projects/guix·blob kernel-updates · refs

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1;;; GNU Guix --- Functional package management for GNU
2;;; Copyright © 2015-2026 Ricardo Wurmus <[email protected]>
3;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <[email protected]>
4;;; Copyright © 2016 Pjotr Prins <[email protected]>
5;;; Copyright © 2016 Ben Woodcroft <[email protected]>
6;;; Copyright © 2017, 2022, 2024 Efraim Flashner <[email protected]>
7;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <[email protected]>
8;;; Copyright © 2019-2023, 2025 Simon Tournier <[email protected]>
9;;; Copyright © 2020 Peter Lo <[email protected]>
10;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu <[email protected]>
11;;; Copyright © 2020 Jakub Kądziołka <[email protected]>
12;;; Copyright © 2021 Hong Li <[email protected]>
13;;; Copyright © 2021 Tim Howes <[email protected]>
14;;; Copyright © 2021 Nicolas Vallet <[email protected]>
15;;; Copyright © 2023 Navid Afkhami <[email protected]>
16;;; Copyright © 2024 Spencer King <[email protected]>
17;;; Copyright © 2024, 2025 Janneke Nieuwenhuizen <[email protected]>
18;;;
19;;; This file is part of GNU Guix.
20;;;
21;;; GNU Guix is free software; you can redistribute it and/or modify it
22;;; under the terms of the GNU General Public License as published by
23;;; the Free Software Foundation; either version 3 of the License, or (at
24;;; your option) any later version.
25;;;
26;;; GNU Guix is distributed in the hope that it will be useful, but
27;;; WITHOUT ANY WARRANTY; without even the implied warranty of
28;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
29;;; GNU General Public License for more details.
30;;;
31;;; You should have received a copy of the GNU General Public License
32;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
33
34(define-module (gnu packages bioconductor)
35 #:use-module ((guix licenses) #:prefix license:)
36 #:use-module (guix packages)
37 #:use-module (guix download)
38 #:use-module (guix gexp)
39 #:use-module (guix utils)
40 #:use-module (guix git-download)
41 #:use-module (guix build-system r)
42 #:use-module (gnu packages)
43 #:use-module (gnu packages algebra)
44 #:use-module (gnu packages autotools)
45 #:use-module (gnu packages base)
46 #:use-module (gnu packages bioinformatics)
47 #:use-module (gnu packages boost)
48 #:use-module (gnu packages chemistry)
49 #:use-module (gnu packages cmake)
50 #:use-module (gnu packages cran)
51 #:use-module (gnu packages compression)
52 #:use-module (gnu packages containers)
53 #:use-module (gnu packages curl)
54 #:use-module (gnu packages gcc)
55 #:use-module (gnu packages ghostscript)
56 #:use-module (gnu packages graph)
57 #:use-module (gnu packages graphviz)
58 #:use-module (gnu packages haskell-xyz)
59 #:use-module (gnu packages image)
60 #:use-module (gnu packages java)
61 #:use-module (gnu packages javascript)
62 #:use-module (gnu packages maths)
63 #:use-module (gnu packages ncurses)
64 #:use-module (gnu packages netpbm)
65 #:use-module (gnu packages python)
66 #:use-module (gnu packages python-science)
67 #:use-module (gnu packages python-xyz)
68 #:use-module (gnu packages perl)
69 #:use-module (gnu packages pkg-config)
70 #:use-module (gnu packages protobuf)
71 #:use-module (gnu packages statistics)
72 #:use-module (gnu packages tex)
73 #:use-module (gnu packages tls)
74 #:use-module (gnu packages web)
75 #:use-module (gnu packages xml)
76 #:use-module ((srfi srfi-1) #:hide (zip)))
77
78
79;;; Annotations
80
81(define-public r-bsgenome-drerio-ucsc-danrer7
82 (package
83 (name "r-bsgenome-drerio-ucsc-danrer7")
84 (version "1.4.0")
85 (source
86 (origin
87 (method url-fetch)
88 (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer7" version
89 'annotation))
90 (sha256
91 (base32 "17x3hj08jag05y8q4aziy455jy15dpwkdbh97v3byzcda0kpwbpg"))))
92 (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer7")))
93 (build-system r-build-system)
94 (propagated-inputs (list r-bsgenome))
95 (home-page
96 "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer7")
97 (synopsis "Full genome sequences for Danio rerio (UCSC version danRer7)")
98 (description
99 "This package provides full genome sequences for Danio rerio (Zebrafish)
100as provided by UCSC (@code{danRer7}, Jul. 2010) and stored in Biostrings
101objects.")
102 (license license:artistic2.0)))
103
104(define-public r-bsgenome-drerio-ucsc-danrer10
105 (package
106 (name "r-bsgenome-drerio-ucsc-danrer10")
107 (version "1.4.2")
108 (source
109 (origin
110 (method url-fetch)
111 (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer10" version
112 'annotation))
113 (sha256
114 (base32 "1grlxihdx65fwgb9gbp1jibbqan9a5667w4jgswhg0qsia608lzs"))))
115 (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer10")))
116 (build-system r-build-system)
117 (propagated-inputs (list r-bsgenome))
118 (home-page
119 "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer10")
120 (synopsis "Full genome sequences for Danio rerio (UCSC version danRer10)")
121 (description
122 "This package provides full genome sequences for Danio rerio (Zebrafish)
123as provided by UCSC (@code{danRer10}, Sep. 2014) and stored in
124@code{Biostrings} objects.")
125 (license license:artistic2.0)))
126
127(define-public r-bsgenome-hsapiens-ucsc-hg38-masked
128 (package
129 (name "r-bsgenome-hsapiens-ucsc-hg38-masked")
130 (version "1.4.5")
131 (source
132 (origin
133 (method url-fetch)
134 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38.masked" version
135 'annotation))
136 (sha256
137 (base32 "0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m"))))
138 (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38.masked")))
139 (build-system r-build-system)
140 (propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg38
141 r-genomeinfodb))
142 (home-page
143 "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked")
144 (synopsis
145 "Full masked genomic sequences for Homo sapiens (UCSC version hg38)")
146 (description
147 "This package provides the complete genome sequences for Homo sapiens as
148provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).
149The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each
150of them has the 4 following masks on top:
151
152@enumerate
153@item the mask of assembly gaps (AGAPS mask);
154@item the mask of intra-contig ambiguities (AMB mask);
155@item the mask of repeats from @code{RepeatMasker} (RM mask);
156@item the mask of repeats from Tandem Repeats Finder (TRF mask).
157@end enumerate
158
159Only the AGAPS and AMB masks are \"active\" by default. The sequences are stored
160in @code{MaskedDNAString} objects.")
161 (license license:artistic2.0)))
162
163(define-public r-ensdb-hsapiens-v79
164 (package
165 (name "r-ensdb-hsapiens-v79")
166 (version "2.99.0")
167 (source
168 (origin
169 (method url-fetch)
170 (uri (bioconductor-uri "EnsDb.Hsapiens.v79" version
171 'annotation))
172 (sha256
173 (base32 "0k94iml0417m3k086d0bzd83fndyb2kn7pimsfzcdmafgy6sxwgg"))))
174 (properties `((upstream-name . "EnsDb.Hsapiens.v79")))
175 (build-system r-build-system)
176 (propagated-inputs (list r-ensembldb))
177 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v79")
178 (synopsis "Ensembl based annotation package")
179 (description "This package exposes an annotation database generated from
180Ensembl.")
181 (license license:artistic2.0)))
182
183(define-public r-genomewidesnp6crlmm
184 (package
185 (name "r-genomewidesnp6crlmm")
186 (version "1.0.7")
187 (source
188 (origin
189 (method url-fetch)
190 (uri (bioconductor-uri "genomewidesnp6Crlmm" version
191 'annotation))
192 (sha256
193 (base32 "16qcxa32fmbdcv5dck0grsnqyfcqql7wpxa1l6andv9hrvabv2jx"))))
194 (properties `((upstream-name . "genomewidesnp6Crlmm")))
195 (build-system r-build-system)
196 (home-page "https://bioconductor.org/packages/genomewidesnp6Crlmm")
197 (synopsis "Metadata for fast genotyping with the crlmm package")
198 (description
199 "This is a package with metadata for fast genotyping Affymetrix
200@code{GenomeWideSnp_6} arrays using the @code{crlmm} package.")
201 (license license:artistic2.0)))
202
203(define-public r-hgu95a-db
204 (package
205 (name "r-hgu95a-db")
206 (version "3.13.0")
207 (source
208 (origin
209 (method url-fetch)
210 (uri (bioconductor-uri "hgu95a.db" version
211 'annotation))
212 (sha256
213 (base32 "1krmnl5kqfvb4jvrqy72x0s8z7rha96d5nwcbnarpflf12k4hrha"))))
214 (properties `((upstream-name . "hgu95a.db")))
215 (build-system r-build-system)
216 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
217 (native-inputs (list r-runit))
218 (home-page "https://bioconductor.org/packages/hgu95a.db")
219 (synopsis "Affymetrix HG_U95A Array annotation data (chip hgu95a)")
220 (description
221 "This package provides Affymetrix HG_U95A Array annotation data (chip
222hgu95a) assembled using data from public repositories.")
223 (license license:artistic2.0)))
224
225(define-public r-hgu95av2
226 (package
227 (name "r-hgu95av2")
228 (version "2.2.0")
229 (source
230 (origin
231 (method url-fetch)
232 (uri (bioconductor-uri "hgu95av2" version
233 'annotation))
234 (sha256
235 (base32 "181bady90v89yx2gzwahhcl63aiypcx33pkfnjxkyq45qgb18bqi"))))
236 (properties `((upstream-name . "hgu95av2")))
237 (build-system r-build-system)
238 (home-page "https://bioconductor.org/packages/hgu95av2")
239 (synopsis "Affymetrix Human Genome U95 Set annotation data (hgu95av2)")
240 (description
241 "This package provides Affymetrix Human Genome U95 Set annotation
242data (hgu95av2) assembled using data from public data repositories.")
243 (license license:artistic2.0)))
244
245(define-public r-hgu95av2-db
246 (package
247 (name "r-hgu95av2-db")
248 (version "3.13.0")
249 (source
250 (origin
251 (method url-fetch)
252 (uri (bioconductor-uri "hgu95av2.db" version
253 'annotation))
254 (sha256
255 (base32 "1zk3mb9p8z2xabqr6y9jdiwidjzkgn22jlqyqg1bq0iahmj2ywpz"))))
256 (properties `((upstream-name . "hgu95av2.db")))
257 (build-system r-build-system)
258 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
259 (native-inputs (list r-runit))
260 (home-page "https://bioconductor.org/packages/hgu95av2.db")
261 (synopsis
262 "Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2)")
263 (description
264 "This package provides Affymetrix HG_U95Av2 Array annotation
265data (chip hgu95av2) assembled using data from public repositories.")
266 (license license:artistic2.0)))
267
268(define-public r-hgu95av2cdf
269 (package
270 (name "r-hgu95av2cdf")
271 (version "2.18.0")
272 (source
273 (origin
274 (method url-fetch)
275 (uri (bioconductor-uri "hgu95av2cdf" version
276 'annotation))
277 (sha256
278 (base32 "1zp1y5awnkprkmk01rmn881y50bslfi8s33i8bws39am5xma0jfl"))))
279 (properties `((upstream-name . "hgu95av2cdf")))
280 (build-system r-build-system)
281 (propagated-inputs (list r-annotationdbi))
282 (home-page "https://bioconductor.org/packages/hgu95av2cdf")
283 (synopsis "hgu95av2cdf")
284 (description
285 "This package provides a package containing an environment representing
286the HG_U95Av2.CDF file.")
287 (license license:lgpl2.0+)))
288
289(define-public r-hgu133a-db
290 (package
291 (name "r-hgu133a-db")
292 (version "3.13.0")
293 (source
294 (origin
295 (method url-fetch)
296 (uri (bioconductor-uri "hgu133a.db" version
297 'annotation))
298 (sha256
299 (base32 "00jcginfs161ls9hxsvynbrghg3awjrphnc54b8g0gj8g6x22pll"))))
300 (properties `((upstream-name . "hgu133a.db")))
301 (build-system r-build-system)
302 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
303 (native-inputs (list r-runit))
304 (home-page "https://bioconductor.org/packages/hgu133a.db")
305 (synopsis "Affymetrix HG-U133A Array annotation data (chip hgu133a)")
306 (description
307 "This package provides Affymetrix HG-U133A Array annotation data (chip
308hgu133a) assembled using data from public repositories.")
309 (license license:artistic2.0)))
310
311(define-public r-hpo-db
312 (package
313 (name "r-hpo-db")
314 (version "0.99.2")
315 (source
316 (origin
317 (method url-fetch)
318 (uri (bioconductor-uri "HPO.db" version
319 'annotation))
320 (sha256
321 (base32 "1brzrnafvyh76h8a663gk5lprhixxpi9xi65vwgxwf7jh6yw0was"))))
322 (properties `((upstream-name . "HPO.db")))
323 (build-system r-build-system)
324 (arguments
325 (list
326 #:phases
327 #~(modify-phases %standard-phases
328 (add-after 'unpack 'avoid-internet-access
329 (lambda* (#:key inputs #:allow-other-keys)
330 (let* ((cache (string-append #$output "/share/HPO.db/cache"))
331 (file (string-append cache "/118333")))
332 (mkdir-p cache)
333 (copy-file #$(this-package-native-input "HPO.sqlite") file)
334 (substitute* "R/zzz.R"
335 (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m)
336 (string-append
337 "if (Sys.getenv(\"NIX_BUILD_TOP\") == \"\") { " m " };"))
338 (("dbfile <- ah.*" m)
339 (string-append
340 "if (Sys.getenv(\"NIX_BUILD_TOP\") != \"\") { dbfile <- \""
341 file "\";} else { " m " }\n")))))))))
342 (propagated-inputs
343 (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi))
344 (native-inputs
345 `(("r-knitr" ,r-knitr)
346 ("r-testthat" ,r-testthat)
347 ("HPO.sqlite"
348 ,(origin
349 (method url-fetch)
350 (uri "https://annotationhub.bioconductor.org/fetch/118333")
351 (file-name "HPO.sqlite")
352 (sha256
353 (base32 "1wwdwf27iil0p41183qgygh2ifphhmlljjkgjm2h8sr25qycf0md"))))))
354 (home-page "https://bioconductor.org/packages/HPO.db")
355 (synopsis
356 "Annotation maps describing the entire Human Phenotype Ontology")
357 (description
358 "Human Phenotype Ontology (HPO) was developed to create a consistent
359description of gene products with disease perspectives, and is essential for
360supporting functional genomics in disease context. Accurate disease
361descriptions can discover new relationships between genes and disease, and new
362functions for previous uncharacteried genes and alleles.")
363 (license license:artistic2.0)))
364
365(define-public r-human370v1ccrlmm
366 (package
367 (name "r-human370v1ccrlmm")
368 (version "1.0.2")
369 (source
370 (origin
371 (method url-fetch)
372 (uri (bioconductor-uri "human370v1cCrlmm" version
373 'annotation))
374 (sha256
375 (base32 "1fhvgc6phhy8fqrl8bwjyskjl95bwlc08jyrkhsivml3ngbsfdf7"))))
376 (properties `((upstream-name . "human370v1cCrlmm")))
377 (build-system r-build-system)
378 (home-page "https://bioconductor.org/packages/human370v1cCrlmm")
379 (synopsis "Metadata for fast genotyping with the 'crlmm' package")
380 (description
381 "This is a package with metadata for genotyping Illumina 370k arrays
382using the crlmm package.")
383 (license license:artistic2.0)))
384
385(define-public r-illuminahumanmethylationepicanno-ilm10b2-hg19
386 (package
387 (name "r-illuminahumanmethylationepicanno-ilm10b2-hg19")
388 (version "0.6.0")
389 (source
390 (origin
391 (method url-fetch)
392 (uri (bioconductor-uri "IlluminaHumanMethylationEPICanno.ilm10b2.hg19"
393 version
394 'annotation))
395 (sha256
396 (base32 "0sfdx0lpiw3l4passx93pjfswd0iv3hxdc7ciazh53baib3xpv2d"))))
397 (properties `((upstream-name . "IlluminaHumanMethylationEPICanno.ilm10b2.hg19")))
398 (build-system r-build-system)
399 (propagated-inputs (list r-minfi))
400 (home-page "https://bitbucket.com/kasperdanielhansen/Illumina_EPIC")
401 (synopsis "Annotation for Illumina's EPIC methylation arrays")
402 (description
403 "This is an annotation package for Illumina's EPIC methylation arrays.")
404 (license license:artistic2.0)))
405
406(define-public r-jaspar2020
407 (package
408 (name "r-jaspar2020")
409 (version "0.99.10")
410 (source
411 (origin
412 (method url-fetch)
413 (uri (bioconductor-uri "JASPAR2020" version 'annotation))
414 (sha256
415 (base32 "0nrp63z7q2ivv5h87f7inpp2qll2dfgj4227l4rbnzii38a2vfdr"))))
416 (properties `((upstream-name . "JASPAR2020")))
417 (build-system r-build-system)
418 (native-inputs (list r-knitr))
419 (home-page "https://jaspar.elixir.no/")
420 (synopsis "Data package for JASPAR database (version 2020)")
421 (description "Data package for JASPAR2020. To explore these databases,
422utilize the TFBSTools package (version 1.23.1 or higher).")
423 (license license:gpl2)))
424
425(define-public r-mafdb-1kgenomes-phase1-hs37d5
426 (package
427 (name "r-mafdb-1kgenomes-phase1-hs37d5")
428 (version "3.10.0")
429 (source
430 (origin
431 (method url-fetch)
432 (uri (bioconductor-uri "MafDb.1Kgenomes.phase1.hs37d5" version
433 'annotation))
434 (sha256
435 (base32 "0vsjik59qa36w402bcrd5z27wc9vyp4gl0ffcwskd9iwjqim0phi"))))
436 (properties `((upstream-name . "MafDb.1Kgenomes.phase1.hs37d5")))
437 (build-system r-build-system)
438 (propagated-inputs (list r-bsgenome
439 r-genomeinfodb
440 r-genomicranges
441 r-genomicscores
442 r-iranges
443 r-s4vectors))
444 (home-page
445 "https://bioconductor.org/packages/MafDb.1Kgenomes.phase1.hs37d5")
446 (synopsis
447 "Minor allele frequency data from 1000 Genomes Phase 1 for hs37d5")
448 (description
449 "Store minor allele frequency data from the Phase 1 of the 1000 Genomes
450Project for the human genome version hs37d5.")
451 (license license:artistic2.0)))
452
453(define-public r-mafh5-gnomad-v3-1-2-grch38
454 (package
455 (name "r-mafh5-gnomad-v3-1-2-grch38")
456 (version "3.15.1")
457 (source
458 (origin
459 (method url-fetch)
460 (uri (bioconductor-uri "MafH5.gnomAD.v3.1.2.GRCh38" version
461 'annotation))
462 (sha256
463 (base32 "1q9hlva814sjfz8vm9bzw7xzppbcfy5qq7nnz9w742yr59cjb6mp"))))
464 (properties `((upstream-name . "MafH5.gnomAD.v3.1.2.GRCh38")))
465 (build-system r-build-system)
466 (propagated-inputs (list r-bsgenome
467 r-genomeinfodb
468 r-genomicranges
469 r-genomicscores
470 r-hdf5array
471 r-iranges
472 r-rhdf5
473 r-s4vectors))
474 (home-page "https://bioconductor.org/packages/MafH5.gnomAD.v3.1.2.GRCh38")
475 (synopsis
476 "Minor allele frequency data from gnomAD version 3.1.2 for GRCh38")
477 (description
478 "This package is designed to store minor allele frequency data.
479It retrieves this data from the Genome Aggregation Database
480(@code{gnomAD} version 3.1.2) for the human genome version GRCh38.")
481 (license license:artistic2.0)))
482
483(define-public r-mpo-db
484 (package
485 (name "r-mpo-db")
486 (version "0.99.8")
487 (source
488 (origin
489 (method url-fetch)
490 (uri (bioconductor-uri "MPO.db" version
491 'annotation))
492 (sha256
493 (base32 "1aaz4s8ydcqxx5qwfqxxs7fc20bjbdjxzg700gwd59kjgk6ijm92"))))
494 (properties `((upstream-name . "MPO.db")))
495 (build-system r-build-system)
496 (arguments
497 (list
498 #:phases
499 #~(modify-phases %standard-phases
500 (add-after 'unpack 'avoid-internet-access
501 (lambda* (#:key inputs #:allow-other-keys)
502 (let* ((cache (string-append #$output "/share/MPO.db/cache"))
503 (file (string-append cache "/118299")))
504 (mkdir-p cache)
505 (copy-file #$(this-package-native-input "MPO.sqlite") file)
506 (substitute* "R/zzz.R"
507 (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m)
508 (string-append
509 "if (Sys.getenv(\"NIX_BUILD_TOP\") == \"\") { " m " };"))
510 (("dbfile <- ah\\[\\[\"AH117057\".*" m)
511 (string-append
512 "if (Sys.getenv(\"NIX_BUILD_TOP\") != \"\") { dbfile <- \""
513 file "\";} else { " m " }\n")))))))))
514 (propagated-inputs
515 (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi))
516 (native-inputs
517 `(("r-knitr" ,r-knitr)
518 ("r-testthat" ,r-testthat)
519 ("MPO.sqlite"
520 ,(origin
521 (method url-fetch)
522 (uri "https://annotationhub.bioconductor.org/fetch/118299")
523 (file-name "MPO.sqlite")
524 (sha256
525 (base32 "12rf5dpnjrpw55bgnbn68dni2g0p87nvs9c7mamqk0ayafs61zl0"))))))
526 (home-page "https://github.com/YuLab-SMU/MPO.db")
527 (synopsis "Set of annotation maps describing the Mouse Phenotype Ontology")
528 (description
529 "This is the human disease ontology R package HDO.db, which provides the
530semantic relationship between human diseases. Relying on the DOSE and
531GO@code{SemSim} packages, this package can carry out disease enrichment and
532semantic similarity analyses. Many biological studies are achieved through
533mouse models, and a large number of data indicate the association between
534genotypes and phenotypes or diseases. The study of model organisms can be
535transformed into useful knowledge about normal human biology and disease to
536facilitate treatment and early screening for diseases. Organism-specific
537genotype-phenotypic associations can be applied to cross-species phenotypic
538studies to clarify previously unknown phenotypic connections in other species.
539Using the same principle to diseases can identify genetic associations and
540even help to identify disease associations that are not obvious.")
541 (license license:artistic2.0)))
542
543(define-public r-oligodata
544 (package
545 (name "r-oligodata")
546 (version "1.8.0")
547 (source
548 (origin
549 (method url-fetch)
550 (uri (bioconductor-uri "oligoData" version
551 'annotation))
552 (sha256
553 (base32 "1d1yfms3jv2c4s255xnh8yxwijrj35skw3nxds7l46y88lg3qn8y"))))
554 (properties `((upstream-name . "oligoData")))
555 (build-system r-build-system)
556 (propagated-inputs (list r-oligo))
557 (home-page "https://bioconductor.org/packages/oligoData")
558 (synopsis "Dataset samples for the oligo package")
559 (description
560 "This package provides dataset samples (Affymetrix: Expression, Gene,
561Exon, SNP; @code{NimbleGen}: Expression, Tiling) to be used with the
562@code{oligo} package.")
563 (license license:lgpl2.0+)))
564
565(define-public r-org-eck12-eg-db
566 (package
567 (name "r-org-eck12-eg-db")
568 (version "3.22.0")
569 (source
570 (origin
571 (method url-fetch)
572 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
573 (sha256
574 (base32 "1m19yms6g0np99myxg54phszz5zzl89hwcr0dhmixfzb2w3fh8bp"))))
575 (properties
576 `((upstream-name . "org.EcK12.eg.db")
577 (updater-extra-native-inputs . ("r-runit"))))
578 (build-system r-build-system)
579 (propagated-inputs
580 (list r-annotationdbi))
581 (native-inputs (list r-annotate r-go-db r-runit))
582 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
583 (synopsis "Genome wide annotation for E coli strain K12")
584 (description
585 "This package provides genome wide annotation for E coli strain K12,
586primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
587National Center for Biotechnology Information (NCBI)’s database for
588gene-specific information. Entrez Gene maintains records from genomes which
589have been completely sequenced, which have an active research community to
590submit gene-specific information, or which are scheduled for intense sequence
591analysis.")
592 (license license:artistic2.0)))
593
594(define-public r-org-bt-eg-db
595 (package
596 (name "r-org-bt-eg-db")
597 (version "3.22.0")
598 (source
599 (origin
600 (method url-fetch)
601 (uri (bioconductor-uri "org.Bt.eg.db" version 'annotation))
602 (sha256
603 (base32
604 "0d9kjbacg8avn541k5vblcazqj3h22jn56klp25q32mghal4ama1"))))
605 (properties
606 '((upstream-name . "org.Bt.eg.db")
607 (updater-extra-native-inputs . ("r-runit"))))
608 (build-system r-build-system)
609 (propagated-inputs
610 (list r-annotationdbi))
611 (native-inputs (list r-annotate r-go-db r-runit))
612 (home-page "https://bioconductor.org/packages/org.Bt.eg.db")
613 (synopsis "Genome wide annotation for Bovine")
614 (description
615 "This package provides genome wide annotations for Bovine, primarily
616based on mapping using Entrez Gene identifiers.")
617 (license license:artistic2.0)))
618
619(define-public r-org-sc-sgd-db
620 (package
621 (name "r-org-sc-sgd-db")
622 (version "3.22.0")
623 (source
624 (origin
625 (method url-fetch)
626 (uri (bioconductor-uri "org.Sc.sgd.db" version
627 'annotation))
628 (sha256
629 (base32 "15xb6v06v0242yy358zw8ylli6vgl7i7w88byan7wh4k500mb7zf"))))
630 (properties
631 '((upstream-name . "org.Sc.sgd.db")
632 (updater-extra-native-inputs . ("r-runit"))))
633 (build-system r-build-system)
634 (propagated-inputs (list r-annotationdbi))
635 (native-inputs (list r-annotate r-go-db r-runit))
636 (home-page "https://bioconductor.org/packages/org.Sc.sgd.db")
637 (synopsis "Genome wide annotation for Yeast")
638 (description
639 "This package provides genome wide annotation for Yeast, primarily based
640on mapping using ORF identifiers from @acronym{SGD, Saccharomyces Genome
641Database}.")
642 (license license:artistic2.0)))
643
644(define-public r-pd-mapping50k-hind240
645 (package
646 (name "r-pd-mapping50k-hind240")
647 (version "3.12.0")
648 (source
649 (origin
650 (method url-fetch)
651 (uri (bioconductor-uri "pd.mapping50k.hind240" version
652 'annotation))
653 (sha256
654 (base32 "1whpjdr4aql846cm8nzgs613pi12qdqfixhqcfv8wrqyks27kq6s"))))
655 (properties `((upstream-name . "pd.mapping50k.hind240")))
656 (build-system r-build-system)
657 (propagated-inputs (list r-biostrings
658 r-dbi
659 r-iranges
660 r-oligo
661 r-oligoclasses
662 r-rsqlite
663 r-s4vectors))
664 (home-page "https://bioconductor.org/packages/pd.mapping50k.hind240")
665 (synopsis "Platform Design Info for Affymetrix Mapping50K_Hind240")
666 (description "This package provides platform design info for Affymetrix
667Mapping50K_Hind240.")
668 (license license:artistic2.0)))
669
670(define-public r-pd-mapping50k-xba240
671 (package
672 (name "r-pd-mapping50k-xba240")
673 (version "3.12.0")
674 (source
675 (origin
676 (method url-fetch)
677 (uri (bioconductor-uri "pd.mapping50k.xba240" version
678 'annotation))
679 (sha256
680 (base32 "1a1f3lh5ywhyjawdbj2fzban85c8jz70lfcv3pagd5piincjwxq8"))))
681 (properties `((upstream-name . "pd.mapping50k.xba240")))
682 (build-system r-build-system)
683 (propagated-inputs
684 (list r-biostrings
685 r-dbi
686 r-iranges
687 r-oligo
688 r-oligoclasses
689 r-rsqlite
690 r-s4vectors))
691 (home-page "https://bioconductor.org/packages/pd.mapping50k.xba240")
692 (synopsis "Platform design info for Affymetrix Mapping50K_Xba240")
693 (description "This package provides platform design info for Affymetrix
694Mapping50K_Xba240 (pd.mapping50k.xba240).")
695 (license license:artistic2.0)))
696
697(define-public r-polyphen-hsapiens-dbsnp131
698 (package
699 (name "r-polyphen-hsapiens-dbsnp131")
700 (version "1.0.2")
701 (source
702 (origin
703 (method url-fetch)
704 (uri (bioconductor-uri "PolyPhen.Hsapiens.dbSNP131" version
705 'annotation))
706 (sha256
707 (base32 "1kikygkli41sn3rqihz0924prmqg2264ifj29vmg1a7qccm0kf7c"))))
708 (properties `((upstream-name . "PolyPhen.Hsapiens.dbSNP131")))
709 (build-system r-build-system)
710 (propagated-inputs (list r-annotationdbi r-rsqlite r-variantannotation))
711 (home-page "https://bioconductor.org/packages/PolyPhen.Hsapiens.dbSNP131")
712 (synopsis "PolyPhen predictions for Homo sapiens dbSNP build 131")
713 (description
714 "This package provides a database of @code{PolyPhen} predictions for Homo
715sapiens @code{dbSNP} build 131.")
716 (license license:artistic2.0)))
717
718(define-public r-reactome-db
719 (package
720 (name "r-reactome-db")
721 (version "1.96.0")
722 (source
723 (origin
724 (method url-fetch)
725 (uri (bioconductor-uri "reactome.db" version 'annotation))
726 (sha256
727 (base32
728 "0b43ri3clg6ynp197vy24936n762k0f43v9m51g1lar2w4qc2zhb"))))
729 (properties `((upstream-name . "reactome.db")))
730 (build-system r-build-system)
731 (propagated-inputs
732 (list r-annotationdbi))
733 (home-page "https://bioconductor.org/packages/reactome.db/")
734 (synopsis "Annotation maps for reactome")
735 (description
736 "This package provides a set of annotation maps for the REACTOME
737database, assembled using data from REACTOME.")
738 (license license:cc-by4.0)))
739
740(define-public r-sift-hsapiens-dbsnp137
741 (package
742 (name "r-sift-hsapiens-dbsnp137")
743 (version "1.0.0")
744 (source
745 (origin
746 (method url-fetch)
747 (uri (bioconductor-uri "SIFT.Hsapiens.dbSNP137" version
748 'annotation))
749 (sha256
750 (base32 "1472abqanbwziyynr851xzhg7ck8w1n98ymmggg7s46hzix5mlj8"))))
751 (properties `((upstream-name . "SIFT.Hsapiens.dbSNP137")))
752 (build-system r-build-system)
753 (propagated-inputs (list r-annotationdbi r-rsqlite r-variantannotation))
754 (home-page "https://bioconductor.org/packages/SIFT.Hsapiens.dbSNP137")
755 (synopsis "PROVEAN/SIFT predictions for Homo sapiens dbSNP build 137")
756 (description
757 "This package provides a database of PROVEAN/SIFT predictions for Homo
758sapiens @code{dbSNP} build 137.")
759 (license license:artistic2.0)))
760
761(define-public r-bsgenome-btaurus-ucsc-bostau8
762 (package
763 (name "r-bsgenome-btaurus-ucsc-bostau8")
764 (version "1.4.2")
765 (source (origin
766 (method url-fetch)
767 (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8"
768 version 'annotation))
769 (sha256
770 (base32
771 "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"))))
772 (properties
773 `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
774 (build-system r-build-system)
775 (propagated-inputs
776 (list r-bsgenome))
777 (home-page
778 "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
779 (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
780 (description "This package provides the full genome sequences for Bos
781taurus (UCSC version bosTau8).")
782 (license license:artistic2.0)))
783
784(define-public r-bsgenome-celegans-ucsc-ce6
785 (package
786 (name "r-bsgenome-celegans-ucsc-ce6")
787 (version "1.4.0")
788 (source (origin
789 (method url-fetch)
790 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
791 version 'annotation))
792 (sha256
793 (base32
794 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
795 (properties
796 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
797 (build-system r-build-system)
798 (propagated-inputs
799 (list r-bsgenome))
800 (home-page
801 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
802 (synopsis "Full genome sequences for Worm")
803 (description
804 "This package provides full genome sequences for Caenorhabditis
805elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
806objects.")
807 (license license:artistic2.0)))
808
809(define-public r-bsgenome-celegans-ucsc-ce10
810 (package
811 (name "r-bsgenome-celegans-ucsc-ce10")
812 (version "1.4.0")
813 (source (origin
814 (method url-fetch)
815 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
816 version 'annotation))
817 (sha256
818 (base32
819 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
820 (properties
821 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
822 (build-system r-build-system)
823 (propagated-inputs
824 (list r-bsgenome))
825 (home-page
826 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
827 (synopsis "Full genome sequences for Worm")
828 (description
829 "This package provides full genome sequences for Caenorhabditis
830elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
831objects.")
832 (license license:artistic2.0)))
833
834(define-public r-bsgenome-dmelanogaster-ucsc-dm6
835 (package
836 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
837 (version "1.4.1")
838 (source (origin
839 (method url-fetch)
840 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
841 version 'annotation))
842 (sha256
843 (base32
844 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
845 (properties
846 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
847 (build-system r-build-system)
848 (propagated-inputs
849 (list r-bsgenome))
850 (home-page
851 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
852 (synopsis "Full genome sequences for Fly")
853 (description
854 "This package provides full genome sequences for Drosophila
855melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
856objects.")
857 (license license:artistic2.0)))
858
859(define-public r-bsgenome-dmelanogaster-ucsc-dm3
860 (package
861 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
862 (version "1.4.0")
863 (source (origin
864 (method url-fetch)
865 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
866 version 'annotation))
867 (sha256
868 (base32
869 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
870 (properties
871 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
872 (build-system r-build-system)
873 (propagated-inputs
874 (list r-bsgenome))
875 (home-page
876 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
877 (synopsis "Full genome sequences for Fly")
878 (description
879 "This package provides full genome sequences for Drosophila
880melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
881Biostrings objects.")
882 (license license:artistic2.0)))
883
884(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
885 (package
886 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
887 (version "1.3.99")
888 (source (origin
889 (method url-fetch)
890 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
891 version 'annotation))
892 (sha256
893 (base32
894 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
895 (properties
896 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
897 (build-system r-build-system)
898 (propagated-inputs
899 (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3))
900 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
901 (synopsis "Full masked genome sequences for Fly")
902 (description
903 "This package provides full masked genome sequences for Drosophila
904melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
905Biostrings objects. The sequences are the same as in
906BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
907masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
908intra-contig ambiguities (AMB mask), (3) the mask of repeats from
909RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
910Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
911 (license license:artistic2.0)))
912
913(define-public r-bsgenome-drerio-ucsc-danrer11
914 (package
915 (name "r-bsgenome-drerio-ucsc-danrer11")
916 (version "1.4.2")
917 (source
918 (origin
919 (method url-fetch)
920 (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer11"
921 version 'annotation))
922 (sha256
923 (base32 "08a928mqzv2jxngjcs4yr6ni1b9z9al6jdngwi438j8hm41cwk4v"))))
924 (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11")))
925 (build-system r-build-system)
926 (propagated-inputs
927 (list r-bsgenome))
928 (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11")
929 (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)")
930 (description
931 "This package provides full genome sequences for Danio rerio (Zebrafish)
932as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
933 (license license:artistic2.0)))
934
935(define-public r-bsgenome-ecoli-ncbi-20080805
936 (package
937 (name "r-bsgenome-ecoli-ncbi-20080805")
938 (version "1.3.1000")
939 (source
940 (origin
941 (method url-fetch)
942 (uri (bioconductor-uri "BSgenome.Ecoli.NCBI.20080805" version
943 'annotation))
944 (sha256
945 (base32 "1l7mjyys1kaq4mbia9jamyw6sd0ij1wypwxvwy8aksan3gcfnh27"))))
946 (properties `((upstream-name . "BSgenome.Ecoli.NCBI.20080805")))
947 (build-system r-build-system)
948 (propagated-inputs (list r-bsgenome))
949 (home-page
950 "https://bioconductor.org/packages/BSgenome.Ecoli.NCBI.20080805")
951 (synopsis "Escherichia coli full genomes")
952 (description
953 "This package provides Escherichia coli full genomes for several strains
954as provided by NCBI on 2008/08/05 and stored in Biostrings objects.")
955 (license license:artistic2.0)))
956
957(define-public r-bsgenome-hsapiens-1000genomes-hs37d5
958 (package
959 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
960 (version "0.99.1")
961 (source (origin
962 (method url-fetch)
963 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
964 version 'annotation))
965 (sha256
966 (base32
967 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
968 (properties
969 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
970 (build-system r-build-system)
971 (propagated-inputs
972 (list r-bsgenome))
973 (home-page
974 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
975 (synopsis "Full genome sequences for Homo sapiens")
976 (description
977 "This package provides full genome sequences for Homo sapiens from
9781000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
979 (license license:artistic2.0)))
980
981(define-public r-bsgenome-hsapiens-ncbi-grch38
982 (package
983 (name "r-bsgenome-hsapiens-ncbi-grch38")
984 (version "1.3.1000")
985 (source
986 (origin
987 (method url-fetch)
988 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
989 version 'annotation))
990 (sha256
991 (base32
992 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
993 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
994 (build-system r-build-system)
995 (propagated-inputs (list r-bsgenome))
996 (home-page
997 "https://bioconductor.org/packages/release/data/annotation/html/\
998BSgenome.Hsapiens.NCBI.GRCh38.html")
999 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
1000 (description
1001 "This package provides full genome sequences for Homo sapiens (Human) as
1002provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
1003 (license license:artistic2.0)))
1004
1005(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
1006 (package
1007 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
1008 (version "1.3.993")
1009 (source
1010 (origin
1011 (method url-fetch)
1012 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
1013 version 'annotation))
1014 (sha256
1015 (base32 "19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9"))))
1016 (properties
1017 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
1018 (build-system r-build-system)
1019 (propagated-inputs
1020 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19))
1021 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
1022 (synopsis "Full masked genome sequences for Homo sapiens")
1023 (description
1024 "This package provides full genome sequences for Homo sapiens (Human) as
1025provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
1026sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
1027them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
1028mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
1029repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
1030Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
1031default.")
1032 (license license:artistic2.0)))
1033
1034(define-public r-bsgenome-mmusculus-ucsc-mm9
1035 (package
1036 (name "r-bsgenome-mmusculus-ucsc-mm9")
1037 (version "1.4.0")
1038 (source (origin
1039 (method url-fetch)
1040 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
1041 version 'annotation))
1042 (sha256
1043 (base32
1044 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
1045 (properties
1046 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
1047 (build-system r-build-system)
1048 (propagated-inputs
1049 (list r-bsgenome))
1050 (home-page
1051 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
1052 (synopsis "Full genome sequences for Mouse")
1053 (description
1054 "This package provides full genome sequences for Mus musculus (Mouse) as
1055provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
1056 (license license:artistic2.0)))
1057
1058(define-public r-bsgenome-mmusculus-ucsc-mm9-masked
1059 (package
1060 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
1061 (version "1.3.99")
1062 (source (origin
1063 (method url-fetch)
1064 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
1065 version 'annotation))
1066 (sha256
1067 (base32
1068 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
1069 (properties
1070 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
1071 (build-system r-build-system)
1072 (propagated-inputs
1073 (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9))
1074 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
1075 (synopsis "Full masked genome sequences for Mouse")
1076 (description
1077 "This package provides full genome sequences for Mus musculus (Mouse) as
1078provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
1079sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
1080them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
1081mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
1082repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
1083Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
1084default." )
1085 (license license:artistic2.0)))
1086
1087(define-public r-bsgenome-mmusculus-ucsc-mm10
1088 (package
1089 (name "r-bsgenome-mmusculus-ucsc-mm10")
1090 (version "1.4.3")
1091 (source (origin
1092 (method url-fetch)
1093 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
1094 version 'annotation))
1095 (sha256
1096 (base32
1097 "1vprkywr72nqf847vzmgymylcdb45g4hy30fwx6fzwddkyzh5xnw"))))
1098 (properties
1099 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
1100 (build-system r-build-system)
1101 (propagated-inputs
1102 (list r-bsgenome))
1103 (home-page
1104 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
1105 (synopsis "Full genome sequences for Mouse")
1106 (description
1107 "This package provides full genome sequences for Mus
1108musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
1109in Biostrings objects.")
1110 (license license:artistic2.0)))
1111
1112(define-public r-genomeinfodbdata
1113 (package
1114 (name "r-genomeinfodbdata")
1115 (version "1.2.15")
1116 (source (origin
1117 (method url-fetch)
1118 (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
1119 (sha256
1120 (base32
1121 "1n1ag8dgmhzv0xbxh5af7z411w10w80ng6l53gzjkivmc3ci5w5f"))))
1122 (properties
1123 `((upstream-name . "GenomeInfoDbData")))
1124 (build-system r-build-system)
1125 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
1126 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
1127 (description "This package contains data for mapping between NCBI taxonomy
1128ID and species. It is used by functions in the GenomeInfoDb package.")
1129 (license license:artistic2.0)))
1130
1131(define-public r-go-db
1132 (package
1133 (name "r-go-db")
1134 (version "3.23.1")
1135 (source (origin
1136 (method url-fetch)
1137 (uri (bioconductor-uri "GO.db" version 'annotation))
1138 (sha256
1139 (base32
1140 "0ays2n3jivigpr7m3y3rba8gjyqr7g3qxdslppww0z0zzm4m808z"))))
1141 (properties
1142 `((upstream-name . "GO.db")))
1143 (build-system r-build-system)
1144 (propagated-inputs
1145 (list r-annotationdbi))
1146 (home-page "https://bioconductor.org/packages/GO.db")
1147 (synopsis "Annotation maps describing the entire Gene Ontology")
1148 (description
1149 "The purpose of this GO.db annotation package is to provide detailed
1150information about the latest version of the Gene Ontologies.")
1151 (license license:artistic2.0)))
1152
1153(define-public r-hdo-db
1154 (package
1155 (name "r-hdo-db")
1156 (version "1.0.0")
1157 (source (origin
1158 (method url-fetch)
1159 (uri (bioconductor-uri "HDO.db" version 'annotation))
1160 (sha256
1161 (base32
1162 "0h026xkncm8nc1q8z7qk3nlw445rf3dncaf20b80x7xfl2nm3f84"))))
1163 (properties `((upstream-name . "HDO.db")))
1164 (build-system r-build-system)
1165 (propagated-inputs
1166 (list r-annotationdbi r-dbi))
1167 (native-inputs
1168 (list r-knitr r-testthat))
1169 (home-page "https://bioconductor.org/packages/HDO.db")
1170 (synopsis "Annotation maps describing the entire Human Disease Ontology")
1171 (description
1172 "This package provides a set of annotation maps describing the entire
1173Human Disease Ontology. The annotation data comes from
1174@url{Humam Disease Ontology repository,
1175https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.")
1176 (license license:artistic2.0)))
1177
1178(define-public r-homo-sapiens
1179 (package
1180 (name "r-homo-sapiens")
1181 (version "1.3.1")
1182 (source (origin
1183 (method url-fetch)
1184 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
1185 (sha256
1186 (base32
1187 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
1188 (properties
1189 `((upstream-name . "Homo.sapiens")))
1190 (build-system r-build-system)
1191 (propagated-inputs
1192 (list r-annotationdbi
1193 r-genomicfeatures
1194 r-go-db
1195 r-org-hs-eg-db
1196 r-organismdbi
1197 r-txdb-hsapiens-ucsc-hg19-knowngene))
1198 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
1199 (synopsis "Annotation package for the Homo.sapiens object")
1200 (description
1201 "This package contains the Homo.sapiens object to access data from
1202several related annotation packages.")
1203 (license license:artistic2.0)))
1204
1205(define-public r-mus-musculus
1206 (package
1207 (name "r-mus-musculus")
1208 (version "1.3.1")
1209 (source
1210 (origin
1211 (method url-fetch)
1212 (uri (bioconductor-uri "Mus.musculus" version 'annotation))
1213 (sha256
1214 (base32
1215 "143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y"))))
1216 (properties `((upstream-name . "Mus.musculus")))
1217 (build-system r-build-system)
1218 (propagated-inputs
1219 (list r-annotationdbi
1220 r-genomicfeatures
1221 r-go-db
1222 r-org-mm-eg-db
1223 r-organismdbi
1224 r-txdb-mmusculus-ucsc-mm10-knowngene))
1225 (home-page "https://bioconductor.org/packages/Mus.musculus")
1226 (synopsis "Annotation package for the Mus.musculus object")
1227 (description
1228 "This package contains the @code{Mus.musculus} object to access data
1229from several related annotation packages.")
1230 (license license:artistic2.0)))
1231
1232(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
1233 (package
1234 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
1235 (version "0.6.1")
1236 (source
1237 (origin
1238 (method url-fetch)
1239 (uri (bioconductor-uri
1240 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
1241 version 'annotation))
1242 (sha256
1243 (base32
1244 "1272n72fvj4agszd9cv8l9h9qr2pzmd0rbvdz83x7x03cdddf9rn"))))
1245 (properties
1246 `((upstream-name
1247 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
1248 (build-system r-build-system)
1249 (propagated-inputs (list r-minfi))
1250 (home-page
1251 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
1252 (synopsis "Annotation for Illumina's 450k methylation arrays")
1253 (description
1254 "This package provides manifests and annotation for Illumina's 450k array
1255data.")
1256 (license license:artistic2.0)))
1257
1258(define-public r-illuminahumanmethylation450kmanifest
1259 (package
1260 (name "r-illuminahumanmethylation450kmanifest")
1261 (version "0.4.0")
1262 (source (origin
1263 (method url-fetch)
1264 (uri (bioconductor-uri
1265 "IlluminaHumanMethylation450kmanifest"
1266 version 'annotation))
1267 (sha256
1268 (base32
1269 "0qx75xwifrbkqmbkd8dhf44c34ibmbivqh7y8rvgrsizmi5ybcj1"))))
1270 (properties `((upstream-name . "IlluminaHumanMethylation450kmanifest")))
1271 (build-system r-build-system)
1272 (propagated-inputs (list r-minfi))
1273 (home-page
1274 "https://bioconductor.org/packages/IlluminaHumanMethylation450kmanifest")
1275 (synopsis "Annotation for Illumina's 450k methylation arrays")
1276 (description "This package provides a manifest for Illumina's 450k array
1277data.")
1278 (license license:artistic2.0)))
1279
1280(define-public r-illuminahumanmethylationepicanno-ilm10b4-hg19
1281 (package
1282 (name "r-illuminahumanmethylationepicanno-ilm10b4-hg19")
1283 (version "0.6.0")
1284 (source (origin
1285 (method url-fetch)
1286 (uri (bioconductor-uri
1287 "IlluminaHumanMethylationEPICanno.ilm10b4.hg19"
1288 version 'annotation))
1289 (sha256
1290 (base32
1291 "0687b4k8hwfc18qgdd9ypv1skp37jd204fszba0gmrv3dc92i09c"))))
1292 (properties `((upstream-name . "IlluminaHumanMethylationEPICanno.ilm10b4.hg19")))
1293 (build-system r-build-system)
1294 (propagated-inputs (list r-minfi))
1295 (home-page
1296 "https://doi.org/doi:10.18129/B9.bioc.IlluminaHumanMethylationEPICanno.ilm10b4.hg19")
1297 (synopsis "Annotation for Illumina's EPIC methylation arrays")
1298 (description
1299 "This is an annotation package for Illumina's EPIC methylation arrays.")
1300 (license license:artistic2.0)))
1301
1302(define-public r-illuminahumanmethylationepicv2anno-20a1-hg38
1303 (package
1304 (name "r-illuminahumanmethylationepicv2anno-20a1-hg38")
1305 (version "1.0.1")
1306 (source
1307 (origin
1308 (method url-fetch)
1309 (uri (bioconductor-uri "IlluminaHumanMethylationEPICv2anno.20a1.hg38"
1310 version
1311 'annotation))
1312 (sha256
1313 (base32 "18y92h02dh3pcc27dn1m9jr4m6srwv7w25a4wg3c6jlrggnm5210"))))
1314 (properties `((upstream-name . "IlluminaHumanMethylationEPICv2anno.20a1.hg38")))
1315 (build-system r-build-system)
1316 (propagated-inputs (list r-minfi))
1317 (native-inputs (list r-knitr))
1318 (home-page
1319 "https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html")
1320 (synopsis "Annotation for Illumina's EPIC v2.0 methylation arrays")
1321 (description
1322 "This is an annotation package for Illumina's EPIC v2.0 methylation
1323arrays. The version 2 covers more than 935K CpG sites in the human genome
1324hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K
1325methylation array).")
1326 (license license:artistic2.0)))
1327
1328(define-public r-org-ce-eg-db
1329 (package
1330 (name "r-org-ce-eg-db")
1331 (version "3.22.0")
1332 (source (origin
1333 (method url-fetch)
1334 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
1335 (sha256
1336 (base32
1337 "1mizfwq16mynjhx1s6y8f5df08k5p0vh2rg6b52v21yl4bksma05"))))
1338 (properties
1339 `((upstream-name . "org.Ce.eg.db")
1340 (updater-extra-native-inputs . ("r-runit"))))
1341 (build-system r-build-system)
1342 (propagated-inputs
1343 (list r-annotationdbi))
1344 (native-inputs (list r-annotate r-go-db r-runit))
1345 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
1346 (synopsis "Genome wide annotation for Worm")
1347 (description
1348 "This package provides mappings from Entrez gene identifiers to various
1349annotations for the genome of the model worm Caenorhabditis elegans.")
1350 (license license:artistic2.0)))
1351
1352(define-public r-org-dm-eg-db
1353 (package
1354 (name "r-org-dm-eg-db")
1355 (version "3.22.0")
1356 (source (origin
1357 (method url-fetch)
1358 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
1359 (sha256
1360 (base32
1361 "1p2ii104zqfig7x70pb1c8qwng9rbzvxvg20z3dxpcxl4ri38zq5"))))
1362 (properties
1363 `((upstream-name . "org.Dm.eg.db")
1364 (updater-extra-native-inputs . ("r-runit"))))
1365 (build-system r-build-system)
1366 (propagated-inputs
1367 (list r-annotationdbi))
1368 (native-inputs (list r-annotate r-go-db r-runit))
1369 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
1370 (synopsis "Genome wide annotation for Fly")
1371 (description
1372 "This package provides mappings from Entrez gene identifiers to various
1373annotations for the genome of the model fruit fly Drosophila melanogaster.")
1374 (license license:artistic2.0)))
1375
1376(define-public r-org-dr-eg-db
1377 (package
1378 (name "r-org-dr-eg-db")
1379 (version "3.22.0")
1380 (source (origin
1381 (method url-fetch)
1382 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
1383 (sha256
1384 (base32
1385 "13p3yvx4jpmca73nniiqiy3krwaw7sws549in3nswwn4875j5r93"))))
1386 (properties
1387 '((upstream-name . "org.Dr.eg.db")
1388 (updater-extra-native-inputs . ("r-runit"))))
1389 (build-system r-build-system)
1390 (propagated-inputs
1391 (list r-annotationdbi))
1392 (native-inputs (list r-annotate r-go-db r-runit))
1393 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
1394 (synopsis "Annotation for Zebrafish")
1395 (description
1396 "This package provides genome wide annotations for Zebrafish, primarily
1397based on mapping using Entrez Gene identifiers.")
1398 (license license:artistic2.0)))
1399
1400(define-public r-org-hs-eg-db
1401 (package
1402 (name "r-org-hs-eg-db")
1403 (version "3.23.1")
1404 (source (origin
1405 (method url-fetch)
1406 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
1407 (sha256
1408 (base32
1409 "1zlwsk1hq40xi8xd7wc974jp8gky6x7icc9788ch77glbik201j7"))))
1410 (properties
1411 `((upstream-name . "org.Hs.eg.db")
1412 (updater-extra-native-inputs . ("r-runit"))))
1413 (build-system r-build-system)
1414 (propagated-inputs
1415 (list r-annotationdbi))
1416 (native-inputs (list r-annotate r-go-db r-runit))
1417 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
1418 (synopsis "Genome wide annotation for Human")
1419 (description
1420 "This package contains genome-wide annotations for Human, primarily based
1421on mapping using Entrez Gene identifiers.")
1422 (license license:artistic2.0)))
1423
1424(define-public r-org-mm-eg-db
1425 (package
1426 (name "r-org-mm-eg-db")
1427 (version "3.23.0")
1428 (source (origin
1429 (method url-fetch)
1430 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
1431 (sha256
1432 (base32
1433 "0i252737v6wk0im41gnksz4qkzf286kwgfq60yqc1mfva77m8yjh"))))
1434 (properties
1435 '((upstream-name . "org.Mm.eg.db")
1436 (updater-extra-native-inputs . ("r-runit"))))
1437 (build-system r-build-system)
1438 (propagated-inputs
1439 (list r-annotationdbi))
1440 (native-inputs (list r-annotate r-go-db r-runit))
1441 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
1442 (synopsis "Genome wide annotation for Mouse")
1443 (description
1444 "This package provides mappings from Entrez gene identifiers to various
1445annotations for the genome of the model mouse Mus musculus.")
1446 (license license:artistic2.0)))
1447
1448(define-public r-bsgenome-hsapiens-ucsc-hg19
1449 (package
1450 (name "r-bsgenome-hsapiens-ucsc-hg19")
1451 (version "1.4.3")
1452 (source (origin
1453 (method url-fetch)
1454 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
1455 version 'annotation))
1456 (sha256
1457 (base32
1458 "06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv"))))
1459 (properties
1460 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
1461 (build-system r-build-system)
1462 (propagated-inputs
1463 (list r-bsgenome))
1464 (home-page
1465 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
1466 (synopsis "Full genome sequences for Homo sapiens")
1467 (description
1468 "This package provides full genome sequences for Homo sapiens as provided
1469by UCSC (hg19, February 2009) and stored in Biostrings objects.")
1470 (license license:artistic2.0)))
1471
1472(define-public r-bsgenome-hsapiens-ucsc-hg38
1473 (package
1474 (name "r-bsgenome-hsapiens-ucsc-hg38")
1475 (version "1.4.5")
1476 (source (origin
1477 (method url-fetch)
1478 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
1479 version 'annotation))
1480 (sha256
1481 (base32 "0lp94r9dsx8sl1ifysavgjf4aamhjc4n71zif5jyfnwmzpj7g4ml"))))
1482 (properties
1483 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
1484 (build-system r-build-system)
1485 (propagated-inputs
1486 (list r-bsgenome r-genomeinfodb))
1487 (home-page
1488 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
1489 (synopsis "Full genome sequences for Homo sapiens")
1490 (description
1491 "This package provides full genome sequences for Homo sapiens (Human)
1492as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
1493 (license license:artistic2.0)))
1494
1495(define-public r-ensdb-hsapiens-v75
1496 (package
1497 (name "r-ensdb-hsapiens-v75")
1498 (version "2.99.0")
1499 (source
1500 (origin
1501 (method url-fetch)
1502 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
1503 (sha256
1504 (base32
1505 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
1506 (properties
1507 `((upstream-name . "EnsDb.Hsapiens.v75")))
1508 (build-system r-build-system)
1509 (propagated-inputs
1510 (list r-ensembldb))
1511 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
1512 (synopsis "Ensembl based annotation package")
1513 (description
1514 "This package exposes an annotation database generated from Ensembl.")
1515 (license license:artistic2.0)))
1516
1517(define-public r-ensdb-hsapiens-v86
1518 (package
1519 (name "r-ensdb-hsapiens-v86")
1520 (version "2.99.0")
1521 (source
1522 (origin
1523 (method url-fetch)
1524 (uri (bioconductor-uri "EnsDb.Hsapiens.v86" version 'annotation))
1525 (sha256
1526 (base32 "1gp7xrzddpvmh2vrcp571wyy00skxgxfl39ksj4h0hm1qay0fb2m"))))
1527 (properties `((upstream-name . "EnsDb.Hsapiens.v86")))
1528 (build-system r-build-system)
1529 (propagated-inputs (list r-ensembldb))
1530 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v86")
1531 (synopsis "Ensembl based annotation package")
1532 (description "This package exposes an annotation database generated from
1533Ensembl.")
1534 (license license:artistic2.0)))
1535
1536(define-public r-ensdb-mmusculus-v79
1537 (package
1538 (name "r-ensdb-mmusculus-v79")
1539 (version "2.99.0")
1540 (source
1541 (origin
1542 (method url-fetch)
1543 (uri (bioconductor-uri "EnsDb.Mmusculus.v79" version 'annotation))
1544 (sha256
1545 (base32 "1zpmq7v55if6q9r0h883q9k8l70ym20b01m9hxf121wb256rl9f7"))))
1546 (properties `((upstream-name . "EnsDb.Mmusculus.v79")))
1547 (build-system r-build-system)
1548 (propagated-inputs (list r-ensembldb))
1549 (home-page "https://bioconductor.org/packages/EnsDb.Mmusculus.v79")
1550 (synopsis "Ensembl based annotation package")
1551 (description "This package exposes an annotation database generated from
1552Ensembl.")
1553 (license license:artistic2.0)))
1554
1555(define-public r-sift-hsapiens-dbsnp132
1556 (package
1557 (name "r-sift-hsapiens-dbsnp132")
1558 (version "1.0.2")
1559 (source
1560 (origin
1561 (method url-fetch)
1562 (uri (bioconductor-uri "SIFT.Hsapiens.dbSNP132" version
1563 'annotation))
1564 (sha256
1565 (base32 "1akqhmv9hp41q2jrvz4xvpdi30c4c6v4xbz6ykn6pdf0217p7xry"))))
1566 (properties `((upstream-name . "SIFT.Hsapiens.dbSNP132")))
1567 (build-system r-build-system)
1568 (propagated-inputs (list r-annotationdbi r-rsqlite r-variantannotation))
1569 (home-page "https://bioconductor.org/packages/SIFT.Hsapiens.dbSNP132")
1570 (synopsis "SIFT Predictions for Homo sapiens dbSNP build 132")
1571 (description
1572 "This package provides a database of SIFT predictions for Homo sapiens
1573@code{dbSNP} build 132.")
1574 (license license:artistic2.0)))
1575
1576(define-public r-snplocs-hsapiens-dbsnp144-grch37
1577 (package
1578 (name "r-snplocs-hsapiens-dbsnp144-grch37")
1579 (version "0.99.20")
1580 (source (origin
1581 (method url-fetch)
1582 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
1583 version 'annotation))
1584 (sha256
1585 (base32
1586 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
1587 (build-system r-build-system)
1588 ;; As this package provides little more than a very large data file it
1589 ;; doesn't make sense to build substitutes.
1590 (arguments `(#:substitutable? #f))
1591 (propagated-inputs
1592 (list r-biocgenerics
1593 r-bsgenome
1594 r-genomeinfodb
1595 r-genomicranges
1596 r-iranges
1597 r-s4vectors))
1598 (home-page
1599 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
1600 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
1601 (description "This package provides SNP locations and alleles for Homo
1602sapiens extracted from NCBI dbSNP Build 144. The source data files used for
1603this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
1604to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
1605patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
1606X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
1607the mitochondrion chromosome. Therefore, the SNPs in this package can be
1608injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
1609correct position but this injection will exclude chrM (i.e. nothing will be
1610injected in that sequence).")
1611 (license license:artistic2.0)))
1612
1613(define-public r-txdb-dmelanogaster-ucsc-dm3-ensgene
1614 (package
1615 (name "r-txdb-dmelanogaster-ucsc-dm3-ensgene")
1616 (version "3.2.2")
1617 (source
1618 (origin
1619 (method url-fetch)
1620 (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm3.ensGene" version
1621 'annotation))
1622 (sha256
1623 (base32 "1337x23rdmiiza83ms225kri37h16q5hw1lw0m577abcgip3d7c7"))))
1624 (properties `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm3.ensGene")))
1625 (build-system r-build-system)
1626 (propagated-inputs (list r-annotationdbi r-genomicfeatures))
1627 (home-page
1628 "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm3.ensGene")
1629 (synopsis "Annotation package for TxDb object(s)")
1630 (description
1631 "This package exposes an annotation databases generated from UCSC by
1632exposing these as @code{TxDb} objects.")
1633 (license license:artistic2.0)))
1634
1635(define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
1636 (package
1637 (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
1638 (version "3.12.0")
1639 (source
1640 (origin
1641 (method url-fetch)
1642 (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
1643 version 'annotation))
1644 (sha256
1645 (base32
1646 "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
1647 (properties
1648 `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
1649 (build-system r-build-system)
1650 (propagated-inputs
1651 (list r-annotationdbi r-genomicfeatures))
1652 (home-page
1653 "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
1654 (synopsis "Annotation package for TxDb object(s)")
1655 (description
1656 "This package exposes an annotation databases generated from UCSC by
1657exposing these as TxDb objects.")
1658 (license license:artistic2.0)))
1659
1660(define-public r-txdb-hsapiens-ucsc-hg19-knowngene
1661 (package
1662 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
1663 (version "3.22.1")
1664 (source (origin
1665 (method url-fetch)
1666 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
1667 version 'annotation))
1668 (sha256
1669 (base32
1670 "1cdzvidz3c912lbq1pbqk1dp35i15c6s4ih6r13mhy2l4vc2zdmf"))))
1671 (properties
1672 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
1673 (build-system r-build-system)
1674 (propagated-inputs
1675 (list r-annotationdbi r-genomicfeatures))
1676 (home-page
1677 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
1678 (synopsis "Annotation package for human genome in TxDb format")
1679 (description
1680 "This package provides an annotation database of Homo sapiens genome
1681data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
1682track. The database is exposed as a @code{TxDb} object.")
1683 (license license:artistic2.0)))
1684
1685(define-public r-txdb-hsapiens-ucsc-hg38-knowngene
1686 (package
1687 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
1688 (version "3.22.0")
1689 (source (origin
1690 (method url-fetch)
1691 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
1692 version 'annotation))
1693 (sha256
1694 (base32 "0kizsm1rm1d99b21inzjxhpx4wv05vlr0g3h4fa98x6qlqk13dpy"))))
1695 (properties
1696 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
1697 (build-system r-build-system)
1698 (propagated-inputs
1699 (list r-annotationdbi r-genomicfeatures))
1700 (home-page
1701 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
1702 (synopsis "Annotation package for human genome in TxDb format")
1703 (description
1704 "This package provides an annotation database of Homo sapiens genome
1705data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
1706track. The database is exposed as a @code{TxDb} object.")
1707 (license license:artistic2.0)))
1708
1709(define-public r-txdb-mmusculus-ucsc-mm9-knowngene
1710 (package
1711 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
1712 (version "3.2.2")
1713 (source (origin
1714 (method url-fetch)
1715 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
1716 version 'annotation))
1717 (sha256
1718 (base32
1719 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
1720 (properties
1721 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
1722 (build-system r-build-system)
1723 (propagated-inputs
1724 (list r-annotationdbi r-genomicfeatures))
1725 (home-page
1726 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
1727 (synopsis "Annotation package for mouse genome in TxDb format")
1728 (description
1729 "This package provides an annotation database of Mouse genome data. It
1730is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
1731database is exposed as a @code{TxDb} object.")
1732 (license license:artistic2.0)))
1733
1734(define-public r-txdb-mmusculus-ucsc-mm10-ensgene
1735 (package
1736 (name "r-txdb-mmusculus-ucsc-mm10-ensgene")
1737 (version "3.4.0")
1738 (source
1739 (origin
1740 (method url-fetch)
1741 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.ensGene" version
1742 'annotation))
1743 (sha256
1744 (base32 "0saxi1fdiwd38sfvy1rynd3v44rbp158jv6sjqcivvaqnd84zg9s"))))
1745 (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.ensGene")))
1746 (build-system r-build-system)
1747 (propagated-inputs (list r-annotationdbi r-genomicfeatures))
1748 (home-page
1749 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.ensGene")
1750 (synopsis "Annotation package for TxDb object(s)")
1751 (description
1752 "This package exposes an annotation databases generated from UCSC by
1753exposing these as @code{TxDb} objects.")
1754 (license license:artistic2.0)))
1755
1756(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
1757 (package
1758 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
1759 (version "3.10.0")
1760 (source (origin
1761 (method url-fetch)
1762 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
1763 version 'annotation))
1764 (sha256
1765 (base32
1766 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
1767 (properties
1768 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
1769 (build-system r-build-system)
1770 (propagated-inputs
1771 (list r-annotationdbi r-genomicfeatures))
1772 (home-page
1773 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
1774 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
1775 (description
1776 "This package loads a TxDb object, which is an R interface to
1777prefabricated databases contained in this package. This package provides
1778the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
1779based on the knownGene track.")
1780 (license license:artistic2.0)))
1781
1782(define-public r-txdb-celegans-ucsc-ce6-ensgene
1783 (package
1784 (name "r-txdb-celegans-ucsc-ce6-ensgene")
1785 (version "3.2.2")
1786 (source
1787 (origin
1788 (method url-fetch)
1789 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
1790 version 'annotation))
1791 (sha256
1792 (base32
1793 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
1794 (properties
1795 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
1796 (build-system r-build-system)
1797 (propagated-inputs
1798 (list r-annotationdbi r-genomicfeatures))
1799 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
1800 (synopsis "Annotation package for C elegans TxDb objects")
1801 (description
1802 "This package exposes a C elegans annotation database generated from UCSC
1803by exposing these as TxDb objects.")
1804 (license license:artistic2.0)))
1805
1806(define-public r-fdb-infiniummethylation-hg19
1807 (package
1808 (name "r-fdb-infiniummethylation-hg19")
1809 (version "2.2.0")
1810 (source (origin
1811 (method url-fetch)
1812 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
1813 version 'annotation))
1814 (sha256
1815 (base32
1816 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
1817 (properties
1818 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
1819 (build-system r-build-system)
1820 (propagated-inputs
1821 (list r-annotationdbi r-biostrings r-genomicfeatures r-org-hs-eg-db
1822 r-txdb-hsapiens-ucsc-hg19-knowngene))
1823 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
1824 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
1825 (description
1826 "This is an annotation package for Illumina Infinium DNA methylation
1827probes. It contains the compiled HumanMethylation27 and HumanMethylation450
1828annotations.")
1829 (license license:artistic2.0)))
1830
1831(define-public r-illuminahumanmethylationepicmanifest
1832 (package
1833 (name "r-illuminahumanmethylationepicmanifest")
1834 (version "0.3.0")
1835 (source (origin
1836 (method url-fetch)
1837 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
1838 version 'annotation))
1839 (sha256
1840 (base32
1841 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
1842 (properties
1843 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
1844 (build-system r-build-system)
1845 (propagated-inputs
1846 (list r-minfi))
1847 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
1848 (synopsis "Manifest for Illumina's EPIC methylation arrays")
1849 (description
1850 "This is a manifest package for Illumina's EPIC methylation arrays.")
1851 (license license:artistic2.0)))
1852
1853(define-public r-illuminahumanmethylationepicv2manifest
1854 (package
1855 (name "r-illuminahumanmethylationepicv2manifest")
1856 (version "1.0.1")
1857 (source
1858 (origin
1859 (method url-fetch)
1860 (uri (bioconductor-uri "IlluminaHumanMethylationEPICv2manifest"
1861 version 'annotation))
1862 (sha256
1863 (base32 "0dwynwhjf3dnbw6975fxvncrqk5si22vrcyf6wivvgak1zim9bjl"))))
1864 (properties `((upstream-name . "IlluminaHumanMethylationEPICv2manifest")))
1865 (build-system r-build-system)
1866 (propagated-inputs (list r-minfi))
1867 (native-inputs (list r-knitr))
1868 (home-page
1869 "https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html")
1870 (synopsis "Manifest for Illumina's EPIC v2.0 methylation arrays")
1871 (description
1872 "This package provides a manifest package for Illumina's EPIC v2.0
1873methylation arrays. The version 2 covers more than 935K CpG sites in the
1874human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the
1875850K methylation array).")
1876 (license license:artistic2.0)))
1877
1878(define-public r-do-db
1879 (package
1880 (name "r-do-db")
1881 (version "2.9")
1882 (source (origin
1883 (method url-fetch)
1884 (uri (bioconductor-uri "DO.db" version 'annotation))
1885 (sha256
1886 (base32
1887 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
1888 (properties
1889 `((upstream-name . "DO.db")))
1890 (build-system r-build-system)
1891 (propagated-inputs
1892 (list r-annotationdbi))
1893 (home-page "https://www.bioconductor.org/packages/DO.db/")
1894 (synopsis "Annotation maps describing the entire Disease Ontology")
1895 (description
1896 "This package provides a set of annotation maps describing the entire
1897Disease Ontology.")
1898 (license license:artistic2.0)))
1899
1900(define-public r-hgu133plus2-db
1901 (package
1902 (name "r-hgu133plus2-db")
1903 (version "3.13.0")
1904 (source
1905 (origin
1906 (method url-fetch)
1907 (uri (bioconductor-uri "hgu133plus2.db" version 'annotation))
1908 (sha256
1909 (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx"))))
1910 (properties `((upstream-name . "hgu133plus2.db")))
1911 (build-system r-build-system)
1912 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
1913 (native-inputs (list r-runit))
1914 (home-page "https://bioconductor.org/packages/hgu133plus2.db")
1915 (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data")
1916 (description
1917 "This package provides Affymetrix HG-U133_Plus_2 array annotation
1918data (chip hgu133plus2) assembled using data from public repositories.")
1919 (license license:artistic2.0)))
1920
1921(define-public r-pfam-db
1922 (package
1923 (name "r-pfam-db")
1924 (version "3.22.0")
1925 (source
1926 (origin
1927 (method url-fetch)
1928 (uri (bioconductor-uri "PFAM.db" version 'annotation))
1929 (sha256
1930 (base32 "1maxfmvgiaxl0bfyhbvx8bh3wzkfcfljn8whsy1rlqhahih17cz2"))))
1931 (properties `((upstream-name . "PFAM.db")))
1932 (build-system r-build-system)
1933 (propagated-inputs
1934 (list r-annotationdbi))
1935 (home-page "https://bioconductor.org/packages/PFAM.db")
1936 (synopsis "Set of protein ID mappings for PFAM")
1937 (description
1938 "This package provides a set of protein ID mappings for PFAM, assembled
1939using data from public repositories.")
1940 (license license:artistic2.0)))
1941
1942(define-public r-phastcons100way-ucsc-hg19
1943 (package
1944 (name "r-phastcons100way-ucsc-hg19")
1945 (version "3.7.2")
1946 (source
1947 (origin
1948 (method url-fetch)
1949 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
1950 version 'annotation))
1951 (sha256
1952 (base32
1953 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
1954 (properties
1955 `((upstream-name . "phastCons100way.UCSC.hg19")))
1956 (build-system r-build-system)
1957 (propagated-inputs
1958 (list r-bsgenome
1959 r-genomeinfodb
1960 r-genomicranges
1961 r-genomicscores
1962 r-iranges
1963 r-s4vectors))
1964 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
1965 (synopsis "UCSC phastCons conservation scores for hg19")
1966 (description
1967 "This package provides UCSC phastCons conservation scores for the human
1968genome (hg19) calculated from multiple alignments with other 99 vertebrate
1969species.")
1970 (license license:artistic2.0)))
1971
1972
1973;;; Experiment data
1974
1975(define-public r-abadata
1976 (package
1977 (name "r-abadata")
1978 (version "1.12.0")
1979 (source (origin
1980 (method url-fetch)
1981 (uri (bioconductor-uri "ABAData" version 'experiment))
1982 (sha256
1983 (base32
1984 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
1985 (properties
1986 `((upstream-name . "ABAData")))
1987 (build-system r-build-system)
1988 (propagated-inputs
1989 (list r-annotationdbi))
1990 (home-page "https://www.bioconductor.org/packages/ABAData/")
1991 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
1992 (description
1993 "This package provides the data for the gene expression enrichment
1994analysis conducted in the package ABAEnrichment. The package includes three
1995datasets which are derived from the Allen Brain Atlas:
1996
1997@enumerate
1998@item Gene expression data from Human Brain (adults) averaged across donors,
1999@item Gene expression data from the Developing Human Brain pooled into five
2000 age categories and averaged across donors, and
2001@item a developmental effect score based on the Developing Human Brain
2002 expression data.
2003@end enumerate
2004
2005All datasets are restricted to protein coding genes.")
2006 (license license:gpl2+)))
2007
2008(define-public r-adductdata
2009 (package
2010 (name "r-adductdata")
2011 (version "1.28.0")
2012 (source (origin
2013 (method url-fetch)
2014 (uri (bioconductor-uri "adductData" version 'experiment))
2015 (sha256
2016 (base32 "0m1nm9k4addh27xrq30fsyyc80iwpj5qw5sa92c8gm5nricrf7fn"))))
2017 (properties `((upstream-name . "adductData")))
2018 (build-system r-build-system)
2019 (propagated-inputs (list r-annotationhub r-experimenthub))
2020 (native-inputs (list r-knitr))
2021 (home-page "https://bioconductor.org/packages/adductData")
2022 (synopsis "Data from untargeted mass spectrometry of modifications to Cys34")
2023 (description
2024 "This package contains data from untargeted @dfn{mass spectrometry} (MS)
2025of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum
2026albumin} (HSA).")
2027 (license license:artistic2.0)))
2028
2029(define-public r-airway
2030 (package
2031 (name "r-airway")
2032 (version "1.32.0")
2033 (source
2034 (origin
2035 (method url-fetch)
2036 (uri (bioconductor-uri "airway" version
2037 'experiment))
2038 (sha256
2039 (base32 "06gyqwqbrzyik3jjryj5gj29xrkj8s6qlkjp23ccjnh7r17nb7w2"))))
2040 (properties `((upstream-name . "airway")))
2041 (build-system r-build-system)
2042 (propagated-inputs (list r-summarizedexperiment))
2043 (native-inputs (list r-knitr))
2044 (home-page "https://bioconductor.org/packages/airway")
2045 (synopsis
2046 "RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells")
2047 (description
2048 "This package provides a @code{RangedSummarizedExperiment} object of read
2049counts in genes for an RNA-Seq experiment on four human airway smooth muscle
2050cell lines treated with dexamethasone. Details on the gene model and read
2051counting procedure are provided in the package vignette. The citation for the
2052experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B,
2053Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R
2054Jr, Tantisira KG, Weiss ST, Lu Q. RNA-Seq Transcriptome Profiling Identifies
2055CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function
2056in Airway Smooth Muscle Cells. P@code{LoS} One. 2014 Jun 13;9(6):e99625.
2057PMID: 24926665. GEO: GSE52778.")
2058 (license license:lgpl2.0+)))
2059
2060(define-public r-aneufinderdata
2061 (package
2062 (name "r-aneufinderdata")
2063 (version "1.38.0")
2064 (source (origin
2065 (method url-fetch)
2066 (uri (bioconductor-uri "AneuFinderData" version 'experiment))
2067 (sha256
2068 (base32 "0k7xj1kb5cdz9j4hnf10kh9qp6hkc2vlsj6z01ybs9g9fski86v7"))))
2069 (build-system r-build-system)
2070 (home-page "https://bioconductor.org/packages/AneuFinderData/")
2071 (synopsis "Data package for @code{AneuFinder}")
2072 (description "This package contains whole-genome single cell sequencing data for
2073demonstration purposes in the @code{AneuFinder} package.")
2074 (license license:artistic2.0)))
2075
2076(define-public r-arrmdata
2077 (package
2078 (name "r-arrmdata")
2079 (version "1.48.0")
2080 (source (origin
2081 (method url-fetch)
2082 (uri (bioconductor-uri "ARRmData" version 'experiment))
2083 (sha256
2084 (base32 "1hg1n8khf9dgq1lghi5px8awcf4aywgm78ab5rwv70f47ys6igj1"))))
2085 (properties
2086 `((upstream-name . "ARRmData")))
2087 (build-system r-build-system)
2088 (home-page "https://www.bioconductor.org/packages/ARRmData/")
2089 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
2090 (description
2091 "This package provides raw beta values from 36 samples across 3 groups
2092from Illumina 450k methylation arrays.")
2093 (license license:artistic2.0)))
2094
2095(define-public r-bcellviper
2096 (package
2097 (name "r-bcellviper")
2098 (version "1.48.0")
2099 (source (origin
2100 (method url-fetch)
2101 (uri (bioconductor-uri "bcellViper" version
2102 'experiment))
2103 (sha256
2104 (base32
2105 "0pyg0xap1pdba852sy0nvldb78dcycx7jz2hxa5aij856zrnmfzz"))))
2106 (properties `((upstream-name . "bcellViper")))
2107 (build-system r-build-system)
2108 (propagated-inputs (list r-biobase))
2109 (home-page "https://bioconductor.org/packages/bcellViper")
2110 (synopsis
2111 "Transcriptional interactome and normal human B-cell expression data")
2112 (description
2113 "This is a tool for human B-cell context-specific transcriptional
2114regulatory network. In addition, this package provides a human normal B-cells
2115dataset for the examples in package viper.")
2116 (license license:gpl2+)))
2117
2118(define-public r-biotmledata
2119 (package
2120 (name "r-biotmledata")
2121 (version "1.36.0")
2122 (source
2123 (origin
2124 (method url-fetch)
2125 (uri (bioconductor-uri "biotmleData" version
2126 'experiment))
2127 (sha256
2128 (base32 "0ndfr5x8kfa8cfmm07c63w4adqdp7cj6sb34wvk4wpm20lid7h5v"))))
2129 (properties `((upstream-name . "biotmleData")))
2130 (build-system r-build-system)
2131 (home-page "https://bioconductor.org/packages/biotmleData")
2132 (synopsis
2133 "Example experimental microarray data set for the \"biotmle\" R package")
2134 (description
2135 "This package provides microarray data (from the Illumina Ref-8 BeadChips
2136platform) and phenotype-level data from an epidemiological investigation of
2137benzene exposure, packaged using @code{SummarizedExperiemnt}, for use as an
2138example with the @code{biotmle} R package.")
2139 (license license:expat)))
2140
2141(define-public r-bladderbatch
2142 (package
2143 (name "r-bladderbatch")
2144 (version "1.50.0")
2145 (source (origin
2146 (method url-fetch)
2147 (uri (bioconductor-uri "bladderbatch" version
2148 'experiment))
2149 (sha256
2150 (base32
2151 "0x6yx733b2j1flvphgcgbnbifmkkwri62bbsi5m707vm5cp6q6s3"))))
2152 (properties `((upstream-name . "bladderbatch")))
2153 (build-system r-build-system)
2154 (propagated-inputs (list r-biobase))
2155 (home-page "https://bioconductor.org/packages/bladderbatch")
2156 (synopsis "Bladder gene expression data illustrating batch effects")
2157 (description
2158 "This package contains microarray gene expression data on 57 bladder samples from
21595 batches. The data are used as an illustrative example for the sva package.")
2160 (license license:artistic2.0)))
2161
2162(define-public r-bodymaprat
2163 (package
2164 (name "r-bodymaprat")
2165 (version "1.28.0")
2166 (source
2167 (origin
2168 (method url-fetch)
2169 (uri (bioconductor-uri "bodymapRat" version
2170 'experiment))
2171 (sha256
2172 (base32 "0031jjm1w98gx37bfhp7hxp59m1f0qdwx56p5yj0m6b5f32ffrqy"))))
2173 (properties `((upstream-name . "bodymapRat")))
2174 (build-system r-build-system)
2175 (arguments
2176 (list
2177 ;; Tests fail with: could not find function "bodymapRat"
2178 #:tests? #false
2179 #:phases
2180 '(modify-phases %standard-phases
2181 (add-after 'unpack 'set-HOME
2182 (lambda _
2183 (setenv "HOME" "/tmp")))
2184 (add-after 'unpack 'avoid-internet-access
2185 (lambda _
2186 (setenv "GUIX_BUILD" "yes")
2187 (substitute* "R/zzz.R"
2188 (("createHubAccessors.*" m)
2189 (string-append
2190 "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m "}"))))))))
2191 (propagated-inputs (list r-experimenthub r-summarizedexperiment))
2192 (native-inputs (list r-knitr r-testthat))
2193 (home-page "https://bioconductor.org/packages/bodymapRat")
2194 (synopsis "Experimental dataset from the rat BodyMap project")
2195 (description
2196 "This package contains a @code{SummarizedExperiment} from the Yu et
2197al. (2013) paper that performed the rat @code{BodyMap} across 11 organs and 4
2198developmental stages. Raw FASTQ files were downloaded and mapped using
2199STAR. Data is available on @code{ExperimentHub} as a data package.")
2200 (license license:cc-by4.0)))
2201
2202(define-public r-biscuiteerdata
2203 (package
2204 (name "r-biscuiteerdata")
2205 (version "1.26.0")
2206 (source
2207 (origin
2208 (method url-fetch)
2209 (uri (bioconductor-uri "biscuiteerData" version 'experiment))
2210 (sha256
2211 (base32 "0l0ajihw7hrjrygvwrx3i06v2ixkz9m0j4yl5a89yjdwfqczyd65"))))
2212 (properties
2213 `((upstream-name . "biscuiteerData")))
2214 (build-system r-build-system)
2215 (propagated-inputs
2216 (list r-annotationhub r-curl r-experimenthub r-genomicranges))
2217 (native-inputs (list r-knitr))
2218 (home-page "https://bioconductor.org/packages/biscuiteerData")
2219 (synopsis "Data package for Biscuiteer")
2220 (description
2221 "This package contains default datasets used by the Bioconductor package
2222biscuiteer.")
2223 (license license:gpl3)))
2224
2225(define-public r-breakpointrdata
2226 (package
2227 (name "r-breakpointrdata")
2228 (version "1.30.0")
2229 (source (origin
2230 (method url-fetch)
2231 (uri (bioconductor-uri "breakpointRdata" version 'experiment))
2232 (sha256
2233 (base32
2234 "1i2xd9j2vswi1yvqazq84xmqa60fjp5nkmn3nsccq612z8vv3a43"))))
2235 (properties `((upstream-name . "breakpointRdata")))
2236 (build-system r-build-system)
2237 (native-inputs (list r-biocstyle r-knitr))
2238 (home-page "https://github.com/daewoooo/breakpointRdata")
2239 (synopsis "Strand-seq data for demonstration purposes")
2240 (description
2241 "This package is a collection of Strand-seq data. The main purpose is to
2242demonstrate functionalities of the @code{breakpointR} package.")
2243 (license license:expat)))
2244
2245(define-public r-breastcancervdx
2246 (package
2247 (name "r-breastcancervdx")
2248 (version "1.50.0")
2249 (source
2250 (origin
2251 (method url-fetch)
2252 (uri (bioconductor-uri "breastCancerVDX" version
2253 'experiment))
2254 (sha256
2255 (base32 "0vhzafn8jmhpjhgc5rayll86ahp53qv8p0cadb9mq5wmmv78ik1q"))))
2256 (properties `((upstream-name . "breastCancerVDX")))
2257 (build-system r-build-system)
2258 (home-page "https://bioconductor.org/packages/breastCancerVDX")
2259 (synopsis "Gene expression datasets")
2260 (description
2261 "This package is a collection of gene expression data from a breast
2262cancer study published in Wang et al. 2005 and Minn et al 2007.")
2263 (license license:artistic2.0)))
2264
2265(define-public r-celldex
2266 (package
2267 (name "r-celldex")
2268 (version "1.22.0")
2269 (source
2270 (origin
2271 (method url-fetch)
2272 (uri (bioconductor-uri "celldex" version 'experiment))
2273 (sha256
2274 (base32 "0sf2b2p5bgwlr8zvvgq5q2ldzfikfd0yi7jll1bqxi4i3i0gvfaw"))))
2275 (properties `((upstream-name . "celldex")))
2276 (build-system r-build-system)
2277 ;; Tests access the internet via r-gypsum.
2278 (arguments (list #:tests? #false))
2279 (propagated-inputs
2280 (list r-alabaster-base
2281 r-alabaster-matrix
2282 r-alabaster-se
2283 r-annotationdbi
2284 r-annotationhub
2285 r-dbi
2286 r-delayedarray
2287 r-delayedmatrixstats
2288 r-experimenthub
2289 r-gypsum
2290 r-jsonlite
2291 r-matrix
2292 r-rsqlite
2293 r-s4vectors
2294 r-summarizedexperiment))
2295 (native-inputs (list r-biocmanager r-knitr r-testthat))
2296 (home-page "https://github.com/LTLA/celldex")
2297 (synopsis "Reference index for cell types")
2298 (description
2299 "This package provides a collection of reference expression datasets with
2300curated cell type labels, for use in procedures like automated annotation of
2301single-cell data or deconvolution of bulk RNA-seq.")
2302 (license license:gpl3)))
2303
2304(define-public r-champdata
2305 (package
2306 (name "r-champdata")
2307 (version "2.44.0")
2308 (source (origin
2309 (method url-fetch)
2310 (uri (bioconductor-uri "ChAMPdata" version 'experiment))
2311 (sha256
2312 (base32
2313 "01v40dchdpb3sqlr2fz0lgfyass3qr5yds7m257m2pirr5qjdj2a"))))
2314 (properties `((upstream-name . "ChAMPdata")))
2315 (build-system r-build-system)
2316 (propagated-inputs (list r-biocgenerics r-genomicranges))
2317 (home-page "https://bioconductor.org/packages/ChAMPdata")
2318 (synopsis "Data packages for ChAMP package")
2319 (description
2320 "This package provides datasets needed for ChAMP including a test dataset
2321and blood controls for CNA analysis.")
2322 (license license:gpl3)))
2323
2324(define-public r-chipexoqualexample
2325 (package
2326 (name "r-chipexoqualexample")
2327 (version "1.36.0")
2328 (source
2329 (origin
2330 (method url-fetch)
2331 (uri (bioconductor-uri "ChIPexoQualExample" version
2332 'experiment))
2333 (sha256
2334 (base32 "16lv5pr9rxvz7zgvxkigyd6z4ra35gn1b2yrpk51cm0py5hjsbj7"))))
2335 (properties `((upstream-name . "ChIPexoQualExample")))
2336 (build-system r-build-system)
2337 (native-inputs (list r-knitr))
2338 (home-page "https://www.github.com/keleslab/ChIPexoQualExample")
2339 (synopsis "Example data for the ChIPexoQual package")
2340 (description
2341 "This package contains data for the @code{ChIPexoQual} package,
2342consisting of 3 chromosome 1 aligned reads from a @code{ChIP-exo} experiment
2343for @code{FoxA1} in mouse liver cell lines aligned to the mm9 genome.")
2344 (license license:gpl2+)))
2345
2346(define-public r-chromstardata
2347 (package
2348 (name "r-chromstardata")
2349 (version "1.36.0")
2350 (source
2351 (origin
2352 (method url-fetch)
2353 (uri (bioconductor-uri "chromstaRData" version 'experiment))
2354 (sha256
2355 (base32 "0v8blcacwixqzdpqalx3bajakn0nmkmagpdzccfpi7ry3sazl2f4"))))
2356 (properties `((upstream-name . "chromstaRData")))
2357 (build-system r-build-system)
2358 (home-page "https://bioconductor.org/packages/chromstaRData/")
2359 (synopsis "ChIP-seq data for demonstration purposes")
2360 (description
2361 "This package provides ChIP-seq data for demonstration purposes in the
2362chromstaR package.")
2363 (license license:gpl3)))
2364
2365(define-public r-copyhelper
2366 (package
2367 (name "r-copyhelper")
2368 (version "1.44.0")
2369 (source
2370 (origin
2371 (method url-fetch)
2372 (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
2373 (sha256
2374 (base32 "1w10dz2jccrax7xhyi5bdc46a0p24n503p8nq5fj1dfgl2csjk13"))))
2375 (properties `((upstream-name . "CopyhelpeR")))
2376 (build-system r-build-system)
2377 (native-inputs (list r-biocstyle))
2378 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
2379 (synopsis "Helper files for CopywriteR")
2380 (description
2381 "This package contains the helper files that are required to run the
2382Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
2383and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
2384mm10. In addition, it contains a blacklist filter to remove regions that
2385display copy number variation. Files are stored as GRanges objects from the
2386GenomicRanges Bioconductor package.")
2387 (license license:gpl2)))
2388
2389(define-public r-derfinderdata
2390 (package
2391 (name "r-derfinderdata")
2392 (version "2.30.0")
2393 (source
2394 (origin
2395 (method url-fetch)
2396 (uri (bioconductor-uri "derfinderData" version
2397 'experiment))
2398 (sha256
2399 (base32 "05mnf4pglfl0gl7bswc6i4ipcbrl58jivpkf1xsmgqnsy453cbck"))))
2400 (properties `((upstream-name . "derfinderData")))
2401 (build-system r-build-system)
2402 (native-inputs (list r-knitr))
2403 (home-page "https://github.com/leekgroup/derfinderData")
2404 (synopsis "Processed BigWigs from BrainSpan for examples")
2405 (description
2406 "This package provides processed 22 samples from @code{BrainSpan} keeping
2407only the information for chromosome 21. Data is stored in the @code{BigWig}
2408format and is used for examples in other packages.")
2409 (license license:artistic2.0)))
2410
2411(define-public r-faahko
2412 (package
2413 (name "r-faahko")
2414 (version "1.52.0")
2415 (source
2416 (origin
2417 (method url-fetch)
2418 (uri (bioconductor-uri "faahKO" version
2419 'experiment))
2420 (sha256
2421 (base32 "12bz5ampa411xcw8mcjis9cam5j0q8c1y2c50wprmi7iz9jxymn3"))))
2422 (properties `((upstream-name . "faahKO")))
2423 (build-system r-build-system)
2424 (propagated-inputs (list r-xcms))
2425 (home-page "http://dx.doi.org/10.1021/bi0480335")
2426 (synopsis "Saghatelian et al. (2004) FAAH knockout LC/MS data")
2427 (description
2428 "This package includes positive ionization mode data in @code{NetCDF}
2429file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data
2430originally reported in \"Assignment of Endogenous Substrates to Enzymes by
2431Global Metabolite Profiling\" Biochemistry; 2004; 43(45). It also includes
2432detected peaks in an @code{xcmsSet}.")
2433 (license license:lgpl2.0+)))
2434
2435(define-public r-flowsorted-blood-450k
2436 (package
2437 (name "r-flowsorted-blood-450k")
2438 (version "1.50.0")
2439 (source (origin
2440 (method url-fetch)
2441 (uri (bioconductor-uri "FlowSorted.Blood.450k"
2442 version 'experiment))
2443 (sha256
2444 (base32
2445 "00kz0wyhxaw5mph2qw088l8bxp8kx4xkiadg4mlmks0zzccxcxk2"))))
2446 (properties `((upstream-name . "FlowSorted.Blood.450k")))
2447 (build-system r-build-system)
2448 (propagated-inputs (list r-minfi))
2449 (home-page "https://bioconductor.org/packages/FlowSorted.Blood.450k")
2450 (synopsis
2451 "Illumina HumanMethylation data on sorted blood cell populations")
2452 (description
2453 "This package provides raw data objects for the Illumina 450k DNA
2454methylation microarrays, and an object depicting which CpGs on the array are
2455associated with cell type.")
2456 (license license:artistic2.0)))
2457
2458(define-public r-flowsorted-blood-epic
2459 (package
2460 (name "r-flowsorted-blood-epic")
2461 (version "2.16.0")
2462 (source (origin
2463 (method url-fetch)
2464 (uri (bioconductor-uri "FlowSorted.Blood.EPIC" version
2465 'experiment))
2466 (sha256
2467 (base32
2468 "1jhls1adg9q5c45daabfv114mwj113zmha4f91kry32iy8a681yy"))))
2469 (properties `((upstream-name . "FlowSorted.Blood.EPIC")))
2470 (build-system r-build-system)
2471 ;; Tests require Internet access via ExperimentHub.
2472 (arguments (list #:tests? #false))
2473 (propagated-inputs
2474 (list r-annotationhub
2475 r-experimenthub
2476 r-genefilter
2477 r-minfi
2478 r-nlme
2479 r-quadprog
2480 r-s4vectors
2481 r-summarizedexperiment))
2482 (native-inputs (list r-knitr r-testthat))
2483 (home-page "https://github.com/immunomethylomics/FlowSorted.Blood.EPIC")
2484 (synopsis
2485 "Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells")
2486 (description
2487 "This package provides raw data objects to be used for blood cell
2488proportion estimation in minfi and similar packages. The
2489@code{FlowSorted.Blood.EPIC} object is based in samples assayed by Brock
2490Christensen and colleagues; for details see Salas et al. 2018.
2491https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.")
2492 (license license:gpl3)))
2493
2494(define-public r-flowworkspacedata
2495 (package
2496 (name "r-flowworkspacedata")
2497 (version "3.24.0")
2498 (source
2499 (origin
2500 (method url-fetch)
2501 (uri (bioconductor-uri "flowWorkspaceData" version
2502 'experiment))
2503 (sha256
2504 (base32 "1k379pd12d0l0j5x2nvn6cy7fqpdaamy6a4yn7f2akm9w8j5k4qs"))))
2505 (properties `((upstream-name . "flowWorkspaceData")))
2506 (build-system r-build-system)
2507 (home-page "https://bioconductor.org/packages/flowWorkspaceData")
2508 (synopsis "Data for flowWorkspace tests and vignettes")
2509 (description
2510 "The necessary external data to run the @code{flowWorkspace} and
2511@code{openCyto} vignette is found in this package. This data package contains
2512two flowJo, one diva xml workspace and the associated @code{fcs} files as well
2513as three @code{GatingSets} for testing the @code{flowWorkspace},
2514@code{openCyto} and @code{CytoML} packages.")
2515 (license license:gpl2)))
2516
2517(define-public r-genelendatabase
2518 (package
2519 (name "r-genelendatabase")
2520 (version "1.48.0")
2521 (source
2522 (origin
2523 (method url-fetch)
2524 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
2525 (sha256
2526 (base32 "00y68axad1j9h7zf1gsviw7sv5znjbi4safabd1rp6rgykx96q6n"))))
2527 (properties
2528 `((upstream-name . "geneLenDataBase")))
2529 (build-system r-build-system)
2530 (propagated-inputs
2531 (list r-genomicfeatures r-rtracklayer r-txdbmaker))
2532 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
2533 (synopsis "Lengths of mRNA transcripts for a number of genomes")
2534 (description
2535 "This package provides the lengths of mRNA transcripts for a number of
2536genomes and gene ID formats, largely based on the UCSC table browser.")
2537 (license license:lgpl2.0+)))
2538
2539(define-public r-genomationdata
2540 (package
2541 (name "r-genomationdata")
2542 (version "1.44.0")
2543 (source
2544 (origin
2545 (method url-fetch)
2546 (uri (bioconductor-uri "genomationData" version 'experiment))
2547 (sha256
2548 (base32 "1k4zb3pa599n79s93559wl8ikn1kdj7j8ad0wb60hzy7camvai7i"))))
2549 (properties
2550 `((upstream-name . "genomationData")))
2551 (build-system r-build-system)
2552 ;; As this package provides little more than large data files, it doesn't
2553 ;; make sense to build substitutes.
2554 (arguments `(#:substitutable? #f))
2555 (native-inputs
2556 (list r-knitr))
2557 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
2558 (synopsis "Experimental data for use with the genomation package")
2559 (description
2560 "This package contains experimental genetic data for use with the
2561genomation package. Included are Chip Seq, Methylation and Cage data,
2562downloaded from Encode.")
2563 (license license:gpl3+)))
2564
2565(define-public r-golubesets
2566 (package
2567 (name "r-golubesets")
2568 (version "1.54.0")
2569 (source
2570 (origin
2571 (method url-fetch)
2572 (uri (bioconductor-uri "golubEsets" version
2573 'experiment))
2574 (sha256
2575 (base32 "08hzy0xlrs687m1xql99qjls05nvp7x51brsws02rwr2jgsbpij7"))))
2576 (properties `((upstream-name . "golubEsets")))
2577 (build-system r-build-system)
2578 (propagated-inputs (list r-biobase))
2579 (home-page "https://bioconductor.org/packages/golubEsets")
2580 (synopsis "ExpressionSets for golub leukemia data")
2581 (description
2582 "This is a representation of public golub data with some covariate data
2583of provenance unknown to the maintainer at present; it now employs
2584@code{ExpressionSet} format.")
2585 (license license:lgpl2.0+)))
2586
2587(define-public r-gsvadata
2588 (package
2589 (name "r-gsvadata")
2590 (version "1.48.0")
2591 (source
2592 (origin
2593 (method url-fetch)
2594 (uri (bioconductor-uri "GSVAdata" version
2595 'experiment))
2596 (sha256
2597 (base32 "0b974c28wnskx7clz54qj1hvm9fiaclbl9r6z2ygbgbphs4lwa2s"))))
2598 (properties `((upstream-name . "GSVAdata")))
2599 (build-system r-build-system)
2600 (propagated-inputs (list r-biobase r-gseabase r-matrix r-spatialexperiment
2601 r-summarizedexperiment))
2602 (home-page "https://bioconductor.org/packages/GSVAdata")
2603 (synopsis "Data employed in the vignette of the GSVA package")
2604 (description
2605 "This package stores the data employed in the vignette of the GSVA package.
2606These data belong to the following publications: Armstrong et al. Nat Genet
260730:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard,
2608Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et
2609al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak
2610et al. Cancer Cell 17:98-110, 2010; Costa et al. FEBS J, 288:2311-2331,
26112021.")
2612 (license license:artistic2.0)))
2613
2614(define-public r-hellorangesdata
2615 (package
2616 (name "r-hellorangesdata")
2617 (version "1.38.0")
2618 (source
2619 (origin
2620 (method url-fetch)
2621 (uri (bioconductor-uri "HelloRangesData" version
2622 'experiment))
2623 (sha256
2624 (base32 "0y8qg7kb6igvxbmp9fnbbvzvgbdmjr0m0g0anvydd02j93ag3hn6"))))
2625 (properties `((upstream-name . "HelloRangesData")))
2626 (build-system r-build-system)
2627 (native-inputs (list r-biocstyle))
2628 (home-page "https://bioconductor.org/packages/HelloRangesData")
2629 (synopsis "Data for the HelloRanges tutorial vignette")
2630 (description
2631 "This package provides the data that were used in the @url{bedtools
2632tutorial by Aaron Quinlan,
2633http://quinlanlab.org/tutorials/bedtools/bedtools.html}. It includes a subset
2634of the @code{DnaseI} hypersensitivity data from \"Maurano et al. Systematic
2635Localization of Common Disease-Associated Variation in Regulatory
2636DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195.\" The rest of the
2637tracks were originally downloaded from the UCSC table browser. See the
2638@code{HelloRanges} vignette for a port of the bedtools tutorial to R.")
2639 (license license:gpl2+)))
2640
2641(define-public r-hdcytodata
2642 (package
2643 (name "r-hdcytodata")
2644 (version "1.32.0")
2645 (source (origin
2646 (method url-fetch)
2647 (uri (bioconductor-uri "HDCytoData" version 'experiment))
2648 (sha256
2649 (base32
2650 "1zah1xd9kksd8apvxisjp3w6xhwcqzb2kvrfgikf5jhv2kn98vcz"))))
2651 (properties `((upstream-name . "HDCytoData")))
2652 (build-system r-build-system)
2653 (arguments
2654 (list
2655 #:phases
2656 '(modify-phases %standard-phases
2657 (add-after 'unpack 'set-HOME
2658 (lambda _
2659 (setenv "HOME" "/tmp")))
2660 (add-after 'unpack 'avoid-internet-access
2661 (lambda _
2662 (setenv "GUIX_BUILD" "yes")
2663 (substitute* "R/zzz.R"
2664 (("createHubAccessors.*" m)
2665 (string-append
2666 "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m "}"))))))))
2667 (propagated-inputs
2668 (list r-experimenthub r-flowcore r-summarizedexperiment))
2669 (native-inputs (list r-knitr))
2670 (home-page "https://github.com/lmweber/HDCytoData")
2671 (synopsis
2672 "Set of high-dimensional flow cytometry and mass cytometry benchmark datasets")
2673 (description
2674 "HDCytoData contains a set of high-dimensional cytometry benchmark
2675datasets. These datasets are formatted into SummarizedExperiment and flowSet
2676Bioconductor object formats, including all required metadata. Row metadata
2677includes sample IDs, group IDs, patient IDs, reference cell population or
2678cluster labels and labels identifying spiked in cells. Column metadata
2679includes channel names, protein marker names, and protein marker classes.")
2680 (license license:expat)))
2681
2682(define-public r-illumina450probevariants-db
2683 (package
2684 (name "r-illumina450probevariants-db")
2685 (version "1.48.0")
2686 (source (origin
2687 (method url-fetch)
2688 (uri (bioconductor-uri "Illumina450ProbeVariants.db"
2689 version 'experiment))
2690 (sha256
2691 (base32
2692 "0c253i6hygwcazxpww0rkq5dya031v34s6kj9smni1gyr9j517g0"))))
2693 (properties `((upstream-name . "Illumina450ProbeVariants.db")))
2694 (build-system r-build-system)
2695 (home-page "https://bioconductor.org/packages/Illumina450ProbeVariants.db")
2696 (synopsis
2697 "Variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes")
2698 (description
2699 "This package includes details on variants for each probe on the 450k
2700bead chip for each of the four populations (Asian, American, African and
2701European).")
2702 (license license:gpl3)))
2703
2704(define-public r-illuminadatatestfiles
2705 (package
2706 (name "r-illuminadatatestfiles")
2707 (version "1.50.0")
2708 (source
2709 (origin
2710 (method url-fetch)
2711 (uri (bioconductor-uri "IlluminaDataTestFiles" version
2712 'experiment))
2713 (sha256
2714 (base32 "09d897v4r24xdr54d1x00w6vxvm9imcfnz0d8nkmkrbr4z8k6x3b"))))
2715 (properties `((upstream-name . "IlluminaDataTestFiles")))
2716 (build-system r-build-system)
2717 (home-page "https://bioconductor.org/packages/IlluminaDataTestFiles")
2718 (synopsis "Illumina microarray files (IDAT) for testing")
2719 (description
2720 "This package contains example data for Illumina microarray output files,
2721for testing purposes.")
2722 (license license:artistic2.0)))
2723
2724(define-public r-italicsdata
2725 (package
2726 (name "r-italicsdata")
2727 (version "2.50.0")
2728 (source
2729 (origin
2730 (method url-fetch)
2731 (uri (bioconductor-uri "ITALICSData" version 'experiment))
2732 (sha256
2733 (base32 "1wb1ifjiim7cwd5q4pgk3xl4365bgfw1fdxianqrv2znxbai3m1l"))))
2734 (properties `((upstream-name . "ITALICSData")))
2735 (build-system r-build-system)
2736 (home-page "http://bioinfo.curie.fr")
2737 (synopsis "ITALICS data")
2738 (description "This package provides data needed to use the ITALICS
2739package.")
2740 ;; Expanded from GPL
2741 (license (list license:gpl2+ license:gpl3+))))
2742
2743(define-public r-jaspar2016
2744 (package
2745 (name "r-jaspar2016")
2746 (version "1.40.0")
2747 (source
2748 (origin
2749 (method url-fetch)
2750 (uri (bioconductor-uri "JASPAR2016" version 'experiment))
2751 (sha256
2752 (base32 "06xk14h9dgpw9asqn8napwb2q71ylpgk2hmy3nmhp7qmmdqlckds"))))
2753 (properties `((upstream-name . "JASPAR2016")))
2754 (build-system r-build-system)
2755 (home-page "https://jaspar.elixir.no/")
2756 (synopsis "Data package for JASPAR 2016")
2757 (description
2758 "This is a data package for JASPAR 2016. To search this databases,
2759please use the package TFBSTools.")
2760 (license license:gpl2)))
2761
2762(define-public r-leukemiaseset
2763 (package
2764 (name "r-leukemiaseset")
2765 (version "1.48.0")
2766 (source
2767 (origin
2768 (method url-fetch)
2769 (uri (bioconductor-uri "leukemiasEset" version 'experiment))
2770 (sha256
2771 (base32 "1r11290yl0n8p26phb0nn5b05xhxrqfl1vw03rvwj7parqnydl06"))))
2772 (properties `((upstream-name . "leukemiasEset")))
2773 (build-system r-build-system)
2774 (propagated-inputs (list r-biobase))
2775 (home-page "https://bioconductor.org/packages/leukemiasEset")
2776 (synopsis "Leukemia's microarray gene expression data (expressionSet)")
2777 (description
2778 "This package provides an @code{expressionSet} containing gene expression
2779data from 60 bone marrow samples of patients with one of the four main types
2780of leukemia (ALL, AML, CLL, CML) or non-leukemia.")
2781 (license license:gpl2+)))
2782
2783(define-public r-lungcancerlines
2784 (package
2785 (name "r-lungcancerlines")
2786 (version "0.50.0")
2787 (source
2788 (origin
2789 (method url-fetch)
2790 (uri (bioconductor-uri "LungCancerLines" version
2791 'experiment))
2792 (sha256
2793 (base32 "0pags7zjx6vazfisn2j458b1x25979fq8wfbcvfyq73ia7wpfsrv"))))
2794 (properties `((upstream-name . "LungCancerLines")))
2795 (build-system r-build-system)
2796 (propagated-inputs (list r-rsamtools))
2797 (home-page "https://bioconductor.org/packages/LungCancerLines")
2798 (synopsis "Reads from Two Lung Cancer Cell Lines")
2799 (description
2800 "This package contains reads from an RNA-seq experiment between two lung
2801cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as
2802Fastq files and are meant for use with the TP53Genome object in the
2803@code{gmapR} package.")
2804 (license license:artistic2.0)))
2805
2806(define-public r-macrophage
2807 (package
2808 (name "r-macrophage")
2809 (version "1.28.0")
2810 (source (origin
2811 (method url-fetch)
2812 (uri (bioconductor-uri "macrophage" version
2813 'experiment))
2814 (sha256
2815 (base32
2816 "1slm3cn1b04nl6jys2gz5p4aidgw475h4xi5a60f0l9j96b360ds"))))
2817 (properties `((upstream-name . "macrophage")))
2818 (build-system r-build-system)
2819 (native-inputs (list r-knitr))
2820 (home-page "https://bioconductor.org/packages/macrophage")
2821 (synopsis "Human macrophage immune response data")
2822 (description
2823 "This package provides the output of running @code{Salmon} on a set of 24
2824RNA-seq samples from Alasoo, et al. \"Shared genetic effects on chromatin and
2825gene expression indicate a role for enhancer priming in immune response\", published
2826in Nature Genetics, January 2018.")
2827 (license license:gpl2+)))
2828
2829(define-public r-methylaiddata
2830 (package
2831 (name "r-methylaiddata")
2832 (version "1.44.0")
2833 (source
2834 (origin
2835 (method url-fetch)
2836 (uri (bioconductor-uri "MethylAidData" version
2837 'experiment))
2838 (sha256
2839 (base32 "0v1ndz8ldnbych597ngxrz944rzibffpph7wsy63yliyqi1liy5v"))))
2840 (properties `((upstream-name . "MethylAidData")))
2841 (build-system r-build-system)
2842 (propagated-inputs (list r-methylaid))
2843 (native-inputs (list r-biocstyle r-knitr))
2844 (home-page "https://bioconductor.org/packages/MethylAidData")
2845 (synopsis
2846 "MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples")
2847 (description
2848 "This package provides a data package containing summarized Illumina 450k
2849array data on 2800 samples and summarized EPIC data for 2620 samples. The
2850data can be use as a background data set in the interactive application.")
2851 (license license:gpl2+)))
2852
2853(define-public r-methylclockdata
2854 (package
2855 (name "r-methylclockdata")
2856 (version "1.20.0")
2857 (source
2858 (origin
2859 (method url-fetch)
2860 (uri (bioconductor-uri "methylclockData" version
2861 'experiment))
2862 (sha256
2863 (base32 "0w099crxrphsk9avzs7fgggxcdskl7j2m2kari0xxzyfqpcmla7y"))))
2864 (properties `((upstream-name . "methylclockData")))
2865 (build-system r-build-system)
2866 (propagated-inputs (list r-experimenthub r-experimenthubdata))
2867 (native-inputs (list r-knitr))
2868 (home-page "https://github.com/isglobal-brge/methylclockData")
2869 (synopsis "Data for methylclock package")
2870 (description
2871 "This package contains a collection of 9 datasets, andrews and bakulski
2872cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete,
2873combined cord blood, cord bloo d gse68456, gervin and lyle cord blood,
2874guintivano dlpfc and saliva gse48472. The data are used to estimate cell
2875counts using Extrinsic epigenetic age acceleration (EEAA) method. It also
2876contains a collection of 12 datasets to use with @code{MethylClock} package to
2877estimate chronological and gestational DNA methylation with estimators to use
2878with different methylation clocks.")
2879 (license license:expat)))
2880
2881(define-public r-mousegastrulationdata
2882 (package
2883 (name "r-mousegastrulationdata")
2884 (version "1.26.0")
2885 (source (origin
2886 (method url-fetch)
2887 (uri (bioconductor-uri "MouseGastrulationData" version
2888 'experiment))
2889 (sha256
2890 (base32
2891 "0hjng4p8nc55b8vmfw658hnc1kgg60c9179s4yh3zvgimp1hj9gb"))))
2892 (properties `((upstream-name . "MouseGastrulationData")))
2893 (build-system r-build-system)
2894 ;; Tests require Internet access thanks to ExperimentHub.
2895 (arguments (list #:tests? #false))
2896 (propagated-inputs (list r-biocgenerics
2897 r-bumpymatrix
2898 r-experimenthub
2899 r-s4vectors
2900 r-singlecellexperiment
2901 r-spatialexperiment
2902 r-summarizedexperiment))
2903 (native-inputs (list r-knitr r-testthat))
2904 (home-page "https://github.com/MarioniLab/MouseGastrulationData")
2905 (synopsis
2906 "Single-Cell omics data across mouse gastrulation and early organogenesis")
2907 (description
2908 "This package provides processed and raw count data for single-cell RNA
2909sequencing. In addition, this package offers single-cell ATAC-seq, and
2910@code{seqFISH} (spatial transcriptomic) experiments performed along a
2911timecourse of mouse gastrulation and early organogenesis.")
2912 (license license:gpl3)))
2913
2914(define-public r-minfidata
2915 (package
2916 (name "r-minfidata")
2917 (version "0.58.0")
2918 (source (origin
2919 (method url-fetch)
2920 (uri (bioconductor-uri "minfiData" version 'experiment))
2921 (sha256
2922 (base32
2923 "02diyhp3dl9aldz41qsnj8mm6fcpckd91yk0j0k2qmp6fcnbk0xz"))))
2924 (properties `((upstream-name . "minfiData")))
2925 (build-system r-build-system)
2926 (propagated-inputs
2927 (list r-illuminahumanmethylation450kanno-ilmn12-hg19
2928 r-illuminahumanmethylation450kmanifest
2929 r-minfi))
2930 (home-page "https://bioconductor.org/packages/minfiData")
2931 (synopsis "Example data for the Illumina Methylation 450k array")
2932 (description
2933 "This package provides data from 6 samples across 2 groups from 450k
2934methylation arrays.")
2935 (license license:artistic2.0)))
2936
2937(define-public r-minfidataepic
2938 (package
2939 (name "r-minfidataepic")
2940 (version "1.38.0")
2941 (source
2942 (origin
2943 (method url-fetch)
2944 (uri (bioconductor-uri "minfiDataEPIC" version
2945 'experiment))
2946 (sha256
2947 (base32 "1ssqck324gs6b5r3r2wchywmmh8khkqp6sia92ahcmnsf2r2ngd7"))))
2948 (properties `((upstream-name . "minfiDataEPIC")))
2949 (build-system r-build-system)
2950 (propagated-inputs (list r-illuminahumanmethylationepicanno-ilm10b2-hg19
2951 r-illuminahumanmethylationepicmanifest r-minfi))
2952 (home-page "https://bioconductor.org/packages/minfiDataEPIC")
2953 (synopsis "Example data for the Illumina Methylation EPIC array")
2954 (description
2955 "This package provides data from 3 technical replicates of the cell line
2956GM12878 from the EPIC methylation array.")
2957 (license license:artistic2.0)))
2958
2959(define-public r-minionsummarydata
2960 (package
2961 (name "r-minionsummarydata")
2962 (version "1.42.0")
2963 (source
2964 (origin
2965 (method url-fetch)
2966 (uri (bioconductor-uri "minionSummaryData" version
2967 'experiment))
2968 (sha256
2969 (base32 "0ybjgwg0lclf3hf8y2dkpqhbbvaihmb6mszwnxl58l8gv8swh1cr"))))
2970 (properties `((upstream-name . "minionSummaryData")))
2971 (build-system r-build-system)
2972 (native-inputs (list r-knitr))
2973 (home-page "https://bioconductor.org/packages/minionSummaryData")
2974 (synopsis
2975 "Summarized MinION sequencing data published by Ashton et al. 2015")
2976 (description
2977 "This package provides summarized @code{MinION} sequencing data for
2978Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are
2979each provided as @code{Fast5Summary} objects.")
2980 (license license:expat)))
2981
2982(define-public r-msdata
2983 (package
2984 (name "r-msdata")
2985 (version "0.52.0")
2986 (source
2987 (origin
2988 (method url-fetch)
2989 (uri (bioconductor-uri "msdata" version 'experiment))
2990 (sha256
2991 (base32 "0k1pag9m4nwrzp3vigpbk7bz8k79jzgx7m64yq3x3ch20ida18kk"))))
2992 (properties `((upstream-name . "msdata")))
2993 (build-system r-build-system)
2994 (home-page "https://bioconductor.org/packages/msdata")
2995 (synopsis "Various Mass Spectrometry raw data example files")
2996 (description
2997 "This package provides Ion Trap positive ionization mode data in mzML file
2998format. It includes a subset from 500-850 m/z and 1190-1310 seconds,
2999including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex
3000III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5;
3001LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
3002files for various search engines.")
3003 (license license:gpl2+)))
3004
3005(define-public r-msigdb
3006 (package
3007 (name "r-msigdb")
3008 (version "1.20.0")
3009 (source (origin
3010 (method url-fetch)
3011 (uri (bioconductor-uri "msigdb" version
3012 'experiment))
3013 (sha256
3014 (base32
3015 "1rgbf28nlyf84ax7nv70mlqbmdqkp18x8n8np8qgvncyi595x0qr"))))
3016 (properties `((upstream-name . "msigdb")))
3017 (build-system r-build-system)
3018 ;; Tests require Internet access.
3019 (arguments (list #:tests? #false))
3020 (propagated-inputs (list r-annotationdbi
3021 r-annotationhub
3022 r-experimenthub
3023 r-gseabase
3024 r-org-hs-eg-db
3025 r-org-mm-eg-db))
3026 (native-inputs (list r-knitr r-testthat))
3027 (home-page "https://doi.org/doi:10.18129/B9.bioc.msigdb")
3028 (synopsis "ExperimentHub package for the molecular signatures database")
3029 (description
3030 "R-msigdb provides the Molecular Signatures Database in a R accessible
3031objects. Signatures are stored in @code{GeneSet} class objects form the
3032GSEABase package and the entire database is stored in a
3033@code{GeneSetCollection} object. These data are then hosted on the
3034@code{ExperimentHub}. Data used in this package was obtained from the
3035@code{MSigDB} of the Broad Institute. Metadata for each gene set is stored
3036along with the gene set in the @code{GeneSet} class object.")
3037 (license license:cc-by4.0)))
3038
3039(define-public r-pasilla
3040 (package
3041 (name "r-pasilla")
3042 (version "1.40.0")
3043 (source
3044 (origin
3045 (method url-fetch)
3046 (uri (bioconductor-uri "pasilla" version 'experiment))
3047 (sha256
3048 (base32 "1d9xrd3hbcnczrmhzrzp9r8c8y399ygbrffijhz5sh9cxd2js4km"))))
3049 (build-system r-build-system)
3050 (propagated-inputs (list r-dexseq))
3051 (native-inputs (list r-knitr))
3052 (home-page "https://www.bioconductor.org/packages/pasilla/")
3053 (synopsis "Data package with per-exon and per-gene read counts")
3054 (description "This package provides per-exon and per-gene read counts
3055computed for selected genes from RNA-seq data that were presented in the
3056article 'Conservation of an RNA regulatory map between Drosophila and mammals'
3057by Brooks et al., Genome Research 2011.")
3058 (license license:lgpl2.1+)))
3059
3060(define-public r-pasillabamsubset
3061 (package
3062 (name "r-pasillabamsubset")
3063 (version "0.50.0")
3064 (source
3065 (origin
3066 (method url-fetch)
3067 (uri (bioconductor-uri "pasillaBamSubset" version
3068 'experiment))
3069 (sha256
3070 (base32 "02r6b1y2hmz623hjipcnzdwas7j3nif34hkzylkc7bds8b9cdzh0"))))
3071 (properties `((upstream-name . "pasillaBamSubset")))
3072 (build-system r-build-system)
3073 (home-page "https://bioconductor.org/packages/pasillaBamSubset")
3074 (synopsis "Subset of BAM files from \"Pasilla\" experiment")
3075 (description
3076 "This package provides a subset of BAM files untreated1.bam (single-end
3077reads) and untreated3.bam (paired-end reads) from \"Pasilla\"
3078experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See
3079the vignette in the pasilla data package for how BAM files untreated1.bam and
3080untreated3.bam were obtained from the RNA-Seq read sequence data that is
3081provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to
3082GSM461181. It also contains the DNA sequence for fly chromosome 4 to which
3083the reads can be mapped.")
3084 (license license:lgpl2.0+)))
3085
3086(define-public r-prolocdata
3087 (package
3088 (name "r-prolocdata")
3089 (version "1.50.0")
3090 (source
3091 (origin
3092 (method url-fetch)
3093 (uri (bioconductor-uri "pRolocdata" version
3094 'experiment))
3095 (sha256
3096 (base32 "1qjrbkfh2j8y36wydybfy6fcc3ljdsybrri671v743bk898p5k7n"))))
3097 (properties `((upstream-name . "pRolocdata")))
3098 (build-system r-build-system)
3099 (propagated-inputs (list r-biobase r-msnbase))
3100 (native-inputs (list r-testthat))
3101 (home-page "https://github.com/lgatto/pRolocdata")
3102 (synopsis "Data accompanying the pRoloc package")
3103 (description
3104 "This package provides mass-spectrometry based spatial proteomics data
3105sets and protein complex separation data. It also contains the time course
3106expression experiment from Mulvey et al. (2015).")
3107 (license license:gpl2)))
3108
3109(define-public r-hsmmsinglecell
3110 (package
3111 (name "r-hsmmsinglecell")
3112 (version "1.32.0")
3113 (source
3114 (origin
3115 (method url-fetch)
3116 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
3117 (sha256
3118 (base32 "1z13byq43ahj4i19asp3w0wn9ifj6fn8ljy3zm607j3vs8yzb9z9"))))
3119 (properties
3120 '((upstream-name . "HSMMSingleCell")
3121 ;; Avoid dependency cycle.
3122 (updater-ignored-native-inputs . ("r-monocle"))))
3123 (build-system r-build-system)
3124 (native-inputs
3125 (list r-biobase r-ggplot2 r-knitr r-reshape2))
3126 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
3127 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
3128 (description
3129 "Skeletal myoblasts undergo a well-characterized sequence of
3130morphological and transcriptional changes during differentiation. In this
3131experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
3132under high mitogen conditions (GM) and then differentiated by switching to
3133low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
3134hundred cells taken over a time-course of serum-induced differentiation.
3135Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
313672 hours) following serum switch using the Fluidigm C1 microfluidic system.
3137RNA from each cell was isolated and used to construct mRNA-Seq libraries,
3138which were then sequenced to a depth of ~4 million reads per library,
3139resulting in a complete gene expression profile for each cell.")
3140 (license license:artistic2.0)))
3141
3142(define-public r-all
3143 (package
3144 (name "r-all")
3145 (version "1.54.0")
3146 (source
3147 (origin
3148 (method url-fetch)
3149 (uri (bioconductor-uri "ALL" version 'experiment))
3150 (sha256
3151 (base32 "1dr5i4h7c1s5hz7lcpv3gh3y9f48676a1wg07xbaig6yim7y6zix"))))
3152 (properties `((upstream-name . "ALL")))
3153 (build-system r-build-system)
3154 (propagated-inputs (list r-biobase))
3155 (native-inputs (list r-rpart))
3156 (home-page "https://bioconductor.org/packages/ALL")
3157 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
3158 (description
3159 "The data consist of microarrays from 128 different individuals with
3160@dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
3161are available. The data have been normalized (using rma) and it is the
3162jointly normalized data that are available here. The data are presented in
3163the form of an @code{exprSet} object.")
3164 (license license:artistic2.0)))
3165
3166(define-public r-affydata
3167 (package
3168 (name "r-affydata")
3169 (version "1.60.0")
3170 (source
3171 (origin
3172 (method url-fetch)
3173 (uri (bioconductor-uri "affydata" version 'experiment))
3174 (sha256
3175 (base32 "0hjkv4pg92a7bwn7wppvmwvj2n8ws6njfdi522fa7ay8d3vg8rfi"))))
3176 (properties `((upstream-name . "affydata")))
3177 (build-system r-build-system)
3178 (propagated-inputs (list r-affy))
3179 (native-inputs (list r-biobase))
3180 (home-page "https://bioconductor.org/packages/affydata/")
3181 (synopsis "Affymetrix data for demonstration purposes")
3182 (description
3183 "This package provides example datasets that represent 'real world
3184examples' of Affymetrix data, unlike the artificial examples included in the
3185package @code{affy}.")
3186 (license license:gpl2+)))
3187
3188(define-public r-gagedata
3189 (package
3190 (name "r-gagedata")
3191 (version "2.50.0")
3192 (source
3193 (origin
3194 (method url-fetch)
3195 (uri (bioconductor-uri "gageData" version 'experiment))
3196 (sha256
3197 (base32 "0kjvr007b0xnkxn5c8x0q6pw5nilrwkyghddk893gs2w2z5x6q98"))))
3198 (properties `((upstream-name . "gageData")))
3199 (build-system r-build-system)
3200 (home-page "https://bioconductor.org/packages/gageData")
3201 (synopsis "Auxiliary data for the gage package")
3202 (description
3203 "This is a supportive data package for the software package @code{gage}.
3204However, the data supplied here are also useful for gene set or pathway
3205analysis or microarray data analysis in general. In this package, we provide
3206two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
3207BMP6 (originally published as an demo dataset for GAGE, also registered as
3208GSE13604 in GEO). This package also includes commonly used gene set data based
3209on KEGG pathways and GO terms for major research species, including human,
3210mouse, rat and budding yeast. Mapping data between common gene IDs for budding
3211yeast are also included.")
3212 (license license:gpl2+)))
3213
3214(define-public r-curatedtcgadata
3215 (package
3216 (name "r-curatedtcgadata")
3217 (version "1.34.0")
3218 (source
3219 (origin
3220 (method url-fetch)
3221 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
3222 (sha256
3223 (base32 "05aj6vn381fzd5v6m6yw6gghaa3j9im7va1xq4c8qmm2k26p426q"))))
3224 (properties
3225 `((upstream-name . "curatedTCGAData")))
3226 (build-system r-build-system)
3227 ;; Tests require Internet access because of ExperimentHub.
3228 (arguments (list #:tests? #false))
3229 (propagated-inputs
3230 (list r-annotationhub
3231 r-experimenthub
3232 r-hdf5array
3233 r-multiassayexperiment
3234 r-s4vectors
3235 r-summarizedexperiment))
3236 (native-inputs (list r-knitr r-testthat))
3237 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
3238 (synopsis "Curated data from The Cancer Genome Atlas")
3239 (description
3240 "This package provides publicly available data from The Cancer Genome
3241Atlas (TCGA) as @code{MultiAssayExperiment} objects.
3242@code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
3243number, mutation, microRNA, protein, and others) with clinical / pathological
3244data. It also links assay barcodes with patient identifiers, enabling
3245harmonized subsetting of rows (features) and columns (patients / samples)
3246across the entire multi-'omics experiment.")
3247 (license license:artistic2.0)))
3248
3249(define-public r-parathyroidse
3250 (package
3251 (name "r-parathyroidse")
3252 (version "1.46.0")
3253 (source (origin
3254 (method url-fetch)
3255 (uri (bioconductor-uri "parathyroidSE" version
3256 'experiment))
3257 (sha256
3258 (base32
3259 "1mdjg7k943kjpzy33gdbbi05g466mms95gpjighicifcxxqbx7ns"))))
3260 (properties `((upstream-name . "parathyroidSE")))
3261 (build-system r-build-system)
3262 (propagated-inputs (list r-summarizedexperiment))
3263 (home-page "https://bioconductor.org/packages/parathyroidSE")
3264 (synopsis "RangedSummarizedExperiment for RNA-Seq of parathyroid tumors")
3265 (description
3266 "This package provides @code{RangedSummarizedExperiment} objects of read
3267counts in genes and exonic parts for paired-end RNA-Seq data from experiments on
3268primary cultures of parathyroid tumors. The sequencing was performed on tumor
3269cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).")
3270 ;; The author(s) mentions only LGPL without any specific version.
3271 (license license:lgpl2.1+)))
3272
3273(define-public r-rcistarget-hg19-motifdbs-cisbponly-500bp
3274 (package
3275 (name "r-rcistarget-hg19-motifdbs-cisbponly-500bp")
3276 (version "1.32.0")
3277 (source
3278 (origin
3279 (method url-fetch)
3280 (uri (bioconductor-uri "RcisTarget.hg19.motifDBs.cisbpOnly.500bp"
3281 version
3282 'experiment))
3283 (sha256
3284 (base32 "1bp9l13k566ac43148nmc6mhi3cxd7llvrn36ph5i4xx0fymv8gp"))))
3285 (properties `((upstream-name . "RcisTarget.hg19.motifDBs.cisbpOnly.500bp")))
3286 (build-system r-build-system)
3287 (propagated-inputs (list r-data-table))
3288 (home-page "https://scenic.aertslab.org")
3289 (synopsis
3290 "RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs")
3291 (description
3292 "This package provides @code{RcisTarget} databases: Gene-based motif
3293rankings and annotation to transcription factors. This package contains a
3294subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and
3295the TSS. See @code{RcisTarget} tutorial to download the full databases,
3296containing 20k motifs and search space up to 10kbp around the TSS.")
3297 (license license:gpl3)))
3298
3299(define-public r-rnaseqdata-hnrnpc-bam-chr14
3300 (package
3301 (name "r-rnaseqdata-hnrnpc-bam-chr14")
3302 (version "0.50.0")
3303 (source
3304 (origin
3305 (method url-fetch)
3306 (uri (bioconductor-uri "RNAseqData.HNRNPC.bam.chr14" version
3307 'experiment))
3308 (sha256
3309 (base32 "0s20i4b7mpb1s524qjsii7aaay4l0mqp89fp3l5l90zqxlsqkx3z"))))
3310 (properties `((upstream-name . "RNAseqData.HNRNPC.bam.chr14")))
3311 (build-system r-build-system)
3312 (home-page "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/")
3313 (synopsis
3314 "Aligned reads from RNAseq experiment")
3315 (description
3316 "The package contains 8 BAM files, 1 per sequencing run. Each BAM file
3317was obtained by aligning the reads (paired-end) to the full hg19 genome with
3318@code{TopHat2}, and then subsetting to keep only alignments on chr14. See
3319accession number E-MTAB-1147 in the @code{ArrayExpress} database for details
3320about the experiment, including links to the published study (by Zarnack et
3321al., 2012) and to the FASTQ files.")
3322 (license license:lgpl2.0+)))
3323
3324(define-public r-rnbeads-hg19
3325 (package
3326 (name "r-rnbeads-hg19")
3327 (version "1.44.0")
3328 (source
3329 (origin
3330 (method url-fetch)
3331 (uri (bioconductor-uri "RnBeads.hg19" version
3332 'experiment))
3333 (sha256
3334 (base32 "10mlkhv445n8ng9wzjwjcqdd65as4fh5iv682g1di6rhqrvn607h"))))
3335 (properties `((upstream-name . "RnBeads.hg19")))
3336 (build-system r-build-system)
3337 (propagated-inputs (list r-genomicranges))
3338 (home-page "https://bioconductor.org/packages/RnBeads.hg19")
3339 (synopsis "RnBeads annotation package for hg19 assembly")
3340 (description
3341 "This package is an automatically generated @code{RnBeads} annotation
3342package for the assembly hg19.")
3343 (license license:gpl3)))
3344
3345(define-public r-rtcga-rnaseq
3346 (package
3347 (name "r-rtcga-rnaseq")
3348 (version "20151101.42.0")
3349 (source
3350 (origin
3351 (method url-fetch)
3352 (uri (bioconductor-uri "RTCGA.rnaseq" version
3353 'experiment))
3354 (sha256
3355 (base32 "1cmc3jxmn23qvsp0ady34zjlp2y8ykyzml7khx5sirfm6ramcfrj"))))
3356 (properties `((upstream-name . "RTCGA.rnaseq")))
3357 (build-system r-build-system)
3358 (propagated-inputs (list r-rtcga))
3359 (native-inputs (list r-knitr))
3360 (home-page "https://bioconductor.org/packages/RTCGA.rnaseq")
3361 (synopsis "Rna-seq datasets from The Cancer Genome Atlas Project")
3362 (description
3363 "This package provides rna-seq datasets from The Cancer Genome Atlas
3364Project for all cohorts types from @url{http://gdac.broadinstitute.org/}. The
3365Rna-seq data format is explained here
3366@url{https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2}. The data source
3367is Illumina hiseq Level 3 RSEM normalized expression data from 2015-11-01
3368snapshot.")
3369 (license license:gpl2)))
3370
3371(define-public r-scpdata
3372 (package
3373 (name "r-scpdata")
3374 (version "1.20.0")
3375 (source
3376 (origin
3377 (method url-fetch)
3378 (uri (bioconductor-uri "scpdata" version
3379 'experiment))
3380 (sha256
3381 (base32 "0fnx1qkiqhpnhhln8hcbhqdrxqymq14j39zv7s5sg6374wi2w9f8"))))
3382 (properties `((upstream-name . "scpdata")))
3383 (build-system r-build-system)
3384 (arguments
3385 ;; Tests require internet access via r-experimenthub
3386 (list #:tests? #f))
3387 (propagated-inputs (list r-annotationhub r-experimenthub r-qfeatures
3388 r-s4vectors r-singlecellexperiment))
3389 (native-inputs (list r-knitr r-testthat))
3390 (home-page "https://bioconductor.org/packages/scpdata")
3391 (synopsis "Single-cell proteomics data package")
3392 (description
3393 "The package disseminates mass spectrometry (MS)-based single-cell proteomics
3394(SCP) datasets. The data were collected from published work and formatted
3395using the `scp` data structure. The data sets contain quantitative
3396information at spectrum, peptide and/or protein level for single cells or
3397minute sample amounts.")
3398 (license license:gpl2)))
3399
3400(define-public r-sesamedata
3401 (package
3402 (name "r-sesamedata")
3403 (version "1.30.0")
3404 (source (origin
3405 (method url-fetch)
3406 (uri (bioconductor-uri "sesameData" version
3407 'experiment))
3408 (sha256
3409 (base32
3410 "17hdpwnrhc6axcnl5xl2jndwckmis42iiqi86jd87zy8vy6fvj0i"))))
3411 (properties
3412 `((upstream-name . "sesameData")
3413 ;; Avoid dependency cycle.
3414 (updater-ignored-native-inputs . ("r-sesame"))))
3415 (build-system r-build-system)
3416 ;; Tests need r-sesame.
3417 (arguments (list #:tests? #false))
3418 (propagated-inputs (list r-annotationhub
3419 r-experimenthub
3420 r-genomicranges
3421 r-iranges
3422 r-readr
3423 r-s4vectors
3424 r-seqinfo
3425 r-stringr))
3426 (native-inputs (list r-knitr r-testthat))
3427 (home-page "https://bioconductor.org/packages/sesameData")
3428 (synopsis "Supporting Data for SeSAMe Package")
3429 (description
3430 "This package provides supporting annotation and test data for
3431@code{SeSAMe} package. This includes chip tango addresses, mapping
3432information, performance annotation, and trained predictor for Infinium array
3433data. This package provides user access to essential annotation data for
3434working with many generations of the Infinium DNA methylation array. It
3435currently supports human array (HM27, HM450, EPIC), mouse array (MM285) and
3436the @code{HorvathMethylChip40} (Mammal40) array.")
3437 (license license:artistic2.0)))
3438
3439(define-public r-systempiperdata
3440 (package
3441 (name "r-systempiperdata")
3442 (version "2.16.0")
3443 (source
3444 (origin
3445 (method url-fetch)
3446 (uri (bioconductor-uri "systemPipeRdata" version
3447 'experiment))
3448 (sha256
3449 (base32 "118yfnmiyvixds0gwlsz2db28m8g0bsc1sn56dlw0sgshyqp8sci"))))
3450 (properties `((upstream-name . "systemPipeRdata")))
3451 (build-system r-build-system)
3452 (propagated-inputs (list r-biocgenerics r-biostrings r-jsonlite r-remotes))
3453 (native-inputs (list r-knitr))
3454 (home-page "https://github.com/tgirke/systemPipeRdata")
3455 (synopsis "Workflow templates and sample data")
3456 (description
3457 "@code{systemPipeRdata} complements the @code{systemPipeR} workflow
3458management system (WMS) by offering a collection of pre-designed data analysis
3459workflow templates. These templates are easily accessible and can be readily
3460loaded onto a user's system with a single command. Once loaded, the WMS can
3461immediately utilize these templates for efficient end-to-end analysis, serving
3462a wide range of data analysis needs.")
3463 (license license:artistic2.0)))
3464
3465(define-public r-tcgabiolinksgui-data
3466 (package
3467 (name "r-tcgabiolinksgui-data")
3468 (version "1.32.0")
3469 (source
3470 (origin
3471 (method url-fetch)
3472 (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment))
3473 (sha256
3474 (base32 "0fdmb80xs1glr5dvpjsidl1wjz21pdlvk3cb83m69h1xd1pqkh9r"))))
3475 (properties `((upstream-name . "TCGAbiolinksGUI.data")))
3476 (build-system r-build-system)
3477 (native-inputs (list r-knitr))
3478 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data")
3479 (synopsis "Data for the TCGAbiolinksGUI package")
3480 (description "This package provides supporting data for the
3481TCGAbiolinksGUI package.")
3482 (license license:gpl3)))
3483
3484(define-public r-tximportdata
3485 (package
3486 (name "r-tximportdata")
3487 (version "1.40.0")
3488 (source (origin
3489 (method url-fetch)
3490 (uri (bioconductor-uri "tximportData" version
3491 'experiment))
3492 (sha256
3493 (base32
3494 "01wncrlzasx3v35k9yq787pgqqxq71ca0vvrr4xwrm014nldrmm7"))))
3495 (properties `((upstream-name . "tximportData")))
3496 (build-system r-build-system)
3497 (native-inputs (list r-knitr))
3498 (home-page "https://bioconductor.org/packages/tximportData")
3499 (synopsis "Data for the tximport package")
3500 (description
3501 "This package provides the output of running various transcript abundance
3502quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The
3503quantifiers were @code{Cufflinks}, @code{RSEM}, @code{kallisto}, @code{Salmon}
3504and @code{Sailfish}. Alevin example output is also included.")
3505 (license license:gpl2+)))
3506
3507(define-public r-zebrafishrnaseq
3508 (package
3509 (name "r-zebrafishrnaseq")
3510 (version "1.32.0")
3511 (source
3512 (origin
3513 (method url-fetch)
3514 (uri (bioconductor-uri "zebrafishRNASeq" version
3515 'experiment))
3516 (sha256
3517 (base32 "111pa6zq0ijl1950yawmmxv72i9zx41zxsr1scv6iq8q0fykzvcg"))))
3518 (properties `((upstream-name . "zebrafishRNASeq")))
3519 (build-system r-build-system)
3520 (native-inputs (list r-knitr))
3521 (home-page "https://bioconductor.org/packages/zebrafishRNASeq")
3522 (synopsis
3523 "Zebrafish RNA-Seq experimental data from Ferreira et al. (2014)")
3524 (description
3525 "This package provides gene-level read counts from RNA-Seq for
3526gallein-treated and control zebrafish.")
3527 (license (list license:gpl2+ license:gpl3+))))
3528
3529
3530
3531;;; Packages
3532
3533(define-public r-abarray
3534 (package
3535 (name "r-abarray")
3536 (version "1.80.0")
3537 (source (origin
3538 (method url-fetch)
3539 (uri (bioconductor-uri "ABarray" version))
3540 (sha256
3541 (base32
3542 "1vvl8c2ljs551d2krd4kz3k8ik769q5ic07wab78qd537xzd142q"))))
3543 (properties `((upstream-name . "ABarray")))
3544 (build-system r-build-system)
3545 (propagated-inputs (list r-biobase r-multtest))
3546 (home-page "https://bioconductor.org/packages/ABarray")
3547 (synopsis
3548 "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
3549 (description
3550 "The package @code{ABarray} is designed to work with Applied Biosystems
3551whole genome microarray platform, as well as any other platform whose data can
3552be transformed into expression data matrix. Functions include data
3553preprocessing, filtering, control probe analysis, statistical analysis in one
3554single function. A @dfn{graphical user interface} (GUI) is also provided. The
3555raw data, processed data, graphics output and statistical results are organized
3556into folders according to the analysis settings used.")
3557 (license license:gpl2+)))
3558
3559(define-public r-absseq
3560 (package
3561 (name "r-absseq")
3562 (version "1.66.0")
3563 (source (origin
3564 (method url-fetch)
3565 (uri (bioconductor-uri "ABSSeq" version))
3566 (sha256
3567 (base32
3568 "1knrgj3lqzds0vpwxa30d28ng3jwcwng3lykgq8gp9p32glzlwaa"))))
3569 (properties `((upstream-name . "ABSSeq")))
3570 (build-system r-build-system)
3571 (propagated-inputs (list r-limma r-locfit))
3572 (home-page "https://bioconductor.org/packages/ABSSeq")
3573 (synopsis
3574 "RNA-Seq analysis based on modelling absolute expression differences")
3575 (description
3576 "This package implements a new RNA-Seq analysis method and integrates two
3577modules: a basic model for pairwise comparison and a linear model for complex
3578design. RNA-Seq quantifies gene expression with reads count, which usually
3579consists of conditions (or treatments) and several replicates for each
3580condition. This software infers differential expression directly by the
3581counts difference between conditions. It assumes that the sum counts
3582difference between conditions follow a negative binomial distribution. In
3583addition, @code{ABSSeq} moderates the fold-changes by two steps: the
3584expression level and gene-specific dispersion, that might facilitate the gene
3585ranking by fold-change and visualization.")
3586 (license license:gpl3+)))
3587
3588(define-public r-adacgh2
3589 (package
3590 (name "r-adacgh2")
3591 (version "2.52.0")
3592 (source
3593 (origin
3594 (method url-fetch)
3595 (uri (bioconductor-uri "ADaCGH2" version))
3596 (sha256
3597 (base32 "0b3cxs6yjs3wxk512d60zlix41pxypw49n9a5a9v7z48drp5akfv"))))
3598 (properties
3599 `((upstream-name . "ADaCGH2")
3600 (updater-extra-inputs . ("python-wrapper"))))
3601 (build-system r-build-system)
3602 (arguments
3603 (list
3604 #:phases
3605 '(modify-phases %standard-phases
3606 (add-after 'unpack 'python3-compatibility
3607 (lambda _
3608 (substitute* "inst/imagemap-example/toMap.py"
3609 (("print nameMap") "print(nameMap)")))))))
3610 (inputs (list python-wrapper))
3611 (propagated-inputs
3612 (list r-acgh
3613 r-bit
3614 r-cluster
3615 r-dnacopy
3616 r-ff
3617 r-tilingarray
3618 r-waveslim))
3619 (home-page "https://github.com/rdiaz02/adacgh2")
3620 (synopsis "Big data analysis from aCGH experiments")
3621 (description
3622 "This package analyzes and creates plots of array @acronym{CGH,
3623comparative genomic hybridization} data. Also, it allows usage of
3624@acronym{CBS, Circular Binary Segementation}, wavelet-based smoothing, HMM,
3625BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking
3626or with clusters, including MPI and sockets clusters) and use @code{ff} for
3627storing data.")
3628 (license license:gpl3+)))
3629
3630(define-public r-adam
3631 (package
3632 (name "r-adam")
3633 (version "1.28.0")
3634 (source (origin
3635 (method url-fetch)
3636 (uri (bioconductor-uri "ADAM" version))
3637 (sha256
3638 (base32
3639 "173wy9fkgz0z7irwy260q5vd733kp9cj2m1q4fgwqlbmcagc9jd9"))))
3640 (properties `((upstream-name . "ADAM")))
3641 (build-system r-build-system)
3642 (propagated-inputs (list r-dplyr
3643 r-dt
3644 r-go-db
3645 r-keggrest
3646 r-knitr
3647 r-pbapply
3648 r-rcpp
3649 r-stringr
3650 r-summarizedexperiment))
3651 (native-inputs (list r-knitr r-testthat))
3652 (home-page "https://bioconductor.org/packages/ADAM")
3653 (synopsis "Gene activity and diversity analysis module")
3654 (description
3655 "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA)
3656package created to group a set of genes from comparative samples (control
3657versus experiment) belonging to different species according to their respective
3658functions. The corresponding roles are extracted from the default collections
3659like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG).
3660@code{ADAM} show their significance by calculating the p-values referring to
3661gene diversity and activity. Each group of genes is called @dfn{Group of
3662functionally associated genes} (GFAG).")
3663 (license license:gpl2+)))
3664
3665(define-public r-adamgui
3666 (package
3667 (name "r-adamgui")
3668 (version "1.28.0")
3669 (source (origin
3670 (method url-fetch)
3671 (uri (bioconductor-uri "ADAMgui" version))
3672 (sha256
3673 (base32
3674 "1ljipdxf5b5wakqmw1ap5b70jgpy10h270dwx3j24r3jy2fav6g3"))))
3675 (properties `((upstream-name . "ADAMgui")))
3676 (build-system r-build-system)
3677 (propagated-inputs
3678 (list r-adam
3679 r-colorramps
3680 r-data-table
3681 r-dplyr
3682 r-dt
3683 r-ggplot2
3684 r-ggpubr
3685 r-ggrepel
3686 r-ggsignif
3687 r-go-db
3688 r-gridextra
3689 r-knitr
3690 r-rcolorbrewer
3691 r-reshape2
3692 r-shiny
3693 r-shinyjs
3694 r-stringi
3695 r-stringr
3696 r-testthat
3697 r-varhandle))
3698 (native-inputs (list r-knitr))
3699 (home-page "https://bioconductor.org/packages/ADAMgui/")
3700 (synopsis "GUI for gene activity and diversity analysis")
3701 (description
3702 "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI)
3703for the @code{ADAM} package. The @code{ADAMgui} package provides two
3704shiny-based applications that allows the user to study the output of the
3705@code{ADAM} package files through different plots. It's possible, for
3706example, to choose a specific @dfn{group of functionally associated
3707genes} (GFAG) and observe the gene expression behavior with the plots created
3708with the @code{GFAGtargetUi} function. Features such as differential
3709expression and fold change can be easily seen with aid of the plots made with
3710the @code{GFAGpathUi} function.")
3711 (license license:gpl2+)))
3712
3713(define-public r-adimpute
3714 (package
3715 (name "r-adimpute")
3716 (version "1.22.0")
3717 (source (origin
3718 (method url-fetch)
3719 (uri (bioconductor-uri "ADImpute" version))
3720 (sha256
3721 (base32
3722 "0j5xjba36ari9h77iznwva6dbfjwrz8xjlzls877rf36snsirqb0"))))
3723 (properties `((upstream-name . "ADImpute")))
3724 (build-system r-build-system)
3725 (propagated-inputs
3726 (list r-biocparallel
3727 r-checkmate
3728 r-data-table
3729 r-drimpute
3730 r-kernlab
3731 r-mass
3732 r-matrix
3733 r-rsvd
3734 r-s4vectors
3735 r-saver
3736 r-singlecellexperiment
3737 r-summarizedexperiment))
3738 (native-inputs (list r-knitr r-testthat))
3739 (home-page "https://bioconductor.org/packages/ADImpute")
3740 (synopsis "Adaptive computational prediction for dropout imputations")
3741 (description
3742 "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically
3743unable to quantify the expression levels of all genes in a cell, creating a
3744need for the computational prediction of missing values (dropout imputation).
3745Most existing dropout imputation methods are limited in the sense that they
3746exclusively use the scRNA-seq dataset at hand and do not exploit external
3747gene-gene relationship information. The @code{ADImpute} package proposes two
3748methods to address this issue:
3749
3750@enumerate
3751@item a gene regulatory network-based approach using gene-gene relationships
3752 learnt from external data;
3753@item a baseline approach corresponding to a sample-wide average.
3754@end enumerate
3755
3756@code{ADImpute} implements these novel methods and also combines them with
3757existing imputation methods like @code{DrImpute} and @code{SAVER}.
3758@code{ADImpute} can learn the best performing method per gene and combine the
3759results from different methods into an ensemble.")
3760 (license license:gpl3+)))
3761
3762(define-public r-adsplit
3763 (package
3764 (name "r-adsplit")
3765 (version "1.82.0")
3766 (source (origin
3767 (method url-fetch)
3768 (uri (bioconductor-uri "adSplit" version))
3769 (sha256
3770 (base32
3771 "1f9iqqhh23agm0agrgwqrjx0mms7c9vhp48ymq5vaq6xz2d10m08"))))
3772 (properties `((upstream-name . "adSplit")))
3773 (build-system r-build-system)
3774 (propagated-inputs
3775 (list r-annotationdbi
3776 r-biobase
3777 r-cluster
3778 r-go-db
3779 r-keggrest
3780 r-multtest))
3781 (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml")
3782 (synopsis "Annotation-driven splits in microarray data")
3783 (description
3784 "This package implements clustering of microarray gene expression
3785profiles according to functional annotations. For each term genes are
3786annotated to, splits into two subclasses are computed and a significance of
3787the supporting gene set is determined.")
3788 (license license:gpl2+)))
3789
3790(define-public r-affixcan
3791 (package
3792 (name "r-affixcan")
3793 (version "1.30.0")
3794 (source (origin
3795 (method url-fetch)
3796 (uri (bioconductor-uri "AffiXcan" version))
3797 (sha256
3798 (base32
3799 "1ykf4pyp1z50y102q4yhai13mmykdlrgkx3mkbci54cmyh34g5z5"))))
3800 (properties `((upstream-name . "AffiXcan")))
3801 (build-system r-build-system)
3802 (propagated-inputs
3803 (list r-biocparallel
3804 r-crayon
3805 r-multiassayexperiment
3806 r-summarizedexperiment))
3807 (native-inputs (list r-knitr))
3808 (home-page "https://bioconductor.org/packages/AffiXcan")
3809 (synopsis "Functional approach to impute genetically regulated expression")
3810 (description
3811 "The @code{AffiXcan} package imputes a @dfn{genetically regulated
3812expression} (GReX) for a set of genes in a sample of individuals, using a
3813method based on the @dfn{total binding affinity} (TBA). Statistical models to
3814impute GReX can be trained with a training dataset where the real total
3815expression values are known.")
3816 (license license:gpl3)))
3817
3818(define-public r-affyilm
3819 (package
3820 (name "r-affyilm")
3821 (version "1.64.0")
3822 (source
3823 (origin
3824 (method url-fetch)
3825 (uri (bioconductor-uri "affyILM" version))
3826 (sha256
3827 (base32 "16xck7day4xqzaqkw5p2xd5j9jgjmlwdjsplm7m08a8946n74l0w"))))
3828 (properties `((upstream-name . "affyILM")))
3829 (build-system r-build-system)
3830 (propagated-inputs
3831 (list r-affxparser
3832 r-affy
3833 r-biobase
3834 r-gcrma))
3835 (home-page "https://bioconductor.org/packages/affyILM")
3836 (synopsis
3837 "Linear model of background subtraction and the Langmuir isotherm")
3838 (description
3839 "The affyILM package is a preprocessing tool which estimates gene
3840expression levels for Affymetrix Gene Chips. Input from physical chemistry is
3841employed to first background subtract intensities before calculating
3842concentrations on behal of the Langmuir model.")
3843 (license license:gpl3)))
3844
3845(define-public r-affylmgui
3846 (package
3847 (name "r-affylmgui")
3848 (version "1.86.0")
3849 (source
3850 (origin
3851 (method url-fetch)
3852 (uri (bioconductor-uri "affylmGUI" version))
3853 (sha256
3854 (base32 "0jabj6lssr34gipg68bzmjpdhcjszcarzspn9w8fhldzc9s07hb5"))))
3855 (properties `((upstream-name . "affylmGUI")))
3856 (build-system r-build-system)
3857 (propagated-inputs
3858 (list r-affy
3859 r-affyio
3860 r-affyplm
3861 r-annotationdbi
3862 r-biocgenerics
3863 r-biocmanager
3864 r-gcrma
3865 r-limma
3866 r-r2html
3867 r-tkrplot
3868 r-xtable))
3869 (home-page "https://bioinf.wehi.edu.au/affylmGUI/")
3870 (synopsis "GUI for limma package with Affymetrix microarrays")
3871 (description
3872 "This package provides a @acronym{GUI, Graphical User Interface} for
3873analysis of Affymetrix microarray gene expression data using the affy and
3874limma packages.")
3875 (license license:gpl2+)))
3876
3877(define-public r-affyplm
3878 (package
3879 (name "r-affyplm")
3880 (version "1.88.0")
3881 (source
3882 (origin
3883 (method url-fetch)
3884 (uri (bioconductor-uri "affyPLM" version))
3885 (sha256
3886 (base32 "13m9fpa9cak7qi1p61wjvwdidyf3k36bw60dg22kyns4hnk0brk1"))))
3887 (properties
3888 `((upstream-name . "affyPLM")
3889 (updater-extra-native-inputs . ("r-hgu95av2cdf" "r-kernsmooth"))))
3890 (build-system r-build-system)
3891 (inputs (list zlib))
3892 (propagated-inputs
3893 (list r-affy r-biobase r-biocgenerics r-gcrma r-preprocesscore))
3894 (native-inputs
3895 (list pkg-config r-affydata r-hgu95av2cdf r-kernsmooth r-mass))
3896 (home-page "https://github.com/bmbolstad/affyPLM")
3897 (synopsis "Methods for fitting probe-level models")
3898 (description
3899 "The affyPLM provides a package that extends and improves the
3900functionality of the base affy package. For speeding up the runs, it includes
3901routines that make heavy use of compiled code. The central focus is on
3902implementation of methods for fitting probe-level models and tools using these
3903models. @acronym{PLM, probe-level models} based quality assessment tools are
3904also provided.")
3905 (license license:gpl2+)))
3906
3907(define-public r-affyrnadegradation
3908 (package
3909 (name "r-affyrnadegradation")
3910 (version "1.58.0")
3911 (source (origin
3912 (method url-fetch)
3913 (uri (bioconductor-uri "AffyRNADegradation" version))
3914 (sha256
3915 (base32
3916 "0jzcsk26asgqcwmh619drv872fmq2rrs9rxnjzcx3r62bgcxwy8p"))))
3917 (properties `((upstream-name . "AffyRNADegradation")))
3918 (build-system r-build-system)
3919 (propagated-inputs (list r-affy))
3920 (home-page "https://bioconductor.org/packages/AffyRNADegradation")
3921 (synopsis
3922 "Analyze and correct probe positional bias in data due to RNA degradation")
3923 (description
3924 "The @code{AffyRNADegradation} package helps with the assessment and
3925correction of RNA degradation effects in Affymetrix 3 expression arrays. The
3926parameter @code{d} gives a robust and accurate measure of RNA integrity. The
3927correction removes the probe positional bias, and thus improves comparability
3928of samples that are affected by RNA degradation.")
3929 ;; the R file header specifies GPL2 or later
3930 (license license:gpl2+)))
3931
3932(define-public r-agdex
3933 (package
3934 (name "r-agdex")
3935 (version "1.60.0")
3936 (source (origin
3937 (method url-fetch)
3938 (uri (bioconductor-uri "AGDEX" version))
3939 (sha256
3940 (base32
3941 "1lyji0svcn75ymjgagzam3v5876byqlrw0yyqdq1awcr3b0ma835"))))
3942 (properties `((upstream-name . "AGDEX")))
3943 (build-system r-build-system)
3944 (propagated-inputs (list r-biobase r-gseabase))
3945 (home-page "https://bioconductor.org/packages/AGDEX")
3946 (synopsis
3947 "Evaluate agreement of differential expression for cross-species genomics")
3948 (description
3949 "The objective of @code{AGDEX} is to evaluate whether the results of a
3950pair of two-group differential expression analysis comparisons show a level of
3951agreement that is greater than expected if the group labels for each two-group
3952comparison are randomly assigned. The agreement is evaluated for the entire
3953transcriptome and (optionally) for a collection of pre-defined gene-sets.
3954Additionally, the procedure performs permutation-based differential expression
3955and meta analysis at both gene and gene-set levels of the data from each
3956experiment.")
3957 (license license:gpl2+)))
3958
3959(define-public r-aggregatebiovar
3960 (package
3961 (name "r-aggregatebiovar")
3962 (version "1.22.0")
3963 (source (origin
3964 (method url-fetch)
3965 (uri (bioconductor-uri "aggregateBioVar" version))
3966 (sha256
3967 (base32
3968 "0rkbfxnf13a6f2q7jgk1vlgpkqdcpkg3s2ycrd9li8y55pg4v9ym"))))
3969 (properties `((upstream-name . "aggregateBioVar")))
3970 (build-system r-build-system)
3971 (propagated-inputs
3972 (list r-matrix
3973 r-rlang
3974 r-s4vectors
3975 r-singlecellexperiment
3976 r-summarizedexperiment
3977 r-tibble))
3978 (native-inputs (list r-knitr r-testthat))
3979 (home-page "https://github.com/jasonratcliff/aggregateBioVar")
3980 (synopsis "Differential gene expression analysis for multi-subject scRNA-seq")
3981 (description
3982 "This package @code{aggregateBioVar} contains tools to summarize single
3983cell gene expression profiles at the level of subject for single cell RNA-seq
3984data collected from more than one subject (e.g. biological sample or technical
3985replicates). A @code{SingleCellExperiment} object is taken as input and
3986converted to a list of @code{SummarizedExperiment} objects, where each list
3987element corresponds to an assigned cell type. The @code{SummarizedExperiment}
3988objects contain aggregate gene-by-subject count matrices and inter-subject
3989column metadata for individual subjects that can be processed using downstream
3990bulk RNA-seq tools.")
3991 (license license:gpl3)))
3992
3993(define-public r-agilp
3994 (package
3995 (name "r-agilp")
3996 (version "3.44.0")
3997 (source (origin
3998 (method url-fetch)
3999 (uri (bioconductor-uri "agilp" version))
4000 (sha256
4001 (base32
4002 "1sqqfk21p0g7j6midqcjyc96qsm777p8ygv22vkxw1fk4ngf8cnw"))))
4003 (properties `((upstream-name . "agilp")))
4004 (build-system r-build-system)
4005 (home-page "https://bioconductor.org/packages/agilp")
4006 (synopsis "Processing of Agilent expression array")
4007 (description
4008 "This package aims to provide a pipeline for the low-level analysis of
4009gene expression microarray data, primarily focused on the Agilent platform,
4010but which also provides utilities which may be useful for other platforms.")
4011 ;; Some files are under GPLv2+ but the combined work is released under the
4012 ;; GPLv3.
4013 (license license:gpl3)))
4014
4015(define-public r-adductomicsr
4016 (package
4017 (name "r-adductomicsr")
4018 (version "1.27.0")
4019 (source (origin
4020 (method url-fetch)
4021 (uri (bioconductor-uri "adductomicsR" version))
4022 (sha256
4023 (base32
4024 "1g7hxgbbipnanjb7b7nga3s9axsdwmcn0l3pz8y19lpxxw40mwbd"))))
4025 (properties `((upstream-name . "adductomicsR")))
4026 (build-system r-build-system)
4027 ;; Tests connect to the internet via r-experimenthub.
4028 (arguments (list #:tests? #false))
4029 (propagated-inputs
4030 (list r-adductdata
4031 r-ade4
4032 r-annotationhub
4033 r-bootstrap
4034 r-data-table
4035 r-dosnow
4036 r-dplyr
4037 r-dt
4038 r-experimenthub
4039 r-fastcluster
4040 r-foreach
4041 r-fpc
4042 r-mzr
4043 r-orgmassspecr
4044 r-pastecs
4045 r-pracma
4046 r-rcppeigen
4047 r-reshape2
4048 r-rvest
4049 r-smoother
4050 r-zoo))
4051 (native-inputs (list r-knitr r-testthat))
4052 (home-page "https://bioconductor.org/packages/adductomicsR")
4053 (synopsis "Processing of adductomic mass spectral datasets")
4054 (description
4055 "This package @code{adductomicsR} processes data generated by the
4056@dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
4057peptides from spectra that has been corrected for mass drift and retention
4058time drift and quantifies level mass spectral peaks from @dfn{first stage of
4059mass spectrometry} (MS1) data.")
4060 (license license:artistic2.0)))
4061
4062(define-public r-agimicrorna
4063 (package
4064 (name "r-agimicrorna")
4065 (version "2.62.0")
4066 (source (origin
4067 (method url-fetch)
4068 (uri (bioconductor-uri "AgiMicroRna" version))
4069 (sha256
4070 (base32
4071 "0dvjksrgz5ckn9iskp2vjzawkkgax2v0jmkjynh34zxnyqy5h24v"))))
4072 (properties `((upstream-name . "AgiMicroRna")))
4073 (build-system r-build-system)
4074 (propagated-inputs
4075 (list r-affy
4076 r-affycoretools
4077 r-biobase
4078 r-limma
4079 r-preprocesscore))
4080 (home-page "https://git.bioconductor.org/packages/AgiMicroRna")
4081 (synopsis
4082 "Processing and differential expression analysis of Agilent microRNA chips")
4083 (description
4084 "@code{AgiMicroRna} provides useful functionality for the processing,
4085quality assessment and differential expression analysis of Agilent microRNA
4086array data. The package uses a limma-like structure to generate the processed
4087data in order to make statistical inferences about differential expression
4088using the linear model features implemented in limma. Standard Bioconductor
4089objects are used so that other packages could be used as well.")
4090 (license license:gpl3)))
4091
4092(define-public r-aims
4093 (package
4094 (name "r-aims")
4095 (version "1.44.0")
4096 (source (origin
4097 (method url-fetch)
4098 (uri (bioconductor-uri "AIMS" version))
4099 (sha256
4100 (base32
4101 "0gr3czzxaz9gmh02f4wm9j1g6f222dn6x2r267sljgnpc1lssmpr"))))
4102 (properties `((upstream-name . "AIMS")))
4103 (build-system r-build-system)
4104 (propagated-inputs (list r-biobase r-e1071))
4105 (native-inputs (list r-biocgenerics r-breastcancervdx r-hgu133a-db r-runit))
4106 (home-page "https://git.bioconductor.org/packages/AIMS")
4107 (synopsis
4108 "Absolute assignment of breast cancer intrinsic molecular subtype")
4109 (description
4110 "This package contains an implementation of @code{AIMS} -- Absolute
4111Intrinsic Molecular Subtyping. It contains necessary functions to assign the
4112five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched,
4113Basal-like, Normal-like). Assignments could be done on individual samples as
4114well as on dataset of gene expression data.")
4115 (license license:artistic2.0)))
4116
4117(define-public r-airpart
4118 (package
4119 (name "r-airpart")
4120 (version "1.20.0")
4121 (source (origin
4122 (method url-fetch)
4123 (uri (bioconductor-uri "airpart" version))
4124 (sha256
4125 (base32
4126 "1phg6856cw64ivhl7fppfmpckkdlhg5hk9l4v909ygpy0jqrn00i"))))
4127 (properties `((upstream-name . "airpart")))
4128 (build-system r-build-system)
4129 (propagated-inputs
4130 (list r-apeglm
4131 r-clue
4132 r-complexheatmap
4133 r-dplyr
4134 r-dynamictreecut
4135 r-emdbook
4136 r-forestplot
4137 r-ggplot2
4138 r-lpsolve
4139 r-matrixstats
4140 r-mclust
4141 r-pbapply
4142 r-plyr
4143 r-rcolorbrewer
4144 r-rlang
4145 r-s4vectors
4146 r-scater
4147 r-singlecellexperiment
4148 r-smurf
4149 r-summarizedexperiment))
4150 (native-inputs (list r-knitr r-testthat))
4151 (home-page "https://bioconductor.org/packages/airpart")
4152 (synopsis "Differential cell-type-specific allelic imbalance")
4153 (description
4154 "The airpart package identifies sets of genes displaying differential
4155cell-type-specific allelic imbalance across cell types or states, utilizing
4156single-cell allelic counts. It makes use of a generalized fused lasso with
4157binomial observations of allelic counts to partition cell types by their
4158allelic imbalance. Alternatively, a nonparametric method for partitioning
4159cell types is offered. The package includes a number of visualizations and
4160quality control functions for examining single cell allelic imbalance
4161datasets.")
4162 (license license:gpl2)))
4163
4164(define-public r-alabaster-base
4165 (package
4166 (name "r-alabaster-base")
4167 (version "1.12.0")
4168 (source
4169 (origin
4170 (method url-fetch)
4171 (uri (bioconductor-uri "alabaster.base" version))
4172 (sha256
4173 (base32 "08bs3jiv355035kdzsjwn8zd0lwdlz0jy3l33y70j1pjq2ss0zzb"))))
4174 (properties
4175 '((upstream-name . "alabaster.base")))
4176 (build-system r-build-system)
4177 (inputs (list zlib))
4178 (propagated-inputs (list r-alabaster-schemas
4179 r-assorthead
4180 r-digest ;suggested
4181 r-jsonlite
4182 r-jsonvalidate
4183 r-rcpp
4184 r-rhdf5
4185 r-rhdf5lib
4186 r-s4vectors))
4187 (native-inputs (list r-knitr r-matrix r-testthat))
4188 (home-page "https://bioconductor.org/packages/alabaster.base")
4189 (synopsis "Save Bioconductor objects to file")
4190 (description
4191 "This is a package for saving Bioconductor data structures into file
4192artifacts, and loading them back into memory. This is a more robust and
4193portable alternative to serialization of such objects into RDS files. Each
4194artifact is associated with metadata for further interpretation; downstream
4195applications can enrich this metadata with context-specific properties.")
4196 (license license:expat)))
4197
4198(define-public r-alabaster-matrix
4199 (package
4200 (name "r-alabaster-matrix")
4201 (version "1.12.0")
4202 (source
4203 (origin
4204 (method url-fetch)
4205 (uri (bioconductor-uri "alabaster.matrix" version))
4206 (sha256
4207 (base32 "0ki3h4y2s6llz1pby1zg9xfj9ln9p6yjk5ghds392v313la50aqi"))))
4208 (properties
4209 '((upstream-name . "alabaster.matrix")
4210 (updater-extra-native-inputs . ("r-chihaya"))))
4211 (build-system r-build-system)
4212 (propagated-inputs (list r-alabaster-base
4213 r-biocgenerics
4214 r-delayedarray
4215 r-hdf5array
4216 r-matrix
4217 r-rcpp
4218 r-rhdf5
4219 r-s4arrays
4220 r-s4vectors
4221 r-sparsearray))
4222 (native-inputs
4223 (list r-biocsingular r-chihaya r-knitr r-residualmatrix r-testthat))
4224 (home-page "https://bioconductor.org/packages/alabaster.matrix")
4225 (synopsis "Load and save artifacts from file")
4226 (description
4227 "This is a package for saving matrices, arrays and similar objects into
4228file artifacts, and loading them back into memory. This is a more portable
4229alternative to serialization of such objects into RDS files. Each artifact is
4230associated with metadata for further interpretation; downstream applications
4231can enrich this metadata with context-specific properties.")
4232 (license license:expat)))
4233
4234(define-public r-alabaster-ranges
4235 (package
4236 (name "r-alabaster-ranges")
4237 (version "1.12.0")
4238 (source
4239 (origin
4240 (method url-fetch)
4241 (uri (bioconductor-uri "alabaster.ranges" version))
4242 (sha256
4243 (base32 "1i0ws3qr2vz7jmzqa873rbv3dgw44s7cck93zz96smph58yj7xdz"))))
4244 (properties `((upstream-name . "alabaster.ranges")))
4245 (build-system r-build-system)
4246 (propagated-inputs (list r-alabaster-base
4247 r-biocgenerics
4248 r-genomicranges
4249 r-iranges
4250 r-rhdf5
4251 r-s4vectors
4252 r-seqinfo))
4253 (native-inputs (list r-jsonlite r-knitr r-testthat))
4254 (home-page "https://bioconductor.org/packages/alabaster.ranges")
4255 (synopsis "Load and save Ranges-related artifacts from file")
4256 (description
4257 "This is a package for saving @code{GenomicRanges}, @code{IRanges} and
4258related data structures into file artifacts, and loading them back into
4259memory. This is a more portable alternative to serialization of such objects
4260into RDS files. Each artifact is associated with metadata for further
4261interpretation; downstream applications can enrich this metadata with
4262context-specific properties.")
4263 (license license:expat)))
4264
4265(define-public r-alabaster-sce
4266 (package
4267 (name "r-alabaster-sce")
4268 (version "1.12.0")
4269 (source
4270 (origin
4271 (method url-fetch)
4272 (uri (bioconductor-uri "alabaster.sce" version))
4273 (sha256
4274 (base32 "12bz4j1h2y699dzxi2zfl0a4zdlqk5ic2v7yyvkk5x268fs9q5zc"))))
4275 (properties `((upstream-name . "alabaster.sce")))
4276 (build-system r-build-system)
4277 (propagated-inputs (list r-alabaster-base r-alabaster-se r-jsonlite
4278 r-singlecellexperiment))
4279 (native-inputs (list r-knitr r-testthat))
4280 (home-page "https://bioconductor.org/packages/alabaster.sce")
4281 (synopsis "Load and save SingleCellExperiment from file")
4282 (description
4283 "This is a package for saving @code{SingleCellExperiment} into file
4284artifacts, and loading them back into memory. This is a more portable
4285alternative to serialization of such objects into RDS files. Each artifact is
4286associated with metadata for further interpretation; downstream applications
4287can enrich this metadata with context-specific properties.")
4288 (license license:expat)))
4289
4290(define-public r-alabaster-schemas
4291 (package
4292 (name "r-alabaster-schemas")
4293 (version "1.12.0")
4294 (source
4295 (origin
4296 (method url-fetch)
4297 (uri (bioconductor-uri "alabaster.schemas" version))
4298 (sha256
4299 (base32 "0g5wk9vjdv22anwg8ra02wq029xya9zng187lbq2zy6wzsk5vkxm"))))
4300 (properties `((upstream-name . "alabaster.schemas")))
4301 (build-system r-build-system)
4302 (native-inputs (list r-knitr))
4303 (home-page "https://bioconductor.org/packages/alabaster.schemas")
4304 (synopsis "Schemas for the Alabaster framework")
4305 (description
4306 "This package stores all schemas required by various @code{alabaster.*}
4307packages. No computation should be performed by this package, as that is
4308handled by @code{alabaster.base}.")
4309 (license license:expat)))
4310
4311(define-public r-alabaster-se
4312 (package
4313 (name "r-alabaster-se")
4314 (version "1.12.0")
4315 (source
4316 (origin
4317 (method url-fetch)
4318 (uri (bioconductor-uri "alabaster.se" version))
4319 (sha256
4320 (base32 "1sb13gv8656dwb40jii7xga74s0z7q168skn78yk87axsp4hj668"))))
4321 (properties `((upstream-name . "alabaster.se")))
4322 (build-system r-build-system)
4323 (propagated-inputs (list r-alabaster-base
4324 r-alabaster-matrix
4325 r-alabaster-ranges
4326 r-biocgenerics
4327 r-genomicranges
4328 r-iranges
4329 r-jsonlite
4330 r-s4vectors
4331 r-summarizedexperiment))
4332 (native-inputs (list r-knitr r-testthat))
4333 (home-page "https://bioconductor.org/packages/alabaster.se")
4334 (synopsis "Load and save SummarizedExperiments from file")
4335 (description
4336 "This is a package for saving @code{SummarizedExperiments} into file
4337artifacts, and loading them back into memory. This is a more portable
4338alternative to serialization of such objects into RDS files. Each artifact is
4339associated with metadata for further interpretation; downstream applications
4340can enrich this metadata with context-specific properties.")
4341 (license license:expat)))
4342
4343(define-public r-amountain
4344 (package
4345 (name "r-amountain")
4346 (version "1.38.0")
4347 (source (origin
4348 (method url-fetch)
4349 (uri (bioconductor-uri "AMOUNTAIN" version))
4350 (sha256
4351 (base32
4352 "1ds3qjgglvkmmkwljkxhr0bcah38c1jvcysb5k0b6jamh8j81sa9"))))
4353 (properties `((upstream-name . "AMOUNTAIN")))
4354 (build-system r-build-system)
4355 (inputs (list gsl))
4356 (native-inputs (list r-knitr))
4357 (home-page "https://bioconductor.org/packages/AMOUNTAIN")
4358 (synopsis "Modules for multilayer weighted gene co-expression networks")
4359 (description
4360 "This package provides a pure data-driven gene network, @dfn{WGCN}(weighted
4361gene co-expression network) could be constructed only from expression profile.
4362Different layers in such networks may represent different time points, multiple
4363conditions or various species. @code{AMOUNTAIN} aims to search active modules
4364in multi-layer WGCN using a continuous optimization approach.")
4365 (license license:gpl2+)))
4366
4367(define-public r-amplican
4368 (package
4369 (name "r-amplican")
4370 (version "1.34.0")
4371 (source (origin
4372 (method url-fetch)
4373 (uri (bioconductor-uri "amplican" version))
4374 (sha256
4375 (base32
4376 "0gxkmx63bpla5hblh5qvah82p453547yvj1wxx0cbqywdbnrf4vk"))))
4377 (properties `((upstream-name . "amplican")))
4378 (build-system r-build-system)
4379 (propagated-inputs
4380 (list r-biocgenerics
4381 r-biocparallel
4382 r-biostrings
4383 r-cluster
4384 r-data-table
4385 r-genomicranges
4386 r-ggplot2
4387 r-ggthemes
4388 r-gridextra
4389 r-gtable
4390 r-iranges
4391 r-knitr
4392 r-matrix
4393 r-matrixstats
4394 r-pwalign
4395 r-rcpp
4396 r-rlang
4397 r-rmarkdown
4398 r-s4vectors
4399 r-seqinfo
4400 r-shortread
4401 r-stringr))
4402 (native-inputs (list r-devtools r-knitr r-testthat))
4403 (home-page "https://github.com/valenlab/amplican")
4404 (synopsis "Automated analysis of CRISPR experiments")
4405 (description
4406 "The package performs alignment of the amplicon reads, normalizes
4407gathered data, calculates multiple statistics (e.g. cut rates, frameshifts)
4408and presents the results in the form of aggregated reports. Data and
4409statistics can be broken down by experiments, barcodes, user defined groups,
4410guides and amplicons allowing for quick identification of potential
4411problems.")
4412 (license license:gpl3)))
4413
4414(define-public r-amaretto
4415 (package
4416 (name "r-amaretto")
4417 (version "1.28.0")
4418 (source (origin
4419 (method url-fetch)
4420 (uri (bioconductor-uri "AMARETTO" version))
4421 (sha256
4422 (base32
4423 "16m3pz5bff8s89fh45afbc4mwvbk8l7027algw7zag7cl9fkvxly"))))
4424 (properties `((upstream-name . "AMARETTO")))
4425 (build-system r-build-system)
4426 (propagated-inputs
4427 (list r-biocfilecache
4428 r-callr
4429 r-circlize
4430 r-complexheatmap
4431 r-curatedtcgadata
4432 r-doparallel
4433 r-dplyr
4434 r-dt
4435 r-foreach
4436 r-ggplot2
4437 r-glmnet
4438 r-gridextra
4439 r-httr
4440 r-impute
4441 r-knitr
4442 r-limma
4443 r-matrix
4444 r-matrixstats
4445 r-multiassayexperiment
4446 r-rcpp
4447 r-readr
4448 r-reshape2
4449 r-rmarkdown
4450 r-tibble))
4451 (native-inputs (list r-knitr r-testthat))
4452 (home-page "https://bioconductor.org/packages/AMARETTO")
4453 (synopsis "Regulatory network inference and driver gene evaluation")
4454 (description
4455 "This package @code{AMARETTO} represents an algorithm that integrates copy
4456number, DNA methylation and gene expression data to identify a set of driver
4457genes by analyzing cancer samples and connects them to clusters of co-expressed
4458genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer
4459setting to identify cancer driver genes and their modules on multiple cancer
4460sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle
4461and EMT, and modules that accurately predict survival and molecular subtypes.
4462This allows @code{AMARETTO} to identify novel cancer driver genes directing
4463canonical cancer pathways.")
4464 (license license:asl2.0)))
4465
4466(define-public r-anaquin
4467 (package
4468 (name "r-anaquin")
4469 (version "2.36.0")
4470 (source (origin
4471 (method url-fetch)
4472 (uri (bioconductor-uri "Anaquin" version))
4473 (sha256
4474 (base32
4475 "179329714g8xhkq4rsiwjxmfsp807hyfq2z9d4x422c6adb7h6d1"))))
4476 (properties `((upstream-name . "Anaquin")))
4477 (build-system r-build-system)
4478 (propagated-inputs
4479 (list r-deseq2
4480 r-ggplot2
4481 r-knitr
4482 r-locfit
4483 r-plyr
4484 r-qvalue
4485 r-rocr))
4486 (native-inputs (list r-knitr r-runit))
4487 (home-page "https://www.sequinstandards.com/")
4488 (synopsis "Statistical analysis of sequins")
4489 (description
4490 "The project is intended to support the use of @dfn{sequins}(synthetic
4491sequencing spike-in controls) owned and made available by the Garvan Institute
4492of Medical Research. The goal is to provide a standard library for quantitative
4493analysis, modelling, and visualization of spike-in controls.")
4494 (license license:bsd-3)))
4495
4496(define-public r-ancombc
4497 (package
4498 (name "r-ancombc")
4499 (version "2.14.0")
4500 (source (origin
4501 (method url-fetch)
4502 (uri (bioconductor-uri "ANCOMBC" version))
4503 (sha256
4504 (base32
4505 "18mcllrnjmyym412m35m6wbavhi3wk6bnzqk2fgvilkqz897d7n0"))))
4506 (properties
4507 '((upstream-name . "ANCOMBC")
4508 (updater-extra-native-inputs . ("r-microbiome"))))
4509 (build-system r-build-system)
4510 (propagated-inputs
4511 (list r-desctools
4512 r-doparallel
4513 r-dorng
4514 r-energy
4515 r-foreach
4516 r-gtools
4517 r-hmisc
4518 r-lme4
4519 r-lmertest
4520 r-mass
4521 r-matrix
4522 r-multcomp
4523 r-nloptr
4524 r-quadprog
4525 r-rdpack))
4526 (native-inputs (list r-knitr r-microbiome r-phyloseq r-testthat))
4527 (home-page "https://github.com/FrederickHuangLin/ANCOMBC")
4528 (synopsis "Analysis of compositions of microbiomes with bias correction")
4529 (description
4530 "@code{ANCOMBC} is a package containing @dfn{differential abundance} (DA)
4531and correlation analyses for microbiome data. Specifically, the package
4532includes @dfn{Analysis of Compositions of Microbiomes with Bias
4533Correction}(ANCOM-BC) and @dfn{Analysis of Composition of Microbiomes} (ANCOM)
4534for DA analysis, and @dfn{Sparse Estimation of Correlations among
4535Microbiomes} (SECOM) for correlation analysis. Microbiome data are typically
4536subject to two sources of biases: unequal sampling fractions (sample-specific
4537biases) and differential sequencing efficiencies (taxon-specific biases).
4538Methodologies included in the @code{ANCOMBC} package were designed to correct
4539these biases and construct statistically consistent estimators.")
4540 (license license:artistic2.0)))
4541
4542(define-public r-animalcules
4543 (package
4544 (name "r-animalcules")
4545 (version "1.28.0")
4546 (source (origin
4547 (method url-fetch)
4548 (uri (bioconductor-uri "animalcules" version))
4549 (sha256
4550 (base32
4551 "06csh9bap7dvy2lclhfjr7ljsf6blszs8g8bkvladlcw6x80fxx4"))))
4552 (properties
4553 '((upstream-name . "animalcules")
4554 (updater-extra-native-inputs . ("r-glmnet"))))
4555 (build-system r-build-system)
4556 (arguments
4557 (list
4558 #:skipped-tests
4559 ;; This test needs Internet access.
4560 '(("test-examples.R" ".*find_taxonomy\\(\\) is working.*"))))
4561 (propagated-inputs
4562 (list r-ape
4563 r-assertthat
4564 r-caret
4565 r-covr
4566 r-deseq2
4567 r-dplyr
4568 r-dt
4569 r-forcats
4570 r-ggforce
4571 r-ggplot2
4572 r-gunifrac
4573 r-lattice
4574 r-limma
4575 r-magrittr
4576 r-matrix
4577 r-multiassayexperiment
4578 r-plotly
4579 r-rentrez
4580 r-reshape2
4581 r-rocit
4582 r-s4vectors
4583 r-scales
4584 r-shiny
4585 r-shinyjs
4586 r-summarizedexperiment
4587 r-tibble
4588 r-tidyr
4589 r-tsne
4590 r-umap
4591 r-vegan
4592 r-xml))
4593 (native-inputs (list r-glmnet r-knitr r-testthat))
4594 (home-page "https://github.com/compbiomed/animalcules")
4595 (synopsis "Interactive microbiome analysis toolkit")
4596 (description
4597 "Animalcules is an R package for utilizing up-to-date data analytics,
4598visualization methods, and machine learning models to provide users an
4599easy-to-use interactive microbiome analysis framework. It can be used as a
4600standalone software package or users can explore their data with the
4601accompanying interactive R Shiny application. Traditional microbiome analysis
4602such as alpha/beta diversity and differential abundance analysis are enhanced,
4603while new methods like biomarker identification are introduced by animalcules.
4604Powerful interactive and dynamic figures generated by animalcules enable users
4605to understand their data better and discover new insights.")
4606 (license license:artistic2.0)))
4607
4608(define-public r-anndatar
4609 (package
4610 (name "r-anndatar")
4611 (version "1.2.0")
4612 (source
4613 (origin
4614 (method url-fetch)
4615 (uri (bioconductor-uri "anndataR" version))
4616 (sha256
4617 (base32 "1s8c69hgs1jv58pinsbc237fzwc4w29fw541y2hmwm13i7qcjw2m"))))
4618 (properties `((upstream-name . "anndataR")))
4619 (build-system r-build-system)
4620 (arguments
4621 (list
4622 #:skipped-tests
4623 ;; Division by zero in Python, raised while reading key '_index' of
4624 ;; <class 'zarr.core.Array'> from /obs. This happens only in test
4625 ;; "Writing an AnnData with layer 'empty' .zarr. works", but we cannot
4626 ;; easily select it.
4627 '("test-roundtrip-empty.R")
4628 #:phases
4629 '(modify-phases %standard-phases
4630 (add-after 'unpack 'find-python
4631 (lambda _
4632 (setenv "RETICULATE_PYTHON" (which "python3")))))))
4633 (propagated-inputs (list r-cli
4634 r-lifecycle
4635 r-matrix
4636 r-purrr
4637 r-r6
4638 r-reticulate
4639 r-rlang))
4640 (inputs (list python-wrapper
4641 python-anndata))
4642 (native-inputs (list r-knitr
4643 r-processx
4644 r-rarr
4645 r-rhdf5
4646 r-s4vectors
4647 r-seurat
4648 r-seuratobject
4649 r-singlecellexperiment
4650 r-spelling
4651 r-testthat
4652 r-withr))
4653 (home-page "https://anndatar.data-intuitive.com")
4654 (synopsis "AnnData interoperability in R")
4655 (description
4656 "This package aims to bring the power and flexibility of @code{AnnData}
4657to the R ecosystem, allowing you to effortlessly manipulate and analyze your
4658single-cell data. This package lets you work with backed h5ad and zarr files,
4659directly access various slots (e.g. X, obs, var), or convert the data into
4660@code{SingleCellExperiment} and Seurat objects.")
4661 (license license:expat)))
4662
4663(define-public r-annotationhubdata
4664 (package
4665 (name "r-annotationhubdata")
4666 (version "1.42.0")
4667 (source
4668 (origin
4669 (method url-fetch)
4670 (uri (bioconductor-uri "AnnotationHubData" version))
4671 (sha256
4672 (base32 "1w9q9n5fwd23f2vdw6gjcs9g7zq21hkfhikz9cx2qiv5g5h113yz"))))
4673 (properties `((upstream-name . "AnnotationHubData")))
4674 (build-system r-build-system)
4675 (arguments
4676 (list
4677 #:test-directory "inst/unitTests"
4678 ;; These tests require internet access.
4679 #:skipped-tests
4680 '("test_recipe.R"
4681 "test_webAccessFunctions.R")
4682 #:phases
4683 '(modify-phases %standard-phases
4684 (add-before 'install 'set-home
4685 (lambda _ (setenv "HOME" "/tmp"))))))
4686 (propagated-inputs
4687 (list r-annotationdbi
4688 r-annotationforge
4689 r-annotationhub
4690 r-biobase
4691 r-bioccheck
4692 r-biocgenerics
4693 r-biocmanager
4694 r-biocviews
4695 r-biostrings
4696 r-dbi
4697 r-futile-logger
4698 r-genomeinfodb
4699 r-genomicfeatures
4700 r-genomicranges
4701 r-graph
4702 r-iranges
4703 r-jsonlite
4704 r-organismdbi
4705 r-rcurl
4706 r-rsamtools
4707 r-rsqlite
4708 r-rtracklayer
4709 r-s4vectors
4710 r-seqinfo
4711 r-xml))
4712 (native-inputs (list r-genomeinfodbdata r-knitr r-runit))
4713 (home-page "https://bioconductor.org/packages/AnnotationHubData")
4714 (synopsis "Transform public data resources into Bioconductor data structures")
4715 (description
4716 "This package provides tools to acquire, annotate, convert and store data
4717for use in Bioconductor’s AnnotationHub.")
4718 (license license:artistic2.0)))
4719
4720(define-public r-anvil
4721 (package
4722 (name "r-anvil")
4723 (version "1.24.0")
4724 (source (origin
4725 (method url-fetch)
4726 (uri (bioconductor-uri "AnVIL" version))
4727 (sha256
4728 (base32
4729 "1571kb60bmrk6a8fg26jzdzgp3criy2c7f9rknw4s1sarc6ifrkk"))))
4730 (properties `((upstream-name . "AnVIL")))
4731 (build-system r-build-system)
4732 ;; Tests require Internet access.
4733 (arguments (list #:tests? #false))
4734 (propagated-inputs
4735 (list r-anvilbase
4736 r-biocbaseutils
4737 r-digest
4738 r-dplyr
4739 r-dt
4740 r-futile-logger
4741 r-gcptools
4742 r-htmltools
4743 r-httr
4744 r-jsonlite
4745 r-keyring
4746 r-miniui
4747 r-rapiclient
4748 r-shiny
4749 r-tibble
4750 r-yaml))
4751 (native-inputs (list r-knitr r-testthat))
4752 (home-page "https://bioconductor.org/packages/AnVIL")
4753 (synopsis "Provides access to AnVIL, Terra, Leonardo and other projects")
4754 (description
4755 "The AnVIL is a cloud computing resource developed in part by the
4756National Human Genome Research Institute. The AnVIL package provides end-user
4757and developer functionality. AnVIL provides fast binary package installation,
4758utilities for working with Terra/AnVIL table and data resources, and
4759convenient functions for file movement to and from Google cloud storage. For
4760developers, AnVIL provides programmatic access to the Terra, Leonardo, Rawls,
4761Dockstore, and Gen3 RESTful programming interface, including helper functions
4762to transform JSON responses to formats more amenable to manipulation in R.")
4763 (license license:artistic2.0)))
4764
4765(define-public r-anvilbase
4766 (package
4767 (name "r-anvilbase")
4768 (version "1.6.0")
4769 (source
4770 (origin
4771 (method url-fetch)
4772 (uri (bioconductor-uri "AnVILBase" version))
4773 (sha256
4774 (base32 "11kgihy6p1bqqwg7j43pl0wpqzwqq5kcb7kkbxbky34yqcf4dvqc"))))
4775 (properties `((upstream-name . "AnVILBase")))
4776 (build-system r-build-system)
4777 (propagated-inputs (list r-dplyr r-httr r-httr2 r-jsonlite r-tibble))
4778 (native-inputs (list r-knitr r-testthat))
4779 (home-page "https://github.com/Bioconductor/AnVILBase")
4780 (synopsis "Generic functions for interacting with the AnVIL system")
4781 (description
4782 "This package provides generic functions for interacting with the
4783@code{AnVIL} system. Packages that use either GCP or Azure in @code{AnVIL}
4784are built on top of @code{AnVILBase}. Extension packages will provide methods
4785for interacting with other cloud providers.")
4786 (license license:artistic2.0)))
4787
4788(define-public r-anvilgcp
4789 (package
4790 (name "r-anvilgcp")
4791 (version "1.6.2")
4792 (source
4793 (origin
4794 (method url-fetch)
4795 (uri (bioconductor-uri "AnVILGCP" version))
4796 (sha256
4797 (base32 "0fcqbh2ykbdjybbc1l893dk4s6v9ag1lpmhh04lpkn5zr4lb8jys"))))
4798 (properties `((upstream-name . "AnVILGCP")))
4799 (build-system r-build-system)
4800 (propagated-inputs (list r-anvilbase
4801 r-biocbaseutils
4802 r-dplyr
4803 r-gcptools
4804 r-httr
4805 r-jsonlite
4806 r-rlang
4807 r-tibble
4808 r-tidyr))
4809 (native-inputs (list r-knitr r-testthat))
4810 (home-page "https://github.com/Bioconductor/AnVILGCP")
4811 (synopsis "GCP R client for the AnVIL")
4812 (description
4813 "The package provides a set of functions to interact with the @dfn{Google
4814Cloud Platform} (GCP) services on the @code{AnVIL} platform. The package is
4815designed to work with the @code{AnVIL} package. User-level interaction with
4816this package should be minimal.")
4817 (license license:artistic2.0)))
4818
4819(define-public r-aldex2
4820 (package
4821 (name "r-aldex2")
4822 (version "1.44.0")
4823 (source (origin
4824 (method url-fetch)
4825 (uri (bioconductor-uri "ALDEx2" version))
4826 (sha256
4827 (base32
4828 "1nrjmzahdvwfx0v55kk37lnhs49w2zppcvhhjkxvb41srhkriizp"))))
4829 (properties `((upstream-name . "ALDEx2")))
4830 (build-system r-build-system)
4831 (propagated-inputs
4832 (list r-biocparallel
4833 r-directlabels
4834 r-genomicranges
4835 r-iranges
4836 r-lattice
4837 r-latticeextra
4838 r-multtest
4839 r-rfast
4840 r-s4vectors
4841 r-summarizedexperiment
4842 r-zcompositions))
4843 (native-inputs (list r-knitr r-testthat))
4844 (home-page "https://github.com/ggloor/ALDEx_bioc")
4845 (synopsis "Analysis of differential abundance taking sample variation into account")
4846 (description
4847 "This package provides a differential abundance analysis for the
4848comparison of two or more conditions. Useful for analyzing data from standard
4849RNA-seq or meta-RNA-seq assays as well as selected and unselected values from
4850in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer
4851abundance from counts, optimized for three or more experimental replicates.
4852The method infers biological and sampling variation to calculate the expected
4853false discovery rate, given the variation, based on a Wilcoxon Rank Sum test
4854and Welch's t-test, a Kruskal-Wallis test, a generalized linear model, or a
4855correlation test. All tests report p-values and Benjamini-Hochberg corrected
4856p-values. ALDEx2 also calculates expected standardized effect sizes for
4857paired or unpaired study designs.")
4858 ;; The code for the function "rdirichlet" is from the R package
4859 ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the
4860 ;; package's LICENSE is specified as GPL-3.
4861 (license (list license:agpl3+ license:gpl2+ license:gpl3))))
4862
4863(define-public r-alevinqc
4864 (package
4865 (name "r-alevinqc")
4866 (version "1.28.0")
4867 (source (origin
4868 (method url-fetch)
4869 (uri (bioconductor-uri "alevinQC" version))
4870 (sha256
4871 (base32
4872 "1qpbz4zcgb1yzm4cx2m88qx2ysjnkrshc7phnv1jxarr50y4gi6n"))))
4873 (properties
4874 '((upstream-name . "alevinQC")))
4875 (build-system r-build-system)
4876 (propagated-inputs
4877 (list r-cowplot
4878 r-dplyr
4879 r-dt
4880 r-ggally
4881 r-ggplot2
4882 r-rcpp
4883 r-rjson
4884 r-rlang
4885 r-rmarkdown
4886 r-shiny
4887 r-shinydashboard
4888 r-tximport))
4889 (native-inputs (list r-biocstyle r-knitr r-testthat))
4890 (home-page "https://github.com/csoneson/alevinQC")
4891 (synopsis "Quality control reports for @code{Alevin} output")
4892 (description
4893 "The package @code{r-alevinqc} generates quality control reports
4894summarizing the output from an @code{alevin} run. The reports can be
4895generated as HTML or PDF files, or as Shiny applications.")
4896 (license license:expat)))
4897
4898(define-public r-alphabeta
4899 (package
4900 (name "r-alphabeta")
4901 (version "1.26.0")
4902 (source (origin
4903 (method url-fetch)
4904 (uri (bioconductor-uri "AlphaBeta" version))
4905 (sha256
4906 (base32
4907 "1c6l6r5mb8dqi0g7p6ipaimclj68mhm007hb82labh21s9cf4kqf"))))
4908 (properties `((upstream-name . "AlphaBeta")))
4909 (build-system r-build-system)
4910 (propagated-inputs
4911 (list r-biocparallel
4912 r-data-table
4913 r-dplyr
4914 r-expm
4915 r-ggplot2
4916 r-gtools
4917 r-igraph
4918 r-optimx
4919 r-plotly
4920 r-stringr))
4921 (native-inputs (list r-knitr))
4922 (home-page "https://bioconductor.org/packages/AlphaBeta")
4923 (synopsis "Estimate epimutation rates and spectra from DNA methylations in plants")
4924 (description
4925 "The package @code{AlphaBeta} is a computational method for estimating
4926epimutation rates and spectra from high-throughput DNA methylation data in
4927plants. The method has been specifically designed to:
4928
4929@itemize
4930@item analyze @emph{germline} epimutations in the context of
4931 multi-generational mutation accumulation lines;
4932@item analyze @emph{somatic} epimutations in the context of plant development
4933 and aging.
4934@end itemize")
4935 (license license:gpl3)))
4936
4937(define-public r-alpine
4938 (package
4939 (name "r-alpine")
4940 (version "1.26.0")
4941 (source (origin
4942 (method url-fetch)
4943 (uri (bioconductor-uri "alpine" version))
4944 (sha256
4945 (base32
4946 "1md4m9ln1mpxf7d2h7jnsjyi4zrviiqn9fzk1gkz2n6qj7jwpqbb"))))
4947 (properties `((upstream-name . "alpine")))
4948 (build-system r-build-system)
4949 ;; Tests require Internet access because alpineData uses ExperimentHub.
4950 (arguments (list #:tests? #false))
4951 (propagated-inputs
4952 (list r-biostrings
4953 r-genomeinfodb
4954 r-genomicalignments
4955 r-genomicfeatures
4956 r-genomicranges
4957 r-graph
4958 r-iranges
4959 r-rbgl
4960 r-rsamtools
4961 r-s4vectors
4962 r-speedglm
4963 r-stringr
4964 r-summarizedexperiment))
4965 (native-inputs (list r-knitr r-testthat))
4966 (home-page "https://bioconductor.org/packages/alpine")
4967 (synopsis "Modeling and correcting fragment sequence bias")
4968 (description
4969 "The package @code{alpine} helps to model bias parameters and then using
4970those parameters to estimate RNA-seq transcript abundance. @code{Alpine} is a
4971package for estimating and visualizing many forms of sample-specific biases that
4972can arise in RNA-seq, including fragment length distribution, positional bias on
4973the transcript, read start bias (random hexamer priming), and fragment GC-content
4974(amplification). It also offers bias-corrected estimates of transcript
4975abundance in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million
4976mapped reads). It is currently designed for un-stranded paired-end RNA-seq
4977data.")
4978 (license license:gpl2+)))
4979
4980(define-public r-alpsnmr
4981 (package
4982 (name "r-alpsnmr")
4983 (version "4.14.0")
4984 (source (origin
4985 (method url-fetch)
4986 (uri (bioconductor-uri "AlpsNMR" version))
4987 (sha256
4988 (base32
4989 "01lldpaqybrqx1kfpyz1kl42jy3is103r2bmspwwwiqym264f2an"))))
4990 (properties
4991 '((upstream-name . "AlpsNMR")
4992 ;; This is not needed for running tests.
4993 (updater-ignored-native-inputs . ("r-chemospec"))))
4994 (build-system r-build-system)
4995 (propagated-inputs
4996 (list r-baseline
4997 r-biocparallel
4998 r-cli
4999 r-dplyr
5000 r-fs
5001 r-generics
5002 r-ggplot2
5003 r-glue
5004 r-htmltools
5005 r-magrittr
5006 r-matrixstats
5007 r-mixomics
5008 r-pcapp
5009 r-purrr
5010 r-readxl
5011 r-reshape2
5012 r-rlang
5013 r-rmarkdown
5014 r-scales
5015 r-signal
5016 r-speaq
5017 r-stringr
5018 r-tibble
5019 r-tidyr
5020 r-tidyselect
5021 r-vctrs))
5022 (native-inputs (list r-knitr r-testthat))
5023 (home-page "https://sipss.github.io/AlpsNMR/")
5024 (synopsis "Automated spectral processing system for NMR")
5025 (description
5026 "This package reads Bruker @acronym{NMR, Nuclear Magnetic Resonance} data
5027directories both zipped and unzipped. It provides automated and efficient
5028signal processing for untargeted NMR metabolomics. It is able to interpolate
5029the samples, detect outliers, exclude regions, normalize, detect peaks, align
5030the spectra, integrate peaks, manage metadata and visualize the spectra.
5031After spectra processing, it can apply multivariate analysis on extracted
5032data. Efficient plotting with 1-D data is also available. Basic reading of
50331D ACD/Labs exported JDX samples is also available.")
5034 (license license:expat)))
5035
5036(define-public r-altcdfenvs
5037 (package
5038 (name "r-altcdfenvs")
5039 (version "2.74.0")
5040 (source (origin
5041 (method url-fetch)
5042 (uri (bioconductor-uri "altcdfenvs" version))
5043 (sha256
5044 (base32
5045 "0bj50m6hafqwi5c80ni2dmy5qrgqsdvskq016scv7y6i6wdjjp0k"))))
5046 (properties `((upstream-name . "altcdfenvs")))
5047 (build-system r-build-system)
5048 (propagated-inputs
5049 (list r-affy
5050 r-biobase
5051 r-biocgenerics
5052 r-biostrings
5053 r-hypergraph
5054 r-makecdfenv
5055 r-s4vectors))
5056 (home-page "https://bioconductor.org/packages/altcdfenvs")
5057 (synopsis
5058 "Convenience data structures and functions to handle CDF environments")
5059 (description
5060 "The package is usable with Affymetrix GeneChip short oligonucleotide
5061arrays, and it can be adapted or extended to other platforms. It is able to
5062modify or replace the grouping of probes in the probe sets. Also, the package
5063contains simple functions to read R connections in the FASTA format and it can
5064create an alternative mapping from sequences.")
5065 (license license:gpl2+)))
5066
5067(define-public r-aneufinder
5068 (package
5069 (name "r-aneufinder")
5070 (version "1.35.0")
5071 (source (origin
5072 (method url-fetch)
5073 (uri (bioconductor-uri "AneuFinder" version))
5074 (sha256
5075 (base32
5076 "0zx0brvcyi9id7xli9h5nk9an7j46p7zgjj3qmwr3jm4b95qahpl"))))
5077 (build-system r-build-system)
5078 (arguments
5079 (list
5080 #:phases
5081 #~(modify-phases %standard-phases
5082 (add-before 'install 'fix-r-4.5.0
5083 ;; Changes in R 4.5.0: C-Level Facilities.
5084 ;; Strict R headers are now the default. This removes the legacy
5085 ;; definitions of PI, Calloc, Realloc and Free: use M_PI,
5086 ;; R_Calloc, R_Realloc or R_Free instead.
5087 ;; https://cran.r-project.org/doc/manuals/r-release/NEWS.html
5088 (lambda _
5089 (substitute* '("src/densities.cpp"
5090 "src/loghmm.cpp"
5091 "src/scalehmm.cpp"
5092 "src/utility.cpp")
5093 (("Calloc\\(") "R_Calloc(")
5094 (("Free\\(") "R_Free(")))))))
5095 (native-inputs
5096 (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat))
5097 (propagated-inputs
5098 (list r-aneufinderdata
5099 r-bamsignals
5100 r-biocgenerics
5101 r-biostrings
5102 r-cowplot
5103 r-dnacopy
5104 r-doparallel
5105 r-ecp
5106 r-foreach
5107 r-genomeinfodb
5108 r-genomicalignments
5109 r-genomicranges
5110 r-ggdendro
5111 r-ggplot2
5112 r-ggrepel
5113 r-iranges
5114 r-mclust
5115 r-reshape2
5116 r-rsamtools
5117 r-s4vectors))
5118 (home-page "https://bioconductor.org/packages/AneuFinder/")
5119 (synopsis "Copy number variation analysis in single-cell-sequencing data")
5120 (description "This package implements functions for copy number variant
5121calling, plotting, export and analysis from whole-genome single cell
5122sequencing data.")
5123 (license license:artistic2.0)))
5124
5125(define-public r-anf
5126 (package
5127 (name "r-anf")
5128 (version "1.34.0")
5129 (source (origin
5130 (method url-fetch)
5131 (uri (bioconductor-uri "ANF" version))
5132 (sha256
5133 (base32
5134 "106qxs1fr748ipa7z7f4ngr07dqwr1gihlqpzvcxp4bkdsn7s016"))))
5135 (properties `((upstream-name . "ANF")))
5136 (build-system r-build-system)
5137 ;; Tests attempt to download data files.
5138 (arguments (list #:tests? #false))
5139 (propagated-inputs
5140 (list r-biobase
5141 r-igraph
5142 r-mass
5143 r-rcolorbrewer
5144 r-survival))
5145 (native-inputs (list r-experimenthub r-knitr r-testthat))
5146 (home-page "https://bioconductor.org/packages/ANF")
5147 (synopsis "Affinity network fusion for complex patient clustering")
5148 (description
5149 "The package @dfn{ANF}(Affinity Network Fusion) provides methods for affinity
5150matrix construction and fusion as well as spectral clustering. This package is
5151used for complex patient clustering by integrating multi-omic data through affinity
5152network fusion.")
5153 (license license:gpl3)))
5154
5155(define-public r-annmap
5156 (package
5157 (name "r-annmap")
5158 (version "1.54.0")
5159 (source (origin
5160 (method url-fetch)
5161 (uri (bioconductor-uri "annmap" version))
5162 (sha256
5163 (base32
5164 "0k1n6125rd5f60lkldiq0vc54nyrx1fx6xc684ikfnb7a4cn60x8"))))
5165 (properties `((upstream-name . "annmap")))
5166 (build-system r-build-system)
5167 (arguments
5168 (list
5169 #:phases
5170 '(modify-phases %standard-phases
5171 ;; Needed for tests.
5172 (add-after 'unpack 'set-HOME
5173 (lambda _ (setenv "HOME" "/tmp"))))))
5174 (propagated-inputs
5175 (list r-biobase
5176 r-biocgenerics
5177 r-dbi
5178 r-digest
5179 r-genefilter
5180 r-genomicranges
5181 r-iranges
5182 r-lattice
5183 r-rmysql
5184 r-rsamtools))
5185 (home-page "https://github.com/cruk-mi/annmap")
5186 (synopsis
5187 "Genome annotation and visualisation for Affymetrix arrays and NGS analysis")
5188 (description
5189 "This package @code{annmap} provides annotation mappings for Affymetrix exon
5190arrays and coordinate based queries to support deep sequencing data analysis.
5191Database access is hidden behind the API which provides a set of functions such
5192as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc.
5193Functions to plot gene architecture and BAM file data are also provided.")
5194 (license license:gpl2)))
5195
5196(define-public r-antiprofiles
5197 (package
5198 (name "r-antiprofiles")
5199 (version "1.52.0")
5200 (source (origin
5201 (method url-fetch)
5202 (uri (bioconductor-uri "antiProfiles" version))
5203 (sha256
5204 (base32
5205 "0p9cg4y6s121qvg3wl0b7v0ip19dw2cg301nwmrjgjwqh7zm3044"))))
5206 (properties `((upstream-name . "antiProfiles")))
5207 (build-system r-build-system)
5208 (propagated-inputs
5209 (list r-locfit
5210 r-matrixstats))
5211 (home-page "https://github.com/HCBravoLab/antiProfiles")
5212 (synopsis "Implementation of gene expression anti-profiles")
5213 (description
5214 "This package implements the gene expression anti-profiles method.
5215Anti-profiles are a new approach for developing cancer genomic signatures that
5216specifically take advantage of gene expression heterogeneity. They explicitly
5217model increased gene expression variability in cancer to define robust and
5218reproducible gene expression signatures capable of accurately distinguishing
5219tumor samples from healthy controls.")
5220 (license license:artistic2.0)))
5221
5222(define-public r-arrayexpress
5223 (package
5224 (name "r-arrayexpress")
5225 (version "1.72.0")
5226 (source (origin
5227 (method url-fetch)
5228 (uri (bioconductor-uri "ArrayExpress" version))
5229 (sha256
5230 (base32
5231 "0as081hjm6q9s136mz62y9hya5b12ri7mclx3pa6xmdjfklsjmg7"))))
5232 (properties `((upstream-name . "ArrayExpress")))
5233 (build-system r-build-system)
5234 (propagated-inputs
5235 (list r-biobase
5236 r-httr
5237 r-jsonlite
5238 r-limma
5239 r-oligo
5240 r-rlang))
5241 (home-page "https://bioconductor.org/packages/ArrayExpress")
5242 (synopsis "Building R objects from ArrayExpress datasets")
5243 (description
5244 "This package offers the possibility to access the ArrayExpress repository
5245at @dfn{EBI} (European Bioinformatics Institute) and build Bioconductor data
5246structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
5247 (license license:artistic2.0)))
5248
5249(define-public r-arrayqualitymetrics
5250 (package
5251 (name "r-arrayqualitymetrics")
5252 (version "3.68.0")
5253 (source (origin
5254 (method url-fetch)
5255 (uri (bioconductor-uri "arrayQualityMetrics" version))
5256 (sha256
5257 (base32
5258 "1j44zj6pivygzvvd394jrc907bd3pf289n3fkfms3i5sn8g2bvvs"))))
5259 (properties
5260 '((upstream-name . "arrayQualityMetrics")
5261 ;; We don't need these.
5262 (updater-ignored-native-inputs . ("r-allmll" "r-ccl4"))))
5263 (build-system r-build-system)
5264 (propagated-inputs (list r-affy
5265 r-affyplm
5266 r-beadarray
5267 r-biobase
5268 r-genefilter
5269 r-gridsvg
5270 r-hmisc
5271 r-hwriter
5272 r-jsonlite
5273 r-lattice
5274 r-latticeextra
5275 r-limma
5276 r-rcolorbrewer
5277 r-setrng
5278 r-svglite
5279 r-vsn
5280 r-xml))
5281 (native-inputs (list r-knitr))
5282 (home-page "https://bioconductor.org/packages/arrayQualityMetrics")
5283 (synopsis "Quality metrics report for microarray data sets")
5284 (description
5285 "This package generates microarray quality metrics reports for data in
5286Bioconductor microarray data containers @code{(ExpressionSet},
5287@code{NChannelSet}, @code{AffyBatch}). One and two color array platforms are
5288supported.")
5289 (license license:lgpl2.0+)))
5290
5291(define-public r-arraymvout
5292 (package
5293 (name "r-arraymvout")
5294 (version "1.70.0")
5295 (source
5296 (origin
5297 (method url-fetch)
5298 (uri (bioconductor-uri "arrayMvout" version))
5299 (sha256
5300 (base32 "1a5vzcgqj969mrxvy1zf0bc0xn7d5j97k82dq491rj5qqalwasdj"))))
5301 (properties `((upstream-name . "arrayMvout")))
5302 (build-system r-build-system)
5303 (arguments
5304 (list
5305 #:phases
5306 '(modify-phases %standard-phases
5307 (add-before 'install 'change-home-dir
5308 (lambda _
5309 ;; Change from /homeless-shelter to /tmp for write permission.
5310 (setenv "HOME" "/tmp"))))))
5311 (propagated-inputs
5312 (list r-affy
5313 r-affycontam
5314 r-biobase
5315 r-lumi
5316 r-mdqc
5317 r-parody))
5318 (home-page "https://bioconductor.org/packages/arrayMvout")
5319 (synopsis "Multivariate outlier detection for expression array QA")
5320 (description
5321 "This package supports the application of diverse quality metrics to
5322AffyBatch instances, summarizing these metrics via PCA, and then performing
5323parametric outlier detection on the PCs to identify aberrant arrays with a
5324fixed Type I error rate.")
5325 (license license:artistic2.0)))
5326
5327(define-public r-arrayquality
5328 (package
5329 (name "r-arrayquality")
5330 (version "1.90.0")
5331 (source
5332 (origin
5333 (method url-fetch)
5334 (uri (bioconductor-uri "arrayQuality" version))
5335 (sha256
5336 (base32 "0y9bzvd8wskvbfmz89ipmg3gs78cf8kk3jdbam5kywg5dvcz8kgy"))))
5337 (properties `((upstream-name . "arrayQuality")))
5338 (build-system r-build-system)
5339 (propagated-inputs
5340 (list r-gridbase
5341 r-hexbin
5342 r-limma
5343 r-marray
5344 r-rcolorbrewer))
5345 (home-page "http://arrays.ucsf.edu/")
5346 (synopsis "Assessing array quality on spotted arrays")
5347 (description
5348 "This package provides functions for performing print-run and array level
5349quality assessment.")
5350 (license license:lgpl2.0+)))
5351
5352(define-public r-asafe
5353 (package
5354 (name "r-asafe")
5355 (version "1.38.0")
5356 (source (origin
5357 (method url-fetch)
5358 (uri (bioconductor-uri "ASAFE" version))
5359 (sha256
5360 (base32
5361 "0fngw5gky8xm1aba1jgp55815xcg1czw8hd2mz4h5r5q7rarykzw"))))
5362 (properties `((upstream-name . "ASAFE")))
5363 (build-system r-build-system)
5364 (native-inputs (list r-knitr r-testthat))
5365 (home-page "https://bioconductor.org/packages/ASAFE")
5366 (synopsis "Ancestry Specific Allele Frequency Estimation")
5367 (description
5368 "The @code{ASAFE} package contains a collection of functions that can be
5369used to carry out an @dfn{EM} (Expectation–maximization) algorithm to estimate
5370ancestry-specific allele frequencies for a bi-allelic genetic marker, e.g. an
5371@dfn{SNP} (single nucleotide polymorphism) from genotypes and ancestry
5372pairs.")
5373 (license license:artistic2.0)))
5374
5375(define-public r-aseb
5376 (package
5377 (name "r-aseb")
5378 (version "1.56.0")
5379 (source (origin
5380 (method url-fetch)
5381 (uri (bioconductor-uri "ASEB" version))
5382 (sha256
5383 (base32
5384 "0l59cbxas1xgg5k95y8vb8j7rlp6nk2iz7904rz0w3wnb6rckhqf"))))
5385 (properties `((upstream-name . "ASEB")))
5386 (build-system r-build-system)
5387 (home-page "https://bioconductor.org/packages/ASEB")
5388 (synopsis "Predict acetylated lysine sites")
5389 (description
5390 "ASEB is an R package to predict lysine sites that can be acetylated by a
5391specific @dfn{KAT} (K-acetyl-transferases) family. Lysine acetylation is a
5392well-studied posttranslational modification on kinds of proteins. About four
5393thousand lysine acetylation sites and over 20 lysine KATs have been
5394identified. However, which KAT is responsible for a given protein or lysine
5395site acetylation is mostly unknown. In this package, we use a
5396@dfn{GSEA}-like (Gene Set Enrichment Analysis) method to make predictions.
5397GSEA method was developed and successfully used to detect coordinated
5398expression changes and find the putative functions of the long non-coding
5399RNAs.")
5400 (license license:gpl3+)))
5401
5402(define-public r-asgsca
5403 (package
5404 (name "r-asgsca")
5405 (version "1.46.0")
5406 (source (origin
5407 (method url-fetch)
5408 (uri (bioconductor-uri "ASGSCA" version))
5409 (sha256
5410 (base32
5411 "1q5zskcwy2h3gcn2868adblnhbfh9jy83qrbgr2w1cklghbkp476"))))
5412 (properties `((upstream-name . "ASGSCA")))
5413 (build-system r-build-system)
5414 (propagated-inputs (list r-mass r-matrix))
5415 (home-page "https://bioconductor.org/packages/ASGSCA")
5416 (synopsis "Analysis of associations between multiple genotypes and traits")
5417 (description
5418 "The package @dfn{ASGSCA} (Association Study using Generalized Structured
5419Component Analysis) provides tools to model and test the association between
5420multiple genotypes and multiple traits, taking into account the prior
5421biological knowledge. Genes, and clinical pathways are incorporated in the
5422model as latent variables.")
5423 (license license:gpl3)))
5424
5425(define-public r-asics
5426 (package
5427 (name "r-asics")
5428 (version "2.28.0")
5429 (source (origin
5430 (method url-fetch)
5431 (uri (bioconductor-uri "ASICS" version))
5432 (sha256
5433 (base32
5434 "0i00fbn34x62g6kh34s90dnx26n0r0scwk7k8fjckk2zvdcla4ky"))))
5435 (properties `((upstream-name . "ASICS")))
5436 (build-system r-build-system)
5437 (propagated-inputs
5438 (list r-biocparallel
5439 r-ggplot2
5440 r-glmnet
5441 r-gridextra
5442 r-matrix
5443 r-mvtnorm
5444 r-pepsnmr
5445 r-plyr
5446 r-quadprog
5447 r-ropls
5448 r-summarizedexperiment
5449 r-zoo))
5450 (native-inputs (list r-knitr r-testthat))
5451 (home-page "https://bioconductor.org/packages/ASICS")
5452 (synopsis "Automatic statistical identification in complex spectra")
5453 (description
5454 "ASICS quantifies concentration of metabolites in a complex spectrum.
5455The identification of metabolites is performed by fitting a mixture model to
5456the spectra of the library with a sparse penalty.")
5457 (license license:gpl2+)))
5458
5459(define-public r-aspli
5460 (package
5461 (name "r-aspli")
5462 (version "2.22.0")
5463 (source (origin
5464 (method url-fetch)
5465 (uri (bioconductor-uri "ASpli" version))
5466 (sha256
5467 (base32
5468 "0fnisaglavwkx5qkm3ssf9bky3dgni2zlv32xlzicg6y75s7fgsa"))))
5469 (properties `((upstream-name . "ASpli")))
5470 (build-system r-build-system)
5471 (propagated-inputs
5472 (list r-annotationdbi
5473 r-biocgenerics
5474 r-biocstyle
5475 r-data-table
5476 r-dt
5477 r-edger
5478 r-genomicalignments
5479 r-genomicfeatures
5480 r-genomicranges
5481 r-gviz
5482 r-htmltools
5483 r-igraph
5484 r-iranges
5485 r-limma
5486 r-mass
5487 r-pbmcapply
5488 r-rsamtools
5489 r-s4vectors
5490 r-tidyr
5491 r-txdbmaker
5492 r-upsetr))
5493 (home-page "https://bioconductor.org/packages/ASpli")
5494 (synopsis "Analysis of alternative splicing using RNA-Seq")
5495 (description
5496 "@dfn{AS} (alternative splicing) is a common mechanism of
5497post-transcriptional gene regulation in eukaryotic organisms that expands the
5498functional and regulatory diversity of a single gene by generating multiple
5499mRNA isoforms that encode structurally and functionally distinct proteins.
5500ASpli is an integrative pipeline and user-friendly R package that facilitates
5501the analysis of changes in both annotated and novel AS events. ASpli
5502integrates several independent signals in order to deal with the complexity
5503that might arise in splicing patterns.")
5504 ;; The authors didn't specify any GPL version in description or in the
5505 ;; sources.
5506 (license (list license:gpl2+ license:gpl3+))))
5507
5508(define-public r-assessorf
5509 (package
5510 (name "r-assessorf")
5511 (version "1.30.0")
5512 (source (origin
5513 (method url-fetch)
5514 (uri (bioconductor-uri "AssessORF" version))
5515 (sha256
5516 (base32
5517 "1h0ij4y213h8wanbfzkvpanr40wf2axd2d84p077zbn1mbfzxqzn"))))
5518 (properties `((upstream-name . "AssessORF")))
5519 (build-system r-build-system)
5520 (propagated-inputs
5521 (list r-biostrings
5522 r-decipher
5523 r-genomicranges
5524 r-iranges))
5525 (native-inputs (list r-knitr))
5526 (home-page "https://bioconductor.org/packages/AssessORF")
5527 (synopsis "Assess gene predictions using proteomics and evolutionary conservation")
5528 (description
5529 "In order to assess the quality of a set of predicted genes for a genome,
5530evidence must first be mapped to that genome. Next, each gene must be
5531categorized based on how strong the evidence is for or against that gene. The
5532AssessORF package provides the functions and class structures necessary for
5533accomplishing those tasks, using proteomics hits and evolutionarily conserved
5534start codons as the forms of evidence.")
5535 (license license:gpl3)))
5536
5537(define-public r-asset
5538 (package
5539 (name "r-asset")
5540 (version "2.30.0")
5541 (source (origin
5542 (method url-fetch)
5543 (uri (bioconductor-uri "ASSET" version))
5544 (sha256
5545 (base32
5546 "04r6knxfdch3qwip2alq0l1jcy9xib25ipizbh7y3nb076m5gfgq"))))
5547 (properties `((upstream-name . "ASSET")))
5548 (build-system r-build-system)
5549 (propagated-inputs (list r-mass r-msm r-rmeta))
5550 (native-inputs (list r-biocgenerics r-knitr r-runit))
5551 (home-page "https://bioconductor.org/packages/ASSET")
5552 (synopsis
5553 "Subset-based association analysis of heterogeneous traits and subtypes")
5554 (description
5555 "This package is an R program for the subset-based analysis of
5556heterogeneous traits and disease subtypes. ASSET allows the user to search
5557through all possible subsets of z-scores to identify the subset of traits
5558giving the best meta-analyzed z-score. Further, it returns a p-value
5559adjusting for the multiple-testing involved in the search. It also allows for
5560searching for the best combination of disease subtypes associated with each
5561variant.")
5562 (license license:gpl2)))
5563
5564(define-public r-assorthead
5565 (package
5566 (name "r-assorthead")
5567 (version "1.6.3")
5568 (source
5569 (origin
5570 (method url-fetch)
5571 (uri (bioconductor-uri "assorthead" version))
5572 (sha256
5573 (base32 "0vh175mpwmdjw30if09ddzlnvrh8r8lr2gxi5l0bjhwxc2xhdhvm"))))
5574 (properties `((upstream-name . "assorthead")))
5575 (build-system r-build-system)
5576 (native-inputs (list r-knitr))
5577 (home-page "https://github.com/LTLA/assorthead")
5578 (synopsis "Assorted header-only C++ libraries")
5579 (description
5580 "This package vendors an assortment of useful header-only C++ libraries.
5581Bioconductor packages can use these libraries in their own C++ code by
5582@code{LinkingTo} this package without introducing any additional dependencies.
5583The use of a central repository avoids duplicate vendoring of libraries across
5584multiple R packages, and enables better coordination of version updates across
5585cohorts of interdependent C++ libraries.")
5586 (license license:expat)))
5587
5588(define-public r-atena
5589 (package
5590 (name "r-atena")
5591 (version "1.18.0")
5592 (source (origin
5593 (method url-fetch)
5594 (uri (bioconductor-uri "atena" version))
5595 (sha256
5596 (base32
5597 "06bc2nqnmivz4ay1rwa22ihfa2xiygvrky7ssp1xlm1c0rcws5ll"))))
5598 (properties `((upstream-name . "atena")))
5599 (build-system r-build-system)
5600 (propagated-inputs
5601 (list r-annotationhub
5602 r-biocgenerics
5603 r-biocparallel
5604 r-cli
5605 r-genomeinfodb
5606 r-genomicalignments
5607 r-genomicfeatures
5608 r-genomicranges
5609 r-iranges
5610 r-matrix
5611 r-matrixgenerics
5612 r-matrixstats
5613 r-rsamtools
5614 r-s4vectors
5615 r-seqinfo
5616 r-sparsematrixstats
5617 r-squarem
5618 r-summarizedexperiment))
5619 (native-inputs (list r-knitr r-runit))
5620 (home-page "https://github.com/functionalgenomics/atena")
5621 (synopsis "Analysis of transposable elements")
5622 (description
5623 "The atena package quantifies expression of @dfn{TEs} (transposable
5624elements) from RNA-seq data through different methods, including ERVmap,
5625TEtranscripts and Telescope. A common interface is provided to use each of
5626these methods, which consists of building a parameter object, calling the
5627quantification function with this object and getting a
5628@code{SummarizedExperiment} object as an output container of the quantified
5629expression profiles. The implementation allows quantifing TEs and gene
5630transcripts in an integrated manner.")
5631 (license license:artistic2.0)))
5632
5633(define-public r-atsnp
5634 (package
5635 (name "r-atsnp")
5636 (version "1.28.0")
5637 (source (origin
5638 (method url-fetch)
5639 (uri (bioconductor-uri "atSNP" version))
5640 (sha256
5641 (base32
5642 "00g9a9llpkp0n9kll61hj0jvgqmhwmng9x43n5d9ah6db868knsq"))))
5643 (properties `((upstream-name . "atSNP")))
5644 (build-system r-build-system)
5645 (propagated-inputs
5646 (list r-biocfilecache
5647 r-biocparallel
5648 r-bsgenome
5649 r-data-table
5650 r-ggplot2
5651 r-lifecycle
5652 r-motifstack
5653 r-rappdirs
5654 r-rcpp
5655 r-testthat))
5656 (native-inputs (list r-knitr))
5657 (home-page "https://github.com/sunyoungshin/atSNP")
5658 (synopsis
5659 "Affinity test for identifying regulatory single nucleotide polymorphisms")
5660 (description
5661 "The atSNP package performs affinity tests of motif matches with the
5662@dfn{SNP} (single nucleotide polymorphism) or the reference genomes and
5663SNP-led changes in motif matches.")
5664 (license license:gpl2)))
5665
5666(define-public r-attract
5667 (package
5668 (name "r-attract")
5669 (version "1.64.0")
5670 (source (origin
5671 (method url-fetch)
5672 (uri (bioconductor-uri "attract" version))
5673 (sha256
5674 (base32
5675 "15nl5qds46dx7dv0sjj61ycndp5a8swva0zjlk8zv265s63g3kac"))))
5676 (properties `((upstream-name . "attract")))
5677 (build-system r-build-system)
5678 (propagated-inputs
5679 (list r-annotationdbi
5680 r-biobase
5681 r-cluster
5682 r-gostats
5683 r-keggrest
5684 r-limma
5685 r-org-hs-eg-db
5686 r-reactome-db))
5687 (home-page "https://bioconductor.org/packages/attract")
5688 (synopsis "Finding drivers of Kauffman's attractor landscape")
5689 (description
5690 "This package contains the functions to find the gene expression modules
5691that represent the drivers of Kauffman's attractor landscape. The modules are
5692the core attractor pathways that discriminate between different cell types of
5693groups of interest. Each pathway has a set of synexpression groups, which show
5694transcriptionally-coordinated changes in gene expression.")
5695 (license license:lgpl2.0+)))
5696
5697(define-public r-awfisher
5698 (package
5699 (name "r-awfisher")
5700 (version "1.26.0")
5701 (source (origin
5702 (method url-fetch)
5703 (uri (bioconductor-uri "AWFisher" version))
5704 (sha256
5705 (base32
5706 "1f0djxm02fkb773m9azb7chnd2n7w9z2wwzhk8f4drkb91bznp20"))))
5707 (properties `((upstream-name . "AWFisher")))
5708 (build-system r-build-system)
5709 (propagated-inputs
5710 (list r-edger
5711 r-limma))
5712 (native-inputs (list r-knitr))
5713 (home-page "https://bioconductor.org/packages/AWFisher")
5714 (synopsis "Fast computing for adaptively weighted fisher's method")
5715 (description
5716 "This package is an implementation of the Adaptively Weighted Fisher's
5717method, including fast p-value computing, variability index, and
5718meta-pattern.")
5719 (license license:gpl3)))
5720
5721(define-public r-awst
5722 (package
5723 (name "r-awst")
5724 (version "1.20.0")
5725 (source (origin
5726 (method url-fetch)
5727 (uri (bioconductor-uri "awst" version))
5728 (sha256
5729 (base32
5730 "1qggpn4wkc3m1b8d3jiaj4bljalqgmhrhg7kb2kgx1wx3hlsg1pa"))))
5731 (properties
5732 '((upstream-name . "awst")
5733 (updater-extra-native-inputs . ("r-edaseq"))))
5734 (build-system r-build-system)
5735 (propagated-inputs (list r-summarizedexperiment))
5736 (native-inputs (list r-edaseq r-knitr r-testthat))
5737 (home-page "https://github.com/drisso/awst")
5738 (synopsis "Asymmetric within-sample transformation")
5739 (description
5740 "This package @dfn{awst} (Asymmetric Within-Sample Transformation) that
5741regularizes RNA-seq read counts and reduces the effect of noise on the
5742classification of samples. AWST comprises two main steps: standardization and
5743smoothing. These steps transform gene expression data to reduce the noise of
5744the lowly expressed features, which suffer from background effects and low
5745signal-to-noise ratio, and the influence of the highly expressed features,
5746which may be the result of amplification bias and other experimental
5747artifacts.")
5748 (license license:expat)))
5749
5750(define-public r-baalchip
5751 (package
5752 (name "r-baalchip")
5753 (version "1.38.0")
5754 (source (origin
5755 (method url-fetch)
5756 (uri (bioconductor-uri "BaalChIP" version))
5757 (sha256
5758 (base32
5759 "18si08w4c8610cahp7x4cww7dg09ivycgawdby370srx4a0q21m0"))))
5760 (properties `((upstream-name . "BaalChIP")))
5761 (build-system r-build-system)
5762 (inputs (list)) ; extra/get.overlaps.v2_chrXY.perl
5763 (propagated-inputs
5764 (list r-coda
5765 r-doby
5766 r-doparallel
5767 r-foreach
5768 r-genomeinfodb
5769 r-genomicalignments
5770 r-genomicranges
5771 r-ggplot2
5772 r-iranges
5773 r-reshape2
5774 r-rsamtools
5775 r-scales))
5776 (native-inputs (list r-biocgenerics r-knitr r-runit))
5777 (home-page "https://bioconductor.org/packages/BaalChIP")
5778 (synopsis
5779 "Analysis of allele-specific transcription factor binding in cancer genomes")
5780 (description
5781 "This package offers functions to process multiple @code{ChIP-seq BAM}
5782files and detect allele-specific events. It computes allele counts at
5783individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality
5784control) steps to remove problematic variants, and utilizes a Bayesian
5785framework to identify statistically significant allele-specific events.
5786BaalChIP is able to account for copy number differences between the two
5787alleles, a known phenotypical feature of cancer samples.")
5788 (license license:artistic2.0)))
5789
5790(define-public r-bags
5791 (package
5792 (name "r-bags")
5793 (version "2.51.0")
5794 (source
5795 (origin
5796 (method url-fetch)
5797 (uri (bioconductor-uri "BAGS" version))
5798 (sha256
5799 (base32 "0fsg0a0qf6127v5ny1ly2m9y1fbq6fipmm2jkad7prw9wbj9z8r4"))))
5800 (properties `((upstream-name . "BAGS")))
5801 (build-system r-build-system)
5802 (propagated-inputs (list r-biobase r-breastcancervdx))
5803 (home-page "https://bioconductor.org/packages/BAGS")
5804 (synopsis "Bayesian approach for geneset selection")
5805 (description
5806 "This R package is providing functions to perform geneset significance
5807analysis over simple cross-sectional data between 2 and 5 phenotypes of
5808interest.")
5809 (license license:artistic2.0)))
5810
5811(define-public r-basespacer
5812 (package
5813 (name "r-basespacer")
5814 (version "1.56.0")
5815 (source (origin
5816 (method url-fetch)
5817 (uri (bioconductor-uri "BaseSpaceR" version))
5818 (sha256
5819 (base32
5820 "1xa8m0n6p47is1b5pbv38z3frlzsrfmxrmzv13iblwzwbiwg7zc8"))))
5821 (properties `((upstream-name . "BaseSpaceR")))
5822 (build-system r-build-system)
5823 (propagated-inputs (list r-rcurl r-rjsonio))
5824 (home-page "https://bioconductor.org/packages/BaseSpaceR")
5825 (synopsis "R SDK for BaseSpace RESTful API")
5826 (description
5827 "This package provides an R interface to Illumina's BaseSpace cloud
5828computing environment, enabling the fast development of data analysis and
5829visualization tools. Besides providing an easy to use set of tools for
5830manipulating the data from BaseSpace, it also facilitates the access to R's
5831rich environment of statistical and data analysis tools.")
5832 (license license:asl2.0)))
5833
5834(define-public r-bac
5835 (package
5836 (name "r-bac")
5837 (version "1.58.0")
5838 (source (origin
5839 (method url-fetch)
5840 (uri (bioconductor-uri "BAC" version))
5841 (sha256
5842 (base32
5843 "00dkhns9n1x4wmlxjcw75h7iwwk37zlv1c2fi0g1mmsw1xvdjzp6"))))
5844 (properties `((upstream-name . "BAC")))
5845 (build-system r-build-system)
5846 (home-page "https://bioconductor.org/packages/BAC")
5847 (synopsis "Bayesian analysis of Chip-chip experiment")
5848 (description
5849 "This package uses a Bayesian hierarchical model to detect enriched
5850regions from ChIP-chip experiments. The common goal in analyzing this
5851ChIP-chip data is to detect DNA-protein interactions from ChIP-chip
5852experiments. The BAC package has mainly been tested with Affymetrix tiling
5853array data. However, we expect it to work with other platforms (e.g. Agilent,
5854Nimblegen, cDNA, etc.). Note that BAC does not deal with normalization, so
5855you will have to normalize your data beforehand.")
5856 (license license:artistic2.0)))
5857
5858(define-public r-bader
5859 (package
5860 (name "r-bader")
5861 (version "1.50.0")
5862 (source (origin
5863 (method url-fetch)
5864 (uri (bioconductor-uri "BADER" version))
5865 (sha256
5866 (base32
5867 "050qnkvvycqqfxwjjq0yc1m6n20bzfnrkzadbzlyan8b21a7fxny"))))
5868 (properties `((upstream-name . "BADER")))
5869 (build-system r-build-system)
5870 (home-page "https://bioconductor.org/packages/BADER")
5871 (synopsis
5872 "Bayesian analysis of differential expression in RNA sequencing data")
5873 (description
5874 "The BADER package is intended for the analysis of RNA sequencing data.
5875The algorithm fits a Bayesian hierarchical model for RNA sequencing count
5876data. BADER returns the posterior probability of differential expression for
5877each gene between two groups A and B. The joint posterior distribution of the
5878variables in the model can be returned in the form of posterior samples, which
5879can be used for further down-stream analyses such as gene set enrichment.")
5880 (license license:gpl2)))
5881
5882(define-public r-badregionfinder
5883 (package
5884 (name "r-badregionfinder")
5885 (version "1.40.0")
5886 (source (origin
5887 (method url-fetch)
5888 (uri (bioconductor-uri "BadRegionFinder" version))
5889 (sha256
5890 (base32
5891 "0zmhhbwdpracxb33yq93xz5ga4nwqxsrav1s7fwsc38a0sxgg58w"))))
5892 (properties `((upstream-name . "BadRegionFinder")))
5893 (build-system r-build-system)
5894 (propagated-inputs
5895 (list r-biomart
5896 r-genomicranges
5897 r-rsamtools
5898 r-s4vectors
5899 r-variantannotation))
5900 (home-page "https://bioconductor.org/packages/BadRegionFinder")
5901 (synopsis "Identifying regions with bad coverage in sequence alignment data")
5902 (description
5903 "BadRegionFinder is a package for identifying regions with a bad,
5904acceptable and good coverage in sequence alignment data available as bam
5905files. The whole genome may be considered as well as a set of target regions.
5906Various visual and textual types of output are available.")
5907 (license license:lgpl3)))
5908
5909(define-public r-bambu
5910 (package
5911 (name "r-bambu")
5912 (version "3.14.0")
5913 (source (origin
5914 (method url-fetch)
5915 (uri (bioconductor-uri "bambu" version))
5916 (sha256
5917 (base32
5918 "0gqif9hgsa3ddd425aj77xl7kk7q4f3wdniqirgcvnxmfbfay29y"))))
5919 (properties `((upstream-name . "bambu")))
5920 (build-system r-build-system)
5921 ;; Tests require Internet access.
5922 (arguments (list #:tests? #false))
5923 (propagated-inputs
5924 (list r-biocgenerics
5925 r-biocparallel
5926 r-bsgenome
5927 r-data-table
5928 r-dplyr
5929 r-genomeinfodb
5930 r-genomicalignments
5931 r-genomicfeatures
5932 r-genomicranges
5933 r-iranges
5934 r-rcpp
5935 r-rcpparmadillo
5936 r-rsamtools
5937 r-s4vectors
5938 r-summarizedexperiment
5939 r-tidyr
5940 r-xgboost))
5941 (native-inputs
5942 (list r-annotationdbi r-ggplot2 r-knitr r-purrr r-testthat))
5943 (home-page "https://github.com/GoekeLab/bambu")
5944 (synopsis
5945 "Isoform reconstruction and quantification for long read RNA-Seq data")
5946 (description
5947 "This R package is for multi-sample transcript discovery and
5948quantification using long read RNA-Seq data. You can use bambu after read
5949alignment to obtain expression estimates for known and novel transcripts and
5950genes. The output from bambu can directly be used for visualisation and
5951downstream analysis, such as differential gene expression or transcript
5952usage.")
5953 (license license:gpl3)))
5954
5955(define-public r-bandits
5956 (package
5957 (name "r-bandits")
5958 (version "1.28.0")
5959 (source (origin
5960 (method url-fetch)
5961 (uri (bioconductor-uri "BANDITS" version))
5962 (sha256
5963 (base32
5964 "0pq8rjc0xgv8jmy284ci0g7kml6ynhs91mzknj02inxr72ad148j"))))
5965 (properties
5966 '((upstream-name . "BANDITS")
5967 (updater-extra-native-inputs . ("r-tximport"))))
5968 (build-system r-build-system)
5969 (propagated-inputs
5970 (list r-biocparallel
5971 r-data-table
5972 r-doparallel
5973 r-dorng
5974 r-drimseq
5975 r-foreach
5976 r-ggplot2
5977 r-mass
5978 r-r-utils
5979 r-rcpp
5980 r-rcpparmadillo))
5981 (native-inputs (list r-knitr r-testthat r-tximport))
5982 (home-page "https://github.com/SimoneTiberi/BANDITS")
5983 (synopsis "Bayesian analysis of differential splicing")
5984 (description
5985 "BANDITS is a Bayesian hierarchical model for detecting differential
5986splicing of genes and transcripts, via @dfn{DTU} (differential transcript
5987usage), between two or more conditions. The method uses a Bayesian
5988hierarchical framework, which allows for sample specific proportions in a
5989Dirichlet-Multinomial model, and samples the allocation of fragments to the
5990transcripts. Parameters are inferred via @dfn{MCMC} (Markov chain Monte
5991Carlo) techniques and a DTU test is performed via a multivariate Wald test on
5992the posterior densities for the average relative abundance of transcripts.")
5993 (license license:gpl3+)))
5994
5995(define-public r-banocc
5996 (package
5997 (name "r-banocc")
5998 (version "1.36.0")
5999 (source (origin
6000 (method url-fetch)
6001 (uri (bioconductor-uri "banocc" version))
6002 (sha256
6003 (base32
6004 "0pdz29iibv2bhls4cbzlad0187mgqfxij8imkc665chzfl343ck1"))))
6005 (properties `((upstream-name . "banocc")))
6006 (build-system r-build-system)
6007 (propagated-inputs
6008 (list r-coda
6009 r-mvtnorm
6010 r-rstan
6011 r-stringr))
6012 (native-inputs (list r-knitr r-testthat))
6013 (home-page "https://bioconductor.org/packages/banocc")
6014 (synopsis "Bayesian analysis of compositional covariance")
6015 (description
6016 "BAnOCC is a package designed for compositional data, where each sample
6017sums to one. It infers the approximate covariance of the unconstrained data
6018using a Bayesian model coded with @code{rstan}. It provides as output the
6019@code{stanfit} object as well as posterior median and credible interval
6020estimates for each correlation element.")
6021 (license license:expat)))
6022
6023(define-public r-barcodetrackr
6024 (package
6025 (name "r-barcodetrackr")
6026 (version "1.16.0")
6027 (source (origin
6028 (method url-fetch)
6029 (uri (bioconductor-uri "barcodetrackR" version))
6030 (sha256
6031 (base32
6032 "1n2rj50gwqmqj5gs5d3asd3gcs0iv1rr1zh12s55lcsdxyfgp1ar"))))
6033 (properties `((upstream-name . "barcodetrackR")))
6034 (build-system r-build-system)
6035 ;; These 13 tests fail with this error:
6036 ;; Expected `barcodetrackR::...` to have type "list".
6037 ;; Actual type: "object"
6038 ;; These errors also exist in the current development version 1.19.0 for
6039 ;; Bioconductor 3.23.
6040 (arguments
6041 (list
6042 #:skipped-tests
6043 '(("test-clonal-bias-functions.R"
6044 "bias_(histogram|ridge_plot|lineplot) works")
6045 ("test-clonal-diversity-functions.R"
6046 "clonal_count works"
6047 "clonal_diversity works"
6048 "mds_plot works"
6049 "rank_abundance works")
6050 ("test-clonal-pattern-functions.R"
6051 "barcode_binary_heatmap works"
6052 "barcode_ggheatmap works"
6053 "barcode_ggheatmap_stat works"
6054 "clonal_contribution works")
6055 ("test-shared-clonality-functions.R"
6056 "cor_plot works"
6057 "scatter_plot works"))))
6058 (propagated-inputs
6059 (list r-circlize
6060 r-cowplot
6061 r-dplyr
6062 r-ggdendro
6063 r-ggplot2
6064 r-ggridges
6065 r-magrittr
6066 r-plyr
6067 r-proxy
6068 r-rcolorbrewer
6069 r-rlang
6070 r-s4vectors
6071 r-scales
6072 r-shiny
6073 r-summarizedexperiment
6074 r-tibble
6075 r-tidyr
6076 r-vegan
6077 r-viridis))
6078 (native-inputs (list r-knitr r-testthat))
6079 (home-page "https://github.com/dunbarlabNIH/barcodetrackR")
6080 (synopsis "Functions for analyzing cellular barcoding data")
6081 (description
6082 "This package is developed for the analysis and visualization of clonal
6083tracking data. The required data is formed by samples and tag abundances in
6084matrix form, usually from cellular barcoding experiments, integration site
6085retrieval analyses, or similar technologies.")
6086 (license license:cc0)))
6087
6088(define-public r-biocmake
6089 (package
6090 (name "r-biocmake")
6091 (version "1.4.0")
6092 (source
6093 (origin
6094 (method url-fetch)
6095 (uri (bioconductor-uri "biocmake" version))
6096 (sha256
6097 (base32 "0391ag380ac0da0rk397s60f0qg1zfhk4ksw9vkvbafwcpymk30m"))))
6098 (properties
6099 '((upstream-name . "biocmake")
6100 (updater-extra-propagated-inputs . ("cmake"))))
6101 (build-system r-build-system)
6102 (arguments
6103 (list
6104 ;; This requires internet access.
6105 #:skipped-tests '("test-download.R")))
6106 (propagated-inputs (list cmake r-dir-expiry))
6107 (native-inputs (list r-knitr r-testthat))
6108 (home-page "https://github.com/LTLA/biocmake")
6109 (synopsis "CMake for Bioconductor")
6110 (description
6111 "This package manages the installation of CMake for building Bioconductor
6112packages. This avoids the need for end-users to manually install CMake on
6113their system. No action is performed if a suitable version of CMake is
6114already available.")
6115 (license license:expat)))
6116
6117(define-public r-biocversion
6118 (package
6119 (name "r-biocversion")
6120 (version "3.23.1")
6121 (source
6122 (origin
6123 (method url-fetch)
6124 (uri (bioconductor-uri "BiocVersion" version))
6125 (sha256
6126 (base32
6127 "1x34d379lj9vbwss5zjrzg8p5j6d2bgaxn58ab3sr7z6a0pxv7vs"))))
6128 (properties `((upstream-name . "BiocVersion")))
6129 (build-system r-build-system)
6130 (home-page "https://bioconductor.org/packages/BiocVersion/")
6131 (synopsis "Set the appropriate version of Bioconductor packages")
6132 (description
6133 "This package provides repository information for the appropriate version
6134of Bioconductor.")
6135 (license license:artistic2.0)))
6136
6137(define-public r-biocgenerics
6138 (package
6139 (name "r-biocgenerics")
6140 (version "0.58.1")
6141 (source (origin
6142 (method url-fetch)
6143 (uri (bioconductor-uri "BiocGenerics" version))
6144 (sha256
6145 (base32
6146 "160s075v9h5gxg1mqhi3kd84hq2cm8w6f6yj3h40fnib1fgma4b9"))))
6147 (properties
6148 `((upstream-name . "BiocGenerics")))
6149 (build-system r-build-system)
6150 ;; Tests require r-iranges, which needs this package.
6151 (arguments (list #:tests? #false))
6152 (propagated-inputs (list r-generics))
6153 (home-page "https://bioconductor.org/packages/BiocGenerics")
6154 (synopsis "S4 generic functions for Bioconductor")
6155 (description
6156 "This package provides S4 generic functions needed by many Bioconductor
6157packages.")
6158 (license license:artistic2.0)))
6159
6160(define-public r-breakpointr
6161 (package
6162 (name "r-breakpointr")
6163 (version "1.30.0")
6164 (source (origin
6165 (method url-fetch)
6166 (uri (bioconductor-uri "breakpointR" version))
6167 (sha256
6168 (base32
6169 "0pnvg417fi2vjfzhi0vxxiax0kp9g7qff12sqgkif215wrlx8hh4"))))
6170 (properties `((upstream-name . "breakpointR")))
6171 (build-system r-build-system)
6172 (propagated-inputs
6173 (list r-biocgenerics
6174 r-breakpointrdata
6175 r-cowplot
6176 r-doparallel
6177 r-foreach
6178 r-genomeinfodb
6179 r-genomicalignments
6180 r-genomicranges
6181 r-ggplot2
6182 r-gtools
6183 r-iranges
6184 r-rsamtools
6185 r-s4vectors))
6186 (native-inputs (list r-biocstyle r-knitr r-testthat))
6187 (home-page "https://github.com/daewoooo/BreakPointR")
6188 (synopsis "Find breakpoints in Strand-seq data")
6189 (description
6190 "This package implements functions for finding breakpoints, plotting and
6191export of Strand-seq data.")
6192 (license license:expat)))
6193
6194(define-public r-cardelino
6195 (package
6196 (name "r-cardelino")
6197 (version "1.14.0")
6198 (source (origin
6199 (method url-fetch)
6200 (uri (bioconductor-uri "cardelino" version))
6201 (sha256
6202 (base32
6203 "11s9jzrpz5g9nvk7wxccb6hfgnmhvmnb4blxa9kisx6z7j1whsny"))))
6204 (properties `((upstream-name . "cardelino")))
6205 (build-system r-build-system)
6206 (propagated-inputs (list r-combinat
6207 r-genomeinfodb
6208 r-genomicranges
6209 r-ggplot2
6210 r-ggtree
6211 r-matrix
6212 r-matrixstats
6213 r-pheatmap
6214 r-s4vectors
6215 r-snpstats
6216 r-variantannotation
6217 r-vcfr))
6218 (native-inputs (list r-covr r-knitr r-testthat))
6219 (home-page "https://github.com/single-cell-genetics/cardelino")
6220 (synopsis "Clone identification from single cell data")
6221 (description
6222 "This package provides methods to infer clonal tree configuration for a
6223population of cells using single-cell RNA-seq data (scRNA-seq), and possibly
6224other data modalities. Methods are also provided to assign cells to inferred
6225clones and explore differences in gene expression between clones. These
6226methods can flexibly integrate information from imperfect clonal trees
6227inferred based on bulk exome-seq data, and sparse variant alleles expressed in
6228scRNA-seq data. A flexible beta-binomial error model that accounts for
6229stochastic dropout events as well as systematic allelic imbalance is used.")
6230 (license license:gpl3)))
6231
6232(define-public r-ccfindr
6233 (package
6234 (name "r-ccfindr")
6235 (version "1.32.0")
6236 (source
6237 (origin
6238 (method url-fetch)
6239 (uri (bioconductor-uri "ccfindR" version))
6240 (sha256
6241 (base32 "1dwy6kxc3gnx13482ndc244m7wna35p61jb0i0ivpqj9bc7ivnrl"))))
6242 (properties
6243 `((upstream-name . "ccfindR")
6244 (updater-extra-inputs . ("gsl"))))
6245 (build-system r-build-system)
6246 (inputs (list gsl))
6247 (propagated-inputs (list r-ape
6248 r-gtools
6249 r-irlba
6250 r-matrix
6251 r-rcolorbrewer
6252 r-rcpp
6253 r-rcppeigen
6254 r-rdpack
6255 r-rmpi
6256 r-rtsne
6257 r-s4vectors
6258 r-singlecellexperiment
6259 r-summarizedexperiment))
6260 (native-inputs (list r-knitr))
6261 (home-page "https://dx.doi.org/10.26508/lsa.201900443")
6262 (synopsis "Cancer clone finder")
6263 (description
6264 "This package provides a collection of tools for cancer genomic data
6265clustering analyses, including those for single cell RNA-seq. Cell clustering
6266and feature gene selection analysis employ Bayesian (and maximum likelihood)
6267non-negative matrix factorization (NMF) algorithm. Input data set consists of
6268RNA count matrix, gene, and cell bar code annotations. Analysis outputs are
6269factor matrices for multiple ranks and marginal likelihood values for each
6270rank. The package includes utilities for downstream analyses, including
6271meta-gene identification, visualization, and construction of rank-based trees
6272for clusters.")
6273 (license license:gpl2+)))
6274
6275(define-public r-cellid
6276 (package
6277 (name "r-cellid")
6278 (version "1.19.0")
6279 (source (origin
6280 (method url-fetch)
6281 (uri (bioconductor-uri "CelliD" version))
6282 (sha256
6283 (base32
6284 "1497qfxif0a5pil7an0m9js6cdwrdcryjwkcg3xd45x7gkmsv1x8"))))
6285 (properties `((upstream-name . "CelliD")))
6286 (build-system r-build-system)
6287 (arguments
6288 (list
6289 #:phases
6290 #~(modify-phases %standard-phases
6291 ;; "The `slot` argument of `GetAssayData()` was deprecated in
6292 ;; SeuratObject 5.0.0 and is now defunct.", i = "Please use
6293 ;; the `layer` argument instead."
6294 (add-after 'unpack 'fix-deprecated-argument
6295 (lambda _
6296 (substitute* '("R/mca.R" "tests/testthat/test_CelliD.R")
6297 (("slot") "layer")))))))
6298 (propagated-inputs
6299 (list r-biocparallel
6300 r-data-table
6301 r-fastmatch
6302 r-fgsea
6303 r-ggplot2
6304 r-glue
6305 r-irlba
6306 r-matrix
6307 r-matrixstats
6308 r-pbapply
6309 r-rcpp
6310 r-rcpparmadillo
6311 r-reticulate
6312 r-rtsne
6313 r-scater
6314 r-seurat
6315 r-singlecellexperiment
6316 r-stringr
6317 r-summarizedexperiment
6318 r-tictoc
6319 r-umap))
6320 (native-inputs (list r-knitr r-testthat))
6321 (home-page "https://bioconductor.org/packages/CelliD")
6322 (synopsis
6323 "Single cell gene signature extraction using multiple correspondence analysis")
6324 (description
6325 "CelliD is a clustering-free method for extracting per-cell gene
6326signatures from scRNA-seq. CelliD allows unbiased cell identity recognition
6327across different donors, tissues-of-origin, model organisms and single-cell
6328omics protocols. The package can also be used to explore functional pathways
6329enrichment in single cell data.")
6330 (license license:gpl3)))
6331
6332(define-public r-chihaya
6333 (package
6334 (name "r-chihaya")
6335 (version "1.12.0")
6336 (source
6337 (origin
6338 (method url-fetch)
6339 (uri (bioconductor-uri "chihaya" version))
6340 (sha256
6341 (base32 "0jsm4rlg2zig954lxl7qhrrp5rbrfwgqi71d2pmwbxjj54l5mlw8"))))
6342 (properties `((upstream-name . "chihaya")))
6343 (build-system r-build-system)
6344 (propagated-inputs (list r-delayedarray
6345 r-hdf5array
6346 r-matrix
6347 r-rcpp
6348 r-rhdf5
6349 r-rhdf5lib))
6350 (native-inputs (list r-biocgenerics
6351 r-biocsingular
6352 r-knitr
6353 r-residualmatrix
6354 r-s4vectors
6355 r-testthat))
6356 (home-page "https://github.com/ArtifactDB/chihaya-R")
6357 (synopsis "Save Delayed Operations to a HDF5 File")
6358 (description
6359 "Saves the delayed operations of a @code{DelayedArray} to a HDF5 file. This
6360enables efficient recovery of the @code{DelayedArray's} contents in other
6361languages and analysis frameworks.")
6362 (license license:gpl3)))
6363
6364(define-public r-cigarillo
6365 (package
6366 (name "r-cigarillo")
6367 (version "1.2.0")
6368 (source
6369 (origin
6370 (method url-fetch)
6371 (uri (bioconductor-uri "cigarillo" version))
6372 (sha256
6373 (base32 "0zs2s4zd7rqy6fvrlrmpbqcbi8x6g0s6s0nlqlv99sxk15pv33kr"))))
6374 (properties `((upstream-name . "cigarillo")))
6375 (build-system r-build-system)
6376 (propagated-inputs (list r-biocgenerics r-biostrings r-iranges r-s4vectors))
6377 (native-inputs (list r-knitr r-testthat))
6378 (home-page "https://bioconductor.org/packages/cigarillo")
6379 (synopsis "Efficient manipulation of CIGAR strings")
6380 (description
6381 "CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. CIGAR
6382strings are found in the BAM files produced by most aligners and in the
6383AIRR-formatted output produced by @code{IgBLAST}. The cigarillo package
6384provides functions to parse and inspect CIGAR strings, trim them, turn them
6385into ranges of positions relative to the \"query space\" or \"reference
6386space\", and project positions or sequences from one space to the other. Note
6387that these operations are low-level operations that the user rarely needs to
6388perform directly. More typically, they are performed behind the scene by
6389higher-level functionality implemented in other packages like Bioconductor
6390packages @code{GenomicAlignments} and igblastr.")
6391 (license license:artistic2.0)))
6392
6393(define-public r-convert
6394 (package
6395 (name "r-convert")
6396 (version "1.88.0")
6397 (source
6398 (origin
6399 (method url-fetch)
6400 (uri (bioconductor-uri "convert" version))
6401 (sha256
6402 (base32 "1bhb5gvrpbmks38hb1yb1cadmr1wlq0kq3dhnjz25adzhvbwgjzb"))))
6403 (properties `((upstream-name . "convert")))
6404 (build-system r-build-system)
6405 (propagated-inputs (list r-biobase r-limma r-marray))
6406 (home-page "http://bioinf.wehi.edu.au/limma/convert.html")
6407 (synopsis "Convert microarray data objects")
6408 (description "This package defines coerce methods for microarray data
6409objects.")
6410 (license license:lgpl2.0+)))
6411
6412(define-public r-coregx
6413 (package
6414 (name "r-coregx")
6415 (version "2.16.0")
6416 (source
6417 (origin
6418 (method url-fetch)
6419 (uri (bioconductor-uri "CoreGx" version))
6420 (sha256
6421 (base32 "0p8hiqhi7r3k5c172z1sgdsd8x6razxsvxpmg86njkyadks1vcy1"))))
6422 (properties `((upstream-name . "CoreGx")))
6423 (build-system r-build-system)
6424 (propagated-inputs
6425 (list r-bench
6426 r-biobase
6427 r-biocgenerics
6428 r-biocparallel
6429 r-bumpymatrix
6430 r-checkmate
6431 r-crayon
6432 r-data-table
6433 r-glue
6434 r-lsa
6435 r-matrixgenerics
6436 r-multiassayexperiment
6437 r-piano
6438 r-rlang
6439 r-s4vectors
6440 r-summarizedexperiment))
6441 (native-inputs (list r-knitr r-testthat))
6442 (home-page "https://bioconductor.org/packages/CoreGx")
6443 (synopsis
6444 "Classes and functions to serve as the basis for other Gx packages")
6445 (description
6446 "This package provides a collection of functions and classes which serve
6447as the foundation for packages such as PharmacoGx and RadioGx. It was created
6448to abstract shared functionality to increase ease of maintainability and
6449reduce code repetition in current and future Gx suite programs. Major
6450features include a @code{CoreSet} class, from which RadioSet and PharmacoSet
6451are derived, along with get and set methods for each respective slot.
6452Additional functions related to fitting and plotting dose response curves,
6453quantifying statistical correlation and calculating @acronym{AUC, area under
6454the curve} or @acronym{SF, survival fraction} are included.")
6455 (license license:gpl3+)))
6456
6457(define-public r-coverageview
6458 (package
6459 (name "r-coverageview")
6460 (version "1.50.0")
6461 (source (origin
6462 (method url-fetch)
6463 (uri (bioconductor-uri "CoverageView" version))
6464 (sha256
6465 (base32
6466 "16n3cwj516v7fsi6xlazmdn0y21zm0rqcbva653bbmh8wrzxbdgd"))))
6467 (build-system r-build-system)
6468 (propagated-inputs
6469 (list r-genomicalignments
6470 r-genomicranges
6471 r-iranges
6472 r-rsamtools
6473 r-rtracklayer
6474 r-s4vectors))
6475 (home-page "https://bioconductor.org/packages/CoverageView/")
6476 (synopsis "Coverage visualization package for R")
6477 (description "This package provides a framework for the visualization of
6478genome coverage profiles. It can be used for ChIP-seq experiments, but it can
6479be also used for genome-wide nucleosome positioning experiments or other
6480experiment types where it is important to have a framework in order to inspect
6481how the coverage distributed across the genome.")
6482 (license license:artistic2.0)))
6483
6484;; This is a CRAN package, but it depends on Bioconductor packages.
6485(define-public r-cpp11bigwig
6486 (package
6487 (name "r-cpp11bigwig")
6488 (version "0.1.3")
6489 (source
6490 (origin
6491 (method url-fetch)
6492 (uri (cran-uri "cpp11bigwig" version))
6493 (sha256
6494 (base32 "0p6s8h4a8a1j367iiq2n01bl6f6aijsli9lbm0k98hzfw8bqgdqk"))))
6495 (properties
6496 '((upstream-name . "cpp11bigwig")
6497 (updater-extra-inputs . ("curl"))))
6498 (build-system r-build-system)
6499 (inputs (list curl zlib))
6500 (propagated-inputs (list r-cpp11 r-genomicranges r-iranges r-tibble))
6501 (native-inputs (list r-testthat))
6502 (home-page "https://rnabioco.github.io/cpp11bigwig/")
6503 (synopsis "Read bigWig and bigBed files")
6504 (description
6505 "Read @code{bigWig} and @code{bigBed} files using libBigWig. This
6506package provides lightweight access to the binary bigWig and bigBed formats
6507developed by the UCSC Genome Browser group.")
6508 (license license:expat)))
6509
6510(define-public r-csaw
6511 (package
6512 (name "r-csaw")
6513 (version "1.46.0")
6514 (source
6515 (origin
6516 (method url-fetch)
6517 (uri (bioconductor-uri "csaw" version))
6518 (sha256
6519 (base32 "1cq9dycwv76g7v9gq84b5s8sqxiggw6gb9sgx5pp4w8kf1v56dcd"))))
6520 (properties `((upstream-name . "csaw")))
6521 (build-system r-build-system)
6522 (propagated-inputs (list r-biocgenerics
6523 r-biocparallel
6524 r-edger
6525 r-genomicranges
6526 r-iranges
6527 r-limma
6528 r-matrix
6529 r-metapod
6530 r-rcpp
6531 r-rhtslib
6532 r-rsamtools
6533 r-s4vectors
6534 r-seqinfo
6535 r-summarizedexperiment))
6536 (native-inputs (list r-genomicalignments r-knitr r-org-mm-eg-db r-testthat
6537 r-txdb-mmusculus-ucsc-mm10-knowngene))
6538 (home-page "https://bioconductor.org/packages/csaw")
6539 (synopsis "ChIP-Seq analysis with windows")
6540 (description
6541 "This is a package for detection of differentially bound regions in
6542@code{ChIP-seq} data with sliding windows, with methods for normalization and
6543proper FDR control.")
6544 (license license:gpl3)))
6545
6546(define-public r-cummerbund
6547 (package
6548 (name "r-cummerbund")
6549 (version "2.50.0")
6550 (source (origin
6551 (method url-fetch)
6552 (uri (bioconductor-uri "cummeRbund" version))
6553 (sha256
6554 (base32
6555 "1i1zcrfizp4ix0bgx3gjbd4y4hj7dfs15j4ssh87kkx61y7x6yl8"))))
6556 (build-system r-build-system)
6557 (propagated-inputs
6558 (list r-biobase
6559 r-biocgenerics
6560 r-fastcluster
6561 r-ggplot2
6562 r-gviz
6563 r-plyr
6564 r-reshape2
6565 r-rsqlite
6566 r-rtracklayer
6567 r-s4vectors))
6568 (home-page "https://bioconductor.org/packages/cummeRbund/")
6569 (synopsis "Analyze Cufflinks high-throughput sequencing data")
6570 (description "This package allows for persistent storage, access,
6571exploration, and manipulation of Cufflinks high-throughput sequencing data.
6572In addition, provides numerous plotting functions for commonly used
6573visualizations.")
6574 (license license:artistic2.0)))
6575
6576(define-public r-dama
6577 (package
6578 (name "r-dama")
6579 (version "1.84.0")
6580 (source (origin
6581 (method url-fetch)
6582 (uri (bioconductor-uri "daMA" version))
6583 (sha256
6584 (base32
6585 "0r1m8vmzrpglr3gj39qz0z8b8x72s2sncfisjyh7vvqr5dcpfg3f"))))
6586 (properties `((upstream-name . "daMA")))
6587 (build-system r-build-system)
6588 (propagated-inputs (list r-mass))
6589 (home-page "https://bioconductor.org/packages/release/bioc/html/daMA.html")
6590 (synopsis
6591 "Efficient design and analysis of factorial two-colour microarray data")
6592 (description
6593 "This package contains functions for the efficient design of factorial
6594two-colour microarray experiments and for the statistical analysis of
6595factorial microarray data.")
6596 (license license:gpl2+)))
6597
6598(define-public r-damefinder
6599 (package
6600 (name "r-damefinder")
6601 (version "1.24.0")
6602 (source (origin
6603 (method url-fetch)
6604 (uri (bioconductor-uri "DAMEfinder" version))
6605 (sha256
6606 (base32
6607 "05md0q4q6qiniby8w735dfvxf6amd9akizsyn0g3sazqimmk5yp9"))))
6608 (properties `((upstream-name . "DAMEfinder")))
6609 (build-system r-build-system)
6610 (propagated-inputs
6611 (list r-biocgenerics
6612 r-biostrings
6613 r-bumphunter
6614 r-cowplot
6615 r-genomicalignments
6616 r-genomicranges
6617 r-ggplot2
6618 r-iranges
6619 r-limma
6620 r-plyr
6621 r-readr
6622 r-reshape2
6623 r-rsamtools
6624 r-s4vectors
6625 r-seqinfo
6626 r-stringr
6627 r-summarizedexperiment
6628 r-variantannotation))
6629 (native-inputs (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat))
6630 (home-page "https://bioconductor.org/packages/DAMEfinder")
6631 (synopsis "Differential allelicly methylated regions")
6632 (description
6633 "This package offers functionality for taking methtuple or Bismark
6634outputs to calculate @acronym{ASM, Allele-Specific Methylation} scores and
6635compute @acronym{DAMEs, Differential Allelicly MEthylated} regions. It also
6636offers nice visualization of methyl-circle plots.")
6637 (license license:expat)))
6638
6639(define-public r-dearseq
6640 (package
6641 (name "r-dearseq")
6642 (version "1.24.0")
6643 (source
6644 (origin
6645 (method url-fetch)
6646 (uri (bioconductor-uri "dearseq" version))
6647 (sha256
6648 (base32
6649 "1rgvr6da9y5ipy3dgzwwla51r30fgsbfarrpn059yqpdac4ixvkc"))))
6650 (build-system r-build-system)
6651 (propagated-inputs
6652 (list r-compquadform
6653 r-dplyr
6654 r-ggplot2
6655 r-kernsmooth
6656 r-magrittr
6657 r-matrixstats
6658 r-patchwork
6659 r-pbapply
6660 r-reshape2
6661 r-rlang
6662 r-scattermore
6663 r-statmod
6664 r-survey
6665 r-tibble
6666 r-viridislite))
6667 (native-inputs
6668 (list r-knitr r-testthat))
6669 (home-page "https://github.com/borishejblum/dearseq")
6670 (synopsis "DEA for RNA-seq data through a robust variance component test")
6671 (description
6672 "This is a package for Differential Expression Analysis of RNA-seq data.
6673It features a variance component score test accounting for data
6674heteroscedasticity through precision weights. Perform both gene-wise and gene
6675set analyses, and can deal with repeated or longitudinal data.")
6676 (license license:gpl2)))
6677
6678(define-public r-debcam
6679 (package
6680 (name "r-debcam")
6681 (version "1.26.0")
6682 (source (origin
6683 (method url-fetch)
6684 (uri (bioconductor-uri "debCAM" version))
6685 (sha256
6686 (base32
6687 "1sh8vbhgrkk1xfk139jxi88s2z70pnr4ji2pnb2gb3s5013zrhk8"))
6688 (snippet
6689 '(for-each delete-file
6690 '("inst/java/CornerDetect.jar"
6691 "inst/java/lib/pj20150107.jar")))))
6692 (properties `((upstream-name . "debCAM")))
6693 (build-system r-build-system)
6694 (arguments
6695 (list
6696 #:tests? #false ;require a running JVM.
6697 #:configure-flags '(list "--fake")
6698 #:modules
6699 '((guix build r-build-system)
6700 ((guix build ant-build-system) #:prefix ant:)
6701 (guix build utils))
6702 #:imported-modules
6703 `((guix build ant-build-system)
6704 ,@%r-build-system-modules)
6705 #:phases
6706 '(modify-phases %standard-phases
6707 (add-after 'unpack 'build-jar
6708 (lambda* (#:key inputs #:allow-other-keys)
6709 (install-file
6710 (search-input-file inputs "/share/java/pj20150107.jar")
6711 "inst/java/lib")
6712 (with-directory-excursion "java"
6713 (mkdir "build")
6714 (invoke "javac" "-d" "./build"
6715 "-cp" "../inst/java/lib/pj20150107.jar"
6716 "CornerDetectTopN.java"
6717 "FixSizedPriorityQueue.java")
6718 (with-directory-excursion "build"
6719 (apply invoke "jar" "cvf" "../../inst/java/CornerDetect.jar"
6720 (find-files "."))))))
6721 (add-after 'install 'strip-jar-timestamps
6722 (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))
6723 (inputs
6724 (list (list openjdk11 "jdk")
6725 java-pj))
6726 (propagated-inputs
6727 (list r-apcluster
6728 r-biobase
6729 r-biocparallel
6730 r-corpcor
6731 r-dmwr2
6732 r-geometry
6733 r-nmf
6734 r-nnls
6735 r-pcapp
6736 r-rjava
6737 r-summarizedexperiment))
6738 (native-inputs
6739 (list r-knitr r-testthat zip)) ;zip is needed for repacking the jar
6740 (home-page "https://bioconductor.org/packages/debCAM")
6741 (synopsis "Deconvolution by convex analysis of mixtures")
6742 (description
6743 "This package is an R implementation for fully unsupervised deconvolution
6744of complex tissues. DebCAM provides basic functions to perform unsupervised
6745deconvolution on mixture expression profiles by @acronym{CAM, Convex Analysis
6746of Mixtures} and some auxiliary functions to help understand the
6747subpopulation- specific results. It also implements functions to perform
6748supervised deconvolution based on prior knowledge of molecular markers, S
6749matrix or A matrix. Combining molecular markers from CAM and from prior
6750knowledge can achieve semi-supervised deconvolution of mixtures.")
6751 (license license:gpl2)))
6752
6753(define-public r-decipher
6754 (package
6755 (name "r-decipher")
6756 (version "3.8.0")
6757 (source (origin
6758 (method url-fetch)
6759 (uri (bioconductor-uri "DECIPHER" version))
6760 (sha256
6761 (base32
6762 "00ymkfa828wgm8hiqan4jipwpi02g41fvs0dwcyn5kg0jp12vlxf"))))
6763 (build-system r-build-system)
6764 (propagated-inputs
6765 (list r-biostrings r-dbi r-iranges r-s4vectors r-xvector))
6766 (home-page "https://www.bioconductor.org/packages/DECIPHER/")
6767 (synopsis "Tools for deciphering and managing biological sequences")
6768 (description "This package provides a toolset for deciphering and managing
6769biological sequences.")
6770 (license license:gpl3)))
6771
6772(define-public r-deco
6773 (package
6774 (name "r-deco")
6775 (version "1.13.0")
6776 (source (origin
6777 (method url-fetch)
6778 (uri (bioconductor-uri "deco" version))
6779 (sha256
6780 (base32
6781 "0d4abif3v62cbas6hl7pfw8q8jihh7nsra76k9cm6kz54qw4fbnw"))))
6782 (properties `((upstream-name . "deco")))
6783 (build-system r-build-system)
6784 (propagated-inputs
6785 (list r-ade4
6786 r-annotationdbi
6787 r-biobase
6788 r-biocparallel
6789 r-biocstyle
6790 r-cluster
6791 r-foreign
6792 r-gdata
6793 r-ggplot2
6794 r-gplots
6795 r-gridextra
6796 r-limma
6797 r-locfit
6798 r-made4
6799 r-rcolorbrewer
6800 r-reshape2
6801 r-scatterplot3d
6802 r-sfsmisc
6803 r-summarizedexperiment))
6804 (native-inputs (list r-knitr))
6805 (home-page "https://github.com/fjcamlab/deco")
6806 (synopsis "Decomposing heterogeneous cohorts using omic data profiling")
6807 (description
6808 "This package discovers differential features in hetero- and homogeneous
6809omic data by a two-step method including subsampling LIMMA and NSCA. DECO
6810reveals feature associations to hidden subclasses not exclusively related to
6811higher deregulation levels.")
6812 (license license:gpl3+)))
6813
6814(define-public r-decomplexdisease
6815 (package
6816 (name "r-decomplexdisease")
6817 (version "1.18.0")
6818 (source (origin
6819 (method url-fetch)
6820 (uri (bioconductor-uri "DEComplexDisease" version))
6821 (sha256
6822 (base32
6823 "12gw9b0gdwyih51j2gzay6vxhycgc52n8svd0slv6wsbw5rc19lh"))))
6824 (properties `((upstream-name . "DEComplexDisease")))
6825 (build-system r-build-system)
6826 (propagated-inputs
6827 (list r-biocparallel
6828 r-complexheatmap
6829 r-deseq2
6830 r-edger
6831 r-rcpp
6832 r-summarizedexperiment))
6833 (native-inputs (list r-knitr))
6834 (home-page "https://bioconductor.org/packages/DEComplexDisease")
6835 (synopsis "Investigations of complex diseases by bi-clustering analysis")
6836 (description
6837 "DEComplexDisease is designed to find the @acronym{DEGs, Differential
6838Expressed Genes} for complex disease, which is characterized by the
6839heterogeneous genomic expression profiles. Different from the established DEG
6840analysis tools, it does not assume the patients of complex diseases to share
6841the common DEGs. By applying a bi-clustering algorithm, DEComplexDisease
6842finds the DEGs shared by as many patients. Applying the DEComplexDisease
6843analysis results, users are possible to find the patients affected by the same
6844mechanism based on the shared signatures.")
6845 (license license:gpl3)))
6846
6847(define-public r-decomptumor2sig
6848 (package
6849 (name "r-decomptumor2sig")
6850 (version "2.28.0")
6851 (source (origin
6852 (method url-fetch)
6853 (uri (bioconductor-uri "decompTumor2Sig" version))
6854 (sha256
6855 (base32
6856 "0jxgbp6g1nq3qlsm6hb29ckpmp2qq9xyvyazjdm2j4j0vjia7r2w"))))
6857 (properties `((upstream-name . "decompTumor2Sig")))
6858 (build-system r-build-system)
6859 ;; This package installs Perl scripts: extractSpecColumns.pl,
6860 ;; filterLines.pl, and filterLinesNumeric.pl.
6861 (inputs (list perl))
6862 (propagated-inputs
6863 (list r-biocgenerics
6864 r-biostrings
6865 r-bsgenome-hsapiens-ucsc-hg19
6866 r-data-table
6867 r-genomicfeatures
6868 r-genomicranges
6869 r-ggplot2
6870 r-ggseqlogo
6871 r-gridextra
6872 r-matrix
6873 r-plyr
6874 r-quadprog
6875 r-readxl
6876 r-s4vectors
6877 r-seqinfo
6878 r-summarizedexperiment
6879 r-txdb-hsapiens-ucsc-hg19-knowngene
6880 r-variantannotation))
6881 (native-inputs (list r-knitr))
6882 (home-page "https://rmpiro.net/decompTumor2Sig/")
6883 (synopsis "Decomposition of individual tumors into mutational signatures")
6884 (description
6885 "The package uses quadratic programming for signature refitting, i.e., to
6886decompose the mutation catalog from an individual tumor sample into a set of
6887given mutational signatures (either Alexandrov-model signatures or
6888Shiraishi-model signatures), computing weights that reflect the contributions
6889of the signatures to the mutation load of the tumor.")
6890 (license license:gpl2)))
6891
6892(define-public r-deconrnaseq
6893 (package
6894 (name "r-deconrnaseq")
6895 (version "1.50.0")
6896 (source (origin
6897 (method url-fetch)
6898 (uri (bioconductor-uri "DeconRNASeq" version))
6899 (sha256
6900 (base32
6901 "06dkxdikfgiay72z9p0kmk8bayvdbrg641cl39nwk109dms0vc6f"))))
6902 (properties `((upstream-name . "DeconRNASeq")))
6903 (build-system r-build-system)
6904 (propagated-inputs
6905 (list r-ggplot2
6906 r-limsolve
6907 r-pcamethods))
6908 (home-page "https://bioconductor.org/packages/DeconRNASeq")
6909 (synopsis
6910 "Deconvolution of heterogeneous tissue samples for mRNA-Seq data")
6911 (description
6912 "DeconSeq is an R package for deconvolution of heterogeneous tissues
6913based on mRNA-Seq data. It models the expression levels from heterogeneous
6914cell populations in mRNA-Seq as the weighted average of expression from
6915different constituting cell types and predicted cell type proportions of
6916single expression profiles.")
6917 (license license:gpl2)))
6918
6919(define-public r-decontam
6920 (package
6921 (name "r-decontam")
6922 (version "1.32.0")
6923 (source (origin
6924 (method url-fetch)
6925 (uri (bioconductor-uri "decontam" version))
6926 (sha256
6927 (base32
6928 "1x9f79p5pxjc4vycdsdh3ck3ickdq0wy7awam8w5imbd13ds5d3y"))))
6929 (properties `((upstream-name . "decontam")))
6930 (build-system r-build-system)
6931 (propagated-inputs
6932 (list r-ggplot2 r-reshape2))
6933 (native-inputs (list r-knitr))
6934 (home-page "https://github.com/benjjneb/decontam")
6935 (synopsis
6936 "Identification of contaminants in marker-gene and metagenomics data")
6937 (description
6938 "This package offers simple statistical identification of contaminating
6939sequence features in marker-gene or metagenomics data. It works on any kind
6940of feature derived from environmental sequencing data (e.g. ASVs, OTUs,
6941taxonomic groups, MAGs, etc). Requires DNA quantitation data or sequenced
6942negative control samples.")
6943 (license license:artistic2.0)))
6944
6945(define-public r-deconvr
6946 (package
6947 (name "r-deconvr")
6948 (version "1.18.0")
6949 (source (origin
6950 (method url-fetch)
6951 (uri (bioconductor-uri "deconvR" version))
6952 (sha256
6953 (base32
6954 "075lns93akjpghhrlfn5l4181895d1nih41y48zwrqk0pj97xy2r"))))
6955 (properties `((upstream-name . "deconvR")))
6956 (build-system r-build-system)
6957 (propagated-inputs
6958 (list r-assertthat
6959 r-biocgenerics
6960 r-data-table
6961 r-dplyr
6962 r-e1071
6963 r-foreach
6964 r-genomicranges
6965 r-iranges
6966 r-magrittr
6967 r-mass
6968 r-matrixstats
6969 r-methylkit
6970 r-minfi
6971 r-nnls
6972 r-quadprog
6973 r-rsq
6974 r-s4vectors
6975 r-tidyr))
6976 (native-inputs (list r-knitr r-testthat))
6977 (home-page "https://github.com/BIMSBbioinfo/deconvR")
6978 (synopsis "Simulation and deconvolution of omic profiles")
6979 (description
6980 "This package provides a collection of functions designed for analyzing
6981deconvolution of the bulk sample(s) using an atlas of reference omic signature
6982profiles and a user-selected model. Users are given the option to create or
6983extend a reference atlas and,also simulate the desired size of the bulk
6984signature profile of the reference cell types. The package includes the
6985cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can
6986be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to
6987make mapping WGBS data to their probe IDs easier.")
6988 (license license:artistic2.0)))
6989
6990(define-public r-decoupler
6991 (package
6992 (name "r-decoupler")
6993 (version "2.17.0")
6994 (source
6995 (origin
6996 (method url-fetch)
6997 (uri (bioconductor-uri "decoupleR" version))
6998 (sha256
6999 (base32 "1jpdh7iq91fqbmahx95ba3w8yvz75794vvk6098gh61z151lwahx"))))
7000 (properties
7001 '((upstream-name . "decoupleR")
7002 (updater-extra-native-inputs . ("r-aucell"
7003 "r-fgsea"
7004 "r-gsva"
7005 "r-omnipathr"
7006 "r-ranger"
7007 "r-rpart"))))
7008 (build-system r-build-system)
7009 (arguments
7010 (list
7011 #:skipped-tests
7012 ;; viper is non-free software; this test tries to load it.
7013 '(("test-decoupleR-decouple.R"
7014 "decouple same results as independent functions")
7015 ;; Differences in p values.
7016 ("test-statistic-fgsea.R" "test run_fgsea")
7017 ;; These tests require Internet access.
7018 ("test-omnipath.R"
7019 "test show_resources"
7020 "test get_resource"
7021 "test get_progeny human"
7022 "test get_progeny mouse"
7023 "test get_dorothea human"
7024 "test get_dorothea mouse"
7025 "test get_collectri"))))
7026 (propagated-inputs
7027 (list r-biocparallel
7028 r-broom
7029 r-dplyr
7030 r-magrittr
7031 r-matrix
7032 r-parallelly
7033 r-purrr
7034 r-rlang
7035 r-stringr
7036 r-tibble
7037 r-tidyr
7038 r-tidyselect
7039 r-withr))
7040 (native-inputs (list r-aucell
7041 r-fgsea
7042 r-gsva
7043 r-knitr
7044 r-omnipathr
7045 r-ranger
7046 r-rpart
7047 r-testthat))
7048 (home-page "https://saezlab.github.io/decoupleR/")
7049 (synopsis "Computational methods to infer biological activities from omics data")
7050 (description
7051 "Many methods allow us to extract biological activities from omics data using
7052information from prior knowledge resources, reducing the dimensionality for
7053increased statistical power and better interpretability. decoupleR is a
7054Bioconductor package containing different statistical methods to extract these
7055signatures within a unified framework. decoupleR allows the user to flexibly
7056test any method with any resource. It incorporates methods that take into
7057account the sign and weight of network interactions. decoupleR can be used
7058with any omic, as long as its features can be linked to a biological process
7059based on prior knowledge. For example, in transcriptomics gene sets regulated
7060by a transcription factor, or in phospho-proteomics phosphosites that are
7061targeted by a kinase.")
7062 (license license:gpl3)))
7063
7064(define-public r-deepsnv
7065 (package
7066 (name "r-deepsnv")
7067 (version "1.58.0")
7068 (source (origin
7069 (method url-fetch)
7070 (uri (bioconductor-uri "deepSNV" version))
7071 (sha256
7072 (base32
7073 "0z49mh844c4xzp4bafwcc6swpcyhifmy8dvzax62j78xiqpzjm23"))))
7074 (properties `((upstream-name . "deepSNV")))
7075 (build-system r-build-system)
7076 (propagated-inputs
7077 (list r-biostrings
7078 r-genomicranges
7079 r-iranges
7080 r-rhtslib
7081 r-summarizedexperiment
7082 r-variantannotation
7083 r-vgam))
7084 (native-inputs
7085 (list r-knitr r-rcolorbrewer r-txdb-hsapiens-ucsc-hg19-knowngene))
7086 (home-page "https://github.com/gerstung-lab/deepSNV/")
7087 (synopsis "Detection of subclonal SNVs in deep sequencing data")
7088 (description
7089 "This package provides quantitative variant callers for detecting
7090subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
7091The deepSNV algorithm is used for a comparative setup with a control experiment
7092of the same loci and uses a beta-binomial model and a likelihood ratio test to
7093discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
7094computes a Bayes classifier based on a beta-binomial model for variant calling
7095with multiple samples for precisely estimating model parameters - such as local
7096error rates and dispersion - and prior knowledge, e.g. from variation data
7097bases such as COSMIC.")
7098 (license license:gpl3)))
7099
7100(define-public r-degreport
7101 (package
7102 (name "r-degreport")
7103 (version "1.48.0")
7104 (source (origin
7105 (method url-fetch)
7106 (uri (bioconductor-uri "DEGreport" version))
7107 (sha256
7108 (base32
7109 "122hlall00qar6h4lgvq13q45i6x0fscdqm9yl08v8smw89jgm5c"))
7110 (snippet
7111 '(delete-file "docs/jquery.sticky-kit.min.js"))))
7112 (properties `((upstream-name . "DEGreport")))
7113 (build-system r-build-system)
7114 (arguments
7115 (list
7116 #:phases
7117 '(modify-phases %standard-phases
7118 (add-after 'unpack 'process-javascript
7119 (lambda* (#:key inputs #:allow-other-keys)
7120 (invoke "esbuild"
7121 (assoc-ref inputs "jquery.sticky-kit.js")
7122 "--minify"
7123 "--outfile=docs/jquery.sticky-kit.min.js"))))))
7124 (propagated-inputs (list r-biobase
7125 r-biocgenerics
7126 r-broom
7127 r-circlize
7128 r-cluster
7129 r-complexheatmap
7130 r-consensusclusterplus
7131 r-cowplot
7132 r-dendextend
7133 r-deseq2
7134 r-dplyr
7135 r-edger
7136 r-ggdendro
7137 r-ggplot2
7138 r-ggrepel
7139 r-knitr
7140 r-logging
7141 r-magrittr
7142 r-psych
7143 r-rcolorbrewer
7144 r-reshape
7145 r-rlang
7146 r-s4vectors
7147 r-scales
7148 r-stringi
7149 r-stringr
7150 r-summarizedexperiment
7151 r-tibble
7152 r-tidyr))
7153 (native-inputs
7154 (list esbuild
7155 r-knitr
7156 r-testthat
7157 (origin
7158 (method url-fetch)
7159 (uri "https://raw.githubusercontent.com/leafo/sticky-kit/\
7160v1.1.2/jquery.sticky-kit.js")
7161 (sha256
7162 (base32
7163 "17c3a1hqc3ybwj7hpw8prazajp2x98aq7nyfn71h6lzjvblq297g")))))
7164 (home-page "https://lpantano.github.io/DEGreport/")
7165 (synopsis "Report of DEG analysis")
7166 (description
7167 "This is a package for creating na HTML report of differential expression
7168analyses of count data. It integrates some of the code mentioned in DESeq2
7169and @code{edgeR} vignettes, and report a ranked list of genes according to the
7170fold changes mean and variability for each selected gene.")
7171 (license license:expat)))
7172
7173(define-public r-delayedarray
7174 (package
7175 (name "r-delayedarray")
7176 (version "0.38.2")
7177 (source (origin
7178 (method url-fetch)
7179 (uri (bioconductor-uri "DelayedArray" version))
7180 (sha256
7181 (base32
7182 "1zg3xy6bx76h429lvqvp2dv2dhix854w2ym4m55dygcfixgiklyr"))))
7183 (properties
7184 '((upstream-name . "DelayedArray")
7185 ;; These are needed for tests, which we don't run, because we cannot
7186 ;; add r-hdf5array anyway.
7187 (updater-ignored-native-inputs
7188 . ("r-airway"
7189 "r-biocparallel"
7190 "r-genefilter"
7191 "r-hdf5array"
7192 "r-lobstr"
7193 "r-summarizedexperiment"))))
7194 (build-system r-build-system)
7195 ;; Tests require r-hdf5array, but adding it would lead to a dependency
7196 ;; cycle.
7197 (arguments (list #:tests? #false))
7198 (propagated-inputs
7199 (list r-biocgenerics
7200 r-iranges
7201 r-matrix
7202 r-matrixgenerics
7203 r-s4arrays
7204 r-s4vectors
7205 r-sparsearray))
7206 (native-inputs (list r-knitr))
7207 (home-page "https://bioconductor.org/packages/DelayedArray")
7208 (synopsis "Delayed operations on array-like objects")
7209 (description
7210 "Wrapping an array-like object (typically an on-disk object) in a
7211@code{DelayedArray} object allows one to perform common array operations on it
7212without loading the object in memory. In order to reduce memory usage and
7213optimize performance, operations on the object are either delayed or executed
7214using a block processing mechanism. Note that this also works on in-memory
7215array-like objects like @code{DataFrame} objects (typically with Rle columns),
7216@code{Matrix} objects, and ordinary arrays and data frames.")
7217 (license license:artistic2.0)))
7218
7219(define-public r-densvis
7220 (package
7221 (name "r-densvis")
7222 (version "1.22.0")
7223 (source (origin
7224 (method url-fetch)
7225 (uri (bioconductor-uri "densvis" version))
7226 (sha256
7227 (base32
7228 "1p4ig0jq6y4d5gn5d87g4ipwh600h5cv10abaayqz9f12205527i"))))
7229 (properties `((upstream-name . "densvis")))
7230 (build-system r-build-system)
7231 ;; Due to the use of Basilisk, which forcibly installs a Conda environment
7232 ;; on demand, we cannot run these tests.
7233 (arguments (list #:tests? #false))
7234 (propagated-inputs (list r-assertthat
7235 r-basilisk
7236 r-irlba
7237 r-rcpp
7238 r-reticulate
7239 r-rtsne))
7240 (native-inputs (list r-knitr r-testthat))
7241 (home-page "https://bioconductor.org/packages/densvis")
7242 (synopsis
7243 "Density-preserving data visualization via non-linear dimensionality reduction")
7244 (description
7245 "This package implements the density-preserving modification to t-SNE and
7246UMAP described by Narayan et al. (2020) <doi:10.1101/2020.05.12.077776>.
7247den-SNE and densMAP aim to enable more accurate visual interpretation of
7248high-dimensional datasets by producing lower-dimensional embeddings that
7249accurately represent the heterogeneity of the original high-dimensional space,
7250enabling the identification of homogeneous and heterogeneous cell states.
7251This accuracy is accomplished by including in the optimisation process a term
7252which considers the local density of points in the original high-dimensional
7253space. This can help to create visualisations that are more representative of
7254heterogeneity in the original high-dimensional space.")
7255 (license license:expat)))
7256
7257(define-public r-derfinder
7258 (package
7259 (name "r-derfinder")
7260 (version "1.46.0")
7261 (source (origin
7262 (method url-fetch)
7263 (uri (bioconductor-uri "derfinder" version))
7264 (sha256
7265 (base32
7266 "1n5l8qqyv2l43g7fxqdvdn0fb16flv2p3k4k2h6c9c0k4q96zihk"))))
7267 (properties `((upstream-name . "derfinder")))
7268 (build-system r-build-system)
7269 (propagated-inputs (list r-annotationdbi
7270 r-biocgenerics
7271 r-biocparallel
7272 r-bumphunter
7273 r-derfinderhelper
7274 r-genomeinfodb
7275 r-genomicalignments
7276 r-genomicfeatures
7277 r-genomicfiles
7278 r-genomicranges
7279 r-hmisc
7280 r-iranges
7281 r-qvalue
7282 r-rsamtools
7283 r-rtracklayer
7284 r-s4vectors
7285 r-seqinfo))
7286 (native-inputs (list r-derfinderdata r-knitr r-testthat
7287 r-txdb-hsapiens-ucsc-hg19-knowngene))
7288 (home-page "https://github.com/lcolladotor/derfinder")
7289 (synopsis
7290 "Annotation-agnostic differential expression analysis of RNA-seq data")
7291 (description
7292 "This package provides functions for annotation-agnostic differential
7293expression analysis of RNA-seq data. Two implementations of the DER Finder
7294approach are included in this package:
7295
7296@enumerate
7297@item single base-level F-statistics and
7298@item DER identification at the expressed regions-level.
7299@end enumerate
7300
7301The DER Finder approach can also be used to identify differentially bounded
7302@code{ChIP-seq} peaks.")
7303 (license license:artistic2.0)))
7304
7305(define-public r-derfinderhelper
7306 (package
7307 (name "r-derfinderhelper")
7308 (version "1.46.0")
7309 (source
7310 (origin
7311 (method url-fetch)
7312 (uri (bioconductor-uri "derfinderHelper" version))
7313 (sha256
7314 (base32 "1968l7fsig714l2vj8zkz9jdkpmj57jqxj5nsggv29w5j9prjlap"))))
7315 (properties `((upstream-name . "derfinderHelper")))
7316 (build-system r-build-system)
7317 (propagated-inputs
7318 (list r-iranges r-matrix r-s4vectors))
7319 (native-inputs
7320 (list r-knitr r-testthat))
7321 (home-page "https://github.com/leekgroup/derfinderHelper")
7322 (synopsis "Helper for derfinder")
7323 (description
7324 "This package speeds up the derfinder package when using multiple cores.
7325It is particularly useful when using BiocParallel and it helps reduce the time
7326spent loading the full derfinder package when running the F-statistics
7327calculation in parallel.")
7328 (license license:artistic2.0)))
7329
7330(define-public r-dmrcate
7331 (package
7332 (name "r-dmrcate")
7333 (version "3.8.0")
7334 (source (origin
7335 (method url-fetch)
7336 (uri (bioconductor-uri "DMRcate" version))
7337 (sha256
7338 (base32
7339 "0jg9s05kc8hcgj85vpvz08441vdb8b21dsq46ib23nsbzwjq5z3x"))))
7340 (properties `((upstream-name . "DMRcate")))
7341 (build-system r-build-system)
7342 (propagated-inputs
7343 (list r-annotationhub
7344 r-biomart
7345 r-bsseq
7346 r-edger
7347 r-experimenthub
7348 r-genomicranges
7349 r-gviz
7350 r-iranges
7351 r-limma
7352 r-minfi
7353 r-missmethyl
7354 r-plyr
7355 r-s4vectors
7356 r-seqinfo
7357 r-summarizedexperiment))
7358 (native-inputs (list r-biocmanager r-genomeinfodb r-knitr))
7359 (home-page "https://bioconductor.org/packages/DMRcate")
7360 (synopsis "Methylation array and sequencing spatial analysis methods")
7361 (description
7362 "This is a package for de novo identification and extraction of
7363@dfn{differentially methylated regions} (DMRs) from the human genome using
7364@dfn{Whole Genome Bisulfite Sequencing} (WGBS) and Illumina Infinium
7365Array (450K and EPIC) data. It provides functionality for filtering probes
7366possibly confounded by SNPs and cross-hybridisation. It includes
7367@code{GRanges} generation and plotting functions.")
7368 ;; GPLv3 with additional liability disclaimer.
7369 (license license:gpl3)))
7370
7371(define-public r-drimseq
7372 (package
7373 (name "r-drimseq")
7374 (version "1.40.0")
7375 (source
7376 (origin
7377 (method url-fetch)
7378 (uri (bioconductor-uri "DRIMSeq" version))
7379 (sha256
7380 (base32 "09nzw4b1adyc1lyp4pv9zrbvh4dmfqg7ybwvyly3abni6yrrjy42"))))
7381 (properties
7382 '((upstream-name . "DRIMSeq")
7383 (updater-ignored-native-inputs
7384 . ("r-geuvadistranscriptexpr"
7385 "r-pasillatranscriptexpr"))))
7386 (build-system r-build-system)
7387 (propagated-inputs
7388 (list r-biocgenerics
7389 r-biocparallel
7390 r-edger
7391 r-genomicranges
7392 r-ggplot2
7393 r-iranges
7394 r-limma
7395 r-mass
7396 r-reshape2
7397 r-s4vectors))
7398 (native-inputs (list r-biocstyle r-knitr r-stager r-testthat))
7399 (home-page "https://bioconductor.org/packages/DRIMSeq")
7400 (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
7401 (description
7402 "The package provides two frameworks. One for the differential
7403transcript usage analysis between different conditions and one for the tuQTL
7404analysis. Both are based on modeling the counts of genomic features (i.e.,
7405transcripts) with the Dirichlet-multinomial distribution. The package also
7406makes available functions for visualization and exploration of the data and
7407results.")
7408 (license license:gpl3+)))
7409
7410(define-public r-dropletutils
7411 (package
7412 (name "r-dropletutils")
7413 (version "1.32.0")
7414 (source
7415 (origin
7416 (method url-fetch)
7417 (uri (bioconductor-uri "DropletUtils" version))
7418 (sha256
7419 (base32 "1asx88y94wsj6gm575v8prdyvmlpmi9mhlhld5x64xlpnv1cypmv"))))
7420 (properties `((upstream-name . "DropletUtils")))
7421 (build-system r-build-system)
7422 (propagated-inputs
7423 (list r-assorthead
7424 r-beachmat
7425 r-bh
7426 r-biocgenerics
7427 r-biocparallel
7428 r-delayedarray
7429 r-delayedmatrixstats
7430 r-dqrng
7431 r-edger
7432 r-genomicranges
7433 r-hdf5array
7434 r-iranges
7435 r-matrix
7436 r-r-utils
7437 r-rcpp
7438 r-rhdf5
7439 r-rhdf5lib
7440 r-s4vectors
7441 r-scuttle
7442 r-singlecellexperiment
7443 r-sparsearray
7444 r-summarizedexperiment))
7445 (native-inputs (list r-knitr r-testthat))
7446 (home-page "https://bioconductor.org/packages/DropletUtils")
7447 (synopsis "Utilities for handling single-cell droplet data")
7448 (description
7449 "This package provides a number of utility functions for handling
7450single-cell RNA-seq data from droplet technologies such as 10X Genomics. This
7451includes data loading from count matrices or molecule information files,
7452identification of cells from empty droplets, removal of barcode-swapped
7453pseudo-cells, and downsampling of the count matrix.")
7454 (license license:gpl3)))
7455
7456;; This is a CRAN package, but it depends on r-limma from Bioconductor.
7457(define-public r-dsb
7458 (package
7459 (name "r-dsb")
7460 (version "2.0.1")
7461 (source
7462 (origin
7463 (method url-fetch)
7464 (uri (cran-uri "dsb" version))
7465 (sha256
7466 (base32 "1s02jigpv9ycf43y3l9qzrdbhwbjq75zdqv7glrq409nnlq5qp9h"))))
7467 (properties `((upstream-name . "dsb")))
7468 (build-system r-build-system)
7469 (propagated-inputs (list r-limma r-magrittr r-mclust))
7470 (native-inputs (list r-knitr r-rmarkdown r-spelling r-testthat))
7471 (home-page "https://github.com/niaid/dsb")
7472 (synopsis
7473 "Normalize & denoise droplet single cell protein data (CITE-Seq)")
7474 (description
7475 "R-dsb improves protein expression analysis in droplet-based single-cell
7476studies. The package specifically addresses noise in raw protein UMI counts
7477from methods like CITE-seq. It identifies and removes two main sources of
7478noise—protein-specific noise from unbound antibodies and droplet/cell-specific
7479noise. The package is applicable to various methods, including CITE-seq,
7480REAP-seq, ASAP-seq, TEA-seq, and Mission Bioplatform data. Check the vignette
7481for tutorials on integrating dsb with Seurat and Bioconductor, and using dsb
7482in Python.")
7483 (license license:cc0)))
7484
7485(define-public r-dss
7486 (package
7487 (name "r-dss")
7488 (version "2.60.0")
7489 (source (origin
7490 (method url-fetch)
7491 (uri (bioconductor-uri "DSS" version))
7492 (sha256
7493 (base32
7494 "0a9d6k0jw7r7mn722ci7y5796jbrfdxfa64i9srgz1qzfc33xv5a"))))
7495 (properties `((upstream-name . "DSS")))
7496 (build-system r-build-system)
7497 (propagated-inputs (list r-biobase r-biocparallel r-bsseq))
7498 (native-inputs (list r-knitr))
7499 (home-page "https://bioconductor.org/packages/DSS")
7500 (synopsis "Dispersion shrinkage for sequencing data")
7501 (description
7502 "DSS is an R library performing differential analysis for count-based
7503sequencing data. It detects @dfn{differentially expressed genes} (DEGs) from
7504RNA-seq, and differentially methylated loci or regions (DML/DMRs) from
7505@dfn{bisulfite sequencing} (BS-seq). The core of DSS is a dispersion
7506shrinkage method for estimating the dispersion parameter from Gamma-Poisson or
7507Beta-Binomial distributions.")
7508 ;; Any version of the GPL
7509 (license (list license:gpl2+ license:gpl3+))))
7510
7511(define-public r-dyndoc
7512 (package
7513 (name "r-dyndoc")
7514 (version "1.90.0")
7515 (source (origin
7516 (method url-fetch)
7517 (uri (bioconductor-uri "DynDoc" version))
7518 (sha256
7519 (base32
7520 "1gcc2hmisrcqsvi0lgm2pg7ikpvrqnvr8l0155ymj9dfmlclf7wr"))))
7521 (properties `((upstream-name . "DynDoc")))
7522 (build-system r-build-system)
7523 (home-page "https://bioconductor.org/packages/DynDoc")
7524 (synopsis "Dynamic document tools")
7525 (description
7526 "This package provides a set of functions to create and interact with
7527dynamic documents and vignettes.")
7528 (license license:artistic2.0)))
7529
7530(define-public r-escape
7531 (package
7532 (name "r-escape")
7533 (version "2.8.0")
7534 (source
7535 (origin
7536 (method url-fetch)
7537 (uri (bioconductor-uri "escape" version))
7538 (sha256
7539 (base32 "0c4wpfaw08zi11vi5dpb5spgba2hzbhlcxscnxkcjxy5h0pg92i8"))))
7540 (properties
7541 '((upstream-name . "escape")
7542 (updater-extra-native-inputs
7543 . ("r-delayedmatrixstats" "r-fgsea" "r-gsva"))))
7544 (build-system r-build-system)
7545 (propagated-inputs (list r-ggdist r-ggplot2 r-matrix r-matrixgenerics
7546 r-summarizedexperiment))
7547 (native-inputs (list r-biocparallel
7548 r-delayedmatrixstats
7549 r-dplyr
7550 r-fgsea
7551 r-gseabase
7552 r-gsva
7553 r-knitr
7554 r-rlang
7555 r-seurat
7556 r-seuratobject
7557 r-singlecellexperiment
7558 r-spelling
7559 r-testthat))
7560 (home-page "https://bioconductor.org/packages/escape")
7561 (synopsis "Single cell analysis platform for enrichment")
7562 (description
7563 "R-escape streamlines gene set enrichment analysis for single-cell RNA
7564sequencing. Using raw count information, Seurat objects, or
7565@code{SingleCellExperiment} format, users can perform and visualize GSEA
7566across individual cells.")
7567 (license license:gpl2)))
7568
7569(define-public r-bluster
7570 (package
7571 (name "r-bluster")
7572 (version "1.22.0")
7573 (source (origin
7574 (method url-fetch)
7575 (uri (bioconductor-uri "bluster" version))
7576 (sha256
7577 (base32
7578 "0f60wr5i4l92dvl7riwrcc8mx7w7lsir7k6wr1s8ncrfh9r0741d"))))
7579 (properties
7580 '((upstream-name . "bluster")
7581 (updater-extra-native-inputs
7582 . ("r-dirichletmultinomial"
7583 "r-dynamictreecut"))))
7584 (build-system r-build-system)
7585 (propagated-inputs
7586 (list r-assorthead
7587 r-biocneighbors
7588 r-biocparallel
7589 r-cluster
7590 r-igraph
7591 r-matrix
7592 r-rcpp
7593 r-s4vectors))
7594 (native-inputs
7595 (list r-apcluster
7596 r-dirichletmultinomial
7597 r-dynamictreecut
7598 r-knitr
7599 r-kohonen
7600 r-mbkmeans
7601 r-testthat
7602 r-vegan))
7603 (home-page "https://bioconductor.org/packages/bluster")
7604 (synopsis "Clustering algorithms for Bioconductor")
7605 (description"This package wraps common clustering algorithms in an easily
7606extended S4 framework. Backends are implemented for hierarchical, k-means
7607and graph-based clustering. Several utilities are also provided to compare
7608and evaluate clustering results.")
7609 (license license:gpl3)))
7610
7611(define-public r-ideoviz
7612 (package
7613 (name "r-ideoviz")
7614 (version "1.48.0")
7615 (source (origin
7616 (method url-fetch)
7617 (uri (bioconductor-uri "IdeoViz" version))
7618 (sha256
7619 (base32
7620 "0dgz1fqqv3qm32www8saplcj61fgbh1dhaqbfqrm3r0cxx6pdny7"))))
7621 (build-system r-build-system)
7622 (propagated-inputs
7623 (list r-biobase
7624 r-genomeinfodb
7625 r-genomicranges
7626 r-iranges
7627 r-rcolorbrewer
7628 r-rtracklayer))
7629 (home-page "https://bioconductor.org/packages/IdeoViz/")
7630 (synopsis "Plots data along a chromosomal ideogram")
7631 (description "This package provides functions to plot data associated with
7632arbitrary genomic intervals along chromosomal ideogram.")
7633 (license license:gpl2)))
7634
7635(define-public r-immapex
7636 (package
7637 (name "r-immapex")
7638 (version "1.6.0")
7639 (source
7640 (origin
7641 (method url-fetch)
7642 (uri (bioconductor-uri "immApex" version))
7643 (sha256
7644 (base32 "1x3i6n6rlp2hg6fdwia34z80a0j25067l2n2s53sjzfd2j9w15nf"))))
7645 (properties `((upstream-name . "immApex")))
7646 (build-system r-build-system)
7647 (arguments
7648 (list
7649 #:skipped-tests
7650 '(("test-getIMGT.R"
7651 ;; TRBV_human_aa is NULL
7652 "getIMGT returns expected structure for amino acid sequences"
7653 ;; TRBJ_mouse_nt is NULL
7654 "getIMGT works with different regions and species"
7655 ;; IGHV_rat_nt is NULL
7656 "getIMGT works with nucleotide sequences"
7657 ;; TRBV_rabbit_aa is NULL
7658 "getIMGT works with additional species")
7659 ("test-sequenceDecoder.R"
7660 ;; XXX: fails because "kideraFactors" is an unknown property.
7661 ".propertyDecoder decodes standard sequences correctly"))))
7662 (propagated-inputs (list r-immreferent
7663 r-matrix
7664 r-matrixstats
7665 r-rcpp
7666 r-singlecellexperiment
7667 r-stringr))
7668 (native-inputs (list r-knitr r-spelling r-testthat))
7669 (home-page "https://github.com/BorchLab/immApex/")
7670 (synopsis
7671 "Adaptive immune receptor sequence-based machine and deep learning")
7672 (description
7673 "This package provides a set of tools to for machine and deep learning in
7674R from amino acid and nucleotide sequences focusing on adaptive immune
7675receptors. The package includes pre-processing of sequences, unifying gene
7676nomenclature usage, encoding sequences, and combining models. This package
7677will serve as the basis of future immune receptor sequence
7678functions/packages/models compatible with the @code{scRepertoire} ecosystem.")
7679 (license license:expat)))
7680
7681(define-public r-immreferent
7682 (package
7683 (name "r-immreferent")
7684 (version "1.0.0")
7685 (source
7686 (origin
7687 (method url-fetch)
7688 (uri (bioconductor-uri "immReferent" version))
7689 (sha256
7690 (base32 "194z5bnc2ksja22caf1dk64hp7d8hc521d2pzigk4kkr7wd3s3p8"))))
7691 (properties `((upstream-name . "immReferent")))
7692 (build-system r-build-system)
7693 (propagated-inputs (list r-biostrings
7694 r-httr
7695 r-jsonlite
7696 r-rvest
7697 r-tibble
7698 r-yaml))
7699 (native-inputs (list r-knitr r-spelling r-testthat r-withr))
7700 (home-page "https://github.com/BorchLab/immReferent/")
7701 (synopsis "Interface for immune receptor and HLA gene reference data")
7702 (description
7703 "This package provides a consistent interface for downloading, storing,
7704and accessing immune receptor (TCR/BCR) and HLA sequences from IMGT,
7705IPD-IMGT/HLA, and OGRDB (AIRR-C). It supports export to popular analysis
7706tools including @code{MiXCR}, TRUST4, Cell Ranger, and @code{IgBLAST}. This
7707package serves as a core dependency for immunogenomics packages, ensuring
7708reliable and high-quality sequence access with local caching for
7709reproducibility.")
7710 (license license:expat)))
7711
7712(define-public r-infercnv
7713 (package
7714 (name "r-infercnv")
7715 (version "1.28.0")
7716 (source
7717 (origin
7718 (method url-fetch)
7719 (uri (bioconductor-uri "infercnv" version))
7720 (sha256
7721 (base32
7722 "0wfxrb30bhvmvair8yawbwwhkx6xkh78dickj8x1q00w5mdwjya0"))))
7723 (properties
7724 `((upstream-name . "infercnv")
7725 (updater-extra-inputs . ("python"))))
7726 (build-system r-build-system)
7727 (inputs (list python))
7728 (propagated-inputs
7729 (list r-ape
7730 r-argparse
7731 r-biocgenerics
7732 r-catools
7733 r-coda
7734 r-coin
7735 r-digest
7736 r-doparallel
7737 r-dplyr
7738 r-edger
7739 r-fastcluster
7740 r-fitdistrplus
7741 r-foreach
7742 r-futile-logger
7743 r-future
7744 r-ggplot2
7745 r-gplots
7746 r-gridextra
7747 r-hiddenmarkov
7748 r-igraph
7749 r-matrix
7750 r-paralleldist
7751 r-phyclust
7752 r-rann
7753 r-rcolorbrewer
7754 r-reshape2
7755 r-rjags
7756 r-seurat
7757 r-singlecellexperiment
7758 r-summarizedexperiment
7759 r-tidyr))
7760 (native-inputs (list r-knitr r-testthat))
7761 (home-page "https://github.com/broadinstitute/inferCNV/wiki")
7762 (synopsis "Infer copy number variation from single-cell RNA-Seq data")
7763 (description
7764 "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
7765evidence for somatic large-scale chromosomal copy number alterations, such as gains
7766or deletions of entire chromosomes or large segments of chromosomes. This is done
7767by exploring expression intensity of genes across positions of a tumor genome in
7768comparison to a set of reference \"normal\" cells. A heatmap is generated
7769illustrating the relative expression intensities across each chromosome, and it
7770often becomes readily apparent as to which regions of the tumor genome are
7771over-abundant or less-abundant as compared to that of normal cells.")
7772 (license license:bsd-3)))
7773
7774;; This is a CRAN package, but it depends on r-xllim, which depends on a
7775;; Bioconductor package.
7776(define-public r-infusion
7777 (package
7778 (name "r-infusion")
7779 (version "2.3.12")
7780 (source
7781 (origin
7782 (method url-fetch)
7783 (uri (cran-uri "Infusion" version))
7784 (sha256
7785 (base32 "1k36z7s3vsgr6vqzq2d3vg79z0l8aayh3qrxh596hf04wxdfa8ch"))))
7786 (properties
7787 '((upstream-name . "Infusion")
7788 (updater-ignored-native-inputs . ("r-pkg"))))
7789 (build-system r-build-system)
7790 (propagated-inputs (list r-blackbox
7791 r-boot
7792 r-cli
7793 r-foreach
7794 r-geometry
7795 r-matrixstats
7796 r-mvtnorm
7797 r-nloptr
7798 r-numderiv
7799 r-pbapply
7800 r-proxy
7801 r-ranger
7802 r-spamm
7803 r-viridislite))
7804 (native-inputs (list r-devtools r-testthat r-xllim))
7805 (home-page "https://gitlab.mbb.univ-montp2.fr/francois/Infusion")
7806 (synopsis "Inference using simulation")
7807 (description
7808 "This package implements functions for simulation-based inference. In
7809particular, it implements functions to perform likelihood inference from data
7810summaries whose distributions are simulated. The package implements more
7811advanced methods than the ones first described in: Rousset, Gouy, Almoyna and
7812Courtiol (2017) <doi:10.1111/1755-0998.12627>.")
7813 (license license:cecill)))
7814
7815(define-public r-iranges
7816 (package
7817 (name "r-iranges")
7818 (version "2.46.0")
7819 (source (origin
7820 (method url-fetch)
7821 (uri (bioconductor-uri "IRanges" version))
7822 (sha256
7823 (base32
7824 "1sdkk1l4wh26dqrzfhalq1chnv7whjv8cn0cfwdl2mq35f0rf7m6"))))
7825 (properties
7826 `((upstream-name . "IRanges")))
7827 (build-system r-build-system)
7828 ;; Some tests require r-xvector, causing a dependency cycle.
7829 (arguments (list #:tests? #false))
7830 (propagated-inputs
7831 (list r-biocgenerics r-s4vectors))
7832 (home-page "https://bioconductor.org/packages/IRanges")
7833 (synopsis "Infrastructure for manipulating intervals on sequences")
7834 (description
7835 "This package provides efficient low-level and highly reusable S4 classes
7836for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
7837generally, data that can be organized sequentially (formally defined as
7838@code{Vector} objects), as well as views on these @code{Vector} objects.
7839Efficient list-like classes are also provided for storing big collections of
7840instances of the basic classes. All classes in the package use consistent
7841naming and share the same rich and consistent \"Vector API\" as much as
7842possible.")
7843 (license license:artistic2.0)))
7844
7845(define-public r-isoformswitchanalyzer
7846 (package
7847 (name "r-isoformswitchanalyzer")
7848 (version "2.12.0")
7849 (source
7850 (origin
7851 (method url-fetch)
7852 (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
7853 (sha256
7854 (base32 "011rbnd180pvm04fsybmbr30xrkbhg9rb692akig2z3x58s275nx"))))
7855 (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
7856 (build-system r-build-system)
7857 (propagated-inputs
7858 (list r-biobase
7859 r-biocgenerics
7860 r-biocparallel
7861 r-biostrings
7862 r-bsgenome
7863 r-dbi
7864 r-dexseq
7865 r-dplyr
7866 r-edger
7867 r-futile-logger
7868 r-genomicranges
7869 r-ggplot2
7870 r-gridextra
7871 r-iranges
7872 r-limma
7873 r-magrittr
7874 r-pfamanalyzer
7875 r-plyr
7876 r-pwalign
7877 r-rcolorbrewer
7878 r-rcurl
7879 r-readr
7880 r-reshape2
7881 r-rtracklayer
7882 r-s4vectors
7883 r-saturn
7884 r-seqinfo
7885 r-stringr
7886 r-summarizedexperiment
7887 r-sva
7888 r-tibble
7889 r-tidyr
7890 r-tximeta
7891 r-tximport
7892 r-venndiagram
7893 r-xvector))
7894 (native-inputs
7895 (list r-knitr))
7896 (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
7897 (synopsis "Analyze alternative splicing in RNA-seq data")
7898 (description
7899 "This is a package for the analysis of alternative splicing and isoform
7900switches with predicted functional consequences (e.g. gain/loss of protein
7901domains etc.) from quantification of all types of RNASeq by tools such as
7902Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
7903 (license license:gpl2+)))
7904
7905;; This is a CRAN package, but it depends on qvalue from Bioconductor.
7906(define-public r-isva
7907 (package
7908 (name "r-isva")
7909 (version "1.10")
7910 (source (origin
7911 (method url-fetch)
7912 (uri (cran-uri "isva" version))
7913 (sha256
7914 (base32
7915 "1im1bwbf6l88m4bwwwr0z2x8bvw927s3fqbwc06s5240wc8syjpl"))))
7916 (properties `((upstream-name . "isva")))
7917 (build-system r-build-system)
7918 (propagated-inputs (list r-fastica r-jade r-qvalue))
7919 (home-page "https://cran.r-project.org/package=isva")
7920 (synopsis "Independent surrogate variable analysis")
7921 (description
7922 "Independent Surrogate Variable Analysis is an algorithm for feature
7923selection in the presence of potential confounding factors (see Teschendorff
7924AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).")
7925 (license license:gpl2)))
7926
7927(define-public r-italics
7928 (package
7929 (name "r-italics")
7930 (version "2.72.0")
7931 (source
7932 (origin
7933 (method url-fetch)
7934 (uri (bioconductor-uri "ITALICS" version))
7935 (sha256
7936 (base32 "0rz9wifxxwh9zjz1mfvd6pw1c2mfr6838rybvvvi2sqw4jj86shc"))))
7937 (properties `((upstream-name . "ITALICS")))
7938 (build-system r-build-system)
7939 (propagated-inputs
7940 (list r-affxparser
7941 r-dbi
7942 r-glad
7943 r-italicsdata
7944 r-oligo
7945 r-oligoclasses
7946 r-pd-mapping50k-xba240))
7947 (home-page "http://bioinfo.curie.fr")
7948 (synopsis "Normalizing of the Affymetrix GeneChip human mapping")
7949 (description
7950 "This package provides tools for normalizing and analyzing of GeneChip
7951Mapping 100K and 500K Set. Affymetrix GeneChip Human Mapping 100K and 500K
7952Set allows the DNA copy number mea- surement of respectively 2× 50K and 2×
7953250K SNPs along the genome. Their high density allows a precise localization
7954of genomic alterations and makes them a powerful tool for cancer and copy
7955number polymorphism study.")
7956 (license license:gpl2)))
7957
7958;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
7959(define-public r-absfiltergsea
7960 (package
7961 (name "r-absfiltergsea")
7962 (version "1.5.1")
7963 (source
7964 (origin
7965 (method url-fetch)
7966 (uri (cran-uri "AbsFilterGSEA" version))
7967 (sha256
7968 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
7969 (properties `((upstream-name . "AbsFilterGSEA")))
7970 (build-system r-build-system)
7971 (propagated-inputs
7972 (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
7973 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
7974 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
7975 (description
7976 "This package provides a function that performs gene-permuting of a gene-set
7977enrichment analysis (GSEA) calculation with or without the absolute filtering.
7978 Without filtering, users can perform (original) two-tailed or one-tailed
7979absolute GSEA.")
7980 (license license:gpl2)))
7981
7982;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
7983(define-public r-bisquerna
7984 (package
7985 (name "r-bisquerna")
7986 (version "1.0.5")
7987 (source (origin
7988 (method url-fetch)
7989 (uri (cran-uri "BisqueRNA" version))
7990 (sha256
7991 (base32
7992 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
7993 (properties
7994 '((upstream-name . "BisqueRNA")
7995 (updater-extra-native-inputs . ("r-plyr"))))
7996 (build-system r-build-system)
7997 (propagated-inputs
7998 (list r-biobase r-limsolve))
7999 (native-inputs
8000 (list r-knitr r-plyr r-testthat))
8001 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
8002 (synopsis "Decomposition of bulk expression with single-cell sequencing")
8003 (description "This package provides tools to accurately estimate cell type
8004abundances from heterogeneous bulk expression. A reference-based method
8005utilizes single-cell information to generate a signature matrix and
8006transformation of bulk expression for accurate regression based estimates. A
8007marker-based method utilizes known cell-specific marker genes to measure
8008relative abundances across samples.")
8009 (license license:gpl3)))
8010
8011;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
8012;; from Bioconductor.
8013(define-public r-deconstructsigs
8014 (package
8015 (name "r-deconstructsigs")
8016 (version "1.8.0")
8017 (source (origin
8018 (method url-fetch)
8019 (uri (cran-uri "deconstructSigs" version))
8020 (sha256
8021 (base32
8022 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
8023 (properties
8024 `((upstream-name . "deconstructSigs")))
8025 (build-system r-build-system)
8026 (propagated-inputs
8027 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
8028 r-reshape2))
8029 (home-page "https://github.com/raerose01/deconstructSigs")
8030 (synopsis "Identifies signatures present in a tumor sample")
8031 (description "This package takes sample information in the form of the
8032fraction of mutations in each of 96 trinucleotide contexts and identifies
8033the weighted combination of published signatures that, when summed, most
8034closely reconstructs the mutational profile.")
8035 (license license:gpl2+)))
8036
8037;; This is a CRAN package, but it depends on Bioconductor packages.
8038(define-public r-jetset
8039 (package
8040 (name "r-jetset")
8041 (version "3.4.0")
8042 (source
8043 (origin
8044 (method url-fetch)
8045 (uri (cran-uri "jetset" version))
8046 (sha256
8047 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
8048 (properties `((upstream-name . "jetset")))
8049 (build-system r-build-system)
8050 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
8051 (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
8052 (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
8053 (description
8054 "This package provides a one-to-one mapping from gene to \"best\" probe
8055set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
8056hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single
8057gene may be measured by multiple probe sets. This can present a mild
8058conundrum when attempting to evaluate a gene \"signature\" that is defined by
8059gene names rather than by specific probe sets. This package also includes the
8060pre-calculated probe set quality scores that were used to define the
8061mapping.")
8062 (license license:artistic2.0)))
8063
8064(define-public r-nebulosa
8065 (package
8066 (name "r-nebulosa")
8067 (version "1.22.0")
8068 (source (origin
8069 (method url-fetch)
8070 (uri (bioconductor-uri "Nebulosa" version))
8071 (sha256
8072 (base32
8073 "1sc0fzjzvsbsr7z0xv2dc9zkxjn5l6f9yav2ldpmgyqkv7d5jrkn"))))
8074 (properties
8075 '((upstream-name . "Nebulosa")
8076 (updater-extra-native-inputs . ("r-seurat"))))
8077 (build-system r-build-system)
8078 (propagated-inputs (list r-ggplot2
8079 r-ggrastr
8080 r-ks
8081 r-matrix
8082 r-patchwork
8083 r-seuratobject
8084 r-singlecellexperiment
8085 r-summarizedexperiment))
8086 (native-inputs (list r-knitr r-seurat r-testthat))
8087 (home-page "https://github.com/powellgenomicslab/Nebulosa")
8088 (synopsis
8089 "Single-cell data visualisation using kernel gene-weighted density estimation")
8090 (description
8091 "This package provides a enhanced visualization of single-cell data based
8092on gene-weighted density estimation. Nebulosa recovers the signal from
8093dropped-out features and allows the inspection of the joint expression from
8094multiple features (e.g. genes). @code{Seurat} and @code{SingleCellExperiment}
8095objects can be used within Nebulosa.")
8096 (license license:gpl3)))
8097
8098;; This is a CRAN package but it requires r-rcy3, a Bioconductor package.
8099(define-public r-netgsa
8100 (package
8101 (name "r-netgsa")
8102 (version "4.0.7")
8103 (source
8104 (origin
8105 (method url-fetch)
8106 (uri (cran-uri "netgsa" version))
8107 (sha256
8108 (base32 "0a38gg33h5qmihg61jh8lpckzhp7yrbgsdn8lqk7j0gcp5fc3ylv"))))
8109 (properties `((upstream-name . "netgsa")))
8110 (build-system r-build-system)
8111 (propagated-inputs (list r-annotationdbi
8112 r-corpcor
8113 r-data-table
8114 r-dplyr
8115 r-genefilter
8116 r-glassofast
8117 r-glmnet
8118 r-graph
8119 r-graphite
8120 r-httr
8121 r-igraph
8122 r-magrittr
8123 r-matrix
8124 r-msigdbr
8125 r-quadprog
8126 r-rcpp
8127 r-rcppeigen
8128 r-rcy3
8129 r-reshape2
8130 r-rlang))
8131 (native-inputs (list r-knitr))
8132 (home-page "https://github.com/mikehellstern/netgsa")
8133 (synopsis "Network-Based gene set analysis")
8134 (description
8135 "This package lets you carry out network-based gene set analysis by
8136incorporating external information about interactions among genes, as well as
8137novel interactions learned from data. It implements methods described in
8138Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A,
8139Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A,
8140Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.")
8141 (license license:gpl3+)))
8142
8143;; This is a CRAN package, but it depends on Bioconductor packages.
8144(define-public r-nmf
8145 (package
8146 (name "r-nmf")
8147 (version "0.28")
8148 (source
8149 (origin
8150 (method url-fetch)
8151 (uri (cran-uri "NMF" version))
8152 (sha256
8153 (base32
8154 "1yzf5vcvyb2lypxcfyhah7y2yblkar1is7c50645yppf4frygpvp"))))
8155 (properties `((upstream-name . "NMF")))
8156 (build-system r-build-system)
8157 (propagated-inputs
8158 (list r-biobase
8159 r-biocmanager
8160 r-bigmemory ;suggested
8161 r-cluster
8162 r-codetools
8163 r-colorspace
8164 r-digest
8165 r-doparallel
8166 r-foreach
8167 r-ggplot2
8168 r-gridbase
8169 r-rcolorbrewer
8170 r-registry
8171 r-reshape2
8172 r-rngtools
8173 r-stringr
8174 r-synchronicity)) ;suggested
8175 (native-inputs
8176 (list r-knitr r-runit))
8177 (home-page "https://renozao.github.io/NMF")
8178 (synopsis "Algorithms and framework for nonnegative matrix factorization")
8179 (description
8180 "This package provides a framework to perform Non-negative Matrix
8181Factorization (NMF). The package implements a set of already published
8182algorithms and seeding methods, and provides a framework to test, develop and
8183plug new or custom algorithms. Most of the built-in algorithms have been
8184optimized in C++, and the main interface function provides an easy way of
8185performing parallel computations on multicore machines.")
8186 (license license:gpl2+)))
8187
8188(define-public r-affy
8189 (package
8190 (name "r-affy")
8191 (version "1.90.0")
8192 (source
8193 (origin
8194 (method url-fetch)
8195 (uri (bioconductor-uri "affy" version))
8196 (sha256
8197 (base32
8198 "0ipd0vqcsxg03g7myshbfhrz11bwjs0dns82kv00ajpfmbrbf7wv"))))
8199 (build-system r-build-system)
8200 ;; Some tests require r-affydata, causing a dependency cycle.
8201 (arguments (list #:tests? #false))
8202 (propagated-inputs
8203 (list r-affyio r-biobase r-biocgenerics r-biocmanager r-preprocesscore))
8204 (inputs
8205 (list zlib))
8206 (home-page "https://bioconductor.org/packages/affy")
8207 (synopsis "Methods for affymetrix oligonucleotide arrays")
8208 (description
8209 "This package contains functions for exploratory oligonucleotide array
8210analysis.")
8211 (license license:lgpl2.0+)))
8212
8213(define-public r-affycomp
8214 (package
8215 (name "r-affycomp")
8216 (version "1.88.0")
8217 (source
8218 (origin
8219 (method url-fetch)
8220 (uri (bioconductor-uri "affycomp" version))
8221 (sha256
8222 (base32
8223 "0qk6vds72g5zh2badb55v53zxh3gzsn1yhykds7adn4gvwzp312m"))))
8224 (properties `((upstream-name . "affycomp")))
8225 (build-system r-build-system)
8226 (propagated-inputs (list r-biobase))
8227 (home-page "https://bioconductor.org/packages/affycomp/")
8228 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
8229 (description
8230 "The package contains functions that can be used to compare expression
8231measures for Affymetrix Oligonucleotide Arrays.")
8232 (license license:gpl2+)))
8233
8234(define-public r-affycompatible
8235 (package
8236 (name "r-affycompatible")
8237 (version "1.58.0")
8238 (source
8239 (origin
8240 (method url-fetch)
8241 (uri (bioconductor-uri "AffyCompatible" version))
8242 (sha256
8243 (base32
8244 "1bg7iqasvfsgd9x3ykgpblqnz1q06g3ifmzj4jf2kn8kxj63wfbl"))))
8245 (properties
8246 `((upstream-name . "AffyCompatible")))
8247 (build-system r-build-system)
8248 (arguments
8249 (list
8250 #:phases
8251 `(modify-phases %standard-phases
8252 (add-after 'unpack 'make-reproducible
8253 (lambda _
8254 ;; Order DTD elements before generating R code from them.
8255 (substitute* "R/methods-AffyCompatible.R"
8256 (("dtd <- .*" m)
8257 (string-append m "
8258elements <- dtd$elements
8259ordered <- elements[order(names(elements))]\n"))
8260 (("elt in dtd\\$elements")
8261 "elt in ordered"))
8262 ;; Use a predictable directory name for code generation.
8263 (mkdir-p "/tmp/NetAffxResourcePrototype")
8264 (substitute* "R/DataClasses.R"
8265 (("directory=tempdir\\(\\)")
8266 "directory=\"/tmp/NetAffxResourcePrototype\"")))))))
8267 (propagated-inputs
8268 (list r-biostrings r-rcurl r-xml))
8269 (home-page "https://bioconductor.org/packages/AffyCompatible/")
8270 (synopsis "Work with Affymetrix GeneChip files")
8271 (description
8272 "This package provides an interface to Affymetrix chip annotation and
8273sample attribute files. The package allows an easy way for users to download
8274and manage local data bases of Affynmetrix NetAffx annotation files. It also
8275provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
8276Command Console} (AGCC)-compatible sample annotation files.")
8277 (license license:artistic2.0)))
8278
8279(define-public r-affycontam
8280 (package
8281 (name "r-affycontam")
8282 (version "1.70.0")
8283 (source
8284 (origin
8285 (method url-fetch)
8286 (uri (bioconductor-uri "affyContam" version))
8287 (sha256
8288 (base32
8289 "0xsi05gl1k5wvhqfam6wwx0p6apz3j4v0a47ydjcxzyjrr0j5cca"))))
8290 (properties `((upstream-name . "affyContam")))
8291 (build-system r-build-system)
8292 (propagated-inputs
8293 (list r-affy r-affydata r-biobase))
8294 (home-page "https://bioconductor.org/packages/affyContam/")
8295 (synopsis "Structured corruption of Affymetrix CEL file data")
8296 (description
8297 "Microarray quality assessment is a major concern of microarray analysts.
8298This package provides some simple approaches to in silico creation of quality
8299problems in CEL-level data to help evaluate performance of quality metrics.")
8300 (license license:artistic2.0)))
8301
8302(define-public r-affycoretools
8303 (package
8304 (name "r-affycoretools")
8305 (version "1.84.0")
8306 (source
8307 (origin
8308 (method url-fetch)
8309 (uri (bioconductor-uri "affycoretools" version))
8310 (sha256
8311 (base32
8312 "0s4xs4cqcg0yqynacxb9pm383l2ffzgvgmqx6c1ydvspwp7nprgp"))))
8313 (properties `((upstream-name . "affycoretools")))
8314 (build-system r-build-system)
8315 (propagated-inputs
8316 (list r-affy
8317 r-annotationdbi
8318 r-biobase
8319 r-biocgenerics
8320 r-dbi
8321 r-edger
8322 r-gcrma
8323 r-ggplot2
8324 r-glimma
8325 r-gostats
8326 r-gplots
8327 r-hwriter
8328 r-lattice
8329 r-limma
8330 r-oligoclasses
8331 r-reportingtools
8332 r-rsqlite
8333 r-s4vectors
8334 r-xtable))
8335 (native-inputs
8336 (list r-knitr))
8337 (home-page "https://bioconductor.org/packages/affycoretools/")
8338 (synopsis "Functions for analyses with Affymetrix GeneChips")
8339 (description
8340 "This package provides various wrapper functions that have been written
8341to streamline the more common analyses that a Biostatistician might see.")
8342 (license license:artistic2.0)))
8343
8344(define-public r-affyio
8345 (package
8346 (name "r-affyio")
8347 (version "1.82.0")
8348 (source
8349 (origin
8350 (method url-fetch)
8351 (uri (bioconductor-uri "affyio" version))
8352 (sha256
8353 (base32
8354 "06va62dq065ka5xnfc51fylm5mdm39yh09nh86rs70ln3d1mlr3y"))))
8355 (build-system r-build-system)
8356 (inputs
8357 (list zlib))
8358 (home-page "https://github.com/bmbolstad/affyio")
8359 (synopsis "Tools for parsing Affymetrix data files")
8360 (description
8361 "This package provides routines for parsing Affymetrix data files based
8362upon file format information. The primary focus is on accessing the CEL and
8363CDF file formats.")
8364 (license license:lgpl2.0+)))
8365
8366(define-public r-affxparser
8367 (package
8368 (name "r-affxparser")
8369 (version "1.84.0")
8370 (source
8371 (origin
8372 (method url-fetch)
8373 (uri (bioconductor-uri "affxparser" version))
8374 (sha256
8375 (base32
8376 "08kfkhzb8s532irchm53m23f3gdq3yfi5mad2pjx93qsvwz7lc4f"))))
8377 (properties `((upstream-name . "affxparser")))
8378 (build-system r-build-system)
8379 (home-page "https://github.com/HenrikBengtsson/affxparser")
8380 (synopsis "Affymetrix File Parsing SDK")
8381 (description
8382 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
8383BAR). It provides methods for fast and memory efficient parsing of Affymetrix
8384files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
8385are supported. Currently, there are methods for reading @dfn{chip definition
8386file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
8387either in full or in part. For example, probe signals from a few probesets
8388can be extracted very quickly from a set of CEL files into a convenient list
8389structure.")
8390 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
8391 ;; under LGPLv2+.
8392 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
8393
8394(define-public r-annotate
8395 (package
8396 (name "r-annotate")
8397 (version "1.90.0")
8398 (source
8399 (origin
8400 (method url-fetch)
8401 (uri (bioconductor-uri "annotate" version))
8402 (sha256
8403 (base32
8404 "0d3v2nzng87ygkf60daw3hzv3i4781wiakggg334bvicc7dk4wsk"))))
8405 (properties
8406 '((updater-ignored-native-inputs
8407 . ("r-hgu95av2-db"
8408 "r-org-hs-eg-db"
8409 "r-rae230a-db"
8410 "r-rae230aprobe"))))
8411 (build-system r-build-system)
8412 ;; Tests require a number of annotation packages.
8413 (arguments (list #:tests? #false))
8414 (propagated-inputs
8415 (list r-annotationdbi
8416 r-biobase
8417 r-biocgenerics
8418 r-dbi
8419 r-httr
8420 r-xml
8421 r-xtable))
8422 (native-inputs (list r-biostrings r-go-db r-knitr r-rgraphviz r-runit))
8423 (home-page "https://bioconductor.org/packages/annotate")
8424 (synopsis "Annotation for microarrays")
8425 (description "This package provides R environments for the annotation of
8426microarrays.")
8427 (license license:artistic2.0)))
8428
8429(define-public r-annotationdbi
8430 (package
8431 (name "r-annotationdbi")
8432 (version "1.74.0")
8433 (source (origin
8434 (method url-fetch)
8435 (uri (bioconductor-uri "AnnotationDbi" version))
8436 (sha256
8437 (base32
8438 "0l0k9jym9yb1l070vh1h8q6h05iisp4fqrd9q444f1ivj4nhhlan"))))
8439 (properties
8440 '((upstream-name . "AnnotationDbi")
8441 (updater-ignored-native-inputs
8442 . ("r-annotationforge"
8443 "r-db"
8444 "r-ensdb-hsapiens-v75"
8445 "r-go-db"
8446 "r-hgu95av2-db"
8447 "r-org-at-tair-db"
8448 "r-org-hs-eg-db"
8449 "r-org-sc-sgd-db"
8450 "r-reactome-db"
8451 "r-txdb-hsapiens-ucsc-hg19-knowngene"))))
8452 (build-system r-build-system)
8453 ;; Tests require annotation packages that depend on this package.
8454 (arguments (list #:tests? #false))
8455 (propagated-inputs
8456 (list r-biobase
8457 r-biocgenerics
8458 r-dbi
8459 r-iranges
8460 r-keggrest
8461 r-rsqlite
8462 r-s4vectors))
8463 (native-inputs
8464 (list r-biocstyle r-knitr r-runit))
8465 (home-page "https://bioconductor.org/packages/AnnotationDbi")
8466 (synopsis "Annotation database interface")
8467 (description
8468 "This package provides user interface and database connection code for
8469annotation data packages using SQLite data storage.")
8470 (license license:artistic2.0)))
8471
8472(define-public r-annotationfilter
8473 (package
8474 (name "r-annotationfilter")
8475 (version "1.36.0")
8476 (source (origin
8477 (method url-fetch)
8478 (uri (bioconductor-uri "AnnotationFilter" version))
8479 (sha256
8480 (base32
8481 "0kj6y6629afjfwqk4fnwjacgz219bx834q65243fbzqacj66h27n"))))
8482 (properties
8483 `((upstream-name . "AnnotationFilter")))
8484 (build-system r-build-system)
8485 (propagated-inputs
8486 (list r-genomicranges r-lazyeval))
8487 (native-inputs
8488 (list r-knitr r-testthat))
8489 (home-page "https://github.com/Bioconductor/AnnotationFilter")
8490 (synopsis "Facilities for filtering Bioconductor annotation resources")
8491 (description
8492 "This package provides classes and other infrastructure to implement
8493filters for manipulating Bioconductor annotation resources. The filters are
8494used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
8495 (license license:artistic2.0)))
8496
8497(define-public r-annotationforge
8498 (package
8499 (name "r-annotationforge")
8500 (version "1.54.0")
8501 (source
8502 (origin
8503 (method url-fetch)
8504 (uri (bioconductor-uri "AnnotationForge" version))
8505 (sha256
8506 (base32
8507 "059ymad55nzl1b4jh9ysmqvb07jsczlyvv7766s32j002g6ydh99"))))
8508 (properties
8509 '((upstream-name . "AnnotationForge")
8510 (updater-extra-native-inputs . ("r-go-db" "r-runit"))
8511 (updater-ignored-native-inputs
8512 . ("r-db"
8513 "r-hgu95av2-db"
8514 "r-homo-sapiens"
8515 "r-org-hs-eg-db"))))
8516 (build-system r-build-system)
8517 (propagated-inputs
8518 (list r-annotationdbi
8519 r-biobase
8520 r-biocgenerics
8521 r-dbi
8522 r-rcurl
8523 r-rsqlite
8524 r-s4vectors
8525 r-xml))
8526 (native-inputs
8527 (list r-biocfilecache
8528 r-biocmanager
8529 r-biocstyle
8530 r-biostrings
8531 r-go-db
8532 r-knitr
8533 r-runit))
8534 (home-page "https://bioconductor.org/packages/AnnotationForge")
8535 (synopsis "Code for building annotation database packages")
8536 (description
8537 "This package provides code for generating Annotation packages and their
8538databases. Packages produced are intended to be used with AnnotationDbi.")
8539 (license license:artistic2.0)))
8540
8541(define-public r-annotationhub
8542 (package
8543 (name "r-annotationhub")
8544 (version "4.2.0")
8545 (source
8546 (origin
8547 (method url-fetch)
8548 (uri (bioconductor-uri "AnnotationHub" version))
8549 (sha256
8550 (base32
8551 "0ra9cya4kln8fhsff0qbpp8fjx8i68ka9xrm2vjv2nw2yw8klzk4"))))
8552 (properties
8553 '((upstream-name . "AnnotationHub")
8554 ;; Avoid dependency cycles.
8555 (updater-ignored-native-inputs
8556 . ("r-dbi"
8557 "r-genomeinfodb"
8558 "r-genomicranges"
8559 "r-iranges"
8560 "r-seqinfo"))))
8561 (build-system r-build-system)
8562 ;; Many tests try to download files.
8563 (arguments (list #:tests? #false))
8564 (propagated-inputs
8565 (list r-annotationdbi
8566 r-biocbaseutils
8567 r-biocfilecache
8568 r-biocgenerics
8569 r-biocmanager
8570 r-biocversion
8571 r-curl
8572 r-dplyr
8573 r-httr2
8574 r-rappdirs
8575 r-rsqlite
8576 r-s4vectors
8577 r-yaml))
8578 (native-inputs (list r-knitr r-runit))
8579 (home-page "https://bioconductor.org/packages/AnnotationHub")
8580 (synopsis "Client to access AnnotationHub resources")
8581 (description
8582 "This package provides a client for the Bioconductor AnnotationHub web
8583resource. The AnnotationHub web resource provides a central location where
8584genomic files (e.g. VCF, bed, wig) and other resources from standard
8585locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
8586metadata about each resource, e.g., a textual description, tags, and date of
8587modification. The client creates and manages a local cache of files retrieved
8588by the user, helping with quick and reproducible access.")
8589 (license license:artistic2.0)))
8590
8591(define-public r-aroma-light
8592 (package
8593 (name "r-aroma-light")
8594 (version "3.42.0")
8595 (source
8596 (origin
8597 (method url-fetch)
8598 (uri (bioconductor-uri "aroma.light" version))
8599 (sha256
8600 (base32
8601 "0f7k4ls09cs4yj8cc1q8wrnf4fnsh37w445788sg2iazbksjgzwh"))))
8602 (properties
8603 '((upstream-name . "aroma.light")
8604 ;; Needed for tests.
8605 (updater-extra-native-inputs . ("r-princurve"))))
8606 (build-system r-build-system)
8607 (propagated-inputs
8608 (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
8609 (native-inputs (list r-princurve))
8610 (home-page "https://github.com/HenrikBengtsson/aroma.light")
8611 (synopsis "Methods for normalization and visualization of microarray data")
8612 (description
8613 "This package provides methods for microarray analysis that take basic
8614data types such as matrices and lists of vectors. These methods can be used
8615standalone, be utilized in other packages, or be wrapped up in higher-level
8616classes.")
8617 (license license:gpl2+)))
8618
8619(define-public r-bamsignals
8620 (package
8621 (name "r-bamsignals")
8622 (version "1.44.1")
8623 (source
8624 (origin
8625 (method url-fetch)
8626 (uri (bioconductor-uri "bamsignals" version))
8627 (sha256
8628 (base32
8629 "0r1vs9rdhv83fbgz20zl1hgh1kvyhqc6rv5dph6lzz8m2qhk7476"))))
8630 (build-system r-build-system)
8631 (arguments
8632 (list
8633 #:skipped-tests
8634 '(("test_CountSignals.R"
8635 ;; Three attributes have no name.
8636 "Test CountSignals class and methods"))))
8637 (propagated-inputs
8638 (list r-biocgenerics r-genomicranges r-iranges r-rcpp r-rhtslib))
8639 (native-inputs
8640 (list r-knitr r-rsamtools r-testthat))
8641 (home-page "https://bioconductor.org/packages/bamsignals")
8642 (synopsis "Extract read count signals from bam files")
8643 (description
8644 "This package efficiently obtains count vectors from indexed bam
8645files. It counts the number of nucleotide sequence reads in given genomic
8646ranges and it computes reads profiles and coverage profiles. It also handles
8647paired-end data.")
8648 (license license:gpl2+)))
8649
8650(define-public r-biobase
8651 (package
8652 (name "r-biobase")
8653 (version "2.72.0")
8654 (source (origin
8655 (method url-fetch)
8656 (uri (bioconductor-uri "Biobase" version))
8657 (sha256
8658 (base32
8659 "1pdv64zy2bbh9gx8cywz00ppsxqm3dvym1b2jrmgjlh3hp2z8jnh"))))
8660 (properties
8661 '((upstream-name . "Biobase")
8662 ;; Avoid dependency cycle.
8663 (updater-ignored-native-inputs . ("r-all" "r-convert" "r-golubesets"))))
8664 (build-system r-build-system)
8665 ;; One test depends on golubEsets, which depends on r-biobase.
8666 (arguments (list #:tests? #false))
8667 (propagated-inputs (list r-biocgenerics))
8668 (native-inputs (list r-biocmanager r-knitr r-runit))
8669 (home-page "https://bioconductor.org/packages/Biobase")
8670 (synopsis "Base functions for Bioconductor")
8671 (description
8672 "This package provides functions that are needed by many other packages
8673on Bioconductor or which replace R functions.")
8674 (license license:artistic2.0)))
8675
8676(define-public r-biomart
8677 (package
8678 (name "r-biomart")
8679 (version "2.68.0")
8680 (source (origin
8681 (method url-fetch)
8682 (uri (bioconductor-uri "biomaRt" version))
8683 (sha256
8684 (base32
8685 "05dbv2mx2rj74fk0mqwxa7cambdn30w8v0aynl5kycass783nd0s"))))
8686 (properties
8687 `((upstream-name . "biomaRt")))
8688 (build-system r-build-system)
8689 (arguments
8690 (list
8691 #:skipped-tests
8692 '(("test_ensembl_ssl_settings.R"
8693 ;; This produces unexpected warnings.
8694 "SSL settings are stored in the cache")
8695 ;; These tests attempt to download files.
8696 ("test_ensemblFunctions.R"
8697 "useEnsembl\\(\\) error handling is OK"
8698 "useEnsembl\\(host = \\) is not necessary for ensembl.org"
8699 "Ensembl URLs are constructed correctly")
8700 ("test_getBM.R"
8701 "getBM returns sensible things"
8702 "getBM doesn't convert T/F alleles into TRUE/FALSE")
8703 ("test-getGene.R"
8704 "getGene\\(\\) recognizes new ensembl name as ensembl")
8705 ;; Code run outside of testthat accesses www.ensembl.org
8706 "test_z_cache.R")))
8707 (propagated-inputs
8708 (list r-annotationdbi
8709 r-biocfilecache
8710 r-curl
8711 r-httr2
8712 r-progress
8713 r-stringr
8714 r-xml2))
8715 (native-inputs
8716 (list r-httptest2 r-knitr r-mockery r-testthat r-withr))
8717 (home-page "https://bioconductor.org/packages/biomaRt")
8718 (synopsis "Interface to BioMart databases")
8719 (description
8720 "biomaRt provides an interface to a growing collection of databases
8721implementing the @url{BioMart software suite, http://www.biomart.org}. The
8722package enables retrieval of large amounts of data in a uniform way without
8723the need to know the underlying database schemas or write complex SQL queries.
8724Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
8725Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
8726users direct access to a diverse set of data and enable a wide range of
8727powerful online queries from gene annotation to database mining.")
8728 (license license:artistic2.0)))
8729
8730;; This is a CRAN package, but it depends on a Bioconductor package:
8731;; r-biomart
8732(define-public r-biomartr
8733 (package
8734 (name "r-biomartr")
8735 (version "1.0.7")
8736 (source (origin
8737 (method url-fetch)
8738 (uri (cran-uri "biomartr" version))
8739 (sha256
8740 (base32
8741 "0ic6qbk2xmgrcc0xhxyhjafp1xbf2c5dpbqqrbkprrhynr8mq7cx"))))
8742 (properties `((upstream-name . "biomartr")))
8743 (build-system r-build-system)
8744 (propagated-inputs
8745 (list r-biomart
8746 r-biostrings
8747 r-curl
8748 r-data-table
8749 r-downloader
8750 r-dplyr
8751 r-fs
8752 r-httr
8753 r-jsonlite
8754 r-philentropy
8755 r-purrr
8756 r-r-utils
8757 r-rcurl
8758 r-readr
8759 r-stringr
8760 r-tibble
8761 r-withr
8762 r-xml))
8763 (native-inputs (list r-knitr r-testthat))
8764 (home-page "https://docs.ropensci.org/biomartr/")
8765 (synopsis "Genomic data retrieval")
8766 (description
8767 "Perform large scale genomic data retrieval and functional annotation
8768retrieval. This package aims to provide users with a standardized way to
8769automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome
8770retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases.
8771Furthermore, an interface to the BioMart database allows users to retrieve
8772functional annotation for genomic loci. In addition, users can download
8773entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with
8774only one command.")
8775 (license license:gpl2)))
8776
8777(define-public r-biocparallel
8778 (package
8779 (name "r-biocparallel")
8780 (version "1.46.0")
8781 (source (origin
8782 (method url-fetch)
8783 (uri (bioconductor-uri "BiocParallel" version))
8784 (sha256
8785 (base32
8786 "0f0hkr0if481p0pmcn8iwhfxs0wfq9sb0s5c92d2j5rmnpvl4rnh"))))
8787 (properties
8788 '((upstream-name . "BiocParallel")
8789 (updater-extra-native-inputs . ("r-batchtools"))))
8790 (build-system r-build-system)
8791 (arguments
8792 (list
8793 #:phases
8794 '(modify-phases %standard-phases
8795 (add-after 'unpack 'make-reproducible
8796 (lambda _
8797 ;; Remove generated documentation.
8798 (for-each delete-file
8799 '("inst/doc/BiocParallel_BatchtoolsParam.R"
8800 "inst/doc/Introduction_To_BiocParallel.R"
8801 "inst/doc/Errors_Logs_And_Debugging.R"
8802 "inst/doc/Random_Numbers.R"))
8803
8804 ;; Remove timestamp
8805 (substitute* '("vignettes/Random_Numbers.Rmd"
8806 "vignettes/Introduction_To_BiocParallel.Rmd"
8807 "vignettes/Errors_Logs_And_Debugging.Rmd"
8808 "vignettes/BiocParallel_BatchtoolsParam.Rmd"
8809 "inst/doc/Random_Numbers.Rmd"
8810 "inst/doc/Introduction_To_BiocParallel.Rmd"
8811 "inst/doc/Errors_Logs_And_Debugging.Rmd"
8812 "inst/doc/BiocParallel_BatchtoolsParam.Rmd")
8813 (("Compiled: `r format\\(Sys.time.*`") ""))
8814
8815 ;; Initialize the random number generator seed when building.
8816 (substitute* "R/rng.R"
8817 (("\"L'Ecuyer-CMRG\"\\)" m)
8818 (string-append
8819 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
8820 (propagated-inputs
8821 (list r-bh r-codetools r-cpp11 r-futile-logger r-snow))
8822 (native-inputs
8823 (list r-batchtools
8824 r-biocgenerics
8825 r-doparallel
8826 r-foreach
8827 r-knitr
8828 r-runit))
8829 (home-page "https://bioconductor.org/packages/BiocParallel")
8830 (synopsis "Bioconductor facilities for parallel evaluation")
8831 (description
8832 "This package provides modified versions and novel implementation of
8833functions for parallel evaluation, tailored to use with Bioconductor
8834objects.")
8835 (license (list license:gpl2+ license:gpl3+))))
8836
8837(define-public r-biostrings
8838 (package
8839 (name "r-biostrings")
8840 (version "2.80.1")
8841 (source (origin
8842 (method url-fetch)
8843 (uri (bioconductor-uri "Biostrings" version))
8844 (sha256
8845 (base32
8846 "0sfhnjkm9krqp9qqdi36046spz2v7csmkl12xxblzbi66wmxhmkn"))))
8847 (properties
8848 `((upstream-name . "Biostrings")))
8849 (build-system r-build-system)
8850 (propagated-inputs
8851 (list r-biocgenerics
8852 r-crayon
8853 r-iranges
8854 r-s4vectors
8855 r-seqinfo
8856 r-xvector))
8857 (native-inputs (list r-knitr r-runit r-testthat))
8858 (home-page "https://bioconductor.org/packages/Biostrings")
8859 (synopsis "String objects and algorithms for biological sequences")
8860 (description
8861 "This package provides memory efficient string containers, string
8862matching algorithms, and other utilities, for fast manipulation of large
8863biological sequences or sets of sequences.")
8864 (license license:artistic2.0)))
8865
8866(define-public r-biovizbase
8867 (package
8868 (name "r-biovizbase")
8869 (version "1.60.0")
8870 (source
8871 (origin
8872 (method url-fetch)
8873 (uri (bioconductor-uri "biovizBase" version))
8874 (sha256
8875 (base32
8876 "0jn0bly05la0i9qs2a3fv6x0l96k207fx7c7xpxfp51w788ai4kg"))))
8877 (properties `((upstream-name . "biovizBase")))
8878 (build-system r-build-system)
8879 (propagated-inputs
8880 (list r-annotationdbi
8881 r-annotationfilter
8882 r-biocgenerics
8883 r-biostrings
8884 r-dichromat
8885 r-ensembldb
8886 r-genomeinfodb
8887 r-genomicalignments
8888 r-genomicfeatures
8889 r-genomicranges
8890 r-hmisc
8891 r-iranges
8892 r-rcolorbrewer
8893 r-rlang
8894 r-rsamtools
8895 r-s4vectors
8896 r-scales
8897 r-seqinfo
8898 r-summarizedexperiment
8899 r-variantannotation))
8900 (native-inputs (list r-bsgenome-hsapiens-ucsc-hg19 r-ensdb-hsapiens-v75
8901 r-rtracklayer r-runit))
8902 (home-page "https://bioconductor.org/packages/biovizBase")
8903 (synopsis "Basic graphic utilities for visualization of genomic data")
8904 (description
8905 "The biovizBase package is designed to provide a set of utilities, color
8906schemes and conventions for genomic data. It serves as the base for various
8907high-level packages for biological data visualization. This saves development
8908effort and encourages consistency.")
8909 (license license:artistic2.0)))
8910
8911(define-public r-bsgenome
8912 (package
8913 (name "r-bsgenome")
8914 (version "1.80.0")
8915 (source (origin
8916 (method url-fetch)
8917 (uri (bioconductor-uri "BSgenome" version))
8918 (sha256
8919 (base32
8920 "0rw14vv8m1vcb2rhnljw6w4f9s3rgkzz7c6w7jid65nw1m0zawgx"))))
8921 (properties
8922 `((upstream-name . "BSgenome")
8923 ;; Avoid cycles.
8924 (updater-ignored-native-inputs
8925 . ("r-bsgenome-celegans-ucsc-ce2"
8926 "r-bsgenome-hsapiens-ucsc-hg38-masked"
8927 "r-hgu95av2probe"))))
8928 (build-system r-build-system)
8929 (propagated-inputs
8930 (list r-biocgenerics
8931 r-biocio
8932 r-biostrings
8933 r-genomicranges
8934 r-iranges
8935 r-matrixstats
8936 r-rsamtools
8937 r-rtracklayer
8938 r-s4vectors
8939 r-seqinfo
8940 r-xvector))
8941 (home-page "https://bioconductor.org/packages/BSgenome")
8942 (synopsis "Infrastructure for Biostrings-based genome data packages")
8943 (description
8944 "This package provides infrastructure shared by all Biostrings-based
8945genome data packages and support for efficient SNP representation.")
8946 (license license:artistic2.0)))
8947
8948(define-public r-category
8949 (package
8950 (name "r-category")
8951 (version "2.78.0")
8952 (source
8953 (origin
8954 (method url-fetch)
8955 (uri (bioconductor-uri "Category" version))
8956 (sha256
8957 (base32
8958 "1jg55sj99bxjnsm6y8n52rvbzmhdfk7a1hpxqnfj8pdapnfdjy8s"))))
8959 (properties
8960 `((upstream-name . "Category")
8961 (updater-ignored-native-inputs . ("r-gostats"))))
8962 (build-system r-build-system)
8963 (arguments
8964 (list
8965 ;; Vignettes attempt to connect to rest.kegg.jp.
8966 #:test-types '(list "tests")
8967 #:test-directory "inst/UnitTests"
8968 ;; These tests need r-gostats, which depends on this package.
8969 #:skipped-tests '("hyperGTest_test.R")))
8970 (propagated-inputs
8971 (list r-annotate
8972 r-annotationdbi
8973 r-biobase
8974 r-biocgenerics
8975 r-dbi
8976 r-genefilter
8977 r-graph
8978 r-gseabase
8979 r-matrix
8980 r-rbgl))
8981 (native-inputs (list r-all
8982 r-geneplotter
8983 r-hgu95av2-db
8984 r-karyoploter
8985 r-keggrest
8986 r-lattice
8987 r-limma
8988 r-org-sc-sgd-db
8989 r-rcolorbrewer
8990 r-runit))
8991 (home-page "https://bioconductor.org/packages/Category")
8992 (synopsis "Category analysis")
8993 (description
8994 "This package provides a collection of tools for performing category
8995analysis.")
8996 (license license:artistic2.0)))
8997
8998(define-public r-champ
8999 (package
9000 (name "r-champ")
9001 (version "2.42.0")
9002 (source (origin
9003 (method url-fetch)
9004 (uri (bioconductor-uri "ChAMP" version))
9005 (sha256
9006 (base32
9007 "1q21hl8vdah7v3d456x55lf4917d4alb3m35nlk7bwfqzrm64k1w"))))
9008 (properties `((upstream-name . "ChAMP")))
9009 (build-system r-build-system)
9010 (propagated-inputs
9011 (list r-bumphunter
9012 r-champdata
9013 r-combinat
9014 r-dendextend
9015 r-dmrcate
9016 r-dnacopy
9017 r-doparallel
9018 r-dt
9019 r-genomicranges
9020 r-ggplot2
9021 r-globaltest
9022 r-goseq
9023 r-hmisc
9024 r-illumina450probevariants-db
9025 r-illuminahumanmethylation450kmanifest
9026 r-illuminahumanmethylationepicanno-ilm10b4-hg19
9027 r-illuminahumanmethylationepicmanifest
9028 r-illuminaio
9029 r-impute
9030 r-isva
9031 r-limma
9032 r-marray
9033 r-matrixstats
9034 r-minfi
9035 r-missmethyl
9036 r-plotly
9037 r-plyr
9038 r-preprocesscore
9039 r-prettydoc
9040 r-quadprog
9041 r-qvalue
9042 r-rcolorbrewer
9043 r-rmarkdown
9044 r-rpmm
9045 r-shiny
9046 r-shinythemes
9047 r-sva
9048 r-watermelon))
9049 (native-inputs (list r-knitr))
9050 (home-page "https://bioconductor.org/packages/ChAMP")
9051 (synopsis
9052 "Chip analysis methylation pipeline for Illumina HumanMethylation450 and EPIC")
9053 (description
9054 "The package includes quality control metrics, a selection of
9055normalization methods and novel methods to identify differentially methylated
9056regions and to highlight copy number alterations.")
9057 (license license:gpl3)))
9058
9059(define-public r-chipseeker
9060 (package
9061 (name "r-chipseeker")
9062 (version "1.48.0")
9063 (source (origin
9064 (method url-fetch)
9065 (uri (bioconductor-uri "ChIPseeker" version))
9066 (sha256
9067 (base32
9068 "1h4sc5jk9qszv9f9fj9bxwjlb54v2r5vcb8mxq8ap19wj19l0dkb"))))
9069 (build-system r-build-system)
9070 (native-inputs
9071 (list r-knitr r-testthat r-txdb-hsapiens-ucsc-hg38-knowngene))
9072 (propagated-inputs
9073 (list r-annotationdbi
9074 r-aplot
9075 r-biocgenerics
9076 r-boot
9077 r-dplyr
9078 r-enrichplot
9079 r-genomeinfodb
9080 r-genomicfeatures
9081 r-genomicranges
9082 r-ggplot2
9083 r-gplots
9084 r-gtools
9085 r-iranges
9086 r-magrittr
9087 r-plotrix
9088 r-rcolorbrewer
9089 r-rlang
9090 r-rtracklayer
9091 r-s4vectors
9092 r-scales
9093 r-tibble
9094 r-txdb-hsapiens-ucsc-hg19-knowngene
9095 r-yulab-utils))
9096 (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
9097 (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
9098 (description "This package implements functions to retrieve the nearest
9099genes around the peak, annotate genomic region of the peak, statstical methods
9100for estimate the significance of overlap among ChIP peak data sets, and
9101incorporate GEO database for user to compare the own dataset with those
9102deposited in database. The comparison can be used to infer cooperative
9103regulation and thus can be used to generate hypotheses. Several visualization
9104functions are implemented to summarize the coverage of the peak experiment,
9105average profile and heatmap of peaks binding to TSS regions, genomic
9106annotation, distance to TSS, and overlap of peaks or genes.")
9107 (license license:artistic2.0)))
9108
9109(define-public r-chipseq
9110 (package
9111 (name "r-chipseq")
9112 (version "1.62.0")
9113 (source
9114 (origin
9115 (method url-fetch)
9116 (uri (bioconductor-uri "chipseq" version))
9117 (sha256
9118 (base32
9119 "1m7kajzpy8az3wjya0xda7j1yvki5fblkj5q2v145030bgw3gbsk"))))
9120 (build-system r-build-system)
9121 (propagated-inputs
9122 (list r-biocgenerics
9123 r-genomicranges
9124 r-iranges
9125 r-lattice
9126 r-s4vectors
9127 r-shortread))
9128 (native-inputs (list r-knitr))
9129 (home-page "https://bioconductor.org/packages/chipseq")
9130 (synopsis "Package for analyzing ChIPseq data")
9131 (description
9132 "This package provides tools for processing short read data from ChIPseq
9133experiments.")
9134 (license license:artistic2.0)))
9135
9136(define-public r-complexheatmap
9137 (package
9138 (name "r-complexheatmap")
9139 (version "2.28.0")
9140 (source
9141 (origin
9142 (method url-fetch)
9143 (uri (bioconductor-uri "ComplexHeatmap" version))
9144 (sha256
9145 (base32
9146 "1i8rnj5c7f16g4hjb20r3242z6inhyf1wmld0yhxyp6l3jjmyhxk"))))
9147 (properties
9148 `((upstream-name . "ComplexHeatmap")))
9149 (build-system r-build-system)
9150 (propagated-inputs
9151 (list r-circlize
9152 r-clue
9153 r-codetools
9154 r-colorspace
9155 r-digest
9156 r-doparallel
9157 r-foreach
9158 r-getoptlong
9159 r-globaloptions
9160 r-iranges
9161 r-matrixstats
9162 r-png
9163 r-rcolorbrewer))
9164 (native-inputs
9165 (list r-dendextend
9166 r-genomicranges
9167 r-gplots
9168 r-gridtext
9169 r-knitr
9170 r-testthat))
9171 (home-page
9172 "https://github.com/jokergoo/ComplexHeatmap")
9173 (synopsis "Making Complex Heatmaps")
9174 (description
9175 "Complex heatmaps are efficient to visualize associations between
9176different sources of data sets and reveal potential structures. This package
9177provides a highly flexible way to arrange multiple heatmaps and supports
9178self-defined annotation graphics.")
9179 (license license:gpl2+)))
9180
9181;; This is a CRAN package, but it depends on r-complexheatmap from
9182;; Bioconductor.
9183(define-public r-conos
9184 (package
9185 (name "r-conos")
9186 (version "1.5.4")
9187 (source
9188 (origin
9189 (method url-fetch)
9190 (uri (cran-uri "conos" version))
9191 (sha256
9192 (base32 "16b9fi64m75xrf8bgn6yh8dj4x1d8114kh1b8wlnfdz52hdqy0dk"))))
9193 (properties `((upstream-name . "conos")))
9194 (build-system r-build-system)
9195 (propagated-inputs
9196 (list r-abind
9197 r-complexheatmap
9198 r-cowplot
9199 r-dendextend
9200 r-dplyr
9201 r-ggplot2
9202 r-ggrepel
9203 r-gridextra
9204 r-igraph
9205 r-irlba
9206 r-leidenalg
9207 r-magrittr
9208 r-matrix
9209 r-n2r
9210 r-pagoda2
9211 r-r6
9212 r-rcpp
9213 r-rcpparmadillo
9214 r-rcppeigen
9215 r-rcppprogress
9216 r-reshape2
9217 r-rlang
9218 r-rtsne
9219 r-sccore))
9220 (native-inputs (list r-testthat))
9221 (home-page "https://github.com/kharchenkolab/conos")
9222 (synopsis "Clustering on network of samples")
9223 (description
9224 "This package wires together large collections of single-cell RNA-seq
9225datasets, which allows for both the identification of recurrent cell clusters
9226and the propagation of information between datasets in multi-sample or
9227atlas-scale collections. Conos focuses on the uniform mapping of homologous
9228cell types across heterogeneous sample collections. For instance, users could
9229investigate a collection of dozens of peripheral blood samples from cancer
9230patients combined with dozens of controls, which perhaps includes samples of a
9231related tissue such as lymph nodes.")
9232 (license license:gpl3)))
9233
9234(define-public r-copywriter
9235 (package
9236 (name "r-copywriter")
9237 (version "2.29.0")
9238 (source
9239 (origin
9240 (method url-fetch)
9241 (uri (bioconductor-uri "CopywriteR" version))
9242 (sha256
9243 (base32
9244 "1h4cyrjwdazgk49yzi9lvya8bfz9r4cpq19hyzikvc81ia8zdxs6"))))
9245 (properties `((upstream-name . "CopywriteR")))
9246 (build-system r-build-system)
9247 (propagated-inputs
9248 (list r-biocparallel
9249 r-chipseq
9250 r-copyhelper
9251 r-data-table
9252 r-dnacopy
9253 r-futile-logger
9254 r-genomeinfodb
9255 r-genomicalignments
9256 r-genomicranges
9257 r-gtools
9258 r-iranges
9259 r-matrixstats
9260 r-rsamtools
9261 r-s4vectors))
9262 (home-page "https://github.com/PeeperLab/CopywriteR")
9263 (synopsis "Copy number information from targeted sequencing")
9264 (description
9265 "CopywriteR extracts DNA copy number information from targeted sequencing
9266by utilizing off-target reads. It allows for extracting uniformly distributed
9267copy number information, can be used without reference, and can be applied to
9268sequencing data obtained from various techniques including chromatin
9269immunoprecipitation and target enrichment on small gene panels. Thereby,
9270CopywriteR constitutes a widely applicable alternative to available copy
9271number detection tools.")
9272 (license license:gpl2)))
9273
9274(define-public r-deseq
9275 (package
9276 (name "r-deseq")
9277 (version "1.39.0")
9278 (source
9279 (origin
9280 (method url-fetch)
9281 (uri (bioconductor-uri "DESeq" version))
9282 (sha256
9283 (base32
9284 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
9285 (properties `((upstream-name . "DESeq")))
9286 (build-system r-build-system)
9287 (propagated-inputs
9288 (list r-biobase
9289 r-biocgenerics
9290 r-genefilter
9291 r-geneplotter
9292 r-lattice
9293 r-locfit
9294 r-mass
9295 r-rcolorbrewer))
9296 (home-page "https://www-huber.embl.de/users/anders/DESeq/")
9297 (synopsis "Differential gene expression analysis")
9298 (description
9299 "This package provides tools for estimating variance-mean dependence in
9300count data from high-throughput genetic sequencing assays and for testing for
9301differential expression based on a model using the negative binomial
9302distribution.")
9303 (license license:gpl3+)))
9304
9305(define-public r-deseq2
9306 (package
9307 (name "r-deseq2")
9308 (version "1.52.0")
9309 (source
9310 (origin
9311 (method url-fetch)
9312 (uri (bioconductor-uri "DESeq2" version))
9313 (sha256
9314 (base32
9315 "112rm5i4y8k1b9d02k9aivvlmfzmzpk2q4zcdvk50qrkhs96k4cc"))))
9316 (properties
9317 '((upstream-name . "DESeq2")
9318 (updater-extra-native-inputs
9319 . ("r-apeglm" "r-ashr" "r-glmgampoi"))))
9320 (build-system r-build-system)
9321 (propagated-inputs
9322 (list r-biobase
9323 r-biocgenerics
9324 r-biocparallel
9325 r-genomicranges
9326 r-ggplot2
9327 r-iranges
9328 r-locfit
9329 r-matrixgenerics
9330 r-matrixstats
9331 r-rcpp
9332 r-rcpparmadillo
9333 r-s4vectors
9334 r-summarizedexperiment))
9335 (native-inputs
9336 (list r-apeglm
9337 r-ashr
9338 r-glmgampoi
9339 r-knitr
9340 r-readr
9341 r-rmarkdown
9342 r-testthat
9343 r-tximeta
9344 r-tximport
9345 r-tximportdata))
9346 (home-page "https://bioconductor.org/packages/DESeq2")
9347 (synopsis "Differential gene expression analysis")
9348 (description
9349 "This package provides functions to estimate variance-mean dependence in
9350count data from high-throughput nucleotide sequencing assays and test for
9351differential expression based on a model using the negative binomial
9352distribution.")
9353 (license license:lgpl3+)))
9354
9355(define-public r-dexseq
9356 (package
9357 (name "r-dexseq")
9358 (version "1.58.0")
9359 (source
9360 (origin
9361 (method url-fetch)
9362 (uri (bioconductor-uri "DEXSeq" version))
9363 (sha256
9364 (base32
9365 "1lq10na1c24s9vj1zs5zpspcwf1pc42wkyzrpb4w9z8p3fi7mnib"))))
9366 (properties `((upstream-name . "DEXSeq")))
9367 (build-system r-build-system)
9368 ;; Tests require r-pasilla, which depends on this package.
9369 (arguments (list #:tests? #false))
9370 (propagated-inputs
9371 (list r-annotationdbi
9372 r-biobase
9373 r-biocgenerics
9374 r-biocparallel
9375 r-biomart
9376 r-deseq2
9377 r-genefilter
9378 r-geneplotter
9379 r-genomicranges
9380 r-hwriter
9381 r-iranges
9382 r-rsamtools
9383 r-s4vectors
9384 r-statmod
9385 r-stringr
9386 r-summarizedexperiment))
9387 (native-inputs
9388 (list r-glmgampoi r-knitr r-testthat))
9389 (home-page "https://bioconductor.org/packages/DEXSeq")
9390 (synopsis "Inference of differential exon usage in RNA-Seq")
9391 (description
9392 "This package is focused on finding differential exon usage using RNA-seq
9393exon counts between samples with different experimental designs. It provides
9394functions that allows the user to make the necessary statistical tests based
9395on a model that uses the negative binomial distribution to estimate the
9396variance between biological replicates and generalized linear models for
9397testing. The package also provides functions for the visualization and
9398exploration of the results.")
9399 (license license:gpl3+)))
9400
9401(define-public r-diffcyt
9402 (package
9403 (name "r-diffcyt")
9404 (version "1.32.0")
9405 (source
9406 (origin
9407 (method url-fetch)
9408 (uri (bioconductor-uri "diffcyt" version))
9409 (sha256
9410 (base32 "0h9829j1x2msl01z4s182sg2wb0iwa05cfzb4dffwq6rzc6fx8id"))))
9411 (properties `((upstream-name . "diffcyt")))
9412 (build-system r-build-system)
9413 (propagated-inputs
9414 (list r-circlize
9415 r-complexheatmap
9416 r-dplyr
9417 r-edger
9418 r-flowcore
9419 r-flowsom
9420 r-limma
9421 r-lme4
9422 r-magrittr
9423 r-multcomp
9424 r-reshape2
9425 r-s4vectors
9426 r-summarizedexperiment
9427 r-tidyr))
9428 (native-inputs (list r-knitr r-testthat))
9429 (home-page "https://github.com/lmweber/diffcyt")
9430 (synopsis "Differential discovery in high-dimensional cytometry")
9431 (description
9432 "This package provides statistical methods for differential discovery
9433analyses in high-dimensional cytometry data (including flow cytometry, mass
9434cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a
9435combination of high-resolution clustering and empirical Bayes moderated tests
9436adapted from transcriptomics.")
9437 (license license:expat)))
9438
9439(define-public r-dirichletmultinomial
9440 (package
9441 (name "r-dirichletmultinomial")
9442 (version "1.54.0")
9443 (source
9444 (origin
9445 (method url-fetch)
9446 (uri (bioconductor-uri "DirichletMultinomial" version))
9447 (sha256
9448 (base32
9449 "0fhzq77lmwii9gqna7byjbgnkifi21nxhya5hvyylkm3w4s6shcb"))))
9450 (properties
9451 `((upstream-name . "DirichletMultinomial")))
9452 (build-system r-build-system)
9453 (inputs
9454 (list gsl))
9455 (propagated-inputs
9456 (list r-biocgenerics r-iranges r-s4vectors))
9457 (native-inputs (list r-knitr))
9458 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
9459 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
9460 (description
9461 "Dirichlet-multinomial mixture models can be used to describe variability
9462in microbial metagenomic data. This package is an interface to code
9463originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
94641-15.")
9465 (license license:lgpl3)))
9466
9467(define-public r-dittoseq
9468 (package
9469 (name "r-dittoseq")
9470 (version "1.24.0")
9471 (source (origin
9472 (method url-fetch)
9473 (uri (bioconductor-uri "dittoSeq" version))
9474 (sha256
9475 (base32
9476 "0kj52cz71kg0zvj4bdqsw35zmm3rbq7xa1q5cslmhcg92d4jf22w"))))
9477 (properties
9478 '((upstream-name . "dittoSeq")
9479 (updater-extra-native-inputs
9480 . ("r-complexheatmap"
9481 "r-ggplot-multistats"
9482 "r-ggrastr"))))
9483 (build-system r-build-system)
9484 (propagated-inputs
9485 (list r-colorspace
9486 r-cowplot
9487 r-ggplot2
9488 r-ggrepel
9489 r-ggridges
9490 r-gridextra
9491 r-pheatmap
9492 r-reshape2
9493 r-s4vectors
9494 r-singlecellexperiment
9495 r-summarizedexperiment))
9496 (native-inputs
9497 (list r-complexheatmap
9498 r-deseq2
9499 r-edger
9500 r-ggplot-multistats
9501 r-ggrastr
9502 r-knitr
9503 r-seurat
9504 r-testthat))
9505 (home-page "https://bioconductor.org/packages/dittoSeq")
9506 (synopsis "Single-cell and bulk RNA sequencing visualization")
9507 (description
9508 "This package provides a universal, user friendly, single-cell and bulk RNA
9509sequencing visualization toolkit that allows highly customizable creation of
9510color blindness friendly, publication-quality figures. dittoSeq accepts both
9511SingleCellExperiment (SCE) and Seurat objects, as well as the import and
9512usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data.
9513Visualizations include dimensionality reduction plots, heatmaps, scatterplots,
9514percent composition or expression across groups, and more. Customizations
9515range from size and title adjustments to automatic generation of annotations
9516for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton
9517plot, hidden data overlay upon cursor hovering via ggplotly conversion, and
9518many more. All with simple, discrete inputs. Color blindness friendliness is
9519powered by legend adjustments (enlarged keys), and by allowing the use of
9520shapes or letter-overlay in addition to the carefully selected
9521code{dittoColors()}.")
9522 (license license:expat)))
9523
9524(define-public r-edaseq
9525 (package
9526 (name "r-edaseq")
9527 (version "2.46.0")
9528 (source
9529 (origin
9530 (method url-fetch)
9531 (uri (bioconductor-uri "EDASeq" version))
9532 (sha256
9533 (base32
9534 "1h82mclrlw145fywqwv8hjqf93kczp5js07mzdr0asjhsalpjj6y"))))
9535 (properties `((upstream-name . "EDASeq")))
9536 (build-system r-build-system)
9537 (propagated-inputs
9538 (list r-annotationdbi
9539 r-aroma-light
9540 r-biobase
9541 r-biocgenerics
9542 r-biocmanager
9543 r-biomart
9544 r-biostrings
9545 r-genomicfeatures
9546 r-genomicranges
9547 r-iranges
9548 r-rsamtools
9549 r-shortread))
9550 (native-inputs
9551 (list r-knitr r-testthat))
9552 (home-page "https://github.com/drisso/EDASeq")
9553 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
9554 (description
9555 "This package provides support for numerical and graphical summaries of
9556RNA-Seq genomic read data. Provided within-lane normalization procedures to
9557adjust for GC-content effect (or other gene-level effects) on read counts:
9558loess robust local regression, global-scaling, and full-quantile
9559normalization. Between-lane normalization procedures to adjust for
9560distributional differences between lanes (e.g., sequencing depth):
9561global-scaling and full-quantile normalization.")
9562 (license license:artistic2.0)))
9563
9564(define-public r-edger
9565 (package
9566 (name "r-edger")
9567 (version "4.10.1")
9568 (source (origin
9569 (method url-fetch)
9570 (uri (bioconductor-uri "edgeR" version))
9571 (sha256
9572 (base32
9573 "0yh5w155izrzby1p4nyiwlxzzy2jha8dri6w94831kz1lvl8wgkg"))))
9574 (properties `((upstream-name . "edgeR")))
9575 (build-system r-build-system)
9576 (propagated-inputs
9577 (list r-limma r-locfit))
9578 (native-inputs (list r-knitr))
9579 (home-page "https://bioinf.wehi.edu.au/edgeR")
9580 (synopsis "EdgeR does empirical analysis of digital gene expression data")
9581 (description "This package can do differential expression analysis of
9582RNA-seq expression profiles with biological replication. It implements a range
9583of statistical methodology based on the negative binomial distributions,
9584including empirical Bayes estimation, exact tests, generalized linear models
9585and quasi-likelihood tests. It be applied to differential signal analysis of
9586other types of genomic data that produce counts, including ChIP-seq, SAGE and
9587CAGE.")
9588 (license license:gpl2+)))
9589
9590(define-public r-enhancedvolcano
9591 (package
9592 (name "r-enhancedvolcano")
9593 (version "1.30.0")
9594 (source (origin
9595 (method url-fetch)
9596 (uri (bioconductor-uri "EnhancedVolcano" version))
9597 (sha256
9598 (base32
9599 "1gzimnk4kkacb78sb3iydamp01kr2v44m9r3dqlyzh8cc6kghcfl"))))
9600 (properties `((upstream-name . "EnhancedVolcano")))
9601 (build-system r-build-system)
9602 (propagated-inputs (list r-ggplot2 r-ggrepel r-scales))
9603 (native-inputs (list r-biocgenerics r-knitr r-runit))
9604 (home-page "https://github.com/kevinblighe/EnhancedVolcano")
9605 (synopsis
9606 "Publication-ready volcano plots with enhanced coloring and labeling")
9607 (description
9608 "Volcano plots represent a useful way to visualise the results of
9609differential expression analyses. This package provides a highly-configurable
9610function that produces publication-ready volcano plots. EnhancedVolcano will
9611attempt to fit as many point labels in the plot window as possible, thus
9612avoiding clogging up the plot with labels that could not otherwise have been
9613read. Other functionality allows the user to identify up to 4 different types
9614of attributes in the same plot space via color, shape, size, and shade
9615parameter configurations.")
9616 (license license:gpl3)))
9617
9618(define-public r-enmix
9619 (package
9620 (name "r-enmix")
9621 (version "1.48.0")
9622 (source (origin
9623 (method url-fetch)
9624 (uri (bioconductor-uri "ENmix" version))
9625 (sha256
9626 (base32
9627 "1rbv95gqhklm6mjl2d2cz7dfiyvgrzbsxnwdcynyi6a5zysn2zih"))))
9628 (properties
9629 '((upstream-name . "ENmix")
9630 (updater-extra-native-inputs . ("r-minfidata"))))
9631 (build-system r-build-system)
9632 (propagated-inputs
9633 (list r-annotationhub
9634 r-biobase
9635 r-doparallel
9636 r-dynamictreecut
9637 r-experimenthub
9638 r-foreach
9639 r-genefilter
9640 r-geneplotter
9641 r-gplots
9642 r-gtools
9643 r-illuminaio
9644 r-impute
9645 r-iranges
9646 r-irlba
9647 r-matrixstats
9648 r-minfi
9649 r-quadprog
9650 r-rpmm
9651 r-s4vectors
9652 r-summarizedexperiment))
9653 (native-inputs (list r-biocgenerics r-knitr r-minfidata r-runit))
9654 (home-page "https://bioconductor.org/packages/release/bioc/html/ENmix.html")
9655 (synopsis
9656 "Quality control and analysis tools for Illumina DNA methylation BeadChip")
9657 (description
9658 "This package provides tools for quality control, analysis and
9659visualization of Illumina DNA methylation array data.")
9660 (license license:artistic2.0)))
9661
9662(define-public r-ensembldb
9663 (package
9664 (name "r-ensembldb")
9665 (version "2.36.1")
9666 (source
9667 (origin
9668 (method url-fetch)
9669 (uri (bioconductor-uri "ensembldb" version))
9670 (sha256
9671 (base32
9672 "1rzx68kk6rfjlrax8yqyasx8dw4sgwngd7w99cylxzbq9fxh5ynn"))))
9673 (properties
9674 '((updater-ignored-native-inputs
9675 ;; Avoid dependency cycle.
9676 . ("r-ensdb-hsapiens-v86"))))
9677 (build-system r-build-system)
9678 ;; The tests require r-ensdb-hsapiens-v86, which depends on
9679 ;; this package.
9680 (arguments (list #:tests? #false))
9681 (propagated-inputs
9682 (list r-annotationdbi
9683 r-annotationfilter
9684 r-biobase
9685 r-biocgenerics
9686 r-biostrings
9687 r-curl
9688 r-dbi
9689 r-genomeinfodb
9690 r-genomicfeatures
9691 r-genomicranges
9692 r-iranges
9693 r-protgenerics
9694 r-rsamtools
9695 r-rsqlite
9696 r-rtracklayer
9697 r-s4vectors
9698 r-seqinfo))
9699 (native-inputs
9700 (list r-bsgenome-hsapiens-ncbi-grch38 r-knitr
9701 r-rcurl r-testthat))
9702 (home-page "https://github.com/jotsetung/ensembldb")
9703 (synopsis "Utilities to create and use Ensembl-based annotation databases")
9704 (description
9705 "The package provides functions to create and use transcript-centric
9706annotation databases/packages. The annotation for the databases are directly
9707fetched from Ensembl using their Perl API. The functionality and data is
9708similar to that of the TxDb packages from the @code{GenomicFeatures} package,
9709but, in addition to retrieve all gene/transcript models and annotations from
9710the database, the @code{ensembldb} package also provides a filter framework
9711allowing to retrieve annotations for specific entries like genes encoded on a
9712chromosome region or transcript models of lincRNA genes.")
9713 ;; No version specified
9714 (license license:lgpl3+)))
9715
9716(define-public r-epidish
9717 (package
9718 (name "r-epidish")
9719 (version "2.28.0")
9720 (source
9721 (origin
9722 (method url-fetch)
9723 (uri (bioconductor-uri "EpiDISH" version))
9724 (sha256
9725 (base32 "18m4c28rqyh9ygkx5gy8d0r1bp19k7y2c8y2rpl3455xzhjyh0hj"))))
9726 (properties `((upstream-name . "EpiDISH")))
9727 (build-system r-build-system)
9728 (propagated-inputs (list r-e1071
9729 r-genefilter
9730 r-locfdr
9731 r-mass
9732 r-matrix
9733 r-matrixstats
9734 r-quadprog
9735 r-stringr))
9736 (native-inputs (list r-knitr r-testthat))
9737 (home-page "https://github.com/sjczheng/EpiDISH")
9738 (synopsis "Epigenetic dissection of intra-sample-heterogeneity")
9739 (description
9740 "@code{EpiDISH} is a R package to infer the proportions of a priori known
9741cell-types present in a sample representing a mixture of such cell-types.
9742Right now, the package can be used on DNAm data of whole blood, generic
9743epithelial tissue and breast tissue. Besides, the package provides a function
9744that allows the identification of differentially methylated cell-types and
9745their directionality of change in Epigenome-Wide Association Studies.")
9746 (license license:gpl2)))
9747
9748(define-public r-fastseg
9749 (package
9750 (name "r-fastseg")
9751 (version "1.58.0")
9752 (source
9753 (origin
9754 (method url-fetch)
9755 (uri (bioconductor-uri "fastseg" version))
9756 (sha256
9757 (base32
9758 "07f9hh49h6j8hirwf3rdi2gn9hc7f4jsml1bb57cc2smj4z19ggx"))))
9759 (build-system r-build-system)
9760 (propagated-inputs
9761 (list r-biobase r-biocgenerics r-genomicranges r-iranges
9762 r-s4vectors))
9763 (native-inputs (list r-knitr))
9764 (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
9765 (synopsis "Fast segmentation algorithm for genetic sequencing data")
9766 (description
9767 "Fastseg implements a very fast and efficient segmentation algorithm.
9768It can segment data from DNA microarrays and data from next generation
9769sequencing for example to detect copy number segments. Further it can segment
9770data from RNA microarrays like tiling arrays to identify transcripts. Most
9771generally, it can segment data given as a matrix or as a vector. Various data
9772formats can be used as input to fastseg like expression set objects for
9773microarrays or GRanges for sequencing data.")
9774 (license license:lgpl2.0+)))
9775
9776(define-public r-gage
9777 (package
9778 (name "r-gage")
9779 (version "2.62.0")
9780 (source
9781 (origin
9782 (method url-fetch)
9783 (uri (bioconductor-uri "gage" version))
9784 (sha256
9785 (base32
9786 "03ap9cxjc4ypdl9zgvp7pmxlz54m2ax25a6ml2f4vc2gw69sgyxp"))))
9787 (build-system r-build-system)
9788 (propagated-inputs
9789 (list r-annotationdbi r-go-db r-graph r-keggrest))
9790 (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
9791 "articles/10.1186/1471-2105-10-161"))
9792 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
9793 (description
9794 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
9795analysis. GAGE is generally applicable independent of microarray or RNA-Seq
9796data attributes including sample sizes, experimental designs, assay platforms,
9797and other types of heterogeneity. The gage package provides functions for
9798basic GAGE analysis, result processing and presentation. In addition, it
9799provides demo microarray data and commonly used gene set data based on KEGG
9800pathways and GO terms. These functions and data are also useful for gene set
9801analysis using other methods.")
9802 (license license:gpl2+)))
9803
9804(define-public r-gcptools
9805 (package
9806 (name "r-gcptools")
9807 (version "1.2.1")
9808 (source
9809 (origin
9810 (method url-fetch)
9811 (uri (bioconductor-uri "GCPtools" version))
9812 (sha256
9813 (base32 "035fii0lrzqardv3dnb68vr5gnhx21xciqnigldm8wz0a41c71wq"))))
9814 (properties `((upstream-name . "GCPtools")))
9815 (build-system r-build-system)
9816 (propagated-inputs (list r-anvilbase
9817 r-biocbaseutils
9818 r-dplyr
9819 r-httr
9820 r-rlang
9821 r-tibble
9822 r-tidyr))
9823 (native-inputs (list r-knitr r-testthat r-withr))
9824 (home-page "https://github.com/Bioconductor/GCPtools")
9825 (synopsis "Tools for working with @code{gcloud} and @code{gsutil}")
9826 (description
9827 "This package provides lower-level functionality to interface with Google
9828Cloud Platform tools. @code{gcloud} and @code{gsutil} are both supported.
9829The functionality provided centers around utilities for the @code{AnVIL}
9830platform.")
9831 (license license:artistic2.0)))
9832
9833(define-public r-genefilter
9834 (package
9835 (name "r-genefilter")
9836 (version "1.94.0")
9837 (source
9838 (origin
9839 (method url-fetch)
9840 (uri (bioconductor-uri "genefilter" version))
9841 (sha256
9842 (base32
9843 "01ifq86aj42y4c0sic9hmvvi2s1fxzc30p02rriaaz9i21bkvzlj"))))
9844 (build-system r-build-system)
9845 (native-inputs
9846 (list gfortran r-all r-biocstyle r-knitr))
9847 (propagated-inputs
9848 (list r-annotate r-annotationdbi r-biobase r-matrixgenerics
9849 r-survival))
9850 (home-page "https://bioconductor.org/packages/genefilter")
9851 (synopsis "Filter genes from high-throughput experiments")
9852 (description
9853 "This package provides basic functions for filtering genes from
9854high-throughput sequencing experiments.")
9855 (license license:artistic2.0)))
9856
9857(define-public r-geneoverlap
9858 (package
9859 (name "r-geneoverlap")
9860 (version "1.48.0")
9861 (source (origin
9862 (method url-fetch)
9863 (uri (bioconductor-uri "GeneOverlap" version))
9864 (sha256
9865 (base32
9866 "1dn2w9jygjj4n6ls1ms883695hynsv17algqrzyx48l5crznq37h"))))
9867 (properties
9868 ;; Needed for vignettes.
9869 '((updater-extra-native-inputs . ("r-biocstyle"))))
9870 (build-system r-build-system)
9871 (propagated-inputs
9872 (list r-gplots r-rcolorbrewer))
9873 (native-inputs (list r-biocgenerics r-biocstyle r-runit))
9874 (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
9875 (synopsis "Test and visualize gene overlaps")
9876 (description "This package can be used to test two sets of gene lists
9877and visualize the results.")
9878 (license license:gpl3)))
9879
9880(define-public r-genomation
9881 (package
9882 (name "r-genomation")
9883 (version "1.44.0")
9884 (source (origin
9885 (method url-fetch)
9886 (uri (bioconductor-uri "genomation" version))
9887 (sha256
9888 (base32
9889 "0pka23n8qvjnkb323xndx6n18mgl84fbpz39hp4qw65pcmg42vj4"))))
9890 (properties
9891 '((updater-extra-native-inputs . ("r-runit"))))
9892 (build-system r-build-system)
9893 (propagated-inputs
9894 (list r-biostrings
9895 r-bsgenome
9896 r-data-table
9897 r-genomicalignments
9898 r-genomicranges
9899 r-ggplot2
9900 r-gridbase
9901 r-impute
9902 r-iranges
9903 r-matrixstats
9904 r-plotrix
9905 r-plyr
9906 r-rcpp
9907 r-readr
9908 r-reshape2
9909 r-rsamtools
9910 r-rtracklayer
9911 r-s4vectors
9912 r-seqinfo
9913 r-seqpattern))
9914 (native-inputs
9915 (list r-knitr r-runit))
9916 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
9917 (synopsis "Summary, annotation and visualization of genomic data")
9918 (description
9919 "This package provides a package for summary and annotation of genomic
9920intervals. Users can visualize and quantify genomic intervals over
9921pre-defined functional regions, such as promoters, exons, introns, etc. The
9922genomic intervals represent regions with a defined chromosome position, which
9923may be associated with a score, such as aligned reads from HT-seq experiments,
9924TF binding sites, methylation scores, etc. The package can use any tabular
9925genomic feature data as long as it has minimal information on the locations of
9926genomic intervals. In addition, it can use BAM or BigWig files as input.")
9927 (license license:artistic2.0)))
9928
9929(define-public r-genomeinfodb
9930 (package
9931 (name "r-genomeinfodb")
9932 (version "1.48.0")
9933 (source (origin
9934 (method url-fetch)
9935 (uri (bioconductor-uri "GenomeInfoDb" version))
9936 (sha256
9937 (base32
9938 "10z93cvxdnwla28ncr9as8z5a0xgnacqbf0480ip4fbw5a8zd8a2"))))
9939 (properties
9940 '((upstream-name . "GenomeInfoDb")
9941 (updater-ignored-native-inputs
9942 ;; Avoid dependency cycle.
9943 . ("r-genomicranges"
9944 "r-txdb-dmelanogaster-ucsc-dm3-ensgene"))))
9945 (build-system r-build-system)
9946 ;; Tests attempt to download files.
9947 (arguments (list #:tests? #false))
9948 (propagated-inputs
9949 (list r-biocgenerics r-iranges r-s4vectors r-seqinfo r-ucsc-utils))
9950 (native-inputs (list r-biocstyle r-knitr))
9951 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
9952 (synopsis "Utilities for manipulating chromosome identifiers")
9953 (description
9954 "This package contains data and functions that define and allow
9955translation between different chromosome sequence naming conventions (e.g.,
9956\"chr1\" versus \"1\"), including a function that attempts to place sequence
9957names in their natural, rather than lexicographic, order.")
9958 (license license:artistic2.0)))
9959
9960(define-public r-genomicalignments
9961 (package
9962 (name "r-genomicalignments")
9963 (version "1.48.0")
9964 (source (origin
9965 (method url-fetch)
9966 (uri (bioconductor-uri "GenomicAlignments" version))
9967 (sha256
9968 (base32
9969 "0gjh7ka4b9v8z3zm9xjbard0yh5kg3b5vabvi1xr077gmb2ggh58"))))
9970 (properties
9971 `((upstream-name . "GenomicAlignments")
9972 (updater-extra-native-inputs . ("r-runit"))
9973 (updater-ignored-native-inputs
9974 . ("r-bsgenome-dmelanogaster-ucsc-dm3"
9975 "r-deseq2"
9976 "r-edger"
9977 "r-genomicfeatures"
9978 "r-rtracklayer"
9979 "r-txdb-dmelanogaster-ucsc-dm3-ensgene"))))
9980 (build-system r-build-system)
9981 ;; Vignettes require more packages.
9982 (arguments (list #:test-types '(list "tests")))
9983 (propagated-inputs
9984 (list r-biocgenerics
9985 r-biocparallel
9986 r-biostrings
9987 r-cigarillo
9988 r-genomicranges
9989 r-iranges
9990 r-rsamtools
9991 r-s4vectors
9992 r-seqinfo
9993 r-summarizedexperiment))
9994 (native-inputs (list r-biocmanager r-biocstyle r-knitr r-pasillabamsubset
9995 r-runit))
9996 (home-page "https://bioconductor.org/packages/GenomicAlignments")
9997 (synopsis "Representation and manipulation of short genomic alignments")
9998 (description
9999 "This package provides efficient containers for storing and manipulating
10000short genomic alignments (typically obtained by aligning short reads to a
10001reference genome). This includes read counting, computing the coverage,
10002junction detection, and working with the nucleotide content of the
10003alignments.")
10004 (license license:artistic2.0)))
10005
10006(define-public r-genomicdatacommons
10007 (package
10008 (name "r-genomicdatacommons")
10009 (version "1.36.0")
10010 (source (origin
10011 (method url-fetch)
10012 (uri (bioconductor-uri "GenomicDataCommons" version))
10013 (sha256
10014 (base32
10015 "01ckz4vf0f66bnz1rbnjvjfbfzsl22a8li27ap8xpzx6p0qagl0c"))))
10016 (properties `((upstream-name . "GenomicDataCommons")))
10017 (build-system r-build-system)
10018 (arguments
10019 (list
10020 #:skipped-tests
10021 ;; These tests attempt to download files.
10022 '(("test_clinical.R"
10023 "clinical data is structured properly")
10024 "test_api.R"
10025 "test_data.R")))
10026 (propagated-inputs (list r-dplyr
10027 r-genomicranges
10028 r-httr
10029 r-iranges
10030 r-jsonlite
10031 r-rappdirs
10032 r-readr
10033 r-rlang
10034 r-tibble
10035 r-tidyr
10036 r-xml2))
10037 (native-inputs (list r-knitr r-testthat))
10038 (home-page "https://bioconductor.org/packages/GenomicDataCommons")
10039 (synopsis "NIH/NCI genomic data commons access")
10040 (description
10041 "This package lets you programmatically access the NIH/NCI Genomic Data
10042Commons RESTful service.")
10043 (license license:artistic2.0)))
10044
10045(define-public r-genomicfeatures
10046 (package
10047 (name "r-genomicfeatures")
10048 (version "1.64.0")
10049 (source (origin
10050 (method url-fetch)
10051 (uri (bioconductor-uri "GenomicFeatures" version))
10052 (sha256
10053 (base32
10054 "19j1xps0y3391gicjh8wwgnv88v6al3hmhiv4iqlq0r2zk8k6cn3"))))
10055 (properties
10056 `((upstream-name . "GenomicFeatures")
10057 (updater-ignored-native-inputs
10058 . ("r-txdb-dmelanogaster-ucsc-dm3-ensgene"
10059 "r-txdb-hsapiens-ucsc-hg19-knowngene"
10060 ;; Avoid dependency cycle.
10061 "r-txdbmaker"))))
10062 (build-system r-build-system)
10063 ;; Test require r-txdbmaker, which depends on r-genomicfeatures.
10064 (arguments (list #:tests? #false))
10065 (propagated-inputs
10066 (list r-annotationdbi
10067 r-biocgenerics
10068 r-biostrings
10069 r-dbi
10070 r-genomicranges
10071 r-iranges
10072 r-rtracklayer
10073 r-s4vectors
10074 r-seqinfo
10075 r-xvector))
10076 (native-inputs
10077 (list r-bsgenome-dmelanogaster-ucsc-dm3
10078 r-bsgenome-hsapiens-ucsc-hg19
10079 r-genomeinfodb
10080 r-knitr
10081 r-pasillabamsubset
10082 r-rsamtools
10083 r-runit))
10084 (home-page "https://bioconductor.org/packages/GenomicFeatures")
10085 (synopsis "Tools for working with transcript centric annotations")
10086 (description
10087 "This package provides a set of tools and methods for making and
10088manipulating transcript centric annotations. With these tools the user can
10089easily download the genomic locations of the transcripts, exons and cds of a
10090given organism, from either the UCSC Genome Browser or a BioMart
10091database (more sources will be supported in the future). This information is
10092then stored in a local database that keeps track of the relationship between
10093transcripts, exons, cds and genes. Flexible methods are provided for
10094extracting the desired features in a convenient format.")
10095 (license license:artistic2.0)))
10096
10097(define-public r-genomicfiles
10098 (package
10099 (name "r-genomicfiles")
10100 (version "1.48.0")
10101 (source
10102 (origin
10103 (method url-fetch)
10104 (uri (bioconductor-uri "GenomicFiles" version))
10105 (sha256
10106 (base32
10107 "09pbr4aybs2hgfv9l4aqyag1q49qkhkgasrqaf2996m4kcfcxd1h"))))
10108 (properties `((upstream-name . "GenomicFiles")))
10109 (build-system r-build-system)
10110 (propagated-inputs
10111 (list r-biocbaseutils
10112 r-biocgenerics
10113 r-biocparallel
10114 r-genomeinfodb
10115 r-genomicalignments
10116 r-genomicranges
10117 r-iranges
10118 r-matrixgenerics
10119 r-rsamtools
10120 r-rtracklayer
10121 r-s4vectors
10122 r-seqinfo
10123 r-summarizedexperiment
10124 r-variantannotation))
10125 (native-inputs (list r-knitr r-runit))
10126 (home-page "https://bioconductor.org/packages/GenomicFiles")
10127 (synopsis "Distributed computing by file or by range")
10128 (description
10129 "This package provides infrastructure for parallel computations
10130distributed by file or by range. User defined mapper and reducer functions
10131provide added flexibility for data combination and manipulation.")
10132 (license license:artistic2.0)))
10133
10134(define-public r-genomicranges
10135 (package
10136 (name "r-genomicranges")
10137 (version "1.64.0")
10138 (source (origin
10139 (method url-fetch)
10140 (uri (bioconductor-uri "GenomicRanges" version))
10141 (sha256
10142 (base32
10143 "0xpp8hfvcri1qnlfj97adnws3agy70i0lnx3ix6gbqhbnraybzh9"))))
10144 (properties
10145 `((upstream-name . "GenomicRanges")
10146 (updater-extra-native-inputs . ("r-runit"))
10147 (updater-ignored-native-inputs
10148 . ("r-bsgenome"
10149 "r-bsgenome-hsapiens-ucsc-hg38"
10150 "r-bsgenome-mmusculus-ucsc-mm10"
10151 "r-bsgenome-scerevisiae-ucsc-saccer2"
10152 "r-deseq2"
10153 "r-edger"
10154 "r-genomicalignments"
10155 "r-genomicfeatures"
10156 "r-hgu95av2probe"
10157 "r-kegggraph"
10158 "r-keggrest"
10159 "r-pasillabamsubset"
10160 "r-rnaseqdata-hnrnpc-bam-chr14"
10161 "r-rsamtools"
10162 "r-txdb-athaliana-biomart-plantsmart22"
10163 "r-txdb-dmelanogaster-ucsc-dm3-ensgene"
10164 "r-txdb-hsapiens-ucsc-hg38-knowngene"
10165 "r-txdb-mmusculus-ucsc-mm10-knowngene"
10166 "r-txdbmaker"))))
10167 (build-system r-build-system)
10168 ;; The vignettes require more packages.
10169 (arguments (list #:test-types '(list "tests")))
10170 (propagated-inputs
10171 (list r-biocgenerics r-iranges r-s4vectors r-seqinfo))
10172 (native-inputs
10173 (list r-annotationhub
10174 r-biocstyle
10175 r-biostrings
10176 r-knitr
10177 r-runit))
10178 (home-page "https://bioconductor.org/packages/GenomicRanges")
10179 (synopsis "Representation and manipulation of genomic intervals")
10180 (description
10181 "This package provides tools to efficiently represent and manipulate
10182genomic annotations and alignments is playing a central role when it comes to
10183analyzing high-throughput sequencing data (a.k.a. NGS data). The
10184GenomicRanges package defines general purpose containers for storing and
10185manipulating genomic intervals and variables defined along a genome.")
10186 (license license:artistic2.0)))
10187
10188(define-public r-glad
10189 (package
10190 (name "r-glad")
10191 (version "2.76.0")
10192 (source (origin
10193 (method url-fetch)
10194 (uri (bioconductor-uri "GLAD" version))
10195 (sha256
10196 (base32
10197 "1s10apbd64an545a9g5pixqlp59ik8jp6157802d10c0k4mvhqvh"))))
10198 (properties `((upstream-name . "GLAD")))
10199 (build-system r-build-system)
10200 (inputs (list gsl))
10201 (propagated-inputs (list r-aws))
10202 (native-inputs (list pkg-config))
10203 (home-page "http://bioinfo.curie.fr")
10204 (synopsis "Gain and loss analysis of DNA")
10205 (description
10206 "This package helps with the analysis of array @acronym{CGH, comparative
10207genomic hybridization} data by detecting of the breakpoints in the genomic
10208profiles and assignment of a status (gain, normal or loss) to each chromosomal
10209regions identified.")
10210 (license license:gpl2)))
10211
10212(define-public r-globalancova
10213 (package
10214 (name "r-globalancova")
10215 (version "4.30.0")
10216 (source (origin
10217 (method url-fetch)
10218 (uri (bioconductor-uri "GlobalAncova" version))
10219 (sha256
10220 (base32
10221 "0nm41kmkp569dms07hxv7j8n1gf2zgi0127x31m2xmjcldbmlblv"))))
10222 (properties `((upstream-name . "GlobalAncova")))
10223 (build-system r-build-system)
10224 (propagated-inputs (list r-annotate
10225 r-annotationdbi
10226 r-biobase
10227 r-corpcor
10228 r-dendextend
10229 r-globaltest
10230 r-gseabase
10231 r-vgam))
10232 (home-page "https://bioconductor.org/packages/GlobalAncova")
10233 (synopsis "Global test for groups of variables via model comparisons")
10234 (description
10235 "This package supports the computation of an F-test for the association
10236between expression values and clinical entities. In many cases a two way
10237layout with gene and a dichotomous group as factors will be considered.
10238However, adjustment for other covariates and the analysis of arbitrary
10239clinical variables, interactions, gene co-expression, time series data and so
10240on is also possible. The test is carried out by comparison of corresponding
10241linear models via the extra sum of squares principle.")
10242 (license license:gpl2+)))
10243
10244(define-public r-globaltest
10245 (package
10246 (name "r-globaltest")
10247 (version "5.66.0")
10248 (source (origin
10249 (method url-fetch)
10250 (uri (bioconductor-uri "globaltest" version))
10251 (sha256
10252 (base32
10253 "11cgwn2r855kjvw5f9xzmy7axi7923disbv0c8zh86nhxdlb4xy7"))))
10254 (properties `((upstream-name . "globaltest")))
10255 (build-system r-build-system)
10256 (propagated-inputs
10257 (list r-annotate r-annotationdbi r-biobase r-survival))
10258 (home-page "https://bioconductor.org/packages/globaltest")
10259 (synopsis
10260 "Test groups of covariates for association with a response variable")
10261 (description
10262 "The global test tests groups of covariates (or features) for association
10263with a response variable. This package implements the test with diagnostic
10264plots and multiple testing utilities, along with several functions to
10265facilitate the use of this test for gene set testing of GO and KEGG terms.")
10266 (license license:gpl2+)))
10267
10268(define-public r-gostats
10269 (package
10270 (name "r-gostats")
10271 (version "2.78.0")
10272 (source
10273 (origin
10274 (method url-fetch)
10275 (uri (bioconductor-uri "GOstats" version))
10276 (sha256
10277 (base32
10278 "0hqbdz9si4zq906s93h9z0b7nifgwzgiymf906vswj1sazay199i"))))
10279 (properties `((upstream-name . "GOstats")))
10280 (build-system r-build-system)
10281 (propagated-inputs
10282 (list r-annotate
10283 r-annotationdbi
10284 r-annotationforge
10285 r-biobase
10286 r-category
10287 r-go-db
10288 r-graph
10289 r-rbgl
10290 r-rgraphviz))
10291 (native-inputs (list r-biocgenerics r-hgu95av2-db r-knitr r-runit))
10292 (home-page "https://bioconductor.org/packages/GOstats")
10293 (synopsis "Tools for manipulating GO and microarrays")
10294 (description
10295 "This package provides a set of tools for interacting with GO and
10296microarray data. A variety of basic manipulation tools for graphs, hypothesis
10297testing and other simple calculations.")
10298 (license license:artistic2.0)))
10299
10300(define-public r-gseabase
10301 (package
10302 (name "r-gseabase")
10303 (version "1.74.0")
10304 (source
10305 (origin
10306 (method url-fetch)
10307 (uri (bioconductor-uri "GSEABase" version))
10308 (sha256
10309 (base32
10310 "0hm76h0k5rvz1vla7qwgy1fk25vj04r9593kjslx56gzylxx42hy"))))
10311 (properties
10312 '((upstream-name . "GSEABase")
10313 (updater-extra-native-inputs
10314 . ("r-go-db" "r-hgu95av2" "r-hgu95av2-db"))))
10315 (build-system r-build-system)
10316 (propagated-inputs
10317 (list r-annotate
10318 r-annotationdbi
10319 r-biobase
10320 r-biocgenerics
10321 r-graph
10322 r-xml))
10323 (native-inputs
10324 (list r-go-db
10325 r-hgu95av2
10326 r-hgu95av2-db
10327 r-knitr
10328 r-org-hs-eg-db
10329 r-runit))
10330 (home-page "https://bioconductor.org/packages/GSEABase")
10331 (synopsis "Gene set enrichment data structures and methods")
10332 (description
10333 "This package provides classes and methods to support @dfn{Gene Set
10334Enrichment Analysis} (GSEA).")
10335 (license license:artistic2.0)))
10336
10337(define-public r-gsva
10338 (package
10339 (name "r-gsva")
10340 (version "2.6.2")
10341 (source (origin
10342 (method url-fetch)
10343 (uri (bioconductor-uri "GSVA" version))
10344 (sha256
10345 (base32
10346 "0k86y25ab5h0mflhh7z69v5y8qbskml1mswcbmwqdj1bpcx1qg8k"))))
10347 (properties `((upstream-name . "GSVA")))
10348 (build-system r-build-system)
10349 (arguments
10350 (list
10351 #:test-directory "inst/unitTests"
10352 #:skipped-tests
10353 ;; These all fail with: "no method for coercing this S4 class to a vector"
10354 '("test_genesets.R"
10355 "test_gsvaRanks.R"
10356 "test_inputdatacontainers.R"
10357 "test_ranksserialization.R"
10358 "test_spatial.R")))
10359 (propagated-inputs (list r-biobase
10360 r-biocgenerics
10361 r-biocparallel
10362 r-biocsingular
10363 r-cli
10364 r-delayedarray
10365 r-delayedmatrixstats
10366 r-gseabase
10367 r-hdf5array
10368 r-iranges
10369 r-matrix
10370 r-matrixgenerics
10371 r-memuse
10372 r-s4arrays
10373 r-s4vectors
10374 r-singlecellexperiment
10375 r-sparsearray
10376 r-sparsematrixstats
10377 r-spatialexperiment
10378 r-summarizedexperiment))
10379 (native-inputs (list r-gsvadata r-knitr r-runit))
10380 (home-page "https://github.com/rcastelo/GSVA")
10381 (synopsis "Gene Set Variation Analysis for microarray and RNA-seq data")
10382 (description
10383 "Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised
10384method for estimating variation of gene set enrichment through the samples of
10385a expression data set. GSVA performs a change in coordinate systems,
10386transforming the data from a gene by sample matrix to a gene-set by sample
10387matrix, thereby allowing the evaluation of pathway enrichment for each sample.
10388This new matrix of GSVA enrichment scores facilitates applying standard
10389analytical methods like functional enrichment, survival analysis, clustering,
10390CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric
10391manner.")
10392 (license license:gpl2+)))
10393
10394(define-public r-gypsum
10395 (package
10396 (name "r-gypsum")
10397 (version "1.8.0")
10398 (source
10399 (origin
10400 (method url-fetch)
10401 (uri (bioconductor-uri "gypsum" version))
10402 (sha256
10403 (base32 "00zz8n0rcb09qxgz0iac2jcw1rvmb11m4iq4aivkalf39amqn1ba"))))
10404 (properties `((upstream-name . "gypsum")))
10405 (build-system r-build-system)
10406 ;; Some tests need internet access.
10407 (arguments (list #:tests? #false))
10408 (propagated-inputs (list r-filelock r-httr2 r-jsonlite r-rappdirs))
10409 (native-inputs (list r-dbi r-digest r-knitr r-rsqlite r-testthat))
10410 (home-page "https://github.com/ArtifactDB/gypsum-R")
10411 (synopsis "Interface to the gypsum REST API")
10412 (description
10413 "This package provides a client for the gypsum REST
10414API (https://gypsum.artifactdb.com), a cloud-based file store in the
10415@code{ArtifactDB} ecosystem. This package provides functions for uploads,
10416downloads, and various administrative and management tasks. Check out the
10417documentation at @url{https://github.com/ArtifactDB/gypsum-worker} for more
10418details.")
10419 (license license:expat)))
10420
10421;; This is a CRAN package, but it depends on r-genomicranges from
10422;; Bioconductor.
10423(define-public r-hahmmr
10424 (package
10425 (name "r-hahmmr")
10426 (version "1.0.0")
10427 (source
10428 (origin
10429 (method url-fetch)
10430 (uri (cran-uri "hahmmr" version))
10431 (sha256
10432 (base32 "19bds84pkimr71dy1365b71k7ihn7x86yalgcmagvkxgygpg3409"))))
10433 (properties `((upstream-name . "hahmmr")))
10434 (build-system r-build-system)
10435 (propagated-inputs (list r-data-table
10436 r-dplyr
10437 r-genomicranges
10438 r-ggplot2
10439 r-glue
10440 r-iranges
10441 r-patchwork
10442 r-rcpp
10443 r-rcpparmadillo
10444 r-roptim
10445 r-stringr
10446 r-tibble
10447 r-zoo))
10448 (native-inputs (list r-testthat))
10449 (home-page "https://cran.r-project.org/package=hahmmr")
10450 (synopsis "Haplotype-aware Hidden Markov Model for RNA")
10451 (description
10452 "Haplotype-aware Hidden Markov Model for RNA (@code{HaHMMR}) is a method
10453for detecting copy number variations (CNVs) from bulk RNA-seq data.
10454Additional examples, documentations, and details on the method are available
10455at @url{https://github.com/kharchenkolab/hahmmr/}.")
10456 (license license:expat)))
10457
10458(define-public r-harshlight
10459 (package
10460 (name "r-harshlight")
10461 (version "1.79.0")
10462 (source (origin
10463 (method url-fetch)
10464 (uri (bioconductor-uri "Harshlight" version))
10465 (sha256
10466 (base32
10467 "1jm0ia06ls1m7dsbzp1hk68qi5wbqzhcf6x66534bj1kxdll17k7"))))
10468 (properties `((upstream-name . "Harshlight")))
10469 (build-system r-build-system)
10470 (arguments
10471 (list
10472 #:phases
10473 #~(modify-phases %standard-phases
10474 (add-before 'install 'relax-c-standard
10475 (lambda _
10476 ;; XXX FIXME: $HOME/.R/Makevars seems to be the only way to
10477 ;; set custom CFLAGS for R?
10478 (setenv "HOME" (getcwd))
10479 (mkdir-p ".R")
10480 (with-directory-excursion ".R"
10481 (with-output-to-file "Makevars"
10482 (lambda _
10483 (display (string-append
10484 "CFLAGS=-g -O2"
10485 " -std=gnu11"))))))))))
10486 (propagated-inputs
10487 (list r-affy
10488 r-altcdfenvs
10489 r-biobase))
10490 (home-page "http://asterion.rockefeller.edu/Harshlight/")
10491 (synopsis "Corrective make-up program for microarray chips")
10492 (description
10493 "The package detects extended diffuse and compact blemishes on microarray
10494chips. Harshlight marks the areas in a collection of chips (affybatch
10495objects). A corrected @code{AffyBatch} object will result. The package
10496replaces the defected areas with @code{N/A}s or the median of the values of
10497the same probe. The new version handles the substitute value as a whole
10498matrix to solve the memory problem.")
10499 (license license:gpl2+)))
10500
10501(define-public r-hpar
10502 (package
10503 (name "r-hpar")
10504 (version "1.54.0")
10505 (source
10506 (origin
10507 (method url-fetch)
10508 (uri (bioconductor-uri "hpar" version))
10509 (sha256
10510 (base32
10511 "04jq9j7w720dsbgh3slp33i4jz6672gx4wipnp67kqlah5i1p8zh"))))
10512 (build-system r-build-system)
10513 (arguments
10514 (list
10515 #:phases
10516 '(modify-phases %standard-phases
10517 (add-after 'unpack 'set-HOME
10518 (lambda _
10519 (setenv "HOME" "/tmp")))
10520 (add-after 'unpack 'avoid-internet-access
10521 (lambda _
10522 (setenv "GUIX_BUILD" "yes")
10523 (substitute* "R/zzz.R"
10524 (("ExperimentHub::createHubAccessors.*" m)
10525 (string-append
10526 "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m "}"))))))))
10527 (propagated-inputs (list r-experimenthub))
10528 (native-inputs
10529 (list r-knitr r-testthat))
10530 (home-page "https://bioconductor.org/packages/hpar/")
10531 (synopsis "Human Protein Atlas in R")
10532 (description "This package provides a simple interface to and data from
10533the Human Protein Atlas project.")
10534 (license license:artistic2.0)))
10535
10536(define-public r-r3cseq
10537 (package
10538 (name "r-r3cseq")
10539 (version "1.58.0")
10540 (source
10541 (origin
10542 (method url-fetch)
10543 (uri (bioconductor-uri "r3Cseq" version))
10544 (sha256
10545 (base32 "1jw08rhd3bs4fpxsi44wn7dayjj9a58jawfi35bjch8sfnly9qqy"))))
10546 (properties `((upstream-name . "r3Cseq")))
10547 (build-system r-build-system)
10548 (propagated-inputs
10549 (list r-biostrings
10550 r-data-table
10551 r-genomicranges
10552 r-iranges
10553 r-qvalue
10554 r-rcolorbrewer
10555 r-rsamtools
10556 r-rtracklayer
10557 r-seqinfo
10558 r-sqldf
10559 r-vgam))
10560 (home-page "http://r3cseq.genereg.net/Site/index.html")
10561 (synopsis
10562 "Analysis of Chromosome conformation capture and Next-generation sequencing")
10563 (description
10564 "This package is used for the analysis of long-range chromatin
10565interactions from 3C-seq assay.")
10566 (license license:gpl3)))
10567
10568(define-public r-r4rna
10569 (package
10570 (name "r-r4rna")
10571 (version "1.40.0")
10572 (source
10573 (origin
10574 (method url-fetch)
10575 (uri (bioconductor-uri "R4RNA" version))
10576 (sha256
10577 (base32 "1ib5bjhgpyi6pf7j1qy97ic94jh79pn83frx8kb39kjw1k0d0n0k"))))
10578 (properties `((upstream-name . "R4RNA")))
10579 (build-system r-build-system)
10580 (propagated-inputs (list r-biostrings))
10581 (home-page "https://www.e-rna.org/r-chie/")
10582 (synopsis "RNA visualization and analysis")
10583 (description
10584 "This package provides a package for RNA basepair analysis, including the
10585visualization of basepairs as arc diagrams for easy comparison and annotation of
10586sequence and structure. Arc diagrams can additionally be projected onto
10587multiple sequence alignments to assess basepair conservation and covariation,
10588with numerical methods for computing statistics for each.")
10589 (license license:gpl3)))
10590
10591(define-public r-radiogx
10592 (package
10593 (name "r-radiogx")
10594 (version "2.16.0")
10595 (source
10596 (origin
10597 (method url-fetch)
10598 (uri (bioconductor-uri "RadioGx" version))
10599 (sha256
10600 (base32 "126sb87ws14qr8a5lzzbxwb5bmlbcx1ka8g5hxclgxjyqyad7zi5"))))
10601 (properties `((upstream-name . "RadioGx")))
10602 (build-system r-build-system)
10603 (propagated-inputs
10604 (list r-assertthat
10605 r-biobase
10606 r-biocgenerics
10607 r-biocparallel
10608 r-catools
10609 r-coregx
10610 r-data-table
10611 r-downloader
10612 r-magicaxis
10613 r-matrixstats
10614 r-rcolorbrewer
10615 r-reshape2
10616 r-s4vectors
10617 r-scales
10618 r-summarizedexperiment))
10619 (native-inputs (list r-knitr))
10620 (home-page "https://bioconductor.org/packages/RadioGx")
10621 (synopsis "Analysis of large-scale radio-genomic data")
10622 (description
10623 "This package is a computational tool box for radio-genomic analysis
10624which integrates radio-response data, radio-biological modelling and
10625comprehensive cell line annotations for hundreds of cancer cell lines. The
10626@code{RadioSet} class enables creation and manipulation of standardized
10627datasets including information about cancer cells lines, radio-response assays
10628and dose-response indicators. Included methods allow fitting and plotting
10629dose-response data using established radio-biological models along with
10630quality control to validate results. Additional functions related to fitting
10631and plotting dose response curves, quantifying statistical correlation and
10632calculating @acronym{AUC, area under the curve} or @acronym{SF, survival
10633fraction} are included.")
10634 (license license:gpl3)))
10635
10636(define-public r-raggedexperiment
10637 (package
10638 (name "r-raggedexperiment")
10639 (version "1.36.0")
10640 (source (origin
10641 (method url-fetch)
10642 (uri (bioconductor-uri "RaggedExperiment" version))
10643 (sha256
10644 (base32
10645 "1hh48rq7vmj24bs0gdfdjby74bq7g6l4sx4hnjy8353cx3drymaw"))))
10646 (properties `((upstream-name . "RaggedExperiment")))
10647 (build-system r-build-system)
10648 (propagated-inputs (list r-biocbaseutils
10649 r-biocgenerics
10650 r-genomicranges
10651 r-iranges
10652 r-matrix
10653 r-matrixgenerics
10654 r-s4vectors
10655 r-seqinfo
10656 r-summarizedexperiment))
10657 (native-inputs (list r-knitr r-testthat))
10658 (home-page "https://bioconductor.org/packages/RaggedExperiment")
10659 (synopsis "Representation of sparse experiments and assays across samples")
10660 (description
10661 "This package provides a flexible representation of copy number,
10662mutation, and other data that fit into the ragged array schema for genomic
10663location data. The basic representation of such data provides a rectangular
10664flat table interface to the user with range information in the rows and
10665samples/specimen in the columns. The @code{RaggedExperiment} class derives
10666from a @code{GRangesList} representation and provides a semblance of a
10667rectangular dataset.")
10668 (license license:artistic2.0)))
10669
10670(define-public r-rarr
10671 (package
10672 (name "r-rarr")
10673 (version "2.0.1")
10674 (source
10675 (origin
10676 (method url-fetch)
10677 (uri (bioconductor-uri "Rarr" version))
10678 (sha256
10679 (base32 "1m8sgy7pfqpyf5ipjdzc1zgxsnz9k5jzxvhawk84csyz9azgy2wf"))))
10680 (properties `((upstream-name . "Rarr")))
10681 (build-system r-build-system)
10682 (arguments
10683 (list
10684 #:skipped-tests
10685 ;; This test needs Internet access.
10686 '(("test-attributes.R" "read_zarr_attributes from s3"))))
10687 (inputs (list c-blosc zlib (list zstd "lib")))
10688 (propagated-inputs (list r-curl r-jsonlite r-lifecycle r-paws-storage
10689 r-r-utils))
10690 (native-inputs (list r-knitr r-testthat r-withr))
10691 (home-page "https://huber-group-embl.github.io/Rarr/")
10692 (synopsis "Read Zarr files in R")
10693 (description
10694 "The Zarr specification defines a format for chunked, compressed,
10695N-dimensional arrays. Its design allows efficient access to subsets of the
10696stored array, and supports both local and cloud storage systems. Rarr aims to
10697implement this specification in R with minimal reliance on external tools or
10698libraries.")
10699 (license license:expat)))
10700
10701(define-public r-rdisop
10702 (package
10703 (name "r-rdisop")
10704 (version "1.72.0")
10705 (source (origin
10706 (method url-fetch)
10707 (uri (bioconductor-uri "Rdisop" version))
10708 (sha256
10709 (base32
10710 "1v4limw5i69ivyzxxplpn9m8sndlhscqgzf1zrhyx4srh4j3f631"))))
10711 (properties `((upstream-name . "Rdisop")))
10712 (build-system r-build-system)
10713 (propagated-inputs (list r-rcpp))
10714 (native-inputs (list r-knitr r-testthat))
10715 (home-page "https://github.com/sneumann/Rdisop")
10716 (synopsis "Decomposition of isotopic patterns")
10717 (description
10718 "This is a package for identification of metabolites using high precision
10719mass spectrometry. MS peaks are used to derive a ranked list of sum formulae,
10720alternatively for a given sum formula the theoretical isotope distribution can
10721be calculated to search in MS peak lists.")
10722 (license license:gpl2)))
10723
10724(define-public r-rhtslib
10725 (package
10726 (name "r-rhtslib")
10727 (version "3.8.0")
10728 (source
10729 (origin
10730 (method url-fetch)
10731 (uri (bioconductor-uri "Rhtslib" version))
10732 (sha256
10733 (base32
10734 "1vgdn71npxhqinc3g8xr4ggqrqi6kkimq2cak0pdq2jqmjxm74g8"))))
10735 (properties `((upstream-name . "Rhtslib")))
10736 (build-system r-build-system)
10737 ;; Without this a temporary directory ends up in the Rhtslib.so binary,
10738 ;; which makes R abort the build.
10739 (arguments '(#:configure-flags '("--no-staged-install")))
10740 (propagated-inputs
10741 (list curl zlib ; packages using rhtslib need to link with zlib
10742 r-zlibbioc))
10743 (native-inputs
10744 (list pkg-config r-knitr))
10745 (home-page "https://github.com/nhayden/Rhtslib")
10746 (synopsis "High-throughput sequencing library as an R package")
10747 (description
10748 "This package provides the HTSlib C library for high-throughput
10749nucleotide sequence analysis. The package is primarily useful to developers
10750of other R packages who wish to make use of HTSlib.")
10751 (license license:lgpl2.0+)))
10752
10753(define-public r-rliger
10754 (package
10755 (name "r-rliger")
10756 (version "2.2.1")
10757 (source
10758 (origin
10759 (method git-fetch)
10760 (uri (git-reference
10761 (url "https://github.com/welch-lab/liger")
10762 (commit (string-append "v" version))))
10763 (file-name (git-file-name name version))
10764 (sha256
10765 (base32 "1w849km9b347m56qwr5lr6ymdk7wv22hr224riscm0zrnx402yb3"))))
10766 (properties `((upstream-name . "rliger")))
10767 (build-system r-build-system)
10768 (propagated-inputs (list r-cli
10769 r-delayedarray
10770 r-dplyr
10771 r-ggplot2
10772 r-hdf5array
10773 r-hdf5r
10774 r-leidenalg
10775 r-lifecycle
10776 r-magrittr
10777 r-matrix
10778 r-patchwork
10779 r-rann
10780 r-rcpp
10781 r-rcpparmadillo
10782 r-rcppplanc
10783 r-rcppprogress
10784 r-rlang
10785 r-s4vectors
10786 r-scales
10787 r-uwot))
10788 (native-inputs
10789 (list r-circlize r-complexheatmap r-cowplot r-knitr r-testthat r-viridis))
10790 (home-page "https://github.com/welch-lab/liger")
10791 (synopsis "Linked inference of genomic experimental relationships")
10792 (description
10793 "LIGER is a package for integrating and analyzing multiple single-cell
10794datasets. It relies on integrative non-negative matrix factorization to
10795identify shared and dataset-specific factors.")
10796 (license license:gpl3)))
10797
10798(define-public r-rnbeads
10799 (package
10800 (name "r-rnbeads")
10801 (version "2.30.0")
10802 (source
10803 (origin
10804 (method url-fetch)
10805 (uri (bioconductor-uri "RnBeads" version))
10806 (sha256
10807 (base32 "0alcapsh99z7h81i71c4mlschkkckig59pgg6awkxv5z4zbl674r"))
10808 (modules '((guix build utils)))
10809 (snippet
10810 '(delete-file-recursively "inst/bin"))))
10811 (properties
10812 `((upstream-name . "RnBeads")
10813 (updater-extra-inputs . ("kentutils"))
10814 (updater-extra-native-inputs
10815 . ("r-impute" "r-missmethyl" "r-doparallel" "r-qvalue" "ghostscript"))))
10816 (build-system r-build-system)
10817 (arguments
10818 (list
10819 ;; Vignette ‘RnBeads.Rnw’ overwrites the following ‘tangle’ output by
10820 ;; vignette ‘RnBeads_Annotations.Rnw’: RnBeads_Annotations.R
10821 #:test-types '(list "tests")
10822 #:phases
10823 #~(modify-phases %standard-phases
10824 (add-after 'install 'link-to-executables
10825 (lambda* (#:key inputs #:allow-other-keys)
10826 (let ((bin (string-append #$output
10827 "/site-library/RnBeads/bin/linux_x86.64")))
10828 (mkdir-p bin)
10829 (symlink (search-input-file inputs "/bin/bedToBigBed")
10830 (string-append bin "/bedToBigBed"))
10831 (symlink (search-input-file inputs "/bin/bedGraphToBigWig")
10832 (string-append bin "/bedGraphToBigWig"))))))))
10833 (propagated-inputs
10834 (list r-biocgenerics
10835 r-cluster
10836 r-ff
10837 r-fields
10838 r-genomicranges
10839 r-ggplot2
10840 r-gplots
10841 r-gridextra
10842 r-illuminaio
10843 r-iranges
10844 r-limma
10845 r-mass
10846 r-matrixstats
10847 r-methylumi
10848 r-plyr
10849 r-reshape2
10850 r-s4vectors))
10851 (inputs (list kentutils))
10852 (native-inputs
10853 (list ghostscript
10854 r-biocmanager
10855 r-doparallel
10856 r-impute
10857 r-missmethyl
10858 r-qvalue
10859 r-rnbeads-hg19
10860 r-rtracklayer
10861 r-runit))
10862 (home-page "https://bioconductor.org/packages/RnBeads")
10863 (synopsis "RnBeads")
10864 (description
10865 "@code{RnBeads} facilitates comprehensive analysis of various types of
10866DNA methylation data at the genome scale.")
10867 (license license:gpl3)))
10868
10869(define-public r-rpx
10870 (package
10871 (name "r-rpx")
10872 (version "2.20.0")
10873 (source
10874 (origin
10875 (method url-fetch)
10876 (uri (bioconductor-uri "rpx" version))
10877 (sha256
10878 (base32 "1p3a2dz65ykkk23iwjl2f7g57cbi05fw0sk8p0mqxrzavw1agv57"))))
10879 (properties `((upstream-name . "rpx")))
10880 (build-system r-build-system)
10881 ;; Tests require Internet access.
10882 (arguments (list #:tests? #false))
10883 (propagated-inputs (list r-biocfilecache r-curl r-jsonlite r-rcurl r-xml2))
10884 (native-inputs (list r-biostrings r-knitr r-testthat r-tibble))
10885 (home-page "https://github.com/lgatto/rpx")
10886 (synopsis "R interface to the ProteomeXchange Repository")
10887 (description
10888 "The rpx package implements an interface to proteomics data submitted to
10889the @code{ProteomeXchange} consortium.")
10890 (license license:gpl2)))
10891
10892(define-public r-impute
10893 (package
10894 (name "r-impute")
10895 (version "1.86.0")
10896 (source (origin
10897 (method url-fetch)
10898 (uri (bioconductor-uri "impute" version))
10899 (sha256
10900 (base32
10901 "0k1xyi5j13qnyjpfs77m6cr3kv3fpj63gml90p27gyjpwpxz5a8n"))))
10902 (native-inputs
10903 (list gfortran))
10904 (build-system r-build-system)
10905 (home-page "https://bioconductor.org/packages/impute")
10906 (synopsis "Imputation for microarray data")
10907 (description
10908 "This package provides a function to impute missing gene expression
10909microarray data, using nearest neighbor averaging.")
10910 (license license:gpl2+)))
10911
10912;; This is a CRAN package, but it depends on r-impute, a Bioconductor package.
10913(define-public r-imputelcmd
10914 (package
10915 (name "r-imputelcmd")
10916 (version "2.1")
10917 (source
10918 (origin
10919 (method url-fetch)
10920 (uri (cran-uri "imputeLCMD" version))
10921 (sha256
10922 (base32 "0w6wn9b74phiz9f58b6p95fymgrrlh94avhas046ngzaax6ay71n"))))
10923 (properties `((upstream-name . "imputeLCMD")))
10924 (build-system r-build-system)
10925 (propagated-inputs (list r-impute r-norm r-pcamethods r-tmvtnorm))
10926 (home-page "https://cran.r-project.org/package=imputeLCMD")
10927 (synopsis
10928 "Collection of methods for left-censored missing data imputation")
10929 (description
10930 "This package provides a collection of functions for left-censored
10931missing data imputation. Left-censoring is a special case of missing not at
10932random (MNAR) mechanism that generates non-responses in proteomics
10933experiments. The package also contains functions to artificially generate
10934peptide/protein expression data (log-transformed) as random draws from a
10935multivariate Gaussian distribution as well as a function to generate missing
10936data (both randomly and non-randomly). For comparison reasons, the package
10937also contains several wrapper functions for the imputation of non-responses
10938that are missing at random.")
10939 (license license:gpl2+)))
10940
10941(define-public r-interactivedisplay
10942 (package
10943 (name "r-interactivedisplay")
10944 (version "1.48.0")
10945 (source (origin
10946 (method url-fetch)
10947 (uri (bioconductor-uri "interactiveDisplay" version))
10948 (sha256
10949 (base32
10950 "02amr55nk6jx059a0shrwpnzkgcdfsr2x8k975j7x9y0nwsj6l94"))
10951 (snippet
10952 '(for-each delete-file
10953 '("inst/www/js/d3.v2.js"
10954 "inst/www/js/jquery.js"
10955 "inst/www/js/jquery.min.js"
10956 "inst/www/js/jquery.dataTables.min.js"
10957 "inst/www/js/jquery.dataTables.nightly.js")))))
10958 (properties
10959 '((upstream-name . "interactiveDisplay")
10960 (updater-extra-propagated-inputs . ("r-biocmanager"))))
10961 (build-system r-build-system)
10962 (arguments
10963 (list
10964 #:modules
10965 '((guix build r-build-system)
10966 (guix build minify-build-system)
10967 (guix build utils)
10968 (ice-9 match))
10969 #:imported-modules
10970 `(,@%r-build-system-modules
10971 (guix build minify-build-system))
10972 #:phases
10973 #~(modify-phases (@ (guix build r-build-system) %standard-phases)
10974 (add-after 'unpack 'process-javascript
10975 (lambda* (#:key inputs #:allow-other-keys)
10976 (with-directory-excursion "inst/"
10977 (for-each (match-lambda
10978 ((source . target)
10979 (minify source #:target target)))
10980 `((,(assoc-ref inputs "js-jquery-1.8.2")
10981 . "www/js/jquery.js")
10982 (,(assoc-ref inputs "js-jquery-1.9.1")
10983 . "www/js/jquery.min.js")
10984 (,(search-input-file inputs
10985 "/share/javascript/jquery.dataTables.min.js")
10986 . "www/js/jquery.dataTables.min.js")
10987 (,(string-append (assoc-ref inputs "js-datatables-1.9")
10988 "/share/javascript/jquery.dataTables.min.js")
10989 . "www/js/jquery.dataTables.min.js")
10990 (,(string-append (assoc-ref inputs "js-datatables-1.10")
10991 "/share/javascript/jquery.dataTables.min.js")
10992 . "www/js/jquery.dataTables.nightly.js")
10993 (,(assoc-ref inputs "js-d3-v2")
10994 . "www/js/d3.v2.js")))))))))
10995 (propagated-inputs
10996 (list r-annotationdbi
10997 r-biocgenerics
10998 r-biocmanager ;this is not listed in DESCRIPTION
10999 r-category
11000 r-ggplot2
11001 r-gridsvg
11002 r-interactivedisplaybase
11003 r-plyr
11004 r-rcolorbrewer
11005 r-reshape2
11006 r-shiny
11007 r-xml))
11008 (native-inputs
11009 `(("esbuild" ,esbuild)
11010 ("r-knitr" ,r-knitr)
11011 ;; D3 version 2.10.3
11012 ("js-d3-v2"
11013 ,(origin
11014 (method url-fetch)
11015 (uri "https://web.archive.org/web/20230428092426id_/https://d3js.org/d3.v2.js")
11016 (sha256
11017 (base32
11018 "1m57mxhcynfaz6gz3v0aph5i6hx5jf455jdygyl8yzs9r2dpp5vr"))))
11019 ;; Version 1.9.4 is bundled
11020 ("js-datatables-1.9" ,js-datatables-1.9)
11021 ;; Version 1.10.0 is bundled
11022 ("js-datatables-1.10" ,js-datatables)
11023 ("js-jquery-1.8.2"
11024 ,(origin
11025 (method url-fetch)
11026 (uri "https://code.jquery.com/jquery-1.8.2.js")
11027 (sha256
11028 (base32
11029 "0nikk2clbnyi02k0brvhbd8m43lfh4l1zrya35jya9sy6wb9b9ng"))))
11030 ("js-jquery-1.9.1"
11031 ,(origin
11032 (method url-fetch)
11033 (uri "https://code.jquery.com/jquery-1.9.1.js")
11034 (sha256
11035 (base32
11036 "0h4dk67yc9d0kadqxb6b33585f3x3559p6qmp70l00qwq030vn3v"))))))
11037 (home-page "https://bioconductor.org/packages/interactiveDisplay")
11038 (synopsis "Package for Shiny web displays of Bioconductor objects")
11039 (description
11040 "This package offers interactive Shiny displays for Bioconductor
11041objects. In addition, this package empowers users to develop engaging
11042visualizations and interfaces for working with Bioconductor data.")
11043 (license license:artistic2.0)))
11044
11045(define-public r-interactivedisplaybase
11046 (package
11047 (name "r-interactivedisplaybase")
11048 (version "1.48.0")
11049 (source
11050 (origin
11051 (method url-fetch)
11052 (uri (bioconductor-uri "interactiveDisplayBase" version))
11053 (sha256
11054 (base32
11055 "0slmb7cd9sn0146r1ad0cnaiihh7vh22fx41w7zdnq8c5nykkhad"))))
11056 (properties
11057 `((upstream-name . "interactiveDisplayBase")))
11058 (build-system r-build-system)
11059 (propagated-inputs
11060 (list r-biocgenerics r-dt r-shiny))
11061 (native-inputs
11062 (list r-knitr))
11063 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
11064 (synopsis "Base package for web displays of Bioconductor objects")
11065 (description
11066 "This package contains the basic methods needed to generate interactive
11067Shiny-based display methods for Bioconductor objects.")
11068 (license license:artistic2.0)))
11069
11070(define-public r-keggrest
11071 (package
11072 (name "r-keggrest")
11073 (version "1.52.0")
11074 (source
11075 (origin
11076 (method url-fetch)
11077 (uri (bioconductor-uri "KEGGREST" version))
11078 (sha256
11079 (base32
11080 "1z9xp4pkpqcyadbrzam7qxqcrrqy29pn926n3nqni6cpypbv7jj4"))))
11081 (properties `((upstream-name . "KEGGREST")))
11082 (build-system r-build-system)
11083 ;; Tests contact the internet.
11084 (arguments (list #:tests? #false))
11085 (propagated-inputs
11086 (list r-biostrings r-httr r-png))
11087 (native-inputs
11088 (list r-biocgenerics r-knitr r-runit))
11089 (home-page "https://bioconductor.org/packages/KEGGREST")
11090 (synopsis "Client-side REST access to KEGG")
11091 (description
11092 "This package provides a package that provides a client interface to the
11093@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
11094 (license license:artistic2.0)))
11095
11096(define-public r-lea
11097 (package
11098 (name "r-lea")
11099 (version "3.24.0")
11100 (source (origin
11101 (method url-fetch)
11102 (uri (bioconductor-uri "LEA" version))
11103 (sha256
11104 (base32
11105 "0xvvf86za1q0ljw2n4mpjq8wpby0mbdh1npmb7famhdnqd0476aa"))))
11106 (properties `((upstream-name . "LEA")))
11107 (build-system r-build-system)
11108 (native-inputs (list r-knitr))
11109 (home-page "http://membres-timc.imag.fr/Olivier.Francois/LEA/index.htm")
11110 (synopsis
11111 "R package for landscape and ecological association studies")
11112 (description
11113 "LEA is an R package dedicated to population genomics, landscape genomics
11114and genotype-environment association tests. LEA can run analyses of
11115population structure and genome-wide tests for local adaptation, and also
11116performs imputation of missing genotypes. The package includes statistical
11117methods for estimating ancestry coefficients from large genotypic matrices and
11118for evaluating the number of ancestral populations (snmf). It performs
11119statistical tests using latent factor mixed models for identifying genetic
11120polymorphisms that exhibit association with environmental gradients or
11121phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset
11122statistics based on new or predicted environments (@code{genetic.gap},
11123@code{genetic.offset}). LEA is mainly based on optimized programs that can
11124scale with the dimensions of large data sets.")
11125 (license license:gpl3)))
11126
11127(define-public r-lfa
11128 (package
11129 (name "r-lfa")
11130 (version "2.12.0")
11131 (source
11132 (origin
11133 (method url-fetch)
11134 (uri (bioconductor-uri "lfa" version))
11135 (sha256
11136 (base32 "0sfyphvadhf3w741sjdxy4m94mkax6qv5xqfzw2wcljjqjp3f70i"))))
11137 (properties
11138 '((upstream-name . "lfa")
11139 (updater-ignored-native-inputs . ("r-genio"))))
11140 (build-system r-build-system)
11141 (propagated-inputs (list r-bedmatrix r-corpcor r-genio r-rspectra))
11142 (native-inputs (list r-knitr r-testthat))
11143 (home-page "https://github.com/StoreyLab/lfa")
11144 (synopsis "Logistic Factor Analysis for categorical data")
11145 (description
11146 "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on
11147Binomial data via estimation of latent structure in the natural parameter.")
11148 (license license:gpl3)))
11149
11150(define-public r-limma
11151 (package
11152 (name "r-limma")
11153 (version "3.68.4")
11154 (source (origin
11155 (method url-fetch)
11156 (uri (bioconductor-uri "limma" version))
11157 (sha256
11158 (base32
11159 "0452k5p1v01qjzk6jlip6ix871dfyn0prvxjxpjxdnjl4zbkrz3v"))))
11160 (properties
11161 '((updater-extra-native-inputs
11162 . ("r-go-db" "r-locfit" "r-mass" "r-org-hs-eg-db"))))
11163 (build-system r-build-system)
11164 (native-inputs
11165 (list r-go-db r-knitr r-locfit r-mass r-org-hs-eg-db))
11166 (propagated-inputs (list r-statmod))
11167 (home-page "https://bioinf.wehi.edu.au/limma")
11168 (synopsis "Package for linear models for microarray and RNA-seq data")
11169 (description "This package can be used for the analysis of gene expression
11170studies, especially the use of linear models for analysing designed experiments
11171and the assessment of differential expression. The analysis methods apply to
11172different technologies, including microarrays, RNA-seq, and quantitative PCR.")
11173 (license license:gpl2+)))
11174
11175(define-public r-maaslin2
11176 (package
11177 (name "r-maaslin2")
11178 (version "1.26.0")
11179 (source
11180 (origin
11181 (method url-fetch)
11182 (uri (bioconductor-uri "Maaslin2" version))
11183 (sha256
11184 (base32 "1fbibcajdcm4n9hdl0kv4wr70mv6nkh7s33sszckhnxlfrxd3sfg"))))
11185 (properties `((upstream-name . "Maaslin2")))
11186 (build-system r-build-system)
11187 (propagated-inputs
11188 (list r-biglm
11189 r-car
11190 r-chemometrics
11191 r-cplm
11192 r-data-table
11193 r-dplyr
11194 r-edger
11195 r-ggplot2
11196 r-glmmtmb
11197 r-hash
11198 r-lme4
11199 r-lmertest
11200 r-logging
11201 r-mass
11202 r-metagenomeseq
11203 r-optparse
11204 r-pbapply
11205 r-pcapp
11206 r-pheatmap
11207 r-pscl
11208 r-robustbase
11209 r-tibble
11210 r-vegan))
11211 (native-inputs (list r-knitr r-testthat))
11212 (home-page "http://huttenhower.sph.harvard.edu/maaslin2")
11213 (synopsis
11214 "Multivariable association discovery in population-scale meta-omics studies")
11215 (description
11216 "MaAsLin2 is comprehensive R package for efficiently determining multivariable
11217association between clinical metadata and microbial meta'omic features. This
11218package relies on general linear models to accommodate most modern epidemiological
11219study designs, including cross-sectional and longitudinal, and offers a variety
11220of data exploration, normalization, and transformation methods.")
11221 (license license:expat)))
11222
11223(define-public r-maaslin3
11224 (package
11225 (name "r-maaslin3")
11226 (version "1.4.0")
11227 (source
11228 (origin
11229 (method url-fetch)
11230 (uri (bioconductor-uri "maaslin3" version))
11231 (sha256
11232 (base32 "1k4ifhc1y0cm1b2frv56ya7i3vz0kq8085d4p02p08znkxg4vjw6"))))
11233 (properties `((upstream-name . "maaslin3")))
11234 (build-system r-build-system)
11235 (propagated-inputs (list r-biocgenerics
11236 r-collapse
11237 r-data-table
11238 r-ggnewscale
11239 r-ggplot2
11240 r-lme4
11241 r-lmertest
11242 r-logging
11243 r-mirai
11244 r-multcomp
11245 r-optparse
11246 r-patchwork
11247 r-rcolorbrewer
11248 r-reformulas
11249 r-rlang
11250 r-scales
11251 r-survival))
11252 (native-inputs (list r-dplyr r-knitr r-plyr r-summarizedexperiment
11253 r-testthat))
11254 (home-page "http://huttenhower.sph.harvard.edu/maaslin3")
11255 (synopsis
11256 "Refine multivariate linear models for meta-omic association discovery")
11257 (description
11258 "@code{MaAsLin} 3 refines and extends generalized multivariate linear
11259models for meta-omicron association discovery. It finds abundance and
11260prevalence associations between microbiome meta-omics features and complex
11261metadata in population-scale epidemiological studies. The software includes
11262multiple analysis methods (including support for multiple covariates, repeated
11263measures, and ordered predictors), filtering, normalization, and transform
11264options to customize analysis for your specific study.")
11265 (license license:expat)))
11266
11267(define-public r-made4
11268 (package
11269 (name "r-made4")
11270 (version "1.86.0")
11271 (source (origin
11272 (method url-fetch)
11273 (uri (bioconductor-uri "made4" version))
11274 (sha256
11275 (base32
11276 "14x7f3j0d0wif59pmyfnd97zdnfy2hh11189ls7b1y2qyz5mxmh2"))))
11277 (properties `((upstream-name . "made4")))
11278 (build-system r-build-system)
11279 (propagated-inputs
11280 (list r-ade4
11281 r-biobase
11282 r-gplots
11283 r-rcolorbrewer
11284 r-scatterplot3d
11285 r-summarizedexperiment))
11286 (native-inputs (list r-knitr))
11287 (home-page "http://www.hsph.harvard.edu/aedin-culhane/")
11288 (synopsis "Multivariate analysis of microarray data using ADE4")
11289 (description
11290 "This is a package for multivariate data analysis and graphical display
11291of microarray data. Functions are included for supervised dimension
11292reduction (between group analysis) and joint dimension reduction of two
11293datasets (coinertia analysis).")
11294 (license license:artistic2.0)))
11295
11296(define-public r-makecdfenv
11297 (package
11298 (name "r-makecdfenv")
11299 (version "1.88.0")
11300 (source (origin
11301 (method url-fetch)
11302 (uri (bioconductor-uri "makecdfenv" version))
11303 (sha256
11304 (base32
11305 "14ydf4qj5k6x1jd4zxjh9221l1vxvkv2d1f6kxjq017j0dgahrnh"))))
11306 (properties `((upstream-name . "makecdfenv")))
11307 (build-system r-build-system)
11308 (inputs (list zlib))
11309 (propagated-inputs
11310 (list r-affy r-affyio r-biobase))
11311 (home-page "https://bioconductor.org/packages/makecdfenv")
11312 (synopsis "Chip description file environment maker")
11313 (description
11314 "This package implements two functions. One of them reads an Affymetrix
11315@acronym{CDF, chip description file} and creates a hash table environment
11316containing the location/probe set membership mapping. The other one creates a
11317package that automatically loads that environment.")
11318 (license license:gpl2+)))
11319
11320(define-public r-manor
11321 (package
11322 (name "r-manor")
11323 (version "1.84.0")
11324 (source
11325 (origin
11326 (method url-fetch)
11327 (uri (bioconductor-uri "MANOR" version))
11328 (sha256
11329 (base32 "09wfzvz8k2rhw3y4kp4af3phdazvvxbirhcidwkq5dpggj1rgr7z"))))
11330 (properties `((upstream-name . "MANOR")))
11331 (build-system r-build-system)
11332 (propagated-inputs (list r-glad))
11333 (native-inputs (list r-knitr))
11334 (home-page "http://bioinfo.curie.fr/projects/manor/index.html")
11335 (synopsis "CGH micro-array normalization")
11336 (description
11337 "This package ofers functions for importation, normalization,
11338visualization, and quality control to correct identified sources of
11339variability in array of @acronym{CGH, comparative genomic hybridization}
11340experiments.")
11341 (license license:gpl2)))
11342
11343(define-public r-maser
11344 (package
11345 (name "r-maser")
11346 (version "1.30.0")
11347 (source (origin
11348 (method url-fetch)
11349 (uri (bioconductor-uri "maser" version))
11350 (sha256
11351 (base32
11352 "08k4x9h6lxx79d6fvq3g5frnybb2l6fi2jig15a4z150rx2dfi8s"))))
11353 (properties `((upstream-name . "maser")))
11354 (build-system r-build-system)
11355 (propagated-inputs
11356 (list r-biocgenerics
11357 r-data-table
11358 r-dplyr
11359 r-dt
11360 r-genomicranges
11361 r-ggplot2
11362 r-gviz
11363 r-iranges
11364 r-reshape2
11365 r-rtracklayer
11366 r-seqinfo))
11367 (native-inputs (list r-knitr))
11368 (home-page "https://github.com/DiogoVeiga/maser")
11369 (synopsis "Mapping alternative splicing events to proteins")
11370 (description
11371 "This package provides functionalities for downstream analysis, annotation
11372and visualizaton of alternative splicing events generated by rMATS.")
11373 (license license:expat)))
11374
11375(define-public r-mdqc
11376 (package
11377 (name "r-mdqc")
11378 (version "1.74.0")
11379 (source
11380 (origin
11381 (method url-fetch)
11382 (uri (bioconductor-uri "mdqc" version))
11383 (sha256
11384 (base32 "1p0p9pg863fac2snyp45sbgphdckjjpb5zjj6vq0jjys1g7sp318"))))
11385 (properties `((upstream-name . "mdqc")))
11386 (build-system r-build-system)
11387 (propagated-inputs
11388 (list r-cluster
11389 r-mass))
11390 (home-page "https://bioconductor.org/packages/mdqc")
11391 (synopsis "Mahalanobis distance quality control for microarrays")
11392 (description
11393 "MDQC is a multivariate quality assessment method for microarrays based
11394on quality control (QC) reports. The Mahalanobis distance of an array's
11395quality attributes is used to measure the similarity of the quality of that
11396array against the quality of the other arrays. Then, arrays with unusually
11397high distances can be flagged as potentially low-quality.")
11398 (license license:lgpl2.0+)))
11399
11400(define-public r-metabocoreutils
11401 (package
11402 (name "r-metabocoreutils")
11403 (version "1.20.1")
11404 (source
11405 (origin
11406 (method url-fetch)
11407 (uri (bioconductor-uri "MetaboCoreUtils" version))
11408 (sha256
11409 (base32 "0cr619mn4xiz26cdy4ald4lyfvrbmp9kz56pwpjyl6ww6l8apr10"))))
11410 (properties
11411 '((upstream-name . "MetaboCoreUtils")
11412 (updater-extra-native-inputs . ("r-robustbase"))
11413 ;; Avoid dependency cycle.
11414 (updater-ignored-native-inputs . ("r-spectra"))))
11415 (build-system r-build-system)
11416 (propagated-inputs (list r-biocparallel r-mscoreutils))
11417 (native-inputs (list r-callr r-knitr r-microbenchmark r-robustbase
11418 r-testthat))
11419 (home-page "https://github.com/RforMassSpectrometry/MetaboCoreUtils")
11420 (synopsis "Core utils for Metabolomics data")
11421 (description
11422 "@code{MetaboCoreUtils} defines metabolomics-related core functionality
11423provided as low-level functions to allow a data structure-independent usage
11424across various R packages. This includes functions to calculate between
11425ion (adduct) and compound mass-to-charge ratios and masses or functions to
11426work with chemical formulas. The package provides also a set of adduct
11427definitions and information on some commercially available internal standard
11428mixes commonly used in MS experiments.")
11429 (license license:artistic2.0)))
11430
11431(define-public r-metagenomeseq
11432 (package
11433 (name "r-metagenomeseq")
11434 (version "1.54.0")
11435 (source
11436 (origin
11437 (method url-fetch)
11438 (uri (bioconductor-uri "metagenomeSeq" version))
11439 (sha256
11440 (base32 "0wbr5kp0m5diihra2q2mzxhcsadigbdjqnaqb1bfa24crpjqi51y"))))
11441 (properties `((upstream-name . "metagenomeSeq")))
11442 (build-system r-build-system)
11443 (propagated-inputs
11444 (list r-biobase
11445 r-foreach
11446 r-glmnet
11447 r-gplots
11448 r-limma
11449 r-matrix
11450 r-matrixstats
11451 r-rcolorbrewer
11452 r-wrench))
11453 (native-inputs (list r-annotate r-biomformat r-gss r-knitr r-testthat))
11454 (home-page "https://github.com/HCBravoLab/metagenomeSeq")
11455 (synopsis "Statistical analysis for sparse high-throughput sequencing")
11456 (description
11457 "MetagenomeSeq is designed to determine features (be it @acronym{OTU,
11458Operational Taxanomic Unit}, species, etc.) that are differentially abundant
11459between two or more groups of multiple samples. This package is designed to
11460address the effects of both normalization and under-sampling of microbial
11461communities on disease association detection and the testing of feature
11462correlations.")
11463 (license license:artistic2.0)))
11464
11465(define-public r-metaneighbor
11466 (package
11467 (name "r-metaneighbor")
11468 (version "1.29.0")
11469 (source (origin
11470 (method url-fetch)
11471 (uri (bioconductor-uri "MetaNeighbor" version))
11472 (sha256
11473 (base32
11474 "0fvsnwwpvwbdcq7lgbb2jq9n6scr33ip3s3z14v6nxm7zmf6i5bn"))))
11475 (properties `((upstream-name . "MetaNeighbor")))
11476 (build-system r-build-system)
11477 (propagated-inputs
11478 (list r-beanplot
11479 r-dplyr
11480 r-ggplot2
11481 r-gplots
11482 r-igraph
11483 r-matrix
11484 r-matrixstats
11485 r-rcolorbrewer
11486 r-singlecellexperiment
11487 r-summarizedexperiment
11488 r-tibble
11489 r-tidyr))
11490 (native-inputs (list r-knitr r-testthat))
11491 (home-page "https://bioconductor.org/packages/MetaNeighbor")
11492 (synopsis "Single cell replicability analysis")
11493 (description
11494 "This package implements a method to rapidly assess cell type identity using
11495both functional and random gene sets and it allows users to quantify cell type
11496replicability across datasets using neighbor voting. @code{MetaNeighbor} works
11497on the basis that cells of the same type should have more similar gene expression
11498profiles than cells of different types.")
11499 (license license:expat)))
11500
11501(define-public r-methylaid
11502 (package
11503 (name "r-methylaid")
11504 (version "1.46.0")
11505 (source
11506 (origin
11507 (method url-fetch)
11508 (uri (bioconductor-uri "MethylAid" version))
11509 (sha256
11510 (base32 "1d87j2ijhwdbbz0iz5xi91p40cfmkarh699wh77b1y7j7irhjjy5"))))
11511 (properties
11512 `((upstream-name . "MethylAid")
11513 (updater-ignored-native-inputs . ("r-methylaiddata"))))
11514 (build-system r-build-system)
11515 (propagated-inputs
11516 (list r-biobase
11517 r-biocgenerics
11518 r-biocparallel
11519 r-ggplot2
11520 r-gridbase
11521 r-hexbin
11522 r-matrixstats
11523 r-minfi
11524 r-rcolorbrewer
11525 r-shiny
11526 r-summarizedexperiment))
11527 (native-inputs (list r-biocstyle
11528 r-geoquery
11529 r-knitr
11530 r-minfidata
11531 r-minfidataepic
11532 r-runit))
11533 (home-page "https://git.bioconductor.org/packages/MethylAid")
11534 (synopsis
11535 "Quality control of large Illumina DNA Methylation array data sets")
11536 (description
11537 "This package provides a visual and interactive web application using
11538RStudio's shiny package. Bad quality samples are detected using sample-dependent
11539and sample-independent controls present on the array and user adjustable
11540thresholds. In depth exploration of bad quality samples can be performed using
11541several interactive diagnostic plots of the quality control probes present on
11542the array. Furthermore, the impact of any batch effect provided by the user can
11543be explored.")
11544 (license license:gpl2+)))
11545
11546(define-public r-methylkit
11547 (package
11548 (name "r-methylkit")
11549 (version "1.38.0")
11550 (source (origin
11551 (method url-fetch)
11552 (uri (bioconductor-uri "methylKit" version))
11553 (sha256
11554 (base32
11555 "0ki6zybnwigk7gppc7495phzlg9pixmp79hyg1kfrrskykyr1280"))))
11556 (properties `((upstream-name . "methylKit")))
11557 (build-system r-build-system)
11558 (propagated-inputs
11559 (list r-data-table
11560 r-emdbook
11561 r-fastseg
11562 r-genomicranges
11563 r-gtools
11564 r-iranges
11565 r-kernsmooth
11566 r-limma
11567 r-mclust
11568 r-mgcv
11569 r-qvalue
11570 r-r-utils
11571 r-rcpp
11572 r-rhtslib
11573 r-rsamtools
11574 r-rtracklayer
11575 r-s4vectors
11576 r-seqinfo))
11577 (native-inputs
11578 (list r-knitr r-testthat)) ; for vignettes
11579 (home-page "https://github.com/al2na/methylKit")
11580 (synopsis
11581 "DNA methylation analysis from high-throughput bisulfite sequencing results")
11582 (description
11583 "MethylKit is an R package for DNA methylation analysis and annotation
11584from high-throughput bisulfite sequencing. The package is designed to deal
11585with sequencing data from @dfn{Reduced representation bisulfite
11586sequencing} (RRBS) and its variants, but also target-capture methods and whole
11587genome bisulfite sequencing. It also has functions to analyze base-pair
11588resolution 5hmC data from experimental protocols such as oxBS-Seq and
11589TAB-Seq.")
11590 (license license:artistic2.0)))
11591
11592(define-public r-mfuzz
11593 (package
11594 (name "r-mfuzz")
11595 (version "2.72.0")
11596 (source (origin
11597 (method url-fetch)
11598 (uri (bioconductor-uri "Mfuzz" version))
11599 (sha256
11600 (base32
11601 "11xs6cprfpmk3zwffpc2q5yfb063fvdy1ck51qkxh28pr9gv5ysv"))))
11602 (properties `((upstream-name . "Mfuzz")))
11603 (build-system r-build-system)
11604 (propagated-inputs (list r-biobase r-e1071 r-tkwidgets))
11605 (home-page "http://mfuzz.sysbiolab.eu/")
11606 (synopsis "Soft clustering of time series gene expression data")
11607 (description
11608 "This is a package for noise-robust soft clustering of gene expression
11609time-series data (including a graphical user interface).")
11610 (license license:gpl2)))
11611
11612(define-public r-mmuphin
11613 (package
11614 (name "r-mmuphin")
11615 (version "2.0.0")
11616 (source
11617 (origin
11618 (method url-fetch)
11619 (uri (bioconductor-uri "MMUPHin" version))
11620 (sha256
11621 (base32 "038phah1pdz2n323mpq1mga6bfh1im2cxyllr1pbj9bdjyw3858j"))
11622 ;; Delete generated files.
11623 (snippet
11624 '(for-each delete-file
11625 '("inst/doc/MMUPHin.R"
11626 "inst/doc/MMUPHin.html")))))
11627 (properties `((upstream-name . "MMUPHin")))
11628 (build-system r-build-system)
11629 (arguments
11630 (list
11631 #:phases
11632 #~(modify-phases %standard-phases
11633 (add-after 'unpack 'fix-includes
11634 (lambda _
11635 (substitute* "inst/doc/MMUPHin.Rmd"
11636 (("\\.\\./man/figures")
11637 (string-append (getcwd) "/man/figures"))
11638 (("bibliography: references.bib")
11639 (string-append "bibliography: "
11640 (getcwd) "/vignettes/references.bib")))))
11641 ;; Maaslin2 generates log files with timestamps. We don't need to
11642 ;; keep them. The generated PDF files also contain timestamps, so
11643 ;; we replace them with arbitrary fixed timestamps.
11644 (add-after 'check 'make-reproducible
11645 (lambda _
11646 (for-each delete-file
11647 (find-files #$output "maaslin2.log"))
11648 (with-fluids ((%default-port-encoding "ISO-8859-1"))
11649 (substitute* (find-files #$output "\\.pdf$")
11650 (("/CreationDate \\(D:.*\\)")
11651 "/CreationDate (D:20230301143558)")
11652 (("/ModDate \\(D:.*\\)")
11653 "/ModDate (D:20230301143558)"))))))))
11654 ;; The DESCRIPTION file says that glpk is needed, but this package does
11655 ;; not seem to reference the library directly.
11656 (propagated-inputs
11657 (list r-cowplot
11658 r-dplyr
11659 r-fpc
11660 r-ggplot2
11661 r-igraph
11662 r-maaslin3
11663 r-metafor
11664 r-stringr
11665 r-tidyr))
11666 (native-inputs (list r-knitr r-testthat))
11667 (home-page "https://bioconductor.org/packages/MMUPHin")
11668 (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome")
11669 (description
11670 "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts.
11671It has function interfaces for:
11672@itemize
11673@item covariate-controlled batch- and cohort effect adjustment;
11674@item meta-analysis differential abundance testing;
11675@item meta-analysis unsupervised discrete structure (clustering) discovery;
11676@item meta-analysis unsupervised continuous structure discovery.
11677@end itemize")
11678 (license license:expat)))
11679
11680(define-public r-modstrings
11681 (package
11682 (name "r-modstrings")
11683 (version "1.28.0")
11684 (source
11685 (origin
11686 (method url-fetch)
11687 (uri (bioconductor-uri "Modstrings" version))
11688 (sha256
11689 (base32 "0qxglvznsqb64h253xn6nq9dbk1xfigbyfx7skvpw2yygybbi24l"))))
11690 (properties `((upstream-name . "Modstrings")))
11691 (build-system r-build-system)
11692 (propagated-inputs (list r-biocgenerics
11693 r-biostrings
11694 r-crayon
11695 r-genomicranges
11696 r-iranges
11697 r-s4vectors
11698 r-stringi
11699 r-stringr
11700 r-xvector))
11701 (native-inputs (list r-knitr r-testthat))
11702 (home-page "https://bioconductor.org/packages/Modstrings")
11703 (synopsis "Working with modified nucleotide sequences")
11704 (description
11705 "Representing nucleotide modifications in a nucleotide sequence is
11706usually done via special characters from a number of sources. This represents
11707a challenge to work with in R and the Biostrings package. The Modstrings
11708package implements this functionality for RNA and DNA sequences containing
11709modified nucleotides by translating the character internally in order to work
11710with the infrastructure of the Biostrings package. For this the
11711@code{ModRNAString} and @code{ModDNAString} classes and derivates and
11712functions to construct and modify these objects despite the encoding issues
11713are implemenented. In addition the conversion from sequences to list like
11714location information (and the reverse operation) is implemented as well.")
11715 (license license:artistic2.0)))
11716
11717(define-public r-mosdef
11718 (package
11719 (name "r-mosdef")
11720 (version "1.8.0")
11721 (source
11722 (origin
11723 (method url-fetch)
11724 (uri (bioconductor-uri "mosdef" version))
11725 (sha256
11726 (base32 "08bvbxfh4mxkxbm2gn3bafbxsdn9d1sckykgcqkgk15a5l7gr63z"))))
11727 (properties
11728 `((upstream-name . "mosdef")
11729 ;; Avoid dependency cycle.
11730 (updater-ignored-native-inputs . ("r-pcaexplorer"))))
11731 (build-system r-build-system)
11732 (arguments
11733 (list
11734 #:skipped-tests
11735 '(("test-check_inputs.R"
11736 ;; Genome length information unavailable.
11737 "res_de and de_container are related"))))
11738 (propagated-inputs (list r-annotationdbi
11739 r-clusterprofiler
11740 r-deseq2
11741 r-dt
11742 r-ggforce
11743 r-ggplot2
11744 r-ggrepel
11745 r-go-db
11746 r-goseq
11747 r-htmltools
11748 r-rcolorbrewer
11749 r-rlang
11750 r-s4vectors
11751 r-scales
11752 r-summarizedexperiment
11753 r-topgo))
11754 (native-inputs (list r-knitr r-macrophage r-org-hs-eg-db r-testthat))
11755 (home-page "https://github.com/imbeimainz/mosdef")
11756 (synopsis "Frequently used and useful differential expression functions")
11757 (description
11758 "This package provides functionality to run a number of tasks in the
11759differential expression analysis workflow. This encompasses the most widely
11760used steps, from running various enrichment analysis tools with a unified
11761interface to creating plots and beautifying table components linking to
11762external websites and databases. This streamlines the generation of
11763comprehensive analysis reports.")
11764 (license license:expat)))
11765
11766(define-public r-motifrg
11767 (package
11768 (name "r-motifrg")
11769 (version "1.31.0")
11770 (source
11771 (origin
11772 (method url-fetch)
11773 (uri (bioconductor-uri "motifRG" version))
11774 (sha256
11775 (base32
11776 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
11777 (properties `((upstream-name . "motifRG")))
11778 (build-system r-build-system)
11779 (propagated-inputs
11780 (list r-biostrings
11781 r-bsgenome
11782 r-bsgenome-hsapiens-ucsc-hg19
11783 r-iranges
11784 r-seqlogo
11785 r-xvector))
11786 (home-page "https://bioconductor.org/packages/motifRG")
11787 (synopsis "Discover motifs in high throughput sequencing data")
11788 (description
11789 "This package provides tools for discriminative motif discovery in high
11790throughput genetic sequencing data sets using regression methods.")
11791 (license license:artistic2.0)))
11792
11793(define-public r-muscat
11794 (package
11795 (name "r-muscat")
11796 (version "1.26.0")
11797 (source
11798 (origin
11799 (method url-fetch)
11800 (uri (bioconductor-uri "muscat" version))
11801 (sha256
11802 (base32
11803 "1k34hs05l4x36ycr2cwyb4rw0s9y9rmga9z7sxggbzhl89sqyaar"))))
11804 (properties `((upstream-name . "muscat")))
11805 (build-system r-build-system)
11806 (propagated-inputs
11807 (list r-biocparallel
11808 r-blme
11809 r-complexheatmap
11810 r-dplyr
11811 r-edger
11812 r-ggplot2
11813 r-glmmtmb
11814 r-limma
11815 r-lme4
11816 r-lmertest
11817 r-matrix
11818 r-matrixgenerics
11819 r-matrixstats
11820 r-progress
11821 r-rlang
11822 r-s4vectors
11823 r-scales
11824 r-scater
11825 r-scuttle
11826 r-singlecellexperiment
11827 r-summarizedexperiment
11828 r-variancepartition))
11829 (native-inputs (list r-deseq2 r-knitr r-sctransform r-testthat))
11830 (home-page "https://github.com/HelenaLC/muscat")
11831 (synopsis "Multi-sample multi-group scRNA-seq data analysis tools")
11832 (description
11833 "This package @code{muscat} provides various methods and visualization tools
11834for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group,
11835multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and
11836methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation
11837platform that mimics both single and multi-sample scRNA-seq data.")
11838 (license license:gpl3)))
11839
11840(define-public r-mutationalpatterns
11841 (package
11842 (name "r-mutationalpatterns")
11843 (version "3.22.0")
11844 (source
11845 (origin
11846 (method url-fetch)
11847 (uri (bioconductor-uri "MutationalPatterns" version))
11848 (sha256
11849 (base32
11850 "02js36k18gnqsrx41lmxnxsmrqkw28iv9ibymx58ydrviwa5l4dy"))))
11851 (properties
11852 '((updater-extra-native-inputs . ("r-ccfindr"))))
11853 (build-system r-build-system)
11854 (native-inputs
11855 (list r-ccfindr
11856 r-knitr
11857 r-rtracklayer
11858 r-testthat
11859 r-txdb-hsapiens-ucsc-hg19-knowngene))
11860 (propagated-inputs
11861 (list r-biocgenerics
11862 r-biostrings
11863 r-bsgenome
11864 r-cowplot
11865 r-dplyr
11866 r-genomeinfodb
11867 r-genomicranges
11868 r-ggalluvial
11869 r-ggdendro
11870 r-ggplot2
11871 r-iranges
11872 r-magrittr
11873 r-nmf
11874 r-pracma
11875 r-purrr
11876 r-rcolorbrewer
11877 r-s4vectors
11878 r-seqinfo
11879 r-stringr
11880 r-tibble
11881 r-tidyr
11882 r-variantannotation
11883
11884 ;; These two packages are suggested packages
11885 r-bsgenome-hsapiens-ucsc-hg19
11886 r-txdb-hsapiens-ucsc-hg19-knowngene))
11887 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
11888 (synopsis "Extract and visualize mutational patterns in genomic data")
11889 (description "This package provides an extensive toolset for the
11890characterization and visualization of a wide range of mutational patterns
11891in SNV base substitution data.")
11892 (license license:expat)))
11893
11894(define-public r-msa
11895 (package
11896 (name "r-msa")
11897 (version "1.44.0")
11898 (source (origin
11899 (method url-fetch)
11900 (uri (bioconductor-uri "msa" version))
11901 (sha256
11902 (base32
11903 "0w1kl3p3skf3y7p99qvpmlfqqq197cf0chwazjm5nfbk72cj55kh"))))
11904 (properties `((upstream-name . "msa")))
11905 (build-system r-build-system)
11906 (propagated-inputs
11907 (list r-biocgenerics
11908 r-biostrings
11909 r-iranges
11910 r-rcpp
11911 r-s4vectors))
11912 (native-inputs (list r-ape r-biocmanager r-knitr r-pwalign r-seqinr))
11913 (home-page "http://www.bioinf.jku.at/software/msa/")
11914 (synopsis "Multiple sequence alignment")
11915 (description
11916 "The msa package provides a unified R/Bioconductor interface to the
11917multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle.
11918All three algorithms are integrated in the package, therefore, they do not
11919depend on any external software tools and are available for all major
11920platforms. The multiple sequence alignment algorithms are complemented by a
11921function for pretty-printing multiple sequence alignments using the LaTeX
11922package TeXshade.")
11923 (license license:gpl2+)))
11924
11925(define-public r-msbackendsql
11926 (package
11927 (name "r-msbackendsql")
11928 (version "1.12.0")
11929 (source
11930 (origin
11931 (method url-fetch)
11932 (uri (bioconductor-uri "MsBackendSql" version))
11933 (sha256
11934 (base32 "0sfpr9fma1h7mhilag9zn0z3iinzhplrvzmm0glf0d24vfqkx37v"))))
11935 (properties
11936 '((upstream-name . "MsBackendSql")
11937 (updater-extra-native-inputs . ("r-mzr"))))
11938 (build-system r-build-system)
11939 ;; Thanks to r-msdatahub tests require Internet access.
11940 (arguments (list #:tests? #false))
11941 (propagated-inputs (list r-biocgenerics
11942 r-biocparallel
11943 r-data-table
11944 r-dbi
11945 r-fastmatch
11946 r-iranges
11947 r-mscoreutils
11948 r-progress
11949 r-protgenerics
11950 r-s4vectors
11951 r-spectra
11952 r-stringi))
11953 (native-inputs (list r-knitr r-msdatahub r-mzr r-rsqlite r-testthat))
11954 (home-page "https://github.com/RforMassSpectrometry/MsBackendSql")
11955 (synopsis "SQL-based mass spectrometry data backend")
11956 (description
11957 "This package provides an SQL-based mass spectrometry (MS) data backend
11958supporting also storage and handling of very large data sets. Objects from
11959this package are supposed to be used with the Spectra Bioconductor package.
11960Through the @code{MsBackendSql} with its minimal memory footprint, this
11961package thus provides an alternative MS data representation for very large or
11962remote MS data sets.")
11963 (license license:artistic2.0)))
11964
11965(define-public r-msdatahub
11966 (package
11967 (name "r-msdatahub")
11968 (version "1.12.0")
11969 (source
11970 (origin
11971 (method url-fetch)
11972 (uri (bioconductor-uri "MsDataHub" version))
11973 (sha256
11974 (base32 "06qpfnrn4fizh51c9nahd1bf5z7jinxdyqj3lwla9ry2cd3w2qw8"))))
11975 (properties `((upstream-name . "MsDataHub")))
11976 (build-system r-build-system)
11977 (arguments
11978 (list
11979 #:phases '(modify-phases %standard-phases
11980 (add-after 'unpack 'set-HOME
11981 (lambda _
11982 (setenv "HOME" "/tmp"))))))
11983 (propagated-inputs (list r-experimenthub))
11984 (native-inputs (list r-knitr r-testthat))
11985 (home-page "https://rformassspectrometry.github.io/MsDataHub")
11986 (synopsis "Mass spectrometry data on ExperimentHub")
11987 (description
11988 "The @code{MsDataHub} package uses the @code{ExperimentHub}
11989infrastructure to distribute raw mass spectrometry data files, peptide
11990spectrum matches or quantitative data from proteomics and metabolomics
11991experiments.")
11992 (license license:artistic2.0)))
11993
11994(define-public r-msexperiment
11995 (package
11996 (name "r-msexperiment")
11997 (version "1.14.0")
11998 (source
11999 (origin
12000 (method url-fetch)
12001 (uri (bioconductor-uri "MsExperiment" version))
12002 (sha256
12003 (base32 "1shraa2lh9b26anz4mzsg0glxdq2y1r9lk4mppx8dd4d3wjjyplp"))))
12004 (properties
12005 `((upstream-name . "MsExperiment")
12006 (updater-extra-native-inputs . ("r-mzr"))))
12007 (build-system r-build-system)
12008 ;; Thanks to r-msdatahub the tests need Internet access.
12009 (arguments (list #:tests? #false))
12010 (propagated-inputs (list r-biocgenerics
12011 r-dbi
12012 r-iranges
12013 r-protgenerics
12014 r-qfeatures
12015 r-s4vectors
12016 r-spectra
12017 r-summarizedexperiment))
12018 (native-inputs (list r-knitr
12019 r-msbackendsql
12020 r-msdatahub
12021 r-mzr
12022 r-rsqlite
12023 r-testthat))
12024 (home-page "https://github.com/RforMassSpectrometry/MsExperiment")
12025 (synopsis "Infrastructure for Mass Spectrometry experiments")
12026 (description
12027 "This package provides infrastructure to store and manage all aspects
12028related to a complete proteomics or metabolomics mass spectrometry (MS)
12029experiment. The @code{MsExperiment} package provides light-weight and
12030flexible containers for MS experiments building on the new MS infrastructure
12031provided by the Spectra, QFeatures and related packages. Along with raw data
12032representations, links to original data files and sample annotations,
12033additional metadata or annotations can also be stored within the
12034@code{MsExperiment} container. To guarantee maximum flexibility only minimal
12035constraints are put on the type and content of the data within the
12036containers.")
12037 (license license:artistic2.0)))
12038
12039(define-public r-msnbase
12040 (package
12041 (name "r-msnbase")
12042 (version "2.37.0")
12043 (source
12044 (origin
12045 (method url-fetch)
12046 (uri (bioconductor-uri "MSnbase" version))
12047 (sha256
12048 (base32
12049 "04bcz27ssbljdd2ds1ch52zgaywxl4srs0ggl8pqjkgf6gkjj1s5"))))
12050 (properties
12051 `((upstream-name . "MSnbase")
12052 ;; Avoid dependency cycle.
12053 (updater-ignored-native-inputs . ("r-prolocdata"))))
12054 (build-system r-build-system)
12055 (arguments
12056 (list
12057 ;; r-msdata no longer contains the data file
12058 ;; TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz.
12059 #:tests? #false
12060 #:skipped-tests
12061 ;; These all need Internet access
12062 '("test_MSmap.R"
12063 ("test_MzTab.R"
12064 "MzTab creation and accessors"
12065 "MzTab-M creation and accessors"
12066 "MzTab-M MS-Dial import"
12067 "MzTab reading and writing"
12068 "MzTab-M reading and writing"
12069 "Conversion to MSnSetList")
12070 ("test_MzTab_09.R"
12071 "read MzTab data v 0.9 and 1.0")
12072 ("test_fileNames.R"
12073 "fileNames accessor MzTab")
12074 ;; Fails with: unable to find an inherited method for function
12075 ;; ‘pickPeaks’
12076 ("test_OnDiskMSnExp_other_methods.R"
12077 "Compare OnDiskMSnExp and MSnExp pickPeaks"
12078 "pickPeaks,OnDiskMSnExp works with refineMz")
12079 ;; Fails with: object 'hyperLOPIT2015' not found
12080 ("test_utils.R"
12081 "merging and expanding features")
12082 ;; Fails with: invalid 'description' argument
12083 ("test_io.R"
12084 "readMSnSet2: rownames and fnames")
12085 ;; Attempts to run "hostname"
12086 "test_readMSData2.R")
12087 #:phases
12088 '(modify-phases %standard-phases
12089 (add-after 'unpack 'set-HOME
12090 (lambda _ (setenv "HOME" "/tmp")))
12091 ;; For unknown reasons, the libxml2 features are misreported without
12092 ;; this call prior to running BiocGenerics:::testPackage("mzR").
12093 (add-after 'unpack 'ensure-libxml2-works
12094 (lambda _
12095 (substitute* "tests/testthat.R"
12096 (("library\\(\"MSnbase\"\\)" m)
12097 (string-append "XML::libxmlFeatures()\n" m))))))))
12098 (propagated-inputs
12099 (list r-affy
12100 r-biobase
12101 r-biocgenerics
12102 r-biocparallel
12103 r-digest
12104 r-ggplot2
12105 r-impute
12106 r-iranges
12107 r-lattice
12108 r-maldiquant
12109 r-mass
12110 r-mscoreutils
12111 r-mzid
12112 r-mzr
12113 r-pcamethods
12114 r-plyr
12115 r-protgenerics
12116 r-psmatch
12117 r-rcpp
12118 r-s4vectors
12119 r-scales
12120 r-vsn))
12121 (native-inputs
12122 (list r-knitr
12123 r-msdata
12124 r-rpx
12125 r-spectra
12126 r-summarizedexperiment
12127 r-testthat
12128 r-xml))
12129 (home-page "https://github.com/lgatto/MSnbase")
12130 (synopsis "Base functions and classes for MS-based proteomics")
12131 (description
12132 "This package provides basic plotting, data manipulation and processing
12133of mass spectrometry based proteomics data.")
12134 (license license:artistic2.0)))
12135
12136(define-public r-msnid
12137 (package
12138 (name "r-msnid")
12139 (version "1.46.0")
12140 (source
12141 (origin
12142 (method url-fetch)
12143 (uri (bioconductor-uri "MSnID" version))
12144 (sha256
12145 (base32
12146 "1a36awfdvxvk007b69c5v4bwrsdd3nyqndkq4kqraqnsfn1w0bsk"))))
12147 (properties `((upstream-name . "MSnID")))
12148 (build-system r-build-system)
12149 (arguments
12150 (list
12151 ;; Disable vignettes because they need Internet access.
12152 #:test-types '(list "tests")
12153 #:phases
12154 '(modify-phases %standard-phases
12155 ;; Needed for r-r-cache
12156 (add-after 'unpack 'set-HOME
12157 (lambda _ (setenv "HOME" "/tmp"))))))
12158 (propagated-inputs
12159 (list r-annotationdbi
12160 r-annotationhub
12161 r-biobase
12162 r-biocgenerics
12163 r-biocstyle
12164 r-biostrings
12165 r-data-table
12166 r-doparallel
12167 r-dplyr
12168 r-foreach
12169 r-ggplot2
12170 r-iterators
12171 r-msmstests
12172 r-msnbase
12173 r-mzid
12174 r-mzr
12175 r-protgenerics
12176 r-purrr
12177 r-r-cache
12178 r-rcpp
12179 r-reshape2
12180 r-rlang
12181 r-runit
12182 r-stringr
12183 r-tibble
12184 r-xtable))
12185 (native-inputs (list r-digest))
12186 (home-page "https://bioconductor.org/packages/MSnID")
12187 (synopsis "Utilities for LC-MSn proteomics identifications")
12188 (description
12189 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
12190from mzIdentML (leveraging the mzID package) or text files. After collating
12191the search results from multiple datasets it assesses their identification
12192quality and optimize filtering criteria to achieve the maximum number of
12193identifications while not exceeding a specified false discovery rate. It also
12194contains a number of utilities to explore the MS/MS results and assess missed
12195and irregular enzymatic cleavages, mass measurement accuracy, etc.")
12196 (license license:artistic2.0)))
12197
12198(define-public r-mzid
12199 (package
12200 (name "r-mzid")
12201 (version "1.50.0")
12202 (source
12203 (origin
12204 (method url-fetch)
12205 (uri (bioconductor-uri "mzID" version))
12206 (sha256
12207 (base32
12208 "00rad0qcsg0lyx8nw8a2plng1xbfc36pwi0n3vmqln3hx4821jjm"))))
12209 (properties `((upstream-name . "mzID")))
12210 (build-system r-build-system)
12211 (propagated-inputs
12212 (list r-doparallel
12213 r-foreach
12214 r-iterators
12215 r-plyr
12216 r-protgenerics
12217 r-xml))
12218 (native-inputs
12219 (list r-knitr r-testthat))
12220 (home-page "https://bioconductor.org/packages/mzID")
12221 (synopsis "Parser for mzIdentML files")
12222 (description
12223 "This package provides a parser for mzIdentML files implemented using the
12224XML package. The parser tries to be general and able to handle all types of
12225mzIdentML files with the drawback of having less pretty output than a vendor
12226specific parser.")
12227 (license license:gpl2+)))
12228
12229(define-public r-mzr
12230 (package
12231 (name "r-mzr")
12232 (version "2.46.0")
12233 (source
12234 (origin
12235 (method url-fetch)
12236 (uri (bioconductor-uri "mzR" version))
12237 (sha256
12238 (base32
12239 "0q9sfjzivrhvlavxdwy1pb6l3zx2jv25dy9jy23s3f67ccb8kkf1"))
12240 (modules '((guix build utils)))
12241 (snippet
12242 '(delete-file-recursively "src/boost"))))
12243 (properties
12244 `((upstream-name . "mzR")
12245 (updater-extra-inputs . ("boost"))))
12246 (build-system r-build-system)
12247 (arguments
12248 (list
12249 ;; Almost all tests now depend on ExperimentHub data files and so they
12250 ;; attempt to download files off the Internet.
12251 #:tests? #false
12252 #:phases
12253 '(modify-phases %standard-phases
12254 ;; For unknown reasons, the libxml2 features are misreported without
12255 ;; this call prior to running BiocGenerics:::testPackage("mzR").
12256 (add-after 'unpack 'ensure-libxml2-works
12257 (lambda _
12258 (substitute* "tests/runTests.R"
12259 (("library\\(\"mzR\"\\)" m)
12260 (string-append "XML::libxmlFeatures()\n" m)))))
12261 (add-after 'unpack 'use-system-boost
12262 (lambda _
12263 (substitute* "src/Makevars"
12264 (("\\./boost/libs.*") "")
12265 (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
12266 (("\\ARCH_OBJS=" line)
12267 (string-append line
12268 "\nBOOST_LIBS=-lboost_system -lboost_regex \
12269-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
12270 (inputs
12271 (list boost-1.83 ; use this instead of the bundled boost sources
12272 zlib))
12273 (propagated-inputs
12274 (list r-biobase
12275 r-biocgenerics
12276 r-ncdf4
12277 r-protgenerics
12278 r-rcpp
12279 r-rhdf5lib))
12280 (native-inputs
12281 (list r-knitr r-msdatahub r-mzid r-runit r-xml))
12282 (home-page "https://github.com/sneumann/mzR/")
12283 (synopsis "Parser for mass spectrometry data files")
12284 (description
12285 "The mzR package provides a unified API to the common file formats and
12286parsers available for mass spectrometry data. It comes with a wrapper for the
12287ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
12288The package contains the original code written by the ISB, and a subset of the
12289proteowizard library for mzML and mzIdentML. The netCDF reading code has
12290previously been used in XCMS.")
12291 (license license:artistic2.0)))
12292
12293;; This is a CRAN package, but it depends on a Bioconductor package.
12294(define-public r-numbat
12295 (package
12296 (name "r-numbat")
12297 (version "1.5.2")
12298 (source (origin
12299 (method url-fetch)
12300 (uri (cran-uri "numbat" version))
12301 (sha256
12302 (base32
12303 "0j6p15n0zmm4d8ml4j6ydcd8x3b8gba53hpxjm1qv05blr29b65y"))))
12304 (properties `((upstream-name . "numbat")))
12305 (build-system r-build-system)
12306 (propagated-inputs (list r-ape
12307 r-catools
12308 r-data-table
12309 r-dendextend
12310 r-dplyr
12311 r-genomicranges
12312 r-ggplot2
12313 r-ggraph
12314 r-ggtree
12315 r-glue
12316 r-hahmmr
12317 r-igraph
12318 r-iranges
12319 r-logger
12320 r-magrittr
12321 r-matrix
12322 r-optparse
12323 r-paralleldist
12324 r-patchwork
12325 r-purrr
12326 r-r-utils
12327 r-rcpp
12328 r-rcpparmadillo
12329 r-rhpcblasctl
12330 r-roptim
12331 r-scales
12332 r-scistreer
12333 r-stringr
12334 r-tibble
12335 r-tidygraph
12336 r-tidyr
12337 r-vcfr
12338 r-zoo))
12339 (native-inputs (list r-testthat))
12340 (home-page "https://github.com/kharchenkolab/numbat")
12341 (synopsis "Haplotype-aware CNV analysis from scRNA-Seq")
12342 (description
12343 "This package provides a computational method that infers copy number
12344variations (CNV) in cancer scRNA-seq data and reconstructs the tumor
12345phylogeny. It integrates signals from gene expression, allelic ratio, and
12346population haplotype structures to accurately infer allele-specific CNVs in
12347single cells and reconstruct their lineage relationship. It does not require
12348tumor/normal-paired DNA or genotype data, but operates solely on the donor
12349scRNA-data data (for example, 10x Cell Ranger output). It can be used to:
12350
12351@enumerate
12352@item detect allele-specific copy number variations from single-cells
12353@item differentiate tumor versus normal cells in the tumor microenvironment
12354@item infer the clonal architecture and evolutionary history of profiled tumors
12355@end enumerate
12356
12357For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y,
12358Gao et al in Nature Biotechnology 2022}.")
12359 (license license:expat)))
12360
12361(define-public r-organism-dplyr
12362 (package
12363 (name "r-organism-dplyr")
12364 (version "1.37.1")
12365 (source
12366 (origin
12367 (method url-fetch)
12368 (uri (bioconductor-uri "Organism.dplyr" version))
12369 (sha256
12370 (base32
12371 "0n9qfwx54pniyb849cx5whnf9hbrsiqyd6xn4bqhq4sl29ly3npd"))))
12372 (properties `((upstream-name . "Organism.dplyr")))
12373 (build-system r-build-system)
12374 ;; As of Bioconductor 3.22 there are 37 failing tests due to unexpected
12375 ;; differences.
12376 (arguments (list #:tests? #false))
12377 (propagated-inputs
12378 (list r-annotationdbi
12379 r-annotationfilter
12380 r-biocfilecache
12381 r-dbi
12382 r-dbplyr
12383 r-dplyr
12384 r-genomicfeatures
12385 r-genomicranges
12386 r-iranges
12387 r-rlang
12388 r-rsqlite
12389 r-s4vectors
12390 r-seqinfo
12391 r-tibble))
12392 (native-inputs
12393 (list r-knitr
12394 r-testthat
12395 r-txdb-hsapiens-ucsc-hg38-knowngene
12396 r-txdb-mmusculus-ucsc-mm10-ensgene))
12397 (home-page "https://bioconductor.org/packages/Organism.dplyr")
12398 (synopsis "Dplyr-based access to Bioconductor annotation resources")
12399 (description
12400 "This package provides an alternative interface to Bioconductor @code{
12401annotation} resources, in particular the gene identifier mapping functionality
12402of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate
12403functionality of the @code{TxDb} packages (e.g.,
12404@code{TxDb.Hsapiens.UCSC.hg38.knownGene}).")
12405 (license license:artistic2.0)))
12406
12407(define-public r-organismdbi
12408 (package
12409 (name "r-organismdbi")
12410 (version "1.54.0")
12411 (source
12412 (origin
12413 (method url-fetch)
12414 (uri (bioconductor-uri "OrganismDbi" version))
12415 (sha256
12416 (base32
12417 "112yzs84vs99akgsmn6faqgdp7ajnl0n32kbpxnjgmsll6hr7635"))))
12418 (properties
12419 '((upstream-name . "OrganismDbi")
12420 (updater-ignored-native-inputs
12421 . ("r-fdb-ucsc-trnas"
12422 "r-homo-sapiens"
12423 "r-rattus-norvegicus"))))
12424 (build-system r-build-system)
12425 ;; Tests need r-homo-sapiens, which needs this package.
12426 (arguments (list #:tests? #false))
12427 (propagated-inputs
12428 (list r-annotationdbi
12429 r-biobase
12430 r-biocgenerics
12431 r-biocmanager
12432 r-dbi
12433 r-genomicfeatures
12434 r-genomicranges
12435 r-graph
12436 r-iranges
12437 r-rbgl
12438 r-s4vectors
12439 r-seqinfo))
12440 (native-inputs (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-rsqlite
12441 r-runit r-txdbmaker))
12442 (home-page "https://bioconductor.org/packages/OrganismDbi")
12443 (synopsis "Software to enable the smooth interfacing of database packages")
12444 (description "The package enables a simple unified interface to several
12445annotation packages each of which has its own schema by taking advantage of
12446the fact that each of these packages implements a select methods.")
12447 (license license:artistic2.0)))
12448
12449(define-public r-oscope
12450 (package
12451 (name "r-oscope")
12452 (version "1.42.0")
12453 (source (origin
12454 (method url-fetch)
12455 (uri (bioconductor-uri "Oscope" version))
12456 (sha256
12457 (base32
12458 "1aq2zblqd096flhzpijh55qmnr6zz4jf8vs3zc5sksmil3914z6c"))))
12459 (properties `((upstream-name . "Oscope")))
12460 (build-system r-build-system)
12461 (propagated-inputs (list r-biocparallel r-cluster r-ebseq))
12462 (native-inputs (list r-biocstyle r-testthat))
12463 (home-page "https://bioconductor.org/packages/Oscope")
12464 (synopsis
12465 "Oscillatory genes identifier in unsynchronized single cell RNA-seq")
12466 (description
12467 "Oscope is a oscillatory genes identifier in unsynchronized single cell
12468RNA-seq. This statistical pipeline has been developed to identify and recover
12469the base cycle profiles of oscillating genes in an unsynchronized single cell
12470RNA-seq experiment. The Oscope pipeline includes three modules: a sine model
12471module to search for candidate oscillator pairs; a K-medoids clustering module
12472to cluster candidate oscillators into groups; and an extended nearest
12473insertion module to recover the base cycle order for each oscillator group.")
12474 (license license:asl2.0)))
12475
12476(define-public r-pcaexplorer
12477 (package
12478 (name "r-pcaexplorer")
12479 (version "3.6.0")
12480 (source
12481 (origin
12482 (method url-fetch)
12483 (uri (bioconductor-uri "pcaExplorer" version))
12484 (sha256
12485 (base32
12486 "0r7sn010222rzpm97vf71cnksr7hrm69nrxk5k14baipnqs9bgbk"))))
12487 (properties
12488 '((upstream-name . "pcaExplorer")
12489 (updater-extra-native-inputs . ("r-markdown"))))
12490 (build-system r-build-system)
12491 (propagated-inputs
12492 (list r-annotationdbi
12493 r-base64enc
12494 r-biomart
12495 r-deseq2
12496 r-dt
12497 r-genefilter
12498 r-genomicranges
12499 r-ggplot2
12500 r-ggrepel
12501 r-go-db
12502 r-gostats
12503 r-heatmaply
12504 r-iranges
12505 r-knitr
12506 r-limma
12507 r-mosdef
12508 r-nmf
12509 r-pheatmap
12510 r-plotly
12511 r-plyr
12512 r-rmarkdown
12513 r-s4vectors
12514 r-scales
12515 r-shiny
12516 r-shinyace
12517 r-shinybs
12518 r-shinydashboard
12519 r-summarizedexperiment
12520 r-threejs
12521 r-tidyr
12522 r-topgo))
12523 (native-inputs
12524 (list r-airway r-knitr r-markdown r-org-hs-eg-db r-testthat))
12525 (home-page "https://github.com/federicomarini/pcaExplorer")
12526 (synopsis
12527 "Interactive Visualization of RNA-seq Data Using a Principal Components Approach")
12528 (description
12529 "This package provides functionality for interactive visualization of RNA-seq
12530datasets based on Principal Components Analysis. The methods provided allow for
12531quick information extraction and effective data exploration. A Shiny
12532application encapsulates the whole analysis.")
12533 (license license:expat)))
12534
12535(define-public r-pcamethods
12536 (package
12537 (name "r-pcamethods")
12538 (version "2.4.0")
12539 (source
12540 (origin
12541 (method url-fetch)
12542 (uri (bioconductor-uri "pcaMethods" version))
12543 (sha256
12544 (base32
12545 "1mkb3vv9ypz0c38iblgh35y1kwknj8dmgcxgs38l5z26849i5qi8"))))
12546 (properties `((upstream-name . "pcaMethods")))
12547 (build-system r-build-system)
12548 (propagated-inputs
12549 (list r-biobase r-biocgenerics r-mass r-rcpp))
12550 (home-page "https://github.com/hredestig/pcamethods")
12551 (synopsis "Collection of PCA methods")
12552 (description
12553 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
12554Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
12555for missing value estimation is included for comparison. BPCA, PPCA and
12556NipalsPCA may be used to perform PCA on incomplete data as well as for
12557accurate missing value estimation. A set of methods for printing and plotting
12558the results is also provided. All PCA methods make use of the same data
12559structure (pcaRes) to provide a common interface to the PCA results.")
12560 (license license:gpl3+)))
12561
12562(define-public r-pfamanalyzer
12563 (package
12564 (name "r-pfamanalyzer")
12565 (version "1.12.0")
12566 (source (origin
12567 (method url-fetch)
12568 (uri (bioconductor-uri "pfamAnalyzeR" version))
12569 (sha256
12570 (base32
12571 "1zhw9748f65fzafkjhnina7mh3zi5sj0q8xxsvh510rlpjrl7v0f"))))
12572 (properties `((upstream-name . "pfamAnalyzeR")))
12573 (build-system r-build-system)
12574 (propagated-inputs (list r-dplyr r-magrittr r-readr r-stringr r-tibble))
12575 (native-inputs (list r-knitr))
12576 (home-page "https://bioconductor.org/packages/pfamAnalyzeR")
12577 (synopsis "Identification of domain isotypes in pfam data")
12578 (description
12579 "This R package enables the user to read pfam predictions into R. Most
12580human protein domains exist as multiple distinct variants termed domain
12581isotypes. This R package enables the identification and classification of such
12582domain isotypes from pfam data.")
12583 (license license:expat)))
12584
12585(define-public r-piano
12586 (package
12587 (name "r-piano")
12588 (version "2.28.0")
12589 (source
12590 (origin
12591 (method url-fetch)
12592 (uri (bioconductor-uri "piano" version))
12593 (sha256
12594 (base32 "0rcqdiwv58s4h9j0mzkam2d4bkaw8582k1ry22s4zs6whs1zd3l4"))))
12595 (properties `((upstream-name . "piano")))
12596 (build-system r-build-system)
12597 (propagated-inputs
12598 (list r-biobase
12599 r-biocgenerics
12600 r-dt
12601 r-fgsea
12602 r-gplots
12603 r-htmlwidgets
12604 r-igraph
12605 r-marray
12606 r-relations
12607 r-scales
12608 r-shiny
12609 r-shinydashboard
12610 r-shinyjs
12611 r-visnetwork))
12612 (native-inputs (list r-biocmanager r-biomart r-knitr))
12613 (home-page "https://varemo.github.io/piano/")
12614 (synopsis "Platform for integrative analysis of omics data")
12615 (description
12616 "Piano performs gene set analysis using various statistical methods, from
12617different gene level statistics and a wide range of gene-set collections. The
12618package contains functions for combining the results of multiple runs of gene
12619set analyses.")
12620 (license license:gpl2+)))
12621
12622(define-public r-polyester
12623 (package
12624 (name "r-polyester")
12625 (version "1.39.0")
12626 (source
12627 (origin
12628 (method url-fetch)
12629 (uri (bioconductor-uri "polyester" version))
12630 (sha256
12631 (base32 "0fw0qhmbygjq4ryspyqikb8rxfn33ks000j7sshgfg8hf2rmqg3x"))))
12632 (properties `((upstream-name . "polyester")))
12633 (build-system r-build-system)
12634 (propagated-inputs
12635 (list r-biostrings
12636 r-iranges
12637 r-limma
12638 r-logspline
12639 r-s4vectors
12640 r-zlibbioc))
12641 (native-inputs (list r-knitr))
12642 (home-page "https://bioconductor.org/packages/polyester")
12643 (synopsis "Simulate RNA-seq reads")
12644 (description
12645 "The polyester package simulates RNA-seq reads from differential expression
12646experiments with replicates. The reads can then be aligned and used to perform
12647comparisons of methods for differential expression.")
12648 (license license:artistic2.0)))
12649
12650(define-public r-powertcr
12651 (package
12652 (name "r-powertcr")
12653 (version "1.32.0")
12654 (source
12655 (origin
12656 (method url-fetch)
12657 (uri (bioconductor-uri "powerTCR" version))
12658 (sha256
12659 (base32 "0wg2scbgff43ysm8p525ikh342hs9ms5i1wl6yma50ar73769228"))))
12660 (properties `((upstream-name . "powerTCR")))
12661 (build-system r-build-system)
12662 (propagated-inputs
12663 (list r-cubature
12664 r-doparallel
12665 r-evmix
12666 r-foreach
12667 r-magrittr
12668 r-purrr
12669 r-truncdist
12670 r-vegan
12671 r-vgam))
12672 (native-inputs (list r-biocgenerics r-knitr r-runit))
12673 (home-page "https://bioconductor.org/packages/powerTCR")
12674 (synopsis "Model-based comparative analysis of the TCR repertoire")
12675 (description
12676 "This package provides a model for the clone size distribution of the
12677@acronym{TCR, T-cell receptor} repertoire. Further, it permits comparative
12678analysis of TCR repertoire libraries based on theoretical model fits.")
12679 (license license:artistic2.0)))
12680
12681;; This is a CRAN package, but it depends on a Bioconductor package:
12682;; r-aroma-light, r-dnacopy..
12683(define-public r-pscbs
12684 (package
12685 (name "r-pscbs")
12686 (version "0.68.0")
12687 (source
12688 (origin
12689 (method url-fetch)
12690 (uri (cran-uri "PSCBS" version))
12691 (sha256
12692 (base32 "1xsy4glg60iqbkvnyfwvyyjz5hnqzci45g5w17h9dva94qb62wc7"))))
12693 (properties `((upstream-name . "PSCBS")))
12694 (build-system r-build-system)
12695 (arguments
12696 `(#:phases
12697 (modify-phases %standard-phases
12698 (add-before 'install 'change-home-dir
12699 (lambda _
12700 ;; Change from /homeless-shelter to /tmp for write permission.
12701 (setenv "HOME" "/tmp"))))))
12702 (propagated-inputs
12703 (list r-aroma-light
12704 r-dnacopy
12705 r-future
12706 r-matrixstats
12707 r-r-cache
12708 r-r-methodss3
12709 r-r-oo
12710 r-r-utils))
12711 (native-inputs
12712 (list r-r-rsp))
12713 (home-page "https://github.com/HenrikBengtsson/PSCBS")
12714 (synopsis "Analysis of parent-specific DNA copy numbers")
12715 (description
12716 "This is a package for segmentation of allele-specific DNA copy number
12717data and detection of regions with abnormal copy number within each parental
12718chromosome. Both tumor-normal paired and tumor-only analyses are supported.")
12719 (license license:gpl2+)))
12720
12721(define-public r-psmatch
12722 (package
12723 (name "r-psmatch")
12724 (version "1.16.0")
12725 (source
12726 (origin
12727 (method url-fetch)
12728 (uri (bioconductor-uri "PSMatch" version))
12729 (sha256
12730 (base32 "1gp4w65j2jn09mwvhy4chk0awj7ziiv0kn48lpk830d1j5q05ndh"))))
12731 (properties
12732 '((upstream-name . "PSMatch")
12733 (updater-extra-native-inputs . ("r-mzid" "r-mzr"))))
12734 (build-system r-build-system)
12735 (arguments
12736 (list
12737 #:skipped-tests
12738 ;; These tests attempt to connect to the Internet to download databases.
12739 '("test_PSM.R"
12740 ("test_adjacencyMatrix.R"
12741 "plotAdjacencyMatrix\\(\\) attributes work"
12742 "plotAdjacencyMatrix\\(\\) works"
12743 "makeAjacendyMatrix\\(\\) works on PSM data \\(2\\)"))))
12744 (propagated-inputs (list r-biocgenerics
12745 r-biocparallel
12746 r-igraph
12747 r-matrix
12748 r-mscoreutils
12749 r-protgenerics
12750 r-ptmods
12751 r-qfeatures
12752 r-s4vectors
12753 r-spectra))
12754 (native-inputs
12755 (list r-devtools
12756 r-iranges
12757 r-knitr
12758 r-msdatahub
12759 r-mzid
12760 r-mzr
12761 r-testthat
12762 r-vdiffr))
12763 (home-page "https://github.com/RforMassSpectrometry/PSM")
12764 (synopsis "Handling and managing peptide spectrum matches")
12765 (description
12766 "The PSMatch package helps proteomics practitioners to load, handle and
12767manage peptide spectrum matches. It provides functions to model
12768peptide-protein relations as adjacency matrices and connected components,
12769visualise these as graphs and make informed decision about shared peptide
12770filtering. The package also provides functions to calculate and visualise MS2
12771fragment ions.")
12772 (license license:artistic2.0)))
12773
12774(define-public r-protgear
12775 (package
12776 (name "r-protgear")
12777 (version "1.16.0")
12778 (source
12779 (origin
12780 (method url-fetch)
12781 (uri (bioconductor-uri "protGear" version))
12782 (sha256
12783 (base32 "1xbpbyjsgxyah4v0qxlv9xgflb9j2aw6q3bng8y71q6gh20lb8rm"))))
12784 (properties `((upstream-name . "protGear")))
12785 (build-system r-build-system)
12786 (arguments
12787 (list
12788 #:phases
12789 '(modify-phases %standard-phases
12790 ;; Needed by styler for writing to caches.
12791 (add-after 'unpack 'set-HOME
12792 (lambda _ (setenv "HOME" "/tmp"))))))
12793 (propagated-inputs (list r-biobase
12794 r-data-table
12795 r-dplyr
12796 r-factoextra
12797 r-factominer
12798 r-flexdashboard
12799 r-genefilter
12800 r-ggally
12801 r-ggplot2
12802 r-ggpubr
12803 r-gtools
12804 r-htmltools
12805 r-kendall
12806 r-knitr
12807 r-limma
12808 r-magrittr
12809 r-mass
12810 r-pheatmap
12811 r-plotly
12812 r-plyr
12813 r-purrr
12814 r-readr
12815 r-remotes
12816 r-rlang
12817 r-rmarkdown
12818 r-shiny
12819 r-shinydashboard
12820 r-styler
12821 r-tibble
12822 r-tidyr
12823 r-vsn))
12824 (native-inputs (list r-knitr))
12825 (home-page "https://github.com/Keniajin/protGear")
12826 (synopsis
12827 "Protein micro array data management and interactive visualization")
12828 (description
12829 "This package provides a generic three-step pre-processing package for
12830protein microarray data. This package contains different data pre-processing
12831procedures to allow comparison of their performance. These steps are
12832background correction, the coefficient of variation (CV) based filtering,
12833batch correction and normalization.")
12834 (license license:gpl3)))
12835
12836(define-public r-protgenerics
12837 (package
12838 (name "r-protgenerics")
12839 (version "1.44.0")
12840 (source
12841 (origin
12842 (method url-fetch)
12843 (uri (bioconductor-uri "ProtGenerics" version))
12844 (sha256
12845 (base32
12846 "0sd5rfxf98rqcdss2m4wkzqyr2bzhzrbp17cpn0iphmy1y86dbhj"))))
12847 (properties `((upstream-name . "ProtGenerics")))
12848 (build-system r-build-system)
12849 (native-inputs (list r-testthat))
12850 (home-page "https://github.com/lgatto/ProtGenerics")
12851 (synopsis "S4 generic functions for proteomics infrastructure")
12852 (description
12853 "This package provides S4 generic functions needed by Bioconductor
12854proteomics packages.")
12855 (license license:artistic2.0)))
12856
12857(define-public r-ptmods
12858 (package
12859 (name "r-ptmods")
12860 (version "1.0.0")
12861 (source
12862 (origin
12863 (method url-fetch)
12864 (uri (bioconductor-uri "PTMods" version))
12865 (sha256
12866 (base32 "131a483r9jrmr7f7pbm0dl6h69zg5p2fjw0d6ab1w9gfxs0myj0w"))))
12867 (properties `((upstream-name . "PTMods")))
12868 (build-system r-build-system)
12869 (arguments
12870 (list
12871 #:skipped-tests
12872 ;; This file contains code that attempts to connect to http://www.unimod.org.
12873 '("test_datasets.R"
12874 ;; These tests fail with this error: object 'aminoacids' not found
12875 ("test_mass.R" ".aamass" ".mass"))))
12876 (native-inputs (list r-biostrings r-knitr r-testthat r-xml2))
12877 (home-page "https://github.com/RforMassSpectrometry/PTMods")
12878 (synopsis "Managing post-translational modifications in R")
12879 (description
12880 "This package provides an interface to the community supported database
12881for amino acid/protein modifications using mass spectrometry.")
12882 (license license:gpl3)))
12883
12884(define-public r-pwalign
12885 (package
12886 (name "r-pwalign")
12887 (version "1.8.0")
12888 (source
12889 (origin
12890 (method url-fetch)
12891 (uri (bioconductor-uri "pwalign" version))
12892 (sha256
12893 (base32 "11940saxi8j056k424xcrmbn4dvvix2kz0dw8k55hmhppbf7vnal"))))
12894 (properties
12895 '((upstream-name . "pwalign")
12896 (updater-extra-native-inputs . ("r-runit"))))
12897 (build-system r-build-system)
12898 (propagated-inputs (list r-biocgenerics r-biostrings r-iranges r-s4vectors
12899 r-xvector))
12900 (native-inputs (list r-runit))
12901 (home-page "https://bioconductor.org/packages/pwalign")
12902 (synopsis "Perform pairwise sequence alignments")
12903 (description
12904 "The two main functions in the package are @code{pairwiseAlignment} and
12905@code{stringDist}. The former solves (Needleman-Wunsch) global alignment,
12906(Smith-Waterman) local alignment, and (ends-free) overlap alignment problems.
12907The latter computes the Levenshtein edit distance or pairwise alignment score
12908matrix for a set of strings.")
12909 (license license:artistic2.0)))
12910
12911(define-public r-rbgl
12912 (package
12913 (name "r-rbgl")
12914 (version "1.88.0")
12915 (source
12916 (origin
12917 (method url-fetch)
12918 (uri (bioconductor-uri "RBGL" version))
12919 (sha256
12920 (base32
12921 "0cmya6wncfi1b6yafrp67r8kz15flhn75485z2vjfysy6w5zhkpq"))))
12922 (properties `((upstream-name . "RBGL")))
12923 (build-system r-build-system)
12924 (propagated-inputs
12925 (list r-bh r-graph))
12926 (native-inputs (list r-biocgenerics r-knitr r-runit))
12927 (home-page "https://www.bioconductor.org/packages/RBGL")
12928 (synopsis "Interface to the Boost graph library")
12929 (description
12930 "This package provides a fairly extensive and comprehensive interface to
12931the graph algorithms contained in the Boost library.")
12932 (license license:artistic2.0)))
12933
12934(define-public r-rcas
12935 (package
12936 (name "r-rcas")
12937 (version "1.38.0")
12938 (source (origin
12939 (method url-fetch)
12940 (uri (bioconductor-uri "RCAS" version))
12941 (sha256
12942 (base32
12943 "1b8m1k32kjnf2lpfc6jn12crx2hp5i2b2r8zdhpvdqwab2aarri9"))))
12944 (properties `((upstream-name . "RCAS")))
12945 (build-system r-build-system)
12946 (arguments
12947 (list
12948 #:skipped-tests
12949 ;; Code running outside testthat accesses the Internet
12950 '("test_motif.R"
12951 ;; These tests attempt to download data.
12952 ("test_database_functions.R"
12953 "Testing createDB function")
12954 ("test_report.R"
12955 "Testing runReport function"))
12956 #:phases
12957 '(modify-phases %standard-phases
12958 (add-after 'unpack 'set-HOME
12959 (lambda _ (setenv "HOME" "/tmp"))))))
12960 (inputs (list pandoc))
12961 (propagated-inputs
12962 (list r-biocgenerics
12963 r-biostrings
12964 r-bsgenome
12965 r-bsgenome-hsapiens-ucsc-hg19
12966 r-cowplot
12967 r-data-table
12968 r-dt
12969 r-genomation
12970 r-genomeinfodb
12971 r-genomicfeatures
12972 r-genomicranges
12973 r-ggplot2
12974 r-gprofiler2
12975 r-iranges
12976 r-knitr
12977 r-pbapply
12978 r-pheatmap
12979 r-plotly
12980 r-plotrix
12981 r-proxy
12982 r-ranger
12983 r-rmarkdown
12984 r-rsqlite
12985 r-rtracklayer
12986 r-s4vectors
12987 r-seqlogo
12988 r-txdbmaker))
12989 (native-inputs
12990 (list r-knitr r-testthat))
12991 (synopsis "RNA-centric annotation system")
12992 (description
12993 "RCAS aims to be a standalone RNA-centric annotation system that provides
12994intuitive reports and publication-ready graphics. This package provides the R
12995library implementing most of the pipeline's features.")
12996 (home-page "https://github.com/BIMSBbioinfo/RCAS")
12997 (license license:artistic2.0)))
12998
12999(define-public r-rcy3
13000 (package
13001 (name "r-rcy3")
13002 (version "2.32.0")
13003 (source
13004 (origin
13005 (method url-fetch)
13006 (uri (bioconductor-uri "RCy3" version))
13007 (sha256
13008 (base32 "1i41jsyxq9y9dd5rd3c8z7shgf4lx2zknl9zs5l0wb4yvdshsfxz"))))
13009 (properties `((upstream-name . "RCy3")))
13010 (build-system r-build-system)
13011 (propagated-inputs (list r-base64enc
13012 r-base64url
13013 r-biocgenerics
13014 r-fs
13015 r-glue
13016 r-gplots
13017 r-graph
13018 r-httr
13019 r-irdisplay
13020 r-irkernel
13021 r-rcolorbrewer
13022 r-rcurl
13023 r-rjsonio
13024 r-stringi
13025 r-uuid
13026 r-xml))
13027 (native-inputs (list r-knitr r-runit))
13028 (home-page "https://github.com/cytoscape/RCy3")
13029 (synopsis "Functions to access and control Cytoscape")
13030 (description
13031 "Vizualize, analyze and explore networks using Cytoscape via R. Anything
13032you can do using the graphical user interface of Cytoscape, you can now do
13033with a single RCy3 function.")
13034 (license license:expat)))
13035
13036(define-public r-recount
13037 (package
13038 (name "r-recount")
13039 (version "1.38.0")
13040 (source
13041 (origin
13042 (method url-fetch)
13043 (uri (bioconductor-uri "recount" version))
13044 (sha256
13045 (base32 "1xkrw7brfr4xiabh5cd7dznv2y15kjvig85wzhmlxm6jyq2cvd79"))))
13046 (properties `((upstream-name . "recount")))
13047 (build-system r-build-system)
13048 ;; 3 tests attempt to download data.
13049 (arguments (list #:tests? #false))
13050 (propagated-inputs (list r-biocparallel
13051 r-derfinder
13052 r-downloader
13053 r-genomeinfodb
13054 r-genomicranges
13055 r-geoquery
13056 r-iranges
13057 r-rcurl
13058 r-rentrez
13059 r-rtracklayer
13060 r-s4vectors
13061 r-summarizedexperiment))
13062 (native-inputs (list r-knitr r-testthat))
13063 (home-page "https://github.com/leekgroup/recount")
13064 (synopsis "Explore and download data from the recount project")
13065 (description
13066 "Explore and download data from the recount project available at
13067https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you
13068can download @code{RangedSummarizedExperiment} objects at the gene, exon or
13069exon-exon junctions level, the raw counts, the phenotype metadata used, the
13070urls to the sample coverage @code{bigWig} files or the mean coverage
13071@code{bigWig} file for a particular study. The
13072@code{RangedSummarizedExperiment} objects can be used by different packages
13073for performing differential expression analysis. Using
13074http://bioconductor.org/packages/derfinder you can perform annotation-agnostic
13075differential expression analyses with the data from the recount project as
13076described at
13077@url{https://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html}.")
13078 (license license:artistic2.0)))
13079
13080(define-public r-regioner
13081 (package
13082 (name "r-regioner")
13083 (version "1.44.0")
13084 (source
13085 (origin
13086 (method url-fetch)
13087 (uri (bioconductor-uri "regioneR" version))
13088 (sha256
13089 (base32
13090 "0ksvzj0aawsx7wgdm5npcmhkj5cpk0cxpkyfm96i52jrslh0fkmq"))))
13091 (properties `((upstream-name . "regioneR")))
13092 (build-system r-build-system)
13093 (arguments
13094 (list
13095 #:skipped-tests
13096 ;; These tests require internet access.
13097 '("test_randomizationFunctions.R"
13098 ("test_toGRanges.R"
13099 " toGRanges works for a data.frame"))))
13100 (propagated-inputs
13101 (list r-biostrings
13102 r-bsgenome
13103 r-genomeinfodb
13104 r-genomicranges
13105 r-iranges
13106 r-memoise
13107 r-rtracklayer
13108 r-s4vectors
13109 r-seqinfo))
13110 (native-inputs
13111 (list r-knitr r-testthat))
13112 (home-page "https://bioconductor.org/packages/regioneR/")
13113 (synopsis "Association analysis of genomic regions")
13114 (description "This package offers a statistical framework based on
13115customizable permutation tests to assess the association between genomic
13116region sets and other genomic features.")
13117 (license license:artistic2.0)))
13118
13119(define-public r-reportingtools
13120 (package
13121 (name "r-reportingtools")
13122 (version "2.52.0")
13123 (source
13124 (origin
13125 (method url-fetch)
13126 (uri (bioconductor-uri "ReportingTools" version))
13127 (sha256
13128 (base32
13129 "13ady91bj8xdkwv5l8qbjimh3w7vizznrxgbg95dn2diwysfnfjl"))
13130 (snippet
13131 '(delete-file "inst/extdata/jslib/jquery-1.8.0.min.js"))))
13132 (properties
13133 `((upstream-name . "ReportingTools")
13134 ;; This is mentioned in microarrayAnalysis.Rnw, but the package doesn't
13135 ;; exist and apparently isn't needed after all.
13136 (updater-ignored-native-inputs . ("r-gsealm"))))
13137 (build-system r-build-system)
13138 (arguments
13139 (list
13140 #:modules '((guix build utils)
13141 (guix build r-build-system)
13142 (guix build minify-build-system)
13143 (ice-9 match))
13144 #:imported-modules
13145 `(,@%r-build-system-modules
13146 (guix build minify-build-system))
13147 #:phases
13148 '(modify-phases (@ (guix build r-build-system) %standard-phases)
13149 (add-after 'unpack 'process-javascript
13150 (lambda* (#:key inputs #:allow-other-keys)
13151 (for-each (match-lambda
13152 ((source . target)
13153 (minify source #:target target)))
13154 `((,(assoc-ref inputs "jquery-1.8.0.js")
13155 . "inst/extdata/jslib/jquery-1.8.0.min.js"))))))))
13156 (propagated-inputs
13157 (list r-annotate
13158 r-annotationdbi
13159 r-biobase
13160 r-biocgenerics
13161 r-category
13162 r-deseq2
13163 r-edger
13164 r-ggbio
13165 r-ggplot2
13166 r-gostats
13167 r-gseabase
13168 r-hwriter
13169 r-iranges
13170 r-knitr
13171 r-lattice
13172 r-limma
13173 r-pfam-db
13174 r-r-utils
13175 r-xml))
13176 (native-inputs
13177 (list esbuild
13178 r-all
13179 r-genefilter
13180 r-hgu95av2-db
13181 r-org-hs-eg-db
13182 r-org-mm-eg-db
13183 r-org-sc-sgd-db
13184 r-pasilla
13185 r-rmarkdown
13186 r-runit
13187 r-shiny
13188 (origin
13189 (method url-fetch)
13190 (uri "https://code.jquery.com/jquery-1.8.0.js")
13191 (sha256
13192 (base32
13193 "02vnwfxrrfsqm6qbmxyv9rdg32qyzs81d1snk62fy08gv7r62hfk")))))
13194 (home-page "https://bioconductor.org/packages/ReportingTools/")
13195 (synopsis "Tools for making reports in various formats")
13196 (description
13197 "The ReportingTools package enables users to easily display reports of
13198analysis results generated from sources such as microarray and sequencing
13199data. The package allows users to create HTML pages that may be viewed on a
13200web browser, or in other formats. Users can generate tables with sortable and
13201filterable columns, make and display plots, and link table entries to other
13202data sources such as NCBI or larger plots within the HTML page. Using the
13203package, users can also produce a table of contents page to link various
13204reports together for a particular project that can be viewed in a web
13205browser.")
13206 (license license:artistic2.0)))
13207
13208(define-public r-rhdf5
13209 (package
13210 (name "r-rhdf5")
13211 (version "2.56.0")
13212 (source (origin
13213 (method url-fetch)
13214 (uri (bioconductor-uri "rhdf5" version))
13215 (sha256
13216 (base32
13217 "00wp6gj1zq0cypj39zkf1j0xwvq6bnh242kkld0spbv83wca974k"))))
13218 (build-system r-build-system)
13219 (arguments
13220 (list
13221 #:skipped-tests
13222 ;; Some of the tests expect to be able to use the proprietary
13223 ;; SZIP, which we've removed from r-rhdf5lib.
13224 '(("test_H5P_dcpl.R"
13225 "Filters can be set"
13226 "Filter information can be retrieved")
13227 ;; It is unclear why this would fail, but it says that the size
13228 ;; difference is zero. Perhaps it's related to a failure to read the
13229 ;; test file?
13230 ("test_external_filters.R"
13231 "BLOSC filter works when reading")
13232 ("test_h5read.R"
13233 "Reading SZIP"
13234 ;; It is unclear why this fails with "H5Identifier not valid."
13235 "Failing to read BLOSC"))))
13236 (propagated-inputs
13237 (list r-rhdf5filters r-rhdf5lib))
13238 (native-inputs
13239 (list r-bit64 r-knitr r-testthat r-withr))
13240 (home-page "https://bioconductor.org/packages/rhdf5")
13241 (synopsis "HDF5 interface to R")
13242 (description
13243 "This R/Bioconductor package provides an interface between HDF5 and R.
13244HDF5's main features are the ability to store and access very large and/or
13245complex datasets and a wide variety of metadata on mass storage (disk) through
13246a completely portable file format. The rhdf5 package is thus suited for the
13247exchange of large and/or complex datasets between R and other software
13248package, and for letting R applications work on datasets that are larger than
13249the available RAM.")
13250 (license license:artistic2.0)))
13251
13252(define-public r-rhdf5filters
13253 (package
13254 (name "r-rhdf5filters")
13255 (version "1.24.0")
13256 (source
13257 (origin
13258 (method url-fetch)
13259 (uri (bioconductor-uri "rhdf5filters" version))
13260 (sha256
13261 (base32
13262 "11ymlsgvm5pwnhgx0pm5sp7n3kr2xkv35lwxyabg9gjckzd17k3s"))))
13263 (properties
13264 '((upstream-name . "rhdf5filters")
13265 (updater-extra-inputs
13266 . ("bzip2" "c-blosc"))))
13267 (build-system r-build-system)
13268 (arguments
13269 (list
13270 ;; Tests require r-rhdf5, which depends on this package.
13271 #:tests? #false
13272 #:configure-flags
13273 '(list "--without-bundled-libraries")
13274 #:phases
13275 #~(modify-phases %standard-phases
13276 (add-after 'unpack 'patch-build-system
13277 (lambda _
13278 #$@(if (target-aarch64?)
13279 '((substitute* '("src/vbz/third_party/streamvbyte/Makefile"
13280 "src/vbz/third_party/streamvbyte/Makefile.in")
13281 (("\\$\\(STREAM_BYTE_CFLAGS\\)" m)
13282 (string-append m " -D__ARM_NEON__"))))
13283 '())
13284 (substitute* "src/lzf/lzf/Makefile"
13285 ;; Use the default rules for building .o from .c
13286 ((" \\$\\(CC\\) .*") ""))
13287 (substitute* "src/vbz/vbz/Makefile.in"
13288 ;; Use the default rules for building .o from .c
13289 ((" $(CXX) $(FLAGS).*") "")
13290 ;; Remove PKG_CPPFLAGS which clears the header search path.
13291 (("\\$\\(PKG_CPPFLAGS\\)") ""))
13292 ;; Remove PKG_CPPFLAGS which clears the header search path.
13293 (substitute* '("src/lzf/Makefile"
13294 "src/vbz/Makefile.in")
13295 (("\\$\\(PKG_CPPFLAGS\\)") "")))))))
13296 (propagated-inputs
13297 (list r-rhdf5lib))
13298 (inputs
13299 (list bzip2 c-blosc zlib (list zstd "lib")))
13300 (native-inputs
13301 (list r-knitr r-testthat))
13302 (home-page "https://github.com/grimbough/rhdf5filters")
13303 (synopsis "HDF5 compression filters")
13304 (description
13305 "This package provides a collection of compression filters for use with
13306HDF5 datasets.")
13307 (license license:bsd-2)))
13308
13309(define-public r-rnaagecalc
13310 (package
13311 (name "r-rnaagecalc")
13312 (version "1.24.0")
13313 (source
13314 (origin
13315 (method url-fetch)
13316 (uri (bioconductor-uri "RNAAgeCalc" version))
13317 (sha256
13318 (base32 "00mskzn6fzvzf9089v2gs9qa484340r4ypy6jy0ipdb7x21a6gf6"))))
13319 (properties `((upstream-name . "RNAAgeCalc")))
13320 (build-system r-build-system)
13321 (propagated-inputs (list r-annotationdbi
13322 r-ggplot2
13323 r-impute
13324 r-org-hs-eg-db
13325 r-recount
13326 r-summarizedexperiment))
13327 (native-inputs (list r-knitr r-testthat))
13328 (home-page "https://github.com/reese3928/RNAAgeCalc")
13329 (synopsis "Multi-tissue transcriptional age calculator")
13330 (description
13331 "It has been shown that both DNA methylation and RNA transcription are
13332linked to chronological age and age related diseases. Several estimators have
13333been developed to predict human aging from DNA level and RNA level. Most of
13334the human transcriptional age predictor are based on microarray data and
13335limited to only a few tissues. To date, transcriptional studies on aging
13336using RNASeq data from different human tissues is limited. The aim of this
13337package is to provide a tool for across-tissue and tissue-specific
13338transcriptional age calculation based on GTEx RNASeq data.")
13339 (license license:gpl2)))
13340
13341(define-public r-rsamtools
13342 (package
13343 (name "r-rsamtools")
13344 (version "2.28.0")
13345 (source (origin
13346 (method url-fetch)
13347 (uri (bioconductor-uri "Rsamtools" version))
13348 (sha256
13349 (base32
13350 "0c5pdxihnxwzybainlz2nlm3mr9d29jp4r2lixh5bgqqa01z2h2q"))))
13351 (properties
13352 `((upstream-name . "Rsamtools")))
13353 (build-system r-build-system)
13354 (arguments
13355 `(#:phases
13356 (modify-phases %standard-phases
13357 (add-after 'unpack 'use-system-zlib
13358 (lambda _
13359 (substitute* "DESCRIPTION"
13360 (("zlibbioc, ") ""))
13361 (substitute* "NAMESPACE"
13362 (("import\\(zlibbioc\\)") "")))))))
13363 (propagated-inputs
13364 (list r-biocgenerics
13365 r-biocparallel
13366 r-biostrings
13367 r-bitops
13368 r-genomicranges
13369 r-iranges
13370 r-rhtslib
13371 r-s4vectors
13372 r-seqinfo
13373 r-xvector))
13374 (native-inputs (list r-knitr r-runit))
13375 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
13376 (synopsis "Interface to samtools, bcftools, and tabix")
13377 (description
13378 "This package provides an interface to the @code{samtools},
13379@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
13380Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
13381tab-delimited (tabix) files.")
13382 (license license:expat)))
13383
13384;; This is a CRAN package, but it depends on a Bioconductor package:
13385;; s4vectors.
13386(define-public r-restfulr
13387 (package
13388 (name "r-restfulr")
13389 (version "0.0.17")
13390 (source
13391 (origin
13392 (method url-fetch)
13393 (uri (cran-uri "restfulr" version))
13394 (sha256
13395 (base32
13396 "0ms06268iki490zdqsapghp2d5yyshj9zy0hjrm7bww6k159q2z5"))))
13397 (properties `((upstream-name . "restfulr")))
13398 (build-system r-build-system)
13399 (propagated-inputs
13400 (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
13401 (home-page "https://cran.r-project.org/package=restfulr")
13402 (synopsis "R interface to RESTful web services")
13403 (description
13404 "This package models a RESTful service as if it were a nested R list.")
13405 (license license:artistic2.0)))
13406
13407(define-public r-rtcga
13408 (package
13409 (name "r-rtcga")
13410 (version "1.41.0")
13411 (source (origin
13412 (method url-fetch)
13413 (uri (bioconductor-uri "RTCGA" version))
13414 (sha256
13415 (base32
13416 "1q33npwadbj9jp0k4dp1abg6vbsiis3542194hag0impx01zidcf"))))
13417 (properties
13418 '((upstream-name . "RTCGA")
13419 (updater-ignored-native-inputs . ("r-rtcga-rnaseq"))))
13420 (build-system r-build-system)
13421 ;; Tests need r-rtcga-rnaseq, which depends on this package.
13422 (arguments (list #:tests? #false))
13423 (propagated-inputs (list r-assertthat
13424 r-data-table
13425 r-dplyr
13426 r-ggplot2
13427 r-ggthemes
13428 r-htmltools
13429 r-knitr
13430 r-purrr
13431 r-rcurl
13432 r-rmarkdown
13433 r-rvest
13434 r-scales
13435 r-stringi
13436 r-survival
13437 r-survminer
13438 r-viridis
13439 r-xml
13440 r-xml2))
13441 (native-inputs (list r-biobase r-genomicranges r-knitr
13442 r-testthat))
13443 (home-page "https://rtcga.github.io/RTCGA/")
13444 (synopsis "The Cancer Genome Atlas data integration")
13445 (description
13446 "The Cancer Genome Atlas (TCGA) Data Portal provides a platform for
13447researchers to search, download, and analyze data sets generated by TCGA. It
13448contains clinical information, genomic characterization data, and high level
13449sequence analysis of the tumor genomes. The key is to understand genomics to
13450improve cancer care. RTCGA package offers download and integration of the
13451variety and volume of TCGA data using patient barcode key, what enables easier
13452data possession. This may have an benefcial infuence on impact on development
13453of science and improvement of patients treatment. Furthermore, RTCGA package
13454transforms TCGA data to tidy form which is convenient to use.")
13455 (license license:gpl2)))
13456
13457(define-public r-rtcgatoolbox
13458 (package
13459 (name "r-rtcgatoolbox")
13460 (version "2.42.0")
13461 (source (origin
13462 (method url-fetch)
13463 (uri (bioconductor-uri "RTCGAToolbox" version))
13464 (sha256
13465 (base32
13466 "132g0n8dhrix9k8gs88j31wn03vjbfkywq6j9zcg9cszrdq3w7n2"))))
13467 (properties `((upstream-name . "RTCGAToolbox")))
13468 (build-system r-build-system)
13469 (propagated-inputs (list r-biocgenerics
13470 r-data-table
13471 r-delayedarray
13472 r-genomicranges
13473 r-httr
13474 r-raggedexperiment
13475 r-rcurl
13476 r-rjsonio
13477 r-rvest
13478 r-s4vectors
13479 r-seqinfo
13480 r-stringr
13481 r-summarizedexperiment
13482 r-tcgautils))
13483 (native-inputs (list r-knitr))
13484 (home-page "http://mksamur.github.io/RTCGAToolbox/")
13485 (synopsis "Export TCGA Firehose data")
13486 (description
13487 "Managing data from large scale projects such as The Cancer Genome
13488Atlas (TCGA) for further analysis is an important and time consuming step for
13489research projects. Several efforts, such as Firehose project, make TCGA
13490pre-processed data publicly available via web services and data portals but it
13491requires managing, downloading and preparing the data for following steps.
13492This package provides an extensible R based data client for Firehose
13493pre-processed data.")
13494 (license license:gpl2)))
13495
13496(define-public r-rtracklayer
13497 (package
13498 (name "r-rtracklayer")
13499 (version "1.72.0")
13500 (source (origin
13501 (method url-fetch)
13502 (uri (bioconductor-uri "rtracklayer" version))
13503 (sha256
13504 (base32
13505 "1ps8acpzl7mj3lyfsy55128zam1mabvgbavkr82hizp71y55v26x"))))
13506 (properties
13507 '((updater-ignored-native-inputs
13508 . ("r-bsgenome-hsapiens-ucsc-hg19"
13509 "r-humanstemcell"
13510 "r-microrna"))))
13511 (build-system r-build-system)
13512 (arguments
13513 (list
13514 ;; Tests require internet access.
13515 #:tests? #false
13516 #:phases
13517 '(modify-phases %standard-phases
13518 (add-after 'unpack 'use-system-zlib
13519 (lambda _
13520 (substitute* "DESCRIPTION"
13521 ((" zlibbioc,") ""))
13522 (substitute* "NAMESPACE"
13523 (("import\\(zlibbioc\\)") "")))))))
13524 (native-inputs
13525 (list pkg-config
13526 r-genefilter
13527 r-genomeinfodb
13528 r-hgu133plus2-db
13529 r-limma
13530 r-org-hs-eg-db))
13531 (inputs
13532 (list curl zlib))
13533 (propagated-inputs
13534 (list r-biocgenerics
13535 r-biocio
13536 r-biostrings
13537 r-curl
13538 r-genomicalignments
13539 r-genomicranges
13540 r-httr
13541 r-iranges
13542 r-restfulr
13543 r-rsamtools
13544 r-s4vectors
13545 r-seqinfo
13546 r-xml
13547 r-xvector))
13548 (home-page "https://bioconductor.org/packages/rtracklayer")
13549 (synopsis "R interface to genome browsers and their annotation tracks")
13550 (description
13551 "rtracklayer is an extensible framework for interacting with multiple
13552genome browsers (currently UCSC built-in) and manipulating annotation tracks
13553in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
13554built-in). The user may export/import tracks to/from the supported browsers,
13555as well as query and modify the browser state, such as the current viewport.")
13556 (license license:artistic2.0)))
13557
13558;; This is a CRAN package, but it depends on a Bioconductor package.
13559(define-public r-samr
13560 (package
13561 (name "r-samr")
13562 (version "3.0.1")
13563 (source
13564 (origin
13565 (method url-fetch)
13566 (uri (cran-uri "samr" version))
13567 (sha256
13568 (base32
13569 "1qdsm9dj4vql1ah3h12zcslx09g09hr34idc4xiqcd6q7lp2c109"))))
13570 (properties `((upstream-name . "samr")))
13571 (build-system r-build-system)
13572 (propagated-inputs
13573 (list r-gsa
13574 r-impute
13575 r-matrixstats
13576 r-openxlsx
13577 r-shiny
13578 r-shinyfiles))
13579 (native-inputs (list gfortran))
13580 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
13581 (synopsis "Significance analysis of Microarrays")
13582 (description
13583 "This is a package for significance analysis of Microarrays for
13584differential expression analysis, RNAseq data and related problems.")
13585 ;; Any version of the LGPL
13586 (license license:lgpl3+)))
13587
13588(define-public r-saturn
13589 (package
13590 (name "r-saturn")
13591 (version "1.20.0")
13592 (source (origin
13593 (method url-fetch)
13594 (uri (bioconductor-uri "satuRn" version))
13595 (sha256
13596 (base32
13597 "0bcp69x6c51qxkg9zr11j7akwhp22ld9hq4cgpfl0b4347x0nrp0"))))
13598 (properties `((upstream-name . "satuRn")))
13599 (build-system r-build-system)
13600 (propagated-inputs (list r-biocparallel
13601 r-boot
13602 r-ggplot2
13603 r-limma
13604 r-locfdr
13605 r-matrix
13606 r-pbapply
13607 r-summarizedexperiment))
13608 (native-inputs (list r-delayedarray r-knitr r-testthat))
13609 (home-page "https://github.com/statOmics/satuRn")
13610 (synopsis
13611 "Analysis of differential transcript usage for scRNA-seq applications")
13612 (description
13613 "satuRn provides a framework for performing differential transcript usage
13614analyses. The package consists of three main functions. The first function,
13615@code{fitDTU}, fits quasi-binomial generalized linear models that model
13616transcript usage in different groups of interest. The second function,
13617@code{testDTU}, tests for differential usage of transcripts between groups of
13618interest. Finally, @code{plotDTU} visualizes the usage profiles of
13619transcripts in groups of interest.")
13620 (license license:artistic2.0)))
13621
13622(define-public r-scannotatr
13623 (package
13624 (name "r-scannotatr")
13625 (version "1.18.0")
13626 (source
13627 (origin
13628 (method url-fetch)
13629 (uri (bioconductor-uri "scAnnotatR" version))
13630 (sha256
13631 (base32 "0pw907bdpfb79r61kzgf08s3849rdg4i96p5siywrzz3hwwrsqqk"))))
13632 (properties `((upstream-name . "scAnnotatR")))
13633 (build-system r-build-system)
13634 ;; 6 tests require connecting to a database over the Internet.
13635 (arguments (list #:tests? #false))
13636 (propagated-inputs
13637 (list r-annotationhub
13638 r-ape
13639 r-caret
13640 r-data-tree
13641 r-dplyr
13642 r-e1071
13643 r-ggplot2
13644 r-kernlab
13645 r-proc
13646 r-rocr
13647 r-seurat
13648 r-singlecellexperiment
13649 r-summarizedexperiment))
13650 (native-inputs (list r-knitr r-testthat))
13651 (home-page "https://github.com/grisslab/scAnnotatR")
13652 (synopsis "Pretrained models for prediction on single cell RNA-sequencing data")
13653 (description
13654 "This package comprises a set of pretrained machine learning models to
13655predict basic immune cell types. This enables to quickly get a first
13656annotation of the cell types present in the dataset without requiring prior
13657knowledge. The package also lets you train using own models to predict new
13658cell types based on specific research needs.")
13659 (license license:expat)))
13660
13661(define-public r-scdblfinder
13662 (package
13663 (name "r-scdblfinder")
13664 (version "1.26.2")
13665 (source
13666 (origin
13667 (method url-fetch)
13668 (uri (bioconductor-uri "scDblFinder" version))
13669 (sha256
13670 (base32 "1anxrlq0hvkxnpm6cffm1ag5ga6v77b1vfd8hzvg1yjvlm40ss36"))))
13671 (properties `((upstream-name . "scDblFinder")))
13672 (build-system r-build-system)
13673 (propagated-inputs
13674 (list r-biocgenerics
13675 r-biocneighbors
13676 r-biocparallel
13677 r-biocsingular
13678 r-bluster
13679 r-delayedarray
13680 r-genomeinfodb
13681 r-genomicranges
13682 r-igraph
13683 r-iranges
13684 r-mass
13685 r-matrix
13686 r-rsamtools
13687 r-rtracklayer
13688 r-s4vectors
13689 r-scater
13690 r-scran
13691 r-scuttle
13692 r-singlecellexperiment
13693 r-summarizedexperiment
13694 r-xgboost))
13695 (native-inputs (list r-knitr r-testthat))
13696 (home-page "https://github.com/plger/scDblFinder")
13697 (synopsis "Detect multiplets in single-cell RNA sequencing data")
13698 (description
13699 "The scDblFinder package gathers various methods for the detection and
13700handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
13701multiple cells captured within the same droplet or reaction volume). It
13702includes methods formerly found in the scran package, and the new fast and
13703comprehensive scDblFinder method.")
13704 (license license:gpl3)))
13705
13706;; This is a CRAN package, but it depends on packages from Bioconductor.
13707(define-public r-scgate
13708 (package
13709 (name "r-scgate")
13710 (version "1.7.2")
13711 (source
13712 (origin
13713 (method url-fetch)
13714 (uri (cran-uri "scGate" version))
13715 (sha256
13716 (base32 "050a23wlmzp2pijzi8dgjzjy349mzs9apiiz8i4q7j6ak63lcij9"))))
13717 (properties `((upstream-name . "scGate")))
13718 (build-system r-build-system)
13719 (propagated-inputs
13720 (list r-biocparallel
13721 r-colorspace
13722 r-dplyr
13723 r-ggplot2
13724 r-ggridges
13725 r-patchwork
13726 r-reshape2
13727 r-seurat
13728 r-ucell))
13729 (native-inputs (list r-knitr))
13730 (home-page "https://github.com/carmonalab/scGate")
13731 (synopsis
13732 "Marker-based cell type purification for single-cell sequencing data")
13733 (description
13734 "This package provides a method to purify a cell type or cell population
13735of interest from heterogeneous datasets. scGate package automatizes
13736marker-based purification of specific cell populations, without requiring
13737training data or reference gene expression profiles. scGate takes as input a
13738gene expression matrix stored in a Seurat object and a @acronym{GM, gating
13739model}, consisting of a set of marker genes that define the cell population of
13740interest. It evaluates the strength of signature marker expression in each
13741cell using the rank-based method UCell, and then performs @acronym{kNN,
13742k-nearest neighbor} smoothing by calculating the mean UCell score across
13743neighboring cells. kNN-smoothing aims at compensating for the large degree of
13744sparsity in scRNAseq data. Finally, a universal threshold over kNN-smoothed
13745signature scores is applied in binary decision trees generated from the
13746user-provided gating model, to annotate cells as either “pure” or “impure”,
13747with respect to the cell population of interest.")
13748 (license license:gpl3)))
13749
13750;; This is a CRAN package, but it depends on packages from Bioconductor.
13751(define-public r-scistreer
13752 (package
13753 (name "r-scistreer")
13754 (version "1.2.1")
13755 (source (origin
13756 (method url-fetch)
13757 (uri (cran-uri "scistreer" version))
13758 (sha256
13759 (base32
13760 "0v8pwz0skkan9gbpr9jffkkz0y22gm063mcw516c43xy3bgrxmgk"))))
13761 (properties `((upstream-name . "scistreer")))
13762 (build-system r-build-system)
13763 (propagated-inputs (list r-ape
13764 r-dplyr
13765 r-ggplot2
13766 r-ggtree
13767 r-igraph
13768 r-paralleldist
13769 r-patchwork
13770 r-phangorn
13771 r-rcpp
13772 r-rcpparmadillo
13773 r-rcppparallel
13774 r-reshape2
13775 r-rhpcblasctl
13776 r-stringr
13777 r-tidygraph))
13778 (native-inputs (list r-testthat))
13779 (home-page "https://github.com/kharchenkolab/scistreer")
13780 (synopsis "Maximum-likelihood perfect phylogeny Inference at scale")
13781 (description
13782 "This package provides fast maximum-likelihood phylogeny inference from
13783noisy single-cell data using the ScisTree algorithm proposed by
13784@code{doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019)}. It makes the
13785method applicable to massive single-cell datasets (>10,000 cells).")
13786 (license license:gpl3)))
13787
13788(define-public r-scmap
13789 (package
13790 (name "r-scmap")
13791 (version "1.34.0")
13792 (source
13793 (origin
13794 (method url-fetch)
13795 (uri (bioconductor-uri "scmap" version))
13796 (sha256
13797 (base32 "0a8ccz8y76cw702xhv8s27jvab8hfmzp9c9g9cb4x0286pqvbxzl"))))
13798 (properties `((upstream-name . "scmap")))
13799 (build-system r-build-system)
13800 (propagated-inputs
13801 (list r-biobase
13802 r-biocgenerics
13803 r-dplyr
13804 r-e1071
13805 r-ggplot2
13806 r-googlevis
13807 r-matrixstats
13808 r-proxy
13809 r-randomforest
13810 r-rcpp
13811 r-rcpparmadillo
13812 r-reshape2
13813 r-s4vectors
13814 r-singlecellexperiment
13815 r-summarizedexperiment))
13816 (native-inputs (list r-knitr))
13817 (home-page "https://github.com/hemberg-lab/scmap")
13818 (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
13819 (description
13820 "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
13821composition of complex tissues since the technology allows researchers to
13822define cell-types using unsupervised clustering of the transcriptome.
13823However, due to differences in experimental methods and computational
13824analyses, it is often challenging to directly compare the cells identified in
13825two different experiments. @code{scmap} is a method for projecting cells from
13826a scRNA-seq experiment onto the cell-types or individual cells identified in a
13827different experiment.")
13828 (license license:gpl3)))
13829
13830(define-public r-scp
13831 (package
13832 (name "r-scp")
13833 (version "1.22.0")
13834 (source
13835 (origin
13836 (method url-fetch)
13837 (uri (bioconductor-uri "scp" version))
13838 (sha256
13839 (base32 "1b2279xvkq7xgl30rkmnnp6wpycjn64wwrnks8r8vvhgi967y0zz"))))
13840 (properties
13841 '((upstream-name . "scp")
13842 (updater-extra-native-inputs . ("r-preprocesscore" "r-vsn"))))
13843 (build-system r-build-system)
13844 (arguments
13845 (list
13846 #:skipped-tests
13847 ;; These tests require Internet access via r-experimenthub
13848 '(("test-readSCP.R"
13849 "readSCPfromDIANN"
13850 "readSCPfromDIANN with sce"))))
13851 (propagated-inputs (list r-ggplot2
13852 r-ggrepel
13853 r-ihw
13854 r-matrixstats
13855 r-metapod
13856 r-mscoreutils
13857 r-multiassayexperiment
13858 r-nipals
13859 r-qfeatures
13860 r-rcolorbrewer
13861 r-s4vectors
13862 r-singlecellexperiment
13863 r-summarizedexperiment))
13864 (native-inputs (list r-biocgenerics r-knitr r-msdatahub r-preprocesscore
13865 r-testthat r-vdiffr r-vsn))
13866 (home-page "https://UCLouvain-CBIO.github.io/scp")
13867 (synopsis "Mass Spectrometry-based Single-Cell Proteomics data analysis")
13868 (description
13869 "This package provides utility functions for manipulating, processing,
13870and analyzing mass spectrometry-based single-cell proteomics data. The
13871package is an extension to the @code{QFeatures} package and relies on
13872@code{SingleCellExpirement} to enable single-cell proteomics analyses. The
13873package offers the user the functionality to process quantitative table (as
13874generated by MaxQuant, Proteome Discoverer, and more) into data tables ready
13875for downstream analysis and data visualization.")
13876 (license license:artistic2.0)))
13877
13878(define-public r-screpertoire
13879 (package
13880 (name "r-screpertoire")
13881 (version "2.8.0")
13882 (source
13883 (origin
13884 (method url-fetch)
13885 (uri (bioconductor-uri "scRepertoire" version))
13886 (sha256
13887 (base32 "0swz9ww8h57k04jm1lz12w1pz5dhm0zm4fy2jrc7w4d1k4j5dl6f"))))
13888 (properties
13889 '((upstream-name . "scRepertoire")))
13890 (build-system r-build-system)
13891 (arguments
13892 (list
13893 #:skipped-tests
13894 ;; There is code running outside of testthat that tries to
13895 ;; download files off the Internet.
13896 '("test-combineContigs.R"
13897 ;; These attempt to connect to the Internet.
13898 ("test-getContigDoublets.R"
13899 "getContigDoublets works for no doublets"
13900 "getContigDoublets works for inputs with doublets")
13901 ("test-loadContigs.R"
13902 "loadContigs correctly auto-detects and processes various formats"
13903 "loadContigs correctly processes various formats from URL")
13904 ;; These fail with: Unknown property set: 'kideraFactors'.
13905 ("test-positionalProperty.R"
13906 "positionalProperty: Output structure is correct"
13907 "positionalProperty: ggplot object is correctly formed"))))
13908 (propagated-inputs
13909 (list r-dplyr
13910 r-evmix
13911 r-ggalluvial
13912 r-ggdendro
13913 r-ggplot2
13914 r-ggraph
13915 r-igraph
13916 r-immapex
13917 r-inext
13918 r-lifecycle
13919 r-matrix
13920 r-purrr
13921 r-quantreg
13922 r-rcpp
13923 r-rjson
13924 r-rlang
13925 r-s4vectors
13926 r-seuratobject
13927 r-singlecellexperiment
13928 r-summarizedexperiment
13929 r-tidygraph))
13930 (native-inputs (list r-knitr r-spelling r-testthat))
13931 (home-page "https://bioconductor.org/packages/scRepertoire")
13932 (synopsis "Toolkit for single-cell immune receptor profiling")
13933 (description
13934 "The scRepertoire package was built to process data derived from the 10x
13935Genomics Chromium Immune Profiling for both @acronym{TCR, T-cell receptor} and
13936@acronym{Ig, immunoglobulin} enrichment workflows and subsequently interacts with
13937the popular Seurat and SingleCellExperiment R packages. It also allows for
13938general analysis of single-cell clonotype information without the use of
13939expression information. The package functions as a wrapper for Startrac and
13940powerTCR R packages.")
13941 (license license:gpl2)))
13942
13943(define-public r-scrnaseq
13944 (package
13945 (name "r-scrnaseq")
13946 (version "2.26.0")
13947 (source
13948 (origin
13949 (method url-fetch)
13950 (uri (bioconductor-uri "scRNAseq" version
13951 'experiment))
13952 (sha256
13953 (base32 "18p5xjf4473iyfjj3f66ydh4pavpgx55bgf96si7s87cljbak1mk"))))
13954 (properties `((upstream-name . "scRNAseq")))
13955 (build-system r-build-system)
13956 ;; Some tests require Internet access.
13957 (arguments (list #:tests? #false))
13958 (propagated-inputs (list r-alabaster-base
13959 r-alabaster-matrix
13960 r-alabaster-sce
13961 r-annotationdbi
13962 r-annotationhub
13963 r-biocgenerics
13964 r-dbi
13965 r-delayedarray
13966 r-ensembldb
13967 r-experimenthub
13968 r-genomicfeatures
13969 r-genomicranges
13970 r-gypsum
13971 r-jsonlite
13972 r-matrix
13973 r-rsqlite
13974 r-s4vectors
13975 r-singlecellexperiment
13976 r-sparsearray
13977 r-summarizedexperiment))
13978 (native-inputs (list r-biocmanager r-knitr r-testthat))
13979 (home-page "https://bioconductor.org/packages/scRNAseq")
13980 (synopsis "Collection of public single-cell RNA-seq datasets")
13981 (description
13982 "This package contains gene-level counts for a collection of public
13983@code{scRNA-seq} datasets, provided as @code{SingleCellExperiment} objects
13984with cell- and gene-level metadata.")
13985 (license license:cc0)))
13986
13987(define-public r-scry
13988 (package
13989 (name "r-scry")
13990 (version "1.24.0")
13991 (source (origin
13992 (method url-fetch)
13993 (uri (bioconductor-uri "scry" version))
13994 (sha256
13995 (base32
13996 "0d1ldv60g2kniib3dinhybp06bajhn8ahhhy3jcw7pjnsak4z6f5"))))
13997 (properties
13998 '((upstream-name . "scry")
13999 (updater-extra-native-inputs . ("r-hdf5array"))))
14000 (build-system r-build-system)
14001 (propagated-inputs
14002 (list r-biocsingular
14003 r-delayedarray
14004 r-glmpca
14005 r-matrix
14006 r-singlecellexperiment
14007 r-summarizedexperiment))
14008 (native-inputs (list r-hdf5array r-knitr r-testthat))
14009 (home-page "https://bioconductor.org/packages/scry.html")
14010 (synopsis "Small-count analysis methods for high-dimensional data")
14011 (description
14012 "Many modern biological datasets consist of small counts that are not
14013well fit by standard linear-Gaussian methods such as principal component
14014analysis. This package provides implementations of count-based feature
14015selection and dimension reduction algorithms. These methods can be used to
14016facilitate unsupervised analysis of any high-dimensional data such as
14017single-cell RNA-seq.")
14018 (license license:artistic2.0)))
14019
14020(define-public r-seqarray
14021 (package
14022 (name "r-seqarray")
14023 (version "1.52.1")
14024 (source (origin
14025 (method url-fetch)
14026 (uri (bioconductor-uri "SeqArray" version))
14027 (sha256
14028 (base32
14029 "00sdj7xr8rlb22c51c1dbb0hfh1fza729ngmzhsdxi032asi10b0"))))
14030 (properties
14031 '((upstream-name . "SeqArray")
14032 (updater-extra-native-inputs . ("r-digest"))))
14033 (build-system r-build-system)
14034 (propagated-inputs (list r-biostrings
14035 r-digest
14036 r-gdsfmt
14037 r-genomicranges
14038 r-iranges
14039 r-s4vectors
14040 r-seqinfo))
14041 (native-inputs
14042 (list r-biocgenerics r-digest r-knitr r-runit r-variantannotation))
14043 (home-page "https://github.com/zhengxwen/SeqArray")
14044 (synopsis
14045 "Data management of large-scale whole-genome sequence variant calls")
14046 (description
14047 "This package supports data management of large-scale whole-genome
14048sequencing variant calls with thousands of individuals: genotypic data (e.g.,
14049SNVs, indels and structural variation calls) and annotations in SeqArray GDS
14050files are stored in an array-oriented and compressed manner, with efficient
14051data access using the R programming language.")
14052 (license license:gpl3)))
14053
14054(define-public r-seqinfo
14055 (package
14056 (name "r-seqinfo")
14057 (version "1.2.0")
14058 (source
14059 (origin
14060 (method url-fetch)
14061 (uri (bioconductor-uri "Seqinfo" version))
14062 (sha256
14063 (base32 "0wx0ldp3ap5g61iz057yj0vfasr5d06h8h63g57xq97zjvyr6rpq"))))
14064 (properties
14065 '((upstream-name . "Seqinfo")
14066 (updater-extra-native-inputs . ("r-runit"))
14067 ;; Avoid dependency cycle.
14068 (updater-ignored-native-inputs . ("r-genomicranges"))))
14069 (build-system r-build-system)
14070 ;; Tests require r-genomicranges.
14071 (arguments (list #:tests? #false))
14072 (propagated-inputs (list r-biocgenerics r-iranges r-s4vectors))
14073 (native-inputs (list r-knitr r-runit))
14074 (home-page "https://bioconductor.org/packages/Seqinfo")
14075 (synopsis
14076 "S4 class for storing basic information about a collection of genomic sequences")
14077 (description
14078 "The @code{Seqinfo} class stores the names, lengths, circularity flags,
14079and genomes for a particular collection of sequences. These sequences are
14080typically the chromosomes and/or scaffolds of a specific genome assembly of a
14081given organism. @code{Seqinfo} objects are rarely used as standalone objects.
14082Instead, they are used as part of higher-level objects to represent their
14083@code{seqinfo()} component. Examples of such higher-level objects are
14084@code{GRanges}, @code{RangedSummarizedExperiment}, @code{VCF},
14085@code{GAlignments}, etc@dots{} defined in other Bioconductor infrastructure
14086packages.")
14087 (license license:artistic2.0)))
14088
14089(define-public r-seqlogo
14090 (package
14091 (name "r-seqlogo")
14092 (version "1.78.0")
14093 (source
14094 (origin
14095 (method url-fetch)
14096 (uri (bioconductor-uri "seqLogo" version))
14097 (sha256
14098 (base32
14099 "1kglbwfw6jkdkjf06181m1yyajxkvlkf58c68qpysm87pcdzjpj4"))))
14100 (properties `((upstream-name . "seqLogo")))
14101 (build-system r-build-system)
14102 (native-inputs
14103 (list r-knitr r-testthat))
14104 (home-page "https://bioconductor.org/packages/seqLogo")
14105 (synopsis "Sequence logos for DNA sequence alignments")
14106 (description
14107 "seqLogo takes the position weight matrix of a DNA sequence motif and
14108plots the corresponding sequence logo as introduced by Schneider and
14109Stephens (1990).")
14110 (license license:lgpl2.0+)))
14111
14112(define-public r-seqpattern
14113 (package
14114 (name "r-seqpattern")
14115 (version "1.44.0")
14116 (source (origin
14117 (method url-fetch)
14118 (uri (bioconductor-uri "seqPattern" version))
14119 (sha256
14120 (base32
14121 "11wx63wfnmcsbfdpdx32f5hwmgf3jwk88qn36h1hhhjg2hp3mlx8"))))
14122 (properties
14123 `((upstream-name . "seqPattern")
14124 (updater-extra-native-inputs . ("r-biocstyle"))))
14125 (build-system r-build-system)
14126 (propagated-inputs
14127 (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
14128 (native-inputs
14129 (list r-biocgenerics r-biocstyle r-bsgenome-drerio-ucsc-danrer7 r-runit))
14130 (home-page "https://bioconductor.org/packages/seqPattern")
14131 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
14132 (description
14133 "This package provides tools to visualize oligonucleotide patterns and
14134sequence motif occurrences across a large set of sequences centred at a common
14135reference point and sorted by a user defined feature.")
14136 (license license:gpl3+)))
14137
14138(define-public r-sesame
14139 (package
14140 (name "r-sesame")
14141 (version "1.30.0")
14142 (source (origin
14143 (method url-fetch)
14144 (uri (bioconductor-uri "sesame" version))
14145 (sha256
14146 (base32
14147 "081rjiqip0aqxc23pvzp0vwiyn7lnca2z33jyan629w70nfxy2bb"))))
14148 (properties `((upstream-name . "sesame")))
14149 (build-system r-build-system)
14150 ;; Tests use ExperimentHub, so needs Internet access.
14151 (arguments (list #:tests? #false))
14152 (propagated-inputs (list r-biocfilecache
14153 r-biocparallel
14154 r-dplyr
14155 r-genomicranges
14156 r-ggplot2
14157 r-iranges
14158 r-mass
14159 r-preprocesscore
14160 r-readr
14161 r-reshape2
14162 r-s4vectors
14163 r-seqinfo
14164 r-sesamedata
14165 r-stringr
14166 r-summarizedexperiment
14167 r-tibble
14168 r-wheatmap))
14169 (native-inputs (list r-knitr r-testthat))
14170 (home-page "https://github.com/zwdzwd/sesame")
14171 (synopsis "Step-wise analysis of DNA Methylation BeadChips")
14172 (description
14173 "This package provides tools For analyzing Illumina Infinium DNA
14174methylation arrays. @code{SeSAMe} provides utilities to support analyses of
14175multiple generations of Infinium DNA methylation @code{BeadChips}, including
14176preprocessing, quality control, visualization and inference. @code{SeSAMe}
14177features accurate detection calling, intelligent inference of ethnicity, sex
14178and advanced quality control routines.")
14179 (license license:expat)))
14180
14181(define-public r-shinymethyl
14182 (package
14183 (name "r-shinymethyl")
14184 (version "1.48.0")
14185 (source (origin
14186 (method url-fetch)
14187 (uri (bioconductor-uri "shinyMethyl" version))
14188 (sha256
14189 (base32
14190 "1fi9cm0zhidjhnl9f8zkl4v8xbr6s0nk2b19calqsngfabf7lr4k"))))
14191 (properties `((upstream-name . "shinyMethyl")))
14192 (build-system r-build-system)
14193 (propagated-inputs
14194 (list r-biobase
14195 r-biocgenerics
14196 r-htmltools
14197 r-matrixgenerics
14198 r-minfi
14199 r-rcolorbrewer
14200 r-shiny))
14201 (native-inputs (list r-knitr r-testthat))
14202 (home-page "https://bioconductor.org/packages/shinyMethyl")
14203 (synopsis "Interactive visualization for Illumina methylation arrays")
14204 (description
14205 "This package provides an interactive tool for visualizing Illumina
14206methylation array data. Both the 450k and EPIC array are supported.")
14207 (license license:artistic2.0)))
14208
14209(define-public r-shortread
14210 (package
14211 (name "r-shortread")
14212 (version "1.70.0")
14213 (source
14214 (origin
14215 (method url-fetch)
14216 (uri (bioconductor-uri "ShortRead" version))
14217 (sha256
14218 (base32
14219 "111s382q64b37ybsc4dswja3yr3q3258fqmy255qbwcwvqcgdnpx"))))
14220 (properties
14221 '((upstream-name . "ShortRead")
14222 (updater-ignored-native-inputs . ("r-hilbertvis"))))
14223 (build-system r-build-system)
14224 (inputs (list zlib))
14225 (propagated-inputs
14226 (list r-biobase
14227 r-biocgenerics
14228 r-biocparallel
14229 r-biostrings
14230 r-genomicalignments
14231 r-genomicranges
14232 r-hwriter
14233 r-iranges
14234 r-lattice
14235 r-latticeextra
14236 r-pwalign
14237 r-rhtslib
14238 r-rsamtools
14239 r-s4vectors
14240 r-seqinfo
14241 r-xvector))
14242 (native-inputs (list r-knitr r-runit))
14243 (home-page "https://bioconductor.org/packages/ShortRead")
14244 (synopsis "FASTQ input and manipulation tools")
14245 (description
14246 "This package implements sampling, iteration, and input of FASTQ files.
14247It includes functions for filtering and trimming reads, and for generating a
14248quality assessment report. Data are represented as
14249@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
14250purposes. The package also contains legacy support for early single-end,
14251ungapped alignment formats.")
14252 (license license:artistic2.0)))
14253
14254(define-public r-sictools
14255 (package
14256 (name "r-sictools")
14257 (version "1.42.0")
14258 (source
14259 (origin
14260 (method url-fetch)
14261 (uri (bioconductor-uri "SICtools" version))
14262 (sha256
14263 (base32 "0v6cmzg79q3bh7wnrr47dygc0zd22aqrl4p3nipsx7by3hr8cd16"))))
14264 (properties
14265 `((upstream-name . "SICtools")
14266 (updater-extra-inputs . ("ncurses"))))
14267 (build-system r-build-system)
14268 (arguments
14269 (list
14270 ;; 1 test fails with a string mismatch.
14271 #:tests? #false
14272 #:phases
14273 '(modify-phases %standard-phases
14274 (add-after 'unpack 'patch-curses
14275 (lambda _
14276 (substitute* "src/Makefile"
14277 (("^LIBCURSES.*")
14278 "LIBCURSES=-lncurses\n")))))))
14279 (propagated-inputs (list r-biostrings
14280 r-doparallel
14281 r-genomicranges
14282 r-iranges
14283 r-matrixstats
14284 r-plyr
14285 r-rsamtools
14286 r-stringr))
14287 (inputs (list ncurses))
14288 (native-inputs (list r-biocgenerics r-knitr r-runit))
14289 (home-page "https://bioconductor.org/packages/SICtools")
14290 (synopsis
14291 "Find SNV/Indel differences between two bam files with near relationship")
14292 (description
14293 "This package is to find SNV/Indel differences between two @file{bam}
14294files with near relationship in a way of pairwise comparison through each base
14295position across the genome region of interest. The difference is inferred by
14296Fisher test and euclidean distance, the input of which is the base
14297count (A,T,G,C) in a given position and read counts for indels that span no
14298less than 2bp on both sides of indel region.")
14299 (license license:gpl2+)))
14300
14301(define-public r-simona
14302 (package
14303 (name "r-simona")
14304 (version "1.10.0")
14305 (source
14306 (origin
14307 (method url-fetch)
14308 (uri (bioconductor-uri "simona" version))
14309 (sha256
14310 (base32 "1vs8a4khcf5cpfxsphdwrx9wllg1alk1z1hpl93ql0ayxgv1k12s"))))
14311 (properties
14312 `((upstream-name . "simona")
14313 (updater-extra-native-inputs
14314 . ("r-go-db" "r-org-hs-eg-db" "r-proxyc"))))
14315 (build-system r-build-system)
14316 (inputs (list openjdk perl))
14317 (propagated-inputs (list r-circlize
14318 r-complexheatmap
14319 r-fastmatch
14320 r-getoptlong
14321 r-globaloptions
14322 r-igraph
14323 r-matrixstats
14324 r-polychrome
14325 r-rcpp
14326 r-s4vectors
14327 r-shiny
14328 r-xml2))
14329 (native-inputs (list r-go-db r-knitr r-org-hs-eg-db r-proxyc r-testthat))
14330 (home-page "https://github.com/jokergoo/simona")
14331 (synopsis "Semantic similarity on bio-ontologies")
14332 (description
14333 "This package implements infrastructures for ontology analysis by
14334offering efficient data structures, fast ontology traversal methods, and
14335elegant visualizations. It provides a robust toolbox supporting over 70
14336methods for semantic similarity analysis.")
14337 (license license:expat)))
14338
14339(define-public r-simplifyenrichment
14340 (package
14341 (name "r-simplifyenrichment")
14342 (version "2.6.0")
14343 (source
14344 (origin
14345 (method url-fetch)
14346 (uri (bioconductor-uri "simplifyEnrichment" version))
14347 (sha256
14348 (base32
14349 "1d4fzxfd8ymh2diy4bm991ai83ag9759hrvwzlmrcf5p2qnx5ay1"))))
14350 (properties
14351 `((upstream-name . "simplifyEnrichment")))
14352 (build-system r-build-system)
14353 (propagated-inputs
14354 (list r-annotationdbi
14355 r-circlize
14356 r-clue
14357 r-cluster
14358 r-colorspace
14359 r-complexheatmap
14360 r-digest
14361 r-getoptlong
14362 r-globaloptions
14363 r-go-db
14364 r-simona
14365 r-slam
14366 r-tm))
14367 (native-inputs (list r-knitr r-testthat))
14368 (home-page "https://github.com/jokergoo/simplifyEnrichment")
14369 (synopsis "Simplify functional enrichment results")
14370 (description "This package provides a new clustering algorithm, binary
14371cut, for clustering similarity matrices of functional terms is implemented in
14372this package. It also provides functionalities for visualizing, summarizing
14373and comparing the clusterings.")
14374 (license license:expat)))
14375
14376(define-public r-singscore
14377 (package
14378 (name "r-singscore")
14379 (version "1.32.0")
14380 (source (origin
14381 (method url-fetch)
14382 (uri (bioconductor-uri "singscore" version))
14383 (sha256
14384 (base32
14385 "0npxk2189myjmgmnlv67y9zm20msxdyg9g2rh6f9pjay475wpzxl"))))
14386 (properties
14387 '((upstream-name . "singscore")
14388 (updater-extra-native-inputs . ("r-hexbin"))))
14389 (build-system r-build-system)
14390 (propagated-inputs (list r-biobase
14391 r-biocparallel
14392 r-edger
14393 r-ggplot2
14394 r-ggrepel
14395 r-gseabase
14396 r-magrittr
14397 r-matrixstats
14398 r-plotly
14399 r-plyr
14400 r-rcolorbrewer
14401 r-reshape
14402 r-reshape2
14403 r-s4vectors
14404 r-summarizedexperiment
14405 r-tidyr))
14406 (native-inputs (list r-hexbin r-knitr r-testthat))
14407 (home-page "https://davislaboratory.github.io/singscore/")
14408 (synopsis "Rank-based single-sample gene set scoring method")
14409 (description
14410 "This package provides a simple single-sample gene signature scoring
14411method that uses rank-based statistics to analyze the sample's gene expression
14412profile. It scores the expression activities of gene sets at a single-sample
14413level.")
14414 (license license:gpl3)))
14415
14416(define-public r-tcgautils
14417 (package
14418 (name "r-tcgautils")
14419 (version "1.32.1")
14420 (source (origin
14421 (method url-fetch)
14422 (uri (bioconductor-uri "TCGAutils" version))
14423 (sha256
14424 (base32
14425 "0x7qpgx831m7a56ibmqhp2iszw9kl8xpih8p6yyyc74agjzmadga"))))
14426 (properties `((upstream-name . "TCGAutils")))
14427 (build-system r-build-system)
14428 (arguments
14429 (list
14430 #:skipped-tests
14431 '(("test-ID-translation.R"
14432 ;; These tests require Internet access.
14433 "UUIDhistory correctly returns the appropriate identifiers"
14434 "UUIDtoBarcode shows multiple entries per file_id"
14435 "UUIDtoBarcode translates correctly"
14436 "barcodeToUUID translates correctly"))))
14437 (propagated-inputs (list r-annotationdbi
14438 r-biocbaseutils
14439 r-biocgenerics
14440 r-genomeinfodb
14441 r-genomicdatacommons
14442 r-genomicfeatures
14443 r-genomicranges
14444 r-glue
14445 r-iranges
14446 r-multiassayexperiment
14447 r-raggedexperiment
14448 r-rvest
14449 r-s4vectors
14450 r-seqinfo
14451 r-stringr
14452 r-summarizedexperiment
14453 r-xml2))
14454 (native-inputs (list r-knitr r-testthat))
14455 (home-page "https://bioconductor.org/packages/TCGAutils")
14456 (synopsis "TCGA utility functions for data management")
14457 (description
14458 "This package provides a suite of helper functions for checking and
14459manipulating TCGA data including data obtained from the @code{curatedTCGAData}
14460experiment package. These functions aim to simplify and make working with
14461TCGA data more manageable. Exported functions include those that import data
14462from flat files into Bioconductor objects, convert row annotations, and
14463identifier translation via the GDC API.")
14464 (license license:artistic2.0)))
14465
14466(define-public r-tkwidgets
14467 (package
14468 (name "r-tkwidgets")
14469 (version "1.90.0")
14470 (source (origin
14471 (method url-fetch)
14472 (uri (bioconductor-uri "tkWidgets" version))
14473 (sha256
14474 (base32
14475 "1jx66q3jzqdf1awq183qlk44552rvpx19x89nfmpfvavc3jywhgk"))))
14476 (properties `((upstream-name . "tkWidgets")))
14477 (build-system r-build-system)
14478 (propagated-inputs (list r-dyndoc r-widgettools))
14479 (home-page "https://bioconductor.org/packages/tkWidgets")
14480 (synopsis "R based tk widgets")
14481 (description
14482 "This package implements widgets to provide user interfaces.")
14483 (license license:artistic2.0)))
14484
14485(define-public r-toast
14486 (package
14487 (name "r-toast")
14488 (version "1.26.0")
14489 (source
14490 (origin
14491 (method url-fetch)
14492 (uri (bioconductor-uri "TOAST" version))
14493 (sha256
14494 (base32 "1r9qr9lxfdb314g0p3a66lsx2k796ams3r0bwvymxb4am20r6k6b"))))
14495 (properties `((upstream-name . "TOAST")))
14496 (build-system r-build-system)
14497 (propagated-inputs (list r-corpcor
14498 r-doparallel
14499 r-epidish
14500 r-ggally
14501 r-ggplot2
14502 r-limma
14503 r-nnls
14504 r-quadprog
14505 r-summarizedexperiment
14506 r-tidyr))
14507 (native-inputs (list r-knitr))
14508 (home-page "https://bioconductor.org/packages/TOAST")
14509 (synopsis "Tools for the analysis of heterogeneous tissues")
14510 (description
14511 "This package is devoted to analyzing high-throughput data (e.g. gene
14512expression microarray, DNA methylation microarray, RNA-seq) from complex
14513tissues. Current functionalities include
14514
14515@enumerate
14516@item detect cell-type specific or cross-cell type differential signals
14517@item tree-based differential analysis
14518@item improve variable selection in reference-free deconvolution
14519@item partial reference-free deconvolution with prior knowledge.
14520@end enumerate")
14521 (license license:gpl2)))
14522
14523(define-public r-trackviewer
14524 (package
14525 (name "r-trackviewer")
14526 (version "1.48.0")
14527 (source (origin
14528 (method url-fetch)
14529 (uri (bioconductor-uri "trackViewer" version))
14530 (sha256
14531 (base32
14532 "1xi2cr2b2aaiwycjwm6d3c487jnj5ik03svg06zi5bv2ibfdw11f"))
14533 (snippet
14534 '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js"))))
14535 (properties `((upstream-name . "trackViewer")))
14536 (build-system r-build-system)
14537 (arguments
14538 (list
14539 #:phases
14540 '(modify-phases %standard-phases
14541 (add-after 'unpack 'process-javascript
14542 (lambda* (#:key inputs #:allow-other-keys)
14543 (with-directory-excursion "inst/htmlwidgets/lib/d3"
14544 (let ((source (assoc-ref inputs "d3.v4.js"))
14545 (target "d3.v4.min.js"))
14546 (format #true "Processing ~a --> ~a~%"
14547 source target)
14548 (invoke "esbuild" source "--minify"
14549 (string-append "--outfile=" target)))))))))
14550 (propagated-inputs (list r-annotationdbi
14551 r-biocgenerics
14552 r-genomeinfodb
14553 r-genomicalignments
14554 r-genomicfeatures
14555 r-genomicranges
14556 r-grimport
14557 r-gviz
14558 r-htmlwidgets
14559 r-interactionset
14560 r-iranges
14561 r-rhdf5
14562 r-rsamtools
14563 r-rtracklayer
14564 r-s4vectors
14565 r-scales
14566 r-seqinfo
14567 r-strawr
14568 r-txdbmaker))
14569 (native-inputs
14570 (list esbuild
14571 r-knitr
14572 r-runit
14573 (origin
14574 (method url-fetch)
14575 (uri "https://web.archive.org/web/20230428092426id_/\
14576https://d3js.org/d3.v4.js")
14577 (sha256
14578 (base32
14579 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))
14580 (home-page "https://bioconductor.org/packages/trackViewer")
14581 (synopsis "Web interface for interactive multi-omics data analysis")
14582 (description
14583 "TrackViewer offers multi-omics analysis with web based tracks and
14584lollipops. Visualize mapped reads along with annotation as track layers for
14585NGS datasets such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and
14586methylation data.")
14587 (license license:gpl2+)))
14588
14589(define-public r-transcriptr
14590 (package
14591 (name "r-transcriptr")
14592 (version "1.40.0")
14593 (source
14594 (origin
14595 (method url-fetch)
14596 (uri (bioconductor-uri "transcriptR" version))
14597 (sha256
14598 (base32 "077vnbpx6yhgwp8jima0jnvp81i15d7mb1m0pavhqi1hw3fxrvg3"))))
14599 (properties
14600 '((upstream-name . "transcriptR")
14601 (updater-ignored-native-inputs
14602 . ("r-knowngene"))
14603 (updater-extra-native-inputs
14604 . ("r-txdb-hsapiens-ucsc-hg19-knowngene"))))
14605 (build-system r-build-system)
14606 (propagated-inputs
14607 (list r-biocgenerics
14608 r-caret
14609 r-chipseq
14610 r-genomeinfodb
14611 r-genomicalignments
14612 r-genomicfeatures
14613 r-genomicranges
14614 r-ggplot2
14615 r-iranges
14616 r-proc
14617 r-reshape2
14618 r-rsamtools
14619 r-rtracklayer
14620 r-s4vectors))
14621 (native-inputs
14622 (list r-knitr r-testthat r-txdb-hsapiens-ucsc-hg19-knowngene))
14623 (home-page "https://bioconductor.org/packages/transcriptR")
14624 (synopsis "Primary transcripts detection and quantification")
14625 (description
14626 "The differences in the RNA types being sequenced have an impact on the
14627resulting sequencing profiles. mRNA-seq data is enriched with reads derived
14628from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
14629broader coverage of both exonic and intronic regions. The presence of
14630intronic reads in GRO-seq type of data makes it possible to use it to
14631computationally identify and quantify all de novo continuous regions of
14632transcription distributed across the genome. This type of data, however, is
14633more challenging to interpret and less common practice compared to mRNA-seq.
14634One of the challenges for primary transcript detection concerns the
14635simultaneous transcription of closely spaced genes, which needs to be properly
14636divided into individually transcribed units. The R package transcriptR
14637combines RNA-seq data with ChIP-seq data of histone modifications that mark
14638active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
14639overcome this challenge. The advantage of this approach over the use of, for
14640example, gene annotations is that this approach is data driven and therefore
14641able to deal also with novel and case specific events.")
14642 (license license:gpl3)))
14643
14644(define-public r-trajectoryutils
14645 (package
14646 (name "r-trajectoryutils")
14647 (version "1.20.0")
14648 (source
14649 (origin
14650 (method url-fetch)
14651 (uri (bioconductor-uri "TrajectoryUtils" version))
14652 (sha256
14653 (base32
14654 "148p7l4nlyv0gn7zcna8fin9fycdlmzk0yx1r9qn5nmb0n9j4wdg"))))
14655 (properties
14656 '((upstream-name . "TrajectoryUtils")
14657 (updater-extra-native-inputs . ("r-biocneighbors" "r-biocparallel"))))
14658 (build-system r-build-system)
14659 (propagated-inputs
14660 (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
14661 r-summarizedexperiment))
14662 (native-inputs
14663 (list r-biocneighbors
14664 r-biocparallel
14665 r-delayedmatrixstats
14666 r-knitr
14667 r-testthat))
14668 (home-page "https://bioconductor.org/packages/TrajectoryUtils")
14669 (synopsis "Single-cell trajectory analysis utilities")
14670 (description
14671 "This package implements low-level utilities for single-cell trajectory
14672analysis, primarily intended for re-use inside higher-level packages. It
14673includes a function to create a cluster-level minimum spanning tree and data
14674structures to hold pseudotime inference results.")
14675 (license license:gpl3)))
14676
14677(define-public r-trna
14678 (package
14679 (name "r-trna")
14680 (version "1.30.0")
14681 (source
14682 (origin
14683 (method url-fetch)
14684 (uri (bioconductor-uri "tRNA" version))
14685 (sha256
14686 (base32
14687 "0vaap0lk4zfv8qsaxnsr056wblkgyf4wvq14xc30k7s3jys7vzz0"))))
14688 (properties
14689 `((upstream-name . "tRNA")))
14690 (build-system r-build-system)
14691 (propagated-inputs
14692 (list r-biocgenerics
14693 r-biostrings
14694 r-genomicranges
14695 r-ggplot2
14696 r-iranges
14697 r-modstrings
14698 r-s4vectors
14699 r-scales
14700 r-stringr
14701 r-structstrings
14702 r-xvector))
14703 (native-inputs (list r-knitr r-testthat))
14704 (home-page "https://bioconductor.org/packages/tRNA")
14705 (synopsis "Analyzing tRNA sequences and structures")
14706 (description
14707 "The tRNA package allows tRNA sequences and structures to be accessed and
14708used for subsetting. In addition, it provides visualization tools to compare
14709feature parameters of multiple tRNA sets and correlate them to additional
14710data. The tRNA package uses GRanges objects as inputs requiring only few
14711additional column data sets.")
14712 (license license:gpl3)))
14713
14714(define-public r-trnadbimport
14715 (package
14716 (name "r-trnadbimport")
14717 (version "1.30.0")
14718 (source
14719 (origin
14720 (method url-fetch)
14721 (uri (bioconductor-uri "tRNAdbImport" version))
14722 (sha256
14723 (base32 "1rbrshawck225gxghnw50pry1iig279f5rfrp7hcj6iwd5dpship"))))
14724 (properties `((upstream-name . "tRNAdbImport")))
14725 (build-system r-build-system)
14726 (propagated-inputs (list r-biostrings
14727 r-genomicranges
14728 r-httr2
14729 r-iranges
14730 r-modstrings
14731 r-s4vectors
14732 r-stringr
14733 r-structstrings
14734 r-trna
14735 r-xml2))
14736 (native-inputs (list r-biocgenerics r-httptest r-knitr r-testthat))
14737 (home-page "https://bioconductor.org/packages/tRNAdbImport")
14738 (synopsis "Importing from tRNAdb and mitotRNAdb as GRanges objects")
14739 (description
14740 "@code{tRNAdbImport} imports the entries of the @code{tRNAdb} and
14741@code{mtRNAdb} as GRanges object.")
14742 (license license:gpl3)))
14743
14744(define-public r-scds
14745 (package
14746 (name "r-scds")
14747 (version "2.0.0")
14748 (source (origin
14749 (method url-fetch)
14750 (uri (bioconductor-uri "scds" version))
14751 (sha256
14752 (base32
14753 "0992pmw7swvjqhvpfif384rrg8f6dmc3v3ccksj8g4v5j72y9dzn"))))
14754 (properties `((upstream-name . "scds")))
14755 (build-system r-build-system)
14756 (propagated-inputs (list r-dplyr
14757 r-matrix
14758 r-proc
14759 r-s4vectors
14760 r-singlecellexperiment
14761 r-summarizedexperiment
14762 r-xgboost))
14763 (native-inputs (list r-knitr))
14764 (home-page "https://bioconductor.org/packages/scds")
14765 (synopsis "In-silico doublet annotation for single cell RNA sequencing data")
14766 (description
14767 "This is an R package for doublet annotation of single cell RNA
14768sequencing data. @code{scds} provides methods to annotate doublets in
14769scRNA-seq data computationally.")
14770 (license license:expat)))
14771
14772(define-public r-slingshot
14773 (package
14774 (name "r-slingshot")
14775 (version "2.20.0")
14776 (source (origin
14777 (method url-fetch)
14778 (uri (bioconductor-uri "slingshot" version))
14779 (sha256
14780 (base32
14781 "1ir0i5skfcmnhqlz0vna44rsw5ghaasjy52w70byj5a283lq7qaz"))))
14782 (properties
14783 '((updater-extra-native-inputs . ("r-delayedmatrixstats"))))
14784 (build-system r-build-system)
14785 (propagated-inputs
14786 (list r-igraph
14787 r-matrixstats
14788 r-princurve
14789 r-s4vectors
14790 r-singlecellexperiment
14791 r-summarizedexperiment
14792 r-trajectoryutils))
14793 (native-inputs
14794 (list r-clusterexperiment r-delayedmatrixstats r-knitr r-rgl r-testthat))
14795 (home-page "https://bioconductor.org/packages/slingshot")
14796 (synopsis "Tools for ordering single-cell sequencing")
14797 (description "This package provides functions for inferring continuous,
14798branching lineage structures in low-dimensional data. Slingshot was designed
14799to model developmental trajectories in single-cell RNA sequencing data and
14800serve as a component in an analysis pipeline after dimensionality reduction
14801and clustering. It is flexible enough to handle arbitrarily many branching
14802events and allows for the incorporation of prior knowledge through supervised
14803graph construction.")
14804 (license license:artistic2.0)))
14805
14806;; This is a CRAN package but it depends on a bioconductor package.
14807(define-public r-speaq
14808 (package
14809 (name "r-speaq")
14810 (version "2.7.0")
14811 (source (origin
14812 (method url-fetch)
14813 (uri (cran-uri "speaq" version))
14814 (sha256
14815 (base32
14816 "0z9a3nbfazphp090c6hg892vjq7jp4g4cij3s5wbs1q567inbmlk"))))
14817 (properties `((upstream-name . "speaq")))
14818 (build-system r-build-system)
14819 (propagated-inputs
14820 (list r-cluster
14821 r-data-table
14822 r-dosnow
14823 r-foreach
14824 r-ggplot2
14825 r-gridextra
14826 r-impute
14827 r-massspecwavelet
14828 r-missforest
14829 r-reshape2
14830 r-rfast
14831 r-rvest
14832 r-xml2))
14833 (native-inputs (list r-knitr))
14834 (home-page "https://cran.r-project.org/package=speaq")
14835 (synopsis "Tools for nuclear magnetic resonance spectra alignment")
14836 (description
14837 "This package aims to make @acronym{NMR, Nuclear Magnetic Resonance}
14838spectroscopy data analysis as easy as possible. It only requires a small set
14839of functions to perform an entire analysis. Speaq offers the possibility of
14840raw spectra alignment and quantitation but also an analysis based on features
14841whereby the spectra are converted to peaks which are then grouped and turned
14842into features. These features can be processed with any number of statistical
14843tools either included in speaq or available elsewhere on CRAN.")
14844 (license license:asl2.0)))
14845
14846(define-public r-spectra
14847 (package
14848 (name "r-spectra")
14849 (version "1.22.2")
14850 (source (origin
14851 (method url-fetch)
14852 (uri (bioconductor-uri "Spectra" version))
14853 (sha256
14854 (base32
14855 "0zpy23zr8vzji4g05y51hfc9snf9l8zb4bbg5pyh6jzvqj6m759a"))))
14856 (properties
14857 '((upstream-name . "Spectra")
14858 ;; Avoid dependency cycle.
14859 (updater-ignored-native-inputs . ("r-msdata"))))
14860 (build-system r-build-system)
14861 ;; FIXME Tests fail with: Error in mzR::openMSfile(x): File NA not found
14862 (arguments (list #:tests? #false))
14863 (propagated-inputs (list r-biocgenerics
14864 r-biocparallel
14865 r-data-table
14866 r-fs
14867 r-iranges
14868 r-metabocoreutils
14869 r-mscoreutils
14870 r-protgenerics
14871 r-s4vectors))
14872 (native-inputs (list r-devtools
14873 r-knitr
14874 r-msdatahub
14875 r-patrick
14876 r-rhdf5
14877 r-testthat
14878 r-vdiffr))
14879 (home-page "https://github.com/RforMassSpectrometry/Spectra")
14880 (synopsis "Spectra infrastructure for mass spectrometry data")
14881 (description
14882 "The Spectra package defines an efficient infrastructure for storing and
14883handling mass spectrometry spectra and functionality to subset, process,
14884visualize and compare spectra data. It provides different
14885implementations (backends) to store mass spectrometry data. These comprise
14886backends tuned for fast data access and processing and backends for very large
14887data sets ensuring a small memory footprint.")
14888 (license license:artistic2.0)))
14889
14890(define-public r-stager
14891 (package
14892 (name "r-stager")
14893 (version "1.34.0")
14894 (source
14895 (origin
14896 (method url-fetch)
14897 (uri (bioconductor-uri "stageR" version))
14898 (sha256
14899 (base32 "04zsjzxrnk63qap9ipwbbbsq8dv66sjdxgl4n0nzkm64pgyz2sqk"))))
14900 (properties `((upstream-name . "stageR")))
14901 (build-system r-build-system)
14902 (propagated-inputs (list r-summarizedexperiment))
14903 (native-inputs (list r-knitr r-testthat))
14904 (home-page "https://bioconductor.org/packages/stageR")
14905 (synopsis "Stage-wise analysis of high throughput gene expression data")
14906 (description
14907 "The stageR package allows automated stage-wise analysis of
14908high-throughput gene expression data. The method is published in Genome
14909Biology at
14910@url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.")
14911 (license license:gpl3)))
14912
14913(define-public r-stringdb
14914 (package
14915 (name "r-stringdb")
14916 (version "2.24.0")
14917 (source
14918 (origin
14919 (method url-fetch)
14920 (uri (bioconductor-uri "STRINGdb" version))
14921 (sha256
14922 (base32 "1n83y39pc14p9qdlpjddd97l11h37g5kqbp3qbbdx7l3ibvnbrkd"))))
14923 (properties `((upstream-name . "STRINGdb")))
14924 (build-system r-build-system)
14925 ;; Tests attempt to connect to string-db.org website.
14926 (arguments (list #:tests? #false))
14927 (propagated-inputs
14928 (list r-gplots
14929 r-hash
14930 r-httr
14931 r-igraph
14932 r-plotrix
14933 r-plyr
14934 r-png
14935 r-rcolorbrewer
14936 r-sqldf))
14937 (native-inputs (list r-biocgenerics r-runit))
14938 (home-page "https://git.bioconductor.org/packages/STRINGdb")
14939 (synopsis "Search tool for the retrieval of interacting proteins database")
14940 (description
14941 "The @code{STRINGdb} package provides an R interface to the STRING
14942protein-protein interactions database. @url{https://www.string-db.org,
14943STRING} is a database of known and predicted protein-protein interactions.
14944The interactions include direct (physical) and indirect (functional)
14945associations. Each interaction is associated with a combined confidence score
14946that integrates the various evidences.")
14947 (license license:gpl2)))
14948
14949(define-public r-structstrings
14950 (package
14951 (name "r-structstrings")
14952 (version "1.28.0")
14953 (source
14954 (origin
14955 (method url-fetch)
14956 (uri (bioconductor-uri "Structstrings" version))
14957 (sha256
14958 (base32 "0lcy3kbvifkyxrb6hn6mq9z6mvf4fns1fwlkwl10hjxk7i6r7wr4"))))
14959 (properties `((upstream-name . "Structstrings")))
14960 (build-system r-build-system)
14961 (propagated-inputs (list r-biocgenerics
14962 r-biostrings
14963 r-crayon
14964 r-iranges
14965 r-s4vectors
14966 r-stringi
14967 r-stringr
14968 r-xvector))
14969 (native-inputs (list r-knitr r-testthat))
14970 (home-page "https://github.com/FelixErnst/Structstrings")
14971 (synopsis "Implementation of the dot bracket annotations with Biostrings")
14972 (description
14973 "The Structstrings package implements the widely used dot bracket
14974annotation for storing base pairing information in structured
14975RNA. Structstrings uses the infrastructure provided by the Biostrings package
14976and derives the @code{DotBracketString} and related classes from the BString
14977class. From these, base pair tables can be produced for in depth analysis.
14978In addition, the loop indices of the base pairs can be retrieved as well. For
14979better efficiency, information conversion is implemented in C, inspired to a
14980large extend by the @code{ViennaRNA} package.")
14981 (license license:artistic2.0)))
14982
14983(define-public r-structuralvariantannotation
14984 (package
14985 (name "r-structuralvariantannotation")
14986 (version "1.28.0")
14987 (source
14988 (origin
14989 (method url-fetch)
14990 (uri (bioconductor-uri "StructuralVariantAnnotation" version))
14991 (sha256
14992 (base32 "03sfnm7k69qc6xqfwzshzgs0z85vg62383vs31pm00acc8pfk5gn"))))
14993 (build-system r-build-system)
14994 (propagated-inputs
14995 (list r-assertthat
14996 r-biocgenerics
14997 r-biostrings
14998 r-dplyr
14999 r-genomeinfodb
15000 r-genomicfeatures
15001 r-genomicranges
15002 r-iranges
15003 r-pwalign
15004 r-rlang
15005 r-rtracklayer
15006 r-s4vectors
15007 r-stringr
15008 r-summarizedexperiment
15009 r-variantannotation))
15010 (native-inputs
15011 (list r-bsgenome-hsapiens-ucsc-hg19
15012 r-knitr
15013 r-testthat
15014 r-tictoc
15015 r-tidyverse))
15016 (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
15017 (synopsis "R package designed to simplify structural variant analysis")
15018 (description
15019 "This package contains useful helper functions for dealing with structural
15020variants in VCF format. The packages contains functions for parsing VCFs from
15021a number of popular callers as well as functions for dealing with breakpoints
15022involving two separate genomic loci encoded as GRanges objects.")
15023 (license license:gpl3)))
15024
15025(define-public r-summarizedexperiment
15026 (package
15027 (name "r-summarizedexperiment")
15028 (version "1.42.0")
15029 (source (origin
15030 (method url-fetch)
15031 (uri (bioconductor-uri "SummarizedExperiment" version))
15032 (sha256
15033 (base32
15034 "06m74i539gnrssifq0yrrzzmr7m7fsd39b68mliixr34pf6hn4a0"))))
15035 (properties
15036 `((upstream-name . "SummarizedExperiment")
15037 (updater-extra-native-inputs . ("r-runit"))))
15038 (build-system r-build-system)
15039 (arguments
15040 (list
15041 #:test-directory "inst/unitTests"
15042 ;; This test requires r-txdb-hsapiens-ucsc-hg19-knowngene, but we can't
15043 ;; add it due to a dependency cycle.
15044 #:skipped-tests '("test_makeSummarizedExperimentFromExpressionSet.R")))
15045 (propagated-inputs
15046 (list r-biobase
15047 r-biocgenerics
15048 r-delayedarray
15049 r-genomicranges
15050 r-iranges
15051 r-matrix
15052 r-matrixgenerics
15053 r-s4arrays
15054 r-s4vectors
15055 r-seqinfo))
15056 (native-inputs
15057 (list r-digest r-knitr r-runit))
15058 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
15059 (synopsis "Container for representing genomic ranges by sample")
15060 (description
15061 "The SummarizedExperiment container contains one or more assays, each
15062represented by a matrix-like object of numeric or other mode. The rows
15063typically represent genomic ranges of interest and the columns represent
15064samples.")
15065 (license license:artistic2.0)))
15066
15067(define-public r-survcomp
15068 (package
15069 (name "r-survcomp")
15070 (version "1.62.0")
15071 (source (origin
15072 (method url-fetch)
15073 (uri (bioconductor-uri "survcomp" version))
15074 (sha256
15075 (base32
15076 "0ga480z0775v8g9bj4haaxs5wyvnxc891rn70j26scig6411x2x7"))))
15077 (properties `((upstream-name . "survcomp")))
15078 (build-system r-build-system)
15079 (propagated-inputs (list r-bootstrap
15080 r-ipred
15081 r-kernsmooth
15082 r-prodlim
15083 r-rmeta
15084 r-suppdists
15085 r-survival
15086 r-survivalroc))
15087 (native-inputs (list r-biobase r-biocmanager r-xtable))
15088 (home-page "https://www.pmgenomics.ca/bhklab/")
15089 (synopsis "Performance assessment and comparison for survival analysis")
15090 (description
15091 "This is a package for the assessment and comparison of the performance
15092of risk prediction (survival) models.")
15093 (license license:artistic2.0)))
15094
15095(define-public r-sva
15096 (package
15097 (name "r-sva")
15098 (version "3.60.0")
15099 (source
15100 (origin
15101 (method url-fetch)
15102 (uri (bioconductor-uri "sva" version))
15103 (sha256
15104 (base32
15105 "03xkb1zy9p92dyj68h66d62hf1kls6xxklmva3dfkg2ss0avblnm"))))
15106 (properties
15107 '((updater-extra-native-inputs . ("r-biocstyle"))))
15108 (build-system r-build-system)
15109 ;; Vignettes fail with: could not find function "topTableF"
15110 (arguments (list #:test-types '(list "tests")))
15111 (propagated-inputs
15112 (list r-biocparallel
15113 r-edger
15114 r-genefilter
15115 r-limma
15116 r-matrixstats
15117 r-mgcv))
15118 (native-inputs
15119 (list r-biocstyle r-bladderbatch r-pamr r-testthat r-zebrafishrnaseq))
15120 (home-page "https://bioconductor.org/packages/sva")
15121 (synopsis "Surrogate variable analysis")
15122 (description
15123 "This package contains functions for removing batch effects and other
15124unwanted variation in high-throughput experiment. It also contains functions
15125for identifying and building surrogate variables for high-dimensional data
15126sets. Surrogate variables are covariates constructed directly from
15127high-dimensional data like gene expression/RNA sequencing/methylation/brain
15128imaging data that can be used in subsequent analyses to adjust for unknown,
15129unmodeled, or latent sources of noise.")
15130 (license license:artistic2.0)))
15131
15132(define-public r-systempiper
15133 (package
15134 (name "r-systempiper")
15135 (version "2.18.0")
15136 (source
15137 (origin
15138 (method url-fetch)
15139 (uri (bioconductor-uri "systemPipeR" version))
15140 (sha256
15141 (base32
15142 "0zvlgnb62yhsgm8xc6fpyp250sklbpzjykn4hcpikdknppmzdnhq"))))
15143 (properties `((upstream-name . "systemPipeR")))
15144 (build-system r-build-system)
15145 ;; Tests fail because genWorkenvir fails to set up the environment.
15146 (arguments (list #:tests? #false))
15147 (propagated-inputs
15148 (list r-biocgenerics
15149 r-biostrings
15150 r-crayon
15151 r-genomicranges
15152 r-ggplot2
15153 r-htmlwidgets
15154 r-magrittr
15155 r-rsamtools
15156 r-s4vectors
15157 r-shortread
15158 r-stringr
15159 r-summarizedexperiment
15160 r-yaml))
15161 (native-inputs
15162 (list r-biomart
15163 r-chippeakanno
15164 r-knitr
15165 r-rsubread
15166 r-rtracklayer
15167 r-systempiperdata
15168 r-testthat
15169 r-txdbmaker))
15170 (home-page "https://github.com/tgirke/systemPipeR")
15171 (synopsis "Next generation sequencing workflow and reporting environment")
15172 (description
15173 "This R package provides tools for building and running automated
15174end-to-end analysis workflows for a wide range of @dfn{next generation
15175sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
15176Important features include a uniform workflow interface across different NGS
15177applications, automated report generation, and support for running both R and
15178command-line software, such as NGS aligners or peak/variant callers, on local
15179computers or compute clusters. Efficient handling of complex sample sets and
15180experimental designs is facilitated by a consistently implemented sample
15181annotation infrastructure.")
15182 (license license:artistic2.0)))
15183
15184(define-public r-topgo
15185 (package
15186 (name "r-topgo")
15187 (version "2.64.0")
15188 (source (origin
15189 (method url-fetch)
15190 (uri (bioconductor-uri "topGO" version))
15191 (sha256
15192 (base32
15193 "02g79vhg86q5345vib818srvj96hf3an0b7dfv8ixhc5v1z9ja55"))))
15194 (properties
15195 `((upstream-name . "topGO")))
15196 (build-system r-build-system)
15197 (propagated-inputs
15198 (list r-annotationdbi
15199 r-biobase
15200 r-biocgenerics
15201 r-dbi
15202 r-go-db
15203 r-graph
15204 r-lattice
15205 r-matrixstats
15206 r-sparsem))
15207 (home-page "https://bioconductor.org/packages/topGO")
15208 (synopsis "Enrichment analysis for gene ontology")
15209 (description
15210 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
15211terms while accounting for the topology of the GO graph. Different test
15212statistics and different methods for eliminating local similarities and
15213dependencies between GO terms can be implemented and applied.")
15214 ;; Any version of the LGPL applies.
15215 (license license:lgpl2.1+)))
15216
15217(define-public r-txdbmaker
15218 (package
15219 (name "r-txdbmaker")
15220 (version "1.8.0")
15221 (source
15222 (origin
15223 (method url-fetch)
15224 (uri (bioconductor-uri "txdbmaker" version))
15225 (sha256
15226 (base32 "19133f2rdsw4ryycb5lvcwhp9sxzchd0zpmxm490rzpmd7djyj47"))))
15227 (properties
15228 '((upstream-name . "txdbmaker")
15229 (updater-extra-native-inputs . ("r-genomeinfodbdata" "r-runit"))))
15230 (build-system r-build-system)
15231 (arguments
15232 (list
15233 #:test-directory "inst/unitTests"
15234 #:skipped-tests
15235 ;; These tests attempt to download files.
15236 '("test_makeTxDbFromUCSC.R"
15237 "test_makeTxDbFromBiomart.R")))
15238 (propagated-inputs (list r-annotationdbi
15239 r-biobase
15240 r-biocgenerics
15241 r-biocio
15242 r-biomart
15243 r-dbi
15244 r-genomeinfodb
15245 r-genomicfeatures
15246 r-genomicranges
15247 r-httr
15248 r-iranges
15249 r-rjson
15250 r-rsqlite
15251 r-rtracklayer
15252 r-s4vectors
15253 r-seqinfo
15254 r-ucsc-utils))
15255 (native-inputs (list r-genomeinfodbdata r-knitr r-runit))
15256 (home-page "https://bioconductor.org/packages/txdbmaker")
15257 (synopsis "Tools for making TxDb objects from genomic annotations")
15258 (description
15259 "This package provides a set of tools for making @code{TxDb} objects from
15260genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files).
15261These tools allow the user to download the genomic locations of transcripts,
15262exons, and CDS, for a given assembly, and to import them in a @code{TxDb}
15263object. @code{TxDb} objects are implemented in the @code{GenomicFeatures}
15264package, together with flexible methods for extracting the desired features in
15265convenient formats.")
15266 (license license:artistic2.0)))
15267
15268(define-public r-tximport
15269 (package
15270 (name "r-tximport")
15271 (version "1.40.0")
15272 (source (origin
15273 (method url-fetch)
15274 (uri (bioconductor-uri "tximport" version))
15275 (sha256
15276 (base32
15277 "1y99r6fpycm9ngycx60pfyb1ay7a9sx9ybdg0p5lrxn159mim13j"))))
15278 (properties
15279 '((updater-extra-native-inputs
15280 . ("r-matrix" "r-rhdf5"))))
15281 (build-system r-build-system)
15282 ;; One test fails because the "eds" package is missing, but there is no
15283 ;; such package.
15284 (arguments (list #:tests? #false))
15285 (native-inputs
15286 (list r-knitr
15287 r-matrix
15288 r-matrixstats
15289 r-readr
15290 r-rhdf5
15291 r-testthat
15292 r-tximportdata))
15293 (home-page "https://bioconductor.org/packages/tximport")
15294 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
15295 (description
15296 "This package provides tools to import transcript-level abundance,
15297estimated counts and transcript lengths, and to summarize them into matrices
15298for use with downstream gene-level analysis packages. Average transcript
15299length, weighted by sample-specific transcript abundance estimates, is
15300provided as a matrix which can be used as an offset for different expression
15301of gene-level counts.")
15302 (license license:gpl2+)))
15303
15304;; This is a CRAN package, but it depends on a Bioconductor package.
15305(define-public r-valr
15306 (package
15307 (name "r-valr")
15308 (version "0.9.1")
15309 (source
15310 (origin
15311 (method url-fetch)
15312 (uri (cran-uri "valr" version))
15313 (sha256
15314 (base32
15315 "1f0q7c8mz7w2ih5m3bfb0g5y9lx5lmn1ifj234k75ksffwwi4lz9"))))
15316 (build-system r-build-system)
15317 (propagated-inputs
15318 (list r-broom
15319 r-cli
15320 r-cpp11
15321 r-cpp11bigwig
15322 r-dplyr
15323 r-ggplot2
15324 r-lifecycle
15325 r-readr
15326 r-rlang
15327 r-stringr
15328 r-tibble))
15329 (native-inputs
15330 (list r-knitr r-testthat))
15331 (home-page "https://github.com/rnabioco/valr")
15332 (synopsis "Genome interval arithmetic in R")
15333 (description
15334 "This package enables you to read and manipulate genome intervals and
15335signals. It provides functionality similar to command-line tool suites within
15336R, enabling interactive analysis and visualization of genome-scale data.")
15337 (license license:expat)))
15338
15339(define-public r-variantannotation
15340 (package
15341 (name "r-variantannotation")
15342 (version "1.58.0")
15343 (source (origin
15344 (method url-fetch)
15345 (uri (bioconductor-uri "VariantAnnotation" version))
15346 (sha256
15347 (base32
15348 "1b4b3qv11pk89gqwgv9ya26x1haxc8w3lwwy906da48zi0lzvzmx"))))
15349 (properties
15350 `((upstream-name . "VariantAnnotation")
15351 (updater-ignored-native-inputs
15352 . ("r-sift-hsapiens-dbsnp132"
15353 "r-polyphen-hsapiens-dbsnp131"))
15354 (updater-extra-native-inputs
15355 . ("r-runit"))))
15356 (build-system r-build-system)
15357 (arguments
15358 (list
15359 #:test-directory "inst/unitTests"
15360 ;; These tests depend on SIFT.Hsapiens.dbSNP132, which depends on
15361 ;; r-variantannotation.
15362 #:skipped-tests '("test_SIFTandPolyPhen.R")))
15363 (propagated-inputs
15364 (list r-annotationdbi
15365 r-biobase
15366 r-biocgenerics
15367 r-biostrings
15368 r-bsgenome
15369 r-curl
15370 r-dbi
15371 r-genomicfeatures
15372 r-genomicranges
15373 r-iranges
15374 r-matrixgenerics
15375 r-rhtslib
15376 r-rsamtools
15377 r-rtracklayer
15378 r-s4vectors
15379 r-seqinfo
15380 r-summarizedexperiment
15381 r-xvector))
15382 (native-inputs (list r-bsgenome-hsapiens-ucsc-hg19
15383 r-knitr r-runit r-snpstats
15384 r-txdb-hsapiens-ucsc-hg19-knowngene))
15385 (home-page "https://bioconductor.org/packages/VariantAnnotation")
15386 (synopsis "Package for annotation of genetic variants")
15387 (description "This R package can annotate variants, compute amino acid
15388coding changes and predict coding outcomes.")
15389 (license license:artistic2.0)))
15390
15391(define-public r-vsn
15392 (package
15393 (name "r-vsn")
15394 (version "3.80.0")
15395 (source
15396 (origin
15397 (method url-fetch)
15398 (uri (bioconductor-uri "vsn" version))
15399 (sha256
15400 (base32
15401 "179vgpn3qq4syd66pk8p0j1lisqc7fka1fmwqn988dl943isbrv2"))))
15402 (properties
15403 ;; This is needed for vignettes.
15404 '((updater-extra-native-inputs . ("r-biocstyle"))))
15405 (build-system r-build-system)
15406 (propagated-inputs
15407 (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
15408 (native-inputs
15409 (list r-biocstyle r-knitr r-testthat))
15410 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
15411 (synopsis "Variance stabilization and calibration for microarray data")
15412 (description
15413 "The package implements a method for normalising microarray intensities,
15414and works for single- and multiple-color arrays. It can also be used for data
15415from other technologies, as long as they have similar format. The method uses
15416a robust variant of the maximum-likelihood estimator for an
15417additive-multiplicative error model and affine calibration. The model
15418incorporates data calibration step (a.k.a. normalization), a model for the
15419dependence of the variance on the mean intensity and a variance stabilizing
15420data transformation. Differences between transformed intensities are
15421analogous to \"normalized log-ratios\". However, in contrast to the latter,
15422their variance is independent of the mean, and they are usually more sensitive
15423and specific in detecting differential transcription.")
15424 (license license:artistic2.0)))
15425
15426;; There is no source tarball, so we fetch the code from the Bioconductor git
15427;; repository.
15428(define-public r-xcir
15429 (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
15430 (revision "1"))
15431 (package
15432 (name "r-xcir")
15433 (version (git-version "1.8.0" revision commit))
15434 (source (origin
15435 (method git-fetch)
15436 (uri (git-reference
15437 (url "https://git.bioconductor.org/packages/XCIR")
15438 (commit commit)))
15439 (file-name (git-file-name name version))
15440 (sha256
15441 (base32
15442 "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
15443 (properties `((upstream-name . "XCIR")))
15444 (build-system r-build-system)
15445 (propagated-inputs (list r-biomart
15446 r-biostrings
15447 r-data-table
15448 r-ggplot2
15449 r-iranges
15450 r-readxl
15451 r-s4vectors
15452 r-seqminer
15453 r-variantannotation))
15454 (native-inputs (list r-knitr))
15455 (home-page "https://github.com/SRenan/XCIR")
15456 (synopsis "Analysis of X chromosome inactivation")
15457 (description
15458 "This package is an R package that offers models and tools for subject
15459level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
15460inference.")
15461 (license license:gpl2))))
15462
15463(define-public r-xina
15464 (package
15465 (name "r-xina")
15466 (version "1.30.0")
15467 (source
15468 (origin
15469 (method url-fetch)
15470 (uri (bioconductor-uri "XINA" version))
15471 (sha256
15472 (base32 "0kb23h0gsqgb6a8j81kj0vywjcp2d47lp96lvn0rq8p8rfn8mwqc"))))
15473 (properties `((upstream-name . "XINA")))
15474 (build-system r-build-system)
15475 (propagated-inputs
15476 (list r-alluvial
15477 r-ggplot2
15478 r-gridextra
15479 r-igraph
15480 r-mclust
15481 r-plyr
15482 r-stringdb))
15483 (native-inputs (list r-knitr))
15484 (home-page "https://git.bioconductor.org/packages/XINA")
15485 (synopsis "Identifying proteins that exhibit similar patterns")
15486 (description
15487 "The aim of @code{XINA} is to determine which proteins exhibit similar
15488patterns within and across experimental conditions, since proteins with
15489co-abundance patterns may have common molecular functions. @code{XINA} imports
15490multiple datasets, tags dataset in silico, and combines the data for subsequent
15491subgrouping into multiple clusters. The result is a single output depicting
15492the variation across all conditions. @code{XINA} not only extracts
15493coabundance profiles within and across experiments, but also incorporates
15494protein-protein interaction databases and integrative resources such as
15495@dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
15496molecular functions, respectively, and produces intuitive graphical outputs.")
15497 (license license:gpl3)))
15498
15499;; This is a CRAN package but it depends on r-mixomics from Bioconductor.
15500(define-public r-xllim
15501 (package
15502 (name "r-xllim")
15503 (version "2.3.1")
15504 (source
15505 (origin
15506 (method url-fetch)
15507 (uri (cran-uri "xLLiM" version))
15508 (sha256
15509 (base32 "1h2z6a3j3yi7rj5lyk7gb1iyp2vf516fgmk7wr333gfkvk522n2r"))))
15510 (properties `((upstream-name . "xLLiM")))
15511 (build-system r-build-system)
15512 (propagated-inputs (list r-abind
15513 r-capushe
15514 r-corpcor
15515 r-e1071
15516 r-glmnet
15517 r-igraph
15518 r-mass
15519 r-matrix
15520 r-mda
15521 r-mixomics
15522 r-progress
15523 r-randomforest))
15524 (home-page "https://cran.r-project.org/package=xLLiM")
15525 (synopsis "High dimensional locally-linear mapping")
15526 (description
15527 "This package provides a tool for non linear mapping (non linear
15528regression) using a mixture of regression model and an inverse regression
15529strategy. The methods include the GLLiM model (see Deleforge et al (2015)
15530<DOI:10.1007/s11222-014-9461-5>) based on Gaussian mixtures and a robust
15531version of GLLiM, named SLLiM (see Perthame et al (2016)
15532<DOI:10.1016/j.jmva.2017.09.009>) based on a mixture of Generalized Student
15533distributions. The methods also include BLLiM (see Devijver et al (2017)
15534<@code{arXiv:1701.07899>}) which is an extension of GLLiM with a sparse block
15535diagonal structure for large covariance matrices (particularly interesting for
15536transcriptomic data).")
15537 (license license:gpl2+)))
15538
15539(define-public r-xmapbridge
15540 (package
15541 (name "r-xmapbridge")
15542 (version "1.70.0")
15543 (source
15544 (origin
15545 (method url-fetch)
15546 (uri (bioconductor-uri "xmapbridge" version))
15547 (sha256
15548 (base32 "1bhp69d8rfxgnyvbhbvyyj723pfqqyz01h3cr9vqzwq7lmzwfb11"))))
15549 (properties
15550 '((upstream-name . "xmapbridge")
15551 (updater-extra-native-inputs . ("r-rcolorbrewer"))))
15552 (build-system r-build-system)
15553 (native-inputs (list r-rcolorbrewer))
15554 (home-page "https://git.bioconductor.org/packages/xmapbridge")
15555 (synopsis "Display numeric data in the web based genome browser X:MAP")
15556 (description
15557 "The package @code{xmapbridge} can plot graphs in the X:Map genome
15558browser. X:Map uses the Google Maps API to provide a scrollable view of the
15559genome. It supports a number of species, and can be accessed at
15560@url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a
15561suitable format. Graph plotting in R is done using calls to the functions
15562@code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
15563similar to those used by the standard plot methods in R. These result in data
15564being written to a set of files (in a specific directory structure) that
15565contain the data to be displayed, as well as some additional meta-data
15566describing each of the graphs.")
15567 (license license:lgpl3)))
15568
15569(define-public r-xvector
15570 (package
15571 (name "r-xvector")
15572 (version "0.52.0")
15573 (source (origin
15574 (method url-fetch)
15575 (uri (bioconductor-uri "XVector" version))
15576 (sha256
15577 (base32
15578 "17b053xva3pndaqhygazf1sn5ypz2bvvv9m20vz17np9hk4j1dc0"))))
15579 (properties
15580 '((upstream-name . "XVector")
15581 (updater-extra-native-inputs . ("r-runit"))))
15582 (build-system r-build-system)
15583 (arguments
15584 `(#:phases
15585 (modify-phases %standard-phases
15586 (add-after 'unpack 'use-system-zlib
15587 (lambda _
15588 (substitute* "DESCRIPTION"
15589 (("zlibbioc, ") ""))
15590 (substitute* "NAMESPACE"
15591 (("import\\(zlibbioc\\)") "")))))))
15592 (inputs
15593 (list zlib))
15594 (native-inputs (list r-runit))
15595 (propagated-inputs
15596 (list r-biocgenerics r-iranges r-s4vectors))
15597 (home-page "https://bioconductor.org/packages/XVector")
15598 (synopsis "Representation and manpulation of external sequences")
15599 (description
15600 "This package provides memory efficient S4 classes for storing sequences
15601\"externally\" (behind an R external pointer, or on disk).")
15602 (license license:artistic2.0)))
15603
15604(define-public r-zlibbioc
15605 (package
15606 (name "r-zlibbioc")
15607 (version "1.54.0")
15608 (source (origin
15609 (method url-fetch)
15610 (uri (bioconductor-uri "zlibbioc" version))
15611 (sha256
15612 (base32
15613 "0ll3v5b9yk63rqiwm4g0dwan22mqkj2lv1b6czwghbpl1jpv2jrd"))))
15614 (properties
15615 `((upstream-name . "zlibbioc")))
15616 (build-system r-build-system)
15617 (native-inputs (list r-knitr))
15618 (home-page "https://bioconductor.org/packages/zlibbioc")
15619 (synopsis "Provider for zlib-1.2.5 to R packages")
15620 (description "This package uses the source code of zlib-1.2.5 to create
15621libraries for systems that do not have these available via other means.")
15622 (license license:artistic2.0)))
15623
15624(define-public r-zellkonverter
15625 (package
15626 (name "r-zellkonverter")
15627 (version "1.22.0")
15628 (source
15629 (origin
15630 (method url-fetch)
15631 (uri (bioconductor-uri "zellkonverter" version))
15632 (sha256
15633 (base32 "0k7zlf25y9kckbdzisrkn2pkj79xv4916sypmld8qrfbkcjf1ih4"))))
15634 (properties `((upstream-name . "zellkonverter")))
15635 (build-system r-build-system)
15636 (arguments
15637 (list
15638 #:skipped-tests
15639 ;; In this file code outside of any particular testthat test attempts to
15640 ;; fetch data from gypsum.artifactdb.com.
15641 '("test-write.R")
15642 #:phases
15643 #~(modify-phases %standard-phases
15644 (add-after 'unpack 'basilisk-configuration
15645 ;; This uses r-basilisk, which attempts to set up a Conda
15646 ;; environment. We've patched basilisk to work without Conda when
15647 ;; GUIX_BYPASS_BASILISK is set, so that's what we do here.
15648 (lambda* (#:key inputs #:allow-other-keys)
15649 (setenv "HOME" "/tmp")
15650 (setenv "RETICULATE_PYTHON" (which "python3"))
15651 (setenv "GUIX_BYPASS_BASILISK" "1"))))))
15652 (propagated-inputs
15653 (list r-basilisk
15654 r-cli
15655 r-delayedarray
15656 r-matrix
15657 r-reticulate
15658 r-s4vectors
15659 r-singlecellexperiment
15660 r-sparsearray
15661 r-summarizedexperiment))
15662 (inputs (list python-anndata
15663 python-h5py
15664 python-natsort
15665 python-numpy
15666 python-pandas
15667 python-scipy
15668 python-wrapper))
15669 (native-inputs (list r-biocfilecache
15670 r-hdf5array
15671 r-knitr
15672 r-pkgload
15673 r-scrnaseq
15674 r-spatialexperiment
15675 r-spelling
15676 r-testthat
15677 r-withr))
15678 (home-page "https://github.com/theislab/zellkonverter")
15679 (synopsis "Conversion between AnnData and single-cell experiments objects")
15680 (description
15681 "This package provides methods to convert between Python AnnData objects
15682and SingleCellExperiment objects. These are primarily intended for use by
15683downstream Bioconductor packages that wrap Python methods for single-cell data
15684analysis. It also includes functions to read and write H5AD files used for
15685saving AnnData objects to disk.")
15686 (license license:expat)))
15687
15688(define-public r-geneplotter
15689 (package
15690 (name "r-geneplotter")
15691 (version "1.90.0")
15692 (source
15693 (origin
15694 (method url-fetch)
15695 (uri (bioconductor-uri "geneplotter" version))
15696 (sha256
15697 (base32
15698 "0phvff6vglrris9alc0n8mxal8g90vdx6ppchxrbc7xppbffcrza"))))
15699 (build-system r-build-system)
15700 (propagated-inputs
15701 (list r-annotate
15702 r-annotationdbi
15703 r-biobase
15704 r-biocgenerics
15705 r-lattice
15706 r-rcolorbrewer))
15707 (native-inputs
15708 (list r-knitr))
15709 (home-page "https://bioconductor.org/packages/geneplotter")
15710 (synopsis "Graphics functions for genomic data")
15711 (description
15712 "This package provides functions for plotting genomic data.")
15713 (license license:artistic2.0)))
15714
15715(define-public r-oligoclasses
15716 (package
15717 (name "r-oligoclasses")
15718 (version "1.74.0")
15719 (source
15720 (origin
15721 (method url-fetch)
15722 (uri (bioconductor-uri "oligoClasses" version))
15723 (sha256
15724 (base32
15725 "07fk31gmz6cqlkxlmgh8igz732ma8ryzxh5qffcvgmh1zkh5vxkx"))))
15726 (properties `((upstream-name . "oligoClasses")))
15727 (build-system r-build-system)
15728 ;; Some tests need pd.mapping50k.hind240, which needs this package.
15729 (arguments (list #:tests? #false))
15730 (propagated-inputs
15731 (list r-affyio
15732 r-biobase
15733 r-biocgenerics
15734 r-biocmanager
15735 r-biostrings
15736 r-dbi
15737 r-ff
15738 r-foreach
15739 r-genomicranges
15740 r-iranges
15741 r-rsqlite
15742 r-s4vectors
15743 r-summarizedexperiment))
15744 (home-page "https://bioconductor.org/packages/oligoClasses/")
15745 (synopsis "Classes for high-throughput arrays")
15746 (description
15747 "This package contains class definitions, validity checks, and
15748initialization methods for classes used by the @code{oligo} and @code{crlmm}
15749packages.")
15750 (license license:gpl2+)))
15751
15752(define-public r-oligo
15753 (package
15754 (name "r-oligo")
15755 (version "1.76.0")
15756 (source
15757 (origin
15758 (method url-fetch)
15759 (uri (bioconductor-uri "oligo" version))
15760 (sha256
15761 (base32
15762 "0lzp1k74z3k0rrzsxzj7qswjwz20wkvr6dsnkbp20gnq5bw2zngk"))))
15763 (properties
15764 '((upstream-name . "oligo")
15765 (updater-ignored-native-inputs . ("r-oligodata"))))
15766 (build-system r-build-system)
15767 ;; Tests require r-oligodata, which depends on this package.
15768 (arguments (list #:tests? #false))
15769 (inputs (list zlib))
15770 (propagated-inputs
15771 (list r-affxparser
15772 r-affyio
15773 r-biobase
15774 r-biocgenerics
15775 r-biostrings
15776 r-bit
15777 r-dbi
15778 r-ff
15779 r-oligoclasses
15780 r-preprocesscore
15781 r-rsqlite))
15782 (native-inputs
15783 (list r-knitr r-runit))
15784 (home-page "https://bioconductor.org/packages/oligo/")
15785 (synopsis "Preprocessing tools for oligonucleotide arrays")
15786 (description
15787 "This package provides a package to analyze oligonucleotide
15788arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
15789Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
15790 (license license:lgpl2.0+)))
15791
15792(define-public r-qfeatures
15793 (package
15794 (name "r-qfeatures")
15795 (version "1.22.0")
15796 (source (origin
15797 (method url-fetch)
15798 (uri (bioconductor-uri "QFeatures" version))
15799 (sha256
15800 (base32
15801 "0m0alvmlx177jq638sidxbndqf6s6pl80bjlx8zkh8m9xkqmvbfw"))))
15802 (properties
15803 '((upstream-name . "QFeatures")
15804 (updater-extra-native-inputs
15805 . ("r-impute" "r-preprocesscore" "r-vsn"))
15806 ;; Avoid a dependency cycle.
15807 (updater-ignored-native-inputs
15808 . ("r-psmatch"))))
15809 (build-system r-build-system)
15810 (propagated-inputs (list r-annotationfilter
15811 r-biobase
15812 r-biocgenerics
15813 r-igraph
15814 r-iranges
15815 r-lazyeval
15816 r-mscoreutils
15817 r-multiassayexperiment
15818 r-plotly
15819 r-protgenerics
15820 r-reshape2
15821 r-s4vectors
15822 r-summarizedexperiment
15823 r-tidyr
15824 r-tidyselect))
15825 (native-inputs
15826 (list r-impute
15827 r-knitr
15828 r-matrix
15829 r-matrixstats
15830 r-preprocesscore
15831 r-singlecellexperiment
15832 r-testthat
15833 r-vdiffr
15834 r-vsn))
15835 (home-page "https://github.com/RforMassSpectrometry/QFeatures")
15836 (synopsis "Quantitative features for mass spectrometry data")
15837 (description
15838 "The QFeatures infrastructure enables the management and processing of
15839quantitative features for high-throughput mass spectrometry assays. It
15840provides a familiar Bioconductor user experience to manages quantitative data
15841across different assay levels (such as peptide spectrum matches, peptides and
15842proteins) in a coherent and tractable format.")
15843 (license license:artistic2.0)))
15844
15845(define-public r-quantsmooth
15846 (package
15847 (name "r-quantsmooth")
15848 (version "1.78.0")
15849 (source
15850 (origin
15851 (method url-fetch)
15852 (uri (bioconductor-uri "quantsmooth" version))
15853 (sha256
15854 (base32 "11ry6bgcijflild2qbss2yll7zwcys7vbav02p4zrn3sxkj1irlg"))))
15855 (properties `((upstream-name . "quantsmooth")))
15856 (build-system r-build-system)
15857 (propagated-inputs (list r-quantreg))
15858 (home-page "https://bioconductor.org/packages/quantsmooth")
15859 (synopsis "Quantile smoothing and genomic visualization of array data")
15860 (description
15861 "This package implements quantile smoothing. It contains a dataset used
15862to produce human chromosomal ideograms for plotting purposes and a collection
15863of arrays that contains data of chromosome 14 of 3 colorectal tumors. The
15864package provides functions for painting chromosomal icons, chromosome or
15865chromosomal idiogram and other types of plots. Quantsmooth offers options
15866like converting chromosomal ids to their numeric form, retrieving the human
15867chromosomal length from NCBI data, retrieving regions of interest in a vector
15868of intensities using quantile smoothing, determining cytoband position based
15869on the location of the probe, and other useful tools.")
15870 (license license:gpl2)))
15871
15872(define-public r-qvalue
15873 (package
15874 (name "r-qvalue")
15875 (version "2.44.0")
15876 (source
15877 (origin
15878 (method url-fetch)
15879 (uri (bioconductor-uri "qvalue" version))
15880 (sha256
15881 (base32
15882 "03mxzgwckbz1k56sbh14nw8f8py5lwqvcai1aqch5abzz8r8nyp8"))))
15883 (build-system r-build-system)
15884 (propagated-inputs
15885 (list r-ggplot2 r-reshape2))
15886 (native-inputs
15887 (list r-knitr))
15888 (home-page "https://github.com/StoreyLab/qvalue")
15889 (synopsis "Q-value estimation for false discovery rate control")
15890 (description
15891 "This package takes a list of p-values resulting from the simultaneous
15892testing of many hypotheses and estimates their q-values and local @dfn{false
15893discovery rate} (FDR) values. The q-value of a test measures the proportion
15894of false positives incurred when that particular test is called significant.
15895The local FDR measures the posterior probability the null hypothesis is true
15896given the test's p-value. Various plots are automatically generated, allowing
15897one to make sensible significance cut-offs. The software can be applied to
15898problems in genomics, brain imaging, astrophysics, and data mining.")
15899 ;; Any version of the LGPL.
15900 (license license:lgpl3+)))
15901
15902(define r-rcppnumerical
15903 (package
15904 (name "r-rcppnumerical")
15905 (version "0.4-0")
15906 (source (origin
15907 (method url-fetch)
15908 (uri (cran-uri "RcppNumerical" version))
15909 (sha256
15910 (base32
15911 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
15912 (properties `((upstream-name . "RcppNumerical")))
15913 (build-system r-build-system)
15914 (propagated-inputs
15915 `(("r-rcpp" ,r-rcpp)
15916 ("r-rcppeigen" ,r-rcppeigen)))
15917 (native-inputs
15918 `(("r-knitr" ,r-knitr)))
15919 (home-page "https://github.com/yixuan/RcppNumerical")
15920 (synopsis "Rcpp integration for numerical computing libraries")
15921 (description
15922 "This package provides a collection of libraries for numerical computing
15923(numerical integration, optimization, etc.) and their integration with
15924@code{Rcpp}.")
15925 (license license:gpl2+)))
15926
15927(define-public r-apcomplex
15928 (package
15929 (name "r-apcomplex")
15930 (version "2.78.0")
15931 (source
15932 (origin
15933 (method url-fetch)
15934 (uri (bioconductor-uri "apComplex" version))
15935 (sha256
15936 (base32 "1zrwcvzp6wm466nxxqwjnmmcznrhwj40wa21i54hvxyws21sgjcz"))))
15937 (properties `((upstream-name . "apComplex")))
15938 (build-system r-build-system)
15939 (propagated-inputs
15940 (list r-graph
15941 r-org-sc-sgd-db
15942 r-rbgl
15943 r-rgraphviz))
15944 (home-page "https://bioconductor.org/packages/apComplex")
15945 (synopsis "Estimate protein complex membership using AP-MS protein data")
15946 (description
15947 "This package provides functions to estimate a bipartite graph of protein
15948complex membership using @acronym{AP-MS, affinity purification–mass
15949spectrometry} data.")
15950 (license license:lgpl2.0+)))
15951
15952(define-public r-apeglm
15953 (package
15954 (name "r-apeglm")
15955 (version "1.34.0")
15956 (source (origin
15957 (method url-fetch)
15958 (uri (bioconductor-uri "apeglm" version))
15959 (sha256
15960 (base32
15961 "06j8dpm5l859ald4z749js7d8m615m3akx84294hln07npgf9akq"))))
15962 (properties `((upstream-name . "apeglm")))
15963 (build-system r-build-system)
15964 (propagated-inputs
15965 (list r-emdbook
15966 r-genomicranges
15967 r-rcpp
15968 r-rcppeigen
15969 r-rcppnumerical
15970 r-summarizedexperiment))
15971 (native-inputs (list r-knitr r-rmarkdown r-testthat))
15972 (home-page "https://bioconductor.org/packages/apeglm")
15973 (synopsis "Approximate posterior estimation for GLM coefficients")
15974 (description "This package provides Bayesian shrinkage estimators for
15975effect sizes for a variety of GLM models, using approximation of the
15976posterior for individual coefficients.")
15977 (license license:gpl2)))
15978
15979(define-public r-greylistchip
15980 (package
15981 (name "r-greylistchip")
15982 (version "1.44.0")
15983 (source (origin
15984 (method url-fetch)
15985 (uri (bioconductor-uri "GreyListChIP" version))
15986 (sha256
15987 (base32
15988 "13kmfp7gykr95zcy4rmwfaqs192awilvcylizdkzi2wndpqsnfa6"))))
15989 (properties
15990 '((upstream-name . "GreyListChIP")
15991 (updater-extra-native-inputs . ("r-biocstyle"))))
15992 (build-system r-build-system)
15993 (propagated-inputs
15994 (list r-bsgenome
15995 r-genomicalignments
15996 r-genomicranges
15997 r-mass
15998 r-rsamtools
15999 r-rtracklayer
16000 r-seqinfo
16001 r-summarizedexperiment))
16002 (native-inputs (list r-biocgenerics
16003 r-biocstyle
16004 r-bsgenome-hsapiens-ucsc-hg19
16005 r-runit))
16006 (home-page "https://bioconductor.org/packages/GreyListChIP")
16007 (synopsis "Greylist artefact regions based on ChIP inputs")
16008 (description "This package identifies regions of ChIP experiments with high
16009signal in the input, that lead to spurious peaks during peak calling.")
16010 (license license:artistic2.0)))
16011
16012(define-public r-diffbind
16013 (package
16014 (name "r-diffbind")
16015 (version "3.22.1")
16016 (source
16017 (origin
16018 (method url-fetch)
16019 (uri (bioconductor-uri "DiffBind" version))
16020 (sha256
16021 (base32
16022 "0dzpn84nc4rn84axzx06r78gwpgva20ji05h33cr09da52xbwlly"))))
16023 (properties
16024 `((upstream-name . "DiffBind")
16025 (updater-extra-native-inputs
16026 . ("r-biocstyle" "r-csaw" "r-edger" "r-genomeinfodb"))))
16027 (build-system r-build-system)
16028 ;; Vignettes fail with: "Only one peakset meets specified criteria."
16029 (arguments (list #:test-types '(list "tests")))
16030 (propagated-inputs
16031 (list r-amap
16032 r-apeglm
16033 r-ashr
16034 r-biocparallel
16035 r-deseq2
16036 r-dplyr
16037 r-genomicalignments
16038 r-genomicranges
16039 r-ggplot2
16040 r-ggrepel
16041 r-gplots
16042 r-greylistchip
16043 r-iranges
16044 r-lattice
16045 r-limma
16046 r-locfit
16047 r-rcolorbrewer
16048 r-rcpp
16049 r-rhtslib
16050 r-rsamtools
16051 r-s4vectors
16052 r-summarizedexperiment
16053 r-systempiper))
16054 (native-inputs
16055 (list r-biocstyle
16056 r-csaw
16057 r-deseq
16058 r-edger
16059 r-genomeinfodb
16060 r-testthat
16061 r-xtable))
16062 (home-page "https://bioconductor.org/packages/DiffBind")
16063 (synopsis "Differential binding analysis of ChIP-Seq peak data")
16064 (description
16065 "This package computes differentially bound sites from multiple
16066ChIP-seq experiments using affinity (quantitative) data. Also enables
16067occupancy (overlap) analysis and plotting functions.")
16068 (license license:artistic2.0)))
16069
16070(define-public r-ripseeker
16071 (package
16072 (name "r-ripseeker")
16073 (version "1.26.0")
16074 (source
16075 (origin
16076 (method url-fetch)
16077 (uri (bioconductor-uri "RIPSeeker" version))
16078 (sha256
16079 (base32
16080 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
16081 (properties `((upstream-name . "RIPSeeker")))
16082 (build-system r-build-system)
16083 (propagated-inputs
16084 (list r-s4vectors
16085 r-iranges
16086 r-genomicranges
16087 r-summarizedexperiment
16088 r-rsamtools
16089 r-genomicalignments
16090 r-rtracklayer))
16091 (home-page "https://bioconductor.org/packages/RIPSeeker")
16092 (synopsis
16093 "Identifying protein-associated transcripts from RIP-seq experiments")
16094 (description
16095 "This package infers and discriminates RIP peaks from RIP-seq alignments
16096using two-state HMM with negative binomial emission probability. While
16097RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
16098a suite of bioinformatics tools integrated within this self-contained software
16099package comprehensively addressing issues ranging from post-alignments
16100processing to visualization and annotation.")
16101 (license license:gpl2)))
16102
16103(define-public r-mbecs
16104 (package
16105 (name "r-mbecs")
16106 (version "1.16.0")
16107 (source
16108 (origin
16109 (method url-fetch)
16110 (uri (bioconductor-uri "MBECS" version))
16111 (sha256
16112 (base32 "1rvwazyi156g2wnf0g17bjy47g1wvs5p4jg3nycycawrs18p0a1s"))))
16113 (properties `((upstream-name . "MBECS")))
16114 (build-system r-build-system)
16115 (arguments
16116 (list
16117 #:phases
16118 #~(modify-phases %standard-phases
16119 (add-after 'unpack 'set-HOME
16120 ;; Fontconfig needs a writable cache
16121 (lambda _ (setenv "HOME" "/tmp"))))))
16122 (propagated-inputs
16123 (list r-cluster
16124 r-dplyr
16125 r-ggplot2
16126 r-gridextra
16127 r-limma
16128 r-lme4
16129 r-lmertest
16130 r-magrittr
16131 r-matrix
16132 r-pheatmap
16133 r-phyloseq
16134 r-rmarkdown
16135 r-ruv
16136 r-sva
16137 r-tibble
16138 r-tidyr
16139 r-vegan))
16140 (native-inputs (list r-knitr r-testthat))
16141 (home-page "https://github.com/rmolbrich/MBECS")
16142 (synopsis
16143 "Evaluation and correction of batch effects in microbiome data-sets")
16144 (description
16145 "The @acronym{MBECS, Microbiome Batch Effect Correction Suite} provides a
16146set of functions to evaluate and mitigate unwated noise due to processing in
16147batches. To that end it incorporates a host of batch correcting algorithms
16148(BECA) from various packages. In addition it offers a correction and reporting
16149pipeline that provides a preliminary look at the characteristics of a data-set
16150before and after correcting for batch effects.")
16151 (license license:artistic2.0)))
16152
16153(define-public r-mbkmeans
16154 (package
16155 (name "r-mbkmeans")
16156 (version "1.28.0")
16157 (source (origin
16158 (method url-fetch)
16159 (uri (bioconductor-uri "mbkmeans" version))
16160 (sha256
16161 (base32
16162 "025b6azmc4q6zcjk9r77232jdb2lkk80flrjgg2p560mp0yy1y7m"))))
16163 (build-system r-build-system)
16164 (native-inputs
16165 (list r-hdf5array r-knitr r-testthat))
16166 (propagated-inputs
16167 (list r-beachmat
16168 r-benchmarkme
16169 r-biocparallel
16170 r-clusterr
16171 r-delayedarray
16172 r-matrix
16173 r-rcpp
16174 r-rcpparmadillo
16175 r-rhdf5lib
16176 r-s4vectors
16177 r-singlecellexperiment
16178 r-summarizedexperiment))
16179 (home-page "https://bioconductor.org/packages/mbkmeans")
16180 (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
16181 (description "This package implements the mini-batch k-means algorithm for
16182large datasets, including support for on-disk data representation.")
16183 (license license:expat)))
16184
16185(define-public r-multibac
16186 (package
16187 (name "r-multibac")
16188 (version "1.22.0")
16189 (source
16190 (origin
16191 (method url-fetch)
16192 (uri (bioconductor-uri "MultiBaC" version))
16193 (sha256
16194 (base32 "09z2g521lkpmd7i0mj8k1hf66p1isccqjznqh83qsbc4y9qsb3v1"))))
16195 (properties `((upstream-name . "MultiBaC")))
16196 (build-system r-build-system)
16197 (propagated-inputs
16198 (list r-ggplot2
16199 r-matrix
16200 r-multiassayexperiment
16201 r-pcamethods
16202 r-plotrix
16203 r-ropls))
16204 (native-inputs (list r-knitr))
16205 (home-page "https://bioconductor.org/packages/MultiBaC")
16206 (synopsis "Multiomic batch effect correction")
16207 (description
16208 "MultiBaC is a strategy to correct batch effects from multiomic datasets
16209distributed across different labs or data acquisition events. MultiBaC is
16210able to remove batch effects across different omics generated within separate
16211batches provided that at least one common omic data type is included in all
16212the batches considered.")
16213 (license license:gpl3)))
16214
16215(define-public r-multtest
16216 (package
16217 (name "r-multtest")
16218 (version "2.68.0")
16219 (source
16220 (origin
16221 (method url-fetch)
16222 (uri (bioconductor-uri "multtest" version))
16223 (sha256
16224 (base32
16225 "1lizrqcsljranjnd6a9n43nz8gnw8h677bffz08b09hy84a59fpf"))))
16226 (build-system r-build-system)
16227 (propagated-inputs
16228 (list r-biobase r-biocgenerics r-mass r-survival))
16229 (home-page "https://bioconductor.org/packages/multtest")
16230 (synopsis "Resampling-based multiple hypothesis testing")
16231 (description
16232 "This package can do non-parametric bootstrap and permutation
16233resampling-based multiple testing procedures (including empirical Bayes
16234methods) for controlling the family-wise error rate (FWER), generalized
16235family-wise error rate (gFWER), tail probability of the proportion of
16236false positives (TPPFP), and false discovery rate (FDR). Several choices
16237of bootstrap-based null distribution are implemented (centered, centered
16238and scaled, quantile-transformed). Single-step and step-wise methods are
16239available. Tests based on a variety of T- and F-statistics (including
16240T-statistics based on regression parameters from linear and survival models
16241as well as those based on correlation parameters) are included. When probing
16242hypotheses with T-statistics, users may also select a potentially faster null
16243distribution which is multivariate normal with mean zero and variance
16244covariance matrix derived from the vector influence function. Results are
16245reported in terms of adjusted P-values, confidence regions and test statistic
16246cutoffs. The procedures are directly applicable to identifying differentially
16247expressed genes in DNA microarray experiments.")
16248 (license license:lgpl3)))
16249
16250(define-public r-graph
16251 (package
16252 (name "r-graph")
16253 (version "1.90.0")
16254 (source (origin
16255 (method url-fetch)
16256 (uri (bioconductor-uri "graph" version))
16257 (sha256
16258 (base32
16259 "1rwd2j8x61dspsf5a3yj5i7k5zkl5s1lf37vkc1f7q4l33swyhfy"))))
16260 (properties '((updater-extra-native-inputs . ("r-xml"))))
16261 (build-system r-build-system)
16262 (arguments
16263 (list
16264 #:phases
16265 '(modify-phases %standard-phases
16266 (add-after 'unpack 'disable-bad-test
16267 (lambda _
16268 ;; This one test fails for unknown reasons.
16269 (substitute* "inst/unitTests/graphNEL_test.R"
16270 (("checkEquals\\(\"not a node:.*") "")))))))
16271 (propagated-inputs
16272 (list r-biocgenerics))
16273 (native-inputs (list r-knitr r-multigraph r-runit r-xml))
16274 (home-page "https://bioconductor.org/packages/graph")
16275 (synopsis "Handle graph data structures in R")
16276 (description
16277 "This package implements some simple graph handling capabilities for R.")
16278 (license license:artistic2.0)))
16279
16280;; This is a CRAN package, but it depends on a Bioconductor package.
16281(define-public r-ggm
16282 (package
16283 (name "r-ggm")
16284 (version "2.5.2")
16285 (source
16286 (origin
16287 (method url-fetch)
16288 (uri (cran-uri "ggm" version))
16289 (sha256
16290 (base32
16291 "0nv5m7f2kbjr0abfpcb18g1291ghphpzx0ixf7fpk23ia6xqwvyy"))))
16292 (properties `((upstream-name . "ggm")))
16293 (build-system r-build-system)
16294 (propagated-inputs
16295 (list r-biocmanager r-graph r-igraph))
16296 (home-page "https://cran.r-project.org/package=ggm")
16297 (synopsis "Functions for graphical Markov models")
16298 (description
16299 "This package provides functions and datasets for maximum likelihood
16300fitting of some classes of graphical Markov models.")
16301 (license license:gpl2+)))
16302
16303(define-public r-ggtreeextra
16304 (package
16305 (name "r-ggtreeextra")
16306 (version "1.22.1")
16307 (source (origin
16308 (method url-fetch)
16309 (uri (bioconductor-uri "ggtreeExtra" version))
16310 (sha256
16311 (base32
16312 "17zlm3bpibd18qbs8s6w84j8kpb2zm5b2n0lzj1rgnyq6cb6vxhj"))))
16313 (properties `((upstream-name . "ggtreeExtra")))
16314 (build-system r-build-system)
16315 (propagated-inputs (list r-cli
16316 r-ggnewscale
16317 r-ggplot2
16318 r-ggtree
16319 r-magrittr
16320 r-rlang
16321 r-tidytree
16322 r-yulab-utils))
16323 (native-inputs (list r-knitr r-testthat))
16324 (home-page "https://github.com/YuLab-SMU/ggtreeExtra/")
16325 (synopsis
16326 "Add geometric layers On circular or other layout tree of ggtree")
16327 (description
16328 "ggtreeExtra extends the method for mapping and visualizing associated
16329data on phylogenetic tree using ggtree. These associated data can be
16330presented on the external panels to circular layout, fan layout, or other
16331rectangular layout tree built by ggtree with the grammar of ggplot2.")
16332 (license license:gpl3+)))
16333
16334;; This is a CRAN package, but it depends on a bunch of Bioconductor packages.
16335(define-public r-ggpicrust2
16336 (package
16337 (name "r-ggpicrust2")
16338 (version "2.5.17")
16339 (source (origin
16340 (method url-fetch)
16341 (uri (cran-uri "ggpicrust2" version))
16342 (sha256
16343 (base32
16344 "1fhidxk54a8jjk4rqrvgg3jz91hcs1iyv8nr62c3awrpf4j5s66k"))))
16345 (properties
16346 '((upstream-name . "ggpicrust2")
16347 (updater-extra-native-inputs
16348 . ("r-aldex2" "r-circlize" "r-complexheatmap"
16349 "r-fgsea" "r-ggally" "r-limma"))))
16350 (build-system r-build-system)
16351 (propagated-inputs (list r-aplot
16352 r-dplyr
16353 r-ggh4x
16354 r-ggplot2
16355 r-ggplotify
16356 r-ggprism
16357 r-ggraph
16358 r-magrittr
16359 r-patchwork
16360 r-progress
16361 r-readr
16362 r-tibble
16363 r-tidygraph
16364 r-tidyr))
16365 (native-inputs
16366 (list r-aldex2
16367 r-circlize
16368 r-complexheatmap
16369 r-fgsea
16370 r-ggally
16371 r-knitr
16372 r-limma
16373 r-metagenomeseq
16374 r-testthat))
16375 (home-page "https://github.com/cafferychen777/ggpicrust2")
16376 (synopsis "Make PICRUSt2 output analysis and visualization easier")
16377 (description
16378 "This package provides a convenient way to analyze and visualize PICRUSt2
16379output with pre-defined plots and functions. It allows for generating
16380statistical plots about microbiome functional predictions and offers
16381customization options. It features a one-click option for creating
16382publication-level plots, saving time and effort in producing
16383professional-grade figures. It streamlines the PICRUSt2 analysis and
16384visualization process.")
16385 (license license:expat)))
16386
16387;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
16388(define-public r-perfmeas
16389 (package
16390 (name "r-perfmeas")
16391 (version "1.2.5")
16392 (source
16393 (origin
16394 (method url-fetch)
16395 (uri (cran-uri "PerfMeas" version))
16396 (sha256
16397 (base32
16398 "13yjk0kwpbsqwl056hzf0zj2br1mk4faqcn1whdfxmq348c14hjb"))))
16399 (properties `((upstream-name . "PerfMeas")))
16400 (build-system r-build-system)
16401 (propagated-inputs
16402 (list r-graph r-limma r-rbgl))
16403 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
16404 (synopsis "Performance measures for ranking and classification tasks")
16405 (description
16406 "This package implements different performance measures for
16407classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
16408a given recall, F-score for single and multiple classes are available.")
16409 (license license:gpl2+)))
16410
16411(define-public r-pepsnmr
16412 (package
16413 (name "r-pepsnmr")
16414 (version "1.30.0")
16415 (source (origin
16416 (method url-fetch)
16417 (uri (bioconductor-uri "PepsNMR" version))
16418 (sha256
16419 (base32
16420 "1qp0cpi1ydxvrrnqcz941fv8d5wl5mjj43hp7mc7i27id6qc4p59"))))
16421 (properties `((upstream-name . "PepsNMR")))
16422 (build-system r-build-system)
16423 (propagated-inputs
16424 (list r-ggplot2
16425 r-gridextra
16426 r-matrix
16427 r-matrixstats
16428 r-ptw
16429 r-reshape2))
16430 (native-inputs (list r-knitr))
16431 (home-page "https://github.com/ManonMartin/PepsNMR")
16432 (synopsis "Pre-process 1H-NMR FID signals")
16433 (description
16434 "This package provides R functions for common pre-processing steps that
16435are applied on @acronym{1H-NMR, proton nuclear magnetic resonance} data. It
16436also provides a function to read the @acronym{FID, free induction decay}
16437signals directly in the Bruker format.")
16438 (license license:gpl2)))
16439
16440;; This is a CRAN package, but it depends on a Bioconductor package.
16441(define-public r-codedepends
16442 (package
16443 (name "r-codedepends")
16444 (version "0.6.7")
16445 (source
16446 (origin
16447 (method url-fetch)
16448 (uri (cran-uri "CodeDepends" version))
16449 (sha256
16450 (base32
16451 "02sj40qxq5vywgqay9q9vpv3s6j3jjr46kc8q3v1yw2vbsmlvrz0"))))
16452 (properties `((upstream-name . "CodeDepends")))
16453 (build-system r-build-system)
16454 (propagated-inputs
16455 (list r-codetools r-graph r-xml))
16456 (native-inputs (list r-knitr r-rgraphviz r-runit))
16457 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
16458 (synopsis "Analysis of R code for reproducible research and code comprehension")
16459 (description
16460 "This package provides tools for analyzing R expressions or blocks of
16461code and determining the dependencies between them. It focuses on R scripts,
16462but can be used on the bodies of functions. There are many facilities
16463including the ability to summarize or get a high-level view of code,
16464determining dependencies between variables, code improvement suggestions.")
16465 ;; Any version of the GPL
16466 (license (list license:gpl2+ license:gpl3+))))
16467
16468(define-public r-chippeakanno
16469 (package
16470 (name "r-chippeakanno")
16471 (version "3.46.0")
16472 (source
16473 (origin
16474 (method url-fetch)
16475 (uri (bioconductor-uri "ChIPpeakAnno" version))
16476 (sha256
16477 (base32
16478 "1f4k2z5dv4s341c7592v1s1jman6scgdxyklcnxn93pkp5pvriqa"))))
16479 (properties
16480 '((upstream-name . "ChIPpeakAnno")
16481 (updater-extra-native-inputs . ("r-seqinr"))))
16482 (build-system r-build-system)
16483 (arguments
16484 (list
16485 #:skipped-tests
16486 ;; "sequence MT not found", but it's probably because it tries to access
16487 ;; the Internet earlier
16488 '(("test_getAllPeakSequence.R"
16489 "getAllPeakSequence works not correct"))))
16490 (propagated-inputs
16491 (list r-annotationdbi
16492 r-biocgenerics
16493 r-biomart
16494 r-biostrings
16495 r-data-table
16496 r-dbi
16497 r-dplyr
16498 r-ensembldb
16499 r-genomeinfodb
16500 r-genomicalignments
16501 r-genomicfeatures
16502 r-genomicranges
16503 r-ggplot2
16504 r-graph
16505 r-interactionset
16506 r-iranges
16507 r-keggrest
16508 r-matrixstats
16509 r-multtest
16510 r-pwalign
16511 r-rbgl
16512 r-regioner
16513 r-rsamtools
16514 r-rtracklayer
16515 r-s4vectors
16516 r-scales
16517 r-stringr
16518 r-summarizedexperiment
16519 r-tibble
16520 r-tidyr
16521 r-universalmotif
16522 r-venndiagram))
16523 (native-inputs
16524 (list r-bsgenome-celegans-ucsc-ce10
16525 r-bsgenome-drerio-ucsc-danrer7
16526 r-bsgenome-hsapiens-ucsc-hg19
16527 r-ensdb-hsapiens-v79
16528 r-knitr
16529 r-org-ce-eg-db
16530 r-org-hs-eg-db
16531 r-reactome-db
16532 r-seqinr
16533 r-testthat
16534 r-txdb-hsapiens-ucsc-hg38-knowngene))
16535 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
16536 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
16537 (description
16538 "The package includes functions to retrieve the sequences around the peak,
16539obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
16540custom features such as most conserved elements and other transcription factor
16541binding sites supplied by users. Starting 2.0.5, new functions have been added
16542for finding the peaks with bi-directional promoters with summary statistics
16543(peaksNearBDP), for summarizing the occurrence of motifs in peaks
16544(summarizePatternInPeaks) and for adding other IDs to annotated peaks or
16545enrichedGO (addGeneIDs).")
16546 (license license:gpl2+)))
16547
16548(define-public r-matrixgenerics
16549 (package
16550 (name "r-matrixgenerics")
16551 (version "1.24.0")
16552 (source (origin
16553 (method url-fetch)
16554 (uri (bioconductor-uri "MatrixGenerics" version))
16555 (sha256
16556 (base32
16557 "0ph0g4rm6vawlrx6zbawijaw46cndbv58p2v8rjndb94sfxk479p"))))
16558 (properties
16559 `((upstream-name . "MatrixGenerics")))
16560 (build-system r-build-system)
16561 (propagated-inputs
16562 (list r-matrixstats))
16563 (native-inputs (list r-testthat))
16564 (home-page "https://bioconductor.org/packages/MatrixGenerics")
16565 (synopsis "S4 generic summary statistic functions for matrix-like objects")
16566 (description
16567 "This package provides S4 generic functions modeled after the
16568@code{matrixStats} API for alternative matrix implementations. Packages with
16569alternative matrix implementation can depend on this package and implement the
16570generic functions that are defined here for a useful set of row and column
16571summary statistics. Other package developers can import this package and
16572handle a different matrix implementations without worrying about
16573incompatibilities.")
16574 (license license:artistic2.0)))
16575
16576(define-public r-marray
16577 (package
16578 (name "r-marray")
16579 (version "1.90.0")
16580 (source (origin
16581 (method url-fetch)
16582 (uri (bioconductor-uri "marray" version))
16583 (sha256
16584 (base32 "16g3b673kvjad1q5xzglk9x34hkhip2n9p9qjhna0cih5xxq76yg"))))
16585 (build-system r-build-system)
16586 (propagated-inputs
16587 (list r-limma))
16588 (home-page "https://bioconductor.org/packages/marray")
16589 (synopsis "Exploratory analysis for two-color spotted microarray data")
16590 (description "This package contains class definitions for two-color spotted
16591microarray data. It also includes functions for data input, diagnostic plots,
16592normalization and quality checking.")
16593 (license license:lgpl2.0+)))
16594
16595(define-public r-cghbase
16596 (package
16597 (name "r-cghbase")
16598 (version "1.72.0")
16599 (source (origin
16600 (method url-fetch)
16601 (uri (bioconductor-uri "CGHbase" version))
16602 (sha256
16603 (base32 "1wbp0laymizn937plvwrmi9hzxc69chbvcrygzpfqvwy0q90slcp"))))
16604 (properties `((upstream-name . "CGHbase")))
16605 (build-system r-build-system)
16606 (propagated-inputs
16607 (list r-biobase r-marray))
16608 (home-page "https://bioconductor.org/packages/CGHbase")
16609 (synopsis "Base functions and classes for arrayCGH data analysis")
16610 (description "This package contains functions and classes that are needed by
16611the @code{arrayCGH} packages.")
16612 (license license:gpl2+)))
16613
16614(define-public r-cghcall
16615 (package
16616 (name "r-cghcall")
16617 (version "2.74.0")
16618 (source (origin
16619 (method url-fetch)
16620 (uri (bioconductor-uri "CGHcall" version))
16621 (sha256
16622 (base32 "12qp4173hs52f8jrr8dg05mrv4zrs1wzxlaw9sl5y1xmcf2c8nad"))))
16623 (properties `((upstream-name . "CGHcall")))
16624 (build-system r-build-system)
16625 (propagated-inputs
16626 (list r-biobase r-cghbase r-dnacopy r-impute r-snowfall))
16627 (home-page "https://bioconductor.org/packages/CGHcall")
16628 (synopsis "Base functions and classes for arrayCGH data analysis")
16629 (description "This package contains functions and classes that are needed by
16630@code{arrayCGH} packages.")
16631 (license license:gpl2+)))
16632
16633(define-public r-qdnaseq
16634 (package
16635 (name "r-qdnaseq")
16636 (version "1.48.0")
16637 (source (origin
16638 (method url-fetch)
16639 (uri (bioconductor-uri "QDNAseq" version))
16640 (sha256
16641 (base32 "15j0jwhfrpxh8l2gxz00vq7yj6fj2rlvaxr9wrhqzm726gvff6ns"))))
16642 (properties
16643 '((upstream-name . "QDNAseq")
16644 (updater-extra-native-inputs . ("r-biocstyle"))))
16645 (build-system r-build-system)
16646 (propagated-inputs
16647 (list r-biobase
16648 r-biocgenerics
16649 r-cghbase
16650 r-cghcall
16651 r-dnacopy
16652 r-future-apply
16653 r-genomicranges
16654 r-iranges
16655 r-matrixstats
16656 r-r-utils
16657 r-rsamtools
16658 r-seqinfo))
16659 (native-inputs
16660 (list r-biocstyle
16661 r-bsgenome-hsapiens-ucsc-hg19
16662 r-digest
16663 r-future
16664 r-parallelly))
16665 (home-page "https://bioconductor.org/packages/QDNAseq")
16666 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
16667 (description "The genome is divided into non-overlapping fixed-sized bins,
16668number of sequence reads in each counted, adjusted with a simultaneous
16669two-dimensional loess correction for sequence mappability and GC content, and
16670filtered to remove spurious regions in the genome. Downstream steps of
16671segmentation and calling are also implemented via packages DNAcopy and CGHcall,
16672respectively.")
16673 (license license:gpl2+)))
16674
16675(define-public r-bayseq
16676 (package
16677 (name "r-bayseq")
16678 (version "2.46.0")
16679 (source
16680 (origin
16681 (method url-fetch)
16682 (uri (bioconductor-uri "baySeq" version))
16683 (sha256
16684 (base32
16685 "0dq9b96sidy4lpm55mzv9br4y19aibc0gzfdxx78fyy5s752jawl"))))
16686 (properties `((upstream-name . "baySeq")))
16687 (build-system r-build-system)
16688 (propagated-inputs
16689 (list r-abind r-edger r-genomicranges))
16690 (home-page "https://bioconductor.org/packages/baySeq/")
16691 (synopsis "Bayesian analysis of differential expression patterns in count data")
16692 (description
16693 "This package identifies differential expression in high-throughput count
16694data, such as that derived from next-generation sequencing machines,
16695calculating estimated posterior likelihoods of differential expression (or
16696more complex hypotheses) via empirical Bayesian methods.")
16697 (license license:gpl3)))
16698
16699(define-public r-chipcomp
16700 (package
16701 (name "r-chipcomp")
16702 (version "1.41.0")
16703 (source
16704 (origin
16705 (method url-fetch)
16706 (uri (bioconductor-uri "ChIPComp" version))
16707 (sha256
16708 (base32
16709 "0mp748ixlpp0ikj9gmrjkxk2w33l4w7y22z9sr5ww678lb9kd08k"))))
16710 (properties
16711 '((upstream-name . "ChIPComp")
16712 (updater-extra-native-inputs . ("r-biocstyle"))))
16713 (build-system r-build-system)
16714 (propagated-inputs
16715 (list r-biocgenerics
16716 r-bsgenome-hsapiens-ucsc-hg19
16717 r-bsgenome-mmusculus-ucsc-mm9
16718 r-genomicranges
16719 r-iranges
16720 r-limma
16721 r-rsamtools
16722 r-rtracklayer
16723 r-s4vectors
16724 r-seqinfo))
16725 (native-inputs (list r-biocstyle r-runit))
16726 (home-page "https://bioconductor.org/packages/ChIPComp")
16727 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
16728 (description
16729 "ChIPComp implements a statistical method for quantitative comparison of
16730multiple ChIP-seq datasets. It detects differentially bound sharp binding
16731sites across multiple conditions considering matching control in ChIP-seq
16732datasets.")
16733 ;; Any version of the GPL.
16734 (license license:gpl3+)))
16735
16736(define-public r-riboprofiling
16737 (package
16738 (name "r-riboprofiling")
16739 (version "1.39.1")
16740 (source
16741 (origin
16742 (method url-fetch)
16743 (uri (bioconductor-uri "RiboProfiling" version))
16744 (sha256
16745 (base32
16746 "0yqmk7cgfahyiy4gcrfr4iyf9sa6sl42h41xaj65b4dx6mhgqrs9"))))
16747 (properties
16748 '((upstream-name . "RiboProfiling")
16749 (updater-extra-native-inputs
16750 . ("r-txdb-hsapiens-ucsc-hg19-knowngene"))))
16751 (build-system r-build-system)
16752 (propagated-inputs
16753 (list r-biocgenerics
16754 r-biostrings
16755 r-data-table
16756 r-genomicalignments
16757 r-genomicfeatures
16758 r-genomicranges
16759 r-ggbio
16760 r-ggplot2
16761 r-iranges
16762 r-plyr
16763 r-reshape2
16764 r-rsamtools
16765 r-rtracklayer
16766 r-s4vectors
16767 r-seqinfo
16768 r-sqldf))
16769 (native-inputs
16770 (list r-knitr r-testthat r-txdb-hsapiens-ucsc-hg19-knowngene))
16771 (home-page "https://bioconductor.org/packages/RiboProfiling/")
16772 (synopsis "Ribosome profiling data analysis")
16773 (description "Starting with a BAM file, this package provides the
16774necessary functions for quality assessment, read start position recalibration,
16775the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
16776of count data: pairs, log fold-change, codon frequency and coverage
16777assessment, principal component analysis on codon coverage.")
16778 (license license:gpl3)))
16779
16780(define-public r-riboseqr
16781 (package
16782 (name "r-riboseqr")
16783 (version "1.46.0")
16784 (source
16785 (origin
16786 (method url-fetch)
16787 (uri (bioconductor-uri "riboSeqR" version))
16788 (sha256
16789 (base32
16790 "1hlllqyxiww22gvg7z96d0k6jzg6xjqy7hjihk6gip6q5h3sm02v"))))
16791 (properties
16792 '((upstream-name . "riboSeqR")
16793 (updater-extra-native-inputs . ("r-biocstyle"))))
16794 (build-system r-build-system)
16795 (propagated-inputs
16796 (list r-abind
16797 r-bayseq
16798 r-genomicranges
16799 r-iranges
16800 r-rsamtools
16801 r-s4vectors
16802 r-seqinfo
16803 r-seqlogo))
16804 (native-inputs (list r-biocgenerics r-biocstyle r-runit))
16805 (home-page "https://bioconductor.org/packages/riboSeqR/")
16806 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
16807 (description
16808 "This package provides plotting functions, frameshift detection and
16809parsing of genetic sequencing data from ribosome profiling experiments.")
16810 (license license:gpl3)))
16811
16812(define-public r-interactionset
16813 (package
16814 (name "r-interactionset")
16815 (version "1.40.0")
16816 (source
16817 (origin
16818 (method url-fetch)
16819 (uri (bioconductor-uri "InteractionSet" version))
16820 (sha256
16821 (base32
16822 "15a52jjr19i4swqapzkv1616mbflsr4jq64j0y5lwsj3m76gf149"))))
16823 (properties
16824 `((upstream-name . "InteractionSet")))
16825 (build-system r-build-system)
16826 (propagated-inputs
16827 (list r-biocgenerics
16828 r-genomicranges
16829 r-iranges
16830 r-matrix
16831 r-rcpp
16832 r-s4vectors
16833 r-seqinfo
16834 r-summarizedexperiment))
16835 (native-inputs
16836 (list r-knitr r-testthat))
16837 (home-page "https://bioconductor.org/packages/InteractionSet")
16838 (synopsis "Base classes for storing genomic interaction data")
16839 (description
16840 "This package provides the @code{GInteractions},
16841@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
16842for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
16843experiments.")
16844 (license license:gpl3)))
16845
16846(define-public r-genomicinteractions
16847 (package
16848 (name "r-genomicinteractions")
16849 (version "1.46.0")
16850 (source
16851 (origin
16852 (method url-fetch)
16853 (uri (bioconductor-uri "GenomicInteractions" version))
16854 (sha256
16855 (base32
16856 "1lcxsvb74ikqmzgvsllhk8f93ysqphwc06dakh5bxy9jy5a0iaaz"))))
16857 (properties
16858 `((upstream-name . "GenomicInteractions")))
16859 (build-system r-build-system)
16860 (propagated-inputs
16861 (list r-biobase
16862 r-biocgenerics
16863 r-data-table
16864 r-dplyr
16865 r-genomicranges
16866 r-ggplot2
16867 r-gridextra
16868 r-gviz
16869 r-igraph
16870 r-interactionset
16871 r-iranges
16872 r-rsamtools
16873 r-rtracklayer
16874 r-s4vectors
16875 r-seqinfo
16876 r-stringr))
16877 (native-inputs
16878 (list r-knitr r-testthat))
16879 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
16880 (synopsis "R package for handling genomic interaction data")
16881 (description
16882 "This R package provides tools for handling genomic interaction data,
16883such as ChIA-PET/Hi-C, annotating genomic features with interaction
16884information and producing various plots and statistics.")
16885 (license license:gpl3)))
16886
16887(define-public r-ctc
16888 (package
16889 (name "r-ctc")
16890 (version "1.86.0")
16891 (source
16892 (origin
16893 (method url-fetch)
16894 (uri (bioconductor-uri "ctc" version))
16895 (sha256
16896 (base32
16897 "0mjcsr1yclsp3xjmzzi0b4kqynsc0dazl8xac12jbaiiqa12by8p"))))
16898 (build-system r-build-system)
16899 (propagated-inputs (list r-amap))
16900 (home-page "https://bioconductor.org/packages/ctc/")
16901 (synopsis "Cluster and tree conversion")
16902 (description
16903 "This package provides tools for exporting and importing classification
16904trees and clusters to other programs.")
16905 (license license:gpl2)))
16906
16907(define-public r-goseq
16908 (package
16909 (name "r-goseq")
16910 (version "1.64.0")
16911 (source
16912 (origin
16913 (method url-fetch)
16914 (uri (bioconductor-uri "goseq" version))
16915 (sha256
16916 (base32
16917 "0796rcy9jvbg8sh3dx58cg43cjyjxxdjwwvbl76r20xfq1zvaxs0"))))
16918 (build-system r-build-system)
16919 (propagated-inputs
16920 (list r-annotationdbi
16921 r-biasedurn
16922 r-biocgenerics
16923 r-genelendatabase
16924 r-genomicfeatures
16925 r-go-db
16926 r-mgcv
16927 r-rtracklayer
16928 r-seqinfo))
16929 (home-page "https://bioconductor.org/packages/goseq/")
16930 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
16931 (description
16932 "This package provides tools to detect Gene Ontology and/or other user
16933defined categories which are over/under represented in RNA-seq data.")
16934 (license license:lgpl2.0+)))
16935
16936(define-public r-glimma
16937 (package
16938 (name "r-glimma")
16939 (version "2.21.0")
16940 (source
16941 (origin
16942 (method url-fetch)
16943 (uri (bioconductor-uri "Glimma" version))
16944 (sha256
16945 (base32
16946 "1n3x7nm65mszjz558zcfs8hrpc1wd0vf91xrh2r0pcjbgwqkmg9b"))
16947 (modules '((guix build utils)))
16948 (snippet
16949 '(with-directory-excursion "inst/htmlwidgets/lib/"
16950 (for-each delete-file
16951 ;; XXX: we keep inst/v1/js/glimma.min.js because
16952 ;; it's not clear how to build it.
16953 (cons* "vega/vega.min.js"
16954 "jquery/jquery-3.6.1.min.js"
16955 (find-files "datatables"
16956 "\\.min\\.js$")))))))
16957 (properties `((upstream-name . "Glimma")))
16958 (build-system r-build-system)
16959 (arguments
16960 (list
16961 #:modules
16962 '((guix build r-build-system)
16963 (guix build minify-build-system)
16964 (guix build utils)
16965 (srfi srfi-1)
16966 (ice-9 match))
16967 #:imported-modules
16968 `(,@%r-build-system-modules
16969 (guix build minify-build-system))
16970 #:phases
16971 '(modify-phases (@ (guix build r-build-system) %standard-phases)
16972 (add-after 'unpack 'process-javascript
16973 (lambda* (#:key inputs #:allow-other-keys)
16974 (with-directory-excursion "inst/htmlwidgets/lib/"
16975 (let ((files (list "datatables/Buttons-2.3.3/js/buttons.bootstrap.js"
16976 "datatables/Buttons-2.3.3/js/buttons.bootstrap4.js"
16977 "datatables/Buttons-2.3.3/js/buttons.bootstrap5.js"
16978 "datatables/Buttons-2.3.3/js/buttons.bulma.js"
16979 "datatables/Buttons-2.3.3/js/buttons.colVis.js"
16980 "datatables/Buttons-2.3.3/js/buttons.dataTables.js"
16981 "datatables/Buttons-2.3.3/js/buttons.foundation.js"
16982 "datatables/Buttons-2.3.3/js/buttons.html5.js"
16983 "datatables/Buttons-2.3.3/js/buttons.jqueryui.js"
16984 "datatables/Buttons-2.3.3/js/buttons.print.js"
16985 "datatables/Buttons-2.3.3/js/buttons.semanticui.js"
16986 "datatables/Buttons-2.3.3/js/dataTables.buttons.js"
16987 "datatables/DataTables-1.13.1/js/dataTables.bootstrap.js"
16988 "datatables/DataTables-1.13.1/js/dataTables.bootstrap4.js"
16989 "datatables/DataTables-1.13.1/js/dataTables.bootstrap5.js"
16990 "datatables/DataTables-1.13.1/js/dataTables.bulma.js"
16991 "datatables/DataTables-1.13.1/js/dataTables.dataTables.js"
16992 "datatables/DataTables-1.13.1/js/dataTables.foundation.js"
16993 "datatables/DataTables-1.13.1/js/dataTables.jqueryui.js"
16994 "datatables/DataTables-1.13.1/js/dataTables.semanticui.js"
16995 "datatables/DataTables-1.13.1/js/jquery.dataTables.js"
16996 "datatables/JSZip-2.5.0/jszip.js"
16997 "datatables/Scroller-2.0.7/js/dataTables.scroller.js"
16998 "datatables/Scroller-2.0.7/js/scroller.bootstrap.js"
16999 "datatables/Scroller-2.0.7/js/scroller.bootstrap4.js"
17000 "datatables/Scroller-2.0.7/js/scroller.bootstrap5.js"
17001 "datatables/Scroller-2.0.7/js/scroller.bulma.js"
17002 "datatables/Scroller-2.0.7/js/scroller.dataTables.js"
17003 "datatables/Scroller-2.0.7/js/scroller.foundation.js"
17004 "datatables/Scroller-2.0.7/js/scroller.jqueryui.js"
17005 "datatables/Scroller-2.0.7/js/scroller.semanticui.js"
17006 "datatables/datatables.js"
17007 "vega/vega.js")))
17008 (for-each (lambda (source)
17009 (let ((target (string-append (dirname source) "/" (basename source ".js") ".min.js")))
17010 (minify source #:target target)))
17011 files)
17012 (let ((source (assoc-ref inputs "js-jquery"))
17013 (target "jquery/jquery-3.6.1.min.js"))
17014 (minify source #:target target)))))))))
17015 (propagated-inputs
17016 (list r-deseq2
17017 r-edger
17018 r-htmlwidgets
17019 r-jsonlite
17020 r-limma
17021 r-s4vectors
17022 r-summarizedexperiment))
17023 (native-inputs
17024 `(("esbuild" ,esbuild)
17025 ("r-knitr" ,r-knitr)
17026 ("r-testthat" ,r-testthat)
17027 ("js-jquery"
17028 ,(origin
17029 (method url-fetch)
17030 (uri "https://code.jquery.com/jquery-3.6.1.js")
17031 (sha256
17032 (base32
17033 "1lm4zcpvqdi7qi2s7bgci2z74wazq0z0bdvjmlrqbhmfrpk42ffz"))))))
17034 (home-page "https://github.com/Shians/Glimma")
17035 (synopsis "Interactive HTML graphics")
17036 (description
17037 "This package generates interactive visualisations for analysis of
17038RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
17039HTML page. The interactions are built on top of the popular static
17040representations of analysis results in order to provide additional
17041information.")
17042 (license license:lgpl3)))
17043
17044(define-public r-glmgampoi
17045 (package
17046 (name "r-glmgampoi")
17047 (version "1.24.0")
17048 (source (origin
17049 (method url-fetch)
17050 (uri (bioconductor-uri "glmGamPoi" version))
17051 (sha256
17052 (base32
17053 "14kl3sd8hm5nlfw4lzbyl3ss4kgjabrqsn67ans6qjp8x28pzwgs"))))
17054 (properties
17055 '((upstream-name . "glmGamPoi")
17056 (updater-ignored-native-inputs
17057 . ("r-deseq2"
17058 "r-distraltparam"
17059 "r-einsum"))))
17060 (build-system r-build-system)
17061 (arguments
17062 (list
17063 #:skipped-tests
17064 ;; This test needs r-scran/r-deseq2, which depends on this package.
17065 '(("test-size_factors.R"
17066 "estimate size factor works"
17067 "combine_size_factors_and_offset works"))))
17068 (propagated-inputs
17069 (list r-assorthead
17070 r-beachmat
17071 r-biocgenerics
17072 r-delayedarray
17073 r-delayedmatrixstats
17074 r-hdf5array
17075 r-matrix
17076 r-matrixgenerics
17077 r-matrixstats
17078 r-rcpp
17079 r-rcpparmadillo
17080 r-rlang
17081 r-s4vectors
17082 r-singlecellexperiment
17083 r-sparsearray
17084 r-summarizedexperiment
17085 r-vctrs))
17086 (native-inputs
17087 (list r-bench
17088 r-biocparallel
17089 r-edger
17090 r-knitr
17091 r-limma
17092 r-mass
17093 r-mockery
17094 r-mockr
17095 r-nloptr
17096 r-pheatmap
17097 r-sparsematrixstats
17098 r-statmod
17099 r-testthat
17100 r-zoo))
17101 (home-page "https://github.com/const-ae/glmGamPoi")
17102 (synopsis "Fit a Gamma-Poisson Generalized Linear Model")
17103 (description
17104 "Fit linear models to overdispersed count data. The package can estimate
17105the overdispersion and fit repeated models for matrix input. It is designed
17106to handle large input datasets as they typically occur in single cell RNA-seq
17107experiments.")
17108 (license license:gpl3)))
17109
17110(define-public r-rots
17111 (package
17112 (name "r-rots")
17113 (version "2.4.0")
17114 (source
17115 (origin
17116 (method url-fetch)
17117 (uri (bioconductor-uri "ROTS" version))
17118 (sha256
17119 (base32
17120 "11455j8h4772pn2giz6x8rc69mlk7rvb677zw3b6901mfilm04g8"))))
17121 (properties `((upstream-name . "ROTS")))
17122 (build-system r-build-system)
17123 (propagated-inputs
17124 (list r-biobase r-biocparallel r-lme4 r-rcpp r-survival))
17125 (native-inputs (list r-testthat))
17126 (home-page "https://bioconductor.org/packages/ROTS/")
17127 (synopsis "Reproducibility-Optimized Test Statistic")
17128 (description
17129 "This package provides tools for calculating the
17130@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
17131in omics data.")
17132 (license license:gpl2+)))
17133
17134(define-public r-plgem
17135 (package
17136 (name "r-plgem")
17137 (version "1.84.0")
17138 (source
17139 (origin
17140 (method url-fetch)
17141 (uri (bioconductor-uri "plgem" version))
17142 (sha256
17143 (base32
17144 "0cjjzpfqxg3kskqs9wwlrmm7yyyfm0h4xkp7q4nbmqqdg17rm303"))))
17145 (build-system r-build-system)
17146 (propagated-inputs
17147 (list r-biobase r-mass))
17148 (home-page "https://www.genopolis.it")
17149 (synopsis "Detect differential expression in microarray and proteomics datasets")
17150 (description
17151 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
17152model the variance-versus-mean dependence that exists in a variety of
17153genome-wide datasets, including microarray and proteomics data. The use of
17154PLGEM has been shown to improve the detection of differentially expressed
17155genes or proteins in these datasets.")
17156 (license license:gpl2)))
17157
17158(define-public r-plyranges
17159 (package
17160 (name "r-plyranges")
17161 (version "1.32.0")
17162 (source (origin
17163 (method url-fetch)
17164 (uri (bioconductor-uri "plyranges" version))
17165 (sha256
17166 (base32
17167 "16yvz5m42c9sqlq1da3w3ss9sf1gfi180pzk27wfn6awba46akad"))))
17168 (properties
17169 '((upstream-name . "plyranges")
17170 (updater-extra-native-inputs . ("r-helloranges"))))
17171 (build-system r-build-system)
17172 (propagated-inputs (list r-biocgenerics
17173 r-dplyr
17174 r-genomicalignments
17175 r-genomicranges
17176 r-iranges
17177 r-magrittr
17178 r-rlang
17179 r-rsamtools
17180 r-rtracklayer
17181 r-s4vectors
17182 r-seqinfo
17183 r-tidyselect))
17184 (native-inputs (list r-bsgenome-hsapiens-ucsc-hg19 r-helloranges r-knitr
17185 r-testthat))
17186 (home-page "https://bioconductor.org/packages/plyranges")
17187 (synopsis "Fluent interface for manipulating GenomicRanges")
17188 (description
17189 "This package provides a dplyr-like interface for interacting with the
17190common Bioconductor classes @code{Ranges} and @code{GenomicRanges}. By
17191providing a grammatical and consistent way of manipulating these classes their
17192accessibility for new Bioconductor users is hopefully increased.")
17193 (license license:artistic2.0)))
17194
17195(define-public r-inspect
17196 (package
17197 (name "r-inspect")
17198 (version "1.42.0")
17199 (source
17200 (origin
17201 (method url-fetch)
17202 (uri (bioconductor-uri "INSPEcT" version))
17203 (sha256
17204 (base32
17205 "0m9p98w2yjnq30jwpzf42cphplyrb6rpw3ar8pdpa05xj2zwx7i7"))))
17206 (properties `((upstream-name . "INSPEcT")))
17207 (build-system r-build-system)
17208 (propagated-inputs
17209 (list r-biobase
17210 r-biocgenerics
17211 r-biocparallel
17212 r-deseq2
17213 r-desolve
17214 r-genomicalignments
17215 r-genomicfeatures
17216 r-genomicranges
17217 r-iranges
17218 r-kernsmooth
17219 r-plgem
17220 r-proc
17221 r-readxl
17222 r-rootsolve
17223 r-rsamtools
17224 r-rtracklayer
17225 r-s4vectors
17226 r-seqinfo
17227 r-shiny
17228 r-summarizedexperiment
17229 r-txdb-mmusculus-ucsc-mm9-knowngene))
17230 (native-inputs
17231 (list r-knitr))
17232 (home-page "https://bioconductor.org/packages/INSPEcT")
17233 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
17234 (description
17235 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
17236Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
17237order to evaluate synthesis, processing and degradation rates and assess via
17238modeling the rates that determines changes in mature mRNA levels.")
17239 (license license:gpl2)))
17240
17241(define-public r-dnabarcodes
17242 (package
17243 (name "r-dnabarcodes")
17244 (version "1.42.0")
17245 (source
17246 (origin
17247 (method url-fetch)
17248 (uri (bioconductor-uri "DNABarcodes" version))
17249 (sha256
17250 (base32
17251 "0bdlpsmv278ncp36yrchl2zwzd4f6xsh029cvhp4wcqg2wrkcb8x"))))
17252 (properties `((upstream-name . "DNABarcodes")))
17253 (build-system r-build-system)
17254 (propagated-inputs
17255 (list r-bh r-matrix r-rcpp))
17256 (native-inputs
17257 (list r-knitr))
17258 (home-page "https://bioconductor.org/packages/DNABarcodes")
17259 (synopsis "Create and analyze DNA barcodes")
17260 (description
17261 "This package offers tools to create DNA barcode sets capable of
17262correcting insertion, deletion, and substitution errors. Existing barcodes
17263can be analyzed regarding their minimal, maximal and average distances between
17264barcodes. Finally, reads that start with a (possibly mutated) barcode can be
17265demultiplexed, i.e. assigned to their original reference barcode.")
17266 (license license:gpl2)))
17267
17268(define-public r-ruvseq
17269 (package
17270 (name "r-ruvseq")
17271 (version "1.46.0")
17272 (source
17273 (origin
17274 (method url-fetch)
17275 (uri (bioconductor-uri "RUVSeq" version))
17276 (sha256
17277 (base32
17278 "0rr3zs1iqf98dypbpw6ry2bsf97iipfqniv6dpq3rwdgvp6g3cpf"))))
17279 (properties `((upstream-name . "RUVSeq")))
17280 (build-system r-build-system)
17281 (propagated-inputs
17282 (list r-biobase r-edaseq r-edger r-mass))
17283 (native-inputs
17284 (list r-knitr))
17285 (home-page "https://github.com/drisso/RUVSeq")
17286 (synopsis "Remove unwanted variation from RNA-Seq data")
17287 (description
17288 "This package implements methods to @dfn{remove unwanted variation} (RUV)
17289of Risso et al. (2014) for the normalization of RNA-Seq read counts between
17290samples.")
17291 (license license:artistic2.0)))
17292
17293(define-public r-biocneighbors
17294 (package
17295 (name "r-biocneighbors")
17296 (version "2.6.0")
17297 (source
17298 (origin
17299 (method url-fetch)
17300 (uri (bioconductor-uri "BiocNeighbors" version))
17301 (sha256
17302 (base32
17303 "13gr8p35accgxfi7iwxfsnbzbyzsmpgywxs31irpfxw7yzivlv9a"))))
17304 (properties `((upstream-name . "BiocNeighbors")))
17305 (build-system r-build-system)
17306 (propagated-inputs
17307 (list r-assorthead r-beachmat r-rcpp))
17308 (native-inputs
17309 (list r-biocparallel r-delayedarray r-knitr r-testthat))
17310 (home-page "https://bioconductor.org/packages/BiocNeighbors")
17311 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
17312 (description
17313 "This package implements exact and approximate methods for nearest
17314neighbor detection, in a framework that allows them to be easily switched
17315within Bioconductor packages or workflows. The exact algorithm is implemented
17316using pre-clustering with the k-means algorithm. Functions are also provided
17317to search for all neighbors within a given distance. Parallelization is
17318achieved for all methods using the BiocParallel framework.")
17319 (license license:gpl3)))
17320
17321(define-public r-scaledmatrix
17322 (package
17323 (name "r-scaledmatrix")
17324 (version "1.20.0")
17325 (source
17326 (origin
17327 (method url-fetch)
17328 (uri (bioconductor-uri "ScaledMatrix" version))
17329 (sha256
17330 (base32
17331 "03imc35qr3hkk6ldcwml6zgrqwjbd9p66wi68r50806xhj229ifk"))))
17332 (properties `((upstream-name . "ScaledMatrix")))
17333 (build-system r-build-system)
17334 (propagated-inputs
17335 (list r-delayedarray r-matrix r-s4vectors))
17336 (native-inputs (list r-knitr r-s4arrays r-testthat))
17337 (home-page "https://github.com/LTLA/ScaledMatrix")
17338 (synopsis "Create a DelayedMatrix of scaled and centered values")
17339 (description
17340 "This package provides delayed computation of a matrix of scaled and
17341centered values. The result is equivalent to using the @code{scale} function
17342but avoids explicit realization of a dense matrix during block processing.
17343This permits greater efficiency in common operations, most notably matrix
17344multiplication.")
17345 (license license:gpl3)))
17346
17347(define-public r-scrapper
17348 (package
17349 (name "r-scrapper")
17350 (version "1.6.3")
17351 (source
17352 (origin
17353 (method url-fetch)
17354 (uri (bioconductor-uri "scrapper" version))
17355 (sha256
17356 (base32 "0d72in6cy9cywx7pvmffycqf0g7p72hqvf0k695k67d348mbx4vk"))))
17357 (properties
17358 '((upstream-name . "scrapper")
17359 (updater-ignored-native-inputs . ("r-rigraphlib"))
17360 (updater-ignored-propagated-inputs . ("r-rigraphlib"))
17361 (updater-extra-native-inputs
17362 . ("pkg-config" "r-delayedmatrixstats" "r-sparsematrixstats"))
17363 (updater-extra-inputs
17364 . ("igraph-for-r-rigraphlib"))))
17365 (build-system r-build-system)
17366 (arguments
17367 (list
17368 #:phases
17369 '(modify-phases %standard-phases
17370 ;; I really don't like the trend on Bioconductor to repackage
17371 ;; libraries as R packages, so we're patching this package to link
17372 ;; with igraph directly instead of statically linking with a
17373 ;; repackaged igraph with bundled dependencies in the Rigraphlib
17374 ;; package.
17375 (add-after 'unpack 'just-use-igraph
17376 (lambda _
17377 (substitute* "DESCRIPTION"
17378 (("^ *Rigraphlib.*") ""))
17379 (substitute* "src/Makevars"
17380 (("^RIGRAPH_FLAGS.*")
17381 "RIGRAPH_FLAGS=`pkg-config --cflags igraph`\n")
17382 (("^RIGRAPH_LIBS=.*")
17383 "RIGRAPH_LIBS=`pkg-config --libs igraph`\n")))))))
17384 (inputs (list igraph-for-r-rigraphlib))
17385 (propagated-inputs (list r-assorthead
17386 r-beachmat
17387 r-biocneighbors
17388 r-delayedarray
17389 r-rcpp
17390 r-s4vectors
17391 r-sparsearray))
17392 (native-inputs (list pkg-config
17393 r-delayedmatrixstats
17394 r-igraph
17395 r-knitr
17396 r-matrix
17397 r-singlecellexperiment
17398 r-sparsematrixstats
17399 r-summarizedexperiment
17400 r-testthat))
17401 (home-page "https://bioconductor.org/packages/scrapper")
17402 (synopsis "Bindings to C++ libraries for Single-Cell analysis")
17403 (description
17404 "This package implements R bindings to C++ code for analyzing single-cell
17405(expression) data, mostly from various libscran libraries. Each function
17406performs an individual step in the single-cell analysis workflow, ranging from
17407quality control to clustering and marker detection. It is mostly intended for
17408other Bioconductor package developers to build more user-friendly end-to-end
17409workflows.")
17410 (license license:expat)))
17411
17412(define-public r-treeio
17413 (package
17414 (name "r-treeio")
17415 (version "1.36.1")
17416 (source
17417 (origin
17418 (method url-fetch)
17419 (uri (bioconductor-uri "treeio" version))
17420 (sha256
17421 (base32
17422 "13iyip9phydmlwb57qp9crxn1xlvh19lnkpq23fcpaw2v7qp1yif"))))
17423 (properties
17424 '((upstream-name . "treeio")
17425 ;; Avoid dependency cycle.
17426 (updater-ignored-native-inputs . ("r-ggtree"))
17427 (updater-extra-native-inputs . ("r-xml2"))))
17428 (build-system r-build-system)
17429 (arguments
17430 (list
17431 #:skipped-tests
17432 ;; Some tests need r-ggtree, which depends on this package.
17433 '("test-merge-tree.R"
17434 "test-tree-subset.R")))
17435 (propagated-inputs
17436 (list r-ape
17437 r-dplyr
17438 r-jsonlite
17439 r-magrittr
17440 r-rlang
17441 r-tibble
17442 r-tidytree
17443 r-yulab-utils))
17444 (native-inputs (list r-igraph r-knitr r-testthat r-tidyr r-xml2))
17445 (home-page "https://github.com/YuLab-SMU/treeio")
17446 (synopsis "Base classes and functions for Phylogenetic tree input and output")
17447 (description
17448 "This is an R package to make it easier to import and store phylogenetic
17449trees with associated data; and to link external data from different sources
17450to phylogeny. It also supports exporting phylogenetic trees with
17451heterogeneous associated data to a single tree file and can be served as a
17452platform for merging tree with associated data and converting file formats.")
17453 (license license:artistic2.0)))
17454
17455(define-public r-treesummarizedexperiment
17456 (package
17457 (name "r-treesummarizedexperiment")
17458 (version "2.20.0")
17459 (source (origin
17460 (method url-fetch)
17461 (uri (bioconductor-uri "TreeSummarizedExperiment" version))
17462 (sha256
17463 (base32
17464 "00j8930s4mvxhl27a8p4aypymbaylf6qdzd13z3a6wxxm3m0qp40"))))
17465 (properties `((upstream-name . "TreeSummarizedExperiment")))
17466 (build-system r-build-system)
17467 (propagated-inputs
17468 (list r-ape
17469 r-biocgenerics
17470 r-biocparallel
17471 r-biostrings
17472 r-dplyr
17473 r-iranges
17474 r-rlang
17475 r-s4vectors
17476 r-singlecellexperiment
17477 r-summarizedexperiment
17478 r-treeio))
17479 (native-inputs (list r-knitr r-testthat))
17480 (home-page "https://bioconductor.org/packages/TreeSummarizedExperiment")
17481 (synopsis "S4 class for data with tree structures")
17482 (description
17483 "@code{TreeSummarizedExperiment} extends @code{SingleCellExperiment} to
17484include hierarchical information on the rows or columns of the rectangular
17485data.")
17486 (license license:gpl2+)))
17487
17488(define-public r-ggtree
17489 (package
17490 (name "r-ggtree")
17491 (version "4.2.0")
17492 (source
17493 (origin
17494 (method url-fetch)
17495 (uri (bioconductor-uri "ggtree" version))
17496 (sha256
17497 (base32
17498 "1vm5k8w04h1s009ga6j1w4yp2v67vdkfnz2nv97k8k4lmxjmrm32"))))
17499 (properties `((upstream-name . "ggtree")))
17500 (build-system r-build-system)
17501 (propagated-inputs
17502 (list r-ape
17503 r-aplot
17504 r-cli
17505 r-dplyr
17506 r-ggfun
17507 r-ggiraph
17508 r-ggplot2
17509 r-magrittr
17510 r-purrr
17511 r-rlang
17512 r-scales
17513 r-tidyr
17514 r-tidytree
17515 r-treeio
17516 r-yulab-utils))
17517 (native-inputs (list r-knitr r-testthat))
17518 (home-page "https://yulab-smu.top/treedata-book/")
17519 (synopsis "R package for visualization of trees and annotation data")
17520 (description
17521 "This package extends the ggplot2 plotting system which implements a
17522grammar of graphics. ggtree is designed for visualization and annotation of
17523phylogenetic trees and other tree-like structures with their annotation
17524data.")
17525 (license license:artistic2.0)))
17526
17527(define-public r-metapod
17528 (package
17529 (name "r-metapod")
17530 (version "1.20.0")
17531 (source
17532 (origin
17533 (method url-fetch)
17534 (uri (bioconductor-uri "metapod" version))
17535 (sha256
17536 (base32
17537 "11vhihimi9k31imdgyy9pxw5rcyccmdzarkr1j1dipvh6xk8v0pb"))))
17538 (properties `((upstream-name . "metapod")))
17539 (build-system r-build-system)
17540 (propagated-inputs
17541 (list r-rcpp))
17542 (native-inputs
17543 (list r-knitr r-testthat))
17544 (home-page "https://bioconductor.org/packages/metapod")
17545 (synopsis "Meta-analyses on p-values of differential analyses")
17546 (description
17547 "This package implements a variety of methods for combining p-values in
17548differential analyses of genome-scale datasets. Functions can combine
17549p-values across different tests in the same analysis (e.g., genomic windows in
17550ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
17551analyses (e.g., replicated comparisons, effect of different treatment
17552conditions). Support is provided for handling log-transformed input p-values,
17553missing values and weighting where appropriate.")
17554 (license license:gpl3)))
17555
17556(define-public r-biocsingular
17557 (package
17558 (name "r-biocsingular")
17559 (version "1.28.0")
17560 (source
17561 (origin
17562 (method url-fetch)
17563 (uri (bioconductor-uri "BiocSingular" version))
17564 (sha256
17565 (base32
17566 "1n6r72m7bpnbcvpnass26zjdgbbxcqmjba0favl54855fc5spcrp"))))
17567 (properties `((upstream-name . "BiocSingular")))
17568 (build-system r-build-system)
17569 (arguments
17570 (list
17571 #:skipped-tests
17572 '(("test-lowrank.R"
17573 ;; Objects equal but not identical
17574 "LowRankMatrix subsetting works as expected"))))
17575 (propagated-inputs
17576 (list r-assorthead
17577 r-beachmat
17578 r-biocgenerics
17579 r-biocparallel
17580 r-delayedarray
17581 r-irlba
17582 r-matrix
17583 r-rcpp
17584 r-rsvd
17585 r-s4vectors
17586 r-scaledmatrix))
17587 (native-inputs
17588 (list r-knitr r-testthat))
17589 (home-page "https://github.com/LTLA/BiocSingular")
17590 (synopsis "Singular value decomposition for Bioconductor packages")
17591 (description
17592 "This package implements exact and approximate methods for singular value
17593decomposition and principal components analysis, in a framework that allows
17594them to be easily switched within Bioconductor packages or workflows. Where
17595possible, parallelization is achieved using the BiocParallel framework.")
17596 (license license:gpl3)))
17597
17598(define-public r-destiny
17599 (package
17600 (name "r-destiny")
17601 (version "3.26.0")
17602 (source
17603 (origin
17604 (method url-fetch)
17605 (uri (bioconductor-uri "destiny" version))
17606 (sha256
17607 (base32
17608 "1qik33fm9mqnnw7idfxp666lmwpm0vbzf01nnnx2hl82s4559ll8"))))
17609 (build-system r-build-system)
17610 (propagated-inputs
17611 (list r-biobase
17612 r-biocgenerics
17613 r-ggplot-multistats
17614 r-ggplot2
17615 r-ggthemes
17616 r-irlba
17617 r-knn-covertree
17618 r-matrix
17619 r-pcamethods
17620 r-proxy
17621 r-rcpp
17622 r-rcppeigen
17623 r-rcpphnsw
17624 r-rlang
17625 r-rspectra
17626 r-scales
17627 r-scatterplot3d
17628 r-singlecellexperiment
17629 r-summarizedexperiment
17630 r-tidyr
17631 r-tidyselect
17632 r-vim))
17633 (native-inputs (list r-knitr r-testthat))
17634 (home-page "https://bioconductor.org/packages/destiny/")
17635 (synopsis "Create and plot diffusion maps")
17636 (description "This package provides tools to create and plot diffusion
17637maps.")
17638 ;; Any version of the GPL
17639 (license license:gpl3+)))
17640
17641(define-public r-savr
17642 (package
17643 (name "r-savr")
17644 (version "1.37.0")
17645 (source
17646 (origin
17647 (method url-fetch)
17648 (uri (bioconductor-uri "savR" version))
17649 (sha256
17650 (base32
17651 "13wiw7isdmpwhynxjrhimy9yglcz1108k7nwa98vq9czq49zpada"))))
17652 (properties `((upstream-name . "savR")))
17653 (build-system r-build-system)
17654 ;; Disable vignettes because they use a removed function in r-ggplot2.
17655 (arguments (list #:test-types '(list "tests")))
17656 (propagated-inputs
17657 (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
17658 (native-inputs (list r-testthat))
17659 (home-page "https://github.com/bcalder/savR")
17660 (synopsis "Parse and analyze Illumina SAV files")
17661 (description
17662 "This package provides tools to parse Illumina Sequence Analysis
17663Viewer (SAV) files, access data, and generate QC plots.")
17664 (license license:agpl3+)))
17665
17666(define-public r-chipexoqual
17667 (package
17668 (name "r-chipexoqual")
17669 (version "1.36.0")
17670 (source
17671 (origin
17672 (method url-fetch)
17673 (uri (bioconductor-uri "ChIPexoQual" version))
17674 (sha256
17675 (base32
17676 "0i08np52kfirjx7k2fr5r2d5nazazqbmhl6vw3l8qasv1clk0h6m"))))
17677 (properties `((upstream-name . "ChIPexoQual")))
17678 (build-system r-build-system)
17679 (propagated-inputs
17680 (list r-biocparallel
17681 r-biovizbase
17682 r-broom
17683 r-data-table
17684 r-dplyr
17685 r-genomicalignments
17686 r-genomicranges
17687 r-ggplot2
17688 r-hexbin
17689 r-iranges
17690 r-rcolorbrewer
17691 r-rmarkdown
17692 r-rsamtools
17693 r-s4vectors
17694 r-scales
17695 r-seqinfo
17696 r-viridis))
17697 (native-inputs
17698 (list r-chipexoqualexample r-knitr r-testthat))
17699 (home-page "https://github.com/keleslab/ChIPexoQual")
17700 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
17701 (description
17702 "This package provides a quality control pipeline for ChIP-exo/nexus
17703sequencing data.")
17704 (license license:gpl2+)))
17705
17706(define-public r-copynumber
17707 (package
17708 (name "r-copynumber")
17709 (version "1.38.0")
17710 (source (origin
17711 (method url-fetch)
17712 (uri (bioconductor-uri "copynumber" version))
17713 (sha256
17714 (base32
17715 "1a664bllaq9pbb5cpd01j919qirylvnm8qd49lwlz89jvqjdri19"))))
17716 (build-system r-build-system)
17717 (propagated-inputs
17718 (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
17719 (home-page "https://bioconductor.org/packages/copynumber")
17720 (synopsis "Segmentation of single- and multi-track copy number data")
17721 (description
17722 "This package segments single- and multi-track copy number data by a
17723penalized least squares regression method.")
17724 (license license:artistic2.0)))
17725
17726(define-public r-dnacopy
17727 (package
17728 (name "r-dnacopy")
17729 (version "1.86.0")
17730 (source
17731 (origin
17732 (method url-fetch)
17733 (uri (bioconductor-uri "DNAcopy" version))
17734 (sha256
17735 (base32
17736 "0939alm8scjb56f9mdxlgw40vcwgldzcbl37b23rx92m07a1lndx"))))
17737 (properties `((upstream-name . "DNAcopy")))
17738 (build-system r-build-system)
17739 (native-inputs (list gfortran))
17740 (home-page "https://bioconductor.org/packages/DNAcopy")
17741 (synopsis "DNA copy number data analysis")
17742 (description
17743 "This package implements the @dfn{circular binary segmentation} (CBS)
17744algorithm to segment DNA copy number data and identify genomic regions with
17745abnormal copy number.")
17746 (license license:gpl2+)))
17747
17748(define-public r-hmmcopy
17749 (package
17750 (name "r-hmmcopy")
17751 (version "1.54.0")
17752 (source
17753 (origin
17754 (method url-fetch)
17755 (uri (bioconductor-uri "HMMcopy" version))
17756 (sha256
17757 (base32 "1j956903rhjcax7cn1w2mqh0lwzpws04q6lzsi4sszbmjmic99pg"))))
17758 (properties `((upstream-name . "HMMcopy")))
17759 (build-system r-build-system)
17760 (propagated-inputs (list r-data-table))
17761 (home-page "https://bioconductor.org/packages/HMMcopy")
17762 (synopsis
17763 "Copy number prediction with correction for GC and mappability bias for HTS data")
17764 (description
17765 "This package corrects GC and mappability biases for
17766readcounts (i.e. coverage) in non-overlapping windows of fixed length for
17767single whole genome samples, yielding a rough estimate of copy number for
17768further analysis. It was designed for rapid correction of high coverage whole
17769genome tumor and normal samples.")
17770 (license license:gpl3)))
17771
17772;; This is a CRAN package, but it uncharacteristically depends on a
17773;; Bioconductor package.
17774(define-public r-htscluster
17775 (package
17776 (name "r-htscluster")
17777 (version "2.0.11")
17778 (source
17779 (origin
17780 (method url-fetch)
17781 (uri (cran-uri "HTSCluster" version))
17782 (sha256
17783 (base32
17784 "0x9shhyla9bldkkh367gfdmf0k72l1ppixb8gzsa6nf8jx8qdpbp"))))
17785 (properties `((upstream-name . "HTSCluster")))
17786 (build-system r-build-system)
17787 (propagated-inputs
17788 (list r-capushe r-edger r-plotrix))
17789 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
17790 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
17791 (description
17792 "This package provides a Poisson mixture model is implemented to cluster
17793genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
17794estimation is performed using either the EM or CEM algorithm, and the slope
17795heuristics are used for model selection (i.e., to choose the number of
17796clusters).")
17797 (license license:gpl3+)))
17798
17799(define-public r-deds
17800 (package
17801 (name "r-deds")
17802 (version "1.60.0")
17803 (source
17804 (origin
17805 (method url-fetch)
17806 (uri (bioconductor-uri "DEDS" version))
17807 (sha256
17808 (base32
17809 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
17810 (properties `((upstream-name . "DEDS")))
17811 (build-system r-build-system)
17812 (home-page "https://bioconductor.org/packages/DEDS/")
17813 (synopsis "Differential expression via distance summary for microarray data")
17814 (description
17815 "This library contains functions that calculate various statistics of
17816differential expression for microarray data, including t statistics, fold
17817change, F statistics, SAM, moderated t and F statistics and B statistics. It
17818also implements a new methodology called DEDS (Differential Expression via
17819Distance Summary), which selects differentially expressed genes by integrating
17820and summarizing a set of statistics using a weighted distance approach.")
17821 ;; Any version of the LGPL.
17822 (license license:lgpl3+)))
17823
17824;; This is a CRAN package, but since it depends on a Bioconductor package we
17825;; put it here.
17826(define-public r-nbpseq
17827 (package
17828 (name "r-nbpseq")
17829 (version "0.3.1")
17830 (source
17831 (origin
17832 (method url-fetch)
17833 (uri (cran-uri "NBPSeq" version))
17834 (sha256
17835 (base32
17836 "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14"))))
17837 (properties `((upstream-name . "NBPSeq")))
17838 (build-system r-build-system)
17839 (propagated-inputs
17840 (list r-qvalue))
17841 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
17842 (synopsis "Negative binomial models for RNA-Seq data")
17843 (description
17844 "This package provides negative binomial models for two-group comparisons
17845and regression inferences from RNA-sequencing data.")
17846 (license license:gpl2)))
17847
17848(define-public r-ebseq
17849 (package
17850 (name "r-ebseq")
17851 (version "2.10.0")
17852 (source
17853 (origin
17854 (method url-fetch)
17855 (uri (bioconductor-uri "EBSeq" version))
17856 (sha256
17857 (base32
17858 "0a150n75idrbgvj54z4cxfgx88r20hp1qp8r208rh56whm277jnf"))))
17859 (properties `((upstream-name . "EBSeq")))
17860 (build-system r-build-system)
17861 (propagated-inputs
17862 (list r-bh
17863 r-blockmodeling
17864 r-gplots
17865 r-rcpp
17866 r-rcppeigen))
17867 (native-inputs (list r-testthat))
17868 (home-page "https://bioconductor.org/packages/EBSeq")
17869 (synopsis "Differential expression analysis of RNA-seq data")
17870 (description
17871 "This package provides tools for differential expression analysis at both
17872gene and isoform level using RNA-seq data")
17873 (license license:artistic2.0)))
17874
17875(define-public r-karyoploter
17876 (package
17877 (name "r-karyoploter")
17878 (version "1.38.0")
17879 (source (origin
17880 (method url-fetch)
17881 (uri (bioconductor-uri "karyoploteR" version))
17882 (sha256
17883 (base32
17884 "18l18prc2bzkhzy1yl0m5gg3a2qlbcrvlp86kz74js1sw8ywk1b3"))))
17885 (build-system r-build-system)
17886 (propagated-inputs
17887 (list r-annotationdbi
17888 r-bamsignals
17889 r-bezier
17890 r-biovizbase
17891 r-digest
17892 r-genomeinfodb
17893 r-genomicfeatures
17894 r-genomicranges
17895 r-iranges
17896 r-memoise
17897 r-regioner
17898 r-rsamtools
17899 r-rtracklayer
17900 r-s4vectors
17901 r-seqinfo
17902 r-variantannotation))
17903 (native-inputs
17904 (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat))
17905 (home-page "https://bioconductor.org/packages/karyoploteR/")
17906 (synopsis "Plot customizable linear genomes displaying arbitrary data")
17907 (description "This package creates karyotype plots of arbitrary genomes and
17908offers a complete set of functions to plot arbitrary data on them. It mimics
17909many R base graphics functions coupling them with a coordinate change function
17910automatically mapping the chromosome and data coordinates into the plot
17911coordinates.")
17912 (license license:artistic2.0)))
17913
17914(define-public r-lpsymphony
17915 (package
17916 (name "r-lpsymphony")
17917 (version "1.40.0")
17918 (source
17919 (origin
17920 (method url-fetch)
17921 (uri (bioconductor-uri "lpsymphony" version))
17922 (sha256
17923 (base32
17924 "1lh6fsjrmadary2pwrzq7118n9wqnyb6l90hcgd4zdsvl8xg62jr"))))
17925 (properties
17926 '((updater-extra-native-inputs . ("gfortran"))))
17927 (build-system r-build-system)
17928 (arguments
17929 (list
17930 #:phases
17931 #~(modify-phases %standard-phases
17932 (add-after 'unpack 'make-build-order-reproducible
17933 (lambda _
17934 (substitute* '("src/SYMPHONY/Cgl/configure.ac"
17935 "src/SYMPHONY/Cgl/configure")
17936 (("for file in `ls \\*/Makefile.in`")
17937 "for file in `ls */Makefile.in | sort`"))))
17938 #$@(if (or (target-aarch64?)
17939 (target-riscv64?))
17940 #~((add-after 'unpack 'update-config-files
17941 (lambda* (#:key native-inputs inputs #:allow-other-keys)
17942 (for-each
17943 (lambda (location)
17944 (for-each (lambda (file)
17945 (install-file
17946 (search-input-file
17947 (or native-inputs inputs)
17948 (string-append "/bin/" file))
17949 (dirname location)))
17950 '("config.guess" "config.sub")))
17951 (find-files "." "config\\.guess")))))
17952 #~()))))
17953 (inputs
17954 (list zlib))
17955 (native-inputs
17956 (append
17957 (list gfortran pkg-config r-biocstyle r-knitr r-testthat)
17958 (if (or (target-aarch64?)
17959 (target-riscv64?))
17960 (list config)
17961 '())))
17962 (home-page "https://r-forge.r-project.org/projects/rsymphony")
17963 (synopsis "Symphony integer linear programming solver in R")
17964 (description
17965 "This package was derived from Rsymphony. The package provides an R
17966interface to SYMPHONY, a linear programming solver written in C++. The main
17967difference between this package and Rsymphony is that it includes the solver
17968source code, while Rsymphony expects to find header and library files on the
17969users' system. Thus the intention of @code{lpsymphony} is to provide an easy
17970to install interface to SYMPHONY.")
17971 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
17972 ;; lpsimphony is released under the same terms.
17973 (license license:epl1.0)))
17974
17975(define-public r-ihw
17976 (package
17977 (name "r-ihw")
17978 (version "1.40.0")
17979 (source
17980 (origin
17981 (method url-fetch)
17982 (uri (bioconductor-uri "IHW" version))
17983 (sha256
17984 (base32
17985 "01ap2ishmsbv3w3b14qsbg79669w5an67yvzlmsjmbywlgasfrvq"))))
17986 (properties
17987 '((upstream-name . "IHW")
17988 (updater-extra-native-inputs . ("r-ggplot2" "r-scales"))))
17989 (build-system r-build-system)
17990 (propagated-inputs
17991 (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
17992 (native-inputs
17993 (list r-ggplot2 r-knitr r-scales r-testthat))
17994 (home-page "https://bioconductor.org/packages/IHW")
17995 (synopsis "Independent hypothesis weighting")
17996 (description
17997 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
17998procedure that increases power compared to the method of Benjamini and
17999Hochberg by assigning data-driven weights to each hypothesis. The input to
18000IHW is a two-column table of p-values and covariates. The covariate can be
18001any continuous-valued or categorical variable that is thought to be
18002informative on the statistical properties of each hypothesis test, while it is
18003independent of the p-value under the null hypothesis.")
18004 (license license:artistic2.0)))
18005
18006(define-public r-icobra
18007 (package
18008 (name "r-icobra")
18009 (version "1.40.0")
18010 (source
18011 (origin
18012 (method url-fetch)
18013 (uri (bioconductor-uri "iCOBRA" version))
18014 (sha256
18015 (base32
18016 "0gb9kvz89b11svnip05bj2yqa27i0kvzlrnfam3jhc619gbn4px4"))))
18017 (properties `((upstream-name . "iCOBRA")))
18018 (build-system r-build-system)
18019 (propagated-inputs
18020 (list r-dplyr
18021 r-dt
18022 r-ggplot2
18023 r-limma
18024 r-prompter
18025 r-reshape2
18026 r-rlang
18027 r-rocr
18028 r-scales
18029 r-shiny
18030 r-shinydashboard
18031 r-upsetr))
18032 (native-inputs
18033 (list r-knitr r-testthat))
18034 (home-page "https://bioconductor.org/packages/iCOBRA")
18035 (synopsis "Comparison and visualization of ranking and assignment methods")
18036 (description
18037 "This package provides functions for calculation and visualization of
18038performance metrics for evaluation of ranking and binary
18039classification (assignment) methods. It also contains a Shiny application for
18040interactive exploration of results.")
18041 (license license:gpl2+)))
18042
18043(define-public r-residualmatrix
18044 (package
18045 (name "r-residualmatrix")
18046 (version "1.22.0")
18047 (source
18048 (origin
18049 (method url-fetch)
18050 (uri (bioconductor-uri "ResidualMatrix" version))
18051 (sha256
18052 (base32
18053 "1vaqv7g0i4yz8p0l79kzy8kq625j1lwr6fxzh683kk0hyzl4d4ix"))))
18054 (properties
18055 `((upstream-name . "ResidualMatrix")))
18056 (build-system r-build-system)
18057 (propagated-inputs
18058 (list r-delayedarray r-matrix r-s4vectors))
18059 (native-inputs
18060 (list r-knitr r-testthat))
18061 (home-page "https://github.com/LTLA/ResidualMatrix")
18062 (synopsis "Create a DelayedMatrix of regression residuals")
18063 (description
18064 "This package implements tools for delayed computation of a matrix of
18065residuals after fitting a linear model to each column of an input matrix. It
18066also supports partial computation of residuals where selected factors are to
18067be preserved in the output matrix. It implements a number of efficient
18068methods for operating on the delayed matrix of residuals, most notably matrix
18069multiplication and calculation of row/column sums or means.")
18070 (license license:gpl3)))
18071
18072(define-public r-batchelor
18073 (package
18074 (name "r-batchelor")
18075 (version "1.28.0")
18076 (source
18077 (origin
18078 (method url-fetch)
18079 (uri (bioconductor-uri "batchelor" version))
18080 (sha256
18081 (base32
18082 "0y4rjpwzknzaz811ag8nxx7as05a7jb4rbg23hfn759gd48lp491"))))
18083 (properties `((upstream-name . "batchelor")))
18084 (build-system r-build-system)
18085 (arguments
18086 (list
18087 #:skipped-tests
18088 ;; Objects equal but not identical
18089 '(("test-cluster-mnn.R"
18090 "clusterMNN behaves like fastMNN on pseudo-bulk samples")
18091 ("test-correct-exps.R"
18092 "correctExperiments works properly")
18093 ("test-reduced-mnn.R"
18094 "reducedMNN works correctly with restriction"))))
18095 (propagated-inputs
18096 (list r-beachmat
18097 r-biocgenerics
18098 r-biocneighbors
18099 r-biocparallel
18100 r-biocsingular
18101 r-delayedarray
18102 r-delayedmatrixstats
18103 r-igraph
18104 r-matrix
18105 r-rcpp
18106 r-residualmatrix
18107 r-s4vectors
18108 r-scaledmatrix
18109 r-scuttle
18110 r-singlecellexperiment
18111 r-sparsearray
18112 r-summarizedexperiment))
18113 (native-inputs (list r-bluster r-knitr r-scran r-testthat))
18114 (home-page "https://bioconductor.org/packages/batchelor")
18115 (synopsis "Single-Cell Batch Correction Methods")
18116 (description
18117 "This package implements a variety of methods for batch correction of
18118single-cell (RNA sequencing) data. This includes methods based on detecting
18119mutually nearest neighbors, as well as several efficient variants of linear
18120regression of the log-expression values. Functions are also provided to
18121perform global rescaling to remove differences in depth between batches, and
18122to perform a principal components analysis that is robust to differences in
18123the numbers of cells across batches.")
18124 (license license:gpl3)))
18125
18126;; TODO: check version of js-jquery-sticky-kit
18127(define-public r-mast
18128 (package
18129 (name "r-mast")
18130 (version "1.38.0")
18131 (source
18132 (origin
18133 (method url-fetch)
18134 (uri (bioconductor-uri "MAST" version))
18135 (sha256
18136 (base32
18137 "175yqh6zirii85qfxv11x0bf2iw03v16wqq6ha7r8bp1slym29p5"))
18138 (snippet
18139 '(delete-file "docs/jquery.sticky-kit.min.js"))))
18140 (properties `((upstream-name . "MAST")))
18141 (build-system r-build-system)
18142 (arguments
18143 (list
18144 #:phases
18145 '(modify-phases %standard-phases
18146 (add-after 'unpack 'process-javascript
18147 (lambda* (#:key inputs #:allow-other-keys)
18148 (invoke "esbuild"
18149 (assoc-ref inputs "jquery.sticky-kit.js")
18150 "--minify"
18151 "--outfile=docs/jquery.sticky-kit.min.js"))))))
18152 (propagated-inputs
18153 (list r-abind
18154 r-biobase
18155 r-biocgenerics
18156 r-data-table
18157 r-ggplot2
18158 r-matrix
18159 r-plyr
18160 r-progress
18161 r-reshape2
18162 r-s4vectors
18163 r-singlecellexperiment
18164 r-stringr
18165 r-summarizedexperiment))
18166 (native-inputs
18167 (list esbuild r-car r-knitr r-reshape r-testthat
18168 (origin
18169 (method url-fetch)
18170 (uri
18171 "https://cdn.jsdelivr.net/gh/leafo/[email protected]/jquery.sticky-kit.js")
18172 (sha256
18173 (base32
18174 "17c3a1hqc3ybwj7hpw8prazajp2x98aq7nyfn71h6lzjvblq297g")))))
18175 (home-page "https://github.com/RGLab/MAST/")
18176 (synopsis "Model-based analysis of single cell transcriptomics")
18177 (description
18178 "This package provides methods and models for handling zero-inflated
18179single cell assay data.")
18180 (license license:gpl2+)))
18181
18182(define-public r-monocle
18183 (package
18184 (name "r-monocle")
18185 (version "2.40.0")
18186 (source
18187 (origin
18188 (method url-fetch)
18189 (uri (bioconductor-uri "monocle" version))
18190 (sha256
18191 (base32
18192 "1d3kqzfi959vrbpcd6n5kiicm7byn4ir1n3xnnbcidzpr1yxgd17"))))
18193 (build-system r-build-system)
18194 (arguments
18195 (list
18196 ;; Test files are not included.
18197 #:tests? #false
18198 #:phases
18199 '(modify-phases %standard-phases
18200 (add-after 'unpack 'patch-tests
18201 (lambda _
18202 (substitute* "inst/tests/basic_tests.R"
18203 (("^load_small_test" m)
18204 (string-append "library(testthat)\n" m))))))))
18205 (propagated-inputs
18206 (list r-biobase
18207 r-biocgenerics
18208 r-biocviews
18209 r-cluster
18210 r-combinat
18211 r-ddrtree
18212 r-dplyr
18213 r-fastica
18214 r-ggplot2
18215 r-hsmmsinglecell
18216 r-igraph
18217 r-irlba
18218 r-leidenbase
18219 r-limma
18220 r-mass
18221 r-matrix
18222 r-matrixstats
18223 r-pheatmap
18224 r-plyr
18225 r-proxy
18226 r-rann
18227 r-rcpp
18228 r-reshape2
18229 r-rtsne
18230 r-slam
18231 r-stringr
18232 r-tibble
18233 r-vgam
18234 r-viridis))
18235 (native-inputs
18236 (list r-knitr r-testthat))
18237 (home-page "https://bioconductor.org/packages/monocle")
18238 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
18239 (description
18240 "Monocle performs differential expression and time-series analysis for
18241single-cell expression experiments. It orders individual cells according to
18242progress through a biological process, without knowing ahead of time which
18243genes define progress through that process. Monocle also performs
18244differential expression analysis, clustering, visualization, and other useful
18245tasks on single cell expression data. It is designed to work with RNA-Seq and
18246qPCR data, but could be used with other types as well.")
18247 (license license:artistic2.0)))
18248
18249(define-public r-sangerseqr
18250 (package
18251 (name "r-sangerseqr")
18252 (version "1.48.0")
18253 (source (origin
18254 (method url-fetch)
18255 (uri (bioconductor-uri "sangerseqR" version))
18256 (sha256
18257 (base32
18258 "0bz9zpdwqvzkyvc83qh1b2pccskyf2h12phwbqkznk5ci6v7w9ii"))))
18259 (properties `((upstream-name . "sangerseqR")))
18260 (build-system r-build-system)
18261 (propagated-inputs (list r-biostrings r-pwalign r-shiny r-stringr))
18262 (native-inputs (list r-biocgenerics r-knitr r-runit))
18263 (home-page "https://bioconductor.org/packages/sangerseqR")
18264 (synopsis "Tools for Sanger Sequencing data in R")
18265 (description
18266 "This package contains several tools for analyzing Sanger Sequencing data
18267files in R, including reading @file{.scf} and @file{.ab1} files, making
18268basecalls and plotting chromatograms.")
18269 (license license:gpl2)))
18270
18271(define-public r-sanssouci
18272 ;; This is the latest commit as of packaging for Guix.
18273 (let ((commit "fcd60da7f3fadfa993a151288f3e67acd3d40b49")
18274 (revision "1"))
18275 (package
18276 (name "r-sanssouci")
18277 (version (git-version "0.16.2" revision commit))
18278 (source (origin
18279 (method git-fetch)
18280 (uri (git-reference
18281 (url "https://github.com/pneuvial/sanssouci.git")
18282 (commit commit)))
18283 (file-name (git-file-name name version))
18284 (sha256
18285 (base32
18286 "0ayfz6l3l1d8wialrgkd61d0p3wzci9jbj1yivgwbyr3a47828im"))))
18287 (build-system r-build-system)
18288 (propagated-inputs
18289 (list r-generics r-matrix r-matrixstats r-matrixtests r-rlang))
18290 (native-inputs (list r-knitr r-testthat))
18291 (home-page "https://pneuvial.github.io/sanssouci")
18292 (synopsis "Post Hoc multiple testing inference")
18293 (description
18294 "The goal of sansSouci is to perform post hoc inference: in a multiple
18295testing context, sansSouci provides statistical guarantees on possibly
18296user-defined and/or data-driven sets of hypotheses.")
18297 (license license:gpl3))))
18298
18299(define-public r-noiseq
18300 (package
18301 (name "r-noiseq")
18302 (version "2.56.0")
18303 (source
18304 (origin
18305 (method url-fetch)
18306 (uri (bioconductor-uri "NOISeq" version))
18307 (sha256
18308 (base32
18309 "1v4zckighnyxx9mmiazqx7q1drcd4wh61vncg26hj4psgdavimvc"))))
18310 (properties `((upstream-name . "NOISeq")))
18311 (build-system r-build-system)
18312 (propagated-inputs
18313 (list r-biobase r-matrix))
18314 (home-page "https://bioconductor.org/packages/NOISeq")
18315 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
18316 (description
18317 "This package provides tools to support the analysis of RNA-seq
18318expression data or other similar kind of data. It provides exploratory plots
18319to evaluate saturation, count distribution, expression per chromosome, type of
18320detected features, features length, etc. It also supports the analysis of
18321differential expression between two experimental conditions with no parametric
18322assumptions.")
18323 (license license:artistic2.0)))
18324
18325(define-public r-scdd
18326 (package
18327 (name "r-scdd")
18328 (version "1.36.0")
18329 (source
18330 (origin
18331 (method url-fetch)
18332 (uri (bioconductor-uri "scDD" version))
18333 (sha256
18334 (base32
18335 "1gjxxbhlq75jwdarvg50q37ar2rg1rl504k0gwz7bav9qmwlr20x"))))
18336 (properties
18337 '((upstream-name . "scDD")
18338 (updater-extra-native-inputs . ("r-testthat"))))
18339 (build-system r-build-system)
18340 (propagated-inputs
18341 (list r-arm
18342 r-biocparallel
18343 r-ebseq
18344 r-fields
18345 r-ggplot2
18346 r-mclust
18347 r-outliers
18348 r-s4vectors
18349 r-scran
18350 r-singlecellexperiment
18351 r-summarizedexperiment))
18352 (native-inputs
18353 (list r-biocstyle r-gridextra r-knitr r-testthat))
18354 (home-page "https://github.com/kdkorthauer/scDD")
18355 (synopsis "Mixture modeling of single-cell RNA-seq data")
18356 (description
18357 "This package implements a method to analyze single-cell RNA-seq data
18358utilizing flexible Dirichlet Process mixture models. Genes with differential
18359distributions of expression are classified into several interesting patterns
18360of differences between two conditions. The package also includes functions
18361for simulating data with these patterns from negative binomial
18362distributions.")
18363 (license license:gpl2)))
18364
18365(define-public r-scone
18366 (package
18367 (name "r-scone")
18368 (version "1.36.0")
18369 (source
18370 (origin
18371 (method url-fetch)
18372 (uri (bioconductor-uri "scone" version))
18373 (sha256
18374 (base32
18375 "1cc38h9dpgzg7djhnf504bzyvj9s0ja6rm4cd8hrdcvimbbzjric"))))
18376 (build-system r-build-system)
18377 (propagated-inputs
18378 (list r-aroma-light
18379 r-biocparallel
18380 r-boot
18381 r-class
18382 r-cluster
18383 r-compositions
18384 r-delayedmatrixstats
18385 r-diptest
18386 r-edger
18387 r-fpc
18388 r-gplots
18389 r-hexbin
18390 r-limma
18391 r-matrixgenerics
18392 r-matrixstats
18393 r-mixtools
18394 r-rarpack
18395 r-rcolorbrewer
18396 r-rhdf5
18397 r-ruvseq
18398 r-singlecellexperiment
18399 r-sparsearray
18400 r-sparsematrixstats
18401 r-summarizedexperiment))
18402 (native-inputs
18403 (list r-delayedarray r-knitr r-testthat))
18404 (home-page "https://bioconductor.org/packages/scone")
18405 (synopsis "Single cell overview of normalized expression data")
18406 (description
18407 "SCONE is an R package for comparing and ranking the performance of
18408different normalization schemes for single-cell RNA-seq and other
18409high-throughput analyses.")
18410 (license license:artistic2.0)))
18411
18412(define-public r-geoquery
18413 (package
18414 (name "r-geoquery")
18415 (version "2.80.0")
18416 (source
18417 (origin
18418 (method url-fetch)
18419 (uri (bioconductor-uri "GEOquery" version))
18420 (sha256
18421 (base32
18422 "1snb9r6qp7h0rbhl695yb0jalmq7kncinf4ldbjh3yjav5g86a97"))))
18423 (properties `((upstream-name . "GEOquery")))
18424 (build-system r-build-system)
18425 ;; Tests attempt to download data files.
18426 (arguments (list #:tests? #false))
18427 (propagated-inputs
18428 (list r-biobase
18429 r-curl
18430 r-data-table
18431 r-dplyr
18432 r-httr2
18433 r-limma
18434 r-magrittr
18435 r-r-utils
18436 r-readr
18437 r-rentrez
18438 r-rvest
18439 r-s4vectors
18440 r-stringr
18441 r-summarizedexperiment
18442 r-tidyr
18443 r-xml2))
18444 (native-inputs
18445 (list r-quarto r-testthat))
18446 (home-page "https://github.com/seandavi/GEOquery/")
18447 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
18448 (description
18449 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
18450microarray data. Given the rich and varied nature of this resource, it is
18451only natural to want to apply BioConductor tools to these data. GEOquery is
18452the bridge between GEO and BioConductor.")
18453 (license license:gpl2)))
18454
18455(define-public r-illuminaio
18456 (package
18457 (name "r-illuminaio")
18458 (version "0.54.0")
18459 (source
18460 (origin
18461 (method url-fetch)
18462 (uri (bioconductor-uri "illuminaio" version))
18463 (sha256
18464 (base32
18465 "1jdnlqhxxhrlp2rdvy6wmd250j3ci9abkdi7kwd4s7zfqmcw5qq2"))))
18466 (properties
18467 ;; This is needed for vignettes.
18468 '((updater-extra-native-inputs . ("r-biocstyle"))))
18469 (build-system r-build-system)
18470 (propagated-inputs
18471 (list r-base64))
18472 (native-inputs
18473 (list r-biocstyle
18474 r-illuminadatatestfiles
18475 r-runit))
18476 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
18477 (synopsis "Parse Illumina microarray output files")
18478 (description
18479 "This package provides tools for parsing Illumina's microarray output
18480files, including IDAT.")
18481 (license license:gpl2)))
18482
18483(define-public r-siggenes
18484 (package
18485 (name "r-siggenes")
18486 (version "1.86.0")
18487 (source
18488 (origin
18489 (method url-fetch)
18490 (uri (bioconductor-uri "siggenes" version))
18491 (sha256
18492 (base32
18493 "1x96kac4y7cffp3i11v7rbfg5w5lp2r6gl21qx7j6p2v7x9gi3zx"))))
18494 (build-system r-build-system)
18495 (propagated-inputs
18496 (list r-biobase r-multtest r-scrime))
18497 (home-page "https://bioconductor.org/packages/siggenes/")
18498 (synopsis
18499 "Multiple testing using SAM and Efron's empirical Bayes approaches")
18500 (description
18501 "This package provides tools for the identification of differentially
18502expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
18503both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
18504Bayes Analyses of Microarrays} (EBAM).")
18505 (license license:lgpl2.0+)))
18506
18507(define-public r-bumphunter
18508 (package
18509 (name "r-bumphunter")
18510 (version "1.54.0")
18511 (source
18512 (origin
18513 (method url-fetch)
18514 (uri (bioconductor-uri "bumphunter" version))
18515 (sha256
18516 (base32
18517 "1qqhf13lr935dp9ny03czqpwhwngf7n94bi9hm0ba1xr5nm2qrrw"))))
18518 (build-system r-build-system)
18519 (arguments
18520 (list
18521 ;; Test in test_annotation attempt to download a data file. There are
18522 ;; no other tests.
18523 #:tests? #false))
18524 (propagated-inputs
18525 (list r-annotationdbi
18526 r-biocgenerics
18527 r-dorng
18528 r-foreach
18529 r-genomicfeatures
18530 r-genomicranges
18531 r-iranges
18532 r-iterators
18533 r-limma
18534 r-locfit
18535 r-matrixstats
18536 r-s4vectors
18537 r-seqinfo))
18538 (native-inputs
18539 (list r-doparallel
18540 r-genomeinfodb
18541 r-rtracklayer
18542 r-runit
18543 r-testthat
18544 r-txdb-hsapiens-ucsc-hg19-knowngene
18545 r-txdbmaker))
18546 (home-page "https://github.com/ririzarr/bumphunter")
18547 (synopsis "Find bumps in genomic data")
18548 (description
18549 "This package provides tools for finding bumps in genomic data in order
18550to identify differentially methylated regions in epigenetic epidemiology
18551studies.")
18552 (license license:artistic2.0)))
18553
18554(define-public r-bumpymatrix
18555 (package
18556 (name "r-bumpymatrix")
18557 (version "1.20.0")
18558 (source (origin
18559 (method url-fetch)
18560 (uri (bioconductor-uri "BumpyMatrix" version))
18561 (sha256
18562 (base32
18563 "139vgz85lj6hmkzpqbvgx2al38v2wi2jbzj0zcxn94i0xr13hg12"))))
18564 (properties `((upstream-name . "BumpyMatrix")))
18565 (build-system r-build-system)
18566 (propagated-inputs (list r-iranges r-matrix r-s4vectors))
18567 (native-inputs (list r-knitr r-testthat))
18568 (home-page "https://bioconductor.org/packages/BumpyMatrix")
18569 (synopsis "Bumpy matrix of non-scalar objects")
18570 (description
18571 "This package provides a class and subclasses for storing non-scalar
18572objects in matrix entries. This is akin to a ragged array but the raggedness
18573is in the third dimension, much like a bumpy surface--hence the name. Of
18574particular interest is the @code{BumpyDataFrameMatrix}, where each entry is a
18575Bioconductor data frame. This allows us to naturally represent multivariate
18576data in a format that is compatible with two-dimensional containers like the
18577@code{SummarizedExperiment} and @code{MultiAssayExperiment} objects.")
18578 (license license:expat)))
18579
18580(define-public r-mia
18581 (package
18582 (name "r-mia")
18583 (version "1.20.0")
18584 (source (origin
18585 (method url-fetch)
18586 (uri (bioconductor-uri "mia" version))
18587 (sha256
18588 (base32
18589 "117j9rmamd8khsb3mq4prmal1w2x3kb9bjwa5nc4z569npzm7zab"))))
18590 (properties
18591 '((upstream-name . "mia")
18592 (updater-ignored-native-inputs
18593 . ("r-goodmankruskal"
18594 "r-microbiomedatasets"
18595 "r-philr"
18596 "r-topicdoc"))))
18597 (build-system r-build-system)
18598 (propagated-inputs
18599 (list r-ape
18600 r-biocgenerics
18601 r-biocparallel
18602 r-biostrings
18603 r-bluster
18604 r-decipher
18605 r-decontam
18606 r-delayedarray
18607 r-delayedmatrixstats
18608 r-dirichletmultinomial
18609 r-dplyr
18610 r-ecodive
18611 r-iranges
18612 r-mass
18613 r-matrixgenerics
18614 r-multiassayexperiment
18615 r-rcpp
18616 r-rlang
18617 r-s4vectors
18618 r-scater
18619 r-singlecellexperiment
18620 r-stringr
18621 r-summarizedexperiment
18622 r-tibble
18623 r-tidyr
18624 r-treesummarizedexperiment
18625 r-vegan))
18626 (native-inputs (list r-biomformat
18627 r-dada2
18628 r-knitr
18629 r-mediation
18630 r-microbiome
18631 r-nmf
18632 r-phyloseq
18633 r-reldist
18634 r-scuttle
18635 r-testthat
18636 r-topicmodels))
18637 (home-page "https://github.com/microbiome/mia")
18638 (synopsis "Microbiome analysis")
18639 (description
18640 "The mia package implements tools for microbiome analysis based on the
18641@code{SummarizedExperiment}, @code{SingleCellExperiment} and
18642@code{TreeSummarizedExperiment} infrastructure. Data wrangling and analysis
18643in the context of taxonomic data is the main scope. Additional functions for
18644common task are implemented such as community indices calculation and
18645summarization.")
18646 (license license:artistic2.0)))
18647
18648(define-public r-microbiome
18649 (package
18650 (name "r-microbiome")
18651 (version "1.34.0")
18652 (source (origin
18653 (method url-fetch)
18654 (uri (bioconductor-uri "microbiome" version))
18655 (sha256
18656 (base32
18657 "0w6pl5d2hsscf99s5pci99pkwama01fns7zqwnnlp30mqwx7ym0k"))))
18658 (properties `((upstream-name . "microbiome")))
18659 (build-system r-build-system)
18660 (propagated-inputs
18661 (list r-biostrings
18662 r-compositions
18663 r-dplyr
18664 r-ggplot2
18665 r-phyloseq
18666 r-reshape2
18667 r-rtsne
18668 r-scales
18669 r-tibble
18670 r-tidyr
18671 r-vegan))
18672 (native-inputs (list r-knitr r-testthat))
18673 (home-page "https://microbiome.github.io/microbiome/")
18674 (synopsis "Tools for microbiome analysis")
18675 (description
18676 "This package facilitates phyloseq exploration and analysis of taxonomic
18677profiling data. This package provides tools for the manipulation, statistical
18678analysis, and visualization of taxonomic profiling data. In addition to
18679targeted case-control studies, microbiome facilitates scalable exploration of
18680population cohorts. This package supports the independent phyloseq data
18681format and expands the available toolkit in order to facilitate the
18682standardization of the analyses and the development of best practices.")
18683 (license license:bsd-2)))
18684
18685;; This is a CRAN package but it depends on phyloseq, which is from
18686;; Bioconductor.
18687(define-public r-microbiomestat
18688 (package
18689 (name "r-microbiomestat")
18690 (version "1.4")
18691 (source (origin
18692 (method url-fetch)
18693 (uri (cran-uri "MicrobiomeStat" version))
18694 (sha256
18695 (base32
18696 "0in28lzds3sv1xa25vs8q5mmm1ax78s2axhq7mi23njqip5xmsr1"))))
18697 (properties
18698 '((upstream-name . "MicrobiomeStat")
18699 (updater-extra-inputs . ("nlopt"))
18700 (updater-extra-native-inputs . ("pkg-config"))))
18701 (build-system r-build-system)
18702 (inputs (list nlopt))
18703 (native-inputs (list pkg-config))
18704 (propagated-inputs (list r-bbotk
18705 r-dplyr
18706 r-foreach
18707 r-ggplot2
18708 r-ggrepel
18709 r-lmertest
18710 r-mass
18711 r-matrix
18712 r-matrixstats
18713 r-mlr3
18714 r-mlr3mbo
18715 r-modeest
18716 r-paradox
18717 r-rcpp
18718 r-rcpparmadillo
18719 r-statmod))
18720 (home-page "https://cran.r-project.org/package=MicrobiomeStat")
18721 (synopsis "Statistical methods for microbiome compositional data")
18722 (description
18723 "This package provides a suite of methods for powerful and robust
18724microbiome data analysis addressing zero-inflation, phylogenetic structure and
18725compositional effects. The methods can be applied to the analysis of
18726other (high-dimensional) compositional data arising from sequencing
18727experiments.")
18728 (license license:gpl3)))
18729
18730(define-public r-milor
18731 (package
18732 (name "r-milor")
18733 (version "2.8.1")
18734 (source (origin
18735 (method url-fetch)
18736 (uri (bioconductor-uri "miloR" version))
18737 (sha256
18738 (base32
18739 "1734zfn5ibcmihrdxm6nms90rsf7kf0qfvmy0gvlx3n73zx6wygm"))))
18740 (properties `((upstream-name . "miloR")))
18741 (build-system r-build-system)
18742 (propagated-inputs
18743 (list r-biocgenerics
18744 r-biocneighbors
18745 r-biocparallel
18746 r-biocsingular
18747 r-cowplot
18748 r-dplyr
18749 r-edger
18750 r-ggbeeswarm
18751 r-ggplot2
18752 r-ggraph
18753 r-ggrepel
18754 r-gtools
18755 r-igraph
18756 r-irlba
18757 r-limma
18758 r-matrix
18759 r-matrixgenerics
18760 r-matrixstats
18761 r-numderiv
18762 r-patchwork
18763 r-pracma
18764 r-rcolorbrewer
18765 r-rcpp
18766 r-rcpparmadillo
18767 r-s4vectors
18768 r-singlecellexperiment
18769 r-stringr
18770 r-summarizedexperiment
18771 r-tibble
18772 r-tidyr))
18773 (native-inputs (list r-knitr
18774 r-mass
18775 r-mvtnorm
18776 r-scater
18777 r-scran
18778 r-testthat))
18779 (home-page "https://marionilab.github.io/miloR")
18780 (synopsis "Differential neighbourhood abundance testing on a graph")
18781 (description
18782 "Milo performs single-cell differential abundance testing. Cell states
18783are modelled as representative neighbourhoods on a nearest neighbour graph.
18784Hypothesis testing is performed using a negative bionomial generalized linear
18785model.")
18786 (license license:gpl3)))
18787
18788(define-public r-minfi
18789 (package
18790 (name "r-minfi")
18791 (version "1.58.0")
18792 (source
18793 (origin
18794 (method url-fetch)
18795 (uri (bioconductor-uri "minfi" version))
18796 (sha256
18797 (base32
18798 "0lk0ndhh6rldpsm73qw3856wsawm1gpavy4z3j4r5p61kwcjikcs"))))
18799 (properties
18800 '((updater-ignored-native-inputs . ("r-minfidata"))))
18801 (build-system r-build-system)
18802 ;; Tests require r-minfidata, which depends on this package.
18803 (arguments (list #:tests? #false))
18804 (propagated-inputs
18805 (list r-beanplot
18806 r-biobase
18807 r-biocgenerics
18808 r-biocparallel
18809 r-biostrings
18810 r-bumphunter
18811 r-data-table
18812 r-delayedarray
18813 r-delayedmatrixstats
18814 r-genefilter
18815 r-genomicranges
18816 r-geoquery
18817 r-hdf5array
18818 r-illuminaio
18819 r-iranges
18820 r-lattice
18821 r-limma
18822 r-mass
18823 r-mclust
18824 r-nlme
18825 r-nor1mix
18826 r-preprocesscore
18827 r-quadprog
18828 r-rcolorbrewer
18829 r-reshape
18830 r-s4vectors
18831 r-seqinfo
18832 r-siggenes
18833 r-summarizedexperiment))
18834 (native-inputs
18835 (list r-biocstyle r-knitr r-runit))
18836 (home-page "https://github.com/hansenlab/minfi")
18837 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
18838 (description
18839 "This package provides tools to analyze and visualize Illumina Infinium
18840methylation arrays.")
18841 (license license:artistic2.0)))
18842
18843(define-public r-missmethyl
18844 (package
18845 (name "r-missmethyl")
18846 (version "1.46.0")
18847 (source (origin
18848 (method url-fetch)
18849 (uri (bioconductor-uri "missMethyl" version))
18850 (sha256
18851 (base32
18852 "1398riwl6azivdxirwg5gdi4l94wcy1vxxyampv18rdljwah4rdj"))))
18853 (properties `((upstream-name . "missMethyl")))
18854 (build-system r-build-system)
18855 (propagated-inputs
18856 (list r-annotationdbi
18857 r-biasedurn
18858 r-biobase
18859 r-biocgenerics
18860 r-genomeinfodb
18861 r-genomicranges
18862 r-go-db
18863 r-illuminahumanmethylation450kanno-ilmn12-hg19
18864 r-illuminahumanmethylation450kmanifest
18865 r-illuminahumanmethylationepicanno-ilm10b4-hg19
18866 r-illuminahumanmethylationepicmanifest
18867 r-illuminahumanmethylationepicv2anno-20a1-hg38
18868 r-illuminahumanmethylationepicv2manifest
18869 r-iranges
18870 r-limma
18871 r-methylumi
18872 r-minfi
18873 r-org-hs-eg-db
18874 r-ruv
18875 r-s4vectors
18876 r-statmod
18877 r-stringr
18878 r-summarizedexperiment))
18879 (native-inputs (list r-knitr))
18880 (home-page "https://bioconductor.org/packages/missMethyl")
18881 (synopsis "Analyzing Illumina HumanMethylation BeadChip data")
18882 (description
18883 "This is a package for normalization, testing for differential
18884variability and differential methylation and gene set testing for data from
18885Illumina's Infinium HumanMethylation arrays. The normalization procedure is
18886subset-quantile within-array normalization (SWAN), which allows Infinium I and
18887II type probes on a single array to be normalized together. The test for
18888differential variability is based on an empirical Bayes version of Levene's
18889test. Differential methylation testing is performed using RUV, which can
18890adjust for systematic errors of unknown origin in high-dimensional data by
18891using negative control probes. Gene ontology analysis is performed by taking
18892into account the number of probes per gene on the array, as well as taking
18893into account multi-gene associated probes.")
18894 (license license:gpl2)))
18895
18896(define-public r-methylumi
18897 (package
18898 (name "r-methylumi")
18899 (version "2.58.0")
18900 (source
18901 (origin
18902 (method url-fetch)
18903 (uri (bioconductor-uri "methylumi" version))
18904 (sha256
18905 (base32
18906 "0lwb99ijybs9hjif2ii5mdiw8hwlmv7bhs7bs2n5kfvwmlza6wy0"))))
18907 (properties
18908 '((updater-ignored-native-inputs
18909 . ("r-tcgamethylation450k" "r-lumi"))))
18910 (build-system r-build-system)
18911 (propagated-inputs
18912 (list r-annotate
18913 r-annotationdbi
18914 r-biobase
18915 r-biocgenerics
18916 r-fdb-infiniummethylation-hg19
18917 r-genefilter
18918 r-genomeinfodb
18919 r-genomicfeatures
18920 r-genomicranges
18921 r-ggplot2
18922 r-illuminaio
18923 r-iranges
18924 r-lattice
18925 r-matrixstats
18926 r-minfi
18927 r-reshape2
18928 r-s4vectors
18929 r-scales
18930 r-summarizedexperiment))
18931 (native-inputs
18932 (list r-homo-sapiens
18933 r-illuminahumanmethylation450kanno-ilmn12-hg19
18934 r-knitr
18935 r-limma
18936 r-txdb-hsapiens-ucsc-hg19-knowngene
18937 r-xtable))
18938 (home-page "https://bioconductor.org/packages/methylumi")
18939 (synopsis "Handle Illumina methylation data")
18940 (description
18941 "This package provides classes for holding and manipulating Illumina
18942methylation data. Based on eSet, it can contain MIAME information, sample
18943information, feature information, and multiple matrices of data. An
18944\"intelligent\" import function, methylumiR can read the Illumina text files
18945and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
18946HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
18947background correction, and quality control features for GoldenGate, Infinium,
18948and Infinium HD arrays are also included.")
18949 (license license:gpl2)))
18950
18951(define-public r-lefser
18952 (package
18953 (name "r-lefser")
18954 (version "1.22.0")
18955 (source (origin
18956 (method url-fetch)
18957 (uri (bioconductor-uri "lefser" version))
18958 (sha256
18959 (base32
18960 "06b8c3ps4n47bv4ijv2njyj2f2bq9bhm3sg7pavmr7zzx9kh2d9a"))))
18961 (properties
18962 `((upstream-name . "lefser")
18963 (updater-extra-native-inputs . ("r-mia"))))
18964 (build-system r-build-system)
18965 (propagated-inputs
18966 (list r-ape
18967 r-biocgenerics
18968 r-coin
18969 r-dplyr
18970 r-forcats
18971 r-ggplot2
18972 r-ggrepel
18973 r-ggtree
18974 r-mass
18975 r-mia
18976 r-purrr
18977 r-s4vectors
18978 r-stringr
18979 r-summarizedexperiment
18980 r-testthat
18981 r-tibble
18982 r-tidyr
18983 r-tidyselect
18984 r-treeio))
18985 (native-inputs (list r-knitr r-mia r-withr))
18986 (home-page "https://github.com/waldronlab/lefser")
18987 (synopsis "LEfSE method for microbiome biomarker discovery")
18988 (description
18989 "Lefser is an implementation in R of the popular \"LDA Effect
18990Size\" (LEfSe) method for microbiome biomarker discovery. It uses the
18991Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis
18992to find biomarkers of groups and sub-groups.")
18993 (license license:artistic2.0)))
18994
18995(define-public r-lumi
18996 (package
18997 (name "r-lumi")
18998 (version "2.64.0")
18999 (source
19000 (origin
19001 (method url-fetch)
19002 (uri (bioconductor-uri "lumi" version))
19003 (sha256
19004 (base32
19005 "1443pjgqbgch7pk14n3sbn2xmqvhngg6fbm6xifjdcx2pd4gd2l2"))))
19006 (build-system r-build-system)
19007 (propagated-inputs
19008 (list r-affy
19009 r-annotate
19010 r-annotationdbi
19011 r-biobase
19012 r-dbi
19013 r-genomicfeatures
19014 r-genomicranges
19015 r-kernsmooth
19016 r-lattice
19017 r-mass
19018 r-methylumi
19019 r-mgcv
19020 r-nleqslv
19021 r-preprocesscore
19022 r-rsqlite))
19023 (home-page "https://bioconductor.org/packages/lumi")
19024 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
19025 (description
19026 "The lumi package provides an integrated solution for the Illumina
19027microarray data analysis. It includes functions of Illumina
19028BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
19029variance stabilization, normalization and gene annotation at the probe level.
19030It also includes the functions of processing Illumina methylation microarrays,
19031especially Illumina Infinium methylation microarrays.")
19032 (license license:lgpl2.0+)))
19033
19034(define-public r-linnorm
19035 (package
19036 (name "r-linnorm")
19037 (version "2.36.0")
19038 (source
19039 (origin
19040 (method url-fetch)
19041 (uri (bioconductor-uri "Linnorm" version))
19042 (sha256
19043 (base32
19044 "1lxd38lyimgsb6azddq5ywypq3xz2s7ysgp1cxjywqcyq4av3di4"))))
19045 (properties `((upstream-name . "Linnorm")))
19046 (build-system r-build-system)
19047 (propagated-inputs
19048 (list r-amap
19049 r-apcluster
19050 r-ellipse
19051 r-fastcluster
19052 r-fpc
19053 r-ggdendro
19054 r-ggplot2
19055 r-gmodels
19056 r-igraph
19057 r-limma
19058 r-mass
19059 r-mclust
19060 r-rcpp
19061 r-rcpparmadillo
19062 r-rtsne
19063 r-statmod
19064 r-vegan
19065 r-zoo))
19066 (native-inputs
19067 (list r-knitr r-matrixstats r-moments r-testthat))
19068 (home-page "http://www.jjwanglab.org/Linnorm/")
19069 (synopsis "Linear model and normality based transformation method")
19070 (description
19071 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
19072count data or any large scale count data. It transforms such datasets for
19073parametric tests. In addition to the transformtion function (@code{Linnorm}),
19074the following pipelines are implemented:
19075
19076@enumerate
19077@item Library size/batch effect normalization (@code{Linnorm.Norm})
19078@item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
19079 clustering or hierarchical clustering (@code{Linnorm.tSNE},
19080 @code{Linnorm.PCA}, @code{Linnorm.HClust})
19081@item Differential expression analysis or differential peak detection using
19082 limma (@code{Linnorm.limma})
19083@item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
19084@item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
19085@item Stable gene selection for scRNA-seq data; for users without or who do
19086 not want to rely on spike-in genes (@code{Linnorm.SGenes})
19087@item Data imputation (@code{Linnorm.DataImput}).
19088@end enumerate
19089
19090Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
19091@code{RnaXSim} function is included for simulating RNA-seq data for the
19092evaluation of DEG analysis methods.")
19093 (license license:expat)))
19094
19095(define-public r-ioniser
19096 (package
19097 (name "r-ioniser")
19098 (version "2.35.0")
19099 (source
19100 (origin
19101 (method url-fetch)
19102 (uri (bioconductor-uri "IONiseR" version))
19103 (sha256
19104 (base32
19105 "1ga6i8g9sbwpli9lyjcfmcnd329dqmkaf5mmcg6ks87zx32cqmax"))))
19106 (properties `((upstream-name . "IONiseR")))
19107 (build-system r-build-system)
19108 (arguments
19109 ;; This test uses dplyr's summarise_each(), which has been removed.
19110 (list #:skipped-tests '("test_plotting.R")))
19111 (propagated-inputs
19112 (list r-biocgenerics
19113 r-biocparallel
19114 r-biostrings
19115 r-bit64
19116 r-dplyr
19117 r-ggplot2
19118 r-magrittr
19119 r-rhdf5
19120 r-shortread
19121 r-stringr
19122 r-tibble
19123 r-tidyr
19124 r-xvector))
19125 (native-inputs
19126 (list r-knitr r-minionsummarydata r-testthat))
19127 (home-page "https://bioconductor.org/packages/IONiseR/")
19128 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
19129 (description
19130 "IONiseR provides tools for the quality assessment of Oxford Nanopore
19131MinION data. It extracts summary statistics from a set of fast5 files and can
19132be used either before or after base calling. In addition to standard
19133summaries of the read-types produced, it provides a number of plots for
19134visualising metrics relative to experiment run time or spatially over the
19135surface of a flowcell.")
19136 (license license:expat)))
19137
19138;; This is a CRAN package, but it depends on multtest from Bioconductor.
19139(define-public r-mutoss
19140 (package
19141 (name "r-mutoss")
19142 (version "0.1-14")
19143 (source
19144 (origin
19145 (method url-fetch)
19146 (uri (cran-uri "mutoss" version))
19147 (sha256
19148 (base32
19149 "1gswlg6n2pz1z8gyap6syggvyv3bfzr5kmxcwimhbixm36xzfkhz"))))
19150 (properties `((upstream-name . "mutoss")))
19151 (build-system r-build-system)
19152 (propagated-inputs
19153 (list r-multcomp r-multtest r-mvtnorm r-plotrix))
19154 (native-inputs (list r-testthat))
19155 (home-page "https://github.com/kornl/mutoss/")
19156 (synopsis "Unified multiple testing procedures")
19157 (description
19158 "This package is designed to ease the application and comparison of
19159multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
19160are standardized and usable by the accompanying mutossGUI package.")
19161 ;; Any version of the GPL.
19162 (license (list license:gpl2+ license:gpl3+))))
19163
19164;; This is a CRAN package, but it depends on mutoss, which depends on multtest
19165;; from Bioconductor, so we put it here.
19166(define-public r-metap
19167 (package
19168 (name "r-metap")
19169 (version "1.14")
19170 (source
19171 (origin
19172 (method url-fetch)
19173 (uri (cran-uri "metap" version))
19174 (sha256
19175 (base32
19176 "1w0jmh9l3jisa1byfbz11mxsaffmq27rsic90xjbk3fm3f8nanwn"))))
19177 (build-system r-build-system)
19178 (propagated-inputs
19179 (list r-lattice
19180 r-mathjaxr
19181 r-mutoss
19182 r-qqconf
19183 r-rdpack
19184 r-tfisher))
19185 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
19186 (synopsis "Meta-analysis of significance values")
19187 (description
19188 "The canonical way to perform meta-analysis involves using effect sizes.
19189When they are not available this package provides a number of methods for
19190meta-analysis of significance values including the methods of Edgington,
19191Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
19192published results; and a routine for graphical display.")
19193 (license license:gpl2)))
19194
19195(define-public r-tradeseq
19196 (package
19197 (name "r-tradeseq")
19198 (version "1.26.0")
19199 (source (origin
19200 (method url-fetch)
19201 (uri (bioconductor-uri "tradeSeq" version))
19202 (sha256
19203 (base32
19204 "151yrskr8v3h8pa5lq8wl4951nq7nk6ws60lkyh4lxnf03r1a2ip"))))
19205 (properties
19206 '((updater-extra-native-inputs
19207 . ("r-clusterexperiment" "r-delayedmatrixstats"))))
19208 (build-system r-build-system)
19209 (propagated-inputs
19210 (list r-biobase
19211 r-biocparallel
19212 r-edger
19213 r-ggplot2
19214 r-igraph
19215 r-magrittr
19216 r-mass
19217 r-matrix
19218 r-matrixstats
19219 r-mgcv
19220 r-pbapply
19221 r-princurve
19222 r-rcolorbrewer
19223 r-s4vectors
19224 r-singlecellexperiment
19225 r-slingshot
19226 r-summarizedexperiment
19227 r-tibble
19228 r-trajectoryutils
19229 r-viridis))
19230 (native-inputs
19231 (list r-clusterexperiment r-delayedmatrixstats r-knitr r-testthat))
19232 (home-page "https://statomics.github.io/tradeSeq/index.html")
19233 (synopsis "Trajectory-based differential expression analysis")
19234 (description
19235 "This package provides a flexible method for fitting regression models that
19236can be used to find genes that are differentially expressed along one or
19237multiple lineages in a trajectory. Based on the fitted models, it uses a
19238variety of tests suited to answer different questions of interest, e.g. the
19239discovery of genes for which expression is associated with pseudotime, or which
19240are differentially expressed (in a specific region) along the trajectory. It
19241fits a negative binomial generalized additive model (GAM) for each gene, and
19242performs inference on the parameters of the GAM.")
19243 (license license:expat)))
19244
19245(define-public r-triform
19246 (package
19247 (name "r-triform")
19248 (version "1.29.0")
19249 (source
19250 (origin
19251 (method url-fetch)
19252 (uri (bioconductor-uri "triform" version))
19253 (sha256
19254 (base32
19255 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
19256 (build-system r-build-system)
19257 ;; Vignettes need deprecated package RangedData.
19258 (arguments (list #:test-types '(list "tests")))
19259 (propagated-inputs
19260 (list r-biocgenerics r-iranges r-yaml))
19261 (native-inputs (list r-runit))
19262 (home-page "https://bioconductor.org/packages/triform/")
19263 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
19264 (description
19265 "The Triform algorithm uses model-free statistics to identify peak-like
19266distributions of TF ChIP sequencing reads, taking advantage of an improved
19267peak definition in combination with known profile characteristics.")
19268 (license license:gpl2)))
19269
19270(define-public r-varianttools
19271 (package
19272 (name "r-varianttools")
19273 (version "1.54.0")
19274 (source
19275 (origin
19276 (method url-fetch)
19277 (uri (bioconductor-uri "VariantTools" version))
19278 (sha256
19279 (base32
19280 "1js9snyd83w445431bsjkq52kl1162ifq4c08k7gl7mx9v97klhf"))))
19281 (properties
19282 '((upstream-name . "VariantTools")
19283 ;; This package is not needed for tests, which is great because we
19284 ;; haven't packaged it.
19285 (updater-ignored-native-inputs . ("r-gmapr"))))
19286 (build-system r-build-system)
19287 (propagated-inputs
19288 (list r-biobase
19289 r-biocgenerics
19290 r-biocparallel
19291 r-biostrings
19292 r-bsgenome
19293 r-genomeinfodb
19294 r-genomicfeatures
19295 r-genomicranges
19296 r-iranges
19297 r-matrix
19298 r-rsamtools
19299 r-rtracklayer
19300 r-s4vectors
19301 r-variantannotation))
19302 (native-inputs (list r-lungcancerlines))
19303 (home-page "https://bioconductor.org/packages/VariantTools/")
19304 (synopsis "Tools for exploratory analysis of variant calls")
19305 (description
19306 "Explore, diagnose, and compare variant calls using filters. The
19307VariantTools package supports a workflow for loading data, calling single
19308sample variants and tumor-specific somatic mutations or other sample-specific
19309variant types (e.g., RNA editing). Most of the functions operate on
19310alignments (BAM files) or datasets of called variants. The user is expected
19311to have already aligned the reads with a separate tool, e.g., GSNAP via
19312gmapR.")
19313 (license license:artistic2.0)))
19314
19315(define-public r-heatplus
19316 (package
19317 (name "r-heatplus")
19318 (version "3.20.0")
19319 (source
19320 (origin
19321 (method url-fetch)
19322 (uri (bioconductor-uri "Heatplus" version))
19323 (sha256
19324 (base32
19325 "0rzq3vff8fsh0y3vvzn3ayfvqxp706fmwvympq4r33l7gy6jn6n4"))))
19326 (properties `((upstream-name . "Heatplus")))
19327 (build-system r-build-system)
19328 (propagated-inputs
19329 (list r-rcolorbrewer))
19330 (home-page "https://github.com/alexploner/Heatplus")
19331 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
19332 (description
19333 "This package provides tools to display a rectangular heatmap (intensity
19334plot) of a data matrix. By default, both samples (columns) and features (row)
19335of the matrix are sorted according to a hierarchical clustering, and the
19336corresponding dendrogram is plotted. Optionally, panels with additional
19337information about samples and features can be added to the plot.")
19338 (license license:gpl2+)))
19339
19340(define-public r-helloranges
19341 (package
19342 (name "r-helloranges")
19343 (version "1.38.0")
19344 (source
19345 (origin
19346 (method url-fetch)
19347 (uri (bioconductor-uri "HelloRanges" version))
19348 (sha256
19349 (base32 "1mh1cmwxfccv2j7mk7cgb4mlr1jywiral0k691fp66df1wy7z35f"))))
19350 (properties
19351 '((upstream-name . "HelloRanges")
19352 (updater-extra-native-inputs . ("r-biocstyle" "r-runit"))))
19353 (build-system r-build-system)
19354 ;; Vignettes need Internet access.
19355 (arguments (list #:test-types '(list "tests")))
19356 (propagated-inputs (list r-biocgenerics
19357 r-biocio
19358 r-biostrings
19359 r-bsgenome
19360 r-docopt
19361 r-genomicalignments
19362 r-genomicfeatures
19363 r-genomicranges
19364 r-iranges
19365 r-rsamtools
19366 r-rtracklayer
19367 r-s4vectors
19368 r-seqinfo
19369 r-summarizedexperiment
19370 r-variantannotation))
19371 (native-inputs
19372 (list r-biocstyle r-hellorangesdata r-runit
19373 r-txdb-hsapiens-ucsc-hg19-knowngene))
19374 (home-page "https://bioconductor.org/packages/HelloRanges")
19375 (synopsis "Introduce *Ranges to bedtools users")
19376 (description
19377 "This package translates bedtools command-line invocations to R code
19378calling functions from the Bioconductor @code{*Ranges} infrastructure. This
19379is intended to educate novice Bioconductor users and to compare the syntax and
19380semantics of the two frameworks.")
19381 (license license:gpl2+)))
19382
19383(define-public r-gosemsim
19384 (package
19385 (name "r-gosemsim")
19386 (version "2.38.0")
19387 (source
19388 (origin
19389 (method url-fetch)
19390 (uri (bioconductor-uri "GOSemSim" version))
19391 (sha256
19392 (base32
19393 "1bfrxb6zm9lms264wb4xzxdb50py97zdr6lh3mharzxnngbri4d7"))))
19394 (properties
19395 '((upstream-name . "GOSemSim")
19396 (updater-extra-native-inputs . ("r-org-hs-eg-db"))))
19397 (build-system r-build-system)
19398 (propagated-inputs
19399 (list r-annotationdbi
19400 r-dbi
19401 r-digest
19402 r-go-db
19403 r-rcpp
19404 r-rlang
19405 r-yulab-utils))
19406 (native-inputs
19407 (list r-knitr r-org-hs-eg-db r-testthat))
19408 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
19409 (synopsis "GO-terms semantic similarity measures")
19410 (description
19411 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
19412quantitative ways to compute similarities between genes and gene groups, and
19413have became important basis for many bioinformatics analysis approaches.
19414GOSemSim is an R package for semantic similarity computation among GO terms,
19415sets of GO terms, gene products and gene clusters.")
19416 (license license:artistic2.0)))
19417
19418(define-public r-anota
19419 (package
19420 (name "r-anota")
19421 (version "1.60.0")
19422 (source
19423 (origin
19424 (method url-fetch)
19425 (uri (bioconductor-uri "anota" version))
19426 (sha256
19427 (base32
19428 "0kq566k3wky66pyz6ypbw91x04djcw1v27zgxfiy3xbpahccij9m"))))
19429 (build-system r-build-system)
19430 (propagated-inputs
19431 (list r-multtest r-qvalue))
19432 (home-page "https://bioconductor.org/packages/anota/")
19433 (synopsis "Analysis of translational activity")
19434 (description
19435 "Genome wide studies of translational control is emerging as a tool to
19436study various biological conditions. The output from such analysis is both
19437the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
19438involved in translation (the actively translating mRNA level) for each mRNA.
19439The standard analysis of such data strives towards identifying differential
19440translational between two or more sample classes - i.e., differences in
19441actively translated mRNA levels that are independent of underlying differences
19442in cytosolic mRNA levels. This package allows for such analysis using partial
19443variances and the random variance model. As 10s of thousands of mRNAs are
19444analyzed in parallel the library performs a number of tests to assure that
19445the data set is suitable for such analysis.")
19446 (license license:gpl3)))
19447
19448(define-public r-anota2seq
19449 (package
19450 (name "r-anota2seq")
19451 (version "1.34.0")
19452 (source
19453 (origin
19454 (method url-fetch)
19455 (uri (bioconductor-uri "anota2seq" version))
19456 (sha256
19457 (base32 "1y3qnx98jml8956vy94kyvc7kgn27226jxl4716wp7rgs9bkni68"))))
19458 (properties `((upstream-name . "anota2seq")))
19459 (build-system r-build-system)
19460 (propagated-inputs
19461 (list r-deseq2
19462 r-edger
19463 r-limma
19464 r-multtest
19465 r-qvalue
19466 r-rcolorbrewer
19467 r-summarizedexperiment))
19468 (native-inputs (list r-biocstyle r-knitr))
19469 (home-page "https://bioconductor.org/packages/anota2seq")
19470 (synopsis "Transcriptome-wide analysis of translational efficiency")
19471 (description
19472 "The anota2seq package provides analysis of translational efficiency and
19473differential expression analysis for polysome-profiling and ribosome-profiling
19474studies (two or more sample classes) quantified by RNA sequencing or
19475DNA-microarray. Polysome-profiling and ribosome-profiling typically generate
19476data for two RNA sources, translated mRNA and total mRNA. Analysis of
19477differential expression is used to estimate changes within each RNA source.
19478Analysis of translational efficiency aims to identify changes in translation
19479efficiency leading to altered protein levels that are independent of total
19480mRNA levels or buffering, a mechanism regulating translational efficiency so
19481that protein levels remain constant despite fluctuating total mRNA levels.")
19482 (license license:gpl3)))
19483
19484(define-public r-fcscan
19485 (package
19486 (name "r-fcscan")
19487 (version "1.26.0")
19488 (source
19489 (origin
19490 (method url-fetch)
19491 (uri (bioconductor-uri "fcScan" version))
19492 (sha256
19493 (base32 "1r6gl2qqv76czf6pcp8kql5qarb4mbbpchs8adb1bhw8arxryq0v"))))
19494 (properties `((upstream-name . "fcScan")))
19495 (build-system r-build-system)
19496 (propagated-inputs
19497 (list r-doparallel
19498 r-foreach
19499 r-genomicranges
19500 r-iranges
19501 r-plyr
19502 r-rtracklayer
19503 r-summarizedexperiment
19504 r-variantannotation))
19505 (native-inputs (list r-biocgenerics r-knitr r-runit))
19506 (home-page "https://bioconductor.org/packages/fcScan")
19507 (synopsis "Detect clusters of coordinates with user defined options")
19508 (description
19509 "This package is used to detect combination of genomic coordinates
19510falling within a user defined window size along with user defined overlap
19511between identified neighboring clusters. It can be used for genomic data
19512where the clusters are built on a specific chromosome or specific strand.
19513Clustering can be performed with a \"greedy\" option allowing thus the
19514presence of additional sites within the allowed window size.")
19515 (license license:artistic2.0)))
19516
19517(define-public r-fgsea
19518 (package
19519 (name "r-fgsea")
19520 (version "1.38.0")
19521 (source
19522 (origin
19523 (method url-fetch)
19524 (uri (bioconductor-uri "fgsea" version))
19525 (sha256
19526 (base32
19527 "13vrf7w5rbr3qcjkap7wmrv08grpgw6s8lcyjyjzij61q7jysgi2"))))
19528 (build-system r-build-system)
19529 (propagated-inputs
19530 (list r-bh
19531 r-biocparallel
19532 r-cowplot
19533 r-data-table
19534 r-fastmatch
19535 r-ggplot2
19536 r-matrix
19537 r-rcpp
19538 r-scales))
19539 (native-inputs
19540 (list r-knitr r-testthat))
19541 (home-page "https://github.com/ctlab/fgsea/")
19542 (synopsis "Fast gene set enrichment analysis")
19543 (description
19544 "The package implements an algorithm for fast gene set enrichment
19545analysis. Using the fast algorithm makes more permutations and gets
19546more fine grained p-values, which allows using accurate standard approaches
19547to multiple hypothesis correction.")
19548 (license license:expat)))
19549
19550(define-public r-dose
19551 (package
19552 (name "r-dose")
19553 (version "4.6.0")
19554 (source
19555 (origin
19556 (method url-fetch)
19557 (uri (bioconductor-uri "DOSE" version))
19558 (sha256
19559 (base32
19560 "0zkl7lgwhzwx01xcnvsbhv4fxxsr4cvgc2gc6j28dnxqa3za7ng0"))))
19561 (properties `((upstream-name . "DOSE")))
19562 (build-system r-build-system)
19563 ;; Tests attempt to download data from the Internet via r-gosemsim.
19564 (arguments (list #:tests? #false))
19565 (propagated-inputs
19566 (list r-annotationdbi
19567 r-enrichit
19568 r-ggplot2
19569 r-gosemsim
19570 r-reshape2
19571 r-yulab-utils))
19572 (native-inputs
19573 (list r-knitr r-testthat))
19574 (home-page "https://guangchuangyu.github.io/software/DOSE/")
19575 (synopsis "Disease ontology semantic and enrichment analysis")
19576 (description
19577 "This package implements five methods proposed by Resnik, Schlicker,
19578Jiang, Lin and Wang, respectively, for measuring semantic similarities among
19579@dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
19580including hypergeometric model and gene set enrichment analysis are also
19581implemented for discovering disease associations of high-throughput biological
19582data.")
19583 (license license:artistic2.0)))
19584
19585(define-public r-enrichedheatmap
19586 (package
19587 (name "r-enrichedheatmap")
19588 (version "1.42.0")
19589 (source (origin
19590 (method url-fetch)
19591 (uri (bioconductor-uri "EnrichedHeatmap" version))
19592 (sha256
19593 (base32
19594 "1a0736xq0qqfh5iyw5y2fnbiqdc7fxipjpas4yzri313mpjz42qh"))))
19595 (properties `((upstream-name . "EnrichedHeatmap")))
19596 (build-system r-build-system)
19597 (propagated-inputs (list r-circlize
19598 r-complexheatmap
19599 r-genomicranges
19600 r-getoptlong
19601 r-iranges
19602 r-locfit
19603 r-matrixstats
19604 r-rcpp))
19605 (native-inputs (list r-knitr r-testthat))
19606 (home-page "https://github.com/jokergoo/EnrichedHeatmap")
19607 (synopsis "Enriched heatmaps")
19608 (description
19609 "Enriched heatmap is a special type of heatmap which visualizes the
19610enrichment of genomic signals on specific target regions. This type of
19611heatmap is just a normal heatmap but with some special settings, with the
19612functionality of @code{ComplexHeatmap}, it would be much easier to customize
19613the heatmap as well as concatenating to a list of heatmaps to show
19614correspondence between different data sources.")
19615 (license license:expat)))
19616
19617(define-public r-enrichplot
19618 (package
19619 (name "r-enrichplot")
19620 (version "1.32.0")
19621 (source
19622 (origin
19623 (method url-fetch)
19624 (uri (bioconductor-uri "enrichplot" version))
19625 (sha256
19626 (base32
19627 "0jlkqhh29w57ssay97n3n8dzfl8gvscjvfjbq3hlzrffyzc1wyxq"))))
19628 (build-system r-build-system)
19629 (propagated-inputs
19630 (list r-aplot
19631 r-dose
19632 r-dplyr
19633 r-enrichit
19634 r-ggfun
19635 r-ggnewscale
19636 r-ggplot2
19637 r-ggrepel
19638 r-ggtangle
19639 r-ggtree
19640 r-gosemsim
19641 r-igraph
19642 r-purrr
19643 r-rcolorbrewer
19644 r-reshape2
19645 r-rlang
19646 r-scatterpie
19647 r-tidydr
19648 r-yulab-utils))
19649 (native-inputs
19650 (list r-quarto))
19651 (home-page "https://github.com/GuangchuangYu/enrichplot")
19652 (synopsis "Visualization of functional enrichment result")
19653 (description
19654 "The enrichplot package implements several visualization methods for
19655interpreting functional enrichment results obtained from ORA or GSEA analyses.
19656All the visualization methods are developed based on ggplot2 graphics.")
19657 (license license:artistic2.0)))
19658
19659;; This is a CRAN package, but it depends on Bioconductor packages, so we
19660;; added it here.
19661(define-public r-classdiscovery
19662 (package
19663 (name "r-classdiscovery")
19664 (version "3.4.9")
19665 (source (origin
19666 (method url-fetch)
19667 (uri (cran-uri "ClassDiscovery" version))
19668 (sha256
19669 (base32
19670 "05bajszkrflvbi2390r71r5xna4wb4zxw1lkgpfm81h4x8fsvldw"))))
19671 (properties `((upstream-name . "ClassDiscovery")))
19672 (build-system r-build-system)
19673 (propagated-inputs
19674 (list r-biobase r-cluster r-mclust r-oompabase r-oompadata))
19675 (native-inputs
19676 (list r-xtable)) ;for vignettes
19677 (home-page "https://oompa.r-forge.r-project.org/")
19678 (synopsis
19679 "Classes and methods for \"Class Discovery\" with Microarrays or Proteomics")
19680 (description
19681 "This package defines classes for \"class discovery\" in the OOMPA project.
19682Class discovery primarily consists of unsupervised clustering methods with
19683attempts to assess their statistical significance.")
19684 (license license:asl2.0)))
19685
19686(define-public r-clusterprofiler
19687 (package
19688 (name "r-clusterprofiler")
19689 (version "4.20.0")
19690 (source
19691 (origin
19692 (method url-fetch)
19693 (uri (bioconductor-uri "clusterProfiler" version))
19694 (sha256
19695 (base32
19696 "0y7f3a6ww0ba7zanzpmhd4vxvdg1yklz33q3xf8syi8im5p4jl04"))))
19697 (properties
19698 '((upstream-name . "clusterProfiler")
19699 (updater-extra-native-inputs . ("r-org-hs-eg-db"))))
19700 (build-system r-build-system)
19701 (propagated-inputs
19702 (list r-aisdk
19703 r-annotationdbi
19704 r-dplyr
19705 r-enrichit
19706 r-enrichplot
19707 r-ggplot2
19708 r-go-db
19709 r-gosemsim
19710 r-gson
19711 r-httr
19712 r-igraph
19713 r-jsonlite
19714 r-magrittr
19715 r-plyr
19716 r-qvalue
19717 r-rlang
19718 r-tidyr
19719 r-yulab-utils))
19720 (native-inputs
19721 (list r-org-hs-eg-db r-quarto r-testthat))
19722 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
19723 (synopsis "Analysis and visualization of functional profiles for gene clusters")
19724 (description
19725 "This package implements methods to analyze and visualize functional
19726profiles (GO and KEGG) of gene and gene clusters.")
19727 (license license:artistic2.0)))
19728
19729(define-public r-clusterexperiment
19730 (package
19731 (name "r-clusterexperiment")
19732 (version "2.32.0")
19733 (source (origin
19734 (method url-fetch)
19735 (uri (bioconductor-uri "clusterExperiment" version))
19736 (sha256
19737 (base32
19738 "0k0pmgz7sy5vvbqyshgbfgzvhw99wnmksx03vb68hcjd9x53nhby"))))
19739 (build-system r-build-system)
19740 (native-inputs
19741 (list r-knitr r-testthat))
19742 (propagated-inputs
19743 (list r-ape
19744 r-biocgenerics
19745 r-biocsingular
19746 r-cluster
19747 r-delayedarray
19748 r-edger
19749 r-hdf5array
19750 r-kernlab
19751 r-limma
19752 r-locfdr
19753 r-matrix
19754 r-matrixstats
19755 r-mbkmeans
19756 r-nmf
19757 r-phylobase
19758 r-pracma
19759 r-rcolorbrewer
19760 r-rcpp
19761 r-s4vectors
19762 r-scales
19763 r-singlecellexperiment
19764 r-stringr
19765 r-summarizedexperiment
19766 r-zinbwave))
19767 (home-page "https://bioconductor.org/packages/clusterExperiment/")
19768 (synopsis "Compare clusterings for single-cell sequencing")
19769 (description "This package provides functionality for running and comparing
19770many different clusterings of single-cell sequencing data or other large mRNA
19771expression data sets.")
19772 (license license:artistic2.0)))
19773
19774(define-public r-mlinterfaces
19775 (package
19776 (name "r-mlinterfaces")
19777 (version "1.92.0")
19778 (source
19779 (origin
19780 (method url-fetch)
19781 (uri (bioconductor-uri "MLInterfaces" version))
19782 (sha256
19783 (base32
19784 "0vzixaicm3rmirgpbknzxg2fvl93svx0yyy4159hq9l5xk8m1k1j"))))
19785 (properties
19786 '((upstream-name . "MLInterfaces")
19787 (updater-extra-native-inputs . ("r-e1071"))))
19788 (build-system r-build-system)
19789 (propagated-inputs
19790 (list r-annotate
19791 r-biobase
19792 r-biocgenerics
19793 r-cluster
19794 r-fpc
19795 r-gbm
19796 r-gdata
19797 r-genefilter
19798 r-ggvis
19799 r-hwriter
19800 r-magrittr
19801 r-mass
19802 r-mlbench
19803 r-pls
19804 r-rcolorbrewer
19805 r-rcpp
19806 r-rpart
19807 r-sfsmisc
19808 r-shiny
19809 r-summarizedexperiment
19810 r-threejs))
19811 (native-inputs (list r-e1071 r-golubesets r-knitr r-snow r-testthat))
19812 (home-page "https://bioconductor.org/packages/MLInterfaces/")
19813 (synopsis "Interfaces to R machine learning procedures")
19814 (description
19815 "This package provides uniform interfaces to machine learning code for
19816data in R and Bioconductor containers.")
19817 ;; Any version of the LGPL.
19818 (license license:lgpl2.1+)))
19819
19820(define-public r-annaffy
19821 (package
19822 (name "r-annaffy")
19823 (version "1.84.0")
19824 (source
19825 (origin
19826 (method url-fetch)
19827 (uri (bioconductor-uri "annaffy" version))
19828 (sha256
19829 (base32
19830 "07phh7wn77lvvlr4pm1g0rbj6lwlc15p4ijkyfirp96hfmrq59yq"))))
19831 (build-system r-build-system)
19832 (arguments
19833 `(#:phases
19834 (modify-phases %standard-phases
19835 (add-after 'unpack 'remove-reference-to-non-free-data
19836 (lambda _
19837 (substitute* "DESCRIPTION"
19838 ((", KEGG.db") "")))))))
19839 (propagated-inputs
19840 (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
19841 (home-page "https://bioconductor.org/packages/annaffy/")
19842 (synopsis "Annotation tools for Affymetrix biological metadata")
19843 (description
19844 "This package provides functions for handling data from Bioconductor
19845Affymetrix annotation data packages. It produces compact HTML and text
19846reports including experimental data and URL links to many online databases.
19847It allows searching of biological metadata using various criteria.")
19848 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
19849 ;; the LGPL 2.1 is included.
19850 (license license:lgpl2.1+)))
19851
19852(define-public r-a4core
19853 (package
19854 (name "r-a4core")
19855 (version "1.60.0")
19856 (source
19857 (origin
19858 (method url-fetch)
19859 (uri (bioconductor-uri "a4Core" version))
19860 (sha256
19861 (base32
19862 "146ybha1729mw4l9ywwaj5083sp98mnxymlamnjbc1c2j2sqsc8f"))))
19863 (properties `((upstream-name . "a4Core")))
19864 (build-system r-build-system)
19865 (propagated-inputs
19866 (list r-biobase r-glmnet))
19867 (native-inputs
19868 (list r-knitr))
19869 (home-page "https://bioconductor.org/packages/a4Core")
19870 (synopsis "Automated Affymetrix array analysis core package")
19871 (description
19872 "This is the core package for the automated analysis of Affymetrix
19873arrays.")
19874 (license license:gpl3)))
19875
19876(define-public r-a4classif
19877 (package
19878 (name "r-a4classif")
19879 (version "1.60.0")
19880 (source
19881 (origin
19882 (method url-fetch)
19883 (uri (bioconductor-uri "a4Classif" version))
19884 (sha256
19885 (base32
19886 "02zmzx08l9kv9fl8318vbhwnqw0v710sqwv8rbddillfqzx2x0bi"))))
19887 (properties `((upstream-name . "a4Classif")))
19888 (build-system r-build-system)
19889 (propagated-inputs
19890 (list r-a4core
19891 r-a4preproc
19892 r-biobase
19893 r-glmnet
19894 r-pamr
19895 r-rocr
19896 r-varselrf))
19897 (native-inputs
19898 (list r-knitr))
19899 (home-page "https://bioconductor.org/packages/a4Classif/")
19900 (synopsis "Automated Affymetrix array analysis classification package")
19901 (description
19902 "This is the classification package for the automated analysis of
19903Affymetrix arrays.")
19904 (license license:gpl3)))
19905
19906(define-public r-a4preproc
19907 (package
19908 (name "r-a4preproc")
19909 (version "1.60.0")
19910 (source
19911 (origin
19912 (method url-fetch)
19913 (uri (bioconductor-uri "a4Preproc" version))
19914 (sha256
19915 (base32
19916 "0408cd44hmcb19npn7nbr7rxn5d7bs28wlhfmi60gasiifxr05qp"))))
19917 (properties `((upstream-name . "a4Preproc")))
19918 (build-system r-build-system)
19919 (propagated-inputs
19920 (list r-biobase r-biocgenerics))
19921 (native-inputs
19922 (list r-knitr))
19923 (home-page "https://bioconductor.org/packages/a4Preproc/")
19924 (synopsis "Automated Affymetrix array analysis preprocessing package")
19925 (description
19926 "This is a package for the automated analysis of Affymetrix arrays. It
19927is used for preprocessing the arrays.")
19928 (license license:gpl3)))
19929
19930(define-public r-a4reporting
19931 (package
19932 (name "r-a4reporting")
19933 (version "1.60.0")
19934 (source
19935 (origin
19936 (method url-fetch)
19937 (uri (bioconductor-uri "a4Reporting" version))
19938 (sha256
19939 (base32
19940 "18ya7dw0wnwzrs19gv8zg2flays164iq3d3g0c1qdy7iqs1hqwlp"))))
19941 (properties `((upstream-name . "a4Reporting")))
19942 (build-system r-build-system)
19943 (propagated-inputs
19944 (list r-xtable))
19945 (native-inputs
19946 (list r-knitr))
19947 (home-page "https://bioconductor.org/packages/a4Reporting/")
19948 (synopsis "Automated Affymetrix array analysis reporting package")
19949 (description
19950 "This is a package for the automated analysis of Affymetrix arrays. It
19951provides reporting features.")
19952 (license license:gpl3)))
19953
19954(define-public r-a4base
19955 (package
19956 (name "r-a4base")
19957 (version "1.60.0")
19958 (source
19959 (origin
19960 (method url-fetch)
19961 (uri (bioconductor-uri "a4Base" version))
19962 (sha256
19963 (base32
19964 "0ra6ipn4lkhq530aiwyw44hlqwb77wi8jd36ic29yy45fiiz6l1r"))))
19965 (properties `((upstream-name . "a4Base")))
19966 (build-system r-build-system)
19967 (propagated-inputs
19968 (list r-a4core
19969 r-a4preproc
19970 r-annaffy
19971 r-biobase
19972 r-genefilter
19973 r-glmnet
19974 r-gplots
19975 r-limma
19976 r-mpm
19977 r-multtest))
19978 (home-page "https://bioconductor.org/packages/a4Base/")
19979 (synopsis "Automated Affymetrix array analysis base package")
19980 (description
19981 "This package provides basic features for the automated analysis of
19982Affymetrix arrays.")
19983 (license license:gpl3)))
19984
19985(define-public r-a4
19986 (package
19987 (name "r-a4")
19988 (version "1.60.0")
19989 (source
19990 (origin
19991 (method url-fetch)
19992 (uri (bioconductor-uri "a4" version))
19993 (sha256
19994 (base32
19995 "0wkldy3z2k3hbp6qnls9v5zqyi8kk5b9av4b5v8yzb29syhpiyb0"))))
19996 (build-system r-build-system)
19997 (propagated-inputs
19998 (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
19999 (home-page "https://bioconductor.org/packages/a4/")
20000 (synopsis "Automated Affymetrix array analysis umbrella package")
20001 (description
20002 "This package provides a software suite for the automated analysis of
20003Affymetrix arrays.")
20004 (license license:gpl3)))
20005
20006(define-public r-abseqr
20007 (package
20008 (name "r-abseqr")
20009 (version "1.30.0")
20010 (source
20011 (origin
20012 (method url-fetch)
20013 (uri (bioconductor-uri "abseqR" version))
20014 (sha256
20015 (base32
20016 "181a7b1gr8qh1lmski8cvg7fslm3lm58j91pgigdzcd25xs7bhp0"))))
20017 (properties `((upstream-name . "abseqR")))
20018 (build-system r-build-system)
20019 (inputs
20020 (list pandoc))
20021 (propagated-inputs
20022 (list r-biocparallel
20023 r-biocstyle
20024 r-circlize
20025 r-flexdashboard
20026 r-ggcorrplot
20027 r-ggdendro
20028 r-ggplot2
20029 r-gridextra
20030 r-knitr
20031 r-plotly
20032 r-plyr
20033 r-png
20034 r-rcolorbrewer
20035 r-reshape2
20036 r-rmarkdown
20037 r-stringr
20038 r-vegan
20039 r-venndiagram))
20040 (native-inputs
20041 (list r-knitr r-testthat))
20042 (home-page "https://github.com/malhamdoosh/abseqR")
20043 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
20044 (description
20045 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
20046sequencing datasets generated from antibody libraries and abseqR is one of its
20047packages. AbseqR empowers the users of abseqPy with plotting and reporting
20048capabilities and allows them to generate interactive HTML reports for the
20049convenience of viewing and sharing with other researchers. Additionally,
20050abseqR extends abseqPy to compare multiple repertoire analyses and perform
20051further downstream analysis on its output.")
20052 (license license:gpl3)))
20053
20054(define-public r-bacon
20055 (package
20056 (name "r-bacon")
20057 (version "1.40.0")
20058 (source
20059 (origin
20060 (method url-fetch)
20061 (uri (bioconductor-uri "bacon" version))
20062 (sha256
20063 (base32
20064 "0alqljzd6nlj0k6a5lmvn4zx70l4kjbjxsa7krvnz1pawjggsqnc"))))
20065 (build-system r-build-system)
20066 (propagated-inputs
20067 (list r-biocparallel r-ellipse r-ggplot2))
20068 (native-inputs
20069 (list r-knitr r-testthat))
20070 (home-page "https://bioconductor.org/packages/bacon/")
20071 (synopsis "Controlling bias and inflation in association studies")
20072 (description
20073 "Bacon can be used to remove inflation and bias often observed in
20074epigenome- and transcriptome-wide association studies. To this end bacon
20075constructs an empirical null distribution using a Gibbs Sampling algorithm by
20076fitting a three-component normal mixture on z-scores.")
20077 (license license:gpl2+)))
20078
20079(define-public r-rgadem
20080 (package
20081 (name "r-rgadem")
20082 (version "2.55.0")
20083 (source
20084 (origin
20085 (method url-fetch)
20086 (uri (bioconductor-uri "rGADEM" version))
20087 (sha256
20088 (base32
20089 "1fjqvkayam7xpvvbdlz6nafgsrw46vgmbkl96mfvm4szclrxzs8g"))))
20090 (properties `((upstream-name . "rGADEM")))
20091 (build-system r-build-system)
20092 (propagated-inputs
20093 (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
20094 (home-page "https://bioconductor.org/packages/rGADEM/")
20095 (synopsis "De novo sequence motif discovery")
20096 (description
20097 "rGADEM is an efficient de novo motif discovery tool for large-scale
20098genomic sequence data.")
20099 (license license:artistic2.0)))
20100
20101(define-public r-motiv
20102 (package
20103 (name "r-motiv")
20104 (version "1.43.0")
20105 (source
20106 (origin
20107 (method url-fetch)
20108 (uri (bioconductor-uri "MotIV" version))
20109 (sha256
20110 (base32
20111 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
20112 (properties `((upstream-name . "MotIV")))
20113 (build-system r-build-system)
20114 (inputs
20115 (list gsl))
20116 (propagated-inputs
20117 (list r-biocgenerics
20118 r-biostrings
20119 r-genomicranges
20120 r-iranges
20121 r-lattice
20122 r-rgadem
20123 r-s4vectors))
20124 (home-page "https://bioconductor.org/packages/MotIV/")
20125 (synopsis "Motif identification and validation")
20126 (description
20127 "This package is used for the identification and validation of sequence
20128motifs. It makes use of STAMP for comparing a set of motifs to a given
20129database (e.g. JASPAR). It can also be used to visualize motifs, motif
20130distributions, modules and filter motifs.")
20131 (license license:gpl2)))
20132
20133(define-public r-motifdb
20134 (package
20135 (name "r-motifdb")
20136 (version "1.54.0")
20137 (source (origin
20138 (method url-fetch)
20139 (uri (bioconductor-uri "MotifDb" version))
20140 (sha256
20141 (base32 "0kkvnjssrr0l9qw93xg2s5n8rsphl4hfx8m5w6ykqdmqmmnr1hsw"))))
20142 (properties
20143 '((upstream-name . "MotifDb")
20144 (updater-ignored-native-inputs . ("r-fos"))))
20145 (build-system r-build-system)
20146 (propagated-inputs
20147 (list r-biocgenerics
20148 r-biostrings
20149 r-genomicranges
20150 r-iranges
20151 r-rtracklayer
20152 r-s4vectors
20153 r-splitstackshape))
20154 (native-inputs
20155 (list r-formatr
20156 r-knitr
20157 r-markdown
20158 r-motiv
20159 r-rmarkdown
20160 r-runit
20161 r-seqlogo))
20162 (home-page "https://www.bioconductor.org/packages/MotifDb/")
20163 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
20164 (description "This package provides more than 2000 annotated position
20165frequency matrices from nine public sources, for multiple organisms.")
20166 (license license:artistic2.0)))
20167
20168(define-public r-motifbreakr
20169 (package
20170 (name "r-motifbreakr")
20171 (version "2.24.0")
20172 (source (origin
20173 (method url-fetch)
20174 (uri (bioconductor-uri "motifbreakR" version))
20175 (sha256
20176 (base32 "0ksxil00v1s282zvsj0gjzybq46kcfay849y2syh7la7pgdw3x63"))))
20177 (properties `((upstream-name . "motifbreakR")))
20178 (build-system r-build-system)
20179 (propagated-inputs
20180 (list r-biocfilecache
20181 r-biocgenerics
20182 r-biocparallel
20183 r-biomart
20184 r-biostrings
20185 r-bsgenome
20186 r-bsicons
20187 r-bslib
20188 r-dt
20189 r-genomeinfodb
20190 r-genomicranges
20191 r-gviz
20192 r-iranges
20193 r-matrixstats
20194 r-motifdb
20195 r-motifstack
20196 r-pwalign
20197 r-rtracklayer
20198 r-s4vectors
20199 r-shiny
20200 r-stringr
20201 r-summarizedexperiment
20202 r-tfmpvalue
20203 r-variantannotation
20204 r-vroom))
20205 (native-inputs
20206 (list r-knitr))
20207 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
20208 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
20209 (description "This package allows biologists to judge in the first place
20210whether the sequence surrounding the polymorphism is a good match, and in
20211the second place how much information is gained or lost in one allele of
20212the polymorphism relative to another. This package gives a choice of
20213algorithms for interrogation of genomes with motifs from public sources:
20214@enumerate
20215@item a weighted-sum probability matrix;
20216@item log-probabilities;
20217@item weighted by relative entropy.
20218@end enumerate
20219
20220This package can predict effects for novel or previously described variants in
20221public databases, making it suitable for tasks beyond the scope of its original
20222design. Lastly, it can be used to interrogate any genome curated within
20223Bioconductor.")
20224 (license license:gpl2+)))
20225
20226(define-public r-motifstack
20227 (package
20228 (name "r-motifstack")
20229 (version "1.56.0")
20230 (source
20231 (origin
20232 (method url-fetch)
20233 (uri (bioconductor-uri "motifStack" version))
20234 (sha256
20235 (base32
20236 "16s2s64j5rpddcvghjf7zxpb6fhi20q0s2qysarcak440w7zjj83"))
20237 (snippet
20238 '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js"))))
20239 (properties `((upstream-name . "motifStack")))
20240 (build-system r-build-system)
20241 (arguments
20242 (list
20243 #:phases
20244 '(modify-phases %standard-phases
20245 (add-after 'unpack 'process-javascript
20246 (lambda* (#:key inputs #:allow-other-keys)
20247 (with-directory-excursion "inst/htmlwidgets/lib/d3"
20248 (let ((source (assoc-ref inputs "d3.v4.js"))
20249 (target "d3.v4.min.js"))
20250 (invoke "esbuild" source "--minify"
20251 (string-append "--outfile=" target)))))))))
20252 (propagated-inputs
20253 (list r-ade4
20254 r-biostrings
20255 r-ggplot2
20256 r-htmlwidgets
20257 r-tfbstools
20258 r-xml))
20259 (native-inputs
20260 (list esbuild
20261 r-biocgenerics
20262 r-knitr r-runit
20263 (origin
20264 (method url-fetch)
20265 (uri "https://web.archive.org/web/20230428092426id_/\
20266https://d3js.org/d3.v4.js")
20267 (sha256
20268 (base32
20269 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))
20270 (home-page "https://bioconductor.org/packages/motifStack/")
20271 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
20272 (description
20273 "The motifStack package is designed for graphic representation of
20274multiple motifs with different similarity scores. It works with both DNA/RNA
20275sequence motifs and amino acid sequence motifs. In addition, it provides the
20276flexibility for users to customize the graphic parameters such as the font
20277type and symbol colors.")
20278 (license license:gpl2+)))
20279
20280(define-public r-genomicscores
20281 (package
20282 (name "r-genomicscores")
20283 (version "2.24.0")
20284 (source
20285 (origin
20286 (method url-fetch)
20287 (uri (bioconductor-uri "GenomicScores" version))
20288 (sha256
20289 (base32
20290 "0xnj2w9p5ngaz0slpi0cgv0bb4v4imyl6z081vlzkh9qsa3j09nz"))))
20291 (properties `((upstream-name . "GenomicScores")))
20292 (build-system r-build-system)
20293 (propagated-inputs
20294 (list r-annotationhub
20295 r-biobase
20296 r-biocfilecache
20297 r-biocgenerics
20298 r-biocmanager
20299 r-biostrings
20300 r-delayedarray
20301 r-genomeinfodb
20302 r-genomicranges
20303 r-hdf5array
20304 r-httr
20305 r-iranges
20306 r-rhdf5
20307 r-s4vectors
20308 r-seqinfo
20309 r-xml))
20310 (native-inputs
20311 (list r-knitr r-runit))
20312 (home-page "https://github.com/rcastelo/GenomicScores/")
20313 (synopsis "Work with genome-wide position-specific scores")
20314 (description
20315 "This package provides infrastructure to store and access genome-wide
20316position-specific scores within R and Bioconductor.")
20317 (license license:artistic2.0)))
20318
20319(define-public r-genomicstate
20320 (package
20321 (name "r-genomicstate")
20322 (version "0.99.17")
20323 (source
20324 (origin
20325 (method url-fetch)
20326 (uri (bioconductor-uri "GenomicState" version
20327 'annotation))
20328 (sha256
20329 (base32 "1hdzf75rqq63dx2mjjjpiqvsvlqpk4ymkcll6j763wr1rdagdh3r"))))
20330 (properties `((upstream-name . "GenomicState")))
20331 (build-system r-build-system)
20332 ;; Tests require Internet access.
20333 (arguments (list #:tests? #false))
20334 (propagated-inputs (list r-annotationdbi
20335 r-annotationhub
20336 r-bumphunter
20337 r-derfinder
20338 r-genomicfeatures
20339 r-iranges
20340 r-org-hs-eg-db
20341 r-rtracklayer
20342 r-seqinfo
20343 r-txdbmaker))
20344 (native-inputs (list r-knitr r-testthat))
20345 (home-page "https://github.com/LieberInstitute/GenomicState")
20346 (synopsis "Build and access GenomicState objects")
20347 (description
20348 "This package contains functions for building @code{GenomicState} objects
20349from different annotation sources such as Gencode. It also provides access to
20350these files at JHPCE.")
20351 (license license:artistic2.0)))
20352
20353(define-public r-atacseqqc
20354 (package
20355 (name "r-atacseqqc")
20356 (version "1.36.0")
20357 (source
20358 (origin
20359 (method url-fetch)
20360 (uri (bioconductor-uri "ATACseqQC" version))
20361 (sha256
20362 (base32
20363 "1flikjhvjml25hwwhmm67ymch0ppmgxx12dl43rfw5y8bzb1gm7p"))))
20364 (properties `((upstream-name . "ATACseqQC")))
20365 (build-system r-build-system)
20366 (propagated-inputs
20367 (list r-biocgenerics
20368 r-biocparallel
20369 r-biostrings
20370 r-bsgenome
20371 r-chippeakanno
20372 r-edger
20373 r-genomeinfodb
20374 r-genomicalignments
20375 r-genomicranges
20376 r-genomicscores
20377 r-iranges
20378 r-kernsmooth
20379 r-limma
20380 r-motifstack
20381 r-preseqr
20382 r-randomforest
20383 r-rsamtools
20384 r-rtracklayer
20385 r-s4vectors))
20386 (native-inputs
20387 (list r-knitr r-testthat))
20388 (home-page "https://bioconductor.org/packages/ATACseqQC/")
20389 (synopsis "ATAC-seq quality control")
20390 (description
20391 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
20392sequencing, is a rapid and sensitive method for chromatin accessibility
20393analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
20394and DNAse-seq. The ATACseqQC package was developed to help users to quickly
20395assess whether their ATAC-seq experiment is successful. It includes
20396diagnostic plots of fragment size distribution, proportion of mitochondria
20397reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
20398footprints.")
20399 (license license:gpl2+)))
20400
20401(define-public r-gofuncr
20402 (package
20403 (name "r-gofuncr")
20404 (version "1.31.0")
20405 (source
20406 (origin
20407 (method url-fetch)
20408 (uri (bioconductor-uri "GOfuncR" version))
20409 (sha256
20410 (base32
20411 "1ff3micf0pnrx6za3zyrx3b42ah4q0k306wsdimn3a6i2lfyl1cf"))))
20412 (properties `((upstream-name . "GOfuncR")))
20413 (build-system r-build-system)
20414 (propagated-inputs
20415 (list r-annotationdbi
20416 r-genomicranges
20417 r-gtools
20418 r-iranges
20419 r-mapplots
20420 r-rcpp
20421 r-vioplot))
20422 (native-inputs
20423 (list r-knitr r-testthat))
20424 (home-page "https://bioconductor.org/packages/GOfuncR/")
20425 (synopsis "Gene ontology enrichment using FUNC")
20426 (description
20427 "GOfuncR performs a gene ontology enrichment analysis based on the
20428ontology enrichment software FUNC. GO-annotations are obtained from
20429OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
20430included in the package and updated regularly. GOfuncR provides the standard
20431candidate vs background enrichment analysis using the hypergeometric test, as
20432well as three additional tests:
20433
20434@enumerate
20435@item the Wilcoxon rank-sum test that is used when genes are ranked,
20436@item a binomial test that is used when genes are associated with two counts,
20437 and
20438@item a Chi-square or Fisher's exact test that is used in cases when genes are
20439associated with four counts.
20440@end enumerate
20441
20442To correct for multiple testing and interdependency of the tests, family-wise
20443error rates are computed based on random permutations of the gene-associated
20444variables. GOfuncR also provides tools for exploring the ontology graph and
20445the annotations, and options to take gene-length or spatial clustering of
20446genes into account. It is also possible to provide custom gene coordinates,
20447annotations and ontologies.")
20448 (license license:gpl2+)))
20449
20450(define-public r-abaenrichment
20451 (package
20452 (name "r-abaenrichment")
20453 (version "1.24.0")
20454 (source
20455 (origin
20456 (method url-fetch)
20457 (uri (bioconductor-uri "ABAEnrichment" version))
20458 (sha256
20459 (base32
20460 "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
20461 (properties `((upstream-name . "ABAEnrichment")))
20462 (arguments
20463 (list
20464 #:phases
20465 '(modify-phases %standard-phases
20466 ;; These deprecated procedures have been removed in testthat.
20467 (add-after 'unpack 'testthat-compatibility
20468 (lambda _
20469 (substitute* '("tests/testthat/test_0load_by_name.R"
20470 "tests/testthat/test_aba_enrich.R"
20471 "tests/testthat/test_detect_identifier.R"
20472 "tests/testthat/test_get_superstructures.R")
20473 (("is_true\\(\\)") "expect_true")
20474 (("is_false\\(\\)") "expect_false")))))))
20475 (build-system r-build-system)
20476 (propagated-inputs
20477 (list r-abadata
20478 r-data-table
20479 r-gofuncr
20480 r-gplots
20481 r-gtools
20482 r-rcpp))
20483 (native-inputs
20484 (list r-knitr r-testthat))
20485 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
20486 (synopsis "Gene expression enrichment in human brain regions")
20487 (description
20488 "The package ABAEnrichment is designed to test for enrichment of user
20489defined candidate genes in the set of expressed genes in different human brain
20490regions. The core function @code{aba_enrich} integrates the expression of the
20491candidate gene set (averaged across donors) and the structural information of
20492the brain using an ontology, both provided by the Allen Brain Atlas project.")
20493 (license license:gpl2+)))
20494
20495(define-public r-annotationfuncs
20496 (package
20497 (name "r-annotationfuncs")
20498 (version "1.40.0")
20499 (source
20500 (origin
20501 (method url-fetch)
20502 (uri (bioconductor-uri "AnnotationFuncs" version))
20503 (sha256
20504 (base32
20505 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
20506 (properties
20507 `((upstream-name . "AnnotationFuncs")))
20508 (build-system r-build-system)
20509 (propagated-inputs
20510 (list r-annotationdbi r-dbi))
20511 (home-page "https://www.iysik.com/r/annotationfuncs")
20512 (synopsis "Annotation translation functions")
20513 (description
20514 "This package provides functions for handling translating between
20515different identifieres using the Biocore Data Team data-packages (e.g.
20516@code{org.Bt.eg.db}).")
20517 (license license:gpl2)))
20518
20519(define-public r-annotationtools
20520 (package
20521 (name "r-annotationtools")
20522 (version "1.86.0")
20523 (source
20524 (origin
20525 (method url-fetch)
20526 (uri (bioconductor-uri "annotationTools" version))
20527 (sha256
20528 (base32
20529 "0sw08jl7h5v2irz7d8klf9apiiw0cq75zzls4wmm58x7mjnqs3hh"))))
20530 (properties
20531 `((upstream-name . "annotationTools")))
20532 (build-system r-build-system)
20533 (propagated-inputs (list r-biobase))
20534 (home-page "https://bioconductor.org/packages/annotationTools/")
20535 (synopsis "Annotate microarrays and perform gene expression analyses")
20536 (description
20537 "This package provides functions to annotate microarrays, find orthologs,
20538and integrate heterogeneous gene expression profiles using annotation and
20539other molecular biology information available as flat file database (plain
20540text files).")
20541 ;; Any version of the GPL.
20542 (license (list license:gpl2+))))
20543
20544(define-public r-allelicimbalance
20545 (package
20546 (name "r-allelicimbalance")
20547 (version "1.50.0")
20548 (source
20549 (origin
20550 (method url-fetch)
20551 (uri (bioconductor-uri "AllelicImbalance" version))
20552 (sha256
20553 (base32
20554 "09dzajwnkg4k2psjz332gbn53vs5g4wf56gwh83cp4ldmx7ifqa6"))))
20555 (properties
20556 `((upstream-name . "AllelicImbalance")))
20557 (build-system r-build-system)
20558 (propagated-inputs
20559 (list r-annotationdbi
20560 r-biocgenerics
20561 r-biostrings
20562 r-bsgenome
20563 r-genomeinfodb
20564 r-genomicalignments
20565 r-genomicfeatures
20566 r-genomicranges
20567 r-gridextra
20568 r-gviz
20569 r-iranges
20570 r-lattice
20571 r-latticeextra
20572 r-nlme
20573 r-rsamtools
20574 r-s4vectors
20575 r-seqinr
20576 r-summarizedexperiment
20577 r-variantannotation))
20578 (native-inputs
20579 (list r-knitr r-testthat))
20580 (home-page "https://github.com/pappewaio/AllelicImbalance")
20581 (synopsis "Investigate allele-specific expression")
20582 (description
20583 "This package provides a framework for allele-specific expression
20584investigation using RNA-seq data.")
20585 (license license:gpl3)))
20586
20587(define-public r-aucell
20588 (package
20589 (name "r-aucell")
20590 (version "1.34.0")
20591 (source
20592 (origin
20593 (method url-fetch)
20594 (uri (bioconductor-uri "AUCell" version))
20595 (sha256
20596 (base32
20597 "0ryqbhg78aylzqxf4jx2af3db3z86c7wxbma1i4wcsmdwvjhdix7"))))
20598 (properties `((upstream-name . "AUCell")))
20599 (build-system r-build-system)
20600 (propagated-inputs
20601 (list r-biocgenerics
20602 r-data-table
20603 r-delayedarray
20604 r-delayedmatrixstats
20605 r-gseabase
20606 r-matrix
20607 r-mixtools
20608 r-r-utils
20609 r-summarizedexperiment))
20610 (native-inputs
20611 (list r-biobase r-knitr r-testthat))
20612 (home-page "https://bioconductor.org/packages/AUCell/")
20613 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
20614 (description
20615 "AUCell identifies cells with active gene sets (e.g. signatures,
20616gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
20617Under the Curve} (AUC) to calculate whether a critical subset of the input
20618gene set is enriched within the expressed genes for each cell. The
20619distribution of AUC scores across all the cells allows exploring the relative
20620expression of the signature. Since the scoring method is ranking-based,
20621AUCell is independent of the gene expression units and the normalization
20622procedure. In addition, since the cells are evaluated individually, it can
20623easily be applied to bigger datasets, subsetting the expression matrix if
20624needed.")
20625 (license license:gpl3)))
20626
20627(define-public r-ebimage
20628 (package
20629 (name "r-ebimage")
20630 (version "4.54.0")
20631 (source
20632 (origin
20633 (method url-fetch)
20634 (uri (bioconductor-uri "EBImage" version))
20635 (sha256
20636 (base32
20637 "1zpafm4gfkxmi02hiavb22zf27mp8swr284k78g92fcvdskqbi08"))))
20638 (properties `((upstream-name . "EBImage")))
20639 (build-system r-build-system)
20640 (propagated-inputs
20641 (list r-abind
20642 r-biocgenerics
20643 r-fftwtools
20644 r-htmltools
20645 r-htmlwidgets
20646 r-jpeg
20647 r-locfit
20648 r-png
20649 r-rcurl
20650 r-tiff))
20651 (native-inputs
20652 (list r-digest r-knitr)) ; for vignettes
20653 (home-page "https://github.com/aoles/EBImage")
20654 (synopsis "Image processing and analysis toolbox for R")
20655 (description
20656 "EBImage provides general purpose functionality for image processing and
20657analysis. In the context of (high-throughput) microscopy-based cellular
20658assays, EBImage offers tools to segment cells and extract quantitative
20659cellular descriptors. This allows the automation of such tasks using the R
20660programming language and facilitates the use of other tools in the R
20661environment for signal processing, statistical modeling, machine learning and
20662visualization with image data.")
20663 ;; Any version of the LGPL.
20664 (license license:lgpl2.1+)))
20665
20666(define-public r-yamss
20667 (package
20668 (name "r-yamss")
20669 (version "1.38.0")
20670 (source
20671 (origin
20672 (method url-fetch)
20673 (uri (bioconductor-uri "yamss" version))
20674 (sha256
20675 (base32
20676 "14qv7qicb5k5szmrbqmxnhvdm9r2yfja2xvxw39xv9pkjsk9jv7d"))))
20677 (build-system r-build-system)
20678 (propagated-inputs
20679 (list r-biocgenerics
20680 r-data-table
20681 r-ebimage
20682 r-iranges
20683 r-limma
20684 r-matrix
20685 r-mzr
20686 r-s4vectors
20687 r-summarizedexperiment))
20688 (native-inputs
20689 (list r-knitr r-testthat))
20690 (home-page "https://github.com/hansenlab/yamss")
20691 (synopsis "Tools for high-throughput metabolomics")
20692 (description
20693 "This package provides tools to analyze and visualize high-throughput
20694metabolomics data acquired using chromatography-mass spectrometry. These tools
20695preprocess data in a way that enables reliable and powerful differential
20696analysis.")
20697 (license license:artistic2.0)))
20698
20699(define-public r-gtrellis
20700 (package
20701 (name "r-gtrellis")
20702 (version "1.44.0")
20703 (source
20704 (origin
20705 (method url-fetch)
20706 (uri (bioconductor-uri "gtrellis" version))
20707 (sha256
20708 (base32
20709 "111c4znmfd2swdqd4gpa7shdkv96nlm9l8bhfb0668m9a4axjf91"))))
20710 (build-system r-build-system)
20711 (propagated-inputs
20712 (list r-circlize r-genomicranges r-getoptlong r-iranges))
20713 (native-inputs
20714 (list r-knitr r-testthat))
20715 (home-page "https://github.com/jokergoo/gtrellis")
20716 (synopsis "Genome level Trellis layout")
20717 (description
20718 "Genome level Trellis graph visualizes genomic data conditioned by
20719genomic categories (e.g. chromosomes). For each genomic category, multiple
20720dimensional data which are represented as tracks describe different features
20721from different aspects. This package provides high flexibility to arrange
20722genomic categories and to add self-defined graphics in the plot.")
20723 (license license:expat)))
20724
20725(define-public r-somaticsignatures
20726 (package
20727 (name "r-somaticsignatures")
20728 (version "2.48.0")
20729 (source
20730 (origin
20731 (method url-fetch)
20732 (uri (bioconductor-uri "SomaticSignatures" version))
20733 (sha256
20734 (base32
20735 "1l9d1fcjnf9an0l3ai1ckscz6zwzr0rllym31l7jcbn4fbrw3sa5"))))
20736 (properties
20737 `((upstream-name . "SomaticSignatures")))
20738 (build-system r-build-system)
20739 (propagated-inputs
20740 (list r-biobase
20741 r-biostrings
20742 r-genomicranges
20743 r-ggbio
20744 r-ggplot2
20745 r-iranges
20746 r-nmf
20747 r-pcamethods
20748 r-proxy
20749 r-reshape2
20750 r-s4vectors
20751 r-seqinfo
20752 r-variantannotation))
20753 (native-inputs
20754 (list r-knitr r-testthat))
20755 (home-page "https://github.com/juliangehring/SomaticSignatures")
20756 (synopsis "Somatic signatures")
20757 (description
20758 "This package identifies mutational signatures of @dfn{single nucleotide
20759variants} (SNVs). It provides a infrastructure related to the methodology
20760described in Nik-Zainal (2012, Cell), with flexibility in the matrix
20761decomposition algorithms.")
20762 (license license:expat)))
20763
20764(define-public r-yapsa
20765 (package
20766 (name "r-yapsa")
20767 (version "1.38.0")
20768 (source
20769 (origin
20770 (method url-fetch)
20771 (uri (bioconductor-uri "YAPSA" version))
20772 (sha256
20773 (base32
20774 "0yrhdkisijhbbnjr6p95hm47bkvbnxhq88gyjfafwb0cqfbfjzh8"))))
20775 (properties `((upstream-name . "YAPSA")))
20776 (build-system r-build-system)
20777 (propagated-inputs
20778 (list r-biostrings
20779 r-bsgenome-hsapiens-ucsc-hg19
20780 r-circlize
20781 r-complexheatmap
20782 r-corrplot
20783 r-dendextend
20784 r-doparallel
20785 r-dplyr
20786 r-genomicranges
20787 r-getoptlong
20788 r-ggbeeswarm
20789 r-ggplot2
20790 r-gridextra
20791 r-gtrellis
20792 r-keggrest
20793 r-limsolve
20794 r-magrittr
20795 r-pmcmrplus
20796 r-pracma
20797 r-reshape2
20798 r-seqinfo
20799 r-somaticsignatures
20800 r-variantannotation))
20801 (native-inputs
20802 (list r-knitr r-testthat))
20803 (home-page "https://bioconductor.org/packages/YAPSA/")
20804 (synopsis "Yet another package for signature analysis")
20805 (description
20806 "This package provides functions and routines useful in the analysis of
20807somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
20808functions to perform a signature analysis with known signatures and a
20809signature analysis on @dfn{stratified mutational catalogue} (SMC) are
20810provided.")
20811 (license license:gpl3)))
20812
20813(define-public r-gcrma
20814 (package
20815 (name "r-gcrma")
20816 (version "2.84.0")
20817 (source
20818 (origin
20819 (method url-fetch)
20820 (uri (bioconductor-uri "gcrma" version))
20821 (sha256
20822 (base32
20823 "0cn16f7qy69gp3403jw9b3m2l8sma8gd8y55qsqssi8cq3jadk01"))))
20824 (build-system r-build-system)
20825 (propagated-inputs
20826 (list r-affy
20827 r-affyio
20828 r-biobase
20829 r-biocmanager
20830 r-biostrings
20831 r-xvector))
20832 (home-page "https://bioconductor.org/packages/gcrma/")
20833 (synopsis "Background adjustment using sequence information")
20834 (description
20835 "Gcrma adjusts for background intensities in Affymetrix array data which
20836include optical noise and @dfn{non-specific binding} (NSB). The main function
20837@code{gcrma} converts background adjusted probe intensities to expression
20838measures using the same normalization and summarization methods as a
20839@dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
20840to estimate probe affinity to NSB. The sequence information is summarized in
20841a more complex way than the simple GC content. Instead, the base types (A, T,
20842G or C) at each position along the probe determine the affinity of each probe.
20843The parameters of the position-specific base contributions to the probe
20844affinity is estimated in an NSB experiment in which only NSB but no
20845gene-specific binding is expected.")
20846 ;; Any version of the LGPL
20847 (license license:lgpl2.1+)))
20848
20849(define-public r-simpleaffy
20850 (package
20851 (name "r-simpleaffy")
20852 (version "2.66.0")
20853 (source
20854 (origin
20855 (method url-fetch)
20856 (uri (bioconductor-uri "simpleaffy" version))
20857 (sha256
20858 (base32
20859 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
20860 (build-system r-build-system)
20861 (arguments
20862 (list
20863 #:phases
20864 #~(modify-phases %standard-phases
20865 (add-before 'install 'relax-gcc-14-strictness
20866 (lambda _
20867 ;; XXX FIXME: $HOME/.R/Makevars seems to be the only way to
20868 ;; set custom CFLAGS for R?
20869 (setenv "HOME" (getcwd))
20870 (mkdir-p ".R")
20871 (with-directory-excursion ".R"
20872 (with-output-to-file "Makevars"
20873 (lambda _
20874 (display (string-append
20875 "CFLAGS=-g -O2"
20876 " -Wno-error=incompatible-pointer-types\n"))))))))))
20877 (propagated-inputs
20878 (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
20879 (home-page "https://bioconductor.org/packages/simpleaffy/")
20880 (synopsis "Very simple high level analysis of Affymetrix data")
20881 (description
20882 "This package provides high level functions for reading Affy @file{.CEL}
20883files, phenotypic data, and then computing simple things with it, such as
20884t-tests, fold changes and the like. It makes heavy use of the @code{affy}
20885library. It also has some basic scatter plot functions and mechanisms for
20886generating high resolution journal figures.")
20887 (license license:gpl2+)))
20888
20889(define-public r-yaqcaffy
20890 (package
20891 (name "r-yaqcaffy")
20892 (version "1.50.0")
20893 (source
20894 (origin
20895 (method url-fetch)
20896 (uri (bioconductor-uri "yaqcaffy" version))
20897 (sha256
20898 (base32
20899 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
20900 (build-system r-build-system)
20901 (propagated-inputs
20902 (list r-simpleaffy))
20903 (home-page "https://bioconductor.org/packages/yaqcaffy/")
20904 (synopsis "Affymetrix quality control and reproducibility analysis")
20905 (description
20906 "This is a package that can be used for quality control of Affymetrix
20907GeneChip expression data and reproducibility analysis of human whole genome
20908chips with the MAQC reference datasets.")
20909 (license license:artistic2.0)))
20910
20911(define-public r-quantro
20912 (package
20913 (name "r-quantro")
20914 (version "1.46.0")
20915 (source
20916 (origin
20917 (method url-fetch)
20918 (uri (bioconductor-uri "quantro" version))
20919 (sha256
20920 (base32
20921 "14lz9xc2g9y1g37gq9br2vgvpdmw1r10dx0jksw7mfb6zvklhc8q"))))
20922 (build-system r-build-system)
20923 (propagated-inputs
20924 (list r-biobase
20925 r-doparallel
20926 r-foreach
20927 r-ggplot2
20928 r-iterators
20929 r-minfi
20930 r-rcolorbrewer))
20931 (native-inputs
20932 (list r-biocgenerics r-knitr r-runit))
20933 (home-page "https://bioconductor.org/packages/quantro/")
20934 (synopsis "Test for when to use quantile normalization")
20935 (description
20936 "This package provides a data-driven test for the assumptions of quantile
20937normalization using raw data such as objects that inherit eSets (e.g.
20938ExpressionSet, MethylSet). Group level information about each sample (such as
20939Tumor / Normal status) must also be provided because the test assesses if
20940there are global differences in the distributions between the user-defined
20941groups.")
20942 (license license:gpl3+)))
20943
20944(define-public r-yarn
20945 (package
20946 (name "r-yarn")
20947 (version "1.38.0")
20948 (source
20949 (origin
20950 (method url-fetch)
20951 (uri (bioconductor-uri "yarn" version))
20952 (sha256
20953 (base32
20954 "019qpzy1mhbqkzfrqgnnx4gjqv924a21v0f3ljrg31w7lf4fbb0x"))))
20955 (build-system r-build-system)
20956 (propagated-inputs
20957 (list r-biobase
20958 r-biomart
20959 r-downloader
20960 r-edger
20961 r-gplots
20962 r-limma
20963 r-matrixstats
20964 r-preprocesscore
20965 r-quantro
20966 r-rcolorbrewer
20967 r-readr))
20968 (native-inputs
20969 (list r-knitr r-testthat))
20970 (home-page "https://bioconductor.org/packages/yarn/")
20971 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
20972 (description
20973 "Expedite large RNA-Seq analyses using a combination of previously
20974developed tools. YARN is meant to make it easier for the user in performing
20975basic mis-annotation quality control, filtering, and condition-aware
20976normalization. YARN leverages many Bioconductor tools and statistical
20977techniques to account for the large heterogeneity and sparsity found in very
20978large RNA-seq experiments.")
20979 (license license:artistic2.0)))
20980
20981(define-public r-roar
20982 (package
20983 (name "r-roar")
20984 (version "1.48.0")
20985 (source
20986 (origin
20987 (method url-fetch)
20988 (uri (bioconductor-uri "roar" version))
20989 (sha256
20990 (base32
20991 "1v5hc65yzn6dsvvdwscr1vq1p2jzp09m8kr0wamh7dal63n64r8a"))))
20992 (build-system r-build-system)
20993 (propagated-inputs
20994 (list r-biocgenerics
20995 r-genomeinfodb
20996 r-genomicalignments
20997 r-genomicranges
20998 r-iranges
20999 r-rtracklayer
21000 r-s4vectors
21001 r-summarizedexperiment))
21002 (native-inputs (list r-rnaseqdata-hnrnpc-bam-chr14 r-testthat))
21003 (home-page "https://github.com/vodkatad/roar/")
21004 (synopsis "Identify differential APA usage from RNA-seq alignments")
21005 (description
21006 "This package provides tools for identifying preferential usage of APA
21007sites, comparing two biological conditions, starting from known alternative
21008sites and alignments obtained from standard RNA-seq experiments.")
21009 (license license:gpl3)))
21010
21011(define-public r-xbseq
21012 (package
21013 (name "r-xbseq")
21014 (version "1.22.0")
21015 (source
21016 (origin
21017 (method url-fetch)
21018 (uri (bioconductor-uri "XBSeq" version))
21019 (sha256
21020 (base32
21021 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
21022 (properties `((upstream-name . "XBSeq")))
21023 (build-system r-build-system)
21024 (propagated-inputs
21025 (list r-biobase
21026 r-deseq2
21027 r-dplyr
21028 r-ggplot2
21029 r-locfit
21030 r-magrittr
21031 r-matrixstats
21032 r-pracma
21033 r-roar))
21034 (native-inputs
21035 (list r-knitr r-testthat))
21036 (home-page "https://github.com/Liuy12/XBSeq")
21037 (synopsis "Test for differential expression for RNA-seq data")
21038 (description
21039 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
21040expression} (DE), where a statistical model was established based on the
21041assumption that observed signals are the convolution of true expression
21042signals and sequencing noises. The mapped reads in non-exonic regions are
21043considered as sequencing noises, which follows a Poisson distribution. Given
21044measurable observed signal and background noise from RNA-seq data, true
21045expression signals, assuming governed by the negative binomial distribution,
21046can be delineated and thus the accurate detection of differential expressed
21047genes.")
21048 (license license:gpl3+)))
21049
21050(define-public r-massspecwavelet
21051 (package
21052 (name "r-massspecwavelet")
21053 (version "1.78.0")
21054 (source
21055 (origin
21056 (method url-fetch)
21057 (uri (bioconductor-uri "MassSpecWavelet" version))
21058 (sha256
21059 (base32
21060 "000139fcxlrfr5fysz1zf8dhrnz3krnqj2qqgnbgnpp1llli9lv8"))))
21061 (properties
21062 '((upstream-name . "MassSpecWavelet")
21063 (updater-extra-native-inputs . ("r-runit"))))
21064 (build-system r-build-system)
21065 (native-inputs
21066 (list r-knitr r-runit))
21067 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
21068 (synopsis "Mass spectrum processing by wavelet-based algorithms")
21069 (description
21070 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
21071data mainly through the use of wavelet transforms. It supports peak detection
21072based on @dfn{Continuous Wavelet Transform} (CWT).")
21073 (license license:lgpl2.0+)))
21074
21075(define-public r-xcms
21076 (package
21077 (name "r-xcms")
21078 (version "4.10.0")
21079 (source
21080 (origin
21081 (method url-fetch)
21082 (uri (bioconductor-uri "xcms" version))
21083 (sha256
21084 (base32
21085 "0hawwzr1115c4k8hf9i5m5pajpr195zpc26cv9hc1cp23qr5pyz4"))))
21086 (properties
21087 '((upstream-name . "xcms")
21088 ;; Avoid dependency cycle.
21089 (updater-ignored-native-inputs . ("r-faahko"))))
21090 (build-system r-build-system)
21091 ;; Tests require faahKO, which depends on this package.
21092 (arguments (list #:tests? #false))
21093 (propagated-inputs
21094 (list r-biobase
21095 r-biocgenerics
21096 r-biocparallel
21097 r-data-table
21098 r-iranges
21099 r-lattice
21100 r-massspecwavelet
21101 r-metabocoreutils
21102 r-mscoreutils
21103 r-msexperiment
21104 r-msfeatures
21105 r-msnbase
21106 r-mzr
21107 r-progress
21108 r-protgenerics
21109 r-rcolorbrewer
21110 r-s4vectors
21111 r-spectra
21112 r-summarizedexperiment))
21113 (native-inputs
21114 (list r-knitr r-msdatahub r-rhdf5 r-testthat))
21115 (home-page "https://bioconductor.org/packages/xcms/")
21116 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
21117 (description
21118 "This package provides a framework for processing and visualization of
21119chromatographically separated and single-spectra mass spectral data. It
21120imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
21121data for high-throughput, untargeted analyte profiling.")
21122 (license license:gpl2+)))
21123
21124(define-public r-wppi
21125 (package
21126 (name "r-wppi")
21127 (version "1.19.0")
21128 (source (origin
21129 (method url-fetch)
21130 (uri (bioconductor-uri "wppi" version))
21131 (sha256
21132 (base32
21133 "1smi3b541vdgffxrwhhh4vh4krfvvni9xf93rpcpanbsbkj7rdqn"))))
21134 (properties `((upstream-name . "wppi")))
21135 (build-system r-build-system)
21136 ;; This is necessary because omnipathr attempts to write a configuration
21137 ;; file to HOME.
21138 (arguments
21139 `(#:phases
21140 (modify-phases %standard-phases
21141 (add-after 'unpack 'set-HOME
21142 (lambda _ (setenv "HOME" "/tmp"))))))
21143 (propagated-inputs (list r-dplyr
21144 r-igraph
21145 r-logger
21146 r-magrittr
21147 r-matrix
21148 r-omnipathr
21149 r-progress
21150 r-purrr
21151 r-rcurl
21152 r-rlang
21153 r-tibble
21154 r-tidyr))
21155 (native-inputs (list r-knitr))
21156 (home-page "https://github.com/AnaGalhoz37/wppi")
21157 (synopsis "Weighting protein-protein interactions")
21158 (description
21159 "This package predicts functional relevance of protein-protein
21160interactions based on functional annotations such as Human Protein Ontology
21161and Gene Ontology, and prioritizes genes based on network topology, functional
21162scores and a path search algorithm.")
21163 (license license:expat)))
21164
21165(define-public r-wrench
21166 (package
21167 (name "r-wrench")
21168 (version "1.30.0")
21169 (source
21170 (origin
21171 (method url-fetch)
21172 (uri (bioconductor-uri "Wrench" version))
21173 (sha256
21174 (base32
21175 "113s2q1v6mia5c28k1zgyym70faq4kvw8cjgif1md7wmsfg1pmdp"))))
21176 (properties `((upstream-name . "Wrench")))
21177 (build-system r-build-system)
21178 (propagated-inputs
21179 (list r-limma r-locfit r-matrixstats))
21180 (native-inputs
21181 (list r-knitr))
21182 (home-page "https://github.com/HCBravoLab/Wrench")
21183 (synopsis "Wrench normalization for sparse count data")
21184 (description
21185 "Wrench is a package for normalization sparse genomic count data, like
21186that arising from 16s metagenomic surveys.")
21187 (license license:artistic2.0)))
21188
21189(define-public r-wiggleplotr
21190 (package
21191 (name "r-wiggleplotr")
21192 (version "1.36.0")
21193 (source
21194 (origin
21195 (method url-fetch)
21196 (uri (bioconductor-uri "wiggleplotr" version))
21197 (sha256
21198 (base32
21199 "03g7w7x1gsbwpjnxkxkf4kkvq28fgdl5iwhhsii17h321flamcb8"))))
21200 (build-system r-build-system)
21201 (propagated-inputs
21202 (list r-assertthat
21203 r-cowplot
21204 r-dplyr
21205 r-genomeinfodb
21206 r-genomicranges
21207 r-ggplot2
21208 r-iranges
21209 r-purrr
21210 r-rtracklayer
21211 r-s4vectors))
21212 (native-inputs
21213 (list r-knitr r-testthat))
21214 (home-page "https://bioconductor.org/packages/wiggleplotr/")
21215 (synopsis "Make read coverage plots from BigWig files")
21216 (description
21217 "This package provides tools to visualize read coverage from sequencing
21218experiments together with genomic annotations (genes, transcripts, peaks).
21219Introns of long transcripts can be rescaled to a fixed length for better
21220visualization of exonic read coverage.")
21221 (license license:asl2.0)))
21222
21223(define-public r-widgettools
21224 (package
21225 (name "r-widgettools")
21226 (version "1.90.0")
21227 (source
21228 (origin
21229 (method url-fetch)
21230 (uri (bioconductor-uri "widgetTools" version))
21231 (sha256
21232 (base32
21233 "0jmdj3apybax32v3lwg8d57mnv11lk34s89jilyjzqlka9sixkb1"))))
21234 (properties `((upstream-name . "widgetTools")))
21235 (build-system r-build-system)
21236 (home-page "https://bioconductor.org/packages/widgetTools/")
21237 (synopsis "Tools for creating interactive tcltk widgets")
21238 (description
21239 "This package contains tools to support the construction of tcltk
21240widgets in R.")
21241 ;; Any version of the LGPL.
21242 (license license:lgpl3+)))
21243
21244(define-public r-webbioc
21245 (package
21246 (name "r-webbioc")
21247 (version "1.84.0")
21248 (source
21249 (origin
21250 (method url-fetch)
21251 (uri (bioconductor-uri "webbioc" version))
21252 (sha256
21253 (base32
21254 "1g9yyafqn4pzk7mk3q6z2h17fnxwcfb7slipd7v427n441gjngys"))))
21255 (build-system r-build-system)
21256 (inputs
21257 (list netpbm perl))
21258 (propagated-inputs
21259 (list r-affy
21260 r-annaffy
21261 r-biobase
21262 r-biocmanager
21263 r-gcrma
21264 r-multtest
21265 r-qvalue
21266 r-vsn))
21267 (home-page "https://www.bioconductor.org/")
21268 (synopsis "Bioconductor web interface")
21269 (description
21270 "This package provides an integrated web interface for doing microarray
21271analysis using several of the Bioconductor packages. It is intended to be
21272deployed as a centralized bioinformatics resource for use by many users.
21273Currently only Affymetrix oligonucleotide analysis is supported.")
21274 (license license:gpl2+)))
21275
21276(define-public r-zinbwave
21277 (package
21278 (name "r-zinbwave")
21279 (version "1.34.0")
21280 (source
21281 (origin
21282 (method url-fetch)
21283 (uri (bioconductor-uri "zinbwave" version))
21284 (sha256
21285 (base32
21286 "0wbkhawribxl6pw9l4hlb7j76c8wvgi1k2bi8lx38bgrd22hbmlv"))))
21287 (build-system r-build-system)
21288 (propagated-inputs
21289 (list r-biocparallel
21290 r-edger
21291 r-genefilter
21292 r-matrix
21293 r-singlecellexperiment
21294 r-softimpute
21295 r-summarizedexperiment))
21296 (native-inputs
21297 (list r-knitr r-testthat))
21298 (home-page "https://bioconductor.org/packages/zinbwave")
21299 (synopsis "Zero-inflated negative binomial model for RNA-seq data")
21300 (description "This package implements a general and flexible zero-inflated
21301negative binomial model that can be used to provide a low-dimensional
21302representations of single-cell RNA-seq data. The model accounts for zero
21303inflation (dropouts), over-dispersion, and the count nature of the data.
21304The model also accounts for the difference in library sizes and optionally
21305for batch effects and/or other covariates, avoiding the need for pre-normalize
21306the data.")
21307 (license license:artistic2.0)))
21308
21309(define-public r-zfpkm
21310 (package
21311 (name "r-zfpkm")
21312 (version "1.34.0")
21313 (source
21314 (origin
21315 (method url-fetch)
21316 (uri (bioconductor-uri "zFPKM" version))
21317 (sha256
21318 (base32
21319 "0avyzw86gifxvd4sbmnda5jjcnfdwjalvsxij1hhcri6n3da6iia"))))
21320 (properties `((upstream-name . "zFPKM")))
21321 (build-system r-build-system)
21322 (propagated-inputs
21323 (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
21324 (native-inputs
21325 (list r-knitr))
21326 (home-page "https://github.com/ronammar/zFPKM/")
21327 (synopsis "Functions to facilitate zFPKM transformations")
21328 (description
21329 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
21330This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
2133124215113).")
21332 (license license:gpl3)))
21333
21334(define-public r-rbowtie2
21335 (package
21336 (name "r-rbowtie2")
21337 (version "2.18.0")
21338 (source
21339 (origin
21340 (method url-fetch)
21341 (uri (bioconductor-uri "Rbowtie2" version))
21342 (sha256
21343 (base32
21344 "19rg1arvya09fp4d3rb56fgr1rhmc4dpqya0d4jaff60a60kvzng"))))
21345 (properties `((upstream-name . "Rbowtie2")))
21346 (build-system r-build-system)
21347 (propagated-inputs
21348 (list r-magrittr r-rsamtools))
21349 (inputs
21350 (list samtools))
21351 (native-inputs
21352 (list r-knitr))
21353 (home-page "https://bioconductor.org/packages/Rbowtie2/")
21354 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
21355 (description
21356 "This package provides an R wrapper of the popular @code{bowtie2}
21357sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
21358rapid adapter trimming, identification, and read merging.")
21359 (license license:gpl3+)))
21360
21361(define-public r-progeny
21362 (package
21363 (name "r-progeny")
21364 (version "1.34.0")
21365 (source
21366 (origin
21367 (method url-fetch)
21368 (uri (bioconductor-uri "progeny" version))
21369 (sha256
21370 (base32
21371 "1lcifxsskzyyiq0r2p1qpnl8l6mqw3py928h99z5hkpjxqkfk3ry"))))
21372 (build-system r-build-system)
21373 (propagated-inputs
21374 (list r-biobase
21375 r-decoupler
21376 r-dplyr
21377 r-ggplot2
21378 r-ggrepel
21379 r-gridextra
21380 r-reshape2
21381 r-tidyr))
21382 (native-inputs
21383 (list r-knitr r-testthat))
21384 (home-page "https://github.com/saezlab/progeny")
21385 (synopsis "Pathway responsive gene activity inference")
21386 (description
21387 "This package provides a function to infer pathway activity from gene
21388expression. It contains the linear model inferred in the publication
21389\"Perturbation-response genes reveal signaling footprints in cancer gene
21390expression\".")
21391 (license license:asl2.0)))
21392
21393(define-public r-arrmnormalization
21394 (package
21395 (name "r-arrmnormalization")
21396 (version "1.52.0")
21397 (source
21398 (origin
21399 (method url-fetch)
21400 (uri (bioconductor-uri "ARRmNormalization" version))
21401 (sha256
21402 (base32
21403 "1m2k342sxhc6b25mmwhz9imzk8wh50w3lpn0q2jk5r6rpbvabyva"))))
21404 (properties
21405 `((upstream-name . "ARRmNormalization")))
21406 (build-system r-build-system)
21407 (propagated-inputs (list r-arrmdata))
21408 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
21409 (synopsis "Adaptive robust regression normalization for methylation data")
21410 (description
21411 "This is a package to perform the @dfn{Adaptive Robust Regression
21412method} (ARRm) for the normalization of methylation data from the Illumina
21413Infinium HumanMethylation 450k assay.")
21414 (license license:artistic2.0)))
21415
21416(define-public r-biocfilecache
21417 (package
21418 (name "r-biocfilecache")
21419 (version "3.2.0")
21420 (source
21421 (origin
21422 (method url-fetch)
21423 (uri (bioconductor-uri "BiocFileCache" version))
21424 (sha256
21425 (base32
21426 "0gf1mhzy47fjs44bwlx7p57gd4wxim5qm6qa790p2zl4l9j5kzd6"))))
21427 (properties `((upstream-name . "BiocFileCache")))
21428 (build-system r-build-system)
21429 ;; Tests require internet access.
21430 (arguments (list #:tests? #false))
21431 (propagated-inputs
21432 (list r-curl
21433 r-dbi
21434 r-dbplyr
21435 r-dplyr
21436 r-filelock
21437 r-httr2
21438 r-rsqlite))
21439 (native-inputs
21440 (list r-knitr r-testthat))
21441 (home-page "https://bioconductor.org/packages/BiocFileCache/")
21442 (synopsis "Manage files across sessions")
21443 (description
21444 "This package creates a persistent on-disk cache of files that the user
21445can add, update, and retrieve. It is useful for managing resources (such as
21446custom Txdb objects) that are costly or difficult to create, web resources,
21447and data files used across sessions.")
21448 (license license:artistic2.0)))
21449
21450(define-public r-iclusterplus
21451 (package
21452 (name "r-iclusterplus")
21453 (version "1.48.0")
21454 (source
21455 (origin
21456 (method url-fetch)
21457 (uri (bioconductor-uri "iClusterPlus" version))
21458 (sha256
21459 (base32
21460 "19zyji2kknc23ja79frc1rcsz85pdhqsp315va9xiqdqvqpn1hsk"))))
21461 (properties `((upstream-name . "iClusterPlus")))
21462 (build-system r-build-system)
21463 (propagated-inputs (list r-irlba))
21464 (native-inputs (list gfortran r-biocgenerics r-runit))
21465 (home-page "https://bioconductor.org/packages/iClusterPlus/")
21466 (synopsis "Integrative clustering of multi-type genomic data")
21467 (description
21468 "iClusterPlus is developed for integrative clustering analysis of
21469multi-type genomic data and is an enhanced version of iCluster proposed and
21470developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
21471from the experiments where biological samples (e.g. tumor samples) are
21472analyzed by multiple techniques, for instance, @dfn{array comparative genomic
21473hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
21474on. In the iClusterPlus model, binary observations such as somatic mutation
21475are modeled as Binomial processes; categorical observations such as copy
21476number states are realizations of Multinomial random variables; counts are
21477modeled as Poisson random processes; and continuous measures are modeled by
21478Gaussian distributions.")
21479 (license license:gpl2+)))
21480
21481(define-public r-rbowtie
21482 (package
21483 (name "r-rbowtie")
21484 (version "1.52.0")
21485 (source
21486 (origin
21487 (method url-fetch)
21488 (uri (bioconductor-uri "Rbowtie" version))
21489 (sha256
21490 (base32
21491 "1lsqd6hsx0sq9zfn27c0gjkzlij0rj80ynwn2bslhzc0k8vffpfk"))))
21492 (properties `((upstream-name . "Rbowtie")))
21493 (build-system r-build-system)
21494 (arguments
21495 `(#:phases
21496 ;; Disable unsupported `popcnt' instructions on
21497 ;; architectures other than x86_64
21498 ,(if (string-prefix? "x86_64"
21499 (or (%current-target-system)
21500 (%current-system)))
21501 '%standard-phases
21502 '(modify-phases %standard-phases
21503 (add-after 'unpack 'patch-sources
21504 (lambda _
21505 (setenv "POPCNT_CAPABILITY" "0")))))))
21506 (inputs (list zlib))
21507 (native-inputs
21508 (list r-knitr r-testthat))
21509 (home-page "https://bioconductor.org/packages/Rbowtie/")
21510 (synopsis "R bowtie wrapper")
21511 (description
21512 "This package provides an R wrapper around the popular bowtie short read
21513aligner and around SpliceMap, a de novo splice junction discovery and
21514alignment tool.")
21515 (license license:artistic2.0)))
21516
21517(define-public r-sgseq
21518 (package
21519 (name "r-sgseq")
21520 (version "1.46.0")
21521 (source
21522 (origin
21523 (method url-fetch)
21524 (uri (bioconductor-uri "SGSeq" version))
21525 (sha256
21526 (base32
21527 "1w4m80j1fim81pgsrl6f7fwjzjvs2m9d818jsjb47bw9yhysywgk"))))
21528 (properties `((upstream-name . "SGSeq")))
21529 (build-system r-build-system)
21530 (propagated-inputs
21531 (list r-annotationdbi
21532 r-biocgenerics
21533 r-biostrings
21534 r-genomeinfodb
21535 r-genomicalignments
21536 r-genomicfeatures
21537 r-genomicranges
21538 r-igraph
21539 r-iranges
21540 r-rsamtools
21541 r-rtracklayer
21542 r-runit
21543 r-s4vectors
21544 r-seqinfo
21545 r-summarizedexperiment))
21546 (native-inputs
21547 (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr))
21548 (home-page "https://bioconductor.org/packages/SGSeq/")
21549 (synopsis "Splice event prediction and quantification from RNA-seq data")
21550 (description
21551 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
21552data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
21553represented as a splice graph, which can be obtained from existing annotation
21554or predicted from the mapped sequence reads. Splice events are identified
21555from the graph and are quantified locally using structurally compatible reads
21556at the start or end of each splice variant. The software includes functions
21557for splice event prediction, quantification, visualization and
21558interpretation.")
21559 (license license:artistic2.0)))
21560
21561(define-public r-rhisat2
21562 (package
21563 (name "r-rhisat2")
21564 (version "1.28.0")
21565 (source
21566 (origin
21567 (method url-fetch)
21568 (uri (bioconductor-uri "Rhisat2" version))
21569 (sha256
21570 (base32
21571 "04095x4yh1fj3hs1vk6bc2qrcqc8xib61dsjz55gj69igj3xp0ks"))))
21572 (properties `((upstream-name . "Rhisat2")))
21573 (build-system r-build-system)
21574 (arguments
21575 `(#:phases
21576 (modify-phases %standard-phases
21577 (add-after 'unpack 'make-reproducible
21578 (lambda _
21579 (substitute* "src/Makefile"
21580 (("`hostname`") "guix")
21581 (("`date`") "0")
21582 ;; Avoid shelling out to "which".
21583 (("^CC =.*") (which "gcc"))
21584 (("^CPP =.*") (which "g++")))
21585 #t)))))
21586 (propagated-inputs
21587 (list r-genomicranges r-sgseq r-txdbmaker))
21588 (native-inputs
21589 (list r-knitr r-testthat))
21590 (home-page "https://github.com/fmicompbio/Rhisat2")
21591 (synopsis "R Wrapper for HISAT2 sequence aligner")
21592 (description
21593 "This package provides an R interface to the HISAT2 spliced short-read
21594aligner by Kim et al. (2015). The package contains wrapper functions to
21595create a genome index and to perform the read alignment to the generated
21596index.")
21597 (license license:gpl3)))
21598
21599(define-public r-quasr
21600 (package
21601 (name "r-quasr")
21602 (version "1.52.0")
21603 (source
21604 (origin
21605 (method url-fetch)
21606 (uri (bioconductor-uri "QuasR" version))
21607 (sha256
21608 (base32
21609 "08n28mniyf6g4f6r4vz2jh3lq84kkc0b38f2kri2dqb4yww6r6cd"))))
21610 (properties
21611 `((upstream-name . "QuasR")
21612 (updater-extra-native-inputs . ("r-rhisat2"))))
21613 (build-system r-build-system)
21614 (propagated-inputs
21615 (list r-annotationdbi
21616 r-biobase
21617 r-biocgenerics
21618 r-biocparallel
21619 r-biostrings
21620 r-bsgenome
21621 r-genomicfeatures
21622 r-genomicfiles
21623 r-genomicranges
21624 r-iranges
21625 r-rbowtie
21626 r-rhtslib
21627 r-rsamtools
21628 r-rtracklayer
21629 r-s4vectors
21630 r-seqinfo
21631 r-shortread
21632 r-txdbmaker))
21633 (native-inputs
21634 (list r-genomicalignments r-knitr r-rhisat2 r-testthat))
21635 (home-page "https://bioconductor.org/packages/QuasR/")
21636 (synopsis "Quantify and annotate short reads in R")
21637 (description
21638 "This package provides a framework for the quantification and analysis of
21639short genomic reads. It covers a complete workflow starting from raw sequence
21640reads, over creation of alignments and quality control plots, to the
21641quantification of genomic regions of interest.")
21642 (license license:gpl2)))
21643
21644(define-public r-rqc
21645 (package
21646 (name "r-rqc")
21647 (version "1.46.0")
21648 (source
21649 (origin
21650 (method url-fetch)
21651 (uri (bioconductor-uri "Rqc" version))
21652 (sha256
21653 (base32
21654 "01wlqcqhy87sc4088cg38afb3m9my454i9sjkv0czk2bvps7007m"))))
21655 (properties `((upstream-name . "Rqc")))
21656 (build-system r-build-system)
21657 (propagated-inputs
21658 (list r-biocgenerics
21659 r-biocparallel
21660 r-biocstyle
21661 r-biostrings
21662 r-biovizbase
21663 r-genomicalignments
21664 r-genomicfiles
21665 r-ggplot2
21666 r-iranges
21667 r-knitr
21668 r-markdown
21669 r-plyr
21670 r-rcpp
21671 r-reshape2
21672 r-rsamtools
21673 r-s4vectors
21674 r-shiny
21675 r-shortread))
21676 (native-inputs
21677 (list r-knitr r-testthat))
21678 (home-page "https://github.com/labbcb/Rqc")
21679 (synopsis "Quality control tool for high-throughput sequencing data")
21680 (description
21681 "Rqc is an optimized tool designed for quality control and assessment of
21682high-throughput sequencing data. It performs parallel processing of entire
21683files and produces a report which contains a set of high-resolution
21684graphics.")
21685 (license license:gpl2+)))
21686
21687(define-public r-birewire
21688 (package
21689 (name "r-birewire")
21690 (version "3.41.0")
21691 (source
21692 (origin
21693 (method url-fetch)
21694 (uri (bioconductor-uri "BiRewire" version))
21695 (sha256
21696 (base32
21697 "18ckdn0ls29z7i51k6ilnd4d65ci33zcy9lidmr34djyjh732b4v"))))
21698 (properties `((upstream-name . "BiRewire")))
21699 (build-system r-build-system)
21700 ;; Vignettes cannot be built:
21701 ;; Error in mde(x) : 'list' object cannot be coerced to type 'double'
21702 (arguments (list #:test-types '(list "tests")))
21703 (propagated-inputs
21704 (list r-igraph r-matrix r-rtsne r-slam))
21705 (native-inputs (list r-biocgenerics r-runit))
21706 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
21707 (synopsis "Tools for randomization of bipartite graphs")
21708 (description
21709 "This package provides functions for bipartite network rewiring through N
21710consecutive switching steps and for the computation of the minimal number of
21711switching steps to be performed in order to maximise the dissimilarity with
21712respect to the original network. It includes functions for the analysis of
21713the introduced randomness across the switching steps and several other
21714routines to analyse the resulting networks and their natural projections.")
21715 (license license:gpl3)))
21716
21717(define-public r-birta
21718 (package
21719 (name "r-birta")
21720 (version "1.31.0")
21721 (source
21722 (origin
21723 (method url-fetch)
21724 (uri (bioconductor-uri "birta" version))
21725 (sha256
21726 (base32
21727 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
21728 (build-system r-build-system)
21729 (propagated-inputs
21730 (list r-biobase r-limma r-mass))
21731 (home-page "https://bioconductor.org/packages/birta")
21732 (synopsis "Bayesian inference of regulation of transcriptional activity")
21733 (description
21734 "Expression levels of mRNA molecules are regulated by different
21735processes, comprising inhibition or activation by transcription factors and
21736post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
21737Inference of Regulation of Transcriptional Activity) uses the regulatory
21738networks of transcription factors and miRNAs together with mRNA and miRNA
21739expression data to predict switches in regulatory activity between two
21740conditions. A Bayesian network is used to model the regulatory structure and
21741Markov-Chain-Monte-Carlo is applied to sample the activity states.")
21742 (license license:gpl2+)))
21743
21744(define-public r-multidataset
21745 (package
21746 (name "r-multidataset")
21747 (version "1.40.0")
21748 (source
21749 (origin
21750 (method url-fetch)
21751 (uri (bioconductor-uri "MultiDataSet" version))
21752 (sha256
21753 (base32
21754 "1cs6l8aad7a40q6qkdwrnw5crhwc7i3jghs7spiccvy5lzr9vrk6"))))
21755 (properties `((upstream-name . "MultiDataSet")))
21756 (build-system r-build-system)
21757 (propagated-inputs
21758 (list r-biobase
21759 r-biocgenerics
21760 r-genomicranges
21761 r-ggplot2
21762 r-ggrepel
21763 r-iranges
21764 r-limma
21765 r-qqman
21766 r-s4vectors
21767 r-summarizedexperiment))
21768 (native-inputs
21769 (list r-knitr))
21770 (home-page "https://bioconductor.org/packages/MultiDataSet/")
21771 (synopsis "Implementation of MultiDataSet and ResultSet")
21772 (description
21773 "This package provides an implementation of the BRGE's (Bioinformatic
21774Research Group in Epidemiology from Center for Research in Environmental
21775Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
21776integrating multi omics data sets and ResultSet is a container for omics
21777results. This package contains base classes for MEAL and rexposome
21778packages.")
21779 (license license:expat)))
21780
21781(define-public r-ropls
21782 (package
21783 (name "r-ropls")
21784 (version "1.44.0")
21785 (source
21786 (origin
21787 (method url-fetch)
21788 (uri (bioconductor-uri "ropls" version))
21789 (sha256
21790 (base32
21791 "0087c5k0ma2czxzjh01qgykr7gklh0zb28bgxkn19q5n0yrig276"))))
21792 (build-system r-build-system)
21793 (propagated-inputs
21794 (list r-biobase
21795 r-ggplot2
21796 r-multiassayexperiment
21797 r-multidataset
21798 r-plotly
21799 r-summarizedexperiment))
21800 (native-inputs
21801 (list r-knitr r-testthat)) ; for vignettes
21802 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
21803 (synopsis "Multivariate analysis and feature selection of omics data")
21804 (description
21805 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
21806and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
21807regression, classification, and feature selection of omics data where the
21808number of variables exceeds the number of samples and with multicollinearity
21809among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
21810separately model the variation correlated (predictive) to the factor of
21811interest and the uncorrelated (orthogonal) variation. While performing
21812similarly to PLS, OPLS facilitates interpretation.
21813
21814This package provides imlementations of PCA, PLS, and OPLS for multivariate
21815analysis and feature selection of omics data. In addition to scores, loadings
21816and weights plots, the package provides metrics and graphics to determine the
21817optimal number of components (e.g. with the R2 and Q2 coefficients), check the
21818validity of the model by permutation testing, detect outliers, and perform
21819feature selection (e.g. with Variable Importance in Projection or regression
21820coefficients).")
21821 (license license:cecill)))
21822
21823(define-public r-biosigner
21824 (package
21825 (name "r-biosigner")
21826 (version "1.40.0")
21827 (source
21828 (origin
21829 (method url-fetch)
21830 (uri (bioconductor-uri "biosigner" version))
21831 (sha256
21832 (base32
21833 "10b9rn5awva9g6jy261n8vkb8iand3cds9dmqn8zhcr7zn9h3290"))))
21834 (build-system r-build-system)
21835 (propagated-inputs
21836 (list r-biobase
21837 r-e1071
21838 r-multiassayexperiment
21839 r-multidataset
21840 r-randomforest
21841 r-ropls
21842 r-summarizedexperiment))
21843 (native-inputs
21844 (list r-knitr r-testthat))
21845 (home-page "https://bioconductor.org/packages/biosigner/")
21846 (synopsis "Signature discovery from omics data")
21847 (description
21848 "Feature selection is critical in omics data analysis to extract
21849restricted and meaningful molecular signatures from complex and high-dimension
21850data, and to build robust classifiers. This package implements a method to
21851assess the relevance of the variables for the prediction performances of the
21852classifier. The approach can be run in parallel with the PLS-DA, Random
21853Forest, and SVM binary classifiers. The signatures and the corresponding
21854'restricted' models are returned, enabling future predictions on new
21855datasets.")
21856 (license license:cecill)))
21857
21858(define-public r-annotatr
21859 (package
21860 (name "r-annotatr")
21861 (version "1.38.0")
21862 (source
21863 (origin
21864 (method url-fetch)
21865 (uri (bioconductor-uri "annotatr" version))
21866 (sha256
21867 (base32
21868 "0j85hy1b6cj8kxcpdmbcdvllsbxiywax95j8j9cmsm8x4yh5v768"))))
21869 (build-system r-build-system)
21870 ;; 5 tests need internet access.
21871 (arguments (list #:tests? #false))
21872 (propagated-inputs
21873 (list r-annotationdbi
21874 r-annotationhub
21875 r-dplyr
21876 r-genomicfeatures
21877 r-genomicranges
21878 r-ggplot2
21879 r-iranges
21880 r-readr
21881 r-regioner
21882 r-reshape2
21883 r-rlang
21884 r-rtracklayer
21885 r-s4vectors
21886 r-seqinfo))
21887 (native-inputs
21888 (list r-knitr r-testthat))
21889 (home-page "https://bioconductor.org/packages/annotatr/")
21890 (synopsis "Annotation of genomic regions to genomic annotations")
21891 (description
21892 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
21893differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
21894to investigate the intersecting genomic annotations. Such annotations include
21895those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
21896CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
21897enhancers. The annotatr package provides an easy way to summarize and
21898visualize the intersection of genomic sites/regions with genomic
21899annotations.")
21900 (license license:gpl3)))
21901
21902(define-public r-rsubread
21903 (package
21904 (name "r-rsubread")
21905 (version "2.26.0")
21906 (source
21907 (origin
21908 (method url-fetch)
21909 (uri (bioconductor-uri "Rsubread" version))
21910 (sha256
21911 (base32
21912 "0j8yvsayjf3li9yzarxpnxl12y9nj7c3amqkzahm2chv27yc09wa"))))
21913 (properties `((upstream-name . "Rsubread")))
21914 (build-system r-build-system)
21915 (inputs (list zlib))
21916 (propagated-inputs
21917 (list r-matrix))
21918 (home-page "https://bioconductor.org/packages/Rsubread/")
21919 (synopsis "Subread sequence alignment and counting for R")
21920 (description
21921 "This package provides tools for alignment, quantification and analysis
21922of second and third generation sequencing data. It includes functionality for
21923read mapping, read counting, SNP calling, structural variant detection and
21924gene fusion discovery. It can be applied to all major sequencing techologies
21925and to both short and long sequence reads.")
21926 (license license:gpl3)))
21927
21928(define-public r-flames
21929 (package
21930 (name "r-flames")
21931 (version "2.6.0")
21932 (source
21933 (origin
21934 (method url-fetch)
21935 (uri (bioconductor-uri "FLAMES" version))
21936 (sha256
21937 (base32 "081f52cs92slr4b644dgpyy2b0rkiggygvpnfvz16yv2cyvd715h"))
21938 (modules '((guix build utils)))
21939 (snippet
21940 '(delete-file-recursively "src/submodule/minimap2"))))
21941 (properties `((upstream-name . "FLAMES")))
21942 (build-system r-build-system)
21943 (arguments
21944 (list
21945 #:skipped-tests
21946 ;; These tests expect the optional oarfish to be installed.
21947 '("test-run_FLAMES.R")
21948 #:phases
21949 '(modify-phases %standard-phases
21950 (add-after 'unpack 'do-not-build-minimap2
21951 (lambda _
21952 (substitute* "src/Makevars"
21953 (("all: strippedLib ../inst/bin/minimap2 ../inst/bin/oarfish")
21954 "all: strippedLib"))))
21955 (add-after 'unpack 'fix-build-system
21956 (lambda _
21957 ;; One target uses & instead of &&, which leads to a command
21958 ;; being run despite the check failing.
21959 (substitute* "src/Makevars"
21960 ((" & ") " && ")))))))
21961 (inputs
21962 (list minimap2 zlib))
21963 (propagated-inputs
21964 (list r-abind
21965 r-bambu
21966 r-basilisk
21967 r-biocgenerics
21968 r-biocparallel
21969 r-biostrings
21970 r-circlize
21971 r-cli
21972 r-complexheatmap
21973 r-cowplot
21974 r-crew
21975 r-dplyr
21976 r-genomicalignments
21977 r-genomicfeatures
21978 r-genomicranges
21979 r-ggplot2
21980 r-gridextra
21981 r-igraph
21982 r-iranges
21983 r-jsonlite
21984 r-magick
21985 r-magrittr
21986 r-matrix
21987 r-matrixgenerics
21988 r-r-utils
21989 r-rcolorbrewer
21990 r-rcpp
21991 r-readr
21992 r-reticulate
21993 r-rhtslib
21994 r-rsamtools
21995 r-rtracklayer
21996 r-s4arrays
21997 r-s4vectors
21998 r-scater
21999 r-scatterpie
22000 r-scran
22001 r-scrapper
22002 r-scuttle
22003 r-seqinfo
22004 r-shortread
22005 r-singlecellexperiment
22006 r-spatialexperiment
22007 r-stringr
22008 r-summarizedexperiment
22009 r-testthat
22010 r-tibble
22011 r-tidyr
22012 r-tidyselect
22013 r-withr))
22014 (native-inputs (list r-knitr which))
22015 (home-page "https://github.com/OliverVoogd/FLAMES")
22016 (synopsis
22017 "Full Length Analysis of Mutations and Splicing in long read RNA-seq data")
22018 (description
22019 "This is a package for semi-supervised isoform detection and annotation
22020from both bulk and single-cell long read RNA-seq data. Flames provides
22021automated pipelines for analysing isoforms, as well as intermediate functions
22022for manual execution.")
22023 (license license:gpl2+)))
22024
22025(define-public r-flowai
22026 (package
22027 (name "r-flowai")
22028 (version "1.42.0")
22029 (source (origin
22030 (method url-fetch)
22031 (uri (bioconductor-uri "flowAI" version))
22032 (sha256
22033 (base32
22034 "0zjrgvsb06zcbf8nabzg71f54c9gjzcv50xdnws16zhq5gd6wzs4"))))
22035 (properties `((upstream-name . "flowAI")))
22036 (build-system r-build-system)
22037 (propagated-inputs
22038 (list r-changepoint
22039 r-flowcore
22040 r-ggplot2
22041 r-knitr
22042 r-plyr
22043 r-rcolorbrewer
22044 r-reshape2
22045 r-rmarkdown
22046 r-scales))
22047 (native-inputs (list r-knitr))
22048 (home-page "https://bioconductor.org/packages/flowAI")
22049 (synopsis
22050 "Automatic and interactive quality control for flow cytometry data")
22051 (description
22052 "This package is able to perform an automatic or interactive quality
22053control on FCS data acquired using flow cytometry instruments. By evaluating
22054three different properties:
22055
22056@enumerate
22057@item flow rate
22058@item signal acquisition, and
22059@item dynamic range,
22060@end enumerate
22061
22062the quality control enables the detection and removal of anomalies.")
22063 (license license:gpl2+)))
22064
22065(define-public r-flowutils
22066 (package
22067 (name "r-flowutils")
22068 (version "1.59.0")
22069 (source
22070 (origin
22071 (method url-fetch)
22072 (uri (bioconductor-uri "flowUtils" version))
22073 (sha256
22074 (base32
22075 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
22076 (properties `((upstream-name . "flowUtils")))
22077 (build-system r-build-system)
22078 (propagated-inputs
22079 (list r-biobase
22080 r-corpcor
22081 r-flowcore
22082 r-graph
22083 r-runit
22084 r-xml))
22085 (home-page "https://github.com/jspidlen/flowUtils")
22086 (synopsis "Utilities for flow cytometry")
22087 (description
22088 "This package provides utilities for flow cytometry data.")
22089 (license license:artistic2.0)))
22090
22091(define-public r-consensusclusterplus
22092 (package
22093 (name "r-consensusclusterplus")
22094 (version "1.76.0")
22095 (source
22096 (origin
22097 (method url-fetch)
22098 (uri (bioconductor-uri "ConsensusClusterPlus" version))
22099 (sha256
22100 (base32
22101 "06wdqpy0kk8jflbmzr6wv2ccfbkvpxrrh134dhw02hm39sxbccml"))))
22102 (properties
22103 `((upstream-name . "ConsensusClusterPlus")))
22104 (build-system r-build-system)
22105 (propagated-inputs
22106 (list r-all r-biobase r-cluster))
22107 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
22108 (synopsis "Clustering algorithm")
22109 (description
22110 "This package provides an implementation of an algorithm for determining
22111cluster count and membership by stability evidence in unsupervised analysis.")
22112 (license license:gpl2)))
22113
22114;; This is the latest commit and it solves a bug from the latest release.
22115(define-public r-cycombine
22116 (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1"))
22117 (package
22118 (name "r-cycombine")
22119 (version (git-version "0.2.6" revision commit))
22120 (source (origin
22121 (method git-fetch)
22122 (uri (git-reference
22123 (url "https://github.com/biosurf/cyCombine")
22124 (commit commit)))
22125 (file-name (git-file-name name version))
22126 (sha256
22127 (base32
22128 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm"))))
22129 (properties `((upstream-name . "cyCombine")))
22130 (build-system r-build-system)
22131 (propagated-inputs
22132 (list r-biobase
22133 r-cytolib
22134 r-dplyr
22135 r-flowcore
22136 r-ggplot2
22137 r-knitr
22138 r-kohonen
22139 r-magrittr
22140 r-purrr
22141 r-rcolorbrewer
22142 r-readr
22143 r-readxl
22144 r-stringr
22145 r-sva
22146 r-tibble
22147 r-tidyr))
22148 (native-inputs (list r-knitr r-testthat))
22149 (home-page "https://github.com/biosurf/cyCombine")
22150 (synopsis "Integration of single-cell cytometry datasets")
22151 (description
22152 "This package provides a method for combining single-cell cytometry
22153datasets, which increases the analytical flexibility and the statistical power
22154of the analyses while minimizing technical noise.")
22155 (license license:expat))))
22156
22157;; This package bundles a version of Boost. We cannot use the latest version
22158;; of Boost here, as we also need to make sure that the BH (r-bh) package is
22159;; compatible with whatever this package bundles.
22160(define-public r-cytolib
22161 (package
22162 (name "r-cytolib")
22163 (version "2.24.0")
22164 (source
22165 (origin
22166 (method url-fetch)
22167 (uri (bioconductor-uri "cytolib" version))
22168 (sha256
22169 (base32
22170 "14vsd62mr2gyxg3k02pwnrxb8y98bscl59wvhhwpn395khvkapzp"))))
22171 (properties `((upstream-name . "cytolib")))
22172 (build-system r-build-system)
22173 (native-inputs
22174 (list r-knitr))
22175 (propagated-inputs
22176 (list r-bh r-rhdf5lib r-rprotobuflib))
22177 (home-page "https://bioconductor.org/packages/cytolib/")
22178 (synopsis "C++ infrastructure for working with gated cytometry")
22179 (description
22180 "This package provides the core data structure and API to represent and
22181interact with gated cytometry data.")
22182 (license license:artistic2.0)))
22183
22184(define-public r-flowcore
22185 (package
22186 (name "r-flowcore")
22187 (version "2.24.0")
22188 (source
22189 (origin
22190 (method url-fetch)
22191 (uri (bioconductor-uri "flowCore" version))
22192 (sha256
22193 (base32
22194 "01r7rgxlfzh9dqb71mqsssl2xyq3d2y4nx5cg3vkb5b5xb6hcacy"))))
22195 (properties
22196 '((upstream-name . "flowCore")
22197 (updater-ignored-native-inputs
22198 . ("r-flowstats"
22199 "r-flowworkspace"
22200 "r-ggcyto"))))
22201 (build-system r-build-system)
22202 ;; Tests need r-flowstats, which depends on this package
22203 (arguments
22204 (list
22205 #:tests? #false
22206 #:phases
22207 '(modify-phases %standard-phases
22208 (add-after 'unpack 'R-4.6.0-compatibility
22209 (lambda _
22210 (substitute* "src/Makevars"
22211 (("^PKG_LIBS.*") "\
22212RHDF5_LIBS= $(shell echo 'Rhdf5lib::pkgconfig(\"PKG_CXX_LIBS\")'|\
22213 \"${R_HOME}/bin/R\" --vanilla --slave)
22214
22215PKG_LIBS = `${R_HOME}/bin/Rscript -e \"cytolib:::cytolib_LdFlags()\"` $(RHDF5_LIBS)")))))))
22216 (propagated-inputs
22217 (list r-bh
22218 r-biobase
22219 r-biocgenerics
22220 r-cpp11
22221 r-cytolib
22222 r-matrixstats
22223 r-rcpp
22224 r-rprotobuflib
22225 r-s4vectors))
22226 (native-inputs
22227 (list r-devtools
22228 r-gridextra
22229 r-knitr
22230 r-testthat))
22231 (home-page "https://bioconductor.org/packages/flowCore")
22232 (synopsis "Basic structures for flow cytometry data")
22233 (description
22234 "This package provides S4 data structures and basic functions to deal
22235with flow cytometry data.")
22236 (license license:artistic2.0)))
22237
22238(define-public r-flowmeans
22239 (package
22240 (name "r-flowmeans")
22241 (version "1.72.0")
22242 (source
22243 (origin
22244 (method url-fetch)
22245 (uri (bioconductor-uri "flowMeans" version))
22246 (sha256
22247 (base32
22248 "0pdkksrqvnjk22kr2zplnicwqikm2yjg3alxvajpa7j5an2shfri"))))
22249 (properties `((upstream-name . "flowMeans")))
22250 (build-system r-build-system)
22251 (propagated-inputs
22252 (list r-biobase r-feature r-flowcore r-rrcov))
22253 (home-page "https://bioconductor.org/packages/flowMeans")
22254 (synopsis "Non-parametric flow cytometry data gating")
22255 (description
22256 "This package provides tools to identify cell populations in Flow
22257Cytometry data using non-parametric clustering and segmented-regression-based
22258change point detection.")
22259 (license license:artistic2.0)))
22260
22261(define-public r-ncdfflow
22262 (package
22263 (name "r-ncdfflow")
22264 (version "2.58.0")
22265 (source
22266 (origin
22267 (method url-fetch)
22268 (uri (bioconductor-uri "ncdfFlow" version))
22269 (sha256
22270 (base32
22271 "08prn22idh4a2r2yc99p9ba7fqhw9if6v9wb0i7mvmcnvm2ks51j"))))
22272 (properties
22273 `((upstream-name . "ncdfFlow")
22274 ;; Avoid dependency cycle.
22275 (updater-ignored-native-inputs . ("r-flowstats"))))
22276 (build-system r-build-system)
22277 (propagated-inputs
22278 (list r-bh
22279 r-biobase
22280 r-biocgenerics
22281 r-cpp11
22282 r-flowcore
22283 r-rhdf5lib))
22284 (native-inputs
22285 (list r-devtools r-knitr r-testthat))
22286 (home-page "https://bioconductor.org/packages/ncdfFlow/")
22287 (synopsis "HDF5 based storage for flow cytometry data")
22288 (description
22289 "This package provides HDF5 storage based methods and functions for
22290manipulation of flow cytometry data.")
22291 (license license:artistic2.0)))
22292
22293(define-public r-ggcyto
22294 (package
22295 (name "r-ggcyto")
22296 (version "1.40.0")
22297 (source
22298 (origin
22299 (method url-fetch)
22300 (uri (bioconductor-uri "ggcyto" version))
22301 (sha256
22302 (base32
22303 "15v4k4f08pcq0j3ab0zkp1v1b2r4rf0lh848vbx3bpkk1lnrbivk"))))
22304 (properties
22305 `((upstream-name . "ggcyto")
22306 ;; Avoid dependency cycle.
22307 (updater-ignored-native-inputs . ("r-flowstats"))
22308 (updater-extra-native-inputs . ("r-flowworkspacedata"))))
22309 (build-system r-build-system)
22310 (propagated-inputs
22311 (list r-data-table
22312 r-flowcore
22313 r-flowworkspace
22314 r-ggplot2
22315 r-gridextra
22316 r-hexbin
22317 r-ncdfflow
22318 r-plyr
22319 r-rcolorbrewer
22320 r-rlang
22321 r-scales))
22322 (native-inputs
22323 (list r-flowworkspacedata r-knitr r-opencyto r-testthat r-vdiffr))
22324 (home-page "https://github.com/RGLab/ggcyto/issues")
22325 (synopsis "Visualize Cytometry data with ggplot")
22326 (description
22327 "With the dedicated fortify method implemented for @code{flowSet},
22328@code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
22329cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
22330and some custom layers also make it easy to add gates and population
22331statistics to the plot.")
22332 (license license:artistic2.0)))
22333
22334(define-public r-flowviz
22335 (package
22336 (name "r-flowviz")
22337 (version "1.76.0")
22338 (source
22339 (origin
22340 (method url-fetch)
22341 (uri (bioconductor-uri "flowViz" version))
22342 (sha256
22343 (base32
22344 "0102nmzh6cnr7v8av2gpj2z9276c427v2qfh5jrs3w1jh0z6948s"))))
22345 (properties
22346 `((upstream-name . "flowViz")
22347 ;; Avoid dependency cycle.
22348 (updater-ignored-native-inputs . ("r-flowstats"))))
22349 (build-system r-build-system)
22350 ;; There is only one test file and it depends on r-flowstats, which
22351 ;; depends on this package.
22352 (arguments (list #:tests? #false))
22353 (propagated-inputs
22354 (list r-biobase
22355 r-flowcore
22356 r-hexbin
22357 r-idpmisc
22358 r-kernsmooth
22359 r-lattice
22360 r-latticeextra
22361 r-mass
22362 r-rcolorbrewer))
22363 (native-inputs
22364 (list r-knitr r-ncdfflow r-testthat))
22365 (home-page "https://bioconductor.org/packages/flowViz/")
22366 (synopsis "Visualization for flow cytometry")
22367 (description
22368 "This package provides visualization tools for flow cytometry data.")
22369 (license license:artistic2.0)))
22370
22371(define-public r-flowclust
22372 (package
22373 (name "r-flowclust")
22374 (version "3.50.0")
22375 (source
22376 (origin
22377 (method url-fetch)
22378 (uri (bioconductor-uri "flowClust" version))
22379 (sha256
22380 (base32
22381 "1kk4gfwagn4kjldg3ffj4ns6j32b73m35zxrss1rmab9wbx93fnf"))))
22382 (properties
22383 `((upstream-name . "flowClust")
22384 ;; Avoid dependency cycle.
22385 (updater-ignored-native-inputs . ("r-opencyto"))))
22386 (build-system r-build-system)
22387 (arguments
22388 (list
22389 #:configure-flags
22390 '(list "--configure-args=--enable-bundled-gsl=no")
22391 #:skipped-tests
22392 ;; "argument is of length zero"
22393 '("test_1d_gated_data.R"
22394 ;; This test eventually times out.
22395 ("test_1d.R" "flowClust:SSH-H, 1 mode")
22396 ;; "invalid subscript type 'list'"
22397 "test_2d.R")))
22398 (propagated-inputs
22399 (list r-biobase
22400 r-biocgenerics
22401 r-flowcore
22402 r-graph))
22403 (inputs (list gsl))
22404 (native-inputs
22405 (list pkg-config
22406 r-devtools
22407 r-ellipse
22408 r-flowworkspace
22409 r-knitr
22410 r-testthat))
22411 (home-page "https://bioconductor.org/packages/flowClust")
22412 (synopsis "Clustering for flow cytometry")
22413 (description
22414 "This package provides robust model-based clustering using a t-mixture
22415model with Box-Cox transformation.")
22416 (license license:artistic2.0)))
22417
22418;; TODO: this package bundles an old version of protobuf. It's not easy to
22419;; make it use our protobuf package instead.
22420(define-public r-rprotobuflib
22421 (package
22422 (name "r-rprotobuflib")
22423 (version "2.24.0")
22424 (source
22425 (origin
22426 (method url-fetch)
22427 (uri (bioconductor-uri "RProtoBufLib" version))
22428 (sha256
22429 (base32
22430 "1m23cyp12w0d7k4sva8xcy0k3zssgkgfk8xxrs6vymnmk4ma1mns"))))
22431 (properties `((upstream-name . "RProtoBufLib")))
22432 (build-system r-build-system)
22433 (arguments
22434 `(#:phases
22435 (modify-phases %standard-phases
22436 (add-after 'unpack 'unpack-bundled-sources
22437 (lambda _
22438 (with-directory-excursion "src"
22439 (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
22440 (native-inputs
22441 (list r-knitr))
22442 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
22443 (synopsis "C++ headers and static libraries of Protocol buffers")
22444 (description
22445 "This package provides the headers and static library of Protocol buffers
22446for other R packages to compile and link against.")
22447 (license license:bsd-3)))
22448
22449(define-public r-flowworkspace
22450 (package
22451 (name "r-flowworkspace")
22452 (version "4.24.0")
22453 (source
22454 (origin
22455 (method url-fetch)
22456 (uri (bioconductor-uri "flowWorkspace" version))
22457 (sha256
22458 (base32
22459 "1g0kdql245nmk7mry9kbg2kg3wpmhqcr94j9gdmpdf2x3hmv9n6k"))))
22460 (properties
22461 `((upstream-name . "flowWorkspace")
22462 ;; Avoid dependency cycles.
22463 (updater-ignored-native-inputs . ("r-cytoml" "r-opencyto"))))
22464 (build-system r-build-system)
22465 ;; Tests fail with: 'NA' is not a valid file
22466 (arguments (list #:tests? #false))
22467 (propagated-inputs
22468 (list r-bh
22469 r-biobase
22470 r-biocgenerics
22471 r-cpp11
22472 r-cytolib
22473 r-data-table
22474 r-delayedarray
22475 r-dplyr
22476 r-flowcore
22477 r-ggplot2
22478 r-graph
22479 r-matrixstats
22480 r-ncdfflow
22481 r-rbgl
22482 r-rgraphviz
22483 r-rhdf5lib
22484 r-rprotobuflib
22485 r-s4vectors
22486 r-scales
22487 r-xml))
22488 (native-inputs
22489 (list r-digest r-knitr r-testthat))
22490 (home-page "https://bioconductor.org/packages/flowWorkspace/")
22491 (synopsis "Infrastructure for working with cytometry data")
22492 (description
22493 "This package is designed to facilitate comparison of automated gating
22494methods against manual gating done in flowJo. This package allows you to
22495import basic flowJo workspaces into BioConductor and replicate the gating from
22496flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
22497samples, compensation, and transformation are performed so that the output
22498matches the flowJo analysis.")
22499 (license license:artistic2.0)))
22500
22501(define-public r-flowstats
22502 (package
22503 (name "r-flowstats")
22504 (version "4.24.0")
22505 (source
22506 (origin
22507 (method url-fetch)
22508 (uri (bioconductor-uri "flowStats" version))
22509 (sha256
22510 (base32
22511 "0qfn4m7qvf0d8swy22namavrf9x6kpqcamvqikhi8f1h533fnvga"))))
22512 (properties `((upstream-name . "flowStats")))
22513 (build-system r-build-system)
22514 (propagated-inputs
22515 (list r-biobase
22516 r-biocgenerics
22517 r-clue
22518 r-cluster
22519 r-corpcor
22520 r-fda
22521 r-flowcore
22522 r-flowviz
22523 r-flowworkspace
22524 r-kernsmooth
22525 r-ks
22526 r-lattice
22527 r-mass
22528 r-mnormt
22529 r-ncdfflow
22530 r-rcolorbrewer
22531 r-rrcov))
22532 (native-inputs (list r-devtools
22533 r-ggcyto
22534 r-ggridges
22535 r-gridextra
22536 r-opencyto
22537 r-scales
22538 r-testthat
22539 r-xtable))
22540 (home-page "http://www.github.com/RGLab/flowStats")
22541 (synopsis "Statistical methods for the analysis of flow cytometry data")
22542 (description
22543 "This package provides methods and functionality to analyze flow data
22544that is beyond the basic infrastructure provided by the @code{flowCore}
22545package.")
22546 (license license:artistic2.0)))
22547
22548(define-public r-opencyto
22549 (package
22550 (name "r-opencyto")
22551 (version "2.24.0")
22552 (source
22553 (origin
22554 (method url-fetch)
22555 (uri (bioconductor-uri "openCyto" version))
22556 (sha256
22557 (base32
22558 "0bm916paq8jkzf0bw4r3rb0fink7n3c2wjn5ik0si5kk6lyq23vy"))))
22559 (properties
22560 `((upstream-name . "openCyto")
22561 (updater-extra-native-inputs . ("r-flowworkspacedata"))
22562 (updater-ignored-native-inputs . ("r-flowstats"))))
22563 (build-system r-build-system)
22564 (propagated-inputs
22565 (list r-bh
22566 r-biobase
22567 r-biocgenerics
22568 r-cpp11
22569 r-data-table
22570 r-flowclust
22571 r-flowcore
22572 r-flowviz
22573 r-flowworkspace
22574 r-graph
22575 r-ncdfflow
22576 r-rbgl
22577 r-rcolorbrewer))
22578 (native-inputs
22579 (list r-flowworkspacedata r-knitr r-mass r-testthat))
22580 (home-page "https://bioconductor.org/packages/openCyto")
22581 (synopsis "Hierarchical gating pipeline for flow cytometry data")
22582 (description
22583 "This package is designed to facilitate the automated gating methods in a
22584sequential way to mimic the manual gating strategy.")
22585 (license license:artistic2.0)))
22586
22587(define-public r-cytoml
22588 (package
22589 (name "r-cytoml")
22590 (version "2.24.0")
22591 (source
22592 (origin
22593 (method url-fetch)
22594 (uri (bioconductor-uri "CytoML" version))
22595 (sha256
22596 (base32
22597 "1mvb8r47q87p7mj5v0zdm7yn8s0q372nhp2nacd67fjxl4vbgi46"))))
22598 (properties
22599 `((upstream-name . "CytoML")
22600 (updater-extra-native-inputs . ("r-flowworkspacedata"))
22601 (updater-ignored-native-inputs . ("r-cytoml-old"))))
22602 (build-system r-build-system)
22603 (inputs
22604 (list libxml2 zlib))
22605 (propagated-inputs
22606 (list r-bh
22607 r-biobase
22608 r-cpp11
22609 r-cytolib
22610 r-data-table
22611 r-dplyr
22612 r-flowcore
22613 r-flowworkspace
22614 r-ggcyto
22615 r-graph
22616 r-jsonlite
22617 r-opencyto
22618 r-rbgl
22619 r-rgraphviz
22620 r-rhdf5lib
22621 r-rprotobuflib
22622 r-tibble
22623 r-xml
22624 r-yaml))
22625 (native-inputs
22626 (list r-devtools
22627 r-flowclust
22628 r-flowstats
22629 r-flowworkspacedata
22630 r-knitr
22631 r-testthat))
22632 (home-page "https://github.com/RGLab/CytoML")
22633 (synopsis "GatingML interface for cross platform cytometry data sharing")
22634 (description
22635 "This package provides an interface to implementations of the GatingML2.0
22636standard to exchange gated cytometry data with other software platforms.")
22637 (license license:artistic2.0)))
22638
22639(define-public r-flowsom
22640 (package
22641 (name "r-flowsom")
22642 (version "2.20.0")
22643 (source
22644 (origin
22645 (method url-fetch)
22646 (uri (bioconductor-uri "FlowSOM" version))
22647 (sha256
22648 (base32
22649 "176mi6msrmqm8w1mdz8mn0f8wng5lw6583wwd8790dx4cvm2qlan"))))
22650 (properties `((upstream-name . "FlowSOM")))
22651 (build-system r-build-system)
22652 (propagated-inputs
22653 (list r-biocgenerics
22654 r-colorramps
22655 r-consensusclusterplus
22656 r-dplyr
22657 r-flowcore
22658 r-ggforce
22659 r-ggnewscale
22660 r-ggplot2
22661 r-ggpubr
22662 r-igraph
22663 r-magrittr
22664 r-rlang
22665 r-rtsne
22666 r-tidyr
22667 r-xml))
22668 (native-inputs (list r-biocmanager r-biocstyle r-flowworkspace))
22669 (home-page "https://bioconductor.org/packages/FlowSOM/")
22670 (synopsis "Visualize and interpret cytometry data")
22671 (description
22672 "FlowSOM offers visualization options for cytometry data, by using
22673self-organizing map clustering and minimal spanning trees.")
22674 (license license:gpl2+)))
22675
22676(define-public r-mixomics
22677 (package
22678 (name "r-mixomics")
22679 (version "6.36.0")
22680 (source
22681 (origin
22682 (method url-fetch)
22683 (uri (bioconductor-uri "mixOmics" version))
22684 (sha256
22685 (base32
22686 "1cyh85ny93nj8h1q7j3lv96awkvdmqcgq8qffy58y24jm13gfb33"))))
22687 (properties `((upstream-name . "mixOmics")))
22688 (build-system r-build-system)
22689 (propagated-inputs
22690 (list r-biocparallel
22691 r-corpcor
22692 r-dplyr
22693 r-ellipse
22694 r-ggplot2
22695 r-ggrepel
22696 r-gridextra
22697 r-igraph
22698 r-lattice
22699 r-mass
22700 r-matrixstats
22701 r-rarpack
22702 r-rcolorbrewer
22703 r-reshape2
22704 r-rgl
22705 r-rlang
22706 r-tidyr))
22707 (native-inputs
22708 (list r-knitr r-testthat r-vdiffr))
22709 (home-page "http://www.mixOmics.org")
22710 (synopsis "Multivariate methods for exploration of biological datasets")
22711 (description
22712 "mixOmics offers a wide range of multivariate methods for the exploration
22713and integration of biological datasets with a particular focus on variable
22714selection. The package proposes several sparse multivariate models we have
22715developed to identify the key variables that are highly correlated, and/or
22716explain the biological outcome of interest. The data that can be analysed
22717with mixOmics may come from high throughput sequencing technologies, such as
22718omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
22719also beyond the realm of omics (e.g. spectral imaging). The methods
22720implemented in mixOmics can also handle missing values without having to
22721delete entire rows with missing data.")
22722 (license license:gpl2+)))
22723
22724(define-public r-depecher
22725 (package ;Source/Weave error
22726 (name "r-depecher")
22727 (version "1.28.0")
22728 (source
22729 (origin
22730 (method url-fetch)
22731 (uri (bioconductor-uri "DepecheR" version))
22732 (sha256
22733 (base32
22734 "15nr1qmzsqilawrpyva47ixd4z9p7n5qq12l0pn851a5kn2m41vf"))))
22735 (properties `((upstream-name . "DepecheR")))
22736 (build-system r-build-system)
22737 (propagated-inputs
22738 (list r-beanplot
22739 r-clusterr
22740 r-collapse
22741 r-dosnow
22742 r-dplyr
22743 r-fnn
22744 r-foreach
22745 r-ggplot2
22746 r-gmodels
22747 r-gplots
22748 r-mass
22749 r-matrixstats
22750 r-mixomics
22751 r-moments
22752 r-rcpp
22753 r-rcppeigen
22754 r-reshape2
22755 r-robustbase
22756 r-viridis))
22757 (native-inputs
22758 (list r-knitr r-testthat))
22759 (home-page "https://bioconductor.org/packages/DepecheR/")
22760 (synopsis "Identify traits of clusters in high-dimensional entities")
22761 (description
22762 "The purpose of this package is to identify traits in a dataset that can
22763separate groups. This is done on two levels. First, clustering is performed,
22764using an implementation of sparse K-means. Secondly, the generated clusters
22765are used to predict outcomes of groups of individuals based on their
22766distribution of observations in the different clusters. As certain clusters
22767with separating information will be identified, and these clusters are defined
22768by a sparse number of variables, this method can reduce the complexity of
22769data, to only emphasize the data that actually matters.")
22770 (license license:expat)))
22771
22772(define-public r-rcistarget
22773 (package
22774 (name "r-rcistarget")
22775 (version "1.29.0")
22776 (source
22777 (origin
22778 (method url-fetch)
22779 (uri (bioconductor-uri "RcisTarget" version))
22780 (sha256
22781 (base32
22782 "0y028c8vrfcqy9ddn7p4y285bjb3hw5n1rwax4ggwbf18cfk1ql2"))))
22783 (properties
22784 '((upstream-name . "RcisTarget")
22785 (updater-extra-native-inputs
22786 . ("r-doparallel"))))
22787 (build-system r-build-system)
22788 (propagated-inputs
22789 (list r-arrow
22790 r-aucell
22791 r-biocgenerics
22792 r-data-table
22793 r-dplyr
22794 r-genomeinfodb
22795 r-genomicranges
22796 r-gseabase
22797 r-r-utils
22798 r-s4vectors
22799 r-summarizedexperiment
22800 r-tibble
22801 r-zoo))
22802 (native-inputs
22803 (list r-doparallel
22804 r-knitr
22805 r-rcistarget-hg19-motifdbs-cisbponly-500bp
22806 r-testthat))
22807 (home-page "https://aertslab.org/#scenic")
22808 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
22809 (description
22810 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
22811over-represented on a gene list. In a first step, RcisTarget selects DNA
22812motifs that are significantly over-represented in the surroundings of the
22813@dfn{transcription start site} (TSS) of the genes in the gene-set. This is
22814achieved by using a database that contains genome-wide cross-species rankings
22815for each motif. The motifs that are then annotated to TFs and those that have
22816a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
22817each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
22818genes in the gene-set that are ranked above the leading edge).")
22819 (license license:gpl3)))
22820
22821(define-public r-chicago
22822 (package
22823 (name "r-chicago")
22824 (version "1.40.0")
22825 (source
22826 (origin
22827 (method url-fetch)
22828 (uri (bioconductor-uri "Chicago" version))
22829 (sha256
22830 (base32
22831 "029kwb3grwfzl4v6h5kma3mdbj3gvyr5j2qnjyzlkaarvgwmdqs1"))))
22832 (properties `((upstream-name . "Chicago")))
22833 (build-system r-build-system)
22834 (propagated-inputs
22835 (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
22836 (native-inputs (list r-knitr r-testthat))
22837 (home-page "https://bioconductor.org/packages/Chicago")
22838 (synopsis "Capture Hi-C analysis of genomic organization")
22839 (description
22840 "This package provides a pipeline for analysing Capture Hi-C data.")
22841 (license license:artistic2.0)))
22842
22843;; This is a CRAN package, but it depends on Bioconductor packages, so we put
22844;; it here.
22845(define-public r-ciara
22846 (package
22847 (name "r-ciara")
22848 (version "0.1.0")
22849 (source (origin
22850 (method url-fetch)
22851 (uri (cran-uri "CIARA" version))
22852 (sha256
22853 (base32
22854 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf"))))
22855 (properties `((upstream-name . "CIARA")))
22856 (build-system r-build-system)
22857 (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr))
22858 (native-inputs (list r-knitr r-testthat))
22859 (home-page "https://cran.r-project.org/package=CIARA")
22860 (synopsis "Cluster-independent algorithm for rare cell types identification")
22861 (description
22862 "This is a package to support identification of markers of rare cell
22863types by looking at genes whose expression is confined in small regions of the
22864expression space.")
22865 (license license:artistic2.0)))
22866
22867(define-public r-cicero
22868 (package
22869 (name "r-cicero")
22870 (version "1.30.0")
22871 (source
22872 (origin
22873 (method url-fetch)
22874 (uri (bioconductor-uri "cicero" version))
22875 (sha256
22876 (base32
22877 "1x11zhq9sgsmxq777xxvnwbnr88vp062achpn2iswd4skxr5q6bv"))))
22878 (build-system r-build-system)
22879 (propagated-inputs
22880 (list r-assertthat
22881 r-biobase
22882 r-biocgenerics
22883 r-data-table
22884 r-dplyr
22885 r-fnn
22886 r-genomicranges
22887 r-ggplot2
22888 r-glasso
22889 r-gviz
22890 r-igraph
22891 r-iranges
22892 r-matrix
22893 r-monocle
22894 r-plyr
22895 r-reshape2
22896 r-s4vectors
22897 r-stringi
22898 r-stringr
22899 r-tibble
22900 r-tidyr
22901 r-vgam))
22902 (native-inputs
22903 (list r-knitr r-testthat r-vdiffr))
22904 (home-page "https://bioconductor.org/packages/cicero/")
22905 (synopsis "Predict cis-co-accessibility from single-cell data")
22906 (description
22907 "Cicero computes putative cis-regulatory maps from single-cell chromatin
22908accessibility data. It also extends the monocle package for use in chromatin
22909accessibility data.")
22910 (license license:expat)))
22911
22912(define-public r-circrnaprofiler
22913 (package
22914 (name "r-circrnaprofiler")
22915 (version "1.26.0")
22916 (source
22917 (origin
22918 (method url-fetch)
22919 (uri (bioconductor-uri "circRNAprofiler" version))
22920 (sha256
22921 (base32
22922 "0k2xagwvs90693hzwc00chrlhlymszkppyqckh3pljsns8vvh46m"))))
22923 (properties
22924 `((upstream-name . "circRNAprofiler")))
22925 (build-system r-build-system)
22926 (propagated-inputs
22927 (list r-annotationhub
22928 r-biostrings
22929 r-bsgenome
22930 r-bsgenome-hsapiens-ucsc-hg19
22931 r-deseq2
22932 r-dplyr
22933 r-edger
22934 r-genomeinfodb
22935 r-genomicranges
22936 r-ggplot2
22937 r-gwascat
22938 r-iranges
22939 r-magrittr
22940 r-r-utils
22941 r-readr
22942 r-reshape2
22943 r-rlang
22944 r-rtracklayer
22945 r-s4vectors
22946 r-seqinr
22947 r-stringi
22948 r-stringr
22949 r-universalmotif))
22950 (native-inputs
22951 (list r-knitr r-testthat))
22952 (home-page
22953 "https://github.com/Aufiero/circRNAprofiler")
22954 (synopsis
22955 "Computational framework for the downstream analysis of circular RNA's")
22956 (description
22957 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
22958in silico analysis of @dfn{circular RNA} (circRNAs). This computational
22959framework allows combining and analyzing circRNAs previously detected by
22960multiple publicly available annotation-based circRNA detection tools. It
22961covers different aspects of circRNAs analysis from differential expression
22962analysis, evolutionary conservation, biogenesis to functional analysis.")
22963 (license license:gpl3)))
22964
22965(define-public r-cistopic
22966 (package
22967 (name "r-cistopic")
22968 (version "2.1.0")
22969 (source
22970 (origin
22971 (method git-fetch)
22972 (uri (git-reference
22973 (url "https://github.com/aertslab/cisTopic")
22974 (commit (string-append "v" version))))
22975 (file-name (git-file-name name version))
22976 (sha256
22977 (base32
22978 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
22979 (build-system r-build-system)
22980 (propagated-inputs
22981 (list r-aucell
22982 r-data-table
22983 r-dplyr
22984 r-dosnow
22985 r-dt
22986 r-feather
22987 r-fitdistrplus
22988 r-genomicranges
22989 r-ggplot2
22990 r-lda
22991 r-matrix
22992 r-plyr
22993 r-rcistarget
22994 r-rtracklayer
22995 r-s4vectors))
22996 (home-page "https://github.com/aertslab/cisTopic")
22997 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
22998 (description
22999 "The sparse nature of single cell epigenomics data can be overruled using
23000probabilistic modelling methods such as @dfn{Latent Dirichlet
23001Allocation} (LDA). This package allows the probabilistic modelling of
23002cis-regulatory topics (cisTopics) from single cell epigenomics data, and
23003includes functionalities to identify cell states based on the contribution of
23004cisTopics and explore the nature and regulatory proteins driving them.")
23005 (license license:gpl3)))
23006
23007(define-public r-cistopic-next
23008 (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803")
23009 (revision "1"))
23010 (package
23011 (inherit r-cistopic)
23012 (name "r-cistopic-next")
23013 ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd
23014 ;; since the previous release is 2.1.0. Oh well.
23015 (version (git-version "0.3.0" revision commit))
23016 (source
23017 (origin
23018 (method git-fetch)
23019 (uri (git-reference
23020 (url "https://github.com/aertslab/cisTopic")
23021 (commit commit)))
23022 (file-name (git-file-name name version))
23023 (sha256
23024 (base32
23025 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
23026 (properties `((upstream-name . "cisTopic")))
23027 (propagated-inputs
23028 (list r-aucell
23029 r-data-table
23030 r-dosnow
23031 r-dplyr
23032 r-dt
23033 r-feather
23034 r-fitdistrplus
23035 r-genomicranges
23036 r-ggplot2
23037 r-lda
23038 r-matrix
23039 r-plyr
23040 r-rcistarget
23041 r-rtracklayer
23042 r-s4vectors
23043 r-text2vec))
23044 (native-inputs
23045 (list r-knitr)))))
23046
23047(define-public r-genie3
23048 (package
23049 (name "r-genie3")
23050 (version "1.34.0")
23051 (source
23052 (origin
23053 (method url-fetch)
23054 (uri (bioconductor-uri "GENIE3" version))
23055 (sha256
23056 (base32
23057 "0p1v9w40v6afhc5kg27zi04a6v9p5wq792kmnfb1pjm1mh2f1lkj"))))
23058 (properties
23059 '((upstream-name . "GENIE3")))
23060 (build-system r-build-system)
23061 (propagated-inputs
23062 (list r-dplyr r-reshape2))
23063 (native-inputs
23064 (list r-biobase
23065 r-knitr
23066 r-scater
23067 r-summarizedexperiment
23068 r-testthat))
23069 (home-page "https://bioconductor.org/packages/GENIE3")
23070 (synopsis "Gene network inference with ensemble of trees")
23071 (description
23072 "This package implements the GENIE3 algorithm for inferring gene
23073regulatory networks from expression data.")
23074 (license license:gpl2+)))
23075
23076(define-public r-roc
23077 (package
23078 (name "r-roc")
23079 (version "1.88.0")
23080 (source
23081 (origin
23082 (method url-fetch)
23083 (uri (bioconductor-uri "ROC" version))
23084 (sha256
23085 (base32
23086 "1na3v20iwg1icxn434yzg3fp4vd85grd493126zbmg2wdndgqzj8"))))
23087 (properties `((upstream-name . "ROC")))
23088 (build-system r-build-system)
23089 (native-inputs
23090 (list r-knitr))
23091 (home-page "https://www.bioconductor.org/packages/ROC/")
23092 (synopsis "Utilities for ROC curves")
23093 (description
23094 "This package provides utilities for @dfn{Receiver Operating
23095Characteristic} (ROC) curves, with a focus on micro arrays.")
23096 (license license:artistic2.0)))
23097
23098(define-public r-watermelon
23099 (package
23100 (name "r-watermelon")
23101 (version "2.18.0")
23102 (source
23103 (origin
23104 (method url-fetch)
23105 (uri (bioconductor-uri "wateRmelon" version))
23106 (sha256
23107 (base32
23108 "0k7jgwm8fq40d03mqfq05aj1ksvma5aknkg5dqwp2w3hdr87jp90"))))
23109 (properties `((upstream-name . "wateRmelon")))
23110 (build-system r-build-system)
23111 (propagated-inputs
23112 (list r-biobase
23113 r-illuminahumanmethylation450kanno-ilmn12-hg19
23114 r-illuminaio
23115 r-limma
23116 r-lumi
23117 r-matrixstats
23118 r-methylumi
23119 r-roc))
23120 (native-inputs
23121 (list r-knitr))
23122 (home-page "https://bioconductor.org/packages/wateRmelon/")
23123 (synopsis "Illumina 450 methylation array normalization and metrics")
23124 (description
23125 "The standard index of DNA methylation (beta) is computed from methylated
23126and unmethylated signal intensities. Betas calculated from raw signal
23127intensities perform well, but using 11 methylomic datasets we demonstrate that
23128quantile normalization methods produce marked improvement. The commonly used
23129procedure of normalizing betas is inferior to the separate normalization of M
23130and U, and it is also advantageous to normalize Type I and Type II assays
23131separately. This package provides 15 flavours of betas and three performance
23132metrics, with methods for objects produced by the @code{methylumi} and
23133@code{minfi} packages.")
23134 (license license:gpl3)))
23135
23136(define-public r-gdsfmt
23137 (package
23138 (name "r-gdsfmt")
23139 (version "1.48.1")
23140 (source
23141 (origin
23142 (method url-fetch)
23143 (uri (bioconductor-uri "gdsfmt" version))
23144 (sha256
23145 (base32
23146 "001l93k5912fgiqp7a6h1lmlxvwn5kbgs1cal9qyl2v1i5q6ggbr"))
23147 (modules '((guix build utils)))
23148 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
23149 ;; them and link with system libraries instead.
23150 (snippet
23151 '(begin
23152 (for-each delete-file-recursively
23153 '("src/LZ4"
23154 "src/XZ"
23155 "src/ZLIB"))
23156 (substitute* "src/Makevars"
23157 (("all: \\$\\(SHLIB\\)") "all:")
23158 (("\\$\\(SHLIB\\): liblzma.a") "")
23159 (("^ (ZLIB|LZ4)/.*") "")
23160 (("CoreArray/dVLIntGDS.cpp.*")
23161 "CoreArray/dVLIntGDS.cpp")
23162 (("CoreArray/dVLIntGDS.o.*")
23163 "CoreArray/dVLIntGDS.o")
23164 (("PKG_LIBS = ./liblzma.a")
23165 "PKG_LIBS = -llz4"))
23166 (substitute* "src/CoreArray/dStream.h"
23167 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
23168 (string-append "include <" header ">")))))))
23169 (properties
23170 `((upstream-name . "gdsfmt")
23171 (updater-extra-inputs . ("lz4" "xz" "zlib"))
23172 (updater-extra-native-inputs . ("r-matrix"))))
23173 (build-system r-build-system)
23174 (inputs
23175 (list lz4 xz zlib))
23176 (native-inputs
23177 (list r-biocgenerics r-digest r-knitr r-matrix r-runit))
23178 (home-page "http://corearray.sourceforge.net/")
23179 (synopsis
23180 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
23181 (description
23182 "This package provides a high-level R interface to CoreArray @dfn{Genomic
23183Data Structure} (GDS) data files, which are portable across platforms with
23184hierarchical structure to store multiple scalable array-oriented data sets
23185with metadata information. It is suited for large-scale datasets, especially
23186for data which are much larger than the available random-access memory. The
23187@code{gdsfmt} package offers efficient operations specifically designed for
23188integers of less than 8 bits, since a diploid genotype, like
23189@dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
23190byte. Data compression and decompression are available with relatively
23191efficient random access. It is also allowed to read a GDS file in parallel
23192with multiple R processes supported by the package @code{parallel}.")
23193 (license license:lgpl3)))
23194
23195(define-public r-bigmelon
23196 (package
23197 (name "r-bigmelon")
23198 (version "1.38.0")
23199 (source
23200 (origin
23201 (method url-fetch)
23202 (uri (bioconductor-uri "bigmelon" version))
23203 (sha256
23204 (base32
23205 "16qqk6cv344ynzi7bwprayr7gb9rd4dxzhfajzz0wv585vdck5va"))))
23206 (properties
23207 '((upstream-name . "bigmelon")
23208 (updater-extra-native-inputs . ("r-biocstyle" "r-knitr"))))
23209 (build-system r-build-system)
23210 (propagated-inputs
23211 (list r-biobase
23212 r-biocgenerics
23213 r-gdsfmt
23214 r-geoquery
23215 r-illuminaio
23216 r-methylumi
23217 r-minfi
23218 r-watermelon))
23219 (native-inputs (list r-biocmanager r-biocstyle r-knitr r-runit))
23220 (home-page "https://bioconductor.org/packages/bigmelon/")
23221 (synopsis "Illumina methylation array analysis for large experiments")
23222 (description
23223 "This package provides methods for working with Illumina arrays using the
23224@code{gdsfmt} package.")
23225 (license license:gpl3)))
23226
23227(define-public r-wavcluster
23228 (package
23229 (name "r-wavcluster")
23230 (version "2.46.0")
23231 (source
23232 (origin
23233 (method url-fetch)
23234 (uri (bioconductor-uri "wavClusteR" version))
23235 (sha256
23236 (base32
23237 "03hrpfmc1smnahsdyhhxjx76f6zv4rmrhjvcdzpl9b0gbm6dfy3x"))))
23238 (properties `((upstream-name . "wavClusteR")))
23239 (build-system r-build-system)
23240 (propagated-inputs
23241 (list r-biocgenerics
23242 r-biostrings
23243 r-foreach
23244 r-genomicfeatures
23245 r-genomicranges
23246 r-ggplot2
23247 r-hmisc
23248 r-iranges
23249 r-mclust
23250 r-rsamtools
23251 r-rtracklayer
23252 r-s4vectors
23253 r-seqinr
23254 r-stringr
23255 r-txdbmaker))
23256 (native-inputs
23257 (list r-knitr))
23258 (home-page "https://bioconductor.org/packages/wavClusteR/")
23259 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
23260 (description
23261 "This package provides an integrated pipeline for the analysis of
23262PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
23263sequencing errors, SNPs and additional non-experimental sources by a non-
23264parametric mixture model. The protein binding sites (clusters) are then
23265resolved at high resolution and cluster statistics are estimated using a
23266rigorous Bayesian framework. Post-processing of the results, data export for
23267UCSC genome browser visualization and motif search analysis are provided. In
23268addition, the package integrates RNA-Seq data to estimate the False
23269Discovery Rate of cluster detection. Key functions support parallel multicore
23270computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
23271be applied to the analysis of other NGS data obtained from experimental
23272procedures that induce nucleotide substitutions (e.g. BisSeq).")
23273 (license license:gpl2)))
23274
23275(define-public r-tilingarray
23276 (package
23277 (name "r-tilingarray")
23278 (version "1.90.0")
23279 (source (origin
23280 (method url-fetch)
23281 (uri (bioconductor-uri "tilingArray" version))
23282 (sha256
23283 (base32
23284 "0mg5kvilqv76fc4i4rkr6wcj3l8yywp7m8dd2cb1gv15aqx2zwjp"))))
23285 (properties `((upstream-name . "tilingArray")))
23286 (build-system r-build-system)
23287 (propagated-inputs
23288 (list r-affy
23289 r-biobase
23290 r-genefilter
23291 r-pixmap
23292 r-rcolorbrewer
23293 r-strucchange
23294 r-vsn))
23295 (home-page "https://bioconductor.org/packages/tilingArray")
23296 (synopsis "Transcript mapping with high-density oligonucleotide tiling arrays")
23297 (description
23298 "The package provides functionality that can be useful for the analysis
23299of the high-density tiling microarray data (such as from Affymetrix genechips)
23300or for measuring the transcript abundance and the architecture. The main
23301functionalities of the package are:
23302
23303@enumerate
23304@item the class segmentation for representing partitionings of a linear series
23305 of data;
23306@item the function segment for fitting piecewise constant models using a
23307 dynamic programming algorithm that is both fast and exact;
23308@item the function @code{confint} for calculating confidence intervals using
23309 the @code{strucchange} package;
23310@item the function @code{plotAlongChrom} for generating pretty plots;
23311@item the function @code{normalizeByReference} for probe-sequence dependent
23312 response adjustment from a (set of) reference hybridizations.
23313@end enumerate")
23314 (license license:artistic2.0)))
23315
23316(define-public r-timeseriesexperiment
23317 (package
23318 (name "r-timeseriesexperiment")
23319 (version "1.13.0")
23320 (source
23321 (origin
23322 (method url-fetch)
23323 (uri (bioconductor-uri "TimeSeriesExperiment" version))
23324 (sha256
23325 (base32
23326 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
23327 (properties
23328 `((upstream-name . "TimeSeriesExperiment")))
23329 (build-system r-build-system)
23330 (propagated-inputs
23331 (list r-deseq2
23332 r-dplyr
23333 r-dynamictreecut
23334 r-edger
23335 r-ggplot2
23336 r-hmisc
23337 r-limma
23338 r-magrittr
23339 r-proxy
23340 r-s4vectors
23341 r-summarizedexperiment
23342 r-tibble
23343 r-tidyr
23344 r-vegan
23345 r-viridis))
23346 (native-inputs
23347 (list r-knitr))
23348 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
23349 (synopsis "Analysis for short time-series data")
23350 (description
23351 "This package is a visualization and analysis toolbox for short time
23352course data which includes dimensionality reduction, clustering, two-sample
23353differential expression testing and gene ranking techniques. The package also
23354provides methods for retrieving enriched pathways.")
23355 (license license:lgpl3+)))
23356
23357(define-public r-variantfiltering
23358 (package
23359 (name "r-variantfiltering")
23360 (version "1.48.0")
23361 (source
23362 (origin
23363 (method url-fetch)
23364 (uri (bioconductor-uri "VariantFiltering" version))
23365 (sha256
23366 (base32
23367 "0hb5gcs7s1kdmaxrcpsiwqwfn9dh82hgxyp1hydb09c667jplq34"))))
23368 (properties
23369 `((upstream-name . "VariantFiltering")
23370 (updater-extra-native-inputs
23371 . ("r-biocstyle"
23372 "r-bsgenome-hsapiens-1000genomes-hs37d5"
23373 "r-org-hs-eg-db"
23374 "r-txdb-hsapiens-ucsc-hg19-knowngene"))))
23375 (build-system r-build-system)
23376 (arguments
23377 (list
23378 ;; Vignettes require an obscene amount of humongous annotation packages
23379 ;; and *still* attempt to download additional files off the Internet.
23380 ;; Enough is enough.
23381 #:test-types '(list "tests")))
23382 (propagated-inputs
23383 (list r-annotationdbi
23384 r-biobase
23385 r-biocgenerics
23386 r-biocparallel
23387 r-biostrings
23388 r-bsgenome
23389 r-dt
23390 r-genomeinfodb
23391 r-genomicfeatures
23392 r-genomicranges
23393 r-genomicscores
23394 r-graph
23395 r-gviz
23396 r-iranges
23397 r-rbgl
23398 r-rsamtools
23399 r-s4vectors
23400 r-seqinfo
23401 r-shiny
23402 r-shinyjs
23403 r-shinythemes
23404 r-shinytree
23405 r-summarizedexperiment
23406 r-variantannotation
23407 r-xvector))
23408 (native-inputs
23409 (list r-biocstyle
23410 r-bsgenome-hsapiens-1000genomes-hs37d5
23411 r-org-hs-eg-db
23412 r-runit
23413 r-txdb-hsapiens-ucsc-hg19-knowngene))
23414 (home-page "https://github.com/rcastelo/VariantFiltering")
23415 (synopsis "Filtering of coding and non-coding genetic variants")
23416 (description
23417 "Filter genetic variants using different criteria such as inheritance
23418model, amino acid change consequence, minor allele frequencies across human
23419populations, splice site strength, conservation, etc.")
23420 (license license:artistic2.0)))
23421
23422(define-public r-variancepartition
23423 (package
23424 (name "r-variancepartition")
23425 (version "1.42.0")
23426 (source
23427 (origin
23428 (method url-fetch)
23429 (uri (bioconductor-uri "variancePartition" version))
23430 (sha256
23431 (base32
23432 "00p8nw13fm46r1mw1mavnk2pycxycqgj7lhric8rawxsk186wq6w"))))
23433 (properties
23434 '((upstream-name . "variancePartition")
23435 (updater-extra-native-inputs . ("r-rfast"))))
23436 (build-system r-build-system)
23437 (propagated-inputs
23438 (list r-aod
23439 r-biobase
23440 r-biocparallel
23441 r-corpcor
23442 r-fancova
23443 r-ggplot2
23444 r-gplots
23445 r-gtools
23446 r-iterators
23447 r-limma
23448 r-lme4
23449 r-lmertest
23450 r-mass
23451 r-matrix
23452 r-matrixstats
23453 r-pbkrtest
23454 r-rdpack
23455 r-reformulas
23456 r-remacor
23457 r-reshape2
23458 r-rhpcblasctl
23459 r-rlang
23460 r-scales))
23461 (native-inputs
23462 (list r-biocgenerics
23463 r-cowplot
23464 r-devtools
23465 r-edger
23466 r-knitr
23467 r-rfast
23468 r-runit))
23469 (home-page "https://bioconductor.org/packages/variancePartition/")
23470 (synopsis "Analyze variation in gene expression experiments")
23471 (description
23472 "This is a package providing tools to quantify and interpret multiple
23473sources of biological and technical variation in gene expression experiments.
23474It uses a linear mixed model to quantify variation in gene expression
23475attributable to individual, tissue, time point, or technical variables. The
23476package includes dream differential expression analysis for repeated
23477measures.")
23478 (license license:gpl2+)))
23479
23480(define-public r-htqpcr
23481 (package
23482 (name "r-htqpcr")
23483 (version "1.66.0")
23484 (source
23485 (origin
23486 (method url-fetch)
23487 (uri (bioconductor-uri "HTqPCR" version))
23488 (sha256
23489 (base32
23490 "15z9wvdpwjdr5sv9n0ynka58n4q72b54qfg7ywamjf3ig4wmmc3x"))))
23491 (properties `((upstream-name . "HTqPCR")))
23492 (build-system r-build-system)
23493 (propagated-inputs
23494 (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
23495 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
23496 "groups/bertone/software/HTqPCR.pdf"))
23497 (synopsis "Automated analysis of high-throughput qPCR data")
23498 (description
23499 "Analysis of Ct values from high throughput quantitative real-time
23500PCR (qPCR) assays across multiple conditions or replicates. The input data
23501can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
23502OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
23503Laboratories; conventional 96- or 384-well plates; or microfluidic devices
23504such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
23505loading, quality assessment, normalization, visualization and parametric or
23506non-parametric testing for statistical significance in Ct values between
23507features (e.g. genes, microRNAs).")
23508 (license license:artistic2.0)))
23509
23510(define-public r-ucell
23511 (package
23512 (name "r-ucell")
23513 (version "2.16.0")
23514 (source (origin
23515 (method url-fetch)
23516 (uri (bioconductor-uri "UCell" version))
23517 (sha256
23518 (base32
23519 "172wkwgcnsrdipndcyf1y9pimm9b9ibqqbs3qv58x5dj9zy2crc1"))))
23520 (properties `((upstream-name . "UCell")))
23521 (build-system r-build-system)
23522 (propagated-inputs (list r-biocneighbors
23523 r-biocparallel
23524 r-data-table
23525 r-matrix
23526 r-singlecellexperiment
23527 r-summarizedexperiment))
23528 (native-inputs (list r-knitr))
23529 (home-page "https://github.com/carmonalab/UCell")
23530 (synopsis "Rank-based signature enrichment analysis for single-cell data")
23531 (description
23532 "UCell is a package for evaluating gene signatures in single-cell datasets.
23533UCell signature scores, based on the Mann-Whitney U statistic, are robust to
23534dataset size and heterogeneity, and their calculation demands less computing
23535time and memory than other available methods, enabling the processing of large
23536datasets in a few minutes even on machines with limited computing power.
23537UCell can be applied to any single-cell data matrix, and includes functions to
23538directly interact with SingleCellExperiment and Seurat objects.")
23539 (license license:gpl3)))
23540
23541(define-public r-ucsc-utils
23542 (package
23543 (name "r-ucsc-utils")
23544 (version "1.8.0")
23545 (source
23546 (origin
23547 (method url-fetch)
23548 (uri (bioconductor-uri "UCSC.utils" version))
23549 (sha256
23550 (base32 "12la3f2vdn5mgr4f80iqk0llmx3ywcz523drclq7k008aiq5s88y"))))
23551 (properties `((upstream-name . "UCSC.utils")))
23552 (build-system r-build-system)
23553 ;; Tests require Internet access.
23554 (arguments (list #:tests? #false))
23555 (propagated-inputs (list r-httr r-jsonlite r-s4vectors))
23556 (native-inputs (list r-knitr r-testthat))
23557 (home-page "https://bioconductor.org/packages/UCSC.utils")
23558 (synopsis
23559 "Low-level utilities to retrieve data from the UCSC Genome Browser")
23560 (description
23561 "This package provides a set of low-level utilities to retrieve data from the
23562UCSC Genome Browser. Most functions in the package access the data via the UCSC
23563REST API but some of them query the UCSC @code{MySQL} server directly. Note
23564that the primary purpose of the package is to support higher-level
23565functionalities implemented in downstream packages like @code{GenomeInfoDb} or
23566txdbmaker.")
23567 (license license:artistic2.0)))
23568
23569(define-public r-unifiedwmwqpcr
23570 (package
23571 (name "r-unifiedwmwqpcr")
23572 (version "1.48.0")
23573 (source
23574 (origin
23575 (method url-fetch)
23576 (uri (bioconductor-uri "unifiedWMWqPCR" version))
23577 (sha256
23578 (base32
23579 "1c1pw7mv240z37w7lyi0cijbyszz21jxi1laamvdzw2zgaa3dvnf"))))
23580 (properties
23581 `((upstream-name . "unifiedWMWqPCR")))
23582 (build-system r-build-system)
23583 (propagated-inputs
23584 (list r-biocgenerics r-limma))
23585 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
23586 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
23587 (description
23588 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
23589data. This modified test allows for testing differential expression in qPCR
23590data.")
23591 (license license:gpl2+)))
23592
23593(define-public r-universalmotif
23594 (package
23595 (name "r-universalmotif")
23596 (version "1.30.1")
23597 (source
23598 (origin
23599 (method url-fetch)
23600 (uri (bioconductor-uri "universalmotif" version))
23601 (sha256
23602 (base32
23603 "0g0fnqk2kp8qcx8fhv6wgx561q4px9fabm2fwgisnyyr95sdmxhi"))))
23604 (properties
23605 '((upstream-name . "universalmotif")
23606 (updater-extra-native-inputs . ("r-ape" "r-ggtree"))))
23607 (build-system r-build-system)
23608 (arguments
23609 (list
23610 #:skipped-tests
23611 (if (target-32bit?)
23612 ;; The length of `freqs` must be the power of the number of letters
23613 ;; in the sequence alphabet.
23614 '(("test_create_sequences.R" "sequence creation works"))
23615 '())
23616 #:phases
23617 '(modify-phases %standard-phases
23618 (add-after 'unpack 'fix-reference-to-strip
23619 (lambda _
23620 (substitute* "src/Makevars"
23621 (("/usr/bin/strip") (which "strip"))))))))
23622 (propagated-inputs
23623 (list r-biocgenerics
23624 r-biostrings
23625 r-ggplot2
23626 r-iranges
23627 r-mass
23628 r-matrixgenerics
23629 r-rcpp
23630 r-rcppthread
23631 r-rlang
23632 r-s4vectors
23633 r-yaml))
23634 (native-inputs
23635 (list r-ape r-ggtree r-knitr r-spelling r-testthat))
23636 (home-page
23637 "https://bioconductor.org/packages/universalmotif/")
23638 (synopsis
23639 "Specific structures importer, modifier, and exporter for R")
23640 (description
23641 "This package allows importing most common @dfn{specific structure}
23642(motif) types into R for use by functions provided by other Bioconductor
23643motif-related packages. Motifs can be exported into most major motif formats
23644from various classes as defined by other Bioconductor packages. A suite of
23645motif and sequence manipulation and analysis functions are included, including
23646enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
23647motifs, and others.")
23648 (license license:gpl3)))
23649
23650(define-public r-ace
23651 (package
23652 (name "r-ace")
23653 (version "1.30.0")
23654 (source (origin
23655 (method url-fetch)
23656 (uri (bioconductor-uri "ACE" version))
23657 (sha256
23658 (base32
23659 "1cycpcxg0c5rrzp5fnqll04z6a1lv9h3ihkkcy4q98l6bdplkkrc"))))
23660 (properties `((upstream-name . "ACE")))
23661 (build-system r-build-system)
23662 (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
23663 (native-inputs (list r-knitr))
23664 (home-page "https://github.com/tgac-vumc/ACE")
23665 (synopsis
23666 "Absolute copy number estimation from low-coverage whole genome sequencing")
23667 (description
23668 "This package uses segmented copy number data to estimate tumor cell
23669percentage and produce copy number plots displaying absolute copy numbers. For
23670this it uses segmented data from the @code{QDNAseq} package, which in turn uses
23671a number of dependencies to turn mapped reads into segmented data. @code{ACE}
23672will run @code{QDNAseq} or use its output rds-file of segmented data. It will
23673subsequently run through all samples in the object(s), for which it will create
23674individual subdirectories. For each sample, it will calculate how well the
23675segments fit (the relative error) to integer copy numbers for each percentage
23676of @dfn{tumor cells} (cells with divergent segments).")
23677 (license license:gpl2)))
23678
23679(define-public r-acgh
23680 (package
23681 (name "r-acgh")
23682 (version "1.90.0")
23683 (source (origin
23684 (method url-fetch)
23685 (uri (bioconductor-uri "aCGH" version))
23686 (sha256
23687 (base32
23688 "0zff06h9jswckvfr9k3nxgf7vdzb5bzwxvxg26s95za3mkl737r6"))))
23689 (properties `((upstream-name . "aCGH")))
23690 (build-system r-build-system)
23691 (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
23692 (home-page "https://bioconductor.org/packages/aCGH")
23693 (synopsis
23694 "Classes and functions for array comparative genomic hybridization data")
23695 (description
23696 "This package provides functions for reading
23697@dfn{array comparative genomic hybridization} (aCGH) data from image analysis
23698output files and clone information files, creation of @code{aCGH} objects for
23699storing these data. Basic methods are accessing/replacing, subsetting,
23700printing and plotting @code{aCGH} objects.")
23701 (license license:gpl2)))
23702
23703(define-public r-acme
23704 (package
23705 (name "r-acme")
23706 (version "2.68.0")
23707 (source (origin
23708 (method url-fetch)
23709 (uri (bioconductor-uri "ACME" version))
23710 (sha256
23711 (base32
23712 "0dnfb7f5ng0minl6p0m9g6l5is5cxlnhlnp40fv9zbyxlm142sk5"))))
23713 (properties `((upstream-name . "ACME")))
23714 (build-system r-build-system)
23715 (arguments
23716 (list
23717 #:phases
23718 #~(modify-phases %standard-phases
23719 (add-before 'install 'relax-gcc-14-strictness
23720 (lambda _
23721 ;; XXX FIXME: $HOME/.R/Makevars seems to be the only way to
23722 ;; set custom CFLAGS for R?
23723 (setenv "HOME" (getcwd))
23724 (mkdir-p ".R")
23725 (with-directory-excursion ".R"
23726 (with-output-to-file "Makevars"
23727 (lambda _
23728 (display
23729 (string-append
23730 "CFLAGS=-g -O2"
23731 " -Wno-error=incompatible-pointer-types\n"))))))))))
23732 (propagated-inputs (list r-biobase r-biocgenerics))
23733 (home-page "https://bioconductor.org/packages/aCGH/")
23734 (synopsis "Calculating microarray enrichment")
23735 (description
23736 "This package implements @dfn{algorithms for calculating microarray
23737enrichment} (ACME), and it is a set of tools for analysing tiling array of
23738@dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
23739DNAse hypersensitivity, or other experiments that result in regions of the
23740genome showing enrichment. It does not rely on a specific array technology
23741(although the array should be a tiling array), is very general (can be applied
23742in experiments resulting in regions of enrichment), and is very insensitive to
23743array noise or normalization methods. It is also very fast and can be applied
23744on whole-genome tiling array experiments quite easily with enough memory.")
23745 (license license:gpl2+)))
23746
23747(define-public r-acde
23748 (package
23749 (name "r-acde")
23750 (version "1.42.0")
23751 (source (origin
23752 (method url-fetch)
23753 (uri (bioconductor-uri "acde" version))
23754 (sha256
23755 (base32
23756 "1ps5gjczm0x2jdm9n313877hc0izl08kc73mrxp544ziglga4a74"))))
23757 (properties `((upstream-name . "acde")))
23758 (build-system r-build-system)
23759 ;; FIXME One test fails.
23760 (arguments (list #:tests? #false))
23761 (propagated-inputs (list r-boot))
23762 (native-inputs (list r-biocgenerics r-runit))
23763 (home-page "https://bioconductor.org/packages/acde")
23764 (synopsis
23765 "Identification of differentially expressed genes with artificial components")
23766 (description
23767 "This package provides a multivariate inferential analysis method for
23768detecting differentially expressed genes in gene expression data. It uses
23769artificial components, close to the data's principal components but with an
23770exact interpretation in terms of differential genetic expression, to identify
23771differentially expressed genes while controlling the @dfn{false discovery
23772rate} (FDR).")
23773 (license license:gpl3)))
23774
23775;; This is a CRAN package, but it depends on Bioconductor packages, so we put
23776;; it here.
23777(define-public r-activedriverwgs
23778 (package
23779 (name "r-activedriverwgs")
23780 (version "1.2.1")
23781 (source
23782 (origin
23783 (method url-fetch)
23784 (uri (cran-uri "ActiveDriverWGS" version))
23785 (sha256
23786 (base32
23787 "1v6lnzbaksqpc33q3bp4mwij6rrfbqhi5wk1qx32h2wr2hr4208y"))))
23788 (properties
23789 `((upstream-name . "ActiveDriverWGS")))
23790 (build-system r-build-system)
23791 (propagated-inputs
23792 (list r-biostrings
23793 r-bsgenome
23794 r-genomeinfodb
23795 r-genomicranges
23796 r-iranges
23797 r-s4vectors))
23798 (native-inputs
23799 (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat))
23800 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
23801 (synopsis "Driver discovery tool for cancer whole genomes")
23802 (description
23803 "This package provides a method for finding an enrichment of cancer
23804simple somatic mutations (SNVs and Indels) in functional elements across the
23805human genome. ActiveDriverWGS detects coding and noncoding driver elements
23806using whole genome sequencing data.")
23807 (license license:gpl3)))
23808
23809;; This is a CRAN package, but it depends on Bioconductor packages, so we put
23810;; it here.
23811(define-public r-activepathways
23812 (package
23813 (name "r-activepathways")
23814 (version "2.0.6")
23815 (source
23816 (origin
23817 (method url-fetch)
23818 (uri (cran-uri "ActivePathways" version))
23819 (sha256
23820 (base32
23821 "16icf52xh0659b59x7w5mv35dbi0wqkr3ya55vvyg3akwvcj48zn"))))
23822 (properties
23823 `((upstream-name . "ActivePathways")))
23824 (build-system r-build-system)
23825 (propagated-inputs
23826 (list r-data-table r-ggplot2))
23827 (native-inputs
23828 (list r-knitr r-testthat))
23829 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
23830 (synopsis "Multivariate pathway enrichment analysis")
23831 (description
23832 "This package represents an integrative method of analyzing multi omics
23833data that conducts enrichment analysis of annotated gene sets. ActivePathways
23834uses a statistical data fusion approach, rationalizes contributing evidence
23835and highlights associated genes, improving systems-level understanding of
23836cellular organization in health and disease.")
23837 (license license:gpl3)))
23838
23839(define-public r-bgmix
23840 (package
23841 (name "r-bgmix")
23842 (version "1.59.0")
23843 (source
23844 (origin
23845 (method url-fetch)
23846 (uri (bioconductor-uri "BGmix" version))
23847 (sha256
23848 (base32
23849 "16fzgxcy4sk0kd67vzdxqz81s84dvh4bqss9cbl9bn6vhpfsnfyf"))))
23850 (properties `((upstream-name . "BGmix")))
23851 (build-system r-build-system)
23852 (arguments
23853 (list
23854 #:phases
23855 '(modify-phases %standard-phases
23856 ;; GCC's c++/bits/specfun.h (included by cmath) provides a std::beta
23857 ;; procedure.
23858 (add-after 'unpack 'avoid-naming-conflict
23859 (lambda _
23860 (substitute* "src/BGmix_main.cpp"
23861 (("\\bbeta\\b") "::beta")
23862 (("\\*\\*::beta,") "**beta,")))))))
23863 (propagated-inputs
23864 (list r-kernsmooth))
23865 (home-page "https://bioconductor.org/packages/BGmix/")
23866 (synopsis "Bayesian models for differential gene expression")
23867 (description
23868 "This package provides fully Bayesian mixture models for differential
23869gene expression.")
23870 (license license:gpl2)))
23871
23872(define-public r-bgx
23873 (package
23874 (name "r-bgx")
23875 (version "1.70.0")
23876 (source
23877 (origin
23878 (method url-fetch)
23879 (uri (bioconductor-uri "bgx" version))
23880 (sha256
23881 (base32
23882 "0sglk8q12fvqk6m699v3lajwr1zb8wnrldfv2n8y7jjy2fqcvs19"))))
23883 (properties `((upstream-name . "bgx")))
23884 (build-system r-build-system)
23885 (arguments
23886 (list
23887 #:phases
23888 '(modify-phases %standard-phases
23889 (add-after 'unpack 'do-not-tune-cflags-for-reproducibility
23890 (lambda _
23891 (substitute* "configure.ac"
23892 (("AX_GCC_ARCHFLAG.*") ""))
23893 (delete-file "configure")
23894 (invoke "autoreconf" "-vif"))))))
23895 (inputs
23896 (list boost))
23897 (propagated-inputs
23898 (list r-affy r-biobase r-gcrma r-rcpp))
23899 (native-inputs
23900 (list autoconf automake))
23901 (home-page "https://bioconductor.org/packages/bgx/")
23902 (synopsis "Bayesian gene expression")
23903 (description
23904 "This package provides tools for Bayesian integrated analysis of
23905Affymetrix GeneChips.")
23906 (license license:gpl2)))
23907
23908(define-public r-bhc
23909 (package
23910 (name "r-bhc")
23911 (version "1.56.0")
23912 (source
23913 (origin
23914 (method url-fetch)
23915 (uri (bioconductor-uri "BHC" version))
23916 (sha256
23917 (base32
23918 "1fam1k42dwd0gh7dw2gz4yl6bnbkfrw0bd44v8sdpvwwyd1dq1r8"))))
23919 (properties `((upstream-name . "BHC")))
23920 (build-system r-build-system)
23921 (home-page "https://bioconductor.org/packages/BHC/")
23922 (synopsis "Bayesian hierarchical clustering")
23923 (description
23924 "The method implemented in this package performs bottom-up hierarchical
23925clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
23926in the data and Bayesian model selection to decide at each step which clusters
23927to merge. This avoids several limitations of traditional methods, for example
23928how many clusters there should be and how to choose a principled distance
23929metric. This implementation accepts multinomial (i.e. discrete, with 2+
23930categories) or time-series data. This version also includes a randomised
23931algorithm which is more efficient for larger data sets.")
23932 (license license:gpl3)))
23933
23934(define-public r-bicare
23935 (package
23936 (name "r-bicare")
23937 (version "1.70.0")
23938 (source
23939 (origin
23940 (method url-fetch)
23941 (uri (bioconductor-uri "BicARE" version))
23942 (sha256
23943 (base32
23944 "0skdbqxzz8f53ryyxhjmij9w1gxnjla0m2841xn0scsiyldq340q"))))
23945 (properties `((upstream-name . "BicARE")))
23946 (build-system r-build-system)
23947 (propagated-inputs
23948 (list r-biobase r-go-db r-gseabase r-multtest))
23949 (home-page "http://bioinfo.curie.fr")
23950 (synopsis "Biclustering analysis and results exploration")
23951 (description
23952 "This is a package for biclustering analysis and exploration of
23953results.")
23954 (license license:gpl2)))
23955
23956(define-public r-bifet
23957 (package
23958 (name "r-bifet")
23959 (version "1.32.0")
23960 (source
23961 (origin
23962 (method url-fetch)
23963 (uri (bioconductor-uri "BiFET" version))
23964 (sha256
23965 (base32
23966 "0dg1b2h8yrr03ppbv9myjmbfyxyyyr5ivn5x0v2mzmq4mrjdhbzw"))))
23967 (properties `((upstream-name . "BiFET")))
23968 (build-system r-build-system)
23969 (propagated-inputs
23970 (list r-genomicranges r-poibin))
23971 (native-inputs
23972 (list r-knitr r-testthat))
23973 (home-page "https://bioconductor.org/packages/BiFET")
23974 (synopsis "Bias-free footprint enrichment test")
23975 (description
23976 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
23977over-represented in target regions compared to background regions after
23978correcting for the bias arising from the imbalance in read counts and GC
23979contents between the target and background regions. For a given TF k, BiFET
23980tests the null hypothesis that the target regions have the same probability of
23981having footprints for the TF k as the background regions while correcting for
23982the read count and GC content bias.")
23983 (license license:gpl3)))
23984
23985(define-public r-rsbml
23986 (package
23987 (name "r-rsbml")
23988 (version "2.70.0")
23989 (source
23990 (origin
23991 (method url-fetch)
23992 (uri (bioconductor-uri "rsbml" version))
23993 (sha256
23994 (base32
23995 "0cklj8mm1hs7r9w00ihn7ak462k7g99n2j2zx0lmvfyd3l1igcfq"))))
23996 (properties `((upstream-name . "rsbml")))
23997 (build-system r-build-system)
23998 (inputs
23999 (list libsbml))
24000 (propagated-inputs
24001 (list r-biocgenerics r-graph))
24002 (native-inputs
24003 (list pkg-config))
24004 (home-page "http://www.sbml.org")
24005 (synopsis "R support for SBML")
24006 (description
24007 "This package provides an R interface to libsbml for SBML parsing,
24008validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
24009 (license license:artistic2.0)))
24010
24011(define-public r-hybridmtest
24012 (package
24013 (name "r-hybridmtest")
24014 (version "1.56.0")
24015 (source
24016 (origin
24017 (method url-fetch)
24018 (uri (bioconductor-uri "HybridMTest" version))
24019 (sha256
24020 (base32 "1wxqc6cf9xwydvvazyhkwrin3jmfg0vilj6y496s5k3sinpmzhs0"))))
24021 (properties `((upstream-name . "HybridMTest")))
24022 (build-system r-build-system)
24023 (propagated-inputs
24024 (list r-biobase
24025 r-fdrtool
24026 r-mass
24027 r-survival))
24028 (home-page "https://bioconductor.org/packages/HybridMTest")
24029 (synopsis "Hybrid multiple testing")
24030 (description
24031 "This package performs hybrid multiple testing that incorporates method
24032selection and assumption evaluations into the analysis using @acronym{EBP,
24033empirical Bayes probability} estimates obtained by Grenander density
24034estimation. For instance, for 3-group comparison analysis, Hybrid Multiple
24035testing considers EBPs as weighted EBPs between F-test and H-test with EBPs
24036from Shapiro Wilk test of normality as weight. Instead of just using EBPs
24037from F-test only or using H-test only, this methodology combines both types of
24038EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses
24039then the law of total EBPs.")
24040 (license license:gpl2+)))
24041
24042(define-public r-hypergraph
24043 (package
24044 (name "r-hypergraph")
24045 (version "1.84.0")
24046 (source
24047 (origin
24048 (method url-fetch)
24049 (uri (bioconductor-uri "hypergraph" version))
24050 (sha256
24051 (base32
24052 "0vydq6gb6mjfm6rf3bwsp3dqsb56n024ci2kx2qqy0n766bwzfqm"))))
24053 (properties `((upstream-name . "hypergraph")))
24054 (build-system r-build-system)
24055 (propagated-inputs
24056 (list r-graph))
24057 (native-inputs (list r-biocgenerics r-runit))
24058 (home-page "https://bioconductor.org/packages/hypergraph")
24059 (synopsis "Hypergraph data structures")
24060 (description
24061 "This package implements some simple capabilities for representing and
24062manipulating hypergraphs.")
24063 (license license:artistic2.0)))
24064
24065(define-public r-hyperdraw
24066 (package
24067 (name "r-hyperdraw")
24068 (version "1.64.0")
24069 (source
24070 (origin
24071 (method url-fetch)
24072 (uri (bioconductor-uri "hyperdraw" version))
24073 (sha256
24074 (base32
24075 "176air0kxca3bm40824ls7pxg5g01dnajcbyka83rvk7smvab9vr"))))
24076 (properties `((upstream-name . "hyperdraw")))
24077 (build-system r-build-system)
24078 (inputs (list graphviz))
24079 (propagated-inputs
24080 (list r-graph r-hypergraph r-rgraphviz))
24081 (home-page "https://bioconductor.org/packages/hyperdraw")
24082 (synopsis "Visualizing hypergraphs")
24083 (description
24084 "This package provides functions for visualizing hypergraphs.")
24085 (license license:gpl2+)))
24086
24087(define-public r-biggr
24088 (package
24089 (name "r-biggr")
24090 (version "1.44.0")
24091 (source
24092 (origin
24093 (method url-fetch)
24094 (uri (bioconductor-uri "BiGGR" version))
24095 (sha256
24096 (base32
24097 "1awdwwg54cfnsn8kp0lw6a7c3mgix024ry7mxn9vb5xq4hp1gflb"))))
24098 (properties `((upstream-name . "BiGGR")))
24099 (build-system r-build-system)
24100 (propagated-inputs
24101 (list r-hyperdraw
24102 r-hypergraph
24103 r-lim
24104 r-limsolve
24105 r-rsbml
24106 r-stringr))
24107 (home-page "https://bioconductor.org/packages/BiGGR/")
24108 (synopsis "Constraint based modeling using metabolic reconstruction databases")
24109 (description
24110 "This package provides an interface to simulate metabolic reconstruction
24111from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
24112reconstruction databases. The package facilitates @dfn{flux balance
24113analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
24114networks and estimated fluxes can be visualized with hypergraphs.")
24115 (license license:gpl3+)))
24116
24117(define-public r-bigmemoryextras
24118 (package
24119 (name "r-bigmemoryextras")
24120 (version "1.38.0")
24121 (source
24122 (origin
24123 (method url-fetch)
24124 (uri (bioconductor-uri "bigmemoryExtras" version))
24125 (sha256
24126 (base32
24127 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
24128 (properties
24129 `((upstream-name . "bigmemoryExtras")))
24130 (build-system r-build-system)
24131 ;; One test may fail with "Error: C stack usage 7969984 is too close to
24132 ;; the limit", dependent on settings of the build node. Better to ignore
24133 ;; this test, but unfortunately we cannot easily disable just this one
24134 ;; test called "We can reattach saved objects".
24135 (arguments (list #:tests? #false))
24136 (propagated-inputs
24137 (list r-bigmemory))
24138 (native-inputs
24139 (list r-knitr r-testthat))
24140 (home-page "https://github.com/phaverty/bigmemoryExtras")
24141 (synopsis "Extension of the bigmemory package")
24142 (description
24143 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
24144safety and convenience features to the @code{filebacked.big.matrix} class from
24145the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
24146monitoring and gracefully restoring the connection to on-disk data and it also
24147protects against accidental data modification with a file-system-based
24148permissions system. Utilities are provided for using @code{BigMatrix}-derived
24149classes as @code{assayData} matrices within the @code{Biobase} package's
24150@code{eSet} family of classes. @code{BigMatrix} provides some optimizations
24151related to attaching to, and indexing into, file-backed matrices with
24152dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
24153a file-backed matrix with factor properties.")
24154 (license license:artistic2.0)))
24155
24156(define-public r-bigpint
24157 (package
24158 (name "r-bigpint")
24159 (version "1.15.0")
24160 (source
24161 (origin
24162 (method url-fetch)
24163 (uri (bioconductor-uri "bigPint" version))
24164 (sha256
24165 (base32
24166 "1r9gr5f9as09ifagal5k7713h95qjw508cf8ny3j1jmqd24v6xhs"))))
24167 (properties `((upstream-name . "bigPint")))
24168 (build-system r-build-system)
24169 ;; 4 tests fail with "cannot xtfrm data frames"
24170 (arguments (list #:tests? #false))
24171 (propagated-inputs
24172 (list r-delayedarray
24173 r-dplyr
24174 r-ggally
24175 r-ggplot2
24176 r-gridextra
24177 r-hexbin
24178 r-hmisc
24179 r-htmlwidgets
24180 r-plotly
24181 r-plyr
24182 r-rcolorbrewer
24183 r-reshape
24184 r-shiny
24185 r-shinycssloaders
24186 r-shinydashboard
24187 r-stringr
24188 r-summarizedexperiment
24189 r-tidyr))
24190 (native-inputs
24191 (list r-knitr r-runit))
24192 (home-page "https://github.com/lindsayrutter/bigPint")
24193 (synopsis "Big multivariate data plotted interactively")
24194 (description
24195 "This package provides methods for visualizing large multivariate
24196datasets using static and interactive scatterplot matrices, parallel
24197coordinate plots, volcano plots, and litre plots. It includes examples for
24198visualizing RNA-sequencing datasets and differentially expressed genes.")
24199 (license license:gpl3)))
24200
24201(define-public r-chemmineob
24202 (package
24203 (name "r-chemmineob")
24204 (version "1.50.0")
24205 (source
24206 (origin
24207 (method url-fetch)
24208 (uri (bioconductor-uri "ChemmineOB" version))
24209 (sha256
24210 (base32 "1l1z5hffs0d5m3mhj7svggjpx810qh3ipm21almlfkf4kp8vwjb0"))))
24211 (properties
24212 '((upstream-name . "ChemmineOB")
24213 (updater-extra-inputs . ("eigen" "openbabel"))
24214 (updater-ignored-native-inputs . ("r-chemminer"))))
24215 (build-system r-build-system)
24216 (arguments
24217 (list
24218 ;; Tests require r-chemminer; adding it would lead to mutually recursive
24219 ;; dependency declarations. The tests also complain that Cairo is not
24220 ;; loaded.
24221 #:test-types '(list "vignettes")
24222 #:phases
24223 #~(modify-phases %standard-phases
24224 (add-after 'unpack 'patch-makefile
24225 (lambda _
24226 (substitute* "src/Makevars.in"
24227 (("/usr/include/openbabel3")
24228 (string-append #$(this-package-input "openbabel")
24229 "/include/openbabel3"))
24230 (("/usr/include/eigen3")
24231 (string-append #$(this-package-input "eigen")
24232 "/include/eigen3"))))))))
24233 (inputs (list eigen openbabel zlib))
24234 (propagated-inputs (list r-bh r-biocgenerics r-rcpp))
24235 (native-inputs (list pkg-config r-knitr r-runit))
24236 (home-page "https://github.com/girke-lab/ChemmineOB")
24237 (synopsis "R interface to a subset of OpenBabel functionalities")
24238 (description
24239 "@code{ChemmineOB} provides an R interface to a subset of cheminformatics
24240functionalities implemented by the @code{OpelBabel} C++ project.
24241@code{OpenBabel} is a free cheminformatics toolbox that includes
24242utilities for structure format interconversions, descriptor calculations,
24243compound similarity searching and more. @code{ChemineOB} aims to make a subset
24244of these utilities available from within R. For non-developers,
24245@code{ChemineOB} is primarily intended to be used from @code{ChemmineR} as an
24246add-on package rather than used directly.")
24247 (license license:asl2.0)))
24248
24249(define-public r-chemminer
24250 (package
24251 (name "r-chemminer")
24252 (version "3.64.0")
24253 (source
24254 (origin
24255 (method url-fetch)
24256 (uri (bioconductor-uri "ChemmineR" version))
24257 (sha256
24258 (base32
24259 "1m0x66c454zii8176yifqbqdam05cf7zzlhqiifm42jysxa7jlxh"))))
24260 (properties
24261 '((upstream-name . "ChemmineR")
24262 ;; Needed for tests.
24263 ;; Snow is needed because of a test dependency on "makeSOCKcluster".
24264 (updater-extra-native-inputs . ("r-chemmineob" "r-rsqlite" "r-snow"))
24265 ;; Avoid dependency cycle.
24266 (updater-ignored-native-inputs . ("r-fmcsr"))))
24267 (build-system r-build-system)
24268 (propagated-inputs
24269 (list r-base64enc
24270 r-bh
24271 r-biocgenerics
24272 r-dbi
24273 r-digest
24274 r-dt
24275 r-ggplot2
24276 r-gridextra
24277 r-jsonlite
24278 r-png
24279 r-rcpp
24280 r-rcurl
24281 r-rjson
24282 r-rsvg
24283 r-stringi))
24284 (native-inputs
24285 (list r-biocmanager
24286 r-biocstyle
24287 r-chemmineob
24288 r-gplots
24289 r-knitr
24290 r-rgl
24291 r-rsqlite
24292 r-runit
24293 r-scatterplot3d
24294 r-snow))
24295 (home-page "https://github.com/girke-lab/ChemmineR")
24296 (synopsis "Cheminformatics toolkit for R")
24297 (description
24298 "ChemmineR is a cheminformatics package for analyzing drug-like small
24299molecule data in R. It contains functions for efficient processing of large
24300numbers of molecules, physicochemical/structural property predictions,
24301structural similarity searching, classification and clustering of compound
24302libraries with a wide spectrum of algorithms. In addition, it offers
24303visualization functions for compound clustering results and chemical
24304structures.")
24305 (license license:artistic2.0)))
24306
24307(define-public r-fmcsr
24308 (package
24309 (name "r-fmcsr")
24310 (version "1.54.0")
24311 (source
24312 (origin
24313 (method url-fetch)
24314 (uri (bioconductor-uri "fmcsR" version))
24315 (sha256
24316 (base32 "05059a7yfmc71sq12k8aa4zcvaf350msdvriszqgc91vzbyi6q8l"))))
24317 (properties `((upstream-name . "fmcsR")))
24318 (build-system r-build-system)
24319 (propagated-inputs
24320 (list r-biocgenerics r-chemminer))
24321 (native-inputs (list r-knitr r-runit))
24322 (home-page "https://github.com/girke-lab/fmcsR")
24323 (synopsis "Mismatch tolerant maximum common substructure searching")
24324 (description
24325 "The fmcsR package introduces an efficient @dfn{maximum common
24326substructure} (MCS) algorithms combined with a novel matching strategy that
24327allows for atom and/or bond mismatches in the substructures shared among two
24328small molecules. The resulting flexible MCSs (FMCSs) are often larger than
24329strict MCSs, resulting in the identification of more common features in their
24330source structures, as well as a higher sensitivity in finding compounds with
24331weak structural similarities. The fmcsR package provides several utilities to
24332use the FMCS algorithm for pairwise compound comparisons, structure similarity
24333searching and clustering.")
24334 (license license:artistic2.0)))
24335
24336(define-public r-bioassayr
24337 (package
24338 (name "r-bioassayr")
24339 (version "1.50.0")
24340 (source
24341 (origin
24342 (method url-fetch)
24343 (uri (bioconductor-uri "bioassayR" version))
24344 (sha256
24345 (base32
24346 "1rask82v46qpz10rvkdy5mjckjppivwhh1cv08rd895rijpn2jcx"))))
24347 (properties `((upstream-name . "bioassayR")))
24348 (build-system r-build-system)
24349 (propagated-inputs
24350 (list r-biocgenerics
24351 r-chemminer
24352 r-dbi
24353 r-matrix
24354 r-rjson
24355 r-rsqlite
24356 r-xml))
24357 (native-inputs
24358 (list r-knitr r-testthat))
24359 (home-page "https://github.com/girke-lab/bioassayR")
24360 (synopsis "Cross-target analysis of small molecule bioactivity")
24361 (description
24362 "bioassayR is a computational tool that enables simultaneous analysis of
24363thousands of bioassay experiments performed over a diverse set of compounds
24364and biological targets. Unique features include support for large-scale
24365cross-target analyses of both public and custom bioassays, generation of
24366@dfn{high throughput screening fingerprints} (HTSFPs), and an optional
24367preloaded database that provides access to a substantial portion of publicly
24368available bioactivity data.")
24369 (license license:artistic2.0)))
24370
24371(define-public r-biobroom
24372 (package
24373 (name "r-biobroom")
24374 (version "1.43.0")
24375 (source
24376 (origin
24377 (method url-fetch)
24378 (uri (bioconductor-uri "biobroom" version))
24379 (sha256
24380 (base32
24381 "01kz5qwygwl5ycw02sjwdabcklvm0dc3j98akyjx29z381pmnd9q"))))
24382 (properties `((upstream-name . "biobroom")))
24383 (build-system r-build-system)
24384 (arguments
24385 (list
24386 #:phases
24387 '(modify-phases %standard-phases
24388 (add-after 'unpack 'dplyr-compatibility
24389 (lambda _
24390 (substitute* "R/utilities.R"
24391 (("dplyr::tbl_df") "tibble::as_tibble")))))))
24392 (propagated-inputs
24393 (list r-biobase r-broom r-dplyr r-tidyr))
24394 (native-inputs
24395 (list r-deseq2 r-edger r-knitr r-magrittr r-testthat))
24396 (home-page "https://github.com/StoreyLab/biobroom")
24397 (synopsis "Turn Bioconductor objects into tidy data frames")
24398 (description
24399 "This package contains methods for converting standard objects
24400constructed by bioinformatics packages, especially those in Bioconductor, and
24401converting them to @code{tidy} data. It thus serves as a complement to the
24402@code{broom} package, and follows the same tidy, augment, glance division of
24403tidying methods. Tidying data makes it easy to recombine, reshape and
24404visualize bioinformatics analyses.")
24405 ;; Any version of the LGPL.
24406 (license license:lgpl3+)))
24407
24408(define-public r-graphite
24409 (package
24410 (name "r-graphite")
24411 (version "1.58.0")
24412 (source
24413 (origin
24414 (method url-fetch)
24415 (uri (bioconductor-uri "graphite" version))
24416 (sha256
24417 (base32
24418 "0c11dlv2mmh6mg8pdcy1d9kj66mgyib0p8i7isf87ffzypk38xbb"))))
24419 (properties `((upstream-name . "graphite")))
24420 (build-system r-build-system)
24421 ;; Tests need internet access.
24422 (arguments (list #:tests? #false))
24423 (propagated-inputs
24424 (list r-annotationdbi
24425 r-dir-expiry
24426 r-graph
24427 r-httr
24428 r-lifecycle
24429 r-purrr
24430 r-rappdirs
24431 r-rlang))
24432 (native-inputs (list r-a4preproc
24433 r-all
24434 r-biocstyle
24435 r-checkmate
24436 r-hgu133plus2-db
24437 r-r-rsp
24438 r-testthat))
24439 (home-page "https://bioconductor.org/packages/graphite/")
24440 (synopsis "Networks from pathway databases")
24441 (description
24442 "Graphite provides networks derived from eight public pathway databases,
24443and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
24444symbols).")
24445 (license license:agpl3+)))
24446
24447(define-public r-reactomepa
24448 (package
24449 (name "r-reactomepa")
24450 (version "1.56.0")
24451 (source
24452 (origin
24453 (method url-fetch)
24454 (uri (bioconductor-uri "ReactomePA" version))
24455 (sha256
24456 (base32
24457 "0wpgq27j5jcfm4yjy7xb5f4p8n4fsvq31dhj5h036lvjqlqmxip8"))))
24458 (properties `((upstream-name . "ReactomePA")))
24459 (build-system r-build-system)
24460 (propagated-inputs
24461 (list r-annotationdbi
24462 r-enrichit
24463 r-enrichplot
24464 r-ggplot2
24465 r-ggraph
24466 r-graphite
24467 r-gson
24468 r-igraph
24469 r-reactome-db
24470 r-yulab-utils))
24471 (native-inputs
24472 (list r-knitr r-testthat))
24473 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
24474 (synopsis "Reactome pathway analysis")
24475 (description
24476 "This package provides functions for pathway analysis based on the
24477REACTOME pathway database. It implements enrichment analysis, gene set
24478enrichment analysis and several functions for visualization.")
24479 (license license:gpl2)))
24480
24481(define-public r-ebarrays
24482 (package
24483 (name "r-ebarrays")
24484 (version "2.76.0")
24485 (source
24486 (origin
24487 (method url-fetch)
24488 (uri (bioconductor-uri "EBarrays" version))
24489 (sha256
24490 (base32
24491 "0dd9l3ca2am4734a2gw0vbbc10h1c0mnhlvm0dnxay0dcy3dvqwf"))))
24492 (properties `((upstream-name . "EBarrays")))
24493 (build-system r-build-system)
24494 (propagated-inputs
24495 (list r-biobase r-cluster r-lattice))
24496 (home-page "https://bioconductor.org/packages/EBarrays/")
24497 (synopsis "Gene clustering and differential expression identification")
24498 (description
24499 "EBarrays provides tools for the analysis of replicated/unreplicated
24500microarray data.")
24501 (license license:gpl2+)))
24502
24503(define-public r-biocbaseutils
24504 (package
24505 (name "r-biocbaseutils")
24506 (version "1.14.2")
24507 (source (origin
24508 (method url-fetch)
24509 (uri (bioconductor-uri "BiocBaseUtils" version))
24510 (sha256
24511 (base32
24512 "1fijpvdy26sqqk3m16yan7k8yw5rky3dwy2adnchz1ql43dnixyi"))))
24513 (properties `((upstream-name . "BiocBaseUtils")))
24514 (build-system r-build-system)
24515 (native-inputs (list r-knitr r-tinytest))
24516 (home-page "https://bioconductor.org/packages/BiocBaseUtils")
24517 (synopsis "General utility functions for developing Bioconductor packages")
24518 (description
24519 "The package provides utility functions related to package development.
24520These include functions that replace slots, and selectors for show methods.
24521It aims to coalesce the various helper functions often re-used throughout the
24522Bioconductor ecosystem.")
24523 (license license:artistic2.0)))
24524
24525(define-public r-bioccasestudies
24526 (package
24527 (name "r-bioccasestudies")
24528 (version "1.52.0")
24529 (source
24530 (origin
24531 (method url-fetch)
24532 (uri (bioconductor-uri "BiocCaseStudies" version))
24533 (sha256
24534 (base32
24535 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
24536 (properties
24537 `((upstream-name . "BiocCaseStudies")))
24538 (build-system r-build-system)
24539 (propagated-inputs (list r-biobase))
24540 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
24541 (synopsis "Support for the case studies monograph")
24542 (description
24543 "This package provides software and data to support the case studies
24544monograph.")
24545 (license license:artistic2.0)))
24546
24547(define-public r-bioccheck
24548 (package
24549 (name "r-bioccheck")
24550 (version "1.48.0")
24551 (source (origin
24552 (method url-fetch)
24553 (uri (bioconductor-uri "BiocCheck" version))
24554 (sha256
24555 (base32
24556 "149avgqaslz276hhihr062agsgkar0imfyjg3in2xib7257dki3r"))))
24557 (properties
24558 `((upstream-name . "BiocCheck")))
24559 (build-system r-build-system)
24560 ;; One of the tests requires Internet access to validate Bioconductor
24561 ;; version.
24562 (arguments (list #:tests? #false))
24563 (propagated-inputs
24564 (list r-biocbaseutils
24565 r-biocfilecache
24566 r-biocmanager
24567 r-biocviews
24568 r-callr
24569 r-cli
24570 r-codetools
24571 r-commonmark
24572 r-graph
24573 r-httr2
24574 r-knitr
24575 r-rvest
24576 r-stringdist
24577 r-xml2))
24578 (native-inputs
24579 (list r-knitr r-tinytest))
24580 (home-page "https://bioconductor.org/packages/BiocCheck")
24581 (synopsis "Executes Bioconductor-specific package checks")
24582 (description "This package contains tools to perform additional quality
24583checks on R packages that are to be submitted to the Bioconductor repository.")
24584 (license license:artistic2.0)))
24585
24586(define-public r-biocgraph
24587 (package
24588 (name "r-biocgraph")
24589 (version "1.74.0")
24590 (source
24591 (origin
24592 (method url-fetch)
24593 (uri (bioconductor-uri "biocGraph" version))
24594 (sha256
24595 (base32
24596 "16qxalkh0gv0hhd7lzpx8g0p79madrva77pn8vfi97r09sdzfqhx"))))
24597 (properties `((upstream-name . "biocGraph")))
24598 (build-system r-build-system)
24599 (propagated-inputs
24600 (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
24601 (home-page "https://bioconductor.org/packages/biocGraph/")
24602 (synopsis "Graph examples and use cases in Bioinformatics")
24603 (description
24604 "This package provides examples and code that make use of the
24605different graph related packages produced by Bioconductor.")
24606 (license license:artistic2.0)))
24607
24608(define-public r-biocstyle
24609 (package
24610 (name "r-biocstyle")
24611 (version "2.40.0")
24612 (source (origin
24613 (method url-fetch)
24614 (uri (bioconductor-uri "BiocStyle" version))
24615 (sha256
24616 (base32
24617 "0jb8pgsavn3jpz920bzg7zc5n8xdgd7xk829qvxbwxvdbdxnz9a1"))))
24618 (properties
24619 `((upstream-name . "BiocStyle")))
24620 (build-system r-build-system)
24621 (arguments
24622 (if (target-32bit?)
24623 (list
24624 #:phases
24625 '(modify-phases %standard-phases
24626 ;; XXX: On i686 pandoc segfaults when building self contained
24627 ;; reports.
24628 (add-after 'unpack 'prevent-pandoc-segfault
24629 (lambda _
24630 (substitute* "inst/rmarkdown/templates/html_document/skeleton/skeleton.Rmd"
24631 ((" BiocStyle::html_document")
24632 "\
24633 BiocStyle::html_document:
24634 self_contained: FALSE"))))))
24635 '()))
24636 (propagated-inputs
24637 (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
24638 (native-inputs
24639 (list ghostscript
24640 r-biocgenerics r-knitr r-runit
24641 (texlive-local-tree
24642 (list texlive-bera
24643 texlive-booktabs
24644 texlive-caption
24645 texlive-changepage
24646 texlive-enumitem
24647 texlive-etoolbox
24648 texlive-etoolbox
24649 texlive-fancyhdr
24650 texlive-fancyvrb
24651 texlive-footmisc
24652 texlive-framed
24653 texlive-geometry
24654 texlive-helvetic
24655 texlive-marginfix
24656 texlive-mathtools
24657 texlive-nowidow
24658 texlive-parnotes
24659 texlive-parskip
24660 texlive-pdfcrop
24661 texlive-placeins
24662 texlive-preprint ;authblk
24663 texlive-ragged2e
24664 texlive-soul
24665 texlive-titlesec
24666 texlive-titling
24667 texlive-xcolor
24668 texlive-xstring))))
24669 (home-page "https://bioconductor.org/packages/BiocStyle")
24670 (synopsis "Bioconductor formatting styles")
24671 (description "This package provides standard formatting styles for
24672Bioconductor PDF and HTML documents. Package vignettes illustrate use and
24673functionality.")
24674 (license license:artistic2.0)))
24675
24676(define-public r-biocviews
24677 (package
24678 (name "r-biocviews")
24679 (version "1.80.0")
24680 (source (origin
24681 (method url-fetch)
24682 (uri (bioconductor-uri "biocViews" version))
24683 (sha256
24684 (base32
24685 "0ygv58zab20js6kp8phim4r751anm2p9vh7385av6glc30kzmbhr"))))
24686 (properties
24687 `((upstream-name . "biocViews")))
24688 (build-system r-build-system)
24689 ;; Tests attempt to access http://bioconductor.org/js/versions.js
24690 (arguments (list #:tests? #false))
24691 (propagated-inputs
24692 (list r-biobase
24693 r-biocmanager
24694 r-graph
24695 r-rbgl
24696 r-rcurl
24697 r-runit
24698 r-xml))
24699 (native-inputs (list r-biocgenerics r-knitr))
24700 (home-page "https://bioconductor.org/packages/biocViews")
24701 (synopsis "Bioconductor package categorization helper")
24702 (description "The purpose of biocViews is to create HTML pages that
24703categorize packages in a Bioconductor package repository according to keywords,
24704also known as views, in a controlled vocabulary.")
24705 (license license:artistic2.0)))
24706
24707(define-public r-experimenthub
24708 (package
24709 (name "r-experimenthub")
24710 (version "3.2.0")
24711 (source
24712 (origin
24713 (method url-fetch)
24714 (uri (bioconductor-uri "ExperimentHub" version))
24715 (sha256
24716 (base32
24717 "07gyhw5fqkvk9gw1k2qfdm0nmdsfi0qrfypv4wvhlsp47cz0sa5n"))))
24718 (properties `((upstream-name . "ExperimentHub")))
24719 (build-system r-build-system)
24720 (propagated-inputs
24721 (list r-annotationhub
24722 r-biocfilecache
24723 r-biocgenerics
24724 r-biocmanager
24725 r-rappdirs
24726 r-s4vectors))
24727 (native-inputs
24728 (list r-knitr))
24729 (home-page "https://bioconductor.org/packages/ExperimentHub/")
24730 (synopsis "Client to access ExperimentHub resources")
24731 (description
24732 "This package provides a client for the Bioconductor ExperimentHub web
24733resource. ExperimentHub provides a central location where curated data from
24734experiments, publications or training courses can be accessed. Each resource
24735has associated metadata, tags and date of modification. The client creates
24736and manages a local cache of files retrieved enabling quick and reproducible
24737access.")
24738 (license license:artistic2.0)))
24739
24740(define-public r-experimenthubdata
24741 (package
24742 (name "r-experimenthubdata")
24743 (version "1.38.0")
24744 (source
24745 (origin
24746 (method url-fetch)
24747 (uri (bioconductor-uri "ExperimentHubData" version))
24748 (sha256
24749 (base32 "0saaslbmj4q944kjvglgc2c5vzxd1l0hwisxvwxqsjm1wbl9bx8h"))))
24750 (properties `((upstream-name . "ExperimentHubData")))
24751 (build-system r-build-system)
24752 (propagated-inputs (list r-annotationhubdata
24753 r-biocgenerics
24754 r-biocmanager
24755 r-curl
24756 r-dbi
24757 r-experimenthub
24758 r-httr
24759 r-s4vectors))
24760 (native-inputs (list r-knitr))
24761 (home-page "https://bioconductor.org/packages/ExperimentHubData")
24762 (synopsis "Add resources to ExperimentHub")
24763 (description
24764 "This package provides functions to add metadata to @code{ExperimentHub}
24765db and resource files to AWS S3 buckets.")
24766 (license license:artistic2.0)))
24767
24768(define-public r-grohmm
24769 (package
24770 (name "r-grohmm")
24771 (version "1.46.0")
24772 (source
24773 (origin
24774 (method url-fetch)
24775 (uri (bioconductor-uri "groHMM" version))
24776 (sha256
24777 (base32
24778 "0psz9rz9qmp9pni03cs1i14565fslq19y8xcnz9ppnqfvdrj7xq9"))))
24779 (properties `((upstream-name . "groHMM")))
24780 (build-system r-build-system)
24781 (propagated-inputs
24782 (list r-genomicalignments
24783 r-genomicranges
24784 r-iranges
24785 r-mass
24786 r-rtracklayer
24787 r-s4vectors
24788 r-seqinfo))
24789 (home-page "https://github.com/Kraus-Lab/groHMM")
24790 (synopsis "GRO-seq analysis pipeline")
24791 (description
24792 "This package provides a pipeline for the analysis of GRO-seq data.")
24793 (license license:gpl3+)))
24794
24795(define-public r-multiassayexperiment
24796 (package
24797 (name "r-multiassayexperiment")
24798 (version "1.38.0")
24799 (source
24800 (origin
24801 (method url-fetch)
24802 (uri (bioconductor-uri "MultiAssayExperiment" version))
24803 (sha256
24804 (base32
24805 "008r34ilrsd06clmffilswv69l874b3r907y5s8bzi0ws8wkyj9w"))))
24806 (properties
24807 '((upstream-name . "MultiAssayExperiment")
24808 (updater-extra-native-inputs
24809 . ("r-hdf5array" "r-reshape2"))))
24810 (build-system r-build-system)
24811 (arguments
24812 (list
24813 #:phases
24814 '(modify-phases %standard-phases
24815 ;; For vignette builder.
24816 (add-after 'unpack 'set-HOME
24817 (lambda _ (setenv "HOME" "/tmp"))))))
24818 (propagated-inputs
24819 (list r-biobase
24820 r-biocbaseutils
24821 r-biocgenerics
24822 r-delayedarray
24823 r-genomicranges
24824 r-iranges
24825 r-matrixgenerics
24826 r-s4vectors
24827 r-summarizedexperiment
24828 r-tidyr))
24829 (native-inputs
24830 (list r-hdf5array r-knitr r-raggedexperiment r-reshape2 r-testthat))
24831 (home-page "https://waldronlab.io/MultiAssayExperiment/")
24832 (synopsis "Integration of multi-omics experiments in Bioconductor")
24833 (description
24834 "MultiAssayExperiment harmonizes data management of multiple assays
24835performed on an overlapping set of specimens. It provides a familiar
24836Bioconductor user experience by extending concepts from
24837@code{SummarizedExperiment}, supporting an open-ended mix of standard data
24838classes for individual assays, and allowing subsetting by genomic ranges or
24839rownames.")
24840 (license license:artistic2.0)))
24841
24842(define-public r-biocor
24843 (package
24844 (name "r-biocor")
24845 (version "1.36.0")
24846 (source
24847 (origin
24848 (method url-fetch)
24849 (uri (bioconductor-uri "BioCor" version))
24850 (sha256
24851 (base32
24852 "1m8pc8hx5hldhvfbccw1yk2l4irblhc0z9qs2gsjlhwa0lhcba29"))))
24853 (properties `((upstream-name . "BioCor")))
24854 (build-system r-build-system)
24855 (propagated-inputs
24856 (list r-biocparallel r-gseabase r-matrix))
24857 (native-inputs
24858 (list r-knitr r-reactome-db r-spelling r-testthat))
24859 (home-page "https://llrs.github.io/BioCor/")
24860 (synopsis "Functional similarities")
24861 (description
24862 "This package provides tools to calculate functional similarities based
24863on the pathways described on KEGG and REACTOME or in gene sets. These
24864similarities can be calculated for pathways or gene sets, genes, or clusters
24865and combined with other similarities. They can be used to improve networks,
24866gene selection, testing relationships, and so on.")
24867 (license license:expat)))
24868
24869(define-public r-biocpkgtools
24870 (package
24871 (name "r-biocpkgtools")
24872 (version "1.30.0")
24873 (source
24874 (origin
24875 (method url-fetch)
24876 (uri (bioconductor-uri "BiocPkgTools" version))
24877 (sha256
24878 (base32
24879 "0nv6vq5zkaavbmcbhn4lmgsa6kps6zr38hl1m2h2zrwpzkv368kg"))
24880 (snippet
24881 '(for-each delete-file
24882 '("inst/htmlwidgets/lib/bioc_explore/bootstrap.min.js"
24883 "inst/htmlwidgets/lib/bioc_explore/d3.v3.min.js"
24884 "inst/htmlwidgets/lib/bioc_explore/jquery-2.2.4.min.js"
24885 "inst/htmlwidgets/lib/bioc_explore/underscore-min.js")))))
24886 (properties `((upstream-name . "BiocPkgTools")))
24887 (build-system r-build-system)
24888 (arguments
24889 (list
24890 ;; Tests attempt to connect to the internet.
24891 #:tests? #false
24892 #:modules '((guix build utils)
24893 (guix build r-build-system)
24894 (srfi srfi-1))
24895 #:phases
24896 '(modify-phases %standard-phases
24897 (add-after 'unpack 'process-javascript
24898 (lambda* (#:key inputs #:allow-other-keys)
24899 (with-directory-excursion "inst/htmlwidgets/lib/bioc_explore"
24900 (call-with-values
24901 (lambda ()
24902 (unzip2
24903 `((,(assoc-ref inputs "bootstrap.js")
24904 "bootstrap.min.js")
24905 (,(assoc-ref inputs "d3.v3.js")
24906 "d3.v3.min.js")
24907 (,(assoc-ref inputs "jquery-2.2.4.js")
24908 "jquery-2.2.4.min.js")
24909 (,(search-input-file inputs "/underscore.js")
24910 "underscore-min.js"))))
24911 (lambda (sources targets)
24912 (for-each (lambda (source target)
24913 (format #true "Processing ~a --> ~a~%"
24914 source target)
24915 (invoke "esbuild" source "--minify"
24916 (string-append "--outfile=" target)))
24917 sources targets)))))))))
24918 (propagated-inputs
24919 (list r-biocfilecache
24920 r-biocmanager
24921 r-biocviews
24922 r-curl
24923 r-dplyr
24924 r-dt
24925 r-gh
24926 r-glue
24927 r-graph
24928 r-htmltools
24929 r-htmlwidgets
24930 r-httr
24931 r-httr2
24932 r-igraph
24933 r-jsonlite
24934 r-lubridate
24935 r-purrr
24936 r-rbgl
24937 r-readr
24938 r-rlang
24939 r-rvest
24940 r-stringr
24941 r-tibble
24942 r-tidyr
24943 r-xml2
24944 r-yaml))
24945 (native-inputs
24946 (list esbuild r-knitr r-testthat
24947 (origin
24948 (method url-fetch)
24949 (uri
24950 "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.6/dist/js/bootstrap.js")
24951 (sha256
24952 (base32
24953 "07fm28xbkb7a5n7zgmfxgbl2g5j010r4gvc54y79v1f119s3kz6y")))
24954 ;; 3.5.17
24955 (origin
24956 (method url-fetch)
24957 (uri "https://d3js.org/d3.v3.js")
24958 (sha256
24959 (base32
24960 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))
24961 (origin
24962 (method url-fetch)
24963 (uri "https://code.jquery.com/jquery-2.2.4.js")
24964 (sha256
24965 (base32
24966 "18m6qmmsm3knvybf6gpwmwiasi05y98gcpb364if8qh94gv90gl9")))
24967 (origin
24968 (method git-fetch)
24969 (uri (git-reference
24970 (url "https://github.com/jashkenas/underscore")
24971 (commit "1.8.3")))
24972 (file-name (git-file-name "underscorejs" "1.8.3"))
24973 (sha256
24974 (base32
24975 "1r54smxpl3c6jg6py29xjc2l1z49rlm1h48vr9i57wvnkbnbl0h3")))))
24976 (home-page "https://github.com/seandavi/BiocPkgTools")
24977 (synopsis "Collection of tools for learning about Bioconductor packages")
24978 (description
24979 "Bioconductor has a rich ecosystem of metadata around packages, usage,
24980and build status. This package is a simple collection of functions to access
24981that metadata from R. The goal is to expose metadata for data mining and
24982value-added functionality such as package searching, text mining, and
24983analytics on packages.")
24984 (license license:expat)))
24985
24986(define-public r-biocset
24987 (package
24988 (name "r-biocset")
24989 (version "1.25.0")
24990 (source
24991 (origin
24992 (method url-fetch)
24993 (uri (bioconductor-uri "BiocSet" version))
24994 (sha256
24995 (base32
24996 "1dgwdn9q4gll0drxlfr4ibmw7q6zfvm53g6dq4x1gsca8n1za73n"))))
24997 (properties
24998 '((upstream-name . "BiocSet")
24999 (updater-extra-native-inputs . ("r-gseabase"))))
25000 (build-system r-build-system)
25001 (arguments
25002 (list
25003 #:skipped-tests
25004 ;; One test tries to connect to a website. ("'kegg_sets\\(\\)' works")
25005 '("test_mapping_set.R"
25006 ("test_BiocSet-methods.R"
25007 ;; This test fails because "The `add` argument of `group_by()` was
25008 ;; deprecated in dplyr 1.0.0 and is now defunct."
25009 "'summarise.BiocSet\\(\\)' works"
25010 ;; Expected `es_elementset(es2)$element` to equal
25011 ;; `sort(es_elementset(es)$element)`.
25012 "'arrange.BiocSet\\(\\)' works"
25013 ;; Actual comparison: 17900 < 18105
25014 "'as.list.BiocSet\\(\\)' works")
25015 ("test_tbl_elementset_base-class.R"
25016 ;; `set` must be size 1, not 52.
25017 "'summarise.tbl_elementset_base\\(\\)' works"))))
25018 (propagated-inputs
25019 (list r-annotationdbi
25020 r-biocio
25021 r-dplyr
25022 r-keggrest
25023 r-ontologyindex
25024 r-plyr
25025 r-rlang
25026 r-s4vectors
25027 r-tibble
25028 r-tidyr))
25029 (native-inputs
25030 (list r-go-db r-gseabase r-knitr r-org-hs-eg-db r-testthat))
25031 (home-page "https://bioconductor.org/packages/BiocSet")
25032 (synopsis "Representing different biological sets")
25033 (description
25034 "BiocSet displays different biological sets in a triple tibble format.
25035These three tibbles are @code{element}, @code{set}, and @code{elementset}.
25036The user has the ability to activate one of these three tibbles to perform
25037common functions from the @code{dplyr} package. Mapping functionality and
25038accessing web references for elements/sets are also available in BiocSet.")
25039 (license license:artistic2.0)))
25040
25041(define-public r-biocworkflowtools
25042 (package
25043 (name "r-biocworkflowtools")
25044 (version "1.38.0")
25045 (source
25046 (origin
25047 (method url-fetch)
25048 (uri (bioconductor-uri "BiocWorkflowTools" version))
25049 (sha256
25050 (base32
25051 "051nj8dz78h15jz4gmgrwcykgsq390hc2k98wybs57bhcfdmhjc2"))))
25052 (properties
25053 `((upstream-name . "BiocWorkflowTools")))
25054 (build-system r-build-system)
25055 (propagated-inputs
25056 (list r-biocstyle
25057 r-bookdown
25058 r-git2r
25059 r-httr
25060 r-knitr
25061 r-rmarkdown
25062 r-rstudioapi
25063 r-stringr
25064 r-usethis))
25065 (native-inputs
25066 (list r-knitr))
25067 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
25068 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
25069 (description
25070 "This package provides functions to ease the transition between
25071Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
25072 (license license:expat)))
25073
25074(define-public r-biodist
25075 (package
25076 (name "r-biodist")
25077 (version "1.84.0")
25078 (source
25079 (origin
25080 (method url-fetch)
25081 (uri (bioconductor-uri "bioDist" version))
25082 (sha256
25083 (base32
25084 "11zryj6lxcc9r5xygvx7mw8n6k434kssz0bxijr3vbw2yar1msy1"))))
25085 (properties `((upstream-name . "bioDist")))
25086 (build-system r-build-system)
25087 (propagated-inputs
25088 (list r-biobase r-kernsmooth))
25089 (home-page "https://bioconductor.org/packages/bioDist/")
25090 (synopsis "Different distance measures")
25091 (description
25092 "This package provides a collection of software tools for calculating
25093distance measures.")
25094 (license license:artistic2.0)))
25095
25096(define-public r-pcatools
25097 (package
25098 (name "r-pcatools")
25099 (version "2.24.0")
25100 (source
25101 (origin
25102 (method url-fetch)
25103 (uri (bioconductor-uri "PCAtools" version))
25104 (sha256
25105 (base32
25106 "17sskhb35b2qx28rg5v1dfj5ara4bsk8ad0ys7q9091b6npgyzhc"))))
25107 (properties `((upstream-name . "PCAtools")))
25108 (build-system r-build-system)
25109 (propagated-inputs
25110 (list r-assorthead
25111 r-beachmat
25112 r-bh
25113 r-biocparallel
25114 r-biocsingular
25115 r-cowplot
25116 r-delayedarray
25117 r-delayedmatrixstats
25118 r-dqrng
25119 r-ggplot2
25120 r-ggrepel
25121 r-lattice
25122 r-matrix
25123 r-rcpp
25124 r-reshape2))
25125 (native-inputs (list r-knitr r-scran r-testthat))
25126 (home-page "https://github.com/kevinblighe/PCAtools")
25127 (synopsis "PCAtools: everything Principal Components Analysis")
25128 (description
25129 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
25130structure of the data without the need to build any model to represent it.
25131This \"summary\" of the data is arrived at through a process of reduction that
25132can transform the large number of variables into a lesser number that are
25133uncorrelated (i.e. the 'principal components'), while at the same time being
25134capable of easy interpretation on the original data. PCAtools provides
25135functions for data exploration via PCA, and allows the user to generate
25136publication-ready figures. PCA is performed via @code{BiocSingular}; users
25137can also identify an optimal number of principal components via different
25138metrics, such as the elbow method and Horn's parallel analysis, which has
25139relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
25140dimensional mass cytometry data.")
25141 (license license:gpl3)))
25142
25143(define-public r-rgreat
25144 (package
25145 (name "r-rgreat")
25146 (version "2.14.0")
25147 (source
25148 (origin
25149 (method url-fetch)
25150 (uri (bioconductor-uri "rGREAT" version))
25151 (sha256
25152 (base32
25153 "00n2w6yag3wjhzssz0vx04a9l2is8aqf5zly0pyfnb63xpjl3nyj"))))
25154 (properties `((upstream-name . "rGREAT")))
25155 (build-system r-build-system)
25156 (propagated-inputs
25157 (list r-annotationdbi
25158 r-circlize
25159 r-digest
25160 r-doparallel
25161 r-dt
25162 r-foreach
25163 r-genomeinfodb
25164 r-genomicfeatures
25165 r-genomicranges
25166 r-getoptlong
25167 r-globaloptions
25168 r-go-db
25169 r-iranges
25170 r-org-hs-eg-db
25171 r-progress
25172 r-rcolorbrewer
25173 r-rcpp
25174 r-rcurl
25175 r-rjson
25176 r-s4vectors
25177 r-shiny
25178 r-txdb-hsapiens-ucsc-hg19-knowngene
25179 r-txdb-hsapiens-ucsc-hg38-knowngene))
25180 (native-inputs (list r-knitr r-testthat))
25181 (home-page "https://github.com/jokergoo/rGREAT")
25182 (synopsis "Client for GREAT analysis")
25183 (description
25184 "This package makes GREAT (Genomic Regions Enrichment of Annotations
25185Tool) analysis automatic by constructing a HTTP POST request according to
25186user's input and automatically retrieving results from GREAT web server.")
25187 (license license:expat)))
25188
25189(define-public r-m3c
25190 (package
25191 (name "r-m3c")
25192 (version "1.34.0")
25193 (source
25194 (origin
25195 (method url-fetch)
25196 (uri (bioconductor-uri "M3C" version))
25197 (sha256
25198 (base32
25199 "13k3ynqyz4vhqihwgib69xrmmqb22gnd2ddz0xavzjb2csndadim"))))
25200 (properties `((upstream-name . "M3C")))
25201 (build-system r-build-system)
25202 (propagated-inputs
25203 (list r-cluster
25204 r-corpcor
25205 r-doparallel
25206 r-dosnow
25207 r-foreach
25208 r-ggplot2
25209 r-matrix
25210 r-matrixcalc
25211 r-rtsne
25212 r-umap))
25213 (native-inputs (list r-knitr))
25214 (home-page "https://bioconductor.org/packages/M3C")
25215 (synopsis "Monte Carlo reference-based consensus clustering")
25216 (description
25217 "M3C is a consensus clustering algorithm that uses a Monte Carlo
25218simulation to eliminate overestimation of @code{K} and can reject the null
25219hypothesis @code{K=1}.")
25220 (license license:agpl3+)))
25221
25222(define-public r-icens
25223 (package
25224 (name "r-icens")
25225 (version "1.84.0")
25226 (source
25227 (origin
25228 (method url-fetch)
25229 (uri (bioconductor-uri "Icens" version))
25230 (sha256
25231 (base32
25232 "05g7439yqklzc3l69qmqhbzmdpd4r2ih11l3qlfbbab2z8xrrc71"))))
25233 (properties `((upstream-name . "Icens")))
25234 (build-system r-build-system)
25235 (propagated-inputs
25236 (list r-survival))
25237 (home-page "https://bioconductor.org/packages/Icens")
25238 (synopsis "NPMLE for censored and truncated data")
25239 (description
25240 "This package provides many functions for computing the
25241@dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
25242truncated data.")
25243 (license license:artistic2.0)))
25244
25245;; This is a CRAN package but it depends on r-icens, which is published on
25246;; Bioconductor.
25247(define-public r-interval
25248 (package
25249 (name "r-interval")
25250 (version "1.1-1.0")
25251 (source
25252 (origin
25253 (method url-fetch)
25254 (uri (cran-uri "interval" version))
25255 (sha256
25256 (base32
25257 "0kmz7wpgc4kspr11l0nls4rq0qk2lbsg3s4bpl0zs4r4pjcrwvrx"))))
25258 (properties `((upstream-name . "interval")))
25259 (build-system r-build-system)
25260 (propagated-inputs
25261 (list r-icens r-mlecens r-perm r-survival))
25262 (home-page "https://cran.r-project.org/web/packages/interval/")
25263 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
25264 (description
25265 "This package provides functions to fit nonparametric survival curves,
25266plot them, and perform logrank or Wilcoxon type tests.")
25267 (license license:gpl2+)))
25268
25269;; This is a CRAN package, but it depends on r-interval, which depends on a
25270;; Bioconductor package.
25271(define-public r-fhtest
25272 (package
25273 (name "r-fhtest")
25274 (version "1.5.1")
25275 (source
25276 (origin
25277 (method url-fetch)
25278 (uri (cran-uri "FHtest" version))
25279 (sha256
25280 (base32
25281 "0x7lr88w0b09ng7nps490kgj8aqdjzmp9skv9iwqgn871pnpydms"))))
25282 (properties `((upstream-name . "FHtest")))
25283 (build-system r-build-system)
25284 (propagated-inputs
25285 (list r-interval r-kmsurv r-mass r-perm r-survival))
25286 (home-page "https://cran.r-project.org/web/packages/FHtest/")
25287 (synopsis "Tests for survival data based on the Fleming-Harrington class")
25288 (description
25289 "This package provides functions to compare two or more survival curves
25290with:
25291
25292@itemize
25293@item The Fleming-Harrington test for right-censored data based on
25294 permutations and on counting processes.
25295@item An extension of the Fleming-Harrington test for interval-censored data
25296 based on a permutation distribution and on a score vector distribution.
25297@end itemize
25298")
25299 (license license:gpl2+)))
25300
25301(define-public r-fourcseq
25302 (package
25303 (name "r-fourcseq")
25304 (version "1.24.0")
25305 (source
25306 (origin
25307 (method url-fetch)
25308 (uri (bioconductor-uri "FourCSeq" version))
25309 (sha256
25310 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
25311 (properties `((upstream-name . "FourCSeq")))
25312 (build-system r-build-system)
25313 (propagated-inputs
25314 (list r-biobase
25315 r-biostrings
25316 r-deseq2
25317 r-fda
25318 r-genomicalignments
25319 r-genomicranges
25320 r-ggbio
25321 r-ggplot2
25322 r-gtools
25323 r-lsd
25324 r-matrix
25325 r-reshape2
25326 r-rsamtools
25327 r-rtracklayer
25328 r-summarizedexperiment))
25329 (native-inputs
25330 (list r-knitr))
25331 (home-page
25332 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
25333 (synopsis "Analysis of multiplexed 4C sequencing data")
25334 (description
25335 "This package is an R package dedicated to the analysis of (multiplexed)
253364C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
25337interactions between DNA elements and identify differential interactions
25338between conditions. The statistical analysis in R starts with individual bam
25339files for each sample as inputs. To obtain these files, the package contains
25340a Python script to demultiplex libraries and trim off primer sequences. With
25341a standard alignment software the required bam files can be then be
25342generated.")
25343 (license license:gpl3+)))
25344
25345(define-public r-preprocesscore
25346 (package
25347 (name "r-preprocesscore")
25348 (version "1.74.0")
25349 (source
25350 (origin
25351 (method url-fetch)
25352 (uri (bioconductor-uri "preprocessCore" version))
25353 (sha256
25354 (base32
25355 "1xvzkd96naczph49hfzg3lvhps48psjclw921z2v531ryh91ax9s"))))
25356 (properties
25357 `((upstream-name . "preprocessCore")))
25358 (build-system r-build-system)
25359 (arguments
25360 (list
25361 ;; This is necessary because we use OpenBLAS. See
25362 ;; https://github.com/Bioconductor/bioconductor_docker/issues/22
25363 #:configure-flags '(list "--disable-threading")
25364 #:phases
25365 '(modify-phases %standard-phases
25366 (add-after 'unpack 'disable-threading
25367 (lambda _
25368 ;; Two problems: This package only checks for flexiblas (not
25369 ;; openblas) and "R CMD config BLAS_LIBS" does not mention
25370 ;; openblas.
25371 (substitute* "configure"
25372 (("^BLAS_LIBS=.*") "BLAS_LIBS=flexiblas\n")))))))
25373 (home-page "https://github.com/bmbolstad/preprocessCore")
25374 (synopsis "Collection of pre-processing functions")
25375 (description
25376 "This package provides a library of core pre-processing and normalization
25377routines.")
25378 (license license:lgpl2.0+)))
25379
25380(define-public r-s4arrays
25381 (package
25382 (name "r-s4arrays")
25383 (version "1.12.0")
25384 (source (origin
25385 (method url-fetch)
25386 (uri (bioconductor-uri "S4Arrays" version))
25387 (sha256
25388 (base32
25389 "0f73c47dp8gj248h9mgzf3blnclf4hvdzpqfwxxb2d8w9r8y3x26"))))
25390 (properties
25391 '((upstream-name . "S4Arrays")
25392 (updater-ignored-native-inputs . ("r-delayedarray"))))
25393 (build-system r-build-system)
25394 ;; Tests require r-delayedarray, but adding it would introduce a
25395 ;; dependency cycle.
25396 (arguments (list #:tests? #false))
25397 (propagated-inputs
25398 (list r-abind r-biocgenerics r-iranges r-matrix r-s4vectors))
25399 (native-inputs (list r-knitr r-testthat))
25400 (home-page "https://bioconductor.org/packages/S4Arrays")
25401 (synopsis "Foundation of array-like containers in Bioconductor")
25402 (description
25403 "The S4Arrays package defines the @code{Array} virtual class to be
25404extended by other S4 classes that wish to implement a container with an
25405array-like semantic. It also provides:
25406
25407@enumerate
25408@item low-level functionality meant to help the developer of such container to
25409 implement basic operations like display, subsetting, or coercion of their
25410 array-like objects to an ordinary matrix or array, and
25411@item a framework that facilitates block processing of array-like
25412 objects (typically on-disk objects).
25413@end enumerate
25414")
25415 (license license:artistic2.0)))
25416
25417(define-public r-s4vectors
25418 (package
25419 (name "r-s4vectors")
25420 (version "0.50.1")
25421 (source (origin
25422 (method url-fetch)
25423 (uri (bioconductor-uri "S4Vectors" version))
25424 (sha256
25425 (base32
25426 "03k9kk6w6z1ri2yi8izb7b2v9lmhmdbsniqsa03bq92lcagaqpd8"))))
25427 (properties
25428 '((upstream-name . "S4Vectors")
25429 (updater-ignored-native-inputs
25430 . ("r-genomicranges" "r-graph" "r-iranges" "r-shortread"))))
25431 (build-system r-build-system)
25432 (arguments
25433 (list
25434 ;; These tests require r-iranges and r-genomicranges, which depend on
25435 ;; this package.
25436 #:test-directory "inst/unitTests/"
25437 #:skipped-tests
25438 '("test_DataFrame-class.R"
25439 "test_DataFrame-combine.R"
25440 "test_expand-methods.R"
25441 "test_List-class.R"
25442 "test_List-utils.R"
25443 "test_Pairs-class.R"
25444 "test_Rle-class.R"
25445 "test_Rle-utils.R"
25446 "test_Vector-merge.R")))
25447 (propagated-inputs
25448 (list r-biocgenerics))
25449 (native-inputs (list r-knitr r-runit))
25450 (home-page "https://bioconductor.org/packages/S4Vectors")
25451 (synopsis "S4 implementation of vectors and lists")
25452 (description
25453 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
25454classes and a set of generic functions that extend the semantic of ordinary
25455vectors and lists in R. Package developers can easily implement vector-like
25456or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
25457In addition, a few low-level concrete subclasses of general interest (e.g.
25458@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
25459S4Vectors package itself.")
25460 (license license:artistic2.0)))
25461
25462;; This is a CRAN package, but it depends on preprocessorcore, which is a
25463;; Bioconductor package.
25464(define-public r-wgcna
25465 (package
25466 (name "r-wgcna")
25467 (version "1.74")
25468 (source
25469 (origin
25470 (method url-fetch)
25471 (uri (cran-uri "WGCNA" version))
25472 (sha256
25473 (base32
25474 "1mjmz7qpgnkd07ar02qd9ff4r0d3brf6v4xzc4dz11r2p0by2qag"))))
25475 (properties `((upstream-name . "WGCNA")))
25476 (build-system r-build-system)
25477 (propagated-inputs
25478 (list r-doparallel
25479 r-dynamictreecut
25480 r-fastcluster
25481 r-foreach
25482 r-hmisc
25483 r-impute
25484 r-matrixstats
25485 r-preprocesscore
25486 r-rcpp
25487 r-survival))
25488 (home-page
25489 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
25490 (synopsis "Weighted correlation network analysis")
25491 (description
25492 "This package provides functions necessary to perform Weighted
25493Correlation Network Analysis on high-dimensional data. It includes functions
25494for rudimentary data cleaning, construction and summarization of correlation
25495networks, module identification and functions for relating both variables and
25496modules to sample traits. It also includes a number of utility functions for
25497data manipulation and visualization.")
25498 (license license:gpl2+)))
25499
25500(define-public r-rgraphviz
25501 (package
25502 (name "r-rgraphviz")
25503 (version "2.56.0")
25504 (source
25505 (origin
25506 (method url-fetch)
25507 (uri (bioconductor-uri "Rgraphviz" version))
25508 (sha256
25509 (base32
25510 "1691ivynyjr9mz806vqzgkf2d09yj9nk6nml6vi7bn3dkbfagr3x"))))
25511 (properties `((upstream-name . "Rgraphviz")))
25512 (build-system r-build-system)
25513 (arguments
25514 `(#:phases
25515 (modify-phases %standard-phases
25516 (add-after 'unpack 'make-reproducible
25517 (lambda _
25518 ;; The replacement value is taken from src/graphviz/builddate.h
25519 (substitute* "src/graphviz/configure"
25520 (("VERSION_DATE=.*")
25521 "VERSION_DATE=20200427.2341\n")))))))
25522 ;; FIXME: Rgraphviz bundles the sources of an older variant of
25523 ;; graphviz. It does not build with the latest version of graphviz, so
25524 ;; we do not add graphviz to the inputs.
25525 (inputs (list zlib))
25526 (propagated-inputs
25527 (list r-graph))
25528 (native-inputs
25529 (list pkg-config r-biocgenerics r-runit r-xml))
25530 (home-page "https://bioconductor.org/packages/Rgraphviz")
25531 (synopsis "Plotting capabilities for R graph objects")
25532 (description
25533 "This package interfaces R with the graphviz library for plotting R graph
25534objects from the @code{graph} package.")
25535 (license license:epl1.0)))
25536
25537(define-public r-fishpond
25538 (package
25539 (name "r-fishpond")
25540 (version "2.18.0")
25541 (source (origin
25542 (method url-fetch)
25543 (uri (bioconductor-uri "fishpond" version))
25544 (sha256
25545 (base32
25546 "1ibq2hi3k7gbvmc343ymkm28gjhz0dczm3zisgrzsh67ki647lsl"))))
25547 (properties
25548 '((upstream-name . "fishpond")
25549 (updater-extra-native-inputs . ("r-samr" "r-tximportdata"))))
25550 (build-system r-build-system)
25551 (propagated-inputs
25552 (list r-abind
25553 r-genomicranges
25554 r-gtools
25555 r-iranges
25556 r-jsonlite
25557 r-matrix
25558 r-matrixstats
25559 r-qvalue
25560 r-s4vectors
25561 r-singlecellexperiment
25562 r-summarizedexperiment
25563 r-svmisc))
25564 (native-inputs (list r-annotationhub
25565 r-data-table
25566 r-deseq2
25567 r-ensembldb
25568 r-knitr
25569 r-samr
25570 r-scran
25571 r-testthat
25572 r-tximeta
25573 r-tximportdata))
25574 (home-page "https://github.com/mikelove/fishpond")
25575 (synopsis "Downstream methods and tools for expression data")
25576 (description
25577 "The @code{fishpond} package contains methods for differential transcript
25578and gene expression analysis of RNA-seq data using inferential replicates for
25579uncertainty of abundance quantification, as generated by Gibbs sampling or
25580bootstrap sampling. Also the package contains a number of utilities for
25581working with Salmon and Alevin quantification files.")
25582 (license license:gpl2)))
25583
25584(define-public r-fithic
25585 (package
25586 (name "r-fithic")
25587 (version "1.38.0")
25588 (source (origin
25589 (method url-fetch)
25590 (uri (bioconductor-uri "FitHiC" version))
25591 (sha256
25592 (base32
25593 "1jqnw4ppgrczpdz68gqjxn3d678hajzqkclnllfr0xd33fqcghwr"))))
25594 (properties `((upstream-name . "FitHiC")))
25595 (build-system r-build-system)
25596 (propagated-inputs
25597 (list r-data-table r-fdrtool r-rcpp))
25598 (native-inputs
25599 (list r-knitr))
25600 (home-page "https://bioconductor.org/packages/FitHiC")
25601 (synopsis "Confidence estimation for intra-chromosomal contact maps")
25602 (description
25603 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
25604intra-chromosomal contact maps produced by genome-wide genome architecture
25605assays such as Hi-C.")
25606 (license license:gpl2+)))
25607
25608(define-public r-h5mread
25609 (package
25610 (name "r-h5mread")
25611 (version "1.4.0")
25612 (source
25613 (origin
25614 (method url-fetch)
25615 (uri (bioconductor-uri "h5mread" version))
25616 (sha256
25617 (base32 "19lgkd0n52jbpwqpxjfsp79nngmmv2q36yzk30ny6aasfr5a4dg9"))))
25618 (properties
25619 '((upstream-name . "h5mread")
25620 ;; Avoid dependency cycle.
25621 (updater-ignored-native-inputs . ("r-hdf5array"))))
25622 (build-system r-build-system)
25623 (propagated-inputs (list r-biocgenerics
25624 r-iranges
25625 r-rhdf5
25626 r-rhdf5filters
25627 r-rhdf5lib
25628 r-s4arrays
25629 r-s4vectors
25630 r-sparsearray))
25631 (native-inputs (list r-knitr r-testthat))
25632 (home-page "https://bioconductor.org/packages/h5mread")
25633 (synopsis "Fast HDF5 reader")
25634 (description
25635 "The main function in the h5mread package is @code{h5mread()}, which
25636allows reading arbitrary data from an HDF5 dataset into R, similarly to what
25637the @code{h5read()} function from the rhdf5 package does. In the case of
25638@code{h5mread()}, the implementation has been optimized to make it as fast and
25639memory-efficient as possible.")
25640 (license license:artistic2.0)))
25641
25642(define-public r-hitc
25643 (package
25644 (name "r-hitc")
25645 (version "1.56.0")
25646 (source (origin
25647 (method url-fetch)
25648 (uri (bioconductor-uri "HiTC" version))
25649 (sha256
25650 (base32
25651 "1zm7bhdjzn26hsy2ibx73jzr4d21vs328g7vcg9x0r2wsfr3vy7j"))))
25652 (properties `((upstream-name . "HiTC")))
25653 (build-system r-build-system)
25654 (propagated-inputs
25655 (list r-biostrings
25656 r-genomicranges
25657 r-iranges
25658 r-matrix
25659 r-rcolorbrewer
25660 r-rtracklayer
25661 r-seqinfo))
25662 (home-page "https://bioconductor.org/packages/HiTC")
25663 (synopsis "High throughput chromosome conformation capture analysis")
25664 (description
25665 "The HiTC package was developed to explore high-throughput \"C\" data
25666such as 5C or Hi-C. Dedicated R classes as well as standard methods for
25667quality controls, normalization, visualization, and further analysis are also
25668provided.")
25669 (license license:artistic2.0)))
25670
25671(define-public r-hdf5array
25672 (package
25673 (name "r-hdf5array")
25674 (version "1.40.0")
25675 (source
25676 (origin
25677 (method url-fetch)
25678 (uri (bioconductor-uri "HDF5Array" version))
25679 (sha256
25680 (base32
25681 "1krdy7jvxns28lx8pq6dkcw3kjpy42xc2c9krbq539qiwhl5krka"))))
25682 (properties
25683 '((upstream-name . "HDF5Array")
25684 (updater-ignored-native-inputs . ("r-zellkonverter"))
25685 (updater-extra-native-inputs . ("r-runit"))))
25686 (build-system r-build-system)
25687 (arguments
25688 (list
25689 #:phases
25690 '(modify-phases %standard-phases
25691 (add-after 'unpack 'delete-bad-tests
25692 (lambda _
25693 ;; This file depends on r-zellkonverter, which uses r-basilisk to
25694 ;; set up a Conda environment. We don't want that. It also
25695 ;; leads to a dependency cycle, because zellkonverter directly
25696 ;; and indirectly depends on hdf5array.
25697 (delete-file "inst/unitTests/test_H5ADMatrixSeed-class.R"))))))
25698 (propagated-inputs
25699 (list r-biocgenerics
25700 r-delayedarray
25701 r-h5mread
25702 r-iranges
25703 r-matrix
25704 r-rhdf5
25705 r-s4arrays
25706 r-s4vectors
25707 r-sparsearray))
25708 (native-inputs
25709 (list r-biocparallel r-knitr r-runit r-singlecellexperiment))
25710 (home-page "https://bioconductor.org/packages/HDF5Array")
25711 (synopsis "HDF5 back end for DelayedArray objects")
25712 (description "This package provides an array-like container for convenient
25713access and manipulation of HDF5 datasets. It supports delayed operations and
25714block processing.")
25715 (license license:artistic2.0)))
25716
25717(define-public r-rhdf5lib
25718 (package
25719 (name "r-rhdf5lib")
25720 (version "2.0.0")
25721 (source
25722 (origin
25723 (method url-fetch)
25724 (uri (bioconductor-uri "Rhdf5lib" version))
25725 (sha256
25726 (base32
25727 "10hzw4fasxrrhrnjpbfvpi9ldv6q28sc9pimkiynkjjadx9x7b56"))
25728 (modules '((guix build utils)))
25729 (snippet
25730 '(delete-file-recursively "vendor"))))
25731 (properties
25732 '((upstream-name . "Rhdf5lib")
25733 (updater-extra-propagated-inputs
25734 . ("zlib"))
25735 (updater-extra-native-inputs
25736 . ("r-mockery"))))
25737 (build-system r-build-system)
25738 (arguments
25739 (list
25740 #:test-directory "inst/tinytest"
25741 #:skipped-tests
25742 ;; We don't link with a bundled static library, so these tests fail.
25743 '("test_link_flags.R")
25744 #:phases
25745 #~(modify-phases %standard-phases
25746 (add-after 'unpack 'do-not-use-bundled-hdf5
25747 (lambda* (#:key inputs #:allow-other-keys)
25748 (for-each delete-file '("configure" "configure.win"))
25749 (substitute* "DESCRIPTION"
25750 (("LinkingTo: biocmake.*") ""))
25751 (substitute* "R/zzz.R"
25752 (("libhdf5_cpp.a") "libhdf5_cpp.so")
25753 (("libhdf5.a") "libhdf5.so")
25754 (("libhdf5_hl.a") "libhdf5_hl.so")
25755 (("libhdf5_hl_cpp.a") "libhdf5_hl_cpp.so")
25756 (("system.file\\(\"lib\", package=\"Rhdf5lib\", mustWork=TRUE\\)")
25757 (string-append "\"" #$(this-package-input "hdf5") "/lib/\"\n"))
25758 (("system.file\\(\"lib\", \"libhdf5.settings\",.*")
25759 (string-append "\""
25760 (search-input-file inputs "lib/libhdf5.settings")
25761 "\"\n"))
25762 (("file.path\\(path, \"libhdf5.settings\"\\)")
25763 (string-append "\""
25764 (search-input-file inputs "lib/libhdf5.settings")
25765 "\"\n"))))))))
25766 (propagated-inputs
25767 (list hdf5 zlib))
25768 (native-inputs
25769 (list r-knitr
25770 r-mockery
25771 r-tinytest))
25772 (home-page "https://bioconductor.org/packages/Rhdf5lib")
25773 (synopsis "HDF5 library as an R package")
25774 (description "This package provides C and C++ HDF5 libraries for use in R
25775packages.")
25776 (license license:artistic2.0)))
25777
25778(define-public r-beachmat
25779 (package
25780 (name "r-beachmat")
25781 (version "2.28.0")
25782 (source
25783 (origin
25784 (method url-fetch)
25785 (uri (bioconductor-uri "beachmat" version))
25786 (sha256
25787 (base32
25788 "0fs5qhwkkcwiqlrki0f3dbic9bjjs6iq2spj56csvvsxk6206cib"))))
25789 (build-system r-build-system)
25790 (arguments
25791 (list
25792 #:skipped-tests
25793 '(("test-initializeCpp-other.R"
25794 ;; This test requires r-beachmat-hdf5, but that package depends on
25795 ;; r-beachmat.
25796 "initialization works correctly with the HDF5Arrays"))))
25797 (propagated-inputs
25798 (list r-assorthead
25799 r-biocgenerics
25800 r-delayedarray
25801 r-matrix
25802 r-rcpp
25803 r-sparsearray))
25804 (native-inputs
25805 (list r-biocparallel r-hdf5array r-knitr r-testthat))
25806 (home-page "https://bioconductor.org/packages/beachmat")
25807 (synopsis "Compiling Bioconductor to handle each matrix type")
25808 (description "This package provides a consistent C++ class interface for a
25809variety of commonly used matrix types, including sparse and HDF5-backed
25810matrices.")
25811 (license license:gpl3)))
25812
25813(define-public r-beachmat-hdf5
25814 (package
25815 (name "r-beachmat-hdf5")
25816 (version "1.10.0")
25817 (source
25818 (origin
25819 (method url-fetch)
25820 (uri (bioconductor-uri "beachmat.hdf5" version))
25821 (sha256
25822 (base32 "0p6pl69px5a4npfn3dxm116jzb1a0wnv3ag7xxj8w8qhx85pjkja"))))
25823 (properties `((upstream-name . "beachmat.hdf5")))
25824 (build-system r-build-system)
25825 (propagated-inputs (list r-assorthead
25826 r-beachmat
25827 r-delayedarray
25828 r-hdf5array
25829 r-rcpp
25830 r-rhdf5lib))
25831 (native-inputs (list r-knitr r-matrix r-rhdf5 r-testthat))
25832 (home-page "https://bioconductor.org/packages/beachmat.hdf5")
25833 (synopsis "beachmat bindings for HDF5-backed matrices")
25834 (description
25835 "This package extends beachmat to support initialization of tatami
25836matrices from HDF5-backed arrays. This allows C++ code in downstream packages
25837to directly call the HDF5 C/C++ library to access array data, without the need
25838for block processing via @code{DelayedArray}. Some utilities are also
25839provided for direct creation of an in-memory tatami matrix from a HDF5 file.")
25840 (license license:gpl3)))
25841
25842(define-public r-beadarray
25843 (package
25844 (name "r-beadarray")
25845 (version "2.62.0")
25846 (source (origin
25847 (method url-fetch)
25848 (uri (bioconductor-uri "beadarray" version))
25849 (sha256
25850 (base32
25851 "1p20ny7ykhjkrgsjb7p4py394fl58xijxiww62drjr38dc8nbd64"))))
25852 (properties `((upstream-name . "beadarray")))
25853 (build-system r-build-system)
25854 (propagated-inputs (list r-annotationdbi
25855 r-beaddatapackr
25856 r-biobase
25857 r-biocgenerics
25858 r-genomicranges
25859 r-ggplot2
25860 r-hexbin
25861 r-iranges
25862 r-limma
25863 r-reshape2))
25864 (native-inputs (list r-knitr))
25865 (home-page "https://bioconductor.org/packages/beadarray")
25866 (synopsis
25867 "Quality assessment and low-level analysis for Illumina BeadArray data")
25868 (description
25869 "The package is able to read bead-level data (raw TIFFs and text files)
25870output by BeadScan as well as bead-summary data from BeadStudio. Methods for
25871quality assessment and low-level analysis are provided.")
25872 (license license:expat)))
25873
25874(define-public r-beadarraysnp
25875 (package
25876 (name "r-beadarraysnp")
25877 (version "1.68.0")
25878 (source
25879 (origin
25880 (method url-fetch)
25881 (uri (bioconductor-uri "beadarraySNP" version))
25882 (sha256
25883 (base32 "1vrizh7fpzv1w2gki0qxhphrfj1jj6m6bjsjsbw0b4n4invybzps"))))
25884 (properties `((upstream-name . "beadarraySNP")))
25885 (build-system r-build-system)
25886 (propagated-inputs (list r-biobase r-quantsmooth))
25887 (home-page "https://bioconductor.org/packages/beadarraySNP")
25888 (synopsis "Normalization and reporting of Illumina SNP bead arrays")
25889 (description
25890 "This package is importing data from Illumina SNP experiments and it
25891performs copy number calculations and reports.")
25892 (license license:gpl2)))
25893
25894(define-public r-beaddatapackr
25895 (package
25896 (name "r-beaddatapackr")
25897 (version "1.64.0")
25898 (source (origin
25899 (method url-fetch)
25900 (uri (bioconductor-uri "BeadDataPackR" version))
25901 (sha256
25902 (base32
25903 "0kk7imad42djdjk7ws2ramzssmbr7xdh75mm3rbfcj2qkczbifhb"))))
25904 (properties `((upstream-name . "BeadDataPackR")))
25905 (build-system r-build-system)
25906 (native-inputs (list r-knitr))
25907 (home-page "https://bioconductor.org/packages/BeadDataPackR")
25908 (synopsis "Compression of Illumina BeadArray data")
25909 (description
25910 "This package provides functionality for the compression and
25911decompression of raw bead-level data from the Illumina BeadArray platform.")
25912 (license license:gpl2)))
25913
25914;; This package includes files that have been taken from kentutils. Some
25915;; parts of kentutils are not released under a free license, but this package
25916;; only uses files that are also found in the free parts of kentutils.
25917(define-public r-cner
25918 (package
25919 (name "r-cner")
25920 (version "1.48.0")
25921 (source
25922 (origin
25923 (method url-fetch)
25924 (uri (bioconductor-uri "CNEr" version))
25925 (sha256
25926 (base32 "1gbwg6j8a29hj8z474fh878kgbahi6yh7x6hswbb6g1v0s2570ww"))))
25927 (properties
25928 '((upstream-name . "CNEr")))
25929 (build-system r-build-system)
25930 (inputs (list zlib))
25931 (propagated-inputs
25932 (list r-annotate
25933 r-biocgenerics
25934 r-biostrings
25935 r-dbi
25936 r-genomeinfodb
25937 r-genomicalignments
25938 r-genomicranges
25939 r-ggplot2
25940 r-go-db
25941 r-iranges
25942 r-keggrest
25943 r-powerlaw
25944 r-pwalign
25945 r-r-utils
25946 r-readr
25947 r-reshape2
25948 r-rsqlite
25949 r-rtracklayer
25950 r-s4vectors
25951 r-seqinfo
25952 r-xvector))
25953 (native-inputs
25954 (list r-bsgenome-drerio-ucsc-danrer10
25955 r-bsgenome-hsapiens-ucsc-hg38
25956 r-knitr
25957 r-testthat))
25958 (home-page "https://github.com/ge11232002/CNEr")
25959 (synopsis "CNE Detection and Visualization")
25960 (description
25961 "This package provides tools for large-scale identification and
25962advanced visualization of sets of conserved noncoding elements.")
25963 ;; For all files in src/ucsc "license is hereby granted for all use -
25964 ;; public, private or commercial"; this includes those files that don't
25965 ;; have a license header, because they are included in the free parts of
25966 ;; the kentutils package.
25967 (license (list license:gpl2
25968 (license:non-copyleft
25969 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
25970
25971(define-public r-tfbstools
25972 (package
25973 (name "r-tfbstools")
25974 (version "1.50.0")
25975 (source
25976 (origin
25977 (method url-fetch)
25978 (uri (bioconductor-uri "TFBSTools" version))
25979 (sha256
25980 (base32
25981 "0vgr02da8biy01r6pn5ckkvy8g5zryxb19nn7k5ikmz6g8rnxr09"))))
25982 (properties
25983 '((upstream-name . "TFBSTools")))
25984 (build-system r-build-system)
25985 (propagated-inputs
25986 (list r-biobase
25987 r-biocgenerics
25988 r-biocparallel
25989 r-biostrings
25990 r-bsgenome
25991 r-catools
25992 r-dbi
25993 r-dirichletmultinomial
25994 r-genomicranges
25995 r-gtools
25996 r-iranges
25997 r-pwalign
25998 r-rsqlite
25999 r-rtracklayer
26000 r-s4vectors
26001 r-seqinfo
26002 r-seqlogo
26003 r-tfmpvalue
26004 r-xml
26005 r-xvector))
26006 (native-inputs (list r-jaspar2016 r-knitr r-testthat))
26007 (home-page "https://github.com/ge11232002/TFBSTools")
26008 (synopsis "Transcription factor binding site (TFBS) analysis")
26009 (description
26010 "TFBSTools is a package for the analysis and manipulation of
26011transcription factor binding sites. It includes matrices conversion
26012between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
26013Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
26014scan putative TFBS from sequence/alignment, query JASPAR database and
26015provides a wrapper of de novo motif discovery software.")
26016 (license license:gpl2)))
26017
26018(define-public r-maftools
26019 (package
26020 (name "r-maftools")
26021 (version "2.28.0")
26022 (source
26023 (origin
26024 (method url-fetch)
26025 (uri (bioconductor-uri "maftools" version))
26026 (sha256
26027 (base32 "1f4gn5781hvy7drz551m0xxa5bh2cx1ma0d6lv1m1qjg2q59in1x"))))
26028 (properties `((upstream-name . "maftools")))
26029 (build-system r-build-system)
26030 (propagated-inputs
26031 (list r-data-table
26032 r-dnacopy
26033 r-pheatmap
26034 r-rcolorbrewer
26035 r-rhtslib
26036 r-survival))
26037 (native-inputs (list r-knitr))
26038 (home-page "https://github.com/PoisonAlien/maftools")
26039 (synopsis "Summarize, analyze and visualize MAF files")
26040 (description
26041 "Analyze and visualize Mutation Annotation Format (MAF) files from large
26042scale sequencing studies. This package provides various functions to perform
26043most commonly used analyses in cancer genomics and to create feature rich
26044customizable visualzations with minimal effort.")
26045 (license license:expat)))
26046
26047(define-public r-motifmatchr
26048 (package
26049 (name "r-motifmatchr")
26050 (version "1.34.0")
26051 (source
26052 (origin
26053 (method url-fetch)
26054 (uri (bioconductor-uri "motifmatchr" version))
26055 (sha256
26056 (base32
26057 "0xpd4ahgyp1qdn6n2idi425yhm6jg8rrf5bsj8dyw5bmvjnfqi79"))))
26058 (properties
26059 '((upstream-name . "motifmatchr")
26060 (updater-extra-native-inputs . ("r-bsgenome-hsapiens-ucsc-hg19"))))
26061 (build-system r-build-system)
26062 (propagated-inputs
26063 (list r-biostrings
26064 r-bsgenome
26065 r-genomicranges
26066 r-iranges
26067 r-matrix
26068 r-rcpp
26069 r-rcpparmadillo
26070 r-rsamtools
26071 r-s4vectors
26072 r-seqinfo
26073 r-summarizedexperiment
26074 r-tfbstools))
26075 (native-inputs
26076 (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat r-tfmpvalue))
26077 (home-page "https://bioconductor.org/packages/motifmatchr")
26078 (synopsis "Fast motif matching in R")
26079 (description
26080 "Quickly find motif matches for many motifs and many sequences.
26081This package wraps C++ code from the MOODS motif calling library.")
26082 (license license:gpl3)))
26083
26084(define-public r-chromvar
26085 (package
26086 (name "r-chromvar")
26087 (version "1.34.1")
26088 (source
26089 (origin
26090 (method url-fetch)
26091 (uri (bioconductor-uri "chromVAR" version))
26092 (sha256
26093 (base32 "05d6ff1i5bna4g0gd4n3bcj0igf8cgr82si1sccrd8ap5k8lgqkg"))))
26094 (properties `((upstream-name . "chromVAR")))
26095 (build-system r-build-system)
26096 (arguments
26097 (list
26098 #:skipped-tests
26099 ;; Fails with "more columns than column names".
26100 '(("test_get_counts.R"
26101 "can count fragments with bed file"))))
26102 (propagated-inputs
26103 (list r-biocgenerics
26104 r-biocparallel
26105 r-biostrings
26106 r-bsgenome
26107 r-dt
26108 r-genomicranges
26109 r-ggplot2
26110 r-iranges
26111 r-matrix
26112 r-miniui
26113 r-nabor
26114 r-plotly
26115 r-pwalign
26116 r-rcolorbrewer
26117 r-rcpp
26118 r-rcpparmadillo
26119 r-rsamtools
26120 r-rtsne
26121 r-s4vectors
26122 r-seqinfo
26123 r-shiny
26124 r-summarizedexperiment
26125 r-tfbstools))
26126 (native-inputs (list r-knitr r-testthat))
26127 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
26128 (synopsis "Determine chromatin variation across regions")
26129 (description
26130 "This package @code{r-chromvar} determines variation in chromatin
26131accessibility across sets of annotations or peaks. @code{r-chromvar} is
26132designed primarily for single-cell or sparse chromatin accessibility data like
26133single cell assay for transposase-accessible chromatin using
26134sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
26135sequence (@code{DNAse-seq}) experiments.")
26136 (license license:expat)))
26137
26138(define-public r-singlecellexperiment
26139 (package
26140 (name "r-singlecellexperiment")
26141 (version "1.34.0")
26142 (source
26143 (origin
26144 (method url-fetch)
26145 (uri (bioconductor-uri "SingleCellExperiment" version))
26146 (sha256
26147 (base32
26148 "14aawi3jqvsv9hsixg8krz82p1zzlp0qfq5cj76qaq6gy0v1yr08"))))
26149 (properties
26150 `((upstream-name . "SingleCellExperiment")))
26151 (build-system r-build-system)
26152 (propagated-inputs
26153 (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
26154 r-summarizedexperiment))
26155 (native-inputs
26156 (list r-knitr r-matrix r-testthat))
26157 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
26158 (synopsis "S4 classes for single cell data")
26159 (description "This package defines an S4 class for storing data from
26160single-cell experiments. This includes specialized methods to store and
26161retrieve spike-in information, dimensionality reduction coordinates and size
26162factors for each cell, along with the usual metadata for genes and
26163libraries.")
26164 (license license:gpl3)))
26165
26166(define-public r-singler
26167 (package
26168 (name "r-singler")
26169 (version "2.14.0")
26170 (source
26171 (origin
26172 (method url-fetch)
26173 (uri (bioconductor-uri "SingleR" version))
26174 (sha256
26175 (base32 "0i2p2a1ak4y2p27jhy2j6763a0c8335kgklgkyrm8cd8r0ni16br"))))
26176 (properties
26177 '((upstream-name . "SingleR")
26178 (updater-extra-native-inputs
26179 . ("r-ggplot2" "r-scran" "r-viridis"))))
26180 (build-system r-build-system)
26181 (propagated-inputs
26182 (list r-assorthead
26183 r-beachmat
26184 r-biocgenerics
26185 r-delayedarray
26186 r-matrix
26187 r-rcpp
26188 r-s4vectors
26189 r-summarizedexperiment))
26190 (native-inputs
26191 (list r-biocparallel
26192 r-ggplot2
26193 r-knitr
26194 r-scran
26195 r-scrapper
26196 r-singlecellexperiment
26197 r-testthat
26198 r-viridis))
26199 (home-page "https://github.com/LTLA/SingleR")
26200 (synopsis "Reference-based single-cell RNA-seq annotation")
26201 (description
26202 "This package performs unbiased cell type recognition from single-cell
26203RNA sequencing data, by leveraging reference transcriptomic datasets of pure
26204cell types to infer the cell of origin of each single cell independently.")
26205 (license license:gpl3)))
26206
26207(define-public r-scuttle
26208 (package
26209 (name "r-scuttle")
26210 (version "1.22.0")
26211 (source
26212 (origin
26213 (method url-fetch)
26214 (uri (bioconductor-uri "scuttle" version))
26215 (sha256
26216 (base32
26217 "143v7n2i6rw6qy2krfbl8ky950c3lk74zwr49rxj4srqsci9xhxh"))))
26218 (properties
26219 '((upstream-name . "scuttle")
26220 (updater-extra-native-inputs
26221 . ("r-delayedmatrixstats" "r-sparsematrixstats"))))
26222 (build-system r-build-system)
26223 (propagated-inputs
26224 (list r-assorthead
26225 r-beachmat
26226 r-biocgenerics
26227 r-biocparallel
26228 r-delayedarray
26229 r-genomicranges
26230 r-matrix
26231 r-matrixgenerics
26232 r-rcpp
26233 r-s4arrays
26234 r-s4vectors
26235 r-singlecellexperiment
26236 r-sparsearray
26237 r-summarizedexperiment))
26238 (native-inputs
26239 (list r-delayedmatrixstats r-knitr r-sparsematrixstats r-testthat))
26240 (home-page "https://bioconductor.org/packages/scuttle")
26241 (synopsis "Single-cell RNA-Seq analysis utilities")
26242 (description
26243 "This package provides basic utility functions for performing single-cell
26244analyses, focusing on simple normalization, quality control and data
26245transformations. It also provides some helper functions to assist development
26246of other packages.")
26247 (license license:gpl3)))
26248
26249(define-public r-scater
26250 (package
26251 (name "r-scater")
26252 (version "1.40.1")
26253 (source (origin
26254 (method url-fetch)
26255 (uri (bioconductor-uri "scater" version))
26256 (sha256
26257 (base32
26258 "0kd72ba3nbrrmbphlznrhm937jz9l7lav7qrrvawlp7xlrpq6izf"))))
26259 (build-system r-build-system)
26260 (properties
26261 '((updater-extra-native-inputs
26262 . ("r-delayedmatrixstats"
26263 "r-robustbase"
26264 "r-scattermore"
26265 "r-sparsematrixstats"))))
26266 (propagated-inputs
26267 (list r-beachmat
26268 r-biocgenerics
26269 r-biocneighbors
26270 r-biocparallel
26271 r-biocsingular
26272 r-delayedarray
26273 r-ggbeeswarm
26274 r-ggplot2
26275 r-ggrastr
26276 r-ggrepel
26277 r-matrix
26278 r-matrixgenerics
26279 r-pheatmap
26280 r-rcolorbrewer
26281 r-rcppml
26282 r-rlang
26283 r-rtsne
26284 r-s4vectors
26285 r-scuttle
26286 r-singlecellexperiment
26287 r-sparsearray
26288 r-summarizedexperiment
26289 r-uwot
26290 r-viridis))
26291 (native-inputs
26292 (list r-delayedmatrixstats
26293 r-knitr
26294 r-robustbase
26295 r-scattermore
26296 r-sparsematrixstats
26297 r-testthat))
26298 (home-page "https://github.com/davismcc/scater")
26299 (synopsis "Single-cell analysis toolkit for gene expression data in R")
26300 (description "This package provides a collection of tools for doing
26301various analyses of single-cell RNA-seq gene expression data, with a focus on
26302quality control.")
26303 (license license:gpl2+)))
26304
26305(define-public r-scran
26306 (package
26307 (name "r-scran")
26308 (version "1.40.0")
26309 (source
26310 (origin
26311 (method url-fetch)
26312 (uri (bioconductor-uri "scran" version))
26313 (sha256
26314 (base32
26315 "0vblargck4yx5lwiasigpqbkcshyrx3igajnjw0vr2jxvg5zxni3"))))
26316 (properties
26317 '((updater-extra-native-inputs
26318 . ("r-dynamictreecut"
26319 "r-residualmatrix"))
26320 (updater-ignored-native-inputs . ("r-boost" "r-range"))))
26321 (build-system r-build-system)
26322 (propagated-inputs
26323 (list r-beachmat
26324 r-bh
26325 r-biocgenerics
26326 r-biocparallel
26327 r-biocsingular
26328 r-bluster
26329 r-delayedarray
26330 r-dqrng
26331 r-edger
26332 r-igraph
26333 r-limma
26334 r-matrix
26335 r-matrixgenerics
26336 r-metapod
26337 r-rcpp
26338 r-s4arrays
26339 r-s4vectors
26340 r-scuttle
26341 r-singlecellexperiment
26342 r-statmod
26343 r-summarizedexperiment))
26344 (native-inputs
26345 (list r-delayedmatrixstats
26346 r-deseq2
26347 r-dynamictreecut
26348 r-hdf5array
26349 r-knitr
26350 r-residualmatrix
26351 r-testthat))
26352 (home-page "https://bioconductor.org/packages/scran")
26353 (synopsis "Methods for single-cell RNA-Seq data analysis")
26354 (description "This package implements a variety of low-level analyses of
26355single-cell RNA-seq data. Methods are provided for normalization of
26356cell-specific biases, assignment of cell cycle phase, and detection of highly
26357variable and significantly correlated genes.")
26358 (license license:gpl3)))
26359
26360(define-public r-sparsearray
26361 (package
26362 (name "r-sparsearray")
26363 (version "1.12.2")
26364 (source
26365 (origin
26366 (method url-fetch)
26367 (uri (bioconductor-uri "SparseArray" version))
26368 (sha256
26369 (base32 "1y2r013qjd0vb02wnp29p96ig9rn2ggvd43g8riyylmi7dnqb6gv"))))
26370 (properties `((upstream-name . "SparseArray")))
26371 (build-system r-build-system)
26372 (propagated-inputs (list r-biocgenerics
26373 r-iranges
26374 r-matrix
26375 r-matrixgenerics
26376 r-matrixstats
26377 r-s4arrays
26378 r-s4vectors
26379 r-xvector))
26380 (native-inputs (list r-knitr r-testthat))
26381 (arguments
26382 (list
26383 #:phases
26384 '(modify-phases %standard-phases
26385 (add-after 'unpack 'relax-floating-point-tests
26386 ;; Test files that are modified below contain the following
26387 ;; comment:
26388 ;; "Looks like using expect_identical() is too strict for some
26389 ;; operations on some systems"
26390 ;; then modify the tests to expect_equal for specific functions
26391 ;; on speficic systems. This looks as if we are in the presence
26392 ;; of floating point discrepancies, which are poorly suited for
26393 ;; a strict test suite rejecting builds. Since the tests also
26394 ;; fail in Guix on x86_64 with gcc@14, let us use expect_equal
26395 ;; everywhere.
26396 (lambda _
26397 (substitute*
26398 '("tests/testthat/test-NaArray-Math-methods.R"
26399 "tests/testthat/test-SparseArray-Math-methods.R")
26400 (("expect_identical\\(as") "expect_equal(as")))))))
26401 (home-page "https://bioconductor.org/packages/SparseArray")
26402 (synopsis
26403 "Efficient in-memory representation of multidimensional sparse arrays")
26404 (description
26405 "The @code{SparseArray} package is an infrastructure package that
26406provides an array-like container for efficient in-memory representation of
26407multidimensional sparse data in R. The package defines the @code{SparseArray}
26408virtual class and two concrete subclasses: @code{COO_SparseArray} and
26409@code{SVT_SparseArray}. Each subclass uses its own internal representation of
26410the nonzero multidimensional data, the \"COO layout\" and the \"SVT layout\",
26411respectively. @code{SVT_SparseArray} objects mimic as much as possible the
26412behavior of ordinary matrix and array objects in base R. In particular, they
26413support most of the \"standard matrix and array API\" defined in base R and
26414in the @code{matrixStats} package from CRAN.")
26415 (license license:artistic2.0)))
26416
26417(define-public r-sparsematrixstats
26418 (package
26419 (name "r-sparsematrixstats")
26420 (version "1.24.0")
26421 (source
26422 (origin
26423 (method url-fetch)
26424 (uri (bioconductor-uri "sparseMatrixStats" version))
26425 (sha256
26426 (base32
26427 "0r15z964c7946nj72fa9yf2vijzklc58bfm8hm6ync067wjxra2c"))))
26428 (properties
26429 `((upstream-name . "sparseMatrixStats")))
26430 (build-system r-build-system)
26431 (propagated-inputs
26432 (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
26433 (native-inputs (list r-knitr r-testthat))
26434 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
26435 (synopsis "Summary statistics for rows and columns of sparse matrices")
26436 (description
26437 "This package provides high performance functions for row and column
26438operations on sparse matrices. Currently, the optimizations are limited to
26439data in the column sparse format.")
26440 (license license:expat)))
26441
26442(define-public r-spatialexperiment
26443 (package
26444 (name "r-spatialexperiment")
26445 (version "1.22.0")
26446 (source (origin
26447 (method url-fetch)
26448 (uri (bioconductor-uri "SpatialExperiment" version))
26449 (sha256
26450 (base32
26451 "1crjfic67z9llpwbfnbwqgcfrmfdsgg3laik2if39mj87vllnzx5"))))
26452 (properties `((upstream-name . "SpatialExperiment")))
26453 (build-system r-build-system)
26454 (arguments
26455 (list
26456 ;; 4 tests fail because they need Internet access.
26457 #:tests? #false
26458 #:phases
26459 '(modify-phases %standard-phases
26460 (add-after 'unpack 'set-HOME
26461 (lambda _ (setenv "HOME" "/tmp"))))))
26462 (propagated-inputs (list r-biocfilecache
26463 r-biocgenerics
26464 r-magick
26465 r-rjson
26466 r-s4vectors
26467 r-singlecellexperiment
26468 r-summarizedexperiment))
26469 (native-inputs (list r-knitr r-testthat))
26470 (home-page "https://github.com/drighelli/SpatialExperiment")
26471 (synopsis "S4 class for spatially resolved -omics data")
26472 (description
26473 "This package defines an S4 class for storing data from spatial -omics
26474experiments. The class extends SingleCellExperiment to support storage and
26475retrieval of additional information from spot-based and molecule-based
26476platforms, including spatial coordinates, images, and image metadata. A
26477specialized constructor function is included for data from the 10x Genomics
26478Visium platform.")
26479 (license license:gpl3)))
26480
26481(define-public r-delayedmatrixstats
26482 (package
26483 (name "r-delayedmatrixstats")
26484 (version "1.34.0")
26485 (source
26486 (origin
26487 (method url-fetch)
26488 (uri (bioconductor-uri "DelayedMatrixStats" version))
26489 (sha256
26490 (base32
26491 "070ddm3zq3x8yrpjad3lfq8s0942j8c1j4xc00wcq3ndadqk93h3"))))
26492 (properties
26493 '((upstream-name . "DelayedMatrixStats")
26494 (updater-extra-native-inputs . ("r-hdf5array"))))
26495 (build-system r-build-system)
26496 (propagated-inputs
26497 (list r-delayedarray
26498 r-iranges
26499 r-matrix
26500 r-matrixgenerics
26501 r-s4vectors
26502 r-sparsearray
26503 r-sparsematrixstats))
26504 (native-inputs
26505 (list r-hdf5array r-knitr r-matrixstats r-testthat))
26506 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
26507 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
26508 (description
26509 "This package provides a port of the @code{matrixStats} API for use with
26510@code{DelayedMatrix} objects from the @code{DelayedArray} package. It
26511contains high-performing functions operating on rows and columns of
26512@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
26513@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
26514are optimized per data type and for subsetted calculations such that both
26515memory usage and processing time is minimized.")
26516 (license license:expat)))
26517
26518(define-public r-mscoreutils
26519 (package
26520 (name "r-mscoreutils")
26521 (version "1.24.0")
26522 (source
26523 (origin
26524 (method url-fetch)
26525 (uri (bioconductor-uri "MsCoreUtils" version))
26526 (sha256
26527 (base32
26528 "15zqp2cvlmm0dz6yw633zvh29kvw0xr3p1rksk2dik0h7xhc38qv"))))
26529 (properties
26530 '((upstream-name . "MsCoreUtils")
26531 ;; Avoid dependency cycle.
26532 (updater-ignored-native-inputs . ("r-msnbase"))
26533 (updater-extra-native-inputs . ("r-impute"
26534 "r-imputelcmd"
26535 "r-missforest"
26536 "r-norm"
26537 "r-pcamethods"
26538 "r-preprocesscore"
26539 "r-vsn"))))
26540 (build-system r-build-system)
26541 (propagated-inputs
26542 (list r-clue r-mass r-rcpp r-s4vectors))
26543 (native-inputs
26544 (list r-hdf5array
26545 r-impute
26546 r-imputelcmd
26547 r-knitr
26548 r-matrix
26549 r-missforest
26550 r-norm
26551 r-pcamethods
26552 r-preprocesscore
26553 r-rlang
26554 r-testthat
26555 r-vsn))
26556 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
26557 (synopsis "Core utils for mass spectrometry data")
26558 (description
26559 "This package defines low-level functions for mass spectrometry data and
26560is independent of any high-level data structures. These functions include
26561mass spectra processing functions (noise estimation, smoothing, binning),
26562quantitative aggregation functions (median polish, robust summarisation,
26563etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
26564well as misc helper functions, that are used across high-level data structure
26565within the R for Mass Spectrometry packages.")
26566 (license license:artistic2.0)))
26567
26568(define-public r-msfeatures
26569 (package
26570 (name "r-msfeatures")
26571 (version "1.20.0")
26572 (source
26573 (origin
26574 (method url-fetch)
26575 (uri (bioconductor-uri "MsFeatures" version))
26576 (sha256
26577 (base32 "1ikpnx8cx87w15h0gzydcrydi1zlnkc6i1fid2w4ykqmq6mv4sbi"))))
26578 (properties `((upstream-name . "MsFeatures")))
26579 (build-system r-build-system)
26580 (propagated-inputs
26581 (list r-mscoreutils r-protgenerics r-summarizedexperiment))
26582 (native-inputs
26583 (list r-knitr r-testthat))
26584 (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
26585 (synopsis "Functionality for mass spectrometry features")
26586 (description
26587 "The MsFeature package defines functionality for Mass Spectrometry
26588features. This includes functions to group (LC-MS) features based on some of
26589their properties, such as retention time (coeluting features), or correlation
26590of signals across samples. This package hence can be used to group features, and
26591its results can be used as an input for the @code{QFeatures} package which
26592allows aggregating abundance levels of features within each group. This
26593package defines concepts and functions for base and common data types,
26594implementations for more specific data types are expected to be implemented in
26595the respective packages (such as e.g. @code{xcms}).")
26596 (license license:artistic2.0)))
26597
26598(define-public r-biocio
26599 (package
26600 (name "r-biocio")
26601 (version "1.22.0")
26602 (source
26603 (origin
26604 (method url-fetch)
26605 (uri (bioconductor-uri "BiocIO" version))
26606 (sha256
26607 (base32
26608 "0yy043wh32j0r51ggcc36z79gpdq2xk3416gfyfcs05zqwcfd8x6"))))
26609 (properties `((upstream-name . "BiocIO")))
26610 (build-system r-build-system)
26611 (propagated-inputs
26612 (list r-biocgenerics r-s4vectors))
26613 (native-inputs
26614 (list r-knitr r-testthat))
26615 (home-page "https://bioconductor.org/packages/BiocIO")
26616 (synopsis "Standard input and output for Bioconductor packages")
26617 (description
26618 "This package implements `import()` and `export()` standard generics for
26619importing and exporting biological data formats. `import()` supports
26620whole-file as well as chunk-wise iterative import. The `import()` interface
26621optionally provides a standard mechanism for 'lazy' access via `filter()` (on
26622row or element-like components of the file resource), `select()` (on
26623column-like components of the file resource) and `collect()`. The `import()`
26624interface optionally provides transparent access to remote (e.g. via https)
26625as well as local access. Developers can register a file extension, e.g.,
26626`.loom` for dispatch from character-based URIs to specific `import()` /
26627`export()` methods based on classes representing file types, e.g.,
26628`LoomFile()`.")
26629 (license license:artistic2.0)))
26630
26631(define-public r-msmseda
26632 (package
26633 (name "r-msmseda")
26634 (version "1.50.0")
26635 (source
26636 (origin
26637 (method url-fetch)
26638 (uri (bioconductor-uri "msmsEDA" version))
26639 (sha256
26640 (base32
26641 "0gg4qx52axv6bjag0gq0j0h73l30x8jwgs64bgs0wzd383rl9hwg"))))
26642 (properties `((upstream-name . "msmsEDA")))
26643 (build-system r-build-system)
26644 (propagated-inputs
26645 (list r-gplots r-mass r-msnbase r-rcolorbrewer))
26646 (home-page
26647 "https://bioconductor.org/packages/msmsEDA")
26648 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
26649 (description
26650 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
26651experiments, and visualize de influence of the involved factors.")
26652 (license license:gpl2)))
26653
26654(define-public r-msmstests
26655 (package
26656 (name "r-msmstests")
26657 (version "1.50.0")
26658 (source
26659 (origin
26660 (method url-fetch)
26661 (uri (bioconductor-uri "msmsTests" version))
26662 (sha256
26663 (base32
26664 "15xwg049gn1c9kb5i8d18wn5w97yx0nb70y8jhfqf0l7m3hxqgig"))))
26665 (properties `((upstream-name . "msmsTests")))
26666 (build-system r-build-system)
26667 (propagated-inputs
26668 (list r-edger r-msmseda r-msnbase r-qvalue))
26669 (home-page
26670 "https://bioconductor.org/packages/msmsTests")
26671 (synopsis "Differential LC-MS/MS expression tests")
26672 (description
26673 "This package provides statistical tests for label-free LC-MS/MS data
26674by spectral counts, to discover differentially expressed proteins between two
26675biological conditions. Three tests are available: Poisson GLM regression,
26676quasi-likelihood GLM regression, and the negative binomial of the edgeR
26677package. The three models admit blocking factors to control for nuisance
26678variables. To assure a good level of reproducibility a post-test filter is
26679available, where we may set the minimum effect size considered biologicaly
26680relevant, and the minimum expression of the most abundant condition.")
26681 (license license:gpl2)))
26682
26683(define-public r-catalyst
26684 (package
26685 (name "r-catalyst")
26686 (version "1.36.0")
26687 (source
26688 (origin
26689 (method url-fetch)
26690 (uri (bioconductor-uri "CATALYST" version))
26691 (sha256
26692 (base32
26693 "088236cg5i7hqipyh60ymzvsl1d3mwf074gqsfg1wkxc2wv9qfgn"))))
26694 (properties `((upstream-name . "CATALYST")))
26695 (build-system r-build-system)
26696 (propagated-inputs
26697 (list r-circlize
26698 r-complexheatmap
26699 r-consensusclusterplus
26700 r-cowplot
26701 r-dplyr
26702 r-drc
26703 r-flowcore
26704 r-flowsom
26705 r-ggplot2
26706 r-ggrepel
26707 r-ggridges
26708 r-gridextra
26709 r-matrix
26710 r-matrixstats
26711 r-nnls
26712 r-rcolorbrewer
26713 r-reshape2
26714 r-rtsne
26715 r-s4vectors
26716 r-scales
26717 r-scater
26718 r-singlecellexperiment
26719 r-summarizedexperiment))
26720 (native-inputs
26721 (list r-diffcyt r-knitr r-testthat))
26722 (home-page "https://github.com/HelenaLC/CATALYST")
26723 (synopsis "Cytometry data analysis tools")
26724 (description
26725 "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass
26726cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
26727isotopes rather than fluorescent tags as reporters to label antibodies,
26728thereby substantially decreasing spectral overlap and allowing for examination
26729of over 50 parameters at the single cell level. While spectral overlap is
26730significantly less pronounced in CyTOF than flow cytometry, spillover due to
26731detection sensitivity, isotopic impurities, and oxide formation can impede
26732data interpretability. @code{CATALYST} was designed to provide a pipeline for
26733preprocessing of cytometry data, including:
26734
26735@enumerate
26736@item normalization using bead standards;
26737@item single-cell deconvolution;
26738@item bead-based compensation.
26739@end enumerate
26740")
26741 (license license:gpl2+)))
26742
26743(define-public r-erma
26744 (package
26745 (name "r-erma")
26746 (version "1.24.1")
26747 (source
26748 (origin
26749 (method url-fetch)
26750 (uri (bioconductor-uri "erma" version))
26751 (sha256
26752 (base32
26753 "1s3b2a0iv3rl3sxq1sbqscq2h2gjz4d3vsg9phhnbk1xdhbhqi4d"))))
26754 (build-system r-build-system)
26755 (propagated-inputs
26756 (list r-annotationdbi
26757 r-biobase
26758 r-biocgenerics
26759 r-biocparallel
26760 r-genomeinfodb
26761 r-genomicfiles
26762 r-genomicranges
26763 r-ggplot2
26764 r-homo-sapiens
26765 r-iranges
26766 r-rtracklayer
26767 r-s4vectors
26768 r-shiny
26769 r-summarizedexperiment))
26770 (native-inputs
26771 (list r-knitr))
26772 (home-page "https://bioconductor.org/packages/erma")
26773 (synopsis "Epigenomic road map adventures")
26774 (description
26775 "The epigenomics road map describes locations of epigenetic marks in DNA
26776from a variety of cell types. Of interest are locations of histone
26777modifications, sites of DNA methylation, and regions of accessible chromatin.
26778This package presents a selection of elements of the road map including
26779metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
26780by Ernst and Kellis.")
26781 (license license:artistic2.0)))
26782
26783(define-public r-ggbio
26784 (package
26785 (name "r-ggbio")
26786 (version "1.60.0")
26787 (source
26788 (origin
26789 (method url-fetch)
26790 (uri (bioconductor-uri "ggbio" version))
26791 (sha256
26792 (base32
26793 "119hzv17zykkp1mx2as3cf489yk9fdpcg58pcywjkhn2rwq42ia9"))))
26794 (build-system r-build-system)
26795 (arguments
26796 `(#:phases
26797 (modify-phases %standard-phases
26798 ;; See https://github.com/tengfei/ggbio/issues/117
26799 ;; This fix will be included in the next release.
26800 (add-after 'unpack 'fix-typo
26801 (lambda _
26802 (substitute* "R/GGbio-class.R"
26803 (("fechable") "fetchable"))
26804 #t)))))
26805 (propagated-inputs
26806 (list r-annotationdbi
26807 r-annotationfilter
26808 r-biobase
26809 r-biocgenerics
26810 r-biostrings
26811 r-biovizbase
26812 r-bsgenome
26813 r-ensembldb
26814 r-genomeinfodb
26815 r-genomicalignments
26816 r-genomicfeatures
26817 r-genomicranges
26818 r-ggplot2
26819 r-gridextra
26820 r-gtable
26821 r-hmisc
26822 r-iranges
26823 r-organismdbi
26824 r-reshape2
26825 r-rlang
26826 r-rsamtools
26827 r-rtracklayer
26828 r-s4vectors
26829 r-scales
26830 r-seqinfo
26831 r-summarizedexperiment
26832 r-variantannotation))
26833 (native-inputs
26834 (list r-biocstyle
26835 r-bsgenome-hsapiens-ucsc-hg19
26836 r-ensdb-hsapiens-v75
26837 r-homo-sapiens
26838 r-knitr
26839 r-rcolorbrewer
26840 r-testthat
26841 r-txdb-hsapiens-ucsc-hg19-knowngene))
26842 (home-page "http://www.tengfei.name/ggbio/")
26843 (synopsis "Visualization tools for genomic data")
26844 (description
26845 "The ggbio package extends and specializes the grammar of graphics for
26846biological data. The graphics are designed to answer common scientific
26847questions, in particular those often asked of high throughput genomics data.
26848All core Bioconductor data structures are supported, where appropriate. The
26849package supports detailed views of particular genomic regions, as well as
26850genome-wide overviews. Supported overviews include ideograms and grand linear
26851views. High-level plots include sequence fragment length, edge-linked
26852interval to data view, mismatch pileup, and several splicing summaries.")
26853 (license license:artistic2.0)))
26854
26855(define-public r-gqtlbase
26856 (package
26857 (name "r-gqtlbase")
26858 (version "1.21.1")
26859 (source
26860 (origin
26861 (method url-fetch)
26862 (uri (bioconductor-uri "gQTLBase" version))
26863 (sha256
26864 (base32
26865 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
26866 (properties `((upstream-name . "gQTLBase")))
26867 (build-system r-build-system)
26868 (arguments
26869 (list
26870 ;; Tests fail with "The file does not exist".
26871 #:tests? #false
26872 #:phases
26873 '(modify-phases %standard-phases
26874 ;; This is an upstream bug.
26875 (add-after 'unpack 'fix-imports
26876 (lambda _
26877 (substitute* "NAMESPACE"
26878 ((".*maxffmode.*") "")
26879 (("importFrom\\(ff,.*") "import(ff)\n")))))))
26880 (propagated-inputs
26881 (list r-batchjobs
26882 r-bbmisc
26883 r-biocgenerics
26884 r-bit
26885 r-doparallel
26886 r-ff
26887 r-ffbase
26888 r-foreach
26889 r-genomicfiles
26890 r-genomicranges
26891 r-rtracklayer
26892 r-s4vectors
26893 r-summarizedexperiment))
26894 (native-inputs
26895 (list r-knitr r-runit))
26896 (home-page "https://bioconductor.org/packages/gQTLBase")
26897 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
26898 (description
26899 "The purpose of this package is to simplify the storage and interrogation
26900of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
26901and more.")
26902 (license license:artistic2.0)))
26903
26904(define-public r-gqtlstats
26905 (package
26906 (name "r-gqtlstats")
26907 (version "1.21.3")
26908 (source
26909 (origin
26910 (method url-fetch)
26911 (uri (bioconductor-uri "gQTLstats" version))
26912 (sha256
26913 (base32
26914 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
26915 (properties `((upstream-name . "gQTLstats")))
26916 (build-system r-build-system)
26917 ;; Tests require geuvPack, which has been removed from Bioconductor.
26918 (arguments (list #:tests? #false))
26919 (propagated-inputs
26920 (list r-annotationdbi
26921 r-batchjobs
26922 r-bbmisc
26923 r-beeswarm
26924 r-biobase
26925 r-biocgenerics
26926 r-doparallel
26927 r-dplyr
26928 r-erma
26929 r-ffbase
26930 r-foreach
26931 r-genomeinfodb
26932 r-genomicfeatures
26933 r-genomicfiles
26934 r-genomicranges
26935 r-ggbeeswarm
26936 r-ggplot2
26937 r-gqtlbase
26938 r-hardyweinberg
26939 r-homo-sapiens
26940 r-iranges
26941 r-limma
26942 r-mgcv
26943 r-plotly
26944 r-reshape2
26945 r-s4vectors
26946 r-shiny
26947 r-snpstats
26948 r-summarizedexperiment
26949 r-variantannotation))
26950 (native-inputs
26951 (list r-knitr r-runit))
26952 (home-page "https://bioconductor.org/packages/gQTLstats")
26953 (synopsis "Computationally efficient analysis for eQTL and allied studies")
26954 (description
26955 "This package provides tools for the computationally efficient analysis
26956of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
26957The software in this package aims to support refinements and functional
26958interpretation of members of a collection of association statistics on a
26959family of feature/genome hypotheses.")
26960 (license license:artistic2.0)))
26961
26962(define-public r-gviz
26963 (package
26964 (name "r-gviz")
26965 (version "1.56.0")
26966 (source
26967 (origin
26968 (method url-fetch)
26969 (uri (bioconductor-uri "Gviz" version))
26970 (sha256
26971 (base32
26972 "0pl95b9yf9bcgrzrvxdy80z0ymq8886k3ci154lhl8gh4xkq5r0h"))))
26973 (properties `((upstream-name . "Gviz")))
26974 (build-system r-build-system)
26975 (arguments
26976 (list
26977 #:skipped-tests
26978 (if (target-32bit?)
26979 ;; Sequence is too big
26980 '(("test_Gviz-methods.R" "subseq works"))
26981 '())))
26982 (propagated-inputs
26983 (list r-annotationdbi
26984 r-biobase
26985 r-biocgenerics
26986 r-biomart
26987 r-biostrings
26988 r-biovizbase
26989 r-bsgenome
26990 r-digest
26991 r-ensembldb
26992 r-genomeinfodb
26993 r-genomicalignments
26994 r-genomicfeatures
26995 r-genomicranges
26996 r-iranges
26997 r-lattice
26998 r-latticeextra
26999 r-matrixstats
27000 r-rcolorbrewer
27001 r-rsamtools
27002 r-rtracklayer
27003 r-s4vectors
27004 r-seqinfo
27005 r-xvector))
27006 (native-inputs
27007 (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat))
27008 (home-page "https://bioconductor.org/packages/Gviz")
27009 (synopsis "Plotting data and annotation information along genomic coordinates")
27010 (description
27011 "Genomic data analyses requires integrated visualization of known genomic
27012information and new experimental data. Gviz uses the biomaRt and the
27013rtracklayer packages to perform live annotation queries to Ensembl and UCSC
27014and translates this to e.g. gene/transcript structures in viewports of the
27015grid graphics package. This results in genomic information plotted together
27016with your data.")
27017 (license license:artistic2.0)))
27018
27019(define-public r-gwascat
27020 (package
27021 (name "r-gwascat")
27022 (version "2.44.0")
27023 (source
27024 (origin
27025 (method url-fetch)
27026 (uri (bioconductor-uri "gwascat" version))
27027 (sha256
27028 (base32
27029 "1xpsas0mjygcsn55iznbd9j8m2a4bi8db86wxzyk03aj370c3ads"))))
27030 (build-system r-build-system)
27031 (propagated-inputs
27032 (list r-annotationdbi
27033 r-annotationhub
27034 r-biocfilecache
27035 r-biostrings
27036 r-data-table
27037 r-genomeinfodb
27038 r-genomicfeatures
27039 r-genomicranges
27040 r-iranges
27041 r-readr
27042 r-s4vectors
27043 r-seqinfo
27044 r-snpstats
27045 r-tibble
27046 r-variantannotation))
27047 (native-inputs
27048 (list r-knitr r-testthat))
27049 (home-page "https://bioconductor.org/packages/gwascat")
27050 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
27051 (description
27052 "This package provides tools for representing and modeling data in the
27053EMBL-EBI GWAS catalog.")
27054 (license license:artistic2.0)))
27055
27056(define-public r-gwastools
27057 (package
27058 (name "r-gwastools")
27059 (version "1.58.0")
27060 (source (origin
27061 (method url-fetch)
27062 (uri (bioconductor-uri "GWASTools" version))
27063 (sha256
27064 (base32
27065 "0mcbwgiv1zh4smg0h5146cdb6lr2ngxf1a505dj52vzaq0fhld7m"))))
27066 (properties
27067 '((upstream-name . "GWASTools")
27068 (updater-ignored-native-inputs . ("r-gwasdata"))))
27069 (build-system r-build-system)
27070 ;; TODO: This needs the package GWASdata.
27071 (arguments (list #:tests? #false))
27072 (propagated-inputs (list r-biobase
27073 r-data-table
27074 r-dbi
27075 r-dnacopy
27076 r-gdsfmt
27077 r-gwasexacthw
27078 r-lmtest
27079 r-logistf
27080 r-quantsmooth
27081 r-rsqlite
27082 r-sandwich
27083 r-survival))
27084 (native-inputs (list r-biocgenerics
27085 r-knitr
27086 r-ncdf4
27087 r-runit
27088 r-snprelate
27089 r-variantannotation))
27090 (home-page "https://github.com/smgogarten/GWASTools")
27091 (synopsis "Tools for Genome Wide Association Studies")
27092 (description
27093 "This package provides classes for storing very large GWAS data sets and
27094annotation, and functions for GWAS data cleaning and analysis.")
27095 (license license:artistic2.0)))
27096
27097(define-public r-kegggraph
27098 (package
27099 (name "r-kegggraph")
27100 (version "1.72.0")
27101 (source
27102 (origin
27103 (method url-fetch)
27104 (uri (bioconductor-uri "KEGGgraph" version))
27105 (sha256
27106 (base32 "1d6l1q9f887gd8kidbr31ycv8a8hsf0p5gg6zlidj4d0bcpx4ymi"))))
27107 (properties `((upstream-name . "KEGGgraph")))
27108 (build-system r-build-system)
27109 ;; Vignettes require connection to the internet.
27110 (arguments (list #:test-types '(list "tests")))
27111 (propagated-inputs
27112 (list r-graph r-rcurl r-rgraphviz r-xml))
27113 (native-inputs (list r-biomart
27114 r-hgu133plus2-db
27115 r-org-hs-eg-db
27116 r-rbgl
27117 r-rcolorbrewer
27118 r-testthat))
27119 (home-page "https://bioconductor.org/packages/KEGGgraph")
27120 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
27121 (description
27122 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
27123object as well as a collection of tools to analyze, dissect and visualize these
27124graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
27125maintaining all essential pathway attributes. The package offers
27126functionalities including parsing, graph operation, visualization and etc.")
27127 (license license:gpl2+)))
27128
27129(define-public r-ldblock
27130 (package
27131 (name "r-ldblock")
27132 (version "1.42.0")
27133 (source
27134 (origin
27135 (method url-fetch)
27136 (uri (bioconductor-uri "ldblock" version))
27137 (sha256
27138 (base32
27139 "0w64a1dsbzvjq7iq1rzpy73nqc0z35as4581qdjc8lc9ipjgjiki"))))
27140 (build-system r-build-system)
27141 (propagated-inputs
27142 (list r-biocgenerics r-httr r-matrix r-rlang r-seqinfo))
27143 (native-inputs
27144 (list r-knitr r-runit))
27145 (home-page "https://bioconductor.org/packages/ldblock")
27146 (synopsis "Data structures for linkage disequilibrium measures in populations")
27147 (description
27148 "This package defines data structures for @dfn{linkage
27149disequilibrium} (LD) measures in populations. Its purpose is to simplify
27150handling of existing population-level data for the purpose of flexibly
27151defining LD blocks.")
27152 (license license:artistic2.0)))
27153
27154;; This is a CRAN package, but it depends on r-snpstats, which is a
27155;; Bioconductor package.
27156(define-public r-ldheatmap
27157 (package
27158 (name "r-ldheatmap")
27159 (version "1.0-6")
27160 (source
27161 (origin
27162 (method url-fetch)
27163 (uri (cran-uri "LDheatmap" version))
27164 (sha256
27165 (base32
27166 "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
27167 (properties `((upstream-name . "LDheatmap")))
27168 (build-system r-build-system)
27169 (propagated-inputs
27170 (list r-genetics r-rcpp r-snpstats))
27171 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
27172 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
27173 (description
27174 "This package provides tools to produce a graphical display, as a heat
27175map, of measures of pairwise linkage disequilibria between SNPs. Users may
27176optionally include the physical locations or genetic map distances of each SNP
27177on the plot.")
27178 (license license:gpl3)))
27179
27180;; This is a CRAN package, but it depends on r-rgraphviz, which is a
27181;; Bioconductor package.
27182(define-public r-abn
27183 (package
27184 (name "r-abn")
27185 (version "3.1.13")
27186 (source
27187 (origin
27188 (method url-fetch)
27189 (uri (cran-uri "abn" version))
27190 (sha256
27191 (base32
27192 "1l1yv2rc4aa3zp5w9qsr4n9mbr7g5n5bgldpvpy9z1wf664lxy8w"))))
27193 (build-system r-build-system)
27194 (inputs
27195 (list gsl jags))
27196 (propagated-inputs
27197 (list r-doparallel
27198 r-foreach
27199 r-glmmtmb
27200 r-graph
27201 r-jsonlite
27202 r-lme4
27203 r-mclogit
27204 r-nnet
27205 r-rcpp
27206 r-rcpparmadillo
27207 r-rgraphviz
27208 r-rjags
27209 r-stringi))
27210 (native-inputs
27211 (list r-biocmanager
27212 r-boot
27213 r-brglm
27214 r-entropy
27215 r-knitr
27216 r-moments
27217 r-rhpcblasctl
27218 r-testthat))
27219 (home-page "https://r-bayesian-networks.org/")
27220 (synopsis "Modelling multivariate data with additive bayesian networks")
27221 (description
27222 "Bayesian network analysis is a form of probabilistic graphical models
27223which derives from empirical data a directed acyclic graph, DAG, describing
27224the dependency structure between random variables. An additive Bayesian
27225network model consists of a form of a DAG where each node comprises a
27226@dfn{generalized linear model} (GLM). Additive Bayesian network models are
27227equivalent to Bayesian multivariate regression using graphical modelling, they
27228generalises the usual multivariable regression, GLM, to multiple dependent
27229variables. This package provides routines to help determine optimal Bayesian
27230network models for a given data set, where these models are used to identify
27231statistical dependencies in messy, complex data.")
27232 (license license:gpl2+)))
27233
27234;; This is a CRAN package, but it depends on r-rsamtools, which is a
27235;; Bioconductor package.
27236(define-public r-spp
27237 (package
27238 (name "r-spp")
27239 (version "1.16.0")
27240 (source (origin
27241 (method url-fetch)
27242 (uri (cran-uri "spp" version))
27243 (sha256
27244 (base32
27245 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
27246 (build-system r-build-system)
27247 (inputs
27248 (list zlib))
27249 (propagated-inputs
27250 (list r-bh r-catools r-rcpp r-rsamtools))
27251 (home-page "https://cran.r-project.org/web/packages/spp/")
27252 (synopsis "ChIP-Seq processing pipeline")
27253 (description "This package provides tools for analysis of ChIP-seq and
27254other functional sequencing data.")
27255 (license license:gpl2)))
27256
27257(define-public r-parody
27258 (package
27259 (name "r-parody")
27260 (version "1.70.0")
27261 (source
27262 (origin
27263 (method url-fetch)
27264 (uri (bioconductor-uri "parody" version))
27265 (sha256
27266 (base32 "0xpic2inrbz5wg7c4vphnkyf2dd3xspdh3a9f3yb2ynqgrzlqdck"))))
27267 (properties `((upstream-name . "parody")))
27268 (build-system r-build-system)
27269 (native-inputs (list r-knitr r-testthat))
27270 (home-page "https://bioconductor.org/packages/parody")
27271 (synopsis "Parametric and resistant outlier detection")
27272 (description
27273 "The parody package provides routines for univariate and multivariate
27274outlier detection with a focus on parametric methods, but support for some
27275methods based on resistant statistics.")
27276 (license license:artistic2.0)))
27277
27278(define-public r-pathview
27279 (package
27280 (name "r-pathview")
27281 (version "1.52.0")
27282 (source
27283 (origin
27284 (method url-fetch)
27285 (uri (bioconductor-uri "pathview" version))
27286 (sha256
27287 (base32 "0bsja7y9yvkdbk1sn57nym1wngsxxdby7qh65z2rpr1jj2n9flpd"))))
27288 (properties `((upstream-name . "pathview")))
27289 (build-system r-build-system)
27290 ;; Vignettes attempt to connect to the internet.
27291 (arguments (list #:test-types '(list "tests")))
27292 (propagated-inputs
27293 (list r-annotationdbi
27294 r-graph
27295 r-kegggraph
27296 r-keggrest
27297 r-org-hs-eg-db
27298 r-png
27299 r-rgraphviz
27300 r-xml))
27301 (native-inputs (list r-biocgenerics r-gage r-runit))
27302 (home-page "https://pathview.uncc.edu/")
27303 (synopsis "Tool set for pathway based data integration and visualization")
27304 (description
27305 "@code{r-pathview} is a tool set for pathway based data integration and
27306visualization. It maps and renders a wide variety of biological data on
27307relevant pathway graphs. All users need is to supply their data and specify
27308the target pathway. This package automatically downloads the pathway graph
27309data, parses the data file, maps user data to the pathway, and render pathway
27310graph with the mapped data. In addition, @code{r-pathview} also seamlessly
27311integrates with pathway and gene set (enrichment) analysis tools for
27312large-scale and fully automated analysis.")
27313 (license license:gpl3+)))
27314
27315(define-public r-snprelate
27316 (package
27317 (name "r-snprelate")
27318 (version "1.46.0")
27319 (source (origin
27320 (method url-fetch)
27321 (uri (bioconductor-uri "SNPRelate" version))
27322 (sha256
27323 (base32
27324 "17sq3x00zvkgqmib02n34cx81f4lzkqbf7kkrh23p8nyid19hi6a"))))
27325 (properties
27326 '((upstream-name . "SNPRelate")
27327 (updater-extra-native-inputs . ("r-matrix"))))
27328 (build-system r-build-system)
27329 (propagated-inputs (list r-gdsfmt r-rhpcblasctl))
27330 (native-inputs (list r-biocgenerics r-knitr r-matrix r-runit))
27331 (home-page "https://github.com/zhengxwen/SNPRelate")
27332 (synopsis
27333 "Toolset for relatedness and Principal Component Analysis of SNP data")
27334 (description
27335 "Genome-wide association studies (GWAS) are widely used to investigate
27336the genetic basis of diseases and traits, but they pose many computational
27337challenges. The R package SNPRelate provides a binary format for
27338single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic
27339Data Structure (GDS) data files. The GDS format offers the efficient
27340operations specifically designed for integers with two bits, since a SNP could
27341occupy only two bits. SNPRelate is also designed to accelerate two key
27342computations on SNP data using parallel computing for multi-core symmetric
27343multiprocessing computer architectures: Principal Component Analysis (PCA) and
27344relatedness analysis using Identity-By-Descent measures. The SNP GDS format
27345is also used by the GWASTools package with the support of S4 classes and
27346generic functions. The extended GDS format is implemented in the SeqArray
27347package to support the storage of single nucleotide variations (SNVs),
27348insertion/deletion polymorphism (indel) and structural variation calls in
27349whole-genome and whole-exome variant data.")
27350 (license license:gpl3)))
27351
27352(define-public r-snpstats
27353 (package
27354 (name "r-snpstats")
27355 (version "1.62.0")
27356 (source
27357 (origin
27358 (method url-fetch)
27359 (uri (bioconductor-uri "snpStats" version))
27360 (sha256
27361 (base32
27362 "10cb71ggzahvb8z8sbwwh2rf8dncnl9i34vimvlv2lk0lqiclydc"))))
27363 (properties `((upstream-name . "snpStats")))
27364 (build-system r-build-system)
27365 (inputs (list zlib))
27366 (propagated-inputs
27367 (list r-biocgenerics r-matrix r-survival))
27368 (home-page "https://bioconductor.org/packages/snpStats")
27369 (synopsis "Methods for SNP association studies")
27370 (description
27371 "This package provides classes and statistical methods for large
27372@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
27373the earlier snpMatrix package, allowing for uncertainty in genotypes.")
27374 (license license:gpl3)))
27375
27376(define-public r-chromstar
27377 (package
27378 (name "r-chromstar")
27379 (version "1.32.0")
27380 (source
27381 (origin
27382 (method url-fetch)
27383 (uri (bioconductor-uri "chromstaR" version))
27384 (sha256
27385 (base32
27386 "071aipwk1awr71hvzflps49dzp83p12zm1pbyx4l8d2v3wbj0dlz"))))
27387 (properties `((upstream-name . "chromstaR")))
27388 (build-system r-build-system)
27389 (arguments
27390 (list
27391 #:phases
27392 #~(modify-phases %standard-phases
27393 (add-before 'install 'fix-r-4.5.0
27394 ;; Changes in R 4.5.0: C-Level Facilities.
27395 ;; Strict R headers are now the default. This removes the legacy
27396 ;; definitions of PI, Calloc, Realloc and Free: use M_PI,
27397 ;; R_Calloc, R_Realloc or R_Free instead.
27398 ;; https://cran.r-project.org/doc/manuals/r-release/NEWS.html
27399 (lambda _
27400 (substitute* '("src/densities.cpp"
27401 "src/scalehmm.cpp"
27402 "src/utility.cpp")
27403 (("Calloc\\(") "R_Calloc(")
27404 (("Free\\(") "R_Free(")
27405 (("Realloc\\(") "R_Realloc(")))))))
27406 (propagated-inputs
27407 (list r-bamsignals
27408 r-biocgenerics
27409 r-chromstardata
27410 r-doparallel
27411 r-foreach
27412 r-genomeinfodb
27413 r-genomicalignments
27414 r-genomicranges
27415 r-ggplot2
27416 r-iranges
27417 r-mvtnorm
27418 r-reshape2
27419 r-rsamtools
27420 r-s4vectors))
27421 (native-inputs (list r-biomart r-knitr r-testthat))
27422 (home-page "https://github.com/ataudt/chromstaR")
27423 (synopsis "Chromatin state analysis for ChIP-Seq data")
27424 (description
27425 "This package implements functions for combinatorial and differential
27426analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
27427export to genome browser viewable files, and functions for enrichment
27428analyses.")
27429 (license license:artistic2.0)))
27430
27431(define-public r-guitar
27432 (package
27433 (name "r-guitar")
27434 (version "2.28.0")
27435 (source
27436 (origin
27437 (method url-fetch)
27438 (uri (bioconductor-uri "Guitar" version))
27439 (sha256
27440 (base32
27441 "10xvczafkpj9ffkyvvd910wkbxpmpk8d5jaa4lcrc20cx0s5sfb7"))))
27442 (properties `((upstream-name . "Guitar")))
27443 (build-system r-build-system)
27444 (propagated-inputs
27445 (list r-annotationdbi
27446 r-dplyr
27447 r-genomicfeatures
27448 r-genomicranges
27449 r-ggplot2
27450 r-knitr
27451 r-magrittr
27452 r-rtracklayer))
27453 (native-inputs
27454 (list r-knitr))
27455 (home-page "https://bioconductor.org/packages/Guitar")
27456 (synopsis "Visualize genomic features")
27457 (description
27458 "This package is designed for visualization of RNA-related genomic
27459features with respect to the landmarks of RNA transcripts, i.e., transcription
27460starting site, start codon, stop codon and transcription ending site.")
27461 (license license:gpl2)))
27462
27463(define-public r-sushi
27464 (package
27465 (name "r-sushi")
27466 (version "1.34.0")
27467 (source (origin
27468 (method url-fetch)
27469 (uri (bioconductor-uri "Sushi" version))
27470 (sha256
27471 (base32
27472 "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
27473 (properties `((upstream-name . "Sushi")))
27474 (build-system r-build-system)
27475 (propagated-inputs
27476 (list r-biomart r-zoo))
27477 (home-page "https://bioconductor.org/packages/Sushi")
27478 (synopsis "Tools for visualizing genomics data")
27479 (description
27480 "This package provides flexible, quantitative, and integrative genomic
27481visualizations for publication-quality multi-panel figures.")
27482 (license license:gpl2+)))
27483
27484(define-public r-ballgown
27485 (package
27486 (name "r-ballgown")
27487 (version "2.43.0")
27488 (source
27489 (origin
27490 (method url-fetch)
27491 (uri (bioconductor-uri "ballgown" version))
27492 (sha256
27493 (base32
27494 "1kjg47d1wipvhbjnjppgr6lfvf28g3rqmqsnjzpx8f400g80qd0w"))))
27495 (properties `((upstream-name . "ballgown")))
27496 (build-system r-build-system)
27497 (arguments
27498 (list
27499 #:phases
27500 '(modify-phases %standard-phases
27501 ;; This deprecated procedure has been removed in testthat.
27502 (add-after 'unpack 'testthat-compatibility
27503 (lambda _
27504 (substitute* "tests/testthat/test-annotation.R"
27505 (("is_true\\(\\)") "expect_true")))))))
27506 (propagated-inputs
27507 (list r-biobase
27508 r-genomicranges
27509 r-iranges
27510 r-limma
27511 r-rcolorbrewer
27512 r-rtracklayer
27513 r-s4vectors
27514 r-seqinfo
27515 r-sva))
27516 (native-inputs
27517 (list r-knitr r-testthat))
27518 (home-page "https://bioconductor.org/packages/ballgown")
27519 (synopsis "Flexible, isoform-level differential expression analysis")
27520 (description
27521 "This package provides tools for statistical analysis of assembled
27522transcriptomes, including flexible differential expression analysis,
27523visualization of transcript structures, and matching of assembled transcripts
27524to annotation.")
27525 (license license:artistic2.0)))
27526
27527(define-public r-megadepth
27528 (package
27529 (name "r-megadepth")
27530 (version "1.22.0")
27531 (source
27532 (origin
27533 (method url-fetch)
27534 (uri (bioconductor-uri "megadepth" version))
27535 (sha256
27536 (base32
27537 "1jjqszsrfqjix8qzlya077gdwzfz6qi6jasqwi9xc4pvnrqq85py"))))
27538 (properties
27539 `((upstream-name . "megadepth")
27540 (updater-extra-propagated-inputs . ("megadepth"))))
27541 (build-system r-build-system)
27542 ;; Tests attempt to install latest version of megadepth.
27543 (arguments (list #:tests? #false))
27544 (propagated-inputs
27545 (list megadepth
27546 r-cmdfun
27547 r-dplyr
27548 r-fs
27549 r-genomicranges
27550 r-magrittr
27551 r-readr
27552 r-xfun))
27553 (native-inputs
27554 (list r-knitr r-testthat))
27555 (home-page "https://github.com/LieberInstitute/megadepth")
27556 (synopsis "BigWig and BAM related utilities")
27557 (description
27558 "This package provides an R interface to Megadepth. It is particularly
27559useful for computing the coverage of a set of genomic regions across bigWig or
27560BAM files. With this package, you can build base-pair coverage matrices for
27561regions or annotations of your choice from BigWig files.")
27562 (license license:artistic2.0)))
27563
27564(define-public r-beclear
27565 (package
27566 (name "r-beclear")
27567 (version "2.28.0")
27568 (source
27569 (origin
27570 (method url-fetch)
27571 (uri (bioconductor-uri "BEclear" version))
27572 (sha256
27573 (base32
27574 "00ja1mz7mrcqm0bqwmgjjd098aniv25m0ifk778fn9k664icvvnk"))))
27575 (properties
27576 '((upstream-name . "BEclear")))
27577 (build-system r-build-system)
27578 (propagated-inputs
27579 (list r-abind
27580 r-biocparallel
27581 r-data-table
27582 r-dixontest
27583 r-ids
27584 r-logger
27585 r-matrix
27586 r-rcpp
27587 r-rdpack))
27588 (native-inputs
27589 (list r-knitr r-seewave r-testthat))
27590 (home-page "https://github.com/uds-helms/BEclear")
27591 (synopsis "Correction of batch effects in DNA methylation data")
27592 (description
27593 "This package provides functions to detect and correct for batch effects
27594in DNA methylation data. The core function is based on latent factor models
27595and can also be used to predict missing values in any other matrix containing
27596real numbers.")
27597 (license license:gpl3)))
27598
27599(define-public r-bgeecall
27600 (package
27601 (name "r-bgeecall")
27602 (version "1.28.0")
27603 (source
27604 (origin
27605 (method url-fetch)
27606 (uri (bioconductor-uri "BgeeCall" version))
27607 (sha256
27608 (base32
27609 "0ix45fpl87gzrnpaisddy2nqf5ail5di5mn06lfhy3hdhai1yz4c"))))
27610 (properties
27611 '((upstream-name . "BgeeCall")
27612 (updater-extra-propagated-inputs . ("kallisto"))))
27613 ;; Tests need internet access.
27614 (arguments (list #:tests? #false))
27615 (build-system r-build-system)
27616 (propagated-inputs
27617 (list kallisto
27618 r-annotationdbi
27619 r-biostrings
27620 r-curl
27621 r-data-table
27622 r-dplyr
27623 r-genomicfeatures
27624 r-ggplot2
27625 r-iranges
27626 r-jsonlite
27627 r-rcurl
27628 r-readr
27629 r-rhdf5
27630 r-rslurm
27631 r-rsqlite
27632 r-rtracklayer
27633 r-scales
27634 r-sjmisc
27635 r-spatstat-univar
27636 r-stringr
27637 r-txdbmaker
27638 r-tximport))
27639 (native-inputs (list r-annotationhub r-httr r-knitr r-testthat))
27640 (home-page "https://github.com/BgeeDB/BgeeCall")
27641 (synopsis "RNA-Seq present/absent gene expression calls generation")
27642 (description
27643 "BgeeCall allows generating present/absent gene expression calls without
27644using an arbitrary cutoff like TPM<1. Calls are generated based on reference
27645intergenic sequences. These sequences are generated based on expression of
27646all RNA-Seq libraries of each species integrated in Bgee.")
27647 (license license:gpl3)))
27648
27649(define-public r-bgeedb
27650 (package
27651 (name "r-bgeedb")
27652 (version "2.38.1")
27653 (source
27654 (origin
27655 (method url-fetch)
27656 (uri (bioconductor-uri "BgeeDB" version))
27657 (sha256
27658 (base32
27659 "1kk7vk8ns09h3577k41fk4vy4wcpqk0wczfax24pxh2gc288x61y"))))
27660 (properties `((upstream-name . "BgeeDB")))
27661 (build-system r-build-system)
27662 ;; Tests require Internet access.
27663 (arguments (list #:tests? #false))
27664 (propagated-inputs
27665 (list r-anndata
27666 r-biobase
27667 r-bread
27668 r-curl
27669 r-data-table
27670 r-digest
27671 r-dplyr
27672 r-graph
27673 r-hdf5array
27674 r-r-utils
27675 r-rcurl
27676 r-rsqlite
27677 r-tidyr
27678 r-topgo
27679 r-zellkonverter))
27680 (native-inputs (list r-knitr r-testthat))
27681 (home-page "https://github.com/BgeeDB/BgeeDB_R")
27682 (synopsis "Annotation and gene expression data retrieval from Bgee database")
27683 (description
27684 "This package provides a package for the annotation and gene expression
27685data download from Bgee database, and TopAnat analysis: GO-like enrichment of
27686anatomical terms, mapped to genes by expression patterns.")
27687 (license license:gpl3)))
27688
27689(define-public r-biobtreer
27690 (package
27691 (name "r-biobtreer")
27692 (version "1.24.0")
27693 (source
27694 (origin
27695 (method url-fetch)
27696 (uri (bioconductor-uri "biobtreeR" version))
27697 (sha256
27698 (base32
27699 "1gkkki1pgd3g7vv2281rrdp723ggl40019gg8zlfl46knjid6wv0"))))
27700 (properties `((upstream-name . "biobtreeR")))
27701 (build-system r-build-system)
27702 (propagated-inputs
27703 (list r-httpuv r-httr r-jsonlite r-stringi))
27704 (native-inputs (list r-knitr))
27705 (home-page "https://github.com/tamerh/biobtreeR")
27706 (synopsis "Use biobtree tool from R")
27707 (description
27708 "The biobtreeR package provides an interface to biobtree, a tool which
27709covers large sets of bioinformatics datasets and allows search and chain
27710mappings functionalities.")
27711 (license license:expat)))
27712
27713(define-public r-minet
27714 (package
27715 (name "r-minet")
27716 (version "3.70.0")
27717 (source
27718 (origin
27719 (method url-fetch)
27720 (uri (bioconductor-uri "minet" version))
27721 (sha256
27722 (base32
27723 "0y137wlpb49wjxc8v01r1k2ffl28m7lak0k1lbhhp8kkkf0zsd6c"))))
27724 (properties `((upstream-name . "minet")))
27725 (build-system r-build-system)
27726 (propagated-inputs
27727 (list r-infotheo))
27728 (home-page "http://minet.meyerp.com")
27729 (synopsis "Mutual information networks")
27730 (description
27731 "This package implements various algorithms for inferring mutual
27732information networks from data.")
27733 (license license:artistic2.0)))
27734
27735(define-public r-genetclassifier
27736 (package
27737 (name "r-genetclassifier")
27738 (version "1.52.0")
27739 (source
27740 (origin
27741 (method url-fetch)
27742 (uri (bioconductor-uri "geNetClassifier" version))
27743 (sha256
27744 (base32
27745 "08vxphq82iqm1iv7spv7kqpkliqyvmpqm8axyw94c4hly8473qyb"))))
27746 (properties
27747 `((upstream-name . "geNetClassifier")))
27748 (build-system r-build-system)
27749 (propagated-inputs
27750 (list r-biobase r-e1071 r-ebarrays r-minet))
27751 (native-inputs (list r-biocgenerics r-biocmanager r-leukemiaseset r-runit))
27752 (home-page "https://www.cicancer.org")
27753 (synopsis "Classify diseases and build gene networks using expression profiles")
27754 (description
27755 "This is a comprehensive package to automatically train and validate a
27756multi-class SVM classifier based on gene expression data. It provides
27757transparent selection of gene markers, their coexpression networks, and an
27758interface to query the classifier.")
27759 (license license:gpl2+)))
27760
27761(define-public r-dir-expiry
27762 (package
27763 (name "r-dir-expiry")
27764 (version "1.20.0")
27765 (source
27766 (origin
27767 (method url-fetch)
27768 (uri (bioconductor-uri "dir.expiry" version))
27769 (sha256
27770 (base32
27771 "0p34pi9m768fwcd83d60kqppr5353knglsdsfqifphmjks5hqpw9"))))
27772 (properties
27773 '((upstream-name . "dir.expiry")
27774 (updater-ignored-native-inputs . ("r-expiry"))))
27775 (build-system r-build-system)
27776 (propagated-inputs (list r-filelock))
27777 (native-inputs (list r-knitr r-testthat))
27778 (home-page "https://bioconductor.org/packages/dir.expiry")
27779 (synopsis "Managing expiration for cache directories")
27780 (description
27781 "This package implements an expiration system for access to versioned
27782directories. Directories that have not been accessed by a registered function
27783within a certain time frame are deleted. This aims to reduce disk usage by
27784eliminating obsolete caches generated by old versions of packages.")
27785 (license license:gpl3)))
27786
27787(define-public r-basic4cseq
27788 (package
27789 (name "r-basic4cseq")
27790 (version "1.48.0")
27791 (source
27792 (origin
27793 (method url-fetch)
27794 (uri (bioconductor-uri "Basic4Cseq" version))
27795 (sha256
27796 (base32 "149sf7mx3ddmdvp2p6rz9k8yb5r4p5rfs9pxzi1qxris6v2ba03k"))))
27797 (properties `((upstream-name . "Basic4Cseq")))
27798 (build-system r-build-system)
27799 (propagated-inputs
27800 (list r-biostrings
27801 r-bsgenome-ecoli-ncbi-20080805
27802 r-catools
27803 r-genomicalignments
27804 r-genomicranges
27805 r-rcircos))
27806 (home-page "https://bioconductor.org/packages/Basic4Cseq")
27807 (synopsis "Analyzing 4C-seq data")
27808 (description
27809 "Basic4Cseq is an R package for basic filtering, analysis and subsequent
27810visualization of @acronym{4C-seq, circular chromosome conformation capture
27811sequencing} data. Virtual fragment libraries can be created for any BSGenome
27812package, and filter functions for both reads and fragments and basic quality
27813controls are included. Fragment data in the vicinity of the experiment's
27814viewpoint can be visualized as a coverage plot based on a running median
27815approach and a multi-scale contact profile.")
27816 (license license:lgpl3)))
27817
27818(define-public r-basics
27819 (package
27820 (name "r-basics")
27821 (version "2.24.0")
27822 (source
27823 (origin
27824 (method url-fetch)
27825 (uri (bioconductor-uri "BASiCS" version))
27826 (sha256
27827 (base32 "08sgmg8vs6p3d308wyr42cbcanq66mivxlyqwbwcfq69x20ih970"))))
27828 (properties
27829 '((upstream-name . "BASiCS")
27830 (updater-extra-native-inputs . ("r-scrnaseq"))))
27831 (build-system r-build-system)
27832 (arguments
27833 (list
27834 ;; This test attempts to contact gypsum.artifactdb.com
27835 #:skipped-tests '(("test_misc.R" "ERCC works"))))
27836 (propagated-inputs
27837 (list r-assertthat
27838 r-biobase
27839 r-biocgenerics
27840 r-biocparallel
27841 r-coda
27842 r-cowplot
27843 r-ggextra
27844 r-ggplot2
27845 r-hexbin
27846 r-mass
27847 r-matrix
27848 r-matrixstats
27849 r-posterior
27850 r-rcpp
27851 r-rcpparmadillo
27852 r-reshape2
27853 r-s4vectors
27854 r-scran
27855 r-scuttle
27856 r-singlecellexperiment
27857 r-summarizedexperiment
27858 r-viridis))
27859 (native-inputs (list r-knitr r-scrnaseq r-testthat))
27860 (home-page "https://github.com/catavallejos/BASiCS")
27861 (synopsis "Bayesian analysis of single-cell sequencing data")
27862 (description
27863 "@acronym{BASiCS, Bayesian analysis of single-cell sequencing data} is an
27864integrated Bayesian hierarchical model to perform statistical analyses of
27865single-cell RNA sequencing datasets in the context of supervised experiments
27866(where the groups of cells of interest are known a priori. BASiCS performs
27867built-in data normalisation (global scaling) and technical noise quantification
27868(based on spike-in genes). BASiCS provides an intuitive detection criterion
27869for highly (or lowly) variable genes within a single group of cells.
27870Additionally, BASiCS can compare gene expression patterns between two or more
27871pre-specified groups of cells.")
27872 (license license:gpl3)))
27873
27874(define-public r-basicstarrseq
27875 (package
27876 (name "r-basicstarrseq")
27877 (version "1.40.0")
27878 (source
27879 (origin
27880 (method url-fetch)
27881 (uri (bioconductor-uri "BasicSTARRseq" version))
27882 (sha256
27883 (base32 "1907n76jgl849zcmvp65yy86qlkviqhh2spvfh9f1kyd8fjvcb1g"))))
27884 (properties `((upstream-name . "BasicSTARRseq")))
27885 (build-system r-build-system)
27886 (propagated-inputs
27887 (list r-genomicalignments r-genomicranges r-iranges r-s4vectors r-seqinfo))
27888 (native-inputs (list r-knitr))
27889 (home-page "https://bioconductor.org/packages/BasicSTARRseq")
27890 (synopsis "Basic peak calling on STARR-seq data")
27891 (description
27892 "This package implements a method that aims to identify enhancers on
27893large scale. The STARR-seq data consists of two sequencing datasets of the
27894same targets in a specific genome. The input sequences show which regions
27895where tested for enhancers. Significant enriched peaks i.e. a lot more
27896sequences in one region than in the input where enhancers in the genomic DNA
27897are, can be identified. So the approach pursued is to call peak every region
27898in which there is a lot more
27899(significant in a binomial model) STARR-seq signal than input signal and
27900propose an enhancer at that very same position. Enhancers then are called
27901weak or strong dependent of there degree of enrichment in comparison to
27902input.")
27903 (license license:lgpl3)))
27904
27905(define-public r-basilisk-utils
27906 (package
27907 (name "r-basilisk-utils")
27908 (version "1.24.0")
27909 (source
27910 (origin
27911 (method url-fetch)
27912 (uri (bioconductor-uri "basilisk.utils" version))
27913 (sha256
27914 (base32
27915 "0z4gsack303d6lll1nyc6h2rl08yv4nyv3zwzbpj2a7gfipj4z9p"))))
27916 (properties
27917 '((upstream-name . "basilisk.utils")
27918 (updater-ignored-native-inputs . ("r-expiry"))))
27919 (build-system r-build-system)
27920 ;; 8 tests need Internet access to test that Conda can install software.
27921 (arguments (list #:tests? #false))
27922 (propagated-inputs
27923 (list r-dir-expiry))
27924 (native-inputs (list r-knitr r-testthat))
27925 (home-page "https://bioconductor.org/packages/basilisk.utils")
27926 (synopsis "Basilisk installation utilities")
27927 (description
27928 "This package implements utilities for installation of the basilisk
27929package, primarily for creation of the underlying Conda instance.")
27930 (license license:gpl3)))
27931
27932(define-public r-basilisk
27933 (package
27934 (name "r-basilisk")
27935 (version "1.24.0")
27936 (source
27937 (origin
27938 (method url-fetch)
27939 (uri (bioconductor-uri "basilisk" version))
27940 (sha256
27941 (base32
27942 "0qza9rr89r4qn17wmajjz1j2jk7076kz4r1755jnw35fkm186hb7"))))
27943 (properties
27944 '((upstream-name . "basilisk")
27945 (updater-ignored-native-inputs . ("r-expiry"))))
27946 (build-system r-build-system)
27947 (arguments
27948 (list
27949 ;; Several tests attempt to install things with Conda.
27950 #:tests? #false
27951 #:phases
27952 '(modify-phases %standard-phases
27953 (add-after 'unpack 'patch-for-guix
27954 (lambda _
27955 (substitute* "R/useBasiliskEnv.R"
27956 (("^useBasiliskEnv <- function.*" m)
27957 (string-append m "
27958if (!is.na(Sys.getenv(\"GUIX_BYPASS_BASILISK\"))) {
27959 py_config()
27960 return()
27961}
27962")))
27963 (substitute* "R/basiliskStart.R"
27964 (("^basiliskRun <- function.*" m)
27965 (string-append m "
27966if (!is.na(Sys.getenv(\"GUIX_BYPASS_BASILISK\"))) {
27967 if (is.environment(proc)) {
27968 output <- fun(...)
27969 } else {
27970 proc <- new.env()
27971 proc <- makePSOCKcluster(1)
27972 clusterCall(proc, useBasiliskEnv, envpath=NULL)
27973 on.exit(basiliskStop(proc), add=TRUE)
27974 output <- clusterCall(proc, fun=fun, ...)[[1]]
27975 }
27976 return(output)
27977}
27978"))))))))
27979 (propagated-inputs
27980 (list r-dir-expiry r-reticulate))
27981 (native-inputs (list r-callr r-knitr r-testthat))
27982 (home-page "https://bioconductor.org/packages/basilisk")
27983 (synopsis "Freeze Python dependencies inside Bioconductor packages")
27984 (description
27985 "This package installs a self-contained Conda instance that is managed by
27986the R/Bioconductor installation machinery. This aims to provide a consistent
27987Python environment that can be used reliably by Bioconductor packages.
27988Functions are also provided to enable smooth interoperability of multiple
27989Python environments in a single R session.")
27990 (license license:gpl3)))
27991
27992(define-public r-bayesknockdown
27993 (package
27994 (name "r-bayesknockdown")
27995 (version "1.38.0")
27996 (source
27997 (origin
27998 (method url-fetch)
27999 (uri (bioconductor-uri "BayesKnockdown" version))
28000 (sha256
28001 (base32 "04bfv90g27kpbg3xzp3zvp4g2zazacvcm83dwqfcqgdlb51dg91h"))))
28002 (properties `((upstream-name . "BayesKnockdown")))
28003 (build-system r-build-system)
28004 (propagated-inputs (list r-biobase))
28005 (home-page "https://bioconductor.org/packages/BayesKnockdown")
28006 (synopsis "Posterior probabilities for edges from knockdown data")
28007 (description
28008 "This package provides a simple, fast Bayesian method for computing
28009posterior probabilities for relationships between a single predictor variable
28010and multiple potential outcome variables, incorporating prior probabilities of
28011relationships. In the context of knockdown experiments, the predictor
28012variable is the knocked-down gene, while the other genes are potential
28013targets. It can also be used for differential expression/2-class data.")
28014 (license license:gpl3)))
28015
28016(define-public r-bayesspace
28017 (package
28018 (name "r-bayesspace")
28019 (version "1.22.0")
28020 (source
28021 (origin
28022 (method url-fetch)
28023 (uri (bioconductor-uri "BayesSpace" version))
28024 (sha256
28025 (base32 "142j3ab2ahp5ziaz3snq1pxji6kpz1s9gj0zx95li1i1rm0rz805"))))
28026 (properties `((upstream-name . "BayesSpace")))
28027 (build-system r-build-system)
28028 (propagated-inputs
28029 (list r-arrow
28030 r-assertthat
28031 r-biocfilecache
28032 r-biocparallel
28033 r-biocsingular
28034 r-coda
28035 r-dirichletreg
28036 r-dplyr
28037 r-ggplot2
28038 r-magrittr
28039 r-matrix
28040 r-mclust
28041 r-microbenchmark
28042 r-purrr
28043 r-rcpp
28044 r-rcpparmadillo
28045 r-rcppdist
28046 r-rcppprogress
28047 r-rcurl
28048 r-rhdf5
28049 r-rjson
28050 r-rlang
28051 r-s4vectors
28052 r-scales
28053 r-scater
28054 r-scran
28055 r-singlecellexperiment
28056 r-summarizedexperiment
28057 r-tibble
28058 r-tidyr
28059 r-xgboost))
28060 (native-inputs (list r-knitr r-testthat))
28061 (home-page "https://www.ezstatconsulting.com/BayesSpace/")
28062 (synopsis "Clustering and resolution enhancement of spatial transcriptomes")
28063 (description
28064 "This package provides tools for clustering and enhancing the resolution
28065of spatial gene expression experiments. BayesSpace clusters a low-dimensional
28066representation of the gene expression matrix, incorporating a spatial prior to
28067encourage neighboring spots to cluster together. The method can enhance the
28068resolution of the low-dimensional representation into \"sub-spots\", for which
28069features such as gene expression or cell type composition can be imputed.")
28070 (license license:expat)))
28071
28072(define-public r-baynorm
28073 (package
28074 (name "r-baynorm")
28075 (version "1.30.0")
28076 (source
28077 (origin
28078 (method url-fetch)
28079 (uri (bioconductor-uri "bayNorm" version))
28080 (sha256
28081 (base32 "1653yclrw0zfcwcssm7sn3vmgac5hzddfc91yndmgx093s4s27b3"))))
28082 (properties `((upstream-name . "bayNorm")))
28083 (build-system r-build-system)
28084 (propagated-inputs
28085 (list r-bb
28086 r-biocparallel
28087 r-dosnow
28088 r-fitdistrplus
28089 r-foreach
28090 r-iterators
28091 r-locfit
28092 r-mass
28093 r-matrix
28094 r-rcpp
28095 r-rcpparmadillo
28096 r-rcppprogress
28097 r-singlecellexperiment
28098 r-summarizedexperiment))
28099 (native-inputs (list r-knitr r-testthat))
28100 (home-page "https://github.com/WT215/bayNorm")
28101 (synopsis "Single-cell RNA sequencing data normalization")
28102 (description
28103 "The bayNorm package is used for normalizing single-cell RNA-seq data.
28104The main function is @code{bayNorm}, which is a wrapper function for gene
28105specific prior parameter estimation and normalization. The input is a matrix
28106of scRNA-seq data with rows different genes and columns different cells. The
28107output is either point estimates from posterior (2D array) or samples from
28108posterior (3D array).")
28109 (license license:gpl2+)))
28110
28111(define-public r-bbcanalyzer
28112 (package
28113 (name "r-bbcanalyzer")
28114 (version "1.42.0")
28115 (source
28116 (origin
28117 (method url-fetch)
28118 (uri (bioconductor-uri "BBCAnalyzer" version))
28119 (sha256
28120 (base32 "00zfcn5ii9zycxcvbr1jdgyraqvww66n1n66p29yb4yvyjx7bdbq"))))
28121 (properties `((upstream-name . "BBCAnalyzer")))
28122 (build-system r-build-system)
28123 (propagated-inputs
28124 (list r-biostrings
28125 r-genomicranges
28126 r-iranges
28127 r-rsamtools
28128 r-summarizedexperiment
28129 r-variantannotation))
28130 (home-page "https://bioconductor.org/packages/BBCAnalyzer")
28131 (synopsis "Visualizing base counts")
28132 (description
28133 "BBCAnalyzer is a package for visualizing the relative or absolute number
28134of bases, deletions and insertions at defined positions in sequence alignment
28135data available as bam files in comparison to the reference bases. Markers for
28136the relative base frequencies, the mean quality of the detected bases, known
28137mutations or polymorphisms and variants called in the data may additionally be
28138included in the plots.")
28139 (license license:lgpl3)))
28140
28141(define-public r-bcrank
28142 (package
28143 (name "r-bcrank")
28144 (version "1.74.0")
28145 (source
28146 (origin
28147 (method url-fetch)
28148 (uri (bioconductor-uri "BCRANK" version))
28149 (sha256
28150 (base32 "0m6xwyfz710h8yfgp9a02vlacd1mqgjipdj9y8532ryqcnq622bn"))))
28151 (properties `((upstream-name . "BCRANK")))
28152 (build-system r-build-system)
28153 (propagated-inputs (list r-biostrings))
28154 (home-page "https://bioconductor.org/packages/BCRANK")
28155 (synopsis "Predicting binding site consensus from ranked DNA sequences")
28156 (description
28157 "This package provides functions and classes for de novo prediction of
28158transcription factor binding consensus by heuristic search.")
28159 (license license:gpl2)))
28160
28161(define-public r-biocthis
28162 (package
28163 (name "r-biocthis")
28164 (version "1.22.0")
28165 (source
28166 (origin
28167 (method url-fetch)
28168 (uri (bioconductor-uri "biocthis" version))
28169 (sha256
28170 (base32
28171 "0kkvcl29nv6ndk37y45k8cwdm5n1pqhsz6wfh3a058n2b9x8hk78"))))
28172 (properties `((upstream-name . "biocthis")))
28173 (build-system r-build-system)
28174 (arguments
28175 (list
28176 ;; Tests only attempt to check R and Bioc versions. Looks like this is
28177 ;; really only meant for actual Bioconductor infrastructure.
28178 #:tests? #false
28179 #:phases
28180 '(modify-phases %standard-phases
28181 (add-after 'unpack 'set-HOME
28182 (lambda _ (setenv "HOME" "/tmp"))))))
28183 (propagated-inputs
28184 (list r-biocmanager
28185 r-fs
28186 r-glue
28187 r-rlang
28188 r-styler
28189 r-usethis))
28190 (native-inputs (list r-knitr r-testthat))
28191 (home-page "https://github.com/lcolladotor/biocthis")
28192 (synopsis "Automate package and project setup for Bioconductor packages")
28193 (description
28194 "This package expands the @code{usethis} package with the goal of helping
28195automate the process of creating R packages for Bioconductor or making them
28196Bioconductor-friendly.")
28197 (license license:artistic2.0)))
28198
28199(define-public r-biocdockermanager
28200 (package
28201 (name "r-biocdockermanager")
28202 (version "1.11.0")
28203 (source
28204 (origin
28205 (method url-fetch)
28206 (uri (bioconductor-uri "BiocDockerManager" version))
28207 (sha256
28208 (base32
28209 "0w393f14i253pnk0jzf2ci4g5cnxshwdjmix2r8arlnadh7spjyk"))))
28210 (properties
28211 `((upstream-name . "BiocDockerManager")))
28212 (build-system r-build-system)
28213 ;; Tests require access to hub.docker.com.
28214 (arguments (list #:tests? #false))
28215 (propagated-inputs
28216 (list docker
28217 r-dplyr
28218 r-httr
28219 r-memoise
28220 r-readr
28221 r-whisker))
28222 (native-inputs (list r-knitr r-testthat))
28223 (home-page "https://bioconductor.org/packages/BiocDockerManager")
28224 (synopsis "Access and manage Bioconductor Docker images")
28225 (description
28226 "This package works analogous to BiocManager but for Docker images. Use
28227the BiocDockerManager package to install and manage Docker images provided by
28228the Bioconductor project.")
28229 (license license:artistic2.0)))
28230
28231(define-public r-biodb
28232 (package
28233 (name "r-biodb")
28234 (version "1.20.0")
28235 (source
28236 (origin
28237 (method url-fetch)
28238 (uri (bioconductor-uri "biodb" version))
28239 (sha256
28240 (base32
28241 "0gmkjjv1nyrymc70lwqyh7yz8h97k7fq04ayaw7xqzzimhz76fv8"))))
28242 (properties `((upstream-name . "biodb")))
28243 (build-system r-build-system)
28244 ;; 83 tests fail; 1025 pass. Some of the failing tests attempt to
28245 ;; download files and then operate on them in following tests. Since
28246 ;; these are scattered across many files it is too messy to patch them
28247 ;; all.
28248 (arguments (list #:tests? #false))
28249 (propagated-inputs
28250 (list r-chk
28251 r-fscache
28252 r-jsonlite
28253 r-lgr
28254 r-lifecycle
28255 r-openssl
28256 r-plyr
28257 r-progress
28258 r-r6
28259 r-rappdirs
28260 r-rcpp
28261 r-rsqlite
28262 r-sched
28263 r-sqlq
28264 r-stringr
28265 r-testthat
28266 r-withr
28267 r-xml
28268 r-yaml))
28269 (native-inputs (list r-knitr))
28270 (home-page "https://bioconductor.org/packages/biodb")
28271 (synopsis "Library for connecting to chemical and biological databases")
28272 (description
28273 "The biodb package provides access to standard remote chemical and
28274biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local
28275database files (CSV, SQLite), with easy retrieval of entries, access to web
28276services, search of compounds by mass and/or name, and mass spectra matching
28277for LCMS and MSMS. Its architecture as a development framework facilitates
28278the development of new database connectors for local projects or inside
28279separate published packages.")
28280 (license license:agpl3+)))
28281
28282(define-public r-biomformat
28283 (package
28284 (name "r-biomformat")
28285 (version "1.40.0")
28286 (source
28287 (origin
28288 (method url-fetch)
28289 (uri (bioconductor-uri "biomformat" version))
28290 (sha256
28291 (base32
28292 "1hrfhgffhy70j3i620mk1l6b7n9wg7xqisn53cz23v650yyi1lha"))))
28293 (properties
28294 `((upstream-name . "biomformat")
28295 (updater-extra-propagated-inputs . ("r-rhdf5"))))
28296 (build-system r-build-system)
28297 (propagated-inputs
28298 (list r-jsonlite r-matrix r-rhdf5))
28299 (native-inputs (list r-knitr r-s4vectors r-summarizedexperiment r-testthat
28300 r-tibble))
28301 (home-page "https://github.com/joey711/biomformat/")
28302 (synopsis "Interface package for the BIOM file format")
28303 (description
28304 "This is an R package for interfacing with the BIOM format. This package
28305includes basic tools for reading biom-format files, accessing and subsetting
28306data tables from a biom object (which is more complex than a single table), as
28307well as limited support for writing a biom-object back to a biom-format file.
28308The design of this API is intended to match the Python API and other tools
28309included with the biom-format project, but with a decidedly \"R flavor\" that
28310should be familiar to R users. This includes S4 classes and methods, as well
28311as extensions of common core functions/methods.")
28312 (license license:gpl2)))
28313
28314(define-public r-mvcclass
28315 (package
28316 (name "r-mvcclass")
28317 (version "1.86.0")
28318 (source
28319 (origin
28320 (method url-fetch)
28321 (uri (bioconductor-uri "MVCClass" version))
28322 (sha256
28323 (base32
28324 "17yqjhy4wzj7aj52128m71rgj50yn491xg84rzyziaw6vm4z6341"))))
28325 (properties `((upstream-name . "MVCClass")))
28326 (build-system r-build-system)
28327 (home-page "https://bioconductor.org/packages/MVCClass")
28328 (synopsis "Model-View-Controller (MVC) classes")
28329 (description
28330 "This package contains classes used in model-view-controller (MVC)
28331design.")
28332 (license license:lgpl2.1+)))
28333
28334(define-public r-biomvcclass
28335 (package
28336 (name "r-biomvcclass")
28337 (version "1.80.0")
28338 (source
28339 (origin
28340 (method url-fetch)
28341 (uri (bioconductor-uri "BioMVCClass" version))
28342 (sha256
28343 (base32
28344 "0qx8bnvka6qs03mgsbax08m2apc2y26viw3brcav6y88v1rg27pc"))))
28345 (properties `((upstream-name . "BioMVCClass")))
28346 (build-system r-build-system)
28347 (propagated-inputs
28348 (list r-biobase r-graph r-mvcclass r-rgraphviz))
28349 (home-page "https://bioconductor.org/packages/BioMVCClass")
28350 (synopsis "Model-View-Controller (MVC) classes that use Biobase")
28351 (description
28352 "This package contains classes used in model-view-controller (MVC)
28353design.")
28354 (license license:lgpl2.1+)))
28355
28356(define-public r-biomvrcns
28357 (package
28358 (name "r-biomvrcns")
28359 (version "1.52.0")
28360 (source
28361 (origin
28362 (method url-fetch)
28363 (uri (bioconductor-uri "biomvRCNS" version))
28364 (sha256
28365 (base32
28366 "19i26pr0890c5aa1hm5rk5ad32r0p4si5lyd6hg5xdmm51axdmi3"))))
28367 (properties `((upstream-name . "biomvRCNS")))
28368 (build-system r-build-system)
28369 (arguments
28370 (list
28371 #:phases
28372 '(modify-phases %standard-phases
28373 (add-after 'unpack 'patch-constants
28374 (lambda _
28375 (substitute* "src/biomvRCNS.c"
28376 (("DOUBLE_XMIN") "DBL_MIN")
28377 (("DOUBLE_XMAX") "DBL_MAX")))))))
28378 (propagated-inputs
28379 (list r-genomicranges r-gviz r-iranges r-mvtnorm))
28380 (home-page "https://bioconductor.org/packages/biomvRCNS")
28381 (synopsis "Copy number study and segmentation for multivariate biological data")
28382 (description
28383 "In this package, a @dfn{Hidden Semi Markov Model} (HSMM) and one
28384homogeneous segmentation model are designed and implemented for segmentation
28385genomic data, with the aim of assisting in transcripts detection using high
28386throughput technology like RNA-seq or tiling array, and copy number analysis
28387using aCGH or sequencing.")
28388 (license license:gpl2+)))
28389
28390(define-public r-bionero
28391 (package
28392 (name "r-bionero")
28393 (version "1.20.0")
28394 (source
28395 (origin
28396 (method url-fetch)
28397 (uri (bioconductor-uri "BioNERO" version))
28398 (sha256
28399 (base32
28400 "1idg5rk7bppbrh2vzzp3syls13sd3jvh4lmpk4zhvfqakdrz2nw8"))))
28401 (properties
28402 '((upstream-name . "BioNERO")
28403 (updater-extra-native-inputs . ("r-networkd3"))))
28404 (build-system r-build-system)
28405 (propagated-inputs
28406 (list r-biocparallel
28407 r-complexheatmap
28408 r-dynamictreecut
28409 r-genie3
28410 r-ggdendro
28411 r-ggnetwork
28412 r-ggplot2
28413 r-ggrepel
28414 r-igraph
28415 r-intergraph
28416 r-matrixstats
28417 r-minet
28418 r-netrep
28419 r-patchwork
28420 r-rcolorbrewer
28421 r-reshape2
28422 r-rlang
28423 r-summarizedexperiment
28424 r-sva
28425 r-wgcna))
28426 (native-inputs
28427 (list r-knitr r-networkd3 r-testthat))
28428 (home-page "https://github.com/almeidasilvaf/BioNERO")
28429 (synopsis "Biological network reconstruction omnibus")
28430 (description
28431 "BioNERO aims to integrate all aspects of biological network inference in
28432a single package, including data preprocessing, exploratory analyses, network
28433inference, and analyses for biological interpretations. BioNERO can be used
28434to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs)
28435from gene expression data. Additionally, it can be used to explore
28436topological properties of protein-protein interaction (PPI) networks. GCN
28437inference relies on the popular WGCNA algorithm. GRN inference is based on
28438the \"wisdom of the crowds\" principle, which consists in inferring GRNs with
28439multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average
28440rank for each interaction pair. As all steps of network analyses are included
28441in this package, BioNERO makes users avoid having to learn the syntaxes of
28442several packages and how to communicate between them. Finally, users can also
28443identify consensus modules across independent expression sets and calculate
28444intra and interspecies module preservation statistics between different
28445networks.")
28446 (license license:gpl3)))
28447
28448(define-public r-bionet
28449 (package
28450 (name "r-bionet")
28451 (version "1.72.0")
28452 (source
28453 (origin
28454 (method url-fetch)
28455 (uri (bioconductor-uri "BioNet" version))
28456 (sha256
28457 (base32
28458 "0dwzid3ryrnm239z356c2w37s9q3478glidwghzws7dpm7v80hdd"))))
28459 (properties `((upstream-name . "BioNet")))
28460 (build-system r-build-system)
28461 (propagated-inputs
28462 (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
28463 (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
28464 (synopsis "Functional analysis of biological networks")
28465 (description
28466 "This package provides functions for the integrated analysis of
28467protein-protein interaction networks and the detection of functional modules.
28468Different datasets can be integrated into the network by assigning p-values of
28469statistical tests to the nodes of the network. E.g. p-values obtained from
28470the differential expression of the genes from an Affymetrix array are assigned
28471to the nodes of the network. By fitting a beta-uniform mixture model and
28472calculating scores from the p-values, overall scores of network regions can be
28473calculated and an integer linear programming algorithm identifies the maximum
28474scoring subnetwork.")
28475 (license license:gpl2+)))
28476
28477(define-public r-bionetstat
28478 (package
28479 (name "r-bionetstat")
28480 (version "1.22.0")
28481 (source
28482 (origin
28483 (method url-fetch)
28484 (uri (bioconductor-uri "BioNetStat" version))
28485 (sha256
28486 (base32
28487 "1rbb36v64b9xbk2dsf6wsyrhwwbkysrj8fp1g22y3gisdk170sg8"))
28488 (snippet
28489 '(delete-file "inst/datatables/js/jquery.dataTables.min.js"))))
28490 (properties `((upstream-name . "BioNetStat")))
28491 (build-system r-build-system)
28492 (arguments
28493 (list
28494 #:phases
28495 '(modify-phases %standard-phases
28496 (add-after 'unpack 'process-javascript
28497 (lambda _
28498 (with-directory-excursion "inst/datatables/js/"
28499 (invoke "esbuild"
28500 "jquery.dataTables.js"
28501 "--minify"
28502 "--outfile=jquery.dataTables.min.js")))))))
28503 (propagated-inputs
28504 (list r-biocparallel
28505 r-dt
28506 r-ggplot2
28507 r-hmisc
28508 r-igraph
28509 r-knitr
28510 r-markdown
28511 r-pathview
28512 r-pheatmap
28513 r-plyr
28514 r-psych
28515 r-rcolorbrewer
28516 r-rjsonio
28517 r-rmarkdown
28518 r-shiny
28519 r-shinybs
28520 r-whisker
28521 r-yaml))
28522 (native-inputs
28523 (list esbuild r-knitr r-rmarkdown))
28524 (home-page "https://github.com/jardimViniciusC/BioNetStat")
28525 (synopsis "Biological network analysis")
28526 (description
28527 "This package provides a package to perform differential network
28528analysis, differential node analysis (differential coexpression analysis),
28529network and metabolic pathways view.")
28530 (license license:gpl3+)))
28531
28532(define-public r-bioqc
28533 (package
28534 (name "r-bioqc")
28535 (version "1.40.0")
28536 (source
28537 (origin
28538 (method url-fetch)
28539 (uri (bioconductor-uri "BioQC" version))
28540 (sha256
28541 (base32
28542 "0473kgh2siv9la0gpbfa3s5bj5pjrlhbac5021gsyprw4nwcg6ws"))))
28543 (properties `((upstream-name . "BioQC")))
28544 (build-system r-build-system)
28545 (propagated-inputs
28546 (list r-biobase r-edger r-rcpp))
28547 (native-inputs
28548 (list r-ineq r-knitr r-testthat))
28549 (home-page "https://accio.github.io/BioQC/")
28550 (synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
28551 (description
28552 "BioQC performs quality control of high-throughput expression data based
28553on tissue gene signatures. It can detect tissue heterogeneity in gene
28554expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is
28555optimised for high performance.")
28556 (license license:gpl3+)))
28557
28558(define-public r-biotip
28559 (package
28560 (name "r-biotip")
28561 (version "1.26.0")
28562 (source
28563 (origin
28564 (method url-fetch)
28565 (uri (bioconductor-uri "BioTIP" version))
28566 (sha256
28567 (base32
28568 "02ywxggsak4h558wca7fay9ysgz3a4lg9rq4acg65ppp3y4mv9a5"))))
28569 (properties `((upstream-name . "BioTIP")))
28570 (build-system r-build-system)
28571 (propagated-inputs
28572 (list r-cluster
28573 r-doparallel
28574 r-foreach
28575 r-genomicranges
28576 r-igraph
28577 r-mass
28578 r-psych
28579 r-scran
28580 r-stringr))
28581 (native-inputs
28582 (list r-knitr))
28583 (home-page "https://github.com/xyang2uchicago/BioTIP")
28584 (synopsis "R package for characterization of biological tipping-point")
28585 (description
28586 "This package adopts tipping-point theory to transcriptome profiles to
28587help unravel disease regulatory trajectory.")
28588 (license license:gpl2)))
28589
28590(define-public r-biotmle
28591 (package
28592 (name "r-biotmle")
28593 (version "1.36.0")
28594 (source
28595 (origin
28596 (method url-fetch)
28597 (uri (bioconductor-uri "biotmle" version))
28598 (sha256
28599 (base32
28600 "1ivdz6ahzfpb23d7pchqfxi6ggifdsgpz9ghnpkl1zingcyysccw"))))
28601 (properties `((upstream-name . "biotmle")))
28602 (build-system r-build-system)
28603 ;; Two tests fail with "BiocParallel errors".
28604 (arguments (list #:tests? #false))
28605 (propagated-inputs
28606 (list r-assertthat
28607 r-biocgenerics
28608 r-biocparallel
28609 r-dplyr
28610 r-drtmle
28611 r-ggplot2
28612 r-ggsci
28613 r-limma
28614 r-s4vectors
28615 r-summarizedexperiment
28616 r-superheat
28617 r-tibble))
28618 (native-inputs
28619 (list r-biotmledata r-knitr r-superlearner r-testthat))
28620 (home-page "https://code.nimahejazi.org/biotmle/")
28621 (synopsis "Targeted learning with moderated statistics for biomarker discovery")
28622 (description
28623 "This package provides tools for differential expression biomarker
28624discovery based on microarray and next-generation sequencing data that
28625leverage efficient semiparametric estimators of the average treatment effect
28626for variable importance analysis. Estimation and inference of the (marginal)
28627average treatment effects of potential biomarkers are computed by targeted
28628minimum loss-based estimation, with joint, stable inference constructed across
28629all biomarkers using a generalization of moderated statistics for use with the
28630estimated efficient influence function. The procedure accommodates the use of
28631ensemble machine learning for the estimation of nuisance functions.")
28632 (license license:expat)))
28633
28634(define-public r-bsseq
28635 (package
28636 (name "r-bsseq")
28637 (version "1.48.0")
28638 (source
28639 (origin
28640 (method url-fetch)
28641 (uri (bioconductor-uri "bsseq" version))
28642 (sha256
28643 (base32
28644 "1rkxz5cibpk7mbh2xjg51nk0g9y4ga69q3q0zahmd9z1iik1943l"))))
28645 (properties
28646 '((upstream-name . "bsseq")
28647 (updater-extra-native-inputs . ("r-batchtools" "r-genomeinfodb"))))
28648 (build-system r-build-system)
28649 (propagated-inputs
28650 (list r-assorthead
28651 r-beachmat
28652 r-biobase
28653 r-biocgenerics
28654 r-biocparallel
28655 r-biostrings
28656 r-bsgenome
28657 r-data-table
28658 r-delayedarray
28659 r-delayedmatrixstats
28660 r-genomicranges
28661 r-gtools
28662 r-hdf5array
28663 r-iranges
28664 r-limma
28665 r-locfit
28666 r-permute
28667 r-r-utils
28668 r-rcpp
28669 r-rhdf5
28670 r-s4vectors
28671 r-scales
28672 r-seqinfo
28673 r-summarizedexperiment))
28674 (native-inputs
28675 (list r-batchtools
28676 r-doparallel
28677 r-genomeinfodb
28678 r-knitr
28679 r-matrix
28680 r-testthat))
28681 (home-page "https://github.com/hansenlab/bsseq")
28682 (synopsis "Analyze, manage and store bisulfite sequencing data")
28683 (description
28684 "This package provides a collection of tools for analyzing and
28685visualizing bisulfite sequencing data.")
28686 (license license:artistic2.0)))
28687
28688(define-public r-dada2
28689 (package
28690 (name "r-dada2")
28691 (version "1.40.0")
28692 (source (origin
28693 (method url-fetch)
28694 (uri (bioconductor-uri "dada2" version))
28695 (sha256
28696 (base32
28697 "1bih1958isw8qh3dgwfkiqfyvzs5c0jfcfr77zix7pjj5grd88qx"))))
28698 (properties `((upstream-name . "dada2")))
28699 (build-system r-build-system)
28700 (arguments
28701 (list
28702 #:phases
28703 #~(modify-phases %standard-phases
28704 (add-before 'install 'relax-gcc-14-strictness
28705 (lambda _
28706 (substitute* "src/Makevars"
28707 (("CXX_STD = CXX11")
28708 "CXX_STD = CXX11
28709PKG_CXXFLAGS=-g -O2 -Wno-error=changes-meaning")))))))
28710 (propagated-inputs
28711 (list r-biocgenerics
28712 r-biostrings
28713 r-ggplot2
28714 r-iranges
28715 r-rcpp
28716 r-rcppparallel
28717 r-reshape2
28718 r-shortread
28719 r-xvector))
28720 (native-inputs (list r-knitr))
28721 (home-page "https://benjjneb.github.io/dada2/")
28722 (synopsis
28723 "Accurate, high-resolution sample inference from amplicon sequencing data")
28724 (description
28725 "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs)
28726from high-throughput amplicon sequencing data, replacing the coarser and less
28727accurate OTU clustering approach. The dada2 pipeline takes as input
28728demultiplexed fastq files, and outputs the sequence variants and their
28729sample-wise abundances after removing substitution and chimera errors.
28730Taxonomic classification is available via a native implementation of the RDP
28731naive Bayesian classifier, and species-level assignment to 16S rRNA gene
28732fragments by exact matching.")
28733 (license license:lgpl2.0)))
28734
28735(define-public r-dmrseq
28736 (package
28737 (name "r-dmrseq")
28738 (version "1.32.0")
28739 (source
28740 (origin
28741 (method url-fetch)
28742 (uri (bioconductor-uri "dmrseq" version))
28743 (sha256
28744 (base32
28745 "1c97ywmi79245s0dph1v2pk5kkdk4d7qc0wbsn6lb9yp3khdfimh"))))
28746 (properties `((upstream-name . "dmrseq")))
28747 (build-system r-build-system)
28748 (propagated-inputs
28749 (list r-annotationhub
28750 r-annotatr
28751 r-biocparallel
28752 r-bsseq
28753 r-bumphunter
28754 r-delayedmatrixstats
28755 r-genomicranges
28756 r-ggplot2
28757 r-iranges
28758 r-locfit
28759 r-matrixstats
28760 r-nlme
28761 r-outliers
28762 r-rcolorbrewer
28763 r-rtracklayer
28764 r-s4vectors
28765 r-seqinfo))
28766 (native-inputs
28767 (list r-knitr))
28768 (home-page "https://bioconductor.org/packages/dmrseq")
28769 (synopsis "Detection and inference of differentially methylated regions")
28770 (description
28771 "This package implements an approach for scanning the genome to detect
28772and perform accurate inference on differentially methylated regions from Whole
28773Genome Bisulfite Sequencing data. The method is based on comparing detected
28774regions to a pooled null distribution, that can be implemented even when as
28775few as two samples per population are available. Region-level statistics are
28776obtained by fitting a @dfn{generalized least squares} (GLS) regression model
28777with a nested autoregressive correlated error structure for the effect of
28778interest on transformed methylation proportions.")
28779 (license license:expat)))
28780
28781(define-public r-omicade4
28782 (package
28783 (name "r-omicade4")
28784 (version "1.52.0")
28785 (source (origin
28786 (method url-fetch)
28787 (uri (bioconductor-uri "omicade4" version))
28788 (sha256
28789 (base32
28790 "183h89j5z7k5y02l0mwccldrxn07df80cqnfdzhvhrs1gdibn8dc"))))
28791 (properties `((upstream-name . "omicade4")))
28792 (build-system r-build-system)
28793 (propagated-inputs (list r-ade4 r-biobase r-made4))
28794 (home-page "https://bioconductor.org/packages/omicade4")
28795 (synopsis "Multiple co-inertia analysis of omics datasets")
28796 (description
28797 "This package performs multiple co-inertia analysis of omics datasets.")
28798 (license license:gpl2)))
28799
28800(define-public r-omnipathr
28801 (package
28802 (name "r-omnipathr")
28803 (version "3.14.0")
28804 (source
28805 (origin
28806 (method url-fetch)
28807 (uri (bioconductor-uri "OmnipathR" version))
28808 (sha256
28809 (base32 "14fwdckmsilq7jj1y9rg0qj0z2xrryajwhib8k8wss0ys6sk7fzz"))))
28810 (properties `((upstream-name . "OmnipathR")))
28811 (build-system r-build-system)
28812 (arguments
28813 `(#:phases
28814 (modify-phases %standard-phases
28815 (add-after 'unpack 'set-HOME
28816 (lambda _ (setenv "HOME" "/tmp"))))))
28817 (propagated-inputs
28818 (list r-checkmate
28819 r-crayon
28820 r-curl
28821 r-digest
28822 r-dplyr
28823 r-httr
28824 r-igraph
28825 r-jsonlite
28826 r-later
28827 r-logger
28828 r-lubridate
28829 r-magrittr
28830 r-progress
28831 r-purrr
28832 r-r-utils
28833 r-rappdirs
28834 r-readr
28835 r-readxl
28836 r-rlang
28837 r-rmarkdown
28838 r-rsqlite
28839 r-rvest
28840 r-stringi
28841 r-stringr
28842 r-tibble
28843 r-tidyr
28844 r-tidyselect
28845 r-vctrs
28846 r-withr
28847 r-xml
28848 r-xml2
28849 r-yaml
28850 r-zip))
28851 (native-inputs (list r-knitr r-testthat))
28852 (home-page "https://saezlab.github.io/OmnipathR/")
28853 (synopsis "OmniPath web service client and more")
28854 (description
28855 "This package provides a client for the OmniPath web service and many
28856other resources. It also includes functions to transform and pretty print
28857some of the downloaded data, functions to access a number of other resources.
28858Furthermore, OmnipathR features a close integration with the NicheNet method
28859for ligand activity prediction from transcriptomics data.")
28860 (license license:expat)))
28861
28862(define-public r-biscuiteer
28863 (package
28864 (name "r-biscuiteer")
28865 (version "1.26.0")
28866 (source
28867 (origin
28868 (method url-fetch)
28869 (uri (bioconductor-uri "biscuiteer" version))
28870 (sha256
28871 (base32
28872 "1nabxdb3dii8drmnfy7137dq551hhd9s0vj1rv8ixbp7i82swmh6"))))
28873 (properties `((upstream-name . "biscuiteer")))
28874 (build-system r-build-system)
28875 (propagated-inputs
28876 (list r-biobase
28877 r-biocgenerics
28878 r-biocparallel
28879 r-biscuiteerdata
28880 r-bsseq
28881 r-data-table
28882 r-delayedmatrixstats
28883 r-dmrseq
28884 r-genomeinfodb
28885 r-genomicranges
28886 r-gtools
28887 r-hdf5array
28888 r-homo-sapiens
28889 r-impute
28890 r-iranges
28891 r-matrix
28892 r-matrixstats
28893 r-mus-musculus
28894 r-qdnaseq
28895 r-qualv
28896 r-r-utils
28897 r-readr
28898 r-rsamtools
28899 r-rtracklayer
28900 r-s4vectors
28901 r-summarizedexperiment
28902 r-variantannotation))
28903 (native-inputs
28904 (list r-knitr r-testthat))
28905 (home-page "https://github.com/trichelab/biscuiteer")
28906 (synopsis "Convenience functions for the Biscuit package")
28907 (description
28908 "This package provides a test harness for bsseq loading of Biscuit
28909output, summarization of WGBS data over defined regions and in mappable
28910samples, with or without imputation, dropping of mostly-NA rows, age
28911estimates, etc.")
28912 (license license:gpl3)))
28913
28914(define-public r-tcgabiolinks
28915 (package
28916 (name "r-tcgabiolinks")
28917 (version "2.40.0")
28918 (source
28919 (origin
28920 (method url-fetch)
28921 (uri (bioconductor-uri "TCGAbiolinks" version))
28922 (sha256
28923 (base32 "0piv9g4zz2w119d98qai605w9h7g5l74ypl6jc8cs8jy9fhglv4x"))))
28924 (properties
28925 '((upstream-name . "TCGAbiolinks")
28926 (updater-extra-native-inputs . ("r-edaseq" "r-edger" "r-survminer"))))
28927 (build-system r-build-system)
28928 (propagated-inputs
28929 (list r-biomart
28930 r-data-table
28931 r-downloader
28932 r-dplyr
28933 r-genomicranges
28934 r-ggplot2
28935 r-httr
28936 r-iranges
28937 r-jsonlite
28938 r-knitr
28939 r-plyr
28940 r-purrr
28941 r-r-utils
28942 r-readr
28943 r-rvest
28944 r-s4vectors
28945 r-stringr
28946 r-summarizedexperiment
28947 r-tcgabiolinksgui-data
28948 r-tibble
28949 r-tidyr
28950 r-xml
28951 r-xml2))
28952 (native-inputs (list r-edaseq r-edger r-knitr r-survminer r-testthat))
28953 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks")
28954 (synopsis "Integrative analysis with GDC data")
28955 (description
28956 "The aim of TCGAbiolinks is:
28957
28958@enumerate
28959@item facilitate GDC open-access data retrieval;
28960@item prepare the data using the appropriate pre-processing strategies;
28961@item provide the means to carry out different standard analyses, and;
28962@item to easily reproduce earlier research results.
28963@end enumerate
28964
28965In more detail, the package provides multiple methods for analysis (e.g.,
28966differential expression analysis, identifying differentially methylated
28967regions) and methods for visualization (e.g., survival plots, volcano plots,
28968starburst plots) in order to easily develop complete analysis pipelines.")
28969 (license license:gpl3+)))
28970
28971(define-public r-tricycle
28972 (package
28973 (name "r-tricycle")
28974 (version "1.20.0")
28975 (source (origin
28976 (method url-fetch)
28977 (uri (bioconductor-uri "tricycle" version))
28978 (sha256
28979 (base32
28980 "11l4i4ydha705dfc2bvbm3p8264jk6lb2dhk25dsxbdp60z93sfy"))))
28981 (properties `((upstream-name . "tricycle")))
28982 (build-system r-build-system)
28983 (propagated-inputs
28984 (list r-annotationdbi
28985 r-circular
28986 r-dplyr
28987 r-genomicranges
28988 r-ggnewscale
28989 r-ggplot2
28990 r-iranges
28991 r-rcolorbrewer
28992 r-s4vectors
28993 r-scater
28994 r-scattermore
28995 r-singlecellexperiment
28996 r-summarizedexperiment))
28997 (native-inputs (list r-knitr r-testthat))
28998 (home-page "https://github.com/hansenlab/tricycle")
28999 (synopsis "Transferable representation and inference of cell cycle")
29000 (description
29001 "The package contains functions to infer and visualize cell cycle process
29002using Single-cell RNA-Seq data. It exploits the idea of transfer learning,
29003projecting new data to the previous learned biologically interpretable space.
29004The @code{tricycle} provides a pre-learned cell cycle space, which could be
29005used to infer cell cycle time of human and mouse single cell samples. In
29006addition, it also offer functions to visualize cell cycle time on different
29007embeddings and functions to build new reference.")
29008 (license license:gpl3)))
29009
29010(define-public r-tximeta
29011 (package
29012 (name "r-tximeta")
29013 (version "1.30.0")
29014 (source
29015 (origin
29016 (method url-fetch)
29017 (uri (bioconductor-uri "tximeta" version))
29018 (sha256
29019 (base32
29020 "1dqn301qnvvh5r23nh0w4i70a55jpncg4wh5hjdpjxgxfnkrs5g2"))))
29021 (properties `((upstream-name . "tximeta")))
29022 (build-system r-build-system)
29023 ;; Two tests fail because data files are not included.
29024 (arguments (list #:tests? #false))
29025 (propagated-inputs
29026 (list r-annotationdbi
29027 r-annotationhub
29028 r-biocfilecache
29029 r-biostrings
29030 r-dbi
29031 r-ensembldb
29032 r-genomicfeatures
29033 r-genomicranges
29034 r-iranges
29035 r-jsonlite
29036 r-matrix
29037 r-s4vectors
29038 r-seqinfo
29039 r-summarizedexperiment
29040 r-tibble
29041 r-txdbmaker
29042 r-tximport))
29043 (native-inputs
29044 (list r-edger r-knitr r-org-dm-eg-db r-rmarkdown r-testthat))
29045 (home-page "https://github.com/mikelove/tximeta")
29046 (synopsis "Transcript quantification import with automatic metadata")
29047 (description
29048 "This package implements transcript quantification import from Salmon and
29049alevin with automatic attachment of transcript ranges and release information,
29050and other associated metadata. De novo transcriptomes can be linked to the
29051appropriate sources with linkedTxomes and shared for computational
29052reproducibility.")
29053 (license license:gpl2)))
29054
29055(define-public r-phyloseq
29056 (package
29057 (name "r-phyloseq")
29058 (version "1.56.0")
29059 (source
29060 (origin
29061 (method url-fetch)
29062 (uri (bioconductor-uri "phyloseq" version))
29063 (sha256
29064 (base32 "1avfzqlak080xnkaia8q5kf3r0313r2igrm8gda0km6ga6ap1c2c"))))
29065 (properties `((upstream-name . "phyloseq")))
29066 (build-system r-build-system)
29067 (propagated-inputs
29068 (list r-ade4
29069 r-ape
29070 r-biobase
29071 r-biocgenerics
29072 r-biomformat
29073 r-biostrings
29074 r-cluster
29075 r-data-table
29076 r-foreach
29077 r-ggplot2
29078 r-igraph
29079 r-multtest
29080 r-plyr
29081 r-reshape2
29082 r-scales
29083 r-vegan))
29084 (native-inputs
29085 (list r-genefilter r-knitr r-sparsearray r-testthat))
29086 (home-page "https://github.com/joey711/phyloseq")
29087 (synopsis "Handling and analysis of high-throughput microbiome census data")
29088 (description
29089 "Phyloseq provides a set of classes and tools to facilitate the import,
29090storage, analysis, and graphical display of microbiome census data.")
29091 (license license:agpl3)))
29092
29093;;;
29094;;; Avoid adding new packages to the end of this file. To reduce the chances
29095;;; of a merge conflict, place them above by existing packages with similar
29096;;; functionality or similar names.
29097;;;