gnu: r-chromstar: Fix typo in description.
[jackhill/guix/guix.git] / gnu / packages / bioconductor.scm
1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
7 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
9 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
10 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
11 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
12 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
13 ;;;
14 ;;; This file is part of GNU Guix.
15 ;;;
16 ;;; GNU Guix is free software; you can redistribute it and/or modify it
17 ;;; under the terms of the GNU General Public License as published by
18 ;;; the Free Software Foundation; either version 3 of the License, or (at
19 ;;; your option) any later version.
20 ;;;
21 ;;; GNU Guix is distributed in the hope that it will be useful, but
22 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
23 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
24 ;;; GNU General Public License for more details.
25 ;;;
26 ;;; You should have received a copy of the GNU General Public License
27 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
28
29 (define-module (gnu packages bioconductor)
30 #:use-module ((guix licenses) #:prefix license:)
31 #:use-module (guix packages)
32 #:use-module (guix download)
33 #:use-module (guix git-download)
34 #:use-module (guix build-system r)
35 #:use-module (gnu packages)
36 #:use-module (gnu packages base)
37 #:use-module (gnu packages bioinformatics)
38 #:use-module (gnu packages cran)
39 #:use-module (gnu packages compression)
40 #:use-module (gnu packages gcc)
41 #:use-module (gnu packages graph)
42 #:use-module (gnu packages graphviz)
43 #:use-module (gnu packages haskell-xyz)
44 #:use-module (gnu packages image)
45 #:use-module (gnu packages maths)
46 #:use-module (gnu packages netpbm)
47 #:use-module (gnu packages perl)
48 #:use-module (gnu packages pkg-config)
49 #:use-module (gnu packages statistics)
50 #:use-module (gnu packages web)
51 #:use-module (gnu packages xml)
52 #:use-module (srfi srfi-1))
53
54 \f
55 ;;; Annotations
56
57 (define-public r-org-eck12-eg-db
58 (package
59 (name "r-org-eck12-eg-db")
60 (version "3.12.0")
61 (source
62 (origin
63 (method url-fetch)
64 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
65 (sha256
66 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
67 (properties
68 `((upstream-name . "org.EcK12.eg.db")))
69 (build-system r-build-system)
70 (propagated-inputs
71 `(("r-annotationdbi" ,r-annotationdbi)))
72 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
73 (synopsis "Genome wide annotation for E coli strain K12")
74 (description
75 "This package provides genome wide annotation for E coli strain K12,
76 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
77 National Center for Biotechnology Information (NCBI)’s database for
78 gene-specific information. Entrez Gene maintains records from genomes which
79 have been completely sequenced, which have an active research community to
80 submit gene-specific information, or which are scheduled for intense sequence
81 analysis.")
82 (license license:artistic2.0)))
83
84 (define-public r-reactome-db
85 (package
86 (name "r-reactome-db")
87 (version "1.70.0")
88 (source
89 (origin
90 (method url-fetch)
91 (uri (bioconductor-uri "reactome.db" version 'annotation))
92 (sha256
93 (base32
94 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
95 (properties `((upstream-name . "reactome.db")))
96 (build-system r-build-system)
97 (propagated-inputs
98 `(("r-annotationdbi" ,r-annotationdbi)))
99 (home-page "https://bioconductor.org/packages/reactome.db/")
100 (synopsis "Annotation maps for reactome")
101 (description
102 "This package provides a set of annotation maps for the REACTOME
103 database, assembled using data from REACTOME.")
104 (license license:cc-by4.0)))
105
106 (define-public r-bsgenome-celegans-ucsc-ce6
107 (package
108 (name "r-bsgenome-celegans-ucsc-ce6")
109 (version "1.4.0")
110 (source (origin
111 (method url-fetch)
112 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
113 version 'annotation))
114 (sha256
115 (base32
116 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
117 (properties
118 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
119 (build-system r-build-system)
120 (propagated-inputs
121 `(("r-bsgenome" ,r-bsgenome)))
122 (home-page
123 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
124 (synopsis "Full genome sequences for Worm")
125 (description
126 "This package provides full genome sequences for Caenorhabditis
127 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
128 objects.")
129 (license license:artistic2.0)))
130
131 (define-public r-bsgenome-celegans-ucsc-ce10
132 (package
133 (name "r-bsgenome-celegans-ucsc-ce10")
134 (version "1.4.0")
135 (source (origin
136 (method url-fetch)
137 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
138 version 'annotation))
139 (sha256
140 (base32
141 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
142 (properties
143 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
144 (build-system r-build-system)
145 (propagated-inputs
146 `(("r-bsgenome" ,r-bsgenome)))
147 (home-page
148 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
149 (synopsis "Full genome sequences for Worm")
150 (description
151 "This package provides full genome sequences for Caenorhabditis
152 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
153 objects.")
154 (license license:artistic2.0)))
155
156 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
157 (package
158 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
159 (version "1.4.1")
160 (source (origin
161 (method url-fetch)
162 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
163 version 'annotation))
164 (sha256
165 (base32
166 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
167 (properties
168 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
169 (build-system r-build-system)
170 (propagated-inputs
171 `(("r-bsgenome" ,r-bsgenome)))
172 (home-page
173 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
174 (synopsis "Full genome sequences for Fly")
175 (description
176 "This package provides full genome sequences for Drosophila
177 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
178 objects.")
179 (license license:artistic2.0)))
180
181 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
182 (package
183 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
184 (version "1.4.0")
185 (source (origin
186 (method url-fetch)
187 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
188 version 'annotation))
189 (sha256
190 (base32
191 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
192 (properties
193 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
194 (build-system r-build-system)
195 (propagated-inputs
196 `(("r-bsgenome" ,r-bsgenome)))
197 (home-page
198 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
199 (synopsis "Full genome sequences for Fly")
200 (description
201 "This package provides full genome sequences for Drosophila
202 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
203 Biostrings objects.")
204 (license license:artistic2.0)))
205
206 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
207 (package
208 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
209 (version "1.3.99")
210 (source (origin
211 (method url-fetch)
212 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
213 version 'annotation))
214 (sha256
215 (base32
216 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
217 (properties
218 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
219 (build-system r-build-system)
220 (propagated-inputs
221 `(("r-bsgenome" ,r-bsgenome)
222 ("r-bsgenome-dmelanogaster-ucsc-dm3"
223 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
224 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
225 (synopsis "Full masked genome sequences for Fly")
226 (description
227 "This package provides full masked genome sequences for Drosophila
228 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
229 Biostrings objects. The sequences are the same as in
230 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
231 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
232 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
233 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
234 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
235 (license license:artistic2.0)))
236
237 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
238 (package
239 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
240 (version "0.99.1")
241 (source (origin
242 (method url-fetch)
243 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
244 version 'annotation))
245 (sha256
246 (base32
247 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
248 (properties
249 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
250 (build-system r-build-system)
251 (propagated-inputs
252 `(("r-bsgenome" ,r-bsgenome)))
253 (home-page
254 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
255 (synopsis "Full genome sequences for Homo sapiens")
256 (description
257 "This package provides full genome sequences for Homo sapiens from
258 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
259 (license license:artistic2.0)))
260
261 (define-public r-bsgenome-hsapiens-ncbi-grch38
262 (package
263 (name "r-bsgenome-hsapiens-ncbi-grch38")
264 (version "1.3.1000")
265 (source
266 (origin
267 (method url-fetch)
268 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
269 version 'annotation))
270 (sha256
271 (base32
272 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
273 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
274 (build-system r-build-system)
275 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
276 (home-page
277 "https://bioconductor.org/packages/release/data/annotation/html/\
278 BSgenome.Hsapiens.NCBI.GRCh38.html")
279 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
280 (description
281 "This package provides full genome sequences for Homo sapiens (Human) as
282 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
283 (license license:artistic2.0)))
284
285 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
286 (package
287 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
288 (version "1.3.99")
289 (source (origin
290 (method url-fetch)
291 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
292 version 'annotation))
293 (sha256
294 (base32
295 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
296 (properties
297 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
298 (build-system r-build-system)
299 (propagated-inputs
300 `(("r-bsgenome" ,r-bsgenome)
301 ("r-bsgenome-hsapiens-ucsc-hg19"
302 ,r-bsgenome-hsapiens-ucsc-hg19)))
303 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
304 (synopsis "Full masked genome sequences for Homo sapiens")
305 (description
306 "This package provides full genome sequences for Homo sapiens (Human) as
307 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
308 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
309 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
310 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
311 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
312 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
313 default.")
314 (license license:artistic2.0)))
315
316 (define-public r-bsgenome-mmusculus-ucsc-mm9
317 (package
318 (name "r-bsgenome-mmusculus-ucsc-mm9")
319 (version "1.4.0")
320 (source (origin
321 (method url-fetch)
322 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
323 version 'annotation))
324 (sha256
325 (base32
326 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
327 (properties
328 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
329 (build-system r-build-system)
330 (propagated-inputs
331 `(("r-bsgenome" ,r-bsgenome)))
332 (home-page
333 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
334 (synopsis "Full genome sequences for Mouse")
335 (description
336 "This package provides full genome sequences for Mus musculus (Mouse) as
337 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
338 (license license:artistic2.0)))
339
340 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
341 (package
342 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
343 (version "1.3.99")
344 (source (origin
345 (method url-fetch)
346 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
347 version 'annotation))
348 (sha256
349 (base32
350 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
351 (properties
352 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
353 (build-system r-build-system)
354 (propagated-inputs
355 `(("r-bsgenome" ,r-bsgenome)
356 ("r-bsgenome-mmusculus-ucsc-mm9"
357 ,r-bsgenome-mmusculus-ucsc-mm9)))
358 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
359 (synopsis "Full masked genome sequences for Mouse")
360 (description
361 "This package provides full genome sequences for Mus musculus (Mouse) as
362 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
363 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
364 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
365 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
366 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
367 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
368 default." )
369 (license license:artistic2.0)))
370
371 (define-public r-bsgenome-mmusculus-ucsc-mm10
372 (package
373 (name "r-bsgenome-mmusculus-ucsc-mm10")
374 (version "1.4.0")
375 (source (origin
376 (method url-fetch)
377 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
378 version 'annotation))
379 (sha256
380 (base32
381 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
382 (properties
383 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
384 (build-system r-build-system)
385 (propagated-inputs
386 `(("r-bsgenome" ,r-bsgenome)))
387 (home-page
388 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
389 (synopsis "Full genome sequences for Mouse")
390 (description
391 "This package provides full genome sequences for Mus
392 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
393 in Biostrings objects.")
394 (license license:artistic2.0)))
395
396 (define-public r-genomeinfodbdata
397 (package
398 (name "r-genomeinfodbdata")
399 (version "1.2.0")
400 (source (origin
401 (method url-fetch)
402 (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
403 (sha256
404 (base32
405 "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
406 (properties
407 `((upstream-name . "GenomeInfoDbData")))
408 (build-system r-build-system)
409 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
410 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
411 (description "This package contains data for mapping between NCBI taxonomy
412 ID and species. It is used by functions in the GenomeInfoDb package.")
413 (license license:artistic2.0)))
414
415 (define-public r-homo-sapiens
416 (package
417 (name "r-homo-sapiens")
418 (version "1.3.1")
419 (source (origin
420 (method url-fetch)
421 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
422 (sha256
423 (base32
424 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
425 (properties
426 `((upstream-name . "Homo.sapiens")))
427 (build-system r-build-system)
428 (propagated-inputs
429 `(("r-genomicfeatures" ,r-genomicfeatures)
430 ("r-go-db" ,r-go-db)
431 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
432 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
433 ("r-organismdbi" ,r-organismdbi)
434 ("r-annotationdbi" ,r-annotationdbi)))
435 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
436 (synopsis "Annotation package for the Homo.sapiens object")
437 (description
438 "This package contains the Homo.sapiens object to access data from
439 several related annotation packages.")
440 (license license:artistic2.0)))
441
442 (define-public r-org-ce-eg-db
443 (package
444 (name "r-org-ce-eg-db")
445 (version "3.7.0")
446 (source (origin
447 (method url-fetch)
448 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
449 (sha256
450 (base32
451 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
452 (properties
453 `((upstream-name . "org.Ce.eg.db")))
454 (build-system r-build-system)
455 (propagated-inputs
456 `(("r-annotationdbi" ,r-annotationdbi)))
457 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
458 (synopsis "Genome wide annotation for Worm")
459 (description
460 "This package provides mappings from Entrez gene identifiers to various
461 annotations for the genome of the model worm Caenorhabditis elegans.")
462 (license license:artistic2.0)))
463
464 (define-public r-org-dm-eg-db
465 (package
466 (name "r-org-dm-eg-db")
467 (version "3.7.0")
468 (source (origin
469 (method url-fetch)
470 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
471 (sha256
472 (base32
473 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
474 (properties
475 `((upstream-name . "org.Dm.eg.db")))
476 (build-system r-build-system)
477 (propagated-inputs
478 `(("r-annotationdbi" ,r-annotationdbi)))
479 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
480 (synopsis "Genome wide annotation for Fly")
481 (description
482 "This package provides mappings from Entrez gene identifiers to various
483 annotations for the genome of the model fruit fly Drosophila melanogaster.")
484 (license license:artistic2.0)))
485
486 (define-public r-org-dr-eg-db
487 (package
488 (name "r-org-dr-eg-db")
489 (version "3.7.0")
490 (source (origin
491 (method url-fetch)
492 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
493 (sha256
494 (base32
495 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
496 (properties
497 `((upstream-name . "org.Dr.eg.db")))
498 (build-system r-build-system)
499 (propagated-inputs
500 `(("r-annotationdbi" ,r-annotationdbi)))
501 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
502 (synopsis "Annotation for Zebrafish")
503 (description
504 "This package provides genome wide annotations for Zebrafish, primarily
505 based on mapping using Entrez Gene identifiers.")
506 (license license:artistic2.0)))
507
508 (define-public r-org-hs-eg-db
509 (package
510 (name "r-org-hs-eg-db")
511 (version "3.7.0")
512 (source (origin
513 (method url-fetch)
514 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
515 (sha256
516 (base32
517 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
518 (properties
519 `((upstream-name . "org.Hs.eg.db")))
520 (build-system r-build-system)
521 (propagated-inputs
522 `(("r-annotationdbi" ,r-annotationdbi)))
523 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
524 (synopsis "Genome wide annotation for Human")
525 (description
526 "This package contains genome-wide annotations for Human, primarily based
527 on mapping using Entrez Gene identifiers.")
528 (license license:artistic2.0)))
529
530 (define-public r-org-mm-eg-db
531 (package
532 (name "r-org-mm-eg-db")
533 (version "3.7.0")
534 (source (origin
535 (method url-fetch)
536 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
537 (sha256
538 (base32
539 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
540 (properties
541 `((upstream-name . "org.Mm.eg.db")))
542 (build-system r-build-system)
543 (propagated-inputs
544 `(("r-annotationdbi" ,r-annotationdbi)))
545 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
546 (synopsis "Genome wide annotation for Mouse")
547 (description
548 "This package provides mappings from Entrez gene identifiers to various
549 annotations for the genome of the model mouse Mus musculus.")
550 (license license:artistic2.0)))
551
552 (define-public r-bsgenome-hsapiens-ucsc-hg19
553 (package
554 (name "r-bsgenome-hsapiens-ucsc-hg19")
555 (version "1.4.0")
556 (source (origin
557 (method url-fetch)
558 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
559 version 'annotation))
560 (sha256
561 (base32
562 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
563 (properties
564 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
565 (build-system r-build-system)
566 (propagated-inputs
567 `(("r-bsgenome" ,r-bsgenome)))
568 (home-page
569 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
570 (synopsis "Full genome sequences for Homo sapiens")
571 (description
572 "This package provides full genome sequences for Homo sapiens as provided
573 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
574 (license license:artistic2.0)))
575
576 (define-public r-bsgenome-hsapiens-ucsc-hg38
577 (package
578 (name "r-bsgenome-hsapiens-ucsc-hg38")
579 (version "1.4.1")
580 (source (origin
581 (method url-fetch)
582 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
583 version 'annotation))
584 (sha256
585 (base32
586 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
587 (properties
588 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
589 (build-system r-build-system)
590 (propagated-inputs
591 `(("r-bsgenome" ,r-bsgenome)))
592 (home-page
593 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
594 (synopsis "Full genome sequences for Homo sapiens")
595 (description
596 "This package provides full genome sequences for Homo sapiens (Human)
597 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
598 (license license:artistic2.0)))
599
600 (define-public r-ensdb-hsapiens-v75
601 (package
602 (name "r-ensdb-hsapiens-v75")
603 (version "2.99.0")
604 (source
605 (origin
606 (method url-fetch)
607 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
608 (sha256
609 (base32
610 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
611 (properties
612 `((upstream-name . "EnsDb.Hsapiens.v75")))
613 (build-system r-build-system)
614 (propagated-inputs
615 `(("r-ensembldb" ,r-ensembldb)))
616 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
617 (synopsis "Ensembl based annotation package")
618 (description
619 "This package exposes an annotation database generated from Ensembl.")
620 (license license:artistic2.0)))
621
622 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
623 (package
624 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
625 (version "3.2.2")
626 (source (origin
627 (method url-fetch)
628 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
629 version 'annotation))
630 (sha256
631 (base32
632 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
633 (properties
634 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
635 (build-system r-build-system)
636 (propagated-inputs
637 `(("r-genomicfeatures" ,r-genomicfeatures)))
638 (home-page
639 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
640 (synopsis "Annotation package for human genome in TxDb format")
641 (description
642 "This package provides an annotation database of Homo sapiens genome
643 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
644 track. The database is exposed as a @code{TxDb} object.")
645 (license license:artistic2.0)))
646
647 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
648 (package
649 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
650 (version "3.4.6")
651 (source (origin
652 (method url-fetch)
653 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
654 version 'annotation))
655 (sha256
656 (base32
657 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
658 (properties
659 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
660 (build-system r-build-system)
661 (propagated-inputs
662 `(("r-genomicfeatures" ,r-genomicfeatures)))
663 (home-page
664 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
665 (synopsis "Annotation package for human genome in TxDb format")
666 (description
667 "This package provides an annotation database of Homo sapiens genome
668 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
669 track. The database is exposed as a @code{TxDb} object.")
670 (license license:artistic2.0)))
671
672 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
673 (package
674 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
675 (version "3.2.2")
676 (source (origin
677 (method url-fetch)
678 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
679 version 'annotation))
680 (sha256
681 (base32
682 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
683 (properties
684 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
685 (build-system r-build-system)
686 (propagated-inputs
687 `(("r-genomicfeatures" ,r-genomicfeatures)
688 ("r-annotationdbi" ,r-annotationdbi)))
689 (home-page
690 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
691 (synopsis "Annotation package for mouse genome in TxDb format")
692 (description
693 "This package provides an annotation database of Mouse genome data. It
694 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
695 database is exposed as a @code{TxDb} object.")
696 (license license:artistic2.0)))
697
698 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
699 (package
700 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
701 (version "3.10.0")
702 (source (origin
703 (method url-fetch)
704 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
705 version 'annotation))
706 (sha256
707 (base32
708 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
709 (properties
710 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
711 (build-system r-build-system)
712 (propagated-inputs
713 `(("r-bsgenome" ,r-bsgenome)
714 ("r-genomicfeatures" ,r-genomicfeatures)
715 ("r-annotationdbi" ,r-annotationdbi)))
716 (home-page
717 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
718 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
719 (description
720 "This package loads a TxDb object, which is an R interface to
721 prefabricated databases contained in this package. This package provides
722 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
723 based on the knownGene track.")
724 (license license:artistic2.0)))
725
726 (define-public r-txdb-celegans-ucsc-ce6-ensgene
727 (package
728 (name "r-txdb-celegans-ucsc-ce6-ensgene")
729 (version "3.2.2")
730 (source
731 (origin
732 (method url-fetch)
733 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
734 version 'annotation))
735 (sha256
736 (base32
737 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
738 (properties
739 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
740 (build-system r-build-system)
741 (propagated-inputs
742 `(("r-annotationdbi" ,r-annotationdbi)
743 ("r-genomicfeatures" ,r-genomicfeatures)))
744 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
745 (synopsis "Annotation package for C elegans TxDb objects")
746 (description
747 "This package exposes a C elegans annotation database generated from UCSC
748 by exposing these as TxDb objects.")
749 (license license:artistic2.0)))
750
751 (define-public r-fdb-infiniummethylation-hg19
752 (package
753 (name "r-fdb-infiniummethylation-hg19")
754 (version "2.2.0")
755 (source (origin
756 (method url-fetch)
757 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
758 version 'annotation))
759 (sha256
760 (base32
761 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
762 (properties
763 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
764 (build-system r-build-system)
765 (propagated-inputs
766 `(("r-biostrings" ,r-biostrings)
767 ("r-genomicfeatures" ,r-genomicfeatures)
768 ("r-annotationdbi" ,r-annotationdbi)
769 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
770 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
771 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
772 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
773 (description
774 "This is an annotation package for Illumina Infinium DNA methylation
775 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
776 annotations.")
777 (license license:artistic2.0)))
778
779 (define-public r-illuminahumanmethylationepicmanifest
780 (package
781 (name "r-illuminahumanmethylationepicmanifest")
782 (version "0.3.0")
783 (source (origin
784 (method url-fetch)
785 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
786 version 'annotation))
787 (sha256
788 (base32
789 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
790 (properties
791 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
792 (build-system r-build-system)
793 (propagated-inputs
794 `(("r-minfi" ,r-minfi)))
795 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
796 (synopsis "Manifest for Illumina's EPIC methylation arrays")
797 (description
798 "This is a manifest package for Illumina's EPIC methylation arrays.")
799 (license license:artistic2.0)))
800
801 (define-public r-do-db
802 (package
803 (name "r-do-db")
804 (version "2.9")
805 (source (origin
806 (method url-fetch)
807 (uri (bioconductor-uri "DO.db" version 'annotation))
808 (sha256
809 (base32
810 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
811 (properties
812 `((upstream-name . "DO.db")))
813 (build-system r-build-system)
814 (propagated-inputs
815 `(("r-annotationdbi" ,r-annotationdbi)))
816 (home-page "https://www.bioconductor.org/packages/DO.db/")
817 (synopsis "Annotation maps describing the entire Disease Ontology")
818 (description
819 "This package provides a set of annotation maps describing the entire
820 Disease Ontology.")
821 (license license:artistic2.0)))
822
823 (define-public r-pfam-db
824 (package
825 (name "r-pfam-db")
826 (version "3.8.2")
827 (source
828 (origin
829 (method url-fetch)
830 (uri (bioconductor-uri "PFAM.db" version 'annotation))
831 (sha256
832 (base32
833 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
834 (properties `((upstream-name . "PFAM.db")))
835 (build-system r-build-system)
836 (propagated-inputs
837 `(("r-annotationdbi" ,r-annotationdbi)))
838 (home-page "https://bioconductor.org/packages/PFAM.db")
839 (synopsis "Set of protein ID mappings for PFAM")
840 (description
841 "This package provides a set of protein ID mappings for PFAM, assembled
842 using data from public repositories.")
843 (license license:artistic2.0)))
844
845 (define-public r-phastcons100way-ucsc-hg19
846 (package
847 (name "r-phastcons100way-ucsc-hg19")
848 (version "3.7.2")
849 (source
850 (origin
851 (method url-fetch)
852 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
853 version 'annotation))
854 (sha256
855 (base32
856 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
857 (properties
858 `((upstream-name . "phastCons100way.UCSC.hg19")))
859 (build-system r-build-system)
860 (propagated-inputs
861 `(("r-bsgenome" ,r-bsgenome)
862 ("r-genomeinfodb" ,r-genomeinfodb)
863 ("r-genomicranges" ,r-genomicranges)
864 ("r-genomicscores" ,r-genomicscores)
865 ("r-iranges" ,r-iranges)
866 ("r-s4vectors" ,r-s4vectors)))
867 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
868 (synopsis "UCSC phastCons conservation scores for hg19")
869 (description
870 "This package provides UCSC phastCons conservation scores for the human
871 genome (hg19) calculated from multiple alignments with other 99 vertebrate
872 species.")
873 (license license:artistic2.0)))
874
875 \f
876 ;;; Experiment data
877
878 (define-public r-abadata
879 (package
880 (name "r-abadata")
881 (version "1.12.0")
882 (source (origin
883 (method url-fetch)
884 (uri (bioconductor-uri "ABAData" version 'experiment))
885 (sha256
886 (base32
887 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
888 (properties
889 `((upstream-name . "ABAData")))
890 (build-system r-build-system)
891 (propagated-inputs
892 `(("r-annotationdbi" ,r-annotationdbi)))
893 (home-page "https://www.bioconductor.org/packages/ABAData/")
894 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
895 (description
896 "This package provides the data for the gene expression enrichment
897 analysis conducted in the package ABAEnrichment. The package includes three
898 datasets which are derived from the Allen Brain Atlas:
899
900 @enumerate
901 @item Gene expression data from Human Brain (adults) averaged across donors,
902 @item Gene expression data from the Developing Human Brain pooled into five
903 age categories and averaged across donors, and
904 @item a developmental effect score based on the Developing Human Brain
905 expression data.
906 @end enumerate
907
908 All datasets are restricted to protein coding genes.")
909 (license license:gpl2+)))
910
911 (define-public r-arrmdata
912 (package
913 (name "r-arrmdata")
914 (version "1.18.0")
915 (source (origin
916 (method url-fetch)
917 (uri (bioconductor-uri "ARRmData" version 'experiment))
918 (sha256
919 (base32
920 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
921 (properties
922 `((upstream-name . "ARRmData")))
923 (build-system r-build-system)
924 (home-page "https://www.bioconductor.org/packages/ARRmData/")
925 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
926 (description
927 "This package provides raw beta values from 36 samples across 3 groups
928 from Illumina 450k methylation arrays.")
929 (license license:artistic2.0)))
930
931 (define-public r-chromstardata
932 (package
933 (name "r-chromstardata")
934 (version "1.16.0")
935 (source
936 (origin
937 (method url-fetch)
938 (uri (bioconductor-uri "chromstaRData" version 'experiment))
939 (sha256
940 (base32
941 "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
942 (properties `((upstream-name . "chromstaRData")))
943 (build-system r-build-system)
944 (home-page "https://bioconductor.org/packages/chromstaRData/")
945 (synopsis "ChIP-seq data for demonstration purposes")
946 (description
947 "This package provides ChIP-seq data for demonstration purposes in the
948 chromstaR package.")
949 (license license:gpl3)))
950
951 (define-public r-genelendatabase
952 (package
953 (name "r-genelendatabase")
954 (version "1.18.0")
955 (source
956 (origin
957 (method url-fetch)
958 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
959 (sha256
960 (base32
961 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
962 (properties
963 `((upstream-name . "geneLenDataBase")))
964 (build-system r-build-system)
965 (propagated-inputs
966 `(("r-rtracklayer" ,r-rtracklayer)
967 ("r-genomicfeatures" ,r-genomicfeatures)))
968 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
969 (synopsis "Lengths of mRNA transcripts for a number of genomes")
970 (description
971 "This package provides the lengths of mRNA transcripts for a number of
972 genomes and gene ID formats, largely based on the UCSC table browser.")
973 (license license:lgpl2.0+)))
974
975 (define-public r-pasilla
976 (package
977 (name "r-pasilla")
978 (version "1.14.0")
979 (source (origin
980 (method url-fetch)
981 (uri (string-append
982 "http://bioconductor.org/packages/release/data/experiment"
983 "/src/contrib/pasilla_" version ".tar.gz"))
984 (sha256
985 (base32
986 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
987 (build-system r-build-system)
988 (propagated-inputs
989 `(("r-biocstyle" ,r-biocstyle)
990 ("r-dexseq" ,r-dexseq)
991 ("r-knitr" ,r-knitr)
992 ("r-rmarkdown" ,r-rmarkdown)))
993 (home-page "https://www.bioconductor.org/packages/pasilla/")
994 (synopsis "Data package with per-exon and per-gene read counts")
995 (description "This package provides per-exon and per-gene read counts
996 computed for selected genes from RNA-seq data that were presented in the
997 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
998 by Brooks et al., Genome Research 2011.")
999 (license license:lgpl2.1+)))
1000
1001 (define-public r-hsmmsinglecell
1002 (package
1003 (name "r-hsmmsinglecell")
1004 (version "1.2.0")
1005 (source (origin
1006 (method url-fetch)
1007 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1008 (sha256
1009 (base32
1010 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
1011 (properties
1012 `((upstream-name . "HSMMSingleCell")))
1013 (build-system r-build-system)
1014 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1015 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1016 (description
1017 "Skeletal myoblasts undergo a well-characterized sequence of
1018 morphological and transcriptional changes during differentiation. In this
1019 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1020 under high mitogen conditions (GM) and then differentiated by switching to
1021 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1022 hundred cells taken over a time-course of serum-induced differentiation.
1023 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1024 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1025 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1026 which were then sequenced to a depth of ~4 million reads per library,
1027 resulting in a complete gene expression profile for each cell.")
1028 (license license:artistic2.0)))
1029
1030 (define-public r-all
1031 (package
1032 (name "r-all")
1033 (version "1.26.0")
1034 (source (origin
1035 (method url-fetch)
1036 (uri (bioconductor-uri "ALL" version 'experiment))
1037 (sha256
1038 (base32
1039 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1040 (properties `((upstream-name . "ALL")))
1041 (build-system r-build-system)
1042 (propagated-inputs
1043 `(("r-biobase" ,r-biobase)))
1044 (home-page "https://bioconductor.org/packages/ALL")
1045 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1046 (description
1047 "The data consist of microarrays from 128 different individuals with
1048 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1049 are available. The data have been normalized (using rma) and it is the
1050 jointly normalized data that are available here. The data are presented in
1051 the form of an @code{exprSet} object.")
1052 (license license:artistic2.0)))
1053
1054 (define-public r-affydata
1055 (package
1056 (name "r-affydata")
1057 (version "1.32.0")
1058 (source
1059 (origin
1060 (method url-fetch)
1061 (uri (bioconductor-uri "affydata" version 'experiment))
1062 (sha256
1063 (base32
1064 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1065 (properties `((upstream-name . "affydata")))
1066 (build-system r-build-system)
1067 (propagated-inputs
1068 `(("r-affy" ,r-affy)))
1069 (home-page "https://bioconductor.org/packages/affydata/")
1070 (synopsis "Affymetrix data for demonstration purposes")
1071 (description
1072 "This package provides example datasets that represent 'real world
1073 examples' of Affymetrix data, unlike the artificial examples included in the
1074 package @code{affy}.")
1075 (license license:gpl2+)))
1076
1077 (define-public r-gagedata
1078 (package
1079 (name "r-gagedata")
1080 (version "2.28.0")
1081 (source
1082 (origin
1083 (method url-fetch)
1084 (uri (bioconductor-uri "gageData" version 'experiment))
1085 (sha256
1086 (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn"))))
1087 (properties `((upstream-name . "gageData")))
1088 (build-system r-build-system)
1089 (home-page "https://bioconductor.org/packages/gageData")
1090 (synopsis "Auxillary data for gage package")
1091 (description
1092 "This is a supportive data package for the software package @code{gage}.
1093 However, the data supplied here are also useful for gene set or pathway
1094 analysis or microarray data analysis in general. In this package, we provide
1095 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1096 BMP6 (originally published as an demo dataset for GAGE, also registered as
1097 GSE13604 in GEO). This package also includes commonly used gene set data based
1098 on KEGG pathways and GO terms for major research species, including human,
1099 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1100 yeast are also included.")
1101 (license license:gpl2+)))
1102
1103 (define-public r-curatedtcgadata
1104 (package
1105 (name "r-curatedtcgadata")
1106 (version "1.8.0")
1107 (source
1108 (origin
1109 (method url-fetch)
1110 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1111 (sha256
1112 (base32
1113 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1114 (properties
1115 `((upstream-name . "curatedTCGAData")))
1116 (build-system r-build-system)
1117 (propagated-inputs
1118 `(("r-annotationhub" ,r-annotationhub)
1119 ("r-experimenthub" ,r-experimenthub)
1120 ("r-hdf5array" ,r-hdf5array)
1121 ("r-multiassayexperiment" ,r-multiassayexperiment)
1122 ("r-s4vectors" ,r-s4vectors)
1123 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1124 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1125 (synopsis "Curated data from The Cancer Genome Atlas")
1126 (description
1127 "This package provides publicly available data from The Cancer Genome
1128 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1129 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1130 number, mutation, microRNA, protein, and others) with clinical / pathological
1131 data. It also links assay barcodes with patient identifiers, enabling
1132 harmonized subsetting of rows (features) and columns (patients / samples)
1133 across the entire multi-'omics experiment.")
1134 (license license:artistic2.0)))
1135
1136 \f
1137 ;;; Packages
1138
1139 (define-public r-biocversion
1140 (package
1141 (name "r-biocversion")
1142 (version "3.12.0")
1143 (source
1144 (origin
1145 (method url-fetch)
1146 (uri (bioconductor-uri "BiocVersion" version))
1147 (sha256
1148 (base32
1149 "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
1150 (properties `((upstream-name . "BiocVersion")))
1151 (build-system r-build-system)
1152 (home-page "https://bioconductor.org/packages/BiocVersion/")
1153 (synopsis "Set the appropriate version of Bioconductor packages")
1154 (description
1155 "This package provides repository information for the appropriate version
1156 of Bioconductor.")
1157 (license license:artistic2.0)))
1158
1159 (define-public r-biocgenerics
1160 (package
1161 (name "r-biocgenerics")
1162 (version "0.36.0")
1163 (source (origin
1164 (method url-fetch)
1165 (uri (bioconductor-uri "BiocGenerics" version))
1166 (sha256
1167 (base32
1168 "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
1169 (properties
1170 `((upstream-name . "BiocGenerics")))
1171 (build-system r-build-system)
1172 (home-page "https://bioconductor.org/packages/BiocGenerics")
1173 (synopsis "S4 generic functions for Bioconductor")
1174 (description
1175 "This package provides S4 generic functions needed by many Bioconductor
1176 packages.")
1177 (license license:artistic2.0)))
1178
1179 (define-public r-coverageview
1180 (package
1181 (name "r-coverageview")
1182 (version "1.28.0")
1183 (source (origin
1184 (method url-fetch)
1185 (uri (bioconductor-uri "CoverageView" version))
1186 (sha256
1187 (base32
1188 "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
1189 (build-system r-build-system)
1190 (propagated-inputs
1191 `(("r-s4vectors" ,r-s4vectors)
1192 ("r-iranges" ,r-iranges)
1193 ("r-genomicranges" ,r-genomicranges)
1194 ("r-genomicalignments" ,r-genomicalignments)
1195 ("r-rtracklayer" ,r-rtracklayer)
1196 ("r-rsamtools" ,r-rsamtools)))
1197 (home-page "https://bioconductor.org/packages/CoverageView/")
1198 (synopsis "Coverage visualization package for R")
1199 (description "This package provides a framework for the visualization of
1200 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1201 be also used for genome-wide nucleosome positioning experiments or other
1202 experiment types where it is important to have a framework in order to inspect
1203 how the coverage distributed across the genome.")
1204 (license license:artistic2.0)))
1205
1206 (define-public r-cummerbund
1207 (package
1208 (name "r-cummerbund")
1209 (version "2.32.0")
1210 (source (origin
1211 (method url-fetch)
1212 (uri (bioconductor-uri "cummeRbund" version))
1213 (sha256
1214 (base32
1215 "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
1216 (build-system r-build-system)
1217 (propagated-inputs
1218 `(("r-biobase" ,r-biobase)
1219 ("r-biocgenerics" ,r-biocgenerics)
1220 ("r-fastcluster" ,r-fastcluster)
1221 ("r-ggplot2" ,r-ggplot2)
1222 ("r-gviz" ,r-gviz)
1223 ("r-plyr" ,r-plyr)
1224 ("r-reshape2" ,r-reshape2)
1225 ("r-rsqlite" ,r-rsqlite)
1226 ("r-rtracklayer" ,r-rtracklayer)
1227 ("r-s4vectors" ,r-s4vectors)))
1228 (home-page "https://bioconductor.org/packages/cummeRbund/")
1229 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1230 (description "This package allows for persistent storage, access,
1231 exploration, and manipulation of Cufflinks high-throughput sequencing
1232 data. In addition, provides numerous plotting functions for commonly
1233 used visualizations.")
1234 (license license:artistic2.0)))
1235
1236 (define-public r-delayedarray
1237 (package
1238 (name "r-delayedarray")
1239 (version "0.16.3")
1240 (source (origin
1241 (method url-fetch)
1242 (uri (bioconductor-uri "DelayedArray" version))
1243 (sha256
1244 (base32
1245 "0w1wppy6m2iv41852dscg3y19sq84ahdx3m7c2p2pxjcznmv6hys"))))
1246 (properties
1247 `((upstream-name . "DelayedArray")))
1248 (build-system r-build-system)
1249 (propagated-inputs
1250 `(("r-biocgenerics" ,r-biocgenerics)
1251 ("r-s4vectors" ,r-s4vectors)
1252 ("r-iranges" ,r-iranges)
1253 ("r-matrix" ,r-matrix)
1254 ("r-matrixgenerics" ,r-matrixgenerics)))
1255 (native-inputs
1256 `(("r-knitr" ,r-knitr)))
1257 (home-page "https://bioconductor.org/packages/DelayedArray")
1258 (synopsis "Delayed operations on array-like objects")
1259 (description
1260 "Wrapping an array-like object (typically an on-disk object) in a
1261 @code{DelayedArray} object allows one to perform common array operations on it
1262 without loading the object in memory. In order to reduce memory usage and
1263 optimize performance, operations on the object are either delayed or executed
1264 using a block processing mechanism. Note that this also works on in-memory
1265 array-like objects like @code{DataFrame} objects (typically with Rle columns),
1266 @code{Matrix} objects, and ordinary arrays and data frames.")
1267 (license license:artistic2.0)))
1268
1269 (define-public r-bluster
1270 (package
1271 (name "r-bluster")
1272 (version "1.0.0")
1273 (source (origin
1274 (method url-fetch)
1275 (uri (bioconductor-uri "bluster" version))
1276 (sha256
1277 (base32
1278 "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61"))))
1279 (properties `((upstream-name . "bluster")))
1280 (build-system r-build-system)
1281 (propagated-inputs
1282 `(("r-biocneighbors" ,r-biocneighbors)
1283 ("r-biocparallel" ,r-biocparallel)
1284 ("r-igraph" ,r-igraph)
1285 ("r-matrix" ,r-matrix)
1286 ("r-rcpp" ,r-rcpp)
1287 ("r-s4vectors" ,r-s4vectors)))
1288 (native-inputs
1289 `(("r-knitr" ,r-knitr)))
1290 (home-page "https://bioconductor.org/packages/bluster")
1291 (synopsis "Clustering algorithms for Bioconductor")
1292 (description"This package wraps common clustering algorithms in an easily
1293 extended S4 framework. Backends are implemented for hierarchical, k-means
1294 and graph-based clustering. Several utilities are also provided to compare
1295 and evaluate clustering results.")
1296 (license license:gpl3)))
1297
1298 (define-public r-ideoviz
1299 (package
1300 (name "r-ideoviz")
1301 (version "1.26.0")
1302 (source (origin
1303 (method url-fetch)
1304 (uri (bioconductor-uri "IdeoViz" version))
1305 (sha256
1306 (base32
1307 "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
1308 (build-system r-build-system)
1309 (propagated-inputs
1310 `(("r-biobase" ,r-biobase)
1311 ("r-iranges" ,r-iranges)
1312 ("r-genomicranges" ,r-genomicranges)
1313 ("r-rcolorbrewer" ,r-rcolorbrewer)
1314 ("r-rtracklayer" ,r-rtracklayer)
1315 ("r-genomeinfodb" ,r-genomeinfodb)))
1316 (home-page "https://bioconductor.org/packages/IdeoViz/")
1317 (synopsis "Plots data along a chromosomal ideogram")
1318 (description "This package provides functions to plot data associated with
1319 arbitrary genomic intervals along chromosomal ideogram.")
1320 (license license:gpl2)))
1321
1322 (define-public r-iranges
1323 (package
1324 (name "r-iranges")
1325 (version "2.24.1")
1326 (source (origin
1327 (method url-fetch)
1328 (uri (bioconductor-uri "IRanges" version))
1329 (sha256
1330 (base32
1331 "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52"))))
1332 (properties
1333 `((upstream-name . "IRanges")))
1334 (build-system r-build-system)
1335 (propagated-inputs
1336 `(("r-biocgenerics" ,r-biocgenerics)
1337 ("r-s4vectors" ,r-s4vectors)))
1338 (home-page "https://bioconductor.org/packages/IRanges")
1339 (synopsis "Infrastructure for manipulating intervals on sequences")
1340 (description
1341 "This package provides efficient low-level and highly reusable S4 classes
1342 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
1343 generally, data that can be organized sequentially (formally defined as
1344 @code{Vector} objects), as well as views on these @code{Vector} objects.
1345 Efficient list-like classes are also provided for storing big collections of
1346 instances of the basic classes. All classes in the package use consistent
1347 naming and share the same rich and consistent \"Vector API\" as much as
1348 possible.")
1349 (license license:artistic2.0)))
1350
1351 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
1352 (define-public r-absfiltergsea
1353 (package
1354 (name "r-absfiltergsea")
1355 (version "1.5.1")
1356 (source
1357 (origin
1358 (method url-fetch)
1359 (uri (cran-uri "AbsFilterGSEA" version))
1360 (sha256
1361 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
1362 (properties `((upstream-name . "AbsFilterGSEA")))
1363 (build-system r-build-system)
1364 (propagated-inputs
1365 `(("r-biobase" ,r-biobase)
1366 ("r-deseq" ,r-deseq)
1367 ("r-limma" ,r-limma)
1368 ("r-rcpp" ,r-rcpp)
1369 ("r-rcpparmadillo" ,r-rcpparmadillo)))
1370 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
1371 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
1372 (description
1373 "This package provides a function that performs gene-permuting of a gene-set
1374 enrichment analysis (GSEA) calculation with or without the absolute filtering.
1375 Without filtering, users can perform (original) two-tailed or one-tailed
1376 absolute GSEA.")
1377 (license license:gpl2)))
1378
1379 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
1380 (define-public r-bisquerna
1381 (package
1382 (name "r-bisquerna")
1383 (version "1.0.4")
1384 (source (origin
1385 (method url-fetch)
1386 (uri (cran-uri "BisqueRNA" version))
1387 (sha256
1388 (base32
1389 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
1390 (properties `((upstream-name . "BisqueRNA")))
1391 (build-system r-build-system)
1392 (propagated-inputs
1393 `(("r-biobase" ,r-biobase)
1394 ("r-limsolve" ,r-limsolve)))
1395 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
1396 (synopsis "Decomposition of bulk expression with single-cell sequencing")
1397 (description "This package provides tools to accurately estimate cell type
1398 abundances from heterogeneous bulk expression. A reference-based method
1399 utilizes single-cell information to generate a signature matrix and
1400 transformation of bulk expression for accurate regression based estimates.
1401 A marker-based method utilizes known cell-specific marker genes to measure
1402 relative abundances across samples.")
1403 (license license:gpl3)))
1404
1405 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
1406 ;; from Bioconductor.
1407 (define-public r-deconstructsigs
1408 (package
1409 (name "r-deconstructsigs")
1410 (version "1.8.0")
1411 (source (origin
1412 (method url-fetch)
1413 (uri (cran-uri "deconstructSigs" version))
1414 (sha256
1415 (base32
1416 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
1417 (properties
1418 `((upstream-name . "deconstructSigs")))
1419 (build-system r-build-system)
1420 (propagated-inputs
1421 `(("r-bsgenome" ,r-bsgenome)
1422 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1423 ("r-genomeinfodb" ,r-genomeinfodb)
1424 ("r-reshape2" ,r-reshape2)))
1425 (home-page "https://github.com/raerose01/deconstructSigs")
1426 (synopsis "Identifies signatures present in a tumor sample")
1427 (description "This package takes sample information in the form of the
1428 fraction of mutations in each of 96 trinucleotide contexts and identifies
1429 the weighted combination of published signatures that, when summed, most
1430 closely reconstructs the mutational profile.")
1431 (license license:gpl2+)))
1432
1433 ;; This is a CRAN package, but it depends on Bioconductor packages.
1434 (define-public r-nmf
1435 (package
1436 (name "r-nmf")
1437 (version "0.23.0")
1438 (source
1439 (origin
1440 (method url-fetch)
1441 (uri (cran-uri "NMF" version))
1442 (sha256
1443 (base32
1444 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
1445 (properties `((upstream-name . "NMF")))
1446 (build-system r-build-system)
1447 (propagated-inputs
1448 `(("r-cluster" ,r-cluster)
1449 ("r-biobase" ,r-biobase)
1450 ("r-biocmanager" ,r-biocmanager)
1451 ("r-bigmemory" ,r-bigmemory) ; suggested
1452 ("r-synchronicity" ,r-synchronicity) ; suggested
1453 ("r-colorspace" ,r-colorspace)
1454 ("r-digest" ,r-digest)
1455 ("r-doparallel" ,r-doparallel)
1456 ("r-foreach" ,r-foreach)
1457 ("r-ggplot2" ,r-ggplot2)
1458 ("r-gridbase" ,r-gridbase)
1459 ("r-pkgmaker" ,r-pkgmaker)
1460 ("r-rcolorbrewer" ,r-rcolorbrewer)
1461 ("r-registry" ,r-registry)
1462 ("r-reshape2" ,r-reshape2)
1463 ("r-rngtools" ,r-rngtools)
1464 ("r-stringr" ,r-stringr)))
1465 (native-inputs
1466 `(("r-knitr" ,r-knitr)))
1467 (home-page "http://renozao.github.io/NMF")
1468 (synopsis "Algorithms and framework for nonnegative matrix factorization")
1469 (description
1470 "This package provides a framework to perform Non-negative Matrix
1471 Factorization (NMF). The package implements a set of already published
1472 algorithms and seeding methods, and provides a framework to test, develop and
1473 plug new or custom algorithms. Most of the built-in algorithms have been
1474 optimized in C++, and the main interface function provides an easy way of
1475 performing parallel computations on multicore machines.")
1476 (license license:gpl2+)))
1477
1478 (define-public r-affycomp
1479 (package
1480 (name "r-affycomp")
1481 (version "1.66.0")
1482 (source
1483 (origin
1484 (method url-fetch)
1485 (uri (bioconductor-uri "affycomp" version))
1486 (sha256
1487 (base32
1488 "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
1489 (properties `((upstream-name . "affycomp")))
1490 (build-system r-build-system)
1491 (propagated-inputs `(("r-biobase" ,r-biobase)))
1492 (home-page "https://bioconductor.org/packages/affycomp/")
1493 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1494 (description
1495 "The package contains functions that can be used to compare expression
1496 measures for Affymetrix Oligonucleotide Arrays.")
1497 (license license:gpl2+)))
1498
1499 (define-public r-affycompatible
1500 (package
1501 (name "r-affycompatible")
1502 (version "1.50.0")
1503 (source
1504 (origin
1505 (method url-fetch)
1506 (uri (bioconductor-uri "AffyCompatible" version))
1507 (sha256
1508 (base32
1509 "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
1510 (properties
1511 `((upstream-name . "AffyCompatible")))
1512 (build-system r-build-system)
1513 (propagated-inputs
1514 `(("r-biostrings" ,r-biostrings)
1515 ("r-rcurl" ,r-rcurl)
1516 ("r-xml" ,r-xml)))
1517 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1518 (synopsis "Work with Affymetrix GeneChip files")
1519 (description
1520 "This package provides an interface to Affymetrix chip annotation and
1521 sample attribute files. The package allows an easy way for users to download
1522 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1523 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1524 Command Console} (AGCC)-compatible sample annotation files.")
1525 (license license:artistic2.0)))
1526
1527 (define-public r-affycontam
1528 (package
1529 (name "r-affycontam")
1530 (version "1.48.0")
1531 (source
1532 (origin
1533 (method url-fetch)
1534 (uri (bioconductor-uri "affyContam" version))
1535 (sha256
1536 (base32
1537 "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
1538 (properties `((upstream-name . "affyContam")))
1539 (build-system r-build-system)
1540 (propagated-inputs
1541 `(("r-affy" ,r-affy)
1542 ("r-affydata" ,r-affydata)
1543 ("r-biobase" ,r-biobase)))
1544 (home-page "https://bioconductor.org/packages/affyContam/")
1545 (synopsis "Structured corruption of Affymetrix CEL file data")
1546 (description
1547 "Microarray quality assessment is a major concern of microarray analysts.
1548 This package provides some simple approaches to in silico creation of quality
1549 problems in CEL-level data to help evaluate performance of quality metrics.")
1550 (license license:artistic2.0)))
1551
1552 (define-public r-affycoretools
1553 (package
1554 (name "r-affycoretools")
1555 (version "1.62.0")
1556 (source
1557 (origin
1558 (method url-fetch)
1559 (uri (bioconductor-uri "affycoretools" version))
1560 (sha256
1561 (base32
1562 "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
1563 (properties `((upstream-name . "affycoretools")))
1564 (build-system r-build-system)
1565 (propagated-inputs
1566 `(("r-affy" ,r-affy)
1567 ("r-annotationdbi" ,r-annotationdbi)
1568 ("r-biobase" ,r-biobase)
1569 ("r-biocgenerics" ,r-biocgenerics)
1570 ("r-dbi" ,r-dbi)
1571 ("r-edger" ,r-edger)
1572 ("r-gcrma" ,r-gcrma)
1573 ("r-glimma" ,r-glimma)
1574 ("r-ggplot2" ,r-ggplot2)
1575 ("r-gostats" ,r-gostats)
1576 ("r-gplots" ,r-gplots)
1577 ("r-hwriter" ,r-hwriter)
1578 ("r-lattice" ,r-lattice)
1579 ("r-limma" ,r-limma)
1580 ("r-oligoclasses" ,r-oligoclasses)
1581 ("r-reportingtools" ,r-reportingtools)
1582 ("r-rsqlite" ,r-rsqlite)
1583 ("r-s4vectors" ,r-s4vectors)
1584 ("r-xtable" ,r-xtable)))
1585 (native-inputs
1586 `(("r-knitr" ,r-knitr)))
1587 (home-page "https://bioconductor.org/packages/affycoretools/")
1588 (synopsis "Functions for analyses with Affymetrix GeneChips")
1589 (description
1590 "This package provides various wrapper functions that have been written
1591 to streamline the more common analyses that a Biostatistician might see.")
1592 (license license:artistic2.0)))
1593
1594 (define-public r-affxparser
1595 (package
1596 (name "r-affxparser")
1597 (version "1.62.0")
1598 (source
1599 (origin
1600 (method url-fetch)
1601 (uri (bioconductor-uri "affxparser" version))
1602 (sha256
1603 (base32
1604 "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
1605 (properties `((upstream-name . "affxparser")))
1606 (build-system r-build-system)
1607 (home-page "https://github.com/HenrikBengtsson/affxparser")
1608 (synopsis "Affymetrix File Parsing SDK")
1609 (description
1610 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1611 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1612 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1613 are supported. Currently, there are methods for reading @dfn{chip definition
1614 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1615 either in full or in part. For example, probe signals from a few probesets
1616 can be extracted very quickly from a set of CEL files into a convenient list
1617 structure.")
1618 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1619 ;; under LGPLv2+.
1620 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1621
1622 (define-public r-annotate
1623 (package
1624 (name "r-annotate")
1625 (version "1.68.0")
1626 (source
1627 (origin
1628 (method url-fetch)
1629 (uri (bioconductor-uri "annotate" version))
1630 (sha256
1631 (base32
1632 "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
1633 (build-system r-build-system)
1634 (propagated-inputs
1635 `(("r-annotationdbi" ,r-annotationdbi)
1636 ("r-biobase" ,r-biobase)
1637 ("r-biocgenerics" ,r-biocgenerics)
1638 ("r-dbi" ,r-dbi)
1639 ("r-httr" ,r-httr)
1640 ("r-xml" ,r-xml)
1641 ("r-xtable" ,r-xtable)))
1642 (home-page
1643 "https://bioconductor.org/packages/annotate")
1644 (synopsis "Annotation for microarrays")
1645 (description "This package provides R environments for the annotation of
1646 microarrays.")
1647 (license license:artistic2.0)))
1648
1649 (define-public r-annotationdbi
1650 (package
1651 (name "r-annotationdbi")
1652 (version "1.52.0")
1653 (source (origin
1654 (method url-fetch)
1655 (uri (bioconductor-uri "AnnotationDbi" version))
1656 (sha256
1657 (base32
1658 "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
1659 (properties
1660 `((upstream-name . "AnnotationDbi")))
1661 (build-system r-build-system)
1662 (propagated-inputs
1663 `(("r-biobase" ,r-biobase)
1664 ("r-biocgenerics" ,r-biocgenerics)
1665 ("r-dbi" ,r-dbi)
1666 ("r-iranges" ,r-iranges)
1667 ("r-rsqlite" ,r-rsqlite)
1668 ("r-s4vectors" ,r-s4vectors)))
1669 (native-inputs
1670 `(("r-knitr" ,r-knitr)))
1671 (home-page "https://bioconductor.org/packages/AnnotationDbi")
1672 (synopsis "Annotation database interface")
1673 (description
1674 "This package provides user interface and database connection code for
1675 annotation data packages using SQLite data storage.")
1676 (license license:artistic2.0)))
1677
1678 (define-public r-annotationforge
1679 (package
1680 (name "r-annotationforge")
1681 (version "1.32.0")
1682 (source
1683 (origin
1684 (method url-fetch)
1685 (uri (bioconductor-uri "AnnotationForge" version))
1686 (sha256
1687 (base32
1688 "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
1689 (properties
1690 `((upstream-name . "AnnotationForge")))
1691 (build-system r-build-system)
1692 (propagated-inputs
1693 `(("r-annotationdbi" ,r-annotationdbi)
1694 ("r-biobase" ,r-biobase)
1695 ("r-biocgenerics" ,r-biocgenerics)
1696 ("r-dbi" ,r-dbi)
1697 ("r-rcurl" ,r-rcurl)
1698 ("r-rsqlite" ,r-rsqlite)
1699 ("r-s4vectors" ,r-s4vectors)
1700 ("r-xml" ,r-xml)))
1701 (native-inputs
1702 `(("r-knitr" ,r-knitr)))
1703 (home-page "https://bioconductor.org/packages/AnnotationForge")
1704 (synopsis "Code for building annotation database packages")
1705 (description
1706 "This package provides code for generating Annotation packages and their
1707 databases. Packages produced are intended to be used with AnnotationDbi.")
1708 (license license:artistic2.0)))
1709
1710 (define-public r-biobase
1711 (package
1712 (name "r-biobase")
1713 (version "2.50.0")
1714 (source (origin
1715 (method url-fetch)
1716 (uri (bioconductor-uri "Biobase" version))
1717 (sha256
1718 (base32
1719 "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
1720 (properties
1721 `((upstream-name . "Biobase")))
1722 (build-system r-build-system)
1723 (propagated-inputs
1724 `(("r-biocgenerics" ,r-biocgenerics)))
1725 (home-page "https://bioconductor.org/packages/Biobase")
1726 (synopsis "Base functions for Bioconductor")
1727 (description
1728 "This package provides functions that are needed by many other packages
1729 on Bioconductor or which replace R functions.")
1730 (license license:artistic2.0)))
1731
1732 (define-public r-biomart
1733 (package
1734 (name "r-biomart")
1735 (version "2.46.3")
1736 (source (origin
1737 (method url-fetch)
1738 (uri (bioconductor-uri "biomaRt" version))
1739 (sha256
1740 (base32
1741 "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
1742 (properties
1743 `((upstream-name . "biomaRt")))
1744 (build-system r-build-system)
1745 (propagated-inputs
1746 `(("r-annotationdbi" ,r-annotationdbi)
1747 ("r-biocfilecache" ,r-biocfilecache)
1748 ("r-httr" ,r-httr)
1749 ("r-openssl" ,r-openssl)
1750 ("r-progress" ,r-progress)
1751 ("r-rappdirs" ,r-rappdirs)
1752 ("r-stringr" ,r-stringr)
1753 ("r-xml" ,r-xml)
1754 ("r-xml2" ,r-xml2)))
1755 (native-inputs
1756 `(("r-knitr" ,r-knitr)))
1757 (home-page "https://bioconductor.org/packages/biomaRt")
1758 (synopsis "Interface to BioMart databases")
1759 (description
1760 "biomaRt provides an interface to a growing collection of databases
1761 implementing the @url{BioMart software suite, http://www.biomart.org}. The
1762 package enables retrieval of large amounts of data in a uniform way without
1763 the need to know the underlying database schemas or write complex SQL queries.
1764 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
1765 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
1766 users direct access to a diverse set of data and enable a wide range of
1767 powerful online queries from gene annotation to database mining.")
1768 (license license:artistic2.0)))
1769
1770 (define-public r-biocparallel
1771 (package
1772 (name "r-biocparallel")
1773 (version "1.24.1")
1774 (source (origin
1775 (method url-fetch)
1776 (uri (bioconductor-uri "BiocParallel" version))
1777 (sha256
1778 (base32
1779 "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
1780 (properties
1781 `((upstream-name . "BiocParallel")))
1782 (build-system r-build-system)
1783 (arguments
1784 `(#:phases
1785 (modify-phases %standard-phases
1786 (add-after 'unpack 'make-reproducible
1787 (lambda _
1788 ;; Remove generated documentation.
1789 (for-each delete-file
1790 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
1791 "inst/doc/Introduction_To_BiocParallel.pdf"
1792 "inst/doc/Errors_Logs_And_Debugging.pdf"
1793 "inst/doc/BiocParallel_BatchtoolsParam.R"
1794 "inst/doc/Introduction_To_BiocParallel.R"
1795 "inst/doc/Errors_Logs_And_Debugging.R"))
1796
1797 ;; Remove time-dependent macro
1798 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
1799 "inst/doc/Introduction_To_BiocParallel.Rnw"
1800 "inst/doc/Errors_Logs_And_Debugging.Rnw"
1801 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
1802 "vignettes/Introduction_To_BiocParallel.Rnw"
1803 "vignettes/Errors_Logs_And_Debugging.Rnw")
1804 (("\\today") "later"))
1805
1806 ;; Initialize the random number generator seed when building.
1807 (substitute* "R/internal_rng_stream.R"
1808 (("\"L'Ecuyer-CMRG\"\\)" m)
1809 (string-append
1810 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
1811 (propagated-inputs
1812 `(("r-futile-logger" ,r-futile-logger)
1813 ("r-snow" ,r-snow)
1814 ("r-bh" ,r-bh)))
1815 (native-inputs
1816 `(("r-knitr" ,r-knitr)))
1817 (home-page "https://bioconductor.org/packages/BiocParallel")
1818 (synopsis "Bioconductor facilities for parallel evaluation")
1819 (description
1820 "This package provides modified versions and novel implementation of
1821 functions for parallel evaluation, tailored to use with Bioconductor
1822 objects.")
1823 (license (list license:gpl2+ license:gpl3+))))
1824
1825 (define-public r-biostrings
1826 (package
1827 (name "r-biostrings")
1828 (version "2.58.0")
1829 (source (origin
1830 (method url-fetch)
1831 (uri (bioconductor-uri "Biostrings" version))
1832 (sha256
1833 (base32
1834 "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
1835 (properties
1836 `((upstream-name . "Biostrings")))
1837 (build-system r-build-system)
1838 (propagated-inputs
1839 `(("r-biocgenerics" ,r-biocgenerics)
1840 ("r-crayon" ,r-crayon)
1841 ("r-iranges" ,r-iranges)
1842 ("r-s4vectors" ,r-s4vectors)
1843 ("r-xvector" ,r-xvector)))
1844 (home-page "https://bioconductor.org/packages/Biostrings")
1845 (synopsis "String objects and algorithms for biological sequences")
1846 (description
1847 "This package provides memory efficient string containers, string
1848 matching algorithms, and other utilities, for fast manipulation of large
1849 biological sequences or sets of sequences.")
1850 (license license:artistic2.0)))
1851
1852 (define-public r-category
1853 (package
1854 (name "r-category")
1855 (version "2.56.0")
1856 (source
1857 (origin
1858 (method url-fetch)
1859 (uri (bioconductor-uri "Category" version))
1860 (sha256
1861 (base32
1862 "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
1863 (properties `((upstream-name . "Category")))
1864 (build-system r-build-system)
1865 (propagated-inputs
1866 `(("r-annotate" ,r-annotate)
1867 ("r-annotationdbi" ,r-annotationdbi)
1868 ("r-biobase" ,r-biobase)
1869 ("r-biocgenerics" ,r-biocgenerics)
1870 ("r-genefilter" ,r-genefilter)
1871 ("r-graph" ,r-graph)
1872 ("r-gseabase" ,r-gseabase)
1873 ("r-matrix" ,r-matrix)
1874 ("r-rbgl" ,r-rbgl)
1875 ("r-dbi" ,r-dbi)))
1876 (home-page "https://bioconductor.org/packages/Category")
1877 (synopsis "Category analysis")
1878 (description
1879 "This package provides a collection of tools for performing category
1880 analysis.")
1881 (license license:artistic2.0)))
1882
1883 (define-public r-deseq2
1884 (package
1885 (name "r-deseq2")
1886 (version "1.30.1")
1887 (source
1888 (origin
1889 (method url-fetch)
1890 (uri (bioconductor-uri "DESeq2" version))
1891 (sha256
1892 (base32
1893 "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19"))))
1894 (properties `((upstream-name . "DESeq2")))
1895 (build-system r-build-system)
1896 (propagated-inputs
1897 `(("r-biobase" ,r-biobase)
1898 ("r-biocgenerics" ,r-biocgenerics)
1899 ("r-biocparallel" ,r-biocparallel)
1900 ("r-genefilter" ,r-genefilter)
1901 ("r-geneplotter" ,r-geneplotter)
1902 ("r-genomicranges" ,r-genomicranges)
1903 ("r-ggplot2" ,r-ggplot2)
1904 ("r-iranges" ,r-iranges)
1905 ("r-locfit" ,r-locfit)
1906 ("r-rcpp" ,r-rcpp)
1907 ("r-rcpparmadillo" ,r-rcpparmadillo)
1908 ("r-s4vectors" ,r-s4vectors)
1909 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1910 (native-inputs
1911 `(("r-knitr" ,r-knitr)))
1912 (home-page "https://bioconductor.org/packages/DESeq2")
1913 (synopsis "Differential gene expression analysis")
1914 (description
1915 "This package provides functions to estimate variance-mean dependence in
1916 count data from high-throughput nucleotide sequencing assays and test for
1917 differential expression based on a model using the negative binomial
1918 distribution.")
1919 (license license:lgpl3+)))
1920
1921 (define-public r-dexseq
1922 (package
1923 (name "r-dexseq")
1924 (version "1.36.0")
1925 (source
1926 (origin
1927 (method url-fetch)
1928 (uri (bioconductor-uri "DEXSeq" version))
1929 (sha256
1930 (base32
1931 "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
1932 (properties `((upstream-name . "DEXSeq")))
1933 (build-system r-build-system)
1934 (propagated-inputs
1935 `(("r-annotationdbi" ,r-annotationdbi)
1936 ("r-biobase" ,r-biobase)
1937 ("r-biocgenerics" ,r-biocgenerics)
1938 ("r-biocparallel" ,r-biocparallel)
1939 ("r-biomart" ,r-biomart)
1940 ("r-deseq2" ,r-deseq2)
1941 ("r-genefilter" ,r-genefilter)
1942 ("r-geneplotter" ,r-geneplotter)
1943 ("r-genomicranges" ,r-genomicranges)
1944 ("r-hwriter" ,r-hwriter)
1945 ("r-iranges" ,r-iranges)
1946 ("r-rcolorbrewer" ,r-rcolorbrewer)
1947 ("r-rsamtools" ,r-rsamtools)
1948 ("r-s4vectors" ,r-s4vectors)
1949 ("r-statmod" ,r-statmod)
1950 ("r-stringr" ,r-stringr)
1951 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1952 (native-inputs
1953 `(("r-knitr" ,r-knitr)))
1954 (home-page "https://bioconductor.org/packages/DEXSeq")
1955 (synopsis "Inference of differential exon usage in RNA-Seq")
1956 (description
1957 "This package is focused on finding differential exon usage using RNA-seq
1958 exon counts between samples with different experimental designs. It provides
1959 functions that allows the user to make the necessary statistical tests based
1960 on a model that uses the negative binomial distribution to estimate the
1961 variance between biological replicates and generalized linear models for
1962 testing. The package also provides functions for the visualization and
1963 exploration of the results.")
1964 (license license:gpl3+)))
1965
1966 (define-public r-edger
1967 (package
1968 (name "r-edger")
1969 (version "3.32.1")
1970 (source (origin
1971 (method url-fetch)
1972 (uri (bioconductor-uri "edgeR" version))
1973 (sha256
1974 (base32
1975 "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
1976 (properties `((upstream-name . "edgeR")))
1977 (build-system r-build-system)
1978 (propagated-inputs
1979 `(("r-limma" ,r-limma)
1980 ("r-locfit" ,r-locfit)
1981 ("r-rcpp" ,r-rcpp)
1982 ("r-statmod" ,r-statmod))) ;for estimateDisp
1983 (home-page "http://bioinf.wehi.edu.au/edgeR")
1984 (synopsis "EdgeR does empirical analysis of digital gene expression data")
1985 (description "This package can do differential expression analysis of
1986 RNA-seq expression profiles with biological replication. It implements a range
1987 of statistical methodology based on the negative binomial distributions,
1988 including empirical Bayes estimation, exact tests, generalized linear models
1989 and quasi-likelihood tests. It be applied to differential signal analysis of
1990 other types of genomic data that produce counts, including ChIP-seq, SAGE and
1991 CAGE.")
1992 (license license:gpl2+)))
1993
1994 (define-public r-genefilter
1995 (package
1996 (name "r-genefilter")
1997 (version "1.72.1")
1998 (source
1999 (origin
2000 (method url-fetch)
2001 (uri (bioconductor-uri "genefilter" version))
2002 (sha256
2003 (base32
2004 "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
2005 (build-system r-build-system)
2006 (native-inputs
2007 `(("gfortran" ,gfortran)
2008 ("r-knitr" ,r-knitr)))
2009 (propagated-inputs
2010 `(("r-annotate" ,r-annotate)
2011 ("r-annotationdbi" ,r-annotationdbi)
2012 ("r-biobase" ,r-biobase)
2013 ("r-biocgenerics" ,r-biocgenerics)
2014 ("r-survival" ,r-survival)))
2015 (home-page "https://bioconductor.org/packages/genefilter")
2016 (synopsis "Filter genes from high-throughput experiments")
2017 (description
2018 "This package provides basic functions for filtering genes from
2019 high-throughput sequencing experiments.")
2020 (license license:artistic2.0)))
2021
2022 (define-public r-genomeinfodb
2023 (package
2024 (name "r-genomeinfodb")
2025 (version "1.26.6")
2026 (source (origin
2027 (method url-fetch)
2028 (uri (bioconductor-uri "GenomeInfoDb" version))
2029 (sha256
2030 (base32
2031 "1wy4dwiv0pgim975var802z565py4a0nakx6zdvbhry4c0dfczd1"))))
2032 (properties
2033 `((upstream-name . "GenomeInfoDb")))
2034 (build-system r-build-system)
2035 (propagated-inputs
2036 `(("r-biocgenerics" ,r-biocgenerics)
2037 ("r-genomeinfodbdata" ,r-genomeinfodbdata)
2038 ("r-iranges" ,r-iranges)
2039 ("r-rcurl" ,r-rcurl)
2040 ("r-s4vectors" ,r-s4vectors)))
2041 (native-inputs
2042 `(("r-knitr" ,r-knitr)))
2043 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
2044 (synopsis "Utilities for manipulating chromosome identifiers")
2045 (description
2046 "This package contains data and functions that define and allow
2047 translation between different chromosome sequence naming conventions (e.g.,
2048 \"chr1\" versus \"1\"), including a function that attempts to place sequence
2049 names in their natural, rather than lexicographic, order.")
2050 (license license:artistic2.0)))
2051
2052 (define-public r-genomicranges
2053 (package
2054 (name "r-genomicranges")
2055 (version "1.42.0")
2056 (source (origin
2057 (method url-fetch)
2058 (uri (bioconductor-uri "GenomicRanges" version))
2059 (sha256
2060 (base32
2061 "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
2062 (properties
2063 `((upstream-name . "GenomicRanges")))
2064 (build-system r-build-system)
2065 (propagated-inputs
2066 `(("r-biocgenerics" ,r-biocgenerics)
2067 ("r-genomeinfodb" ,r-genomeinfodb)
2068 ("r-iranges" ,r-iranges)
2069 ("r-s4vectors" ,r-s4vectors)
2070 ("r-xvector" ,r-xvector)))
2071 (native-inputs
2072 `(("r-knitr" ,r-knitr)))
2073 (home-page "https://bioconductor.org/packages/GenomicRanges")
2074 (synopsis "Representation and manipulation of genomic intervals")
2075 (description
2076 "This package provides tools to efficiently represent and manipulate
2077 genomic annotations and alignments is playing a central role when it comes to
2078 analyzing high-throughput sequencing data (a.k.a. NGS data). The
2079 GenomicRanges package defines general purpose containers for storing and
2080 manipulating genomic intervals and variables defined along a genome.")
2081 (license license:artistic2.0)))
2082
2083 (define-public r-gostats
2084 (package
2085 (name "r-gostats")
2086 (version "2.56.0")
2087 (source
2088 (origin
2089 (method url-fetch)
2090 (uri (bioconductor-uri "GOstats" version))
2091 (sha256
2092 (base32
2093 "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
2094 (properties `((upstream-name . "GOstats")))
2095 (build-system r-build-system)
2096 (propagated-inputs
2097 `(("r-annotate" ,r-annotate)
2098 ("r-annotationdbi" ,r-annotationdbi)
2099 ("r-annotationforge" ,r-annotationforge)
2100 ("r-biobase" ,r-biobase)
2101 ("r-category" ,r-category)
2102 ("r-go-db" ,r-go-db)
2103 ("r-graph" ,r-graph)
2104 ("r-rgraphviz" ,r-rgraphviz)
2105 ("r-rbgl" ,r-rbgl)))
2106 (home-page "https://bioconductor.org/packages/GOstats")
2107 (synopsis "Tools for manipulating GO and microarrays")
2108 (description
2109 "This package provides a set of tools for interacting with GO and
2110 microarray data. A variety of basic manipulation tools for graphs, hypothesis
2111 testing and other simple calculations.")
2112 (license license:artistic2.0)))
2113
2114 (define-public r-gseabase
2115 (package
2116 (name "r-gseabase")
2117 (version "1.52.1")
2118 (source
2119 (origin
2120 (method url-fetch)
2121 (uri (bioconductor-uri "GSEABase" version))
2122 (sha256
2123 (base32
2124 "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
2125 (properties `((upstream-name . "GSEABase")))
2126 (build-system r-build-system)
2127 (propagated-inputs
2128 `(("r-annotate" ,r-annotate)
2129 ("r-annotationdbi" ,r-annotationdbi)
2130 ("r-biobase" ,r-biobase)
2131 ("r-biocgenerics" ,r-biocgenerics)
2132 ("r-graph" ,r-graph)
2133 ("r-xml" ,r-xml)))
2134 (native-inputs
2135 `(("r-knitr" ,r-knitr)))
2136 (home-page "https://bioconductor.org/packages/GSEABase")
2137 (synopsis "Gene set enrichment data structures and methods")
2138 (description
2139 "This package provides classes and methods to support @dfn{Gene Set
2140 Enrichment Analysis} (GSEA).")
2141 (license license:artistic2.0)))
2142
2143 (define-public r-hpar
2144 (package
2145 (name "r-hpar")
2146 (version "1.32.1")
2147 (source
2148 (origin
2149 (method url-fetch)
2150 (uri (bioconductor-uri "hpar" version))
2151 (sha256
2152 (base32
2153 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
2154 (build-system r-build-system)
2155 (native-inputs
2156 `(("r-knitr" ,r-knitr)))
2157 (home-page "https://bioconductor.org/packages/hpar/")
2158 (synopsis "Human Protein Atlas in R")
2159 (description "This package provides a simple interface to and data from
2160 the Human Protein Atlas project.")
2161 (license license:artistic2.0)))
2162
2163 (define-public r-limma
2164 (package
2165 (name "r-limma")
2166 (version "3.46.0")
2167 (source (origin
2168 (method url-fetch)
2169 (uri (bioconductor-uri "limma" version))
2170 (sha256
2171 (base32
2172 "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
2173 (build-system r-build-system)
2174 (home-page "http://bioinf.wehi.edu.au/limma")
2175 (synopsis "Package for linear models for microarray and RNA-seq data")
2176 (description "This package can be used for the analysis of gene expression
2177 studies, especially the use of linear models for analysing designed experiments
2178 and the assessment of differential expression. The analysis methods apply to
2179 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
2180 (license license:gpl2+)))
2181
2182 (define-public r-rbgl
2183 (package
2184 (name "r-rbgl")
2185 (version "1.66.0")
2186 (source
2187 (origin
2188 (method url-fetch)
2189 (uri (bioconductor-uri "RBGL" version))
2190 (sha256
2191 (base32
2192 "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
2193 (properties `((upstream-name . "RBGL")))
2194 (build-system r-build-system)
2195 (propagated-inputs
2196 `(("r-bh" ,r-bh)
2197 ("r-graph" ,r-graph)))
2198 (home-page "https://www.bioconductor.org/packages/RBGL")
2199 (synopsis "Interface to the Boost graph library")
2200 (description
2201 "This package provides a fairly extensive and comprehensive interface to
2202 the graph algorithms contained in the Boost library.")
2203 (license license:artistic2.0)))
2204
2205 (define-public r-regioner
2206 (package
2207 (name "r-regioner")
2208 (version "1.22.0")
2209 (source
2210 (origin
2211 (method url-fetch)
2212 (uri (bioconductor-uri "regioneR" version))
2213 (sha256
2214 (base32
2215 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
2216 (properties `((upstream-name . "regioneR")))
2217 (build-system r-build-system)
2218 (propagated-inputs
2219 `(("r-biostrings" ,r-biostrings)
2220 ("r-bsgenome" ,r-bsgenome)
2221 ("r-genomeinfodb" ,r-genomeinfodb)
2222 ("r-genomicranges" ,r-genomicranges)
2223 ("r-iranges" ,r-iranges)
2224 ("r-memoise" ,r-memoise)
2225 ("r-rtracklayer" ,r-rtracklayer)
2226 ("r-s4vectors" ,r-s4vectors)))
2227 (native-inputs
2228 `(("r-knitr" ,r-knitr)))
2229 (home-page "https://bioconductor.org/packages/regioneR/")
2230 (synopsis "Association analysis of genomic regions")
2231 (description "This package offers a statistical framework based on
2232 customizable permutation tests to assess the association between genomic
2233 region sets and other genomic features.")
2234 (license license:artistic2.0)))
2235
2236 (define-public r-reportingtools
2237 (package
2238 (name "r-reportingtools")
2239 (version "2.30.2")
2240 (source
2241 (origin
2242 (method url-fetch)
2243 (uri (bioconductor-uri "ReportingTools" version))
2244 (sha256
2245 (base32
2246 "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb"))))
2247 (properties
2248 `((upstream-name . "ReportingTools")))
2249 (build-system r-build-system)
2250 (propagated-inputs
2251 `(("r-annotate" ,r-annotate)
2252 ("r-annotationdbi" ,r-annotationdbi)
2253 ("r-biobase" ,r-biobase)
2254 ("r-biocgenerics" ,r-biocgenerics)
2255 ("r-category" ,r-category)
2256 ("r-deseq2" ,r-deseq2)
2257 ("r-edger" ,r-edger)
2258 ("r-ggbio" ,r-ggbio)
2259 ("r-ggplot2" ,r-ggplot2)
2260 ("r-gostats" ,r-gostats)
2261 ("r-gseabase" ,r-gseabase)
2262 ("r-hwriter" ,r-hwriter)
2263 ("r-iranges" ,r-iranges)
2264 ("r-knitr" ,r-knitr)
2265 ("r-lattice" ,r-lattice)
2266 ("r-limma" ,r-limma)
2267 ("r-pfam-db" ,r-pfam-db)
2268 ("r-r-utils" ,r-r-utils)
2269 ("r-xml" ,r-xml)))
2270 (native-inputs
2271 `(("r-knitr" ,r-knitr)))
2272 (home-page "https://bioconductor.org/packages/ReportingTools/")
2273 (synopsis "Tools for making reports in various formats")
2274 (description
2275 "The ReportingTools package enables users to easily display reports of
2276 analysis results generated from sources such as microarray and sequencing
2277 data. The package allows users to create HTML pages that may be viewed on a
2278 web browser, or in other formats. Users can generate tables with sortable and
2279 filterable columns, make and display plots, and link table entries to other
2280 data sources such as NCBI or larger plots within the HTML page. Using the
2281 package, users can also produce a table of contents page to link various
2282 reports together for a particular project that can be viewed in a web
2283 browser.")
2284 (license license:artistic2.0)))
2285
2286 (define-public r-rsamtools
2287 (package
2288 (name "r-rsamtools")
2289 (version "2.6.0")
2290 (source (origin
2291 (method url-fetch)
2292 (uri (bioconductor-uri "Rsamtools" version))
2293 (sha256
2294 (base32
2295 "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
2296 (properties
2297 `((upstream-name . "Rsamtools")))
2298 (build-system r-build-system)
2299 (arguments
2300 `(#:phases
2301 (modify-phases %standard-phases
2302 (add-after 'unpack 'use-system-zlib
2303 (lambda _
2304 (substitute* "DESCRIPTION"
2305 (("zlibbioc, ") ""))
2306 (substitute* "NAMESPACE"
2307 (("import\\(zlibbioc\\)") ""))
2308 #t)))))
2309 (propagated-inputs
2310 `(("r-biocgenerics" ,r-biocgenerics)
2311 ("r-biocparallel" ,r-biocparallel)
2312 ("r-biostrings" ,r-biostrings)
2313 ("r-bitops" ,r-bitops)
2314 ("r-genomeinfodb" ,r-genomeinfodb)
2315 ("r-genomicranges" ,r-genomicranges)
2316 ("r-iranges" ,r-iranges)
2317 ("r-rhtslib" ,r-rhtslib)
2318 ("r-s4vectors" ,r-s4vectors)
2319 ("r-xvector" ,r-xvector)))
2320 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
2321 (synopsis "Interface to samtools, bcftools, and tabix")
2322 (description
2323 "This package provides an interface to the @code{samtools},
2324 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
2325 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
2326 tab-delimited (tabix) files.")
2327 (license license:expat)))
2328
2329 (define-public r-shortread
2330 (package
2331 (name "r-shortread")
2332 (version "1.48.0")
2333 (source
2334 (origin
2335 (method url-fetch)
2336 (uri (bioconductor-uri "ShortRead" version))
2337 (sha256
2338 (base32
2339 "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
2340 (properties `((upstream-name . "ShortRead")))
2341 (build-system r-build-system)
2342 (inputs
2343 `(("zlib" ,zlib)))
2344 (propagated-inputs
2345 `(("r-biobase" ,r-biobase)
2346 ("r-biocgenerics" ,r-biocgenerics)
2347 ("r-biocparallel" ,r-biocparallel)
2348 ("r-biostrings" ,r-biostrings)
2349 ("r-genomeinfodb" ,r-genomeinfodb)
2350 ("r-genomicalignments" ,r-genomicalignments)
2351 ("r-genomicranges" ,r-genomicranges)
2352 ("r-rhtslib" ,r-rhtslib)
2353 ("r-hwriter" ,r-hwriter)
2354 ("r-iranges" ,r-iranges)
2355 ("r-lattice" ,r-lattice)
2356 ("r-latticeextra" ,r-latticeextra)
2357 ("r-rsamtools" ,r-rsamtools)
2358 ("r-s4vectors" ,r-s4vectors)
2359 ("r-xvector" ,r-xvector)
2360 ("r-zlibbioc" ,r-zlibbioc)))
2361 (home-page "https://bioconductor.org/packages/ShortRead")
2362 (synopsis "FASTQ input and manipulation tools")
2363 (description
2364 "This package implements sampling, iteration, and input of FASTQ files.
2365 It includes functions for filtering and trimming reads, and for generating a
2366 quality assessment report. Data are represented as
2367 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
2368 purposes. The package also contains legacy support for early single-end,
2369 ungapped alignment formats.")
2370 (license license:artistic2.0)))
2371
2372 (define-public r-systempiper
2373 (package
2374 (name "r-systempiper")
2375 (version "1.24.3")
2376 (source
2377 (origin
2378 (method url-fetch)
2379 (uri (bioconductor-uri "systemPipeR" version))
2380 (sha256
2381 (base32
2382 "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
2383 (properties `((upstream-name . "systemPipeR")))
2384 (build-system r-build-system)
2385 (propagated-inputs
2386 `(("r-annotate" ,r-annotate)
2387 ("r-assertthat" ,r-assertthat)
2388 ("r-batchtools" ,r-batchtools)
2389 ("r-biostrings" ,r-biostrings)
2390 ("r-deseq2" ,r-deseq2)
2391 ("r-dot" ,r-dot)
2392 ("r-edger" ,r-edger)
2393 ("r-genomicfeatures" ,r-genomicfeatures)
2394 ("r-genomicranges" ,r-genomicranges)
2395 ("r-ggplot2" ,r-ggplot2)
2396 ("r-go-db" ,r-go-db)
2397 ("r-gostats" ,r-gostats)
2398 ("r-iranges" ,r-iranges)
2399 ("r-limma" ,r-limma)
2400 ("r-magrittr" ,r-magrittr)
2401 ("r-pheatmap" ,r-pheatmap)
2402 ("r-rjson" ,r-rjson)
2403 ("r-rsamtools" ,r-rsamtools)
2404 ("r-rsvg" ,r-rsvg)
2405 ("r-shortread" ,r-shortread)
2406 ("r-stringr" ,r-stringr)
2407 ("r-summarizedexperiment" ,r-summarizedexperiment)
2408 ("r-yaml" ,r-yaml)
2409 ("r-variantannotation" ,r-variantannotation)))
2410 (native-inputs
2411 `(("r-knitr" ,r-knitr)))
2412 (home-page "https://github.com/tgirke/systemPipeR")
2413 (synopsis "Next generation sequencing workflow and reporting environment")
2414 (description
2415 "This R package provides tools for building and running automated
2416 end-to-end analysis workflows for a wide range of @dfn{next generation
2417 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
2418 Important features include a uniform workflow interface across different NGS
2419 applications, automated report generation, and support for running both R and
2420 command-line software, such as NGS aligners or peak/variant callers, on local
2421 computers or compute clusters. Efficient handling of complex sample sets and
2422 experimental designs is facilitated by a consistently implemented sample
2423 annotation infrastructure.")
2424 (license license:artistic2.0)))
2425
2426 (define-public r-variantannotation
2427 (package
2428 (name "r-variantannotation")
2429 (version "1.36.0")
2430 (source (origin
2431 (method url-fetch)
2432 (uri (bioconductor-uri "VariantAnnotation" version))
2433 (sha256
2434 (base32
2435 "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
2436 (properties
2437 `((upstream-name . "VariantAnnotation")))
2438 (propagated-inputs
2439 `(("r-annotationdbi" ,r-annotationdbi)
2440 ("r-biobase" ,r-biobase)
2441 ("r-biocgenerics" ,r-biocgenerics)
2442 ("r-biostrings" ,r-biostrings)
2443 ("r-bsgenome" ,r-bsgenome)
2444 ("r-dbi" ,r-dbi)
2445 ("r-genomeinfodb" ,r-genomeinfodb)
2446 ("r-genomicfeatures" ,r-genomicfeatures)
2447 ("r-genomicranges" ,r-genomicranges)
2448 ("r-iranges" ,r-iranges)
2449 ("r-matrixgenerics" ,r-matrixgenerics)
2450 ("r-summarizedexperiment" ,r-summarizedexperiment)
2451 ("r-rhtslib" ,r-rhtslib)
2452 ("r-rsamtools" ,r-rsamtools)
2453 ("r-rtracklayer" ,r-rtracklayer)
2454 ("r-s4vectors" ,r-s4vectors)
2455 ("r-xvector" ,r-xvector)
2456 ("r-zlibbioc" ,r-zlibbioc)))
2457 (build-system r-build-system)
2458 (home-page "https://bioconductor.org/packages/VariantAnnotation")
2459 (synopsis "Package for annotation of genetic variants")
2460 (description "This R package can annotate variants, compute amino acid
2461 coding changes and predict coding outcomes.")
2462 (license license:artistic2.0)))
2463
2464 (define-public r-xvector
2465 (package
2466 (name "r-xvector")
2467 (version "0.30.0")
2468 (source (origin
2469 (method url-fetch)
2470 (uri (bioconductor-uri "XVector" version))
2471 (sha256
2472 (base32
2473 "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
2474 (properties
2475 `((upstream-name . "XVector")))
2476 (build-system r-build-system)
2477 (arguments
2478 `(#:phases
2479 (modify-phases %standard-phases
2480 (add-after 'unpack 'use-system-zlib
2481 (lambda _
2482 (substitute* "DESCRIPTION"
2483 (("zlibbioc, ") ""))
2484 (substitute* "NAMESPACE"
2485 (("import\\(zlibbioc\\)") ""))
2486 #t)))))
2487 (inputs
2488 `(("zlib" ,zlib)))
2489 (propagated-inputs
2490 `(("r-biocgenerics" ,r-biocgenerics)
2491 ("r-iranges" ,r-iranges)
2492 ("r-s4vectors" ,r-s4vectors)))
2493 (home-page "https://bioconductor.org/packages/XVector")
2494 (synopsis "Representation and manpulation of external sequences")
2495 (description
2496 "This package provides memory efficient S4 classes for storing sequences
2497 \"externally\" (behind an R external pointer, or on disk).")
2498 (license license:artistic2.0)))
2499
2500 (define-public r-geneplotter
2501 (package
2502 (name "r-geneplotter")
2503 (version "1.68.0")
2504 (source
2505 (origin
2506 (method url-fetch)
2507 (uri (bioconductor-uri "geneplotter" version))
2508 (sha256
2509 (base32
2510 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
2511 (build-system r-build-system)
2512 (propagated-inputs
2513 `(("r-annotate" ,r-annotate)
2514 ("r-annotationdbi" ,r-annotationdbi)
2515 ("r-biobase" ,r-biobase)
2516 ("r-biocgenerics" ,r-biocgenerics)
2517 ("r-lattice" ,r-lattice)
2518 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2519 (home-page "https://bioconductor.org/packages/geneplotter")
2520 (synopsis "Graphics functions for genomic data")
2521 (description
2522 "This package provides functions for plotting genomic data.")
2523 (license license:artistic2.0)))
2524
2525 (define-public r-oligoclasses
2526 (package
2527 (name "r-oligoclasses")
2528 (version "1.52.0")
2529 (source
2530 (origin
2531 (method url-fetch)
2532 (uri (bioconductor-uri "oligoClasses" version))
2533 (sha256
2534 (base32
2535 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
2536 (properties `((upstream-name . "oligoClasses")))
2537 (build-system r-build-system)
2538 (propagated-inputs
2539 `(("r-affyio" ,r-affyio)
2540 ("r-biobase" ,r-biobase)
2541 ("r-biocgenerics" ,r-biocgenerics)
2542 ("r-biocmanager" ,r-biocmanager)
2543 ("r-biostrings" ,r-biostrings)
2544 ("r-dbi" ,r-dbi)
2545 ("r-ff" ,r-ff)
2546 ("r-foreach" ,r-foreach)
2547 ("r-genomicranges" ,r-genomicranges)
2548 ("r-iranges" ,r-iranges)
2549 ("r-rsqlite" ,r-rsqlite)
2550 ("r-s4vectors" ,r-s4vectors)
2551 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2552 (home-page "https://bioconductor.org/packages/oligoClasses/")
2553 (synopsis "Classes for high-throughput arrays")
2554 (description
2555 "This package contains class definitions, validity checks, and
2556 initialization methods for classes used by the @code{oligo} and @code{crlmm}
2557 packages.")
2558 (license license:gpl2+)))
2559
2560 (define-public r-oligo
2561 (package
2562 (name "r-oligo")
2563 (version "1.54.1")
2564 (source
2565 (origin
2566 (method url-fetch)
2567 (uri (bioconductor-uri "oligo" version))
2568 (sha256
2569 (base32
2570 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
2571 (properties `((upstream-name . "oligo")))
2572 (build-system r-build-system)
2573 (inputs `(("zlib" ,zlib)))
2574 (propagated-inputs
2575 `(("r-affxparser" ,r-affxparser)
2576 ("r-affyio" ,r-affyio)
2577 ("r-biobase" ,r-biobase)
2578 ("r-biocgenerics" ,r-biocgenerics)
2579 ("r-biostrings" ,r-biostrings)
2580 ("r-dbi" ,r-dbi)
2581 ("r-ff" ,r-ff)
2582 ("r-oligoclasses" ,r-oligoclasses)
2583 ("r-preprocesscore" ,r-preprocesscore)
2584 ("r-rsqlite" ,r-rsqlite)
2585 ("r-zlibbioc" ,r-zlibbioc)))
2586 (native-inputs
2587 `(("r-knitr" ,r-knitr)))
2588 (home-page "https://bioconductor.org/packages/oligo/")
2589 (synopsis "Preprocessing tools for oligonucleotide arrays")
2590 (description
2591 "This package provides a package to analyze oligonucleotide
2592 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
2593 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
2594 (license license:lgpl2.0+)))
2595
2596 (define-public r-qvalue
2597 (package
2598 (name "r-qvalue")
2599 (version "2.22.0")
2600 (source
2601 (origin
2602 (method url-fetch)
2603 (uri (bioconductor-uri "qvalue" version))
2604 (sha256
2605 (base32
2606 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
2607 (build-system r-build-system)
2608 (propagated-inputs
2609 `(("r-ggplot2" ,r-ggplot2)
2610 ("r-reshape2" ,r-reshape2)))
2611 (native-inputs
2612 `(("r-knitr" ,r-knitr)))
2613 (home-page "https://github.com/StoreyLab/qvalue")
2614 (synopsis "Q-value estimation for false discovery rate control")
2615 (description
2616 "This package takes a list of p-values resulting from the simultaneous
2617 testing of many hypotheses and estimates their q-values and local @dfn{false
2618 discovery rate} (FDR) values. The q-value of a test measures the proportion
2619 of false positives incurred when that particular test is called significant.
2620 The local FDR measures the posterior probability the null hypothesis is true
2621 given the test's p-value. Various plots are automatically generated, allowing
2622 one to make sensible significance cut-offs. The software can be applied to
2623 problems in genomics, brain imaging, astrophysics, and data mining.")
2624 ;; Any version of the LGPL.
2625 (license license:lgpl3+)))
2626
2627 (define r-rcppnumerical
2628 (package
2629 (name "r-rcppnumerical")
2630 (version "0.4-0")
2631 (source (origin
2632 (method url-fetch)
2633 (uri (cran-uri "RcppNumerical" version))
2634 (sha256
2635 (base32
2636 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
2637 (properties `((upstream-name . "RcppNumerical")))
2638 (build-system r-build-system)
2639 (propagated-inputs
2640 `(("r-rcpp" ,r-rcpp)
2641 ("r-rcppeigen" ,r-rcppeigen)))
2642 (native-inputs
2643 `(("r-knitr" ,r-knitr)))
2644 (home-page "https://github.com/yixuan/RcppNumerical")
2645 (synopsis "Rcpp integration for numerical computing libraries")
2646 (description "This package provides a collection of open source libraries
2647 for numerical computing (numerical integration, optimization, etc.) and their
2648 integration with @code{Rcpp}.")
2649 (license license:gpl2+)))
2650
2651 (define-public r-apeglm
2652 (package
2653 (name "r-apeglm")
2654 (version "1.12.0")
2655 (source (origin
2656 (method url-fetch)
2657 (uri (bioconductor-uri "apeglm" version))
2658 (sha256
2659 (base32
2660 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
2661 (properties `((upstream-name . "apeglm")))
2662 (build-system r-build-system)
2663 (propagated-inputs
2664 `(("r-emdbook" ,r-emdbook)
2665 ("r-genomicranges" ,r-genomicranges)
2666 ("r-rcpp" ,r-rcpp)
2667 ("r-rcppeigen" ,r-rcppeigen)
2668 ("r-rcppnumerical" ,r-rcppnumerical)
2669 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2670 (native-inputs `(("r-knitr" ,r-knitr)))
2671 (home-page "https://bioconductor.org/packages/apeglm")
2672 (synopsis "Approximate posterior estimation for GLM coefficients")
2673 (description "This package provides Bayesian shrinkage estimators for
2674 effect sizes for a variety of GLM models, using approximation of the
2675 posterior for individual coefficients.")
2676 (license license:gpl2)))
2677
2678 (define-public r-greylistchip
2679 (package
2680 (name "r-greylistchip")
2681 (version "1.22.0")
2682 (source (origin
2683 (method url-fetch)
2684 (uri (bioconductor-uri "GreyListChIP" version))
2685 (sha256
2686 (base32
2687 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
2688 (properties `((upstream-name . "GreyListChIP")))
2689 (build-system r-build-system)
2690 (propagated-inputs
2691 `(("r-bsgenome" ,r-bsgenome)
2692 ("r-genomeinfodb" ,r-genomeinfodb)
2693 ("r-genomicalignments" ,r-genomicalignments)
2694 ("r-genomicranges" ,r-genomicranges)
2695 ("r-mass" ,r-mass)
2696 ("r-rsamtools" ,r-rsamtools)
2697 ("r-rtracklayer" ,r-rtracklayer)
2698 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2699 (home-page "https://bioconductor.org/packages/GreyListChIP")
2700 (synopsis "Greylist artefact regions based on ChIP inputs")
2701 (description "This package identifies regions of ChIP experiments with high
2702 signal in the input, that lead to spurious peaks during peak calling.")
2703 (license license:artistic2.0)))
2704
2705 (define-public r-diffbind
2706 (package
2707 (name "r-diffbind")
2708 (version "3.0.15")
2709 (source
2710 (origin
2711 (method url-fetch)
2712 (uri (bioconductor-uri "DiffBind" version))
2713 (sha256
2714 (base32
2715 "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi"))))
2716 (properties `((upstream-name . "DiffBind")))
2717 (build-system r-build-system)
2718 (propagated-inputs
2719 `(("r-amap" ,r-amap)
2720 ("r-apeglm" ,r-apeglm)
2721 ("r-ashr" ,r-ashr)
2722 ("r-biocparallel" ,r-biocparallel)
2723 ("r-deseq2" ,r-deseq2)
2724 ("r-dplyr" ,r-dplyr)
2725 ("r-genomicalignments" ,r-genomicalignments)
2726 ("r-genomicranges" ,r-genomicranges)
2727 ("r-ggplot2" ,r-ggplot2)
2728 ("r-ggrepel" ,r-ggrepel)
2729 ("r-gplots" ,r-gplots)
2730 ("r-greylistchip" ,r-greylistchip)
2731 ("r-iranges" ,r-iranges)
2732 ("r-lattice" ,r-lattice)
2733 ("r-limma" ,r-limma)
2734 ("r-locfit" ,r-locfit)
2735 ("r-rcolorbrewer" , r-rcolorbrewer)
2736 ("r-rcpp" ,r-rcpp)
2737 ("r-rhtslib" ,r-rhtslib)
2738 ("r-rsamtools" ,r-rsamtools)
2739 ("r-s4vectors" ,r-s4vectors)
2740 ("r-summarizedexperiment" ,r-summarizedexperiment)
2741 ("r-systempiper" ,r-systempiper)))
2742 (home-page "https://bioconductor.org/packages/DiffBind")
2743 (synopsis "Differential binding analysis of ChIP-Seq peak data")
2744 (description
2745 "This package computes differentially bound sites from multiple
2746 ChIP-seq experiments using affinity (quantitative) data. Also enables
2747 occupancy (overlap) analysis and plotting functions.")
2748 (license license:artistic2.0)))
2749
2750 (define-public r-ripseeker
2751 (package
2752 (name "r-ripseeker")
2753 (version "1.26.0")
2754 (source
2755 (origin
2756 (method url-fetch)
2757 (uri (bioconductor-uri "RIPSeeker" version))
2758 (sha256
2759 (base32
2760 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
2761 (properties `((upstream-name . "RIPSeeker")))
2762 (build-system r-build-system)
2763 (propagated-inputs
2764 `(("r-s4vectors" ,r-s4vectors)
2765 ("r-iranges" ,r-iranges)
2766 ("r-genomicranges" ,r-genomicranges)
2767 ("r-summarizedexperiment" ,r-summarizedexperiment)
2768 ("r-rsamtools" ,r-rsamtools)
2769 ("r-genomicalignments" ,r-genomicalignments)
2770 ("r-rtracklayer" ,r-rtracklayer)))
2771 (home-page "https://bioconductor.org/packages/RIPSeeker")
2772 (synopsis
2773 "Identifying protein-associated transcripts from RIP-seq experiments")
2774 (description
2775 "This package infers and discriminates RIP peaks from RIP-seq alignments
2776 using two-state HMM with negative binomial emission probability. While
2777 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
2778 a suite of bioinformatics tools integrated within this self-contained software
2779 package comprehensively addressing issues ranging from post-alignments
2780 processing to visualization and annotation.")
2781 (license license:gpl2)))
2782
2783 (define-public r-multtest
2784 (package
2785 (name "r-multtest")
2786 (version "2.46.0")
2787 (source
2788 (origin
2789 (method url-fetch)
2790 (uri (bioconductor-uri "multtest" version))
2791 (sha256
2792 (base32
2793 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
2794 (build-system r-build-system)
2795 (propagated-inputs
2796 `(("r-survival" ,r-survival)
2797 ("r-biocgenerics" ,r-biocgenerics)
2798 ("r-biobase" ,r-biobase)
2799 ("r-mass" ,r-mass)))
2800 (home-page "https://bioconductor.org/packages/multtest")
2801 (synopsis "Resampling-based multiple hypothesis testing")
2802 (description
2803 "This package can do non-parametric bootstrap and permutation
2804 resampling-based multiple testing procedures (including empirical Bayes
2805 methods) for controlling the family-wise error rate (FWER), generalized
2806 family-wise error rate (gFWER), tail probability of the proportion of
2807 false positives (TPPFP), and false discovery rate (FDR). Several choices
2808 of bootstrap-based null distribution are implemented (centered, centered
2809 and scaled, quantile-transformed). Single-step and step-wise methods are
2810 available. Tests based on a variety of T- and F-statistics (including
2811 T-statistics based on regression parameters from linear and survival models
2812 as well as those based on correlation parameters) are included. When probing
2813 hypotheses with T-statistics, users may also select a potentially faster null
2814 distribution which is multivariate normal with mean zero and variance
2815 covariance matrix derived from the vector influence function. Results are
2816 reported in terms of adjusted P-values, confidence regions and test statistic
2817 cutoffs. The procedures are directly applicable to identifying differentially
2818 expressed genes in DNA microarray experiments.")
2819 (license license:lgpl3)))
2820
2821 (define-public r-graph
2822 (package
2823 (name "r-graph")
2824 (version "1.68.0")
2825 (source (origin
2826 (method url-fetch)
2827 (uri (bioconductor-uri "graph" version))
2828 (sha256
2829 (base32
2830 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
2831 (build-system r-build-system)
2832 (propagated-inputs
2833 `(("r-biocgenerics" ,r-biocgenerics)))
2834 (home-page "https://bioconductor.org/packages/graph")
2835 (synopsis "Handle graph data structures in R")
2836 (description
2837 "This package implements some simple graph handling capabilities for R.")
2838 (license license:artistic2.0)))
2839
2840 ;; This is a CRAN package, but it depends on a Bioconductor package.
2841 (define-public r-ggm
2842 (package
2843 (name "r-ggm")
2844 (version "2.5")
2845 (source
2846 (origin
2847 (method url-fetch)
2848 (uri (cran-uri "ggm" version))
2849 (sha256
2850 (base32
2851 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
2852 (properties `((upstream-name . "ggm")))
2853 (build-system r-build-system)
2854 (propagated-inputs
2855 `(("r-graph" ,r-graph)
2856 ("r-igraph" ,r-igraph)))
2857 (home-page "https://cran.r-project.org/package=ggm")
2858 (synopsis "Functions for graphical Markov models")
2859 (description
2860 "This package provides functions and datasets for maximum likelihood
2861 fitting of some classes of graphical Markov models.")
2862 (license license:gpl2+)))
2863
2864 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
2865 (define-public r-perfmeas
2866 (package
2867 (name "r-perfmeas")
2868 (version "1.2.1")
2869 (source
2870 (origin
2871 (method url-fetch)
2872 (uri (cran-uri "PerfMeas" version))
2873 (sha256
2874 (base32
2875 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
2876 (properties `((upstream-name . "PerfMeas")))
2877 (build-system r-build-system)
2878 (propagated-inputs
2879 `(("r-graph" ,r-graph)
2880 ("r-limma" ,r-limma)
2881 ("r-rbgl" ,r-rbgl)))
2882 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
2883 (synopsis "Performance measures for ranking and classification tasks")
2884 (description
2885 "This package implements different performance measures for
2886 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
2887 a given recall, F-score for single and multiple classes are available.")
2888 (license license:gpl2+)))
2889
2890 ;; This is a CRAN package, but it depends on a Bioconductor package.
2891 (define-public r-codedepends
2892 (package
2893 (name "r-codedepends")
2894 (version "0.6.5")
2895 (source
2896 (origin
2897 (method url-fetch)
2898 (uri (cran-uri "CodeDepends" version))
2899 (sha256
2900 (base32
2901 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
2902 (properties `((upstream-name . "CodeDepends")))
2903 (build-system r-build-system)
2904 (propagated-inputs
2905 `(("r-codetools" ,r-codetools)
2906 ("r-graph" ,r-graph)
2907 ("r-xml" ,r-xml)))
2908 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
2909 (synopsis "Analysis of R code for reproducible research and code comprehension")
2910 (description
2911 "This package provides tools for analyzing R expressions or blocks of
2912 code and determining the dependencies between them. It focuses on R scripts,
2913 but can be used on the bodies of functions. There are many facilities
2914 including the ability to summarize or get a high-level view of code,
2915 determining dependencies between variables, code improvement suggestions.")
2916 ;; Any version of the GPL
2917 (license (list license:gpl2+ license:gpl3+))))
2918
2919 (define-public r-chippeakanno
2920 (package
2921 (name "r-chippeakanno")
2922 (version "3.24.2")
2923 (source
2924 (origin
2925 (method url-fetch)
2926 (uri (bioconductor-uri "ChIPpeakAnno" version))
2927 (sha256
2928 (base32
2929 "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw"))))
2930 (properties `((upstream-name . "ChIPpeakAnno")))
2931 (build-system r-build-system)
2932 (propagated-inputs
2933 `(("r-annotationdbi" ,r-annotationdbi)
2934 ("r-biocgenerics" ,r-biocgenerics)
2935 ("r-biomart" ,r-biomart)
2936 ("r-biostrings" ,r-biostrings)
2937 ("r-dbi" ,r-dbi)
2938 ("r-dplyr" ,r-dplyr)
2939 ("r-ensembldb" ,r-ensembldb)
2940 ("r-genomeinfodb" ,r-genomeinfodb)
2941 ("r-genomicalignments" ,r-genomicalignments)
2942 ("r-genomicfeatures" ,r-genomicfeatures)
2943 ("r-genomicranges" ,r-genomicranges)
2944 ("r-ggplot2" ,r-ggplot2)
2945 ("r-graph" ,r-graph)
2946 ("r-iranges" ,r-iranges)
2947 ("r-keggrest" ,r-keggrest)
2948 ("r-matrixstats" ,r-matrixstats)
2949 ("r-multtest" ,r-multtest)
2950 ("r-rbgl" ,r-rbgl)
2951 ("r-regioner" ,r-regioner)
2952 ("r-rsamtools" ,r-rsamtools)
2953 ("r-rtracklayer" ,r-rtracklayer)
2954 ("r-s4vectors" ,r-s4vectors)
2955 ("r-summarizedexperiment" ,r-summarizedexperiment)
2956 ("r-venndiagram" ,r-venndiagram)))
2957 (native-inputs
2958 `(("r-knitr" ,r-knitr)))
2959 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
2960 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
2961 (description
2962 "The package includes functions to retrieve the sequences around the peak,
2963 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
2964 custom features such as most conserved elements and other transcription factor
2965 binding sites supplied by users. Starting 2.0.5, new functions have been added
2966 for finding the peaks with bi-directional promoters with summary statistics
2967 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
2968 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
2969 enrichedGO (addGeneIDs).")
2970 (license license:gpl2+)))
2971
2972 (define-public r-matrixgenerics
2973 (package
2974 (name "r-matrixgenerics")
2975 (version "1.2.1")
2976 (source (origin
2977 (method url-fetch)
2978 (uri (bioconductor-uri "MatrixGenerics" version))
2979 (sha256
2980 (base32
2981 "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
2982 (properties
2983 `((upstream-name . "MatrixGenerics")))
2984 (build-system r-build-system)
2985 (propagated-inputs
2986 `(("r-matrixstats" ,r-matrixstats)))
2987 (home-page "https://bioconductor.org/packages/MatrixGenerics")
2988 (synopsis "S4 generic summary statistic functions for matrix-like objects")
2989 (description
2990 "This package provides S4 generic functions modeled after the
2991 @code{matrixStats} API for alternative matrix implementations. Packages with
2992 alternative matrix implementation can depend on this package and implement the
2993 generic functions that are defined here for a useful set of row and column
2994 summary statistics. Other package developers can import this package and
2995 handle a different matrix implementations without worrying about
2996 incompatibilities.")
2997 (license license:artistic2.0)))
2998
2999 (define-public r-marray
3000 (package
3001 (name "r-marray")
3002 (version "1.68.0")
3003 (source (origin
3004 (method url-fetch)
3005 (uri (bioconductor-uri "marray" version))
3006 (sha256
3007 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
3008 (build-system r-build-system)
3009 (propagated-inputs
3010 `(("r-limma" ,r-limma)))
3011 (home-page "https://bioconductor.org/packages/marray")
3012 (synopsis "Exploratory analysis for two-color spotted microarray data")
3013 (description "This package contains class definitions for two-color spotted
3014 microarray data. It also includes functions for data input, diagnostic plots,
3015 normalization and quality checking.")
3016 (license license:lgpl2.0+)))
3017
3018 (define-public r-cghbase
3019 (package
3020 (name "r-cghbase")
3021 (version "1.50.0")
3022 (source (origin
3023 (method url-fetch)
3024 (uri (bioconductor-uri "CGHbase" version))
3025 (sha256
3026 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
3027 (properties `((upstream-name . "CGHbase")))
3028 (build-system r-build-system)
3029 (propagated-inputs
3030 `(("r-biobase" ,r-biobase)
3031 ("r-marray" ,r-marray)))
3032 (home-page "https://bioconductor.org/packages/CGHbase")
3033 (synopsis "Base functions and classes for arrayCGH data analysis")
3034 (description "This package contains functions and classes that are needed by
3035 the @code{arrayCGH} packages.")
3036 (license license:gpl2+)))
3037
3038 (define-public r-cghcall
3039 (package
3040 (name "r-cghcall")
3041 (version "2.52.0")
3042 (source (origin
3043 (method url-fetch)
3044 (uri (bioconductor-uri "CGHcall" version))
3045 (sha256
3046 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
3047 (properties `((upstream-name . "CGHcall")))
3048 (build-system r-build-system)
3049 (propagated-inputs
3050 `(("r-biobase" ,r-biobase)
3051 ("r-cghbase" ,r-cghbase)
3052 ("r-impute" ,r-impute)
3053 ("r-dnacopy" ,r-dnacopy)
3054 ("r-snowfall" ,r-snowfall)))
3055 (home-page "https://bioconductor.org/packages/CGHcall")
3056 (synopsis "Base functions and classes for arrayCGH data analysis")
3057 (description "This package contains functions and classes that are needed by
3058 @code{arrayCGH} packages.")
3059 (license license:gpl2+)))
3060
3061 (define-public r-qdnaseq
3062 (package
3063 (name "r-qdnaseq")
3064 (version "1.26.0")
3065 (source (origin
3066 (method url-fetch)
3067 (uri (bioconductor-uri "QDNAseq" version))
3068 (sha256
3069 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
3070 (properties `((upstream-name . "QDNAseq")))
3071 (build-system r-build-system)
3072 (propagated-inputs
3073 `(("r-biobase" ,r-biobase)
3074 ("r-cghbase" ,r-cghbase)
3075 ("r-cghcall" ,r-cghcall)
3076 ("r-dnacopy" ,r-dnacopy)
3077 ("r-future" ,r-future)
3078 ("r-future-apply" ,r-future-apply)
3079 ("r-genomicranges" ,r-genomicranges)
3080 ("r-iranges" ,r-iranges)
3081 ("r-matrixstats" ,r-matrixstats)
3082 ("r-r-utils" ,r-r-utils)
3083 ("r-rsamtools" ,r-rsamtools)))
3084 (home-page "https://bioconductor.org/packages/QDNAseq")
3085 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
3086 (description "The genome is divided into non-overlapping fixed-sized bins,
3087 number of sequence reads in each counted, adjusted with a simultaneous
3088 two-dimensional loess correction for sequence mappability and GC content, and
3089 filtered to remove spurious regions in the genome. Downstream steps of
3090 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
3091 respectively.")
3092 (license license:gpl2+)))
3093
3094 (define-public r-bayseq
3095 (package
3096 (name "r-bayseq")
3097 (version "2.24.0")
3098 (source
3099 (origin
3100 (method url-fetch)
3101 (uri (bioconductor-uri "baySeq" version))
3102 (sha256
3103 (base32
3104 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
3105 (properties `((upstream-name . "baySeq")))
3106 (build-system r-build-system)
3107 (propagated-inputs
3108 `(("r-abind" ,r-abind)
3109 ("r-edger" ,r-edger)
3110 ("r-genomicranges" ,r-genomicranges)))
3111 (home-page "https://bioconductor.org/packages/baySeq/")
3112 (synopsis "Bayesian analysis of differential expression patterns in count data")
3113 (description
3114 "This package identifies differential expression in high-throughput count
3115 data, such as that derived from next-generation sequencing machines,
3116 calculating estimated posterior likelihoods of differential expression (or
3117 more complex hypotheses) via empirical Bayesian methods.")
3118 (license license:gpl3)))
3119
3120 (define-public r-chipcomp
3121 (package
3122 (name "r-chipcomp")
3123 (version "1.20.0")
3124 (source
3125 (origin
3126 (method url-fetch)
3127 (uri (bioconductor-uri "ChIPComp" version))
3128 (sha256
3129 (base32
3130 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
3131 (properties `((upstream-name . "ChIPComp")))
3132 (build-system r-build-system)
3133 (propagated-inputs
3134 `(("r-biocgenerics" ,r-biocgenerics)
3135 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
3136 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
3137 ("r-genomeinfodb" ,r-genomeinfodb)
3138 ("r-genomicranges" ,r-genomicranges)
3139 ("r-iranges" ,r-iranges)
3140 ("r-limma" ,r-limma)
3141 ("r-rsamtools" ,r-rsamtools)
3142 ("r-rtracklayer" ,r-rtracklayer)
3143 ("r-s4vectors" ,r-s4vectors)))
3144 (home-page "https://bioconductor.org/packages/ChIPComp")
3145 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
3146 (description
3147 "ChIPComp implements a statistical method for quantitative comparison of
3148 multiple ChIP-seq datasets. It detects differentially bound sharp binding
3149 sites across multiple conditions considering matching control in ChIP-seq
3150 datasets.")
3151 ;; Any version of the GPL.
3152 (license license:gpl3+)))
3153
3154 (define-public r-riboprofiling
3155 (package
3156 (name "r-riboprofiling")
3157 (version "1.20.0")
3158 (source
3159 (origin
3160 (method url-fetch)
3161 (uri (bioconductor-uri "RiboProfiling" version))
3162 (sha256
3163 (base32
3164 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
3165 (properties `((upstream-name . "RiboProfiling")))
3166 (build-system r-build-system)
3167 (propagated-inputs
3168 `(("r-biocgenerics" ,r-biocgenerics)
3169 ("r-biostrings" ,r-biostrings)
3170 ("r-data-table" ,r-data-table)
3171 ("r-genomeinfodb" ,r-genomeinfodb)
3172 ("r-genomicalignments" ,r-genomicalignments)
3173 ("r-genomicfeatures" ,r-genomicfeatures)
3174 ("r-genomicranges" ,r-genomicranges)
3175 ("r-ggbio" ,r-ggbio)
3176 ("r-ggplot2" ,r-ggplot2)
3177 ("r-iranges" ,r-iranges)
3178 ("r-plyr" ,r-plyr)
3179 ("r-reshape2" ,r-reshape2)
3180 ("r-rsamtools" ,r-rsamtools)
3181 ("r-rtracklayer" ,r-rtracklayer)
3182 ("r-s4vectors" ,r-s4vectors)
3183 ("r-sqldf" ,r-sqldf)))
3184 (native-inputs
3185 `(("r-knitr" ,r-knitr)))
3186 (home-page "https://bioconductor.org/packages/RiboProfiling/")
3187 (synopsis "Ribosome profiling data analysis")
3188 (description "Starting with a BAM file, this package provides the
3189 necessary functions for quality assessment, read start position recalibration,
3190 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
3191 of count data: pairs, log fold-change, codon frequency and coverage
3192 assessment, principal component analysis on codon coverage.")
3193 (license license:gpl3)))
3194
3195 (define-public r-riboseqr
3196 (package
3197 (name "r-riboseqr")
3198 (version "1.24.0")
3199 (source
3200 (origin
3201 (method url-fetch)
3202 (uri (bioconductor-uri "riboSeqR" version))
3203 (sha256
3204 (base32
3205 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
3206 (properties `((upstream-name . "riboSeqR")))
3207 (build-system r-build-system)
3208 (propagated-inputs
3209 `(("r-abind" ,r-abind)
3210 ("r-bayseq" ,r-bayseq)
3211 ("r-genomeinfodb" ,r-genomeinfodb)
3212 ("r-genomicranges" ,r-genomicranges)
3213 ("r-iranges" ,r-iranges)
3214 ("r-rsamtools" ,r-rsamtools)
3215 ("r-seqlogo" ,r-seqlogo)))
3216 (home-page "https://bioconductor.org/packages/riboSeqR/")
3217 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
3218 (description
3219 "This package provides plotting functions, frameshift detection and
3220 parsing of genetic sequencing data from ribosome profiling experiments.")
3221 (license license:gpl3)))
3222
3223 (define-public r-interactionset
3224 (package ;BROKEN
3225 (name "r-interactionset")
3226 (version "1.18.0")
3227 (source
3228 (origin
3229 (method url-fetch)
3230 (uri (bioconductor-uri "InteractionSet" version))
3231 (sha256
3232 (base32
3233 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
3234 (properties
3235 `((upstream-name . "InteractionSet")))
3236 (build-system r-build-system)
3237 (propagated-inputs
3238 `(("r-biocgenerics" ,r-biocgenerics)
3239 ("r-genomeinfodb" ,r-genomeinfodb)
3240 ("r-genomicranges" ,r-genomicranges)
3241 ("r-iranges" ,r-iranges)
3242 ("r-matrix" ,r-matrix)
3243 ("r-rcpp" ,r-rcpp)
3244 ("r-s4vectors" ,r-s4vectors)
3245 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3246 (native-inputs
3247 `(("r-knitr" ,r-knitr)))
3248 (home-page "https://bioconductor.org/packages/InteractionSet")
3249 (synopsis "Base classes for storing genomic interaction data")
3250 (description
3251 "This package provides the @code{GInteractions},
3252 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
3253 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
3254 experiments.")
3255 (license license:gpl3)))
3256
3257 (define-public r-genomicinteractions
3258 (package
3259 (name "r-genomicinteractions")
3260 (version "1.24.0")
3261 (source
3262 (origin
3263 (method url-fetch)
3264 (uri (bioconductor-uri "GenomicInteractions" version))
3265 (sha256
3266 (base32
3267 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
3268 (properties
3269 `((upstream-name . "GenomicInteractions")))
3270 (build-system r-build-system)
3271 (propagated-inputs
3272 `(("r-biobase" ,r-biobase)
3273 ("r-biocgenerics" ,r-biocgenerics)
3274 ("r-data-table" ,r-data-table)
3275 ("r-dplyr" ,r-dplyr)
3276 ("r-genomeinfodb" ,r-genomeinfodb)
3277 ("r-genomicranges" ,r-genomicranges)
3278 ("r-ggplot2" ,r-ggplot2)
3279 ("r-gridextra" ,r-gridextra)
3280 ("r-gviz" ,r-gviz)
3281 ("r-igraph" ,r-igraph)
3282 ("r-interactionset" ,r-interactionset)
3283 ("r-iranges" ,r-iranges)
3284 ("r-rsamtools" ,r-rsamtools)
3285 ("r-rtracklayer" ,r-rtracklayer)
3286 ("r-s4vectors" ,r-s4vectors)
3287 ("r-stringr" ,r-stringr)))
3288 (native-inputs
3289 `(("r-knitr" ,r-knitr)))
3290 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
3291 (synopsis "R package for handling genomic interaction data")
3292 (description
3293 "This R package provides tools for handling genomic interaction data,
3294 such as ChIA-PET/Hi-C, annotating genomic features with interaction
3295 information and producing various plots and statistics.")
3296 (license license:gpl3)))
3297
3298 (define-public r-ctc
3299 (package
3300 (name "r-ctc")
3301 (version "1.64.0")
3302 (source
3303 (origin
3304 (method url-fetch)
3305 (uri (bioconductor-uri "ctc" version))
3306 (sha256
3307 (base32
3308 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
3309 (build-system r-build-system)
3310 (propagated-inputs `(("r-amap" ,r-amap)))
3311 (home-page "https://bioconductor.org/packages/ctc/")
3312 (synopsis "Cluster and tree conversion")
3313 (description
3314 "This package provides tools for exporting and importing classification
3315 trees and clusters to other programs.")
3316 (license license:gpl2)))
3317
3318 (define-public r-goseq
3319 (package
3320 (name "r-goseq")
3321 (version "1.42.0")
3322 (source
3323 (origin
3324 (method url-fetch)
3325 (uri (bioconductor-uri "goseq" version))
3326 (sha256
3327 (base32
3328 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
3329 (build-system r-build-system)
3330 (propagated-inputs
3331 `(("r-annotationdbi" ,r-annotationdbi)
3332 ("r-biasedurn" ,r-biasedurn)
3333 ("r-biocgenerics" ,r-biocgenerics)
3334 ("r-genelendatabase" ,r-genelendatabase)
3335 ("r-go-db" ,r-go-db)
3336 ("r-mgcv" ,r-mgcv)))
3337 (home-page "https://bioconductor.org/packages/goseq/")
3338 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
3339 (description
3340 "This package provides tools to detect Gene Ontology and/or other user
3341 defined categories which are over/under represented in RNA-seq data.")
3342 (license license:lgpl2.0+)))
3343
3344 (define-public r-glimma
3345 (package
3346 (name "r-glimma")
3347 (version "2.0.0")
3348 (source
3349 (origin
3350 (method url-fetch)
3351 (uri (bioconductor-uri "Glimma" version))
3352 (sha256
3353 (base32
3354 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
3355 (properties `((upstream-name . "Glimma")))
3356 (build-system r-build-system)
3357 (propagated-inputs
3358 `(("r-deseq2" ,r-deseq2)
3359 ("r-edger" ,r-edger)
3360 ("r-htmlwidgets" ,r-htmlwidgets)
3361 ("r-jsonlite" ,r-jsonlite)
3362 ("r-limma" ,r-limma)
3363 ("r-s4vectors" ,r-s4vectors)
3364 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3365 (native-inputs
3366 `(("r-knitr" ,r-knitr)))
3367 (home-page "https://github.com/Shians/Glimma")
3368 (synopsis "Interactive HTML graphics")
3369 (description
3370 "This package generates interactive visualisations for analysis of
3371 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
3372 HTML page. The interactions are built on top of the popular static
3373 representations of analysis results in order to provide additional
3374 information.")
3375 (license license:lgpl3)))
3376
3377 (define-public r-rots
3378 (package
3379 (name "r-rots")
3380 (version "1.18.0")
3381 (source
3382 (origin
3383 (method url-fetch)
3384 (uri (bioconductor-uri "ROTS" version))
3385 (sha256
3386 (base32
3387 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
3388 (properties `((upstream-name . "ROTS")))
3389 (build-system r-build-system)
3390 (propagated-inputs
3391 `(("r-biobase" ,r-biobase)
3392 ("r-rcpp" ,r-rcpp)))
3393 (home-page "https://bioconductor.org/packages/ROTS/")
3394 (synopsis "Reproducibility-Optimized Test Statistic")
3395 (description
3396 "This package provides tools for calculating the
3397 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
3398 in omics data.")
3399 (license license:gpl2+)))
3400
3401 (define-public r-plgem
3402 (package
3403 (name "r-plgem")
3404 (version "1.62.0")
3405 (source
3406 (origin
3407 (method url-fetch)
3408 (uri (bioconductor-uri "plgem" version))
3409 (sha256
3410 (base32
3411 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
3412 (build-system r-build-system)
3413 (propagated-inputs
3414 `(("r-biobase" ,r-biobase)
3415 ("r-mass" ,r-mass)))
3416 (home-page "http://www.genopolis.it")
3417 (synopsis "Detect differential expression in microarray and proteomics datasets")
3418 (description
3419 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
3420 model the variance-versus-mean dependence that exists in a variety of
3421 genome-wide datasets, including microarray and proteomics data. The use of
3422 PLGEM has been shown to improve the detection of differentially expressed
3423 genes or proteins in these datasets.")
3424 (license license:gpl2)))
3425
3426 (define-public r-inspect
3427 (package
3428 (name "r-inspect")
3429 (version "1.20.0")
3430 (source
3431 (origin
3432 (method url-fetch)
3433 (uri (bioconductor-uri "INSPEcT" version))
3434 (sha256
3435 (base32
3436 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
3437 (properties `((upstream-name . "INSPEcT")))
3438 (build-system r-build-system)
3439 (propagated-inputs
3440 `(("r-biobase" ,r-biobase)
3441 ("r-biocgenerics" ,r-biocgenerics)
3442 ("r-biocparallel" ,r-biocparallel)
3443 ("r-deseq2" ,r-deseq2)
3444 ("r-desolve" ,r-desolve)
3445 ("r-gdata" ,r-gdata)
3446 ("r-genomeinfodb" ,r-genomeinfodb)
3447 ("r-genomicalignments" ,r-genomicalignments)
3448 ("r-genomicfeatures" ,r-genomicfeatures)
3449 ("r-genomicranges" ,r-genomicranges)
3450 ("r-iranges" ,r-iranges)
3451 ("r-kernsmooth" ,r-kernsmooth)
3452 ("r-plgem" ,r-plgem)
3453 ("r-proc" ,r-proc)
3454 ("r-rootsolve" ,r-rootsolve)
3455 ("r-rsamtools" ,r-rsamtools)
3456 ("r-rtracklayer" ,r-rtracklayer)
3457 ("r-s4vectors" ,r-s4vectors)
3458 ("r-shiny" ,r-shiny)
3459 ("r-summarizedexperiment" ,r-summarizedexperiment)
3460 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
3461 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
3462 (native-inputs
3463 `(("r-knitr" ,r-knitr)))
3464 (home-page "https://bioconductor.org/packages/INSPEcT")
3465 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
3466 (description
3467 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
3468 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
3469 order to evaluate synthesis, processing and degradation rates and assess via
3470 modeling the rates that determines changes in mature mRNA levels.")
3471 (license license:gpl2)))
3472
3473 (define-public r-dnabarcodes
3474 (package
3475 (name "r-dnabarcodes")
3476 (version "1.20.0")
3477 (source
3478 (origin
3479 (method url-fetch)
3480 (uri (bioconductor-uri "DNABarcodes" version))
3481 (sha256
3482 (base32
3483 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
3484 (properties `((upstream-name . "DNABarcodes")))
3485 (build-system r-build-system)
3486 (propagated-inputs
3487 `(("r-bh" ,r-bh)
3488 ("r-matrix" ,r-matrix)
3489 ("r-rcpp" ,r-rcpp)))
3490 (native-inputs
3491 `(("r-knitr" ,r-knitr)))
3492 (home-page "https://bioconductor.org/packages/DNABarcodes")
3493 (synopsis "Create and analyze DNA barcodes")
3494 (description
3495 "This package offers tools to create DNA barcode sets capable of
3496 correcting insertion, deletion, and substitution errors. Existing barcodes
3497 can be analyzed regarding their minimal, maximal and average distances between
3498 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
3499 demultiplexed, i.e. assigned to their original reference barcode.")
3500 (license license:gpl2)))
3501
3502 (define-public r-ruvseq
3503 (package
3504 (name "r-ruvseq")
3505 (version "1.24.0")
3506 (source
3507 (origin
3508 (method url-fetch)
3509 (uri (bioconductor-uri "RUVSeq" version))
3510 (sha256
3511 (base32
3512 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
3513 (properties `((upstream-name . "RUVSeq")))
3514 (build-system r-build-system)
3515 (propagated-inputs
3516 `(("r-biobase" ,r-biobase)
3517 ("r-edaseq" ,r-edaseq)
3518 ("r-edger" ,r-edger)
3519 ("r-mass" ,r-mass)))
3520 (native-inputs
3521 `(("r-knitr" ,r-knitr)))
3522 (home-page "https://github.com/drisso/RUVSeq")
3523 (synopsis "Remove unwanted variation from RNA-Seq data")
3524 (description
3525 "This package implements methods to @dfn{remove unwanted variation} (RUV)
3526 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
3527 samples.")
3528 (license license:artistic2.0)))
3529
3530 (define-public r-biocneighbors
3531 (package
3532 (name "r-biocneighbors")
3533 (version "1.8.2")
3534 (source
3535 (origin
3536 (method url-fetch)
3537 (uri (bioconductor-uri "BiocNeighbors" version))
3538 (sha256
3539 (base32
3540 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
3541 (properties `((upstream-name . "BiocNeighbors")))
3542 (build-system r-build-system)
3543 (propagated-inputs
3544 `(("r-biocparallel" ,r-biocparallel)
3545 ("r-matrix" ,r-matrix)
3546 ("r-rcpp" ,r-rcpp)
3547 ("r-rcpphnsw" ,r-rcpphnsw)
3548 ("r-s4vectors" ,r-s4vectors)))
3549 (native-inputs
3550 `(("r-knitr" ,r-knitr)))
3551 (home-page "https://bioconductor.org/packages/BiocNeighbors")
3552 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
3553 (description
3554 "This package implements exact and approximate methods for nearest
3555 neighbor detection, in a framework that allows them to be easily switched
3556 within Bioconductor packages or workflows. The exact algorithm is implemented
3557 using pre-clustering with the k-means algorithm. Functions are also provided
3558 to search for all neighbors within a given distance. Parallelization is
3559 achieved for all methods using the BiocParallel framework.")
3560 (license license:gpl3)))
3561
3562 (define-public r-biocsingular
3563 (package
3564 (name "r-biocsingular")
3565 (version "1.6.0")
3566 (source
3567 (origin
3568 (method url-fetch)
3569 (uri (bioconductor-uri "BiocSingular" version))
3570 (sha256
3571 (base32
3572 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
3573 (properties `((upstream-name . "BiocSingular")))
3574 (build-system r-build-system)
3575 (propagated-inputs
3576 `(("r-beachmat" ,r-beachmat)
3577 ("r-biocgenerics" ,r-biocgenerics)
3578 ("r-biocparallel" ,r-biocparallel)
3579 ("r-delayedarray" ,r-delayedarray)
3580 ("r-irlba" ,r-irlba)
3581 ("r-matrix" ,r-matrix)
3582 ("r-rcpp" ,r-rcpp)
3583 ("r-rsvd" ,r-rsvd)
3584 ("r-s4vectors" ,r-s4vectors)))
3585 (native-inputs
3586 `(("r-knitr" ,r-knitr)))
3587 (home-page "https://github.com/LTLA/BiocSingular")
3588 (synopsis "Singular value decomposition for Bioconductor packages")
3589 (description
3590 "This package implements exact and approximate methods for singular value
3591 decomposition and principal components analysis, in a framework that allows
3592 them to be easily switched within Bioconductor packages or workflows. Where
3593 possible, parallelization is achieved using the BiocParallel framework.")
3594 (license license:gpl3)))
3595
3596 (define-public r-destiny
3597 (package
3598 (name "r-destiny")
3599 (version "3.4.0")
3600 (source
3601 (origin
3602 (method url-fetch)
3603 (uri (bioconductor-uri "destiny" version))
3604 (sha256
3605 (base32
3606 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
3607 (build-system r-build-system)
3608 (propagated-inputs
3609 `(("r-biobase" ,r-biobase)
3610 ("r-biocgenerics" ,r-biocgenerics)
3611 ("r-ggplot-multistats" ,r-ggplot-multistats)
3612 ("r-ggplot2" ,r-ggplot2)
3613 ("r-ggthemes" ,r-ggthemes)
3614 ("r-irlba" ,r-irlba)
3615 ("r-knn-covertree" ,r-knn-covertree)
3616 ("r-matrix" ,r-matrix)
3617 ("r-pcamethods" ,r-pcamethods)
3618 ("r-proxy" ,r-proxy)
3619 ("r-rcpp" ,r-rcpp)
3620 ("r-rcppeigen" ,r-rcppeigen)
3621 ("r-rcpphnsw" ,r-rcpphnsw)
3622 ("r-rspectra" ,r-rspectra)
3623 ("r-scales" ,r-scales)
3624 ("r-scatterplot3d" ,r-scatterplot3d)
3625 ("r-singlecellexperiment" ,r-singlecellexperiment)
3626 ("r-smoother" ,r-smoother)
3627 ("r-summarizedexperiment" ,r-summarizedexperiment)
3628 ("r-tidyr" ,r-tidyr)
3629 ("r-tidyselect" ,r-tidyselect)
3630 ("r-vim" ,r-vim)))
3631 (native-inputs
3632 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
3633 (home-page "https://bioconductor.org/packages/destiny/")
3634 (synopsis "Create and plot diffusion maps")
3635 (description "This package provides tools to create and plot diffusion
3636 maps.")
3637 ;; Any version of the GPL
3638 (license license:gpl3+)))
3639
3640 (define-public r-savr
3641 (package
3642 (name "r-savr")
3643 (version "1.28.0")
3644 (source
3645 (origin
3646 (method url-fetch)
3647 (uri (bioconductor-uri "savR" version))
3648 (sha256
3649 (base32
3650 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
3651 (properties `((upstream-name . "savR")))
3652 (build-system r-build-system)
3653 (propagated-inputs
3654 `(("r-ggplot2" ,r-ggplot2)
3655 ("r-gridextra" ,r-gridextra)
3656 ("r-reshape2" ,r-reshape2)
3657 ("r-scales" ,r-scales)
3658 ("r-xml" ,r-xml)))
3659 (home-page "https://github.com/bcalder/savR")
3660 (synopsis "Parse and analyze Illumina SAV files")
3661 (description
3662 "This package provides tools to parse Illumina Sequence Analysis
3663 Viewer (SAV) files, access data, and generate QC plots.")
3664 (license license:agpl3+)))
3665
3666 (define-public r-chipexoqual
3667 (package
3668 (name "r-chipexoqual")
3669 (version "1.14.0")
3670 (source
3671 (origin
3672 (method url-fetch)
3673 (uri (bioconductor-uri "ChIPexoQual" version))
3674 (sha256
3675 (base32
3676 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
3677 (properties `((upstream-name . "ChIPexoQual")))
3678 (build-system r-build-system)
3679 (propagated-inputs
3680 `(("r-biocparallel" ,r-biocparallel)
3681 ("r-biovizbase" ,r-biovizbase)
3682 ("r-broom" ,r-broom)
3683 ("r-data-table" ,r-data-table)
3684 ("r-dplyr" ,r-dplyr)
3685 ("r-genomeinfodb" ,r-genomeinfodb)
3686 ("r-genomicalignments" ,r-genomicalignments)
3687 ("r-genomicranges" ,r-genomicranges)
3688 ("r-ggplot2" ,r-ggplot2)
3689 ("r-hexbin" ,r-hexbin)
3690 ("r-iranges" ,r-iranges)
3691 ("r-rcolorbrewer" ,r-rcolorbrewer)
3692 ("r-rmarkdown" ,r-rmarkdown)
3693 ("r-rsamtools" ,r-rsamtools)
3694 ("r-s4vectors" ,r-s4vectors)
3695 ("r-scales" ,r-scales)
3696 ("r-viridis" ,r-viridis)))
3697 (native-inputs
3698 `(("r-knitr" ,r-knitr)))
3699 (home-page "https://github.com/keleslab/ChIPexoQual")
3700 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
3701 (description
3702 "This package provides a quality control pipeline for ChIP-exo/nexus
3703 sequencing data.")
3704 (license license:gpl2+)))
3705
3706 (define-public r-copynumber
3707 (package
3708 (name "r-copynumber")
3709 (version "1.30.0")
3710 (source (origin
3711 (method url-fetch)
3712 (uri (bioconductor-uri "copynumber" version))
3713 (sha256
3714 (base32
3715 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
3716 (build-system r-build-system)
3717 (propagated-inputs
3718 `(("r-s4vectors" ,r-s4vectors)
3719 ("r-iranges" ,r-iranges)
3720 ("r-genomicranges" ,r-genomicranges)
3721 ("r-biocgenerics" ,r-biocgenerics)))
3722 (home-page "https://bioconductor.org/packages/copynumber")
3723 (synopsis "Segmentation of single- and multi-track copy number data")
3724 (description
3725 "This package segments single- and multi-track copy number data by a
3726 penalized least squares regression method.")
3727 (license license:artistic2.0)))
3728
3729 (define-public r-dnacopy
3730 (package
3731 (name "r-dnacopy")
3732 (version "1.64.0")
3733 (source
3734 (origin
3735 (method url-fetch)
3736 (uri (bioconductor-uri "DNAcopy" version))
3737 (sha256
3738 (base32
3739 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
3740 (properties `((upstream-name . "DNAcopy")))
3741 (build-system r-build-system)
3742 (native-inputs `(("gfortran" ,gfortran)))
3743 (home-page "https://bioconductor.org/packages/DNAcopy")
3744 (synopsis "DNA copy number data analysis")
3745 (description
3746 "This package implements the @dfn{circular binary segmentation} (CBS)
3747 algorithm to segment DNA copy number data and identify genomic regions with
3748 abnormal copy number.")
3749 (license license:gpl2+)))
3750
3751 ;; This is a CRAN package, but it uncharacteristically depends on a
3752 ;; Bioconductor package.
3753 (define-public r-htscluster
3754 (package
3755 (name "r-htscluster")
3756 (version "2.0.8")
3757 (source
3758 (origin
3759 (method url-fetch)
3760 (uri (cran-uri "HTSCluster" version))
3761 (sha256
3762 (base32
3763 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
3764 (properties `((upstream-name . "HTSCluster")))
3765 (build-system r-build-system)
3766 (propagated-inputs
3767 `(("r-capushe" ,r-capushe)
3768 ("r-edger" ,r-edger)
3769 ("r-plotrix" ,r-plotrix)))
3770 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
3771 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
3772 (description
3773 "This package provides a Poisson mixture model is implemented to cluster
3774 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
3775 estimation is performed using either the EM or CEM algorithm, and the slope
3776 heuristics are used for model selection (i.e., to choose the number of
3777 clusters).")
3778 (license license:gpl3+)))
3779
3780 (define-public r-deds
3781 (package
3782 (name "r-deds")
3783 (version "1.60.0")
3784 (source
3785 (origin
3786 (method url-fetch)
3787 (uri (bioconductor-uri "DEDS" version))
3788 (sha256
3789 (base32
3790 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
3791 (properties `((upstream-name . "DEDS")))
3792 (build-system r-build-system)
3793 (home-page "https://bioconductor.org/packages/DEDS/")
3794 (synopsis "Differential expression via distance summary for microarray data")
3795 (description
3796 "This library contains functions that calculate various statistics of
3797 differential expression for microarray data, including t statistics, fold
3798 change, F statistics, SAM, moderated t and F statistics and B statistics. It
3799 also implements a new methodology called DEDS (Differential Expression via
3800 Distance Summary), which selects differentially expressed genes by integrating
3801 and summarizing a set of statistics using a weighted distance approach.")
3802 ;; Any version of the LGPL.
3803 (license license:lgpl3+)))
3804
3805 ;; This is a CRAN package, but since it depends on a Bioconductor package we
3806 ;; put it here.
3807 (define-public r-nbpseq
3808 (package
3809 (name "r-nbpseq")
3810 (version "0.3.0")
3811 (source
3812 (origin
3813 (method url-fetch)
3814 (uri (cran-uri "NBPSeq" version))
3815 (sha256
3816 (base32
3817 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
3818 (properties `((upstream-name . "NBPSeq")))
3819 (build-system r-build-system)
3820 (propagated-inputs
3821 `(("r-qvalue" ,r-qvalue)))
3822 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
3823 (synopsis "Negative binomial models for RNA-Seq data")
3824 (description
3825 "This package provides negative binomial models for two-group comparisons
3826 and regression inferences from RNA-sequencing data.")
3827 (license license:gpl2)))
3828
3829 (define-public r-ebseq
3830 (package
3831 (name "r-ebseq")
3832 (version "1.30.0")
3833 (source
3834 (origin
3835 (method url-fetch)
3836 (uri (bioconductor-uri "EBSeq" version))
3837 (sha256
3838 (base32
3839 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
3840 (properties `((upstream-name . "EBSeq")))
3841 (build-system r-build-system)
3842 (propagated-inputs
3843 `(("r-blockmodeling" ,r-blockmodeling)
3844 ("r-gplots" ,r-gplots)
3845 ("r-testthat" ,r-testthat)))
3846 (home-page "https://bioconductor.org/packages/EBSeq")
3847 (synopsis "Differential expression analysis of RNA-seq data")
3848 (description
3849 "This package provides tools for differential expression analysis at both
3850 gene and isoform level using RNA-seq data")
3851 (license license:artistic2.0)))
3852
3853 (define-public r-karyoploter
3854 (package
3855 (name "r-karyoploter")
3856 (version "1.16.0")
3857 (source (origin
3858 (method url-fetch)
3859 (uri (bioconductor-uri "karyoploteR" version))
3860 (sha256
3861 (base32
3862 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
3863 (build-system r-build-system)
3864 (propagated-inputs
3865 `(("r-annotationdbi" ,r-annotationdbi)
3866 ("r-bamsignals" ,r-bamsignals)
3867 ("r-bezier" ,r-bezier)
3868 ("r-biovizbase" ,r-biovizbase)
3869 ("r-digest" ,r-digest)
3870 ("r-genomeinfodb" ,r-genomeinfodb)
3871 ("r-genomicfeatures" ,r-genomicfeatures)
3872 ("r-genomicranges" ,r-genomicranges)
3873 ("r-iranges" ,r-iranges)
3874 ("r-memoise" ,r-memoise)
3875 ("r-regioner" ,r-regioner)
3876 ("r-rsamtools" ,r-rsamtools)
3877 ("r-rtracklayer" ,r-rtracklayer)
3878 ("r-s4vectors" ,r-s4vectors)
3879 ("r-variantannotation" ,r-variantannotation)))
3880 (native-inputs
3881 `(("r-knitr" ,r-knitr)))
3882 (home-page "https://bioconductor.org/packages/karyoploteR/")
3883 (synopsis "Plot customizable linear genomes displaying arbitrary data")
3884 (description "This package creates karyotype plots of arbitrary genomes and
3885 offers a complete set of functions to plot arbitrary data on them. It mimics
3886 many R base graphics functions coupling them with a coordinate change function
3887 automatically mapping the chromosome and data coordinates into the plot
3888 coordinates.")
3889 (license license:artistic2.0)))
3890
3891 (define-public r-lpsymphony
3892 (package
3893 (name "r-lpsymphony")
3894 (version "1.18.0")
3895 (source
3896 (origin
3897 (method url-fetch)
3898 (uri (bioconductor-uri "lpsymphony" version))
3899 (sha256
3900 (base32
3901 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
3902 (build-system r-build-system)
3903 (inputs
3904 `(("zlib" ,zlib)))
3905 (native-inputs
3906 `(("pkg-config" ,pkg-config)
3907 ("r-knitr" ,r-knitr)))
3908 (home-page "https://r-forge.r-project.org/projects/rsymphony")
3909 (synopsis "Symphony integer linear programming solver in R")
3910 (description
3911 "This package was derived from Rsymphony. The package provides an R
3912 interface to SYMPHONY, a linear programming solver written in C++. The main
3913 difference between this package and Rsymphony is that it includes the solver
3914 source code, while Rsymphony expects to find header and library files on the
3915 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
3916 to install interface to SYMPHONY.")
3917 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
3918 ;; lpsimphony is released under the same terms.
3919 (license license:epl1.0)))
3920
3921 (define-public r-ihw
3922 (package
3923 (name "r-ihw")
3924 (version "1.18.0")
3925 (source
3926 (origin
3927 (method url-fetch)
3928 (uri (bioconductor-uri "IHW" version))
3929 (sha256
3930 (base32
3931 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
3932 (properties `((upstream-name . "IHW")))
3933 (build-system r-build-system)
3934 (propagated-inputs
3935 `(("r-biocgenerics" ,r-biocgenerics)
3936 ("r-fdrtool" ,r-fdrtool)
3937 ("r-lpsymphony" ,r-lpsymphony)
3938 ("r-slam" ,r-slam)))
3939 (native-inputs
3940 `(("r-knitr" ,r-knitr)))
3941 (home-page "https://bioconductor.org/packages/IHW")
3942 (synopsis "Independent hypothesis weighting")
3943 (description
3944 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
3945 procedure that increases power compared to the method of Benjamini and
3946 Hochberg by assigning data-driven weights to each hypothesis. The input to
3947 IHW is a two-column table of p-values and covariates. The covariate can be
3948 any continuous-valued or categorical variable that is thought to be
3949 informative on the statistical properties of each hypothesis test, while it is
3950 independent of the p-value under the null hypothesis.")
3951 (license license:artistic2.0)))
3952
3953 (define-public r-icobra
3954 (package
3955 (name "r-icobra")
3956 (version "1.18.0")
3957 (source
3958 (origin
3959 (method url-fetch)
3960 (uri (bioconductor-uri "iCOBRA" version))
3961 (sha256
3962 (base32
3963 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
3964 (properties `((upstream-name . "iCOBRA")))
3965 (build-system r-build-system)
3966 (propagated-inputs
3967 `(("r-dplyr" ,r-dplyr)
3968 ("r-dt" ,r-dt)
3969 ("r-ggplot2" ,r-ggplot2)
3970 ("r-limma" ,r-limma)
3971 ("r-reshape2" ,r-reshape2)
3972 ("r-rocr" ,r-rocr)
3973 ("r-scales" ,r-scales)
3974 ("r-shiny" ,r-shiny)
3975 ("r-shinybs" ,r-shinybs)
3976 ("r-shinydashboard" ,r-shinydashboard)
3977 ("r-upsetr" ,r-upsetr)))
3978 (native-inputs
3979 `(("r-knitr" ,r-knitr)))
3980 (home-page "https://bioconductor.org/packages/iCOBRA")
3981 (synopsis "Comparison and visualization of ranking and assignment methods")
3982 (description
3983 "This package provides functions for calculation and visualization of
3984 performance metrics for evaluation of ranking and binary
3985 classification (assignment) methods. It also contains a Shiny application for
3986 interactive exploration of results.")
3987 (license license:gpl2+)))
3988
3989 (define-public r-mast
3990 (package
3991 (name "r-mast")
3992 (version "1.16.0")
3993 (source
3994 (origin
3995 (method url-fetch)
3996 (uri (bioconductor-uri "MAST" version))
3997 (sha256
3998 (base32
3999 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
4000 (properties `((upstream-name . "MAST")))
4001 (build-system r-build-system)
4002 (propagated-inputs
4003 `(("r-abind" ,r-abind)
4004 ("r-biobase" ,r-biobase)
4005 ("r-biocgenerics" ,r-biocgenerics)
4006 ("r-data-table" ,r-data-table)
4007 ("r-ggplot2" ,r-ggplot2)
4008 ("r-plyr" ,r-plyr)
4009 ("r-progress" ,r-progress)
4010 ("r-reshape2" ,r-reshape2)
4011 ("r-s4vectors" ,r-s4vectors)
4012 ("r-singlecellexperiment" ,r-singlecellexperiment)
4013 ("r-stringr" ,r-stringr)
4014 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4015 (native-inputs
4016 `(("r-knitr" ,r-knitr)))
4017 (home-page "https://github.com/RGLab/MAST/")
4018 (synopsis "Model-based analysis of single cell transcriptomics")
4019 (description
4020 "This package provides methods and models for handling zero-inflated
4021 single cell assay data.")
4022 (license license:gpl2+)))
4023
4024 (define-public r-monocle
4025 (package
4026 (name "r-monocle")
4027 (version "2.18.0")
4028 (source
4029 (origin
4030 (method url-fetch)
4031 (uri (bioconductor-uri "monocle" version))
4032 (sha256
4033 (base32
4034 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
4035 (build-system r-build-system)
4036 (propagated-inputs
4037 `(("r-biobase" ,r-biobase)
4038 ("r-biocgenerics" ,r-biocgenerics)
4039 ("r-biocviews" ,r-biocviews)
4040 ("r-cluster" ,r-cluster)
4041 ("r-combinat" ,r-combinat)
4042 ("r-ddrtree" ,r-ddrtree)
4043 ("r-densityclust" ,r-densityclust)
4044 ("r-dplyr" ,r-dplyr)
4045 ("r-fastica" ,r-fastica)
4046 ("r-ggplot2" ,r-ggplot2)
4047 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
4048 ("r-igraph" ,r-igraph)
4049 ("r-irlba" ,r-irlba)
4050 ("r-limma" ,r-limma)
4051 ("r-mass" ,r-mass)
4052 ("r-matrix" ,r-matrix)
4053 ("r-matrixstats" ,r-matrixstats)
4054 ("r-pheatmap" ,r-pheatmap)
4055 ("r-plyr" ,r-plyr)
4056 ("r-proxy" ,r-proxy)
4057 ("r-qlcmatrix" ,r-qlcmatrix)
4058 ("r-rann" ,r-rann)
4059 ("r-rcpp" ,r-rcpp)
4060 ("r-reshape2" ,r-reshape2)
4061 ("r-rtsne" ,r-rtsne)
4062 ("r-slam" ,r-slam)
4063 ("r-stringr" ,r-stringr)
4064 ("r-tibble" ,r-tibble)
4065 ("r-vgam" ,r-vgam)
4066 ("r-viridis" ,r-viridis)))
4067 (native-inputs
4068 `(("r-knitr" ,r-knitr)))
4069 (home-page "https://bioconductor.org/packages/monocle")
4070 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
4071 (description
4072 "Monocle performs differential expression and time-series analysis for
4073 single-cell expression experiments. It orders individual cells according to
4074 progress through a biological process, without knowing ahead of time which
4075 genes define progress through that process. Monocle also performs
4076 differential expression analysis, clustering, visualization, and other useful
4077 tasks on single cell expression data. It is designed to work with RNA-Seq and
4078 qPCR data, but could be used with other types as well.")
4079 (license license:artistic2.0)))
4080
4081 (define-public r-monocle3
4082 (package
4083 (name "r-monocle3")
4084 (version "0.1.2")
4085 (source
4086 (origin
4087 (method git-fetch)
4088 (uri (git-reference
4089 (url "https://github.com/cole-trapnell-lab/monocle3")
4090 (commit version)))
4091 (file-name (git-file-name name version))
4092 (sha256
4093 (base32
4094 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
4095 (build-system r-build-system)
4096 (propagated-inputs
4097 `(("r-biobase" ,r-biobase)
4098 ("r-biocgenerics" ,r-biocgenerics)
4099 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
4100 ("r-dplyr" ,r-dplyr)
4101 ("r-ggplot2" ,r-ggplot2)
4102 ("r-ggrepel" ,r-ggrepel)
4103 ("r-grr" ,r-grr)
4104 ("r-htmlwidgets" ,r-htmlwidgets)
4105 ("r-igraph" ,r-igraph)
4106 ("r-irlba" ,r-irlba)
4107 ("r-limma" ,r-limma)
4108 ("r-lmtest" ,r-lmtest)
4109 ("r-mass" ,r-mass)
4110 ("r-matrix" ,r-matrix)
4111 ("r-matrix-utils" ,r-matrix-utils)
4112 ("r-pbapply" ,r-pbapply)
4113 ("r-pbmcapply" ,r-pbmcapply)
4114 ("r-pheatmap" ,r-pheatmap)
4115 ("r-plotly" ,r-plotly)
4116 ("r-pryr" ,r-pryr)
4117 ("r-proxy" ,r-proxy)
4118 ("r-pscl" ,r-pscl)
4119 ("r-purrr" ,r-purrr)
4120 ("r-rann" ,r-rann)
4121 ("r-rcpp" ,r-rcpp)
4122 ("r-rcppparallel" ,r-rcppparallel)
4123 ("r-reshape2" ,r-reshape2)
4124 ("r-reticulate" ,r-reticulate)
4125 ("r-rhpcblasctl" ,r-rhpcblasctl)
4126 ("r-rtsne" ,r-rtsne)
4127 ("r-shiny" ,r-shiny)
4128 ("r-slam" ,r-slam)
4129 ("r-spdep" ,r-spdep)
4130 ("r-speedglm" ,r-speedglm)
4131 ("r-stringr" ,r-stringr)
4132 ("r-singlecellexperiment" ,r-singlecellexperiment)
4133 ("r-tibble" ,r-tibble)
4134 ("r-tidyr" ,r-tidyr)
4135 ("r-uwot" ,r-uwot)
4136 ("r-viridis" ,r-viridis)))
4137 (home-page "https://github.com/cole-trapnell-lab/monocle3")
4138 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
4139 (description
4140 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
4141 (license license:expat)))
4142
4143 (define-public r-noiseq
4144 (package
4145 (name "r-noiseq")
4146 (version "2.34.0")
4147 (source
4148 (origin
4149 (method url-fetch)
4150 (uri (bioconductor-uri "NOISeq" version))
4151 (sha256
4152 (base32
4153 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
4154 (properties `((upstream-name . "NOISeq")))
4155 (build-system r-build-system)
4156 (propagated-inputs
4157 `(("r-biobase" ,r-biobase)
4158 ("r-matrix" ,r-matrix)))
4159 (home-page "https://bioconductor.org/packages/NOISeq")
4160 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
4161 (description
4162 "This package provides tools to support the analysis of RNA-seq
4163 expression data or other similar kind of data. It provides exploratory plots
4164 to evaluate saturation, count distribution, expression per chromosome, type of
4165 detected features, features length, etc. It also supports the analysis of
4166 differential expression between two experimental conditions with no parametric
4167 assumptions.")
4168 (license license:artistic2.0)))
4169
4170 (define-public r-scdd
4171 (package
4172 (name "r-scdd")
4173 (version "1.14.0")
4174 (source
4175 (origin
4176 (method url-fetch)
4177 (uri (bioconductor-uri "scDD" version))
4178 (sha256
4179 (base32
4180 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
4181 (properties `((upstream-name . "scDD")))
4182 (build-system r-build-system)
4183 (propagated-inputs
4184 `(("r-arm" ,r-arm)
4185 ("r-biocparallel" ,r-biocparallel)
4186 ("r-ebseq" ,r-ebseq)
4187 ("r-fields" ,r-fields)
4188 ("r-ggplot2" ,r-ggplot2)
4189 ("r-mclust" ,r-mclust)
4190 ("r-outliers" ,r-outliers)
4191 ("r-s4vectors" ,r-s4vectors)
4192 ("r-scran" ,r-scran)
4193 ("r-singlecellexperiment" ,r-singlecellexperiment)
4194 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4195 (native-inputs
4196 `(("r-knitr" ,r-knitr)))
4197 (home-page "https://github.com/kdkorthauer/scDD")
4198 (synopsis "Mixture modeling of single-cell RNA-seq data")
4199 (description
4200 "This package implements a method to analyze single-cell RNA-seq data
4201 utilizing flexible Dirichlet Process mixture models. Genes with differential
4202 distributions of expression are classified into several interesting patterns
4203 of differences between two conditions. The package also includes functions
4204 for simulating data with these patterns from negative binomial
4205 distributions.")
4206 (license license:gpl2)))
4207
4208 (define-public r-scone
4209 (package
4210 (name "r-scone")
4211 (version "1.14.0")
4212 (source
4213 (origin
4214 (method url-fetch)
4215 (uri (bioconductor-uri "scone" version))
4216 (sha256
4217 (base32
4218 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
4219 (build-system r-build-system)
4220 (propagated-inputs
4221 `(("r-aroma-light" ,r-aroma-light)
4222 ("r-biocparallel" ,r-biocparallel)
4223 ("r-boot" ,r-boot)
4224 ("r-class" ,r-class)
4225 ("r-cluster" ,r-cluster)
4226 ("r-compositions" ,r-compositions)
4227 ("r-diptest" ,r-diptest)
4228 ("r-edger" ,r-edger)
4229 ("r-fpc" ,r-fpc)
4230 ("r-gplots" ,r-gplots)
4231 ("r-hexbin" ,r-hexbin)
4232 ("r-limma" ,r-limma)
4233 ("r-matrixstats" ,r-matrixstats)
4234 ("r-mixtools" ,r-mixtools)
4235 ("r-rarpack" ,r-rarpack)
4236 ("r-rcolorbrewer" ,r-rcolorbrewer)
4237 ("r-rhdf5" ,r-rhdf5)
4238 ("r-ruvseq" ,r-ruvseq)
4239 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4240 (native-inputs
4241 `(("r-knitr" ,r-knitr)))
4242 (home-page "https://bioconductor.org/packages/scone")
4243 (synopsis "Single cell overview of normalized expression data")
4244 (description
4245 "SCONE is an R package for comparing and ranking the performance of
4246 different normalization schemes for single-cell RNA-seq and other
4247 high-throughput analyses.")
4248 (license license:artistic2.0)))
4249
4250 (define-public r-geoquery
4251 (package
4252 (name "r-geoquery")
4253 (version "2.58.0")
4254 (source
4255 (origin
4256 (method url-fetch)
4257 (uri (bioconductor-uri "GEOquery" version))
4258 (sha256
4259 (base32
4260 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
4261 (properties `((upstream-name . "GEOquery")))
4262 (build-system r-build-system)
4263 (propagated-inputs
4264 `(("r-biobase" ,r-biobase)
4265 ("r-dplyr" ,r-dplyr)
4266 ("r-httr" ,r-httr)
4267 ("r-limma" ,r-limma)
4268 ("r-magrittr" ,r-magrittr)
4269 ("r-readr" ,r-readr)
4270 ("r-tidyr" ,r-tidyr)
4271 ("r-xml2" ,r-xml2)))
4272 (native-inputs
4273 `(("r-knitr" ,r-knitr)))
4274 (home-page "https://github.com/seandavi/GEOquery/")
4275 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
4276 (description
4277 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
4278 microarray data. Given the rich and varied nature of this resource, it is
4279 only natural to want to apply BioConductor tools to these data. GEOquery is
4280 the bridge between GEO and BioConductor.")
4281 (license license:gpl2)))
4282
4283 (define-public r-illuminaio
4284 (package
4285 (name "r-illuminaio")
4286 (version "0.32.0")
4287 (source
4288 (origin
4289 (method url-fetch)
4290 (uri (bioconductor-uri "illuminaio" version))
4291 (sha256
4292 (base32
4293 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
4294 (build-system r-build-system)
4295 (propagated-inputs
4296 `(("r-base64" ,r-base64)))
4297 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
4298 (synopsis "Parse Illumina microarray output files")
4299 (description
4300 "This package provides tools for parsing Illumina's microarray output
4301 files, including IDAT.")
4302 (license license:gpl2)))
4303
4304 (define-public r-siggenes
4305 (package
4306 (name "r-siggenes")
4307 (version "1.64.0")
4308 (source
4309 (origin
4310 (method url-fetch)
4311 (uri (bioconductor-uri "siggenes" version))
4312 (sha256
4313 (base32
4314 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
4315 (build-system r-build-system)
4316 (propagated-inputs
4317 `(("r-biobase" ,r-biobase)
4318 ("r-multtest" ,r-multtest)
4319 ("r-scrime" ,r-scrime)))
4320 (home-page "https://bioconductor.org/packages/siggenes/")
4321 (synopsis
4322 "Multiple testing using SAM and Efron's empirical Bayes approaches")
4323 (description
4324 "This package provides tools for the identification of differentially
4325 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
4326 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
4327 Bayes Analyses of Microarrays} (EBAM).")
4328 (license license:lgpl2.0+)))
4329
4330 (define-public r-bumphunter
4331 (package
4332 (name "r-bumphunter")
4333 (version "1.32.0")
4334 (source
4335 (origin
4336 (method url-fetch)
4337 (uri (bioconductor-uri "bumphunter" version))
4338 (sha256
4339 (base32
4340 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
4341 (build-system r-build-system)
4342 (propagated-inputs
4343 `(("r-annotationdbi" ,r-annotationdbi)
4344 ("r-biocgenerics" ,r-biocgenerics)
4345 ("r-dorng" ,r-dorng)
4346 ("r-foreach" ,r-foreach)
4347 ("r-genomeinfodb" ,r-genomeinfodb)
4348 ("r-genomicfeatures" ,r-genomicfeatures)
4349 ("r-genomicranges" ,r-genomicranges)
4350 ("r-iranges" ,r-iranges)
4351 ("r-iterators" ,r-iterators)
4352 ("r-limma" ,r-limma)
4353 ("r-locfit" ,r-locfit)
4354 ("r-matrixstats" ,r-matrixstats)
4355 ("r-s4vectors" ,r-s4vectors)))
4356 (home-page "https://github.com/ririzarr/bumphunter")
4357 (synopsis "Find bumps in genomic data")
4358 (description
4359 "This package provides tools for finding bumps in genomic data in order
4360 to identify differentially methylated regions in epigenetic epidemiology
4361 studies.")
4362 (license license:artistic2.0)))
4363
4364 (define-public r-minfi
4365 (package
4366 (name "r-minfi")
4367 (version "1.36.0")
4368 (source
4369 (origin
4370 (method url-fetch)
4371 (uri (bioconductor-uri "minfi" version))
4372 (sha256
4373 (base32
4374 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
4375 (build-system r-build-system)
4376 (propagated-inputs
4377 `(("r-beanplot" ,r-beanplot)
4378 ("r-biobase" ,r-biobase)
4379 ("r-biocgenerics" ,r-biocgenerics)
4380 ("r-biocparallel" ,r-biocparallel)
4381 ("r-biostrings" ,r-biostrings)
4382 ("r-bumphunter" ,r-bumphunter)
4383 ("r-data-table" ,r-data-table)
4384 ("r-delayedarray" ,r-delayedarray)
4385 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
4386 ("r-genefilter" ,r-genefilter)
4387 ("r-genomeinfodb" ,r-genomeinfodb)
4388 ("r-genomicranges" ,r-genomicranges)
4389 ("r-geoquery" ,r-geoquery)
4390 ("r-hdf5array" ,r-hdf5array)
4391 ("r-illuminaio" ,r-illuminaio)
4392 ("r-iranges" ,r-iranges)
4393 ("r-lattice" ,r-lattice)
4394 ("r-limma" ,r-limma)
4395 ("r-mass" ,r-mass)
4396 ("r-mclust" ,r-mclust)
4397 ("r-nlme" ,r-nlme)
4398 ("r-nor1mix" ,r-nor1mix)
4399 ("r-preprocesscore" ,r-preprocesscore)
4400 ("r-quadprog" ,r-quadprog)
4401 ("r-rcolorbrewer" ,r-rcolorbrewer)
4402 ("r-reshape" ,r-reshape)
4403 ("r-s4vectors" ,r-s4vectors)
4404 ("r-siggenes" ,r-siggenes)
4405 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4406 (native-inputs
4407 `(("r-knitr" ,r-knitr)))
4408 (home-page "https://github.com/hansenlab/minfi")
4409 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
4410 (description
4411 "This package provides tools to analyze and visualize Illumina Infinium
4412 methylation arrays.")
4413 (license license:artistic2.0)))
4414
4415 (define-public r-methylumi
4416 (package
4417 (name "r-methylumi")
4418 (version "2.36.0")
4419 (source
4420 (origin
4421 (method url-fetch)
4422 (uri (bioconductor-uri "methylumi" version))
4423 (sha256
4424 (base32
4425 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
4426 (build-system r-build-system)
4427 (propagated-inputs
4428 `(("r-annotate" ,r-annotate)
4429 ("r-annotationdbi" ,r-annotationdbi)
4430 ("r-biobase" ,r-biobase)
4431 ("r-biocgenerics" ,r-biocgenerics)
4432 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
4433 ("r-genefilter" ,r-genefilter)
4434 ("r-genomeinfodb" ,r-genomeinfodb)
4435 ("r-genomicranges" ,r-genomicranges)
4436 ("r-ggplot2" ,r-ggplot2)
4437 ("r-illuminaio" ,r-illuminaio)
4438 ("r-iranges" ,r-iranges)
4439 ("r-lattice" ,r-lattice)
4440 ("r-matrixstats" ,r-matrixstats)
4441 ("r-minfi" ,r-minfi)
4442 ("r-reshape2" ,r-reshape2)
4443 ("r-s4vectors" ,r-s4vectors)
4444 ("r-scales" ,r-scales)
4445 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4446 (native-inputs
4447 `(("r-knitr" ,r-knitr)))
4448 (home-page "https://bioconductor.org/packages/methylumi")
4449 (synopsis "Handle Illumina methylation data")
4450 (description
4451 "This package provides classes for holding and manipulating Illumina
4452 methylation data. Based on eSet, it can contain MIAME information, sample
4453 information, feature information, and multiple matrices of data. An
4454 \"intelligent\" import function, methylumiR can read the Illumina text files
4455 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
4456 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
4457 background correction, and quality control features for GoldenGate, Infinium,
4458 and Infinium HD arrays are also included.")
4459 (license license:gpl2)))
4460
4461 (define-public r-lumi
4462 (package
4463 (name "r-lumi")
4464 (version "2.42.0")
4465 (source
4466 (origin
4467 (method url-fetch)
4468 (uri (bioconductor-uri "lumi" version))
4469 (sha256
4470 (base32
4471 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
4472 (build-system r-build-system)
4473 (propagated-inputs
4474 `(("r-affy" ,r-affy)
4475 ("r-annotate" ,r-annotate)
4476 ("r-annotationdbi" ,r-annotationdbi)
4477 ("r-biobase" ,r-biobase)
4478 ("r-dbi" ,r-dbi)
4479 ("r-genomicfeatures" ,r-genomicfeatures)
4480 ("r-genomicranges" ,r-genomicranges)
4481 ("r-kernsmooth" ,r-kernsmooth)
4482 ("r-lattice" ,r-lattice)
4483 ("r-mass" ,r-mass)
4484 ("r-methylumi" ,r-methylumi)
4485 ("r-mgcv" ,r-mgcv)
4486 ("r-nleqslv" ,r-nleqslv)
4487 ("r-preprocesscore" ,r-preprocesscore)
4488 ("r-rsqlite" ,r-rsqlite)))
4489 (home-page "https://bioconductor.org/packages/lumi")
4490 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
4491 (description
4492 "The lumi package provides an integrated solution for the Illumina
4493 microarray data analysis. It includes functions of Illumina
4494 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
4495 variance stabilization, normalization and gene annotation at the probe level.
4496 It also includes the functions of processing Illumina methylation microarrays,
4497 especially Illumina Infinium methylation microarrays.")
4498 (license license:lgpl2.0+)))
4499
4500 (define-public r-linnorm
4501 (package
4502 (name "r-linnorm")
4503 (version "2.14.0")
4504 (source
4505 (origin
4506 (method url-fetch)
4507 (uri (bioconductor-uri "Linnorm" version))
4508 (sha256
4509 (base32
4510 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
4511 (properties `((upstream-name . "Linnorm")))
4512 (build-system r-build-system)
4513 (propagated-inputs
4514 `(("r-amap" ,r-amap)
4515 ("r-apcluster" ,r-apcluster)
4516 ("r-ellipse" ,r-ellipse)
4517 ("r-fastcluster" ,r-fastcluster)
4518 ("r-fpc" ,r-fpc)
4519 ("r-ggdendro" ,r-ggdendro)
4520 ("r-ggplot2" ,r-ggplot2)
4521 ("r-gmodels" ,r-gmodels)
4522 ("r-igraph" ,r-igraph)
4523 ("r-limma" ,r-limma)
4524 ("r-mass" ,r-mass)
4525 ("r-mclust" ,r-mclust)
4526 ("r-rcpp" ,r-rcpp)
4527 ("r-rcpparmadillo" ,r-rcpparmadillo)
4528 ("r-rtsne" ,r-rtsne)
4529 ("r-statmod" ,r-statmod)
4530 ("r-vegan" ,r-vegan)
4531 ("r-zoo" ,r-zoo)))
4532 (native-inputs
4533 `(("r-knitr" ,r-knitr)))
4534 (home-page "http://www.jjwanglab.org/Linnorm/")
4535 (synopsis "Linear model and normality based transformation method")
4536 (description
4537 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
4538 count data or any large scale count data. It transforms such datasets for
4539 parametric tests. In addition to the transformtion function (@code{Linnorm}),
4540 the following pipelines are implemented:
4541
4542 @enumerate
4543 @item Library size/batch effect normalization (@code{Linnorm.Norm})
4544 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
4545 clustering or hierarchical clustering (@code{Linnorm.tSNE},
4546 @code{Linnorm.PCA}, @code{Linnorm.HClust})
4547 @item Differential expression analysis or differential peak detection using
4548 limma (@code{Linnorm.limma})
4549 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
4550 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
4551 @item Stable gene selection for scRNA-seq data; for users without or who do
4552 not want to rely on spike-in genes (@code{Linnorm.SGenes})
4553 @item Data imputation (@code{Linnorm.DataImput}).
4554 @end enumerate
4555
4556 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
4557 @code{RnaXSim} function is included for simulating RNA-seq data for the
4558 evaluation of DEG analysis methods.")
4559 (license license:expat)))
4560
4561 (define-public r-ioniser
4562 (package
4563 (name "r-ioniser")
4564 (version "2.14.0")
4565 (source
4566 (origin
4567 (method url-fetch)
4568 (uri (bioconductor-uri "IONiseR" version))
4569 (sha256
4570 (base32
4571 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
4572 (properties `((upstream-name . "IONiseR")))
4573 (build-system r-build-system)
4574 (propagated-inputs
4575 `(("r-biocgenerics" ,r-biocgenerics)
4576 ("r-biocparallel" ,r-biocparallel)
4577 ("r-biostrings" ,r-biostrings)
4578 ("r-bit64" ,r-bit64)
4579 ("r-dplyr" ,r-dplyr)
4580 ("r-ggplot2" ,r-ggplot2)
4581 ("r-magrittr" ,r-magrittr)
4582 ("r-rhdf5" ,r-rhdf5)
4583 ("r-shortread" ,r-shortread)
4584 ("r-stringr" ,r-stringr)
4585 ("r-tibble" ,r-tibble)
4586 ("r-tidyr" ,r-tidyr)
4587 ("r-xvector" ,r-xvector)))
4588 (native-inputs
4589 `(("r-knitr" ,r-knitr)))
4590 (home-page "https://bioconductor.org/packages/IONiseR/")
4591 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
4592 (description
4593 "IONiseR provides tools for the quality assessment of Oxford Nanopore
4594 MinION data. It extracts summary statistics from a set of fast5 files and can
4595 be used either before or after base calling. In addition to standard
4596 summaries of the read-types produced, it provides a number of plots for
4597 visualising metrics relative to experiment run time or spatially over the
4598 surface of a flowcell.")
4599 (license license:expat)))
4600
4601 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
4602 (define-public r-mutoss
4603 (package
4604 (name "r-mutoss")
4605 (version "0.1-12")
4606 (source
4607 (origin
4608 (method url-fetch)
4609 (uri (cran-uri "mutoss" version))
4610 (sha256
4611 (base32
4612 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
4613 (properties `((upstream-name . "mutoss")))
4614 (build-system r-build-system)
4615 (propagated-inputs
4616 `(("r-multcomp" ,r-multcomp)
4617 ("r-multtest" ,r-multtest)
4618 ("r-mvtnorm" ,r-mvtnorm)
4619 ("r-plotrix" ,r-plotrix)))
4620 (home-page "https://github.com/kornl/mutoss/")
4621 (synopsis "Unified multiple testing procedures")
4622 (description
4623 "This package is designed to ease the application and comparison of
4624 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
4625 are standardized and usable by the accompanying mutossGUI package.")
4626 ;; Any version of the GPL.
4627 (license (list license:gpl2+ license:gpl3+))))
4628
4629 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
4630 ;; from Bioconductor, so we put it here.
4631 (define-public r-metap
4632 (package
4633 (name "r-metap")
4634 (version "1.3")
4635 (source
4636 (origin
4637 (method url-fetch)
4638 (uri (cran-uri "metap" version))
4639 (sha256
4640 (base32
4641 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
4642 (build-system r-build-system)
4643 (propagated-inputs
4644 `(("r-lattice" ,r-lattice)
4645 ("r-mutoss" ,r-mutoss)
4646 ("r-rdpack" ,r-rdpack)
4647 ("r-tfisher" ,r-tfisher)))
4648 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
4649 (synopsis "Meta-analysis of significance values")
4650 (description
4651 "The canonical way to perform meta-analysis involves using effect sizes.
4652 When they are not available this package provides a number of methods for
4653 meta-analysis of significance values including the methods of Edgington,
4654 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
4655 published results; and a routine for graphical display.")
4656 (license license:gpl2)))
4657
4658 (define-public r-triform
4659 (package
4660 (name "r-triform")
4661 (version "1.29.0")
4662 (source
4663 (origin
4664 (method url-fetch)
4665 (uri (bioconductor-uri "triform" version))
4666 (sha256
4667 (base32
4668 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
4669 (build-system r-build-system)
4670 (propagated-inputs
4671 `(("r-biocgenerics" ,r-biocgenerics)
4672 ("r-iranges" ,r-iranges)
4673 ("r-yaml" ,r-yaml)))
4674 (home-page "https://bioconductor.org/packages/triform/")
4675 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
4676 (description
4677 "The Triform algorithm uses model-free statistics to identify peak-like
4678 distributions of TF ChIP sequencing reads, taking advantage of an improved
4679 peak definition in combination with known profile characteristics.")
4680 (license license:gpl2)))
4681
4682 (define-public r-varianttools
4683 (package
4684 (name "r-varianttools")
4685 (version "1.32.0")
4686 (source
4687 (origin
4688 (method url-fetch)
4689 (uri (bioconductor-uri "VariantTools" version))
4690 (sha256
4691 (base32
4692 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
4693 (properties `((upstream-name . "VariantTools")))
4694 (build-system r-build-system)
4695 (propagated-inputs
4696 `(("r-biobase" ,r-biobase)
4697 ("r-biocgenerics" ,r-biocgenerics)
4698 ("r-biocparallel" ,r-biocparallel)
4699 ("r-biostrings" ,r-biostrings)
4700 ("r-bsgenome" ,r-bsgenome)
4701 ("r-genomeinfodb" ,r-genomeinfodb)
4702 ("r-genomicfeatures" ,r-genomicfeatures)
4703 ("r-genomicranges" ,r-genomicranges)
4704 ("r-iranges" ,r-iranges)
4705 ("r-matrix" ,r-matrix)
4706 ("r-rsamtools" ,r-rsamtools)
4707 ("r-rtracklayer" ,r-rtracklayer)
4708 ("r-s4vectors" ,r-s4vectors)
4709 ("r-variantannotation" ,r-variantannotation)))
4710 (home-page "https://bioconductor.org/packages/VariantTools/")
4711 (synopsis "Tools for exploratory analysis of variant calls")
4712 (description
4713 "Explore, diagnose, and compare variant calls using filters. The
4714 VariantTools package supports a workflow for loading data, calling single
4715 sample variants and tumor-specific somatic mutations or other sample-specific
4716 variant types (e.g., RNA editing). Most of the functions operate on
4717 alignments (BAM files) or datasets of called variants. The user is expected
4718 to have already aligned the reads with a separate tool, e.g., GSNAP via
4719 gmapR.")
4720 (license license:artistic2.0)))
4721
4722 (define-public r-heatplus
4723 (package
4724 (name "r-heatplus")
4725 (version "2.36.0")
4726 (source
4727 (origin
4728 (method url-fetch)
4729 (uri (bioconductor-uri "Heatplus" version))
4730 (sha256
4731 (base32
4732 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
4733 (properties `((upstream-name . "Heatplus")))
4734 (build-system r-build-system)
4735 (propagated-inputs
4736 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
4737 (home-page "https://github.com/alexploner/Heatplus")
4738 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
4739 (description
4740 "This package provides tools to display a rectangular heatmap (intensity
4741 plot) of a data matrix. By default, both samples (columns) and features (row)
4742 of the matrix are sorted according to a hierarchical clustering, and the
4743 corresponding dendrogram is plotted. Optionally, panels with additional
4744 information about samples and features can be added to the plot.")
4745 (license license:gpl2+)))
4746
4747 (define-public r-gosemsim
4748 (package
4749 (name "r-gosemsim")
4750 (version "2.16.1")
4751 (source
4752 (origin
4753 (method url-fetch)
4754 (uri (bioconductor-uri "GOSemSim" version))
4755 (sha256
4756 (base32
4757 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
4758 (properties `((upstream-name . "GOSemSim")))
4759 (build-system r-build-system)
4760 (propagated-inputs
4761 `(("r-annotationdbi" ,r-annotationdbi)
4762 ("r-go-db" ,r-go-db)
4763 ("r-rcpp" ,r-rcpp)))
4764 (native-inputs
4765 `(("r-knitr" ,r-knitr)))
4766 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
4767 (synopsis "GO-terms semantic similarity measures")
4768 (description
4769 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
4770 quantitative ways to compute similarities between genes and gene groups, and
4771 have became important basis for many bioinformatics analysis approaches.
4772 GOSemSim is an R package for semantic similarity computation among GO terms,
4773 sets of GO terms, gene products and gene clusters.")
4774 (license license:artistic2.0)))
4775
4776 (define-public r-anota
4777 (package
4778 (name "r-anota")
4779 (version "1.38.0")
4780 (source
4781 (origin
4782 (method url-fetch)
4783 (uri (bioconductor-uri "anota" version))
4784 (sha256
4785 (base32
4786 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
4787 (build-system r-build-system)
4788 (propagated-inputs
4789 `(("r-multtest" ,r-multtest)
4790 ("r-qvalue" ,r-qvalue)))
4791 (home-page "https://bioconductor.org/packages/anota/")
4792 (synopsis "Analysis of translational activity")
4793 (description
4794 "Genome wide studies of translational control is emerging as a tool to
4795 study various biological conditions. The output from such analysis is both
4796 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
4797 involved in translation (the actively translating mRNA level) for each mRNA.
4798 The standard analysis of such data strives towards identifying differential
4799 translational between two or more sample classes - i.e. differences in
4800 actively translated mRNA levels that are independent of underlying differences
4801 in cytosolic mRNA levels. This package allows for such analysis using partial
4802 variances and the random variance model. As 10s of thousands of mRNAs are
4803 analyzed in parallel the library performs a number of tests to assure that
4804 the data set is suitable for such analysis.")
4805 (license license:gpl3)))
4806
4807 (define-public r-sigpathway
4808 (package
4809 (name "r-sigpathway")
4810 (version "1.58.0")
4811 (source
4812 (origin
4813 (method url-fetch)
4814 (uri (bioconductor-uri "sigPathway" version))
4815 (sha256
4816 (base32
4817 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
4818 (properties `((upstream-name . "sigPathway")))
4819 (build-system r-build-system)
4820 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
4821 (synopsis "Pathway analysis")
4822 (description
4823 "This package is used to conduct pathway analysis by calculating the NT_k
4824 and NE_k statistics in a statistical framework for determining whether a
4825 specified group of genes for a pathway has a coordinated association with a
4826 phenotype of interest.")
4827 (license license:gpl2)))
4828
4829 (define-public r-fgsea
4830 (package
4831 (name "r-fgsea")
4832 (version "1.16.0")
4833 (source
4834 (origin
4835 (method url-fetch)
4836 (uri (bioconductor-uri "fgsea" version))
4837 (sha256
4838 (base32
4839 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
4840 (build-system r-build-system)
4841 (propagated-inputs
4842 `(("r-bh" ,r-bh)
4843 ("r-biocparallel" ,r-biocparallel)
4844 ("r-data-table" ,r-data-table)
4845 ("r-fastmatch" ,r-fastmatch)
4846 ("r-ggplot2" ,r-ggplot2)
4847 ("r-gridextra" ,r-gridextra)
4848 ("r-matrix" ,r-matrix)
4849 ("r-rcpp" ,r-rcpp)))
4850 (native-inputs
4851 `(("r-knitr" ,r-knitr)))
4852 (home-page "https://github.com/ctlab/fgsea/")
4853 (synopsis "Fast gene set enrichment analysis")
4854 (description
4855 "The package implements an algorithm for fast gene set enrichment
4856 analysis. Using the fast algorithm makes more permutations and gets
4857 more fine grained p-values, which allows using accurate standard approaches
4858 to multiple hypothesis correction.")
4859 (license license:expat)))
4860
4861 (define-public r-dose
4862 (package
4863 (name "r-dose")
4864 (version "3.16.0")
4865 (source
4866 (origin
4867 (method url-fetch)
4868 (uri (bioconductor-uri "DOSE" version))
4869 (sha256
4870 (base32
4871 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
4872 (properties `((upstream-name . "DOSE")))
4873 (build-system r-build-system)
4874 (propagated-inputs
4875 `(("r-annotationdbi" ,r-annotationdbi)
4876 ("r-biocparallel" ,r-biocparallel)
4877 ("r-do-db" ,r-do-db)
4878 ("r-fgsea" ,r-fgsea)
4879 ("r-ggplot2" ,r-ggplot2)
4880 ("r-gosemsim" ,r-gosemsim)
4881 ("r-qvalue" ,r-qvalue)
4882 ("r-reshape2" ,r-reshape2)))
4883 (native-inputs
4884 `(("r-knitr" ,r-knitr)))
4885 (home-page "https://guangchuangyu.github.io/software/DOSE/")
4886 (synopsis "Disease ontology semantic and enrichment analysis")
4887 (description
4888 "This package implements five methods proposed by Resnik, Schlicker,
4889 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
4890 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
4891 including hypergeometric model and gene set enrichment analysis are also
4892 implemented for discovering disease associations of high-throughput biological
4893 data.")
4894 (license license:artistic2.0)))
4895
4896 (define-public r-enrichplot
4897 (package
4898 (name "r-enrichplot")
4899 (version "1.10.2")
4900 (source
4901 (origin
4902 (method url-fetch)
4903 (uri (bioconductor-uri "enrichplot" version))
4904 (sha256
4905 (base32
4906 "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
4907 (build-system r-build-system)
4908 (propagated-inputs
4909 `(("r-cowplot" ,r-cowplot)
4910 ("r-dose" ,r-dose)
4911 ("r-ggplot2" ,r-ggplot2)
4912 ("r-ggraph" ,r-ggraph)
4913 ("r-gosemsim" ,r-gosemsim)
4914 ("r-igraph" ,r-igraph)
4915 ("r-magrittr" ,r-magrittr)
4916 ("r-plyr" ,r-plyr)
4917 ("r-purrr" ,r-purrr)
4918 ("r-rcolorbrewer" ,r-rcolorbrewer)
4919 ("r-reshape2" ,r-reshape2)
4920 ("r-scatterpie" ,r-scatterpie)
4921 ("r-shadowtext" ,r-shadowtext)))
4922 (native-inputs
4923 `(("r-knitr" ,r-knitr)))
4924 (home-page "https://github.com/GuangchuangYu/enrichplot")
4925 (synopsis "Visualization of functional enrichment result")
4926 (description
4927 "The enrichplot package implements several visualization methods for
4928 interpreting functional enrichment results obtained from ORA or GSEA analyses.
4929 All the visualization methods are developed based on ggplot2 graphics.")
4930 (license license:artistic2.0)))
4931
4932 (define-public r-clusterprofiler
4933 (package
4934 (name "r-clusterprofiler")
4935 (version "3.18.1")
4936 (source
4937 (origin
4938 (method url-fetch)
4939 (uri (bioconductor-uri "clusterProfiler" version))
4940 (sha256
4941 (base32
4942 "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
4943 (properties
4944 `((upstream-name . "clusterProfiler")))
4945 (build-system r-build-system)
4946 (propagated-inputs
4947 `(("r-annotationdbi" ,r-annotationdbi)
4948 ("r-dose" ,r-dose)
4949 ("r-downloader" ,r-downloader)
4950 ("r-dplyr" ,r-dplyr)
4951 ("r-enrichplot" ,r-enrichplot)
4952 ("r-go-db" ,r-go-db)
4953 ("r-gosemsim" ,r-gosemsim)
4954 ("r-magrittr" ,r-magrittr)
4955 ("r-plyr" ,r-plyr)
4956 ("r-qvalue" ,r-qvalue)
4957 ("r-rlang" ,r-rlang)
4958 ("r-rvcheck" ,r-rvcheck)
4959 ("r-tidyr" ,r-tidyr)))
4960 (native-inputs
4961 `(("r-knitr" ,r-knitr)))
4962 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
4963 (synopsis "Analysis and visualization of functional profiles for gene clusters")
4964 (description
4965 "This package implements methods to analyze and visualize functional
4966 profiles (GO and KEGG) of gene and gene clusters.")
4967 (license license:artistic2.0)))
4968
4969 (define-public r-mlinterfaces
4970 (package
4971 (name "r-mlinterfaces")
4972 (version "1.70.0")
4973 (source
4974 (origin
4975 (method url-fetch)
4976 (uri (bioconductor-uri "MLInterfaces" version))
4977 (sha256
4978 (base32
4979 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
4980 (properties `((upstream-name . "MLInterfaces")))
4981 (build-system r-build-system)
4982 (propagated-inputs
4983 `(("r-annotate" ,r-annotate)
4984 ("r-biobase" ,r-biobase)
4985 ("r-biocgenerics" ,r-biocgenerics)
4986 ("r-cluster" ,r-cluster)
4987 ("r-fpc" ,r-fpc)
4988 ("r-gbm" ,r-gbm)
4989 ("r-gdata" ,r-gdata)
4990 ("r-genefilter" ,r-genefilter)
4991 ("r-ggvis" ,r-ggvis)
4992 ("r-hwriter" ,r-hwriter)
4993 ("r-mass" ,r-mass)
4994 ("r-mlbench" ,r-mlbench)
4995 ("r-pls" ,r-pls)
4996 ("r-rcolorbrewer" ,r-rcolorbrewer)
4997 ("r-rcpp" ,r-rcpp)
4998 ("r-rpart" ,r-rpart)
4999 ("r-sfsmisc" ,r-sfsmisc)
5000 ("r-shiny" ,r-shiny)
5001 ("r-threejs" ,r-threejs)))
5002 (home-page "https://bioconductor.org/packages/MLInterfaces/")
5003 (synopsis "Interfaces to R machine learning procedures")
5004 (description
5005 "This package provides uniform interfaces to machine learning code for
5006 data in R and Bioconductor containers.")
5007 ;; Any version of the LGPL.
5008 (license license:lgpl2.1+)))
5009
5010 (define-public r-annaffy
5011 (package
5012 (name "r-annaffy")
5013 (version "1.62.0")
5014 (source
5015 (origin
5016 (method url-fetch)
5017 (uri (bioconductor-uri "annaffy" version))
5018 (sha256
5019 (base32
5020 "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
5021 (build-system r-build-system)
5022 (arguments
5023 `(#:phases
5024 (modify-phases %standard-phases
5025 (add-after 'unpack 'remove-reference-to-non-free-data
5026 (lambda _
5027 (substitute* "DESCRIPTION"
5028 ((", KEGG.db") ""))
5029 #t)))))
5030 (propagated-inputs
5031 `(("r-annotationdbi" ,r-annotationdbi)
5032 ("r-biobase" ,r-biobase)
5033 ("r-dbi" ,r-dbi)
5034 ("r-go-db" ,r-go-db)))
5035 (home-page "https://bioconductor.org/packages/annaffy/")
5036 (synopsis "Annotation tools for Affymetrix biological metadata")
5037 (description
5038 "This package provides functions for handling data from Bioconductor
5039 Affymetrix annotation data packages. It produces compact HTML and text
5040 reports including experimental data and URL links to many online databases.
5041 It allows searching of biological metadata using various criteria.")
5042 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
5043 ;; the LGPL 2.1 is included.
5044 (license license:lgpl2.1+)))
5045
5046 (define-public r-a4core
5047 (package
5048 (name "r-a4core")
5049 (version "1.38.0")
5050 (source
5051 (origin
5052 (method url-fetch)
5053 (uri (bioconductor-uri "a4Core" version))
5054 (sha256
5055 (base32
5056 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
5057 (properties `((upstream-name . "a4Core")))
5058 (build-system r-build-system)
5059 (propagated-inputs
5060 `(("r-biobase" ,r-biobase)
5061 ("r-glmnet" ,r-glmnet)))
5062 (native-inputs
5063 `(("r-knitr" ,r-knitr)))
5064 (home-page "https://bioconductor.org/packages/a4Core")
5065 (synopsis "Automated Affymetrix array analysis core package")
5066 (description
5067 "This is the core package for the automated analysis of Affymetrix
5068 arrays.")
5069 (license license:gpl3)))
5070
5071 (define-public r-a4classif
5072 (package
5073 (name "r-a4classif")
5074 (version "1.38.0")
5075 (source
5076 (origin
5077 (method url-fetch)
5078 (uri (bioconductor-uri "a4Classif" version))
5079 (sha256
5080 (base32
5081 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
5082 (properties `((upstream-name . "a4Classif")))
5083 (build-system r-build-system)
5084 (propagated-inputs
5085 `(("r-a4core" ,r-a4core)
5086 ("r-a4preproc" ,r-a4preproc)
5087 ("r-biobase" ,r-biobase)
5088 ("r-glmnet" ,r-glmnet)
5089 ("r-pamr" ,r-pamr)
5090 ("r-rocr" ,r-rocr)
5091 ("r-varselrf" ,r-varselrf)))
5092 (native-inputs
5093 `(("r-knitr" ,r-knitr)))
5094 (home-page "https://bioconductor.org/packages/a4Classif/")
5095 (synopsis "Automated Affymetrix array analysis classification package")
5096 (description
5097 "This is the classification package for the automated analysis of
5098 Affymetrix arrays.")
5099 (license license:gpl3)))
5100
5101 (define-public r-a4preproc
5102 (package
5103 (name "r-a4preproc")
5104 (version "1.38.0")
5105 (source
5106 (origin
5107 (method url-fetch)
5108 (uri (bioconductor-uri "a4Preproc" version))
5109 (sha256
5110 (base32
5111 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
5112 (properties `((upstream-name . "a4Preproc")))
5113 (build-system r-build-system)
5114 (propagated-inputs
5115 `(("r-biobase" ,r-biobase)
5116 ("r-biocgenerics" ,r-biocgenerics)))
5117 (native-inputs
5118 `(("r-knitr" ,r-knitr)))
5119 (home-page "https://bioconductor.org/packages/a4Preproc/")
5120 (synopsis "Automated Affymetrix array analysis preprocessing package")
5121 (description
5122 "This is a package for the automated analysis of Affymetrix arrays. It
5123 is used for preprocessing the arrays.")
5124 (license license:gpl3)))
5125
5126 (define-public r-a4reporting
5127 (package
5128 (name "r-a4reporting")
5129 (version "1.38.0")
5130 (source
5131 (origin
5132 (method url-fetch)
5133 (uri (bioconductor-uri "a4Reporting" version))
5134 (sha256
5135 (base32
5136 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
5137 (properties `((upstream-name . "a4Reporting")))
5138 (build-system r-build-system)
5139 (propagated-inputs
5140 `(("r-xtable" ,r-xtable)))
5141 (native-inputs
5142 `(("r-knitr" ,r-knitr)))
5143 (home-page "https://bioconductor.org/packages/a4Reporting/")
5144 (synopsis "Automated Affymetrix array analysis reporting package")
5145 (description
5146 "This is a package for the automated analysis of Affymetrix arrays. It
5147 provides reporting features.")
5148 (license license:gpl3)))
5149
5150 (define-public r-a4base
5151 (package
5152 (name "r-a4base")
5153 (version "1.38.0")
5154 (source
5155 (origin
5156 (method url-fetch)
5157 (uri (bioconductor-uri "a4Base" version))
5158 (sha256
5159 (base32
5160 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
5161 (properties `((upstream-name . "a4Base")))
5162 (build-system r-build-system)
5163 (propagated-inputs
5164 `(("r-a4core" ,r-a4core)
5165 ("r-a4preproc" ,r-a4preproc)
5166 ("r-annaffy" ,r-annaffy)
5167 ("r-biobase" ,r-biobase)
5168 ("r-genefilter" ,r-genefilter)
5169 ("r-glmnet" ,r-glmnet)
5170 ("r-gplots" ,r-gplots)
5171 ("r-limma" ,r-limma)
5172 ("r-mpm" ,r-mpm)
5173 ("r-multtest" ,r-multtest)))
5174 (home-page "https://bioconductor.org/packages/a4Base/")
5175 (synopsis "Automated Affymetrix array analysis base package")
5176 (description
5177 "This package provides basic features for the automated analysis of
5178 Affymetrix arrays.")
5179 (license license:gpl3)))
5180
5181 (define-public r-a4
5182 (package
5183 (name "r-a4")
5184 (version "1.38.0")
5185 (source
5186 (origin
5187 (method url-fetch)
5188 (uri (bioconductor-uri "a4" version))
5189 (sha256
5190 (base32
5191 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
5192 (build-system r-build-system)
5193 (propagated-inputs
5194 `(("r-a4base" ,r-a4base)
5195 ("r-a4classif" ,r-a4classif)
5196 ("r-a4core" ,r-a4core)
5197 ("r-a4preproc" ,r-a4preproc)
5198 ("r-a4reporting" ,r-a4reporting)))
5199 (home-page "https://bioconductor.org/packages/a4/")
5200 (synopsis "Automated Affymetrix array analysis umbrella package")
5201 (description
5202 "This package provides a software suite for the automated analysis of
5203 Affymetrix arrays.")
5204 (license license:gpl3)))
5205
5206 (define-public r-abseqr
5207 (package
5208 (name "r-abseqr")
5209 (version "1.8.0")
5210 (source
5211 (origin
5212 (method url-fetch)
5213 (uri (bioconductor-uri "abseqR" version))
5214 (sha256
5215 (base32
5216 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
5217 (properties `((upstream-name . "abseqR")))
5218 (build-system r-build-system)
5219 (inputs
5220 `(("pandoc" ,pandoc)))
5221 (propagated-inputs
5222 `(("r-biocparallel" ,r-biocparallel)
5223 ("r-biocstyle" ,r-biocstyle)
5224 ("r-circlize" ,r-circlize)
5225 ("r-flexdashboard" ,r-flexdashboard)
5226 ("r-ggcorrplot" ,r-ggcorrplot)
5227 ("r-ggdendro" ,r-ggdendro)
5228 ("r-ggplot2" ,r-ggplot2)
5229 ("r-gridextra" ,r-gridextra)
5230 ("r-knitr" ,r-knitr)
5231 ("r-plotly" ,r-plotly)
5232 ("r-plyr" ,r-plyr)
5233 ("r-png" ,r-png)
5234 ("r-rcolorbrewer" ,r-rcolorbrewer)
5235 ("r-reshape2" ,r-reshape2)
5236 ("r-rmarkdown" ,r-rmarkdown)
5237 ("r-stringr" ,r-stringr)
5238 ("r-vegan" ,r-vegan)
5239 ("r-venndiagram" ,r-venndiagram)))
5240 (native-inputs
5241 `(("r-knitr" ,r-knitr)))
5242 (home-page "https://github.com/malhamdoosh/abseqR")
5243 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
5244 (description
5245 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
5246 sequencing datasets generated from antibody libraries and abseqR is one of its
5247 packages. AbseqR empowers the users of abseqPy with plotting and reporting
5248 capabilities and allows them to generate interactive HTML reports for the
5249 convenience of viewing and sharing with other researchers. Additionally,
5250 abseqR extends abseqPy to compare multiple repertoire analyses and perform
5251 further downstream analysis on its output.")
5252 (license license:gpl3)))
5253
5254 (define-public r-bacon
5255 (package
5256 (name "r-bacon")
5257 (version "1.18.0")
5258 (source
5259 (origin
5260 (method url-fetch)
5261 (uri (bioconductor-uri "bacon" version))
5262 (sha256
5263 (base32
5264 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
5265 (build-system r-build-system)
5266 (propagated-inputs
5267 `(("r-biocparallel" ,r-biocparallel)
5268 ("r-ellipse" ,r-ellipse)
5269 ("r-ggplot2" ,r-ggplot2)))
5270 (native-inputs
5271 `(("r-knitr" ,r-knitr)))
5272 (home-page "https://bioconductor.org/packages/bacon/")
5273 (synopsis "Controlling bias and inflation in association studies")
5274 (description
5275 "Bacon can be used to remove inflation and bias often observed in
5276 epigenome- and transcriptome-wide association studies. To this end bacon
5277 constructs an empirical null distribution using a Gibbs Sampling algorithm by
5278 fitting a three-component normal mixture on z-scores.")
5279 (license license:gpl2+)))
5280
5281 (define-public r-rgadem
5282 (package
5283 (name "r-rgadem")
5284 (version "2.38.0")
5285 (source
5286 (origin
5287 (method url-fetch)
5288 (uri (bioconductor-uri "rGADEM" version))
5289 (sha256
5290 (base32
5291 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
5292 (properties `((upstream-name . "rGADEM")))
5293 (build-system r-build-system)
5294 (propagated-inputs
5295 `(("r-biostrings" ,r-biostrings)
5296 ("r-bsgenome" ,r-bsgenome)
5297 ("r-genomicranges" ,r-genomicranges)
5298 ("r-iranges" ,r-iranges)
5299 ("r-seqlogo" ,r-seqlogo)))
5300 (home-page "https://bioconductor.org/packages/rGADEM/")
5301 (synopsis "De novo sequence motif discovery")
5302 (description
5303 "rGADEM is an efficient de novo motif discovery tool for large-scale
5304 genomic sequence data.")
5305 (license license:artistic2.0)))
5306
5307 (define-public r-motiv
5308 (package
5309 (name "r-motiv")
5310 (version "1.43.0")
5311 (source
5312 (origin
5313 (method url-fetch)
5314 (uri (bioconductor-uri "MotIV" version))
5315 (sha256
5316 (base32
5317 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
5318 (properties `((upstream-name . "MotIV")))
5319 (build-system r-build-system)
5320 (inputs
5321 `(("gsl" ,gsl)))
5322 (propagated-inputs
5323 `(("r-biocgenerics" ,r-biocgenerics)
5324 ("r-biostrings" ,r-biostrings)
5325 ("r-genomicranges" ,r-genomicranges)
5326 ("r-iranges" ,r-iranges)
5327 ("r-lattice" ,r-lattice)
5328 ("r-rgadem" ,r-rgadem)
5329 ("r-s4vectors" ,r-s4vectors)))
5330 (home-page "https://bioconductor.org/packages/MotIV/")
5331 (synopsis "Motif identification and validation")
5332 (description
5333 "This package is used for the identification and validation of sequence
5334 motifs. It makes use of STAMP for comparing a set of motifs to a given
5335 database (e.g. JASPAR). It can also be used to visualize motifs, motif
5336 distributions, modules and filter motifs.")
5337 (license license:gpl2)))
5338
5339 (define-public r-motifdb
5340 (package
5341 (name "r-motifdb")
5342 (version "1.32.0")
5343 (source (origin
5344 (method url-fetch)
5345 (uri (bioconductor-uri "MotifDb" version))
5346 (sha256
5347 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
5348 (properties `((upstream-name . "MotifDb")))
5349 (build-system r-build-system)
5350 (propagated-inputs
5351 `(("r-biocgenerics" ,r-biocgenerics)
5352 ("r-biostrings" ,r-biostrings)
5353 ("r-genomicranges" ,r-genomicranges)
5354 ("r-iranges" ,r-iranges)
5355 ("r-rtracklayer" ,r-rtracklayer)
5356 ("r-s4vectors" ,r-s4vectors)
5357 ("r-splitstackshape" ,r-splitstackshape)))
5358 (native-inputs
5359 `(("r-knitr" ,r-knitr)))
5360 (home-page "https://www.bioconductor.org/packages/MotifDb/")
5361 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
5362 (description "This package provides more than 2000 annotated position
5363 frequency matrices from nine public sources, for multiple organisms.")
5364 (license license:artistic2.0)))
5365
5366 (define-public r-motifbreakr
5367 (package
5368 (name "r-motifbreakr")
5369 (version "2.4.0")
5370 (source (origin
5371 (method url-fetch)
5372 (uri (bioconductor-uri "motifbreakR" version))
5373 (sha256
5374 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
5375 (properties `((upstream-name . "motifbreakR")))
5376 (build-system r-build-system)
5377 (propagated-inputs
5378 `(("r-biocgenerics" ,r-biocgenerics)
5379 ("r-biocparallel" ,r-biocparallel)
5380 ("r-biostrings" ,r-biostrings)
5381 ("r-bsgenome" ,r-bsgenome)
5382 ("r-genomeinfodb" ,r-genomeinfodb)
5383 ("r-genomicranges" ,r-genomicranges)
5384 ("r-grimport" ,r-grimport)
5385 ("r-gviz" ,r-gviz)
5386 ("r-iranges" ,r-iranges)
5387 ("r-matrixstats" ,r-matrixstats)
5388 ("r-motifdb" ,r-motifdb)
5389 ("r-motifstack" ,r-motifstack)
5390 ("r-rtracklayer" ,r-rtracklayer)
5391 ("r-s4vectors" ,r-s4vectors)
5392 ("r-stringr" ,r-stringr)
5393 ("r-summarizedexperiment" ,r-summarizedexperiment)
5394 ("r-tfmpvalue" ,r-tfmpvalue)
5395 ("r-variantannotation" ,r-variantannotation)))
5396 (native-inputs
5397 `(("r-knitr" ,r-knitr)))
5398 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
5399 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
5400 (description "This package allows biologists to judge in the first place
5401 whether the sequence surrounding the polymorphism is a good match, and in
5402 the second place how much information is gained or lost in one allele of
5403 the polymorphism relative to another. This package gives a choice of
5404 algorithms for interrogation of genomes with motifs from public sources:
5405 @enumerate
5406 @item a weighted-sum probability matrix;
5407 @item log-probabilities;
5408 @item weighted by relative entropy.
5409 @end enumerate
5410
5411 This package can predict effects for novel or previously described variants in
5412 public databases, making it suitable for tasks beyond the scope of its original
5413 design. Lastly, it can be used to interrogate any genome curated within
5414 Bioconductor.")
5415 (license license:gpl2+)))
5416
5417 (define-public r-motifstack
5418 (package
5419 (name "r-motifstack")
5420 (version "1.34.0")
5421 (source
5422 (origin
5423 (method url-fetch)
5424 (uri (bioconductor-uri "motifStack" version))
5425 (sha256
5426 (base32
5427 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
5428 (properties `((upstream-name . "motifStack")))
5429 (build-system r-build-system)
5430 (propagated-inputs
5431 `(("r-ade4" ,r-ade4)
5432 ("r-biostrings" ,r-biostrings)
5433 ("r-ggplot2" ,r-ggplot2)
5434 ("r-htmlwidgets" ,r-htmlwidgets)
5435 ("r-xml" ,r-xml)))
5436 (native-inputs
5437 `(("r-knitr" ,r-knitr)))
5438 (home-page "https://bioconductor.org/packages/motifStack/")
5439 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
5440 (description
5441 "The motifStack package is designed for graphic representation of
5442 multiple motifs with different similarity scores. It works with both DNA/RNA
5443 sequence motifs and amino acid sequence motifs. In addition, it provides the
5444 flexibility for users to customize the graphic parameters such as the font
5445 type and symbol colors.")
5446 (license license:gpl2+)))
5447
5448 (define-public r-genomicscores
5449 (package
5450 (name "r-genomicscores")
5451 (version "2.2.0")
5452 (source
5453 (origin
5454 (method url-fetch)
5455 (uri (bioconductor-uri "GenomicScores" version))
5456 (sha256
5457 (base32
5458 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
5459 (properties `((upstream-name . "GenomicScores")))
5460 (build-system r-build-system)
5461 (propagated-inputs
5462 `(("r-annotationhub" ,r-annotationhub)
5463 ("r-biobase" ,r-biobase)
5464 ("r-biocfilecache" ,r-biocfilecache)
5465 ("r-biocgenerics" ,r-biocgenerics)
5466 ("r-biocmanager" ,r-biocmanager)
5467 ("r-biostrings" ,r-biostrings)
5468 ("r-delayedarray" ,r-delayedarray)
5469 ("r-genomeinfodb" ,r-genomeinfodb)
5470 ("r-genomicranges" ,r-genomicranges)
5471 ("r-hdf5array" ,r-hdf5array)
5472 ("r-iranges" ,r-iranges)
5473 ("r-rhdf5" ,r-rhdf5)
5474 ("r-s4vectors" ,r-s4vectors)
5475 ("r-xml" ,r-xml)))
5476 (native-inputs
5477 `(("r-knitr" ,r-knitr)))
5478 (home-page "https://github.com/rcastelo/GenomicScores/")
5479 (synopsis "Work with genome-wide position-specific scores")
5480 (description
5481 "This package provides infrastructure to store and access genome-wide
5482 position-specific scores within R and Bioconductor.")
5483 (license license:artistic2.0)))
5484
5485 (define-public r-atacseqqc
5486 (package
5487 (name "r-atacseqqc")
5488 (version "1.14.4")
5489 (source
5490 (origin
5491 (method url-fetch)
5492 (uri (bioconductor-uri "ATACseqQC" version))
5493 (sha256
5494 (base32
5495 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
5496 (properties `((upstream-name . "ATACseqQC")))
5497 (build-system r-build-system)
5498 (propagated-inputs
5499 `(("r-biocgenerics" ,r-biocgenerics)
5500 ("r-biostrings" ,r-biostrings)
5501 ("r-bsgenome" ,r-bsgenome)
5502 ("r-chippeakanno" ,r-chippeakanno)
5503 ("r-edger" ,r-edger)
5504 ("r-genomeinfodb" ,r-genomeinfodb)
5505 ("r-genomicalignments" ,r-genomicalignments)
5506 ("r-genomicranges" ,r-genomicranges)
5507 ("r-genomicscores" ,r-genomicscores)
5508 ("r-iranges" ,r-iranges)
5509 ("r-kernsmooth" ,r-kernsmooth)
5510 ("r-limma" ,r-limma)
5511 ("r-motifstack" ,r-motifstack)
5512 ("r-preseqr" ,r-preseqr)
5513 ("r-randomforest" ,r-randomforest)
5514 ("r-rsamtools" ,r-rsamtools)
5515 ("r-rtracklayer" ,r-rtracklayer)
5516 ("r-s4vectors" ,r-s4vectors)))
5517 (native-inputs
5518 `(("r-knitr" ,r-knitr)))
5519 (home-page "https://bioconductor.org/packages/ATACseqQC/")
5520 (synopsis "ATAC-seq quality control")
5521 (description
5522 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
5523 sequencing, is a rapid and sensitive method for chromatin accessibility
5524 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
5525 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
5526 assess whether their ATAC-seq experiment is successful. It includes
5527 diagnostic plots of fragment size distribution, proportion of mitochondria
5528 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
5529 footprints.")
5530 (license license:gpl2+)))
5531
5532 (define-public r-gofuncr
5533 (package
5534 (name "r-gofuncr")
5535 (version "1.10.0")
5536 (source
5537 (origin
5538 (method url-fetch)
5539 (uri (bioconductor-uri "GOfuncR" version))
5540 (sha256
5541 (base32
5542 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
5543 (properties `((upstream-name . "GOfuncR")))
5544 (build-system r-build-system)
5545 (propagated-inputs
5546 `(("r-annotationdbi" ,r-annotationdbi)
5547 ("r-genomicranges" ,r-genomicranges)
5548 ("r-gtools" ,r-gtools)
5549 ("r-iranges" ,r-iranges)
5550 ("r-mapplots" ,r-mapplots)
5551 ("r-rcpp" ,r-rcpp)
5552 ("r-vioplot" ,r-vioplot)))
5553 (native-inputs
5554 `(("r-knitr" ,r-knitr)))
5555 (home-page "https://bioconductor.org/packages/GOfuncR/")
5556 (synopsis "Gene ontology enrichment using FUNC")
5557 (description
5558 "GOfuncR performs a gene ontology enrichment analysis based on the
5559 ontology enrichment software FUNC. GO-annotations are obtained from
5560 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
5561 included in the package and updated regularly. GOfuncR provides the standard
5562 candidate vs background enrichment analysis using the hypergeometric test, as
5563 well as three additional tests:
5564
5565 @enumerate
5566 @item the Wilcoxon rank-sum test that is used when genes are ranked,
5567 @item a binomial test that is used when genes are associated with two counts,
5568 and
5569 @item a Chi-square or Fisher's exact test that is used in cases when genes are
5570 associated with four counts.
5571 @end enumerate
5572
5573 To correct for multiple testing and interdependency of the tests, family-wise
5574 error rates are computed based on random permutations of the gene-associated
5575 variables. GOfuncR also provides tools for exploring the ontology graph and
5576 the annotations, and options to take gene-length or spatial clustering of
5577 genes into account. It is also possible to provide custom gene coordinates,
5578 annotations and ontologies.")
5579 (license license:gpl2+)))
5580
5581 (define-public r-abaenrichment
5582 (package
5583 (name "r-abaenrichment")
5584 (version "1.20.0")
5585 (source
5586 (origin
5587 (method url-fetch)
5588 (uri (bioconductor-uri "ABAEnrichment" version))
5589 (sha256
5590 (base32
5591 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
5592 (properties `((upstream-name . "ABAEnrichment")))
5593 (build-system r-build-system)
5594 (propagated-inputs
5595 `(("r-abadata" ,r-abadata)
5596 ("r-data-table" ,r-data-table)
5597 ("r-gofuncr" ,r-gofuncr)
5598 ("r-gplots" ,r-gplots)
5599 ("r-gtools" ,r-gtools)
5600 ("r-rcpp" ,r-rcpp)))
5601 (native-inputs
5602 `(("r-knitr" ,r-knitr)))
5603 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
5604 (synopsis "Gene expression enrichment in human brain regions")
5605 (description
5606 "The package ABAEnrichment is designed to test for enrichment of user
5607 defined candidate genes in the set of expressed genes in different human brain
5608 regions. The core function @code{aba_enrich} integrates the expression of the
5609 candidate gene set (averaged across donors) and the structural information of
5610 the brain using an ontology, both provided by the Allen Brain Atlas project.")
5611 (license license:gpl2+)))
5612
5613 (define-public r-annotationfuncs
5614 (package
5615 (name "r-annotationfuncs")
5616 (version "1.40.0")
5617 (source
5618 (origin
5619 (method url-fetch)
5620 (uri (bioconductor-uri "AnnotationFuncs" version))
5621 (sha256
5622 (base32
5623 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
5624 (properties
5625 `((upstream-name . "AnnotationFuncs")))
5626 (build-system r-build-system)
5627 (propagated-inputs
5628 `(("r-annotationdbi" ,r-annotationdbi)
5629 ("r-dbi" ,r-dbi)))
5630 (home-page "https://www.iysik.com/r/annotationfuncs")
5631 (synopsis "Annotation translation functions")
5632 (description
5633 "This package provides functions for handling translating between
5634 different identifieres using the Biocore Data Team data-packages (e.g.
5635 @code{org.Bt.eg.db}).")
5636 (license license:gpl2)))
5637
5638 (define-public r-annotationtools
5639 (package
5640 (name "r-annotationtools")
5641 (version "1.64.0")
5642 (source
5643 (origin
5644 (method url-fetch)
5645 (uri (bioconductor-uri "annotationTools" version))
5646 (sha256
5647 (base32
5648 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
5649 (properties
5650 `((upstream-name . "annotationTools")))
5651 (build-system r-build-system)
5652 (propagated-inputs `(("r-biobase" ,r-biobase)))
5653 (home-page "https://bioconductor.org/packages/annotationTools/")
5654 (synopsis "Annotate microarrays and perform gene expression analyses")
5655 (description
5656 "This package provides functions to annotate microarrays, find orthologs,
5657 and integrate heterogeneous gene expression profiles using annotation and
5658 other molecular biology information available as flat file database (plain
5659 text files).")
5660 ;; Any version of the GPL.
5661 (license (list license:gpl2+))))
5662
5663 (define-public r-allelicimbalance
5664 (package
5665 (name "r-allelicimbalance")
5666 (version "1.28.0")
5667 (source
5668 (origin
5669 (method url-fetch)
5670 (uri (bioconductor-uri "AllelicImbalance" version))
5671 (sha256
5672 (base32
5673 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
5674 (properties
5675 `((upstream-name . "AllelicImbalance")))
5676 (build-system r-build-system)
5677 (propagated-inputs
5678 `(("r-annotationdbi" ,r-annotationdbi)
5679 ("r-biocgenerics" ,r-biocgenerics)
5680 ("r-biostrings" ,r-biostrings)
5681 ("r-bsgenome" ,r-bsgenome)
5682 ("r-genomeinfodb" ,r-genomeinfodb)
5683 ("r-genomicalignments" ,r-genomicalignments)
5684 ("r-genomicfeatures" ,r-genomicfeatures)
5685 ("r-genomicranges" ,r-genomicranges)
5686 ("r-gridextra" ,r-gridextra)
5687 ("r-gviz" ,r-gviz)
5688 ("r-iranges" ,r-iranges)
5689 ("r-lattice" ,r-lattice)
5690 ("r-latticeextra" ,r-latticeextra)
5691 ("r-nlme" ,r-nlme)
5692 ("r-rsamtools" ,r-rsamtools)
5693 ("r-s4vectors" ,r-s4vectors)
5694 ("r-seqinr" ,r-seqinr)
5695 ("r-summarizedexperiment" ,r-summarizedexperiment)
5696 ("r-variantannotation" ,r-variantannotation)))
5697 (native-inputs
5698 `(("r-knitr" ,r-knitr)))
5699 (home-page "https://github.com/pappewaio/AllelicImbalance")
5700 (synopsis "Investigate allele-specific expression")
5701 (description
5702 "This package provides a framework for allele-specific expression
5703 investigation using RNA-seq data.")
5704 (license license:gpl3)))
5705
5706 (define-public r-aucell
5707 (package
5708 (name "r-aucell")
5709 (version "1.12.0")
5710 (source
5711 (origin
5712 (method url-fetch)
5713 (uri (bioconductor-uri "AUCell" version))
5714 (sha256
5715 (base32
5716 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
5717 (properties `((upstream-name . "AUCell")))
5718 (build-system r-build-system)
5719 (propagated-inputs
5720 `(("r-biocgenerics" ,r-biocgenerics)
5721 ("r-data-table" ,r-data-table)
5722 ("r-gseabase" ,r-gseabase)
5723 ("r-mixtools" ,r-mixtools)
5724 ("r-r-utils" ,r-r-utils)
5725 ("r-s4vectors" ,r-s4vectors)
5726 ("r-shiny" ,r-shiny)
5727 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5728 (native-inputs
5729 `(("r-knitr" ,r-knitr)))
5730 (home-page "https://bioconductor.org/packages/AUCell/")
5731 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
5732 (description
5733 "AUCell identifies cells with active gene sets (e.g. signatures,
5734 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
5735 Under the Curve} (AUC) to calculate whether a critical subset of the input
5736 gene set is enriched within the expressed genes for each cell. The
5737 distribution of AUC scores across all the cells allows exploring the relative
5738 expression of the signature. Since the scoring method is ranking-based,
5739 AUCell is independent of the gene expression units and the normalization
5740 procedure. In addition, since the cells are evaluated individually, it can
5741 easily be applied to bigger datasets, subsetting the expression matrix if
5742 needed.")
5743 (license license:gpl3)))
5744
5745 (define-public r-ebimage
5746 (package
5747 (name "r-ebimage")
5748 (version "4.32.0")
5749 (source
5750 (origin
5751 (method url-fetch)
5752 (uri (bioconductor-uri "EBImage" version))
5753 (sha256
5754 (base32
5755 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
5756 (properties `((upstream-name . "EBImage")))
5757 (build-system r-build-system)
5758 (propagated-inputs
5759 `(("r-abind" ,r-abind)
5760 ("r-biocgenerics" ,r-biocgenerics)
5761 ("r-fftwtools" ,r-fftwtools)
5762 ("r-htmltools" ,r-htmltools)
5763 ("r-htmlwidgets" ,r-htmlwidgets)
5764 ("r-jpeg" ,r-jpeg)
5765 ("r-locfit" ,r-locfit)
5766 ("r-png" ,r-png)
5767 ("r-rcurl" ,r-rcurl)
5768 ("r-tiff" ,r-tiff)))
5769 (native-inputs
5770 `(("r-knitr" ,r-knitr))) ; for vignettes
5771 (home-page "https://github.com/aoles/EBImage")
5772 (synopsis "Image processing and analysis toolbox for R")
5773 (description
5774 "EBImage provides general purpose functionality for image processing and
5775 analysis. In the context of (high-throughput) microscopy-based cellular
5776 assays, EBImage offers tools to segment cells and extract quantitative
5777 cellular descriptors. This allows the automation of such tasks using the R
5778 programming language and facilitates the use of other tools in the R
5779 environment for signal processing, statistical modeling, machine learning and
5780 visualization with image data.")
5781 ;; Any version of the LGPL.
5782 (license license:lgpl2.1+)))
5783
5784 (define-public r-yamss
5785 (package
5786 (name "r-yamss")
5787 (version "1.16.0")
5788 (source
5789 (origin
5790 (method url-fetch)
5791 (uri (bioconductor-uri "yamss" version))
5792 (sha256
5793 (base32
5794 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
5795 (build-system r-build-system)
5796 (propagated-inputs
5797 `(("r-biocgenerics" ,r-biocgenerics)
5798 ("r-data-table" ,r-data-table)
5799 ("r-ebimage" ,r-ebimage)
5800 ("r-iranges" ,r-iranges)
5801 ("r-limma" ,r-limma)
5802 ("r-matrix" ,r-matrix)
5803 ("r-mzr" ,r-mzr)
5804 ("r-s4vectors" ,r-s4vectors)
5805 ("r-summarizedexperiment"
5806 ,r-summarizedexperiment)))
5807 (native-inputs
5808 `(("r-knitr" ,r-knitr)))
5809 (home-page "https://github.com/hansenlab/yamss")
5810 (synopsis "Tools for high-throughput metabolomics")
5811 (description
5812 "This package provides tools to analyze and visualize high-throughput
5813 metabolomics data acquired using chromatography-mass spectrometry. These tools
5814 preprocess data in a way that enables reliable and powerful differential
5815 analysis.")
5816 (license license:artistic2.0)))
5817
5818 (define-public r-gtrellis
5819 (package
5820 (name "r-gtrellis")
5821 (version "1.22.0")
5822 (source
5823 (origin
5824 (method url-fetch)
5825 (uri (bioconductor-uri "gtrellis" version))
5826 (sha256
5827 (base32
5828 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
5829 (build-system r-build-system)
5830 (propagated-inputs
5831 `(("r-circlize" ,r-circlize)
5832 ("r-genomicranges" ,r-genomicranges)
5833 ("r-getoptlong" ,r-getoptlong)
5834 ("r-iranges" ,r-iranges)))
5835 (native-inputs
5836 `(("r-knitr" ,r-knitr)))
5837 (home-page "https://github.com/jokergoo/gtrellis")
5838 (synopsis "Genome level Trellis layout")
5839 (description
5840 "Genome level Trellis graph visualizes genomic data conditioned by
5841 genomic categories (e.g. chromosomes). For each genomic category, multiple
5842 dimensional data which are represented as tracks describe different features
5843 from different aspects. This package provides high flexibility to arrange
5844 genomic categories and to add self-defined graphics in the plot.")
5845 (license license:expat)))
5846
5847 (define-public r-somaticsignatures
5848 (package
5849 (name "r-somaticsignatures")
5850 (version "2.26.0")
5851 (source
5852 (origin
5853 (method url-fetch)
5854 (uri (bioconductor-uri "SomaticSignatures" version))
5855 (sha256
5856 (base32
5857 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
5858 (properties
5859 `((upstream-name . "SomaticSignatures")))
5860 (build-system r-build-system)
5861 (propagated-inputs
5862 `(("r-biobase" ,r-biobase)
5863 ("r-biostrings" ,r-biostrings)
5864 ("r-genomeinfodb" ,r-genomeinfodb)
5865 ("r-genomicranges" ,r-genomicranges)
5866 ("r-ggbio" ,r-ggbio)
5867 ("r-ggplot2" ,r-ggplot2)
5868 ("r-iranges" ,r-iranges)
5869 ("r-nmf" ,r-nmf)
5870 ("r-pcamethods" ,r-pcamethods)
5871 ("r-proxy" ,r-proxy)
5872 ("r-reshape2" ,r-reshape2)
5873 ("r-s4vectors" ,r-s4vectors)
5874 ("r-variantannotation" ,r-variantannotation)))
5875 (native-inputs
5876 `(("r-knitr" ,r-knitr)))
5877 (home-page "https://github.com/juliangehring/SomaticSignatures")
5878 (synopsis "Somatic signatures")
5879 (description
5880 "This package identifies mutational signatures of @dfn{single nucleotide
5881 variants} (SNVs). It provides a infrastructure related to the methodology
5882 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
5883 decomposition algorithms.")
5884 (license license:expat)))
5885
5886 (define-public r-yapsa
5887 (package
5888 (name "r-yapsa")
5889 (version "1.16.0")
5890 (source
5891 (origin
5892 (method url-fetch)
5893 (uri (bioconductor-uri "YAPSA" version))
5894 (sha256
5895 (base32
5896 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
5897 (properties `((upstream-name . "YAPSA")))
5898 (build-system r-build-system)
5899 (propagated-inputs
5900 `(("r-biostrings" ,r-biostrings)
5901 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
5902 ("r-circlize" ,r-circlize)
5903 ("r-complexheatmap" ,r-complexheatmap)
5904 ("r-corrplot" ,r-corrplot)
5905 ("r-dendextend" ,r-dendextend)
5906 ("r-doparallel" ,r-doparallel)
5907 ("r-dplyr" ,r-dplyr)
5908 ("r-genomeinfodb" ,r-genomeinfodb)
5909 ("r-genomicranges" ,r-genomicranges)
5910 ("r-getoptlong" ,r-getoptlong)
5911 ("r-ggbeeswarm" ,r-ggbeeswarm)
5912 ("r-ggplot2" ,r-ggplot2)
5913 ("r-gridextra" ,r-gridextra)
5914 ("r-gtrellis" ,r-gtrellis)
5915 ("r-keggrest" ,r-keggrest)
5916 ("r-limsolve" ,r-limsolve)
5917 ("r-magrittr" ,r-magrittr)
5918 ("r-pmcmr" ,r-pmcmr)
5919 ("r-pracma" ,r-pracma)
5920 ("r-reshape2" ,r-reshape2)
5921 ("r-somaticsignatures" ,r-somaticsignatures)
5922 ("r-variantannotation" ,r-variantannotation)))
5923 (native-inputs
5924 `(("r-knitr" ,r-knitr)))
5925 (home-page "https://bioconductor.org/packages/YAPSA/")
5926 (synopsis "Yet another package for signature analysis")
5927 (description
5928 "This package provides functions and routines useful in the analysis of
5929 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
5930 functions to perform a signature analysis with known signatures and a
5931 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
5932 provided.")
5933 (license license:gpl3)))
5934
5935 (define-public r-gcrma
5936 (package
5937 (name "r-gcrma")
5938 (version "2.62.0")
5939 (source
5940 (origin
5941 (method url-fetch)
5942 (uri (bioconductor-uri "gcrma" version))
5943 (sha256
5944 (base32
5945 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
5946 (build-system r-build-system)
5947 (propagated-inputs
5948 `(("r-affy" ,r-affy)
5949 ("r-affyio" ,r-affyio)
5950 ("r-biobase" ,r-biobase)
5951 ("r-biocmanager" ,r-biocmanager)
5952 ("r-biostrings" ,r-biostrings)
5953 ("r-xvector" ,r-xvector)))
5954 (home-page "https://bioconductor.org/packages/gcrma/")
5955 (synopsis "Background adjustment using sequence information")
5956 (description
5957 "Gcrma adjusts for background intensities in Affymetrix array data which
5958 include optical noise and @dfn{non-specific binding} (NSB). The main function
5959 @code{gcrma} converts background adjusted probe intensities to expression
5960 measures using the same normalization and summarization methods as a
5961 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
5962 to estimate probe affinity to NSB. The sequence information is summarized in
5963 a more complex way than the simple GC content. Instead, the base types (A, T,
5964 G or C) at each position along the probe determine the affinity of each probe.
5965 The parameters of the position-specific base contributions to the probe
5966 affinity is estimated in an NSB experiment in which only NSB but no
5967 gene-specific binding is expected.")
5968 ;; Any version of the LGPL
5969 (license license:lgpl2.1+)))
5970
5971 (define-public r-simpleaffy
5972 (package
5973 (name "r-simpleaffy")
5974 (version "2.66.0")
5975 (source
5976 (origin
5977 (method url-fetch)
5978 (uri (bioconductor-uri "simpleaffy" version))
5979 (sha256
5980 (base32
5981 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
5982 (build-system r-build-system)
5983 (propagated-inputs
5984 `(("r-affy" ,r-affy)
5985 ("r-biobase" ,r-biobase)
5986 ("r-biocgenerics" ,r-biocgenerics)
5987 ("r-gcrma" ,r-gcrma)
5988 ("r-genefilter" ,r-genefilter)))
5989 (home-page "https://bioconductor.org/packages/simpleaffy/")
5990 (synopsis "Very simple high level analysis of Affymetrix data")
5991 (description
5992 "This package provides high level functions for reading Affy @file{.CEL}
5993 files, phenotypic data, and then computing simple things with it, such as
5994 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
5995 library. It also has some basic scatter plot functions and mechanisms for
5996 generating high resolution journal figures.")
5997 (license license:gpl2+)))
5998
5999 (define-public r-yaqcaffy
6000 (package
6001 (name "r-yaqcaffy")
6002 (version "1.50.0")
6003 (source
6004 (origin
6005 (method url-fetch)
6006 (uri (bioconductor-uri "yaqcaffy" version))
6007 (sha256
6008 (base32
6009 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
6010 (build-system r-build-system)
6011 (propagated-inputs
6012 `(("r-simpleaffy" ,r-simpleaffy)))
6013 (home-page "https://bioconductor.org/packages/yaqcaffy/")
6014 (synopsis "Affymetrix quality control and reproducibility analysis")
6015 (description
6016 "This is a package that can be used for quality control of Affymetrix
6017 GeneChip expression data and reproducibility analysis of human whole genome
6018 chips with the MAQC reference datasets.")
6019 (license license:artistic2.0)))
6020
6021 (define-public r-quantro
6022 (package
6023 (name "r-quantro")
6024 (version "1.24.0")
6025 (source
6026 (origin
6027 (method url-fetch)
6028 (uri (bioconductor-uri "quantro" version))
6029 (sha256
6030 (base32
6031 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
6032 (build-system r-build-system)
6033 (propagated-inputs
6034 `(("r-biobase" ,r-biobase)
6035 ("r-doparallel" ,r-doparallel)
6036 ("r-foreach" ,r-foreach)
6037 ("r-ggplot2" ,r-ggplot2)
6038 ("r-iterators" ,r-iterators)
6039 ("r-minfi" ,r-minfi)
6040 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6041 (native-inputs
6042 `(("r-knitr" ,r-knitr)))
6043 (home-page "https://bioconductor.org/packages/quantro/")
6044 (synopsis "Test for when to use quantile normalization")
6045 (description
6046 "This package provides a data-driven test for the assumptions of quantile
6047 normalization using raw data such as objects that inherit eSets (e.g.
6048 ExpressionSet, MethylSet). Group level information about each sample (such as
6049 Tumor / Normal status) must also be provided because the test assesses if
6050 there are global differences in the distributions between the user-defined
6051 groups.")
6052 (license license:gpl3+)))
6053
6054 (define-public r-yarn
6055 (package
6056 (name "r-yarn")
6057 (version "1.16.0")
6058 (source
6059 (origin
6060 (method url-fetch)
6061 (uri (bioconductor-uri "yarn" version))
6062 (sha256
6063 (base32
6064 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
6065 (build-system r-build-system)
6066 (propagated-inputs
6067 `(("r-biobase" ,r-biobase)
6068 ("r-biomart" ,r-biomart)
6069 ("r-downloader" ,r-downloader)
6070 ("r-edger" ,r-edger)
6071 ("r-gplots" ,r-gplots)
6072 ("r-limma" ,r-limma)
6073 ("r-matrixstats" ,r-matrixstats)
6074 ("r-preprocesscore" ,r-preprocesscore)
6075 ("r-quantro" ,r-quantro)
6076 ("r-rcolorbrewer" ,r-rcolorbrewer)
6077 ("r-readr" ,r-readr)))
6078 (native-inputs
6079 `(("r-knitr" ,r-knitr)))
6080 (home-page "https://bioconductor.org/packages/yarn/")
6081 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
6082 (description
6083 "Expedite large RNA-Seq analyses using a combination of previously
6084 developed tools. YARN is meant to make it easier for the user in performing
6085 basic mis-annotation quality control, filtering, and condition-aware
6086 normalization. YARN leverages many Bioconductor tools and statistical
6087 techniques to account for the large heterogeneity and sparsity found in very
6088 large RNA-seq experiments.")
6089 (license license:artistic2.0)))
6090
6091 (define-public r-roar
6092 (package
6093 (name "r-roar")
6094 (version "1.26.0")
6095 (source
6096 (origin
6097 (method url-fetch)
6098 (uri (bioconductor-uri "roar" version))
6099 (sha256
6100 (base32
6101 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
6102 (build-system r-build-system)
6103 (propagated-inputs
6104 `(("r-biocgenerics" ,r-biocgenerics)
6105 ("r-genomeinfodb" ,r-genomeinfodb)
6106 ("r-genomicalignments" ,r-genomicalignments)
6107 ("r-genomicranges" ,r-genomicranges)
6108 ("r-iranges" ,r-iranges)
6109 ("r-rtracklayer" ,r-rtracklayer)
6110 ("r-s4vectors" ,r-s4vectors)
6111 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6112 (home-page "https://github.com/vodkatad/roar/")
6113 (synopsis "Identify differential APA usage from RNA-seq alignments")
6114 (description
6115 "This package provides tools for identifying preferential usage of APA
6116 sites, comparing two biological conditions, starting from known alternative
6117 sites and alignments obtained from standard RNA-seq experiments.")
6118 (license license:gpl3)))
6119
6120 (define-public r-xbseq
6121 (package
6122 (name "r-xbseq")
6123 (version "1.22.0")
6124 (source
6125 (origin
6126 (method url-fetch)
6127 (uri (bioconductor-uri "XBSeq" version))
6128 (sha256
6129 (base32
6130 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
6131 (properties `((upstream-name . "XBSeq")))
6132 (build-system r-build-system)
6133 (propagated-inputs
6134 `(("r-biobase" ,r-biobase)
6135 ("r-deseq2" ,r-deseq2)
6136 ("r-dplyr" ,r-dplyr)
6137 ("r-ggplot2" ,r-ggplot2)
6138 ("r-locfit" ,r-locfit)
6139 ("r-magrittr" ,r-magrittr)
6140 ("r-matrixstats" ,r-matrixstats)
6141 ("r-pracma" ,r-pracma)
6142 ("r-roar" ,r-roar)))
6143 (native-inputs
6144 `(("r-knitr" ,r-knitr)))
6145 (home-page "https://github.com/Liuy12/XBSeq")
6146 (synopsis "Test for differential expression for RNA-seq data")
6147 (description
6148 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
6149 expression} (DE), where a statistical model was established based on the
6150 assumption that observed signals are the convolution of true expression
6151 signals and sequencing noises. The mapped reads in non-exonic regions are
6152 considered as sequencing noises, which follows a Poisson distribution. Given
6153 measurable observed signal and background noise from RNA-seq data, true
6154 expression signals, assuming governed by the negative binomial distribution,
6155 can be delineated and thus the accurate detection of differential expressed
6156 genes.")
6157 (license license:gpl3+)))
6158
6159 (define-public r-massspecwavelet
6160 (package
6161 (name "r-massspecwavelet")
6162 (version "1.56.0")
6163 (source
6164 (origin
6165 (method url-fetch)
6166 (uri (bioconductor-uri "MassSpecWavelet" version))
6167 (sha256
6168 (base32
6169 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
6170 (properties
6171 `((upstream-name . "MassSpecWavelet")))
6172 (build-system r-build-system)
6173 (propagated-inputs
6174 `(("r-waveslim" ,r-waveslim)))
6175 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
6176 (synopsis "Mass spectrum processing by wavelet-based algorithms")
6177 (description
6178 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
6179 data mainly through the use of wavelet transforms. It supports peak detection
6180 based on @dfn{Continuous Wavelet Transform} (CWT).")
6181 (license license:lgpl2.0+)))
6182
6183 (define-public r-xcms
6184 (package
6185 (name "r-xcms")
6186 (version "3.12.0")
6187 (source
6188 (origin
6189 (method url-fetch)
6190 (uri (bioconductor-uri "xcms" version))
6191 (sha256
6192 (base32
6193 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
6194 (build-system r-build-system)
6195 (propagated-inputs
6196 `(("r-biobase" ,r-biobase)
6197 ("r-biocgenerics" ,r-biocgenerics)
6198 ("r-biocparallel" ,r-biocparallel)
6199 ("r-iranges" ,r-iranges)
6200 ("r-lattice" ,r-lattice)
6201 ("r-massspecwavelet" ,r-massspecwavelet)
6202 ("r-mscoreutils" ,r-mscoreutils)
6203 ("r-msnbase" ,r-msnbase)
6204 ("r-mzr" ,r-mzr)
6205 ("r-plyr" ,r-plyr)
6206 ("r-protgenerics" ,r-protgenerics)
6207 ("r-rann" ,r-rann)
6208 ("r-rcolorbrewer" ,r-rcolorbrewer)
6209 ("r-robustbase" ,r-robustbase)
6210 ("r-s4vectors" ,r-s4vectors)
6211 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6212 (native-inputs
6213 `(("r-knitr" ,r-knitr)))
6214 (home-page "https://bioconductor.org/packages/xcms/")
6215 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
6216 (description
6217 "This package provides a framework for processing and visualization of
6218 chromatographically separated and single-spectra mass spectral data. It
6219 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
6220 data for high-throughput, untargeted analyte profiling.")
6221 (license license:gpl2+)))
6222
6223 (define-public r-wrench
6224 (package
6225 (name "r-wrench")
6226 (version "1.8.0")
6227 (source
6228 (origin
6229 (method url-fetch)
6230 (uri (bioconductor-uri "Wrench" version))
6231 (sha256
6232 (base32
6233 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
6234 (properties `((upstream-name . "Wrench")))
6235 (build-system r-build-system)
6236 (propagated-inputs
6237 `(("r-limma" ,r-limma)
6238 ("r-locfit" ,r-locfit)
6239 ("r-matrixstats" ,r-matrixstats)))
6240 (native-inputs
6241 `(("r-knitr" ,r-knitr)))
6242 (home-page "https://github.com/HCBravoLab/Wrench")
6243 (synopsis "Wrench normalization for sparse count data")
6244 (description
6245 "Wrench is a package for normalization sparse genomic count data, like
6246 that arising from 16s metagenomic surveys.")
6247 (license license:artistic2.0)))
6248
6249 (define-public r-wiggleplotr
6250 (package
6251 (name "r-wiggleplotr")
6252 (version "1.14.0")
6253 (source
6254 (origin
6255 (method url-fetch)
6256 (uri (bioconductor-uri "wiggleplotr" version))
6257 (sha256
6258 (base32
6259 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
6260 (build-system r-build-system)
6261 (propagated-inputs
6262 `(("r-assertthat" ,r-assertthat)
6263 ("r-cowplot" ,r-cowplot)
6264 ("r-dplyr" ,r-dplyr)
6265 ("r-genomeinfodb" ,r-genomeinfodb)
6266 ("r-genomicranges" ,r-genomicranges)
6267 ("r-ggplot2" ,r-ggplot2)
6268 ("r-iranges" ,r-iranges)
6269 ("r-purrr" ,r-purrr)
6270 ("r-rtracklayer" ,r-rtracklayer)
6271 ("r-s4vectors" ,r-s4vectors)))
6272 (native-inputs
6273 `(("r-knitr" ,r-knitr)))
6274 (home-page "https://bioconductor.org/packages/wiggleplotr/")
6275 (synopsis "Make read coverage plots from BigWig files")
6276 (description
6277 "This package provides tools to visualize read coverage from sequencing
6278 experiments together with genomic annotations (genes, transcripts, peaks).
6279 Introns of long transcripts can be rescaled to a fixed length for better
6280 visualization of exonic read coverage.")
6281 (license license:asl2.0)))
6282
6283 (define-public r-widgettools
6284 (package
6285 (name "r-widgettools")
6286 (version "1.68.0")
6287 (source
6288 (origin
6289 (method url-fetch)
6290 (uri (bioconductor-uri "widgetTools" version))
6291 (sha256
6292 (base32
6293 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
6294 (properties `((upstream-name . "widgetTools")))
6295 (build-system r-build-system)
6296 (home-page "https://bioconductor.org/packages/widgetTools/")
6297 (synopsis "Tools for creating interactive tcltk widgets")
6298 (description
6299 "This package contains tools to support the construction of tcltk
6300 widgets in R.")
6301 ;; Any version of the LGPL.
6302 (license license:lgpl3+)))
6303
6304 (define-public r-webbioc
6305 (package
6306 (name "r-webbioc")
6307 (version "1.62.0")
6308 (source
6309 (origin
6310 (method url-fetch)
6311 (uri (bioconductor-uri "webbioc" version))
6312 (sha256
6313 (base32
6314 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
6315 (build-system r-build-system)
6316 (inputs
6317 `(("netpbm" ,netpbm)
6318 ("perl" ,perl)))
6319 (propagated-inputs
6320 `(("r-affy" ,r-affy)
6321 ("r-annaffy" ,r-annaffy)
6322 ("r-biobase" ,r-biobase)
6323 ("r-biocmanager" ,r-biocmanager)
6324 ("r-gcrma" ,r-gcrma)
6325 ("r-multtest" ,r-multtest)
6326 ("r-qvalue" ,r-qvalue)
6327 ("r-vsn" ,r-vsn)))
6328 (home-page "https://www.bioconductor.org/")
6329 (synopsis "Bioconductor web interface")
6330 (description
6331 "This package provides an integrated web interface for doing microarray
6332 analysis using several of the Bioconductor packages. It is intended to be
6333 deployed as a centralized bioinformatics resource for use by many users.
6334 Currently only Affymetrix oligonucleotide analysis is supported.")
6335 (license license:gpl2+)))
6336
6337 (define-public r-zfpkm
6338 (package
6339 (name "r-zfpkm")
6340 (version "1.12.0")
6341 (source
6342 (origin
6343 (method url-fetch)
6344 (uri (bioconductor-uri "zFPKM" version))
6345 (sha256
6346 (base32
6347 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
6348 (properties `((upstream-name . "zFPKM")))
6349 (build-system r-build-system)
6350 (propagated-inputs
6351 `(("r-checkmate" ,r-checkmate)
6352 ("r-dplyr" ,r-dplyr)
6353 ("r-ggplot2" ,r-ggplot2)
6354 ("r-summarizedexperiment" ,r-summarizedexperiment)
6355 ("r-tidyr" ,r-tidyr)))
6356 (native-inputs
6357 `(("r-knitr" ,r-knitr)))
6358 (home-page "https://github.com/ronammar/zFPKM/")
6359 (synopsis "Functions to facilitate zFPKM transformations")
6360 (description
6361 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
6362 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
6363 24215113).")
6364 (license license:gpl3)))
6365
6366 (define-public r-rbowtie2
6367 (package
6368 (name "r-rbowtie2")
6369 (version "1.12.0")
6370 (source
6371 (origin
6372 (method url-fetch)
6373 (uri (bioconductor-uri "Rbowtie2" version))
6374 (sha256
6375 (base32
6376 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
6377 (properties `((upstream-name . "Rbowtie2")))
6378 (build-system r-build-system)
6379 (inputs
6380 `(("zlib" ,zlib)))
6381 (native-inputs
6382 `(("r-knitr" ,r-knitr)))
6383 (home-page "https://bioconductor.org/packages/Rbowtie2/")
6384 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
6385 (description
6386 "This package provides an R wrapper of the popular @code{bowtie2}
6387 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
6388 rapid adapter trimming, identification, and read merging.")
6389 (license license:gpl3+)))
6390
6391 (define-public r-progeny
6392 (package
6393 (name "r-progeny")
6394 (version "1.12.0")
6395 (source
6396 (origin
6397 (method url-fetch)
6398 (uri (bioconductor-uri "progeny" version))
6399 (sha256
6400 (base32
6401 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
6402 (build-system r-build-system)
6403 (propagated-inputs
6404 `(("r-biobase" ,r-biobase)
6405 ("r-dplyr" ,r-dplyr)
6406 ("r-ggplot2" ,r-ggplot2)
6407 ("r-ggrepel" ,r-ggrepel)
6408 ("r-gridextra" ,r-gridextra)
6409 ("r-tidyr" ,r-tidyr)))
6410 (native-inputs
6411 `(("r-knitr" ,r-knitr)))
6412 (home-page "https://github.com/saezlab/progeny")
6413 (synopsis "Pathway responsive gene activity inference")
6414 (description
6415 "This package provides a function to infer pathway activity from gene
6416 expression. It contains the linear model inferred in the publication
6417 \"Perturbation-response genes reveal signaling footprints in cancer gene
6418 expression\".")
6419 (license license:asl2.0)))
6420
6421 (define-public r-arrmnormalization
6422 (package
6423 (name "r-arrmnormalization")
6424 (version "1.30.0")
6425 (source
6426 (origin
6427 (method url-fetch)
6428 (uri (bioconductor-uri "ARRmNormalization" version))
6429 (sha256
6430 (base32
6431 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
6432 (properties
6433 `((upstream-name . "ARRmNormalization")))
6434 (build-system r-build-system)
6435 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
6436 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
6437 (synopsis "Adaptive robust regression normalization for methylation data")
6438 (description
6439 "This is a package to perform the @dfn{Adaptive Robust Regression
6440 method} (ARRm) for the normalization of methylation data from the Illumina
6441 Infinium HumanMethylation 450k assay.")
6442 (license license:artistic2.0)))
6443
6444 (define-public r-biocfilecache
6445 (package
6446 (name "r-biocfilecache")
6447 (version "1.14.0")
6448 (source
6449 (origin
6450 (method url-fetch)
6451 (uri (bioconductor-uri "BiocFileCache" version))
6452 (sha256
6453 (base32
6454 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
6455 (properties `((upstream-name . "BiocFileCache")))
6456 (build-system r-build-system)
6457 (propagated-inputs
6458 `(("r-curl" ,r-curl)
6459 ("r-dbi" ,r-dbi)
6460 ("r-dbplyr" ,r-dbplyr)
6461 ("r-dplyr" ,r-dplyr)
6462 ("r-httr" ,r-httr)
6463 ("r-rappdirs" ,r-rappdirs)
6464 ("r-rsqlite" ,r-rsqlite)))
6465 (native-inputs
6466 `(("r-knitr" ,r-knitr)))
6467 (home-page "https://bioconductor.org/packages/BiocFileCache/")
6468 (synopsis "Manage files across sessions")
6469 (description
6470 "This package creates a persistent on-disk cache of files that the user
6471 can add, update, and retrieve. It is useful for managing resources (such as
6472 custom Txdb objects) that are costly or difficult to create, web resources,
6473 and data files used across sessions.")
6474 (license license:artistic2.0)))
6475
6476 (define-public r-iclusterplus
6477 (package
6478 (name "r-iclusterplus")
6479 (version "1.26.0")
6480 (source
6481 (origin
6482 (method url-fetch)
6483 (uri (bioconductor-uri "iClusterPlus" version))
6484 (sha256
6485 (base32
6486 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
6487 (properties `((upstream-name . "iClusterPlus")))
6488 (build-system r-build-system)
6489 (native-inputs `(("gfortran" ,gfortran)))
6490 (home-page "https://bioconductor.org/packages/iClusterPlus/")
6491 (synopsis "Integrative clustering of multi-type genomic data")
6492 (description
6493 "iClusterPlus is developed for integrative clustering analysis of
6494 multi-type genomic data and is an enhanced version of iCluster proposed and
6495 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
6496 from the experiments where biological samples (e.g. tumor samples) are
6497 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
6498 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
6499 on. In the iClusterPlus model, binary observations such as somatic mutation
6500 are modeled as Binomial processes; categorical observations such as copy
6501 number states are realizations of Multinomial random variables; counts are
6502 modeled as Poisson random processes; and continuous measures are modeled by
6503 Gaussian distributions.")
6504 (license license:gpl2+)))
6505
6506 (define-public r-rbowtie
6507 (package
6508 (name "r-rbowtie")
6509 (version "1.30.0")
6510 (source
6511 (origin
6512 (method url-fetch)
6513 (uri (bioconductor-uri "Rbowtie" version))
6514 (sha256
6515 (base32
6516 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
6517 (properties `((upstream-name . "Rbowtie")))
6518 (build-system r-build-system)
6519 (inputs
6520 `(("zlib" ,zlib)))
6521 (native-inputs
6522 `(("r-knitr" ,r-knitr)))
6523 (home-page "https://bioconductor.org/packages/Rbowtie/")
6524 (synopsis "R bowtie wrapper")
6525 (description
6526 "This package provides an R wrapper around the popular bowtie short read
6527 aligner and around SpliceMap, a de novo splice junction discovery and
6528 alignment tool.")
6529 (license license:artistic2.0)))
6530
6531 (define-public r-sgseq
6532 (package
6533 (name "r-sgseq")
6534 (version "1.24.0")
6535 (source
6536 (origin
6537 (method url-fetch)
6538 (uri (bioconductor-uri "SGSeq" version))
6539 (sha256
6540 (base32
6541 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
6542 (properties `((upstream-name . "SGSeq")))
6543 (build-system r-build-system)
6544 (propagated-inputs
6545 `(("r-annotationdbi" ,r-annotationdbi)
6546 ("r-biocgenerics" ,r-biocgenerics)
6547 ("r-biostrings" ,r-biostrings)
6548 ("r-genomeinfodb" ,r-genomeinfodb)
6549 ("r-genomicalignments" ,r-genomicalignments)
6550 ("r-genomicfeatures" ,r-genomicfeatures)
6551 ("r-genomicranges" ,r-genomicranges)
6552 ("r-igraph" ,r-igraph)
6553 ("r-iranges" ,r-iranges)
6554 ("r-rsamtools" ,r-rsamtools)
6555 ("r-rtracklayer" ,r-rtracklayer)
6556 ("r-runit" ,r-runit)
6557 ("r-s4vectors" ,r-s4vectors)
6558 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6559 (native-inputs
6560 `(("r-knitr" ,r-knitr)))
6561 (home-page "https://bioconductor.org/packages/SGSeq/")
6562 (synopsis "Splice event prediction and quantification from RNA-seq data")
6563 (description
6564 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
6565 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
6566 represented as a splice graph, which can be obtained from existing annotation
6567 or predicted from the mapped sequence reads. Splice events are identified
6568 from the graph and are quantified locally using structurally compatible reads
6569 at the start or end of each splice variant. The software includes functions
6570 for splice event prediction, quantification, visualization and
6571 interpretation.")
6572 (license license:artistic2.0)))
6573
6574 (define-public r-rhisat2
6575 (package
6576 (name "r-rhisat2")
6577 (version "1.6.0")
6578 (source
6579 (origin
6580 (method url-fetch)
6581 (uri (bioconductor-uri "Rhisat2" version))
6582 (sha256
6583 (base32
6584 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
6585 (properties `((upstream-name . "Rhisat2")))
6586 (build-system r-build-system)
6587 (arguments
6588 `(#:phases
6589 (modify-phases %standard-phases
6590 (add-after 'unpack 'make-reproducible
6591 (lambda _
6592 (substitute* "src/Makefile"
6593 (("`hostname`") "guix")
6594 (("`date`") "0")
6595 ;; Avoid shelling out to "which".
6596 (("^CC =.*") (which "gcc"))
6597 (("^CPP =.*") (which "g++")))
6598 #t)))))
6599 (propagated-inputs
6600 `(("r-genomicfeatures" ,r-genomicfeatures)
6601 ("r-genomicranges" ,r-genomicranges)
6602 ("r-sgseq" ,r-sgseq)))
6603 (native-inputs
6604 `(("r-knitr" ,r-knitr)))
6605 (home-page "https://github.com/fmicompbio/Rhisat2")
6606 (synopsis "R Wrapper for HISAT2 sequence aligner")
6607 (description
6608 "This package provides an R interface to the HISAT2 spliced short-read
6609 aligner by Kim et al. (2015). The package contains wrapper functions to
6610 create a genome index and to perform the read alignment to the generated
6611 index.")
6612 (license license:gpl3)))
6613
6614 (define-public r-quasr
6615 (package
6616 (name "r-quasr")
6617 (version "1.30.0")
6618 (source
6619 (origin
6620 (method url-fetch)
6621 (uri (bioconductor-uri "QuasR" version))
6622 (sha256
6623 (base32
6624 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
6625 (properties `((upstream-name . "QuasR")))
6626 (build-system r-build-system)
6627 (propagated-inputs
6628 `(("r-annotationdbi" ,r-annotationdbi)
6629 ("r-biobase" ,r-biobase)
6630 ("r-biocgenerics" ,r-biocgenerics)
6631 ("r-biocmanager" ,r-biocmanager)
6632 ("r-biocparallel" ,r-biocparallel)
6633 ("r-biostrings" ,r-biostrings)
6634 ("r-bsgenome" ,r-bsgenome)
6635 ("r-genomeinfodb" ,r-genomeinfodb)
6636 ("r-genomicalignments" ,r-genomicalignments)
6637 ("r-genomicfeatures" ,r-genomicfeatures)
6638 ("r-genomicfiles" ,r-genomicfiles)
6639 ("r-genomicranges" ,r-genomicranges)
6640 ("r-iranges" ,r-iranges)
6641 ("r-rbowtie" ,r-rbowtie)
6642 ("r-rhisat2" ,r-rhisat2)
6643 ("r-rhtslib" ,r-rhtslib)
6644 ("r-rsamtools" ,r-rsamtools)
6645 ("r-rtracklayer" ,r-rtracklayer)
6646 ("r-s4vectors" ,r-s4vectors)
6647 ("r-shortread" ,r-shortread)))
6648 (native-inputs
6649 `(("r-knitr" ,r-knitr)))
6650 (home-page "https://bioconductor.org/packages/QuasR/")
6651 (synopsis "Quantify and annotate short reads in R")
6652 (description
6653 "This package provides a framework for the quantification and analysis of
6654 short genomic reads. It covers a complete workflow starting from raw sequence
6655 reads, over creation of alignments and quality control plots, to the
6656 quantification of genomic regions of interest.")
6657 (license license:gpl2)))
6658
6659 (define-public r-rqc
6660 (package
6661 (name "r-rqc")
6662 (version "1.24.0")
6663 (source
6664 (origin
6665 (method url-fetch)
6666 (uri (bioconductor-uri "Rqc" version))
6667 (sha256
6668 (base32
6669 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
6670 (properties `((upstream-name . "Rqc")))
6671 (build-system r-build-system)
6672 (propagated-inputs
6673 `(("r-biocgenerics" ,r-biocgenerics)
6674 ("r-biocparallel" ,r-biocparallel)
6675 ("r-biocstyle" ,r-biocstyle)
6676 ("r-biostrings" ,r-biostrings)
6677 ("r-biovizbase" ,r-biovizbase)
6678 ("r-genomicalignments" ,r-genomicalignments)
6679 ("r-genomicfiles" ,r-genomicfiles)
6680 ("r-ggplot2" ,r-ggplot2)
6681 ("r-iranges" ,r-iranges)
6682 ("r-knitr" ,r-knitr)
6683 ("r-markdown" ,r-markdown)
6684 ("r-plyr" ,r-plyr)
6685 ("r-rcpp" ,r-rcpp)
6686 ("r-reshape2" ,r-reshape2)
6687 ("r-rsamtools" ,r-rsamtools)
6688 ("r-s4vectors" ,r-s4vectors)
6689 ("r-shiny" ,r-shiny)
6690 ("r-shortread" ,r-shortread)))
6691 (native-inputs
6692 `(("r-knitr" ,r-knitr)))
6693 (home-page "https://github.com/labbcb/Rqc")
6694 (synopsis "Quality control tool for high-throughput sequencing data")
6695 (description
6696 "Rqc is an optimized tool designed for quality control and assessment of
6697 high-throughput sequencing data. It performs parallel processing of entire
6698 files and produces a report which contains a set of high-resolution
6699 graphics.")
6700 (license license:gpl2+)))
6701
6702 (define-public r-birewire
6703 (package
6704 (name "r-birewire")
6705 (version "3.22.0")
6706 (source
6707 (origin
6708 (method url-fetch)
6709 (uri (bioconductor-uri "BiRewire" version))
6710 (sha256
6711 (base32
6712 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
6713 (properties `((upstream-name . "BiRewire")))
6714 (build-system r-build-system)
6715 (propagated-inputs
6716 `(("r-igraph" ,r-igraph)
6717 ("r-matrix" ,r-matrix)
6718 ("r-slam" ,r-slam)
6719 ("r-tsne" ,r-tsne)))
6720 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
6721 (synopsis "Tools for randomization of bipartite graphs")
6722 (description
6723 "This package provides functions for bipartite network rewiring through N
6724 consecutive switching steps and for the computation of the minimal number of
6725 switching steps to be performed in order to maximise the dissimilarity with
6726 respect to the original network. It includes functions for the analysis of
6727 the introduced randomness across the switching steps and several other
6728 routines to analyse the resulting networks and their natural projections.")
6729 (license license:gpl3)))
6730
6731 (define-public r-birta
6732 (package
6733 (name "r-birta")
6734 (version "1.31.0")
6735 (source
6736 (origin
6737 (method url-fetch)
6738 (uri (bioconductor-uri "birta" version))
6739 (sha256
6740 (base32
6741 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
6742 (build-system r-build-system)
6743 (propagated-inputs
6744 `(("r-biobase" ,r-biobase)
6745 ("r-limma" ,r-limma)
6746 ("r-mass" ,r-mass)))
6747 (home-page "https://bioconductor.org/packages/birta")
6748 (synopsis "Bayesian inference of regulation of transcriptional activity")
6749 (description
6750 "Expression levels of mRNA molecules are regulated by different
6751 processes, comprising inhibition or activation by transcription factors and
6752 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
6753 Inference of Regulation of Transcriptional Activity) uses the regulatory
6754 networks of transcription factors and miRNAs together with mRNA and miRNA
6755 expression data to predict switches in regulatory activity between two
6756 conditions. A Bayesian network is used to model the regulatory structure and
6757 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
6758 (license license:gpl2+)))
6759
6760 (define-public r-multidataset
6761 (package
6762 (name "r-multidataset")
6763 (version "1.18.1")
6764 (source
6765 (origin
6766 (method url-fetch)
6767 (uri (bioconductor-uri "MultiDataSet" version))
6768 (sha256
6769 (base32
6770 "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4"))))
6771 (properties `((upstream-name . "MultiDataSet")))
6772 (build-system r-build-system)
6773 (propagated-inputs
6774 `(("r-biobase" ,r-biobase)
6775 ("r-biocgenerics" ,r-biocgenerics)
6776 ("r-genomicranges" ,r-genomicranges)
6777 ("r-ggplot2" ,r-ggplot2)
6778 ("r-ggrepel" ,r-ggrepel)
6779 ("r-iranges" ,r-iranges)
6780 ("r-limma" ,r-limma)
6781 ("r-qqman" ,r-qqman)
6782 ("r-s4vectors" ,r-s4vectors)
6783 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6784 (native-inputs
6785 `(("r-knitr" ,r-knitr)))
6786 (home-page "https://bioconductor.org/packages/MultiDataSet/")
6787 (synopsis "Implementation of MultiDataSet and ResultSet")
6788 (description
6789 "This package provides an implementation of the BRGE's (Bioinformatic
6790 Research Group in Epidemiology from Center for Research in Environmental
6791 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
6792 integrating multi omics data sets and ResultSet is a container for omics
6793 results. This package contains base classes for MEAL and rexposome
6794 packages.")
6795 (license license:expat)))
6796
6797 (define-public r-ropls
6798 (package
6799 (name "r-ropls")
6800 (version "1.22.0")
6801 (source
6802 (origin
6803 (method url-fetch)
6804 (uri (bioconductor-uri "ropls" version))
6805 (sha256
6806 (base32
6807 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
6808 (build-system r-build-system)
6809 (propagated-inputs
6810 `(("r-biobase" ,r-biobase)
6811 ("r-multidataset" ,r-multidataset)))
6812 (native-inputs
6813 `(("r-knitr" ,r-knitr))) ; for vignettes
6814 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
6815 (synopsis "Multivariate analysis and feature selection of omics data")
6816 (description
6817 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
6818 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
6819 regression, classification, and feature selection of omics data where the
6820 number of variables exceeds the number of samples and with multicollinearity
6821 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
6822 separately model the variation correlated (predictive) to the factor of
6823 interest and the uncorrelated (orthogonal) variation. While performing
6824 similarly to PLS, OPLS facilitates interpretation.
6825
6826 This package provides imlementations of PCA, PLS, and OPLS for multivariate
6827 analysis and feature selection of omics data. In addition to scores, loadings
6828 and weights plots, the package provides metrics and graphics to determine the
6829 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
6830 validity of the model by permutation testing, detect outliers, and perform
6831 feature selection (e.g. with Variable Importance in Projection or regression
6832 coefficients).")
6833 (license license:cecill)))
6834
6835 (define-public r-biosigner
6836 (package
6837 (name "r-biosigner")
6838 (version "1.18.2")
6839 (source
6840 (origin
6841 (method url-fetch)
6842 (uri (bioconductor-uri "biosigner" version))
6843 (sha256
6844 (base32
6845 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
6846 (build-system r-build-system)
6847 (propagated-inputs
6848 `(("r-biobase" ,r-biobase)
6849 ("r-e1071" ,r-e1071)
6850 ("r-multidataset" ,r-multidataset)
6851 ("r-randomforest" ,r-randomforest)
6852 ("r-ropls" ,r-ropls)))
6853 (native-inputs
6854 `(("r-knitr" ,r-knitr)))
6855 (home-page "https://bioconductor.org/packages/biosigner/")
6856 (synopsis "Signature discovery from omics data")
6857 (description
6858 "Feature selection is critical in omics data analysis to extract
6859 restricted and meaningful molecular signatures from complex and high-dimension
6860 data, and to build robust classifiers. This package implements a method to
6861 assess the relevance of the variables for the prediction performances of the
6862 classifier. The approach can be run in parallel with the PLS-DA, Random
6863 Forest, and SVM binary classifiers. The signatures and the corresponding
6864 'restricted' models are returned, enabling future predictions on new
6865 datasets.")
6866 (license license:cecill)))
6867
6868 (define-public r-annotatr
6869 (package
6870 (name "r-annotatr")
6871 (version "1.16.0")
6872 (source
6873 (origin
6874 (method url-fetch)
6875 (uri (bioconductor-uri "annotatr" version))
6876 (sha256
6877 (base32
6878 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
6879 (build-system r-build-system)
6880 (propagated-inputs
6881 `(("r-annotationdbi" ,r-annotationdbi)
6882 ("r-annotationhub" ,r-annotationhub)
6883 ("r-dplyr" ,r-dplyr)
6884 ("r-genomeinfodb" ,r-genomeinfodb)
6885 ("r-genomicfeatures" ,r-genomicfeatures)
6886 ("r-genomicranges" ,r-genomicranges)
6887 ("r-ggplot2" ,r-ggplot2)
6888 ("r-iranges" ,r-iranges)
6889 ("r-readr" ,r-readr)
6890 ("r-regioner" ,r-regioner)
6891 ("r-reshape2" ,r-reshape2)
6892 ("r-rtracklayer" ,r-rtracklayer)
6893 ("r-s4vectors" ,r-s4vectors)))
6894 (native-inputs
6895 `(("r-knitr" ,r-knitr)))
6896 (home-page "https://bioconductor.org/packages/annotatr/")
6897 (synopsis "Annotation of genomic regions to genomic annotations")
6898 (description
6899 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
6900 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
6901 to investigate the intersecting genomic annotations. Such annotations include
6902 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
6903 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
6904 enhancers. The annotatr package provides an easy way to summarize and
6905 visualize the intersection of genomic sites/regions with genomic
6906 annotations.")
6907 (license license:gpl3)))
6908
6909 (define-public r-rsubread
6910 (package
6911 (name "r-rsubread")
6912 (version "2.4.3")
6913 (source
6914 (origin
6915 (method url-fetch)
6916 (uri (bioconductor-uri "Rsubread" version))
6917 (sha256
6918 (base32
6919 "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba"))))
6920 (properties `((upstream-name . "Rsubread")))
6921 (build-system r-build-system)
6922 (inputs `(("zlib" ,zlib)))
6923 (propagated-inputs
6924 `(("r-matrix" ,r-matrix)))
6925 (home-page "https://bioconductor.org/packages/Rsubread/")
6926 (synopsis "Subread sequence alignment and counting for R")
6927 (description
6928 "This package provides tools for alignment, quantification and analysis
6929 of second and third generation sequencing data. It includes functionality for
6930 read mapping, read counting, SNP calling, structural variant detection and
6931 gene fusion discovery. It can be applied to all major sequencing techologies
6932 and to both short and long sequence reads.")
6933 (license license:gpl3)))
6934
6935 (define-public r-flowutils
6936 (package
6937 (name "r-flowutils")
6938 (version "1.54.0")
6939 (source
6940 (origin
6941 (method url-fetch)
6942 (uri (bioconductor-uri "flowUtils" version))
6943 (sha256
6944 (base32
6945 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
6946 (properties `((upstream-name . "flowUtils")))
6947 (build-system r-build-system)
6948 (propagated-inputs
6949 `(("r-biobase" ,r-biobase)
6950 ("r-corpcor" ,r-corpcor)
6951 ("r-flowcore" ,r-flowcore)
6952 ("r-graph" ,r-graph)
6953 ("r-runit" ,r-runit)
6954 ("r-xml" ,r-xml)))
6955 (home-page "https://github.com/jspidlen/flowUtils")
6956 (synopsis "Utilities for flow cytometry")
6957 (description
6958 "This package provides utilities for flow cytometry data.")
6959 (license license:artistic2.0)))
6960
6961 (define-public r-consensusclusterplus
6962 (package
6963 (name "r-consensusclusterplus")
6964 (version "1.54.0")
6965 (source
6966 (origin
6967 (method url-fetch)
6968 (uri (bioconductor-uri "ConsensusClusterPlus" version))
6969 (sha256
6970 (base32
6971 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
6972 (properties
6973 `((upstream-name . "ConsensusClusterPlus")))
6974 (build-system r-build-system)
6975 (propagated-inputs
6976 `(("r-all" ,r-all)
6977 ("r-biobase" ,r-biobase)
6978 ("r-cluster" ,r-cluster)))
6979 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
6980 (synopsis "Clustering algorithm")
6981 (description
6982 "This package provides an implementation of an algorithm for determining
6983 cluster count and membership by stability evidence in unsupervised analysis.")
6984 (license license:gpl2)))
6985
6986 (define-public r-cytolib
6987 (package
6988 (name "r-cytolib")
6989 (version "2.2.1")
6990 (source
6991 (origin
6992 (method url-fetch)
6993 (uri (bioconductor-uri "cytolib" version))
6994 (sha256
6995 (base32
6996 "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
6997 (properties `((upstream-name . "cytolib")))
6998 (build-system r-build-system)
6999 (arguments
7000 `(#:phases
7001 (modify-phases %standard-phases
7002 (add-after 'unpack 'fix-linking
7003 (lambda _
7004 (substitute* "src/Makevars.in"
7005 ;; This is to avoid having a plain directory on the list of
7006 ;; libraries to link.
7007 (("\\(RHDF5_LIBS\\)" match)
7008 (string-append match "/libhdf5.a")))
7009 #t)))))
7010 (native-inputs
7011 `(("r-knitr" ,r-knitr)
7012 ("pkg-config" ,pkg-config)))
7013 (propagated-inputs
7014 `(("r-bh" ,r-bh)
7015 ("r-rcpp" ,r-rcpp)
7016 ("r-rcpparmadillo" ,r-rcpparmadillo)
7017 ("r-rcppparallel" ,r-rcppparallel)
7018 ("r-rhdf5lib" ,r-rhdf5lib)
7019 ("r-rprotobuflib" ,r-rprotobuflib)))
7020 (home-page "https://bioconductor.org/packages/cytolib/")
7021 (synopsis "C++ infrastructure for working with gated cytometry")
7022 (description
7023 "This package provides the core data structure and API to represent and
7024 interact with gated cytometry data.")
7025 (license license:artistic2.0)))
7026
7027 (define-public r-flowcore
7028 (package
7029 (name "r-flowcore")
7030 (version "2.2.0")
7031 (source
7032 (origin
7033 (method url-fetch)
7034 (uri (bioconductor-uri "flowCore" version))
7035 (sha256
7036 (base32
7037 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
7038 (properties `((upstream-name . "flowCore")))
7039 (build-system r-build-system)
7040 (propagated-inputs
7041 `(("r-bh" ,r-bh)
7042 ("r-biobase" ,r-biobase)
7043 ("r-biocgenerics" ,r-biocgenerics)
7044 ("r-cytolib" ,r-cytolib)
7045 ("r-matrixstats" ,r-matrixstats)
7046 ("r-rcpp" ,r-rcpp)
7047 ("r-rcpparmadillo" ,r-rcpparmadillo)
7048 ("r-rprotobuflib" ,r-rprotobuflib)
7049 ("r-s4vectors" ,r-s4vectors)))
7050 (native-inputs
7051 `(("r-knitr" ,r-knitr)))
7052 (home-page "https://bioconductor.org/packages/flowCore")
7053 (synopsis "Basic structures for flow cytometry data")
7054 (description
7055 "This package provides S4 data structures and basic functions to deal
7056 with flow cytometry data.")
7057 (license license:artistic2.0)))
7058
7059 (define-public r-flowmeans
7060 (package
7061 (name "r-flowmeans")
7062 (version "1.50.0")
7063 (source
7064 (origin
7065 (method url-fetch)
7066 (uri (bioconductor-uri "flowMeans" version))
7067 (sha256
7068 (base32
7069 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
7070 (properties `((upstream-name . "flowMeans")))
7071 (build-system r-build-system)
7072 (propagated-inputs
7073 `(("r-biobase" ,r-biobase)
7074 ("r-feature" ,r-feature)
7075 ("r-flowcore" ,r-flowcore)
7076 ("r-rrcov" ,r-rrcov)))
7077 (home-page "https://bioconductor.org/packages/flowMeans")
7078 (synopsis "Non-parametric flow cytometry data gating")
7079 (description
7080 "This package provides tools to identify cell populations in Flow
7081 Cytometry data using non-parametric clustering and segmented-regression-based
7082 change point detection.")
7083 (license license:artistic2.0)))
7084
7085 (define-public r-ncdfflow
7086 (package
7087 (name "r-ncdfflow")
7088 (version "2.36.0")
7089 (source
7090 (origin
7091 (method url-fetch)
7092 (uri (bioconductor-uri "ncdfFlow" version))
7093 (sha256
7094 (base32
7095 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
7096 (properties `((upstream-name . "ncdfFlow")))
7097 (build-system r-build-system)
7098 (arguments
7099 `(#:phases
7100 (modify-phases %standard-phases
7101 (add-after 'unpack 'fix-linking
7102 (lambda _
7103 (substitute* "src/Makevars"
7104 ;; This is to avoid having a plain directory on the list of
7105 ;; libraries to link.
7106 (("\\(RHDF5_LIBS\\)" match)
7107 (string-append match "/libhdf5.a")))
7108 #t)))))
7109 (propagated-inputs
7110 `(("r-bh" ,r-bh)
7111 ("r-biobase" ,r-biobase)
7112 ("r-biocgenerics" ,r-biocgenerics)
7113 ("r-flowcore" ,r-flowcore)
7114 ("r-rcpp" ,r-rcpp)
7115 ("r-rcpparmadillo" ,r-rcpparmadillo)
7116 ("r-rhdf5lib" ,r-rhdf5lib)
7117 ("r-zlibbioc" ,r-zlibbioc)))
7118 (native-inputs
7119 `(("r-knitr" ,r-knitr)))
7120 (home-page "https://bioconductor.org/packages/ncdfFlow/")
7121 (synopsis "HDF5 based storage for flow cytometry data")
7122 (description
7123 "This package provides HDF5 storage based methods and functions for
7124 manipulation of flow cytometry data.")
7125 (license license:artistic2.0)))
7126
7127 (define-public r-ggcyto
7128 (package
7129 (name "r-ggcyto")
7130 (version "1.18.0")
7131 (source
7132 (origin
7133 (method url-fetch)
7134 (uri (bioconductor-uri "ggcyto" version))
7135 (sha256
7136 (base32
7137 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
7138 (properties `((upstream-name . "ggcyto")))
7139 (build-system r-build-system)
7140 (propagated-inputs
7141 `(("r-data-table" ,r-data-table)
7142 ("r-flowcore" ,r-flowcore)
7143 ("r-flowworkspace" ,r-flowworkspace)
7144 ("r-ggplot2" ,r-ggplot2)
7145 ("r-gridextra" ,r-gridextra)
7146 ("r-hexbin" ,r-hexbin)
7147 ("r-ncdfflow" ,r-ncdfflow)
7148 ("r-plyr" ,r-plyr)
7149 ("r-rcolorbrewer" ,r-rcolorbrewer)
7150 ("r-rlang" ,r-rlang)
7151 ("r-scales" ,r-scales)))
7152 (native-inputs
7153 `(("r-knitr" ,r-knitr)))
7154 (home-page "https://github.com/RGLab/ggcyto/issues")
7155 (synopsis "Visualize Cytometry data with ggplot")
7156 (description
7157 "With the dedicated fortify method implemented for @code{flowSet},
7158 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
7159 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
7160 and some custom layers also make it easy to add gates and population
7161 statistics to the plot.")
7162 (license license:artistic2.0)))
7163
7164 (define-public r-flowviz
7165 (package
7166 (name "r-flowviz")
7167 (version "1.54.0")
7168 (source
7169 (origin
7170 (method url-fetch)
7171 (uri (bioconductor-uri "flowViz" version))
7172 (sha256
7173 (base32
7174 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
7175 (properties `((upstream-name . "flowViz")))
7176 (build-system r-build-system)
7177 (propagated-inputs
7178 `(("r-biobase" ,r-biobase)
7179 ("r-flowcore" ,r-flowcore)
7180 ("r-hexbin" ,r-hexbin)
7181 ("r-idpmisc" ,r-idpmisc)
7182 ("r-kernsmooth" ,r-kernsmooth)
7183 ("r-lattice" ,r-lattice)
7184 ("r-latticeextra" ,r-latticeextra)
7185 ("r-mass" ,r-mass)
7186 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7187 (native-inputs
7188 `(("r-knitr" ,r-knitr)))
7189 (home-page "https://bioconductor.org/packages/flowViz/")
7190 (synopsis "Visualization for flow cytometry")
7191 (description
7192 "This package provides visualization tools for flow cytometry data.")
7193 (license license:artistic2.0)))
7194
7195 (define-public r-flowclust
7196 (package
7197 (name "r-flowclust")
7198 (version "3.28.0")
7199 (source
7200 (origin
7201 (method url-fetch)
7202 (uri (bioconductor-uri "flowClust" version))
7203 (sha256
7204 (base32
7205 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
7206 (properties `((upstream-name . "flowClust")))
7207 (build-system r-build-system)
7208 (arguments
7209 `(#:configure-flags
7210 (list "--configure-args=--enable-bundled-gsl=no")))
7211 (propagated-inputs
7212 `(("r-biobase" ,r-biobase)
7213 ("r-biocgenerics" ,r-biocgenerics)
7214 ("r-clue" ,r-clue)
7215 ("r-corpcor" ,r-corpcor)
7216 ("r-ellipse" ,r-ellipse)
7217 ("r-flowcore" ,r-flowcore)
7218 ("r-flowviz" ,r-flowviz)
7219 ("r-graph" ,r-graph)
7220 ("r-mnormt" ,r-mnormt)))
7221 (inputs
7222 `(("gsl" ,gsl)))
7223 (native-inputs
7224 `(("pkg-config" ,pkg-config)
7225 ("r-knitr" ,r-knitr)))
7226 (home-page "https://bioconductor.org/packages/flowClust")
7227 (synopsis "Clustering for flow cytometry")
7228 (description
7229 "This package provides robust model-based clustering using a t-mixture
7230 model with Box-Cox transformation.")
7231 (license license:artistic2.0)))
7232
7233 ;; TODO: this package bundles an old version of protobuf. It's not easy to
7234 ;; make it use our protobuf package instead.
7235 (define-public r-rprotobuflib
7236 (package
7237 (name "r-rprotobuflib")
7238 (version "2.2.0")
7239 (source
7240 (origin
7241 (method url-fetch)
7242 (uri (bioconductor-uri "RProtoBufLib" version))
7243 (sha256
7244 (base32
7245 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
7246 (properties `((upstream-name . "RProtoBufLib")))
7247 (build-system r-build-system)
7248 (arguments
7249 `(#:phases
7250 (modify-phases %standard-phases
7251 (add-after 'unpack 'unpack-bundled-sources
7252 (lambda _
7253 (with-directory-excursion "src"
7254 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
7255 #t)))))
7256 (native-inputs
7257 `(("r-knitr" ,r-knitr)))
7258 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
7259 (synopsis "C++ headers and static libraries of Protocol buffers")
7260 (description
7261 "This package provides the headers and static library of Protocol buffers
7262 for other R packages to compile and link against.")
7263 (license license:bsd-3)))
7264
7265 (define-public r-flowworkspace
7266 (package
7267 (name "r-flowworkspace")
7268 (version "4.2.0")
7269 (source
7270 (origin
7271 (method url-fetch)
7272 (uri (bioconductor-uri "flowWorkspace" version))
7273 (sha256
7274 (base32
7275 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
7276 (properties `((upstream-name . "flowWorkspace")))
7277 (build-system r-build-system)
7278 (arguments
7279 `(#:phases
7280 (modify-phases %standard-phases
7281 (add-after 'unpack 'fix-linking
7282 (lambda _
7283 (substitute* "src/Makevars"
7284 ;; This is to avoid having a plain directory on the list of
7285 ;; libraries to link.
7286 (("\\{h5lib\\}" match)
7287 (string-append match "/libhdf5.a")))
7288 #t)))))
7289 (propagated-inputs
7290 `(("r-aws-s3" ,r-aws-s3)
7291 ("r-aws-signature" ,r-aws-signature)
7292 ("r-bh" ,r-bh)
7293 ("r-biobase" ,r-biobase)
7294 ("r-biocgenerics" ,r-biocgenerics)
7295 ("r-cytolib" ,r-cytolib)
7296 ("r-data-table" ,r-data-table)
7297 ("r-digest" ,r-digest)
7298 ("r-dplyr" ,r-dplyr)
7299 ("r-flowcore" ,r-flowcore)
7300 ("r-ggplot2" ,r-ggplot2)
7301 ("r-graph" ,r-graph)
7302 ("r-lattice" ,r-lattice)
7303 ("r-latticeextra" ,r-latticeextra)
7304 ("r-matrixstats" ,r-matrixstats)
7305 ("r-ncdfflow" ,r-ncdfflow)
7306 ("r-rbgl" ,r-rbgl)
7307 ("r-rcpp" ,r-rcpp)
7308 ("r-rcpparmadillo" ,r-rcpparmadillo)
7309 ("r-rcppparallel" ,r-rcppparallel)
7310 ("r-rgraphviz" ,r-rgraphviz)
7311 ("r-rhdf5lib" ,r-rhdf5lib)
7312 ("r-rprotobuflib" ,r-rprotobuflib)
7313 ("r-scales" ,r-scales)
7314 ("r-xml" ,r-xml)))
7315 (native-inputs
7316 `(("r-knitr" ,r-knitr)))
7317 (home-page "https://bioconductor.org/packages/flowWorkspace/")
7318 (synopsis "Infrastructure for working with cytometry data")
7319 (description
7320 "This package is designed to facilitate comparison of automated gating
7321 methods against manual gating done in flowJo. This package allows you to
7322 import basic flowJo workspaces into BioConductor and replicate the gating from
7323 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
7324 samples, compensation, and transformation are performed so that the output
7325 matches the flowJo analysis.")
7326 (license license:artistic2.0)))
7327
7328 (define-public r-flowstats
7329 (package
7330 (name "r-flowstats")
7331 (version "4.2.0")
7332 (source
7333 (origin
7334 (method url-fetch)
7335 (uri (bioconductor-uri "flowStats" version))
7336 (sha256
7337 (base32
7338 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
7339 (properties `((upstream-name . "flowStats")))
7340 (build-system r-build-system)
7341 (propagated-inputs
7342 `(("r-biobase" ,r-biobase)
7343 ("r-biocgenerics" ,r-biocgenerics)
7344 ("r-cluster" ,r-cluster)
7345 ("r-fda" ,r-fda)
7346 ("r-flowcore" ,r-flowcore)
7347 ("r-flowviz" ,r-flowviz)
7348 ("r-flowworkspace" ,r-flowworkspace)
7349 ("r-kernsmooth" ,r-kernsmooth)
7350 ("r-ks" ,r-ks)
7351 ("r-lattice" ,r-lattice)
7352 ("r-mass" ,r-mass)
7353 ("r-ncdfflow" ,r-ncdfflow)
7354 ("r-rcolorbrewer" ,r-rcolorbrewer)
7355 ("r-rrcov" ,r-rrcov)))
7356 (home-page "http://www.github.com/RGLab/flowStats")
7357 (synopsis "Statistical methods for the analysis of flow cytometry data")
7358 (description
7359 "This package provides methods and functionality to analyze flow data
7360 that is beyond the basic infrastructure provided by the @code{flowCore}
7361 package.")
7362 (license license:artistic2.0)))
7363
7364 (define-public r-opencyto
7365 (package
7366 (name "r-opencyto")
7367 (version "2.2.0")
7368 (source
7369 (origin
7370 (method url-fetch)
7371 (uri (bioconductor-uri "openCyto" version))
7372 (sha256
7373 (base32
7374 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
7375 (properties `((upstream-name . "openCyto")))
7376 (build-system r-build-system)
7377 (propagated-inputs
7378 `(("r-biobase" ,r-biobase)
7379 ("r-biocgenerics" ,r-biocgenerics)
7380 ("r-clue" ,r-clue)
7381 ("r-data-table" ,r-data-table)
7382 ("r-flowclust" ,r-flowclust)
7383 ("r-flowcore" ,r-flowcore)
7384 ("r-flowstats" ,r-flowstats)
7385 ("r-flowviz" ,r-flowviz)
7386 ("r-flowworkspace" ,r-flowworkspace)
7387 ("r-graph" ,r-graph)
7388 ("r-gtools" ,r-gtools)
7389 ("r-ks" ,r-ks)
7390 ("r-lattice" ,r-lattice)
7391 ("r-mass" ,r-mass)
7392 ("r-ncdfflow" ,r-ncdfflow)
7393 ("r-plyr" ,r-plyr)
7394 ("r-r-utils" ,r-r-utils)
7395 ("r-rbgl" ,r-rbgl)
7396 ("r-rcolorbrewer" ,r-rcolorbrewer)
7397 ("r-rcpp" ,r-rcpp)
7398 ("r-rrcov" ,r-rrcov)))
7399 (native-inputs
7400 `(("r-knitr" ,r-knitr)))
7401 (home-page "https://bioconductor.org/packages/openCyto")
7402 (synopsis "Hierarchical gating pipeline for flow cytometry data")
7403 (description
7404 "This package is designed to facilitate the automated gating methods in a
7405 sequential way to mimic the manual gating strategy.")
7406 (license license:artistic2.0)))
7407
7408 (define-public r-cytoml
7409 (package
7410 (name "r-cytoml")
7411 (version "2.2.2")
7412 (source
7413 (origin
7414 (method url-fetch)
7415 (uri (bioconductor-uri "CytoML" version))
7416 (sha256
7417 (base32
7418 "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1"))))
7419 (properties `((upstream-name . "CytoML")))
7420 (build-system r-build-system)
7421 (arguments
7422 `(#:phases
7423 (modify-phases %standard-phases
7424 (add-after 'unpack 'fix-linking
7425 (lambda _
7426 (substitute* "src/Makevars.in"
7427 ;; This is to avoid having a plain directory on the list of
7428 ;; libraries to link.
7429 (("\\{h5lib\\}" match)
7430 (string-append match "/libhdf5.a")))
7431 #t)))))
7432 (inputs
7433 `(("libxml2" ,libxml2)
7434 ("zlib" ,zlib)))
7435 (propagated-inputs
7436 `(("r-base64enc" ,r-base64enc)
7437 ("r-bh" ,r-bh)
7438 ("r-biobase" ,r-biobase)
7439 ("r-corpcor" ,r-corpcor)
7440 ("r-cytolib" ,r-cytolib)
7441 ("r-data-table" ,r-data-table)
7442 ("r-dplyr" ,r-dplyr)
7443 ("r-flowcore" ,r-flowcore)
7444 ("r-flowworkspace" ,r-flowworkspace)
7445 ("r-ggcyto" ,r-ggcyto)
7446 ("r-graph" ,r-graph)
7447 ("r-jsonlite" ,r-jsonlite)
7448 ("r-lattice" ,r-lattice)
7449 ("r-opencyto" ,r-opencyto)
7450 ("r-plyr" ,r-plyr)
7451 ("r-rbgl" ,r-rbgl)
7452 ("r-rcpp" ,r-rcpp)
7453 ("r-rcpparmadillo" ,r-rcpparmadillo)
7454 ("r-rcppparallel" ,r-rcppparallel)
7455 ("r-rgraphviz" ,r-rgraphviz)
7456 ("r-rhdf5lib" ,r-rhdf5lib)
7457 ("r-rprotobuflib" ,r-rprotobuflib)
7458 ("r-runit" ,r-runit)
7459 ("r-tibble" ,r-tibble)
7460 ("r-xml" ,r-xml)
7461 ("r-xml2" ,r-xml2)
7462 ("r-yaml" ,r-yaml)))
7463 (native-inputs
7464 `(("r-knitr" ,r-knitr)))
7465 (home-page "https://github.com/RGLab/CytoML")
7466 (synopsis "GatingML interface for cross platform cytometry data sharing")
7467 (description
7468 "This package provides an interface to implementations of the GatingML2.0
7469 standard to exchange gated cytometry data with other software platforms.")
7470 (license license:artistic2.0)))
7471
7472 (define-public r-flowsom
7473 (package
7474 (name "r-flowsom")
7475 (version "1.22.0")
7476 (source
7477 (origin
7478 (method url-fetch)
7479 (uri (bioconductor-uri "FlowSOM" version))
7480 (sha256
7481 (base32
7482 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
7483 (properties `((upstream-name . "FlowSOM")))
7484 (build-system r-build-system)
7485 (propagated-inputs
7486 `(("r-biocgenerics" ,r-biocgenerics)
7487 ("r-consensusclusterplus" ,r-consensusclusterplus)
7488 ("r-cytoml" ,r-cytoml)
7489 ("r-flowcore" ,r-flowcore)
7490 ("r-flowworkspace" ,r-flowworkspace)
7491 ("r-igraph" ,r-igraph)
7492 ("r-rcolorbrewer" ,r-rcolorbrewer)
7493 ("r-tsne" ,r-tsne)
7494 ("r-xml" ,r-xml)))
7495 (home-page "https://bioconductor.org/packages/FlowSOM/")
7496 (synopsis "Visualize and interpret cytometry data")
7497 (description
7498 "FlowSOM offers visualization options for cytometry data, by using
7499 self-organizing map clustering and minimal spanning trees.")
7500 (license license:gpl2+)))
7501
7502 (define-public r-mixomics
7503 (package
7504 (name "r-mixomics")
7505 (version "6.14.0")
7506 (source
7507 (origin
7508 (method url-fetch)
7509 (uri (bioconductor-uri "mixOmics" version))
7510 (sha256
7511 (base32
7512 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
7513 (properties `((upstream-name . "mixOmics")))
7514 (build-system r-build-system)
7515 (propagated-inputs
7516 `(("r-corpcor" ,r-corpcor)
7517 ("r-dplyr" ,r-dplyr)
7518 ("r-ellipse" ,r-ellipse)
7519 ("r-ggrepel" ,r-ggrepel)
7520 ("r-ggplot2" ,r-ggplot2)
7521 ("r-gridextra" ,r-gridextra)
7522 ("r-igraph" ,r-igraph)
7523 ("r-lattice" ,r-lattice)
7524 ("r-mass" ,r-mass)
7525 ("r-matrixstats" ,r-matrixstats)
7526 ("r-rarpack" ,r-rarpack)
7527 ("r-rcolorbrewer" ,r-rcolorbrewer)
7528 ("r-reshape2" ,r-reshape2)
7529 ("r-tidyr" ,r-tidyr)))
7530 (native-inputs
7531 `(("r-knitr" ,r-knitr)))
7532 (home-page "http://www.mixOmics.org")
7533 (synopsis "Multivariate methods for exploration of biological datasets")
7534 (description
7535 "mixOmics offers a wide range of multivariate methods for the exploration
7536 and integration of biological datasets with a particular focus on variable
7537 selection. The package proposes several sparse multivariate models we have
7538 developed to identify the key variables that are highly correlated, and/or
7539 explain the biological outcome of interest. The data that can be analysed
7540 with mixOmics may come from high throughput sequencing technologies, such as
7541 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
7542 also beyond the realm of omics (e.g. spectral imaging). The methods
7543 implemented in mixOmics can also handle missing values without having to
7544 delete entire rows with missing data.")
7545 (license license:gpl2+)))
7546
7547 (define-public r-depecher
7548 (package ;Source/Weave error
7549 (name "r-depecher")
7550 (version "1.6.0")
7551 (source
7552 (origin
7553 (method url-fetch)
7554 (uri (bioconductor-uri "DepecheR" version))
7555 (sha256
7556 (base32
7557 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
7558 (properties `((upstream-name . "DepecheR")))
7559 (build-system r-build-system)
7560 (propagated-inputs
7561 `(("r-beanplot" ,r-beanplot)
7562 ("r-dosnow" ,r-dosnow)
7563 ("r-dplyr" ,r-dplyr)
7564 ("r-fnn" ,r-fnn)
7565 ("r-foreach" ,r-foreach)
7566 ("r-ggplot2" ,r-ggplot2)
7567 ("r-gmodels" ,r-gmodels)
7568 ("r-gplots" ,r-gplots)
7569 ("r-mass" ,r-mass)
7570 ("r-matrixstats" ,r-matrixstats)
7571 ("r-mixomics" ,r-mixomics)
7572 ("r-moments" ,r-moments)
7573 ("r-rcpp" ,r-rcpp)
7574 ("r-rcppeigen" ,r-rcppeigen)
7575 ("r-reshape2" ,r-reshape2)
7576 ("r-robustbase" ,r-robustbase)
7577 ("r-viridis" ,r-viridis)))
7578 (native-inputs
7579 `(("r-knitr" ,r-knitr)))
7580 (home-page "https://bioconductor.org/packages/DepecheR/")
7581 (synopsis "Identify traits of clusters in high-dimensional entities")
7582 (description
7583 "The purpose of this package is to identify traits in a dataset that can
7584 separate groups. This is done on two levels. First, clustering is performed,
7585 using an implementation of sparse K-means. Secondly, the generated clusters
7586 are used to predict outcomes of groups of individuals based on their
7587 distribution of observations in the different clusters. As certain clusters
7588 with separating information will be identified, and these clusters are defined
7589 by a sparse number of variables, this method can reduce the complexity of
7590 data, to only emphasize the data that actually matters.")
7591 (license license:expat)))
7592
7593 (define-public r-rcistarget
7594 (package
7595 (name "r-rcistarget")
7596 (version "1.10.0")
7597 (source
7598 (origin
7599 (method url-fetch)
7600 (uri (bioconductor-uri "RcisTarget" version))
7601 (sha256
7602 (base32
7603 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
7604 (properties `((upstream-name . "RcisTarget")))
7605 (build-system r-build-system)
7606 (propagated-inputs
7607 `(("r-aucell" ,r-aucell)
7608 ("r-biocgenerics" ,r-biocgenerics)
7609 ("r-data-table" ,r-data-table)
7610 ("r-feather" ,r-feather)
7611 ("r-gseabase" ,r-gseabase)
7612 ("r-r-utils" ,r-r-utils)
7613 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7614 (native-inputs
7615 `(("r-knitr" ,r-knitr)))
7616 (home-page "https://aertslab.org/#scenic")
7617 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
7618 (description
7619 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
7620 over-represented on a gene list. In a first step, RcisTarget selects DNA
7621 motifs that are significantly over-represented in the surroundings of the
7622 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
7623 achieved by using a database that contains genome-wide cross-species rankings
7624 for each motif. The motifs that are then annotated to TFs and those that have
7625 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
7626 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
7627 genes in the gene-set that are ranked above the leading edge).")
7628 (license license:gpl3)))
7629
7630 (define-public r-cicero
7631 (package
7632 (name "r-cicero")
7633 (version "1.8.1")
7634 (source
7635 (origin
7636 (method url-fetch)
7637 (uri (bioconductor-uri "cicero" version))
7638 (sha256
7639 (base32
7640 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
7641 (build-system r-build-system)
7642 (propagated-inputs
7643 `(("r-assertthat" ,r-assertthat)
7644 ("r-biobase" ,r-biobase)
7645 ("r-biocgenerics" ,r-biocgenerics)
7646 ("r-data-table" ,r-data-table)
7647 ("r-dplyr" ,r-dplyr)
7648 ("r-fnn" ,r-fnn)
7649 ("r-genomicranges" ,r-genomicranges)
7650 ("r-ggplot2" ,r-ggplot2)
7651 ("r-glasso" ,r-glasso)
7652 ("r-gviz" ,r-gviz)
7653 ("r-igraph" ,r-igraph)
7654 ("r-iranges" ,r-iranges)
7655 ("r-matrix" ,r-matrix)
7656 ("r-monocle" ,r-monocle)
7657 ("r-plyr" ,r-plyr)
7658 ("r-reshape2" ,r-reshape2)
7659 ("r-s4vectors" ,r-s4vectors)
7660 ("r-stringi" ,r-stringi)
7661 ("r-stringr" ,r-stringr)
7662 ("r-tibble" ,r-tibble)
7663 ("r-tidyr" ,r-tidyr)
7664 ("r-vgam" ,r-vgam)))
7665 (native-inputs
7666 `(("r-knitr" ,r-knitr)))
7667 (home-page "https://bioconductor.org/packages/cicero/")
7668 (synopsis "Predict cis-co-accessibility from single-cell data")
7669 (description
7670 "Cicero computes putative cis-regulatory maps from single-cell chromatin
7671 accessibility data. It also extends the monocle package for use in chromatin
7672 accessibility data.")
7673 (license license:expat)))
7674
7675 ;; This is the latest commit on the "monocle3" branch.
7676 (define-public r-cicero-monocle3
7677 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
7678 (revision "1"))
7679 (package (inherit r-cicero)
7680 (name "r-cicero-monocle3")
7681 (version (git-version "1.3.2" revision commit))
7682 (source
7683 (origin
7684 (method git-fetch)
7685 (uri (git-reference
7686 (url "https://github.com/cole-trapnell-lab/cicero-release")
7687 (commit commit)))
7688 (file-name (git-file-name name version))
7689 (sha256
7690 (base32
7691 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
7692 (propagated-inputs
7693 `(("r-monocle3" ,r-monocle3)
7694 ,@(alist-delete "r-monocle"
7695 (package-propagated-inputs r-cicero)))))))
7696
7697 (define-public r-circrnaprofiler
7698 (package
7699 (name "r-circrnaprofiler")
7700 (version "1.4.2")
7701 (source
7702 (origin
7703 (method url-fetch)
7704 (uri (bioconductor-uri "circRNAprofiler" version))
7705 (sha256
7706 (base32
7707 "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
7708 (properties
7709 `((upstream-name . "circRNAprofiler")))
7710 (build-system r-build-system)
7711 (propagated-inputs
7712 `(("r-annotationhub" ,r-annotationhub)
7713 ("r-biostrings" ,r-biostrings)
7714 ("r-bsgenome" ,r-bsgenome)
7715 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7716 ("r-deseq2" ,r-deseq2)
7717 ("r-dplyr" ,r-dplyr)
7718 ("r-edger" ,r-edger)
7719 ("r-genomeinfodb" ,r-genomeinfodb)
7720 ("r-genomicranges" ,r-genomicranges)
7721 ("r-ggplot2" ,r-ggplot2)
7722 ("r-gwascat" ,r-gwascat)
7723 ("r-iranges" ,r-iranges)
7724 ("r-magrittr" ,r-magrittr)
7725 ("r-r-utils" ,r-r-utils)
7726 ("r-readr" ,r-readr)
7727 ("r-reshape2" ,r-reshape2)
7728 ("r-rlang" ,r-rlang)
7729 ("r-rtracklayer" ,r-rtracklayer)
7730 ("r-s4vectors" ,r-s4vectors)
7731 ("r-seqinr" ,r-seqinr)
7732 ("r-stringi" ,r-stringi)
7733 ("r-stringr" ,r-stringr)
7734 ("r-universalmotif" ,r-universalmotif)))
7735 (native-inputs
7736 `(("r-knitr" ,r-knitr)))
7737 (home-page
7738 "https://github.com/Aufiero/circRNAprofiler")
7739 (synopsis
7740 "Computational framework for the downstream analysis of circular RNA's")
7741 (description
7742 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
7743 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
7744 framework allows to combine and analyze circRNAs previously detected by
7745 multiple publicly available annotation-based circRNA detection tools. It
7746 covers different aspects of circRNAs analysis from differential expression
7747 analysis, evolutionary conservation, biogenesis to functional analysis.")
7748 (license license:gpl3)))
7749
7750 (define-public r-cistopic
7751 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
7752 (revision "0"))
7753 (package
7754 (name "r-cistopic")
7755 (version (git-version "0.2.1" revision commit))
7756 (source
7757 (origin
7758 (method git-fetch)
7759 (uri (git-reference
7760 (url "https://github.com/aertslab/cisTopic")
7761 (commit commit)))
7762 (file-name (git-file-name name version))
7763 (sha256
7764 (base32
7765 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
7766 (build-system r-build-system)
7767 (propagated-inputs
7768 `(("r-aucell" ,r-aucell)
7769 ("r-data-table" ,r-data-table)
7770 ("r-dplyr" ,r-dplyr)
7771 ("r-dosnow" ,r-dosnow)
7772 ("r-dt" ,r-dt)
7773 ("r-feather" ,r-feather)
7774 ("r-fitdistrplus" ,r-fitdistrplus)
7775 ("r-genomicranges" ,r-genomicranges)
7776 ("r-ggplot2" ,r-ggplot2)
7777 ("r-lda" ,r-lda)
7778 ("r-matrix" ,r-matrix)
7779 ("r-plyr" ,r-plyr)
7780 ("r-rcistarget" ,r-rcistarget)
7781 ("r-rtracklayer" ,r-rtracklayer)
7782 ("r-s4vectors" ,r-s4vectors)))
7783 (home-page "https://github.com/aertslab/cisTopic")
7784 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
7785 (description
7786 "The sparse nature of single cell epigenomics data can be overruled using
7787 probabilistic modelling methods such as @dfn{Latent Dirichlet
7788 Allocation} (LDA). This package allows the probabilistic modelling of
7789 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
7790 includes functionalities to identify cell states based on the contribution of
7791 cisTopics and explore the nature and regulatory proteins driving them.")
7792 (license license:gpl3))))
7793
7794 (define-public r-genie3
7795 (package
7796 (name "r-genie3")
7797 (version "1.12.0")
7798 (source
7799 (origin
7800 (method url-fetch)
7801 (uri (bioconductor-uri "GENIE3" version))
7802 (sha256
7803 (base32
7804 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
7805 (properties `((upstream-name . "GENIE3")))
7806 (build-system r-build-system)
7807 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
7808 (native-inputs
7809 `(("r-knitr" ,r-knitr)))
7810 (home-page "https://bioconductor.org/packages/GENIE3")
7811 (synopsis "Gene network inference with ensemble of trees")
7812 (description
7813 "This package implements the GENIE3 algorithm for inferring gene
7814 regulatory networks from expression data.")
7815 (license license:gpl2+)))
7816
7817 (define-public r-roc
7818 (package
7819 (name "r-roc")
7820 (version "1.66.0")
7821 (source
7822 (origin
7823 (method url-fetch)
7824 (uri (bioconductor-uri "ROC" version))
7825 (sha256
7826 (base32
7827 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
7828 (properties `((upstream-name . "ROC")))
7829 (build-system r-build-system)
7830 (propagated-inputs
7831 `(("r-knitr" ,r-knitr)))
7832 (home-page "https://www.bioconductor.org/packages/ROC/")
7833 (synopsis "Utilities for ROC curves")
7834 (description
7835 "This package provides utilities for @dfn{Receiver Operating
7836 Characteristic} (ROC) curves, with a focus on micro arrays.")
7837 (license license:artistic2.0)))
7838
7839 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
7840 (package
7841 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
7842 (version "0.6.0")
7843 (source
7844 (origin
7845 (method url-fetch)
7846 (uri (bioconductor-uri
7847 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
7848 version 'annotation))
7849 (sha256
7850 (base32
7851 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
7852 (properties
7853 `((upstream-name
7854 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
7855 (build-system r-build-system)
7856 (propagated-inputs `(("r-minfi" ,r-minfi)))
7857 (home-page
7858 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
7859 (synopsis "Annotation for Illumina's 450k methylation arrays")
7860 (description
7861 "This package provides manifests and annotation for Illumina's 450k array
7862 data.")
7863 (license license:artistic2.0)))
7864
7865 (define-public r-watermelon
7866 (package
7867 (name "r-watermelon")
7868 (version "1.34.0")
7869 (source
7870 (origin
7871 (method url-fetch)
7872 (uri (bioconductor-uri "wateRmelon" version))
7873 (sha256
7874 (base32
7875 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
7876 (properties `((upstream-name . "wateRmelon")))
7877 (build-system r-build-system)
7878 (propagated-inputs
7879 `(("r-biobase" ,r-biobase)
7880 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
7881 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
7882 ("r-illuminaio" ,r-illuminaio)
7883 ("r-limma" ,r-limma)
7884 ("r-lumi" ,r-lumi)
7885 ("r-matrixstats" ,r-matrixstats)
7886 ("r-methylumi" ,r-methylumi)
7887 ("r-roc" ,r-roc)))
7888 (home-page "https://bioconductor.org/packages/wateRmelon/")
7889 (synopsis "Illumina 450 methylation array normalization and metrics")
7890 (description
7891 "The standard index of DNA methylation (beta) is computed from methylated
7892 and unmethylated signal intensities. Betas calculated from raw signal
7893 intensities perform well, but using 11 methylomic datasets we demonstrate that
7894 quantile normalization methods produce marked improvement. The commonly used
7895 procedure of normalizing betas is inferior to the separate normalization of M
7896 and U, and it is also advantageous to normalize Type I and Type II assays
7897 separately. This package provides 15 flavours of betas and three performance
7898 metrics, with methods for objects produced by the @code{methylumi} and
7899 @code{minfi} packages.")
7900 (license license:gpl3)))
7901
7902 (define-public r-gdsfmt
7903 (package
7904 (name "r-gdsfmt")
7905 (version "1.26.1")
7906 (source
7907 (origin
7908 (method url-fetch)
7909 (uri (bioconductor-uri "gdsfmt" version))
7910 (sha256
7911 (base32
7912 "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
7913 (modules '((guix build utils)))
7914 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
7915 ;; them and link with system libraries instead.
7916 (snippet
7917 '(begin
7918 (for-each delete-file-recursively
7919 '("src/LZ4"
7920 "src/XZ"
7921 "src/ZLIB"))
7922 (substitute* "src/Makevars"
7923 (("all: \\$\\(SHLIB\\)") "all:")
7924 (("\\$\\(SHLIB\\): liblzma.a") "")
7925 (("(ZLIB|LZ4)/.*") "")
7926 (("CoreArray/dVLIntGDS.cpp.*")
7927 "CoreArray/dVLIntGDS.cpp")
7928 (("CoreArray/dVLIntGDS.o.*")
7929 "CoreArray/dVLIntGDS.o")
7930 (("PKG_LIBS = ./liblzma.a")
7931 "PKG_LIBS = -llz4"))
7932 (substitute* "src/CoreArray/dStream.h"
7933 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
7934 (string-append "include <" header ">")))
7935 #t))))
7936 (properties `((upstream-name . "gdsfmt")))
7937 (build-system r-build-system)
7938 (inputs
7939 `(("lz4" ,lz4)
7940 ("xz" ,xz)
7941 ("zlib" ,zlib)))
7942 (native-inputs
7943 `(("r-knitr" ,r-knitr)))
7944 (home-page "http://corearray.sourceforge.net/")
7945 (synopsis
7946 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
7947 (description
7948 "This package provides a high-level R interface to CoreArray @dfn{Genomic
7949 Data Structure} (GDS) data files, which are portable across platforms with
7950 hierarchical structure to store multiple scalable array-oriented data sets
7951 with metadata information. It is suited for large-scale datasets, especially
7952 for data which are much larger than the available random-access memory. The
7953 @code{gdsfmt} package offers efficient operations specifically designed for
7954 integers of less than 8 bits, since a diploid genotype, like
7955 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
7956 byte. Data compression and decompression are available with relatively
7957 efficient random access. It is also allowed to read a GDS file in parallel
7958 with multiple R processes supported by the package @code{parallel}.")
7959 (license license:lgpl3)))
7960
7961 (define-public r-bigmelon
7962 (package
7963 (name "r-bigmelon")
7964 (version "1.16.0")
7965 (source
7966 (origin
7967 (method url-fetch)
7968 (uri (bioconductor-uri "bigmelon" version))
7969 (sha256
7970 (base32
7971 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
7972 (properties `((upstream-name . "bigmelon")))
7973 (build-system r-build-system)
7974 (propagated-inputs
7975 `(("r-biobase" ,r-biobase)
7976 ("r-biocgenerics" ,r-biocgenerics)
7977 ("r-gdsfmt" ,r-gdsfmt)
7978 ("r-geoquery" ,r-geoquery)
7979 ("r-methylumi" ,r-methylumi)
7980 ("r-minfi" ,r-minfi)
7981 ("r-watermelon" ,r-watermelon)))
7982 (home-page "https://bioconductor.org/packages/bigmelon/")
7983 (synopsis "Illumina methylation array analysis for large experiments")
7984 (description
7985 "This package provides methods for working with Illumina arrays using the
7986 @code{gdsfmt} package.")
7987 (license license:gpl3)))
7988
7989 (define-public r-seqbias
7990 (package
7991 (name "r-seqbias")
7992 (version "1.38.0")
7993 (source
7994 (origin
7995 (method url-fetch)
7996 (uri (bioconductor-uri "seqbias" version))
7997 (sha256
7998 (base32
7999 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
8000 (properties `((upstream-name . "seqbias")))
8001 (build-system r-build-system)
8002 (propagated-inputs
8003 `(("r-biostrings" ,r-biostrings)
8004 ("r-genomicranges" ,r-genomicranges)
8005 ("r-rhtslib" ,r-rhtslib)))
8006 (home-page "https://bioconductor.org/packages/seqbias/")
8007 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
8008 (description
8009 "This package implements a model of per-position sequencing bias in
8010 high-throughput sequencing data using a simple Bayesian network, the structure
8011 and parameters of which are trained on a set of aligned reads and a reference
8012 genome sequence.")
8013 (license license:lgpl3)))
8014
8015 (define-public r-snplocs-hsapiens-dbsnp144-grch37
8016 (package
8017 (name "r-snplocs-hsapiens-dbsnp144-grch37")
8018 (version "0.99.20")
8019 (source (origin
8020 (method url-fetch)
8021 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
8022 version 'annotation))
8023 (sha256
8024 (base32
8025 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
8026 (build-system r-build-system)
8027 ;; As this package provides little more than a very large data file it
8028 ;; doesn't make sense to build substitutes.
8029 (arguments `(#:substitutable? #f))
8030 (propagated-inputs
8031 `(("r-biocgenerics" ,r-biocgenerics)
8032 ("r-s4vectors" ,r-s4vectors)
8033 ("r-iranges" ,r-iranges)
8034 ("r-genomeinfodb" ,r-genomeinfodb)
8035 ("r-genomicranges" ,r-genomicranges)
8036 ("r-bsgenome" ,r-bsgenome)
8037 ("r-biostrings" ,r-biostrings)))
8038 (home-page
8039 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
8040 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
8041 (description "This package provides SNP locations and alleles for Homo
8042 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
8043 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
8044 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
8045 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
8046 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
8047 the mitochondrion chromosome. Therefore, the SNPs in this package can be
8048 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
8049 correct position but this injection will exclude chrM (i.e. nothing will be
8050 injected in that sequence).")
8051 (license license:artistic2.0)))
8052
8053 (define-public r-reqon
8054 (package
8055 (name "r-reqon")
8056 (version "1.36.0")
8057 (source
8058 (origin
8059 (method url-fetch)
8060 (uri (bioconductor-uri "ReQON" version))
8061 (sha256
8062 (base32
8063 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
8064 (properties `((upstream-name . "ReQON")))
8065 (build-system r-build-system)
8066 (propagated-inputs
8067 `(("r-rjava" ,r-rjava)
8068 ("r-rsamtools" ,r-rsamtools)
8069 ("r-seqbias" ,r-seqbias)))
8070 (home-page "https://bioconductor.org/packages/ReQON/")
8071 (synopsis "Recalibrating quality of nucleotides")
8072 (description
8073 "This package provides an implementation of an algorithm for
8074 recalibrating the base quality scores for aligned sequencing data in BAM
8075 format.")
8076 (license license:gpl2)))
8077
8078 (define-public r-wavcluster
8079 (package
8080 (name "r-wavcluster")
8081 (version "2.24.0")
8082 (source
8083 (origin
8084 (method url-fetch)
8085 (uri (bioconductor-uri "wavClusteR" version))
8086 (sha256
8087 (base32
8088 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
8089 (properties `((upstream-name . "wavClusteR")))
8090 (build-system r-build-system)
8091 (propagated-inputs
8092 `(("r-biocgenerics" ,r-biocgenerics)
8093 ("r-biostrings" ,r-biostrings)
8094 ("r-foreach" ,r-foreach)
8095 ("r-genomicfeatures" ,r-genomicfeatures)
8096 ("r-genomicranges" ,r-genomicranges)
8097 ("r-ggplot2" ,r-ggplot2)
8098 ("r-hmisc" ,r-hmisc)
8099 ("r-iranges" ,r-iranges)
8100 ("r-mclust" ,r-mclust)
8101 ("r-rsamtools" ,r-rsamtools)
8102 ("r-rtracklayer" ,r-rtracklayer)
8103 ("r-s4vectors" ,r-s4vectors)
8104 ("r-seqinr" ,r-seqinr)
8105 ("r-stringr" ,r-stringr)))
8106 (native-inputs
8107 `(("r-knitr" ,r-knitr)))
8108 (home-page "https://bioconductor.org/packages/wavClusteR/")
8109 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
8110 (description
8111 "This package provides an integrated pipeline for the analysis of
8112 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
8113 sequencing errors, SNPs and additional non-experimental sources by a non-
8114 parametric mixture model. The protein binding sites (clusters) are then
8115 resolved at high resolution and cluster statistics are estimated using a
8116 rigorous Bayesian framework. Post-processing of the results, data export for
8117 UCSC genome browser visualization and motif search analysis are provided. In
8118 addition, the package integrates RNA-Seq data to estimate the False
8119 Discovery Rate of cluster detection. Key functions support parallel multicore
8120 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
8121 be applied to the analysis of other NGS data obtained from experimental
8122 procedures that induce nucleotide substitutions (e.g. BisSeq).")
8123 (license license:gpl2)))
8124
8125 (define-public r-timeseriesexperiment
8126 (package
8127 (name "r-timeseriesexperiment")
8128 (version "1.8.0")
8129 (source
8130 (origin
8131 (method url-fetch)
8132 (uri (bioconductor-uri "TimeSeriesExperiment" version))
8133 (sha256
8134 (base32
8135 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
8136 (properties
8137 `((upstream-name . "TimeSeriesExperiment")))
8138 (build-system r-build-system)
8139 (propagated-inputs
8140 `(("r-deseq2" ,r-deseq2)
8141 ("r-dplyr" ,r-dplyr)
8142 ("r-dynamictreecut" ,r-dynamictreecut)
8143 ("r-edger" ,r-edger)
8144 ("r-ggplot2" ,r-ggplot2)
8145 ("r-hmisc" ,r-hmisc)
8146 ("r-limma" ,r-limma)
8147 ("r-magrittr" ,r-magrittr)
8148 ("r-proxy" ,r-proxy)
8149 ("r-s4vectors" ,r-s4vectors)
8150 ("r-summarizedexperiment" ,r-summarizedexperiment)
8151 ("r-tibble" ,r-tibble)
8152 ("r-tidyr" ,r-tidyr)
8153 ("r-vegan" ,r-vegan)
8154 ("r-viridis" ,r-viridis)))
8155 (native-inputs
8156 `(("r-knitr" ,r-knitr)))
8157 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
8158 (synopsis "Analysis for short time-series data")
8159 (description
8160 "This package is a visualization and analysis toolbox for short time
8161 course data which includes dimensionality reduction, clustering, two-sample
8162 differential expression testing and gene ranking techniques. The package also
8163 provides methods for retrieving enriched pathways.")
8164 (license license:lgpl3+)))
8165
8166 (define-public r-variantfiltering
8167 (package
8168 (name "r-variantfiltering")
8169 (version "1.26.0")
8170 (source
8171 (origin
8172 (method url-fetch)
8173 (uri (bioconductor-uri "VariantFiltering" version))
8174 (sha256
8175 (base32
8176 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
8177 (properties
8178 `((upstream-name . "VariantFiltering")))
8179 (build-system r-build-system)
8180 (propagated-inputs
8181 `(("r-annotationdbi" ,r-annotationdbi)
8182 ("r-biobase" ,r-biobase)
8183 ("r-biocgenerics" ,r-biocgenerics)
8184 ("r-biocparallel" ,r-biocparallel)
8185 ("r-biostrings" ,r-biostrings)
8186 ("r-bsgenome" ,r-bsgenome)
8187 ("r-dt" ,r-dt)
8188 ("r-genomeinfodb" ,r-genomeinfodb)
8189 ("r-genomicfeatures" ,r-genomicfeatures)
8190 ("r-genomicranges" ,r-genomicranges)
8191 ("r-genomicscores" ,r-genomicscores)
8192 ("r-graph" ,r-graph)
8193 ("r-gviz" ,r-gviz)
8194 ("r-iranges" ,r-iranges)
8195 ("r-rbgl" ,r-rbgl)
8196 ("r-rsamtools" ,r-rsamtools)
8197 ("r-s4vectors" ,r-s4vectors)
8198 ("r-shiny" ,r-shiny)
8199 ("r-shinyjs" ,r-shinyjs)
8200 ("r-shinythemes" ,r-shinythemes)
8201 ("r-shinytree" ,r-shinytree)
8202 ("r-summarizedexperiment" ,r-summarizedexperiment)
8203 ("r-variantannotation" ,r-variantannotation)
8204 ("r-xvector" ,r-xvector)))
8205 (home-page "https://github.com/rcastelo/VariantFiltering")
8206 (synopsis "Filtering of coding and non-coding genetic variants")
8207 (description
8208 "Filter genetic variants using different criteria such as inheritance
8209 model, amino acid change consequence, minor allele frequencies across human
8210 populations, splice site strength, conservation, etc.")
8211 (license license:artistic2.0)))
8212
8213 (define-public r-genomegraphs
8214 (package
8215 (name "r-genomegraphs")
8216 (version "1.46.0")
8217 (source
8218 (origin
8219 (method url-fetch)
8220 (uri (bioconductor-uri "GenomeGraphs" version))
8221 (sha256
8222 (base32
8223 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
8224 (properties `((upstream-name . "GenomeGraphs")))
8225 (build-system r-build-system)
8226 (propagated-inputs
8227 `(("r-biomart" ,r-biomart)))
8228 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
8229 (synopsis "Plotting genomic information from Ensembl")
8230 (description
8231 "Genomic data analyses requires integrated visualization of known genomic
8232 information and new experimental data. GenomeGraphs uses the biomaRt package
8233 to perform live annotation queries to Ensembl and translates this to e.g.
8234 gene/transcript structures in viewports of the grid graphics package. This
8235 results in genomic information plotted together with your data. Another
8236 strength of GenomeGraphs is to plot different data types such as array CGH,
8237 gene expression, sequencing and other data, together in one plot using the
8238 same genome coordinate system.")
8239 (license license:artistic2.0)))
8240
8241 (define-public r-wavetiling
8242 (package
8243 (name "r-wavetiling")
8244 (version "1.28.0")
8245 (source
8246 (origin
8247 (method url-fetch)
8248 (uri (bioconductor-uri "waveTiling" version))
8249 (sha256
8250 (base32
8251 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
8252 (properties `((upstream-name . "waveTiling")))
8253 (build-system r-build-system)
8254 (propagated-inputs
8255 `(("r-affy" ,r-affy)
8256 ("r-biobase" ,r-biobase)
8257 ("r-biostrings" ,r-biostrings)
8258 ("r-genomegraphs" ,r-genomegraphs)
8259 ("r-genomicranges" ,r-genomicranges)
8260 ("r-iranges" ,r-iranges)
8261 ("r-oligo" ,r-oligo)
8262 ("r-oligoclasses" ,r-oligoclasses)
8263 ("r-preprocesscore" ,r-preprocesscore)
8264 ("r-waveslim" ,r-waveslim)))
8265 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
8266 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
8267 (description
8268 "This package is designed to conduct transcriptome analysis for tiling
8269 arrays based on fast wavelet-based functional models.")
8270 (license license:gpl2+)))
8271
8272 (define-public r-variancepartition
8273 (package
8274 (name "r-variancepartition")
8275 (version "1.20.0")
8276 (source
8277 (origin
8278 (method url-fetch)
8279 (uri (bioconductor-uri "variancePartition" version))
8280 (sha256
8281 (base32
8282 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
8283 (properties
8284 `((upstream-name . "variancePartition")))
8285 (build-system r-build-system)
8286 (propagated-inputs
8287 `(("r-biobase" ,r-biobase)
8288 ("r-biocparallel" ,r-biocparallel)
8289 ("r-colorramps" ,r-colorramps)
8290 ("r-doparallel" ,r-doparallel)
8291 ("r-foreach" ,r-foreach)
8292 ("r-ggplot2" ,r-ggplot2)
8293 ("r-gplots" ,r-gplots)
8294 ("r-iterators" ,r-iterators)
8295 ("r-limma" ,r-limma)
8296 ("r-lme4" ,r-lme4)
8297 ("r-lmertest" ,r-lmertest)
8298 ("r-mass" ,r-mass)
8299 ("r-pbkrtest" ,r-pbkrtest)
8300 ("r-progress" ,r-progress)
8301 ("r-reshape2" ,r-reshape2)
8302 ("r-scales" ,r-scales)))
8303 (native-inputs
8304 `(("r-knitr" ,r-knitr)))
8305 (home-page "https://bioconductor.org/packages/variancePartition/")
8306 (synopsis "Analyze variation in gene expression experiments")
8307 (description
8308 "This is a package providing tools to quantify and interpret multiple
8309 sources of biological and technical variation in gene expression experiments.
8310 It uses a linear mixed model to quantify variation in gene expression
8311 attributable to individual, tissue, time point, or technical variables. The
8312 package includes dream differential expression analysis for repeated
8313 measures.")
8314 (license license:gpl2+)))
8315
8316 (define-public r-htqpcr
8317 (package
8318 (name "r-htqpcr")
8319 (version "1.44.0")
8320 (source
8321 (origin
8322 (method url-fetch)
8323 (uri (bioconductor-uri "HTqPCR" version))
8324 (sha256
8325 (base32
8326 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
8327 (properties `((upstream-name . "HTqPCR")))
8328 (build-system r-build-system)
8329 (propagated-inputs
8330 `(("r-affy" ,r-affy)
8331 ("r-biobase" ,r-biobase)
8332 ("r-gplots" ,r-gplots)
8333 ("r-limma" ,r-limma)
8334 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8335 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
8336 "groups/bertone/software/HTqPCR.pdf"))
8337 (synopsis "Automated analysis of high-throughput qPCR data")
8338 (description
8339 "Analysis of Ct values from high throughput quantitative real-time
8340 PCR (qPCR) assays across multiple conditions or replicates. The input data
8341 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
8342 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
8343 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
8344 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
8345 loading, quality assessment, normalization, visualization and parametric or
8346 non-parametric testing for statistical significance in Ct values between
8347 features (e.g. genes, microRNAs).")
8348 (license license:artistic2.0)))
8349
8350 (define-public r-unifiedwmwqpcr
8351 (package
8352 (name "r-unifiedwmwqpcr")
8353 (version "1.26.0")
8354 (source
8355 (origin
8356 (method url-fetch)
8357 (uri (bioconductor-uri "unifiedWMWqPCR" version))
8358 (sha256
8359 (base32
8360 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
8361 (properties
8362 `((upstream-name . "unifiedWMWqPCR")))
8363 (build-system r-build-system)
8364 (propagated-inputs
8365 `(("r-biocgenerics" ,r-biocgenerics)
8366 ("r-htqpcr" ,r-htqpcr)))
8367 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
8368 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
8369 (description
8370 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
8371 data. This modified test allows for testing differential expression in qPCR
8372 data.")
8373 (license license:gpl2+)))
8374
8375 (define-public r-universalmotif
8376 (package
8377 (name "r-universalmotif")
8378 (version "1.8.4")
8379 (source
8380 (origin
8381 (method url-fetch)
8382 (uri (bioconductor-uri "universalmotif" version))
8383 (sha256
8384 (base32
8385 "0pmi5mp5v0srr482vlkfmkp28bywq969fvv9g5kjl5rxki963zmr"))))
8386 (properties
8387 `((upstream-name . "universalmotif")))
8388 (build-system r-build-system)
8389 (arguments
8390 `(#:phases
8391 (modify-phases %standard-phases
8392 (add-after 'unpack 'fix-reference-to-strip
8393 (lambda _
8394 (substitute* "src/Makevars"
8395 (("/usr/bin/strip") (which "strip"))))))))
8396 (propagated-inputs
8397 `(("r-biocgenerics" ,r-biocgenerics)
8398 ("r-biostrings" ,r-biostrings)
8399 ("r-ggplot2" ,r-ggplot2)
8400 ("r-ggseqlogo" ,r-ggseqlogo)
8401 ("r-iranges" ,r-iranges)
8402 ("r-mass" ,r-mass)
8403 ("r-rcpp" ,r-rcpp)
8404 ("r-rcppthread" ,r-rcppthread)
8405 ("r-rdpack" ,r-rdpack)
8406 ("r-rlang" ,r-rlang)
8407 ("r-s4vectors" ,r-s4vectors)
8408 ("r-yaml" ,r-yaml)))
8409 (native-inputs
8410 `(("r-knitr" ,r-knitr)))
8411 (home-page
8412 "https://bioconductor.org/packages/universalmotif/")
8413 (synopsis
8414 "Specific structures importer, modifier, and exporter for R")
8415 (description
8416 "This package allows importing most common @dfn{specific structure}
8417 (motif) types into R for use by functions provided by other Bioconductor
8418 motif-related packages. Motifs can be exported into most major motif formats
8419 from various classes as defined by other Bioconductor packages. A suite of
8420 motif and sequence manipulation and analysis functions are included, including
8421 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
8422 motifs, and others.")
8423 (license license:gpl3)))
8424
8425 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
8426 ;; it here.
8427 (define-public r-activedriverwgs
8428 (package
8429 (name "r-activedriverwgs")
8430 (version "1.1.1")
8431 (source
8432 (origin
8433 (method url-fetch)
8434 (uri (cran-uri "ActiveDriverWGS" version))
8435 (sha256
8436 (base32
8437 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
8438 (properties
8439 `((upstream-name . "ActiveDriverWGS")))
8440 (build-system r-build-system)
8441 (propagated-inputs
8442 `(("r-biostrings" ,r-biostrings)
8443 ("r-bsgenome" ,r-bsgenome)
8444 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8445 ("r-genomeinfodb" ,r-genomeinfodb)
8446 ("r-genomicranges" ,r-genomicranges)
8447 ("r-iranges" ,r-iranges)
8448 ("r-s4vectors" ,r-s4vectors)))
8449 (native-inputs
8450 `(("r-knitr" ,r-knitr)))
8451 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
8452 (synopsis "Driver discovery tool for cancer whole genomes")
8453 (description
8454 "This package provides a method for finding an enrichment of cancer
8455 simple somatic mutations (SNVs and Indels) in functional elements across the
8456 human genome. ActiveDriverWGS detects coding and noncoding driver elements
8457 using whole genome sequencing data.")
8458 (license license:gpl3)))
8459
8460 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
8461 ;; it here.
8462 (define-public r-activepathways
8463 (package
8464 (name "r-activepathways")
8465 (version "1.0.2")
8466 (source
8467 (origin
8468 (method url-fetch)
8469 (uri (cran-uri "ActivePathways" version))
8470 (sha256
8471 (base32
8472 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
8473 (properties
8474 `((upstream-name . "ActivePathways")))
8475 (build-system r-build-system)
8476 (propagated-inputs
8477 `(("r-data-table" ,r-data-table)
8478 ("r-ggplot2" ,r-ggplot2)))
8479 (native-inputs
8480 `(("r-knitr" ,r-knitr)))
8481 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
8482 (synopsis "Multivariate pathway enrichment analysis")
8483 (description
8484 "This package represents an integrative method of analyzing multi omics
8485 data that conducts enrichment analysis of annotated gene sets. ActivePathways
8486 uses a statistical data fusion approach, rationalizes contributing evidence
8487 and highlights associated genes, improving systems-level understanding of
8488 cellular organization in health and disease.")
8489 (license license:gpl3)))
8490
8491 (define-public r-bgmix
8492 (package
8493 (name "r-bgmix")
8494 (version "1.50.0")
8495 (source
8496 (origin
8497 (method url-fetch)
8498 (uri (bioconductor-uri "BGmix" version))
8499 (sha256
8500 (base32
8501 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
8502 (properties `((upstream-name . "BGmix")))
8503 (build-system r-build-system)
8504 (propagated-inputs
8505 `(("r-kernsmooth" ,r-kernsmooth)))
8506 (home-page "https://bioconductor.org/packages/BGmix/")
8507 (synopsis "Bayesian models for differential gene expression")
8508 (description
8509 "This package provides fully Bayesian mixture models for differential
8510 gene expression.")
8511 (license license:gpl2)))
8512
8513 (define-public r-bgx
8514 (package
8515 (name "r-bgx")
8516 (version "1.56.0")
8517 (source
8518 (origin
8519 (method url-fetch)
8520 (uri (bioconductor-uri "bgx" version))
8521 (sha256
8522 (base32
8523 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
8524 (properties `((upstream-name . "bgx")))
8525 (build-system r-build-system)
8526 (propagated-inputs
8527 `(("r-affy" ,r-affy)
8528 ("r-biobase" ,r-biobase)
8529 ("r-gcrma" ,r-gcrma)
8530 ("r-rcpp" ,r-rcpp)))
8531 (home-page "https://bioconductor.org/packages/bgx/")
8532 (synopsis "Bayesian gene expression")
8533 (description
8534 "This package provides tools for Bayesian integrated analysis of
8535 Affymetrix GeneChips.")
8536 (license license:gpl2)))
8537
8538 (define-public r-bhc
8539 (package
8540 (name "r-bhc")
8541 (version "1.42.0")
8542 (source
8543 (origin
8544 (method url-fetch)
8545 (uri (bioconductor-uri "BHC" version))
8546 (sha256
8547 (base32
8548 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
8549 (properties `((upstream-name . "BHC")))
8550 (build-system r-build-system)
8551 (home-page "https://bioconductor.org/packages/BHC/")
8552 (synopsis "Bayesian hierarchical clustering")
8553 (description
8554 "The method implemented in this package performs bottom-up hierarchical
8555 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
8556 in the data and Bayesian model selection to decide at each step which clusters
8557 to merge. This avoids several limitations of traditional methods, for example
8558 how many clusters there should be and how to choose a principled distance
8559 metric. This implementation accepts multinomial (i.e. discrete, with 2+
8560 categories) or time-series data. This version also includes a randomised
8561 algorithm which is more efficient for larger data sets.")
8562 (license license:gpl3)))
8563
8564 (define-public r-bicare
8565 (package
8566 (name "r-bicare")
8567 (version "1.48.0")
8568 (source
8569 (origin
8570 (method url-fetch)
8571 (uri (bioconductor-uri "BicARE" version))
8572 (sha256
8573 (base32
8574 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
8575 (properties `((upstream-name . "BicARE")))
8576 (build-system r-build-system)
8577 (propagated-inputs
8578 `(("r-biobase" ,r-biobase)
8579 ("r-gseabase" ,r-gseabase)
8580 ("r-multtest" ,r-multtest)))
8581 (home-page "http://bioinfo.curie.fr")
8582 (synopsis "Biclustering analysis and results exploration")
8583 (description
8584 "This is a package for biclustering analysis and exploration of
8585 results.")
8586 (license license:gpl2)))
8587
8588 (define-public r-bifet
8589 (package
8590 (name "r-bifet")
8591 (version "1.10.0")
8592 (source
8593 (origin
8594 (method url-fetch)
8595 (uri (bioconductor-uri "BiFET" version))
8596 (sha256
8597 (base32
8598 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
8599 (properties `((upstream-name . "BiFET")))
8600 (build-system r-build-system)
8601 (propagated-inputs
8602 `(("r-genomicranges" ,r-genomicranges)
8603 ("r-poibin" ,r-poibin)))
8604 (native-inputs
8605 `(("r-knitr" ,r-knitr)))
8606 (home-page "https://bioconductor.org/packages/BiFET")
8607 (synopsis "Bias-free footprint enrichment test")
8608 (description
8609 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
8610 over-represented in target regions compared to background regions after
8611 correcting for the bias arising from the imbalance in read counts and GC
8612 contents between the target and background regions. For a given TF k, BiFET
8613 tests the null hypothesis that the target regions have the same probability of
8614 having footprints for the TF k as the background regions while correcting for
8615 the read count and GC content bias.")
8616 (license license:gpl3)))
8617
8618 (define-public r-rsbml
8619 (package
8620 (name "r-rsbml")
8621 (version "2.48.0")
8622 (source
8623 (origin
8624 (method url-fetch)
8625 (uri (bioconductor-uri "rsbml" version))
8626 (sha256
8627 (base32
8628 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
8629 (properties `((upstream-name . "rsbml")))
8630 (build-system r-build-system)
8631 (inputs
8632 `(("libsbml" ,libsbml)
8633 ("zlib" ,zlib)))
8634 (propagated-inputs
8635 `(("r-biocgenerics" ,r-biocgenerics)
8636 ("r-graph" ,r-graph)))
8637 (native-inputs
8638 `(("pkg-config" ,pkg-config)))
8639 (home-page "http://www.sbml.org")
8640 (synopsis "R support for SBML")
8641 (description
8642 "This package provides an R interface to libsbml for SBML parsing,
8643 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
8644 (license license:artistic2.0)))
8645
8646 (define-public r-hypergraph
8647 (package
8648 (name "r-hypergraph")
8649 (version "1.62.0")
8650 (source
8651 (origin
8652 (method url-fetch)
8653 (uri (bioconductor-uri "hypergraph" version))
8654 (sha256
8655 (base32
8656 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
8657 (properties `((upstream-name . "hypergraph")))
8658 (build-system r-build-system)
8659 (propagated-inputs
8660 `(("r-graph" ,r-graph)))
8661 (home-page "https://bioconductor.org/packages/hypergraph")
8662 (synopsis "Hypergraph data structures")
8663 (description
8664 "This package implements some simple capabilities for representing and
8665 manipulating hypergraphs.")
8666 (license license:artistic2.0)))
8667
8668 (define-public r-hyperdraw
8669 (package
8670 (name "r-hyperdraw")
8671 (version "1.42.0")
8672 (source
8673 (origin
8674 (method url-fetch)
8675 (uri (bioconductor-uri "hyperdraw" version))
8676 (sha256
8677 (base32
8678 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
8679 (properties `((upstream-name . "hyperdraw")))
8680 (build-system r-build-system)
8681 (inputs `(("graphviz" ,graphviz)))
8682 (propagated-inputs
8683 `(("r-graph" ,r-graph)
8684 ("r-hypergraph" ,r-hypergraph)
8685 ("r-rgraphviz" ,r-rgraphviz)))
8686 (home-page "https://bioconductor.org/packages/hyperdraw")
8687 (synopsis "Visualizing hypergraphs")
8688 (description
8689 "This package provides functions for visualizing hypergraphs.")
8690 (license license:gpl2+)))
8691
8692 (define-public r-biggr
8693 (package
8694 (name "r-biggr")
8695 (version "1.26.0")
8696 (source
8697 (origin
8698 (method url-fetch)
8699 (uri (bioconductor-uri "BiGGR" version))
8700 (sha256
8701 (base32
8702 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
8703 (properties `((upstream-name . "BiGGR")))
8704 (build-system r-build-system)
8705 (propagated-inputs
8706 `(("r-hyperdraw" ,r-hyperdraw)
8707 ("r-hypergraph" ,r-hypergraph)
8708 ("r-lim" ,r-lim)
8709 ("r-limsolve" ,r-limsolve)
8710 ("r-rsbml" ,r-rsbml)
8711 ("r-stringr" ,r-stringr)))
8712 (home-page "https://bioconductor.org/packages/BiGGR/")
8713 (synopsis "Constraint based modeling using metabolic reconstruction databases")
8714 (description
8715 "This package provides an interface to simulate metabolic reconstruction
8716 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
8717 reconstruction databases. The package facilitates @dfn{flux balance
8718 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
8719 networks and estimated fluxes can be visualized with hypergraphs.")
8720 (license license:gpl3+)))
8721
8722 (define-public r-bigmemoryextras
8723 (package
8724 (name "r-bigmemoryextras")
8725 (version "1.38.0")
8726 (source
8727 (origin
8728 (method url-fetch)
8729 (uri (bioconductor-uri "bigmemoryExtras" version))
8730 (sha256
8731 (base32
8732 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
8733 (properties
8734 `((upstream-name . "bigmemoryExtras")))
8735 (build-system r-build-system)
8736 (propagated-inputs
8737 `(("r-bigmemory" ,r-bigmemory)))
8738 (native-inputs
8739 `(("r-knitr" ,r-knitr)))
8740 (home-page "https://github.com/phaverty/bigmemoryExtras")
8741 (synopsis "Extension of the bigmemory package")
8742 (description
8743 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
8744 safety and convenience features to the @code{filebacked.big.matrix} class from
8745 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
8746 monitoring and gracefully restoring the connection to on-disk data and it also
8747 protects against accidental data modification with a file-system-based
8748 permissions system. Utilities are provided for using @code{BigMatrix}-derived
8749 classes as @code{assayData} matrices within the @code{Biobase} package's
8750 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
8751 related to attaching to, and indexing into, file-backed matrices with
8752 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
8753 a file-backed matrix with factor properties.")
8754 (license license:artistic2.0)))
8755
8756 (define-public r-bigpint
8757 (package
8758 (name "r-bigpint")
8759 (version "1.6.0")
8760 (source
8761 (origin
8762 (method url-fetch)
8763 (uri (bioconductor-uri "bigPint" version))
8764 (sha256
8765 (base32
8766 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
8767 (properties `((upstream-name . "bigPint")))
8768 (build-system r-build-system)
8769 (propagated-inputs
8770 `(("r-delayedarray" ,r-delayedarray)
8771 ("r-dplyr" ,r-dplyr)
8772 ("r-ggally" ,r-ggally)
8773 ("r-ggplot2" ,r-ggplot2)
8774 ("r-gridextra" ,r-gridextra)
8775 ("r-hexbin" ,r-hexbin)
8776 ("r-hmisc" ,r-hmisc)
8777 ("r-htmlwidgets" ,r-htmlwidgets)
8778 ("r-plotly" ,r-plotly)
8779 ("r-plyr" ,r-plyr)
8780 ("r-rcolorbrewer" ,r-rcolorbrewer)
8781 ("r-reshape" ,r-reshape)
8782 ("r-shiny" ,r-shiny)
8783 ("r-shinycssloaders" ,r-shinycssloaders)
8784 ("r-shinydashboard" ,r-shinydashboard)
8785 ("r-stringr" ,r-stringr)
8786 ("r-summarizedexperiment" ,r-summarizedexperiment)
8787 ("r-tidyr" ,r-tidyr)))
8788 (native-inputs
8789 `(("r-knitr" ,r-knitr)))
8790 (home-page "https://github.com/lindsayrutter/bigPint")
8791 (synopsis "Big multivariate data plotted interactively")
8792 (description
8793 "This package provides methods for visualizing large multivariate
8794 datasets using static and interactive scatterplot matrices, parallel
8795 coordinate plots, volcano plots, and litre plots. It includes examples for
8796 visualizing RNA-sequencing datasets and differentially expressed genes.")
8797 (license license:gpl3)))
8798
8799 (define-public r-chemminer
8800 (package
8801 (name "r-chemminer")
8802 (version "3.42.2")
8803 (source
8804 (origin
8805 (method url-fetch)
8806 (uri (bioconductor-uri "ChemmineR" version))
8807 (sha256
8808 (base32
8809 "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
8810 (properties `((upstream-name . "ChemmineR")))
8811 (build-system r-build-system)
8812 (propagated-inputs
8813 `(("r-base64enc" ,r-base64enc)
8814 ("r-bh" ,r-bh)
8815 ("r-biocgenerics" ,r-biocgenerics)
8816 ("r-dbi" ,r-dbi)
8817 ("r-digest" ,r-digest)
8818 ("r-dt" ,r-dt)
8819 ("r-ggplot2" ,r-ggplot2)
8820 ("r-gridextra" ,r-gridextra)
8821 ("r-png" ,r-png)
8822 ("r-rcpp" ,r-rcpp)
8823 ("r-rcurl" ,r-rcurl)
8824 ("r-rjson" ,r-rjson)
8825 ("r-rsvg" ,r-rsvg)))
8826 (native-inputs
8827 `(("r-knitr" ,r-knitr)))
8828 (home-page "https://github.com/girke-lab/ChemmineR")
8829 (synopsis "Cheminformatics toolkit for R")
8830 (description
8831 "ChemmineR is a cheminformatics package for analyzing drug-like small
8832 molecule data in R. It contains functions for efficient processing of large
8833 numbers of molecules, physicochemical/structural property predictions,
8834 structural similarity searching, classification and clustering of compound
8835 libraries with a wide spectrum of algorithms. In addition, it offers
8836 visualization functions for compound clustering results and chemical
8837 structures.")
8838 (license license:artistic2.0)))
8839
8840 (define-public r-bioassayr
8841 (package
8842 (name "r-bioassayr")
8843 (version "1.28.2")
8844 (source
8845 (origin
8846 (method url-fetch)
8847 (uri (bioconductor-uri "bioassayR" version))
8848 (sha256
8849 (base32
8850 "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5"))))
8851 (properties `((upstream-name . "bioassayR")))
8852 (build-system r-build-system)
8853 (propagated-inputs
8854 `(("r-biocgenerics" ,r-biocgenerics)
8855 ("r-chemminer" ,r-chemminer)
8856 ("r-dbi" ,r-dbi)
8857 ("r-matrix" ,r-matrix)
8858 ("r-rjson" ,r-rjson)
8859 ("r-rsqlite" ,r-rsqlite)
8860 ("r-xml" ,r-xml)))
8861 (native-inputs
8862 `(("r-knitr" ,r-knitr)))
8863 (home-page "https://github.com/girke-lab/bioassayR")
8864 (synopsis "Cross-target analysis of small molecule bioactivity")
8865 (description
8866 "bioassayR is a computational tool that enables simultaneous analysis of
8867 thousands of bioassay experiments performed over a diverse set of compounds
8868 and biological targets. Unique features include support for large-scale
8869 cross-target analyses of both public and custom bioassays, generation of
8870 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
8871 preloaded database that provides access to a substantial portion of publicly
8872 available bioactivity data.")
8873 (license license:artistic2.0)))
8874
8875 (define-public r-biobroom
8876 (package
8877 (name "r-biobroom")
8878 (version "1.22.0")
8879 (source
8880 (origin
8881 (method url-fetch)
8882 (uri (bioconductor-uri "biobroom" version))
8883 (sha256
8884 (base32
8885 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
8886 (properties `((upstream-name . "biobroom")))
8887 (build-system r-build-system)
8888 (propagated-inputs
8889 `(("r-biobase" ,r-biobase)
8890 ("r-broom" ,r-broom)
8891 ("r-dplyr" ,r-dplyr)
8892 ("r-tidyr" ,r-tidyr)))
8893 (native-inputs
8894 `(("r-knitr" ,r-knitr)))
8895 (home-page "https://github.com/StoreyLab/biobroom")
8896 (synopsis "Turn Bioconductor objects into tidy data frames")
8897 (description
8898 "This package contains methods for converting standard objects
8899 constructed by bioinformatics packages, especially those in Bioconductor, and
8900 converting them to @code{tidy} data. It thus serves as a complement to the
8901 @code{broom} package, and follows the same tidy, augment, glance division of
8902 tidying methods. Tidying data makes it easy to recombine, reshape and
8903 visualize bioinformatics analyses.")
8904 ;; Any version of the LGPL.
8905 (license license:lgpl3+)))
8906
8907 (define-public r-graphite
8908 (package
8909 (name "r-graphite")
8910 (version "1.36.0")
8911 (source
8912 (origin
8913 (method url-fetch)
8914 (uri (bioconductor-uri "graphite" version))
8915 (sha256
8916 (base32
8917 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
8918 (properties `((upstream-name . "graphite")))
8919 (build-system r-build-system)
8920 (propagated-inputs
8921 `(("r-annotationdbi" ,r-annotationdbi)
8922 ("r-checkmate" ,r-checkmate)
8923 ("r-graph" ,r-graph)
8924 ("r-httr" ,r-httr)
8925 ("r-rappdirs" ,r-rappdirs)))
8926 (home-page "https://bioconductor.org/packages/graphite/")
8927 (synopsis "Networks from pathway databases")
8928 (description
8929 "Graphite provides networks derived from eight public pathway databases,
8930 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
8931 symbols).")
8932 (license license:agpl3+)))
8933
8934 (define-public r-reactomepa
8935 (package
8936 (name "r-reactomepa")
8937 (version "1.34.0")
8938 (source
8939 (origin
8940 (method url-fetch)
8941 (uri (bioconductor-uri "ReactomePA" version))
8942 (sha256
8943 (base32
8944 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
8945 (properties `((upstream-name . "ReactomePA")))
8946 (build-system r-build-system)
8947 (propagated-inputs
8948 `(("r-annotationdbi" ,r-annotationdbi)
8949 ("r-dose" ,r-dose)
8950 ("r-enrichplot" ,r-enrichplot)
8951 ("r-ggplot2" ,r-ggplot2)
8952 ("r-ggraph" ,r-ggraph)
8953 ("r-graphite" ,r-graphite)
8954 ("r-igraph" ,r-igraph)
8955 ("r-reactome-db" ,r-reactome-db)))
8956 (native-inputs
8957 `(("r-knitr" ,r-knitr)))
8958 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
8959 (synopsis "Reactome pathway analysis")
8960 (description
8961 "This package provides functions for pathway analysis based on the
8962 REACTOME pathway database. It implements enrichment analysis, gene set
8963 enrichment analysis and several functions for visualization.")
8964 (license license:gpl2)))
8965
8966 (define-public r-ebarrays
8967 (package
8968 (name "r-ebarrays")
8969 (version "2.54.0")
8970 (source
8971 (origin
8972 (method url-fetch)
8973 (uri (bioconductor-uri "EBarrays" version))
8974 (sha256
8975 (base32
8976 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
8977 (properties `((upstream-name . "EBarrays")))
8978 (build-system r-build-system)
8979 (propagated-inputs
8980 `(("r-biobase" ,r-biobase)
8981 ("r-cluster" ,r-cluster)
8982 ("r-lattice" ,r-lattice)))
8983 (home-page "https://bioconductor.org/packages/EBarrays/")
8984 (synopsis "Gene clustering and differential expression identification")
8985 (description
8986 "EBarrays provides tools for the analysis of replicated/unreplicated
8987 microarray data.")
8988 (license license:gpl2+)))
8989
8990 (define-public r-bioccasestudies
8991 (package
8992 (name "r-bioccasestudies")
8993 (version "1.52.0")
8994 (source
8995 (origin
8996 (method url-fetch)
8997 (uri (bioconductor-uri "BiocCaseStudies" version))
8998 (sha256
8999 (base32
9000 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
9001 (properties
9002 `((upstream-name . "BiocCaseStudies")))
9003 (build-system r-build-system)
9004 (propagated-inputs `(("r-biobase" ,r-biobase)))
9005 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
9006 (synopsis "Support for the case studies monograph")
9007 (description
9008 "This package provides software and data to support the case studies
9009 monograph.")
9010 (license license:artistic2.0)))
9011
9012 (define-public r-bioccheck
9013 (package
9014 (name "r-bioccheck")
9015 (version "1.26.0")
9016 (source (origin
9017 (method url-fetch)
9018 (uri (bioconductor-uri "BiocCheck" version))
9019 (sha256
9020 (base32
9021 "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
9022 (properties
9023 `((upstream-name . "BiocCheck")))
9024 (build-system r-build-system)
9025 (arguments
9026 '(#:phases
9027 (modify-phases %standard-phases
9028 ;; This package can be used by calling BiocCheck(<package>) from
9029 ;; within R, or by running R CMD BiocCheck <package>. This phase
9030 ;; makes sure the latter works. For this to work, the BiocCheck
9031 ;; script must be somewhere on the PATH (not the R bin directory).
9032 (add-after 'install 'install-bioccheck-subcommand
9033 (lambda* (#:key outputs #:allow-other-keys)
9034 (let* ((out (assoc-ref outputs "out"))
9035 (dest-dir (string-append out "/bin"))
9036 (script-dir
9037 (string-append out "/site-library/BiocCheck/script/")))
9038 (mkdir-p dest-dir)
9039 (symlink (string-append script-dir "/checkBadDeps.R")
9040 (string-append dest-dir "/checkBadDeps.R"))
9041 (symlink (string-append script-dir "/BiocCheck")
9042 (string-append dest-dir "/BiocCheck")))
9043 #t)))))
9044 (propagated-inputs
9045 `(("r-codetools" ,r-codetools)
9046 ("r-graph" ,r-graph)
9047 ("r-httr" ,r-httr)
9048 ("r-knitr" ,r-knitr)
9049 ("r-optparse" ,r-optparse)
9050 ("r-biocmanager" ,r-biocmanager)
9051 ("r-biocviews" ,r-biocviews)
9052 ("r-stringdist" ,r-stringdist)))
9053 (native-inputs
9054 `(("r-knitr" ,r-knitr)))
9055 (home-page "https://bioconductor.org/packages/BiocCheck")
9056 (synopsis "Executes Bioconductor-specific package checks")
9057 (description "This package contains tools to perform additional quality
9058 checks on R packages that are to be submitted to the Bioconductor repository.")
9059 (license license:artistic2.0)))
9060
9061 (define-public r-biocgraph
9062 (package
9063 (name "r-biocgraph")
9064 (version "1.52.0")
9065 (source
9066 (origin
9067 (method url-fetch)
9068 (uri (bioconductor-uri "biocGraph" version))
9069 (sha256
9070 (base32
9071 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
9072 (properties `((upstream-name . "biocGraph")))
9073 (build-system r-build-system)
9074 (propagated-inputs
9075 `(("r-biocgenerics" ,r-biocgenerics)
9076 ("r-geneplotter" ,r-geneplotter)
9077 ("r-graph" ,r-graph)
9078 ("r-rgraphviz" ,r-rgraphviz)))
9079 (home-page "https://bioconductor.org/packages/biocGraph/")
9080 (synopsis "Graph examples and use cases in Bioinformatics")
9081 (description
9082 "This package provides examples and code that make use of the
9083 different graph related packages produced by Bioconductor.")
9084 (license license:artistic2.0)))
9085
9086 (define-public r-biocstyle
9087 (package
9088 (name "r-biocstyle")
9089 (version "2.18.1")
9090 (source (origin
9091 (method url-fetch)
9092 (uri (bioconductor-uri "BiocStyle" version))
9093 (sha256
9094 (base32
9095 "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
9096 (properties
9097 `((upstream-name . "BiocStyle")))
9098 (build-system r-build-system)
9099 (propagated-inputs
9100 `(("r-biocmanager" ,r-biocmanager)
9101 ("r-bookdown" ,r-bookdown)
9102 ("r-knitr" ,r-knitr)
9103 ("r-rmarkdown" ,r-rmarkdown)
9104 ("r-yaml" ,r-yaml)))
9105 (native-inputs
9106 `(("r-knitr" ,r-knitr)))
9107 (home-page "https://bioconductor.org/packages/BiocStyle")
9108 (synopsis "Bioconductor formatting styles")
9109 (description "This package provides standard formatting styles for
9110 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
9111 functionality.")
9112 (license license:artistic2.0)))
9113
9114 (define-public r-biocviews
9115 (package
9116 (name "r-biocviews")
9117 (version "1.58.1")
9118 (source (origin
9119 (method url-fetch)
9120 (uri (bioconductor-uri "biocViews" version))
9121 (sha256
9122 (base32
9123 "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
9124 (properties
9125 `((upstream-name . "biocViews")))
9126 (build-system r-build-system)
9127 (propagated-inputs
9128 `(("r-biobase" ,r-biobase)
9129 ("r-biocmanager" ,r-biocmanager)
9130 ("r-graph" ,r-graph)
9131 ("r-rbgl" ,r-rbgl)
9132 ("r-rcurl" ,r-rcurl)
9133 ("r-xml" ,r-xml)
9134 ("r-runit" ,r-runit)))
9135 (home-page "https://bioconductor.org/packages/biocViews")
9136 (synopsis "Bioconductor package categorization helper")
9137 (description "The purpose of biocViews is to create HTML pages that
9138 categorize packages in a Bioconductor package repository according to keywords,
9139 also known as views, in a controlled vocabulary.")
9140 (license license:artistic2.0)))
9141
9142 (define-public r-experimenthub
9143 (package
9144 (name "r-experimenthub")
9145 (version "1.16.0")
9146 (source
9147 (origin
9148 (method url-fetch)
9149 (uri (bioconductor-uri "ExperimentHub" version))
9150 (sha256
9151 (base32
9152 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
9153 (properties `((upstream-name . "ExperimentHub")))
9154 (build-system r-build-system)
9155 (propagated-inputs
9156 `(("r-annotationhub" ,r-annotationhub)
9157 ("r-biocfilecache" ,r-biocfilecache)
9158 ("r-biocgenerics" ,r-biocgenerics)
9159 ("r-biocmanager" ,r-biocmanager)
9160 ("r-curl" ,r-curl)
9161 ("r-rappdirs" ,r-rappdirs)
9162 ("r-s4vectors" ,r-s4vectors)))
9163 (native-inputs
9164 `(("r-knitr" ,r-knitr)))
9165 (home-page "https://bioconductor.org/packages/ExperimentHub/")
9166 (synopsis "Client to access ExperimentHub resources")
9167 (description
9168 "This package provides a client for the Bioconductor ExperimentHub web
9169 resource. ExperimentHub provides a central location where curated data from
9170 experiments, publications or training courses can be accessed. Each resource
9171 has associated metadata, tags and date of modification. The client creates
9172 and manages a local cache of files retrieved enabling quick and reproducible
9173 access.")
9174 (license license:artistic2.0)))
9175
9176 (define-public r-grohmm
9177 (package
9178 (name "r-grohmm")
9179 (version "1.24.0")
9180 (source
9181 (origin
9182 (method url-fetch)
9183 (uri (bioconductor-uri "groHMM" version))
9184 (sha256
9185 (base32
9186 "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
9187 (properties `((upstream-name . "groHMM")))
9188 (build-system r-build-system)
9189 (propagated-inputs
9190 `(("r-genomeinfodb" ,r-genomeinfodb)
9191 ("r-genomicalignments" ,r-genomicalignments)
9192 ("r-genomicranges" ,r-genomicranges)
9193 ("r-iranges" ,r-iranges)
9194 ("r-mass" ,r-mass)
9195 ("r-rtracklayer" ,r-rtracklayer)
9196 ("r-s4vectors" ,r-s4vectors)))
9197 (home-page "https://github.com/Kraus-Lab/groHMM")
9198 (synopsis "GRO-seq analysis pipeline")
9199 (description
9200 "This package provides a pipeline for the analysis of GRO-seq data.")
9201 (license license:gpl3+)))
9202
9203 (define-public r-multiassayexperiment
9204 (package
9205 (name "r-multiassayexperiment")
9206 (version "1.16.0")
9207 (source
9208 (origin
9209 (method url-fetch)
9210 (uri (bioconductor-uri "MultiAssayExperiment" version))
9211 (sha256
9212 (base32
9213 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
9214 (properties
9215 `((upstream-name . "MultiAssayExperiment")))
9216 (build-system r-build-system)
9217 (propagated-inputs
9218 `(("r-biobase" ,r-biobase)
9219 ("r-biocgenerics" ,r-biocgenerics)
9220 ("r-genomicranges" ,r-genomicranges)
9221 ("r-iranges" ,r-iranges)
9222 ("r-s4vectors" ,r-s4vectors)
9223 ("r-summarizedexperiment" ,r-summarizedexperiment)
9224 ("r-tidyr" ,r-tidyr)))
9225 (native-inputs
9226 `(("r-knitr" ,r-knitr)))
9227 (home-page "https://waldronlab.io/MultiAssayExperiment/")
9228 (synopsis "Integration of multi-omics experiments in Bioconductor")
9229 (description
9230 "MultiAssayExperiment harmonizes data management of multiple assays
9231 performed on an overlapping set of specimens. It provides a familiar
9232 Bioconductor user experience by extending concepts from
9233 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
9234 classes for individual assays, and allowing subsetting by genomic ranges or
9235 rownames.")
9236 (license license:artistic2.0)))
9237
9238 (define-public r-bioconcotk
9239 (package
9240 (name "r-bioconcotk")
9241 (version "1.10.0")
9242 (source
9243 (origin
9244 (method url-fetch)
9245 (uri (bioconductor-uri "BiocOncoTK" version))
9246 (sha256
9247 (base32
9248 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
9249 (properties `((upstream-name . "BiocOncoTK")))
9250 (build-system r-build-system)
9251 (propagated-inputs
9252 `(("r-bigrquery" ,r-bigrquery)
9253 ("r-car" ,r-car)
9254 ("r-complexheatmap" ,r-complexheatmap)
9255 ("r-curatedtcgadata" ,r-curatedtcgadata)
9256 ("r-dbi" ,r-dbi)
9257 ("r-dplyr" ,r-dplyr)
9258 ("r-dt" ,r-dt)
9259 ("r-genomicfeatures" ,r-genomicfeatures)
9260 ("r-genomicranges" ,r-genomicranges)
9261 ("r-ggplot2" ,r-ggplot2)
9262 ("r-ggpubr" ,r-ggpubr)
9263 ("r-graph" ,r-graph)
9264 ("r-httr" ,r-httr)
9265 ("r-iranges" ,r-iranges)
9266 ("r-magrittr" ,r-magrittr)
9267 ("r-plyr" ,r-plyr)
9268 ("r-rgraphviz" ,r-rgraphviz)
9269 ("r-rjson" ,r-rjson)
9270 ("r-s4vectors" ,r-s4vectors)
9271 ("r-scales" ,r-scales)
9272 ("r-shiny" ,r-shiny)
9273 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9274 (native-inputs
9275 `(("r-knitr" ,r-knitr)))
9276 (home-page "https://bioconductor.org/packages/BiocOncoTK")
9277 (synopsis "Bioconductor components for general cancer genomics")
9278 (description
9279 "The purpose of this package is to provide a central interface to various
9280 tools for genome-scale analysis of cancer studies.")
9281 (license license:artistic2.0)))
9282
9283 (define-public r-biocor
9284 (package
9285 (name "r-biocor")
9286 (version "1.14.0")
9287 (source
9288 (origin
9289 (method url-fetch)
9290 (uri (bioconductor-uri "BioCor" version))
9291 (sha256
9292 (base32
9293 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
9294 (properties `((upstream-name . "BioCor")))
9295 (build-system r-build-system)
9296 (propagated-inputs
9297 `(("r-biocparallel" ,r-biocparallel)
9298 ("r-gseabase" ,r-gseabase)
9299 ("r-matrix" ,r-matrix)))
9300 (native-inputs
9301 `(("r-knitr" ,r-knitr)))
9302 (home-page "https://llrs.github.io/BioCor/")
9303 (synopsis "Functional similarities")
9304 (description
9305 "This package provides tools to calculate functional similarities based
9306 on the pathways described on KEGG and REACTOME or in gene sets. These
9307 similarities can be calculated for pathways or gene sets, genes, or clusters
9308 and combined with other similarities. They can be used to improve networks,
9309 gene selection, testing relationships, and so on.")
9310 (license license:expat)))
9311
9312 (define-public r-biocpkgtools
9313 (package
9314 (name "r-biocpkgtools")
9315 (version "1.8.0")
9316 (source
9317 (origin
9318 (method url-fetch)
9319 (uri (bioconductor-uri "BiocPkgTools" version))
9320 (sha256
9321 (base32
9322 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
9323 (properties `((upstream-name . "BiocPkgTools")))
9324 (build-system r-build-system)
9325 (propagated-inputs
9326 `(("r-biocfilecache" ,r-biocfilecache)
9327 ("r-biocmanager" ,r-biocmanager)
9328 ("r-biocviews" ,r-biocviews)
9329 ("r-dplyr" ,r-dplyr)
9330 ("r-dt" ,r-dt)
9331 ("r-gh" ,r-gh)
9332 ("r-graph" ,r-graph)
9333 ("r-htmltools" ,r-htmltools)
9334 ("r-htmlwidgets" ,r-htmlwidgets)
9335 ("r-httr" ,r-httr)
9336 ("r-igraph" ,r-igraph)
9337 ("r-jsonlite" ,r-jsonlite)
9338 ("r-magrittr" ,r-magrittr)
9339 ("r-rappdirs" ,r-rappdirs)
9340 ("r-rbgl" ,r-rbgl)
9341 ("r-readr" ,r-readr)
9342 ("r-rex" ,r-rex)
9343 ("r-rlang" ,r-rlang)
9344 ("r-rvest" ,r-rvest)
9345 ("r-stringr" ,r-stringr)
9346 ("r-tibble" ,r-tibble)
9347 ("r-tidyr" ,r-tidyr)
9348 ("r-tidyselect" ,r-tidyselect)
9349 ("r-xml2" ,r-xml2)))
9350 (native-inputs
9351 `(("r-knitr" ,r-knitr)))
9352 (home-page "https://github.com/seandavi/BiocPkgTools")
9353 (synopsis "Collection of tools for learning about Bioconductor packages")
9354 (description
9355 "Bioconductor has a rich ecosystem of metadata around packages, usage,
9356 and build status. This package is a simple collection of functions to access
9357 that metadata from R. The goal is to expose metadata for data mining and
9358 value-added functionality such as package searching, text mining, and
9359 analytics on packages.")
9360 (license license:expat)))
9361
9362 (define-public r-biocset
9363 (package
9364 (name "r-biocset")
9365 (version "1.4.0")
9366 (source
9367 (origin
9368 (method url-fetch)
9369 (uri (bioconductor-uri "BiocSet" version))
9370 (sha256
9371 (base32
9372 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
9373 (properties `((upstream-name . "BiocSet")))
9374 (build-system r-build-system)
9375 (propagated-inputs
9376 `(("r-annotationdbi" ,r-annotationdbi)
9377 ("r-biocio" ,r-biocio)
9378 ("r-dplyr" ,r-dplyr)
9379 ("r-keggrest" ,r-keggrest)
9380 ("r-ontologyindex" ,r-ontologyindex)
9381 ("r-plyr" ,r-plyr)
9382 ("r-rlang" ,r-rlang)
9383 ("r-s4vectors" ,r-s4vectors)
9384 ("r-tibble" ,r-tibble)
9385 ("r-tidyr" ,r-tidyr)))
9386 (native-inputs
9387 `(("r-knitr" ,r-knitr)))
9388 (home-page
9389 "https://bioconductor.org/packages/BiocSet")
9390 (synopsis
9391 "Representing Different Biological Sets")
9392 (description
9393 "BiocSet displays different biological sets in a triple tibble format.
9394 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
9395 The user has the ability to activate one of these three tibbles to perform
9396 common functions from the @code{dplyr} package. Mapping functionality and
9397 accessing web references for elements/sets are also available in BiocSet.")
9398 (license license:artistic2.0)))
9399
9400 (define-public r-biocworkflowtools
9401 (package
9402 (name "r-biocworkflowtools")
9403 (version "1.16.0")
9404 (source
9405 (origin
9406 (method url-fetch)
9407 (uri (bioconductor-uri "BiocWorkflowTools" version))
9408 (sha256
9409 (base32
9410 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
9411 (properties
9412 `((upstream-name . "BiocWorkflowTools")))
9413 (build-system r-build-system)
9414 (propagated-inputs
9415 `(("r-biocstyle" ,r-biocstyle)
9416 ("r-bookdown" ,r-bookdown)
9417 ("r-git2r" ,r-git2r)
9418 ("r-httr" ,r-httr)
9419 ("r-knitr" ,r-knitr)
9420 ("r-rmarkdown" ,r-rmarkdown)
9421 ("r-rstudioapi" ,r-rstudioapi)
9422 ("r-stringr" ,r-stringr)
9423 ("r-usethis" ,r-usethis)))
9424 (native-inputs
9425 `(("r-knitr" ,r-knitr)))
9426 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
9427 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
9428 (description
9429 "This package provides functions to ease the transition between
9430 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
9431 (license license:expat)))
9432
9433 (define-public r-biodist
9434 (package
9435 (name "r-biodist")
9436 (version "1.62.0")
9437 (source
9438 (origin
9439 (method url-fetch)
9440 (uri (bioconductor-uri "bioDist" version))
9441 (sha256
9442 (base32
9443 "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
9444 (properties `((upstream-name . "bioDist")))
9445 (build-system r-build-system)
9446 (propagated-inputs
9447 `(("r-biobase" ,r-biobase)
9448 ("r-kernsmooth" ,r-kernsmooth)))
9449 (home-page "https://bioconductor.org/packages/bioDist/")
9450 (synopsis "Different distance measures")
9451 (description
9452 "This package provides a collection of software tools for calculating
9453 distance measures.")
9454 (license license:artistic2.0)))
9455
9456 (define-public r-pcatools
9457 (package
9458 (name "r-pcatools")
9459 (version "2.2.0")
9460 (source
9461 (origin
9462 (method url-fetch)
9463 (uri (bioconductor-uri "PCAtools" version))
9464 (sha256
9465 (base32
9466 "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
9467 (properties `((upstream-name . "PCAtools")))
9468 (build-system r-build-system)
9469 (propagated-inputs
9470 `(("r-beachmat" ,r-beachmat)
9471 ("r-bh" ,r-bh)
9472 ("r-biocparallel" ,r-biocparallel)
9473 ("r-biocsingular" ,r-biocsingular)
9474 ("r-cowplot" ,r-cowplot)
9475 ("r-delayedarray" ,r-delayedarray)
9476 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9477 ("r-dqrng" ,r-dqrng)
9478 ("r-ggplot2" ,r-ggplot2)
9479 ("r-ggrepel" ,r-ggrepel)
9480 ("r-lattice" ,r-lattice)
9481 ("r-matrix" ,r-matrix)
9482 ("r-rcpp" ,r-rcpp)
9483 ("r-reshape2" ,r-reshape2)))
9484 (native-inputs `(("r-knitr" ,r-knitr)))
9485 (home-page "https://github.com/kevinblighe/PCAtools")
9486 (synopsis "PCAtools: everything Principal Components Analysis")
9487 (description
9488 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
9489 structure of the data without the need to build any model to represent it.
9490 This \"summary\" of the data is arrived at through a process of reduction that
9491 can transform the large number of variables into a lesser number that are
9492 uncorrelated (i.e. the 'principal components'), while at the same time being
9493 capable of easy interpretation on the original data. PCAtools provides
9494 functions for data exploration via PCA, and allows the user to generate
9495 publication-ready figures. PCA is performed via @code{BiocSingular}; users
9496 can also identify an optimal number of principal components via different
9497 metrics, such as the elbow method and Horn's parallel analysis, which has
9498 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
9499 dimensional mass cytometry data.")
9500 (license license:gpl3)))
9501
9502 (define-public r-rgreat
9503 (package
9504 (name "r-rgreat")
9505 (version "1.22.0")
9506 (source
9507 (origin
9508 (method url-fetch)
9509 (uri (bioconductor-uri "rGREAT" version))
9510 (sha256
9511 (base32
9512 "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
9513 (properties `((upstream-name . "rGREAT")))
9514 (build-system r-build-system)
9515 (propagated-inputs
9516 `(("r-genomicranges" ,r-genomicranges)
9517 ("r-getoptlong" ,r-getoptlong)
9518 ("r-iranges" ,r-iranges)
9519 ("r-rcurl" ,r-rcurl)
9520 ("r-rjson" ,r-rjson)))
9521 (native-inputs `(("r-knitr" ,r-knitr)))
9522 (home-page "https://github.com/jokergoo/rGREAT")
9523 (synopsis "Client for GREAT analysis")
9524 (description
9525 "This package makes GREAT (Genomic Regions Enrichment of Annotations
9526 Tool) analysis automatic by constructing a HTTP POST request according to
9527 user's input and automatically retrieving results from GREAT web server.")
9528 (license license:expat)))
9529
9530 (define-public r-m3c
9531 (package
9532 (name "r-m3c")
9533 (version "1.12.0")
9534 (source
9535 (origin
9536 (method url-fetch)
9537 (uri (bioconductor-uri "M3C" version))
9538 (sha256
9539 (base32
9540 "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
9541 (properties `((upstream-name . "M3C")))
9542 (build-system r-build-system)
9543 (propagated-inputs
9544 `(("r-cluster" ,r-cluster)
9545 ("r-corpcor" ,r-corpcor)
9546 ("r-doparallel" ,r-doparallel)
9547 ("r-dosnow" ,r-dosnow)
9548 ("r-foreach" ,r-foreach)
9549 ("r-ggplot2" ,r-ggplot2)
9550 ("r-matrix" ,r-matrix)
9551 ("r-matrixcalc" ,r-matrixcalc)
9552 ("r-rtsne" ,r-rtsne)
9553 ("r-umap" ,r-umap)))
9554 (native-inputs `(("r-knitr" ,r-knitr)))
9555 (home-page "https://bioconductor.org/packages/M3C")
9556 (synopsis "Monte Carlo reference-based consensus clustering")
9557 (description
9558 "M3C is a consensus clustering algorithm that uses a Monte Carlo
9559 simulation to eliminate overestimation of @code{K} and can reject the null
9560 hypothesis @code{K=1}.")
9561 (license license:agpl3+)))
9562
9563 (define-public r-icens
9564 (package
9565 (name "r-icens")
9566 (version "1.62.0")
9567 (source
9568 (origin
9569 (method url-fetch)
9570 (uri (bioconductor-uri "Icens" version))
9571 (sha256
9572 (base32
9573 "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
9574 (properties `((upstream-name . "Icens")))
9575 (build-system r-build-system)
9576 (propagated-inputs
9577 `(("r-survival" ,r-survival)))
9578 (home-page "https://bioconductor.org/packages/Icens")
9579 (synopsis "NPMLE for censored and truncated data")
9580 (description
9581 "This package provides many functions for computing the
9582 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
9583 truncated data.")
9584 (license license:artistic2.0)))
9585
9586 ;; This is a CRAN package but it depends on r-icens, which is published on
9587 ;; Bioconductor.
9588 (define-public r-interval
9589 (package
9590 (name "r-interval")
9591 (version "1.1-0.7")
9592 (source
9593 (origin
9594 (method url-fetch)
9595 (uri (cran-uri "interval" version))
9596 (sha256
9597 (base32
9598 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
9599 (properties `((upstream-name . "interval")))
9600 (build-system r-build-system)
9601 (propagated-inputs
9602 `(("r-icens" ,r-icens)
9603 ("r-mlecens" ,r-mlecens)
9604 ("r-perm" ,r-perm)
9605 ("r-survival" ,r-survival)))
9606 (home-page "https://cran.r-project.org/web/packages/interval/")
9607 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
9608 (description
9609 "This package provides functions to fit nonparametric survival curves,
9610 plot them, and perform logrank or Wilcoxon type tests.")
9611 (license license:gpl2+)))
9612
9613 ;; This is a CRAN package, but it depends on r-interval, which depends on a
9614 ;; Bioconductor package.
9615 (define-public r-fhtest
9616 (package
9617 (name "r-fhtest")
9618 (version "1.5")
9619 (source
9620 (origin
9621 (method url-fetch)
9622 (uri (cran-uri "FHtest" version))
9623 (sha256
9624 (base32
9625 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
9626 (properties `((upstream-name . "FHtest")))
9627 (build-system r-build-system)
9628 (propagated-inputs
9629 `(("r-interval" ,r-interval)
9630 ("r-kmsurv" ,r-kmsurv)
9631 ("r-mass" ,r-mass)
9632 ("r-perm" ,r-perm)
9633 ("r-survival" ,r-survival)))
9634 (home-page "https://cran.r-project.org/web/packages/FHtest/")
9635 (synopsis "Tests for survival data based on the Fleming-Harrington class")
9636 (description
9637 "This package provides functions to compare two or more survival curves
9638 with:
9639
9640 @itemize
9641 @item The Fleming-Harrington test for right-censored data based on
9642 permutations and on counting processes.
9643 @item An extension of the Fleming-Harrington test for interval-censored data
9644 based on a permutation distribution and on a score vector distribution.
9645 @end itemize
9646 ")
9647 (license license:gpl2+)))
9648
9649 (define-public r-fourcseq
9650 (package
9651 (name "r-fourcseq")
9652 (version "1.24.0")
9653 (source
9654 (origin
9655 (method url-fetch)
9656 (uri (bioconductor-uri "FourCSeq" version))
9657 (sha256
9658 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
9659 (properties `((upstream-name . "FourCSeq")))
9660 (build-system r-build-system)
9661 (propagated-inputs
9662 `(("r-biobase" ,r-biobase)
9663 ("r-biostrings" ,r-biostrings)
9664 ("r-deseq2" ,r-deseq2)
9665 ("r-fda" ,r-fda)
9666 ("r-genomicalignments" ,r-genomicalignments)
9667 ("r-genomicranges" ,r-genomicranges)
9668 ("r-ggbio" ,r-ggbio)
9669 ("r-ggplot2" ,r-ggplot2)
9670 ("r-gtools" ,r-gtools)
9671 ("r-lsd" ,r-lsd)
9672 ("r-matrix" ,r-matrix)
9673 ("r-reshape2" ,r-reshape2)
9674 ("r-rsamtools" ,r-rsamtools)
9675 ("r-rtracklayer" ,r-rtracklayer)
9676 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9677 (native-inputs
9678 `(("r-knitr" ,r-knitr)))
9679 (home-page
9680 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
9681 (synopsis "Analysis of multiplexed 4C sequencing data")
9682 (description
9683 "This package is an R package dedicated to the analysis of (multiplexed)
9684 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
9685 interactions between DNA elements and identify differential interactions
9686 between conditions. The statistical analysis in R starts with individual bam
9687 files for each sample as inputs. To obtain these files, the package contains
9688 a Python script to demultiplex libraries and trim off primer sequences. With
9689 a standard alignment software the required bam files can be then be
9690 generated.")
9691 (license license:gpl3+)))
9692
9693 (define-public r-preprocesscore
9694 (package
9695 (name "r-preprocesscore")
9696 (version "1.52.1")
9697 (source
9698 (origin
9699 (method url-fetch)
9700 (uri (bioconductor-uri "preprocessCore" version))
9701 (sha256
9702 (base32
9703 "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
9704 (properties
9705 `((upstream-name . "preprocessCore")))
9706 (build-system r-build-system)
9707 (home-page "https://github.com/bmbolstad/preprocessCore")
9708 (synopsis "Collection of pre-processing functions")
9709 (description
9710 "This package provides a library of core pre-processing and normalization
9711 routines.")
9712 (license license:lgpl2.0+)))
9713
9714 (define-public r-s4vectors
9715 (package
9716 (name "r-s4vectors")
9717 (version "0.28.1")
9718 (source (origin
9719 (method url-fetch)
9720 (uri (bioconductor-uri "S4Vectors" version))
9721 (sha256
9722 (base32
9723 "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh"))))
9724 (properties
9725 `((upstream-name . "S4Vectors")))
9726 (build-system r-build-system)
9727 (propagated-inputs
9728 `(("r-biocgenerics" ,r-biocgenerics)))
9729 (home-page "https://bioconductor.org/packages/S4Vectors")
9730 (synopsis "S4 implementation of vectors and lists")
9731 (description
9732 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
9733 classes and a set of generic functions that extend the semantic of ordinary
9734 vectors and lists in R. Package developers can easily implement vector-like
9735 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
9736 In addition, a few low-level concrete subclasses of general interest (e.g.
9737 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
9738 S4Vectors package itself.")
9739 (license license:artistic2.0)))
9740
9741 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
9742 ;; Bioconductor package.
9743 (define-public r-wgcna
9744 (package
9745 (name "r-wgcna")
9746 (version "1.70-3")
9747 (source
9748 (origin
9749 (method url-fetch)
9750 (uri (cran-uri "WGCNA" version))
9751 (sha256
9752 (base32
9753 "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
9754 (properties `((upstream-name . "WGCNA")))
9755 (build-system r-build-system)
9756 (propagated-inputs
9757 `(("r-annotationdbi" ,r-annotationdbi)
9758 ("r-doparallel" ,r-doparallel)
9759 ("r-dynamictreecut" ,r-dynamictreecut)
9760 ("r-fastcluster" ,r-fastcluster)
9761 ("r-foreach" ,r-foreach)
9762 ("r-go-db" ,r-go-db)
9763 ("r-hmisc" ,r-hmisc)
9764 ("r-impute" ,r-impute)
9765 ("r-rcpp" ,r-rcpp)
9766 ("r-survival" ,r-survival)
9767 ("r-matrixstats" ,r-matrixstats)
9768 ("r-preprocesscore" ,r-preprocesscore)))
9769 (home-page
9770 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
9771 (synopsis "Weighted correlation network analysis")
9772 (description
9773 "This package provides functions necessary to perform Weighted
9774 Correlation Network Analysis on high-dimensional data. It includes functions
9775 for rudimentary data cleaning, construction and summarization of correlation
9776 networks, module identification and functions for relating both variables and
9777 modules to sample traits. It also includes a number of utility functions for
9778 data manipulation and visualization.")
9779 (license license:gpl2+)))
9780
9781 (define-public r-rgraphviz
9782 (package
9783 (name "r-rgraphviz")
9784 (version "2.34.0")
9785 (source
9786 (origin
9787 (method url-fetch)
9788 (uri (bioconductor-uri "Rgraphviz" version))
9789 (sha256
9790 (base32
9791 "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
9792 (properties `((upstream-name . "Rgraphviz")))
9793 (build-system r-build-system)
9794 (arguments
9795 `(#:phases
9796 (modify-phases %standard-phases
9797 (add-after 'unpack 'make-reproducible
9798 (lambda _
9799 ;; The replacement value is taken from src/graphviz/builddate.h
9800 (substitute* "src/graphviz/configure"
9801 (("VERSION_DATE=.*")
9802 "VERSION_DATE=20200427.2341\n"))
9803 #t)))))
9804 ;; FIXME: Rgraphviz bundles the sources of an older variant of
9805 ;; graphviz. It does not build with the latest version of graphviz, so
9806 ;; we do not add graphviz to the inputs.
9807 (inputs `(("zlib" ,zlib)))
9808 (propagated-inputs
9809 `(("r-graph" ,r-graph)))
9810 (native-inputs
9811 `(("pkg-config" ,pkg-config)))
9812 (home-page "https://bioconductor.org/packages/Rgraphviz")
9813 (synopsis "Plotting capabilities for R graph objects")
9814 (description
9815 "This package interfaces R with the graphviz library for plotting R graph
9816 objects from the @code{graph} package.")
9817 (license license:epl1.0)))
9818
9819 (define-public r-fithic
9820 (package
9821 (name "r-fithic")
9822 (version "1.16.0")
9823 (source (origin
9824 (method url-fetch)
9825 (uri (bioconductor-uri "FitHiC" version))
9826 (sha256
9827 (base32
9828 "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
9829 (properties `((upstream-name . "FitHiC")))
9830 (build-system r-build-system)
9831 (propagated-inputs
9832 `(("r-data-table" ,r-data-table)
9833 ("r-fdrtool" ,r-fdrtool)
9834 ("r-rcpp" ,r-rcpp)))
9835 (native-inputs
9836 `(("r-knitr" ,r-knitr)))
9837 (home-page "https://bioconductor.org/packages/FitHiC")
9838 (synopsis "Confidence estimation for intra-chromosomal contact maps")
9839 (description
9840 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
9841 intra-chromosomal contact maps produced by genome-wide genome architecture
9842 assays such as Hi-C.")
9843 (license license:gpl2+)))
9844
9845 (define-public r-hitc
9846 (package
9847 (name "r-hitc")
9848 (version "1.34.0")
9849 (source (origin
9850 (method url-fetch)
9851 (uri (bioconductor-uri "HiTC" version))
9852 (sha256
9853 (base32
9854 "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
9855 (properties `((upstream-name . "HiTC")))
9856 (build-system r-build-system)
9857 (propagated-inputs
9858 `(("r-biostrings" ,r-biostrings)
9859 ("r-genomeinfodb" ,r-genomeinfodb)
9860 ("r-genomicranges" ,r-genomicranges)
9861 ("r-iranges" ,r-iranges)
9862 ("r-matrix" ,r-matrix)
9863 ("r-rcolorbrewer" ,r-rcolorbrewer)
9864 ("r-rtracklayer" ,r-rtracklayer)))
9865 (home-page "https://bioconductor.org/packages/HiTC")
9866 (synopsis "High throughput chromosome conformation capture analysis")
9867 (description
9868 "The HiTC package was developed to explore high-throughput \"C\" data
9869 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
9870 quality controls, normalization, visualization, and further analysis are also
9871 provided.")
9872 (license license:artistic2.0)))
9873
9874 (define-public r-hdf5array
9875 (package
9876 (name "r-hdf5array")
9877 (version "1.18.1")
9878 (source
9879 (origin
9880 (method url-fetch)
9881 (uri (bioconductor-uri "HDF5Array" version))
9882 (sha256
9883 (base32
9884 "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
9885 (properties `((upstream-name . "HDF5Array")))
9886 (build-system r-build-system)
9887 (arguments
9888 `(#:phases
9889 (modify-phases %standard-phases
9890 (add-after 'unpack 'fix-linking
9891 (lambda _
9892 (substitute* "src/Makevars"
9893 ;; This is to avoid having a plain directory on the list of
9894 ;; libraries to link.
9895 (("\\(RHDF5LIB_LIBS\\)" match)
9896 (string-append match "/libhdf5.a")))
9897 #t)))))
9898 (inputs
9899 `(("zlib" ,zlib)))
9900 (propagated-inputs
9901 `(("r-biocgenerics" ,r-biocgenerics)
9902 ("r-delayedarray" ,r-delayedarray)
9903 ("r-iranges" ,r-iranges)
9904 ("r-matrix" ,r-matrix)
9905 ("r-rhdf5" ,r-rhdf5)
9906 ("r-rhdf5lib" ,r-rhdf5lib)
9907 ("r-s4vectors" ,r-s4vectors)))
9908 (home-page "https://bioconductor.org/packages/HDF5Array")
9909 (synopsis "HDF5 back end for DelayedArray objects")
9910 (description "This package provides an array-like container for convenient
9911 access and manipulation of HDF5 datasets. It supports delayed operations and
9912 block processing.")
9913 (license license:artistic2.0)))
9914
9915 (define-public r-rhdf5lib
9916 (package
9917 (name "r-rhdf5lib")
9918 (version "1.12.1")
9919 (source
9920 (origin
9921 (method url-fetch)
9922 (uri (bioconductor-uri "Rhdf5lib" version))
9923 (sha256
9924 (base32
9925 "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
9926 (modules '((guix build utils)))
9927 (snippet
9928 '(begin
9929 ;; Delete bundled binaries
9930 (delete-file-recursively "src/wininclude/")
9931 (delete-file-recursively "src/winlib-4.9.3/")
9932 (delete-file-recursively "src/winlib-8.3.0/")
9933 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
9934 #t))))
9935 (properties `((upstream-name . "Rhdf5lib")))
9936 (build-system r-build-system)
9937 (arguments
9938 `(#:phases
9939 (modify-phases %standard-phases
9940 (add-after 'unpack 'do-not-use-bundled-hdf5
9941 (lambda* (#:key inputs #:allow-other-keys)
9942 (for-each delete-file '("configure" "configure.ac"))
9943 ;; Do not make other packages link with the proprietary libsz.
9944 (substitute* "R/zzz.R"
9945 ((" \"%s/libsz.a\"") ""))
9946 (with-directory-excursion "src"
9947 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
9948 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
9949 "hdf5")
9950 ;; Remove timestamp and host system information to make
9951 ;; the build reproducible.
9952 (substitute* "hdf5/src/libhdf5.settings.in"
9953 (("Configured on: @CONFIG_DATE@")
9954 "Configured on: Guix")
9955 (("Uname information:.*")
9956 "Uname information: Linux\n")
9957 ;; Remove unnecessary store reference.
9958 (("C Compiler:.*")
9959 "C Compiler: GCC\n"))
9960 (rename-file "hdf5/src/libhdf5.settings.in"
9961 "hdf5/src/libhdf5.settings")
9962 (rename-file "Makevars.in" "Makevars")
9963 (substitute* "Makevars"
9964 (("@ZLIB_LIB@") "-lz")
9965 (("@ZLIB_INCLUDE@") "")
9966 (("HDF5_CXX_LIB=.*")
9967 (string-append "HDF5_CXX_LIB="
9968 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
9969 (("HDF5_LIB=.*")
9970 (string-append "HDF5_LIB="
9971 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
9972 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
9973 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
9974 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
9975 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
9976 (("HDF5_HL_LIB=.*")
9977 (string-append "HDF5_HL_LIB="
9978 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
9979 (("HDF5_HL_CXX_LIB=.*")
9980 (string-append "HDF5_HL_CXX_LIB="
9981 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
9982 ;; szip is non-free software
9983 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
9984 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
9985 #t)))))
9986 (inputs
9987 `(("zlib" ,zlib)))
9988 (propagated-inputs
9989 `(("hdf5" ,hdf5-1.10)))
9990 (native-inputs
9991 `(("hdf5-source" ,(package-source hdf5-1.10))
9992 ("r-knitr" ,r-knitr)))
9993 (home-page "https://bioconductor.org/packages/Rhdf5lib")
9994 (synopsis "HDF5 library as an R package")
9995 (description "This package provides C and C++ HDF5 libraries for use in R
9996 packages.")
9997 (license license:artistic2.0)))
9998
9999 (define-public r-beachmat
10000 (package
10001 (name "r-beachmat")
10002 (version "2.6.4")
10003 (source
10004 (origin
10005 (method url-fetch)
10006 (uri (bioconductor-uri "beachmat" version))
10007 (sha256
10008 (base32
10009 "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
10010 (build-system r-build-system)
10011 (propagated-inputs
10012 `(("r-biocgenerics" ,r-biocgenerics)
10013 ("r-delayedarray" ,r-delayedarray)
10014 ("r-matrix" ,r-matrix)))
10015 (native-inputs
10016 `(("r-knitr" ,r-knitr)))
10017 (home-page "https://bioconductor.org/packages/beachmat")
10018 (synopsis "Compiling Bioconductor to handle each matrix type")
10019 (description "This package provides a consistent C++ class interface for a
10020 variety of commonly used matrix types, including sparse and HDF5-backed
10021 matrices.")
10022 (license license:gpl3)))
10023
10024 ;; This package includes files that have been taken from kentutils. Some
10025 ;; parts of kentutils are not released under a free license, but this package
10026 ;; only uses files that are also found in the free parts of kentutils.
10027 (define-public r-cner
10028 (package
10029 (name "r-cner")
10030 (version "1.26.0")
10031 (source
10032 (origin
10033 (method url-fetch)
10034 (uri (bioconductor-uri "CNEr" version))
10035 (sha256
10036 (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
10037 (properties `((upstream-name . "CNEr")))
10038 (build-system r-build-system)
10039 (inputs `(("zlib" ,zlib)))
10040 (propagated-inputs
10041 `(("r-annotate" ,r-annotate)
10042 ("r-biocgenerics" ,r-biocgenerics)
10043 ("r-biostrings" ,r-biostrings)
10044 ("r-dbi" ,r-dbi)
10045 ("r-genomeinfodb" ,r-genomeinfodb)
10046 ("r-genomicalignments" ,r-genomicalignments)
10047 ("r-genomicranges" ,r-genomicranges)
10048 ("r-ggplot2" ,r-ggplot2)
10049 ("r-go-db" ,r-go-db)
10050 ("r-iranges" ,r-iranges)
10051 ("r-keggrest" ,r-keggrest)
10052 ("r-powerlaw" ,r-powerlaw)
10053 ("r-r-utils" ,r-r-utils)
10054 ("r-readr" ,r-readr)
10055 ("r-reshape2" ,r-reshape2)
10056 ("r-rsqlite" ,r-rsqlite)
10057 ("r-rtracklayer" ,r-rtracklayer)
10058 ("r-s4vectors" ,r-s4vectors)
10059 ("r-xvector" ,r-xvector)))
10060 (native-inputs
10061 `(("r-knitr" ,r-knitr)))
10062 (home-page "https://github.com/ge11232002/CNEr")
10063 (synopsis "CNE Detection and Visualization")
10064 (description
10065 "This package provides tools for large-scale identification and
10066 advanced visualization of sets of conserved noncoding elements.")
10067 ;; For all files in src/ucsc "license is hereby granted for all use -
10068 ;; public, private or commercial"; this includes those files that don't
10069 ;; have a license header, because they are included in the free parts of
10070 ;; the kentutils package.
10071 (license (list license:gpl2
10072 (license:non-copyleft
10073 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
10074
10075 (define-public r-tfbstools
10076 (package
10077 (name "r-tfbstools")
10078 (version "1.28.0")
10079 (source
10080 (origin
10081 (method url-fetch)
10082 (uri (bioconductor-uri "TFBSTools" version))
10083 (sha256
10084 (base32
10085 "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
10086 (properties `((upstream-name . "TFBSTools")))
10087 (build-system r-build-system)
10088 (propagated-inputs
10089 `(("r-biobase" ,r-biobase)
10090 ("r-biocgenerics" ,r-biocgenerics)
10091 ("r-biocparallel" ,r-biocparallel)
10092 ("r-biostrings" ,r-biostrings)
10093 ("r-bsgenome" ,r-bsgenome)
10094 ("r-catools" ,r-catools)
10095 ("r-cner" ,r-cner)
10096 ("r-dbi" ,r-dbi)
10097 ("r-dirichletmultinomial" ,r-dirichletmultinomial)
10098 ("r-genomeinfodb" ,r-genomeinfodb)
10099 ("r-genomicranges" ,r-genomicranges)
10100 ("r-gtools" ,r-gtools)
10101 ("r-iranges" ,r-iranges)
10102 ("r-rsqlite" ,r-rsqlite)
10103 ("r-rtracklayer" ,r-rtracklayer)
10104 ("r-s4vectors" ,r-s4vectors)
10105 ("r-seqlogo" ,r-seqlogo)
10106 ("r-tfmpvalue" ,r-tfmpvalue)
10107 ("r-xml" ,r-xml)
10108 ("r-xvector" ,r-xvector)))
10109 (native-inputs `(("r-knitr" ,r-knitr)))
10110 (home-page "https://github.com/ge11232002/TFBSTools")
10111 (synopsis "Transcription factor binding site (TFBS) analysis")
10112 (description
10113 "TFBSTools is a package for the analysis and manipulation of
10114 transcription factor binding sites. It includes matrices conversion
10115 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
10116 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
10117 scan putative TFBS from sequence/alignment, query JASPAR database and
10118 provides a wrapper of de novo motif discovery software.")
10119 (license license:gpl2)))
10120
10121 (define-public r-motifmatchr
10122 (package
10123 (name "r-motifmatchr")
10124 (version "1.12.0")
10125 (source
10126 (origin
10127 (method url-fetch)
10128 (uri (bioconductor-uri "motifmatchr" version))
10129 (sha256
10130 (base32
10131 "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z"))))
10132 (properties `((upstream-name . "motifmatchr")))
10133 (build-system r-build-system)
10134 (propagated-inputs
10135 `(("r-biostrings" ,r-biostrings)
10136 ("r-bsgenome" ,r-bsgenome)
10137 ("r-genomeinfodb" ,r-genomeinfodb)
10138 ("r-genomicranges" ,r-genomicranges)
10139 ("r-iranges" ,r-iranges)
10140 ("r-matrix" ,r-matrix)
10141 ("r-rcpp" ,r-rcpp)
10142 ("r-rcpparmadillo" ,r-rcpparmadillo)
10143 ("r-rsamtools" ,r-rsamtools)
10144 ("r-s4vectors" ,r-s4vectors)
10145 ("r-summarizedexperiment" ,r-summarizedexperiment)
10146 ("r-tfbstools" ,r-tfbstools)))
10147 (native-inputs `(("r-knitr" ,r-knitr)))
10148 (home-page "https://bioconductor.org/packages/motifmatchr")
10149 (synopsis "Fast motif matching in R")
10150 (description
10151 "Quickly find motif matches for many motifs and many sequences.
10152 This package wraps C++ code from the MOODS motif calling library.")
10153 (license license:gpl3)))
10154
10155 (define-public r-chromvar
10156 (package
10157 (name "r-chromvar")
10158 (version "1.12.0")
10159 (source
10160 (origin
10161 (method url-fetch)
10162 (uri (bioconductor-uri "chromVAR" version))
10163 (sha256
10164 (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819"))))
10165 (properties `((upstream-name . "chromVAR")))
10166 (build-system r-build-system)
10167 (propagated-inputs
10168 `(("r-biocgenerics" ,r-biocgenerics)
10169 ("r-biocparallel" ,r-biocparallel)
10170 ("r-biostrings" ,r-biostrings)
10171 ("r-bsgenome" ,r-bsgenome)
10172 ("r-dt" ,r-dt)
10173 ("r-genomeinfodb" ,r-genomeinfodb)
10174 ("r-genomicranges" ,r-genomicranges)
10175 ("r-ggplot2" ,r-ggplot2)
10176 ("r-iranges" ,r-iranges)
10177 ("r-matrix" ,r-matrix)
10178 ("r-miniui" ,r-miniui)
10179 ("r-nabor" ,r-nabor)
10180 ("r-plotly" ,r-plotly)
10181 ("r-rcolorbrewer" ,r-rcolorbrewer)
10182 ("r-rcpp" ,r-rcpp)
10183 ("r-rcpparmadillo" ,r-rcpparmadillo)
10184 ("r-rsamtools" ,r-rsamtools)
10185 ("r-rtsne" ,r-rtsne)
10186 ("r-s4vectors" ,r-s4vectors)
10187 ("r-shiny" ,r-shiny)
10188 ("r-summarizedexperiment" ,r-summarizedexperiment)
10189 ("r-tfbstools" ,r-tfbstools)))
10190 (native-inputs `(("r-knitr" ,r-knitr)))
10191 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
10192 (synopsis "Determine chromatin variation across regions")
10193 (description
10194 "This package @code{r-chromvar} determines variation in chromatin
10195 accessibility across sets of annotations or peaks. @code{r-chromvar} is
10196 designed primarily for single-cell or sparse chromatin accessibility data like
10197 single cell assay for transposase-accessible chromatin using
10198 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
10199 sequence (@code{DNAse-seq}) experiments.")
10200 (license license:expat)))
10201
10202 (define-public r-singlecellexperiment
10203 (package
10204 (name "r-singlecellexperiment")
10205 (version "1.12.0")
10206 (source
10207 (origin
10208 (method url-fetch)
10209 (uri (bioconductor-uri "SingleCellExperiment" version))
10210 (sha256
10211 (base32
10212 "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
10213 (properties
10214 `((upstream-name . "SingleCellExperiment")))
10215 (build-system r-build-system)
10216 (propagated-inputs
10217 `(("r-biocgenerics" ,r-biocgenerics)
10218 ("r-s4vectors" ,r-s4vectors)
10219 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10220 (native-inputs
10221 `(("r-knitr" ,r-knitr)))
10222 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
10223 (synopsis "S4 classes for single cell data")
10224 (description "This package defines an S4 class for storing data from
10225 single-cell experiments. This includes specialized methods to store and
10226 retrieve spike-in information, dimensionality reduction coordinates and size
10227 factors for each cell, along with the usual metadata for genes and
10228 libraries.")
10229 (license license:gpl3)))
10230
10231 (define-public r-scuttle
10232 (package
10233 (name "r-scuttle")
10234 (version "1.0.4")
10235 (source
10236 (origin
10237 (method url-fetch)
10238 (uri (bioconductor-uri "scuttle" version))
10239 (sha256
10240 (base32
10241 "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
10242 (properties `((upstream-name . "scuttle")))
10243 (build-system r-build-system)
10244 (propagated-inputs
10245 `(("r-beachmat" ,r-beachmat)
10246 ("r-biocgenerics" ,r-biocgenerics)
10247 ("r-biocparallel" ,r-biocparallel)
10248 ("r-delayedarray" ,r-delayedarray)
10249 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10250 ("r-genomicranges" ,r-genomicranges)
10251 ("r-matrix" ,r-matrix)
10252 ("r-rcpp" ,r-rcpp)
10253 ("r-s4vectors" ,r-s4vectors)
10254 ("r-singlecellexperiment" ,r-singlecellexperiment)
10255 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10256 (native-inputs `(("r-knitr" ,r-knitr)))
10257 (home-page "https://bioconductor.org/packages/scuttle")
10258 (synopsis "Single-cell RNA-Seq analysis utilities")
10259 (description
10260 "This package provides basic utility functions for performing single-cell
10261 analyses, focusing on simple normalization, quality control and data
10262 transformations. It also provides some helper functions to assist development
10263 of other packages.")
10264 (license license:gpl3)))
10265
10266 (define-public r-scater
10267 (package
10268 (name "r-scater")
10269 (version "1.18.6")
10270 (source (origin
10271 (method url-fetch)
10272 (uri (bioconductor-uri "scater" version))
10273 (sha256
10274 (base32
10275 "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609"))))
10276 (build-system r-build-system)
10277 (propagated-inputs
10278 `(("r-biocgenerics" ,r-biocgenerics)
10279 ("r-biocneighbors" ,r-biocneighbors)
10280 ("r-biocparallel" ,r-biocparallel)
10281 ("r-biocsingular" ,r-biocsingular)
10282 ("r-delayedarray" ,r-delayedarray)
10283 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10284 ("r-ggbeeswarm" ,r-ggbeeswarm)
10285 ("r-ggplot2" ,r-ggplot2)
10286 ("r-gridextra" ,r-gridextra)
10287 ("r-matrix" ,r-matrix)
10288 ("r-rlang" ,r-rlang)
10289 ("r-s4vectors" ,r-s4vectors)
10290 ("r-scuttle" ,r-scuttle)
10291 ("r-singlecellexperiment" ,r-singlecellexperiment)
10292 ("r-summarizedexperiment" ,r-summarizedexperiment)
10293 ("r-viridis" ,r-viridis)))
10294 (native-inputs
10295 `(("r-knitr" ,r-knitr)))
10296 (home-page "https://github.com/davismcc/scater")
10297 (synopsis "Single-cell analysis toolkit for gene expression data in R")
10298 (description "This package provides a collection of tools for doing
10299 various analyses of single-cell RNA-seq gene expression data, with a focus on
10300 quality control.")
10301 (license license:gpl2+)))
10302
10303 (define-public r-scran
10304 (package
10305 (name "r-scran")
10306 (version "1.18.5")
10307 (source
10308 (origin
10309 (method url-fetch)
10310 (uri (bioconductor-uri "scran" version))
10311 (sha256
10312 (base32
10313 "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
10314 (build-system r-build-system)
10315 (propagated-inputs
10316 `(("r-beachmat" ,r-beachmat)
10317 ("r-bh" ,r-bh)
10318 ("r-biocgenerics" ,r-biocgenerics)
10319 ("r-biocneighbors" ,r-biocneighbors)
10320 ("r-biocparallel" ,r-biocparallel)
10321 ("r-biocsingular" ,r-biocsingular)
10322 ("r-bluster" ,r-bluster)
10323 ("r-delayedarray" ,r-delayedarray)
10324 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10325 ("r-dqrng" ,r-dqrng)
10326 ("r-edger" ,r-edger)
10327 ("r-igraph" ,r-igraph)
10328 ("r-limma" ,r-limma)
10329 ("r-matrix" ,r-matrix)
10330 ("r-rcpp" ,r-rcpp)
10331 ("r-s4vectors" ,r-s4vectors)
10332 ("r-scuttle" ,r-scuttle)
10333 ("r-singlecellexperiment" ,r-singlecellexperiment)
10334 ("r-statmod" ,r-statmod)
10335 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10336 (native-inputs
10337 `(("r-knitr" ,r-knitr)))
10338 (home-page "https://bioconductor.org/packages/scran")
10339 (synopsis "Methods for single-cell RNA-Seq data analysis")
10340 (description "This package implements a variety of low-level analyses of
10341 single-cell RNA-seq data. Methods are provided for normalization of
10342 cell-specific biases, assignment of cell cycle phase, and detection of highly
10343 variable and significantly correlated genes.")
10344 (license license:gpl3)))
10345
10346 (define-public r-sparsematrixstats
10347 (package
10348 (name "r-sparsematrixstats")
10349 (version "1.2.1")
10350 (source
10351 (origin
10352 (method url-fetch)
10353 (uri (bioconductor-uri "sparseMatrixStats" version))
10354 (sha256
10355 (base32
10356 "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
10357 (properties
10358 `((upstream-name . "sparseMatrixStats")))
10359 (build-system r-build-system)
10360 (propagated-inputs
10361 `(("r-matrix" ,r-matrix)
10362 ("r-matrixgenerics" ,r-matrixgenerics)
10363 ("r-matrixstats" ,r-matrixstats)
10364 ("r-rcpp" ,r-rcpp)))
10365 (native-inputs `(("r-knitr" ,r-knitr)))
10366 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
10367 (synopsis "Summary statistics for rows and columns of sparse matrices")
10368 (description
10369 "This package provides high performance functions for row and column
10370 operations on sparse matrices. Currently, the optimizations are limited to
10371 data in the column sparse format.")
10372 (license license:expat)))
10373
10374 (define-public r-delayedmatrixstats
10375 (package
10376 (name "r-delayedmatrixstats")
10377 (version "1.12.3")
10378 (source
10379 (origin
10380 (method url-fetch)
10381 (uri (bioconductor-uri "DelayedMatrixStats" version))
10382 (sha256
10383 (base32
10384 "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
10385 (properties
10386 `((upstream-name . "DelayedMatrixStats")))
10387 (build-system r-build-system)
10388 (propagated-inputs
10389 `(("r-biocparallel" ,r-biocparallel)
10390 ("r-delayedarray" ,r-delayedarray)
10391 ("r-hdf5array" ,r-hdf5array)
10392 ("r-iranges" ,r-iranges)
10393 ("r-matrix" ,r-matrix)
10394 ("r-matrixgenerics" ,r-matrixgenerics)
10395 ("r-matrixstats" ,r-matrixstats)
10396 ("r-s4vectors" ,r-s4vectors)
10397 ("r-sparsematrixstats" ,r-sparsematrixstats)))
10398 (native-inputs
10399 `(("r-knitr" ,r-knitr)))
10400 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
10401 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
10402 (description
10403 "This package provides a port of the @code{matrixStats} API for use with
10404 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
10405 contains high-performing functions operating on rows and columns of
10406 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
10407 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
10408 are optimized per data type and for subsetted calculations such that both
10409 memory usage and processing time is minimized.")
10410 (license license:expat)))
10411
10412 (define-public r-mscoreutils
10413 (package
10414 (name "r-mscoreutils")
10415 (version "1.2.0")
10416 (source
10417 (origin
10418 (method url-fetch)
10419 (uri (bioconductor-uri "MsCoreUtils" version))
10420 (sha256
10421 (base32
10422 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
10423 (properties `((upstream-name . "MsCoreUtils")))
10424 (build-system r-build-system)
10425 (propagated-inputs
10426 `(("r-mass" ,r-mass)
10427 ("r-rcpp" ,r-rcpp)
10428 ("r-s4vectors" ,r-s4vectors)))
10429 (native-inputs
10430 `(("r-knitr" ,r-knitr)))
10431 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
10432 (synopsis "Core utils for mass spectrometry data")
10433 (description
10434 "This package defines low-level functions for mass spectrometry data and
10435 is independent of any high-level data structures. These functions include
10436 mass spectra processing functions (noise estimation, smoothing, binning),
10437 quantitative aggregation functions (median polish, robust summarisation,
10438 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
10439 well as misc helper functions, that are used across high-level data structure
10440 within the R for Mass Spectrometry packages.")
10441 (license license:artistic2.0)))
10442
10443 (define-public r-biocio
10444 (package
10445 (name "r-biocio")
10446 (version "1.0.1")
10447 (source
10448 (origin
10449 (method url-fetch)
10450 (uri (bioconductor-uri "BiocIO" version))
10451 (sha256
10452 (base32
10453 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
10454 (properties `((upstream-name . "BiocIO")))
10455 (build-system r-build-system)
10456 (propagated-inputs
10457 `(("r-biocgenerics" ,r-biocgenerics)
10458 ("r-genomicranges" ,r-genomicranges)
10459 ("r-rcurl" ,r-rcurl)
10460 ("r-s4vectors" ,r-s4vectors)))
10461 (native-inputs
10462 `(("r-knitr" ,r-knitr)))
10463 (home-page "https://bioconductor.org/packages/BiocIO")
10464 (synopsis "Standard input and output for Bioconductor packages")
10465 (description
10466 "This package implements `import()` and `export()` standard generics for
10467 importing and exporting biological data formats. `import()` supports
10468 whole-file as well as chunk-wise iterative import. The `import()` interface
10469 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
10470 row or element-like components of the file resource), `select()` (on
10471 column-like components of the file resource) and `collect()`. The `import()`
10472 interface optionally provides transparent access to remote (e.g. via https)
10473 as well as local access. Developers can register a file extension, e.g.,
10474 `.loom` for dispatch from character-based URIs to specific `import()` /
10475 `export()` methods based on classes representing file types, e.g.,
10476 `LoomFile()`.")
10477 (license license:artistic2.0)))
10478
10479 (define-public r-msmseda
10480 (package
10481 (name "r-msmseda")
10482 (version "1.28.0")
10483 (source
10484 (origin
10485 (method url-fetch)
10486 (uri (bioconductor-uri "msmsEDA" version))
10487 (sha256
10488 (base32
10489 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
10490 (properties `((upstream-name . "msmsEDA")))
10491 (build-system r-build-system)
10492 (propagated-inputs
10493 `(("r-gplots" ,r-gplots)
10494 ("r-mass" ,r-mass)
10495 ("r-msnbase" ,r-msnbase)
10496 ("r-rcolorbrewer" ,r-rcolorbrewer)))
10497 (home-page
10498 "https://bioconductor.org/packages/msmsEDA")
10499 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
10500 (description
10501 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
10502 experiments, and visualize de influence of the involved factors.")
10503 (license license:gpl2)))
10504
10505 (define-public r-msmstests
10506 (package
10507 (name "r-msmstests")
10508 (version "1.28.0")
10509 (source
10510 (origin
10511 (method url-fetch)
10512 (uri (bioconductor-uri "msmsTests" version))
10513 (sha256
10514 (base32
10515 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
10516 (properties `((upstream-name . "msmsTests")))
10517 (build-system r-build-system)
10518 (propagated-inputs
10519 `(("r-edger" ,r-edger)
10520 ("r-msmseda" ,r-msmseda)
10521 ("r-msnbase" ,r-msnbase)
10522 ("r-qvalue" ,r-qvalue)))
10523 (home-page
10524 "https://bioconductor.org/packages/msmsTests")
10525 (synopsis "Differential LC-MS/MS expression tests")
10526 (description
10527 "This packages provides statistical tests for label-free LC-MS/MS data
10528 by spectral counts, to discover differentially expressed proteins between two
10529 biological conditions. Three tests are available: Poisson GLM regression,
10530 quasi-likelihood GLM regression, and the negative binomial of the edgeR
10531 package. The three models admit blocking factors to control for nuisance
10532 variables. To assure a good level of reproducibility a post-test filter is
10533 available, where we may set the minimum effect size considered biologicaly
10534 relevant, and the minimum expression of the most abundant condition.")
10535 (license license:gpl2)))
10536
10537 (define-public r-catalyst
10538 (package
10539 (name "r-catalyst")
10540 (version "1.14.0")
10541 (source
10542 (origin
10543 (method url-fetch)
10544 (uri (bioconductor-uri "CATALYST" version))
10545 (sha256
10546 (base32
10547 "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
10548 (properties `((upstream-name . "CATALYST")))
10549 (build-system r-build-system)
10550 (propagated-inputs
10551 `(("r-circlize" ,r-circlize)
10552 ("r-complexheatmap" ,r-complexheatmap)
10553 ("r-consensusclusterplus" ,r-consensusclusterplus)
10554 ("r-cowplot" ,r-cowplot)
10555 ("r-data-table" ,r-data-table)
10556 ("r-dplyr" ,r-dplyr)
10557 ("r-drc" ,r-drc)
10558 ("r-flowcore" ,r-flowcore)
10559 ("r-flowsom" ,r-flowsom)
10560 ("r-ggplot2" ,r-ggplot2)
10561 ("r-ggrepel" ,r-ggrepel)
10562 ("r-ggridges" ,r-ggridges)
10563 ("r-gridextra" ,r-gridextra)
10564 ("r-magrittr" ,r-magrittr)
10565 ("r-matrix" ,r-matrix)
10566 ("r-matrixstats" ,r-matrixstats)
10567 ("r-nnls" ,r-nnls)
10568 ("r-purrr" ,r-purrr)
10569 ("r-rcolorbrewer" ,r-rcolorbrewer)
10570 ("r-reshape2" ,r-reshape2)
10571 ("r-rtsne" ,r-rtsne)
10572 ("r-s4vectors" ,r-s4vectors)
10573 ("r-scales" ,r-scales)
10574 ("r-scater" ,r-scater)
10575 ("r-singlecellexperiment" ,r-singlecellexperiment)
10576 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10577 (native-inputs
10578 `(("r-knitr" ,r-knitr)))
10579 (home-page
10580 "https://github.com/HelenaLC/CATALYST")
10581 (synopsis "Cytometry data analysis tools")
10582 (description
10583 "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
10584 cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
10585 reporters to label antibodies, thereby substantially decreasing spectral
10586 overlap and allowing for examination of over 50 parameters at the single cell
10587 level. While spectral overlap is significantly less pronounced in CyTOF than
10588 flow cytometry, spillover due to detection sensitivity, isotopic impurities,
10589 and oxide formation can impede data interpretability. We designed
10590 CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
10591 preprocessing of cytometry data, including i) normalization using bead
10592 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
10593 (license license:gpl2+)))
10594
10595 (define-public r-erma
10596 (package
10597 (name "r-erma")
10598 (version "1.6.0")
10599 (source
10600 (origin
10601 (method url-fetch)
10602 (uri (bioconductor-uri "erma" version))
10603 (sha256
10604 (base32
10605 "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
10606 (build-system r-build-system)
10607 (propagated-inputs
10608 `(("r-annotationdbi" ,r-annotationdbi)
10609 ("r-biobase" ,r-biobase)
10610 ("r-biocgenerics" ,r-biocgenerics)
10611 ("r-biocparallel" ,r-biocparallel)
10612 ("r-genomeinfodb" ,r-genomeinfodb)
10613 ("r-genomicfiles" ,r-genomicfiles)
10614 ("r-genomicranges" ,r-genomicranges)
10615 ("r-ggplot2" ,r-ggplot2)
10616 ("r-homo-sapiens" ,r-homo-sapiens)
10617 ("r-iranges" ,r-iranges)
10618 ("r-rtracklayer" ,r-rtracklayer)
10619 ("r-s4vectors" ,r-s4vectors)
10620 ("r-shiny" ,r-shiny)
10621 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10622 (native-inputs
10623 `(("r-knitr" ,r-knitr)))
10624 (home-page "https://bioconductor.org/packages/erma")
10625 (synopsis "Epigenomic road map adventures")
10626 (description
10627 "The epigenomics road map describes locations of epigenetic marks in DNA
10628 from a variety of cell types. Of interest are locations of histone
10629 modifications, sites of DNA methylation, and regions of accessible chromatin.
10630 This package presents a selection of elements of the road map including
10631 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
10632 by Ernst and Kellis.")
10633 (license license:artistic2.0)))
10634
10635 (define-public r-ggbio
10636 (package
10637 (name "r-ggbio")
10638 (version "1.38.0")
10639 (source
10640 (origin
10641 (method url-fetch)
10642 (uri (bioconductor-uri "ggbio" version))
10643 (sha256
10644 (base32
10645 "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
10646 (build-system r-build-system)
10647 (arguments
10648 `(#:phases
10649 (modify-phases %standard-phases
10650 ;; See https://github.com/tengfei/ggbio/issues/117
10651 ;; This fix will be included in the next release.
10652 (add-after 'unpack 'fix-typo
10653 (lambda _
10654 (substitute* "R/GGbio-class.R"
10655 (("fechable") "fetchable"))
10656 #t)))))
10657 (propagated-inputs
10658 `(("r-annotationdbi" ,r-annotationdbi)
10659 ("r-annotationfilter" ,r-annotationfilter)
10660 ("r-biobase" ,r-biobase)
10661 ("r-biocgenerics" ,r-biocgenerics)
10662 ("r-biostrings" ,r-biostrings)
10663 ("r-biovizbase" ,r-biovizbase)
10664 ("r-bsgenome" ,r-bsgenome)
10665 ("r-ensembldb" ,r-ensembldb)
10666 ("r-genomeinfodb" ,r-genomeinfodb)
10667 ("r-genomicalignments" ,r-genomicalignments)
10668 ("r-genomicfeatures" ,r-genomicfeatures)
10669 ("r-genomicranges" ,r-genomicranges)
10670 ("r-ggally" ,r-ggally)
10671 ("r-ggplot2" ,r-ggplot2)
10672 ("r-gridextra" ,r-gridextra)
10673 ("r-gtable" ,r-gtable)
10674 ("r-hmisc" ,r-hmisc)
10675 ("r-iranges" ,r-iranges)
10676 ("r-organismdbi" ,r-organismdbi)
10677 ("r-reshape2" ,r-reshape2)
10678 ("r-rlang" ,r-rlang)
10679 ("r-rsamtools" ,r-rsamtools)
10680 ("r-rtracklayer" ,r-rtracklayer)
10681 ("r-s4vectors" ,r-s4vectors)
10682 ("r-scales" ,r-scales)
10683 ("r-summarizedexperiment" ,r-summarizedexperiment)
10684 ("r-variantannotation" ,r-variantannotation)))
10685 (native-inputs
10686 `(("r-knitr" ,r-knitr)))
10687 (home-page "http://www.tengfei.name/ggbio/")
10688 (synopsis "Visualization tools for genomic data")
10689 (description
10690 "The ggbio package extends and specializes the grammar of graphics for
10691 biological data. The graphics are designed to answer common scientific
10692 questions, in particular those often asked of high throughput genomics data.
10693 All core Bioconductor data structures are supported, where appropriate. The
10694 package supports detailed views of particular genomic regions, as well as
10695 genome-wide overviews. Supported overviews include ideograms and grand linear
10696 views. High-level plots include sequence fragment length, edge-linked
10697 interval to data view, mismatch pileup, and several splicing summaries.")
10698 (license license:artistic2.0)))
10699
10700 (define-public r-gqtlbase
10701 (package
10702 (name "r-gqtlbase")
10703 (version "1.21.1")
10704 (source
10705 (origin
10706 (method url-fetch)
10707 (uri (bioconductor-uri "gQTLBase" version))
10708 (sha256
10709 (base32
10710 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
10711 (properties `((upstream-name . "gQTLBase")))
10712 (build-system r-build-system)
10713 (arguments
10714 `(#:phases
10715 (modify-phases %standard-phases
10716 ;; This is an upstream bug.
10717 (add-after 'unpack 'fix-imports
10718 (lambda _
10719 (substitute* "NAMESPACE"
10720 ((".*maxffmode.*") "")
10721 (("importFrom\\(ff,.*") "import(ff)\n"))
10722 #t)))))
10723 (propagated-inputs
10724 `(("r-batchjobs" ,r-batchjobs)
10725 ("r-bbmisc" ,r-bbmisc)
10726 ("r-biocgenerics" ,r-biocgenerics)
10727 ("r-bit" ,r-bit)
10728 ("r-doparallel" ,r-doparallel)
10729 ("r-ff" ,r-ff)
10730 ("r-ffbase" ,r-ffbase)
10731 ("r-foreach" ,r-foreach)
10732 ("r-genomicfiles" ,r-genomicfiles)
10733 ("r-genomicranges" ,r-genomicranges)
10734 ("r-rtracklayer" ,r-rtracklayer)
10735 ("r-s4vectors" ,r-s4vectors)
10736 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10737 (native-inputs
10738 `(("r-knitr" ,r-knitr)))
10739 (home-page "https://bioconductor.org/packages/gQTLBase")
10740 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
10741 (description
10742 "The purpose of this package is to simplify the storage and interrogation
10743 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
10744 and more.")
10745 (license license:artistic2.0)))
10746
10747 (define-public r-gqtlstats
10748 (package
10749 (name "r-gqtlstats")
10750 (version "1.21.3")
10751 (source
10752 (origin
10753 (method url-fetch)
10754 (uri (bioconductor-uri "gQTLstats" version))
10755 (sha256
10756 (base32
10757 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
10758 (properties `((upstream-name . "gQTLstats")))
10759 (build-system r-build-system)
10760 (propagated-inputs
10761 `(("r-annotationdbi" ,r-annotationdbi)
10762 ("r-batchjobs" ,r-batchjobs)
10763 ("r-bbmisc" ,r-bbmisc)
10764 ("r-beeswarm" ,r-beeswarm)
10765 ("r-biobase" ,r-biobase)
10766 ("r-biocgenerics" ,r-biocgenerics)
10767 ("r-doparallel" ,r-doparallel)
10768 ("r-dplyr" ,r-dplyr)
10769 ("r-erma" ,r-erma)
10770 ("r-ffbase" ,r-ffbase)
10771 ("r-foreach" ,r-foreach)
10772 ("r-genomeinfodb" ,r-genomeinfodb)
10773 ("r-genomicfeatures" ,r-genomicfeatures)
10774 ("r-genomicfiles" ,r-genomicfiles)
10775 ("r-genomicranges" ,r-genomicranges)
10776 ("r-ggbeeswarm" ,r-ggbeeswarm)
10777 ("r-ggplot2" ,r-ggplot2)
10778 ("r-gqtlbase" ,r-gqtlbase)
10779 ("r-hardyweinberg" ,r-hardyweinberg)
10780 ("r-homo-sapiens" ,r-homo-sapiens)
10781 ("r-iranges" ,r-iranges)
10782 ("r-limma" ,r-limma)
10783 ("r-mgcv" ,r-mgcv)
10784 ("r-plotly" ,r-plotly)
10785 ("r-reshape2" ,r-reshape2)
10786 ("r-s4vectors" ,r-s4vectors)
10787 ("r-shiny" ,r-shiny)
10788 ("r-snpstats" ,r-snpstats)
10789 ("r-summarizedexperiment" ,r-summarizedexperiment)
10790 ("r-variantannotation" ,r-variantannotation)))
10791 (native-inputs
10792 `(("r-knitr" ,r-knitr)))
10793 (home-page "https://bioconductor.org/packages/gQTLstats")
10794 (synopsis "Computationally efficient analysis for eQTL and allied studies")
10795 (description
10796 "This package provides tools for the computationally efficient analysis
10797 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
10798 The software in this package aims to support refinements and functional
10799 interpretation of members of a collection of association statistics on a
10800 family of feature/genome hypotheses.")
10801 (license license:artistic2.0)))
10802
10803 (define-public r-gviz
10804 (package
10805 (name "r-gviz")
10806 (version "1.34.1")
10807 (source
10808 (origin
10809 (method url-fetch)
10810 (uri (bioconductor-uri "Gviz" version))
10811 (sha256
10812 (base32
10813 "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1"))))
10814 (properties `((upstream-name . "Gviz")))
10815 (build-system r-build-system)
10816 (propagated-inputs
10817 `(("r-annotationdbi" ,r-annotationdbi)
10818 ("r-biobase" ,r-biobase)
10819 ("r-biocgenerics" ,r-biocgenerics)
10820 ("r-biomart" ,r-biomart)
10821 ("r-biostrings" ,r-biostrings)
10822 ("r-biovizbase" ,r-biovizbase)
10823 ("r-bsgenome" ,r-bsgenome)
10824 ("r-digest" ,r-digest)
10825 ("r-ensembldb" ,r-ensembldb)
10826 ("r-genomeinfodb" ,r-genomeinfodb)
10827 ("r-genomicalignments" ,r-genomicalignments)
10828 ("r-genomicfeatures" ,r-genomicfeatures)
10829 ("r-genomicranges" ,r-genomicranges)
10830 ("r-iranges" ,r-iranges)
10831 ("r-lattice" ,r-lattice)
10832 ("r-latticeextra" ,r-latticeextra)
10833 ("r-matrixstats" ,r-matrixstats)
10834 ("r-rcolorbrewer" ,r-rcolorbrewer)
10835 ("r-rsamtools" ,r-rsamtools)
10836 ("r-rtracklayer" ,r-rtracklayer)
10837 ("r-s4vectors" ,r-s4vectors)
10838 ("r-xvector" ,r-xvector)))
10839 (native-inputs
10840 `(("r-knitr" ,r-knitr)))
10841 (home-page "https://bioconductor.org/packages/Gviz")
10842 (synopsis "Plotting data and annotation information along genomic coordinates")
10843 (description
10844 "Genomic data analyses requires integrated visualization of known genomic
10845 information and new experimental data. Gviz uses the biomaRt and the
10846 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
10847 and translates this to e.g. gene/transcript structures in viewports of the
10848 grid graphics package. This results in genomic information plotted together
10849 with your data.")
10850 (license license:artistic2.0)))
10851
10852 (define-public r-gwascat
10853 (package
10854 (name "r-gwascat")
10855 (version "2.22.0")
10856 (source
10857 (origin
10858 (method url-fetch)
10859 (uri (bioconductor-uri "gwascat" version))
10860 (sha256
10861 (base32
10862 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
10863 (build-system r-build-system)
10864 (propagated-inputs
10865 `(("r-annotationdbi" ,r-annotationdbi)
10866 ("r-biocfilecache" ,r-biocfilecache)
10867 ("r-biostrings" ,r-biostrings)
10868 ("r-genomeinfodb" ,r-genomeinfodb)
10869 ("r-genomicfeatures" ,r-genomicfeatures)
10870 ("r-genomicranges" ,r-genomicranges)
10871 ("r-iranges" ,r-iranges)
10872 ("r-readr" ,r-readr)
10873 ("r-s4vectors" ,r-s4vectors)
10874 ("r-snpstats" ,r-snpstats)
10875 ("r-variantannotation" ,r-variantannotation)))
10876 (native-inputs
10877 `(("r-knitr" ,r-knitr)))
10878 (home-page "https://bioconductor.org/packages/gwascat")
10879 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
10880 (description
10881 "This package provides tools for representing and modeling data in the
10882 EMBL-EBI GWAS catalog.")
10883 (license license:artistic2.0)))
10884
10885 (define-public r-kegggraph
10886 (package
10887 (name "r-kegggraph")
10888 (version "1.50.0")
10889 (source
10890 (origin
10891 (method url-fetch)
10892 (uri (bioconductor-uri "KEGGgraph" version))
10893 (sha256
10894 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
10895 (properties `((upstream-name . "KEGGgraph")))
10896 (build-system r-build-system)
10897 (propagated-inputs
10898 `(("r-graph" ,r-graph)
10899 ("r-rcurl" ,r-rcurl)
10900 ("r-xml" ,r-xml)))
10901 (home-page "https://bioconductor.org/packages/KEGGgraph")
10902 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
10903 (description
10904 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
10905 object as well as a collection of tools to analyze, dissect and visualize these
10906 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
10907 maintaining all essential pathway attributes. The package offers
10908 functionalities including parsing, graph operation, visualization and etc.")
10909 (license license:gpl2+)))
10910
10911 (define-public r-ldblock
10912 (package
10913 (name "r-ldblock")
10914 (version "1.20.0")
10915 (source
10916 (origin
10917 (method url-fetch)
10918 (uri (bioconductor-uri "ldblock" version))
10919 (sha256
10920 (base32
10921 "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
10922 (build-system r-build-system)
10923 (propagated-inputs
10924 `(("r-biocgenerics" ,r-biocgenerics)
10925 ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
10926 ("r-ensembldb" ,r-ensembldb)
10927 ("r-genomeinfodb" ,r-genomeinfodb)
10928 ("r-genomicfiles" ,r-genomicfiles)
10929 ("r-httr" ,r-httr)
10930 ("r-matrix" ,r-matrix)
10931 ("r-rsamtools" ,r-rsamtools)
10932 ("r-snpstats" ,r-snpstats)
10933 ("r-variantannotation" ,r-variantannotation)))
10934 (native-inputs
10935 `(("r-knitr" ,r-knitr)))
10936 (home-page "https://bioconductor.org/packages/ldblock")
10937 (synopsis "Data structures for linkage disequilibrium measures in populations")
10938 (description
10939 "This package defines data structures for @dfn{linkage
10940 disequilibrium} (LD) measures in populations. Its purpose is to simplify
10941 handling of existing population-level data for the purpose of flexibly
10942 defining LD blocks.")
10943 (license license:artistic2.0)))
10944
10945 ;; This is a CRAN package, but it depends on r-snpstats, which is a
10946 ;; Bioconductor package.
10947 (define-public r-ldheatmap
10948 (package
10949 (name "r-ldheatmap")
10950 (version "1.0-4")
10951 (source
10952 (origin
10953 (method url-fetch)
10954 (uri (cran-uri "LDheatmap" version))
10955 (sha256
10956 (base32
10957 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
10958 (properties `((upstream-name . "LDheatmap")))
10959 (build-system r-build-system)
10960 (propagated-inputs
10961 `(("r-genetics" ,r-genetics)
10962 ("r-rcpp" ,r-rcpp)
10963 ("r-snpstats" ,r-snpstats)))
10964 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
10965 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
10966 (description
10967 "This package provides tools to produce a graphical display, as a heat
10968 map, of measures of pairwise linkage disequilibria between SNPs. Users may
10969 optionally include the physical locations or genetic map distances of each SNP
10970 on the plot.")
10971 (license license:gpl3)))
10972
10973 (define-public r-pathview
10974 (package
10975 (name "r-pathview")
10976 (version "1.30.1")
10977 (source
10978 (origin
10979 (method url-fetch)
10980 (uri (bioconductor-uri "pathview" version))
10981 (sha256
10982 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
10983 (properties `((upstream-name . "pathview")))
10984 (build-system r-build-system)
10985 (propagated-inputs
10986 `(("r-annotationdbi" ,r-annotationdbi)
10987 ("r-graph" ,r-graph)
10988 ("r-kegggraph" ,r-kegggraph)
10989 ("r-keggrest" ,r-keggrest)
10990 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
10991 ("r-png" ,r-png)
10992 ("r-rgraphviz" ,r-rgraphviz)
10993 ("r-xml" ,r-xml)))
10994 (home-page "https://pathview.uncc.edu/")
10995 (synopsis "Tool set for pathway based data integration and visualization")
10996 (description
10997 "@code{r-pathview} is a tool set for pathway based data integration and
10998 visualization. It maps and renders a wide variety of biological data on
10999 relevant pathway graphs. All users need is to supply their data and specify
11000 the target pathway. This package automatically downloads the pathway graph
11001 data, parses the data file, maps user data to the pathway, and render pathway
11002 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
11003 integrates with pathway and gene set (enrichment) analysis tools for
11004 large-scale and fully automated analysis.")
11005 (license license:gpl3+)))
11006
11007 (define-public r-snpstats
11008 (package
11009 (name "r-snpstats")
11010 (version "1.40.0")
11011 (source
11012 (origin
11013 (method url-fetch)
11014 (uri (bioconductor-uri "snpStats" version))
11015 (sha256
11016 (base32
11017 "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
11018 (properties `((upstream-name . "snpStats")))
11019 (build-system r-build-system)
11020 (inputs `(("zlib" ,zlib)))
11021 (propagated-inputs
11022 `(("r-biocgenerics" ,r-biocgenerics)
11023 ("r-matrix" ,r-matrix)
11024 ("r-survival" ,r-survival)
11025 ("r-zlibbioc" ,r-zlibbioc)))
11026 (home-page "https://bioconductor.org/packages/snpStats")
11027 (synopsis "Methods for SNP association studies")
11028 (description
11029 "This package provides classes and statistical methods for large
11030 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
11031 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
11032 (license license:gpl3)))
11033
11034 (define-public r-chromstar
11035 (package
11036 (name "r-chromstar")
11037 (version "1.16.0")
11038 (source
11039 (origin
11040 (method url-fetch)
11041 (uri (bioconductor-uri "chromstaR" version))
11042 (sha256
11043 (base32
11044 "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1"))))
11045 (properties `((upstream-name . "chromstaR")))
11046 (build-system r-build-system)
11047 (propagated-inputs
11048 `(("r-bamsignals" ,r-bamsignals)
11049 ("r-biocgenerics" ,r-biocgenerics)
11050 ("r-chromstardata" ,r-chromstardata)
11051 ("r-doparallel" ,r-doparallel)
11052 ("r-foreach" ,r-foreach)
11053 ("r-genomeinfodb" ,r-genomeinfodb)
11054 ("r-genomicalignments" ,r-genomicalignments)
11055 ("r-genomicranges" ,r-genomicranges)
11056 ("r-ggplot2" ,r-ggplot2)
11057 ("r-iranges" ,r-iranges)
11058 ("r-mvtnorm" ,r-mvtnorm)
11059 ("r-reshape2" ,r-reshape2)
11060 ("r-rsamtools" ,r-rsamtools)
11061 ("r-s4vectors" ,r-s4vectors)))
11062 (native-inputs `(("r-knitr" ,r-knitr)))
11063 (home-page "https://github.com/ataudt/chromstaR")
11064 (synopsis "Chromatin state analysis for ChIP-Seq data")
11065 (description
11066 "This package implements functions for combinatorial and differential
11067 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
11068 export to genome browser viewable files, and functions for enrichment
11069 analyses.")
11070 (license license:artistic2.0)))
11071
11072 (define-public r-sushi
11073 (package
11074 (name "r-sushi")
11075 (version "1.28.0")
11076 (source (origin
11077 (method url-fetch)
11078 (uri (bioconductor-uri "Sushi" version))
11079 (sha256
11080 (base32
11081 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
11082 (properties `((upstream-name . "Sushi")))
11083 (build-system r-build-system)
11084 (propagated-inputs
11085 `(("r-biomart" ,r-biomart)
11086 ("r-zoo" ,r-zoo)))
11087 (home-page "https://bioconductor.org/packages/Sushi")
11088 (synopsis "Tools for visualizing genomics data")
11089 (description
11090 "This package provides flexible, quantitative, and integrative genomic
11091 visualizations for publication-quality multi-panel figures.")
11092 (license license:gpl2+)))