gnu: Update r-msnbase to 2.16.0.
[jackhill/guix/guix.git] / gnu / packages / bioconductor.scm
CommitLineData
fa596599 1;;; GNU Guix --- Functional package management for GNU
f8f181ae 2;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
e8d435f7 3;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
61242625 4;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
25f4e652 5;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com>
488001eb 6;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
f4d920b9 7;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
c61268c1 8;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
fa596599
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9;;;
10;;; This file is part of GNU Guix.
11;;;
12;;; GNU Guix is free software; you can redistribute it and/or modify it
13;;; under the terms of the GNU General Public License as published by
14;;; the Free Software Foundation; either version 3 of the License, or (at
15;;; your option) any later version.
16;;;
17;;; GNU Guix is distributed in the hope that it will be useful, but
18;;; WITHOUT ANY WARRANTY; without even the implied warranty of
19;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
20;;; GNU General Public License for more details.
21;;;
22;;; You should have received a copy of the GNU General Public License
23;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
24
25(define-module (gnu packages bioconductor)
26 #:use-module ((guix licenses) #:prefix license:)
27 #:use-module (guix packages)
28 #:use-module (guix download)
b2dce6b5 29 #:use-module (guix git-download)
fa596599 30 #:use-module (guix build-system r)
183ce988 31 #:use-module (gnu packages)
58656064 32 #:use-module (gnu packages base)
cf9a29b2 33 #:use-module (gnu packages bioinformatics)
a5b56a53
RJ
34 #:use-module (gnu packages cran)
35 #:use-module (gnu packages compression)
c18dccff 36 #:use-module (gnu packages gcc)
cf9a29b2 37 #:use-module (gnu packages graph)
5aef09bd 38 #:use-module (gnu packages graphviz)
dddbc90c 39 #:use-module (gnu packages haskell-xyz)
5cfa4bff 40 #:use-module (gnu packages image)
b64ce4b7 41 #:use-module (gnu packages maths)
6b12f213
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42 #:use-module (gnu packages netpbm)
43 #:use-module (gnu packages perl)
2cb71d81 44 #:use-module (gnu packages pkg-config)
f4235c0e 45 #:use-module (gnu packages statistics)
14bb1c48 46 #:use-module (gnu packages web)
7a62d5e0 47 #:use-module (gnu packages xml)
14bb1c48 48 #:use-module (srfi srfi-1))
fa596599 49
557a1089
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50\f
51;;; Annotations
52
6f15ea24
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53(define-public r-reactome-db
54 (package
55 (name "r-reactome-db")
56 (version "1.70.0")
57 (source
58 (origin
59 (method url-fetch)
60 (uri (bioconductor-uri "reactome.db" version 'annotation))
61 (sha256
62 (base32
63 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
64 (properties `((upstream-name . "reactome.db")))
65 (build-system r-build-system)
66 (propagated-inputs
67 `(("r-annotationdbi" ,r-annotationdbi)))
68 (home-page "https://bioconductor.org/packages/reactome.db/")
69 (synopsis "Annotation maps for reactome")
70 (description
71 "This package provides a set of annotation maps for the REACTOME
72database, assembled using data from REACTOME.")
73 (license license:cc-by4.0)))
74
b7d93cf5
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75(define-public r-bsgenome-celegans-ucsc-ce6
76 (package
77 (name "r-bsgenome-celegans-ucsc-ce6")
78 (version "1.4.0")
79 (source (origin
80 (method url-fetch)
86ced7b2
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81 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
82 version 'annotation))
b7d93cf5
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83 (sha256
84 (base32
85 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
86 (properties
87 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
88 (build-system r-build-system)
b7d93cf5
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89 (propagated-inputs
90 `(("r-bsgenome" ,r-bsgenome)))
91 (home-page
92 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
93 (synopsis "Full genome sequences for Worm")
94 (description
95 "This package provides full genome sequences for Caenorhabditis
96elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
0c792ffb
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97objects.")
98 (license license:artistic2.0)))
99
100(define-public r-bsgenome-celegans-ucsc-ce10
101 (package
102 (name "r-bsgenome-celegans-ucsc-ce10")
103 (version "1.4.0")
104 (source (origin
105 (method url-fetch)
6998ecba
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106 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
107 version 'annotation))
0c792ffb
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108 (sha256
109 (base32
110 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
111 (properties
112 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
113 (build-system r-build-system)
0c792ffb
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114 (propagated-inputs
115 `(("r-bsgenome" ,r-bsgenome)))
116 (home-page
117 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
118 (synopsis "Full genome sequences for Worm")
119 (description
120 "This package provides full genome sequences for Caenorhabditis
121elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
b7d93cf5
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122objects.")
123 (license license:artistic2.0)))
124
183db725
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125(define-public r-bsgenome-dmelanogaster-ucsc-dm6
126 (package
127 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
128 (version "1.4.1")
129 (source (origin
130 (method url-fetch)
149f351f
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131 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
132 version 'annotation))
183db725
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133 (sha256
134 (base32
135 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
136 (properties
137 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
138 (build-system r-build-system)
183db725
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139 (propagated-inputs
140 `(("r-bsgenome" ,r-bsgenome)))
141 (home-page
142 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
143 (synopsis "Full genome sequences for Fly")
144 (description
145 "This package provides full genome sequences for Drosophila
146melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
147objects.")
148 (license license:artistic2.0)))
149
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150(define-public r-bsgenome-dmelanogaster-ucsc-dm3
151 (package
152 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
153 (version "1.4.0")
154 (source (origin
155 (method url-fetch)
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156 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
157 version 'annotation))
13dabd69
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158 (sha256
159 (base32
160 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
161 (properties
162 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
163 (build-system r-build-system)
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164 (propagated-inputs
165 `(("r-bsgenome" ,r-bsgenome)))
166 (home-page
167 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
168 (synopsis "Full genome sequences for Fly")
169 (description
170 "This package provides full genome sequences for Drosophila
171melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
172Biostrings objects.")
173 (license license:artistic2.0)))
174
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175(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
176 (package
177 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
178 (version "1.3.99")
179 (source (origin
180 (method url-fetch)
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181 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
182 version 'annotation))
dfac7eb9
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183 (sha256
184 (base32
185 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
186 (properties
187 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
188 (build-system r-build-system)
189 (propagated-inputs
190 `(("r-bsgenome" ,r-bsgenome)
191 ("r-bsgenome-dmelanogaster-ucsc-dm3"
192 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
193 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
194 (synopsis "Full masked genome sequences for Fly")
195 (description
196 "This package provides full masked genome sequences for Drosophila
197melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
198Biostrings objects. The sequences are the same as in
199BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
200masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
201intra-contig ambiguities (AMB mask), (3) the mask of repeats from
202RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
203Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
204 (license license:artistic2.0)))
205
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206(define-public r-bsgenome-hsapiens-1000genomes-hs37d5
207 (package
208 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
209 (version "0.99.1")
210 (source (origin
211 (method url-fetch)
88e7c7db
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212 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
213 version 'annotation))
40a65057
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214 (sha256
215 (base32
216 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
217 (properties
218 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
219 (build-system r-build-system)
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220 (propagated-inputs
221 `(("r-bsgenome" ,r-bsgenome)))
222 (home-page
223 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
224 (synopsis "Full genome sequences for Homo sapiens")
225 (description
226 "This package provides full genome sequences for Homo sapiens from
2271000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
228 (license license:artistic2.0)))
229
c51c0033
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230(define-public r-bsgenome-hsapiens-ncbi-grch38
231 (package
232 (name "r-bsgenome-hsapiens-ncbi-grch38")
233 (version "1.3.1000")
234 (source
235 (origin
236 (method url-fetch)
237 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
238 version 'annotation))
239 (sha256
240 (base32
241 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
242 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
243 (build-system r-build-system)
244 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
245 (home-page
246 "https://bioconductor.org/packages/release/data/annotation/html/\
247BSgenome.Hsapiens.NCBI.GRCh38.html")
248 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
249 (description
250 "This package provides full genome sequences for Homo sapiens (Human) as
251provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
252 (license license:artistic2.0)))
253
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254(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
255 (package
256 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
257 (version "1.3.99")
258 (source (origin
259 (method url-fetch)
a47646bd
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260 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
261 version 'annotation))
6fbd759b
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262 (sha256
263 (base32
264 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
265 (properties
266 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
267 (build-system r-build-system)
268 (propagated-inputs
269 `(("r-bsgenome" ,r-bsgenome)
270 ("r-bsgenome-hsapiens-ucsc-hg19"
271 ,r-bsgenome-hsapiens-ucsc-hg19)))
272 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
273 (synopsis "Full masked genome sequences for Homo sapiens")
274 (description
275 "This package provides full genome sequences for Homo sapiens (Human) as
276provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
277sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
278them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
279mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
280repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
281Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
282default.")
283 (license license:artistic2.0)))
284
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285(define-public r-bsgenome-mmusculus-ucsc-mm9
286 (package
287 (name "r-bsgenome-mmusculus-ucsc-mm9")
288 (version "1.4.0")
289 (source (origin
290 (method url-fetch)
21f6dae7
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291 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
292 version 'annotation))
5acb9052
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293 (sha256
294 (base32
295 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
296 (properties
297 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
298 (build-system r-build-system)
5acb9052
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299 (propagated-inputs
300 `(("r-bsgenome" ,r-bsgenome)))
301 (home-page
302 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
303 (synopsis "Full genome sequences for Mouse")
304 (description
305 "This package provides full genome sequences for Mus musculus (Mouse) as
306provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
307 (license license:artistic2.0)))
308
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309(define-public r-bsgenome-mmusculus-ucsc-mm9-masked
310 (package
311 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
312 (version "1.3.99")
313 (source (origin
314 (method url-fetch)
51dc4a2d
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315 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
316 version 'annotation))
2bece692
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317 (sha256
318 (base32
319 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
320 (properties
321 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
322 (build-system r-build-system)
323 (propagated-inputs
324 `(("r-bsgenome" ,r-bsgenome)
325 ("r-bsgenome-mmusculus-ucsc-mm9"
326 ,r-bsgenome-mmusculus-ucsc-mm9)))
99db6db7 327 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
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328 (synopsis "Full masked genome sequences for Mouse")
329 (description
330 "This package provides full genome sequences for Mus musculus (Mouse) as
331provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
332sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
333them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
334mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
335repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
336Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
337default." )
338 (license license:artistic2.0)))
339
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340(define-public r-bsgenome-mmusculus-ucsc-mm10
341 (package
342 (name "r-bsgenome-mmusculus-ucsc-mm10")
343 (version "1.4.0")
344 (source (origin
345 (method url-fetch)
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346 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
347 version 'annotation))
c3adc830
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348 (sha256
349 (base32
350 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
351 (properties
352 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
353 (build-system r-build-system)
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354 (propagated-inputs
355 `(("r-bsgenome" ,r-bsgenome)))
356 (home-page
357 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
358 (synopsis "Full genome sequences for Mouse")
359 (description
360 "This package provides full genome sequences for Mus
361musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
362in Biostrings objects.")
363 (license license:artistic2.0)))
364
3a08940e
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365(define-public r-org-ce-eg-db
366 (package
367 (name "r-org-ce-eg-db")
368 (version "3.7.0")
369 (source (origin
370 (method url-fetch)
1c05e637 371 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
3a08940e
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372 (sha256
373 (base32
374 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
375 (properties
376 `((upstream-name . "org.Ce.eg.db")))
377 (build-system r-build-system)
378 (propagated-inputs
379 `(("r-annotationdbi" ,r-annotationdbi)))
380 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
381 (synopsis "Genome wide annotation for Worm")
382 (description
383 "This package provides mappings from Entrez gene identifiers to various
384annotations for the genome of the model worm Caenorhabditis elegans.")
385 (license license:artistic2.0)))
386
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387(define-public r-org-dm-eg-db
388 (package
389 (name "r-org-dm-eg-db")
390 (version "3.7.0")
391 (source (origin
392 (method url-fetch)
b0dfc79b 393 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
f8780e96
RW
394 (sha256
395 (base32
396 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
397 (properties
398 `((upstream-name . "org.Dm.eg.db")))
399 (build-system r-build-system)
400 (propagated-inputs
401 `(("r-annotationdbi" ,r-annotationdbi)))
402 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
403 (synopsis "Genome wide annotation for Fly")
404 (description
405 "This package provides mappings from Entrez gene identifiers to various
406annotations for the genome of the model fruit fly Drosophila melanogaster.")
407 (license license:artistic2.0)))
408
3dad6087
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409(define-public r-org-dr-eg-db
410 (package
411 (name "r-org-dr-eg-db")
412 (version "3.7.0")
413 (source (origin
414 (method url-fetch)
7bb65a22 415 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
3dad6087
RW
416 (sha256
417 (base32
418 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
419 (properties
420 `((upstream-name . "org.Dr.eg.db")))
421 (build-system r-build-system)
422 (propagated-inputs
423 `(("r-annotationdbi" ,r-annotationdbi)))
424 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
425 (synopsis "Annotation for Zebrafish")
426 (description
427 "This package provides genome wide annotations for Zebrafish, primarily
428based on mapping using Entrez Gene identifiers.")
429 (license license:artistic2.0)))
430
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431(define-public r-org-hs-eg-db
432 (package
433 (name "r-org-hs-eg-db")
434 (version "3.7.0")
435 (source (origin
436 (method url-fetch)
f53becc6 437 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
d56df35a
RW
438 (sha256
439 (base32
440 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
441 (properties
442 `((upstream-name . "org.Hs.eg.db")))
443 (build-system r-build-system)
444 (propagated-inputs
445 `(("r-annotationdbi" ,r-annotationdbi)))
446 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
447 (synopsis "Genome wide annotation for Human")
448 (description
449 "This package contains genome-wide annotations for Human, primarily based
450on mapping using Entrez Gene identifiers.")
451 (license license:artistic2.0)))
452
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453(define-public r-org-mm-eg-db
454 (package
455 (name "r-org-mm-eg-db")
456 (version "3.7.0")
457 (source (origin
458 (method url-fetch)
411be88b 459 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
8035819f
RW
460 (sha256
461 (base32
462 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
463 (properties
464 `((upstream-name . "org.Mm.eg.db")))
465 (build-system r-build-system)
466 (propagated-inputs
467 `(("r-annotationdbi" ,r-annotationdbi)))
468 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
469 (synopsis "Genome wide annotation for Mouse")
470 (description
471 "This package provides mappings from Entrez gene identifiers to various
472annotations for the genome of the model mouse Mus musculus.")
473 (license license:artistic2.0)))
474
fe0b76e2
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475(define-public r-bsgenome-hsapiens-ucsc-hg19
476 (package
477 (name "r-bsgenome-hsapiens-ucsc-hg19")
478 (version "1.4.0")
479 (source (origin
480 (method url-fetch)
e7a8cf2e
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481 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
482 version 'annotation))
fe0b76e2
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483 (sha256
484 (base32
485 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
486 (properties
487 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
488 (build-system r-build-system)
fe0b76e2
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489 (propagated-inputs
490 `(("r-bsgenome" ,r-bsgenome)))
491 (home-page
492 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
493 (synopsis "Full genome sequences for Homo sapiens")
494 (description
495 "This package provides full genome sequences for Homo sapiens as provided
496by UCSC (hg19, February 2009) and stored in Biostrings objects.")
497 (license license:artistic2.0)))
498
8ce240fd
RJ
499(define-public r-bsgenome-hsapiens-ucsc-hg38
500 (package
501 (name "r-bsgenome-hsapiens-ucsc-hg38")
502 (version "1.4.1")
503 (source (origin
504 (method url-fetch)
505 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
506 version 'annotation))
507 (sha256
508 (base32
509 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
510 (properties
511 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
512 (build-system r-build-system)
513 (propagated-inputs
514 `(("r-bsgenome" ,r-bsgenome)))
515 (home-page
516 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
517 (synopsis "Full genome sequences for Homo sapiens")
518 (description
519 "This package provides full genome sequences for Homo sapiens (Human)
520as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
521 (license license:artistic2.0)))
522
8324e64c
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523(define-public r-ensdb-hsapiens-v75
524 (package
525 (name "r-ensdb-hsapiens-v75")
526 (version "2.99.0")
527 (source
528 (origin
529 (method url-fetch)
530 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
531 (sha256
532 (base32
533 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
534 (properties
535 `((upstream-name . "EnsDb.Hsapiens.v75")))
536 (build-system r-build-system)
537 (propagated-inputs
538 `(("r-ensembldb" ,r-ensembldb)))
539 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
540 (synopsis "Ensembl based annotation package")
541 (description
542 "This package exposes an annotation database generated from Ensembl.")
543 (license license:artistic2.0)))
544
2cc51108
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545(define-public r-genelendatabase
546 (package
547 (name "r-genelendatabase")
daeb3cd9 548 (version "1.18.0")
2cc51108
RW
549 (source
550 (origin
551 (method url-fetch)
717d7cda 552 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
2cc51108
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553 (sha256
554 (base32
daeb3cd9 555 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
2cc51108
RW
556 (properties
557 `((upstream-name . "geneLenDataBase")))
558 (build-system r-build-system)
559 (propagated-inputs
560 `(("r-rtracklayer" ,r-rtracklayer)
561 ("r-genomicfeatures" ,r-genomicfeatures)))
562 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
563 (synopsis "Lengths of mRNA transcripts for a number of genomes")
564 (description
565 "This package provides the lengths of mRNA transcripts for a number of
566genomes and gene ID formats, largely based on the UCSC table browser.")
567 (license license:lgpl2.0+)))
568
66e35ce6
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569(define-public r-txdb-hsapiens-ucsc-hg19-knowngene
570 (package
571 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
572 (version "3.2.2")
573 (source (origin
574 (method url-fetch)
f2580a13
RW
575 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
576 version 'annotation))
66e35ce6
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577 (sha256
578 (base32
579 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
580 (properties
581 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
582 (build-system r-build-system)
66e35ce6
RW
583 (propagated-inputs
584 `(("r-genomicfeatures" ,r-genomicfeatures)))
585 (home-page
586 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
587 (synopsis "Annotation package for human genome in TxDb format")
588 (description
589 "This package provides an annotation database of Homo sapiens genome
590data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
798b80ce
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591track. The database is exposed as a @code{TxDb} object.")
592 (license license:artistic2.0)))
593
594(define-public r-txdb-hsapiens-ucsc-hg38-knowngene
595 (package
596 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
597 (version "3.4.6")
598 (source (origin
599 (method url-fetch)
d78db088
RW
600 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
601 version 'annotation))
798b80ce
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602 (sha256
603 (base32
604 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
605 (properties
606 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
607 (build-system r-build-system)
608 (propagated-inputs
609 `(("r-genomicfeatures" ,r-genomicfeatures)))
610 (home-page
611 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
612 (synopsis "Annotation package for human genome in TxDb format")
613 (description
614 "This package provides an annotation database of Homo sapiens genome
615data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
66e35ce6
RW
616track. The database is exposed as a @code{TxDb} object.")
617 (license license:artistic2.0)))
618
d220babf
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619(define-public r-txdb-mmusculus-ucsc-mm9-knowngene
620 (package
621 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
622 (version "3.2.2")
623 (source (origin
624 (method url-fetch)
1afdf41b
RW
625 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
626 version 'annotation))
d220babf
RW
627 (sha256
628 (base32
629 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
630 (properties
631 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
632 (build-system r-build-system)
633 (propagated-inputs
634 `(("r-genomicfeatures" ,r-genomicfeatures)
635 ("r-annotationdbi" ,r-annotationdbi)))
636 (home-page
637 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
638 (synopsis "Annotation package for mouse genome in TxDb format")
639 (description
640 "This package provides an annotation database of Mouse genome data. It
641is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
642database is exposed as a @code{TxDb} object.")
643 (license license:artistic2.0)))
644
7bc5d1b0
RW
645(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
646 (package
647 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
b69c7703 648 (version "3.10.0")
7bc5d1b0
RW
649 (source (origin
650 (method url-fetch)
c271d990
RW
651 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
652 version 'annotation))
7bc5d1b0
RW
653 (sha256
654 (base32
b69c7703 655 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
7bc5d1b0
RW
656 (properties
657 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
658 (build-system r-build-system)
7bc5d1b0
RW
659 (propagated-inputs
660 `(("r-bsgenome" ,r-bsgenome)
661 ("r-genomicfeatures" ,r-genomicfeatures)
662 ("r-annotationdbi" ,r-annotationdbi)))
663 (home-page
664 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
665 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
666 (description
667 "This package loads a TxDb object, which is an R interface to
668prefabricated databases contained in this package. This package provides
669the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
670based on the knownGene track.")
671 (license license:artistic2.0)))
672
7cd446fd
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673(define-public r-txdb-celegans-ucsc-ce6-ensgene
674 (package
675 (name "r-txdb-celegans-ucsc-ce6-ensgene")
676 (version "3.2.2")
677 (source
678 (origin
679 (method url-fetch)
680 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
681 version 'annotation))
682 (sha256
683 (base32
684 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
685 (properties
686 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
687 (build-system r-build-system)
688 (propagated-inputs
689 `(("r-annotationdbi" ,r-annotationdbi)
690 ("r-genomicfeatures" ,r-genomicfeatures)))
691 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
692 (synopsis "Annotation package for C elegans TxDb objects")
693 (description
694 "This package exposes a C elegans annotation database generated from UCSC
695by exposing these as TxDb objects.")
696 (license license:artistic2.0)))
697
0f5c9cec
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698(define-public r-fdb-infiniummethylation-hg19
699 (package
700 (name "r-fdb-infiniummethylation-hg19")
701 (version "2.2.0")
702 (source (origin
703 (method url-fetch)
6aca4054
RW
704 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
705 version 'annotation))
0f5c9cec
RW
706 (sha256
707 (base32
708 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
709 (properties
710 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
711 (build-system r-build-system)
712 (propagated-inputs
713 `(("r-biostrings" ,r-biostrings)
714 ("r-genomicfeatures" ,r-genomicfeatures)
715 ("r-annotationdbi" ,r-annotationdbi)
716 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
717 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
718 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
719 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
720 (description
721 "This is an annotation package for Illumina Infinium DNA methylation
722probes. It contains the compiled HumanMethylation27 and HumanMethylation450
723annotations.")
724 (license license:artistic2.0)))
725
9475a248
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726(define-public r-illuminahumanmethylationepicmanifest
727 (package
728 (name "r-illuminahumanmethylationepicmanifest")
729 (version "0.3.0")
730 (source (origin
731 (method url-fetch)
25f567a8
RW
732 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
733 version 'annotation))
9475a248
RW
734 (sha256
735 (base32
736 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
737 (properties
738 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
739 (build-system r-build-system)
740 (propagated-inputs
741 `(("r-minfi" ,r-minfi)))
742 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
743 (synopsis "Manifest for Illumina's EPIC methylation arrays")
744 (description
745 "This is a manifest package for Illumina's EPIC methylation arrays.")
746 (license license:artistic2.0)))
e8d435f7
RJ
747
748(define-public r-ideoviz
749 (package
750 (name "r-ideoviz")
25f4e652 751 (version "1.26.0")
e8d435f7
RJ
752 (source (origin
753 (method url-fetch)
754 (uri (bioconductor-uri "IdeoViz" version))
755 (sha256
756 (base32
25f4e652 757 "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
e8d435f7
RJ
758 (build-system r-build-system)
759 (propagated-inputs
760 `(("r-biobase" ,r-biobase)
761 ("r-iranges" ,r-iranges)
762 ("r-genomicranges" ,r-genomicranges)
763 ("r-rcolorbrewer" ,r-rcolorbrewer)
764 ("r-rtracklayer" ,r-rtracklayer)
765 ("r-genomeinfodb" ,r-genomeinfodb)))
766 (home-page "https://bioconductor.org/packages/IdeoViz/")
767 (synopsis "Plots data along a chromosomal ideogram")
768 (description "This package provides functions to plot data associated with
769arbitrary genomic intervals along chromosomal ideogram.")
770 (license license:gpl2)))
9475a248 771
a38bf7c8
RJ
772;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
773;; from Bioconductor.
774(define-public r-deconstructsigs
775 (package
776 (name "r-deconstructsigs")
777 (version "1.8.0")
778 (source (origin
779 (method url-fetch)
780 (uri (cran-uri "deconstructSigs" version))
781 (sha256
782 (base32
783 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
784 (properties
785 `((upstream-name . "deconstructSigs")))
786 (build-system r-build-system)
787 (propagated-inputs
788 `(("r-bsgenome" ,r-bsgenome)
789 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
790 ("r-genomeinfodb" ,r-genomeinfodb)
791 ("r-reshape2" ,r-reshape2)))
792 (home-page "https://github.com/raerose01/deconstructSigs")
793 (synopsis "Identifies signatures present in a tumor sample")
794 (description "This package takes sample information in the form of the
795fraction of mutations in each of 96 trinucleotide contexts and identifies
796the weighted combination of published signatures that, when summed, most
797closely reconstructs the mutational profile.")
798 (license license:gpl2+)))
799
7c9d8a5d
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800;; This is a CRAN package, but it depends on Bioconductor packages.
801(define-public r-nmf
802 (package
803 (name "r-nmf")
0a41d9be 804 (version "0.23.0")
7c9d8a5d
RW
805 (source
806 (origin
807 (method url-fetch)
808 (uri (cran-uri "NMF" version))
809 (sha256
810 (base32
0a41d9be 811 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
7c9d8a5d
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812 (properties `((upstream-name . "NMF")))
813 (build-system r-build-system)
814 (propagated-inputs
815 `(("r-cluster" ,r-cluster)
be1042b3
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816 ("r-biobase" ,r-biobase)
817 ("r-biocmanager" ,r-biocmanager)
7c9d8a5d
RW
818 ("r-bigmemory" ,r-bigmemory) ; suggested
819 ("r-synchronicity" ,r-synchronicity) ; suggested
820 ("r-colorspace" ,r-colorspace)
821 ("r-digest" ,r-digest)
822 ("r-doparallel" ,r-doparallel)
823 ("r-foreach" ,r-foreach)
824 ("r-ggplot2" ,r-ggplot2)
825 ("r-gridbase" ,r-gridbase)
826 ("r-pkgmaker" ,r-pkgmaker)
827 ("r-rcolorbrewer" ,r-rcolorbrewer)
828 ("r-registry" ,r-registry)
829 ("r-reshape2" ,r-reshape2)
830 ("r-rngtools" ,r-rngtools)
831 ("r-stringr" ,r-stringr)))
0a41d9be
RW
832 (native-inputs
833 `(("r-knitr" ,r-knitr)))
7c9d8a5d
RW
834 (home-page "http://renozao.github.io/NMF")
835 (synopsis "Algorithms and framework for nonnegative matrix factorization")
836 (description
837 "This package provides a framework to perform Non-negative Matrix
838Factorization (NMF). The package implements a set of already published
839algorithms and seeding methods, and provides a framework to test, develop and
840plug new or custom algorithms. Most of the built-in algorithms have been
841optimized in C++, and the main interface function provides an easy way of
842performing parallel computations on multicore machines.")
843 (license license:gpl2+)))
844
f8a5af46
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845(define-public r-do-db
846 (package
847 (name "r-do-db")
848 (version "2.9")
849 (source (origin
850 (method url-fetch)
eed2766a 851 (uri (bioconductor-uri "DO.db" version 'annotation))
f8a5af46
RW
852 (sha256
853 (base32
854 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
855 (properties
856 `((upstream-name . "DO.db")))
857 (build-system r-build-system)
858 (propagated-inputs
859 `(("r-annotationdbi" ,r-annotationdbi)))
860 (home-page "https://www.bioconductor.org/packages/DO.db/")
861 (synopsis "Annotation maps describing the entire Disease Ontology")
862 (description
863 "This package provides a set of annotation maps describing the entire
864Disease Ontology.")
865 (license license:artistic2.0)))
866
ec20858a
RJ
867(define-public r-pasilla
868 (package
869 (name "r-pasilla")
870 (version "1.14.0")
871 (source (origin
872 (method url-fetch)
873 (uri (string-append
874 "http://bioconductor.org/packages/release/data/experiment"
875 "/src/contrib/pasilla_" version ".tar.gz"))
876 (sha256
877 (base32
878 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
879 (build-system r-build-system)
880 (propagated-inputs
881 `(("r-biocstyle" ,r-biocstyle)
882 ("r-dexseq" ,r-dexseq)
883 ("r-knitr" ,r-knitr)
884 ("r-rmarkdown" ,r-rmarkdown)))
885 (home-page "https://www.bioconductor.org/packages/pasilla/")
886 (synopsis "Data package with per-exon and per-gene read counts")
887 (description "This package provides per-exon and per-gene read counts
888computed for selected genes from RNA-seq data that were presented in the
889article 'Conservation of an RNA regulatory map between Drosophila and mammals'
890by Brooks et al., Genome Research 2011.")
891 (license license:lgpl2.1+)))
892
83b42091
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893(define-public r-pfam-db
894 (package
895 (name "r-pfam-db")
896 (version "3.8.2")
897 (source
898 (origin
899 (method url-fetch)
900 (uri (bioconductor-uri "PFAM.db" version 'annotation))
901 (sha256
902 (base32
903 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
904 (properties `((upstream-name . "PFAM.db")))
905 (build-system r-build-system)
906 (propagated-inputs
907 `(("r-annotationdbi" ,r-annotationdbi)))
908 (home-page "https://bioconductor.org/packages/PFAM.db")
909 (synopsis "Set of protein ID mappings for PFAM")
910 (description
911 "This package provides a set of protein ID mappings for PFAM, assembled
912using data from public repositories.")
913 (license license:artistic2.0)))
914
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915(define-public r-phastcons100way-ucsc-hg19
916 (package
917 (name "r-phastcons100way-ucsc-hg19")
918 (version "3.7.2")
919 (source
920 (origin
921 (method url-fetch)
922 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
923 version 'annotation))
924 (sha256
925 (base32
926 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
927 (properties
928 `((upstream-name . "phastCons100way.UCSC.hg19")))
929 (build-system r-build-system)
930 (propagated-inputs
931 `(("r-bsgenome" ,r-bsgenome)
932 ("r-genomeinfodb" ,r-genomeinfodb)
933 ("r-genomicranges" ,r-genomicranges)
934 ("r-genomicscores" ,r-genomicscores)
935 ("r-iranges" ,r-iranges)
936 ("r-s4vectors" ,r-s4vectors)))
937 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
938 (synopsis "UCSC phastCons conservation scores for hg19")
939 (description
940 "This package provides UCSC phastCons conservation scores for the human
941genome (hg19) calculated from multiple alignments with other 99 vertebrate
942species.")
943 (license license:artistic2.0)))
944
2cc51108 945\f
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946;;; Experiment data
947
692bce15
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948(define-public r-abadata
949 (package
950 (name "r-abadata")
951 (version "1.12.0")
952 (source (origin
953 (method url-fetch)
ced61edf 954 (uri (bioconductor-uri "ABAData" version 'experiment))
692bce15
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955 (sha256
956 (base32
957 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
958 (properties
959 `((upstream-name . "ABAData")))
960 (build-system r-build-system)
961 (propagated-inputs
962 `(("r-annotationdbi" ,r-annotationdbi)))
963 (home-page "https://www.bioconductor.org/packages/ABAData/")
964 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
965 (description
966 "This package provides the data for the gene expression enrichment
967analysis conducted in the package ABAEnrichment. The package includes three
968datasets which are derived from the Allen Brain Atlas:
969
970@enumerate
971@item Gene expression data from Human Brain (adults) averaged across donors,
972@item Gene expression data from the Developing Human Brain pooled into five
973 age categories and averaged across donors, and
974@item a developmental effect score based on the Developing Human Brain
975 expression data.
976@end enumerate
977
978All datasets are restricted to protein coding genes.")
979 (license license:gpl2+)))
980
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981(define-public r-arrmdata
982 (package
983 (name "r-arrmdata")
984 (version "1.18.0")
985 (source (origin
986 (method url-fetch)
b86f7746 987 (uri (bioconductor-uri "ARRmData" version 'experiment))
b50c9660
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988 (sha256
989 (base32
990 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
991 (properties
992 `((upstream-name . "ARRmData")))
993 (build-system r-build-system)
994 (home-page "https://www.bioconductor.org/packages/ARRmData/")
995 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
996 (description
997 "This package provides raw beta values from 36 samples across 3 groups
998from Illumina 450k methylation arrays.")
999 (license license:artistic2.0)))
1000
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1001(define-public r-hsmmsinglecell
1002 (package
1003 (name "r-hsmmsinglecell")
1004 (version "1.2.0")
1005 (source (origin
1006 (method url-fetch)
545e67ac 1007 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
557a1089
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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
1018morphological and transcriptional changes during differentiation. In this
1019experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1020under high mitogen conditions (GM) and then differentiated by switching to
1021low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1022hundred cells taken over a time-course of serum-induced differentiation.
1023Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
102472 hours) following serum switch using the Fluidigm C1 microfluidic system.
1025RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1026which were then sequenced to a depth of ~4 million reads per library,
1027resulting in a complete gene expression profile for each cell.")
1028 (license license:artistic2.0)))
ad8f46c6 1029
1030(define-public r-all
1031 (package
1032 (name "r-all")
1033 (version "1.26.0")
1034 (source (origin
1035 (method url-fetch)
41728d23 1036 (uri (bioconductor-uri "ALL" version 'experiment))
ad8f46c6 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
1049are available. The data have been normalized (using rma) and it is the
1050jointly normalized data that are available here. The data are presented in
1051the form of an @code{exprSet} object.")
1052 (license license:artistic2.0)))
557a1089 1053
53b1e10f
RW
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
1073examples' of Affymetrix data, unlike the artificial examples included in the
1074package @code{affy}.")
1075 (license license:gpl2+)))
1076
0c0ef9c5
RJ
1077(define-public r-coverageview
1078 (package
1079 (name "r-coverageview")
5ef637dd 1080 (version "1.28.0")
0c0ef9c5
RJ
1081 (source (origin
1082 (method url-fetch)
1083 (uri (bioconductor-uri "CoverageView" version))
1084 (sha256
1085 (base32
5ef637dd 1086 "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
0c0ef9c5
RJ
1087 (build-system r-build-system)
1088 (propagated-inputs
1089 `(("r-s4vectors" ,r-s4vectors)
1090 ("r-iranges" ,r-iranges)
1091 ("r-genomicranges" ,r-genomicranges)
1092 ("r-genomicalignments" ,r-genomicalignments)
1093 ("r-rtracklayer" ,r-rtracklayer)
1094 ("r-rsamtools" ,r-rsamtools)))
1095 (home-page "https://bioconductor.org/packages/CoverageView/")
1096 (synopsis "Coverage visualization package for R")
1097 (description "This package provides a framework for the visualization of
1098genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1099be also used for genome-wide nucleosome positioning experiments or other
1100experiment types where it is important to have a framework in order to inspect
1101how the coverage distributed across the genome.")
1102 (license license:artistic2.0)))
06fc1a51
RJ
1103
1104(define-public r-cummerbund
1105 (package
1106 (name "r-cummerbund")
a3e2e538 1107 (version "2.32.0")
06fc1a51
RJ
1108 (source (origin
1109 (method url-fetch)
1110 (uri (bioconductor-uri "cummeRbund" version))
1111 (sha256
1112 (base32
a3e2e538 1113 "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
06fc1a51
RJ
1114 (build-system r-build-system)
1115 (propagated-inputs
1116 `(("r-biobase" ,r-biobase)
1117 ("r-biocgenerics" ,r-biocgenerics)
1628d57b 1118 ("r-fastcluster" ,r-fastcluster)
06fc1a51
RJ
1119 ("r-ggplot2" ,r-ggplot2)
1120 ("r-gviz" ,r-gviz)
1121 ("r-plyr" ,r-plyr)
1122 ("r-reshape2" ,r-reshape2)
1123 ("r-rsqlite" ,r-rsqlite)
1124 ("r-rtracklayer" ,r-rtracklayer)
1125 ("r-s4vectors" ,r-s4vectors)))
1126 (home-page "https://bioconductor.org/packages/cummeRbund/")
1127 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1128 (description "This package allows for persistent storage, access,
1129exploration, and manipulation of Cufflinks high-throughput sequencing
1130data. In addition, provides numerous plotting functions for commonly
1131used visualizations.")
1132 (license license:artistic2.0)))
0c0ef9c5 1133
ff1146b9
RW
1134(define-public r-curatedtcgadata
1135 (package
1136 (name "r-curatedtcgadata")
1137 (version "1.8.0")
1138 (source
1139 (origin
1140 (method url-fetch)
1141 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1142 (sha256
1143 (base32
1144 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1145 (properties
1146 `((upstream-name . "curatedTCGAData")))
1147 (build-system r-build-system)
1148 (propagated-inputs
1149 `(("r-annotationhub" ,r-annotationhub)
1150 ("r-experimenthub" ,r-experimenthub)
1151 ("r-hdf5array" ,r-hdf5array)
1152 ("r-multiassayexperiment" ,r-multiassayexperiment)
1153 ("r-s4vectors" ,r-s4vectors)
1154 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1155 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1156 (synopsis "Curated data from The Cancer Genome Atlas")
1157 (description
1158 "This package provides publicly available data from The Cancer Genome
1159Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1160@code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1161number, mutation, microRNA, protein, and others) with clinical / pathological
1162data. It also links assay barcodes with patient identifiers, enabling
1163harmonized subsetting of rows (features) and columns (patients / samples)
1164across the entire multi-'omics experiment.")
1165 (license license:artistic2.0)))
1166
557a1089
RW
1167\f
1168;;; Packages
1169
e5d722fb
RW
1170(define-public r-biocversion
1171 (package
1172 (name "r-biocversion")
70ab9909 1173 (version "3.12.0")
e5d722fb
RW
1174 (source
1175 (origin
1176 (method url-fetch)
1177 (uri (bioconductor-uri "BiocVersion" version))
1178 (sha256
1179 (base32
70ab9909 1180 "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
e5d722fb
RW
1181 (properties `((upstream-name . "BiocVersion")))
1182 (build-system r-build-system)
1183 (home-page "https://bioconductor.org/packages/BiocVersion/")
1184 (synopsis "Set the appropriate version of Bioconductor packages")
1185 (description
1186 "This package provides repository information for the appropriate version
1187of Bioconductor.")
1188 (license license:artistic2.0)))
1189
14bba460
RW
1190(define-public r-biocgenerics
1191 (package
1192 (name "r-biocgenerics")
aa311eaa 1193 (version "0.36.0")
14bba460
RW
1194 (source (origin
1195 (method url-fetch)
1196 (uri (bioconductor-uri "BiocGenerics" version))
1197 (sha256
1198 (base32
aa311eaa 1199 "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
14bba460
RW
1200 (properties
1201 `((upstream-name . "BiocGenerics")))
1202 (build-system r-build-system)
1203 (home-page "https://bioconductor.org/packages/BiocGenerics")
1204 (synopsis "S4 generic functions for Bioconductor")
1205 (description
1206 "This package provides S4 generic functions needed by many Bioconductor
1207packages.")
1208 (license license:artistic2.0)))
1209
5cf940de
RW
1210(define-public r-affycomp
1211 (package
1212 (name "r-affycomp")
c472549f 1213 (version "1.66.0")
5cf940de
RW
1214 (source
1215 (origin
1216 (method url-fetch)
1217 (uri (bioconductor-uri "affycomp" version))
1218 (sha256
1219 (base32
c472549f 1220 "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
5cf940de
RW
1221 (properties `((upstream-name . "affycomp")))
1222 (build-system r-build-system)
1223 (propagated-inputs `(("r-biobase" ,r-biobase)))
1224 (home-page "https://bioconductor.org/packages/affycomp/")
1225 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1226 (description
1227 "The package contains functions that can be used to compare expression
1228measures for Affymetrix Oligonucleotide Arrays.")
1229 (license license:gpl2+)))
1230
5094aa94
RW
1231(define-public r-affycompatible
1232 (package
1233 (name "r-affycompatible")
fa2d16cc 1234 (version "1.50.0")
5094aa94
RW
1235 (source
1236 (origin
1237 (method url-fetch)
1238 (uri (bioconductor-uri "AffyCompatible" version))
1239 (sha256
1240 (base32
fa2d16cc 1241 "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
5094aa94
RW
1242 (properties
1243 `((upstream-name . "AffyCompatible")))
1244 (build-system r-build-system)
1245 (propagated-inputs
1246 `(("r-biostrings" ,r-biostrings)
1247 ("r-rcurl" ,r-rcurl)
1248 ("r-xml" ,r-xml)))
1249 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1250 (synopsis "Work with Affymetrix GeneChip files")
1251 (description
1252 "This package provides an interface to Affymetrix chip annotation and
1253sample attribute files. The package allows an easy way for users to download
1254and manage local data bases of Affynmetrix NetAffx annotation files. It also
1255provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1256Command Console} (AGCC)-compatible sample annotation files.")
1257 (license license:artistic2.0)))
1258
4ca2d6c1
RW
1259(define-public r-affycontam
1260 (package
1261 (name "r-affycontam")
3e82f9cc 1262 (version "1.48.0")
4ca2d6c1
RW
1263 (source
1264 (origin
1265 (method url-fetch)
1266 (uri (bioconductor-uri "affyContam" version))
1267 (sha256
1268 (base32
3e82f9cc 1269 "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
4ca2d6c1
RW
1270 (properties `((upstream-name . "affyContam")))
1271 (build-system r-build-system)
1272 (propagated-inputs
1273 `(("r-affy" ,r-affy)
1274 ("r-affydata" ,r-affydata)
1275 ("r-biobase" ,r-biobase)))
1276 (home-page "https://bioconductor.org/packages/affyContam/")
1277 (synopsis "Structured corruption of Affymetrix CEL file data")
1278 (description
1279 "Microarray quality assessment is a major concern of microarray analysts.
1280This package provides some simple approaches to in silico creation of quality
1281problems in CEL-level data to help evaluate performance of quality metrics.")
1282 (license license:artistic2.0)))
1283
12105c6c
RW
1284(define-public r-affycoretools
1285 (package
1286 (name "r-affycoretools")
a92219b4 1287 (version "1.62.0")
12105c6c
RW
1288 (source
1289 (origin
1290 (method url-fetch)
1291 (uri (bioconductor-uri "affycoretools" version))
1292 (sha256
1293 (base32
a92219b4 1294 "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
12105c6c
RW
1295 (properties `((upstream-name . "affycoretools")))
1296 (build-system r-build-system)
1297 (propagated-inputs
1298 `(("r-affy" ,r-affy)
1299 ("r-annotationdbi" ,r-annotationdbi)
1300 ("r-biobase" ,r-biobase)
1301 ("r-biocgenerics" ,r-biocgenerics)
1302 ("r-dbi" ,r-dbi)
1303 ("r-edger" ,r-edger)
1304 ("r-gcrma" ,r-gcrma)
f8f181ae 1305 ("r-glimma" ,r-glimma)
12105c6c
RW
1306 ("r-ggplot2" ,r-ggplot2)
1307 ("r-gostats" ,r-gostats)
1308 ("r-gplots" ,r-gplots)
1309 ("r-hwriter" ,r-hwriter)
1310 ("r-lattice" ,r-lattice)
1311 ("r-limma" ,r-limma)
1312 ("r-oligoclasses" ,r-oligoclasses)
1313 ("r-reportingtools" ,r-reportingtools)
1314 ("r-rsqlite" ,r-rsqlite)
1315 ("r-s4vectors" ,r-s4vectors)
1316 ("r-xtable" ,r-xtable)))
fa610697
RW
1317 (native-inputs
1318 `(("r-knitr" ,r-knitr)))
12105c6c
RW
1319 (home-page "https://bioconductor.org/packages/affycoretools/")
1320 (synopsis "Functions for analyses with Affymetrix GeneChips")
1321 (description
1322 "This package provides various wrapper functions that have been written
1323to streamline the more common analyses that a Biostatistician might see.")
1324 (license license:artistic2.0)))
1325
d6a5d9b2
RW
1326(define-public r-affxparser
1327 (package
1328 (name "r-affxparser")
8e6a2c32 1329 (version "1.62.0")
d6a5d9b2
RW
1330 (source
1331 (origin
1332 (method url-fetch)
1333 (uri (bioconductor-uri "affxparser" version))
1334 (sha256
1335 (base32
8e6a2c32 1336 "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
d6a5d9b2
RW
1337 (properties `((upstream-name . "affxparser")))
1338 (build-system r-build-system)
1339 (home-page "https://github.com/HenrikBengtsson/affxparser")
1340 (synopsis "Affymetrix File Parsing SDK")
1341 (description
1342 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1343BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1344files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1345are supported. Currently, there are methods for reading @dfn{chip definition
1346file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1347either in full or in part. For example, probe signals from a few probesets
1348can be extracted very quickly from a set of CEL files into a convenient list
1349structure.")
1350 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1351 ;; under LGPLv2+.
1352 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1353
7097c700
RW
1354(define-public r-annotate
1355 (package
1356 (name "r-annotate")
7d563023 1357 (version "1.68.0")
7097c700
RW
1358 (source
1359 (origin
1360 (method url-fetch)
1361 (uri (bioconductor-uri "annotate" version))
1362 (sha256
1363 (base32
7d563023 1364 "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
7097c700
RW
1365 (build-system r-build-system)
1366 (propagated-inputs
1367 `(("r-annotationdbi" ,r-annotationdbi)
1368 ("r-biobase" ,r-biobase)
1369 ("r-biocgenerics" ,r-biocgenerics)
1370 ("r-dbi" ,r-dbi)
7d563023 1371 ("r-httr" ,r-httr)
7097c700
RW
1372 ("r-xml" ,r-xml)
1373 ("r-xtable" ,r-xtable)))
1374 (home-page
1375 "https://bioconductor.org/packages/annotate")
1376 (synopsis "Annotation for microarrays")
1377 (description "This package provides R environments for the annotation of
1378microarrays.")
1379 (license license:artistic2.0)))
1380
fa596599
RW
1381(define-public r-hpar
1382 (package
1383 (name "r-hpar")
fa7578b3 1384 (version "1.32.1")
fa596599
RW
1385 (source
1386 (origin
1387 (method url-fetch)
1388 (uri (bioconductor-uri "hpar" version))
1389 (sha256
1390 (base32
fa7578b3 1391 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
fa596599 1392 (build-system r-build-system)
07bea010
RW
1393 (native-inputs
1394 `(("r-knitr" ,r-knitr)))
fa596599
RW
1395 (home-page "https://bioconductor.org/packages/hpar/")
1396 (synopsis "Human Protein Atlas in R")
1397 (description "This package provides a simple interface to and data from
1398the Human Protein Atlas project.")
1399 (license license:artistic2.0)))
183ce988
RJ
1400
1401(define-public r-regioner
1402 (package
1403 (name "r-regioner")
d1ff3604 1404 (version "1.22.0")
183ce988
RJ
1405 (source
1406 (origin
1407 (method url-fetch)
1408 (uri (bioconductor-uri "regioneR" version))
1409 (sha256
1410 (base32
d1ff3604 1411 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
183ce988
RJ
1412 (properties `((upstream-name . "regioneR")))
1413 (build-system r-build-system)
1414 (propagated-inputs
d639d888 1415 `(("r-biostrings" ,r-biostrings)
183ce988 1416 ("r-bsgenome" ,r-bsgenome)
183ce988 1417 ("r-genomeinfodb" ,r-genomeinfodb)
d639d888 1418 ("r-genomicranges" ,r-genomicranges)
72427c72 1419 ("r-iranges" ,r-iranges)
d639d888
RW
1420 ("r-memoise" ,r-memoise)
1421 ("r-rtracklayer" ,r-rtracklayer)
72427c72 1422 ("r-s4vectors" ,r-s4vectors)))
7f34dd58
RW
1423 (native-inputs
1424 `(("r-knitr" ,r-knitr)))
183ce988
RJ
1425 (home-page "https://bioconductor.org/packages/regioneR/")
1426 (synopsis "Association analysis of genomic regions")
1427 (description "This package offers a statistical framework based on
1428customizable permutation tests to assess the association between genomic
1429region sets and other genomic features.")
1430 (license license:artistic2.0)))
a5b56a53 1431
15184fb3
RW
1432(define-public r-reportingtools
1433 (package
1434 (name "r-reportingtools")
c03c7634 1435 (version "2.30.0")
15184fb3
RW
1436 (source
1437 (origin
1438 (method url-fetch)
1439 (uri (bioconductor-uri "ReportingTools" version))
1440 (sha256
1441 (base32
c03c7634 1442 "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31"))))
15184fb3
RW
1443 (properties
1444 `((upstream-name . "ReportingTools")))
1445 (build-system r-build-system)
1446 (propagated-inputs
1447 `(("r-annotate" ,r-annotate)
1448 ("r-annotationdbi" ,r-annotationdbi)
1449 ("r-biobase" ,r-biobase)
1450 ("r-biocgenerics" ,r-biocgenerics)
1451 ("r-category" ,r-category)
1452 ("r-deseq2" ,r-deseq2)
1453 ("r-edger" ,r-edger)
1454 ("r-ggbio" ,r-ggbio)
1455 ("r-ggplot2" ,r-ggplot2)
1456 ("r-gostats" ,r-gostats)
1457 ("r-gseabase" ,r-gseabase)
1458 ("r-hwriter" ,r-hwriter)
1459 ("r-iranges" ,r-iranges)
1460 ("r-knitr" ,r-knitr)
1461 ("r-lattice" ,r-lattice)
1462 ("r-limma" ,r-limma)
1463 ("r-pfam-db" ,r-pfam-db)
1464 ("r-r-utils" ,r-r-utils)
1465 ("r-xml" ,r-xml)))
7f94cf01
RW
1466 (native-inputs
1467 `(("r-knitr" ,r-knitr)))
15184fb3
RW
1468 (home-page "https://bioconductor.org/packages/ReportingTools/")
1469 (synopsis "Tools for making reports in various formats")
1470 (description
1471 "The ReportingTools package enables users to easily display reports of
1472analysis results generated from sources such as microarray and sequencing
1473data. The package allows users to create HTML pages that may be viewed on a
1474web browser, or in other formats. Users can generate tables with sortable and
1475filterable columns, make and display plots, and link table entries to other
1476data sources such as NCBI or larger plots within the HTML page. Using the
1477package, users can also produce a table of contents page to link various
1478reports together for a particular project that can be viewed in a web
1479browser.")
1480 (license license:artistic2.0)))
1481
bfb93b48
RW
1482(define-public r-geneplotter
1483 (package
1484 (name "r-geneplotter")
d72c4c98 1485 (version "1.68.0")
bfb93b48
RW
1486 (source
1487 (origin
1488 (method url-fetch)
1489 (uri (bioconductor-uri "geneplotter" version))
1490 (sha256
1491 (base32
d72c4c98 1492 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
bfb93b48
RW
1493 (build-system r-build-system)
1494 (propagated-inputs
1495 `(("r-annotate" ,r-annotate)
1496 ("r-annotationdbi" ,r-annotationdbi)
1497 ("r-biobase" ,r-biobase)
1498 ("r-biocgenerics" ,r-biocgenerics)
1499 ("r-lattice" ,r-lattice)
1500 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1501 (home-page "https://bioconductor.org/packages/geneplotter")
1502 (synopsis "Graphics functions for genomic data")
1503 (description
1504 "This package provides functions for plotting genomic data.")
1505 (license license:artistic2.0)))
1506
01c7ba99
RW
1507(define-public r-oligoclasses
1508 (package
1509 (name "r-oligoclasses")
464df5cc 1510 (version "1.52.0")
01c7ba99
RW
1511 (source
1512 (origin
1513 (method url-fetch)
1514 (uri (bioconductor-uri "oligoClasses" version))
1515 (sha256
1516 (base32
464df5cc 1517 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
01c7ba99
RW
1518 (properties `((upstream-name . "oligoClasses")))
1519 (build-system r-build-system)
1520 (propagated-inputs
1521 `(("r-affyio" ,r-affyio)
1522 ("r-biobase" ,r-biobase)
1523 ("r-biocgenerics" ,r-biocgenerics)
1524 ("r-biocmanager" ,r-biocmanager)
1525 ("r-biostrings" ,r-biostrings)
1526 ("r-dbi" ,r-dbi)
1527 ("r-ff" ,r-ff)
1528 ("r-foreach" ,r-foreach)
1529 ("r-genomicranges" ,r-genomicranges)
1530 ("r-iranges" ,r-iranges)
1531 ("r-rsqlite" ,r-rsqlite)
1532 ("r-s4vectors" ,r-s4vectors)
1533 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1534 (home-page "https://bioconductor.org/packages/oligoClasses/")
1535 (synopsis "Classes for high-throughput arrays")
1536 (description
1537 "This package contains class definitions, validity checks, and
1538initialization methods for classes used by the @code{oligo} and @code{crlmm}
1539packages.")
1540 (license license:gpl2+)))
1541
4c63eeb8
RW
1542(define-public r-oligo
1543 (package
1544 (name "r-oligo")
9af6fdf8 1545 (version "1.54.1")
4c63eeb8
RW
1546 (source
1547 (origin
1548 (method url-fetch)
1549 (uri (bioconductor-uri "oligo" version))
1550 (sha256
1551 (base32
9af6fdf8 1552 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
4c63eeb8
RW
1553 (properties `((upstream-name . "oligo")))
1554 (build-system r-build-system)
1555 (inputs `(("zlib" ,zlib)))
1556 (propagated-inputs
1557 `(("r-affxparser" ,r-affxparser)
1558 ("r-affyio" ,r-affyio)
1559 ("r-biobase" ,r-biobase)
1560 ("r-biocgenerics" ,r-biocgenerics)
1561 ("r-biostrings" ,r-biostrings)
1562 ("r-dbi" ,r-dbi)
1563 ("r-ff" ,r-ff)
1564 ("r-oligoclasses" ,r-oligoclasses)
1565 ("r-preprocesscore" ,r-preprocesscore)
1566 ("r-rsqlite" ,r-rsqlite)
1567 ("r-zlibbioc" ,r-zlibbioc)))
ace82f80
RW
1568 (native-inputs
1569 `(("r-knitr" ,r-knitr)))
4c63eeb8
RW
1570 (home-page "https://bioconductor.org/packages/oligo/")
1571 (synopsis "Preprocessing tools for oligonucleotide arrays")
1572 (description
1573 "This package provides a package to analyze oligonucleotide
1574arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1575Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1576 (license license:lgpl2.0+)))
1577
4dc2ecc2
RW
1578(define-public r-qvalue
1579 (package
1580 (name "r-qvalue")
e9b60a29 1581 (version "2.22.0")
4dc2ecc2
RW
1582 (source
1583 (origin
1584 (method url-fetch)
1585 (uri (bioconductor-uri "qvalue" version))
1586 (sha256
1587 (base32
e9b60a29 1588 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
4dc2ecc2
RW
1589 (build-system r-build-system)
1590 (propagated-inputs
1591 `(("r-ggplot2" ,r-ggplot2)
1592 ("r-reshape2" ,r-reshape2)))
f9a24759
RW
1593 (native-inputs
1594 `(("r-knitr" ,r-knitr)))
702a1012 1595 (home-page "https://github.com/StoreyLab/qvalue")
4dc2ecc2
RW
1596 (synopsis "Q-value estimation for false discovery rate control")
1597 (description
1598 "This package takes a list of p-values resulting from the simultaneous
1599testing of many hypotheses and estimates their q-values and local @dfn{false
1600discovery rate} (FDR) values. The q-value of a test measures the proportion
1601of false positives incurred when that particular test is called significant.
1602The local FDR measures the posterior probability the null hypothesis is true
1603given the test's p-value. Various plots are automatically generated, allowing
1604one to make sensible significance cut-offs. The software can be applied to
1605problems in genomics, brain imaging, astrophysics, and data mining.")
1606 ;; Any version of the LGPL.
1607 (license license:lgpl3+)))
1608
a0df9b93
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1609(define r-rcppnumerical
1610 (package
1611 (name "r-rcppnumerical")
1612 (version "0.4-0")
1613 (source (origin
1614 (method url-fetch)
1615 (uri (cran-uri "RcppNumerical" version))
1616 (sha256
1617 (base32
1618 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
1619 (properties `((upstream-name . "RcppNumerical")))
1620 (build-system r-build-system)
1621 (propagated-inputs
1622 `(("r-rcpp" ,r-rcpp)
1623 ("r-rcppeigen" ,r-rcppeigen)))
1624 (native-inputs
1625 `(("r-knitr" ,r-knitr)))
1626 (home-page "https://github.com/yixuan/RcppNumerical")
1627 (synopsis "Rcpp integration for numerical computing libraries")
1628 (description "This package provides a collection of open source libraries
1629for numerical computing (numerical integration, optimization, etc.) and their
1630integration with @code{Rcpp}.")
1631 (license license:gpl2+)))
1632
3b399e51
RJ
1633(define-public r-apeglm
1634 (package
1635 (name "r-apeglm")
1636 (version "1.12.0")
1637 (source (origin
1638 (method url-fetch)
1639 (uri (bioconductor-uri "apeglm" version))
1640 (sha256
1641 (base32
1642 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
1643 (properties `((upstream-name . "apeglm")))
1644 (build-system r-build-system)
1645 (propagated-inputs
1646 `(("r-emdbook" ,r-emdbook)
1647 ("r-genomicranges" ,r-genomicranges)
1648 ("r-rcpp" ,r-rcpp)
1649 ("r-rcppeigen" ,r-rcppeigen)
1650 ("r-rcppnumerical" ,r-rcppnumerical)
1651 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1652 (native-inputs `(("r-knitr" ,r-knitr)))
1653 (home-page "https://bioconductor.org/packages/apeglm")
1654 (synopsis "Approximate posterior estimation for GLM coefficients")
1655 (description "This package provides Bayesian shrinkage estimators for
1656effect sizes for a variety of GLM models, using approximation of the
1657posterior for individual coefficients.")
1658 (license license:gpl2)))
1659
6e396c4b
RJ
1660(define-public r-greylistchip
1661 (package
1662 (name "r-greylistchip")
1663 (version "1.22.0")
1664 (source (origin
1665 (method url-fetch)
1666 (uri (bioconductor-uri "GreyListChIP" version))
1667 (sha256
1668 (base32
1669 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
1670 (properties `((upstream-name . "GreyListChIP")))
1671 (build-system r-build-system)
1672 (propagated-inputs
1673 `(("r-bsgenome" ,r-bsgenome)
1674 ("r-genomeinfodb" ,r-genomeinfodb)
1675 ("r-genomicalignments" ,r-genomicalignments)
1676 ("r-genomicranges" ,r-genomicranges)
1677 ("r-mass" ,r-mass)
1678 ("r-rsamtools" ,r-rsamtools)
1679 ("r-rtracklayer" ,r-rtracklayer)
1680 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1681 (home-page "https://bioconductor.org/packages/GreyListChIP")
1682 (synopsis "Greylist artefact regions based on ChIP inputs")
1683 (description "This package identifies regions of ChIP experiments with high
1684signal in the input, that lead to spurious peaks during peak calling.")
1685 (license license:artistic2.0)))
1686
a5b56a53
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1687(define-public r-diffbind
1688 (package
1689 (name "r-diffbind")
341ebaaa 1690 (version "3.0.7")
a5b56a53
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1691 (source
1692 (origin
1693 (method url-fetch)
1694 (uri (bioconductor-uri "DiffBind" version))
1695 (sha256
1696 (base32
341ebaaa 1697 "0irhqsi6rrkrkc7dhwmfpqfd0mnigs17027czcx8vgbrbra4lcvd"))))
a5b56a53
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1698 (properties `((upstream-name . "DiffBind")))
1699 (build-system r-build-system)
1700 (inputs
1701 `(("zlib" ,zlib)))
1702 (propagated-inputs
1703 `(("r-amap" ,r-amap)
341ebaaa
RJ
1704 ("r-apeglm" ,r-apeglm)
1705 ("r-ashr" ,r-ashr)
a5b56a53
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1706 ("r-biocparallel" ,r-biocparallel)
1707 ("r-deseq2" ,r-deseq2)
1708 ("r-dplyr" ,r-dplyr)
a5b56a53 1709 ("r-genomicalignments" ,r-genomicalignments)
45bbccf4
RW
1710 ("r-genomicranges" ,r-genomicranges)
1711 ("r-ggplot2" ,r-ggplot2)
a5b56a53
RJ
1712 ("r-ggrepel" ,r-ggrepel)
1713 ("r-gplots" ,r-gplots)
341ebaaa 1714 ("r-greylistchip" ,r-greylistchip)
a5b56a53
RJ
1715 ("r-iranges" ,r-iranges)
1716 ("r-lattice" ,r-lattice)
1717 ("r-limma" ,r-limma)
1718 ("r-locfit" ,r-locfit)
1719 ("r-rcolorbrewer" , r-rcolorbrewer)
1720 ("r-rcpp" ,r-rcpp)
4c221b3b 1721 ("r-rhtslib" ,r-rhtslib)
a5b56a53
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1722 ("r-rsamtools" ,r-rsamtools)
1723 ("r-s4vectors" ,r-s4vectors)
45bbccf4 1724 ("r-summarizedexperiment" ,r-summarizedexperiment)
4c221b3b 1725 ("r-systempiper" ,r-systempiper)))
99db6db7 1726 (home-page "https://bioconductor.org/packages/DiffBind")
a5b56a53
RJ
1727 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1728 (description
1729 "This package computes differentially bound sites from multiple
1730ChIP-seq experiments using affinity (quantitative) data. Also enables
1731occupancy (overlap) analysis and plotting functions.")
1732 (license license:artistic2.0)))
6d94bf6b
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1733
1734(define-public r-ripseeker
1735 (package
1736 (name "r-ripseeker")
ba74434f 1737 (version "1.26.0")
6d94bf6b
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1738 (source
1739 (origin
1740 (method url-fetch)
1741 (uri (bioconductor-uri "RIPSeeker" version))
1742 (sha256
1743 (base32
ba74434f 1744 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
6d94bf6b
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1745 (properties `((upstream-name . "RIPSeeker")))
1746 (build-system r-build-system)
1747 (propagated-inputs
1748 `(("r-s4vectors" ,r-s4vectors)
1749 ("r-iranges" ,r-iranges)
1750 ("r-genomicranges" ,r-genomicranges)
1751 ("r-summarizedexperiment" ,r-summarizedexperiment)
1752 ("r-rsamtools" ,r-rsamtools)
1753 ("r-genomicalignments" ,r-genomicalignments)
1754 ("r-rtracklayer" ,r-rtracklayer)))
99db6db7 1755 (home-page "https://bioconductor.org/packages/RIPSeeker")
6d94bf6b
RJ
1756 (synopsis
1757 "Identifying protein-associated transcripts from RIP-seq experiments")
1758 (description
1759 "This package infers and discriminates RIP peaks from RIP-seq alignments
1760using two-state HMM with negative binomial emission probability. While
1761RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1762a suite of bioinformatics tools integrated within this self-contained software
1763package comprehensively addressing issues ranging from post-alignments
1764processing to visualization and annotation.")
1765 (license license:gpl2)))
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1766
1767(define-public r-multtest
1768 (package
1769 (name "r-multtest")
1e6920c5 1770 (version "2.46.0")
a6ae9ffd
RJ
1771 (source
1772 (origin
1773 (method url-fetch)
1774 (uri (bioconductor-uri "multtest" version))
1775 (sha256
1776 (base32
1e6920c5 1777 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
a6ae9ffd
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1778 (build-system r-build-system)
1779 (propagated-inputs
1780 `(("r-survival" ,r-survival)
1781 ("r-biocgenerics" ,r-biocgenerics)
1782 ("r-biobase" ,r-biobase)
1783 ("r-mass" ,r-mass)))
99db6db7 1784 (home-page "https://bioconductor.org/packages/multtest")
a6ae9ffd
RJ
1785 (synopsis "Resampling-based multiple hypothesis testing")
1786 (description
1787 "This package can do non-parametric bootstrap and permutation
1788resampling-based multiple testing procedures (including empirical Bayes
1789methods) for controlling the family-wise error rate (FWER), generalized
1790family-wise error rate (gFWER), tail probability of the proportion of
1791false positives (TPPFP), and false discovery rate (FDR). Several choices
1792of bootstrap-based null distribution are implemented (centered, centered
1793and scaled, quantile-transformed). Single-step and step-wise methods are
1794available. Tests based on a variety of T- and F-statistics (including
1795T-statistics based on regression parameters from linear and survival models
1796as well as those based on correlation parameters) are included. When probing
1797hypotheses with T-statistics, users may also select a potentially faster null
1798distribution which is multivariate normal with mean zero and variance
1799covariance matrix derived from the vector influence function. Results are
1800reported in terms of adjusted P-values, confidence regions and test statistic
1801cutoffs. The procedures are directly applicable to identifying differentially
1802expressed genes in DNA microarray experiments.")
1803 (license license:lgpl3)))
793f83ef 1804
5dfe4912
RW
1805(define-public r-graph
1806 (package
1807 (name "r-graph")
f519b4dc 1808 (version "1.68.0")
5dfe4912
RW
1809 (source (origin
1810 (method url-fetch)
1811 (uri (bioconductor-uri "graph" version))
1812 (sha256
1813 (base32
f519b4dc 1814 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
5dfe4912
RW
1815 (build-system r-build-system)
1816 (propagated-inputs
1817 `(("r-biocgenerics" ,r-biocgenerics)))
1818 (home-page "https://bioconductor.org/packages/graph")
1819 (synopsis "Handle graph data structures in R")
1820 (description
1821 "This package implements some simple graph handling capabilities for R.")
1822 (license license:artistic2.0)))
1823
8017eb0a
RW
1824;; This is a CRAN package, but it depends on a Bioconductor package.
1825(define-public r-ggm
1826 (package
1827 (name "r-ggm")
1828 (version "2.5")
1829 (source
1830 (origin
1831 (method url-fetch)
1832 (uri (cran-uri "ggm" version))
1833 (sha256
1834 (base32
1835 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1836 (properties `((upstream-name . "ggm")))
1837 (build-system r-build-system)
1838 (propagated-inputs
1839 `(("r-graph" ,r-graph)
1840 ("r-igraph" ,r-igraph)))
1841 (home-page "https://cran.r-project.org/package=ggm")
1842 (synopsis "Functions for graphical Markov models")
1843 (description
1844 "This package provides functions and datasets for maximum likelihood
1845fitting of some classes of graphical Markov models.")
1846 (license license:gpl2+)))
1847
a07717cc
RW
1848;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
1849(define-public r-perfmeas
1850 (package
1851 (name "r-perfmeas")
1852 (version "1.2.1")
1853 (source
1854 (origin
1855 (method url-fetch)
1856 (uri (cran-uri "PerfMeas" version))
1857 (sha256
1858 (base32
1859 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
1860 (properties `((upstream-name . "PerfMeas")))
1861 (build-system r-build-system)
1862 (propagated-inputs
1863 `(("r-graph" ,r-graph)
1864 ("r-limma" ,r-limma)
1865 ("r-rbgl" ,r-rbgl)))
1866 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
1867 (synopsis "Performance measures for ranking and classification tasks")
1868 (description
1869 "This package implements different performance measures for
1870classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
1871a given recall, F-score for single and multiple classes are available.")
1872 (license license:gpl2+)))
1873
b17ace24 1874;; This is a CRAN package, but it depends on a Bioconductor package.
a207bca2
RW
1875(define-public r-codedepends
1876 (package
1877 (name "r-codedepends")
1878 (version "0.6.5")
1879 (source
1880 (origin
1881 (method url-fetch)
1882 (uri (cran-uri "CodeDepends" version))
1883 (sha256
1884 (base32
1885 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1886 (properties `((upstream-name . "CodeDepends")))
1887 (build-system r-build-system)
1888 (propagated-inputs
1889 `(("r-codetools" ,r-codetools)
1890 ("r-graph" ,r-graph)
1891 ("r-xml" ,r-xml)))
5e1f2362 1892 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
a207bca2
RW
1893 (synopsis "Analysis of R code for reproducible research and code comprehension")
1894 (description
1895 "This package provides tools for analyzing R expressions or blocks of
1896code and determining the dependencies between them. It focuses on R scripts,
1897but can be used on the bodies of functions. There are many facilities
1898including the ability to summarize or get a high-level view of code,
1899determining dependencies between variables, code improvement suggestions.")
1900 ;; Any version of the GPL
1901 (license (list license:gpl2+ license:gpl3+))))
1902
793f83ef
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1903(define-public r-chippeakanno
1904 (package
1905 (name "r-chippeakanno")
d068d967 1906 (version "3.24.1")
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1907 (source
1908 (origin
1909 (method url-fetch)
1910 (uri (bioconductor-uri "ChIPpeakAnno" version))
1911 (sha256
1912 (base32
d068d967 1913 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
793f83ef
RJ
1914 (properties `((upstream-name . "ChIPpeakAnno")))
1915 (build-system r-build-system)
1916 (propagated-inputs
85c1d20f 1917 `(("r-annotationdbi" ,r-annotationdbi)
85c1d20f 1918 ("r-biocgenerics" ,r-biocgenerics)
793f83ef 1919 ("r-biomart" ,r-biomart)
85c1d20f 1920 ("r-biostrings" ,r-biostrings)
85c1d20f 1921 ("r-dbi" ,r-dbi)
85c1d20f
RW
1922 ("r-ensembldb" ,r-ensembldb)
1923 ("r-genomeinfodb" ,r-genomeinfodb)
1924 ("r-genomicalignments" ,r-genomicalignments)
793f83ef 1925 ("r-genomicfeatures" ,r-genomicfeatures)
f794e85d 1926 ("r-genomicranges" ,r-genomicranges)
d068d967 1927 ("r-ggplot2" ,r-ggplot2)
85c1d20f 1928 ("r-graph" ,r-graph)
f794e85d 1929 ("r-iranges" ,r-iranges)
d068d967 1930 ("r-keggrest" ,r-keggrest)
85c1d20f 1931 ("r-matrixstats" ,r-matrixstats)
793f83ef
RJ
1932 ("r-multtest" ,r-multtest)
1933 ("r-rbgl" ,r-rbgl)
793f83ef 1934 ("r-regioner" ,r-regioner)
85c1d20f
RW
1935 ("r-rsamtools" ,r-rsamtools)
1936 ("r-rtracklayer" ,r-rtracklayer)
f794e85d 1937 ("r-s4vectors" ,r-s4vectors)
793f83ef 1938 ("r-summarizedexperiment" ,r-summarizedexperiment)
793f83ef 1939 ("r-venndiagram" ,r-venndiagram)))
dc24de46
RW
1940 (native-inputs
1941 `(("r-knitr" ,r-knitr)))
99db6db7 1942 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
793f83ef
RJ
1943 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1944 (description
1945 "The package includes functions to retrieve the sequences around the peak,
1946obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1947custom features such as most conserved elements and other transcription factor
1948binding sites supplied by users. Starting 2.0.5, new functions have been added
1949for finding the peaks with bi-directional promoters with summary statistics
1950(peaksNearBDP), for summarizing the occurrence of motifs in peaks
1951(summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1952enrichedGO (addGeneIDs).")
1953 (license license:gpl2+)))
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RJ
1954
1955(define-public r-marray
1956 (package
1957 (name "r-marray")
6e6c6272 1958 (version "1.68.0")
164502d8
RJ
1959 (source (origin
1960 (method url-fetch)
1961 (uri (bioconductor-uri "marray" version))
1962 (sha256
6e6c6272 1963 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
164502d8
RJ
1964 (build-system r-build-system)
1965 (propagated-inputs
67487088 1966 `(("r-limma" ,r-limma)))
99db6db7 1967 (home-page "https://bioconductor.org/packages/marray")
164502d8
RJ
1968 (synopsis "Exploratory analysis for two-color spotted microarray data")
1969 (description "This package contains class definitions for two-color spotted
ab8979fc 1970microarray data. It also includes functions for data input, diagnostic plots,
164502d8
RJ
1971normalization and quality checking.")
1972 (license license:lgpl2.0+)))
0416a0d4
RJ
1973
1974(define-public r-cghbase
1975 (package
1976 (name "r-cghbase")
ee052d05 1977 (version "1.50.0")
0416a0d4
RJ
1978 (source (origin
1979 (method url-fetch)
1980 (uri (bioconductor-uri "CGHbase" version))
1981 (sha256
ee052d05 1982 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
0416a0d4
RJ
1983 (properties `((upstream-name . "CGHbase")))
1984 (build-system r-build-system)
1985 (propagated-inputs
1986 `(("r-biobase" ,r-biobase)
1987 ("r-marray" ,r-marray)))
99db6db7 1988 (home-page "https://bioconductor.org/packages/CGHbase")
0416a0d4
RJ
1989 (synopsis "Base functions and classes for arrayCGH data analysis")
1990 (description "This package contains functions and classes that are needed by
1991the @code{arrayCGH} packages.")
1992 (license license:gpl2+)))
67ee83d6
RJ
1993
1994(define-public r-cghcall
1995 (package
1996 (name "r-cghcall")
72400035 1997 (version "2.52.0")
67ee83d6
RJ
1998 (source (origin
1999 (method url-fetch)
2000 (uri (bioconductor-uri "CGHcall" version))
2001 (sha256
72400035 2002 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
67ee83d6
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2003 (properties `((upstream-name . "CGHcall")))
2004 (build-system r-build-system)
2005 (propagated-inputs
2006 `(("r-biobase" ,r-biobase)
2007 ("r-cghbase" ,r-cghbase)
2008 ("r-impute" ,r-impute)
2009 ("r-dnacopy" ,r-dnacopy)
2010 ("r-snowfall" ,r-snowfall)))
99db6db7 2011 (home-page "https://bioconductor.org/packages/CGHcall")
67ee83d6
RJ
2012 (synopsis "Base functions and classes for arrayCGH data analysis")
2013 (description "This package contains functions and classes that are needed by
2014@code{arrayCGH} packages.")
2015 (license license:gpl2+)))
0ef8cc9c
RJ
2016
2017(define-public r-qdnaseq
2018 (package
2019 (name "r-qdnaseq")
3b648409 2020 (version "1.26.0")
0ef8cc9c
RJ
2021 (source (origin
2022 (method url-fetch)
2023 (uri (bioconductor-uri "QDNAseq" version))
2024 (sha256
3b648409 2025 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
0ef8cc9c
RJ
2026 (properties `((upstream-name . "QDNAseq")))
2027 (build-system r-build-system)
2028 (propagated-inputs
2029 `(("r-biobase" ,r-biobase)
2030 ("r-cghbase" ,r-cghbase)
2031 ("r-cghcall" ,r-cghcall)
2032 ("r-dnacopy" ,r-dnacopy)
23ce5ad1
RW
2033 ("r-future" ,r-future)
2034 ("r-future-apply" ,r-future-apply)
0ef8cc9c
RJ
2035 ("r-genomicranges" ,r-genomicranges)
2036 ("r-iranges" ,r-iranges)
2037 ("r-matrixstats" ,r-matrixstats)
2038 ("r-r-utils" ,r-r-utils)
2039 ("r-rsamtools" ,r-rsamtools)))
99db6db7 2040 (home-page "https://bioconductor.org/packages/QDNAseq")
0ef8cc9c
RJ
2041 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
2042 (description "The genome is divided into non-overlapping fixed-sized bins,
2043number of sequence reads in each counted, adjusted with a simultaneous
2044two-dimensional loess correction for sequence mappability and GC content, and
2045filtered to remove spurious regions in the genome. Downstream steps of
2046segmentation and calling are also implemented via packages DNAcopy and CGHcall,
2047respectively.")
2048 (license license:gpl2+)))
bb15b581
RW
2049
2050(define-public r-bayseq
2051 (package
2052 (name "r-bayseq")
63572b0c 2053 (version "2.24.0")
bb15b581
RW
2054 (source
2055 (origin
2056 (method url-fetch)
2057 (uri (bioconductor-uri "baySeq" version))
2058 (sha256
2059 (base32
63572b0c 2060 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
bb15b581
RW
2061 (properties `((upstream-name . "baySeq")))
2062 (build-system r-build-system)
2063 (propagated-inputs
2064 `(("r-abind" ,r-abind)
2065 ("r-edger" ,r-edger)
2066 ("r-genomicranges" ,r-genomicranges)))
2067 (home-page "https://bioconductor.org/packages/baySeq/")
2068 (synopsis "Bayesian analysis of differential expression patterns in count data")
2069 (description
2070 "This package identifies differential expression in high-throughput count
2071data, such as that derived from next-generation sequencing machines,
2072calculating estimated posterior likelihoods of differential expression (or
2073more complex hypotheses) via empirical Bayesian methods.")
2074 (license license:gpl3)))
609f4ad1
RW
2075
2076(define-public r-chipcomp
2077 (package
2078 (name "r-chipcomp")
ef1d3231 2079 (version "1.18.0")
609f4ad1
RW
2080 (source
2081 (origin
2082 (method url-fetch)
2083 (uri (bioconductor-uri "ChIPComp" version))
2084 (sha256
2085 (base32
ef1d3231 2086 "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp"))))
609f4ad1
RW
2087 (properties `((upstream-name . "ChIPComp")))
2088 (build-system r-build-system)
2089 (propagated-inputs
2090 `(("r-biocgenerics" ,r-biocgenerics)
2091 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
2092 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
2093 ("r-genomeinfodb" ,r-genomeinfodb)
2094 ("r-genomicranges" ,r-genomicranges)
2095 ("r-iranges" ,r-iranges)
2096 ("r-limma" ,r-limma)
2097 ("r-rsamtools" ,r-rsamtools)
2098 ("r-rtracklayer" ,r-rtracklayer)
2099 ("r-s4vectors" ,r-s4vectors)))
2100 (home-page "https://bioconductor.org/packages/ChIPComp")
2101 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2102 (description
2103 "ChIPComp implements a statistical method for quantitative comparison of
2104multiple ChIP-seq datasets. It detects differentially bound sharp binding
2105sites across multiple conditions considering matching control in ChIP-seq
2106datasets.")
2107 ;; Any version of the GPL.
2108 (license license:gpl3+)))
0490f9de
RW
2109
2110(define-public r-riboprofiling
2111 (package
2112 (name "r-riboprofiling")
03b655c5 2113 (version "1.20.0")
0490f9de
RW
2114 (source
2115 (origin
2116 (method url-fetch)
2117 (uri (bioconductor-uri "RiboProfiling" version))
2118 (sha256
2119 (base32
03b655c5 2120 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
0490f9de
RW
2121 (properties `((upstream-name . "RiboProfiling")))
2122 (build-system r-build-system)
2123 (propagated-inputs
2124 `(("r-biocgenerics" ,r-biocgenerics)
2125 ("r-biostrings" ,r-biostrings)
2126 ("r-data-table" ,r-data-table)
2127 ("r-genomeinfodb" ,r-genomeinfodb)
2128 ("r-genomicalignments" ,r-genomicalignments)
2129 ("r-genomicfeatures" ,r-genomicfeatures)
2130 ("r-genomicranges" ,r-genomicranges)
2131 ("r-ggbio" ,r-ggbio)
2132 ("r-ggplot2" ,r-ggplot2)
2133 ("r-iranges" ,r-iranges)
2134 ("r-plyr" ,r-plyr)
2135 ("r-reshape2" ,r-reshape2)
2136 ("r-rsamtools" ,r-rsamtools)
2137 ("r-rtracklayer" ,r-rtracklayer)
2138 ("r-s4vectors" ,r-s4vectors)
2139 ("r-sqldf" ,r-sqldf)))
7aae05a9
RW
2140 (native-inputs
2141 `(("r-knitr" ,r-knitr)))
0490f9de
RW
2142 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2143 (synopsis "Ribosome profiling data analysis")
2144 (description "Starting with a BAM file, this package provides the
2145necessary functions for quality assessment, read start position recalibration,
2146the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2147of count data: pairs, log fold-change, codon frequency and coverage
2148assessment, principal component analysis on codon coverage.")
2149 (license license:gpl3)))
6ffdfe6a
RW
2150
2151(define-public r-riboseqr
2152 (package
2153 (name "r-riboseqr")
3813c9fe 2154 (version "1.24.0")
6ffdfe6a
RW
2155 (source
2156 (origin
2157 (method url-fetch)
2158 (uri (bioconductor-uri "riboSeqR" version))
2159 (sha256
2160 (base32
3813c9fe 2161 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
6ffdfe6a
RW
2162 (properties `((upstream-name . "riboSeqR")))
2163 (build-system r-build-system)
2164 (propagated-inputs
2165 `(("r-abind" ,r-abind)
2166 ("r-bayseq" ,r-bayseq)
2167 ("r-genomeinfodb" ,r-genomeinfodb)
2168 ("r-genomicranges" ,r-genomicranges)
2169 ("r-iranges" ,r-iranges)
2170 ("r-rsamtools" ,r-rsamtools)
2171 ("r-seqlogo" ,r-seqlogo)))
2172 (home-page "https://bioconductor.org/packages/riboSeqR/")
2173 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2174 (description
2175 "This package provides plotting functions, frameshift detection and
2176parsing of genetic sequencing data from ribosome profiling experiments.")
2177 (license license:gpl3)))
a32279ff
RW
2178
2179(define-public r-interactionset
2180 (package
2181 (name "r-interactionset")
861a903f 2182 (version "1.16.0")
a32279ff
RW
2183 (source
2184 (origin
2185 (method url-fetch)
2186 (uri (bioconductor-uri "InteractionSet" version))
2187 (sha256
2188 (base32
861a903f 2189 "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v"))))
a32279ff
RW
2190 (properties
2191 `((upstream-name . "InteractionSet")))
2192 (build-system r-build-system)
2193 (propagated-inputs
2194 `(("r-biocgenerics" ,r-biocgenerics)
2195 ("r-genomeinfodb" ,r-genomeinfodb)
2196 ("r-genomicranges" ,r-genomicranges)
2197 ("r-iranges" ,r-iranges)
2198 ("r-matrix" ,r-matrix)
2199 ("r-rcpp" ,r-rcpp)
2200 ("r-s4vectors" ,r-s4vectors)
2201 ("r-summarizedexperiment" ,r-summarizedexperiment)))
861a903f
RW
2202 (native-inputs
2203 `(("r-knitr" ,r-knitr)))
a32279ff
RW
2204 (home-page "https://bioconductor.org/packages/InteractionSet")
2205 (synopsis "Base classes for storing genomic interaction data")
2206 (description
02fe0976 2207 "This package provides the @code{GInteractions},
a32279ff
RW
2208@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2209for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2210experiments.")
2211 (license license:gpl3)))
cf9a29b2
RW
2212
2213(define-public r-genomicinteractions
2214 (package
2215 (name "r-genomicinteractions")
76dd036e 2216 (version "1.22.0")
cf9a29b2
RW
2217 (source
2218 (origin
2219 (method url-fetch)
2220 (uri (bioconductor-uri "GenomicInteractions" version))
2221 (sha256
2222 (base32
76dd036e 2223 "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy"))))
cf9a29b2
RW
2224 (properties
2225 `((upstream-name . "GenomicInteractions")))
2226 (build-system r-build-system)
2227 (propagated-inputs
2228 `(("r-biobase" ,r-biobase)
2229 ("r-biocgenerics" ,r-biocgenerics)
2230 ("r-data-table" ,r-data-table)
2231 ("r-dplyr" ,r-dplyr)
2232 ("r-genomeinfodb" ,r-genomeinfodb)
2233 ("r-genomicranges" ,r-genomicranges)
2234 ("r-ggplot2" ,r-ggplot2)
2235 ("r-gridextra" ,r-gridextra)
2236 ("r-gviz" ,r-gviz)
2237 ("r-igraph" ,r-igraph)
2238 ("r-interactionset" ,r-interactionset)
2239 ("r-iranges" ,r-iranges)
2240 ("r-rsamtools" ,r-rsamtools)
2241 ("r-rtracklayer" ,r-rtracklayer)
2242 ("r-s4vectors" ,r-s4vectors)
2243 ("r-stringr" ,r-stringr)))
81a37891
RW
2244 (native-inputs
2245 `(("r-knitr" ,r-knitr)))
cf9a29b2
RW
2246 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2247 (synopsis "R package for handling genomic interaction data")
2248 (description
2249 "This R package provides tools for handling genomic interaction data,
2250such as ChIA-PET/Hi-C, annotating genomic features with interaction
2251information and producing various plots and statistics.")
2252 (license license:gpl3)))
27c51606
RW
2253
2254(define-public r-ctc
2255 (package
2256 (name "r-ctc")
d27dfbf7 2257 (version "1.64.0")
27c51606
RW
2258 (source
2259 (origin
2260 (method url-fetch)
2261 (uri (bioconductor-uri "ctc" version))
2262 (sha256
2263 (base32
d27dfbf7 2264 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
27c51606
RW
2265 (build-system r-build-system)
2266 (propagated-inputs `(("r-amap" ,r-amap)))
2267 (home-page "https://bioconductor.org/packages/ctc/")
2268 (synopsis "Cluster and tree conversion")
2269 (description
2270 "This package provides tools for exporting and importing classification
2271trees and clusters to other programs.")
2272 (license license:gpl2)))
5da0e142
RW
2273
2274(define-public r-goseq
2275 (package
2276 (name "r-goseq")
c97bcfbd 2277 (version "1.42.0")
5da0e142
RW
2278 (source
2279 (origin
2280 (method url-fetch)
2281 (uri (bioconductor-uri "goseq" version))
2282 (sha256
2283 (base32
c97bcfbd 2284 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
5da0e142
RW
2285 (build-system r-build-system)
2286 (propagated-inputs
2287 `(("r-annotationdbi" ,r-annotationdbi)
2288 ("r-biasedurn" ,r-biasedurn)
2289 ("r-biocgenerics" ,r-biocgenerics)
2290 ("r-genelendatabase" ,r-genelendatabase)
2291 ("r-go-db" ,r-go-db)
2292 ("r-mgcv" ,r-mgcv)))
2293 (home-page "https://bioconductor.org/packages/goseq/")
2294 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2295 (description
2296 "This package provides tools to detect Gene Ontology and/or other user
2297defined categories which are over/under represented in RNA-seq data.")
2298 (license license:lgpl2.0+)))
f4235c0e
RW
2299
2300(define-public r-glimma
2301 (package
2302 (name "r-glimma")
3dab4570 2303 (version "2.0.0")
f4235c0e
RW
2304 (source
2305 (origin
2306 (method url-fetch)
2307 (uri (bioconductor-uri "Glimma" version))
2308 (sha256
2309 (base32
3dab4570 2310 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
f4235c0e
RW
2311 (properties `((upstream-name . "Glimma")))
2312 (build-system r-build-system)
2313 (propagated-inputs
3dab4570 2314 `(("r-deseq2" ,r-deseq2)
2315 ("r-edger" ,r-edger)
2316 ("r-htmlwidgets" ,r-htmlwidgets)
f4235c0e 2317 ("r-jsonlite" ,r-jsonlite)
3dab4570 2318 ("r-limma" ,r-limma)
2319 ("r-s4vectors" ,r-s4vectors)
2320 ("r-summarizedexperiment" ,r-summarizedexperiment)))
a6251d6e
RW
2321 (native-inputs
2322 `(("r-knitr" ,r-knitr)))
f4235c0e
RW
2323 (home-page "https://github.com/Shians/Glimma")
2324 (synopsis "Interactive HTML graphics")
2325 (description
2326 "This package generates interactive visualisations for analysis of
2327RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2328HTML page. The interactions are built on top of the popular static
2329representations of analysis results in order to provide additional
2330information.")
2331 (license license:lgpl3)))
aa388dc7
RW
2332
2333(define-public r-rots
2334 (package
2335 (name "r-rots")
0ef40b23 2336 (version "1.18.0")
aa388dc7
RW
2337 (source
2338 (origin
2339 (method url-fetch)
2340 (uri (bioconductor-uri "ROTS" version))
2341 (sha256
2342 (base32
0ef40b23 2343 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
aa388dc7
RW
2344 (properties `((upstream-name . "ROTS")))
2345 (build-system r-build-system)
2346 (propagated-inputs
2347 `(("r-biobase" ,r-biobase)
2348 ("r-rcpp" ,r-rcpp)))
2349 (home-page "https://bioconductor.org/packages/ROTS/")
2350 (synopsis "Reproducibility-Optimized Test Statistic")
2351 (description
2352 "This package provides tools for calculating the
2353@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2354in omics data.")
2355 (license license:gpl2+)))
b64ce4b7 2356
cad6fb2d
RW
2357(define-public r-plgem
2358 (package
2359 (name "r-plgem")
1c9bdfcf 2360 (version "1.62.0")
cad6fb2d
RW
2361 (source
2362 (origin
2363 (method url-fetch)
2364 (uri (bioconductor-uri "plgem" version))
2365 (sha256
2366 (base32
1c9bdfcf 2367 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
cad6fb2d
RW
2368 (build-system r-build-system)
2369 (propagated-inputs
2370 `(("r-biobase" ,r-biobase)
2371 ("r-mass" ,r-mass)))
2372 (home-page "http://www.genopolis.it")
2373 (synopsis "Detect differential expression in microarray and proteomics datasets")
2374 (description
2375 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2376model the variance-versus-mean dependence that exists in a variety of
2377genome-wide datasets, including microarray and proteomics data. The use of
2378PLGEM has been shown to improve the detection of differentially expressed
2379genes or proteins in these datasets.")
2380 (license license:gpl2)))
2381
b64ce4b7
RW
2382(define-public r-inspect
2383 (package
2384 (name "r-inspect")
41d6b41f 2385 (version "1.20.0")
b64ce4b7
RW
2386 (source
2387 (origin
2388 (method url-fetch)
2389 (uri (bioconductor-uri "INSPEcT" version))
2390 (sha256
2391 (base32
41d6b41f 2392 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
b64ce4b7
RW
2393 (properties `((upstream-name . "INSPEcT")))
2394 (build-system r-build-system)
2395 (propagated-inputs
2396 `(("r-biobase" ,r-biobase)
2397 ("r-biocgenerics" ,r-biocgenerics)
2398 ("r-biocparallel" ,r-biocparallel)
c86fc969 2399 ("r-deseq2" ,r-deseq2)
b64ce4b7 2400 ("r-desolve" ,r-desolve)
bd824de3 2401 ("r-gdata" ,r-gdata)
74bb4cdf 2402 ("r-genomeinfodb" ,r-genomeinfodb)
b64ce4b7
RW
2403 ("r-genomicalignments" ,r-genomicalignments)
2404 ("r-genomicfeatures" ,r-genomicfeatures)
2405 ("r-genomicranges" ,r-genomicranges)
2406 ("r-iranges" ,r-iranges)
74bb4cdf 2407 ("r-kernsmooth" ,r-kernsmooth)
c86fc969 2408 ("r-plgem" ,r-plgem)
b64ce4b7
RW
2409 ("r-proc" ,r-proc)
2410 ("r-rootsolve" ,r-rootsolve)
2411 ("r-rsamtools" ,r-rsamtools)
437bc4dd 2412 ("r-rtracklayer" ,r-rtracklayer)
c86fc969
RW
2413 ("r-s4vectors" ,r-s4vectors)
2414 ("r-shiny" ,r-shiny)
2415 ("r-summarizedexperiment" ,r-summarizedexperiment)
2416 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2417 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
437bc4dd
RW
2418 (native-inputs
2419 `(("r-knitr" ,r-knitr)))
b64ce4b7
RW
2420 (home-page "https://bioconductor.org/packages/INSPEcT")
2421 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2422 (description
2423 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2424Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2425order to evaluate synthesis, processing and degradation rates and assess via
2426modeling the rates that determines changes in mature mRNA levels.")
2427 (license license:gpl2)))
f6e99763
RW
2428
2429(define-public r-dnabarcodes
2430 (package
2431 (name "r-dnabarcodes")
874a774f 2432 (version "1.20.0")
f6e99763
RW
2433 (source
2434 (origin
2435 (method url-fetch)
2436 (uri (bioconductor-uri "DNABarcodes" version))
2437 (sha256
2438 (base32
874a774f 2439 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
f6e99763
RW
2440 (properties `((upstream-name . "DNABarcodes")))
2441 (build-system r-build-system)
2442 (propagated-inputs
2443 `(("r-bh" ,r-bh)
2444 ("r-matrix" ,r-matrix)
2445 ("r-rcpp" ,r-rcpp)))
14f40ae8
RW
2446 (native-inputs
2447 `(("r-knitr" ,r-knitr)))
f6e99763
RW
2448 (home-page "https://bioconductor.org/packages/DNABarcodes")
2449 (synopsis "Create and analyze DNA barcodes")
2450 (description
2451 "This package offers tools to create DNA barcode sets capable of
2452correcting insertion, deletion, and substitution errors. Existing barcodes
2453can be analyzed regarding their minimal, maximal and average distances between
2454barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2455demultiplexed, i.e. assigned to their original reference barcode.")
2456 (license license:gpl2)))
09aa3d06
RW
2457
2458(define-public r-ruvseq
2459 (package
2460 (name "r-ruvseq")
a55b1622 2461 (version "1.24.0")
09aa3d06
RW
2462 (source
2463 (origin
2464 (method url-fetch)
2465 (uri (bioconductor-uri "RUVSeq" version))
2466 (sha256
2467 (base32
a55b1622 2468 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
09aa3d06
RW
2469 (properties `((upstream-name . "RUVSeq")))
2470 (build-system r-build-system)
2471 (propagated-inputs
2472 `(("r-biobase" ,r-biobase)
2473 ("r-edaseq" ,r-edaseq)
2474 ("r-edger" ,r-edger)
2475 ("r-mass" ,r-mass)))
ae0fcaa6
RW
2476 (native-inputs
2477 `(("r-knitr" ,r-knitr)))
09aa3d06
RW
2478 (home-page "https://github.com/drisso/RUVSeq")
2479 (synopsis "Remove unwanted variation from RNA-Seq data")
2480 (description
2481 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2482of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2483samples.")
2484 (license license:artistic2.0)))
286157dc
RW
2485
2486(define-public r-biocneighbors
2487 (package
2488 (name "r-biocneighbors")
bbae34aa 2489 (version "1.8.1")
286157dc
RW
2490 (source
2491 (origin
2492 (method url-fetch)
2493 (uri (bioconductor-uri "BiocNeighbors" version))
2494 (sha256
2495 (base32
bbae34aa 2496 "0hip1sgi3zkrf8g9bw12alaszivja3difalnybr5s7gvh8qd5sf4"))))
286157dc
RW
2497 (properties `((upstream-name . "BiocNeighbors")))
2498 (build-system r-build-system)
2499 (propagated-inputs
12e2aa96
RW
2500 `(("r-biocparallel" ,r-biocparallel)
2501 ("r-matrix" ,r-matrix)
286157dc
RW
2502 ("r-rcpp" ,r-rcpp)
2503 ("r-rcppannoy" ,r-rcppannoy)
6fc161fc 2504 ("r-rcpphnsw" ,r-rcpphnsw)
286157dc 2505 ("r-s4vectors" ,r-s4vectors)))
f5864c11
RW
2506 (native-inputs
2507 `(("r-knitr" ,r-knitr)))
286157dc
RW
2508 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2509 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2510 (description
2511 "This package implements exact and approximate methods for nearest
2512neighbor detection, in a framework that allows them to be easily switched
2513within Bioconductor packages or workflows. The exact algorithm is implemented
2514using pre-clustering with the k-means algorithm. Functions are also provided
2515to search for all neighbors within a given distance. Parallelization is
2516achieved for all methods using the BiocParallel framework.")
2517 (license license:gpl3)))
8a587c89 2518
99391290
RW
2519(define-public r-biocsingular
2520 (package
2521 (name "r-biocsingular")
a8351d46 2522 (version "1.4.0")
99391290
RW
2523 (source
2524 (origin
2525 (method url-fetch)
2526 (uri (bioconductor-uri "BiocSingular" version))
2527 (sha256
2528 (base32
a8351d46 2529 "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih"))))
99391290
RW
2530 (properties `((upstream-name . "BiocSingular")))
2531 (build-system r-build-system)
2532 (propagated-inputs
2533 `(("r-beachmat" ,r-beachmat)
2534 ("r-biocgenerics" ,r-biocgenerics)
2535 ("r-biocparallel" ,r-biocparallel)
2536 ("r-delayedarray" ,r-delayedarray)
2537 ("r-irlba" ,r-irlba)
2538 ("r-matrix" ,r-matrix)
2539 ("r-rcpp" ,r-rcpp)
2540 ("r-rsvd" ,r-rsvd)
2541 ("r-s4vectors" ,r-s4vectors)))
a8351d46
RW
2542 (native-inputs
2543 `(("r-knitr" ,r-knitr)))
99391290
RW
2544 (home-page "https://github.com/LTLA/BiocSingular")
2545 (synopsis "Singular value decomposition for Bioconductor packages")
2546 (description
2547 "This package implements exact and approximate methods for singular value
2548decomposition and principal components analysis, in a framework that allows
2549them to be easily switched within Bioconductor packages or workflows. Where
2550possible, parallelization is achieved using the BiocParallel framework.")
2551 (license license:gpl3)))
2552
a961ae46
RW
2553(define-public r-destiny
2554 (package
2555 (name "r-destiny")
4217307f 2556 (version "3.4.0")
a961ae46
RW
2557 (source
2558 (origin
2559 (method url-fetch)
2560 (uri (bioconductor-uri "destiny" version))
2561 (sha256
2562 (base32
4217307f 2563 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
a961ae46
RW
2564 (build-system r-build-system)
2565 (propagated-inputs
2566 `(("r-biobase" ,r-biobase)
2567 ("r-biocgenerics" ,r-biocgenerics)
6e10ac07 2568 ("r-ggplot-multistats" ,r-ggplot-multistats)
0aa72f2d 2569 ("r-ggplot2" ,r-ggplot2)
a961ae46 2570 ("r-ggthemes" ,r-ggthemes)
6e10ac07
RW
2571 ("r-irlba" ,r-irlba)
2572 ("r-knn-covertree" ,r-knn-covertree)
a961ae46 2573 ("r-matrix" ,r-matrix)
6e10ac07 2574 ("r-pcamethods" ,r-pcamethods)
a961ae46
RW
2575 ("r-proxy" ,r-proxy)
2576 ("r-rcpp" ,r-rcpp)
2577 ("r-rcppeigen" ,r-rcppeigen)
6e10ac07
RW
2578 ("r-rcpphnsw" ,r-rcpphnsw)
2579 ("r-rspectra" ,r-rspectra)
a961ae46
RW
2580 ("r-scales" ,r-scales)
2581 ("r-scatterplot3d" ,r-scatterplot3d)
6e10ac07 2582 ("r-singlecellexperiment" ,r-singlecellexperiment)
a961ae46
RW
2583 ("r-smoother" ,r-smoother)
2584 ("r-summarizedexperiment" ,r-summarizedexperiment)
6e10ac07
RW
2585 ("r-tidyr" ,r-tidyr)
2586 ("r-tidyselect" ,r-tidyselect)
a961ae46 2587 ("r-vim" ,r-vim)))
3f782a6d
RW
2588 (native-inputs
2589 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
a961ae46
RW
2590 (home-page "https://bioconductor.org/packages/destiny/")
2591 (synopsis "Create and plot diffusion maps")
2592 (description "This package provides tools to create and plot diffusion
2593maps.")
2594 ;; Any version of the GPL
2595 (license license:gpl3+)))
2596
8a587c89
RW
2597(define-public r-savr
2598 (package
2599 (name "r-savr")
967fc583 2600 (version "1.28.0")
8a587c89
RW
2601 (source
2602 (origin
2603 (method url-fetch)
2604 (uri (bioconductor-uri "savR" version))
2605 (sha256
2606 (base32
967fc583 2607 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
8a587c89
RW
2608 (properties `((upstream-name . "savR")))
2609 (build-system r-build-system)
2610 (propagated-inputs
2611 `(("r-ggplot2" ,r-ggplot2)
2612 ("r-gridextra" ,r-gridextra)
2613 ("r-reshape2" ,r-reshape2)
2614 ("r-scales" ,r-scales)
2615 ("r-xml" ,r-xml)))
2616 (home-page "https://github.com/bcalder/savR")
2617 (synopsis "Parse and analyze Illumina SAV files")
2618 (description
2619 "This package provides tools to parse Illumina Sequence Analysis
2620Viewer (SAV) files, access data, and generate QC plots.")
2621 (license license:agpl3+)))
41ffc214
RW
2622
2623(define-public r-chipexoqual
2624 (package
2625 (name "r-chipexoqual")
ff4d0804 2626 (version "1.14.0")
41ffc214
RW
2627 (source
2628 (origin
2629 (method url-fetch)
2630 (uri (bioconductor-uri "ChIPexoQual" version))
2631 (sha256
2632 (base32
ff4d0804 2633 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
41ffc214
RW
2634 (properties `((upstream-name . "ChIPexoQual")))
2635 (build-system r-build-system)
2636 (propagated-inputs
2637 `(("r-biocparallel" ,r-biocparallel)
2638 ("r-biovizbase" ,r-biovizbase)
2639 ("r-broom" ,r-broom)
2640 ("r-data-table" ,r-data-table)
2641 ("r-dplyr" ,r-dplyr)
2642 ("r-genomeinfodb" ,r-genomeinfodb)
2643 ("r-genomicalignments" ,r-genomicalignments)
2644 ("r-genomicranges" ,r-genomicranges)
2645 ("r-ggplot2" ,r-ggplot2)
2646 ("r-hexbin" ,r-hexbin)
2647 ("r-iranges" ,r-iranges)
2648 ("r-rcolorbrewer" ,r-rcolorbrewer)
2649 ("r-rmarkdown" ,r-rmarkdown)
2650 ("r-rsamtools" ,r-rsamtools)
2651 ("r-s4vectors" ,r-s4vectors)
2652 ("r-scales" ,r-scales)
2653 ("r-viridis" ,r-viridis)))
9697afb1
RW
2654 (native-inputs
2655 `(("r-knitr" ,r-knitr)))
41ffc214
RW
2656 (home-page "https://github.com/keleslab/ChIPexoQual")
2657 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2658 (description
2659 "This package provides a quality control pipeline for ChIP-exo/nexus
2660sequencing data.")
2661 (license license:gpl2+)))
c18dccff 2662
3d13b448
RW
2663(define-public r-copynumber
2664 (package
2665 (name "r-copynumber")
43d8db04 2666 (version "1.30.0")
3d13b448
RW
2667 (source (origin
2668 (method url-fetch)
2669 (uri (bioconductor-uri "copynumber" version))
2670 (sha256
2671 (base32
43d8db04 2672 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
3d13b448
RW
2673 (build-system r-build-system)
2674 (propagated-inputs
2675 `(("r-s4vectors" ,r-s4vectors)
2676 ("r-iranges" ,r-iranges)
2677 ("r-genomicranges" ,r-genomicranges)
2678 ("r-biocgenerics" ,r-biocgenerics)))
2679 (home-page "https://bioconductor.org/packages/copynumber")
2680 (synopsis "Segmentation of single- and multi-track copy number data")
2681 (description
2682 "This package segments single- and multi-track copy number data by a
2683penalized least squares regression method.")
2684 (license license:artistic2.0)))
2685
c18dccff
RW
2686(define-public r-dnacopy
2687 (package
2688 (name "r-dnacopy")
850f4c2a 2689 (version "1.64.0")
c18dccff
RW
2690 (source
2691 (origin
2692 (method url-fetch)
2693 (uri (bioconductor-uri "DNAcopy" version))
2694 (sha256
2695 (base32
850f4c2a 2696 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
c18dccff
RW
2697 (properties `((upstream-name . "DNAcopy")))
2698 (build-system r-build-system)
2699 (native-inputs `(("gfortran" ,gfortran)))
2700 (home-page "https://bioconductor.org/packages/DNAcopy")
2701 (synopsis "DNA copy number data analysis")
2702 (description
2703 "This package implements the @dfn{circular binary segmentation} (CBS)
2704algorithm to segment DNA copy number data and identify genomic regions with
2705abnormal copy number.")
2706 (license license:gpl2+)))
3a0babac
RW
2707
2708;; This is a CRAN package, but it uncharacteristically depends on a
2709;; Bioconductor package.
2710(define-public r-htscluster
2711 (package
2712 (name "r-htscluster")
2713 (version "2.0.8")
2714 (source
2715 (origin
2716 (method url-fetch)
2717 (uri (cran-uri "HTSCluster" version))
2718 (sha256
2719 (base32
2720 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2721 (properties `((upstream-name . "HTSCluster")))
2722 (build-system r-build-system)
2723 (propagated-inputs
2724 `(("r-capushe" ,r-capushe)
2725 ("r-edger" ,r-edger)
2726 ("r-plotrix" ,r-plotrix)))
2727 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2728 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2729 (description
2730 "This package provides a Poisson mixture model is implemented to cluster
2731genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2732estimation is performed using either the EM or CEM algorithm, and the slope
2733heuristics are used for model selection (i.e., to choose the number of
2734clusters).")
2735 (license license:gpl3+)))
173c9960
RW
2736
2737(define-public r-deds
2738 (package
2739 (name "r-deds")
96030bf7 2740 (version "1.60.0")
173c9960
RW
2741 (source
2742 (origin
2743 (method url-fetch)
2744 (uri (bioconductor-uri "DEDS" version))
2745 (sha256
2746 (base32
96030bf7 2747 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
173c9960
RW
2748 (properties `((upstream-name . "DEDS")))
2749 (build-system r-build-system)
2750 (home-page "https://bioconductor.org/packages/DEDS/")
2751 (synopsis "Differential expression via distance summary for microarray data")
2752 (description
2753 "This library contains functions that calculate various statistics of
2754differential expression for microarray data, including t statistics, fold
2755change, F statistics, SAM, moderated t and F statistics and B statistics. It
2756also implements a new methodology called DEDS (Differential Expression via
2757Distance Summary), which selects differentially expressed genes by integrating
2758and summarizing a set of statistics using a weighted distance approach.")
2759 ;; Any version of the LGPL.
2760 (license license:lgpl3+)))
7ed869f7
RW
2761
2762;; This is a CRAN package, but since it depends on a Bioconductor package we
2763;; put it here.
2764(define-public r-nbpseq
2765 (package
2766 (name "r-nbpseq")
2767 (version "0.3.0")
2768 (source
2769 (origin
2770 (method url-fetch)
2771 (uri (cran-uri "NBPSeq" version))
2772 (sha256
2773 (base32
2774 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2775 (properties `((upstream-name . "NBPSeq")))
2776 (build-system r-build-system)
2777 (propagated-inputs
2778 `(("r-qvalue" ,r-qvalue)))
2779 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2780 (synopsis "Negative binomial models for RNA-Seq data")
2781 (description
2782 "This package provides negative binomial models for two-group comparisons
2783and regression inferences from RNA-sequencing data.")
2784 (license license:gpl2)))
3087a2f3
RW
2785
2786(define-public r-ebseq
2787 (package
2788 (name "r-ebseq")
939c888d 2789 (version "1.30.0")
3087a2f3
RW
2790 (source
2791 (origin
2792 (method url-fetch)
2793 (uri (bioconductor-uri "EBSeq" version))
2794 (sha256
2795 (base32
939c888d 2796 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
3087a2f3
RW
2797 (properties `((upstream-name . "EBSeq")))
2798 (build-system r-build-system)
2799 (propagated-inputs
2800 `(("r-blockmodeling" ,r-blockmodeling)
2801 ("r-gplots" ,r-gplots)
2802 ("r-testthat" ,r-testthat)))
2803 (home-page "https://bioconductor.org/packages/EBSeq")
2804 (synopsis "Differential expression analysis of RNA-seq data")
2805 (description
2806 "This package provides tools for differential expression analysis at both
2807gene and isoform level using RNA-seq data")
2808 (license license:artistic2.0)))
cb1ab035
RJ
2809
2810(define-public r-karyoploter
2811 (package
2812 (name "r-karyoploter")
37da4513 2813 (version "1.16.0")
cb1ab035
RJ
2814 (source (origin
2815 (method url-fetch)
2816 (uri (bioconductor-uri "karyoploteR" version))
2817 (sha256
2818 (base32
37da4513 2819 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
cb1ab035
RJ
2820 (build-system r-build-system)
2821 (propagated-inputs
6e2dc9e3
RW
2822 `(("r-annotationdbi" ,r-annotationdbi)
2823 ("r-bamsignals" ,r-bamsignals)
2824 ("r-bezier" ,r-bezier)
2825 ("r-biovizbase" ,r-biovizbase)
2826 ("r-digest" ,r-digest)
2827 ("r-genomeinfodb" ,r-genomeinfodb)
2828 ("r-genomicfeatures" ,r-genomicfeatures)
cb1ab035
RJ
2829 ("r-genomicranges" ,r-genomicranges)
2830 ("r-iranges" ,r-iranges)
cb1ab035 2831 ("r-memoise" ,r-memoise)
6e2dc9e3
RW
2832 ("r-regioner" ,r-regioner)
2833 ("r-rsamtools" ,r-rsamtools)
cb1ab035 2834 ("r-rtracklayer" ,r-rtracklayer)
cb1ab035 2835 ("r-s4vectors" ,r-s4vectors)
cb1ab035 2836 ("r-variantannotation" ,r-variantannotation)))
6e2dc9e3
RW
2837 (native-inputs
2838 `(("r-knitr" ,r-knitr)))
cb1ab035
RJ
2839 (home-page "https://bioconductor.org/packages/karyoploteR/")
2840 (synopsis "Plot customizable linear genomes displaying arbitrary data")
2841 (description "This package creates karyotype plots of arbitrary genomes and
7230f6d5 2842offers a complete set of functions to plot arbitrary data on them. It mimics
cb1ab035
RJ
2843many R base graphics functions coupling them with a coordinate change function
2844automatically mapping the chromosome and data coordinates into the plot
2845coordinates.")
2846 (license license:artistic2.0)))
2cb71d81
RW
2847
2848(define-public r-lpsymphony
2849 (package
2850 (name "r-lpsymphony")
378d67c9 2851 (version "1.18.0")
2cb71d81
RW
2852 (source
2853 (origin
2854 (method url-fetch)
2855 (uri (bioconductor-uri "lpsymphony" version))
2856 (sha256
2857 (base32
378d67c9 2858 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
2cb71d81
RW
2859 (build-system r-build-system)
2860 (inputs
0653b8b0 2861 `(("zlib" ,zlib)))
2cb71d81 2862 (native-inputs
0653b8b0
RW
2863 `(("pkg-config" ,pkg-config)
2864 ("r-knitr" ,r-knitr)))
c756328e 2865 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2cb71d81
RW
2866 (synopsis "Symphony integer linear programming solver in R")
2867 (description
2868 "This package was derived from Rsymphony. The package provides an R
2869interface to SYMPHONY, a linear programming solver written in C++. The main
2870difference between this package and Rsymphony is that it includes the solver
2871source code, while Rsymphony expects to find header and library files on the
2872users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2873to install interface to SYMPHONY.")
2874 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2875 ;; lpsimphony is released under the same terms.
2876 (license license:epl1.0)))
704de8f5
RW
2877
2878(define-public r-ihw
2879 (package
2880 (name "r-ihw")
95b1f350 2881 (version "1.18.0")
704de8f5
RW
2882 (source
2883 (origin
2884 (method url-fetch)
2885 (uri (bioconductor-uri "IHW" version))
2886 (sha256
2887 (base32
95b1f350 2888 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
704de8f5
RW
2889 (properties `((upstream-name . "IHW")))
2890 (build-system r-build-system)
2891 (propagated-inputs
2892 `(("r-biocgenerics" ,r-biocgenerics)
2893 ("r-fdrtool" ,r-fdrtool)
2894 ("r-lpsymphony" ,r-lpsymphony)
2895 ("r-slam" ,r-slam)))
359a084a
RW
2896 (native-inputs
2897 `(("r-knitr" ,r-knitr)))
704de8f5
RW
2898 (home-page "https://bioconductor.org/packages/IHW")
2899 (synopsis "Independent hypothesis weighting")
2900 (description
2901 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2902procedure that increases power compared to the method of Benjamini and
2903Hochberg by assigning data-driven weights to each hypothesis. The input to
2904IHW is a two-column table of p-values and covariates. The covariate can be
2905any continuous-valued or categorical variable that is thought to be
2906informative on the statistical properties of each hypothesis test, while it is
2907independent of the p-value under the null hypothesis.")
2908 (license license:artistic2.0)))
251e0830
RW
2909
2910(define-public r-icobra
2911 (package
2912 (name "r-icobra")
e26b5eef 2913 (version "1.18.0")
251e0830
RW
2914 (source
2915 (origin
2916 (method url-fetch)
2917 (uri (bioconductor-uri "iCOBRA" version))
2918 (sha256
2919 (base32
e26b5eef 2920 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
251e0830
RW
2921 (properties `((upstream-name . "iCOBRA")))
2922 (build-system r-build-system)
2923 (propagated-inputs
2924 `(("r-dplyr" ,r-dplyr)
2925 ("r-dt" ,r-dt)
2926 ("r-ggplot2" ,r-ggplot2)
2927 ("r-limma" ,r-limma)
2928 ("r-reshape2" ,r-reshape2)
2929 ("r-rocr" ,r-rocr)
2930 ("r-scales" ,r-scales)
2931 ("r-shiny" ,r-shiny)
2932 ("r-shinybs" ,r-shinybs)
2933 ("r-shinydashboard" ,r-shinydashboard)
2934 ("r-upsetr" ,r-upsetr)))
ee1e8fee
RW
2935 (native-inputs
2936 `(("r-knitr" ,r-knitr)))
251e0830
RW
2937 (home-page "https://bioconductor.org/packages/iCOBRA")
2938 (synopsis "Comparison and visualization of ranking and assignment methods")
2939 (description
2940 "This package provides functions for calculation and visualization of
2941performance metrics for evaluation of ranking and binary
2942classification (assignment) methods. It also contains a Shiny application for
2943interactive exploration of results.")
2944 (license license:gpl2+)))
925fcdbb
RW
2945
2946(define-public r-mast
2947 (package
2948 (name "r-mast")
532b1068 2949 (version "1.16.0")
925fcdbb
RW
2950 (source
2951 (origin
2952 (method url-fetch)
2953 (uri (bioconductor-uri "MAST" version))
2954 (sha256
2955 (base32
532b1068 2956 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
925fcdbb
RW
2957 (properties `((upstream-name . "MAST")))
2958 (build-system r-build-system)
2959 (propagated-inputs
2960 `(("r-abind" ,r-abind)
2961 ("r-biobase" ,r-biobase)
2962 ("r-biocgenerics" ,r-biocgenerics)
2963 ("r-data-table" ,r-data-table)
2964 ("r-ggplot2" ,r-ggplot2)
2965 ("r-plyr" ,r-plyr)
2966 ("r-progress" ,r-progress)
2967 ("r-reshape2" ,r-reshape2)
2968 ("r-s4vectors" ,r-s4vectors)
2969 ("r-singlecellexperiment" ,r-singlecellexperiment)
2970 ("r-stringr" ,r-stringr)
2971 ("r-summarizedexperiment" ,r-summarizedexperiment)))
51d1a7a2
RW
2972 (native-inputs
2973 `(("r-knitr" ,r-knitr)))
925fcdbb
RW
2974 (home-page "https://github.com/RGLab/MAST/")
2975 (synopsis "Model-based analysis of single cell transcriptomics")
2976 (description
2977 "This package provides methods and models for handling zero-inflated
2978single cell assay data.")
2979 (license license:gpl2+)))
2d7627cf
RW
2980
2981(define-public r-monocle
2982 (package
2983 (name "r-monocle")
38bc0bf8 2984 (version "2.18.0")
2d7627cf
RW
2985 (source
2986 (origin
2987 (method url-fetch)
2988 (uri (bioconductor-uri "monocle" version))
2989 (sha256
2990 (base32
38bc0bf8 2991 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
2d7627cf
RW
2992 (build-system r-build-system)
2993 (propagated-inputs
2994 `(("r-biobase" ,r-biobase)
2995 ("r-biocgenerics" ,r-biocgenerics)
2996 ("r-biocviews" ,r-biocviews)
2997 ("r-cluster" ,r-cluster)
2998 ("r-combinat" ,r-combinat)
2999 ("r-ddrtree" ,r-ddrtree)
3000 ("r-densityclust" ,r-densityclust)
3001 ("r-dplyr" ,r-dplyr)
3002 ("r-fastica" ,r-fastica)
3003 ("r-ggplot2" ,r-ggplot2)
3004 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
3005 ("r-igraph" ,r-igraph)
3006 ("r-irlba" ,r-irlba)
3007 ("r-limma" ,r-limma)
3008 ("r-mass" ,r-mass)
3009 ("r-matrix" ,r-matrix)
3010 ("r-matrixstats" ,r-matrixstats)
3011 ("r-pheatmap" ,r-pheatmap)
3012 ("r-plyr" ,r-plyr)
3013 ("r-proxy" ,r-proxy)
3014 ("r-qlcmatrix" ,r-qlcmatrix)
3015 ("r-rann" ,r-rann)
3016 ("r-rcpp" ,r-rcpp)
3017 ("r-reshape2" ,r-reshape2)
3018 ("r-rtsne" ,r-rtsne)
3019 ("r-slam" ,r-slam)
3020 ("r-stringr" ,r-stringr)
3021 ("r-tibble" ,r-tibble)
3022 ("r-vgam" ,r-vgam)
3023 ("r-viridis" ,r-viridis)))
d1f3c371
RW
3024 (native-inputs
3025 `(("r-knitr" ,r-knitr)))
2d7627cf
RW
3026 (home-page "https://bioconductor.org/packages/monocle")
3027 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
3028 (description
3029 "Monocle performs differential expression and time-series analysis for
3030single-cell expression experiments. It orders individual cells according to
3031progress through a biological process, without knowing ahead of time which
3032genes define progress through that process. Monocle also performs
3033differential expression analysis, clustering, visualization, and other useful
3034tasks on single cell expression data. It is designed to work with RNA-Seq and
3035qPCR data, but could be used with other types as well.")
3036 (license license:artistic2.0)))
6213e441 3037
b2dce6b5
RW
3038(define-public r-monocle3
3039 (package
3040 (name "r-monocle3")
3041 (version "0.1.2")
3042 (source
3043 (origin
3044 (method git-fetch)
3045 (uri (git-reference
b0e7b699 3046 (url "https://github.com/cole-trapnell-lab/monocle3")
b2dce6b5
RW
3047 (commit version)))
3048 (file-name (git-file-name name version))
3049 (sha256
3050 (base32
3051 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
3052 (build-system r-build-system)
3053 (propagated-inputs
3054 `(("r-biobase" ,r-biobase)
3055 ("r-biocgenerics" ,r-biocgenerics)
3056 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3057 ("r-dplyr" ,r-dplyr)
3058 ("r-ggplot2" ,r-ggplot2)
3059 ("r-ggrepel" ,r-ggrepel)
3060 ("r-grr" ,r-grr)
3061 ("r-htmlwidgets" ,r-htmlwidgets)
3062 ("r-igraph" ,r-igraph)
3063 ("r-irlba" ,r-irlba)
3064 ("r-limma" ,r-limma)
3065 ("r-lmtest" ,r-lmtest)
3066 ("r-mass" ,r-mass)
3067 ("r-matrix" ,r-matrix)
3068 ("r-matrix-utils" ,r-matrix-utils)
3069 ("r-pbapply" ,r-pbapply)
3070 ("r-pbmcapply" ,r-pbmcapply)
3071 ("r-pheatmap" ,r-pheatmap)
3072 ("r-plotly" ,r-plotly)
3073 ("r-pryr" ,r-pryr)
3074 ("r-proxy" ,r-proxy)
3075 ("r-pscl" ,r-pscl)
3076 ("r-purrr" ,r-purrr)
3077 ("r-rann" ,r-rann)
3078 ("r-rcpp" ,r-rcpp)
3079 ("r-rcppparallel" ,r-rcppparallel)
3080 ("r-reshape2" ,r-reshape2)
3081 ("r-reticulate" ,r-reticulate)
3082 ("r-rhpcblasctl" ,r-rhpcblasctl)
3083 ("r-rtsne" ,r-rtsne)
3084 ("r-shiny" ,r-shiny)
3085 ("r-slam" ,r-slam)
3086 ("r-spdep" ,r-spdep)
3087 ("r-speedglm" ,r-speedglm)
3088 ("r-stringr" ,r-stringr)
3089 ("r-singlecellexperiment" ,r-singlecellexperiment)
3090 ("r-tibble" ,r-tibble)
3091 ("r-tidyr" ,r-tidyr)
3092 ("r-uwot" ,r-uwot)
3093 ("r-viridis" ,r-viridis)))
3094 (home-page "https://github.com/cole-trapnell-lab/monocle3")
3095 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
3096 (description
3097 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
3098 (license license:expat)))
3099
6213e441
RW
3100(define-public r-noiseq
3101 (package
3102 (name "r-noiseq")
8396c45e 3103 (version "2.34.0")
6213e441
RW
3104 (source
3105 (origin
3106 (method url-fetch)
3107 (uri (bioconductor-uri "NOISeq" version))
3108 (sha256
3109 (base32
8396c45e 3110 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
6213e441
RW
3111 (properties `((upstream-name . "NOISeq")))
3112 (build-system r-build-system)
3113 (propagated-inputs
3114 `(("r-biobase" ,r-biobase)
3115 ("r-matrix" ,r-matrix)))
3116 (home-page "https://bioconductor.org/packages/NOISeq")
3117 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3118 (description
3119 "This package provides tools to support the analysis of RNA-seq
3120expression data or other similar kind of data. It provides exploratory plots
3121to evaluate saturation, count distribution, expression per chromosome, type of
3122detected features, features length, etc. It also supports the analysis of
3123differential expression between two experimental conditions with no parametric
3124assumptions.")
3125 (license license:artistic2.0)))
b409c357
RW
3126
3127(define-public r-scdd
3128 (package
3129 (name "r-scdd")
ce9e19bc 3130 (version "1.12.0")
b409c357
RW
3131 (source
3132 (origin
3133 (method url-fetch)
3134 (uri (bioconductor-uri "scDD" version))
3135 (sha256
3136 (base32
ce9e19bc 3137 "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx"))))
b409c357
RW
3138 (properties `((upstream-name . "scDD")))
3139 (build-system r-build-system)
3140 (propagated-inputs
3141 `(("r-arm" ,r-arm)
3142 ("r-biocparallel" ,r-biocparallel)
3143 ("r-ebseq" ,r-ebseq)
3144 ("r-fields" ,r-fields)
3145 ("r-ggplot2" ,r-ggplot2)
3146 ("r-mclust" ,r-mclust)
3147 ("r-outliers" ,r-outliers)
3148 ("r-s4vectors" ,r-s4vectors)
3149 ("r-scran" ,r-scran)
3150 ("r-singlecellexperiment" ,r-singlecellexperiment)
3151 ("r-summarizedexperiment" ,r-summarizedexperiment)))
ce9e19bc
RW
3152 (native-inputs
3153 `(("r-knitr" ,r-knitr)))
b409c357
RW
3154 (home-page "https://github.com/kdkorthauer/scDD")
3155 (synopsis "Mixture modeling of single-cell RNA-seq data")
3156 (description
3157 "This package implements a method to analyze single-cell RNA-seq data
3158utilizing flexible Dirichlet Process mixture models. Genes with differential
3159distributions of expression are classified into several interesting patterns
3160of differences between two conditions. The package also includes functions
3161for simulating data with these patterns from negative binomial
3162distributions.")
3163 (license license:gpl2)))
f0887757
RW
3164
3165(define-public r-scone
3166 (package
3167 (name "r-scone")
bde9dc5b 3168 (version "1.14.0")
f0887757
RW
3169 (source
3170 (origin
3171 (method url-fetch)
3172 (uri (bioconductor-uri "scone" version))
3173 (sha256
3174 (base32
bde9dc5b 3175 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
f0887757
RW
3176 (build-system r-build-system)
3177 (propagated-inputs
3178 `(("r-aroma-light" ,r-aroma-light)
3179 ("r-biocparallel" ,r-biocparallel)
3180 ("r-boot" ,r-boot)
3181 ("r-class" ,r-class)
3182 ("r-cluster" ,r-cluster)
3183 ("r-compositions" ,r-compositions)
3184 ("r-diptest" ,r-diptest)
3185 ("r-edger" ,r-edger)
3186 ("r-fpc" ,r-fpc)
3187 ("r-gplots" ,r-gplots)
3188 ("r-hexbin" ,r-hexbin)
3189 ("r-limma" ,r-limma)
3190 ("r-matrixstats" ,r-matrixstats)
3191 ("r-mixtools" ,r-mixtools)
3192 ("r-rarpack" ,r-rarpack)
3193 ("r-rcolorbrewer" ,r-rcolorbrewer)
3194 ("r-rhdf5" ,r-rhdf5)
3195 ("r-ruvseq" ,r-ruvseq)
3196 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3fc1e039
RW
3197 (native-inputs
3198 `(("r-knitr" ,r-knitr)))
f0887757
RW
3199 (home-page "https://bioconductor.org/packages/scone")
3200 (synopsis "Single cell overview of normalized expression data")
3201 (description
3202 "SCONE is an R package for comparing and ranking the performance of
3203different normalization schemes for single-cell RNA-seq and other
3204high-throughput analyses.")
3205 (license license:artistic2.0)))
f9201d67
RW
3206
3207(define-public r-geoquery
3208 (package
3209 (name "r-geoquery")
5c4edeef 3210 (version "2.58.0")
f9201d67
RW
3211 (source
3212 (origin
3213 (method url-fetch)
3214 (uri (bioconductor-uri "GEOquery" version))
3215 (sha256
3216 (base32
5c4edeef 3217 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
f9201d67
RW
3218 (properties `((upstream-name . "GEOquery")))
3219 (build-system r-build-system)
3220 (propagated-inputs
3221 `(("r-biobase" ,r-biobase)
3222 ("r-dplyr" ,r-dplyr)
3223 ("r-httr" ,r-httr)
3224 ("r-limma" ,r-limma)
3225 ("r-magrittr" ,r-magrittr)
3226 ("r-readr" ,r-readr)
3227 ("r-tidyr" ,r-tidyr)
3228 ("r-xml2" ,r-xml2)))
159e427c
RW
3229 (native-inputs
3230 `(("r-knitr" ,r-knitr)))
f9201d67
RW
3231 (home-page "https://github.com/seandavi/GEOquery/")
3232 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3233 (description
3234 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3235microarray data. Given the rich and varied nature of this resource, it is
3236only natural to want to apply BioConductor tools to these data. GEOquery is
3237the bridge between GEO and BioConductor.")
3238 (license license:gpl2)))
eed6ff03
RW
3239
3240(define-public r-illuminaio
3241 (package
3242 (name "r-illuminaio")
e89966e9 3243 (version "0.32.0")
eed6ff03
RW
3244 (source
3245 (origin
3246 (method url-fetch)
3247 (uri (bioconductor-uri "illuminaio" version))
3248 (sha256
3249 (base32
e89966e9 3250 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
eed6ff03
RW
3251 (build-system r-build-system)
3252 (propagated-inputs
3253 `(("r-base64" ,r-base64)))
3254 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3255 (synopsis "Parse Illumina microarray output files")
3256 (description
3257 "This package provides tools for parsing Illumina's microarray output
3258files, including IDAT.")
3259 (license license:gpl2)))
f4eac096
RW
3260
3261(define-public r-siggenes
3262 (package
3263 (name "r-siggenes")
0fd830fe 3264 (version "1.64.0")
f4eac096
RW
3265 (source
3266 (origin
3267 (method url-fetch)
3268 (uri (bioconductor-uri "siggenes" version))
3269 (sha256
3270 (base32
0fd830fe 3271 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
f4eac096
RW
3272 (build-system r-build-system)
3273 (propagated-inputs
3274 `(("r-biobase" ,r-biobase)
409f4dd6
RW
3275 ("r-multtest" ,r-multtest)
3276 ("r-scrime" ,r-scrime)))
f4eac096
RW
3277 (home-page "https://bioconductor.org/packages/siggenes/")
3278 (synopsis
3279 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3280 (description
3281 "This package provides tools for the identification of differentially
3282expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3283both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3284Bayes Analyses of Microarrays} (EBAM).")
3285 (license license:lgpl2.0+)))
34a24f95
RW
3286
3287(define-public r-bumphunter
3288 (package
3289 (name "r-bumphunter")
50c5fee6 3290 (version "1.32.0")
34a24f95
RW
3291 (source
3292 (origin
3293 (method url-fetch)
3294 (uri (bioconductor-uri "bumphunter" version))
3295 (sha256
3296 (base32
50c5fee6 3297 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
34a24f95
RW
3298 (build-system r-build-system)
3299 (propagated-inputs
3300 `(("r-annotationdbi" ,r-annotationdbi)
3301 ("r-biocgenerics" ,r-biocgenerics)
3302 ("r-dorng" ,r-dorng)
3303 ("r-foreach" ,r-foreach)
3304 ("r-genomeinfodb" ,r-genomeinfodb)
3305 ("r-genomicfeatures" ,r-genomicfeatures)
3306 ("r-genomicranges" ,r-genomicranges)
3307 ("r-iranges" ,r-iranges)
3308 ("r-iterators" ,r-iterators)
3309 ("r-limma" ,r-limma)
3310 ("r-locfit" ,r-locfit)
3311 ("r-matrixstats" ,r-matrixstats)
3312 ("r-s4vectors" ,r-s4vectors)))
3313 (home-page "https://github.com/ririzarr/bumphunter")
3314 (synopsis "Find bumps in genomic data")
3315 (description
3316 "This package provides tools for finding bumps in genomic data in order
3317to identify differentially methylated regions in epigenetic epidemiology
3318studies.")
3319 (license license:artistic2.0)))
0fbaf195
RW
3320
3321(define-public r-minfi
3322 (package
3323 (name "r-minfi")
83e6ffda 3324 (version "1.34.0")
0fbaf195
RW
3325 (source
3326 (origin
3327 (method url-fetch)
3328 (uri (bioconductor-uri "minfi" version))
3329 (sha256
3330 (base32
83e6ffda 3331 "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w"))))
0fbaf195
RW
3332 (build-system r-build-system)
3333 (propagated-inputs
3334 `(("r-beanplot" ,r-beanplot)
3335 ("r-biobase" ,r-biobase)
3336 ("r-biocgenerics" ,r-biocgenerics)
3337 ("r-biocparallel" ,r-biocparallel)
3338 ("r-biostrings" ,r-biostrings)
3339 ("r-bumphunter" ,r-bumphunter)
3340 ("r-data-table" ,r-data-table)
3341 ("r-delayedarray" ,r-delayedarray)
3342 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3343 ("r-genefilter" ,r-genefilter)
3344 ("r-genomeinfodb" ,r-genomeinfodb)
3345 ("r-genomicranges" ,r-genomicranges)
3346 ("r-geoquery" ,r-geoquery)
3347 ("r-hdf5array" ,r-hdf5array)
3348 ("r-illuminaio" ,r-illuminaio)
3349 ("r-iranges" ,r-iranges)
3350 ("r-lattice" ,r-lattice)
3351 ("r-limma" ,r-limma)
3352 ("r-mass" ,r-mass)
3353 ("r-mclust" ,r-mclust)
3354 ("r-nlme" ,r-nlme)
3355 ("r-nor1mix" ,r-nor1mix)
3356 ("r-preprocesscore" ,r-preprocesscore)
3357 ("r-quadprog" ,r-quadprog)
3358 ("r-rcolorbrewer" ,r-rcolorbrewer)
3359 ("r-reshape" ,r-reshape)
3360 ("r-s4vectors" ,r-s4vectors)
3361 ("r-siggenes" ,r-siggenes)
3362 ("r-summarizedexperiment" ,r-summarizedexperiment)))
83e6ffda
RW
3363 (native-inputs
3364 `(("r-knitr" ,r-knitr)))
0fbaf195
RW
3365 (home-page "https://github.com/hansenlab/minfi")
3366 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3367 (description
3368 "This package provides tools to analyze and visualize Illumina Infinium
3369methylation arrays.")
3370 (license license:artistic2.0)))
5ec5ba02
RW
3371
3372(define-public r-methylumi
3373 (package
3374 (name "r-methylumi")
5f25d5f8 3375 (version "2.34.0")
5ec5ba02
RW
3376 (source
3377 (origin
3378 (method url-fetch)
3379 (uri (bioconductor-uri "methylumi" version))
3380 (sha256
3381 (base32
5f25d5f8 3382 "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr"))))
5ec5ba02
RW
3383 (build-system r-build-system)
3384 (propagated-inputs
3385 `(("r-annotate" ,r-annotate)
3386 ("r-annotationdbi" ,r-annotationdbi)
3387 ("r-biobase" ,r-biobase)
3388 ("r-biocgenerics" ,r-biocgenerics)
3389 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3390 ("r-genefilter" ,r-genefilter)
3391 ("r-genomeinfodb" ,r-genomeinfodb)
3392 ("r-genomicranges" ,r-genomicranges)
3393 ("r-ggplot2" ,r-ggplot2)
3394 ("r-illuminaio" ,r-illuminaio)
3395 ("r-iranges" ,r-iranges)
3396 ("r-lattice" ,r-lattice)
3397 ("r-matrixstats" ,r-matrixstats)
3398 ("r-minfi" ,r-minfi)
3399 ("r-reshape2" ,r-reshape2)
3400 ("r-s4vectors" ,r-s4vectors)
3401 ("r-scales" ,r-scales)
3402 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5f25d5f8
RW
3403 (native-inputs
3404 `(("r-knitr" ,r-knitr)))
5ec5ba02
RW
3405 (home-page "https://bioconductor.org/packages/methylumi")
3406 (synopsis "Handle Illumina methylation data")
3407 (description
3408 "This package provides classes for holding and manipulating Illumina
3409methylation data. Based on eSet, it can contain MIAME information, sample
3410information, feature information, and multiple matrices of data. An
3411\"intelligent\" import function, methylumiR can read the Illumina text files
3412and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3413HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3414background correction, and quality control features for GoldenGate, Infinium,
3415and Infinium HD arrays are also included.")
3416 (license license:gpl2)))
09605cb2
RW
3417
3418(define-public r-lumi
3419 (package
3420 (name "r-lumi")
ae1c51a1 3421 (version "2.40.0")
09605cb2
RW
3422 (source
3423 (origin
3424 (method url-fetch)
3425 (uri (bioconductor-uri "lumi" version))
3426 (sha256
3427 (base32
ae1c51a1 3428 "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9"))))
09605cb2
RW
3429 (build-system r-build-system)
3430 (propagated-inputs
3431 `(("r-affy" ,r-affy)
3432 ("r-annotate" ,r-annotate)
3433 ("r-annotationdbi" ,r-annotationdbi)
3434 ("r-biobase" ,r-biobase)
3435 ("r-dbi" ,r-dbi)
3436 ("r-genomicfeatures" ,r-genomicfeatures)
3437 ("r-genomicranges" ,r-genomicranges)
3438 ("r-kernsmooth" ,r-kernsmooth)
3439 ("r-lattice" ,r-lattice)
3440 ("r-mass" ,r-mass)
3441 ("r-methylumi" ,r-methylumi)
3442 ("r-mgcv" ,r-mgcv)
3443 ("r-nleqslv" ,r-nleqslv)
3444 ("r-preprocesscore" ,r-preprocesscore)
3445 ("r-rsqlite" ,r-rsqlite)))
3446 (home-page "https://bioconductor.org/packages/lumi")
3447 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3448 (description
3449 "The lumi package provides an integrated solution for the Illumina
3450microarray data analysis. It includes functions of Illumina
3451BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3452variance stabilization, normalization and gene annotation at the probe level.
3453It also includes the functions of processing Illumina methylation microarrays,
3454especially Illumina Infinium methylation microarrays.")
3455 (license license:lgpl2.0+)))
4291f36a
RW
3456
3457(define-public r-linnorm
3458 (package
3459 (name "r-linnorm")
37e09611 3460 (version "2.14.0")
4291f36a
RW
3461 (source
3462 (origin
3463 (method url-fetch)
3464 (uri (bioconductor-uri "Linnorm" version))
3465 (sha256
3466 (base32
37e09611 3467 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
4291f36a
RW
3468 (properties `((upstream-name . "Linnorm")))
3469 (build-system r-build-system)
3470 (propagated-inputs
3471 `(("r-amap" ,r-amap)
3472 ("r-apcluster" ,r-apcluster)
3473 ("r-ellipse" ,r-ellipse)
3474 ("r-fastcluster" ,r-fastcluster)
3475 ("r-fpc" ,r-fpc)
3476 ("r-ggdendro" ,r-ggdendro)
3477 ("r-ggplot2" ,r-ggplot2)
3478 ("r-gmodels" ,r-gmodels)
3479 ("r-igraph" ,r-igraph)
3480 ("r-limma" ,r-limma)
3481 ("r-mass" ,r-mass)
3482 ("r-mclust" ,r-mclust)
3483 ("r-rcpp" ,r-rcpp)
3484 ("r-rcpparmadillo" ,r-rcpparmadillo)
3485 ("r-rtsne" ,r-rtsne)
3486 ("r-statmod" ,r-statmod)
3487 ("r-vegan" ,r-vegan)
3488 ("r-zoo" ,r-zoo)))
1465873c
RW
3489 (native-inputs
3490 `(("r-knitr" ,r-knitr)))
4291f36a
RW
3491 (home-page "http://www.jjwanglab.org/Linnorm/")
3492 (synopsis "Linear model and normality based transformation method")
3493 (description
3494 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3495count data or any large scale count data. It transforms such datasets for
3496parametric tests. In addition to the transformtion function (@code{Linnorm}),
3497the following pipelines are implemented:
3498
3499@enumerate
3500@item Library size/batch effect normalization (@code{Linnorm.Norm})
3501@item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3502 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3503 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3504@item Differential expression analysis or differential peak detection using
3505 limma (@code{Linnorm.limma})
3506@item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3507@item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3508@item Stable gene selection for scRNA-seq data; for users without or who do
3509 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3510@item Data imputation (@code{Linnorm.DataImput}).
3511@end enumerate
3512
3513Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3514@code{RnaXSim} function is included for simulating RNA-seq data for the
3515evaluation of DEG analysis methods.")
3516 (license license:expat)))
e4a17532
RW
3517
3518(define-public r-ioniser
3519 (package
3520 (name "r-ioniser")
2a1a6d74 3521 (version "2.14.0")
e4a17532
RW
3522 (source
3523 (origin
3524 (method url-fetch)
3525 (uri (bioconductor-uri "IONiseR" version))
3526 (sha256
3527 (base32
2a1a6d74 3528 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
e4a17532
RW
3529 (properties `((upstream-name . "IONiseR")))
3530 (build-system r-build-system)
3531 (propagated-inputs
3532 `(("r-biocgenerics" ,r-biocgenerics)
3533 ("r-biocparallel" ,r-biocparallel)
3534 ("r-biostrings" ,r-biostrings)
3535 ("r-bit64" ,r-bit64)
3536 ("r-dplyr" ,r-dplyr)
3537 ("r-ggplot2" ,r-ggplot2)
3538 ("r-magrittr" ,r-magrittr)
3539 ("r-rhdf5" ,r-rhdf5)
3540 ("r-shortread" ,r-shortread)
3541 ("r-stringr" ,r-stringr)
3542 ("r-tibble" ,r-tibble)
3543 ("r-tidyr" ,r-tidyr)
3544 ("r-xvector" ,r-xvector)))
293fb8a1
RW
3545 (native-inputs
3546 `(("r-knitr" ,r-knitr)))
e4a17532
RW
3547 (home-page "https://bioconductor.org/packages/IONiseR/")
3548 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3549 (description
3550 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3551MinION data. It extracts summary statistics from a set of fast5 files and can
3552be used either before or after base calling. In addition to standard
3553summaries of the read-types produced, it provides a number of plots for
3554visualising metrics relative to experiment run time or spatially over the
3555surface of a flowcell.")
3556 (license license:expat)))
80eb01c7
RW
3557
3558;; This is a CRAN package, but it depends on packages from Bioconductor.
3559(define-public r-gkmsvm
3560 (package
3561 (name "r-gkmsvm")
e1636671 3562 (version "0.81.0")
80eb01c7
RW
3563 (source
3564 (origin
3565 (method url-fetch)
3566 (uri (cran-uri "gkmSVM" version))
3567 (sha256
3568 (base32
e1636671 3569 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
80eb01c7
RW
3570 (properties `((upstream-name . "gkmSVM")))
3571 (build-system r-build-system)
3572 (propagated-inputs
975cfe26 3573 `(("r-kernlab" ,r-kernlab)
80eb01c7
RW
3574 ("r-rcpp" ,r-rcpp)
3575 ("r-rocr" ,r-rocr)
80eb01c7
RW
3576 ("r-seqinr" ,r-seqinr)))
3577 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3578 (synopsis "Gapped-kmer support vector machine")
3579 (description
3580 "This R package provides tools for training gapped-kmer SVM classifiers
3581for DNA and protein sequences. This package supports several sequence
3582kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3583 (license license:gpl2+)))
8a5460b4 3584
f2114762
RW
3585;; This is a CRAN package, but it depends on multtest from Bioconductor.
3586(define-public r-mutoss
3587 (package
3588 (name "r-mutoss")
3589 (version "0.1-12")
3590 (source
3591 (origin
3592 (method url-fetch)
3593 (uri (cran-uri "mutoss" version))
3594 (sha256
3595 (base32
3596 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3597 (properties `((upstream-name . "mutoss")))
3598 (build-system r-build-system)
3599 (propagated-inputs
3600 `(("r-multcomp" ,r-multcomp)
3601 ("r-multtest" ,r-multtest)
3602 ("r-mvtnorm" ,r-mvtnorm)
3603 ("r-plotrix" ,r-plotrix)))
3604 (home-page "https://github.com/kornl/mutoss/")
3605 (synopsis "Unified multiple testing procedures")
3606 (description
3607 "This package is designed to ease the application and comparison of
3608multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3609are standardized and usable by the accompanying mutossGUI package.")
3610 ;; Any version of the GPL.
3611 (license (list license:gpl2+ license:gpl3+))))
3612
bf770d92
RW
3613;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3614;; from Bioconductor, so we put it here.
3615(define-public r-metap
3616 (package
3617 (name "r-metap")
fd6412cd 3618 (version "1.3")
bf770d92
RW
3619 (source
3620 (origin
3621 (method url-fetch)
3622 (uri (cran-uri "metap" version))
3623 (sha256
3624 (base32
fd6412cd 3625 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
bf770d92
RW
3626 (build-system r-build-system)
3627 (propagated-inputs
3628 `(("r-lattice" ,r-lattice)
3629 ("r-mutoss" ,r-mutoss)
3630 ("r-rdpack" ,r-rdpack)
3631 ("r-tfisher" ,r-tfisher)))
3632 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3633 (synopsis "Meta-analysis of significance values")
3634 (description
3635 "The canonical way to perform meta-analysis involves using effect sizes.
3636When they are not available this package provides a number of methods for
3637meta-analysis of significance values including the methods of Edgington,
3638Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3639published results; and a routine for graphical display.")
3640 (license license:gpl2)))
3641
8a5460b4
RW
3642(define-public r-triform
3643 (package
3644 (name "r-triform")
ecb4e165 3645 (version "1.29.0")
8a5460b4
RW
3646 (source
3647 (origin
3648 (method url-fetch)
3649 (uri (bioconductor-uri "triform" version))
3650 (sha256
3651 (base32
ecb4e165 3652 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
8a5460b4
RW
3653 (build-system r-build-system)
3654 (propagated-inputs
3655 `(("r-biocgenerics" ,r-biocgenerics)
3656 ("r-iranges" ,r-iranges)
3657 ("r-yaml" ,r-yaml)))
3658 (home-page "https://bioconductor.org/packages/triform/")
3659 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3660 (description
3661 "The Triform algorithm uses model-free statistics to identify peak-like
3662distributions of TF ChIP sequencing reads, taking advantage of an improved
3663peak definition in combination with known profile characteristics.")
3664 (license license:gpl2)))
c538bcdd
RW
3665
3666(define-public r-varianttools
3667 (package
3668 (name "r-varianttools")
67837d4a 3669 (version "1.32.0")
c538bcdd
RW
3670 (source
3671 (origin
3672 (method url-fetch)
3673 (uri (bioconductor-uri "VariantTools" version))
3674 (sha256
3675 (base32
67837d4a 3676 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
c538bcdd
RW
3677 (properties `((upstream-name . "VariantTools")))
3678 (build-system r-build-system)
3679 (propagated-inputs
3680 `(("r-biobase" ,r-biobase)
3681 ("r-biocgenerics" ,r-biocgenerics)
3682 ("r-biocparallel" ,r-biocparallel)
3683 ("r-biostrings" ,r-biostrings)
3684 ("r-bsgenome" ,r-bsgenome)
3685 ("r-genomeinfodb" ,r-genomeinfodb)
3686 ("r-genomicfeatures" ,r-genomicfeatures)
3687 ("r-genomicranges" ,r-genomicranges)
3688 ("r-iranges" ,r-iranges)
3689 ("r-matrix" ,r-matrix)
3690 ("r-rsamtools" ,r-rsamtools)
3691 ("r-rtracklayer" ,r-rtracklayer)
3692 ("r-s4vectors" ,r-s4vectors)
3693 ("r-variantannotation" ,r-variantannotation)))
3694 (home-page "https://bioconductor.org/packages/VariantTools/")
3695 (synopsis "Tools for exploratory analysis of variant calls")
3696 (description
3697 "Explore, diagnose, and compare variant calls using filters. The
3698VariantTools package supports a workflow for loading data, calling single
3699sample variants and tumor-specific somatic mutations or other sample-specific
3700variant types (e.g., RNA editing). Most of the functions operate on
3701alignments (BAM files) or datasets of called variants. The user is expected
3702to have already aligned the reads with a separate tool, e.g., GSNAP via
3703gmapR.")
3704 (license license:artistic2.0)))
3e41919d
RW
3705
3706(define-public r-heatplus
3707 (package
3708 (name "r-heatplus")
9813d24d 3709 (version "2.36.0")
3e41919d
RW
3710 (source
3711 (origin
3712 (method url-fetch)
3713 (uri (bioconductor-uri "Heatplus" version))
3714 (sha256
3715 (base32
9813d24d 3716 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
3e41919d
RW
3717 (properties `((upstream-name . "Heatplus")))
3718 (build-system r-build-system)
3719 (propagated-inputs
3720 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3721 (home-page "https://github.com/alexploner/Heatplus")
3722 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3723 (description
3724 "This package provides tools to display a rectangular heatmap (intensity
3725plot) of a data matrix. By default, both samples (columns) and features (row)
3726of the matrix are sorted according to a hierarchical clustering, and the
3727corresponding dendrogram is plotted. Optionally, panels with additional
3728information about samples and features can be added to the plot.")
3729 (license license:gpl2+)))
c04f230e
RW
3730
3731(define-public r-gosemsim
3732 (package
3733 (name "r-gosemsim")
b2084e4d 3734 (version "2.16.1")
c04f230e
RW
3735 (source
3736 (origin
3737 (method url-fetch)
3738 (uri (bioconductor-uri "GOSemSim" version))
3739 (sha256
3740 (base32
b2084e4d 3741 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
c04f230e
RW
3742 (properties `((upstream-name . "GOSemSim")))
3743 (build-system r-build-system)
3744 (propagated-inputs
3745 `(("r-annotationdbi" ,r-annotationdbi)
3746 ("r-go-db" ,r-go-db)
3747 ("r-rcpp" ,r-rcpp)))
d5951dc4
RW
3748 (native-inputs
3749 `(("r-knitr" ,r-knitr)))
c04f230e
RW
3750 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3751 (synopsis "GO-terms semantic similarity measures")
3752 (description
3753 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3754quantitative ways to compute similarities between genes and gene groups, and
3755have became important basis for many bioinformatics analysis approaches.
3756GOSemSim is an R package for semantic similarity computation among GO terms,
3757sets of GO terms, gene products and gene clusters.")
3758 (license license:artistic2.0)))
9d0f7942
RW
3759
3760(define-public r-anota
3761 (package
3762 (name "r-anota")
33c905b9 3763 (version "1.38.0")
9d0f7942
RW
3764 (source
3765 (origin
3766 (method url-fetch)
3767 (uri (bioconductor-uri "anota" version))
3768 (sha256
3769 (base32
33c905b9 3770 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
9d0f7942
RW
3771 (build-system r-build-system)
3772 (propagated-inputs
3773 `(("r-multtest" ,r-multtest)
3774 ("r-qvalue" ,r-qvalue)))
3775 (home-page "https://bioconductor.org/packages/anota/")
3776 (synopsis "Analysis of translational activity")
3777 (description
3778 "Genome wide studies of translational control is emerging as a tool to
0cea26bd 3779study various biological conditions. The output from such analysis is both
7230f6d5 3780the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
9d0f7942
RW
3781involved in translation (the actively translating mRNA level) for each mRNA.
3782The standard analysis of such data strives towards identifying differential
3783translational between two or more sample classes - i.e. differences in
3784actively translated mRNA levels that are independent of underlying differences
3785in cytosolic mRNA levels. This package allows for such analysis using partial
3786variances and the random variance model. As 10s of thousands of mRNAs are
4f664004 3787analyzed in parallel the library performs a number of tests to assure that
9d0f7942
RW
3788the data set is suitable for such analysis.")
3789 (license license:gpl3)))
a6d867fe
RW
3790
3791(define-public r-sigpathway
3792 (package
3793 (name "r-sigpathway")
7dabc629 3794 (version "1.58.0")
a6d867fe
RW
3795 (source
3796 (origin
3797 (method url-fetch)
3798 (uri (bioconductor-uri "sigPathway" version))
3799 (sha256
3800 (base32
7dabc629 3801 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
a6d867fe
RW
3802 (properties `((upstream-name . "sigPathway")))
3803 (build-system r-build-system)
3804 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3805 (synopsis "Pathway analysis")
3806 (description
3807 "This package is used to conduct pathway analysis by calculating the NT_k
3808and NE_k statistics in a statistical framework for determining whether a
3809specified group of genes for a pathway has a coordinated association with a
3810phenotype of interest.")
3811 (license license:gpl2)))
af26c7ae
RW
3812
3813(define-public r-fgsea
3814 (package
3815 (name "r-fgsea")
d68a9ffa 3816 (version "1.16.0")
af26c7ae
RW
3817 (source
3818 (origin
3819 (method url-fetch)
3820 (uri (bioconductor-uri "fgsea" version))
3821 (sha256
3822 (base32
d68a9ffa 3823 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
af26c7ae
RW
3824 (build-system r-build-system)
3825 (propagated-inputs
ebffd24c
RW
3826 `(("r-bh" ,r-bh)
3827 ("r-biocparallel" ,r-biocparallel)
af26c7ae
RW
3828 ("r-data-table" ,r-data-table)
3829 ("r-fastmatch" ,r-fastmatch)
3830 ("r-ggplot2" ,r-ggplot2)
3831 ("r-gridextra" ,r-gridextra)
3832 ("r-matrix" ,r-matrix)
3833 ("r-rcpp" ,r-rcpp)))
1dec455c
RW
3834 (native-inputs
3835 `(("r-knitr" ,r-knitr)))
af26c7ae
RW
3836 (home-page "https://github.com/ctlab/fgsea/")
3837 (synopsis "Fast gene set enrichment analysis")
3838 (description
3839 "The package implements an algorithm for fast gene set enrichment
23c8ef71
VC
3840analysis. Using the fast algorithm makes more permutations and gets
3841more fine grained p-values, which allows using accurate standard approaches
af26c7ae
RW
3842to multiple hypothesis correction.")
3843 (license license:expat)))
305050b5
RW
3844
3845(define-public r-dose
3846 (package
3847 (name "r-dose")
aeb1d56f 3848 (version "3.16.0")
305050b5
RW
3849 (source
3850 (origin
3851 (method url-fetch)
3852 (uri (bioconductor-uri "DOSE" version))
3853 (sha256
3854 (base32
aeb1d56f 3855 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
305050b5
RW
3856 (properties `((upstream-name . "DOSE")))
3857 (build-system r-build-system)
3858 (propagated-inputs
3859 `(("r-annotationdbi" ,r-annotationdbi)
3860 ("r-biocparallel" ,r-biocparallel)
3861 ("r-do-db" ,r-do-db)
3862 ("r-fgsea" ,r-fgsea)
3863 ("r-ggplot2" ,r-ggplot2)
3864 ("r-gosemsim" ,r-gosemsim)
3865 ("r-qvalue" ,r-qvalue)
3a80f1cf 3866 ("r-reshape2" ,r-reshape2)))
5ef2b749
RW
3867 (native-inputs
3868 `(("r-knitr" ,r-knitr)))
305050b5
RW
3869 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3870 (synopsis "Disease ontology semantic and enrichment analysis")
3871 (description
3872 "This package implements five methods proposed by Resnik, Schlicker,
3873Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3874@dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3875including hypergeometric model and gene set enrichment analysis are also
3876implemented for discovering disease associations of high-throughput biological
3877data.")
3878 (license license:artistic2.0)))
9c30cf65
RW
3879
3880(define-public r-enrichplot
3881 (package
3882 (name "r-enrichplot")
eb3d17eb 3883 (version "1.10.1")
9c30cf65
RW
3884 (source
3885 (origin
3886 (method url-fetch)
3887 (uri (bioconductor-uri "enrichplot" version))
3888 (sha256
3889 (base32
eb3d17eb 3890 "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd"))))
9c30cf65
RW
3891 (build-system r-build-system)
3892 (propagated-inputs
eb3d17eb 3893 `(("r-cowplot" ,r-cowplot)
9c30cf65 3894 ("r-dose" ,r-dose)
9c30cf65 3895 ("r-ggplot2" ,r-ggplot2)
9c30cf65 3896 ("r-ggraph" ,r-ggraph)
9c30cf65 3897 ("r-gosemsim" ,r-gosemsim)
9c30cf65 3898 ("r-igraph" ,r-igraph)
eb3d17eb 3899 ("r-magrittr" ,r-magrittr)
43fb14ce 3900 ("r-plyr" ,r-plyr)
9c30cf65
RW
3901 ("r-purrr" ,r-purrr)
3902 ("r-rcolorbrewer" ,r-rcolorbrewer)
43fb14ce 3903 ("r-reshape2" ,r-reshape2)
eb3d17eb
RJ
3904 ("r-scatterpie" ,r-scatterpie)
3905 ("r-shadowtext" ,r-shadowtext)))
43fb14ce
RW
3906 (native-inputs
3907 `(("r-knitr" ,r-knitr)))
9c30cf65
RW
3908 (home-page "https://github.com/GuangchuangYu/enrichplot")
3909 (synopsis "Visualization of functional enrichment result")
3910 (description
3911 "The enrichplot package implements several visualization methods for
3912interpreting functional enrichment results obtained from ORA or GSEA analyses.
3913All the visualization methods are developed based on ggplot2 graphics.")
3914 (license license:artistic2.0)))
f8295ee6
RW
3915
3916(define-public r-clusterprofiler
3917 (package
3918 (name "r-clusterprofiler")
3fd84a46 3919 (version "3.18.0")
f8295ee6
RW
3920 (source
3921 (origin
3922 (method url-fetch)
3923 (uri (bioconductor-uri "clusterProfiler" version))
3924 (sha256
3925 (base32
3fd84a46 3926 "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9"))))
f8295ee6
RW
3927 (properties
3928 `((upstream-name . "clusterProfiler")))
3929 (build-system r-build-system)
3930 (propagated-inputs
3931 `(("r-annotationdbi" ,r-annotationdbi)
3932 ("r-dose" ,r-dose)
63c8323a
RW
3933 ("r-downloader" ,r-downloader)
3934 ("r-dplyr" ,r-dplyr)
f8295ee6 3935 ("r-enrichplot" ,r-enrichplot)
f8295ee6
RW
3936 ("r-go-db" ,r-go-db)
3937 ("r-gosemsim" ,r-gosemsim)
3938 ("r-magrittr" ,r-magrittr)
3939 ("r-plyr" ,r-plyr)
3940 ("r-qvalue" ,r-qvalue)
69f3b278 3941 ("r-rlang" ,r-rlang)
f8295ee6
RW
3942 ("r-rvcheck" ,r-rvcheck)
3943 ("r-tidyr" ,r-tidyr)))
63c8323a
RW
3944 (native-inputs
3945 `(("r-knitr" ,r-knitr)))
f8295ee6
RW
3946 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3947 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3948 (description
3949 "This package implements methods to analyze and visualize functional
3950profiles (GO and KEGG) of gene and gene clusters.")
3951 (license license:artistic2.0)))
ce77562a
RW
3952
3953(define-public r-mlinterfaces
3954 (package
3955 (name "r-mlinterfaces")
4f82931d 3956 (version "1.70.0")
ce77562a
RW
3957 (source
3958 (origin
3959 (method url-fetch)
3960 (uri (bioconductor-uri "MLInterfaces" version))
3961 (sha256
3962 (base32
4f82931d 3963 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
ce77562a
RW
3964 (properties `((upstream-name . "MLInterfaces")))
3965 (build-system r-build-system)
3966 (propagated-inputs
3967 `(("r-annotate" ,r-annotate)
3968 ("r-biobase" ,r-biobase)
3969 ("r-biocgenerics" ,r-biocgenerics)
3970 ("r-cluster" ,r-cluster)
3971 ("r-fpc" ,r-fpc)
3972 ("r-gbm" ,r-gbm)
3973 ("r-gdata" ,r-gdata)
3974 ("r-genefilter" ,r-genefilter)
3975 ("r-ggvis" ,r-ggvis)
3976 ("r-hwriter" ,r-hwriter)
3977 ("r-mass" ,r-mass)
3978 ("r-mlbench" ,r-mlbench)
3979 ("r-pls" ,r-pls)
3980 ("r-rcolorbrewer" ,r-rcolorbrewer)
500f7df8 3981 ("r-rcpp" ,r-rcpp)
ce77562a
RW
3982 ("r-rpart" ,r-rpart)
3983 ("r-sfsmisc" ,r-sfsmisc)
3984 ("r-shiny" ,r-shiny)
3985 ("r-threejs" ,r-threejs)))
3986 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3987 (synopsis "Interfaces to R machine learning procedures")
3988 (description
3989 "This package provides uniform interfaces to machine learning code for
3990data in R and Bioconductor containers.")
3991 ;; Any version of the LGPL.
3992 (license license:lgpl2.1+)))
a793e88c
RW
3993
3994(define-public r-annaffy
3995 (package
3996 (name "r-annaffy")
d200b4dc 3997 (version "1.60.0")
a793e88c
RW
3998 (source
3999 (origin
4000 (method url-fetch)
4001 (uri (bioconductor-uri "annaffy" version))
4002 (sha256
4003 (base32
d200b4dc 4004 "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4"))))
a793e88c
RW
4005 (build-system r-build-system)
4006 (arguments
4007 `(#:phases
4008 (modify-phases %standard-phases
4009 (add-after 'unpack 'remove-reference-to-non-free-data
4010 (lambda _
4011 (substitute* "DESCRIPTION"
4012 ((", KEGG.db") ""))
4013 #t)))))
4014 (propagated-inputs
4015 `(("r-annotationdbi" ,r-annotationdbi)
4016 ("r-biobase" ,r-biobase)
4017 ("r-dbi" ,r-dbi)
4018 ("r-go-db" ,r-go-db)))
4019 (home-page "https://bioconductor.org/packages/annaffy/")
4020 (synopsis "Annotation tools for Affymetrix biological metadata")
4021 (description
4022 "This package provides functions for handling data from Bioconductor
4023Affymetrix annotation data packages. It produces compact HTML and text
4024reports including experimental data and URL links to many online databases.
4025It allows searching of biological metadata using various criteria.")
4026 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
4027 ;; the LGPL 2.1 is included.
4028 (license license:lgpl2.1+)))
0ec0a5ec
RW
4029
4030(define-public r-a4core
4031 (package
4032 (name "r-a4core")
c47a8cd9 4033 (version "1.38.0")
0ec0a5ec
RW
4034 (source
4035 (origin
4036 (method url-fetch)
4037 (uri (bioconductor-uri "a4Core" version))
4038 (sha256
4039 (base32
c47a8cd9 4040 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
0ec0a5ec
RW
4041 (properties `((upstream-name . "a4Core")))
4042 (build-system r-build-system)
4043 (propagated-inputs
4044 `(("r-biobase" ,r-biobase)
4045 ("r-glmnet" ,r-glmnet)))
c47a8cd9 4046 (native-inputs
4047 `(("r-knitr" ,r-knitr)))
0ec0a5ec
RW
4048 (home-page "https://bioconductor.org/packages/a4Core")
4049 (synopsis "Automated Affymetrix array analysis core package")
4050 (description
4051 "This is the core package for the automated analysis of Affymetrix
4052arrays.")
4053 (license license:gpl3)))
9ae37581
RW
4054
4055(define-public r-a4classif
4056 (package
4057 (name "r-a4classif")
fa51705f 4058 (version "1.38.0")
9ae37581
RW
4059 (source
4060 (origin
4061 (method url-fetch)
4062 (uri (bioconductor-uri "a4Classif" version))
4063 (sha256
4064 (base32
fa51705f 4065 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
9ae37581
RW
4066 (properties `((upstream-name . "a4Classif")))
4067 (build-system r-build-system)
4068 (propagated-inputs
4069 `(("r-a4core" ,r-a4core)
4070 ("r-a4preproc" ,r-a4preproc)
fa51705f 4071 ("r-biobase" ,r-biobase)
9ae37581 4072 ("r-glmnet" ,r-glmnet)
9ae37581
RW
4073 ("r-pamr" ,r-pamr)
4074 ("r-rocr" ,r-rocr)
4075 ("r-varselrf" ,r-varselrf)))
fa51705f 4076 (native-inputs
4077 `(("r-knitr" ,r-knitr)))
9ae37581
RW
4078 (home-page "https://bioconductor.org/packages/a4Classif/")
4079 (synopsis "Automated Affymetrix array analysis classification package")
4080 (description
4081 "This is the classification package for the automated analysis of
4082Affymetrix arrays.")
4083 (license license:gpl3)))
b8d13e2c
RW
4084
4085(define-public r-a4preproc
4086 (package
4087 (name "r-a4preproc")
85155e2e 4088 (version "1.38.0")
b8d13e2c
RW
4089 (source
4090 (origin
4091 (method url-fetch)
4092 (uri (bioconductor-uri "a4Preproc" version))
4093 (sha256
4094 (base32
85155e2e 4095 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
b8d13e2c
RW
4096 (properties `((upstream-name . "a4Preproc")))
4097 (build-system r-build-system)
4098 (propagated-inputs
85155e2e 4099 `(("r-biobase" ,r-biobase)
4100 ("r-biocgenerics" ,r-biocgenerics)))
4101 (native-inputs
4102 `(("r-knitr" ,r-knitr)))
b8d13e2c
RW
4103 (home-page "https://bioconductor.org/packages/a4Preproc/")
4104 (synopsis "Automated Affymetrix array analysis preprocessing package")
4105 (description
4106 "This is a package for the automated analysis of Affymetrix arrays. It
4107is used for preprocessing the arrays.")
4108 (license license:gpl3)))
8e15f861
RW
4109
4110(define-public r-a4reporting
4111 (package
4112 (name "r-a4reporting")
2fb8298c 4113 (version "1.38.0")
8e15f861
RW
4114 (source
4115 (origin
4116 (method url-fetch)
4117 (uri (bioconductor-uri "a4Reporting" version))
4118 (sha256
4119 (base32
2fb8298c 4120 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
8e15f861
RW
4121 (properties `((upstream-name . "a4Reporting")))
4122 (build-system r-build-system)
4123 (propagated-inputs
2fb8298c 4124 `(("r-xtable" ,r-xtable)))
4125 (native-inputs
4126 `(("r-knitr" ,r-knitr)))
8e15f861
RW
4127 (home-page "https://bioconductor.org/packages/a4Reporting/")
4128 (synopsis "Automated Affymetrix array analysis reporting package")
4129 (description
4130 "This is a package for the automated analysis of Affymetrix arrays. It
4131provides reporting features.")
4132 (license license:gpl3)))
dbfe3375
RW
4133
4134(define-public r-a4base
4135 (package
4136 (name "r-a4base")
564d4279 4137 (version "1.38.0")
dbfe3375
RW
4138 (source
4139 (origin
4140 (method url-fetch)
4141 (uri (bioconductor-uri "a4Base" version))
4142 (sha256
4143 (base32
564d4279 4144 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
dbfe3375
RW
4145 (properties `((upstream-name . "a4Base")))
4146 (build-system r-build-system)
4147 (propagated-inputs
4148 `(("r-a4core" ,r-a4core)
4149 ("r-a4preproc" ,r-a4preproc)
4150 ("r-annaffy" ,r-annaffy)
dbfe3375
RW
4151 ("r-biobase" ,r-biobase)
4152 ("r-genefilter" ,r-genefilter)
4153 ("r-glmnet" ,r-glmnet)
4154 ("r-gplots" ,r-gplots)
4155 ("r-limma" ,r-limma)
4156 ("r-mpm" ,r-mpm)
4157 ("r-multtest" ,r-multtest)))
4158 (home-page "https://bioconductor.org/packages/a4Base/")
4159 (synopsis "Automated Affymetrix array analysis base package")
4160 (description
4161 "This package provides basic features for the automated analysis of
4162Affymetrix arrays.")
4163 (license license:gpl3)))
84ad024e
RW
4164
4165(define-public r-a4
4166 (package
4167 (name "r-a4")
68efaafe 4168 (version "1.38.0")
84ad024e
RW
4169 (source
4170 (origin
4171 (method url-fetch)
4172 (uri (bioconductor-uri "a4" version))
4173 (sha256
4174 (base32
68efaafe 4175 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
84ad024e
RW
4176 (build-system r-build-system)
4177 (propagated-inputs
4178 `(("r-a4base" ,r-a4base)
4179 ("r-a4classif" ,r-a4classif)
4180 ("r-a4core" ,r-a4core)
4181 ("r-a4preproc" ,r-a4preproc)
4182 ("r-a4reporting" ,r-a4reporting)))
4183 (home-page "https://bioconductor.org/packages/a4/")
4184 (synopsis "Automated Affymetrix array analysis umbrella package")
4185 (description
4186 "This package provides a software suite for the automated analysis of
4187Affymetrix arrays.")
4188 (license license:gpl3)))
59d331f1
RW
4189
4190(define-public r-abseqr
4191 (package
4192 (name "r-abseqr")
8816139e 4193 (version "1.8.0")
59d331f1
RW
4194 (source
4195 (origin
4196 (method url-fetch)
4197 (uri (bioconductor-uri "abseqR" version))
4198 (sha256
4199 (base32
8816139e 4200 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
59d331f1
RW
4201 (properties `((upstream-name . "abseqR")))
4202 (build-system r-build-system)
4203 (inputs
8816139e 4204 `(("pandoc" ,pandoc)))
59d331f1
RW
4205 (propagated-inputs
4206 `(("r-biocparallel" ,r-biocparallel)
4207 ("r-biocstyle" ,r-biocstyle)
4208 ("r-circlize" ,r-circlize)
4209 ("r-flexdashboard" ,r-flexdashboard)
4210 ("r-ggcorrplot" ,r-ggcorrplot)
4211 ("r-ggdendro" ,r-ggdendro)
4212 ("r-ggplot2" ,r-ggplot2)
4213 ("r-gridextra" ,r-gridextra)
4214 ("r-knitr" ,r-knitr)
4215 ("r-plotly" ,r-plotly)
4216 ("r-plyr" ,r-plyr)
4217 ("r-png" ,r-png)
4218 ("r-rcolorbrewer" ,r-rcolorbrewer)
4219 ("r-reshape2" ,r-reshape2)
4220 ("r-rmarkdown" ,r-rmarkdown)
4221 ("r-stringr" ,r-stringr)
4222 ("r-vegan" ,r-vegan)
4223 ("r-venndiagram" ,r-venndiagram)))
35bcfaef
RW
4224 (native-inputs
4225 `(("r-knitr" ,r-knitr)))
59d331f1
RW
4226 (home-page "https://github.com/malhamdoosh/abseqR")
4227 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4228 (description
4229 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4230sequencing datasets generated from antibody libraries and abseqR is one of its
4231packages. AbseqR empowers the users of abseqPy with plotting and reporting
4232capabilities and allows them to generate interactive HTML reports for the
4233convenience of viewing and sharing with other researchers. Additionally,
4234abseqR extends abseqPy to compare multiple repertoire analyses and perform
4235further downstream analysis on its output.")
4236 (license license:gpl3)))
41aab7d1
RW
4237
4238(define-public r-bacon
4239 (package
4240 (name "r-bacon")
d5dcf1bb 4241 (version "1.18.0")
41aab7d1
RW
4242 (source
4243 (origin
4244 (method url-fetch)
4245 (uri (bioconductor-uri "bacon" version))
4246 (sha256
4247 (base32
d5dcf1bb 4248 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
41aab7d1
RW
4249 (build-system r-build-system)
4250 (propagated-inputs
4251 `(("r-biocparallel" ,r-biocparallel)
4252 ("r-ellipse" ,r-ellipse)
4253 ("r-ggplot2" ,r-ggplot2)))
506cbeab
RW
4254 (native-inputs
4255 `(("r-knitr" ,r-knitr)))
41aab7d1
RW
4256 (home-page "https://bioconductor.org/packages/bacon/")
4257 (synopsis "Controlling bias and inflation in association studies")
4258 (description
4259 "Bacon can be used to remove inflation and bias often observed in
4260epigenome- and transcriptome-wide association studies. To this end bacon
4261constructs an empirical null distribution using a Gibbs Sampling algorithm by
4262fitting a three-component normal mixture on z-scores.")
4263 (license license:gpl2+)))
051e8e1a
RW
4264
4265(define-public r-rgadem
4266 (package
4267 (name "r-rgadem")
41071edc 4268 (version "2.38.0")
051e8e1a
RW
4269 (source
4270 (origin
4271 (method url-fetch)
4272 (uri (bioconductor-uri "rGADEM" version))
4273 (sha256
4274 (base32
41071edc 4275 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
051e8e1a
RW
4276 (properties `((upstream-name . "rGADEM")))
4277 (build-system r-build-system)
4278 (propagated-inputs
4279 `(("r-biostrings" ,r-biostrings)
4280 ("r-bsgenome" ,r-bsgenome)
07189489 4281 ("r-genomicranges" ,r-genomicranges)
051e8e1a
RW
4282 ("r-iranges" ,r-iranges)
4283 ("r-seqlogo" ,r-seqlogo)))
4284 (home-page "https://bioconductor.org/packages/rGADEM/")
4285 (synopsis "De novo sequence motif discovery")
4286 (description
4287 "rGADEM is an efficient de novo motif discovery tool for large-scale
4288genomic sequence data.")
4289 (license license:artistic2.0)))
229f97c3
RW
4290
4291(define-public r-motiv
4292 (package
4293 (name "r-motiv")
352cfa34 4294 (version "1.43.0")
229f97c3
RW
4295 (source
4296 (origin
4297 (method url-fetch)
4298 (uri (bioconductor-uri "MotIV" version))
4299 (sha256
4300 (base32
352cfa34 4301 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
229f97c3
RW
4302 (properties `((upstream-name . "MotIV")))
4303 (build-system r-build-system)
4304 (inputs
4305 `(("gsl" ,gsl)))
4306 (propagated-inputs
4307 `(("r-biocgenerics" ,r-biocgenerics)
4308 ("r-biostrings" ,r-biostrings)
35a1b3ec 4309 ("r-genomicranges" ,r-genomicranges)
229f97c3
RW
4310 ("r-iranges" ,r-iranges)
4311 ("r-lattice" ,r-lattice)
4312 ("r-rgadem" ,r-rgadem)
4313 ("r-s4vectors" ,r-s4vectors)))
4314 (home-page "https://bioconductor.org/packages/MotIV/")
4315 (synopsis "Motif identification and validation")
4316 (description
4317 "This package is used for the identification and validation of sequence
4318motifs. It makes use of STAMP for comparing a set of motifs to a given
4319database (e.g. JASPAR). It can also be used to visualize motifs, motif
4320distributions, modules and filter motifs.")
4321 (license license:gpl2)))
2a72ef56 4322
3699bcf5
RJ
4323(define-public r-motifdb
4324 (package
4325 (name "r-motifdb")
a2bae167 4326 (version "1.32.0")
3699bcf5
RJ
4327 (source (origin
4328 (method url-fetch)
4329 (uri (bioconductor-uri "MotifDb" version))
4330 (sha256
a2bae167 4331 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
3699bcf5
RJ
4332 (properties `((upstream-name . "MotifDb")))
4333 (build-system r-build-system)
4334 (propagated-inputs
4335 `(("r-biocgenerics" ,r-biocgenerics)
4336 ("r-biostrings" ,r-biostrings)
da6a75fe 4337 ("r-genomicranges" ,r-genomicranges)
3699bcf5
RJ
4338 ("r-iranges" ,r-iranges)
4339 ("r-rtracklayer" ,r-rtracklayer)
4340 ("r-s4vectors" ,r-s4vectors)
4341 ("r-splitstackshape" ,r-splitstackshape)))
da6a75fe
RW
4342 (native-inputs
4343 `(("r-knitr" ,r-knitr)))
3699bcf5
RJ
4344 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4345 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4346 (description "This package provides more than 2000 annotated position
4347frequency matrices from nine public sources, for multiple organisms.")
4348 (license license:artistic2.0)))
4349
886125d7
RJ
4350(define-public r-motifbreakr
4351 (package
4352 (name "r-motifbreakr")
301e549c 4353 (version "2.4.0")
886125d7
RJ
4354 (source (origin
4355 (method url-fetch)
4356 (uri (bioconductor-uri "motifbreakR" version))
4357 (sha256
301e549c 4358 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
886125d7
RJ
4359 (properties `((upstream-name . "motifbreakR")))
4360 (build-system r-build-system)
4361 (propagated-inputs
e65783e0
RW
4362 `(("r-biocgenerics" ,r-biocgenerics)
4363 ("r-biocparallel" ,r-biocparallel)
886125d7
RJ
4364 ("r-biostrings" ,r-biostrings)
4365 ("r-bsgenome" ,r-bsgenome)
e65783e0
RW
4366 ("r-genomeinfodb" ,r-genomeinfodb)
4367 ("r-genomicranges" ,r-genomicranges)
4368 ("r-grimport" ,r-grimport)
886125d7 4369 ("r-gviz" ,r-gviz)
e65783e0 4370 ("r-iranges" ,r-iranges)
886125d7 4371 ("r-matrixstats" ,r-matrixstats)
e65783e0
RW
4372 ("r-motifdb" ,r-motifdb)
4373 ("r-motifstack" ,r-motifstack)
4374 ("r-rtracklayer" ,r-rtracklayer)
4375 ("r-s4vectors" ,r-s4vectors)
4376 ("r-stringr" ,r-stringr)
4377 ("r-summarizedexperiment" ,r-summarizedexperiment)
886125d7 4378 ("r-tfmpvalue" ,r-tfmpvalue)
e65783e0
RW
4379 ("r-variantannotation" ,r-variantannotation)))
4380 (native-inputs
4381 `(("r-knitr" ,r-knitr)))
886125d7
RJ
4382 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4383 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4384 (description "This package allows biologists to judge in the first place
4385whether the sequence surrounding the polymorphism is a good match, and in
4386the second place how much information is gained or lost in one allele of
4387the polymorphism relative to another. This package gives a choice of
4388algorithms for interrogation of genomes with motifs from public sources:
4389@enumerate
4390@item a weighted-sum probability matrix;
4391@item log-probabilities;
4392@item weighted by relative entropy.
4393@end enumerate
4394
4395This package can predict effects for novel or previously described variants in
4396public databases, making it suitable for tasks beyond the scope of its original
4397design. Lastly, it can be used to interrogate any genome curated within
4398Bioconductor.")
4399 (license license:gpl2+)))
4400
2a72ef56
RW
4401(define-public r-motifstack
4402 (package
4403 (name "r-motifstack")
4b4cd2b8 4404 (version "1.34.0")
2a72ef56
RW
4405 (source
4406 (origin
4407 (method url-fetch)
4408 (uri (bioconductor-uri "motifStack" version))
4409 (sha256
4410 (base32
4b4cd2b8 4411 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
2a72ef56
RW
4412 (properties `((upstream-name . "motifStack")))
4413 (build-system r-build-system)
4414 (propagated-inputs
4415 `(("r-ade4" ,r-ade4)
4416 ("r-biostrings" ,r-biostrings)
dda936ca 4417 ("r-ggplot2" ,r-ggplot2)
2a72ef56 4418 ("r-htmlwidgets" ,r-htmlwidgets)
2a72ef56 4419 ("r-xml" ,r-xml)))
e6fbaf0c
RW
4420 (native-inputs
4421 `(("r-knitr" ,r-knitr)))
2a72ef56
RW
4422 (home-page "https://bioconductor.org/packages/motifStack/")
4423 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4424 (description
4425 "The motifStack package is designed for graphic representation of
4426multiple motifs with different similarity scores. It works with both DNA/RNA
4427sequence motifs and amino acid sequence motifs. In addition, it provides the
4428flexibility for users to customize the graphic parameters such as the font
4429type and symbol colors.")
4430 (license license:gpl2+)))
e5bff307
RW
4431
4432(define-public r-genomicscores
4433 (package
4434 (name "r-genomicscores")
39280618 4435 (version "2.2.0")
e5bff307
RW
4436 (source
4437 (origin
4438 (method url-fetch)
4439 (uri (bioconductor-uri "GenomicScores" version))
4440 (sha256
4441 (base32
39280618 4442 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
e5bff307
RW
4443 (properties `((upstream-name . "GenomicScores")))
4444 (build-system r-build-system)
4445 (propagated-inputs
4446 `(("r-annotationhub" ,r-annotationhub)
4447 ("r-biobase" ,r-biobase)
39280618 4448 ("r-biocfilecache" ,r-biocfilecache)
e5bff307 4449 ("r-biocgenerics" ,r-biocgenerics)
39280618 4450 ("r-biocmanager" ,r-biocmanager)
e5bff307 4451 ("r-biostrings" ,r-biostrings)
785c7596 4452 ("r-delayedarray" ,r-delayedarray)
e5bff307
RW
4453 ("r-genomeinfodb" ,r-genomeinfodb)
4454 ("r-genomicranges" ,r-genomicranges)
785c7596 4455 ("r-hdf5array" ,r-hdf5array)
e5bff307 4456 ("r-iranges" ,r-iranges)
785c7596 4457 ("r-rhdf5" ,r-rhdf5)
e5bff307
RW
4458 ("r-s4vectors" ,r-s4vectors)
4459 ("r-xml" ,r-xml)))
785c7596
RW
4460 (native-inputs
4461 `(("r-knitr" ,r-knitr)))
e5bff307
RW
4462 (home-page "https://github.com/rcastelo/GenomicScores/")
4463 (synopsis "Work with genome-wide position-specific scores")
4464 (description
4465 "This package provides infrastructure to store and access genome-wide
4466position-specific scores within R and Bioconductor.")
4467 (license license:artistic2.0)))
32e0f906
RW
4468
4469(define-public r-atacseqqc
4470 (package
4471 (name "r-atacseqqc")
2ba61c67 4472 (version "1.14.4")
32e0f906
RW
4473 (source
4474 (origin
4475 (method url-fetch)
4476 (uri (bioconductor-uri "ATACseqQC" version))
4477 (sha256
4478 (base32
2ba61c67 4479 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
32e0f906
RW
4480 (properties `((upstream-name . "ATACseqQC")))
4481 (build-system r-build-system)
4482 (propagated-inputs
4483 `(("r-biocgenerics" ,r-biocgenerics)
4484 ("r-biostrings" ,r-biostrings)
4485 ("r-bsgenome" ,r-bsgenome)
4486 ("r-chippeakanno" ,r-chippeakanno)
bcc233c1 4487 ("r-edger" ,r-edger)
32e0f906
RW
4488 ("r-genomeinfodb" ,r-genomeinfodb)
4489 ("r-genomicalignments" ,r-genomicalignments)
4490 ("r-genomicranges" ,r-genomicranges)
4491 ("r-genomicscores" ,r-genomicscores)
4492 ("r-iranges" ,r-iranges)
4493 ("r-kernsmooth" ,r-kernsmooth)
4494 ("r-limma" ,r-limma)
4495 ("r-motifstack" ,r-motifstack)
4496 ("r-preseqr" ,r-preseqr)
4497 ("r-randomforest" ,r-randomforest)
4498 ("r-rsamtools" ,r-rsamtools)
4499 ("r-rtracklayer" ,r-rtracklayer)
4500 ("r-s4vectors" ,r-s4vectors)))
dc30cc03
RW
4501 (native-inputs
4502 `(("r-knitr" ,r-knitr)))
32e0f906
RW
4503 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4504 (synopsis "ATAC-seq quality control")
4505 (description
4506 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4507sequencing, is a rapid and sensitive method for chromatin accessibility
4508analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4509and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4510assess whether their ATAC-seq experiment is successful. It includes
4511diagnostic plots of fragment size distribution, proportion of mitochondria
4512reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4513footprints.")
4514 (license license:gpl2+)))
3972cfce
RW
4515
4516(define-public r-gofuncr
4517 (package
4518 (name "r-gofuncr")
c3b69d63 4519 (version "1.10.0")
3972cfce
RW
4520 (source
4521 (origin
4522 (method url-fetch)
4523 (uri (bioconductor-uri "GOfuncR" version))
4524 (sha256
4525 (base32
c3b69d63 4526 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
3972cfce
RW
4527 (properties `((upstream-name . "GOfuncR")))
4528 (build-system r-build-system)
4529 (propagated-inputs
4530 `(("r-annotationdbi" ,r-annotationdbi)
4531 ("r-genomicranges" ,r-genomicranges)
4532 ("r-gtools" ,r-gtools)
4533 ("r-iranges" ,r-iranges)
4534 ("r-mapplots" ,r-mapplots)
4535 ("r-rcpp" ,r-rcpp)
4536 ("r-vioplot" ,r-vioplot)))
028fd6f7
RW
4537 (native-inputs
4538 `(("r-knitr" ,r-knitr)))
3972cfce
RW
4539 (home-page "https://bioconductor.org/packages/GOfuncR/")
4540 (synopsis "Gene ontology enrichment using FUNC")
4541 (description
4542 "GOfuncR performs a gene ontology enrichment analysis based on the
4543ontology enrichment software FUNC. GO-annotations are obtained from
4544OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4545included in the package and updated regularly. GOfuncR provides the standard
4546candidate vs background enrichment analysis using the hypergeometric test, as
4547well as three additional tests:
4548
4549@enumerate
4550@item the Wilcoxon rank-sum test that is used when genes are ranked,
4551@item a binomial test that is used when genes are associated with two counts,
4552 and
4553@item a Chi-square or Fisher's exact test that is used in cases when genes are
4554associated with four counts.
4555@end enumerate
4556
4557To correct for multiple testing and interdependency of the tests, family-wise
4558error rates are computed based on random permutations of the gene-associated
4559variables. GOfuncR also provides tools for exploring the ontology graph and
4560the annotations, and options to take gene-length or spatial clustering of
4561genes into account. It is also possible to provide custom gene coordinates,
4562annotations and ontologies.")
4563 (license license:gpl2+)))
9bf4bb19
RW
4564
4565(define-public r-abaenrichment
4566 (package
4567 (name "r-abaenrichment")
8a7f7112 4568 (version "1.20.0")
9bf4bb19
RW
4569 (source
4570 (origin
4571 (method url-fetch)
4572 (uri (bioconductor-uri "ABAEnrichment" version))
4573 (sha256
4574 (base32
8a7f7112 4575 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
9bf4bb19
RW
4576 (properties `((upstream-name . "ABAEnrichment")))
4577 (build-system r-build-system)
4578 (propagated-inputs
4579 `(("r-abadata" ,r-abadata)
4580 ("r-data-table" ,r-data-table)
4581 ("r-gofuncr" ,r-gofuncr)
4582 ("r-gplots" ,r-gplots)
4583 ("r-gtools" ,r-gtools)
4584 ("r-rcpp" ,r-rcpp)))
6a65ac15
RW
4585 (native-inputs
4586 `(("r-knitr" ,r-knitr)))
9bf4bb19
RW
4587 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4588 (synopsis "Gene expression enrichment in human brain regions")
4589 (description
4590 "The package ABAEnrichment is designed to test for enrichment of user
4591defined candidate genes in the set of expressed genes in different human brain
4592regions. The core function @code{aba_enrich} integrates the expression of the
4593candidate gene set (averaged across donors) and the structural information of
4594the brain using an ontology, both provided by the Allen Brain Atlas project.")
4595 (license license:gpl2+)))
0b91b7b9
RW
4596
4597(define-public r-annotationfuncs
4598 (package
4599 (name "r-annotationfuncs")
bc12a4b6 4600 (version "1.40.0")
0b91b7b9
RW
4601 (source
4602 (origin
4603 (method url-fetch)
4604 (uri (bioconductor-uri "AnnotationFuncs" version))
4605 (sha256
4606 (base32
bc12a4b6 4607 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
0b91b7b9
RW
4608 (properties
4609 `((upstream-name . "AnnotationFuncs")))
4610 (build-system r-build-system)
4611 (propagated-inputs
4612 `(("r-annotationdbi" ,r-annotationdbi)
4613 ("r-dbi" ,r-dbi)))
4614 (home-page "https://www.iysik.com/r/annotationfuncs")
4615 (synopsis "Annotation translation functions")
4616 (description
4617 "This package provides functions for handling translating between
4618different identifieres using the Biocore Data Team data-packages (e.g.
4619@code{org.Bt.eg.db}).")
4620 (license license:gpl2)))
adf7d813
RW
4621
4622(define-public r-annotationtools
4623 (package
4624 (name "r-annotationtools")
57791542 4625 (version "1.64.0")
adf7d813
RW
4626 (source
4627 (origin
4628 (method url-fetch)
4629 (uri (bioconductor-uri "annotationTools" version))
4630 (sha256
4631 (base32
57791542 4632 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
adf7d813
RW
4633 (properties
4634 `((upstream-name . "annotationTools")))
4635 (build-system r-build-system)
4636 (propagated-inputs `(("r-biobase" ,r-biobase)))
4637 (home-page "https://bioconductor.org/packages/annotationTools/")
4638 (synopsis "Annotate microarrays and perform gene expression analyses")
4639 (description
4640 "This package provides functions to annotate microarrays, find orthologs,
4641and integrate heterogeneous gene expression profiles using annotation and
4642other molecular biology information available as flat file database (plain
4643text files).")
4644 ;; Any version of the GPL.
4645 (license (list license:gpl2+))))
f31e10f8
RW
4646
4647(define-public r-allelicimbalance
4648 (package
4649 (name "r-allelicimbalance")
85c6636b 4650 (version "1.28.0")
f31e10f8
RW
4651 (source
4652 (origin
4653 (method url-fetch)
4654 (uri (bioconductor-uri "AllelicImbalance" version))
4655 (sha256
4656 (base32
85c6636b 4657 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
f31e10f8
RW
4658 (properties
4659 `((upstream-name . "AllelicImbalance")))
4660 (build-system r-build-system)
4661 (propagated-inputs
4662 `(("r-annotationdbi" ,r-annotationdbi)
4663 ("r-biocgenerics" ,r-biocgenerics)
4664 ("r-biostrings" ,r-biostrings)
4665 ("r-bsgenome" ,r-bsgenome)
4666 ("r-genomeinfodb" ,r-genomeinfodb)
4667 ("r-genomicalignments" ,r-genomicalignments)
4668 ("r-genomicfeatures" ,r-genomicfeatures)
4669 ("r-genomicranges" ,r-genomicranges)
4670 ("r-gridextra" ,r-gridextra)
4671 ("r-gviz" ,r-gviz)
4672 ("r-iranges" ,r-iranges)
4673 ("r-lattice" ,r-lattice)
4674 ("r-latticeextra" ,r-latticeextra)
4675 ("r-nlme" ,r-nlme)
4676 ("r-rsamtools" ,r-rsamtools)
4677 ("r-s4vectors" ,r-s4vectors)
4678 ("r-seqinr" ,r-seqinr)
4679 ("r-summarizedexperiment" ,r-summarizedexperiment)
4680 ("r-variantannotation" ,r-variantannotation)))
63149388
RW
4681 (native-inputs
4682 `(("r-knitr" ,r-knitr)))
f31e10f8
RW
4683 (home-page "https://github.com/pappewaio/AllelicImbalance")
4684 (synopsis "Investigate allele-specific expression")
4685 (description
4686 "This package provides a framework for allele-specific expression
4687investigation using RNA-seq data.")
4688 (license license:gpl3)))
ffe7029b
RW
4689
4690(define-public r-aucell
4691 (package
4692 (name "r-aucell")
ff8b9153 4693 (version "1.12.0")
ffe7029b
RW
4694 (source
4695 (origin
4696 (method url-fetch)
4697 (uri (bioconductor-uri "AUCell" version))
4698 (sha256
4699 (base32
ff8b9153 4700 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
ffe7029b
RW
4701 (properties `((upstream-name . "AUCell")))
4702 (build-system r-build-system)
4703 (propagated-inputs
3a35d274
RW
4704 `(("r-biocgenerics" ,r-biocgenerics)
4705 ("r-data-table" ,r-data-table)
ffe7029b
RW
4706 ("r-gseabase" ,r-gseabase)
4707 ("r-mixtools" ,r-mixtools)
4708 ("r-r-utils" ,r-r-utils)
3a35d274 4709 ("r-s4vectors" ,r-s4vectors)
ffe7029b
RW
4710 ("r-shiny" ,r-shiny)
4711 ("r-summarizedexperiment" ,r-summarizedexperiment)))
e059ab25
RW
4712 (native-inputs
4713 `(("r-knitr" ,r-knitr)))
ffe7029b
RW
4714 (home-page "https://bioconductor.org/packages/AUCell/")
4715 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4716 (description
8c4bf6c2 4717 "AUCell identifies cells with active gene sets (e.g. signatures,
ffe7029b
RW
4718gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4719Under the Curve} (AUC) to calculate whether a critical subset of the input
4720gene set is enriched within the expressed genes for each cell. The
4721distribution of AUC scores across all the cells allows exploring the relative
4722expression of the signature. Since the scoring method is ranking-based,
4723AUCell is independent of the gene expression units and the normalization
4724procedure. In addition, since the cells are evaluated individually, it can
4725easily be applied to bigger datasets, subsetting the expression matrix if
4726needed.")
4727 (license license:gpl3)))
5cfa4bff
RW
4728
4729(define-public r-ebimage
4730 (package
4731 (name "r-ebimage")
ba0bf98d 4732 (version "4.32.0")
5cfa4bff
RW
4733 (source
4734 (origin
4735 (method url-fetch)
4736 (uri (bioconductor-uri "EBImage" version))
4737 (sha256
4738 (base32
ba0bf98d 4739 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
5cfa4bff
RW
4740 (properties `((upstream-name . "EBImage")))
4741 (build-system r-build-system)
4742 (propagated-inputs
4743 `(("r-abind" ,r-abind)
4744 ("r-biocgenerics" ,r-biocgenerics)
4745 ("r-fftwtools" ,r-fftwtools)
4746 ("r-htmltools" ,r-htmltools)
4747 ("r-htmlwidgets" ,r-htmlwidgets)
4748 ("r-jpeg" ,r-jpeg)
4749 ("r-locfit" ,r-locfit)
4750 ("r-png" ,r-png)
4751 ("r-rcurl" ,r-rcurl)
4752 ("r-tiff" ,r-tiff)))
4753 (native-inputs
4754 `(("r-knitr" ,r-knitr))) ; for vignettes
4755 (home-page "https://github.com/aoles/EBImage")
4756 (synopsis "Image processing and analysis toolbox for R")
4757 (description
4758 "EBImage provides general purpose functionality for image processing and
4759analysis. In the context of (high-throughput) microscopy-based cellular
4760assays, EBImage offers tools to segment cells and extract quantitative
4761cellular descriptors. This allows the automation of such tasks using the R
4762programming language and facilitates the use of other tools in the R
4763environment for signal processing, statistical modeling, machine learning and
4764visualization with image data.")
4765 ;; Any version of the LGPL.
4766 (license license:lgpl2.1+)))
51e98f7e
RW
4767
4768(define-public r-yamss
4769 (package
4770 (name "r-yamss")
65ba4ba5 4771 (version "1.16.0")
51e98f7e
RW
4772 (source
4773 (origin
4774 (method url-fetch)
4775 (uri (bioconductor-uri "yamss" version))
4776 (sha256
4777 (base32
65ba4ba5 4778 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
51e98f7e
RW
4779 (build-system r-build-system)
4780 (propagated-inputs
4781 `(("r-biocgenerics" ,r-biocgenerics)
4782 ("r-data-table" ,r-data-table)
4783 ("r-ebimage" ,r-ebimage)
4784 ("r-iranges" ,r-iranges)
4785 ("r-limma" ,r-limma)
4786 ("r-matrix" ,r-matrix)
4787 ("r-mzr" ,r-mzr)
4788 ("r-s4vectors" ,r-s4vectors)
4789 ("r-summarizedexperiment"
4790 ,r-summarizedexperiment)))
6e397aad
RW
4791 (native-inputs
4792 `(("r-knitr" ,r-knitr)))
51e98f7e
RW
4793 (home-page "https://github.com/hansenlab/yamss")
4794 (synopsis "Tools for high-throughput metabolomics")
4795 (description
4796 "This package provides tools to analyze and visualize high-throughput
9b19734c 4797metabolomics data acquired using chromatography-mass spectrometry. These tools
51e98f7e
RW
4798preprocess data in a way that enables reliable and powerful differential
4799analysis.")
4800 (license license:artistic2.0)))
398c4a93
RW
4801
4802(define-public r-gtrellis
4803 (package
4804 (name "r-gtrellis")
0836ef6b 4805 (version "1.22.0")
398c4a93
RW
4806 (source
4807 (origin
4808 (method url-fetch)
4809 (uri (bioconductor-uri "gtrellis" version))
4810 (sha256
4811 (base32
0836ef6b 4812 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
398c4a93
RW
4813 (build-system r-build-system)
4814 (propagated-inputs
4815 `(("r-circlize" ,r-circlize)
4816 ("r-genomicranges" ,r-genomicranges)
4817 ("r-getoptlong" ,r-getoptlong)
4818 ("r-iranges" ,r-iranges)))
a471def0
RW
4819 (native-inputs
4820 `(("r-knitr" ,r-knitr)))
398c4a93
RW
4821 (home-page "https://github.com/jokergoo/gtrellis")
4822 (synopsis "Genome level Trellis layout")
4823 (description
4824 "Genome level Trellis graph visualizes genomic data conditioned by
4825genomic categories (e.g. chromosomes). For each genomic category, multiple
4826dimensional data which are represented as tracks describe different features
4827from different aspects. This package provides high flexibility to arrange
4828genomic categories and to add self-defined graphics in the plot.")
4829 (license license:expat)))
28098414
RW
4830
4831(define-public r-somaticsignatures
4832 (package
4833 (name "r-somaticsignatures")
36f3a19a 4834 (version "2.26.0")
28098414
RW
4835 (source
4836 (origin
4837 (method url-fetch)
4838 (uri (bioconductor-uri "SomaticSignatures" version))
4839 (sha256
4840 (base32
36f3a19a 4841 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
28098414
RW
4842 (properties
4843 `((upstream-name . "SomaticSignatures")))
4844 (build-system r-build-system)
4845 (propagated-inputs
4846 `(("r-biobase" ,r-biobase)
4847 ("r-biostrings" ,r-biostrings)
4848 ("r-genomeinfodb" ,r-genomeinfodb)
4849 ("r-genomicranges" ,r-genomicranges)
4850 ("r-ggbio" ,r-ggbio)
4851 ("r-ggplot2" ,r-ggplot2)
4852 ("r-iranges" ,r-iranges)
4853 ("r-nmf" ,r-nmf)
4854 ("r-pcamethods" ,r-pcamethods)
4855 ("r-proxy" ,r-proxy)
4856 ("r-reshape2" ,r-reshape2)
4857 ("r-s4vectors" ,r-s4vectors)
4858 ("r-variantannotation" ,r-variantannotation)))
63c14717
RW
4859 (native-inputs
4860 `(("r-knitr" ,r-knitr)))
28098414
RW
4861 (home-page "https://github.com/juliangehring/SomaticSignatures")
4862 (synopsis "Somatic signatures")
4863 (description
4864 "This package identifies mutational signatures of @dfn{single nucleotide
4865variants} (SNVs). It provides a infrastructure related to the methodology
4866described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4867decomposition algorithms.")
4868 (license license:expat)))
303f2ed1
RW
4869
4870(define-public r-yapsa
4871 (package
4872 (name "r-yapsa")
8a5abc62 4873 (version "1.14.0")
303f2ed1
RW
4874 (source
4875 (origin
4876 (method url-fetch)
4877 (uri (bioconductor-uri "YAPSA" version))
4878 (sha256
4879 (base32
8a5abc62 4880 "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k"))))
303f2ed1
RW
4881 (properties `((upstream-name . "YAPSA")))
4882 (build-system r-build-system)
4883 (propagated-inputs
8a5abc62
RW
4884 `(("r-biostrings" ,r-biostrings)
4885 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
4886 ("r-circlize" ,r-circlize)
303f2ed1
RW
4887 ("r-complexheatmap" ,r-complexheatmap)
4888 ("r-corrplot" ,r-corrplot)
4889 ("r-dendextend" ,r-dendextend)
8a5abc62
RW
4890 ("r-doparallel" ,r-doparallel)
4891 ("r-dplyr" ,r-dplyr)
303f2ed1
RW
4892 ("r-genomeinfodb" ,r-genomeinfodb)
4893 ("r-genomicranges" ,r-genomicranges)
4894 ("r-getoptlong" ,r-getoptlong)
8a5abc62 4895 ("r-ggbeeswarm" ,r-ggbeeswarm)
303f2ed1
RW
4896 ("r-ggplot2" ,r-ggplot2)
4897 ("r-gridextra" ,r-gridextra)
4898 ("r-gtrellis" ,r-gtrellis)
4899 ("r-keggrest" ,r-keggrest)
4900 ("r-lsei" ,r-lsei)
8a5abc62 4901 ("r-magrittr" ,r-magrittr)
303f2ed1 4902 ("r-pmcmr" ,r-pmcmr)
8a5abc62 4903 ("r-pracma" ,r-pracma)
303f2ed1
RW
4904 ("r-reshape2" ,r-reshape2)
4905 ("r-somaticsignatures" ,r-somaticsignatures)
4906 ("r-variantannotation" ,r-variantannotation)))
8a5abc62
RW
4907 (native-inputs
4908 `(("r-knitr" ,r-knitr)))
303f2ed1
RW
4909 (home-page "https://bioconductor.org/packages/YAPSA/")
4910 (synopsis "Yet another package for signature analysis")
4911 (description
4912 "This package provides functions and routines useful in the analysis of
4913somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4914functions to perform a signature analysis with known signatures and a
4915signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4916provided.")
4917 (license license:gpl3)))
e99380d6
RW
4918
4919(define-public r-gcrma
4920 (package
4921 (name "r-gcrma")
3d41f0c2 4922 (version "2.62.0")
e99380d6
RW
4923 (source
4924 (origin
4925 (method url-fetch)
4926 (uri (bioconductor-uri "gcrma" version))
4927 (sha256
4928 (base32
3d41f0c2 4929 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
e99380d6
RW
4930 (build-system r-build-system)
4931 (propagated-inputs
4932 `(("r-affy" ,r-affy)
4933 ("r-affyio" ,r-affyio)
4934 ("r-biobase" ,r-biobase)
4935 ("r-biocmanager" ,r-biocmanager)
4936 ("r-biostrings" ,r-biostrings)
4937 ("r-xvector" ,r-xvector)))
4938 (home-page "https://bioconductor.org/packages/gcrma/")
4939 (synopsis "Background adjustment using sequence information")
4940 (description
4941 "Gcrma adjusts for background intensities in Affymetrix array data which
4942include optical noise and @dfn{non-specific binding} (NSB). The main function
4943@code{gcrma} converts background adjusted probe intensities to expression
4944measures using the same normalization and summarization methods as a
4945@dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4946to estimate probe affinity to NSB. The sequence information is summarized in
4947a more complex way than the simple GC content. Instead, the base types (A, T,
4948G or C) at each position along the probe determine the affinity of each probe.
4949The parameters of the position-specific base contributions to the probe
4950affinity is estimated in an NSB experiment in which only NSB but no
7230f6d5 4951gene-specific binding is expected.")
e99380d6
RW
4952 ;; Any version of the LGPL
4953 (license license:lgpl2.1+)))
4675b3cf
RW
4954
4955(define-public r-simpleaffy
4956 (package
4957 (name "r-simpleaffy")
48aaef23 4958 (version "2.66.0")
4675b3cf
RW
4959 (source
4960 (origin
4961 (method url-fetch)
4962 (uri (bioconductor-uri "simpleaffy" version))
4963 (sha256
4964 (base32
48aaef23 4965 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
4675b3cf
RW
4966 (build-system r-build-system)
4967 (propagated-inputs
4968 `(("r-affy" ,r-affy)
4969 ("r-biobase" ,r-biobase)
4970 ("r-biocgenerics" ,r-biocgenerics)
4971 ("r-gcrma" ,r-gcrma)
4972 ("r-genefilter" ,r-genefilter)))
4973 (home-page "https://bioconductor.org/packages/simpleaffy/")
4974 (synopsis "Very simple high level analysis of Affymetrix data")
4975 (description
4976 "This package provides high level functions for reading Affy @file{.CEL}
4977files, phenotypic data, and then computing simple things with it, such as
4978t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4979library. It also has some basic scatter plot functions and mechanisms for
4980generating high resolution journal figures.")
4981 (license license:gpl2+)))
f562c90a
RW
4982
4983(define-public r-yaqcaffy
4984 (package
4985 (name "r-yaqcaffy")
94dee0af 4986 (version "1.50.0")
f562c90a
RW
4987 (source
4988 (origin
4989 (method url-fetch)
4990 (uri (bioconductor-uri "yaqcaffy" version))
4991 (sha256
4992 (base32
94dee0af 4993 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
f562c90a
RW
4994 (build-system r-build-system)
4995 (propagated-inputs
4996 `(("r-simpleaffy" ,r-simpleaffy)))
4997 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4998 (synopsis "Affymetrix quality control and reproducibility analysis")
4999 (description
5000 "This is a package that can be used for quality control of Affymetrix
5001GeneChip expression data and reproducibility analysis of human whole genome
5002chips with the MAQC reference datasets.")
5003 (license license:artistic2.0)))
59cf2629
RW
5004
5005(define-public r-quantro
5006 (package
5007 (name "r-quantro")
70d90ae7 5008 (version "1.22.0")
59cf2629
RW
5009 (source
5010 (origin
5011 (method url-fetch)
5012 (uri (bioconductor-uri "quantro" version))
5013 (sha256
5014 (base32
70d90ae7 5015 "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz"))))
59cf2629
RW
5016 (build-system r-build-system)
5017 (propagated-inputs
5018 `(("r-biobase" ,r-biobase)
5019 ("r-doparallel" ,r-doparallel)
5020 ("r-foreach" ,r-foreach)
5021 ("r-ggplot2" ,r-ggplot2)
5022 ("r-iterators" ,r-iterators)
5023 ("r-minfi" ,r-minfi)
5024 ("r-rcolorbrewer" ,r-rcolorbrewer)))
70d90ae7
RW
5025 (native-inputs
5026 `(("r-knitr" ,r-knitr)))
59cf2629
RW
5027 (home-page "https://bioconductor.org/packages/quantro/")
5028 (synopsis "Test for when to use quantile normalization")
5029 (description
5030 "This package provides a data-driven test for the assumptions of quantile
5031normalization using raw data such as objects that inherit eSets (e.g.
5032ExpressionSet, MethylSet). Group level information about each sample (such as
5033Tumor / Normal status) must also be provided because the test assesses if
5034there are global differences in the distributions between the user-defined
5035groups.")
5036 (license license:gpl3+)))
98a2af31
RW
5037
5038(define-public r-yarn
5039 (package
5040 (name "r-yarn")
a37a6ffb 5041 (version "1.14.0")
98a2af31
RW
5042 (source
5043 (origin
5044 (method url-fetch)
5045 (uri (bioconductor-uri "yarn" version))
5046 (sha256
5047 (base32
a37a6ffb 5048 "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx"))))
98a2af31
RW
5049 (build-system r-build-system)
5050 (propagated-inputs
5051 `(("r-biobase" ,r-biobase)
5052 ("r-biomart" ,r-biomart)
5053 ("r-downloader" ,r-downloader)
5054 ("r-edger" ,r-edger)
5055 ("r-gplots" ,r-gplots)
5056 ("r-limma" ,r-limma)
5057 ("r-matrixstats" ,r-matrixstats)
5058 ("r-preprocesscore" ,r-preprocesscore)
5059 ("r-quantro" ,r-quantro)
5060 ("r-rcolorbrewer" ,r-rcolorbrewer)
5061 ("r-readr" ,r-readr)))
a37a6ffb
RW
5062 (native-inputs
5063 `(("r-knitr" ,r-knitr)))
98a2af31
RW
5064 (home-page "https://bioconductor.org/packages/yarn/")
5065 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
5066 (description
5067 "Expedite large RNA-Seq analyses using a combination of previously
5068developed tools. YARN is meant to make it easier for the user in performing
5069basic mis-annotation quality control, filtering, and condition-aware
5070normalization. YARN leverages many Bioconductor tools and statistical
5071techniques to account for the large heterogeneity and sparsity found in very
5072large RNA-seq experiments.")
5073 (license license:artistic2.0)))
a6e1eb1a
RW
5074
5075(define-public r-roar
5076 (package
5077 (name "r-roar")
72476ade 5078 (version "1.26.0")
a6e1eb1a
RW
5079 (source
5080 (origin
5081 (method url-fetch)
5082 (uri (bioconductor-uri "roar" version))
5083 (sha256
5084 (base32
72476ade 5085 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
a6e1eb1a
RW
5086 (build-system r-build-system)
5087 (propagated-inputs
5088 `(("r-biocgenerics" ,r-biocgenerics)
5089 ("r-genomeinfodb" ,r-genomeinfodb)
5090 ("r-genomicalignments" ,r-genomicalignments)
5091 ("r-genomicranges" ,r-genomicranges)
5092 ("r-iranges" ,r-iranges)
5093 ("r-rtracklayer" ,r-rtracklayer)
5094 ("r-s4vectors" ,r-s4vectors)
5095 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5096 (home-page "https://github.com/vodkatad/roar/")
5097 (synopsis "Identify differential APA usage from RNA-seq alignments")
5098 (description
5099 "This package provides tools for identifying preferential usage of APA
5100sites, comparing two biological conditions, starting from known alternative
5101sites and alignments obtained from standard RNA-seq experiments.")
5102 (license license:gpl3)))
50d91770
RW
5103
5104(define-public r-xbseq
5105 (package
5106 (name "r-xbseq")
7f71341e 5107 (version "1.22.0")
50d91770
RW
5108 (source
5109 (origin
5110 (method url-fetch)
5111 (uri (bioconductor-uri "XBSeq" version))
5112 (sha256
5113 (base32
7f71341e 5114 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
50d91770
RW
5115 (properties `((upstream-name . "XBSeq")))
5116 (build-system r-build-system)
5117 (propagated-inputs
5118 `(("r-biobase" ,r-biobase)
5119 ("r-deseq2" ,r-deseq2)
5120 ("r-dplyr" ,r-dplyr)
5121 ("r-ggplot2" ,r-ggplot2)
5122 ("r-locfit" ,r-locfit)
5123 ("r-magrittr" ,r-magrittr)
5124 ("r-matrixstats" ,r-matrixstats)
5125 ("r-pracma" ,r-pracma)
5126 ("r-roar" ,r-roar)))
bcd06bdb
RW
5127 (native-inputs
5128 `(("r-knitr" ,r-knitr)))
50d91770
RW
5129 (home-page "https://github.com/Liuy12/XBSeq")
5130 (synopsis "Test for differential expression for RNA-seq data")
5131 (description
5132 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5133expression} (DE), where a statistical model was established based on the
5134assumption that observed signals are the convolution of true expression
5135signals and sequencing noises. The mapped reads in non-exonic regions are
5136considered as sequencing noises, which follows a Poisson distribution. Given
5137measurable observed signal and background noise from RNA-seq data, true
5138expression signals, assuming governed by the negative binomial distribution,
5139can be delineated and thus the accurate detection of differential expressed
5140genes.")
5141 (license license:gpl3+)))
c8310056
RW
5142
5143(define-public r-massspecwavelet
5144 (package
5145 (name "r-massspecwavelet")
f4e19e62 5146 (version "1.56.0")
c8310056
RW
5147 (source
5148 (origin
5149 (method url-fetch)
5150 (uri (bioconductor-uri "MassSpecWavelet" version))
5151 (sha256
5152 (base32
f4e19e62 5153 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
c8310056
RW
5154 (properties
5155 `((upstream-name . "MassSpecWavelet")))
5156 (build-system r-build-system)
5157 (propagated-inputs
5158 `(("r-waveslim" ,r-waveslim)))
5159 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5160 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5161 (description
5162 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5163data mainly through the use of wavelet transforms. It supports peak detection
5164based on @dfn{Continuous Wavelet Transform} (CWT).")
5165 (license license:lgpl2.0+)))
ec12e537
RW
5166
5167(define-public r-xcms
5168 (package
5169 (name "r-xcms")
40b86e20 5170 (version "3.10.2")
ec12e537
RW
5171 (source
5172 (origin
5173 (method url-fetch)
5174 (uri (bioconductor-uri "xcms" version))
5175 (sha256
5176 (base32
40b86e20 5177 "0sk53jcl7sjrpw2ncdpl8sw1b1j9mizlrj517rinr1qrbm6lsn8f"))))
ec12e537
RW
5178 (build-system r-build-system)
5179 (propagated-inputs
5180 `(("r-biobase" ,r-biobase)
5181 ("r-biocgenerics" ,r-biocgenerics)
5182 ("r-biocparallel" ,r-biocparallel)
4fb52345 5183 ("r-iranges" ,r-iranges)
ec12e537
RW
5184 ("r-lattice" ,r-lattice)
5185 ("r-massspecwavelet" ,r-massspecwavelet)
5186 ("r-msnbase" ,r-msnbase)
ec12e537
RW
5187 ("r-mzr" ,r-mzr)
5188 ("r-plyr" ,r-plyr)
5189 ("r-protgenerics" ,r-protgenerics)
5190 ("r-rann" ,r-rann)
5191 ("r-rcolorbrewer" ,r-rcolorbrewer)
5192 ("r-robustbase" ,r-robustbase)
ff9f179a
RW
5193 ("r-s4vectors" ,r-s4vectors)
5194 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5195 (native-inputs
5196 `(("r-knitr" ,r-knitr)))
ec12e537
RW
5197 (home-page "https://bioconductor.org/packages/xcms/")
5198 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5199 (description
5200 "This package provides a framework for processing and visualization of
5201chromatographically separated and single-spectra mass spectral data. It
5202imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5203data for high-throughput, untargeted analyte profiling.")
5204 (license license:gpl2+)))
8830664d
RW
5205
5206(define-public r-wrench
5207 (package
5208 (name "r-wrench")
996f07b5 5209 (version "1.6.0")
8830664d
RW
5210 (source
5211 (origin
5212 (method url-fetch)
5213 (uri (bioconductor-uri "Wrench" version))
5214 (sha256
5215 (base32
996f07b5 5216 "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6"))))
8830664d
RW
5217 (properties `((upstream-name . "Wrench")))
5218 (build-system r-build-system)
5219 (propagated-inputs
5220 `(("r-limma" ,r-limma)
5221 ("r-locfit" ,r-locfit)
5222 ("r-matrixstats" ,r-matrixstats)))
996f07b5
RW
5223 (native-inputs
5224 `(("r-knitr" ,r-knitr)))
8830664d
RW
5225 (home-page "https://github.com/HCBravoLab/Wrench")
5226 (synopsis "Wrench normalization for sparse count data")
5227 (description
5228 "Wrench is a package for normalization sparse genomic count data, like
5229that arising from 16s metagenomic surveys.")
5230 (license license:artistic2.0)))
b9b8b447
RW
5231
5232(define-public r-wiggleplotr
5233 (package
5234 (name "r-wiggleplotr")
015ff0bf 5235 (version "1.12.1")
b9b8b447
RW
5236 (source
5237 (origin
5238 (method url-fetch)
5239 (uri (bioconductor-uri "wiggleplotr" version))
5240 (sha256
5241 (base32
015ff0bf 5242 "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp"))))
b9b8b447
RW
5243 (build-system r-build-system)
5244 (propagated-inputs
5245 `(("r-assertthat" ,r-assertthat)
5246 ("r-cowplot" ,r-cowplot)
5247 ("r-dplyr" ,r-dplyr)
5248 ("r-genomeinfodb" ,r-genomeinfodb)
5249 ("r-genomicranges" ,r-genomicranges)
5250 ("r-ggplot2" ,r-ggplot2)
5251 ("r-iranges" ,r-iranges)
5252 ("r-purrr" ,r-purrr)
5253 ("r-rtracklayer" ,r-rtracklayer)
5254 ("r-s4vectors" ,r-s4vectors)))
ee0f7460
RW
5255 (native-inputs
5256 `(("r-knitr" ,r-knitr)))
b9b8b447
RW
5257 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5258 (synopsis "Make read coverage plots from BigWig files")
5259 (description
5260 "This package provides tools to visualize read coverage from sequencing
5261experiments together with genomic annotations (genes, transcripts, peaks).
5262Introns of long transcripts can be rescaled to a fixed length for better
5263visualization of exonic read coverage.")
5264 (license license:asl2.0)))
7b5101c5
RW
5265
5266(define-public r-widgettools
5267 (package
5268 (name "r-widgettools")
08c4d314 5269 (version "1.66.0")
7b5101c5
RW
5270 (source
5271 (origin
5272 (method url-fetch)
5273 (uri (bioconductor-uri "widgetTools" version))
5274 (sha256
5275 (base32
08c4d314 5276 "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx"))))
7b5101c5
RW
5277 (properties `((upstream-name . "widgetTools")))
5278 (build-system r-build-system)
5279 (home-page "https://bioconductor.org/packages/widgetTools/")
5280 (synopsis "Tools for creating interactive tcltk widgets")
5281 (description
337bdc17 5282 "This package contains tools to support the construction of tcltk
7b5101c5
RW
5283widgets in R.")
5284 ;; Any version of the LGPL.
5285 (license license:lgpl3+)))
6b12f213
RW
5286
5287(define-public r-webbioc
5288 (package
5289 (name "r-webbioc")
620cc4d9 5290 (version "1.60.0")
6b12f213
RW
5291 (source
5292 (origin
5293 (method url-fetch)
5294 (uri (bioconductor-uri "webbioc" version))
5295 (sha256
5296 (base32
620cc4d9 5297 "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f"))))
6b12f213
RW
5298 (build-system r-build-system)
5299 (inputs
5300 `(("netpbm" ,netpbm)
5301 ("perl" ,perl)))
5302 (propagated-inputs
5303 `(("r-affy" ,r-affy)
5304 ("r-annaffy" ,r-annaffy)
5305 ("r-biobase" ,r-biobase)
5306 ("r-biocmanager" ,r-biocmanager)
5307 ("r-gcrma" ,r-gcrma)
5308 ("r-multtest" ,r-multtest)
5309 ("r-qvalue" ,r-qvalue)
5310 ("r-vsn" ,r-vsn)))
5311 (home-page "https://www.bioconductor.org/")
5312 (synopsis "Bioconductor web interface")
5313 (description
5314 "This package provides an integrated web interface for doing microarray
5315analysis using several of the Bioconductor packages. It is intended to be
5316deployed as a centralized bioinformatics resource for use by many users.
5317Currently only Affymetrix oligonucleotide analysis is supported.")
5318 (license license:gpl2+)))
9800d859
RW
5319
5320(define-public r-zfpkm
5321 (package
5322 (name "r-zfpkm")
8fdca89b 5323 (version "1.10.0")
9800d859
RW
5324 (source
5325 (origin
5326 (method url-fetch)
5327 (uri (bioconductor-uri "zFPKM" version))
5328 (sha256
5329 (base32
8fdca89b 5330 "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys"))))
9800d859
RW
5331 (properties `((upstream-name . "zFPKM")))
5332 (build-system r-build-system)
5333 (propagated-inputs
5334 `(("r-checkmate" ,r-checkmate)
5335 ("r-dplyr" ,r-dplyr)
5336 ("r-ggplot2" ,r-ggplot2)
5337 ("r-summarizedexperiment" ,r-summarizedexperiment)
5338 ("r-tidyr" ,r-tidyr)))
8fdca89b
RW
5339 (native-inputs
5340 `(("r-knitr" ,r-knitr)))
9800d859
RW
5341 (home-page "https://github.com/ronammar/zFPKM/")
5342 (synopsis "Functions to facilitate zFPKM transformations")
5343 (description
5344 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5345This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
534624215113).")
5347 (license license:gpl3)))
2bdc88fc
RW
5348
5349(define-public r-rbowtie2
5350 (package
5351 (name "r-rbowtie2")
82cb9a99 5352 (version "1.10.1")
2bdc88fc
RW
5353 (source
5354 (origin
5355 (method url-fetch)
5356 (uri (bioconductor-uri "Rbowtie2" version))
5357 (sha256
5358 (base32
82cb9a99 5359 "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7"))))
2bdc88fc
RW
5360 (properties `((upstream-name . "Rbowtie2")))
5361 (build-system r-build-system)
5362 (inputs
5363 `(("zlib" ,zlib)))
297854e6
RW
5364 (native-inputs
5365 `(("r-knitr" ,r-knitr)))
2bdc88fc
RW
5366 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5367 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5368 (description
5369 "This package provides an R wrapper of the popular @code{bowtie2}
5370sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5371rapid adapter trimming, identification, and read merging.")
5372 (license license:gpl3+)))
5622628f
RW
5373
5374(define-public r-progeny
5375 (package
5376 (name "r-progeny")
8e5933a8 5377 (version "1.10.0")
5622628f
RW
5378 (source
5379 (origin
5380 (method url-fetch)
5381 (uri (bioconductor-uri "progeny" version))
5382 (sha256
5383 (base32
8e5933a8 5384 "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh"))))
5622628f 5385 (build-system r-build-system)
8e5933a8
RW
5386 (propagated-inputs
5387 `(("r-biobase" ,r-biobase)
5388 ("r-dplyr" ,r-dplyr)
5389 ("r-ggplot2" ,r-ggplot2)
5390 ("r-ggrepel" ,r-ggrepel)
5391 ("r-gridextra" ,r-gridextra)
5392 ("r-tidyr" ,r-tidyr)))
5393 (native-inputs
5394 `(("r-knitr" ,r-knitr)))
5622628f
RW
5395 (home-page "https://github.com/saezlab/progeny")
5396 (synopsis "Pathway responsive gene activity inference")
5397 (description
5398 "This package provides a function to infer pathway activity from gene
5399expression. It contains the linear model inferred in the publication
5400\"Perturbation-response genes reveal signaling footprints in cancer gene
5401expression\".")
5402 (license license:asl2.0)))
307586c1
RW
5403
5404(define-public r-arrmnormalization
5405 (package
5406 (name "r-arrmnormalization")
989b7bb6 5407 (version "1.28.0")
307586c1
RW
5408 (source
5409 (origin
5410 (method url-fetch)
5411 (uri (bioconductor-uri "ARRmNormalization" version))
5412 (sha256
5413 (base32
989b7bb6 5414 "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv"))))
307586c1
RW
5415 (properties
5416 `((upstream-name . "ARRmNormalization")))
5417 (build-system r-build-system)
5418 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5419 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5420 (synopsis "Adaptive robust regression normalization for methylation data")
5421 (description
5422 "This is a package to perform the @dfn{Adaptive Robust Regression
5423method} (ARRm) for the normalization of methylation data from the Illumina
5424Infinium HumanMethylation 450k assay.")
5425 (license license:artistic2.0)))
fbf34949
RW
5426
5427(define-public r-biocfilecache
5428 (package
5429 (name "r-biocfilecache")
4a504b80 5430 (version "1.12.1")
fbf34949
RW
5431 (source
5432 (origin
5433 (method url-fetch)
5434 (uri (bioconductor-uri "BiocFileCache" version))
5435 (sha256
5436 (base32
4a504b80 5437 "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf"))))
fbf34949
RW
5438 (properties `((upstream-name . "BiocFileCache")))
5439 (build-system r-build-system)
5440 (propagated-inputs
5441 `(("r-curl" ,r-curl)
5442 ("r-dbi" ,r-dbi)
5443 ("r-dbplyr" ,r-dbplyr)
5444 ("r-dplyr" ,r-dplyr)
5445 ("r-httr" ,r-httr)
5446 ("r-rappdirs" ,r-rappdirs)
5447 ("r-rsqlite" ,r-rsqlite)))
173844fc
RW
5448 (native-inputs
5449 `(("r-knitr" ,r-knitr)))
fbf34949
RW
5450 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5451 (synopsis "Manage files across sessions")
5452 (description
5453 "This package creates a persistent on-disk cache of files that the user
5454can add, update, and retrieve. It is useful for managing resources (such as
5455custom Txdb objects) that are costly or difficult to create, web resources,
5456and data files used across sessions.")
5457 (license license:artistic2.0)))
8c42f8f6
RW
5458
5459(define-public r-iclusterplus
5460 (package
5461 (name "r-iclusterplus")
ca8d80c9 5462 (version "1.24.0")
8c42f8f6
RW
5463 (source
5464 (origin
5465 (method url-fetch)
5466 (uri (bioconductor-uri "iClusterPlus" version))
5467 (sha256
5468 (base32
ca8d80c9 5469 "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w"))))
8c42f8f6
RW
5470 (properties `((upstream-name . "iClusterPlus")))
5471 (build-system r-build-system)
5472 (native-inputs `(("gfortran" ,gfortran)))
5473 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5474 (synopsis "Integrative clustering of multi-type genomic data")
5475 (description
5476 "iClusterPlus is developed for integrative clustering analysis of
5477multi-type genomic data and is an enhanced version of iCluster proposed and
5478developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5479from the experiments where biological samples (e.g. tumor samples) are
5480analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5481hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5482on. In the iClusterPlus model, binary observations such as somatic mutation
5483are modeled as Binomial processes; categorical observations such as copy
5484number states are realizations of Multinomial random variables; counts are
5485modeled as Poisson random processes; and continuous measures are modeled by
5486Gaussian distributions.")
5487 (license license:gpl2+)))
4d06ef4b
RW
5488
5489(define-public r-rbowtie
5490 (package
5491 (name "r-rbowtie")
a20538ab 5492 (version "1.28.1")
4d06ef4b
RW
5493 (source
5494 (origin
5495 (method url-fetch)
5496 (uri (bioconductor-uri "Rbowtie" version))
5497 (sha256
5498 (base32
a20538ab 5499 "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3"))))
4d06ef4b
RW
5500 (properties `((upstream-name . "Rbowtie")))
5501 (build-system r-build-system)
5502 (inputs
5503 `(("zlib" ,zlib)))
568c3929
RW
5504 (native-inputs
5505 `(("r-knitr" ,r-knitr)))
4d06ef4b
RW
5506 (home-page "https://bioconductor.org/packages/Rbowtie/")
5507 (synopsis "R bowtie wrapper")
5508 (description
5509 "This package provides an R wrapper around the popular bowtie short read
5510aligner and around SpliceMap, a de novo splice junction discovery and
5511alignment tool.")
5512 (license license:artistic2.0)))
14441539
RW
5513
5514(define-public r-sgseq
5515 (package
5516 (name "r-sgseq")
201902bc 5517 (version "1.22.0")
14441539
RW
5518 (source
5519 (origin
5520 (method url-fetch)
5521 (uri (bioconductor-uri "SGSeq" version))
5522 (sha256
5523 (base32
201902bc 5524 "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c"))))
14441539
RW
5525 (properties `((upstream-name . "SGSeq")))
5526 (build-system r-build-system)
5527 (propagated-inputs
5528 `(("r-annotationdbi" ,r-annotationdbi)
5529 ("r-biocgenerics" ,r-biocgenerics)
5530 ("r-biostrings" ,r-biostrings)
5531 ("r-genomeinfodb" ,r-genomeinfodb)
5532 ("r-genomicalignments" ,r-genomicalignments)
5533 ("r-genomicfeatures" ,r-genomicfeatures)
5534 ("r-genomicranges" ,r-genomicranges)
5535 ("r-igraph" ,r-igraph)
5536 ("r-iranges" ,r-iranges)
5537 ("r-rsamtools" ,r-rsamtools)
5538 ("r-rtracklayer" ,r-rtracklayer)
5539 ("r-runit" ,r-runit)
5540 ("r-s4vectors" ,r-s4vectors)
5541 ("r-summarizedexperiment" ,r-summarizedexperiment)))
201902bc
RW
5542 (native-inputs
5543 `(("r-knitr" ,r-knitr)))
14441539
RW
5544 (home-page "https://bioconductor.org/packages/SGSeq/")
5545 (synopsis "Splice event prediction and quantification from RNA-seq data")
5546 (description
5547 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5548data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5549represented as a splice graph, which can be obtained from existing annotation
5550or predicted from the mapped sequence reads. Splice events are identified
5551from the graph and are quantified locally using structurally compatible reads
5552at the start or end of each splice variant. The software includes functions
5553for splice event prediction, quantification, visualization and
5554interpretation.")
5555 (license license:artistic2.0)))
58656064
RW
5556
5557(define-public r-rhisat2
5558 (package
5559 (name "r-rhisat2")
2aff2724 5560 (version "1.4.0")
58656064
RW
5561 (source
5562 (origin
5563 (method url-fetch)
5564 (uri (bioconductor-uri "Rhisat2" version))
5565 (sha256
5566 (base32
2aff2724 5567 "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a"))))
58656064
RW
5568 (properties `((upstream-name . "Rhisat2")))
5569 (build-system r-build-system)
3dd2450e
RW
5570 (arguments
5571 `(#:phases
5572 (modify-phases %standard-phases
5573 (add-after 'unpack 'make-reproducible
5574 (lambda _
5575 (substitute* "src/Makefile"
5576 (("`hostname`") "guix")
5577 (("`date`") "0")
5578 ;; Avoid shelling out to "which".
5579 (("^CC =.*") (which "gcc"))
5580 (("^CPP =.*") (which "g++")))
5581 #t)))))
58656064
RW
5582 (propagated-inputs
5583 `(("r-genomicfeatures" ,r-genomicfeatures)
5584 ("r-genomicranges" ,r-genomicranges)
5585 ("r-sgseq" ,r-sgseq)))
2aff2724
RW
5586 (native-inputs
5587 `(("r-knitr" ,r-knitr)))
58656064
RW
5588 (home-page "https://github.com/fmicompbio/Rhisat2")
5589 (synopsis "R Wrapper for HISAT2 sequence aligner")
5590 (description
5591 "This package provides an R interface to the HISAT2 spliced short-read
5592aligner by Kim et al. (2015). The package contains wrapper functions to
5593create a genome index and to perform the read alignment to the generated
5594index.")
5595 (license license:gpl3)))
5e0241db
RW
5596
5597(define-public r-quasr
5598 (package
5599 (name "r-quasr")
a84abf43 5600 (version "1.28.0")
5e0241db
RW
5601 (source
5602 (origin
5603 (method url-fetch)
5604 (uri (bioconductor-uri "QuasR" version))
5605 (sha256
5606 (base32
a84abf43 5607 "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8"))))
5e0241db
RW
5608 (properties `((upstream-name . "QuasR")))
5609 (build-system r-build-system)
5610 (inputs
5611 `(("zlib" ,zlib)))
5612 (propagated-inputs
5613 `(("r-annotationdbi" ,r-annotationdbi)
5614 ("r-biobase" ,r-biobase)
5615 ("r-biocgenerics" ,r-biocgenerics)
5616 ("r-biocmanager" ,r-biocmanager)
5617 ("r-biocparallel" ,r-biocparallel)
5618 ("r-biostrings" ,r-biostrings)
5619 ("r-bsgenome" ,r-bsgenome)
5620 ("r-genomeinfodb" ,r-genomeinfodb)
5621 ("r-genomicalignments" ,r-genomicalignments)
5622 ("r-genomicfeatures" ,r-genomicfeatures)
5623 ("r-genomicfiles" ,r-genomicfiles)
5624 ("r-genomicranges" ,r-genomicranges)
5625 ("r-iranges" ,r-iranges)
5626 ("r-rbowtie" ,r-rbowtie)
5627 ("r-rhisat2" ,r-rhisat2)
5628 ("r-rhtslib" ,r-rhtslib)
5629 ("r-rsamtools" ,r-rsamtools)
5630 ("r-rtracklayer" ,r-rtracklayer)
5631 ("r-s4vectors" ,r-s4vectors)
5632 ("r-shortread" ,r-shortread)))
a84abf43
RW
5633 (native-inputs
5634 `(("r-knitr" ,r-knitr)))
5e0241db
RW
5635 (home-page "https://bioconductor.org/packages/QuasR/")
5636 (synopsis "Quantify and annotate short reads in R")
5637 (description
5638 "This package provides a framework for the quantification and analysis of
5639short genomic reads. It covers a complete workflow starting from raw sequence
5640reads, over creation of alignments and quality control plots, to the
5641quantification of genomic regions of interest.")
5642 (license license:gpl2)))
496b024f
RW
5643
5644(define-public r-rqc
5645 (package
5646 (name "r-rqc")
1c5360ac 5647 (version "1.22.0")
496b024f
RW
5648 (source
5649 (origin
5650 (method url-fetch)
5651 (uri (bioconductor-uri "Rqc" version))
5652 (sha256
5653 (base32
1c5360ac 5654 "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3"))))
496b024f
RW
5655 (properties `((upstream-name . "Rqc")))
5656 (build-system r-build-system)
5657 (propagated-inputs
5658 `(("r-biocgenerics" ,r-biocgenerics)
5659 ("r-biocparallel" ,r-biocparallel)
5660 ("r-biocstyle" ,r-biocstyle)
5661 ("r-biostrings" ,r-biostrings)
5662 ("r-biovizbase" ,r-biovizbase)
5663 ("r-genomicalignments" ,r-genomicalignments)
5664 ("r-genomicfiles" ,r-genomicfiles)
5665 ("r-ggplot2" ,r-ggplot2)
5666 ("r-iranges" ,r-iranges)
5667 ("r-knitr" ,r-knitr)
5668 ("r-markdown" ,r-markdown)
5669 ("r-plyr" ,r-plyr)
5670 ("r-rcpp" ,r-rcpp)
5671 ("r-reshape2" ,r-reshape2)
5672 ("r-rsamtools" ,r-rsamtools)
5673 ("r-s4vectors" ,r-s4vectors)
5674 ("r-shiny" ,r-shiny)
5675 ("r-shortread" ,r-shortread)))
1c5360ac
RW
5676 (native-inputs
5677 `(("r-knitr" ,r-knitr)))
496b024f
RW
5678 (home-page "https://github.com/labbcb/Rqc")
5679 (synopsis "Quality control tool for high-throughput sequencing data")
5680 (description
5681 "Rqc is an optimized tool designed for quality control and assessment of
5682high-throughput sequencing data. It performs parallel processing of entire
5683files and produces a report which contains a set of high-resolution
5684graphics.")
5685 (license license:gpl2+)))
81e3de01
RW
5686
5687(define-public r-birewire
5688 (package
5689 (name "r-birewire")
f50609ab 5690 (version "3.20.0")
81e3de01
RW
5691 (source
5692 (origin
5693 (method url-fetch)
5694 (uri (bioconductor-uri "BiRewire" version))
5695 (sha256
5696 (base32
f50609ab 5697 "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g"))))
81e3de01
RW
5698 (properties `((upstream-name . "BiRewire")))
5699 (build-system r-build-system)
5700 (propagated-inputs
5701 `(("r-igraph" ,r-igraph)
5702 ("r-matrix" ,r-matrix)
5703 ("r-slam" ,r-slam)
5704 ("r-tsne" ,r-tsne)))
5705 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5706 (synopsis "Tools for randomization of bipartite graphs")
5707 (description
5708 "This package provides functions for bipartite network rewiring through N
5709consecutive switching steps and for the computation of the minimal number of
5710switching steps to be performed in order to maximise the dissimilarity with
5711respect to the original network. It includes functions for the analysis of
5712the introduced randomness across the switching steps and several other
5713routines to analyse the resulting networks and their natural projections.")
5714 (license license:gpl3)))
1a24f855
RW
5715
5716(define-public r-birta
5717 (package
5718 (name "r-birta")
cb941ca0 5719 (version "1.31.0")
1a24f855
RW
5720 (source
5721 (origin
5722 (method url-fetch)
5723 (uri (bioconductor-uri "birta" version))
5724 (sha256
5725 (base32
cb941ca0 5726 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
1a24f855
RW
5727 (build-system r-build-system)
5728 (propagated-inputs
5729 `(("r-biobase" ,r-biobase)
5730 ("r-limma" ,r-limma)
5731 ("r-mass" ,r-mass)))
5732 (home-page "https://bioconductor.org/packages/birta")
5733 (synopsis "Bayesian inference of regulation of transcriptional activity")
5734 (description
5735 "Expression levels of mRNA molecules are regulated by different
5736processes, comprising inhibition or activation by transcription factors and
5737post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5738Inference of Regulation of Transcriptional Activity) uses the regulatory
5739networks of transcription factors and miRNAs together with mRNA and miRNA
5740expression data to predict switches in regulatory activity between two
5741conditions. A Bayesian network is used to model the regulatory structure and
5742Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5743 (license license:gpl2+)))
a9fac3f4 5744
b4a22cca
RW
5745(define-public r-multidataset
5746 (package
5747 (name "r-multidataset")
905bbb13 5748 (version "1.16.0")
b4a22cca
RW
5749 (source
5750 (origin
5751 (method url-fetch)
5752 (uri (bioconductor-uri "MultiDataSet" version))
5753 (sha256
5754 (base32
905bbb13 5755 "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39"))))
b4a22cca
RW
5756 (properties `((upstream-name . "MultiDataSet")))
5757 (build-system r-build-system)
5758 (propagated-inputs
5759 `(("r-biobase" ,r-biobase)
5760 ("r-biocgenerics" ,r-biocgenerics)
5761 ("r-genomicranges" ,r-genomicranges)
5762 ("r-ggplot2" ,r-ggplot2)
5763 ("r-ggrepel" ,r-ggrepel)
5764 ("r-iranges" ,r-iranges)
5765 ("r-limma" ,r-limma)
5766 ("r-qqman" ,r-qqman)
5767 ("r-s4vectors" ,r-s4vectors)
5768 ("r-summarizedexperiment" ,r-summarizedexperiment)))
905bbb13
RW
5769 (native-inputs
5770 `(("r-knitr" ,r-knitr)))
b4a22cca
RW
5771 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5772 (synopsis "Implementation of MultiDataSet and ResultSet")
5773 (description
5774 "This package provides an implementation of the BRGE's (Bioinformatic
5775Research Group in Epidemiology from Center for Research in Environmental
5776Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5777integrating multi omics data sets and ResultSet is a container for omics
5778results. This package contains base classes for MEAL and rexposome
5779packages.")
5780 (license license:expat)))
5781
a9fac3f4
RW
5782(define-public r-ropls
5783 (package
5784 (name "r-ropls")
77334168 5785 (version "1.20.0")
a9fac3f4
RW
5786 (source
5787 (origin
5788 (method url-fetch)
5789 (uri (bioconductor-uri "ropls" version))
5790 (sha256
5791 (base32
77334168 5792 "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx"))))
a9fac3f4 5793 (build-system r-build-system)
643aaf7e
RW
5794 (propagated-inputs
5795 `(("r-biobase" ,r-biobase)
5796 ("r-multidataset" ,r-multidataset)))
a9fac3f4
RW
5797 (native-inputs
5798 `(("r-knitr" ,r-knitr))) ; for vignettes
5799 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5800 (synopsis "Multivariate analysis and feature selection of omics data")
5801 (description
5802 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5803and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5804regression, classification, and feature selection of omics data where the
5805number of variables exceeds the number of samples and with multicollinearity
5806among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5807separately model the variation correlated (predictive) to the factor of
5808interest and the uncorrelated (orthogonal) variation. While performing
5809similarly to PLS, OPLS facilitates interpretation.
5810
5811This package provides imlementations of PCA, PLS, and OPLS for multivariate
5812analysis and feature selection of omics data. In addition to scores, loadings
5813and weights plots, the package provides metrics and graphics to determine the
5814optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5815validity of the model by permutation testing, detect outliers, and perform
5816feature selection (e.g. with Variable Importance in Projection or regression
5817coefficients).")
5818 (license license:cecill)))
075a9094
RW
5819
5820(define-public r-biosigner
5821 (package
5822 (name "r-biosigner")
8b6f26e6 5823 (version "1.16.0")
075a9094
RW
5824 (source
5825 (origin
5826 (method url-fetch)
5827 (uri (bioconductor-uri "biosigner" version))
5828 (sha256
5829 (base32
8b6f26e6 5830 "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06"))))
075a9094
RW
5831 (build-system r-build-system)
5832 (propagated-inputs
5833 `(("r-biobase" ,r-biobase)
5834 ("r-e1071" ,r-e1071)
7d29dc9c 5835 ("r-multidataset" ,r-multidataset)
075a9094
RW
5836 ("r-randomforest" ,r-randomforest)
5837 ("r-ropls" ,r-ropls)))
5838 (native-inputs
f7100eda 5839 `(("r-knitr" ,r-knitr)))
075a9094
RW
5840 (home-page "https://bioconductor.org/packages/biosigner/")
5841 (synopsis "Signature discovery from omics data")
5842 (description
5843 "Feature selection is critical in omics data analysis to extract
5844restricted and meaningful molecular signatures from complex and high-dimension
5845data, and to build robust classifiers. This package implements a method to
5846assess the relevance of the variables for the prediction performances of the
5847classifier. The approach can be run in parallel with the PLS-DA, Random
5848Forest, and SVM binary classifiers. The signatures and the corresponding
5849'restricted' models are returned, enabling future predictions on new
5850datasets.")
5851 (license license:cecill)))
ae6fa185
RW
5852
5853(define-public r-annotatr
5854 (package
5855 (name "r-annotatr")
5ca991bf 5856 (version "1.14.0")
ae6fa185
RW
5857 (source
5858 (origin
5859 (method url-fetch)
5860 (uri (bioconductor-uri "annotatr" version))
5861 (sha256
5862 (base32
5ca991bf 5863 "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl"))))
ae6fa185
RW
5864 (build-system r-build-system)
5865 (propagated-inputs
5866 `(("r-annotationdbi" ,r-annotationdbi)
5867 ("r-annotationhub" ,r-annotationhub)
5868 ("r-dplyr" ,r-dplyr)
5869 ("r-genomeinfodb" ,r-genomeinfodb)
5870 ("r-genomicfeatures" ,r-genomicfeatures)
5871 ("r-genomicranges" ,r-genomicranges)
5872 ("r-ggplot2" ,r-ggplot2)
5873 ("r-iranges" ,r-iranges)
5874 ("r-readr" ,r-readr)
5875 ("r-regioner" ,r-regioner)
5876 ("r-reshape2" ,r-reshape2)
5877 ("r-rtracklayer" ,r-rtracklayer)
5878 ("r-s4vectors" ,r-s4vectors)))
5ca991bf
RW
5879 (native-inputs
5880 `(("r-knitr" ,r-knitr)))
ae6fa185
RW
5881 (home-page "https://bioconductor.org/packages/annotatr/")
5882 (synopsis "Annotation of genomic regions to genomic annotations")
5883 (description
5884 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5885differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5886to investigate the intersecting genomic annotations. Such annotations include
5887those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5888CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5889enhancers. The annotatr package provides an easy way to summarize and
5890visualize the intersection of genomic sites/regions with genomic
5891annotations.")
5892 (license license:gpl3)))
2cb738a6
RW
5893
5894(define-public r-rsubread
5895 (package
5896 (name "r-rsubread")
1bf63066 5897 (version "2.2.6")
2cb738a6
RW
5898 (source
5899 (origin
5900 (method url-fetch)
5901 (uri (bioconductor-uri "Rsubread" version))
5902 (sha256
5903 (base32
1bf63066 5904 "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm"))))
2cb738a6
RW
5905 (properties `((upstream-name . "Rsubread")))
5906 (build-system r-build-system)
5907 (inputs `(("zlib" ,zlib)))
5d63f69b
RW
5908 (propagated-inputs
5909 `(("r-matrix" ,r-matrix)))
2cb738a6
RW
5910 (home-page "https://bioconductor.org/packages/Rsubread/")
5911 (synopsis "Subread sequence alignment and counting for R")
5912 (description
5913 "This package provides tools for alignment, quantification and analysis
5914of second and third generation sequencing data. It includes functionality for
5915read mapping, read counting, SNP calling, structural variant detection and
5916gene fusion discovery. It can be applied to all major sequencing techologies
5917and to both short and long sequence reads.")
5918 (license license:gpl3)))
a6fedf1f 5919
a0422d18 5920(define-public r-flowutils
5921 (package
5922 (name "r-flowutils")
6954950f 5923 (version "1.52.0")
a0422d18 5924 (source
5925 (origin
5926 (method url-fetch)
5927 (uri (bioconductor-uri "flowUtils" version))
5928 (sha256
5929 (base32
6954950f 5930 "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4"))))
a0422d18 5931 (properties `((upstream-name . "flowUtils")))
5932 (build-system r-build-system)
5933 (propagated-inputs
5934 `(("r-biobase" ,r-biobase)
5935 ("r-corpcor" ,r-corpcor)
5936 ("r-flowcore" ,r-flowcore)
5937 ("r-graph" ,r-graph)
5938 ("r-runit" ,r-runit)
5939 ("r-xml" ,r-xml)))
5940 (home-page "https://github.com/jspidlen/flowUtils")
5941 (synopsis "Utilities for flow cytometry")
5942 (description
5943 "This package provides utilities for flow cytometry data.")
5944 (license license:artistic2.0)))
5945
ed6f49fc 5946(define-public r-consensusclusterplus
5947 (package
5948 (name "r-consensusclusterplus")
0c2573e7 5949 (version "1.52.0")
ed6f49fc 5950 (source
5951 (origin
5952 (method url-fetch)
5953 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5954 (sha256
5955 (base32
0c2573e7 5956 "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq"))))
ed6f49fc 5957 (properties
5958 `((upstream-name . "ConsensusClusterPlus")))
5959 (build-system r-build-system)
5960 (propagated-inputs
5961 `(("r-all" ,r-all)
5962 ("r-biobase" ,r-biobase)
5963 ("r-cluster" ,r-cluster)))
5964 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5965 (synopsis "Clustering algorithm")
5966 (description
5967 "This package provides an implementation of an algorithm for determining
5968cluster count and membership by stability evidence in unsupervised analysis.")
5969 (license license:gpl2)))
5970
b4aee31d
RW
5971(define-public r-cytolib
5972 (package
5973 (name "r-cytolib")
3c73d7c5 5974 (version "2.0.3")
b4aee31d
RW
5975 (source
5976 (origin
5977 (method url-fetch)
5978 (uri (bioconductor-uri "cytolib" version))
5979 (sha256
5980 (base32
3c73d7c5 5981 "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj"))))
b4aee31d
RW
5982 (properties `((upstream-name . "cytolib")))
5983 (build-system r-build-system)
3c73d7c5
RW
5984 (inputs
5985 `(("zlib" ,zlib)))
5986 (native-inputs
5987 `(("r-knitr" ,r-knitr)))
5988 (propagated-inputs
5989 `(("r-bh" ,r-bh)
5990 ("r-rcpp" ,r-rcpp)
5991 ("r-rcpparmadillo" ,r-rcpparmadillo)
5992 ("r-rcppparallel" ,r-rcppparallel)
5993 ("r-rhdf5lib" ,r-rhdf5lib)
5994 ("r-rprotobuflib" ,r-rprotobuflib)))
b4aee31d
RW
5995 (home-page "https://bioconductor.org/packages/cytolib/")
5996 (synopsis "C++ infrastructure for working with gated cytometry")
5997 (description
5998 "This package provides the core data structure and API to represent and
5999interact with gated cytometry data.")
6000 (license license:artistic2.0)))
6001
a6fedf1f 6002(define-public r-flowcore
6003 (package
6004 (name "r-flowcore")
faff2de0 6005 (version "2.0.1")
a6fedf1f 6006 (source
6007 (origin
6008 (method url-fetch)
6009 (uri (bioconductor-uri "flowCore" version))
6010 (sha256
6011 (base32
faff2de0 6012 "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p"))))
a6fedf1f 6013 (properties `((upstream-name . "flowCore")))
6014 (build-system r-build-system)
6015 (propagated-inputs
6016 `(("r-bh" ,r-bh)
6017 ("r-biobase" ,r-biobase)
6018 ("r-biocgenerics" ,r-biocgenerics)
b2a2f321 6019 ("r-cytolib" ,r-cytolib)
a6fedf1f 6020 ("r-matrixstats" ,r-matrixstats)
faff2de0
RW
6021 ("r-rcpp" ,r-rcpp)
6022 ("r-rcpparmadillo" ,r-rcpparmadillo)
6023 ("r-rprotobuflib" ,r-rprotobuflib)))
6024 (native-inputs
6025 `(("r-knitr" ,r-knitr)))
a6fedf1f 6026 (home-page "https://bioconductor.org/packages/flowCore")
6027 (synopsis "Basic structures for flow cytometry data")
6028 (description
6029 "This package provides S4 data structures and basic functions to deal
6030with flow cytometry data.")
6031 (license license:artistic2.0)))
e0cb053e 6032
6033(define-public r-flowmeans
6034 (package
6035 (name "r-flowmeans")
76b163d6 6036 (version "1.48.0")
e0cb053e 6037 (source
6038 (origin
6039 (method url-fetch)
6040 (uri (bioconductor-uri "flowMeans" version))
6041 (sha256
6042 (base32
76b163d6 6043 "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7"))))
e0cb053e 6044 (properties `((upstream-name . "flowMeans")))
6045 (build-system r-build-system)
6046 (propagated-inputs
6047 `(("r-biobase" ,r-biobase)
6048 ("r-feature" ,r-feature)
6049 ("r-flowcore" ,r-flowcore)
6050 ("r-rrcov" ,r-rrcov)))
6051 (home-page "https://bioconductor.org/packages/flowMeans")
6052 (synopsis "Non-parametric flow cytometry data gating")
6053 (description
6054 "This package provides tools to identify cell populations in Flow
6055Cytometry data using non-parametric clustering and segmented-regression-based
6056change point detection.")
6057 (license license:artistic2.0)))
1502751b 6058
15ac0c19
RW
6059(define-public r-ncdfflow
6060 (package
6061 (name "r-ncdfflow")
631b12ca 6062 (version "2.34.0")
15ac0c19
RW
6063 (source
6064 (origin
6065 (method url-fetch)
6066 (uri (bioconductor-uri "ncdfFlow" version))
6067 (sha256
6068 (base32
631b12ca 6069 "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f"))))
15ac0c19
RW
6070 (properties `((upstream-name . "ncdfFlow")))
6071 (build-system r-build-system)
6072 (inputs
6073 `(("zlib" ,zlib)))
6074 (propagated-inputs
6075 `(("r-bh" ,r-bh)
6076 ("r-biobase" ,r-biobase)
6077 ("r-biocgenerics" ,r-biocgenerics)
6078 ("r-flowcore" ,r-flowcore)
6079 ("r-rcpp" ,r-rcpp)
6080 ("r-rcpparmadillo" ,r-rcpparmadillo)
6081 ("r-rhdf5lib" ,r-rhdf5lib)
6082 ("r-zlibbioc" ,r-zlibbioc)))
631b12ca
RW
6083 (native-inputs
6084 `(("r-knitr" ,r-knitr)))
15ac0c19
RW
6085 (home-page "https://bioconductor.org/packages/ncdfFlow/")
6086 (synopsis "HDF5 based storage for flow cytometry data")
6087 (description
6088 "This package provides HDF5 storage based methods and functions for
6089manipulation of flow cytometry data.")
6090 (license license:artistic2.0)))
6091
f5f44031
RW
6092(define-public r-ggcyto
6093 (package
6094 (name "r-ggcyto")
3407dfa6 6095 (version "1.16.0")
f5f44031
RW
6096 (source
6097 (origin
6098 (method url-fetch)
6099 (uri (bioconductor-uri "ggcyto" version))
6100 (sha256
6101 (base32
3407dfa6 6102 "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0"))))
f5f44031
RW
6103 (properties `((upstream-name . "ggcyto")))
6104 (build-system r-build-system)
6105 (propagated-inputs
6106 `(("r-data-table" ,r-data-table)
6107 ("r-flowcore" ,r-flowcore)
6108 ("r-flowworkspace" ,r-flowworkspace)
6109 ("r-ggplot2" ,r-ggplot2)
6110 ("r-gridextra" ,r-gridextra)
3407dfa6 6111 ("r-hexbin" ,r-hexbin)
f5f44031
RW
6112 ("r-ncdfflow" ,r-ncdfflow)
6113 ("r-plyr" ,r-plyr)
6114 ("r-rcolorbrewer" ,r-rcolorbrewer)
6115 ("r-rlang" ,r-rlang)
6116 ("r-scales" ,r-scales)))
0754fefb
RW
6117 (native-inputs
6118 `(("r-knitr" ,r-knitr)))
f5f44031
RW
6119 (home-page "https://github.com/RGLab/ggcyto/issues")
6120 (synopsis "Visualize Cytometry data with ggplot")
6121 (description
6122 "With the dedicated fortify method implemented for @code{flowSet},
6123@code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6124cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6125and some custom layers also make it easy to add gates and population
6126statistics to the plot.")
6127 (license license:artistic2.0)))
6128
0dd4b7d7
RW
6129(define-public r-flowviz
6130 (package
6131 (name "r-flowviz")
062789b8 6132 (version "1.52.0")
0dd4b7d7
RW
6133 (source
6134 (origin
6135 (method url-fetch)
6136 (uri (bioconductor-uri "flowViz" version))
6137 (sha256
6138 (base32
062789b8 6139 "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq"))))
0dd4b7d7
RW
6140 (properties `((upstream-name . "flowViz")))
6141 (build-system r-build-system)
6142 (propagated-inputs
6143 `(("r-biobase" ,r-biobase)
6144 ("r-flowcore" ,r-flowcore)
6145 ("r-hexbin" ,r-hexbin)
6146 ("r-idpmisc" ,r-idpmisc)
6147 ("r-kernsmooth" ,r-kernsmooth)
6148 ("r-lattice" ,r-lattice)
6149 ("r-latticeextra" ,r-latticeextra)
6150 ("r-mass" ,r-mass)
6151 ("r-rcolorbrewer" ,r-rcolorbrewer)))
062789b8
RW
6152 (native-inputs
6153 `(("r-knitr" ,r-knitr)))
0dd4b7d7
RW
6154 (home-page "https://bioconductor.org/packages/flowViz/")
6155 (synopsis "Visualization for flow cytometry")
6156 (description
6157 "This package provides visualization tools for flow cytometry data.")
6158 (license license:artistic2.0)))
6159
c8ab9eb1
RW
6160(define-public r-flowclust
6161 (package
6162 (name "r-flowclust")
b347d6c3 6163 (version "3.26.0")
c8ab9eb1
RW
6164 (source
6165 (origin
6166 (method url-fetch)
6167 (uri (bioconductor-uri "flowClust" version))
6168 (sha256
6169 (base32
b347d6c3 6170 "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b"))))
c8ab9eb1
RW
6171 (properties `((upstream-name . "flowClust")))
6172 (build-system r-build-system)
6173 (arguments
6174 `(#:configure-flags
6175 (list "--configure-args=--enable-bundled-gsl=no")))
6176 (propagated-inputs
6177 `(("r-biobase" ,r-biobase)
6178 ("r-biocgenerics" ,r-biocgenerics)
6179 ("r-clue" ,r-clue)
6180 ("r-corpcor" ,r-corpcor)
6181 ("r-ellipse" ,r-ellipse)
6182 ("r-flowcore" ,r-flowcore)
6183 ("r-flowviz" ,r-flowviz)
6184 ("r-graph" ,r-graph)
6185 ("r-mnormt" ,r-mnormt)))
6186 (inputs
6187 `(("gsl" ,gsl)))
6188 (native-inputs
b347d6c3
RW
6189 `(("pkg-config" ,pkg-config)
6190 ("r-knitr" ,r-knitr)))
c8ab9eb1
RW
6191 (home-page "https://bioconductor.org/packages/flowClust")
6192 (synopsis "Clustering for flow cytometry")
6193 (description
6194 "This package provides robust model-based clustering using a t-mixture
6195model with Box-Cox transformation.")
6196 (license license:artistic2.0)))
6197
f1964519
RW
6198;; TODO: this package bundles an old version of protobuf. It's not easy to
6199;; make it use our protobuf package instead.
6200(define-public r-rprotobuflib
6201 (package
6202 (name "r-rprotobuflib")
bafade83 6203 (version "2.0.0")
f1964519
RW
6204 (source
6205 (origin
6206 (method url-fetch)
6207 (uri (bioconductor-uri "RProtoBufLib" version))
6208 (sha256
6209 (base32
bafade83 6210 "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps"))))
f1964519
RW
6211 (properties `((upstream-name . "RProtoBufLib")))
6212 (build-system r-build-system)
6213 (arguments
6214 `(#:phases
6215 (modify-phases %standard-phases
6216 (add-after 'unpack 'unpack-bundled-sources
6217 (lambda _
6218 (with-directory-excursion "src"
bafade83 6219 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
f1964519 6220 #t)))))
bafade83
RW
6221 (native-inputs
6222 `(("r-knitr" ,r-knitr)))
f1964519
RW
6223 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6224 (synopsis "C++ headers and static libraries of Protocol buffers")
6225 (description
6226 "This package provides the headers and static library of Protocol buffers
6227for other R packages to compile and link against.")
6228 (license license:bsd-3)))
6229
82c11117
RW
6230(define-public r-flowworkspace
6231 (package
6232 (name "r-flowworkspace")
214ee827 6233 (version "4.0.6")
82c11117
RW
6234 (source
6235 (origin
6236 (method url-fetch)
6237 (uri (bioconductor-uri "flowWorkspace" version))
6238 (sha256
6239 (base32
214ee827 6240 "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v"))))
82c11117
RW
6241 (properties `((upstream-name . "flowWorkspace")))
6242 (build-system r-build-system)
6243 (propagated-inputs
6244 `(("r-bh" ,r-bh)
6245 ("r-biobase" ,r-biobase)
6246 ("r-biocgenerics" ,r-biocgenerics)
6247 ("r-cytolib" ,r-cytolib)
6248 ("r-data-table" ,r-data-table)
6249 ("r-digest" ,r-digest)
6250 ("r-dplyr" ,r-dplyr)
6251 ("r-flowcore" ,r-flowcore)
a9af09df 6252 ("r-ggplot2" ,r-ggplot2)
82c11117 6253 ("r-graph" ,r-graph)
82c11117
RW
6254 ("r-lattice" ,r-lattice)
6255 ("r-latticeextra" ,r-latticeextra)
6256 ("r-matrixstats" ,r-matrixstats)
6257 ("r-ncdfflow" ,r-ncdfflow)
6258 ("r-rbgl" ,r-rbgl)
82c11117 6259 ("r-rcpp" ,r-rcpp)
a9af09df 6260 ("r-rcpparmadillo" ,r-rcpparmadillo)
82c11117
RW
6261 ("r-rcppparallel" ,r-rcppparallel)
6262 ("r-rgraphviz" ,r-rgraphviz)
a9af09df 6263 ("r-rhdf5lib" ,r-rhdf5lib)
82c11117
RW
6264 ("r-rprotobuflib" ,r-rprotobuflib)
6265 ("r-scales" ,r-scales)
a9af09df
RW
6266 ("r-stringr" ,r-stringr)
6267 ("r-xml" ,r-xml)))
6268 (native-inputs
6269 `(("r-knitr" ,r-knitr)))
82c11117
RW
6270 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6271 (synopsis "Infrastructure for working with cytometry data")
6272 (description
6273 "This package is designed to facilitate comparison of automated gating
6274methods against manual gating done in flowJo. This package allows you to
6275import basic flowJo workspaces into BioConductor and replicate the gating from
6276flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6277samples, compensation, and transformation are performed so that the output
6278matches the flowJo analysis.")
6279 (license license:artistic2.0)))
6280
b700b9ec
RW
6281(define-public r-flowstats
6282 (package
6283 (name "r-flowstats")
372caae6 6284 (version "4.0.0")
b700b9ec
RW
6285 (source
6286 (origin
6287 (method url-fetch)
6288 (uri (bioconductor-uri "flowStats" version))
6289 (sha256
6290 (base32
372caae6 6291 "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir"))))
b700b9ec
RW
6292 (properties `((upstream-name . "flowStats")))
6293 (build-system r-build-system)
6294 (propagated-inputs
6295 `(("r-biobase" ,r-biobase)
6296 ("r-biocgenerics" ,r-biocgenerics)
6297 ("r-cluster" ,r-cluster)
6298 ("r-fda" ,r-fda)
6299 ("r-flowcore" ,r-flowcore)
6300 ("r-flowviz" ,r-flowviz)
6301 ("r-flowworkspace" ,r-flowworkspace)
6302 ("r-kernsmooth" ,r-kernsmooth)
6303 ("r-ks" ,r-ks)
6304 ("r-lattice" ,r-lattice)
6305 ("r-mass" ,r-mass)
6306 ("r-ncdfflow" ,r-ncdfflow)
6307 ("r-rcolorbrewer" ,r-rcolorbrewer)
6308 ("r-rrcov" ,r-rrcov)))
6309 (home-page "http://www.github.com/RGLab/flowStats")
6310 (synopsis "Statistical methods for the analysis of flow cytometry data")
6311 (description
6312 "This package provides methods and functionality to analyze flow data
6313that is beyond the basic infrastructure provided by the @code{flowCore}
6314package.")
6315 (license license:artistic2.0)))
6316
6aedc805
RW
6317(define-public r-opencyto
6318 (package
6319 (name "r-opencyto")
8f5e1674 6320 (version "2.0.0")
6aedc805
RW
6321 (source
6322 (origin
6323 (method url-fetch)
6324 (uri (bioconductor-uri "openCyto" version))
6325 (sha256
6326 (base32
8f5e1674 6327 "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m"))))
6aedc805
RW
6328 (properties `((upstream-name . "openCyto")))
6329 (build-system r-build-system)
6330 (propagated-inputs
6331 `(("r-biobase" ,r-biobase)
6332 ("r-biocgenerics" ,r-biocgenerics)
6333 ("r-clue" ,r-clue)
6334 ("r-data-table" ,r-data-table)
6335 ("r-flowclust" ,r-flowclust)
6336 ("r-flowcore" ,r-flowcore)
6337 ("r-flowstats" ,r-flowstats)
6338 ("r-flowviz" ,r-flowviz)
6339 ("r-flowworkspace" ,r-flowworkspace)
6340 ("r-graph" ,r-graph)
6341 ("r-gtools" ,r-gtools)
6342 ("r-ks" ,r-ks)
6343 ("r-lattice" ,r-lattice)
6344 ("r-mass" ,r-mass)
6345 ("r-ncdfflow" ,r-ncdfflow)
6346 ("r-plyr" ,r-plyr)
6347 ("r-r-utils" ,r-r-utils)
6348 ("r-rbgl" ,r-rbgl)
6349 ("r-rcolorbrewer" ,r-rcolorbrewer)
6350 ("r-rcpp" ,r-rcpp)
6351 ("r-rrcov" ,r-rrcov)))
8f5e1674
RW
6352 (native-inputs
6353 `(("r-knitr" ,r-knitr)))
6aedc805
RW
6354 (home-page "https://bioconductor.org/packages/openCyto")
6355 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6356 (description
6357 "This package is designed to facilitate the automated gating methods in a
6358sequential way to mimic the manual gating strategy.")
6359 (license license:artistic2.0)))
6360
7a62d5e0
RW
6361(define-public r-cytoml
6362 (package
6363 (name "r-cytoml")
ef588757 6364 (version "2.0.5")
7a62d5e0
RW
6365 (source
6366 (origin
6367 (method url-fetch)
6368 (uri (bioconductor-uri "CytoML" version))
6369 (sha256
6370 (base32
ef588757 6371 "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n"))))
7a62d5e0
RW
6372 (properties `((upstream-name . "CytoML")))
6373 (build-system r-build-system)
6374 (inputs
6375 `(("libxml2" ,libxml2)))
6376 (propagated-inputs
6377 `(("r-base64enc" ,r-base64enc)
6378 ("r-bh" ,r-bh)
6379 ("r-biobase" ,r-biobase)
6380 ("r-corpcor" ,r-corpcor)
6381 ("r-cytolib" ,r-cytolib)
6382 ("r-data-table" ,r-data-table)
6383 ("r-dplyr" ,r-dplyr)
6384 ("r-flowcore" ,r-flowcore)
6385 ("r-flowworkspace" ,r-flowworkspace)
6386 ("r-ggcyto" ,r-ggcyto)
6387 ("r-graph" ,r-graph)
6388 ("r-jsonlite" ,r-jsonlite)
6389 ("r-lattice" ,r-lattice)
7a62d5e0
RW
6390 ("r-opencyto" ,r-opencyto)
6391 ("r-plyr" ,r-plyr)
6392 ("r-rbgl" ,r-rbgl)
6393 ("r-rcpp" ,r-rcpp)
8d5a83b7 6394 ("r-rcpparmadillo" ,r-rcpparmadillo)
7a62d5e0
RW
6395 ("r-rcppparallel" ,r-rcppparallel)
6396 ("r-rgraphviz" ,r-rgraphviz)
8d5a83b7 6397 ("r-rhdf5lib" ,r-rhdf5lib)
7a62d5e0
RW
6398 ("r-rprotobuflib" ,r-rprotobuflib)
6399 ("r-runit" ,r-runit)
8d5a83b7 6400 ("r-tibble" ,r-tibble)
7a62d5e0 6401 ("r-xml" ,r-xml)
ef588757 6402 ("r-xml2" ,r-xml2)
7a62d5e0 6403 ("r-yaml" ,r-yaml)))
d49e3f01
RW
6404 (native-inputs
6405 `(("r-knitr" ,r-knitr)))
7a62d5e0
RW
6406 (home-page "https://github.com/RGLab/CytoML")
6407 (synopsis "GatingML interface for cross platform cytometry data sharing")
6408 (description
6409 "This package provides an interface to implementations of the GatingML2.0
6410standard to exchange gated cytometry data with other software platforms.")
6411 (license license:artistic2.0)))
6412
1502751b 6413(define-public r-flowsom
6414 (package
6415 (name "r-flowsom")
32bd0295 6416 (version "1.20.0")
1502751b 6417 (source
6418 (origin
6419 (method url-fetch)
6420 (uri (bioconductor-uri "FlowSOM" version))
6421 (sha256
6422 (base32
32bd0295 6423 "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78"))))
1502751b 6424 (properties `((upstream-name . "FlowSOM")))
6425 (build-system r-build-system)
6426 (propagated-inputs
6427 `(("r-biocgenerics" ,r-biocgenerics)
6428 ("r-consensusclusterplus" ,r-consensusclusterplus)
ba71567a 6429 ("r-cytoml" ,r-cytoml)
1502751b 6430 ("r-flowcore" ,r-flowcore)
ba71567a 6431 ("r-flowworkspace" ,r-flowworkspace)
1502751b 6432 ("r-igraph" ,r-igraph)
ba71567a 6433 ("r-rcolorbrewer" ,r-rcolorbrewer)
1502751b 6434 ("r-tsne" ,r-tsne)
6435 ("r-xml" ,r-xml)))
6436 (home-page "https://bioconductor.org/packages/FlowSOM/")
6437 (synopsis "Visualize and interpret cytometry data")
6438 (description
6439 "FlowSOM offers visualization options for cytometry data, by using
6440self-organizing map clustering and minimal spanning trees.")
6441 (license license:gpl2+)))
1adb9cbc 6442
6443(define-public r-mixomics
6444 (package
6445 (name "r-mixomics")
6bc6a711 6446 (version "6.12.2")
1adb9cbc 6447 (source
6448 (origin
6449 (method url-fetch)
6450 (uri (bioconductor-uri "mixOmics" version))
6451 (sha256
6452 (base32
6bc6a711 6453 "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc"))))
1adb9cbc 6454 (properties `((upstream-name . "mixOmics")))
6455 (build-system r-build-system)
6456 (propagated-inputs
6457 `(("r-corpcor" ,r-corpcor)
6458 ("r-dplyr" ,r-dplyr)
6459 ("r-ellipse" ,r-ellipse)
6460 ("r-ggplot2" ,r-ggplot2)
6461 ("r-gridextra" ,r-gridextra)
6462 ("r-igraph" ,r-igraph)
6463 ("r-lattice" ,r-lattice)
6464 ("r-mass" ,r-mass)
6465 ("r-matrixstats" ,r-matrixstats)
6466 ("r-rarpack" ,r-rarpack)
6467 ("r-rcolorbrewer" ,r-rcolorbrewer)
6468 ("r-reshape2" ,r-reshape2)
6469 ("r-tidyr" ,r-tidyr)))
9669bc17
RW
6470 (native-inputs
6471 `(("r-knitr" ,r-knitr)))
1adb9cbc 6472 (home-page "http://www.mixOmics.org")
6473 (synopsis "Multivariate methods for exploration of biological datasets")
6474 (description
6475 "mixOmics offers a wide range of multivariate methods for the exploration
6476and integration of biological datasets with a particular focus on variable
6477selection. The package proposes several sparse multivariate models we have
6478developed to identify the key variables that are highly correlated, and/or
6479explain the biological outcome of interest. The data that can be analysed
6480with mixOmics may come from high throughput sequencing technologies, such as
6481omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6482also beyond the realm of omics (e.g. spectral imaging). The methods
6483implemented in mixOmics can also handle missing values without having to
6484delete entire rows with missing data.")
6485 (license license:gpl2+)))
a0efa069 6486
6487(define-public r-depecher
6488 (package
6489 (name "r-depecher")
54e04fed 6490 (version "1.4.1")
a0efa069 6491 (source
6492 (origin
6493 (method url-fetch)
6494 (uri (bioconductor-uri "DepecheR" version))
6495 (sha256
6496 (base32
54e04fed 6497 "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v"))))
a0efa069 6498 (properties `((upstream-name . "DepecheR")))
6499 (build-system r-build-system)
a0efa069 6500 (propagated-inputs
6501 `(("r-beanplot" ,r-beanplot)
a0efa069 6502 ("r-dosnow" ,r-dosnow)
6503 ("r-dplyr" ,r-dplyr)
2c8433ca 6504 ("r-fnn" ,r-fnn)
a0efa069 6505 ("r-foreach" ,r-foreach)
6506 ("r-ggplot2" ,r-ggplot2)
6507 ("r-gplots" ,r-gplots)
6508 ("r-mass" ,r-mass)
6509 ("r-matrixstats" ,r-matrixstats)
6510 ("r-mixomics" ,r-mixomics)
6511 ("r-moments" ,r-moments)
6512 ("r-rcpp" ,r-rcpp)
6513 ("r-rcppeigen" ,r-rcppeigen)
6514 ("r-reshape2" ,r-reshape2)
2c8433ca 6515 ("r-robustbase" ,r-robustbase)
a0efa069 6516 ("r-viridis" ,r-viridis)))
bf3722f9
RW
6517 (native-inputs
6518 `(("r-knitr" ,r-knitr)))
a0efa069 6519 (home-page "https://bioconductor.org/packages/DepecheR/")
6520 (synopsis "Identify traits of clusters in high-dimensional entities")
6521 (description
6522 "The purpose of this package is to identify traits in a dataset that can
6523separate groups. This is done on two levels. First, clustering is performed,
6524using an implementation of sparse K-means. Secondly, the generated clusters
6525are used to predict outcomes of groups of individuals based on their
6526distribution of observations in the different clusters. As certain clusters
6527with separating information will be identified, and these clusters are defined
6528by a sparse number of variables, this method can reduce the complexity of
6529data, to only emphasize the data that actually matters.")
6530 (license license:expat)))
b46a0ee7 6531
bb88417f
RW
6532(define-public r-rcistarget
6533 (package
6534 (name "r-rcistarget")
93235b1e 6535 (version "1.8.0")
bb88417f
RW
6536 (source
6537 (origin
6538 (method url-fetch)
6539 (uri (bioconductor-uri "RcisTarget" version))
6540 (sha256
6541 (base32
93235b1e 6542 "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i"))))
bb88417f
RW
6543 (properties `((upstream-name . "RcisTarget")))
6544 (build-system r-build-system)
6545 (propagated-inputs
6546 `(("r-aucell" ,r-aucell)
6547 ("r-biocgenerics" ,r-biocgenerics)
6548 ("r-data-table" ,r-data-table)
6549 ("r-feather" ,r-feather)
6550 ("r-gseabase" ,r-gseabase)
6551 ("r-r-utils" ,r-r-utils)
6552 ("r-summarizedexperiment" ,r-summarizedexperiment)))
93235b1e
RW
6553 (native-inputs
6554 `(("r-knitr" ,r-knitr)))
bb88417f
RW
6555 (home-page "https://aertslab.org/#scenic")
6556 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6557 (description
6558 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6559over-represented on a gene list. In a first step, RcisTarget selects DNA
6560motifs that are significantly over-represented in the surroundings of the
6561@dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6562achieved by using a database that contains genome-wide cross-species rankings
6563for each motif. The motifs that are then annotated to TFs and those that have
6564a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6565each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6566genes in the gene-set that are ranked above the leading edge).")
6567 (license license:gpl3)))
6568
b46a0ee7
RW
6569(define-public r-cicero
6570 (package
6571 (name "r-cicero")
40f378e1 6572 (version "1.6.2")
b46a0ee7
RW
6573 (source
6574 (origin
6575 (method url-fetch)
6576 (uri (bioconductor-uri "cicero" version))
6577 (sha256
6578 (base32
40f378e1 6579 "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh"))))
b46a0ee7
RW
6580 (build-system r-build-system)
6581 (propagated-inputs
6582 `(("r-assertthat" ,r-assertthat)
6583 ("r-biobase" ,r-biobase)
6584 ("r-biocgenerics" ,r-biocgenerics)
6585 ("r-data-table" ,r-data-table)
6586 ("r-dplyr" ,r-dplyr)
6587 ("r-fnn" ,r-fnn)
6588 ("r-genomicranges" ,r-genomicranges)
6589 ("r-ggplot2" ,r-ggplot2)
6590 ("r-glasso" ,r-glasso)
6591 ("r-gviz" ,r-gviz)
6592 ("r-igraph" ,r-igraph)
6593 ("r-iranges" ,r-iranges)
6594 ("r-matrix" ,r-matrix)
6595 ("r-monocle" ,r-monocle)
6596 ("r-plyr" ,r-plyr)
6597 ("r-reshape2" ,r-reshape2)
6598 ("r-s4vectors" ,r-s4vectors)
1893092d 6599 ("r-stringi" ,r-stringi)
b46a0ee7
RW
6600 ("r-stringr" ,r-stringr)
6601 ("r-tibble" ,r-tibble)
5ea4f604 6602 ("r-tidyr" ,r-tidyr)
b46a0ee7 6603 ("r-vgam" ,r-vgam)))
6bd6097e
RW
6604 (native-inputs
6605 `(("r-knitr" ,r-knitr)))
b46a0ee7
RW
6606 (home-page "https://bioconductor.org/packages/cicero/")
6607 (synopsis "Predict cis-co-accessibility from single-cell data")
6608 (description
6609 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6610accessibility data. It also extends the monocle package for use in chromatin
6611accessibility data.")
6612 (license license:expat)))
14bb1c48
RW
6613
6614;; This is the latest commit on the "monocle3" branch.
6615(define-public r-cicero-monocle3
6616 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6617 (revision "1"))
6618 (package (inherit r-cicero)
6619 (name "r-cicero-monocle3")
6620 (version (git-version "1.3.2" revision commit))
6621 (source
6622 (origin
6623 (method git-fetch)
6624 (uri (git-reference
b0e7b699 6625 (url "https://github.com/cole-trapnell-lab/cicero-release")
14bb1c48
RW
6626 (commit commit)))
6627 (file-name (git-file-name name version))
6628 (sha256
6629 (base32
6630 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6631 (propagated-inputs
6632 `(("r-monocle3" ,r-monocle3)
6633 ,@(alist-delete "r-monocle"
6634 (package-propagated-inputs r-cicero)))))))
a9815a6c
RW
6635
6636(define-public r-cistopic
6637 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6638 (revision "0"))
6639 (package
6640 (name "r-cistopic")
6641 (version (git-version "0.2.1" revision commit))
6642 (source
6643 (origin
6644 (method git-fetch)
6645 (uri (git-reference
b0e7b699 6646 (url "https://github.com/aertslab/cisTopic")
a9815a6c
RW
6647 (commit commit)))
6648 (file-name (git-file-name name version))
6649 (sha256
6650 (base32
6651 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6652 (build-system r-build-system)
6653 (propagated-inputs
6654 `(("r-aucell" ,r-aucell)
6655 ("r-data-table" ,r-data-table)
6656 ("r-dplyr" ,r-dplyr)
6657 ("r-dosnow" ,r-dosnow)
6658 ("r-dt" ,r-dt)
6659 ("r-feather" ,r-feather)
6660 ("r-fitdistrplus" ,r-fitdistrplus)
6661 ("r-genomicranges" ,r-genomicranges)
6662 ("r-ggplot2" ,r-ggplot2)
6663 ("r-lda" ,r-lda)
6664 ("r-matrix" ,r-matrix)
6665 ("r-plyr" ,r-plyr)
6666 ("r-rcistarget" ,r-rcistarget)
6667 ("r-rtracklayer" ,r-rtracklayer)
6668 ("r-s4vectors" ,r-s4vectors)))
6669 (home-page "https://github.com/aertslab/cisTopic")
6670 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6671 (description
6672 "The sparse nature of single cell epigenomics data can be overruled using
6673probabilistic modelling methods such as @dfn{Latent Dirichlet
6674Allocation} (LDA). This package allows the probabilistic modelling of
6675cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6676includes functionalities to identify cell states based on the contribution of
6677cisTopics and explore the nature and regulatory proteins driving them.")
6678 (license license:gpl3))))
d85c0f98
RW
6679
6680(define-public r-genie3
6681 (package
6682 (name "r-genie3")
b3280883 6683 (version "1.10.0")
d85c0f98
RW
6684 (source
6685 (origin
6686 (method url-fetch)
6687 (uri (bioconductor-uri "GENIE3" version))
6688 (sha256
6689 (base32
b3280883 6690 "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7"))))
d85c0f98
RW
6691 (properties `((upstream-name . "GENIE3")))
6692 (build-system r-build-system)
6693 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
b3280883
RW
6694 (native-inputs
6695 `(("r-knitr" ,r-knitr)))
d85c0f98
RW
6696 (home-page "https://bioconductor.org/packages/GENIE3")
6697 (synopsis "Gene network inference with ensemble of trees")
6698 (description
6699 "This package implements the GENIE3 algorithm for inferring gene
6700regulatory networks from expression data.")
6701 (license license:gpl2+)))
db316d73
RW
6702
6703(define-public r-roc
6704 (package
6705 (name "r-roc")
cad8a509 6706 (version "1.64.0")
db316d73
RW
6707 (source
6708 (origin
6709 (method url-fetch)
6710 (uri (bioconductor-uri "ROC" version))
6711 (sha256
6712 (base32
cad8a509 6713 "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89"))))
db316d73
RW
6714 (properties `((upstream-name . "ROC")))
6715 (build-system r-build-system)
3672b74f
RW
6716 (propagated-inputs
6717 `(("r-knitr" ,r-knitr)))
db316d73
RW
6718 (home-page "https://www.bioconductor.org/packages/ROC/")
6719 (synopsis "Utilities for ROC curves")
6720 (description
6721 "This package provides utilities for @dfn{Receiver Operating
6722Characteristic} (ROC) curves, with a focus on micro arrays.")
6723 (license license:artistic2.0)))
46721dea
RW
6724
6725(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6726 (package
6727 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6728 (version "0.6.0")
6729 (source
6730 (origin
6731 (method url-fetch)
6732 (uri (bioconductor-uri
6733 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6734 version 'annotation))
6735 (sha256
6736 (base32
6737 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6738 (properties
6739 `((upstream-name
6740 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6741 (build-system r-build-system)
6742 (propagated-inputs `(("r-minfi" ,r-minfi)))
6743 (home-page
6744 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6745 (synopsis "Annotation for Illumina's 450k methylation arrays")
6746 (description
6747 "This package provides manifests and annotation for Illumina's 450k array
6748data.")
6749 (license license:artistic2.0)))
38babeaa
RW
6750
6751(define-public r-watermelon
6752 (package
6753 (name "r-watermelon")
939ace96 6754 (version "1.32.0")
38babeaa
RW
6755 (source
6756 (origin
6757 (method url-fetch)
6758 (uri (bioconductor-uri "wateRmelon" version))
6759 (sha256
6760 (base32
939ace96 6761 "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn"))))
38babeaa
RW
6762 (properties `((upstream-name . "wateRmelon")))
6763 (build-system r-build-system)
6764 (propagated-inputs
6765 `(("r-biobase" ,r-biobase)
6766 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6767 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6768 ("r-illuminaio" ,r-illuminaio)
6769 ("r-limma" ,r-limma)
6770 ("r-lumi" ,r-lumi)
6771 ("r-matrixstats" ,r-matrixstats)
6772 ("r-methylumi" ,r-methylumi)
6773 ("r-roc" ,r-roc)))
6774 (home-page "https://bioconductor.org/packages/wateRmelon/")
6775 (synopsis "Illumina 450 methylation array normalization and metrics")
6776 (description
6777 "The standard index of DNA methylation (beta) is computed from methylated
6778and unmethylated signal intensities. Betas calculated from raw signal
6779intensities perform well, but using 11 methylomic datasets we demonstrate that
6780quantile normalization methods produce marked improvement. The commonly used
6781procedure of normalizing betas is inferior to the separate normalization of M
6782and U, and it is also advantageous to normalize Type I and Type II assays
6783separately. This package provides 15 flavours of betas and three performance
6784metrics, with methods for objects produced by the @code{methylumi} and
6785@code{minfi} packages.")
6786 (license license:gpl3)))
7d2cb646
RW
6787
6788(define-public r-gdsfmt
6789 (package
6790 (name "r-gdsfmt")
f7d5721b 6791 (version "1.24.1")
7d2cb646
RW
6792 (source
6793 (origin
6794 (method url-fetch)
6795 (uri (bioconductor-uri "gdsfmt" version))
6796 (sha256
6797 (base32
f7d5721b 6798 "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67"))
7d2cb646
RW
6799 (modules '((guix build utils)))
6800 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6801 ;; them and link with system libraries instead.
6802 (snippet
6803 '(begin
6804 (for-each delete-file-recursively
6805 '("src/LZ4"
6806 "src/XZ"
6807 "src/ZLIB"))
6808 (substitute* "src/Makevars"
6809 (("all: \\$\\(SHLIB\\)") "all:")
6810 (("\\$\\(SHLIB\\): liblzma.a") "")
6811 (("(ZLIB|LZ4)/.*") "")
6812 (("CoreArray/dVLIntGDS.cpp.*")
6813 "CoreArray/dVLIntGDS.cpp")
6814 (("CoreArray/dVLIntGDS.o.*")
6815 "CoreArray/dVLIntGDS.o")
6816 (("PKG_LIBS = ./liblzma.a")
6817 "PKG_LIBS = -llz4"))
6818 (substitute* "src/CoreArray/dStream.h"
6819 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6820 (string-append "include <" header ">")))
6821 #t))))
6822 (properties `((upstream-name . "gdsfmt")))
6823 (build-system r-build-system)
6824 (inputs
6825 `(("lz4" ,lz4)
6826 ("xz" ,xz)
6827 ("zlib" ,zlib)))
f4954b0b
RW
6828 (native-inputs
6829 `(("r-knitr" ,r-knitr)))
7d2cb646
RW
6830 (home-page "http://corearray.sourceforge.net/")
6831 (synopsis
6832 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6833 (description
6834 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6835Data Structure} (GDS) data files, which are portable across platforms with
6836hierarchical structure to store multiple scalable array-oriented data sets
6837with metadata information. It is suited for large-scale datasets, especially
6838for data which are much larger than the available random-access memory. The
6839@code{gdsfmt} package offers efficient operations specifically designed for
6840integers of less than 8 bits, since a diploid genotype, like
6841@dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6842byte. Data compression and decompression are available with relatively
6843efficient random access. It is also allowed to read a GDS file in parallel
6844with multiple R processes supported by the package @code{parallel}.")
6845 (license license:lgpl3)))
6b5f59c7
RW
6846
6847(define-public r-bigmelon
6848 (package
6849 (name "r-bigmelon")
8112796d 6850 (version "1.14.0")
6b5f59c7
RW
6851 (source
6852 (origin
6853 (method url-fetch)
6854 (uri (bioconductor-uri "bigmelon" version))
6855 (sha256
6856 (base32
8112796d 6857 "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y"))))
6b5f59c7
RW
6858 (properties `((upstream-name . "bigmelon")))
6859 (build-system r-build-system)
6860 (propagated-inputs
6861 `(("r-biobase" ,r-biobase)
6862 ("r-biocgenerics" ,r-biocgenerics)
6863 ("r-gdsfmt" ,r-gdsfmt)
6864 ("r-geoquery" ,r-geoquery)
6865 ("r-methylumi" ,r-methylumi)
6866 ("r-minfi" ,r-minfi)
6867 ("r-watermelon" ,r-watermelon)))
6868 (home-page "https://bioconductor.org/packages/bigmelon/")
6869 (synopsis "Illumina methylation array analysis for large experiments")
6870 (description
6871 "This package provides methods for working with Illumina arrays using the
6872@code{gdsfmt} package.")
6873 (license license:gpl3)))
739b2d10 6874
e5dfcd8e
RW
6875(define-public r-seqbias
6876 (package
6877 (name "r-seqbias")
83b7625c 6878 (version "1.36.0")
e5dfcd8e
RW
6879 (source
6880 (origin
6881 (method url-fetch)
6882 (uri (bioconductor-uri "seqbias" version))
6883 (sha256
6884 (base32
83b7625c 6885 "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai"))))
e5dfcd8e
RW
6886 (properties `((upstream-name . "seqbias")))
6887 (build-system r-build-system)
6888 (propagated-inputs
6889 `(("r-biostrings" ,r-biostrings)
6890 ("r-genomicranges" ,r-genomicranges)
6891 ("r-rhtslib" ,r-rhtslib)))
6892 (inputs
6893 `(("zlib" ,zlib))) ; This comes from rhtslib.
6894 (home-page "https://bioconductor.org/packages/seqbias/")
6895 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6896 (description
6897 "This package implements a model of per-position sequencing bias in
6898high-throughput sequencing data using a simple Bayesian network, the structure
6899and parameters of which are trained on a set of aligned reads and a reference
6900genome sequence.")
6901 (license license:lgpl3)))
6902
63daca1e
RJ
6903(define-public r-snplocs-hsapiens-dbsnp144-grch37
6904 (package
6905 (name "r-snplocs-hsapiens-dbsnp144-grch37")
6906 (version "0.99.20")
6907 (source (origin
6908 (method url-fetch)
6909 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
6910 version 'annotation))
6911 (sha256
6912 (base32
6913 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
6914 (build-system r-build-system)
6915 ;; As this package provides little more than a very large data file it
6916 ;; doesn't make sense to build substitutes.
6917 (arguments `(#:substitutable? #f))
6918 (propagated-inputs
6919 `(("r-biocgenerics" ,r-biocgenerics)
6920 ("r-s4vectors" ,r-s4vectors)
6921 ("r-iranges" ,r-iranges)
6922 ("r-genomeinfodb" ,r-genomeinfodb)
6923 ("r-genomicranges" ,r-genomicranges)
6924 ("r-bsgenome" ,r-bsgenome)
6925 ("r-biostrings" ,r-biostrings)))
6926 (home-page
6927 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
6928 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
6929 (description "This package provides SNP locations and alleles for Homo
6930sapiens extracted from NCBI dbSNP Build 144. The source data files used for
6931this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
6932to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
6933patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
1408e2ab 6934X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
63daca1e
RJ
6935the mitochondrion chromosome. Therefore, the SNPs in this package can be
6936injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
6937correct position but this injection will exclude chrM (i.e. nothing will be
6938injected in that sequence).")
6939 (license license:artistic2.0)))
6940
bb0024dc
RW
6941(define-public r-reqon
6942 (package
6943 (name "r-reqon")
efb44ebc 6944 (version "1.34.0")
bb0024dc
RW
6945 (source
6946 (origin
6947 (method url-fetch)
6948 (uri (bioconductor-uri "ReQON" version))
6949 (sha256
6950 (base32
efb44ebc 6951 "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz"))))
bb0024dc
RW
6952 (properties `((upstream-name . "ReQON")))
6953 (build-system r-build-system)
6954 (propagated-inputs
6955 `(("r-rjava" ,r-rjava)
6956 ("r-rsamtools" ,r-rsamtools)
6957 ("r-seqbias" ,r-seqbias)))
6958 (home-page "https://bioconductor.org/packages/ReQON/")
6959 (synopsis "Recalibrating quality of nucleotides")
6960 (description
6961 "This package provides an implementation of an algorithm for
6962recalibrating the base quality scores for aligned sequencing data in BAM
6963format.")
6964 (license license:gpl2)))
6965
739b2d10
RW
6966(define-public r-wavcluster
6967 (package
6968 (name "r-wavcluster")
12b255f2 6969 (version "2.22.0")
739b2d10
RW
6970 (source
6971 (origin
6972 (method url-fetch)
6973 (uri (bioconductor-uri "wavClusteR" version))
6974 (sha256
6975 (base32
12b255f2 6976 "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk"))))
739b2d10
RW
6977 (properties `((upstream-name . "wavClusteR")))
6978 (build-system r-build-system)
6979 (propagated-inputs
6980 `(("r-biocgenerics" ,r-biocgenerics)
6981 ("r-biostrings" ,r-biostrings)
6982 ("r-foreach" ,r-foreach)
6983 ("r-genomicfeatures" ,r-genomicfeatures)
6984 ("r-genomicranges" ,r-genomicranges)
6985 ("r-ggplot2" ,r-ggplot2)
6986 ("r-hmisc" ,r-hmisc)
6987 ("r-iranges" ,r-iranges)
6988 ("r-mclust" ,r-mclust)
6989 ("r-rsamtools" ,r-rsamtools)
6990 ("r-rtracklayer" ,r-rtracklayer)
6991 ("r-s4vectors" ,r-s4vectors)
6992 ("r-seqinr" ,r-seqinr)
6993 ("r-stringr" ,r-stringr)
6994 ("r-wmtsa" ,r-wmtsa)))
12b255f2
RW
6995 (native-inputs
6996 `(("r-knitr" ,r-knitr)))
739b2d10
RW
6997 (home-page "https://bioconductor.org/packages/wavClusteR/")
6998 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6999 (description
7000 "This package provides an integrated pipeline for the analysis of
7001PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
7002sequencing errors, SNPs and additional non-experimental sources by a non-
7003parametric mixture model. The protein binding sites (clusters) are then
7004resolved at high resolution and cluster statistics are estimated using a
7005rigorous Bayesian framework. Post-processing of the results, data export for
7006UCSC genome browser visualization and motif search analysis are provided. In
e40ecf8a 7007addition, the package integrates RNA-Seq data to estimate the False
739b2d10
RW
7008Discovery Rate of cluster detection. Key functions support parallel multicore
7009computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
7010be applied to the analysis of other NGS data obtained from experimental
7011procedures that induce nucleotide substitutions (e.g. BisSeq).")
7012 (license license:gpl2)))
853211a5
RW
7013
7014(define-public r-timeseriesexperiment
7015 (package
7016 (name "r-timeseriesexperiment")
49dd5041 7017 (version "1.6.0")
853211a5
RW
7018 (source
7019 (origin
7020 (method url-fetch)
7021 (uri (bioconductor-uri "TimeSeriesExperiment" version))
7022 (sha256
7023 (base32
49dd5041 7024 "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3"))))
853211a5
RW
7025 (properties
7026 `((upstream-name . "TimeSeriesExperiment")))
7027 (build-system r-build-system)
7028 (propagated-inputs
7029 `(("r-deseq2" ,r-deseq2)
7030 ("r-dplyr" ,r-dplyr)
7031 ("r-dynamictreecut" ,r-dynamictreecut)
7032 ("r-edger" ,r-edger)
7033 ("r-ggplot2" ,r-ggplot2)
7034 ("r-hmisc" ,r-hmisc)
7035 ("r-limma" ,r-limma)
7036 ("r-magrittr" ,r-magrittr)
7037 ("r-proxy" ,r-proxy)
7038 ("r-s4vectors" ,r-s4vectors)
7039 ("r-summarizedexperiment" ,r-summarizedexperiment)
7040 ("r-tibble" ,r-tibble)
7041 ("r-tidyr" ,r-tidyr)
7042 ("r-vegan" ,r-vegan)
7043 ("r-viridis" ,r-viridis)))
49dd5041
RW
7044 (native-inputs
7045 `(("r-knitr" ,r-knitr)))
853211a5
RW
7046 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
7047 (synopsis "Analysis for short time-series data")
7048 (description
7049 "This package is a visualization and analysis toolbox for short time
7050course data which includes dimensionality reduction, clustering, two-sample
7051differential expression testing and gene ranking techniques. The package also
7052provides methods for retrieving enriched pathways.")
7053 (license license:lgpl3+)))
df8576e5
RW
7054
7055(define-public r-variantfiltering
7056 (package
7057 (name "r-variantfiltering")
41f7fe4a 7058 (version "1.24.0")
df8576e5
RW
7059 (source
7060 (origin
7061 (method url-fetch)
7062 (uri (bioconductor-uri "VariantFiltering" version))
7063 (sha256
7064 (base32
41f7fe4a 7065 "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4"))))
df8576e5
RW
7066 (properties
7067 `((upstream-name . "VariantFiltering")))
7068 (build-system r-build-system)
7069 (propagated-inputs
7070 `(("r-annotationdbi" ,r-annotationdbi)
7071 ("r-biobase" ,r-biobase)
7072 ("r-biocgenerics" ,r-biocgenerics)
7073 ("r-biocparallel" ,r-biocparallel)
7074 ("r-biostrings" ,r-biostrings)
7075 ("r-bsgenome" ,r-bsgenome)
7076 ("r-dt" ,r-dt)
7077 ("r-genomeinfodb" ,r-genomeinfodb)
7078 ("r-genomicfeatures" ,r-genomicfeatures)
7079 ("r-genomicranges" ,r-genomicranges)
7080 ("r-genomicscores" ,r-genomicscores)
7081 ("r-graph" ,r-graph)
7082 ("r-gviz" ,r-gviz)
7083 ("r-iranges" ,r-iranges)
7084 ("r-rbgl" ,r-rbgl)
7085 ("r-rsamtools" ,r-rsamtools)
7086 ("r-s4vectors" ,r-s4vectors)
7087 ("r-shiny" ,r-shiny)
7088 ("r-shinyjs" ,r-shinyjs)
7089 ("r-shinythemes" ,r-shinythemes)
7090 ("r-shinytree" ,r-shinytree)
7091 ("r-summarizedexperiment" ,r-summarizedexperiment)
7092 ("r-variantannotation" ,r-variantannotation)
7093 ("r-xvector" ,r-xvector)))
7094 (home-page "https://github.com/rcastelo/VariantFiltering")
7095 (synopsis "Filtering of coding and non-coding genetic variants")
7096 (description
7097 "Filter genetic variants using different criteria such as inheritance
7098model, amino acid change consequence, minor allele frequencies across human
7099populations, splice site strength, conservation, etc.")
7100 (license license:artistic2.0)))
f5349b4d
RW
7101
7102(define-public r-genomegraphs
7103 (package
7104 (name "r-genomegraphs")
053a2127 7105 (version "1.46.0")
f5349b4d
RW
7106 (source
7107 (origin
7108 (method url-fetch)
7109 (uri (bioconductor-uri "GenomeGraphs" version))
7110 (sha256
7111 (base32
053a2127 7112 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
f5349b4d
RW
7113 (properties `((upstream-name . "GenomeGraphs")))
7114 (build-system r-build-system)
7115 (propagated-inputs
7116 `(("r-biomart" ,r-biomart)))
7117 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7118 (synopsis "Plotting genomic information from Ensembl")
7119 (description
7120 "Genomic data analyses requires integrated visualization of known genomic
7121information and new experimental data. GenomeGraphs uses the biomaRt package
7122to perform live annotation queries to Ensembl and translates this to e.g.
7123gene/transcript structures in viewports of the grid graphics package. This
7124results in genomic information plotted together with your data. Another
7125strength of GenomeGraphs is to plot different data types such as array CGH,
7126gene expression, sequencing and other data, together in one plot using the
7127same genome coordinate system.")
7128 (license license:artistic2.0)))
2a360cf6
RW
7129
7130(define-public r-wavetiling
7131 (package
7132 (name "r-wavetiling")
e13f9773 7133 (version "1.28.0")
2a360cf6
RW
7134 (source
7135 (origin
7136 (method url-fetch)
7137 (uri (bioconductor-uri "waveTiling" version))
7138 (sha256
7139 (base32
e13f9773 7140 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
2a360cf6
RW
7141 (properties `((upstream-name . "waveTiling")))
7142 (build-system r-build-system)
7143 (propagated-inputs
7144 `(("r-affy" ,r-affy)
7145 ("r-biobase" ,r-biobase)
7146 ("r-biostrings" ,r-biostrings)
7147 ("r-genomegraphs" ,r-genomegraphs)
7148 ("r-genomicranges" ,r-genomicranges)
7149 ("r-iranges" ,r-iranges)
7150 ("r-oligo" ,r-oligo)
7151 ("r-oligoclasses" ,r-oligoclasses)
7152 ("r-preprocesscore" ,r-preprocesscore)
7153 ("r-waveslim" ,r-waveslim)))
7154 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7155 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7156 (description
7157 "This package is designed to conduct transcriptome analysis for tiling
7158arrays based on fast wavelet-based functional models.")
7159 (license license:gpl2+)))
d80a1569
RW
7160
7161(define-public r-variancepartition
7162 (package
7163 (name "r-variancepartition")
1bdc770d 7164 (version "1.18.3")
d80a1569
RW
7165 (source
7166 (origin
7167 (method url-fetch)
7168 (uri (bioconductor-uri "variancePartition" version))
7169 (sha256
7170 (base32
1bdc770d 7171 "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0"))))
d80a1569
RW
7172 (properties
7173 `((upstream-name . "variancePartition")))
7174 (build-system r-build-system)
7175 (propagated-inputs
7176 `(("r-biobase" ,r-biobase)
326746e1 7177 ("r-biocparallel" ,r-biocparallel)
d80a1569
RW
7178 ("r-colorramps" ,r-colorramps)
7179 ("r-doparallel" ,r-doparallel)
7180 ("r-foreach" ,r-foreach)
7181 ("r-ggplot2" ,r-ggplot2)
7182 ("r-gplots" ,r-gplots)
7183 ("r-iterators" ,r-iterators)
7184 ("r-limma" ,r-limma)
7185 ("r-lme4" ,r-lme4)
7186 ("r-lmertest" ,r-lmertest)
7187 ("r-mass" ,r-mass)
7188 ("r-pbkrtest" ,r-pbkrtest)
7189 ("r-progress" ,r-progress)
7190 ("r-reshape2" ,r-reshape2)
7191 ("r-scales" ,r-scales)))
fbbaf5ae
RW
7192 (native-inputs
7193 `(("r-knitr" ,r-knitr)))
d80a1569
RW
7194 (home-page "https://bioconductor.org/packages/variancePartition/")
7195 (synopsis "Analyze variation in gene expression experiments")
7196 (description
7197 "This is a package providing tools to quantify and interpret multiple
7198sources of biological and technical variation in gene expression experiments.
7199It uses a linear mixed model to quantify variation in gene expression
7200attributable to individual, tissue, time point, or technical variables. The
7201package includes dream differential expression analysis for repeated
7202measures.")
7203 (license license:gpl2+)))
16e2e4f2 7204
7205(define-public r-htqpcr
7206 (package
7207 (name "r-htqpcr")
518050a7 7208 (version "1.42.0")
16e2e4f2 7209 (source
7210 (origin
7211 (method url-fetch)
7212 (uri (bioconductor-uri "HTqPCR" version))
7213 (sha256
7214 (base32
518050a7 7215 "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j"))))
16e2e4f2 7216 (properties `((upstream-name . "HTqPCR")))
7217 (build-system r-build-system)
7218 (propagated-inputs
7219 `(("r-affy" ,r-affy)
7220 ("r-biobase" ,r-biobase)
7221 ("r-gplots" ,r-gplots)
7222 ("r-limma" ,r-limma)
7223 ("r-rcolorbrewer" ,r-rcolorbrewer)))
486a0800
TGR
7224 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7225 "groups/bertone/software/HTqPCR.pdf"))
16e2e4f2 7226 (synopsis "Automated analysis of high-throughput qPCR data")
7227 (description
7228 "Analysis of Ct values from high throughput quantitative real-time
7229PCR (qPCR) assays across multiple conditions or replicates. The input data
7230can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7231OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7232Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7233such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7234loading, quality assessment, normalization, visualization and parametric or
7235non-parametric testing for statistical significance in Ct values between
7236features (e.g. genes, microRNAs).")
7237 (license license:artistic2.0)))
86fb2c63 7238
7239(define-public r-unifiedwmwqpcr
7240 (package
7241 (name "r-unifiedwmwqpcr")
a9148d06 7242 (version "1.24.0")
86fb2c63 7243 (source
7244 (origin
7245 (method url-fetch)
7246 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7247 (sha256
7248 (base32
a9148d06 7249 "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81"))))
86fb2c63 7250 (properties
7251 `((upstream-name . "unifiedWMWqPCR")))
7252 (build-system r-build-system)
7253 (propagated-inputs
7254 `(("r-biocgenerics" ,r-biocgenerics)
7255 ("r-htqpcr" ,r-htqpcr)))
7256 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7257 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7258 (description
b5b0ee3b 7259 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
86fb2c63 7260data. This modified test allows for testing differential expression in qPCR
7261data.")
7262 (license license:gpl2+)))
72b67e0b
RW
7263
7264;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7265;; it here.
7266(define-public r-activedriverwgs
7267 (package
7268 (name "r-activedriverwgs")
5412da84 7269 (version "1.1.1")
72b67e0b
RW
7270 (source
7271 (origin
7272 (method url-fetch)
7273 (uri (cran-uri "ActiveDriverWGS" version))
7274 (sha256
7275 (base32
5412da84 7276 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
72b67e0b
RW
7277 (properties
7278 `((upstream-name . "ActiveDriverWGS")))
7279 (build-system r-build-system)
7280 (propagated-inputs
7281 `(("r-biostrings" ,r-biostrings)
7282 ("r-bsgenome" ,r-bsgenome)
7283 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7284 ("r-genomeinfodb" ,r-genomeinfodb)
7285 ("r-genomicranges" ,r-genomicranges)
7286 ("r-iranges" ,r-iranges)
72b67e0b 7287 ("r-s4vectors" ,r-s4vectors)))
e1ce10e3
RW
7288 (native-inputs
7289 `(("r-knitr" ,r-knitr)))
72b67e0b
RW
7290 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7291 (synopsis "Driver discovery tool for cancer whole genomes")
7292 (description
7293 "This package provides a method for finding an enrichment of cancer
7294simple somatic mutations (SNVs and Indels) in functional elements across the
7295human genome. ActiveDriverWGS detects coding and noncoding driver elements
7296using whole genome sequencing data.")
7297 (license license:gpl3)))
8e6f63dd
RW
7298
7299;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7300;; it here.
7301(define-public r-activepathways
7302 (package
7303 (name "r-activepathways")
a9a91280 7304 (version "1.0.2")
8e6f63dd
RW
7305 (source
7306 (origin
7307 (method url-fetch)
7308 (uri (cran-uri "ActivePathways" version))
7309 (sha256
7310 (base32
a9a91280 7311 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
8e6f63dd
RW
7312 (properties
7313 `((upstream-name . "ActivePathways")))
7314 (build-system r-build-system)
7315 (propagated-inputs
7316 `(("r-data-table" ,r-data-table)
a9a91280 7317 ("r-ggplot2" ,r-ggplot2)))
229736aa
RW
7318 (native-inputs
7319 `(("r-knitr" ,r-knitr)))
8e6f63dd
RW
7320 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7321 (synopsis "Multivariate pathway enrichment analysis")
7322 (description
7323 "This package represents an integrative method of analyzing multi omics
7324data that conducts enrichment analysis of annotated gene sets. ActivePathways
7325uses a statistical data fusion approach, rationalizes contributing evidence
7326and highlights associated genes, improving systems-level understanding of
7327cellular organization in health and disease.")
7328 (license license:gpl3)))
d11d6fea
RW
7329
7330(define-public r-bgmix
7331 (package
7332 (name "r-bgmix")
296992be 7333 (version "1.48.0")
d11d6fea
RW
7334 (source
7335 (origin
7336 (method url-fetch)
7337 (uri (bioconductor-uri "BGmix" version))
7338 (sha256
7339 (base32
296992be 7340 "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n"))))
d11d6fea
RW
7341 (properties `((upstream-name . "BGmix")))
7342 (build-system r-build-system)
7343 (propagated-inputs
7344 `(("r-kernsmooth" ,r-kernsmooth)))
7345 (home-page "https://bioconductor.org/packages/BGmix/")
7346 (synopsis "Bayesian models for differential gene expression")
7347 (description
7348 "This package provides fully Bayesian mixture models for differential
7349gene expression.")
7350 (license license:gpl2)))
75eb1149
RW
7351
7352(define-public r-bgx
7353 (package
7354 (name "r-bgx")
7337615d 7355 (version "1.54.1")
75eb1149
RW
7356 (source
7357 (origin
7358 (method url-fetch)
7359 (uri (bioconductor-uri "bgx" version))
7360 (sha256
7361 (base32
7337615d 7362 "0a10fg9n5p024jrmbis102gqpbz23sc6vdn1sal2697hlxikzb46"))))
75eb1149
RW
7363 (properties `((upstream-name . "bgx")))
7364 (build-system r-build-system)
7365 (propagated-inputs
7366 `(("r-affy" ,r-affy)
7367 ("r-biobase" ,r-biobase)
7368 ("r-gcrma" ,r-gcrma)
7369 ("r-rcpp" ,r-rcpp)))
7370 (home-page "https://bioconductor.org/packages/bgx/")
7371 (synopsis "Bayesian gene expression")
7372 (description
7373 "This package provides tools for Bayesian integrated analysis of
7374Affymetrix GeneChips.")
7375 (license license:gpl2)))
6bd50acf
RW
7376
7377(define-public r-bhc
7378 (package
7379 (name "r-bhc")
2415576e 7380 (version "1.40.0")
6bd50acf
RW
7381 (source
7382 (origin
7383 (method url-fetch)
7384 (uri (bioconductor-uri "BHC" version))
7385 (sha256
7386 (base32
2415576e 7387 "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr"))))
6bd50acf
RW
7388 (properties `((upstream-name . "BHC")))
7389 (build-system r-build-system)
7390 (home-page "https://bioconductor.org/packages/BHC/")
7391 (synopsis "Bayesian hierarchical clustering")
7392 (description
7393 "The method implemented in this package performs bottom-up hierarchical
7394clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7395in the data and Bayesian model selection to decide at each step which clusters
7396to merge. This avoids several limitations of traditional methods, for example
7397how many clusters there should be and how to choose a principled distance
7398metric. This implementation accepts multinomial (i.e. discrete, with 2+
7399categories) or time-series data. This version also includes a randomised
7400algorithm which is more efficient for larger data sets.")
7401 (license license:gpl3)))
de9374b7
RW
7402
7403(define-public r-bicare
7404 (package
7405 (name "r-bicare")
76425173 7406 (version "1.46.0")
de9374b7
RW
7407 (source
7408 (origin
7409 (method url-fetch)
7410 (uri (bioconductor-uri "BicARE" version))
7411 (sha256
7412 (base32
76425173 7413 "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y"))))
de9374b7
RW
7414 (properties `((upstream-name . "BicARE")))
7415 (build-system r-build-system)
7416 (propagated-inputs
7417 `(("r-biobase" ,r-biobase)
7418 ("r-gseabase" ,r-gseabase)
7419 ("r-multtest" ,r-multtest)))
7420 (home-page "http://bioinfo.curie.fr")
7421 (synopsis "Biclustering analysis and results exploration")
7422 (description
7423 "This is a package for biclustering analysis and exploration of
7424results.")
7425 (license license:gpl2)))
40fe63ad
RW
7426
7427(define-public r-bifet
7428 (package
7429 (name "r-bifet")
a54fd409 7430 (version "1.8.0")
40fe63ad
RW
7431 (source
7432 (origin
7433 (method url-fetch)
7434 (uri (bioconductor-uri "BiFET" version))
7435 (sha256
7436 (base32
a54fd409 7437 "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5"))))
40fe63ad
RW
7438 (properties `((upstream-name . "BiFET")))
7439 (build-system r-build-system)
7440 (propagated-inputs
7441 `(("r-genomicranges" ,r-genomicranges)
7442 ("r-poibin" ,r-poibin)))
a54fd409
RW
7443 (native-inputs
7444 `(("r-knitr" ,r-knitr)))
40fe63ad
RW
7445 (home-page "https://bioconductor.org/packages/BiFET")
7446 (synopsis "Bias-free footprint enrichment test")
7447 (description
7448 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7449over-represented in target regions compared to background regions after
7450correcting for the bias arising from the imbalance in read counts and GC
7451contents between the target and background regions. For a given TF k, BiFET
7452tests the null hypothesis that the target regions have the same probability of
7453having footprints for the TF k as the background regions while correcting for
7454the read count and GC content bias.")
7455 (license license:gpl3)))
e823337c
RW
7456
7457(define-public r-rsbml
7458 (package
7459 (name "r-rsbml")
d65bdbb2 7460 (version "2.46.0")
e823337c
RW
7461 (source
7462 (origin
7463 (method url-fetch)
7464 (uri (bioconductor-uri "rsbml" version))
7465 (sha256
7466 (base32
d65bdbb2 7467 "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx"))))
e823337c
RW
7468 (properties `((upstream-name . "rsbml")))
7469 (build-system r-build-system)
7470 (inputs
7471 `(("libsbml" ,libsbml)
7472 ("zlib" ,zlib)))
7473 (propagated-inputs
7474 `(("r-biocgenerics" ,r-biocgenerics)
7475 ("r-graph" ,r-graph)))
7476 (native-inputs
7477 `(("pkg-config" ,pkg-config)))
7478 (home-page "http://www.sbml.org")
7479 (synopsis "R support for SBML")
7480 (description
7481 "This package provides an R interface to libsbml for SBML parsing,
7482validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7483 (license license:artistic2.0)))
75a8bb31
RW
7484
7485(define-public r-hypergraph
7486 (package
7487 (name "r-hypergraph")
0ff72461 7488 (version "1.60.0")
75a8bb31
RW
7489 (source
7490 (origin
7491 (method url-fetch)
7492 (uri (bioconductor-uri "hypergraph" version))
7493 (sha256
7494 (base32
0ff72461 7495 "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7"))))
75a8bb31
RW
7496 (properties `((upstream-name . "hypergraph")))
7497 (build-system r-build-system)
7498 (propagated-inputs
7499 `(("r-graph" ,r-graph)))
7500 (home-page "https://bioconductor.org/packages/hypergraph")
7501 (synopsis "Hypergraph data structures")
7502 (description
7503 "This package implements some simple capabilities for representing and
7504manipulating hypergraphs.")
7505 (license license:artistic2.0)))
5aef09bd
RW
7506
7507(define-public r-hyperdraw
7508 (package
7509 (name "r-hyperdraw")
31169986 7510 (version "1.40.0")
5aef09bd
RW
7511 (source
7512 (origin
7513 (method url-fetch)
7514 (uri (bioconductor-uri "hyperdraw" version))
7515 (sha256
7516 (base32
31169986 7517 "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf"))))
5aef09bd
RW
7518 (properties `((upstream-name . "hyperdraw")))
7519 (build-system r-build-system)
7520 (inputs `(("graphviz" ,graphviz)))
7521 (propagated-inputs
7522 `(("r-graph" ,r-graph)
7523 ("r-hypergraph" ,r-hypergraph)
7524 ("r-rgraphviz" ,r-rgraphviz)))
7525 (home-page "https://bioconductor.org/packages/hyperdraw")
7526 (synopsis "Visualizing hypergraphs")
7527 (description
7528 "This package provides functions for visualizing hypergraphs.")
7529 (license license:gpl2+)))
6ca6f866
RW
7530
7531(define-public r-biggr
7532 (package
7533 (name "r-biggr")
f31edb01 7534 (version "1.24.0")
6ca6f866
RW
7535 (source
7536 (origin
7537 (method url-fetch)
7538 (uri (bioconductor-uri "BiGGR" version))
7539 (sha256
7540 (base32
f31edb01 7541 "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk"))))
6ca6f866
RW
7542 (properties `((upstream-name . "BiGGR")))
7543 (build-system r-build-system)
7544 (propagated-inputs
7545 `(("r-hyperdraw" ,r-hyperdraw)
7546 ("r-hypergraph" ,r-hypergraph)
7547 ("r-lim" ,r-lim)
7548 ("r-limsolve" ,r-limsolve)
7549 ("r-rsbml" ,r-rsbml)
7550 ("r-stringr" ,r-stringr)))
7551 (home-page "https://bioconductor.org/packages/BiGGR/")
7552 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7553 (description
7554 "This package provides an interface to simulate metabolic reconstruction
7555from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7556reconstruction databases. The package facilitates @dfn{flux balance
7557analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7558networks and estimated fluxes can be visualized with hypergraphs.")
7559 (license license:gpl3+)))
820373db
RW
7560
7561(define-public r-bigmemoryextras
7562 (package
7563 (name "r-bigmemoryextras")
eef9c99c 7564 (version "1.36.0")
820373db
RW
7565 (source
7566 (origin
7567 (method url-fetch)
7568 (uri (bioconductor-uri "bigmemoryExtras" version))
7569 (sha256
7570 (base32
eef9c99c 7571 "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g"))))
820373db
RW
7572 (properties
7573 `((upstream-name . "bigmemoryExtras")))
7574 (build-system r-build-system)
7575 (propagated-inputs
7576 `(("r-bigmemory" ,r-bigmemory)))
eef9c99c
RW
7577 (native-inputs
7578 `(("r-knitr" ,r-knitr)))
820373db
RW
7579 (home-page "https://github.com/phaverty/bigmemoryExtras")
7580 (synopsis "Extension of the bigmemory package")
7581 (description
7582 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7583safety and convenience features to the @code{filebacked.big.matrix} class from
7584the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7585monitoring and gracefully restoring the connection to on-disk data and it also
7230f6d5 7586protects against accidental data modification with a file-system-based
820373db
RW
7587permissions system. Utilities are provided for using @code{BigMatrix}-derived
7588classes as @code{assayData} matrices within the @code{Biobase} package's
7589@code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7590related to attaching to, and indexing into, file-backed matrices with
7591dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7592a file-backed matrix with factor properties.")
7593 (license license:artistic2.0)))
d38775b1
RW
7594
7595(define-public r-bigpint
7596 (package
7597 (name "r-bigpint")
d0badcc1 7598 (version "1.4.0")
d38775b1
RW
7599 (source
7600 (origin
7601 (method url-fetch)
7602 (uri (bioconductor-uri "bigPint" version))
7603 (sha256
7604 (base32
d0badcc1 7605 "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8"))))
d38775b1
RW
7606 (properties `((upstream-name . "bigPint")))
7607 (build-system r-build-system)
7608 (propagated-inputs
d0badcc1
RW
7609 `(("r-delayedarray" ,r-delayedarray)
7610 ("r-dplyr" ,r-dplyr)
d38775b1
RW
7611 ("r-ggally" ,r-ggally)
7612 ("r-ggplot2" ,r-ggplot2)
7613 ("r-gridextra" ,r-gridextra)
7614 ("r-hexbin" ,r-hexbin)
7615 ("r-hmisc" ,r-hmisc)
7616 ("r-htmlwidgets" ,r-htmlwidgets)
7617 ("r-plotly" ,r-plotly)
7618 ("r-plyr" ,r-plyr)
7619 ("r-rcolorbrewer" ,r-rcolorbrewer)
7620 ("r-reshape" ,r-reshape)
7621 ("r-shiny" ,r-shiny)
7622 ("r-shinycssloaders" ,r-shinycssloaders)
7623 ("r-shinydashboard" ,r-shinydashboard)
7624 ("r-stringr" ,r-stringr)
d0badcc1 7625 ("r-summarizedexperiment" ,r-summarizedexperiment)
d38775b1 7626 ("r-tidyr" ,r-tidyr)))
1f2f01ae
RW
7627 (native-inputs
7628 `(("r-knitr" ,r-knitr)))
d38775b1
RW
7629 (home-page "https://github.com/lindsayrutter/bigPint")
7630 (synopsis "Big multivariate data plotted interactively")
7631 (description
7632 "This package provides methods for visualizing large multivariate
7633datasets using static and interactive scatterplot matrices, parallel
7634coordinate plots, volcano plots, and litre plots. It includes examples for
7635visualizing RNA-sequencing datasets and differentially expressed genes.")
7636 (license license:gpl3)))
991554fc
RW
7637
7638(define-public r-chemminer
7639 (package
7640 (name "r-chemminer")
06908a73 7641 (version "3.40.0")
991554fc
RW
7642 (source
7643 (origin
7644 (method url-fetch)
7645 (uri (bioconductor-uri "ChemmineR" version))
7646 (sha256
7647 (base32
06908a73 7648 "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf"))))
991554fc
RW
7649 (properties `((upstream-name . "ChemmineR")))
7650 (build-system r-build-system)
7651 (propagated-inputs
7652 `(("r-base64enc" ,r-base64enc)
7653 ("r-bh" ,r-bh)
7654 ("r-biocgenerics" ,r-biocgenerics)
7655 ("r-dbi" ,r-dbi)
7656 ("r-digest" ,r-digest)
7657 ("r-dt" ,r-dt)
7658 ("r-ggplot2" ,r-ggplot2)
7659 ("r-gridextra" ,r-gridextra)
7660 ("r-png" ,r-png)
7661 ("r-rcpp" ,r-rcpp)
7662 ("r-rcurl" ,r-rcurl)
7663 ("r-rjson" ,r-rjson)
7664 ("r-rsvg" ,r-rsvg)))
06908a73
RW
7665 (native-inputs
7666 `(("r-knitr" ,r-knitr)))
991554fc
RW
7667 (home-page "https://github.com/girke-lab/ChemmineR")
7668 (synopsis "Cheminformatics toolkit for R")
7669 (description
7670 "ChemmineR is a cheminformatics package for analyzing drug-like small
7671molecule data in R. It contains functions for efficient processing of large
7672numbers of molecules, physicochemical/structural property predictions,
7673structural similarity searching, classification and clustering of compound
7674libraries with a wide spectrum of algorithms. In addition, it offers
7675visualization functions for compound clustering results and chemical
7676structures.")
7677 (license license:artistic2.0)))
48bcbef0
RW
7678
7679(define-public r-bioassayr
7680 (package
7681 (name "r-bioassayr")
c8cbde9f 7682 (version "1.26.0")
48bcbef0
RW
7683 (source
7684 (origin
7685 (method url-fetch)
7686 (uri (bioconductor-uri "bioassayR" version))
7687 (sha256
7688 (base32
c8cbde9f 7689 "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy"))))
48bcbef0
RW
7690 (properties `((upstream-name . "bioassayR")))
7691 (build-system r-build-system)
7692 (propagated-inputs
7693 `(("r-biocgenerics" ,r-biocgenerics)
7694 ("r-chemminer" ,r-chemminer)
7695 ("r-dbi" ,r-dbi)
7696 ("r-matrix" ,r-matrix)
7697 ("r-rjson" ,r-rjson)
7698 ("r-rsqlite" ,r-rsqlite)
7699 ("r-xml" ,r-xml)))
faaf2b35
RW
7700 (native-inputs
7701 `(("r-knitr" ,r-knitr)))
48bcbef0
RW
7702 (home-page "https://github.com/TylerBackman/bioassayR")
7703 (synopsis "Cross-target analysis of small molecule bioactivity")
7704 (description
7705 "bioassayR is a computational tool that enables simultaneous analysis of
7706thousands of bioassay experiments performed over a diverse set of compounds
7707and biological targets. Unique features include support for large-scale
7708cross-target analyses of both public and custom bioassays, generation of
7709@dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7710preloaded database that provides access to a substantial portion of publicly
7711available bioactivity data.")
7712 (license license:artistic2.0)))
29fd736a
RW
7713
7714(define-public r-biobroom
7715 (package
7716 (name "r-biobroom")
e09ca033 7717 (version "1.20.0")
29fd736a
RW
7718 (source
7719 (origin
7720 (method url-fetch)
7721 (uri (bioconductor-uri "biobroom" version))
7722 (sha256
7723 (base32
e09ca033 7724 "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf"))))
29fd736a
RW
7725 (properties `((upstream-name . "biobroom")))
7726 (build-system r-build-system)
7727 (propagated-inputs
7728 `(("r-biobase" ,r-biobase)
7729 ("r-broom" ,r-broom)
7730 ("r-dplyr" ,r-dplyr)
7731 ("r-tidyr" ,r-tidyr)))
e09ca033
RW
7732 (native-inputs
7733 `(("r-knitr" ,r-knitr)))
29fd736a
RW
7734 (home-page "https://github.com/StoreyLab/biobroom")
7735 (synopsis "Turn Bioconductor objects into tidy data frames")
7736 (description
7737 "This package contains methods for converting standard objects
7738constructed by bioinformatics packages, especially those in Bioconductor, and
7739converting them to @code{tidy} data. It thus serves as a complement to the
7740@code{broom} package, and follows the same tidy, augment, glance division of
7741tidying methods. Tidying data makes it easy to recombine, reshape and
7742visualize bioinformatics analyses.")
7743 ;; Any version of the LGPL.
7744 (license license:lgpl3+)))
c373223e
RW
7745
7746(define-public r-graphite
7747 (package
7748 (name "r-graphite")
29b17027 7749 (version "1.34.0")
c373223e
RW
7750 (source
7751 (origin
7752 (method url-fetch)
7753 (uri (bioconductor-uri "graphite" version))
7754 (sha256
7755 (base32
29b17027 7756 "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p"))))
c373223e
RW
7757 (properties `((upstream-name . "graphite")))
7758 (build-system r-build-system)
7759 (propagated-inputs
7760 `(("r-annotationdbi" ,r-annotationdbi)
7761 ("r-checkmate" ,r-checkmate)
7762 ("r-graph" ,r-graph)
7763 ("r-httr" ,r-httr)
7764 ("r-rappdirs" ,r-rappdirs)))
7765 (home-page "https://bioconductor.org/packages/graphite/")
7766 (synopsis "Networks from pathway databases")
7767 (description
7768 "Graphite provides networks derived from eight public pathway databases,
7769and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7770symbols).")
7771 (license license:agpl3+)))
f388834e
RW
7772
7773(define-public r-reactomepa
7774 (package
7775 (name "r-reactomepa")
affb4ab3 7776 (version "1.32.0")
f388834e
RW
7777 (source
7778 (origin
7779 (method url-fetch)
7780 (uri (bioconductor-uri "ReactomePA" version))
7781 (sha256
7782 (base32
affb4ab3 7783 "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x"))))
f388834e
RW
7784 (properties `((upstream-name . "ReactomePA")))
7785 (build-system r-build-system)
7786 (propagated-inputs
7787 `(("r-annotationdbi" ,r-annotationdbi)
7788 ("r-dose" ,r-dose)
7789 ("r-enrichplot" ,r-enrichplot)
7790 ("r-ggplot2" ,r-ggplot2)
7791 ("r-ggraph" ,r-ggraph)
7792 ("r-graphite" ,r-graphite)
7793 ("r-igraph" ,r-igraph)
7794 ("r-reactome-db" ,r-reactome-db)))
affb4ab3
RW
7795 (native-inputs
7796 `(("r-knitr" ,r-knitr)))
f388834e
RW
7797 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7798 (synopsis "Reactome pathway analysis")
7799 (description
7800 "This package provides functions for pathway analysis based on the
7801REACTOME pathway database. It implements enrichment analysis, gene set
7802enrichment analysis and several functions for visualization.")
7803 (license license:gpl2)))
21afe920
RW
7804
7805(define-public r-ebarrays
7806 (package
7807 (name "r-ebarrays")
a74a427b 7808 (version "2.52.0")
21afe920
RW
7809 (source
7810 (origin
7811 (method url-fetch)
7812 (uri (bioconductor-uri "EBarrays" version))
7813 (sha256
7814 (base32
a74a427b 7815 "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf"))))
21afe920
RW
7816 (properties `((upstream-name . "EBarrays")))
7817 (build-system r-build-system)
7818 (propagated-inputs
7819 `(("r-biobase" ,r-biobase)
7820 ("r-cluster" ,r-cluster)
7821 ("r-lattice" ,r-lattice)))
7822 (home-page "https://bioconductor.org/packages/EBarrays/")
7823 (synopsis "Gene clustering and differential expression identification")
7824 (description
7825 "EBarrays provides tools for the analysis of replicated/unreplicated
7826microarray data.")
7827 (license license:gpl2+)))
f180be29
RW
7828
7829(define-public r-bioccasestudies
7830 (package
7831 (name "r-bioccasestudies")
8b71b141 7832 (version "1.50.0")
f180be29
RW
7833 (source
7834 (origin
7835 (method url-fetch)
7836 (uri (bioconductor-uri "BiocCaseStudies" version))
7837 (sha256
7838 (base32
8b71b141 7839 "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix"))))
f180be29
RW
7840 (properties
7841 `((upstream-name . "BiocCaseStudies")))
7842 (build-system r-build-system)
7843 (propagated-inputs `(("r-biobase" ,r-biobase)))
7844 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7845 (synopsis "Support for the case studies monograph")
7846 (description
7847 "This package provides software and data to support the case studies
7848monograph.")
7849 (license license:artistic2.0)))
49f0860b
RW
7850
7851(define-public r-biocgraph
7852 (package
7853 (name "r-biocgraph")
543c63f2 7854 (version "1.50.0")
49f0860b
RW
7855 (source
7856 (origin
7857 (method url-fetch)
7858 (uri (bioconductor-uri "biocGraph" version))
7859 (sha256
7860 (base32
543c63f2 7861 "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj"))))
49f0860b
RW
7862 (properties `((upstream-name . "biocGraph")))
7863 (build-system r-build-system)
7864 (propagated-inputs
7865 `(("r-biocgenerics" ,r-biocgenerics)
7866 ("r-geneplotter" ,r-geneplotter)
7867 ("r-graph" ,r-graph)
7868 ("r-rgraphviz" ,r-rgraphviz)))
7869 (home-page "https://bioconductor.org/packages/biocGraph/")
7870 (synopsis "Graph examples and use cases in Bioinformatics")
7871 (description
7872 "This package provides examples and code that make use of the
7873different graph related packages produced by Bioconductor.")
7874 (license license:artistic2.0)))
244270e6
RW
7875
7876(define-public r-experimenthub
7877 (package
7878 (name "r-experimenthub")
a27a402e 7879 (version "1.14.2")
244270e6
RW
7880 (source
7881 (origin
7882 (method url-fetch)
7883 (uri (bioconductor-uri "ExperimentHub" version))
7884 (sha256
7885 (base32
a27a402e 7886 "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x"))))
244270e6
RW
7887 (properties `((upstream-name . "ExperimentHub")))
7888 (build-system r-build-system)
7889 (propagated-inputs
7890 `(("r-annotationhub" ,r-annotationhub)
7891 ("r-biocfilecache" ,r-biocfilecache)
7892 ("r-biocgenerics" ,r-biocgenerics)
7893 ("r-biocmanager" ,r-biocmanager)
7894 ("r-curl" ,r-curl)
7895 ("r-rappdirs" ,r-rappdirs)
7896 ("r-s4vectors" ,r-s4vectors)))
b56a3462
RW
7897 (native-inputs
7898 `(("r-knitr" ,r-knitr)))
244270e6
RW
7899 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7900 (synopsis "Client to access ExperimentHub resources")
7901 (description
7902 "This package provides a client for the Bioconductor ExperimentHub web
7903resource. ExperimentHub provides a central location where curated data from
7904experiments, publications or training courses can be accessed. Each resource
7905has associated metadata, tags and date of modification. The client creates
7906and manages a local cache of files retrieved enabling quick and reproducible
7907access.")
7908 (license license:artistic2.0)))
06784793
RW
7909
7910(define-public r-multiassayexperiment
7911 (package
7912 (name "r-multiassayexperiment")
4091eae2 7913 (version "1.14.0")
06784793
RW
7914 (source
7915 (origin
7916 (method url-fetch)
7917 (uri (bioconductor-uri "MultiAssayExperiment" version))
7918 (sha256
7919 (base32
4091eae2 7920 "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh"))))
06784793
RW
7921 (properties
7922 `((upstream-name . "MultiAssayExperiment")))
7923 (build-system r-build-system)
7924 (propagated-inputs
7925 `(("r-biobase" ,r-biobase)
7926 ("r-biocgenerics" ,r-biocgenerics)
7927 ("r-genomicranges" ,r-genomicranges)
7928 ("r-iranges" ,r-iranges)
7929 ("r-s4vectors" ,r-s4vectors)
7930 ("r-summarizedexperiment" ,r-summarizedexperiment)
7931 ("r-tidyr" ,r-tidyr)))
5d45d711
RW
7932 (native-inputs
7933 `(("r-knitr" ,r-knitr)))
798ca8d0 7934 (home-page "https://waldronlab.io/MultiAssayExperiment/")
06784793
RW
7935 (synopsis "Integration of multi-omics experiments in Bioconductor")
7936 (description
7937 "MultiAssayExperiment harmonizes data management of multiple assays
7938performed on an overlapping set of specimens. It provides a familiar
7939Bioconductor user experience by extending concepts from
7940@code{SummarizedExperiment}, supporting an open-ended mix of standard data
7941classes for individual assays, and allowing subsetting by genomic ranges or
7942rownames.")
7943 (license license:artistic2.0)))
c2b36a04
RW
7944
7945(define-public r-bioconcotk
7946 (package
7947 (name "r-bioconcotk")
1c518215 7948 (version "1.8.0")
c2b36a04
RW
7949 (source
7950 (origin
7951 (method url-fetch)
7952 (uri (bioconductor-uri "BiocOncoTK" version))
7953 (sha256
7954 (base32
1c518215 7955 "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk"))))
c2b36a04
RW
7956 (properties `((upstream-name . "BiocOncoTK")))
7957 (build-system r-build-system)
7958 (propagated-inputs
7959 `(("r-bigrquery" ,r-bigrquery)
7960 ("r-car" ,r-car)
7961 ("r-complexheatmap" ,r-complexheatmap)
7962 ("r-curatedtcgadata" ,r-curatedtcgadata)
7963 ("r-dbi" ,r-dbi)
7964 ("r-dplyr" ,r-dplyr)
7965 ("r-dt" ,r-dt)
7966 ("r-genomicfeatures" ,r-genomicfeatures)
7967 ("r-genomicranges" ,r-genomicranges)
7968 ("r-ggplot2" ,r-ggplot2)
7969 ("r-ggpubr" ,r-ggpubr)
7970 ("r-graph" ,r-graph)
7971 ("r-httr" ,r-httr)
7972 ("r-iranges" ,r-iranges)
7973 ("r-magrittr" ,r-magrittr)
7974 ("r-plyr" ,r-plyr)
7975 ("r-rgraphviz" ,r-rgraphviz)
7976 ("r-rjson" ,r-rjson)
7977 ("r-s4vectors" ,r-s4vectors)
7978 ("r-scales" ,r-scales)
7979 ("r-shiny" ,r-shiny)
7980 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1c518215
RW
7981 (native-inputs
7982 `(("r-knitr" ,r-knitr)))
c2b36a04
RW
7983 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7984 (synopsis "Bioconductor components for general cancer genomics")
7985 (description
7986 "The purpose of this package is to provide a central interface to various
7987tools for genome-scale analysis of cancer studies.")
7988 (license license:artistic2.0)))
4d12c1e3
RW
7989
7990(define-public r-biocor
7991 (package
7992 (name "r-biocor")
132abe5f 7993 (version "1.12.0")
4d12c1e3
RW
7994 (source
7995 (origin
7996 (method url-fetch)
7997 (uri (bioconductor-uri "BioCor" version))
7998 (sha256
7999 (base32
132abe5f 8000 "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy"))))
4d12c1e3
RW
8001 (properties `((upstream-name . "BioCor")))
8002 (build-system r-build-system)
8003 (propagated-inputs
8004 `(("r-biocparallel" ,r-biocparallel)
8005 ("r-gseabase" ,r-gseabase)
8006 ("r-matrix" ,r-matrix)))
132abe5f
RW
8007 (native-inputs
8008 `(("r-knitr" ,r-knitr)))
4d12c1e3
RW
8009 (home-page "https://llrs.github.io/BioCor/")
8010 (synopsis "Functional similarities")
8011 (description
8012 "This package provides tools to calculate functional similarities based
8013on the pathways described on KEGG and REACTOME or in gene sets. These
8014similarities can be calculated for pathways or gene sets, genes, or clusters
8015and combined with other similarities. They can be used to improve networks,
8016gene selection, testing relationships, and so on.")
8017 (license license:expat)))
4a18112d
RW
8018
8019(define-public r-biocpkgtools
8020 (package
8021 (name "r-biocpkgtools")
1759a13d 8022 (version "1.6.0")
4a18112d
RW
8023 (source
8024 (origin
8025 (method url-fetch)
8026 (uri (bioconductor-uri "BiocPkgTools" version))
8027 (sha256
8028 (base32
1759a13d 8029 "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr"))))
4a18112d
RW
8030 (properties `((upstream-name . "BiocPkgTools")))
8031 (build-system r-build-system)
8032 (propagated-inputs
2d6a7bca
RW
8033 `(("r-biocfilecache" ,r-biocfilecache)
8034 ("r-biocmanager" ,r-biocmanager)
4a18112d
RW
8035 ("r-biocviews" ,r-biocviews)
8036 ("r-dplyr" ,r-dplyr)
8037 ("r-dt" ,r-dt)
8038 ("r-gh" ,r-gh)
8039 ("r-graph" ,r-graph)
8040 ("r-htmltools" ,r-htmltools)
8041 ("r-htmlwidgets" ,r-htmlwidgets)
8042 ("r-httr" ,r-httr)
8043 ("r-igraph" ,r-igraph)
8044 ("r-jsonlite" ,r-jsonlite)
8045 ("r-magrittr" ,r-magrittr)
2d6a7bca 8046 ("r-rappdirs" ,r-rappdirs)
4a18112d
RW
8047 ("r-rbgl" ,r-rbgl)
8048 ("r-readr" ,r-readr)
8049 ("r-rex" ,r-rex)
2d6a7bca 8050 ("r-rlang" ,r-rlang)
4a18112d
RW
8051 ("r-rvest" ,r-rvest)
8052 ("r-stringr" ,r-stringr)
8053 ("r-tibble" ,r-tibble)
8054 ("r-tidyr" ,r-tidyr)
2d6a7bca 8055 ("r-tidyselect" ,r-tidyselect)
4a18112d 8056 ("r-xml2" ,r-xml2)))
2d6a7bca
RW
8057 (native-inputs
8058 `(("r-knitr" ,r-knitr)))
4a18112d
RW
8059 (home-page "https://github.com/seandavi/BiocPkgTools")
8060 (synopsis "Collection of tools for learning about Bioconductor packages")
8061 (description
8062 "Bioconductor has a rich ecosystem of metadata around packages, usage,
8063and build status. This package is a simple collection of functions to access
8064that metadata from R. The goal is to expose metadata for data mining and
8065value-added functionality such as package searching, text mining, and
8066analytics on packages.")
8067 (license license:expat)))
43b66e3f
RW
8068
8069(define-public r-biocset
8070 (package
8071 (name "r-biocset")
b828c3ea 8072 (version "1.2.2")
43b66e3f
RW
8073 (source
8074 (origin
8075 (method url-fetch)
8076 (uri (bioconductor-uri "BiocSet" version))
8077 (sha256
8078 (base32
b828c3ea 8079 "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj"))))
43b66e3f
RW
8080 (properties `((upstream-name . "BiocSet")))
8081 (build-system r-build-system)
8082 (propagated-inputs
8083 `(("r-annotationdbi" ,r-annotationdbi)
8084 ("r-dplyr" ,r-dplyr)
8085 ("r-keggrest" ,r-keggrest)
8086 ("r-plyr" ,r-plyr)
8087 ("r-rlang" ,r-rlang)
8088 ("r-rtracklayer" ,r-rtracklayer)
8089 ("r-tibble" ,r-tibble)))
723fa00d
RW
8090 (native-inputs
8091 `(("r-knitr" ,r-knitr)))
43b66e3f
RW
8092 (home-page
8093 "https://bioconductor.org/packages/BiocSet")
8094 (synopsis
8095 "Representing Different Biological Sets")
8096 (description
8097 "BiocSet displays different biological sets in a triple tibble format.
8098These three tibbles are @code{element}, @code{set}, and @code{elementset}.
5b98473a 8099The user has the ability to activate one of these three tibbles to perform
43b66e3f
RW
8100common functions from the @code{dplyr} package. Mapping functionality and
8101accessing web references for elements/sets are also available in BiocSet.")
8102 (license license:artistic2.0)))
0156297f
RW
8103
8104(define-public r-biocworkflowtools
8105 (package
8106 (name "r-biocworkflowtools")
6a88291d 8107 (version "1.14.0")
0156297f
RW
8108 (source
8109 (origin
8110 (method url-fetch)
8111 (uri (bioconductor-uri "BiocWorkflowTools" version))
8112 (sha256
8113 (base32
6a88291d 8114 "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy"))))
0156297f
RW
8115 (properties
8116 `((upstream-name . "BiocWorkflowTools")))
8117 (build-system r-build-system)
8118 (propagated-inputs
8119 `(("r-biocstyle" ,r-biocstyle)
8120 ("r-bookdown" ,r-bookdown)
8121 ("r-git2r" ,r-git2r)
8122 ("r-httr" ,r-httr)
8123 ("r-knitr" ,r-knitr)
8124 ("r-rmarkdown" ,r-rmarkdown)
8125 ("r-rstudioapi" ,r-rstudioapi)
8126 ("r-stringr" ,r-stringr)
8127 ("r-usethis" ,r-usethis)))
4ecba230
RW
8128 (native-inputs
8129 `(("r-knitr" ,r-knitr)))
0156297f
RW
8130 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8131 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8132 (description
8133 "This package provides functions to ease the transition between
8134Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8135 (license license:expat)))
77e2de36
RW
8136
8137(define-public r-biodist
8138 (package
8139 (name "r-biodist")
6b9e3b92 8140 (version "1.60.0")
77e2de36
RW
8141 (source
8142 (origin
8143 (method url-fetch)
8144 (uri (bioconductor-uri "bioDist" version))
8145 (sha256
8146 (base32
6b9e3b92 8147 "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp"))))
77e2de36
RW
8148 (properties `((upstream-name . "bioDist")))
8149 (build-system r-build-system)
8150 (propagated-inputs
8151 `(("r-biobase" ,r-biobase)
8152 ("r-kernsmooth" ,r-kernsmooth)))
8153 (home-page "https://bioconductor.org/packages/bioDist/")
8154 (synopsis "Different distance measures")
8155 (description
8156 "This package provides a collection of software tools for calculating
8157distance measures.")
8158 (license license:artistic2.0)))
9bc516ba
RW
8159
8160(define-public r-pcatools
8161 (package
8162 (name "r-pcatools")
8163 (version "2.0.0")
8164 (source
8165 (origin
8166 (method url-fetch)
8167 (uri (bioconductor-uri "PCAtools" version))
8168 (sha256
8169 (base32
8170 "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc"))))
8171 (properties `((upstream-name . "PCAtools")))
8172 (build-system r-build-system)
8173 (propagated-inputs
8174 `(("r-beachmat" ,r-beachmat)
8175 ("r-bh" ,r-bh)
8176 ("r-biocparallel" ,r-biocparallel)
8177 ("r-biocsingular" ,r-biocsingular)
8178 ("r-cowplot" ,r-cowplot)
8179 ("r-delayedarray" ,r-delayedarray)
8180 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8181 ("r-dqrng" ,r-dqrng)
8182 ("r-ggplot2" ,r-ggplot2)
8183 ("r-ggrepel" ,r-ggrepel)
8184 ("r-lattice" ,r-lattice)
8185 ("r-matrix" ,r-matrix)
8186 ("r-rcpp" ,r-rcpp)
8187 ("r-reshape2" ,r-reshape2)))
8188 (native-inputs `(("r-knitr" ,r-knitr)))
8189 (home-page "https://github.com/kevinblighe/PCAtools")
8190 (synopsis "PCAtools: everything Principal Components Analysis")
8191 (description
8192 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8193structure of the data without the need to build any model to represent it.
8194This \"summary\" of the data is arrived at through a process of reduction that
8195can transform the large number of variables into a lesser number that are
8196uncorrelated (i.e. the 'principal components'), while at the same time being
8197capable of easy interpretation on the original data. PCAtools provides
8198functions for data exploration via PCA, and allows the user to generate
8199publication-ready figures. PCA is performed via @code{BiocSingular}; users
8200can also identify an optimal number of principal components via different
8201metrics, such as the elbow method and Horn's parallel analysis, which has
8202relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8203dimensional mass cytometry data.")
8204 (license license:gpl3)))
c89afe75
RW
8205
8206(define-public r-rgreat
8207 (package
8208 (name "r-rgreat")
8209 (version "1.20.0")
8210 (source
8211 (origin
8212 (method url-fetch)
8213 (uri (bioconductor-uri "rGREAT" version))
8214 (sha256
8215 (base32
8216 "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v"))))
8217 (properties `((upstream-name . "rGREAT")))
8218 (build-system r-build-system)
8219 (propagated-inputs
8220 `(("r-genomicranges" ,r-genomicranges)
8221 ("r-getoptlong" ,r-getoptlong)
8222 ("r-iranges" ,r-iranges)
8223 ("r-rcurl" ,r-rcurl)
8224 ("r-rjson" ,r-rjson)))
8225 (native-inputs `(("r-knitr" ,r-knitr)))
8226 (home-page "https://github.com/jokergoo/rGREAT")
8227 (synopsis "Client for GREAT analysis")
8228 (description
8229 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8230Tool) analysis automatic by constructing a HTTP POST request according to
8231user's input and automatically retrieving results from GREAT web server.")
8232 (license license:expat)))
0b8c7e4b
RW
8233
8234(define-public r-m3c
8235 (package
8236 (name "r-m3c")
8237 (version "1.10.0")
8238 (source
8239 (origin
8240 (method url-fetch)
8241 (uri (bioconductor-uri "M3C" version))
8242 (sha256
8243 (base32
8244 "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y"))))
8245 (properties `((upstream-name . "M3C")))
8246 (build-system r-build-system)
8247 (propagated-inputs
8248 `(("r-cluster" ,r-cluster)
8249 ("r-corpcor" ,r-corpcor)
8250 ("r-doparallel" ,r-doparallel)
8251 ("r-dosnow" ,r-dosnow)
8252 ("r-foreach" ,r-foreach)
8253 ("r-ggplot2" ,r-ggplot2)
8254 ("r-matrix" ,r-matrix)
8255 ("r-matrixcalc" ,r-matrixcalc)
8256 ("r-rtsne" ,r-rtsne)
8257 ("r-umap" ,r-umap)))
8258 (native-inputs `(("r-knitr" ,r-knitr)))
8259 (home-page "https://bioconductor.org/packages/M3C")
8260 (synopsis "Monte Carlo reference-based consensus clustering")
8261 (description
8262 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8263simulation to eliminate overestimation of @code{K} and can reject the null
8264hypothesis @code{K=1}.")
8265 (license license:agpl3+)))
488001eb
PL
8266
8267(define-public r-icens
8268 (package
8269 (name "r-icens")
8270 (version "1.60.0")
8271 (source
8272 (origin
8273 (method url-fetch)
8274 (uri (bioconductor-uri "Icens" version))
8275 (sha256
8276 (base32
8277 "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))
8278 (properties `((upstream-name . "Icens")))
8279 (build-system r-build-system)
8280 (propagated-inputs
8281 `(("r-survival" ,r-survival)))
8282 (home-page "https://bioconductor.org/packages/Icens")
8283 (synopsis "NPMLE for censored and truncated data")
8284 (description
8285 "This package provides many functions for computing the
8286@dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8287truncated data.")
8288 (license license:artistic2.0)))
655c4bb2
PL
8289
8290;; This is a CRAN package but it depends on r-icens, which is published on
8291;; Bioconductor.
8292(define-public r-interval
8293 (package
8294 (name "r-interval")
65e361f9 8295 (version "1.1-0.7")
655c4bb2
PL
8296 (source
8297 (origin
8298 (method url-fetch)
8299 (uri (cran-uri "interval" version))
8300 (sha256
8301 (base32
65e361f9 8302 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
655c4bb2
PL
8303 (properties `((upstream-name . "interval")))
8304 (build-system r-build-system)
8305 (propagated-inputs
8306 `(("r-icens" ,r-icens)
8307 ("r-mlecens" ,r-mlecens)
8308 ("r-perm" ,r-perm)
8309 ("r-survival" ,r-survival)))
8310 (home-page "https://cran.r-project.org/web/packages/interval/")
8311 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8312 (description
8313 "This package provides functions to fit nonparametric survival curves,
8314plot them, and perform logrank or Wilcoxon type tests.")
8315 (license license:gpl2+)))
7e88ee9f
PL
8316
8317;; This is a CRAN package, but it depends on r-interval, which depends on a
8318;; Bioconductor package.
8319(define-public r-fhtest
8320 (package
8321 (name "r-fhtest")
d7cfdc12 8322 (version "1.5")
7e88ee9f
PL
8323 (source
8324 (origin
8325 (method url-fetch)
8326 (uri (cran-uri "FHtest" version))
8327 (sha256
8328 (base32
d7cfdc12 8329 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
7e88ee9f
PL
8330 (properties `((upstream-name . "FHtest")))
8331 (build-system r-build-system)
8332 (propagated-inputs
8333 `(("r-interval" ,r-interval)
8334 ("r-kmsurv" ,r-kmsurv)
8335 ("r-mass" ,r-mass)
8336 ("r-perm" ,r-perm)
8337 ("r-survival" ,r-survival)))
8338 (home-page "https://cran.r-project.org/web/packages/FHtest/")
8339 (synopsis "Tests for survival data based on the Fleming-Harrington class")
8340 (description
8341 "This package provides functions to compare two or more survival curves
8342with:
8343
8344@itemize
8345@item The Fleming-Harrington test for right-censored data based on
8346 permutations and on counting processes.
8347@item An extension of the Fleming-Harrington test for interval-censored data
8348 based on a permutation distribution and on a score vector distribution.
8349@end itemize
8350")
8351 (license license:gpl2+)))
f4d920b9 8352
8353(define-public r-fourcseq
8354 (package
8355 (name "r-fourcseq")
8356 (version "1.22.1")
8357 (source
8358 (origin
8359 (method url-fetch)
8360 (uri (bioconductor-uri "FourCSeq" version))
8361 (sha256
8362 (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
8363 (properties `((upstream-name . "FourCSeq")))
8364 (build-system r-build-system)
8365 (propagated-inputs
8366 `(("r-biobase" ,r-biobase)
8367 ("r-biostrings" ,r-biostrings)
8368 ("r-deseq2" ,r-deseq2)
8369 ("r-fda" ,r-fda)
8370 ("r-genomicalignments" ,r-genomicalignments)
8371 ("r-genomicranges" ,r-genomicranges)
8372 ("r-ggbio" ,r-ggbio)
8373 ("r-ggplot2" ,r-ggplot2)
8374 ("r-gtools" ,r-gtools)
8375 ("r-lsd" ,r-lsd)
8376 ("r-matrix" ,r-matrix)
8377 ("r-reshape2" ,r-reshape2)
8378 ("r-rsamtools" ,r-rsamtools)
8379 ("r-rtracklayer" ,r-rtracklayer)
8380 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8381 (native-inputs
8382 `(("r-knitr" ,r-knitr)))
8383 (home-page
8384 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
8385 (synopsis "Analysis of multiplexed 4C sequencing data")
8386 (description
8387 "This package is an R package dedicated to the analysis of (multiplexed)
83884C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
8389interactions between DNA elements and identify differential interactions
8390between conditions. The statistical analysis in R starts with individual bam
8391files for each sample as inputs. To obtain these files, the package contains
8392a Python script to demultiplex libraries and trim off primer sequences. With
8393a standard alignment software the required bam files can be then be
8394generated.")
8395 (license license:gpl3+)))
6e0ab26f 8396
8397(define-public r-preprocesscore
8398 (package
8399 (name "r-preprocesscore")
8400 (version "1.50.0")
8401 (source
8402 (origin
8403 (method url-fetch)
8404 (uri (bioconductor-uri "preprocessCore" version))
8405 (sha256
8406 (base32
8407 "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
8408 (properties
8409 `((upstream-name . "preprocessCore")))
8410 (build-system r-build-system)
8411 (home-page "https://github.com/bmbolstad/preprocessCore")
8412 (synopsis "Collection of pre-processing functions")
8413 (description
8414 "This package provides a library of core pre-processing and normalization
8415routines.")
8416 (license license:lgpl2.0+)))
b3a99837 8417
3159fcf1
RW
8418;; This is a CRAN package, but it depends on preprocessorcore, which is a
8419;; Bioconductor package.
8420(define-public r-wgcna
8421 (package
8422 (name "r-wgcna")
8423 (version "1.69")
8424 (source
8425 (origin
8426 (method url-fetch)
8427 (uri (cran-uri "WGCNA" version))
8428 (sha256
8429 (base32
8430 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
8431 (properties `((upstream-name . "WGCNA")))
8432 (build-system r-build-system)
8433 (propagated-inputs
8434 `(("r-annotationdbi" ,r-annotationdbi)
8435 ("r-doparallel" ,r-doparallel)
8436 ("r-dynamictreecut" ,r-dynamictreecut)
8437 ("r-fastcluster" ,r-fastcluster)
8438 ("r-foreach" ,r-foreach)
8439 ("r-go-db" ,r-go-db)
8440 ("r-hmisc" ,r-hmisc)
8441 ("r-impute" ,r-impute)
8442 ("r-rcpp" ,r-rcpp)
8443 ("r-survival" ,r-survival)
8444 ("r-matrixstats" ,r-matrixstats)
8445 ("r-preprocesscore" ,r-preprocesscore)))
8446 (home-page
8447 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8448 (synopsis "Weighted correlation network analysis")
8449 (description
8450 "This package provides functions necessary to perform Weighted
8451Correlation Network Analysis on high-dimensional data. It includes functions
8452for rudimentary data cleaning, construction and summarization of correlation
8453networks, module identification and functions for relating both variables and
8454modules to sample traits. It also includes a number of utility functions for
8455data manipulation and visualization.")
8456 (license license:gpl2+)))
8457
b3a99837 8458(define-public r-rgraphviz
8459 (package
8460 (name "r-rgraphviz")
8461 (version "2.32.0")
8462 (source
8463 (origin
8464 (method url-fetch)
8465 (uri (bioconductor-uri "Rgraphviz" version))
8466 (sha256
8467 (base32
8468 "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
8469 (properties `((upstream-name . "Rgraphviz")))
8470 (build-system r-build-system)
8471 (arguments
8472 `(#:phases
8473 (modify-phases %standard-phases
8474 (add-after 'unpack 'make-reproducible
8475 (lambda _
8476 ;; The replacement value is taken from src/graphviz/builddate.h
8477 (substitute* "src/graphviz/configure"
8478 (("VERSION_DATE=.*")
8479 "VERSION_DATE=20200427.2341\n"))
8480 #t)))))
8481 ;; FIXME: Rgraphviz bundles the sources of an older variant of
8482 ;; graphviz. It does not build with the latest version of graphviz, so
8483 ;; we do not add graphviz to the inputs.
8484 (inputs `(("zlib" ,zlib)))
8485 (propagated-inputs
8486 `(("r-graph" ,r-graph)))
8487 (native-inputs
8488 `(("pkg-config" ,pkg-config)))
8489 (home-page "https://bioconductor.org/packages/Rgraphviz")
8490 (synopsis "Plotting capabilities for R graph objects")
8491 (description
8492 "This package interfaces R with the graphviz library for plotting R graph
8493objects from the @code{graph} package.")
8494 (license license:epl1.0)))
8c7c6db4 8495
3292f6ed 8496(define-public r-fithic
8497 (package
8498 (name "r-fithic")
8499 (version "1.14.0")
8500 (source (origin
8501 (method url-fetch)
8502 (uri (bioconductor-uri "FitHiC" version))
8503 (sha256
8504 (base32
8505 "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
8506 (properties `((upstream-name . "FitHiC")))
8507 (build-system r-build-system)
8508 (propagated-inputs
8509 `(("r-data-table" ,r-data-table)
8510 ("r-fdrtool" ,r-fdrtool)
8511 ("r-rcpp" ,r-rcpp)))
8512 (native-inputs
8513 `(("r-knitr" ,r-knitr)))
8514 (home-page "https://bioconductor.org/packages/FitHiC")
8515 (synopsis "Confidence estimation for intra-chromosomal contact maps")
8516 (description
8517 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
8518intra-chromosomal contact maps produced by genome-wide genome architecture
8519assays such as Hi-C.")
8520 (license license:gpl2+)))
8521
7df42d37 8522(define-public r-hitc
8523 (package
8524 (name "r-hitc")
8525 (version "1.32.0")
8526 (source (origin
8527 (method url-fetch)
8528 (uri (bioconductor-uri "HiTC" version))
8529 (sha256
8530 (base32
8531 "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
8532 (properties `((upstream-name . "HiTC")))
8533 (build-system r-build-system)
8534 (propagated-inputs
8535 `(("r-biostrings" ,r-biostrings)
8536 ("r-genomeinfodb" ,r-genomeinfodb)
8537 ("r-genomicranges" ,r-genomicranges)
8538 ("r-iranges" ,r-iranges)
8539 ("r-matrix" ,r-matrix)
8540 ("r-rcolorbrewer" ,r-rcolorbrewer)
8541 ("r-rtracklayer" ,r-rtracklayer)))
8542 (home-page "https://bioconductor.org/packages/HiTC")
8543 (synopsis "High throughput chromosome conformation capture analysis")
8544 (description
8545 "The HiTC package was developed to explore high-throughput \"C\" data
8546such as 5C or Hi-C. Dedicated R classes as well as standard methods for
8547quality controls, normalization, visualization, and further analysis are also
8548provided.")
8549 (license license:artistic2.0)))
8550
63b75c01 8551(define-public r-hdf5array
8552 (package
8553 (name "r-hdf5array")
8554 (version "1.16.1")
8555 (source
8556 (origin
8557 (method url-fetch)
8558 (uri (bioconductor-uri "HDF5Array" version))
8559 (sha256
8560 (base32
8561 "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
8562 (properties `((upstream-name . "HDF5Array")))
8563 (build-system r-build-system)
8564 (inputs
8565 `(("zlib" ,zlib)))
8566 (propagated-inputs
8567 `(("r-biocgenerics" ,r-biocgenerics)
8568 ("r-delayedarray" ,r-delayedarray)
8569 ("r-iranges" ,r-iranges)
8570 ("r-matrix" ,r-matrix)
8571 ("r-rhdf5" ,r-rhdf5)
8572 ("r-rhdf5lib" ,r-rhdf5lib)
8573 ("r-s4vectors" ,r-s4vectors)))
8574 (home-page "https://bioconductor.org/packages/HDF5Array")
8575 (synopsis "HDF5 back end for DelayedArray objects")
8576 (description "This package provides an array-like container for convenient
8577access and manipulation of HDF5 datasets. It supports delayed operations and
8578block processing.")
8579 (license license:artistic2.0)))
8580
c61268c1 8581(define-public r-rhdf5lib
8582 (package
8583 (name "r-rhdf5lib")
8584 (version "1.10.1")
8585 (source
8586 (origin
8587 (method url-fetch)
8588 (uri (bioconductor-uri "Rhdf5lib" version))
8589 (sha256
8590 (base32
8591 "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
8592 (modules '((guix build utils)))
8593 (snippet
8594 '(begin
8595 ;; Delete bundled binaries
8596 (delete-file-recursively "src/wininclude/")
8597 (delete-file-recursively "src/winlib-4.9.3/")
8598 (delete-file-recursively "src/winlib-8.3.0/")
8599 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
8600 #t))))
8601 (properties `((upstream-name . "Rhdf5lib")))
8602 (build-system r-build-system)
8603 (arguments
8604 `(#:phases
8605 (modify-phases %standard-phases
8606 (add-after 'unpack 'do-not-use-bundled-hdf5
8607 (lambda* (#:key inputs #:allow-other-keys)
8608 (for-each delete-file '("configure" "configure.ac"))
8609 ;; Do not make other packages link with the proprietary libsz.
8610 (substitute* "R/zzz.R"
8611 ((" \"%s/libsz.a\"") ""))
8612 (with-directory-excursion "src"
8613 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
8614 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
8615 "hdf5")
8616 ;; Remove timestamp and host system information to make
8617 ;; the build reproducible.
8618 (substitute* "hdf5/src/libhdf5.settings.in"
8619 (("Configured on: @CONFIG_DATE@")
8620 "Configured on: Guix")
8621 (("Uname information:.*")
8622 "Uname information: Linux\n")
8623 ;; Remove unnecessary store reference.
8624 (("C Compiler:.*")
8625 "C Compiler: GCC\n"))
8626 (rename-file "Makevars.in" "Makevars")
8627 (substitute* "Makevars"
8628 (("@ZLIB_LIB@") "-lz")
8629 (("@ZLIB_INCLUDE@") "")
8630 (("HDF5_CXX_LIB=.*")
8631 (string-append "HDF5_CXX_LIB="
8632 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
8633 (("HDF5_LIB=.*")
8634 (string-append "HDF5_LIB="
8635 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
8636 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
8637 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
8638 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
8639 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
8640 (("HDF5_HL_LIB=.*")
8641 (string-append "HDF5_HL_LIB="
8642 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
8643 (("HDF5_HL_CXX_LIB=.*")
8644 (string-append "HDF5_HL_CXX_LIB="
8645 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
8646 ;; szip is non-free software
8647 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
8648 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
8649 #t)))))
8650 (inputs
8651 `(("zlib" ,zlib)))
8652 (propagated-inputs
8653 `(("hdf5" ,hdf5-1.10)))
8654 (native-inputs
8655 `(("hdf5-source" ,(package-source hdf5-1.10))
8656 ("r-knitr" ,r-knitr)))
8657 (home-page "https://bioconductor.org/packages/Rhdf5lib")
8658 (synopsis "HDF5 library as an R package")
8659 (description "This package provides C and C++ HDF5 libraries for use in R
8660packages.")
8661 (license license:artistic2.0)))
8662
8863c14c 8663(define-public r-beachmat
8664 (package
8665 (name "r-beachmat")
8666 (version "2.4.0")
8667 (source
8668 (origin
8669 (method url-fetch)
8670 (uri (bioconductor-uri "beachmat" version))
8671 (sha256
8672 (base32
8673 "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
8674 (build-system r-build-system)
8675 (propagated-inputs
8676 `(("r-biocgenerics" ,r-biocgenerics)
8677 ("r-delayedarray" ,r-delayedarray)
8678 ("r-matrix" ,r-matrix)))
8679 (native-inputs
8680 `(("r-knitr" ,r-knitr)))
8681 (home-page "https://bioconductor.org/packages/beachmat")
8682 (synopsis "Compiling Bioconductor to handle each matrix type")
8683 (description "This package provides a consistent C++ class interface for a
8684variety of commonly used matrix types, including sparse and HDF5-backed
8685matrices.")
8686 (license license:gpl3)))
8687
916a3e59 8688(define-public r-singlecellexperiment
8689 (package
8690 (name "r-singlecellexperiment")
8691 (version "1.10.1")
8692 (source
8693 (origin
8694 (method url-fetch)
8695 (uri (bioconductor-uri "SingleCellExperiment" version))
8696 (sha256
8697 (base32
8698 "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
8699 (properties
8700 `((upstream-name . "SingleCellExperiment")))
8701 (build-system r-build-system)
8702 (propagated-inputs
8703 `(("r-biocgenerics" ,r-biocgenerics)
8704 ("r-s4vectors" ,r-s4vectors)
8705 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8706 (native-inputs
8707 `(("r-knitr" ,r-knitr)))
8708 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
8709 (synopsis "S4 classes for single cell data")
8710 (description "This package defines an S4 class for storing data from
8711single-cell experiments. This includes specialized methods to store and
8712retrieve spike-in information, dimensionality reduction coordinates and size
8713factors for each cell, along with the usual metadata for genes and
8714libraries.")
8715 (license license:gpl3)))
8716
6b1946b3 8717(define-public r-scater
8718 (package
8719 (name "r-scater")
8720 (version "1.16.2")
8721 (source (origin
8722 (method url-fetch)
8723 (uri (bioconductor-uri "scater" version))
8724 (sha256
8725 (base32
8726 "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
8727 (build-system r-build-system)
8728 (propagated-inputs
8729 `(("r-beachmat" ,r-beachmat)
8730 ("r-biocgenerics" ,r-biocgenerics)
8731 ("r-biocneighbors" ,r-biocneighbors)
8732 ("r-biocparallel" ,r-biocparallel)
8733 ("r-biocsingular" ,r-biocsingular)
8734 ("r-delayedarray" ,r-delayedarray)
8735 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8736 ("r-ggbeeswarm" ,r-ggbeeswarm)
8737 ("r-ggplot2" ,r-ggplot2)
8738 ("r-matrix" ,r-matrix)
8739 ("r-rcpp" ,r-rcpp)
8740 ("r-rlang" ,r-rlang)
8741 ("r-s4vectors" ,r-s4vectors)
8742 ("r-singlecellexperiment" ,r-singlecellexperiment)
8743 ("r-summarizedexperiment" ,r-summarizedexperiment)
8744 ("r-viridis" ,r-viridis)))
8745 (native-inputs
8746 `(("r-knitr" ,r-knitr)))
8747 (home-page "https://github.com/davismcc/scater")
8748 (synopsis "Single-cell analysis toolkit for gene expression data in R")
8749 (description "This package provides a collection of tools for doing
8750various analyses of single-cell RNA-seq gene expression data, with a focus on
8751quality control.")
8752 (license license:gpl2+)))
8753
1193b77e 8754(define-public r-scran
8755 (package
8756 (name "r-scran")
8757 (version "1.16.0")
8758 (source
8759 (origin
8760 (method url-fetch)
8761 (uri (bioconductor-uri "scran" version))
8762 (sha256
8763 (base32
8764 "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
8765 (build-system r-build-system)
8766 (propagated-inputs
8767 `(("r-beachmat" ,r-beachmat)
8768 ("r-bh" ,r-bh)
8769 ("r-biocgenerics" ,r-biocgenerics)
8770 ("r-biocneighbors" ,r-biocneighbors)
8771 ("r-biocparallel" ,r-biocparallel)
8772 ("r-biocsingular" ,r-biocsingular)
8773 ("r-delayedarray" ,r-delayedarray)
8774 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8775 ("r-dqrng" ,r-dqrng)
8776 ("r-edger" ,r-edger)
8777 ("r-igraph" ,r-igraph)
8778 ("r-iranges" ,r-iranges)
8779 ("r-limma" ,r-limma)
8780 ("r-matrix" ,r-matrix)
8781 ("r-rcpp" ,r-rcpp)
8782 ("r-s4vectors" ,r-s4vectors)
8783 ("r-scater" ,r-scater)
8784 ("r-singlecellexperiment" ,r-singlecellexperiment)
8785 ("r-statmod" ,r-statmod)
8786 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8787 (native-inputs
8788 `(("r-knitr" ,r-knitr)))
8789 (home-page "https://bioconductor.org/packages/scran")
8790 (synopsis "Methods for single-cell RNA-Seq data analysis")
8791 (description "This package implements a variety of low-level analyses of
8792single-cell RNA-seq data. Methods are provided for normalization of
8793cell-specific biases, assignment of cell cycle phase, and detection of highly
8794variable and significantly correlated genes.")
8795 (license license:gpl3)))
8796
8c7c6db4 8797(define-public r-delayedmatrixstats
8798 (package
8799 (name "r-delayedmatrixstats")
8800 (version "1.10.1")
8801 (source
8802 (origin
8803 (method url-fetch)
8804 (uri (bioconductor-uri "DelayedMatrixStats" version))
8805 (sha256
8806 (base32
8807 "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
8808 (properties
8809 `((upstream-name . "DelayedMatrixStats")))
8810 (build-system r-build-system)
8811 (propagated-inputs
8812 `(("r-biocparallel" ,r-biocparallel)
8813 ("r-delayedarray" ,r-delayedarray)
8814 ("r-hdf5array" ,r-hdf5array)
8815 ("r-iranges" ,r-iranges)
8816 ("r-matrix" ,r-matrix)
8817 ("r-matrixstats" ,r-matrixstats)
8818 ("r-s4vectors" ,r-s4vectors)))
8819 (native-inputs
8820 `(("r-knitr" ,r-knitr)))
8821 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
8822 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
8823 (description
8824 "This package provides a port of the @code{matrixStats} API for use with
8825@code{DelayedMatrix} objects from the @code{DelayedArray} package. It
8826contains high-performing functions operating on rows and columns of
8827@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
8828@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
8829are optimized per data type and for subsetted calculations such that both
8830memory usage and processing time is minimized.")
8831 (license license:expat)))