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fa596599 1;;; GNU Guix --- Functional package management for GNU
6aa896d8
RW		 2;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
bfb93b48 4;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
fa596599
RW		 5;;;
6;;; This file is part of GNU Guix.
7;;;
8;;; GNU Guix is free software; you can redistribute it and/or modify it
9;;; under the terms of the GNU General Public License as published by
10;;; the Free Software Foundation; either version 3 of the License, or (at
11;;; your option) any later version.
12;;;
13;;; GNU Guix is distributed in the hope that it will be useful, but
14;;; WITHOUT ANY WARRANTY; without even the implied warranty of
15;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16;;; GNU General Public License for more details.
17;;;
18;;; You should have received a copy of the GNU General Public License
19;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
20
21(define-module (gnu packages bioconductor)
22 #:use-module ((guix licenses) #:prefix license:)
23 #:use-module (guix packages)
24 #:use-module (guix download)
25 #:use-module (guix build-system r)
183ce988 26 #:use-module (gnu packages)
cf9a29b2 27 #:use-module (gnu packages bioinformatics)
a5b56a53
RJ		 28 #:use-module (gnu packages cran)
29 #:use-module (gnu packages compression)
c18dccff 30 #:use-module (gnu packages gcc)
cf9a29b2 31 #:use-module (gnu packages graph)
59d331f1 32 #:use-module (gnu packages haskell)
b64ce4b7 33 #:use-module (gnu packages maths)
2cb71d81 34 #:use-module (gnu packages pkg-config)
f4235c0e
RW		 35 #:use-module (gnu packages statistics)
36 #:use-module (gnu packages web))
fa596599 37
557a1089
RW		 38\f
39;;; Annotations
40
b7d93cf5
RW		 41(define-public r-bsgenome-celegans-ucsc-ce6
42 (package
43 (name "r-bsgenome-celegans-ucsc-ce6")
44 (version "1.4.0")
45 (source (origin
46 (method url-fetch)
47 ;; We cannot use bioconductor-uri here because this tarball is
48 ;; located under "data/annotation/" instead of "bioc/".
49 (uri (string-append "https://www.bioconductor.org/packages/"
50 "release/data/annotation/src/contrib/"
51 "BSgenome.Celegans.UCSC.ce6_"
52 version ".tar.gz"))
53 (sha256
54 (base32
55 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
56 (properties
57 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
58 (build-system r-build-system)
59 ;; As this package provides little more than a very large data file it
60 ;; doesn't make sense to build substitutes.
61 (arguments `(#:substitutable? #f))
62 (propagated-inputs
63 `(("r-bsgenome" ,r-bsgenome)))
64 (home-page
65 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
66 (synopsis "Full genome sequences for Worm")
67 (description
68 "This package provides full genome sequences for Caenorhabditis
69elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
0c792ffb
RW		 70objects.")
71 (license license:artistic2.0)))
72
73(define-public r-bsgenome-celegans-ucsc-ce10
74 (package
75 (name "r-bsgenome-celegans-ucsc-ce10")
76 (version "1.4.0")
77 (source (origin
78 (method url-fetch)
79 ;; We cannot use bioconductor-uri here because this tarball is
80 ;; located under "data/annotation/" instead of "bioc/".
81 (uri (string-append "https://www.bioconductor.org/packages/"
82 "release/data/annotation/src/contrib/"
83 "BSgenome.Celegans.UCSC.ce10_"
84 version ".tar.gz"))
85 (sha256
86 (base32
87 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
88 (properties
89 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
90 (build-system r-build-system)
91 ;; As this package provides little more than a very large data file it
92 ;; doesn't make sense to build substitutes.
93 (arguments `(#:substitutable? #f))
94 (propagated-inputs
95 `(("r-bsgenome" ,r-bsgenome)))
96 (home-page
97 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
98 (synopsis "Full genome sequences for Worm")
99 (description
100 "This package provides full genome sequences for Caenorhabditis
101elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
b7d93cf5
RW		 102objects.")
103 (license license:artistic2.0)))
104
183db725
RW		 105(define-public r-bsgenome-dmelanogaster-ucsc-dm6
106 (package
107 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
108 (version "1.4.1")
109 (source (origin
110 (method url-fetch)
111 ;; We cannot use bioconductor-uri here because this tarball is
112 ;; located under "data/annotation/" instead of "bioc/".
113 (uri (string-append "https://www.bioconductor.org/packages/"
114 "release/data/annotation/src/contrib/"
115 "BSgenome.Dmelanogaster.UCSC.dm6_"
116 version ".tar.gz"))
117 (sha256
118 (base32
119 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
120 (properties
121 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
122 (build-system r-build-system)
123 ;; As this package provides little more than a very large data file it
124 ;; doesn't make sense to build substitutes.
125 (arguments `(#:substitutable? #f))
126 (propagated-inputs
127 `(("r-bsgenome" ,r-bsgenome)))
128 (home-page
129 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
130 (synopsis "Full genome sequences for Fly")
131 (description
132 "This package provides full genome sequences for Drosophila
133melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
134objects.")
135 (license license:artistic2.0)))
136
13dabd69
RW		 137(define-public r-bsgenome-dmelanogaster-ucsc-dm3
138 (package
139 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
140 (version "1.4.0")
141 (source (origin
142 (method url-fetch)
143 ;; We cannot use bioconductor-uri here because this tarball is
144 ;; located under "data/annotation/" instead of "bioc/".
145 (uri (string-append "https://www.bioconductor.org/packages/"
146 "release/data/annotation/src/contrib/"
147 "BSgenome.Dmelanogaster.UCSC.dm3_"
148 version ".tar.gz"))
149 (sha256
150 (base32
151 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
152 (properties
153 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
154 (build-system r-build-system)
155 ;; As this package provides little more than a very large data file it
156 ;; doesn't make sense to build substitutes.
157 (arguments `(#:substitutable? #f))
158 (propagated-inputs
159 `(("r-bsgenome" ,r-bsgenome)))
160 (home-page
161 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
162 (synopsis "Full genome sequences for Fly")
163 (description
164 "This package provides full genome sequences for Drosophila
165melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
166Biostrings objects.")
167 (license license:artistic2.0)))
168
dfac7eb9
RW		 169(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
170 (package
171 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
172 (version "1.3.99")
173 (source (origin
174 (method url-fetch)
175 ;; We cannot use bioconductor-uri here because this tarball is
176 ;; located under "data/annotation/" instead of "bioc/".
177 (uri (string-append "http://www.bioconductor.org/packages/"
178 "release/data/annotation/src/contrib/"
179 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
180 version ".tar.gz"))
181 (sha256
182 (base32
183 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
184 (properties
185 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
186 (build-system r-build-system)
187 (propagated-inputs
188 `(("r-bsgenome" ,r-bsgenome)
189 ("r-bsgenome-dmelanogaster-ucsc-dm3"
190 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
191 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
192 (synopsis "Full masked genome sequences for Fly")
193 (description
194 "This package provides full masked genome sequences for Drosophila
195melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
196Biostrings objects. The sequences are the same as in
197BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
198masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
199intra-contig ambiguities (AMB mask), (3) the mask of repeats from
200RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
201Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
202 (license license:artistic2.0)))
203
40a65057
RW		 204(define-public r-bsgenome-hsapiens-1000genomes-hs37d5
205 (package
206 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
207 (version "0.99.1")
208 (source (origin
209 (method url-fetch)
210 ;; We cannot use bioconductor-uri here because this tarball is
211 ;; located under "data/annotation/" instead of "bioc/".
212 (uri (string-append "https://www.bioconductor.org/packages/"
213 "release/data/annotation/src/contrib/"
214 "BSgenome.Hsapiens.1000genomes.hs37d5_"
215 version ".tar.gz"))
216 (sha256
217 (base32
218 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
219 (properties
220 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
221 (build-system r-build-system)
222 ;; As this package provides little more than a very large data file it
223 ;; doesn't make sense to build substitutes.
224 (arguments `(#:substitutable? #f))
225 (propagated-inputs
226 `(("r-bsgenome" ,r-bsgenome)))
227 (home-page
228 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
229 (synopsis "Full genome sequences for Homo sapiens")
230 (description
231 "This package provides full genome sequences for Homo sapiens from
2321000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
233 (license license:artistic2.0)))
234
6fbd759b
RW		 235(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
236 (package
237 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
238 (version "1.3.99")
239 (source (origin
240 (method url-fetch)
241 ;; We cannot use bioconductor-uri here because this tarball is
242 ;; located under "data/annotation/" instead of "bioc/".
243 (uri (string-append "http://www.bioconductor.org/packages/"
244 "release/data/annotation/src/contrib/"
245 "BSgenome.Hsapiens.UCSC.hg19.masked_"
246 version ".tar.gz"))
247 (sha256
248 (base32
249 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
250 (properties
251 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
252 (build-system r-build-system)
253 (propagated-inputs
254 `(("r-bsgenome" ,r-bsgenome)
255 ("r-bsgenome-hsapiens-ucsc-hg19"
256 ,r-bsgenome-hsapiens-ucsc-hg19)))
257 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
258 (synopsis "Full masked genome sequences for Homo sapiens")
259 (description
260 "This package provides full genome sequences for Homo sapiens (Human) as
261provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
262sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
263them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
264mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
265repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
266Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
267default.")
268 (license license:artistic2.0)))
269
5acb9052
RW		 270(define-public r-bsgenome-mmusculus-ucsc-mm9
271 (package
272 (name "r-bsgenome-mmusculus-ucsc-mm9")
273 (version "1.4.0")
274 (source (origin
275 (method url-fetch)
276 ;; We cannot use bioconductor-uri here because this tarball is
277 ;; located under "data/annotation/" instead of "bioc/".
278 (uri (string-append "https://www.bioconductor.org/packages/"
279 "release/data/annotation/src/contrib/"
280 "BSgenome.Mmusculus.UCSC.mm9_"
281 version ".tar.gz"))
282 (sha256
283 (base32
284 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
285 (properties
286 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
287 (build-system r-build-system)
288 ;; As this package provides little more than a very large data file it
289 ;; doesn't make sense to build substitutes.
290 (arguments `(#:substitutable? #f))
291 (propagated-inputs
292 `(("r-bsgenome" ,r-bsgenome)))
293 (home-page
294 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
295 (synopsis "Full genome sequences for Mouse")
296 (description
297 "This package provides full genome sequences for Mus musculus (Mouse) as
298provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
299 (license license:artistic2.0)))
300
2bece692
RW		 301(define-public r-bsgenome-mmusculus-ucsc-mm9-masked
302 (package
303 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
304 (version "1.3.99")
305 (source (origin
306 (method url-fetch)
307 ;; We cannot use bioconductor-uri here because this tarball is
308 ;; located under "data/annotation/" instead of "bioc/".
309 (uri (string-append "http://www.bioconductor.org/packages/"
310 "release/data/annotation/src/contrib/"
311 "BSgenome.Mmusculus.UCSC.mm9.masked_"
312 version ".tar.gz"))
313 (sha256
314 (base32
315 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
316 (properties
317 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
318 (build-system r-build-system)
319 (propagated-inputs
320 `(("r-bsgenome" ,r-bsgenome)
321 ("r-bsgenome-mmusculus-ucsc-mm9"
322 ,r-bsgenome-mmusculus-ucsc-mm9)))
323 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
324 (synopsis "Full masked genome sequences for Mouse")
325 (description
326 "This package provides full genome sequences for Mus musculus (Mouse) as
327provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
328sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
329them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
330mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
331repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
332Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
333default." )
334 (license license:artistic2.0)))
335
c3adc830
RW		 336(define-public r-bsgenome-mmusculus-ucsc-mm10
337 (package
338 (name "r-bsgenome-mmusculus-ucsc-mm10")
339 (version "1.4.0")
340 (source (origin
341 (method url-fetch)
342 ;; We cannot use bioconductor-uri here because this tarball is
343 ;; located under "data/annotation/" instead of "bioc/".
344 (uri (string-append "https://www.bioconductor.org/packages/"
345 "release/data/annotation/src/contrib/"
346 "BSgenome.Mmusculus.UCSC.mm10_"
347 version ".tar.gz"))
348 (sha256
349 (base32
350 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
351 (properties
352 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
353 (build-system r-build-system)
354 ;; As this package provides little more than a very large data file it
355 ;; doesn't make sense to build substitutes.
356 (arguments `(#:substitutable? #f))
357 (propagated-inputs
358 `(("r-bsgenome" ,r-bsgenome)))
359 (home-page
360 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
361 (synopsis "Full genome sequences for Mouse")
362 (description
363 "This package provides full genome sequences for Mus
364musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
365in Biostrings objects.")
366 (license license:artistic2.0)))
367
3a08940e
RW		 368(define-public r-org-ce-eg-db
369 (package
370 (name "r-org-ce-eg-db")
371 (version "3.7.0")
372 (source (origin
373 (method url-fetch)
374 ;; We cannot use bioconductor-uri here because this tarball is
375 ;; located under "data/annotation/" instead of "bioc/".
376 (uri (string-append "https://www.bioconductor.org/packages/"
377 "release/data/annotation/src/contrib/"
378 "org.Ce.eg.db_" version ".tar.gz"))
379 (sha256
380 (base32
381 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
382 (properties
383 `((upstream-name . "org.Ce.eg.db")))
384 (build-system r-build-system)
385 (propagated-inputs
386 `(("r-annotationdbi" ,r-annotationdbi)))
387 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
388 (synopsis "Genome wide annotation for Worm")
389 (description
390 "This package provides mappings from Entrez gene identifiers to various
391annotations for the genome of the model worm Caenorhabditis elegans.")
392 (license license:artistic2.0)))
393
f8780e96
RW		 394(define-public r-org-dm-eg-db
395 (package
396 (name "r-org-dm-eg-db")
397 (version "3.7.0")
398 (source (origin
399 (method url-fetch)
400 ;; We cannot use bioconductor-uri here because this tarball is
401 ;; located under "data/annotation/" instead of "bioc/".
402 (uri (string-append "https://www.bioconductor.org/packages/"
403 "release/data/annotation/src/contrib/"
404 "org.Dm.eg.db_" version ".tar.gz"))
405 (sha256
406 (base32
407 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
408 (properties
409 `((upstream-name . "org.Dm.eg.db")))
410 (build-system r-build-system)
411 (propagated-inputs
412 `(("r-annotationdbi" ,r-annotationdbi)))
413 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
414 (synopsis "Genome wide annotation for Fly")
415 (description
416 "This package provides mappings from Entrez gene identifiers to various
417annotations for the genome of the model fruit fly Drosophila melanogaster.")
418 (license license:artistic2.0)))
419
3dad6087
RW		 420(define-public r-org-dr-eg-db
421 (package
422 (name "r-org-dr-eg-db")
423 (version "3.7.0")
424 (source (origin
425 (method url-fetch)
426 ;; We cannot use bioconductor-uri here because this tarball is
427 ;; located under "data/annotation/" instead of "bioc/".
428 (uri (string-append "https://www.bioconductor.org/packages/"
429 "release/data/annotation/src/contrib/"
430 "org.Dr.eg.db_" version ".tar.gz"))
431 (sha256
432 (base32
433 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
434 (properties
435 `((upstream-name . "org.Dr.eg.db")))
436 (build-system r-build-system)
437 (propagated-inputs
438 `(("r-annotationdbi" ,r-annotationdbi)))
439 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
440 (synopsis "Annotation for Zebrafish")
441 (description
442 "This package provides genome wide annotations for Zebrafish, primarily
443based on mapping using Entrez Gene identifiers.")
444 (license license:artistic2.0)))
445
d56df35a
RW		 446(define-public r-org-hs-eg-db
447 (package
448 (name "r-org-hs-eg-db")
449 (version "3.7.0")
450 (source (origin
451 (method url-fetch)
452 ;; We cannot use bioconductor-uri here because this tarball is
453 ;; located under "data/annotation/" instead of "bioc/".
454 (uri (string-append "https://www.bioconductor.org/packages/"
455 "release/data/annotation/src/contrib/"
456 "org.Hs.eg.db_" version ".tar.gz"))
457 (sha256
458 (base32
459 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
460 (properties
461 `((upstream-name . "org.Hs.eg.db")))
462 (build-system r-build-system)
463 (propagated-inputs
464 `(("r-annotationdbi" ,r-annotationdbi)))
465 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
466 (synopsis "Genome wide annotation for Human")
467 (description
468 "This package contains genome-wide annotations for Human, primarily based
469on mapping using Entrez Gene identifiers.")
470 (license license:artistic2.0)))
471
8035819f
RW		 472(define-public r-org-mm-eg-db
473 (package
474 (name "r-org-mm-eg-db")
475 (version "3.7.0")
476 (source (origin
477 (method url-fetch)
478 ;; We cannot use bioconductor-uri here because this tarball is
479 ;; located under "data/annotation/" instead of "bioc/".
480 (uri (string-append "https://www.bioconductor.org/packages/"
481 "release/data/annotation/src/contrib/"
482 "org.Mm.eg.db_" version ".tar.gz"))
483 (sha256
484 (base32
485 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
486 (properties
487 `((upstream-name . "org.Mm.eg.db")))
488 (build-system r-build-system)
489 (propagated-inputs
490 `(("r-annotationdbi" ,r-annotationdbi)))
491 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
492 (synopsis "Genome wide annotation for Mouse")
493 (description
494 "This package provides mappings from Entrez gene identifiers to various
495annotations for the genome of the model mouse Mus musculus.")
496 (license license:artistic2.0)))
497
fe0b76e2
RW		 498(define-public r-bsgenome-hsapiens-ucsc-hg19
499 (package
500 (name "r-bsgenome-hsapiens-ucsc-hg19")
501 (version "1.4.0")
502 (source (origin
503 (method url-fetch)
504 ;; We cannot use bioconductor-uri here because this tarball is
505 ;; located under "data/annotation/" instead of "bioc/".
506 (uri (string-append "https://www.bioconductor.org/packages/"
507 "release/data/annotation/src/contrib/"
508 "BSgenome.Hsapiens.UCSC.hg19_"
509 version ".tar.gz"))
510 (sha256
511 (base32
512 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
513 (properties
514 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
515 (build-system r-build-system)
516 ;; As this package provides little more than a very large data file it
517 ;; doesn't make sense to build substitutes.
518 (arguments `(#:substitutable? #f))
519 (propagated-inputs
520 `(("r-bsgenome" ,r-bsgenome)))
521 (home-page
522 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
523 (synopsis "Full genome sequences for Homo sapiens")
524 (description
525 "This package provides full genome sequences for Homo sapiens as provided
526by UCSC (hg19, February 2009) and stored in Biostrings objects.")
527 (license license:artistic2.0)))
528
2cc51108
RW		 529(define-public r-genelendatabase
530 (package
531 (name "r-genelendatabase")
daeb3cd9 532 (version "1.18.0")
2cc51108
RW		 533 (source
534 (origin
535 (method url-fetch)
536 ;; We cannot use bioconductor-uri here because this tarball is
537 ;; located under "data/experiment/" instead of "bioc/".
538 (uri (string-append "https://bioconductor.org/packages/"
539 "release/data/experiment/src/contrib"
540 "/geneLenDataBase_" version ".tar.gz"))
541 (sha256
542 (base32
daeb3cd9 543 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
2cc51108
RW		 544 (properties
545 `((upstream-name . "geneLenDataBase")))
546 (build-system r-build-system)
547 (propagated-inputs
548 `(("r-rtracklayer" ,r-rtracklayer)
549 ("r-genomicfeatures" ,r-genomicfeatures)))
550 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
551 (synopsis "Lengths of mRNA transcripts for a number of genomes")
552 (description
553 "This package provides the lengths of mRNA transcripts for a number of
554genomes and gene ID formats, largely based on the UCSC table browser.")
555 (license license:lgpl2.0+)))
556
66e35ce6
RW		 557(define-public r-txdb-hsapiens-ucsc-hg19-knowngene
558 (package
559 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
560 (version "3.2.2")
561 (source (origin
562 (method url-fetch)
563 ;; We cannot use bioconductor-uri here because this tarball is
564 ;; located under "data/annotation/" instead of "bioc/".
565 (uri (string-append "https://bioconductor.org/packages/"
566 "release/data/annotation/src/contrib"
567 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
568 version ".tar.gz"))
569 (sha256
570 (base32
571 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
572 (properties
573 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
574 (build-system r-build-system)
575 ;; As this package provides little more than a very large data file it
576 ;; doesn't make sense to build substitutes.
577 (arguments `(#:substitutable? #f))
578 (propagated-inputs
579 `(("r-genomicfeatures" ,r-genomicfeatures)))
580 (home-page
581 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
582 (synopsis "Annotation package for human genome in TxDb format")
583 (description
584 "This package provides an annotation database of Homo sapiens genome
585data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
586track. The database is exposed as a @code{TxDb} object.")
587 (license license:artistic2.0)))
588
d220babf
RW		 589(define-public r-txdb-mmusculus-ucsc-mm9-knowngene
590 (package
591 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
592 (version "3.2.2")
593 (source (origin
594 (method url-fetch)
595 ;; We cannot use bioconductor-uri here because this tarball is
596 ;; located under "data/annotation/" instead of "bioc/".
597 (uri (string-append "https://bioconductor.org/packages/"
598 "release/data/annotation/src/contrib"
599 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
600 version ".tar.gz"))
601 (sha256
602 (base32
603 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
604 (properties
605 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
606 (build-system r-build-system)
607 (propagated-inputs
608 `(("r-genomicfeatures" ,r-genomicfeatures)
609 ("r-annotationdbi" ,r-annotationdbi)))
610 (home-page
611 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
612 (synopsis "Annotation package for mouse genome in TxDb format")
613 (description
614 "This package provides an annotation database of Mouse genome data. It
615is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
616database is exposed as a @code{TxDb} object.")
617 (license license:artistic2.0)))
618
7bc5d1b0
RW		 619(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
620 (package
621 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
622 (version "3.4.4")
623 (source (origin
624 (method url-fetch)
625 ;; We cannot use bioconductor-uri here because this tarball is
626 ;; located under "data/annotation/" instead of "bioc/".
627 (uri (string-append "https://www.bioconductor.org/packages/"
628 "release/data/annotation/src/contrib/"
629 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
630 version ".tar.gz"))
631 (sha256
632 (base32
633 "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
634 (properties
635 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
636 (build-system r-build-system)
637 ;; As this package provides little more than a very large data file it
638 ;; doesn't make sense to build substitutes.
639 (arguments `(#:substitutable? #f))
640 (propagated-inputs
641 `(("r-bsgenome" ,r-bsgenome)
642 ("r-genomicfeatures" ,r-genomicfeatures)
643 ("r-annotationdbi" ,r-annotationdbi)))
644 (home-page
645 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
646 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
647 (description
648 "This package loads a TxDb object, which is an R interface to
649prefabricated databases contained in this package. This package provides
650the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
651based on the knownGene track.")
652 (license license:artistic2.0)))
653
0f5c9cec
RW		 654(define-public r-fdb-infiniummethylation-hg19
655 (package
656 (name "r-fdb-infiniummethylation-hg19")
657 (version "2.2.0")
658 (source (origin
659 (method url-fetch)
660 ;; We cannot use bioconductor-uri here because this tarball is
661 ;; located under "data/annotation/" instead of "bioc/".
662 (uri (string-append "https://www.bioconductor.org/packages/"
663 "release/data/annotation/src/contrib/"
664 "FDb.InfiniumMethylation.hg19_"
665 version ".tar.gz"))
666 (sha256
667 (base32
668 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
669 (properties
670 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
671 (build-system r-build-system)
672 (propagated-inputs
673 `(("r-biostrings" ,r-biostrings)
674 ("r-genomicfeatures" ,r-genomicfeatures)
675 ("r-annotationdbi" ,r-annotationdbi)
676 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
677 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
678 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
679 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
680 (description
681 "This is an annotation package for Illumina Infinium DNA methylation
682probes. It contains the compiled HumanMethylation27 and HumanMethylation450
683annotations.")
684 (license license:artistic2.0)))
685
9475a248
RW		 686(define-public r-illuminahumanmethylationepicmanifest
687 (package
688 (name "r-illuminahumanmethylationepicmanifest")
689 (version "0.3.0")
690 (source (origin
691 (method url-fetch)
692 ;; We cannot use bioconductor-uri here because this tarball is
693 ;; located under "data/annotation/" instead of "bioc/".
694 (uri (string-append "https://www.bioconductor.org/packages/"
695 "release/data/annotation/src/contrib/"
696 "IlluminaHumanMethylationEPICmanifest_"
697 version ".tar.gz"))
698 (sha256
699 (base32
700 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
701 (properties
702 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
703 (build-system r-build-system)
704 (propagated-inputs
705 `(("r-minfi" ,r-minfi)))
706 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
707 (synopsis "Manifest for Illumina's EPIC methylation arrays")
708 (description
709 "This is a manifest package for Illumina's EPIC methylation arrays.")
710 (license license:artistic2.0)))
711
f8a5af46
RW		 712(define-public r-do-db
713 (package
714 (name "r-do-db")
715 (version "2.9")
716 (source (origin
717 (method url-fetch)
718 ;; We cannot use bioconductor-uri here because this tarball is
719 ;; located under "data/annotation/" instead of "bioc/".
720 (uri (string-append "https://www.bioconductor.org/packages/"
721 "release/data/annotation/src/contrib/"
722 "DO.db_" version ".tar.gz"))
723 (sha256
724 (base32
725 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
726 (properties
727 `((upstream-name . "DO.db")))
728 (build-system r-build-system)
729 (propagated-inputs
730 `(("r-annotationdbi" ,r-annotationdbi)))
731 (home-page "https://www.bioconductor.org/packages/DO.db/")
732 (synopsis "Annotation maps describing the entire Disease Ontology")
733 (description
734 "This package provides a set of annotation maps describing the entire
735Disease Ontology.")
736 (license license:artistic2.0)))
737
2cc51108 738\f
557a1089
RW		 739;;; Experiment data
740
692bce15
RW		 741(define-public r-abadata
742 (package
743 (name "r-abadata")
744 (version "1.12.0")
745 (source (origin
746 (method url-fetch)
747 ;; We cannot use bioconductor-uri here because this tarball is
748 ;; located under "data/experiment/" instead of "bioc/".
749 (uri (string-append "https://www.bioconductor.org/packages/"
750 "release/data/experiment/src/contrib/"
751 "ABAData_" version ".tar.gz"))
752 (sha256
753 (base32
754 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
755 (properties
756 `((upstream-name . "ABAData")))
757 (build-system r-build-system)
758 (propagated-inputs
759 `(("r-annotationdbi" ,r-annotationdbi)))
760 (home-page "https://www.bioconductor.org/packages/ABAData/")
761 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
762 (description
763 "This package provides the data for the gene expression enrichment
764analysis conducted in the package ABAEnrichment. The package includes three
765datasets which are derived from the Allen Brain Atlas:
766
767@enumerate
768@item Gene expression data from Human Brain (adults) averaged across donors,
769@item Gene expression data from the Developing Human Brain pooled into five
770 age categories and averaged across donors, and
771@item a developmental effect score based on the Developing Human Brain
772 expression data.
773@end enumerate
774
775All datasets are restricted to protein coding genes.")
776 (license license:gpl2+)))
777
557a1089
RW		 778(define-public r-hsmmsinglecell
779 (package
780 (name "r-hsmmsinglecell")
781 (version "1.2.0")
782 (source (origin
783 (method url-fetch)
784 ;; We cannot use bioconductor-uri here because this tarball is
785 ;; located under "data/experiment/" instead of "bioc/".
786 (uri (string-append "https://www.bioconductor.org/packages/"
787 "release/data/experiment/src/contrib/"
788 "HSMMSingleCell_" version ".tar.gz"))
789 (sha256
790 (base32
791 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
792 (properties
793 `((upstream-name . "HSMMSingleCell")))
794 (build-system r-build-system)
795 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
796 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
797 (description
798 "Skeletal myoblasts undergo a well-characterized sequence of
799morphological and transcriptional changes during differentiation. In this
800experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
801under high mitogen conditions (GM) and then differentiated by switching to
802low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
803hundred cells taken over a time-course of serum-induced differentiation.
804Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
80572 hours) following serum switch using the Fluidigm C1 microfluidic system.
806RNA from each cell was isolated and used to construct mRNA-Seq libraries,
807which were then sequenced to a depth of ~4 million reads per library,
808resulting in a complete gene expression profile for each cell.")
809 (license license:artistic2.0)))
810
811\f
812;;; Packages
813
14bba460
RW		 814(define-public r-biocgenerics
815 (package
816 (name "r-biocgenerics")
817 (version "0.28.0")
818 (source (origin
819 (method url-fetch)
820 (uri (bioconductor-uri "BiocGenerics" version))
821 (sha256
822 (base32
823 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
824 (properties
825 `((upstream-name . "BiocGenerics")))
826 (build-system r-build-system)
827 (home-page "https://bioconductor.org/packages/BiocGenerics")
828 (synopsis "S4 generic functions for Bioconductor")
829 (description
830 "This package provides S4 generic functions needed by many Bioconductor
831packages.")
832 (license license:artistic2.0)))
833
7097c700
RW		 834(define-public r-annotate
835 (package
836 (name "r-annotate")
877fd189 837 (version "1.60.1")
7097c700
RW		 838 (source
839 (origin
840 (method url-fetch)
841 (uri (bioconductor-uri "annotate" version))
842 (sha256
843 (base32
877fd189 844 "0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"))))
7097c700
RW		 845 (build-system r-build-system)
846 (propagated-inputs
847 `(("r-annotationdbi" ,r-annotationdbi)
848 ("r-biobase" ,r-biobase)
849 ("r-biocgenerics" ,r-biocgenerics)
850 ("r-dbi" ,r-dbi)
851 ("r-rcurl" ,r-rcurl)
852 ("r-xml" ,r-xml)
853 ("r-xtable" ,r-xtable)))
854 (home-page
855 "https://bioconductor.org/packages/annotate")
856 (synopsis "Annotation for microarrays")
857 (description "This package provides R environments for the annotation of
858microarrays.")
859 (license license:artistic2.0)))
860
fa596599
RW		 861(define-public r-hpar
862 (package
863 (name "r-hpar")
61686921 864 (version "1.24.0")
fa596599
RW		 865 (source
866 (origin
867 (method url-fetch)
868 (uri (bioconductor-uri "hpar" version))
869 (sha256
870 (base32
61686921 871 "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
fa596599
RW		 872 (build-system r-build-system)
873 (home-page "https://bioconductor.org/packages/hpar/")
874 (synopsis "Human Protein Atlas in R")
875 (description "This package provides a simple interface to and data from
876the Human Protein Atlas project.")
877 (license license:artistic2.0)))
183ce988
RJ		 878
879(define-public r-regioner
880 (package
881 (name "r-regioner")
d639d888 882 (version "1.14.0")
183ce988
RJ		 883 (source
884 (origin
885 (method url-fetch)
886 (uri (bioconductor-uri "regioneR" version))
887 (sha256
888 (base32
d639d888 889 "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
183ce988
RJ		 890 (properties `((upstream-name . "regioneR")))
891 (build-system r-build-system)
892 (propagated-inputs
d639d888 893 `(("r-biostrings" ,r-biostrings)
183ce988 894 ("r-bsgenome" ,r-bsgenome)
183ce988 895 ("r-genomeinfodb" ,r-genomeinfodb)
d639d888 896 ("r-genomicranges" ,r-genomicranges)
72427c72 897 ("r-iranges" ,r-iranges)
d639d888
RW		 898 ("r-memoise" ,r-memoise)
899 ("r-rtracklayer" ,r-rtracklayer)
72427c72 900 ("r-s4vectors" ,r-s4vectors)))
183ce988
RJ		 901 (home-page "https://bioconductor.org/packages/regioneR/")
902 (synopsis "Association analysis of genomic regions")
903 (description "This package offers a statistical framework based on
904customizable permutation tests to assess the association between genomic
905region sets and other genomic features.")
906 (license license:artistic2.0)))
a5b56a53 907
bfb93b48
RW		 908(define-public r-geneplotter
909 (package
910 (name "r-geneplotter")
911 (version "1.60.0")
912 (source
913 (origin
914 (method url-fetch)
915 (uri (bioconductor-uri "geneplotter" version))
916 (sha256
917 (base32
918 "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
919 (build-system r-build-system)
920 (propagated-inputs
921 `(("r-annotate" ,r-annotate)
922 ("r-annotationdbi" ,r-annotationdbi)
923 ("r-biobase" ,r-biobase)
924 ("r-biocgenerics" ,r-biocgenerics)
925 ("r-lattice" ,r-lattice)
926 ("r-rcolorbrewer" ,r-rcolorbrewer)))
927 (home-page "https://bioconductor.org/packages/geneplotter")
928 (synopsis "Graphics functions for genomic data")
929 (description
930 "This package provides functions for plotting genomic data.")
931 (license license:artistic2.0)))
932
4dc2ecc2
RW		 933(define-public r-qvalue
934 (package
935 (name "r-qvalue")
936 (version "2.14.1")
937 (source
938 (origin
939 (method url-fetch)
940 (uri (bioconductor-uri "qvalue" version))
941 (sha256
942 (base32
943 "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
944 (build-system r-build-system)
945 (propagated-inputs
946 `(("r-ggplot2" ,r-ggplot2)
947 ("r-reshape2" ,r-reshape2)))
948 (home-page "http://github.com/jdstorey/qvalue")
949 (synopsis "Q-value estimation for false discovery rate control")
950 (description
951 "This package takes a list of p-values resulting from the simultaneous
952testing of many hypotheses and estimates their q-values and local @dfn{false
953discovery rate} (FDR) values. The q-value of a test measures the proportion
954of false positives incurred when that particular test is called significant.
955The local FDR measures the posterior probability the null hypothesis is true
956given the test's p-value. Various plots are automatically generated, allowing
957one to make sensible significance cut-offs. The software can be applied to
958problems in genomics, brain imaging, astrophysics, and data mining.")
959 ;; Any version of the LGPL.
960 (license license:lgpl3+)))
961
a5b56a53
RJ		 962(define-public r-diffbind
963 (package
964 (name "r-diffbind")
98652568 965 (version "2.10.0")
a5b56a53
RJ		 966 (source
967 (origin
968 (method url-fetch)
969 (uri (bioconductor-uri "DiffBind" version))
970 (sha256
971 (base32
98652568 972 "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
a5b56a53
RJ		 973 (properties `((upstream-name . "DiffBind")))
974 (build-system r-build-system)
975 (inputs
976 `(("zlib" ,zlib)))
977 (propagated-inputs
978 `(("r-amap" ,r-amap)
979 ("r-biocparallel" ,r-biocparallel)
980 ("r-deseq2" ,r-deseq2)
981 ("r-dplyr" ,r-dplyr)
982 ("r-edger" ,r-edger)
983 ("r-genomicalignments" ,r-genomicalignments)
45bbccf4
RW		 984 ("r-genomicranges" ,r-genomicranges)
985 ("r-ggplot2" ,r-ggplot2)
a5b56a53
RJ		 986 ("r-ggrepel" ,r-ggrepel)
987 ("r-gplots" ,r-gplots)
988 ("r-iranges" ,r-iranges)
989 ("r-lattice" ,r-lattice)
990 ("r-limma" ,r-limma)
991 ("r-locfit" ,r-locfit)
992 ("r-rcolorbrewer" , r-rcolorbrewer)
993 ("r-rcpp" ,r-rcpp)
994 ("r-rsamtools" ,r-rsamtools)
995 ("r-s4vectors" ,r-s4vectors)
45bbccf4 996 ("r-summarizedexperiment" ,r-summarizedexperiment)
a5b56a53
RJ		 997 ("r-systempiper" ,r-systempiper)
998 ("r-zlibbioc" ,r-zlibbioc)))
999 (home-page "http://bioconductor.org/packages/DiffBind")
1000 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1001 (description
1002 "This package computes differentially bound sites from multiple
1003ChIP-seq experiments using affinity (quantitative) data. Also enables
1004occupancy (overlap) analysis and plotting functions.")
1005 (license license:artistic2.0)))
6d94bf6b
RJ		 1006
1007(define-public r-ripseeker
1008 (package
1009 (name "r-ripseeker")
e9427b2c 1010 (version "1.22.0")
6d94bf6b
RJ		 1011 (source
1012 (origin
1013 (method url-fetch)
1014 (uri (bioconductor-uri "RIPSeeker" version))
1015 (sha256
1016 (base32
e9427b2c 1017 "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
6d94bf6b
RJ		 1018 (properties `((upstream-name . "RIPSeeker")))
1019 (build-system r-build-system)
1020 (propagated-inputs
1021 `(("r-s4vectors" ,r-s4vectors)
1022 ("r-iranges" ,r-iranges)
1023 ("r-genomicranges" ,r-genomicranges)
1024 ("r-summarizedexperiment" ,r-summarizedexperiment)
1025 ("r-rsamtools" ,r-rsamtools)
1026 ("r-genomicalignments" ,r-genomicalignments)
1027 ("r-rtracklayer" ,r-rtracklayer)))
1028 (home-page "http://bioconductor.org/packages/RIPSeeker")
1029 (synopsis
1030 "Identifying protein-associated transcripts from RIP-seq experiments")
1031 (description
1032 "This package infers and discriminates RIP peaks from RIP-seq alignments
1033using two-state HMM with negative binomial emission probability. While
1034RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1035a suite of bioinformatics tools integrated within this self-contained software
1036package comprehensively addressing issues ranging from post-alignments
1037processing to visualization and annotation.")
1038 (license license:gpl2)))
a6ae9ffd
RJ		 1039
1040(define-public r-multtest
1041 (package
1042 (name "r-multtest")
95ee4a46 1043 (version "2.38.0")
a6ae9ffd
RJ		 1044 (source
1045 (origin
1046 (method url-fetch)
1047 (uri (bioconductor-uri "multtest" version))
1048 (sha256
1049 (base32
95ee4a46 1050 "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
a6ae9ffd
RJ		 1051 (build-system r-build-system)
1052 (propagated-inputs
1053 `(("r-survival" ,r-survival)
1054 ("r-biocgenerics" ,r-biocgenerics)
1055 ("r-biobase" ,r-biobase)
1056 ("r-mass" ,r-mass)))
1057 (home-page "http://bioconductor.org/packages/multtest")
1058 (synopsis "Resampling-based multiple hypothesis testing")
1059 (description
1060 "This package can do non-parametric bootstrap and permutation
1061resampling-based multiple testing procedures (including empirical Bayes
1062methods) for controlling the family-wise error rate (FWER), generalized
1063family-wise error rate (gFWER), tail probability of the proportion of
1064false positives (TPPFP), and false discovery rate (FDR). Several choices
1065of bootstrap-based null distribution are implemented (centered, centered
1066and scaled, quantile-transformed). Single-step and step-wise methods are
1067available. Tests based on a variety of T- and F-statistics (including
1068T-statistics based on regression parameters from linear and survival models
1069as well as those based on correlation parameters) are included. When probing
1070hypotheses with T-statistics, users may also select a potentially faster null
1071distribution which is multivariate normal with mean zero and variance
1072covariance matrix derived from the vector influence function. Results are
1073reported in terms of adjusted P-values, confidence regions and test statistic
1074cutoffs. The procedures are directly applicable to identifying differentially
1075expressed genes in DNA microarray experiments.")
1076 (license license:lgpl3)))
793f83ef 1077
5dfe4912
RW		 1078(define-public r-graph
1079 (package
1080 (name "r-graph")
14520b64 1081 (version "1.60.0")
5dfe4912
RW		 1082 (source (origin
1083 (method url-fetch)
1084 (uri (bioconductor-uri "graph" version))
1085 (sha256
1086 (base32
14520b64 1087 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
5dfe4912
RW		 1088 (build-system r-build-system)
1089 (propagated-inputs
1090 `(("r-biocgenerics" ,r-biocgenerics)))
1091 (home-page "https://bioconductor.org/packages/graph")
1092 (synopsis "Handle graph data structures in R")
1093 (description
1094 "This package implements some simple graph handling capabilities for R.")
1095 (license license:artistic2.0)))
1096
a207bca2
RW		 1097(define-public r-codedepends
1098 (package
1099 (name "r-codedepends")
1100 (version "0.6.5")
1101 (source
1102 (origin
1103 (method url-fetch)
1104 (uri (cran-uri "CodeDepends" version))
1105 (sha256
1106 (base32
1107 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1108 (properties `((upstream-name . "CodeDepends")))
1109 (build-system r-build-system)
1110 (propagated-inputs
1111 `(("r-codetools" ,r-codetools)
1112 ("r-graph" ,r-graph)
1113 ("r-xml" ,r-xml)))
1114 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1115 (synopsis "Analysis of R code for reproducible research and code comprehension")
1116 (description
1117 "This package provides tools for analyzing R expressions or blocks of
1118code and determining the dependencies between them. It focuses on R scripts,
1119but can be used on the bodies of functions. There are many facilities
1120including the ability to summarize or get a high-level view of code,
1121determining dependencies between variables, code improvement suggestions.")
1122 ;; Any version of the GPL
1123 (license (list license:gpl2+ license:gpl3+))))
1124
793f83ef
RJ		 1125(define-public r-chippeakanno
1126 (package
1127 (name "r-chippeakanno")
add2b195 1128 (version "3.16.1")
793f83ef
RJ		 1129 (source
1130 (origin
1131 (method url-fetch)
1132 (uri (bioconductor-uri "ChIPpeakAnno" version))
1133 (sha256
1134 (base32
add2b195 1135 "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
793f83ef
RJ		 1136 (properties `((upstream-name . "ChIPpeakAnno")))
1137 (build-system r-build-system)
1138 (propagated-inputs
1139 `(("r-biocgenerics" ,r-biocgenerics)
57d2fcd9 1140 ("r-biocmanager" ,r-biocmanager)
f794e85d
RW		 1141 ("r-biostrings" ,r-biostrings)
1142 ("r-delayedarray" ,r-delayedarray)
793f83ef
RJ		 1143 ("r-go-db" ,r-go-db)
1144 ("r-biomart" ,r-biomart)
1145 ("r-bsgenome" ,r-bsgenome)
1146 ("r-genomicfeatures" ,r-genomicfeatures)
f794e85d 1147 ("r-genomicranges" ,r-genomicranges)
793f83ef 1148 ("r-genomeinfodb" ,r-genomeinfodb)
f794e85d 1149 ("r-iranges" ,r-iranges)
793f83ef
RJ		 1150 ("r-matrixstats" ,r-matrixstats)
1151 ("r-annotationdbi" ,r-annotationdbi)
1152 ("r-limma" ,r-limma)
1153 ("r-multtest" ,r-multtest)
1154 ("r-rbgl" ,r-rbgl)
1155 ("r-graph" ,r-graph)
793f83ef
RJ		 1156 ("r-regioner" ,r-regioner)
1157 ("r-dbi" ,r-dbi)
1158 ("r-ensembldb" ,r-ensembldb)
1159 ("r-biobase" ,r-biobase)
f794e85d 1160 ("r-s4vectors" ,r-s4vectors)
793f83ef
RJ		 1161 ("r-seqinr" ,r-seqinr)
1162 ("r-idr" ,r-idr)
1163 ("r-genomicalignments" ,r-genomicalignments)
1164 ("r-summarizedexperiment" ,r-summarizedexperiment)
1165 ("r-rsamtools" ,r-rsamtools)
1166 ("r-venndiagram" ,r-venndiagram)))
1167 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1168 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1169 (description
1170 "The package includes functions to retrieve the sequences around the peak,
1171obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1172custom features such as most conserved elements and other transcription factor
1173binding sites supplied by users. Starting 2.0.5, new functions have been added
1174for finding the peaks with bi-directional promoters with summary statistics
1175(peaksNearBDP), for summarizing the occurrence of motifs in peaks
1176(summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1177enrichedGO (addGeneIDs).")
1178 (license license:gpl2+)))
164502d8
RJ		 1179
1180(define-public r-marray
1181 (package
1182 (name "r-marray")
f1c606ce 1183 (version "1.60.0")
164502d8
RJ		 1184 (source (origin
1185 (method url-fetch)
1186 (uri (bioconductor-uri "marray" version))
1187 (sha256
f1c606ce 1188 (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
164502d8
RJ		 1189 (build-system r-build-system)
1190 (propagated-inputs
67487088 1191 `(("r-limma" ,r-limma)))
164502d8
RJ		 1192 (home-page "http://bioconductor.org/packages/marray")
1193 (synopsis "Exploratory analysis for two-color spotted microarray data")
1194 (description "This package contains class definitions for two-color spotted
1195microarray data. It also includes fuctions for data input, diagnostic plots,
1196normalization and quality checking.")
1197 (license license:lgpl2.0+)))
0416a0d4
RJ		 1198
1199(define-public r-cghbase
1200 (package
1201 (name "r-cghbase")
46cdceef 1202 (version "1.42.0")
0416a0d4
RJ		 1203 (source (origin
1204 (method url-fetch)
1205 (uri (bioconductor-uri "CGHbase" version))
1206 (sha256
46cdceef 1207 (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
0416a0d4
RJ		 1208 (properties `((upstream-name . "CGHbase")))
1209 (build-system r-build-system)
1210 (propagated-inputs
1211 `(("r-biobase" ,r-biobase)
1212 ("r-marray" ,r-marray)))
1213 (home-page "http://bioconductor.org/packages/CGHbase")
1214 (synopsis "Base functions and classes for arrayCGH data analysis")
1215 (description "This package contains functions and classes that are needed by
1216the @code{arrayCGH} packages.")
1217 (license license:gpl2+)))
67ee83d6
RJ		 1218
1219(define-public r-cghcall
1220 (package
1221 (name "r-cghcall")
9add0933 1222 (version "2.44.0")
67ee83d6
RJ		 1223 (source (origin
1224 (method url-fetch)
1225 (uri (bioconductor-uri "CGHcall" version))
1226 (sha256
9add0933 1227 (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
67ee83d6
RJ		 1228 (properties `((upstream-name . "CGHcall")))
1229 (build-system r-build-system)
1230 (propagated-inputs
1231 `(("r-biobase" ,r-biobase)
1232 ("r-cghbase" ,r-cghbase)
1233 ("r-impute" ,r-impute)
1234 ("r-dnacopy" ,r-dnacopy)
1235 ("r-snowfall" ,r-snowfall)))
1236 (home-page "http://bioconductor.org/packages/CGHcall")
1237 (synopsis "Base functions and classes for arrayCGH data analysis")
1238 (description "This package contains functions and classes that are needed by
1239@code{arrayCGH} packages.")
1240 (license license:gpl2+)))
0ef8cc9c
RJ		 1241
1242(define-public r-qdnaseq
1243 (package
1244 (name "r-qdnaseq")
a92f5230 1245 (version "1.18.0")
0ef8cc9c
RJ		 1246 (source (origin
1247 (method url-fetch)
1248 (uri (bioconductor-uri "QDNAseq" version))
1249 (sha256
a92f5230 1250 (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
0ef8cc9c
RJ		 1251 (properties `((upstream-name . "QDNAseq")))
1252 (build-system r-build-system)
1253 (propagated-inputs
1254 `(("r-biobase" ,r-biobase)
81b0181b 1255 ("r-biocparallel" ,r-biocparallel)
0ef8cc9c
RJ		 1256 ("r-cghbase" ,r-cghbase)
1257 ("r-cghcall" ,r-cghcall)
1258 ("r-dnacopy" ,r-dnacopy)
1259 ("r-genomicranges" ,r-genomicranges)
1260 ("r-iranges" ,r-iranges)
1261 ("r-matrixstats" ,r-matrixstats)
1262 ("r-r-utils" ,r-r-utils)
1263 ("r-rsamtools" ,r-rsamtools)))
1264 (home-page "http://bioconductor.org/packages/QDNAseq")
1265 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1266 (description "The genome is divided into non-overlapping fixed-sized bins,
1267number of sequence reads in each counted, adjusted with a simultaneous
1268two-dimensional loess correction for sequence mappability and GC content, and
1269filtered to remove spurious regions in the genome. Downstream steps of
1270segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1271respectively.")
1272 (license license:gpl2+)))
bb15b581
RW		 1273
1274(define-public r-bayseq
1275 (package
1276 (name "r-bayseq")
4728e275 1277 (version "2.16.0")
bb15b581
RW		 1278 (source
1279 (origin
1280 (method url-fetch)
1281 (uri (bioconductor-uri "baySeq" version))
1282 (sha256
1283 (base32
4728e275 1284 "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
bb15b581
RW		 1285 (properties `((upstream-name . "baySeq")))
1286 (build-system r-build-system)
1287 (propagated-inputs
1288 `(("r-abind" ,r-abind)
1289 ("r-edger" ,r-edger)
1290 ("r-genomicranges" ,r-genomicranges)))
1291 (home-page "https://bioconductor.org/packages/baySeq/")
1292 (synopsis "Bayesian analysis of differential expression patterns in count data")
1293 (description
1294 "This package identifies differential expression in high-throughput count
1295data, such as that derived from next-generation sequencing machines,
1296calculating estimated posterior likelihoods of differential expression (or
1297more complex hypotheses) via empirical Bayesian methods.")
1298 (license license:gpl3)))
609f4ad1
RW		 1299
1300(define-public r-chipcomp
1301 (package
1302 (name "r-chipcomp")
aa802eaf 1303 (version "1.12.0")
609f4ad1
RW		 1304 (source
1305 (origin
1306 (method url-fetch)
1307 (uri (bioconductor-uri "ChIPComp" version))
1308 (sha256
1309 (base32
aa802eaf 1310 "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
609f4ad1
RW		 1311 (properties `((upstream-name . "ChIPComp")))
1312 (build-system r-build-system)
1313 (propagated-inputs
1314 `(("r-biocgenerics" ,r-biocgenerics)
1315 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1316 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1317 ("r-genomeinfodb" ,r-genomeinfodb)
1318 ("r-genomicranges" ,r-genomicranges)
1319 ("r-iranges" ,r-iranges)
1320 ("r-limma" ,r-limma)
1321 ("r-rsamtools" ,r-rsamtools)
1322 ("r-rtracklayer" ,r-rtracklayer)
1323 ("r-s4vectors" ,r-s4vectors)))
1324 (home-page "https://bioconductor.org/packages/ChIPComp")
1325 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1326 (description
1327 "ChIPComp implements a statistical method for quantitative comparison of
1328multiple ChIP-seq datasets. It detects differentially bound sharp binding
1329sites across multiple conditions considering matching control in ChIP-seq
1330datasets.")
1331 ;; Any version of the GPL.
1332 (license license:gpl3+)))
0490f9de
RW		 1333
1334(define-public r-riboprofiling
1335 (package
1336 (name "r-riboprofiling")
e22e462b 1337 (version "1.12.0")
0490f9de
RW		 1338 (source
1339 (origin
1340 (method url-fetch)
1341 (uri (bioconductor-uri "RiboProfiling" version))
1342 (sha256
1343 (base32
e22e462b 1344 "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
0490f9de
RW		 1345 (properties `((upstream-name . "RiboProfiling")))
1346 (build-system r-build-system)
1347 (propagated-inputs
1348 `(("r-biocgenerics" ,r-biocgenerics)
1349 ("r-biostrings" ,r-biostrings)
1350 ("r-data-table" ,r-data-table)
1351 ("r-genomeinfodb" ,r-genomeinfodb)
1352 ("r-genomicalignments" ,r-genomicalignments)
1353 ("r-genomicfeatures" ,r-genomicfeatures)
1354 ("r-genomicranges" ,r-genomicranges)
1355 ("r-ggbio" ,r-ggbio)
1356 ("r-ggplot2" ,r-ggplot2)
1357 ("r-iranges" ,r-iranges)
1358 ("r-plyr" ,r-plyr)
1359 ("r-reshape2" ,r-reshape2)
1360 ("r-rsamtools" ,r-rsamtools)
1361 ("r-rtracklayer" ,r-rtracklayer)
1362 ("r-s4vectors" ,r-s4vectors)
1363 ("r-sqldf" ,r-sqldf)))
1364 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1365 (synopsis "Ribosome profiling data analysis")
1366 (description "Starting with a BAM file, this package provides the
1367necessary functions for quality assessment, read start position recalibration,
1368the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1369of count data: pairs, log fold-change, codon frequency and coverage
1370assessment, principal component analysis on codon coverage.")
1371 (license license:gpl3)))
6ffdfe6a
RW		 1372
1373(define-public r-riboseqr
1374 (package
1375 (name "r-riboseqr")
c4fed658 1376 (version "1.16.0")
6ffdfe6a
RW		 1377 (source
1378 (origin
1379 (method url-fetch)
1380 (uri (bioconductor-uri "riboSeqR" version))
1381 (sha256
1382 (base32
c4fed658 1383 "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
6ffdfe6a
RW		 1384 (properties `((upstream-name . "riboSeqR")))
1385 (build-system r-build-system)
1386 (propagated-inputs
1387 `(("r-abind" ,r-abind)
1388 ("r-bayseq" ,r-bayseq)
1389 ("r-genomeinfodb" ,r-genomeinfodb)
1390 ("r-genomicranges" ,r-genomicranges)
1391 ("r-iranges" ,r-iranges)
1392 ("r-rsamtools" ,r-rsamtools)
1393 ("r-seqlogo" ,r-seqlogo)))
1394 (home-page "https://bioconductor.org/packages/riboSeqR/")
1395 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1396 (description
1397 "This package provides plotting functions, frameshift detection and
1398parsing of genetic sequencing data from ribosome profiling experiments.")
1399 (license license:gpl3)))
a32279ff
RW		 1400
1401(define-public r-interactionset
1402 (package
1403 (name "r-interactionset")
bbc4787c 1404 (version "1.10.0")
a32279ff
RW		 1405 (source
1406 (origin
1407 (method url-fetch)
1408 (uri (bioconductor-uri "InteractionSet" version))
1409 (sha256
1410 (base32
bbc4787c 1411 "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
a32279ff
RW		 1412 (properties
1413 `((upstream-name . "InteractionSet")))
1414 (build-system r-build-system)
1415 (propagated-inputs
1416 `(("r-biocgenerics" ,r-biocgenerics)
1417 ("r-genomeinfodb" ,r-genomeinfodb)
1418 ("r-genomicranges" ,r-genomicranges)
1419 ("r-iranges" ,r-iranges)
1420 ("r-matrix" ,r-matrix)
1421 ("r-rcpp" ,r-rcpp)
1422 ("r-s4vectors" ,r-s4vectors)
1423 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1424 (home-page "https://bioconductor.org/packages/InteractionSet")
1425 (synopsis "Base classes for storing genomic interaction data")
1426 (description
1427 "This packages provides the @code{GInteractions},
1428@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1429for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1430experiments.")
1431 (license license:gpl3)))
cf9a29b2
RW		 1432
1433(define-public r-genomicinteractions
1434 (package
1435 (name "r-genomicinteractions")
5f2d0e63 1436 (version "1.16.0")
cf9a29b2
RW		 1437 (source
1438 (origin
1439 (method url-fetch)
1440 (uri (bioconductor-uri "GenomicInteractions" version))
1441 (sha256
1442 (base32
5f2d0e63 1443 "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
cf9a29b2
RW		 1444 (properties
1445 `((upstream-name . "GenomicInteractions")))
1446 (build-system r-build-system)
1447 (propagated-inputs
1448 `(("r-biobase" ,r-biobase)
1449 ("r-biocgenerics" ,r-biocgenerics)
1450 ("r-data-table" ,r-data-table)
1451 ("r-dplyr" ,r-dplyr)
1452 ("r-genomeinfodb" ,r-genomeinfodb)
1453 ("r-genomicranges" ,r-genomicranges)
1454 ("r-ggplot2" ,r-ggplot2)
1455 ("r-gridextra" ,r-gridextra)
1456 ("r-gviz" ,r-gviz)
1457 ("r-igraph" ,r-igraph)
1458 ("r-interactionset" ,r-interactionset)
1459 ("r-iranges" ,r-iranges)
1460 ("r-rsamtools" ,r-rsamtools)
1461 ("r-rtracklayer" ,r-rtracklayer)
1462 ("r-s4vectors" ,r-s4vectors)
1463 ("r-stringr" ,r-stringr)))
1464 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1465 (synopsis "R package for handling genomic interaction data")
1466 (description
1467 "This R package provides tools for handling genomic interaction data,
1468such as ChIA-PET/Hi-C, annotating genomic features with interaction
1469information and producing various plots and statistics.")
1470 (license license:gpl3)))
27c51606
RW		 1471
1472(define-public r-ctc
1473 (package
1474 (name "r-ctc")
b858338c 1475 (version "1.56.0")
27c51606
RW		 1476 (source
1477 (origin
1478 (method url-fetch)
1479 (uri (bioconductor-uri "ctc" version))
1480 (sha256
1481 (base32
b858338c 1482 "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
27c51606
RW		 1483 (build-system r-build-system)
1484 (propagated-inputs `(("r-amap" ,r-amap)))
1485 (home-page "https://bioconductor.org/packages/ctc/")
1486 (synopsis "Cluster and tree conversion")
1487 (description
1488 "This package provides tools for exporting and importing classification
1489trees and clusters to other programs.")
1490 (license license:gpl2)))
5da0e142
RW		 1491
1492(define-public r-goseq
1493 (package
1494 (name "r-goseq")
7f2b1c4a 1495 (version "1.34.1")
5da0e142
RW		 1496 (source
1497 (origin
1498 (method url-fetch)
1499 (uri (bioconductor-uri "goseq" version))
1500 (sha256
1501 (base32
7f2b1c4a 1502 "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
5da0e142
RW		 1503 (build-system r-build-system)
1504 (propagated-inputs
1505 `(("r-annotationdbi" ,r-annotationdbi)
1506 ("r-biasedurn" ,r-biasedurn)
1507 ("r-biocgenerics" ,r-biocgenerics)
1508 ("r-genelendatabase" ,r-genelendatabase)
1509 ("r-go-db" ,r-go-db)
1510 ("r-mgcv" ,r-mgcv)))
1511 (home-page "https://bioconductor.org/packages/goseq/")
1512 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1513 (description
1514 "This package provides tools to detect Gene Ontology and/or other user
1515defined categories which are over/under represented in RNA-seq data.")
1516 (license license:lgpl2.0+)))
f4235c0e
RW		 1517
1518(define-public r-glimma
1519 (package
1520 (name "r-glimma")
0b469ee2 1521 (version "1.10.1")
f4235c0e
RW		 1522 (source
1523 (origin
1524 (method url-fetch)
1525 (uri (bioconductor-uri "Glimma" version))
1526 (sha256
1527 (base32
0b469ee2 1528 "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
f4235c0e
RW		 1529 (properties `((upstream-name . "Glimma")))
1530 (build-system r-build-system)
1531 (propagated-inputs
1532 `(("r-edger" ,r-edger)
1533 ("r-jsonlite" ,r-jsonlite)
1534 ("r-s4vectors" ,r-s4vectors)))
1535 (home-page "https://github.com/Shians/Glimma")
1536 (synopsis "Interactive HTML graphics")
1537 (description
1538 "This package generates interactive visualisations for analysis of
1539RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1540HTML page. The interactions are built on top of the popular static
1541representations of analysis results in order to provide additional
1542information.")
1543 (license license:lgpl3)))
aa388dc7
RW		 1544
1545(define-public r-rots
1546 (package
1547 (name "r-rots")
45dcd7dc 1548 (version "1.10.1")
aa388dc7
RW		 1549 (source
1550 (origin
1551 (method url-fetch)
1552 (uri (bioconductor-uri "ROTS" version))
1553 (sha256
1554 (base32
45dcd7dc 1555 "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
aa388dc7
RW		 1556 (properties `((upstream-name . "ROTS")))
1557 (build-system r-build-system)
1558 (propagated-inputs
1559 `(("r-biobase" ,r-biobase)
1560 ("r-rcpp" ,r-rcpp)))
1561 (home-page "https://bioconductor.org/packages/ROTS/")
1562 (synopsis "Reproducibility-Optimized Test Statistic")
1563 (description
1564 "This package provides tools for calculating the
1565@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1566in omics data.")
1567 (license license:gpl2+)))
b64ce4b7 1568
cad6fb2d
RW		 1569(define-public r-plgem
1570 (package
1571 (name "r-plgem")
1572 (version "1.54.1")
1573 (source
1574 (origin
1575 (method url-fetch)
1576 (uri (bioconductor-uri "plgem" version))
1577 (sha256
1578 (base32
1579 "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
1580 (build-system r-build-system)
1581 (propagated-inputs
1582 `(("r-biobase" ,r-biobase)
1583 ("r-mass" ,r-mass)))
1584 (home-page "http://www.genopolis.it")
1585 (synopsis "Detect differential expression in microarray and proteomics datasets")
1586 (description
1587 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1588model the variance-versus-mean dependence that exists in a variety of
1589genome-wide datasets, including microarray and proteomics data. The use of
1590PLGEM has been shown to improve the detection of differentially expressed
1591genes or proteins in these datasets.")
1592 (license license:gpl2)))
1593
b64ce4b7
RW		 1594(define-public r-inspect
1595 (package
1596 (name "r-inspect")
c86fc969 1597 (version "1.12.1")
b64ce4b7
RW		 1598 (source
1599 (origin
1600 (method url-fetch)
1601 (uri (bioconductor-uri "INSPEcT" version))
1602 (sha256
1603 (base32
c86fc969 1604 "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
b64ce4b7
RW		 1605 (properties `((upstream-name . "INSPEcT")))
1606 (build-system r-build-system)
1607 (propagated-inputs
1608 `(("r-biobase" ,r-biobase)
1609 ("r-biocgenerics" ,r-biocgenerics)
1610 ("r-biocparallel" ,r-biocparallel)
c86fc969 1611 ("r-deseq2" ,r-deseq2)
b64ce4b7
RW		 1612 ("r-desolve" ,r-desolve)
1613 ("r-genomicalignments" ,r-genomicalignments)
1614 ("r-genomicfeatures" ,r-genomicfeatures)
1615 ("r-genomicranges" ,r-genomicranges)
1616 ("r-iranges" ,r-iranges)
c86fc969 1617 ("r-plgem" ,r-plgem)
b64ce4b7
RW		 1618 ("r-preprocesscore" ,r-preprocesscore)
1619 ("r-proc" ,r-proc)
1620 ("r-rootsolve" ,r-rootsolve)
1621 ("r-rsamtools" ,r-rsamtools)
c86fc969
RW		 1622 ("r-s4vectors" ,r-s4vectors)
1623 ("r-shiny" ,r-shiny)
1624 ("r-summarizedexperiment" ,r-summarizedexperiment)
1625 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1626 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
b64ce4b7
RW		 1627 (home-page "https://bioconductor.org/packages/INSPEcT")
1628 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1629 (description
1630 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1631Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1632order to evaluate synthesis, processing and degradation rates and assess via
1633modeling the rates that determines changes in mature mRNA levels.")
1634 (license license:gpl2)))
f6e99763
RW		 1635
1636(define-public r-dnabarcodes
1637 (package
1638 (name "r-dnabarcodes")
318bcbc4 1639 (version "1.12.0")
f6e99763
RW		 1640 (source
1641 (origin
1642 (method url-fetch)
1643 (uri (bioconductor-uri "DNABarcodes" version))
1644 (sha256
1645 (base32
318bcbc4 1646 "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
f6e99763
RW		 1647 (properties `((upstream-name . "DNABarcodes")))
1648 (build-system r-build-system)
1649 (propagated-inputs
1650 `(("r-bh" ,r-bh)
1651 ("r-matrix" ,r-matrix)
1652 ("r-rcpp" ,r-rcpp)))
1653 (home-page "https://bioconductor.org/packages/DNABarcodes")
1654 (synopsis "Create and analyze DNA barcodes")
1655 (description
1656 "This package offers tools to create DNA barcode sets capable of
1657correcting insertion, deletion, and substitution errors. Existing barcodes
1658can be analyzed regarding their minimal, maximal and average distances between
1659barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1660demultiplexed, i.e. assigned to their original reference barcode.")
1661 (license license:gpl2)))
09aa3d06
RW		 1662
1663(define-public r-ruvseq
1664 (package
1665 (name "r-ruvseq")
c6e9b494 1666 (version "1.16.1")
09aa3d06
RW		 1667 (source
1668 (origin
1669 (method url-fetch)
1670 (uri (bioconductor-uri "RUVSeq" version))
1671 (sha256
1672 (base32
c6e9b494 1673 "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
09aa3d06
RW		 1674 (properties `((upstream-name . "RUVSeq")))
1675 (build-system r-build-system)
1676 (propagated-inputs
1677 `(("r-biobase" ,r-biobase)
1678 ("r-edaseq" ,r-edaseq)
1679 ("r-edger" ,r-edger)
1680 ("r-mass" ,r-mass)))
1681 (home-page "https://github.com/drisso/RUVSeq")
1682 (synopsis "Remove unwanted variation from RNA-Seq data")
1683 (description
1684 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1685of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1686samples.")
1687 (license license:artistic2.0)))
286157dc
RW		 1688
1689(define-public r-biocneighbors
1690 (package
1691 (name "r-biocneighbors")
1692 (version "1.0.0")
1693 (source
1694 (origin
1695 (method url-fetch)
1696 (uri (bioconductor-uri "BiocNeighbors" version))
1697 (sha256
1698 (base32
1699 "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
1700 (properties `((upstream-name . "BiocNeighbors")))
1701 (build-system r-build-system)
1702 (propagated-inputs
1703 `(("r-biocparallel" ,r-biocparallel)
1704 ("r-rcpp" ,r-rcpp)
1705 ("r-rcppannoy" ,r-rcppannoy)
1706 ("r-s4vectors" ,r-s4vectors)))
1707 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1708 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1709 (description
1710 "This package implements exact and approximate methods for nearest
1711neighbor detection, in a framework that allows them to be easily switched
1712within Bioconductor packages or workflows. The exact algorithm is implemented
1713using pre-clustering with the k-means algorithm. Functions are also provided
1714to search for all neighbors within a given distance. Parallelization is
1715achieved for all methods using the BiocParallel framework.")
1716 (license license:gpl3)))
8a587c89 1717
a961ae46
RW		 1718(define-public r-destiny
1719 (package
1720 (name "r-destiny")
1721 (version "2.12.0")
1722 (source
1723 (origin
1724 (method url-fetch)
1725 (uri (bioconductor-uri "destiny" version))
1726 (sha256
1727 (base32
1728 "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
1729 (build-system r-build-system)
1730 (propagated-inputs
1731 `(("r-biobase" ,r-biobase)
1732 ("r-biocgenerics" ,r-biocgenerics)
1733 ("r-fnn" ,r-fnn)
1734 ("r-ggthemes" ,r-ggthemes)
1735 ("r-hmisc" ,r-hmisc)
1736 ("r-igraph" ,r-igraph)
1737 ("r-matrix" ,r-matrix)
1738 ("r-proxy" ,r-proxy)
1739 ("r-rcpp" ,r-rcpp)
1740 ("r-rcppeigen" ,r-rcppeigen)
1741 ("r-scales" ,r-scales)
1742 ("r-scatterplot3d" ,r-scatterplot3d)
1743 ("r-smoother" ,r-smoother)
1744 ("r-summarizedexperiment" ,r-summarizedexperiment)
1745 ("r-vim" ,r-vim)))
1746 (home-page "https://bioconductor.org/packages/destiny/")
1747 (synopsis "Create and plot diffusion maps")
1748 (description "This package provides tools to create and plot diffusion
1749maps.")
1750 ;; Any version of the GPL
1751 (license license:gpl3+)))
1752
8a587c89
RW		 1753(define-public r-savr
1754 (package
1755 (name "r-savr")
1756 (version "1.20.0")
1757 (source
1758 (origin
1759 (method url-fetch)
1760 (uri (bioconductor-uri "savR" version))
1761 (sha256
1762 (base32
1763 "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
1764 (properties `((upstream-name . "savR")))
1765 (build-system r-build-system)
1766 (propagated-inputs
1767 `(("r-ggplot2" ,r-ggplot2)
1768 ("r-gridextra" ,r-gridextra)
1769 ("r-reshape2" ,r-reshape2)
1770 ("r-scales" ,r-scales)
1771 ("r-xml" ,r-xml)))
1772 (home-page "https://github.com/bcalder/savR")
1773 (synopsis "Parse and analyze Illumina SAV files")
1774 (description
1775 "This package provides tools to parse Illumina Sequence Analysis
1776Viewer (SAV) files, access data, and generate QC plots.")
1777 (license license:agpl3+)))
41ffc214
RW		 1778
1779(define-public r-chipexoqual
1780 (package
1781 (name "r-chipexoqual")
1782 (version "1.6.0")
1783 (source
1784 (origin
1785 (method url-fetch)
1786 (uri (bioconductor-uri "ChIPexoQual" version))
1787 (sha256
1788 (base32
1789 "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
1790 (properties `((upstream-name . "ChIPexoQual")))
1791 (build-system r-build-system)
1792 (propagated-inputs
1793 `(("r-biocparallel" ,r-biocparallel)
1794 ("r-biovizbase" ,r-biovizbase)
1795 ("r-broom" ,r-broom)
1796 ("r-data-table" ,r-data-table)
1797 ("r-dplyr" ,r-dplyr)
1798 ("r-genomeinfodb" ,r-genomeinfodb)
1799 ("r-genomicalignments" ,r-genomicalignments)
1800 ("r-genomicranges" ,r-genomicranges)
1801 ("r-ggplot2" ,r-ggplot2)
1802 ("r-hexbin" ,r-hexbin)
1803 ("r-iranges" ,r-iranges)
1804 ("r-rcolorbrewer" ,r-rcolorbrewer)
1805 ("r-rmarkdown" ,r-rmarkdown)
1806 ("r-rsamtools" ,r-rsamtools)
1807 ("r-s4vectors" ,r-s4vectors)
1808 ("r-scales" ,r-scales)
1809 ("r-viridis" ,r-viridis)))
1810 (home-page "https://github.com/keleslab/ChIPexoQual")
1811 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1812 (description
1813 "This package provides a quality control pipeline for ChIP-exo/nexus
1814sequencing data.")
1815 (license license:gpl2+)))
c18dccff 1816
3d13b448
RW		 1817(define-public r-copynumber
1818 (package
1819 (name "r-copynumber")
1820 (version "1.22.0")
1821 (source (origin
1822 (method url-fetch)
1823 (uri (bioconductor-uri "copynumber" version))
1824 (sha256
1825 (base32
1826 "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
1827 (build-system r-build-system)
1828 (propagated-inputs
1829 `(("r-s4vectors" ,r-s4vectors)
1830 ("r-iranges" ,r-iranges)
1831 ("r-genomicranges" ,r-genomicranges)
1832 ("r-biocgenerics" ,r-biocgenerics)))
1833 (home-page "https://bioconductor.org/packages/copynumber")
1834 (synopsis "Segmentation of single- and multi-track copy number data")
1835 (description
1836 "This package segments single- and multi-track copy number data by a
1837penalized least squares regression method.")
1838 (license license:artistic2.0)))
1839
c18dccff
RW		 1840(define-public r-dnacopy
1841 (package
1842 (name "r-dnacopy")
1843 (version "1.56.0")
1844 (source
1845 (origin
1846 (method url-fetch)
1847 (uri (bioconductor-uri "DNAcopy" version))
1848 (sha256
1849 (base32
1850 "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
1851 (properties `((upstream-name . "DNAcopy")))
1852 (build-system r-build-system)
1853 (native-inputs `(("gfortran" ,gfortran)))
1854 (home-page "https://bioconductor.org/packages/DNAcopy")
1855 (synopsis "DNA copy number data analysis")
1856 (description
1857 "This package implements the @dfn{circular binary segmentation} (CBS)
1858algorithm to segment DNA copy number data and identify genomic regions with
1859abnormal copy number.")
1860 (license license:gpl2+)))
3a0babac
RW		 1861
1862;; This is a CRAN package, but it uncharacteristically depends on a
1863;; Bioconductor package.
1864(define-public r-htscluster
1865 (package
1866 (name "r-htscluster")
1867 (version "2.0.8")
1868 (source
1869 (origin
1870 (method url-fetch)
1871 (uri (cran-uri "HTSCluster" version))
1872 (sha256
1873 (base32
1874 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1875 (properties `((upstream-name . "HTSCluster")))
1876 (build-system r-build-system)
1877 (propagated-inputs
1878 `(("r-capushe" ,r-capushe)
1879 ("r-edger" ,r-edger)
1880 ("r-plotrix" ,r-plotrix)))
1881 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1882 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1883 (description
1884 "This package provides a Poisson mixture model is implemented to cluster
1885genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
1886estimation is performed using either the EM or CEM algorithm, and the slope
1887heuristics are used for model selection (i.e., to choose the number of
1888clusters).")
1889 (license license:gpl3+)))
173c9960
RW		 1890
1891(define-public r-deds
1892 (package
1893 (name "r-deds")
1894 (version "1.56.0")
1895 (source
1896 (origin
1897 (method url-fetch)
1898 (uri (bioconductor-uri "DEDS" version))
1899 (sha256
1900 (base32
1901 "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
1902 (properties `((upstream-name . "DEDS")))
1903 (build-system r-build-system)
1904 (home-page "https://bioconductor.org/packages/DEDS/")
1905 (synopsis "Differential expression via distance summary for microarray data")
1906 (description
1907 "This library contains functions that calculate various statistics of
1908differential expression for microarray data, including t statistics, fold
1909change, F statistics, SAM, moderated t and F statistics and B statistics. It
1910also implements a new methodology called DEDS (Differential Expression via
1911Distance Summary), which selects differentially expressed genes by integrating
1912and summarizing a set of statistics using a weighted distance approach.")
1913 ;; Any version of the LGPL.
1914 (license license:lgpl3+)))
7ed869f7
RW		 1915
1916;; This is a CRAN package, but since it depends on a Bioconductor package we
1917;; put it here.
1918(define-public r-nbpseq
1919 (package
1920 (name "r-nbpseq")
1921 (version "0.3.0")
1922 (source
1923 (origin
1924 (method url-fetch)
1925 (uri (cran-uri "NBPSeq" version))
1926 (sha256
1927 (base32
1928 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
1929 (properties `((upstream-name . "NBPSeq")))
1930 (build-system r-build-system)
1931 (propagated-inputs
1932 `(("r-qvalue" ,r-qvalue)))
1933 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
1934 (synopsis "Negative binomial models for RNA-Seq data")
1935 (description
1936 "This package provides negative binomial models for two-group comparisons
1937and regression inferences from RNA-sequencing data.")
1938 (license license:gpl2)))
3087a2f3
RW		 1939
1940(define-public r-ebseq
1941 (package
1942 (name "r-ebseq")
1943 (version "1.22.1")
1944 (source
1945 (origin
1946 (method url-fetch)
1947 (uri (bioconductor-uri "EBSeq" version))
1948 (sha256
1949 (base32
1950 "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
1951 (properties `((upstream-name . "EBSeq")))
1952 (build-system r-build-system)
1953 (propagated-inputs
1954 `(("r-blockmodeling" ,r-blockmodeling)
1955 ("r-gplots" ,r-gplots)
1956 ("r-testthat" ,r-testthat)))
1957 (home-page "https://bioconductor.org/packages/EBSeq")
1958 (synopsis "Differential expression analysis of RNA-seq data")
1959 (description
1960 "This package provides tools for differential expression analysis at both
1961gene and isoform level using RNA-seq data")
1962 (license license:artistic2.0)))
2cb71d81
RW		 1963
1964(define-public r-lpsymphony
1965 (package
1966 (name "r-lpsymphony")
1967 (version "1.10.0")
1968 (source
1969 (origin
1970 (method url-fetch)
1971 (uri (bioconductor-uri "lpsymphony" version))
1972 (sha256
1973 (base32
1974 "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
1975 (build-system r-build-system)
1976 (inputs
1977 `(("gfortran" ,gfortran)
1978 ("zlib" ,zlib)))
1979 (native-inputs
1980 `(("pkg-config" ,pkg-config)))
1981 (home-page "http://r-forge.r-project.org/projects/rsymphony")
1982 (synopsis "Symphony integer linear programming solver in R")
1983 (description
1984 "This package was derived from Rsymphony. The package provides an R
1985interface to SYMPHONY, a linear programming solver written in C++. The main
1986difference between this package and Rsymphony is that it includes the solver
1987source code, while Rsymphony expects to find header and library files on the
1988users' system. Thus the intention of @code{lpsymphony} is to provide an easy
1989to install interface to SYMPHONY.")
1990 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
1991 ;; lpsimphony is released under the same terms.
1992 (license license:epl1.0)))
704de8f5
RW		 1993
1994(define-public r-ihw
1995 (package
1996 (name "r-ihw")
1997 (version "1.10.1")
1998 (source
1999 (origin
2000 (method url-fetch)
2001 (uri (bioconductor-uri "IHW" version))
2002 (sha256
2003 (base32
2004 "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
2005 (properties `((upstream-name . "IHW")))
2006 (build-system r-build-system)
2007 (propagated-inputs
2008 `(("r-biocgenerics" ,r-biocgenerics)
2009 ("r-fdrtool" ,r-fdrtool)
2010 ("r-lpsymphony" ,r-lpsymphony)
2011 ("r-slam" ,r-slam)))
2012 (home-page "https://bioconductor.org/packages/IHW")
2013 (synopsis "Independent hypothesis weighting")
2014 (description
2015 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2016procedure that increases power compared to the method of Benjamini and
2017Hochberg by assigning data-driven weights to each hypothesis. The input to
2018IHW is a two-column table of p-values and covariates. The covariate can be
2019any continuous-valued or categorical variable that is thought to be
2020informative on the statistical properties of each hypothesis test, while it is
2021independent of the p-value under the null hypothesis.")
2022 (license license:artistic2.0)))
251e0830
RW		 2023
2024(define-public r-icobra
2025 (package
2026 (name "r-icobra")
2027 (version "1.10.0")
2028 (source
2029 (origin
2030 (method url-fetch)
2031 (uri (bioconductor-uri "iCOBRA" version))
2032 (sha256
2033 (base32
2034 "0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"))))
2035 (properties `((upstream-name . "iCOBRA")))
2036 (build-system r-build-system)
2037 (propagated-inputs
2038 `(("r-dplyr" ,r-dplyr)
2039 ("r-dt" ,r-dt)
2040 ("r-ggplot2" ,r-ggplot2)
2041 ("r-limma" ,r-limma)
2042 ("r-reshape2" ,r-reshape2)
2043 ("r-rocr" ,r-rocr)
2044 ("r-scales" ,r-scales)
2045 ("r-shiny" ,r-shiny)
2046 ("r-shinybs" ,r-shinybs)
2047 ("r-shinydashboard" ,r-shinydashboard)
2048 ("r-upsetr" ,r-upsetr)))
2049 (home-page "https://bioconductor.org/packages/iCOBRA")
2050 (synopsis "Comparison and visualization of ranking and assignment methods")
2051 (description
2052 "This package provides functions for calculation and visualization of
2053performance metrics for evaluation of ranking and binary
2054classification (assignment) methods. It also contains a Shiny application for
2055interactive exploration of results.")
2056 (license license:gpl2+)))
925fcdbb
RW		 2057
2058(define-public r-mast
2059 (package
2060 (name "r-mast")
2061 (version "1.8.2")
2062 (source
2063 (origin
2064 (method url-fetch)
2065 (uri (bioconductor-uri "MAST" version))
2066 (sha256
2067 (base32
2068 "0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"))))
2069 (properties `((upstream-name . "MAST")))
2070 (build-system r-build-system)
2071 (propagated-inputs
2072 `(("r-abind" ,r-abind)
2073 ("r-biobase" ,r-biobase)
2074 ("r-biocgenerics" ,r-biocgenerics)
2075 ("r-data-table" ,r-data-table)
2076 ("r-ggplot2" ,r-ggplot2)
2077 ("r-plyr" ,r-plyr)
2078 ("r-progress" ,r-progress)
2079 ("r-reshape2" ,r-reshape2)
2080 ("r-s4vectors" ,r-s4vectors)
2081 ("r-singlecellexperiment" ,r-singlecellexperiment)
2082 ("r-stringr" ,r-stringr)
2083 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2084 (home-page "https://github.com/RGLab/MAST/")
2085 (synopsis "Model-based analysis of single cell transcriptomics")
2086 (description
2087 "This package provides methods and models for handling zero-inflated
2088single cell assay data.")
2089 (license license:gpl2+)))
2d7627cf
RW		 2090
2091(define-public r-monocle
2092 (package
2093 (name "r-monocle")
2094 (version "2.10.1")
2095 (source
2096 (origin
2097 (method url-fetch)
2098 (uri (bioconductor-uri "monocle" version))
2099 (sha256
2100 (base32
2101 "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
2102 (build-system r-build-system)
2103 (propagated-inputs
2104 `(("r-biobase" ,r-biobase)
2105 ("r-biocgenerics" ,r-biocgenerics)
2106 ("r-biocviews" ,r-biocviews)
2107 ("r-cluster" ,r-cluster)
2108 ("r-combinat" ,r-combinat)
2109 ("r-ddrtree" ,r-ddrtree)
2110 ("r-densityclust" ,r-densityclust)
2111 ("r-dplyr" ,r-dplyr)
2112 ("r-fastica" ,r-fastica)
2113 ("r-ggplot2" ,r-ggplot2)
2114 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2115 ("r-igraph" ,r-igraph)
2116 ("r-irlba" ,r-irlba)
2117 ("r-limma" ,r-limma)
2118 ("r-mass" ,r-mass)
2119 ("r-matrix" ,r-matrix)
2120 ("r-matrixstats" ,r-matrixstats)
2121 ("r-pheatmap" ,r-pheatmap)
2122 ("r-plyr" ,r-plyr)
2123 ("r-proxy" ,r-proxy)
2124 ("r-qlcmatrix" ,r-qlcmatrix)
2125 ("r-rann" ,r-rann)
2126 ("r-rcpp" ,r-rcpp)
2127 ("r-reshape2" ,r-reshape2)
2128 ("r-rtsne" ,r-rtsne)
2129 ("r-slam" ,r-slam)
2130 ("r-stringr" ,r-stringr)
2131 ("r-tibble" ,r-tibble)
2132 ("r-vgam" ,r-vgam)
2133 ("r-viridis" ,r-viridis)))
2134 (home-page "https://bioconductor.org/packages/monocle")
2135 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2136 (description
2137 "Monocle performs differential expression and time-series analysis for
2138single-cell expression experiments. It orders individual cells according to
2139progress through a biological process, without knowing ahead of time which
2140genes define progress through that process. Monocle also performs
2141differential expression analysis, clustering, visualization, and other useful
2142tasks on single cell expression data. It is designed to work with RNA-Seq and
2143qPCR data, but could be used with other types as well.")
2144 (license license:artistic2.0)))
6213e441
RW		 2145
2146(define-public r-noiseq
2147 (package
2148 (name "r-noiseq")
2149 (version "2.26.1")
2150 (source
2151 (origin
2152 (method url-fetch)
2153 (uri (bioconductor-uri "NOISeq" version))
2154 (sha256
2155 (base32
2156 "1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"))))
2157 (properties `((upstream-name . "NOISeq")))
2158 (build-system r-build-system)
2159 (propagated-inputs
2160 `(("r-biobase" ,r-biobase)
2161 ("r-matrix" ,r-matrix)))
2162 (home-page "https://bioconductor.org/packages/NOISeq")
2163 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2164 (description
2165 "This package provides tools to support the analysis of RNA-seq
2166expression data or other similar kind of data. It provides exploratory plots
2167to evaluate saturation, count distribution, expression per chromosome, type of
2168detected features, features length, etc. It also supports the analysis of
2169differential expression between two experimental conditions with no parametric
2170assumptions.")
2171 (license license:artistic2.0)))
b409c357
RW		 2172
2173(define-public r-scdd
2174 (package
2175 (name "r-scdd")
2176 (version "1.6.1")
2177 (source
2178 (origin
2179 (method url-fetch)
2180 (uri (bioconductor-uri "scDD" version))
2181 (sha256
2182 (base32
2183 "0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"))))
2184 (properties `((upstream-name . "scDD")))
2185 (build-system r-build-system)
2186 (propagated-inputs
2187 `(("r-arm" ,r-arm)
2188 ("r-biocparallel" ,r-biocparallel)
2189 ("r-ebseq" ,r-ebseq)
2190 ("r-fields" ,r-fields)
2191 ("r-ggplot2" ,r-ggplot2)
2192 ("r-mclust" ,r-mclust)
2193 ("r-outliers" ,r-outliers)
2194 ("r-s4vectors" ,r-s4vectors)
2195 ("r-scran" ,r-scran)
2196 ("r-singlecellexperiment" ,r-singlecellexperiment)
2197 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2198 (home-page "https://github.com/kdkorthauer/scDD")
2199 (synopsis "Mixture modeling of single-cell RNA-seq data")
2200 (description
2201 "This package implements a method to analyze single-cell RNA-seq data
2202utilizing flexible Dirichlet Process mixture models. Genes with differential
2203distributions of expression are classified into several interesting patterns
2204of differences between two conditions. The package also includes functions
2205for simulating data with these patterns from negative binomial
2206distributions.")
2207 (license license:gpl2)))
f0887757
RW		 2208
2209(define-public r-scone
2210 (package
2211 (name "r-scone")
2212 (version "1.6.1")
2213 (source
2214 (origin
2215 (method url-fetch)
2216 (uri (bioconductor-uri "scone" version))
2217 (sha256
2218 (base32
2219 "0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"))))
2220 (build-system r-build-system)
2221 (propagated-inputs
2222 `(("r-aroma-light" ,r-aroma-light)
2223 ("r-biocparallel" ,r-biocparallel)
2224 ("r-boot" ,r-boot)
2225 ("r-class" ,r-class)
2226 ("r-cluster" ,r-cluster)
2227 ("r-compositions" ,r-compositions)
2228 ("r-diptest" ,r-diptest)
2229 ("r-edger" ,r-edger)
2230 ("r-fpc" ,r-fpc)
2231 ("r-gplots" ,r-gplots)
2232 ("r-hexbin" ,r-hexbin)
2233 ("r-limma" ,r-limma)
2234 ("r-matrixstats" ,r-matrixstats)
2235 ("r-mixtools" ,r-mixtools)
2236 ("r-rarpack" ,r-rarpack)
2237 ("r-rcolorbrewer" ,r-rcolorbrewer)
2238 ("r-rhdf5" ,r-rhdf5)
2239 ("r-ruvseq" ,r-ruvseq)
2240 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2241 (home-page "https://bioconductor.org/packages/scone")
2242 (synopsis "Single cell overview of normalized expression data")
2243 (description
2244 "SCONE is an R package for comparing and ranking the performance of
2245different normalization schemes for single-cell RNA-seq and other
2246high-throughput analyses.")
2247 (license license:artistic2.0)))
f9201d67
RW		 2248
2249(define-public r-geoquery
2250 (package
2251 (name "r-geoquery")
2252 (version "2.50.5")
2253 (source
2254 (origin
2255 (method url-fetch)
2256 (uri (bioconductor-uri "GEOquery" version))
2257 (sha256
2258 (base32
2259 "074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"))))
2260 (properties `((upstream-name . "GEOquery")))
2261 (build-system r-build-system)
2262 (propagated-inputs
2263 `(("r-biobase" ,r-biobase)
2264 ("r-dplyr" ,r-dplyr)
2265 ("r-httr" ,r-httr)
2266 ("r-limma" ,r-limma)
2267 ("r-magrittr" ,r-magrittr)
2268 ("r-readr" ,r-readr)
2269 ("r-tidyr" ,r-tidyr)
2270 ("r-xml2" ,r-xml2)))
2271 (home-page "https://github.com/seandavi/GEOquery/")
2272 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2273 (description
2274 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2275microarray data. Given the rich and varied nature of this resource, it is
2276only natural to want to apply BioConductor tools to these data. GEOquery is
2277the bridge between GEO and BioConductor.")
2278 (license license:gpl2)))
eed6ff03
RW		 2279
2280(define-public r-illuminaio
2281 (package
2282 (name "r-illuminaio")
2283 (version "0.24.0")
2284 (source
2285 (origin
2286 (method url-fetch)
2287 (uri (bioconductor-uri "illuminaio" version))
2288 (sha256
2289 (base32
2290 "1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"))))
2291 (build-system r-build-system)
2292 (propagated-inputs
2293 `(("r-base64" ,r-base64)))
2294 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2295 (synopsis "Parse Illumina microarray output files")
2296 (description
2297 "This package provides tools for parsing Illumina's microarray output
2298files, including IDAT.")
2299 (license license:gpl2)))
f4eac096
RW		 2300
2301(define-public r-siggenes
2302 (package
2303 (name "r-siggenes")
2304 (version "1.56.0")
2305 (source
2306 (origin
2307 (method url-fetch)
2308 (uri (bioconductor-uri "siggenes" version))
2309 (sha256
2310 (base32
2311 "0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"))))
2312 (build-system r-build-system)
2313 (propagated-inputs
2314 `(("r-biobase" ,r-biobase)
2315 ("r-multtest" ,r-multtest)))
2316 (home-page "https://bioconductor.org/packages/siggenes/")
2317 (synopsis
2318 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2319 (description
2320 "This package provides tools for the identification of differentially
2321expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2322both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2323Bayes Analyses of Microarrays} (EBAM).")
2324 (license license:lgpl2.0+)))
34a24f95
RW		 2325
2326(define-public r-bumphunter
2327 (package
2328 (name "r-bumphunter")
2329 (version "1.24.5")
2330 (source
2331 (origin
2332 (method url-fetch)
2333 (uri (bioconductor-uri "bumphunter" version))
2334 (sha256
2335 (base32
2336 "1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"))))
2337 (build-system r-build-system)
2338 (propagated-inputs
2339 `(("r-annotationdbi" ,r-annotationdbi)
2340 ("r-biocgenerics" ,r-biocgenerics)
2341 ("r-dorng" ,r-dorng)
2342 ("r-foreach" ,r-foreach)
2343 ("r-genomeinfodb" ,r-genomeinfodb)
2344 ("r-genomicfeatures" ,r-genomicfeatures)
2345 ("r-genomicranges" ,r-genomicranges)
2346 ("r-iranges" ,r-iranges)
2347 ("r-iterators" ,r-iterators)
2348 ("r-limma" ,r-limma)
2349 ("r-locfit" ,r-locfit)
2350 ("r-matrixstats" ,r-matrixstats)
2351 ("r-s4vectors" ,r-s4vectors)))
2352 (home-page "https://github.com/ririzarr/bumphunter")
2353 (synopsis "Find bumps in genomic data")
2354 (description
2355 "This package provides tools for finding bumps in genomic data in order
2356to identify differentially methylated regions in epigenetic epidemiology
2357studies.")
2358 (license license:artistic2.0)))
0fbaf195
RW		 2359
2360(define-public r-minfi
2361 (package
2362 (name "r-minfi")
2363 (version "1.28.4")
2364 (source
2365 (origin
2366 (method url-fetch)
2367 (uri (bioconductor-uri "minfi" version))
2368 (sha256
2369 (base32
2370 "1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"))))
2371 (build-system r-build-system)
2372 (propagated-inputs
2373 `(("r-beanplot" ,r-beanplot)
2374 ("r-biobase" ,r-biobase)
2375 ("r-biocgenerics" ,r-biocgenerics)
2376 ("r-biocparallel" ,r-biocparallel)
2377 ("r-biostrings" ,r-biostrings)
2378 ("r-bumphunter" ,r-bumphunter)
2379 ("r-data-table" ,r-data-table)
2380 ("r-delayedarray" ,r-delayedarray)
2381 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2382 ("r-genefilter" ,r-genefilter)
2383 ("r-genomeinfodb" ,r-genomeinfodb)
2384 ("r-genomicranges" ,r-genomicranges)
2385 ("r-geoquery" ,r-geoquery)
2386 ("r-hdf5array" ,r-hdf5array)
2387 ("r-illuminaio" ,r-illuminaio)
2388 ("r-iranges" ,r-iranges)
2389 ("r-lattice" ,r-lattice)
2390 ("r-limma" ,r-limma)
2391 ("r-mass" ,r-mass)
2392 ("r-mclust" ,r-mclust)
2393 ("r-nlme" ,r-nlme)
2394 ("r-nor1mix" ,r-nor1mix)
2395 ("r-preprocesscore" ,r-preprocesscore)
2396 ("r-quadprog" ,r-quadprog)
2397 ("r-rcolorbrewer" ,r-rcolorbrewer)
2398 ("r-reshape" ,r-reshape)
2399 ("r-s4vectors" ,r-s4vectors)
2400 ("r-siggenes" ,r-siggenes)
2401 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2402 (home-page "https://github.com/hansenlab/minfi")
2403 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2404 (description
2405 "This package provides tools to analyze and visualize Illumina Infinium
2406methylation arrays.")
2407 (license license:artistic2.0)))
5ec5ba02
RW		 2408
2409(define-public r-methylumi
2410 (package
2411 (name "r-methylumi")
2412 (version "2.28.0")
2413 (source
2414 (origin
2415 (method url-fetch)
2416 (uri (bioconductor-uri "methylumi" version))
2417 (sha256
2418 (base32
2419 "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"))))
2420 (build-system r-build-system)
2421 (propagated-inputs
2422 `(("r-annotate" ,r-annotate)
2423 ("r-annotationdbi" ,r-annotationdbi)
2424 ("r-biobase" ,r-biobase)
2425 ("r-biocgenerics" ,r-biocgenerics)
2426 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2427 ("r-genefilter" ,r-genefilter)
2428 ("r-genomeinfodb" ,r-genomeinfodb)
2429 ("r-genomicranges" ,r-genomicranges)
2430 ("r-ggplot2" ,r-ggplot2)
2431 ("r-illuminaio" ,r-illuminaio)
2432 ("r-iranges" ,r-iranges)
2433 ("r-lattice" ,r-lattice)
2434 ("r-matrixstats" ,r-matrixstats)
2435 ("r-minfi" ,r-minfi)
2436 ("r-reshape2" ,r-reshape2)
2437 ("r-s4vectors" ,r-s4vectors)
2438 ("r-scales" ,r-scales)
2439 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2440 (home-page "https://bioconductor.org/packages/methylumi")
2441 (synopsis "Handle Illumina methylation data")
2442 (description
2443 "This package provides classes for holding and manipulating Illumina
2444methylation data. Based on eSet, it can contain MIAME information, sample
2445information, feature information, and multiple matrices of data. An
2446\"intelligent\" import function, methylumiR can read the Illumina text files
2447and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2448HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2449background correction, and quality control features for GoldenGate, Infinium,
2450and Infinium HD arrays are also included.")
2451 (license license:gpl2)))
09605cb2
RW		 2452
2453(define-public r-lumi
2454 (package
2455 (name "r-lumi")
2456 (version "2.34.0")
2457 (source
2458 (origin
2459 (method url-fetch)
2460 (uri (bioconductor-uri "lumi" version))
2461 (sha256
2462 (base32
2463 "1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"))))
2464 (build-system r-build-system)
2465 (propagated-inputs
2466 `(("r-affy" ,r-affy)
2467 ("r-annotate" ,r-annotate)
2468 ("r-annotationdbi" ,r-annotationdbi)
2469 ("r-biobase" ,r-biobase)
2470 ("r-dbi" ,r-dbi)
2471 ("r-genomicfeatures" ,r-genomicfeatures)
2472 ("r-genomicranges" ,r-genomicranges)
2473 ("r-kernsmooth" ,r-kernsmooth)
2474 ("r-lattice" ,r-lattice)
2475 ("r-mass" ,r-mass)
2476 ("r-methylumi" ,r-methylumi)
2477 ("r-mgcv" ,r-mgcv)
2478 ("r-nleqslv" ,r-nleqslv)
2479 ("r-preprocesscore" ,r-preprocesscore)
2480 ("r-rsqlite" ,r-rsqlite)))
2481 (home-page "https://bioconductor.org/packages/lumi")
2482 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2483 (description
2484 "The lumi package provides an integrated solution for the Illumina
2485microarray data analysis. It includes functions of Illumina
2486BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2487variance stabilization, normalization and gene annotation at the probe level.
2488It also includes the functions of processing Illumina methylation microarrays,
2489especially Illumina Infinium methylation microarrays.")
2490 (license license:lgpl2.0+)))
4291f36a
RW		 2491
2492(define-public r-linnorm
2493 (package
2494 (name "r-linnorm")
2495 (version "2.6.1")
2496 (source
2497 (origin
2498 (method url-fetch)
2499 (uri (bioconductor-uri "Linnorm" version))
2500 (sha256
2501 (base32
2502 "1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"))))
2503 (properties `((upstream-name . "Linnorm")))
2504 (build-system r-build-system)
2505 (propagated-inputs
2506 `(("r-amap" ,r-amap)
2507 ("r-apcluster" ,r-apcluster)
2508 ("r-ellipse" ,r-ellipse)
2509 ("r-fastcluster" ,r-fastcluster)
2510 ("r-fpc" ,r-fpc)
2511 ("r-ggdendro" ,r-ggdendro)
2512 ("r-ggplot2" ,r-ggplot2)
2513 ("r-gmodels" ,r-gmodels)
2514 ("r-igraph" ,r-igraph)
2515 ("r-limma" ,r-limma)
2516 ("r-mass" ,r-mass)
2517 ("r-mclust" ,r-mclust)
2518 ("r-rcpp" ,r-rcpp)
2519 ("r-rcpparmadillo" ,r-rcpparmadillo)
2520 ("r-rtsne" ,r-rtsne)
2521 ("r-statmod" ,r-statmod)
2522 ("r-vegan" ,r-vegan)
2523 ("r-zoo" ,r-zoo)))
2524 (home-page "http://www.jjwanglab.org/Linnorm/")
2525 (synopsis "Linear model and normality based transformation method")
2526 (description
2527 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2528count data or any large scale count data. It transforms such datasets for
2529parametric tests. In addition to the transformtion function (@code{Linnorm}),
2530the following pipelines are implemented:
2531
2532@enumerate
2533@item Library size/batch effect normalization (@code{Linnorm.Norm})
2534@item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2535 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2536 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2537@item Differential expression analysis or differential peak detection using
2538 limma (@code{Linnorm.limma})
2539@item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2540@item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2541@item Stable gene selection for scRNA-seq data; for users without or who do
2542 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2543@item Data imputation (@code{Linnorm.DataImput}).
2544@end enumerate
2545
2546Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2547@code{RnaXSim} function is included for simulating RNA-seq data for the
2548evaluation of DEG analysis methods.")
2549 (license license:expat)))
e4a17532
RW		 2550
2551(define-public r-ioniser
2552 (package
2553 (name "r-ioniser")
2554 (version "2.6.0")
2555 (source
2556 (origin
2557 (method url-fetch)
2558 (uri (bioconductor-uri "IONiseR" version))
2559 (sha256
2560 (base32
2561 "01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"))))
2562 (properties `((upstream-name . "IONiseR")))
2563 (build-system r-build-system)
2564 (propagated-inputs
2565 `(("r-biocgenerics" ,r-biocgenerics)
2566 ("r-biocparallel" ,r-biocparallel)
2567 ("r-biostrings" ,r-biostrings)
2568 ("r-bit64" ,r-bit64)
2569 ("r-dplyr" ,r-dplyr)
2570 ("r-ggplot2" ,r-ggplot2)
2571 ("r-magrittr" ,r-magrittr)
2572 ("r-rhdf5" ,r-rhdf5)
2573 ("r-shortread" ,r-shortread)
2574 ("r-stringr" ,r-stringr)
2575 ("r-tibble" ,r-tibble)
2576 ("r-tidyr" ,r-tidyr)
2577 ("r-xvector" ,r-xvector)))
2578 (home-page "https://bioconductor.org/packages/IONiseR/")
2579 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2580 (description
2581 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2582MinION data. It extracts summary statistics from a set of fast5 files and can
2583be used either before or after base calling. In addition to standard
2584summaries of the read-types produced, it provides a number of plots for
2585visualising metrics relative to experiment run time or spatially over the
2586surface of a flowcell.")
2587 (license license:expat)))
80eb01c7
RW		 2588
2589;; This is a CRAN package, but it depends on packages from Bioconductor.
2590(define-public r-gkmsvm
2591 (package
2592 (name "r-gkmsvm")
2593 (version "0.79.0")
2594 (source
2595 (origin
2596 (method url-fetch)
2597 (uri (cran-uri "gkmSVM" version))
2598 (sha256
2599 (base32
2600 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2601 (properties `((upstream-name . "gkmSVM")))
2602 (build-system r-build-system)
2603 (propagated-inputs
2604 `(("r-biocgenerics" ,r-biocgenerics)
2605 ("r-biostrings" ,r-biostrings)
2606 ("r-genomeinfodb" ,r-genomeinfodb)
2607 ("r-genomicranges" ,r-genomicranges)
2608 ("r-iranges" ,r-iranges)
2609 ("r-kernlab" ,r-kernlab)
2610 ("r-rcpp" ,r-rcpp)
2611 ("r-rocr" ,r-rocr)
2612 ("r-rtracklayer" ,r-rtracklayer)
2613 ("r-s4vectors" ,r-s4vectors)
2614 ("r-seqinr" ,r-seqinr)))
2615 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2616 (synopsis "Gapped-kmer support vector machine")
2617 (description
2618 "This R package provides tools for training gapped-kmer SVM classifiers
2619for DNA and protein sequences. This package supports several sequence
2620kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2621 (license license:gpl2+)))
8a5460b4
RW		 2622
2623(define-public r-triform
2624 (package
2625 (name "r-triform")
2626 (version "1.24.0")
2627 (source
2628 (origin
2629 (method url-fetch)
2630 (uri (bioconductor-uri "triform" version))
2631 (sha256
2632 (base32
2633 "12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s"))))
2634 (build-system r-build-system)
2635 (propagated-inputs
2636 `(("r-biocgenerics" ,r-biocgenerics)
2637 ("r-iranges" ,r-iranges)
2638 ("r-yaml" ,r-yaml)))
2639 (home-page "https://bioconductor.org/packages/triform/")
2640 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2641 (description
2642 "The Triform algorithm uses model-free statistics to identify peak-like
2643distributions of TF ChIP sequencing reads, taking advantage of an improved
2644peak definition in combination with known profile characteristics.")
2645 (license license:gpl2)))
c538bcdd
RW		 2646
2647(define-public r-varianttools
2648 (package
2649 (name "r-varianttools")
2650 (version "1.24.0")
2651 (source
2652 (origin
2653 (method url-fetch)
2654 (uri (bioconductor-uri "VariantTools" version))
2655 (sha256
2656 (base32
2657 "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
2658 (properties `((upstream-name . "VariantTools")))
2659 (build-system r-build-system)
2660 (propagated-inputs
2661 `(("r-biobase" ,r-biobase)
2662 ("r-biocgenerics" ,r-biocgenerics)
2663 ("r-biocparallel" ,r-biocparallel)
2664 ("r-biostrings" ,r-biostrings)
2665 ("r-bsgenome" ,r-bsgenome)
2666 ("r-genomeinfodb" ,r-genomeinfodb)
2667 ("r-genomicfeatures" ,r-genomicfeatures)
2668 ("r-genomicranges" ,r-genomicranges)
2669 ("r-iranges" ,r-iranges)
2670 ("r-matrix" ,r-matrix)
2671 ("r-rsamtools" ,r-rsamtools)
2672 ("r-rtracklayer" ,r-rtracklayer)
2673 ("r-s4vectors" ,r-s4vectors)
2674 ("r-variantannotation" ,r-variantannotation)))
2675 (home-page "https://bioconductor.org/packages/VariantTools/")
2676 (synopsis "Tools for exploratory analysis of variant calls")
2677 (description
2678 "Explore, diagnose, and compare variant calls using filters. The
2679VariantTools package supports a workflow for loading data, calling single
2680sample variants and tumor-specific somatic mutations or other sample-specific
2681variant types (e.g., RNA editing). Most of the functions operate on
2682alignments (BAM files) or datasets of called variants. The user is expected
2683to have already aligned the reads with a separate tool, e.g., GSNAP via
2684gmapR.")
2685 (license license:artistic2.0)))
3e41919d
RW		 2686
2687(define-public r-heatplus
2688 (package
2689 (name "r-heatplus")
2690 (version "2.28.0")
2691 (source
2692 (origin
2693 (method url-fetch)
2694 (uri (bioconductor-uri "Heatplus" version))
2695 (sha256
2696 (base32
2697 "0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48"))))
2698 (properties `((upstream-name . "Heatplus")))
2699 (build-system r-build-system)
2700 (propagated-inputs
2701 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2702 (home-page "https://github.com/alexploner/Heatplus")
2703 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2704 (description
2705 "This package provides tools to display a rectangular heatmap (intensity
2706plot) of a data matrix. By default, both samples (columns) and features (row)
2707of the matrix are sorted according to a hierarchical clustering, and the
2708corresponding dendrogram is plotted. Optionally, panels with additional
2709information about samples and features can be added to the plot.")
2710 (license license:gpl2+)))
c04f230e
RW		 2711
2712(define-public r-gosemsim
2713 (package
2714 (name "r-gosemsim")
2715 (version "2.8.0")
2716 (source
2717 (origin
2718 (method url-fetch)
2719 (uri (bioconductor-uri "GOSemSim" version))
2720 (sha256
2721 (base32
2722 "0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib"))))
2723 (properties `((upstream-name . "GOSemSim")))
2724 (build-system r-build-system)
2725 (propagated-inputs
2726 `(("r-annotationdbi" ,r-annotationdbi)
2727 ("r-go-db" ,r-go-db)
2728 ("r-rcpp" ,r-rcpp)))
2729 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2730 (synopsis "GO-terms semantic similarity measures")
2731 (description
2732 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2733quantitative ways to compute similarities between genes and gene groups, and
2734have became important basis for many bioinformatics analysis approaches.
2735GOSemSim is an R package for semantic similarity computation among GO terms,
2736sets of GO terms, gene products and gene clusters.")
2737 (license license:artistic2.0)))
9d0f7942
RW		 2738
2739(define-public r-anota
2740 (package
2741 (name "r-anota")
2742 (version "1.30.0")
2743 (source
2744 (origin
2745 (method url-fetch)
2746 (uri (bioconductor-uri "anota" version))
2747 (sha256
2748 (base32
2749 "182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"))))
2750 (build-system r-build-system)
2751 (propagated-inputs
2752 `(("r-multtest" ,r-multtest)
2753 ("r-qvalue" ,r-qvalue)))
2754 (home-page "https://bioconductor.org/packages/anota/")
2755 (synopsis "Analysis of translational activity")
2756 (description
2757 "Genome wide studies of translational control is emerging as a tool to
2758study verious biological conditions. The output from such analysis is both
2759the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2760involved in translation (the actively translating mRNA level) for each mRNA.
2761The standard analysis of such data strives towards identifying differential
2762translational between two or more sample classes - i.e. differences in
2763actively translated mRNA levels that are independent of underlying differences
2764in cytosolic mRNA levels. This package allows for such analysis using partial
2765variances and the random variance model. As 10s of thousands of mRNAs are
2766analyzed in parallell the library performs a number of tests to assure that
2767the data set is suitable for such analysis.")
2768 (license license:gpl3)))
a6d867fe
RW		 2769
2770(define-public r-sigpathway
2771 (package
2772 (name "r-sigpathway")
2773 (version "1.50.0")
2774 (source
2775 (origin
2776 (method url-fetch)
2777 (uri (bioconductor-uri "sigPathway" version))
2778 (sha256
2779 (base32
2780 "0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3"))))
2781 (properties `((upstream-name . "sigPathway")))
2782 (build-system r-build-system)
2783 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
2784 (synopsis "Pathway analysis")
2785 (description
2786 "This package is used to conduct pathway analysis by calculating the NT_k
2787and NE_k statistics in a statistical framework for determining whether a
2788specified group of genes for a pathway has a coordinated association with a
2789phenotype of interest.")
2790 (license license:gpl2)))
af26c7ae
RW		 2791
2792(define-public r-fgsea
2793 (package
2794 (name "r-fgsea")
2795 (version "1.8.0")
2796 (source
2797 (origin
2798 (method url-fetch)
2799 (uri (bioconductor-uri "fgsea" version))
2800 (sha256
2801 (base32
2802 "0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"))))
2803 (build-system r-build-system)
2804 (propagated-inputs
2805 `(("r-biocparallel" ,r-biocparallel)
2806 ("r-data-table" ,r-data-table)
2807 ("r-fastmatch" ,r-fastmatch)
2808 ("r-ggplot2" ,r-ggplot2)
2809 ("r-gridextra" ,r-gridextra)
2810 ("r-matrix" ,r-matrix)
2811 ("r-rcpp" ,r-rcpp)))
2812 (home-page "https://github.com/ctlab/fgsea/")
2813 (synopsis "Fast gene set enrichment analysis")
2814 (description
2815 "The package implements an algorithm for fast gene set enrichment
2816analysis. Using the fast algorithm allows to make more permutations and get
2817more fine grained p-values, which allows to use accurate stantard approaches
2818to multiple hypothesis correction.")
2819 (license license:expat)))
305050b5
RW		 2820
2821(define-public r-dose
2822 (package
2823 (name "r-dose")
2824 (version "3.8.2")
2825 (source
2826 (origin
2827 (method url-fetch)
2828 (uri (bioconductor-uri "DOSE" version))
2829 (sha256
2830 (base32
2831 "1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa"))))
2832 (properties `((upstream-name . "DOSE")))
2833 (build-system r-build-system)
2834 (propagated-inputs
2835 `(("r-annotationdbi" ,r-annotationdbi)
2836 ("r-biocparallel" ,r-biocparallel)
2837 ("r-do-db" ,r-do-db)
2838 ("r-fgsea" ,r-fgsea)
2839 ("r-ggplot2" ,r-ggplot2)
2840 ("r-gosemsim" ,r-gosemsim)
2841 ("r-qvalue" ,r-qvalue)
2842 ("r-reshape2" ,r-reshape2)
2843 ("r-s4vectors" ,r-s4vectors)))
2844 (home-page "https://guangchuangyu.github.io/software/DOSE/")
2845 (synopsis "Disease ontology semantic and enrichment analysis")
2846 (description
2847 "This package implements five methods proposed by Resnik, Schlicker,
2848Jiang, Lin and Wang, respectively, for measuring semantic similarities among
2849@dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
2850including hypergeometric model and gene set enrichment analysis are also
2851implemented for discovering disease associations of high-throughput biological
2852data.")
2853 (license license:artistic2.0)))
9c30cf65
RW		 2854
2855(define-public r-enrichplot
2856 (package
2857 (name "r-enrichplot")
2858 (version "1.2.0")
2859 (source
2860 (origin
2861 (method url-fetch)
2862 (uri (bioconductor-uri "enrichplot" version))
2863 (sha256
2864 (base32
2865 "0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"))))
2866 (build-system r-build-system)
2867 (propagated-inputs
2868 `(("r-annotationdbi" ,r-annotationdbi)
2869 ("r-cowplot" ,r-cowplot)
2870 ("r-dose" ,r-dose)
2871 ("r-europepmc" ,r-europepmc)
2872 ("r-ggplot2" ,r-ggplot2)
2873 ("r-ggplotify" ,r-ggplotify)
2874 ("r-ggraph" ,r-ggraph)
2875 ("r-ggridges" ,r-ggridges)
2876 ("r-gosemsim" ,r-gosemsim)
2877 ("r-gridextra" ,r-gridextra)
2878 ("r-igraph" ,r-igraph)
2879 ("r-purrr" ,r-purrr)
2880 ("r-rcolorbrewer" ,r-rcolorbrewer)
2881 ("r-reshape2" ,r-reshape2)
2882 ("r-upsetr" ,r-upsetr)))
2883 (home-page "https://github.com/GuangchuangYu/enrichplot")
2884 (synopsis "Visualization of functional enrichment result")
2885 (description
2886 "The enrichplot package implements several visualization methods for
2887interpreting functional enrichment results obtained from ORA or GSEA analyses.
2888All the visualization methods are developed based on ggplot2 graphics.")
2889 (license license:artistic2.0)))
f8295ee6
RW		 2890
2891(define-public r-clusterprofiler
2892 (package
2893 (name "r-clusterprofiler")
2894 (version "3.10.1")
2895 (source
2896 (origin
2897 (method url-fetch)
2898 (uri (bioconductor-uri "clusterProfiler" version))
2899 (sha256
2900 (base32
2901 "1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm"))))
2902 (properties
2903 `((upstream-name . "clusterProfiler")))
2904 (build-system r-build-system)
2905 (propagated-inputs
2906 `(("r-annotationdbi" ,r-annotationdbi)
2907 ("r-dose" ,r-dose)
2908 ("r-enrichplot" ,r-enrichplot)
2909 ("r-ggplot2" ,r-ggplot2)
2910 ("r-go-db" ,r-go-db)
2911 ("r-gosemsim" ,r-gosemsim)
2912 ("r-magrittr" ,r-magrittr)
2913 ("r-plyr" ,r-plyr)
2914 ("r-qvalue" ,r-qvalue)
2915 ("r-rvcheck" ,r-rvcheck)
2916 ("r-tidyr" ,r-tidyr)))
2917 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
2918 (synopsis "Analysis and visualization of functional profiles for gene clusters")
2919 (description
2920 "This package implements methods to analyze and visualize functional
2921profiles (GO and KEGG) of gene and gene clusters.")
2922 (license license:artistic2.0)))
ce77562a
RW		 2923
2924(define-public r-mlinterfaces
2925 (package
2926 (name "r-mlinterfaces")
2927 (version "1.62.0")
2928 (source
2929 (origin
2930 (method url-fetch)
2931 (uri (bioconductor-uri "MLInterfaces" version))
2932 (sha256
2933 (base32
2934 "12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8"))))
2935 (properties `((upstream-name . "MLInterfaces")))
2936 (build-system r-build-system)
2937 (propagated-inputs
2938 `(("r-annotate" ,r-annotate)
2939 ("r-biobase" ,r-biobase)
2940 ("r-biocgenerics" ,r-biocgenerics)
2941 ("r-cluster" ,r-cluster)
2942 ("r-fpc" ,r-fpc)
2943 ("r-gbm" ,r-gbm)
2944 ("r-gdata" ,r-gdata)
2945 ("r-genefilter" ,r-genefilter)
2946 ("r-ggvis" ,r-ggvis)
2947 ("r-hwriter" ,r-hwriter)
2948 ("r-mass" ,r-mass)
2949 ("r-mlbench" ,r-mlbench)
2950 ("r-pls" ,r-pls)
2951 ("r-rcolorbrewer" ,r-rcolorbrewer)
2952 ("r-rda" ,r-rda)
2953 ("r-rpart" ,r-rpart)
2954 ("r-sfsmisc" ,r-sfsmisc)
2955 ("r-shiny" ,r-shiny)
2956 ("r-threejs" ,r-threejs)))
2957 (home-page "https://bioconductor.org/packages/MLInterfaces/")
2958 (synopsis "Interfaces to R machine learning procedures")
2959 (description
2960 "This package provides uniform interfaces to machine learning code for
2961data in R and Bioconductor containers.")
2962 ;; Any version of the LGPL.
2963 (license license:lgpl2.1+)))
a793e88c
RW		 2964
2965(define-public r-annaffy
2966 (package
2967 (name "r-annaffy")
2968 (version "1.54.0")
2969 (source
2970 (origin
2971 (method url-fetch)
2972 (uri (bioconductor-uri "annaffy" version))
2973 (sha256
2974 (base32
2975 "16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5"))))
2976 (build-system r-build-system)
2977 (arguments
2978 `(#:phases
2979 (modify-phases %standard-phases
2980 (add-after 'unpack 'remove-reference-to-non-free-data
2981 (lambda _
2982 (substitute* "DESCRIPTION"
2983 ((", KEGG.db") ""))
2984 #t)))))
2985 (propagated-inputs
2986 `(("r-annotationdbi" ,r-annotationdbi)
2987 ("r-biobase" ,r-biobase)
2988 ("r-dbi" ,r-dbi)
2989 ("r-go-db" ,r-go-db)))
2990 (home-page "https://bioconductor.org/packages/annaffy/")
2991 (synopsis "Annotation tools for Affymetrix biological metadata")
2992 (description
2993 "This package provides functions for handling data from Bioconductor
2994Affymetrix annotation data packages. It produces compact HTML and text
2995reports including experimental data and URL links to many online databases.
2996It allows searching of biological metadata using various criteria.")
2997 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
2998 ;; the LGPL 2.1 is included.
2999 (license license:lgpl2.1+)))
0ec0a5ec
RW		 3000
3001(define-public r-a4core
3002 (package
3003 (name "r-a4core")
3004 (version "1.30.0")
3005 (source
3006 (origin
3007 (method url-fetch)
3008 (uri (bioconductor-uri "a4Core" version))
3009 (sha256
3010 (base32
3011 "1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr"))))
3012 (properties `((upstream-name . "a4Core")))
3013 (build-system r-build-system)
3014 (propagated-inputs
3015 `(("r-biobase" ,r-biobase)
3016 ("r-glmnet" ,r-glmnet)))
3017 (home-page "https://bioconductor.org/packages/a4Core")
3018 (synopsis "Automated Affymetrix array analysis core package")
3019 (description
3020 "This is the core package for the automated analysis of Affymetrix
3021arrays.")
3022 (license license:gpl3)))
9ae37581
RW		 3023
3024(define-public r-a4classif
3025 (package
3026 (name "r-a4classif")
3027 (version "1.30.0")
3028 (source
3029 (origin
3030 (method url-fetch)
3031 (uri (bioconductor-uri "a4Classif" version))
3032 (sha256
3033 (base32
3034 "02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j"))))
3035 (properties `((upstream-name . "a4Classif")))
3036 (build-system r-build-system)
3037 (propagated-inputs
3038 `(("r-a4core" ,r-a4core)
3039 ("r-a4preproc" ,r-a4preproc)
3040 ("r-glmnet" ,r-glmnet)
3041 ("r-mlinterfaces" ,r-mlinterfaces)
3042 ("r-pamr" ,r-pamr)
3043 ("r-rocr" ,r-rocr)
3044 ("r-varselrf" ,r-varselrf)))
3045 (home-page "https://bioconductor.org/packages/a4Classif/")
3046 (synopsis "Automated Affymetrix array analysis classification package")
3047 (description
3048 "This is the classification package for the automated analysis of
3049Affymetrix arrays.")
3050 (license license:gpl3)))
b8d13e2c
RW		 3051
3052(define-public r-a4preproc
3053 (package
3054 (name "r-a4preproc")
3055 (version "1.30.0")
3056 (source
3057 (origin
3058 (method url-fetch)
3059 (uri (bioconductor-uri "a4Preproc" version))
3060 (sha256
3061 (base32
3062 "1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp"))))
3063 (properties `((upstream-name . "a4Preproc")))
3064 (build-system r-build-system)
3065 (propagated-inputs
3066 `(("r-annotationdbi" ,r-annotationdbi)))
3067 (home-page "https://bioconductor.org/packages/a4Preproc/")
3068 (synopsis "Automated Affymetrix array analysis preprocessing package")
3069 (description
3070 "This is a package for the automated analysis of Affymetrix arrays. It
3071is used for preprocessing the arrays.")
3072 (license license:gpl3)))
8e15f861
RW		 3073
3074(define-public r-a4reporting
3075 (package
3076 (name "r-a4reporting")
3077 (version "1.30.0")
3078 (source
3079 (origin
3080 (method url-fetch)
3081 (uri (bioconductor-uri "a4Reporting" version))
3082 (sha256
3083 (base32
3084 "124774z3bfdjgxx2ad40795h92aam21yfx0rw0n01nk2wf6k7xc4"))))
3085 (properties `((upstream-name . "a4Reporting")))
3086 (build-system r-build-system)
3087 (propagated-inputs
3088 `(("r-annaffy" ,r-annaffy)
3089 ("r-xtable" ,r-xtable)))
3090 (home-page "https://bioconductor.org/packages/a4Reporting/")
3091 (synopsis "Automated Affymetrix array analysis reporting package")
3092 (description
3093 "This is a package for the automated analysis of Affymetrix arrays. It
3094provides reporting features.")
3095 (license license:gpl3)))
dbfe3375
RW		 3096
3097(define-public r-a4base
3098 (package
3099 (name "r-a4base")
3100 (version "1.30.0")
3101 (source
3102 (origin
3103 (method url-fetch)
3104 (uri (bioconductor-uri "a4Base" version))
3105 (sha256
3106 (base32
3107 "0k9k3bv99msbwf2y416cz316ssaha2dxvmaddbl7z9037p8mjr70"))))
3108 (properties `((upstream-name . "a4Base")))
3109 (build-system r-build-system)
3110 (propagated-inputs
3111 `(("r-a4core" ,r-a4core)
3112 ("r-a4preproc" ,r-a4preproc)
3113 ("r-annaffy" ,r-annaffy)
3114 ("r-annotationdbi" ,r-annotationdbi)
3115 ("r-biobase" ,r-biobase)
3116 ("r-genefilter" ,r-genefilter)
3117 ("r-glmnet" ,r-glmnet)
3118 ("r-gplots" ,r-gplots)
3119 ("r-limma" ,r-limma)
3120 ("r-mpm" ,r-mpm)
3121 ("r-multtest" ,r-multtest)))
3122 (home-page "https://bioconductor.org/packages/a4Base/")
3123 (synopsis "Automated Affymetrix array analysis base package")
3124 (description
3125 "This package provides basic features for the automated analysis of
3126Affymetrix arrays.")
3127 (license license:gpl3)))
84ad024e
RW		 3128
3129(define-public r-a4
3130 (package
3131 (name "r-a4")
3132 (version "1.30.0")
3133 (source
3134 (origin
3135 (method url-fetch)
3136 (uri (bioconductor-uri "a4" version))
3137 (sha256
3138 (base32
3139 "1iqjy35rqx3m2y0dm2bk4cnzdm1qvbi608bfmrid88w6wmwz3qlk"))))
3140 (build-system r-build-system)
3141 (propagated-inputs
3142 `(("r-a4base" ,r-a4base)
3143 ("r-a4classif" ,r-a4classif)
3144 ("r-a4core" ,r-a4core)
3145 ("r-a4preproc" ,r-a4preproc)
3146 ("r-a4reporting" ,r-a4reporting)))
3147 (home-page "https://bioconductor.org/packages/a4/")
3148 (synopsis "Automated Affymetrix array analysis umbrella package")
3149 (description
3150 "This package provides a software suite for the automated analysis of
3151Affymetrix arrays.")
3152 (license license:gpl3)))
59d331f1
RW		 3153
3154(define-public r-abseqr
3155 (package
3156 (name "r-abseqr")
3157 (version "1.0.0")
3158 (source
3159 (origin
3160 (method url-fetch)
3161 (uri (bioconductor-uri "abseqR" version))
3162 (sha256
3163 (base32
3164 "0w0ngxnilcrxlixsz7ls3zm99gyabxwn7w1r3r45n96d4aj075ry"))))
3165 (properties `((upstream-name . "abseqR")))
3166 (build-system r-build-system)
3167 (inputs
3168 `(("pandoc" ,ghc-pandoc)))
3169 (propagated-inputs
3170 `(("r-biocparallel" ,r-biocparallel)
3171 ("r-biocstyle" ,r-biocstyle)
3172 ("r-circlize" ,r-circlize)
3173 ("r-flexdashboard" ,r-flexdashboard)
3174 ("r-ggcorrplot" ,r-ggcorrplot)
3175 ("r-ggdendro" ,r-ggdendro)
3176 ("r-ggplot2" ,r-ggplot2)
3177 ("r-gridextra" ,r-gridextra)
3178 ("r-knitr" ,r-knitr)
3179 ("r-plotly" ,r-plotly)
3180 ("r-plyr" ,r-plyr)
3181 ("r-png" ,r-png)
3182 ("r-rcolorbrewer" ,r-rcolorbrewer)
3183 ("r-reshape2" ,r-reshape2)
3184 ("r-rmarkdown" ,r-rmarkdown)
3185 ("r-stringr" ,r-stringr)
3186 ("r-vegan" ,r-vegan)
3187 ("r-venndiagram" ,r-venndiagram)))
3188 (home-page "https://github.com/malhamdoosh/abseqR")
3189 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3190 (description
3191 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3192sequencing datasets generated from antibody libraries and abseqR is one of its
3193packages. AbseqR empowers the users of abseqPy with plotting and reporting
3194capabilities and allows them to generate interactive HTML reports for the
3195convenience of viewing and sharing with other researchers. Additionally,
3196abseqR extends abseqPy to compare multiple repertoire analyses and perform
3197further downstream analysis on its output.")
3198 (license license:gpl3)))
41aab7d1
RW		 3199
3200(define-public r-bacon
3201 (package
3202 (name "r-bacon")
3203 (version "1.10.1")
3204 (source
3205 (origin
3206 (method url-fetch)
3207 (uri (bioconductor-uri "bacon" version))
3208 (sha256
3209 (base32
3210 "1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df"))))
3211 (build-system r-build-system)
3212 (propagated-inputs
3213 `(("r-biocparallel" ,r-biocparallel)
3214 ("r-ellipse" ,r-ellipse)
3215 ("r-ggplot2" ,r-ggplot2)))
3216 (home-page "https://bioconductor.org/packages/bacon/")
3217 (synopsis "Controlling bias and inflation in association studies")
3218 (description
3219 "Bacon can be used to remove inflation and bias often observed in
3220epigenome- and transcriptome-wide association studies. To this end bacon
3221constructs an empirical null distribution using a Gibbs Sampling algorithm by
3222fitting a three-component normal mixture on z-scores.")
3223 (license license:gpl2+)))
051e8e1a
RW		 3224
3225(define-public r-rgadem
3226 (package
3227 (name "r-rgadem")
3228 (version "2.30.0")
3229 (source
3230 (origin
3231 (method url-fetch)
3232 (uri (bioconductor-uri "rGADEM" version))
3233 (sha256
3234 (base32
3235 "1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2"))))
3236 (properties `((upstream-name . "rGADEM")))
3237 (build-system r-build-system)
3238 (propagated-inputs
3239 `(("r-biostrings" ,r-biostrings)
3240 ("r-bsgenome" ,r-bsgenome)
3241 ("r-iranges" ,r-iranges)
3242 ("r-seqlogo" ,r-seqlogo)))
3243 (home-page "https://bioconductor.org/packages/rGADEM/")
3244 (synopsis "De novo sequence motif discovery")
3245 (description
3246 "rGADEM is an efficient de novo motif discovery tool for large-scale
3247genomic sequence data.")
3248 (license license:artistic2.0)))
229f97c3
RW		 3249
3250(define-public r-motiv
3251 (package
3252 (name "r-motiv")
3253 (version "1.38.0")
3254 (source
3255 (origin
3256 (method url-fetch)
3257 (uri (bioconductor-uri "MotIV" version))
3258 (sha256
3259 (base32
3260 "1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8"))))
3261 (properties `((upstream-name . "MotIV")))
3262 (build-system r-build-system)
3263 (inputs
3264 `(("gsl" ,gsl)))
3265 (propagated-inputs
3266 `(("r-biocgenerics" ,r-biocgenerics)
3267 ("r-biostrings" ,r-biostrings)
3268 ("r-iranges" ,r-iranges)
3269 ("r-lattice" ,r-lattice)
3270 ("r-rgadem" ,r-rgadem)
3271 ("r-s4vectors" ,r-s4vectors)))
3272 (home-page "https://bioconductor.org/packages/MotIV/")
3273 (synopsis "Motif identification and validation")
3274 (description
3275 "This package is used for the identification and validation of sequence
3276motifs. It makes use of STAMP for comparing a set of motifs to a given
3277database (e.g. JASPAR). It can also be used to visualize motifs, motif
3278distributions, modules and filter motifs.")
3279 (license license:gpl2)))
2a72ef56
RW		 3280
3281(define-public r-motifstack
3282 (package
3283 (name "r-motifstack")
3284 (version "1.26.0")
3285 (source
3286 (origin
3287 (method url-fetch)
3288 (uri (bioconductor-uri "motifStack" version))
3289 (sha256
3290 (base32
3291 "1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf"))))
3292 (properties `((upstream-name . "motifStack")))
3293 (build-system r-build-system)
3294 (propagated-inputs
3295 `(("r-ade4" ,r-ade4)
3296 ("r-biostrings" ,r-biostrings)
3297 ("r-grimport" ,r-grimport)
3298 ("r-htmlwidgets" ,r-htmlwidgets)
3299 ("r-motiv" ,r-motiv)
3300 ("r-scales" ,r-scales)
3301 ("r-xml" ,r-xml)))
3302 (home-page "https://bioconductor.org/packages/motifStack/")
3303 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3304 (description
3305 "The motifStack package is designed for graphic representation of
3306multiple motifs with different similarity scores. It works with both DNA/RNA
3307sequence motifs and amino acid sequence motifs. In addition, it provides the
3308flexibility for users to customize the graphic parameters such as the font
3309type and symbol colors.")
3310 (license license:gpl2+)))
e5bff307
RW		 3311
3312(define-public r-genomicscores
3313 (package
3314 (name "r-genomicscores")
3315 (version "1.6.0")
3316 (source
3317 (origin
3318 (method url-fetch)
3319 (uri (bioconductor-uri "GenomicScores" version))
3320 (sha256
3321 (base32
3322 "0lrhkcblvnki6kncwpavs01gbcz22yza6ma8zvfmbrrkfaxqzh8n"))))
3323 (properties `((upstream-name . "GenomicScores")))
3324 (build-system r-build-system)
3325 (propagated-inputs
3326 `(("r-annotationhub" ,r-annotationhub)
3327 ("r-biobase" ,r-biobase)
3328 ("r-biocgenerics" ,r-biocgenerics)
3329 ("r-biostrings" ,r-biostrings)
3330 ("r-bsgenome" ,r-bsgenome)
3331 ("r-genomeinfodb" ,r-genomeinfodb)
3332 ("r-genomicranges" ,r-genomicranges)
3333 ("r-iranges" ,r-iranges)
3334 ("r-s4vectors" ,r-s4vectors)
3335 ("r-xml" ,r-xml)))
3336 (home-page "https://github.com/rcastelo/GenomicScores/")
3337 (synopsis "Work with genome-wide position-specific scores")
3338 (description
3339 "This package provides infrastructure to store and access genome-wide
3340position-specific scores within R and Bioconductor.")
3341 (license license:artistic2.0)))
32e0f906
RW		 3342
3343(define-public r-atacseqqc
3344 (package
3345 (name "r-atacseqqc")
3346 (version "1.6.4")
3347 (source
3348 (origin
3349 (method url-fetch)
3350 (uri (bioconductor-uri "ATACseqQC" version))
3351 (sha256
3352 (base32
3353 "1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn"))))
3354 (properties `((upstream-name . "ATACseqQC")))
3355 (build-system r-build-system)
3356 (propagated-inputs
3357 `(("r-biocgenerics" ,r-biocgenerics)
3358 ("r-biostrings" ,r-biostrings)
3359 ("r-bsgenome" ,r-bsgenome)
3360 ("r-chippeakanno" ,r-chippeakanno)
3361 ("r-genomeinfodb" ,r-genomeinfodb)
3362 ("r-genomicalignments" ,r-genomicalignments)
3363 ("r-genomicranges" ,r-genomicranges)
3364 ("r-genomicscores" ,r-genomicscores)
3365 ("r-iranges" ,r-iranges)
3366 ("r-kernsmooth" ,r-kernsmooth)
3367 ("r-limma" ,r-limma)
3368 ("r-motifstack" ,r-motifstack)
3369 ("r-preseqr" ,r-preseqr)
3370 ("r-randomforest" ,r-randomforest)
3371 ("r-rsamtools" ,r-rsamtools)
3372 ("r-rtracklayer" ,r-rtracklayer)
3373 ("r-s4vectors" ,r-s4vectors)))
3374 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3375 (synopsis "ATAC-seq quality control")
3376 (description
3377 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3378sequencing, is a rapid and sensitive method for chromatin accessibility
3379analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3380and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3381assess whether their ATAC-seq experiment is successful. It includes
3382diagnostic plots of fragment size distribution, proportion of mitochondria
3383reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3384footprints.")
3385 (license license:gpl2+)))
3972cfce
RW		 3386
3387(define-public r-gofuncr
3388 (package
3389 (name "r-gofuncr")
3390 (version "1.2.0")
3391 (source
3392 (origin
3393 (method url-fetch)
3394 (uri (bioconductor-uri "GOfuncR" version))
3395 (sha256
3396 (base32
3397 "021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk"))))
3398 (properties `((upstream-name . "GOfuncR")))
3399 (build-system r-build-system)
3400 (propagated-inputs
3401 `(("r-annotationdbi" ,r-annotationdbi)
3402 ("r-genomicranges" ,r-genomicranges)
3403 ("r-gtools" ,r-gtools)
3404 ("r-iranges" ,r-iranges)
3405 ("r-mapplots" ,r-mapplots)
3406 ("r-rcpp" ,r-rcpp)
3407 ("r-vioplot" ,r-vioplot)))
3408 (home-page "https://bioconductor.org/packages/GOfuncR/")
3409 (synopsis "Gene ontology enrichment using FUNC")
3410 (description
3411 "GOfuncR performs a gene ontology enrichment analysis based on the
3412ontology enrichment software FUNC. GO-annotations are obtained from
3413OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3414included in the package and updated regularly. GOfuncR provides the standard
3415candidate vs background enrichment analysis using the hypergeometric test, as
3416well as three additional tests:
3417
3418@enumerate
3419@item the Wilcoxon rank-sum test that is used when genes are ranked,
3420@item a binomial test that is used when genes are associated with two counts,
3421 and
3422@item a Chi-square or Fisher's exact test that is used in cases when genes are
3423associated with four counts.
3424@end enumerate
3425
3426To correct for multiple testing and interdependency of the tests, family-wise
3427error rates are computed based on random permutations of the gene-associated
3428variables. GOfuncR also provides tools for exploring the ontology graph and
3429the annotations, and options to take gene-length or spatial clustering of
3430genes into account. It is also possible to provide custom gene coordinates,
3431annotations and ontologies.")
3432 (license license:gpl2+)))
jackhill's copy of GNU Guix: https://guix.gnu.org/