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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)
5cfa4bff 33 #:use-module (gnu packages image)
b64ce4b7 34 #:use-module (gnu packages maths)
2cb71d81 35 #:use-module (gnu packages pkg-config)
f4235c0e
RW		 36 #:use-module (gnu packages statistics)
37 #:use-module (gnu packages web))
fa596599 38
557a1089
RW		 39\f
40;;; Annotations
41
b7d93cf5
RW		 42(define-public r-bsgenome-celegans-ucsc-ce6
43 (package
44 (name "r-bsgenome-celegans-ucsc-ce6")
45 (version "1.4.0")
46 (source (origin
47 (method url-fetch)
48 ;; We cannot use bioconductor-uri here because this tarball is
49 ;; located under "data/annotation/" instead of "bioc/".
50 (uri (string-append "https://www.bioconductor.org/packages/"
51 "release/data/annotation/src/contrib/"
52 "BSgenome.Celegans.UCSC.ce6_"
53 version ".tar.gz"))
54 (sha256
55 (base32
56 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
57 (properties
58 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
59 (build-system r-build-system)
60 ;; As this package provides little more than a very large data file it
61 ;; doesn't make sense to build substitutes.
62 (arguments `(#:substitutable? #f))
63 (propagated-inputs
64 `(("r-bsgenome" ,r-bsgenome)))
65 (home-page
66 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
67 (synopsis "Full genome sequences for Worm")
68 (description
69 "This package provides full genome sequences for Caenorhabditis
70elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
0c792ffb
RW		 71objects.")
72 (license license:artistic2.0)))
73
74(define-public r-bsgenome-celegans-ucsc-ce10
75 (package
76 (name "r-bsgenome-celegans-ucsc-ce10")
77 (version "1.4.0")
78 (source (origin
79 (method url-fetch)
80 ;; We cannot use bioconductor-uri here because this tarball is
81 ;; located under "data/annotation/" instead of "bioc/".
82 (uri (string-append "https://www.bioconductor.org/packages/"
83 "release/data/annotation/src/contrib/"
84 "BSgenome.Celegans.UCSC.ce10_"
85 version ".tar.gz"))
86 (sha256
87 (base32
88 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
89 (properties
90 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
91 (build-system r-build-system)
92 ;; As this package provides little more than a very large data file it
93 ;; doesn't make sense to build substitutes.
94 (arguments `(#:substitutable? #f))
95 (propagated-inputs
96 `(("r-bsgenome" ,r-bsgenome)))
97 (home-page
98 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
99 (synopsis "Full genome sequences for Worm")
100 (description
101 "This package provides full genome sequences for Caenorhabditis
102elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
b7d93cf5
RW		 103objects.")
104 (license license:artistic2.0)))
105
183db725
RW		 106(define-public r-bsgenome-dmelanogaster-ucsc-dm6
107 (package
108 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
109 (version "1.4.1")
110 (source (origin
111 (method url-fetch)
112 ;; We cannot use bioconductor-uri here because this tarball is
113 ;; located under "data/annotation/" instead of "bioc/".
114 (uri (string-append "https://www.bioconductor.org/packages/"
115 "release/data/annotation/src/contrib/"
116 "BSgenome.Dmelanogaster.UCSC.dm6_"
117 version ".tar.gz"))
118 (sha256
119 (base32
120 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
121 (properties
122 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
123 (build-system r-build-system)
124 ;; As this package provides little more than a very large data file it
125 ;; doesn't make sense to build substitutes.
126 (arguments `(#:substitutable? #f))
127 (propagated-inputs
128 `(("r-bsgenome" ,r-bsgenome)))
129 (home-page
130 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
131 (synopsis "Full genome sequences for Fly")
132 (description
133 "This package provides full genome sequences for Drosophila
134melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
135objects.")
136 (license license:artistic2.0)))
137
13dabd69
RW		 138(define-public r-bsgenome-dmelanogaster-ucsc-dm3
139 (package
140 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
141 (version "1.4.0")
142 (source (origin
143 (method url-fetch)
144 ;; We cannot use bioconductor-uri here because this tarball is
145 ;; located under "data/annotation/" instead of "bioc/".
146 (uri (string-append "https://www.bioconductor.org/packages/"
147 "release/data/annotation/src/contrib/"
148 "BSgenome.Dmelanogaster.UCSC.dm3_"
149 version ".tar.gz"))
150 (sha256
151 (base32
152 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
153 (properties
154 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
155 (build-system r-build-system)
156 ;; As this package provides little more than a very large data file it
157 ;; doesn't make sense to build substitutes.
158 (arguments `(#:substitutable? #f))
159 (propagated-inputs
160 `(("r-bsgenome" ,r-bsgenome)))
161 (home-page
162 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
163 (synopsis "Full genome sequences for Fly")
164 (description
165 "This package provides full genome sequences for Drosophila
166melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
167Biostrings objects.")
168 (license license:artistic2.0)))
169
dfac7eb9
RW		 170(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
171 (package
172 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
173 (version "1.3.99")
174 (source (origin
175 (method url-fetch)
176 ;; We cannot use bioconductor-uri here because this tarball is
177 ;; located under "data/annotation/" instead of "bioc/".
178 (uri (string-append "http://www.bioconductor.org/packages/"
179 "release/data/annotation/src/contrib/"
180 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
181 version ".tar.gz"))
182 (sha256
183 (base32
184 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
185 (properties
186 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
187 (build-system r-build-system)
188 (propagated-inputs
189 `(("r-bsgenome" ,r-bsgenome)
190 ("r-bsgenome-dmelanogaster-ucsc-dm3"
191 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
192 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
193 (synopsis "Full masked genome sequences for Fly")
194 (description
195 "This package provides full masked genome sequences for Drosophila
196melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
197Biostrings objects. The sequences are the same as in
198BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
199masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
200intra-contig ambiguities (AMB mask), (3) the mask of repeats from
201RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
202Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
203 (license license:artistic2.0)))
204
40a65057
RW		 205(define-public r-bsgenome-hsapiens-1000genomes-hs37d5
206 (package
207 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
208 (version "0.99.1")
209 (source (origin
210 (method url-fetch)
211 ;; We cannot use bioconductor-uri here because this tarball is
212 ;; located under "data/annotation/" instead of "bioc/".
213 (uri (string-append "https://www.bioconductor.org/packages/"
214 "release/data/annotation/src/contrib/"
215 "BSgenome.Hsapiens.1000genomes.hs37d5_"
216 version ".tar.gz"))
217 (sha256
218 (base32
219 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
220 (properties
221 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
222 (build-system r-build-system)
223 ;; As this package provides little more than a very large data file it
224 ;; doesn't make sense to build substitutes.
225 (arguments `(#:substitutable? #f))
226 (propagated-inputs
227 `(("r-bsgenome" ,r-bsgenome)))
228 (home-page
229 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
230 (synopsis "Full genome sequences for Homo sapiens")
231 (description
232 "This package provides full genome sequences for Homo sapiens from
2331000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
234 (license license:artistic2.0)))
235
6fbd759b
RW		 236(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
237 (package
238 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
239 (version "1.3.99")
240 (source (origin
241 (method url-fetch)
242 ;; We cannot use bioconductor-uri here because this tarball is
243 ;; located under "data/annotation/" instead of "bioc/".
244 (uri (string-append "http://www.bioconductor.org/packages/"
245 "release/data/annotation/src/contrib/"
246 "BSgenome.Hsapiens.UCSC.hg19.masked_"
247 version ".tar.gz"))
248 (sha256
249 (base32
250 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
251 (properties
252 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
253 (build-system r-build-system)
254 (propagated-inputs
255 `(("r-bsgenome" ,r-bsgenome)
256 ("r-bsgenome-hsapiens-ucsc-hg19"
257 ,r-bsgenome-hsapiens-ucsc-hg19)))
258 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
259 (synopsis "Full masked genome sequences for Homo sapiens")
260 (description
261 "This package provides full genome sequences for Homo sapiens (Human) as
262provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
263sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
264them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
265mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
266repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
267Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
268default.")
269 (license license:artistic2.0)))
270
5acb9052
RW		 271(define-public r-bsgenome-mmusculus-ucsc-mm9
272 (package
273 (name "r-bsgenome-mmusculus-ucsc-mm9")
274 (version "1.4.0")
275 (source (origin
276 (method url-fetch)
277 ;; We cannot use bioconductor-uri here because this tarball is
278 ;; located under "data/annotation/" instead of "bioc/".
279 (uri (string-append "https://www.bioconductor.org/packages/"
280 "release/data/annotation/src/contrib/"
281 "BSgenome.Mmusculus.UCSC.mm9_"
282 version ".tar.gz"))
283 (sha256
284 (base32
285 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
286 (properties
287 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
288 (build-system r-build-system)
289 ;; As this package provides little more than a very large data file it
290 ;; doesn't make sense to build substitutes.
291 (arguments `(#:substitutable? #f))
292 (propagated-inputs
293 `(("r-bsgenome" ,r-bsgenome)))
294 (home-page
295 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
296 (synopsis "Full genome sequences for Mouse")
297 (description
298 "This package provides full genome sequences for Mus musculus (Mouse) as
299provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
300 (license license:artistic2.0)))
301
2bece692
RW		 302(define-public r-bsgenome-mmusculus-ucsc-mm9-masked
303 (package
304 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
305 (version "1.3.99")
306 (source (origin
307 (method url-fetch)
308 ;; We cannot use bioconductor-uri here because this tarball is
309 ;; located under "data/annotation/" instead of "bioc/".
310 (uri (string-append "http://www.bioconductor.org/packages/"
311 "release/data/annotation/src/contrib/"
312 "BSgenome.Mmusculus.UCSC.mm9.masked_"
313 version ".tar.gz"))
314 (sha256
315 (base32
316 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
317 (properties
318 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
319 (build-system r-build-system)
320 (propagated-inputs
321 `(("r-bsgenome" ,r-bsgenome)
322 ("r-bsgenome-mmusculus-ucsc-mm9"
323 ,r-bsgenome-mmusculus-ucsc-mm9)))
324 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
325 (synopsis "Full masked genome sequences for Mouse")
326 (description
327 "This package provides full genome sequences for Mus musculus (Mouse) as
328provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
329sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
330them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
331mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
332repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
333Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
334default." )
335 (license license:artistic2.0)))
336
c3adc830
RW		 337(define-public r-bsgenome-mmusculus-ucsc-mm10
338 (package
339 (name "r-bsgenome-mmusculus-ucsc-mm10")
340 (version "1.4.0")
341 (source (origin
342 (method url-fetch)
343 ;; We cannot use bioconductor-uri here because this tarball is
344 ;; located under "data/annotation/" instead of "bioc/".
345 (uri (string-append "https://www.bioconductor.org/packages/"
346 "release/data/annotation/src/contrib/"
347 "BSgenome.Mmusculus.UCSC.mm10_"
348 version ".tar.gz"))
349 (sha256
350 (base32
351 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
352 (properties
353 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
354 (build-system r-build-system)
355 ;; As this package provides little more than a very large data file it
356 ;; doesn't make sense to build substitutes.
357 (arguments `(#:substitutable? #f))
358 (propagated-inputs
359 `(("r-bsgenome" ,r-bsgenome)))
360 (home-page
361 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
362 (synopsis "Full genome sequences for Mouse")
363 (description
364 "This package provides full genome sequences for Mus
365musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
366in Biostrings objects.")
367 (license license:artistic2.0)))
368
3a08940e
RW		 369(define-public r-org-ce-eg-db
370 (package
371 (name "r-org-ce-eg-db")
372 (version "3.7.0")
373 (source (origin
374 (method url-fetch)
375 ;; We cannot use bioconductor-uri here because this tarball is
376 ;; located under "data/annotation/" instead of "bioc/".
377 (uri (string-append "https://www.bioconductor.org/packages/"
378 "release/data/annotation/src/contrib/"
379 "org.Ce.eg.db_" version ".tar.gz"))
380 (sha256
381 (base32
382 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
383 (properties
384 `((upstream-name . "org.Ce.eg.db")))
385 (build-system r-build-system)
386 (propagated-inputs
387 `(("r-annotationdbi" ,r-annotationdbi)))
388 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
389 (synopsis "Genome wide annotation for Worm")
390 (description
391 "This package provides mappings from Entrez gene identifiers to various
392annotations for the genome of the model worm Caenorhabditis elegans.")
393 (license license:artistic2.0)))
394
f8780e96
RW		 395(define-public r-org-dm-eg-db
396 (package
397 (name "r-org-dm-eg-db")
398 (version "3.7.0")
399 (source (origin
400 (method url-fetch)
401 ;; We cannot use bioconductor-uri here because this tarball is
402 ;; located under "data/annotation/" instead of "bioc/".
403 (uri (string-append "https://www.bioconductor.org/packages/"
404 "release/data/annotation/src/contrib/"
405 "org.Dm.eg.db_" version ".tar.gz"))
406 (sha256
407 (base32
408 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
409 (properties
410 `((upstream-name . "org.Dm.eg.db")))
411 (build-system r-build-system)
412 (propagated-inputs
413 `(("r-annotationdbi" ,r-annotationdbi)))
414 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
415 (synopsis "Genome wide annotation for Fly")
416 (description
417 "This package provides mappings from Entrez gene identifiers to various
418annotations for the genome of the model fruit fly Drosophila melanogaster.")
419 (license license:artistic2.0)))
420
3dad6087
RW		 421(define-public r-org-dr-eg-db
422 (package
423 (name "r-org-dr-eg-db")
424 (version "3.7.0")
425 (source (origin
426 (method url-fetch)
427 ;; We cannot use bioconductor-uri here because this tarball is
428 ;; located under "data/annotation/" instead of "bioc/".
429 (uri (string-append "https://www.bioconductor.org/packages/"
430 "release/data/annotation/src/contrib/"
431 "org.Dr.eg.db_" version ".tar.gz"))
432 (sha256
433 (base32
434 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
435 (properties
436 `((upstream-name . "org.Dr.eg.db")))
437 (build-system r-build-system)
438 (propagated-inputs
439 `(("r-annotationdbi" ,r-annotationdbi)))
440 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
441 (synopsis "Annotation for Zebrafish")
442 (description
443 "This package provides genome wide annotations for Zebrafish, primarily
444based on mapping using Entrez Gene identifiers.")
445 (license license:artistic2.0)))
446
d56df35a
RW		 447(define-public r-org-hs-eg-db
448 (package
449 (name "r-org-hs-eg-db")
450 (version "3.7.0")
451 (source (origin
452 (method url-fetch)
453 ;; We cannot use bioconductor-uri here because this tarball is
454 ;; located under "data/annotation/" instead of "bioc/".
455 (uri (string-append "https://www.bioconductor.org/packages/"
456 "release/data/annotation/src/contrib/"
457 "org.Hs.eg.db_" version ".tar.gz"))
458 (sha256
459 (base32
460 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
461 (properties
462 `((upstream-name . "org.Hs.eg.db")))
463 (build-system r-build-system)
464 (propagated-inputs
465 `(("r-annotationdbi" ,r-annotationdbi)))
466 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
467 (synopsis "Genome wide annotation for Human")
468 (description
469 "This package contains genome-wide annotations for Human, primarily based
470on mapping using Entrez Gene identifiers.")
471 (license license:artistic2.0)))
472
8035819f
RW		 473(define-public r-org-mm-eg-db
474 (package
475 (name "r-org-mm-eg-db")
476 (version "3.7.0")
477 (source (origin
478 (method url-fetch)
479 ;; We cannot use bioconductor-uri here because this tarball is
480 ;; located under "data/annotation/" instead of "bioc/".
481 (uri (string-append "https://www.bioconductor.org/packages/"
482 "release/data/annotation/src/contrib/"
483 "org.Mm.eg.db_" version ".tar.gz"))
484 (sha256
485 (base32
486 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
487 (properties
488 `((upstream-name . "org.Mm.eg.db")))
489 (build-system r-build-system)
490 (propagated-inputs
491 `(("r-annotationdbi" ,r-annotationdbi)))
492 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
493 (synopsis "Genome wide annotation for Mouse")
494 (description
495 "This package provides mappings from Entrez gene identifiers to various
496annotations for the genome of the model mouse Mus musculus.")
497 (license license:artistic2.0)))
498
fe0b76e2
RW		 499(define-public r-bsgenome-hsapiens-ucsc-hg19
500 (package
501 (name "r-bsgenome-hsapiens-ucsc-hg19")
502 (version "1.4.0")
503 (source (origin
504 (method url-fetch)
505 ;; We cannot use bioconductor-uri here because this tarball is
506 ;; located under "data/annotation/" instead of "bioc/".
507 (uri (string-append "https://www.bioconductor.org/packages/"
508 "release/data/annotation/src/contrib/"
509 "BSgenome.Hsapiens.UCSC.hg19_"
510 version ".tar.gz"))
511 (sha256
512 (base32
513 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
514 (properties
515 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
516 (build-system r-build-system)
517 ;; As this package provides little more than a very large data file it
518 ;; doesn't make sense to build substitutes.
519 (arguments `(#:substitutable? #f))
520 (propagated-inputs
521 `(("r-bsgenome" ,r-bsgenome)))
522 (home-page
523 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
524 (synopsis "Full genome sequences for Homo sapiens")
525 (description
526 "This package provides full genome sequences for Homo sapiens as provided
527by UCSC (hg19, February 2009) and stored in Biostrings objects.")
528 (license license:artistic2.0)))
529
2cc51108
RW		 530(define-public r-genelendatabase
531 (package
532 (name "r-genelendatabase")
daeb3cd9 533 (version "1.18.0")
2cc51108
RW		 534 (source
535 (origin
536 (method url-fetch)
537 ;; We cannot use bioconductor-uri here because this tarball is
538 ;; located under "data/experiment/" instead of "bioc/".
539 (uri (string-append "https://bioconductor.org/packages/"
540 "release/data/experiment/src/contrib"
541 "/geneLenDataBase_" version ".tar.gz"))
542 (sha256
543 (base32
daeb3cd9 544 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
2cc51108
RW		 545 (properties
546 `((upstream-name . "geneLenDataBase")))
547 (build-system r-build-system)
548 (propagated-inputs
549 `(("r-rtracklayer" ,r-rtracklayer)
550 ("r-genomicfeatures" ,r-genomicfeatures)))
551 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
552 (synopsis "Lengths of mRNA transcripts for a number of genomes")
553 (description
554 "This package provides the lengths of mRNA transcripts for a number of
555genomes and gene ID formats, largely based on the UCSC table browser.")
556 (license license:lgpl2.0+)))
557
66e35ce6
RW		 558(define-public r-txdb-hsapiens-ucsc-hg19-knowngene
559 (package
560 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
561 (version "3.2.2")
562 (source (origin
563 (method url-fetch)
564 ;; We cannot use bioconductor-uri here because this tarball is
565 ;; located under "data/annotation/" instead of "bioc/".
566 (uri (string-append "https://bioconductor.org/packages/"
567 "release/data/annotation/src/contrib"
568 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
569 version ".tar.gz"))
570 (sha256
571 (base32
572 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
573 (properties
574 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
575 (build-system r-build-system)
576 ;; As this package provides little more than a very large data file it
577 ;; doesn't make sense to build substitutes.
578 (arguments `(#:substitutable? #f))
579 (propagated-inputs
580 `(("r-genomicfeatures" ,r-genomicfeatures)))
581 (home-page
582 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
583 (synopsis "Annotation package for human genome in TxDb format")
584 (description
585 "This package provides an annotation database of Homo sapiens genome
586data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
587track. The database is exposed as a @code{TxDb} object.")
588 (license license:artistic2.0)))
589
d220babf
RW		 590(define-public r-txdb-mmusculus-ucsc-mm9-knowngene
591 (package
592 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
593 (version "3.2.2")
594 (source (origin
595 (method url-fetch)
596 ;; We cannot use bioconductor-uri here because this tarball is
597 ;; located under "data/annotation/" instead of "bioc/".
598 (uri (string-append "https://bioconductor.org/packages/"
599 "release/data/annotation/src/contrib"
600 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
601 version ".tar.gz"))
602 (sha256
603 (base32
604 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
605 (properties
606 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
607 (build-system r-build-system)
608 (propagated-inputs
609 `(("r-genomicfeatures" ,r-genomicfeatures)
610 ("r-annotationdbi" ,r-annotationdbi)))
611 (home-page
612 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
613 (synopsis "Annotation package for mouse genome in TxDb format")
614 (description
615 "This package provides an annotation database of Mouse genome data. It
616is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
617database is exposed as a @code{TxDb} object.")
618 (license license:artistic2.0)))
619
7bc5d1b0
RW		 620(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
621 (package
622 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
623 (version "3.4.4")
624 (source (origin
625 (method url-fetch)
626 ;; We cannot use bioconductor-uri here because this tarball is
627 ;; located under "data/annotation/" instead of "bioc/".
628 (uri (string-append "https://www.bioconductor.org/packages/"
629 "release/data/annotation/src/contrib/"
630 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
631 version ".tar.gz"))
632 (sha256
633 (base32
634 "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
635 (properties
636 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
637 (build-system r-build-system)
638 ;; As this package provides little more than a very large data file it
639 ;; doesn't make sense to build substitutes.
640 (arguments `(#:substitutable? #f))
641 (propagated-inputs
642 `(("r-bsgenome" ,r-bsgenome)
643 ("r-genomicfeatures" ,r-genomicfeatures)
644 ("r-annotationdbi" ,r-annotationdbi)))
645 (home-page
646 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
647 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
648 (description
649 "This package loads a TxDb object, which is an R interface to
650prefabricated databases contained in this package. This package provides
651the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
652based on the knownGene track.")
653 (license license:artistic2.0)))
654
0f5c9cec
RW		 655(define-public r-fdb-infiniummethylation-hg19
656 (package
657 (name "r-fdb-infiniummethylation-hg19")
658 (version "2.2.0")
659 (source (origin
660 (method url-fetch)
661 ;; We cannot use bioconductor-uri here because this tarball is
662 ;; located under "data/annotation/" instead of "bioc/".
663 (uri (string-append "https://www.bioconductor.org/packages/"
664 "release/data/annotation/src/contrib/"
665 "FDb.InfiniumMethylation.hg19_"
666 version ".tar.gz"))
667 (sha256
668 (base32
669 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
670 (properties
671 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
672 (build-system r-build-system)
673 (propagated-inputs
674 `(("r-biostrings" ,r-biostrings)
675 ("r-genomicfeatures" ,r-genomicfeatures)
676 ("r-annotationdbi" ,r-annotationdbi)
677 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
678 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
679 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
680 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
681 (description
682 "This is an annotation package for Illumina Infinium DNA methylation
683probes. It contains the compiled HumanMethylation27 and HumanMethylation450
684annotations.")
685 (license license:artistic2.0)))
686
9475a248
RW		 687(define-public r-illuminahumanmethylationepicmanifest
688 (package
689 (name "r-illuminahumanmethylationepicmanifest")
690 (version "0.3.0")
691 (source (origin
692 (method url-fetch)
693 ;; We cannot use bioconductor-uri here because this tarball is
694 ;; located under "data/annotation/" instead of "bioc/".
695 (uri (string-append "https://www.bioconductor.org/packages/"
696 "release/data/annotation/src/contrib/"
697 "IlluminaHumanMethylationEPICmanifest_"
698 version ".tar.gz"))
699 (sha256
700 (base32
701 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
702 (properties
703 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
704 (build-system r-build-system)
705 (propagated-inputs
706 `(("r-minfi" ,r-minfi)))
707 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
708 (synopsis "Manifest for Illumina's EPIC methylation arrays")
709 (description
710 "This is a manifest package for Illumina's EPIC methylation arrays.")
711 (license license:artistic2.0)))
712
f8a5af46
RW		 713(define-public r-do-db
714 (package
715 (name "r-do-db")
716 (version "2.9")
717 (source (origin
718 (method url-fetch)
719 ;; We cannot use bioconductor-uri here because this tarball is
720 ;; located under "data/annotation/" instead of "bioc/".
721 (uri (string-append "https://www.bioconductor.org/packages/"
722 "release/data/annotation/src/contrib/"
723 "DO.db_" version ".tar.gz"))
724 (sha256
725 (base32
726 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
727 (properties
728 `((upstream-name . "DO.db")))
729 (build-system r-build-system)
730 (propagated-inputs
731 `(("r-annotationdbi" ,r-annotationdbi)))
732 (home-page "https://www.bioconductor.org/packages/DO.db/")
733 (synopsis "Annotation maps describing the entire Disease Ontology")
734 (description
735 "This package provides a set of annotation maps describing the entire
736Disease Ontology.")
737 (license license:artistic2.0)))
738
2cc51108 739\f
557a1089
RW		 740;;; Experiment data
741
692bce15
RW		 742(define-public r-abadata
743 (package
744 (name "r-abadata")
745 (version "1.12.0")
746 (source (origin
747 (method url-fetch)
748 ;; We cannot use bioconductor-uri here because this tarball is
749 ;; located under "data/experiment/" instead of "bioc/".
750 (uri (string-append "https://www.bioconductor.org/packages/"
751 "release/data/experiment/src/contrib/"
752 "ABAData_" version ".tar.gz"))
753 (sha256
754 (base32
755 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
756 (properties
757 `((upstream-name . "ABAData")))
758 (build-system r-build-system)
759 (propagated-inputs
760 `(("r-annotationdbi" ,r-annotationdbi)))
761 (home-page "https://www.bioconductor.org/packages/ABAData/")
762 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
763 (description
764 "This package provides the data for the gene expression enrichment
765analysis conducted in the package ABAEnrichment. The package includes three
766datasets which are derived from the Allen Brain Atlas:
767
768@enumerate
769@item Gene expression data from Human Brain (adults) averaged across donors,
770@item Gene expression data from the Developing Human Brain pooled into five
771 age categories and averaged across donors, and
772@item a developmental effect score based on the Developing Human Brain
773 expression data.
774@end enumerate
775
776All datasets are restricted to protein coding genes.")
777 (license license:gpl2+)))
778
557a1089
RW		 779(define-public r-hsmmsinglecell
780 (package
781 (name "r-hsmmsinglecell")
782 (version "1.2.0")
783 (source (origin
784 (method url-fetch)
785 ;; We cannot use bioconductor-uri here because this tarball is
786 ;; located under "data/experiment/" instead of "bioc/".
787 (uri (string-append "https://www.bioconductor.org/packages/"
788 "release/data/experiment/src/contrib/"
789 "HSMMSingleCell_" version ".tar.gz"))
790 (sha256
791 (base32
792 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
793 (properties
794 `((upstream-name . "HSMMSingleCell")))
795 (build-system r-build-system)
796 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
797 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
798 (description
799 "Skeletal myoblasts undergo a well-characterized sequence of
800morphological and transcriptional changes during differentiation. In this
801experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
802under high mitogen conditions (GM) and then differentiated by switching to
803low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
804hundred cells taken over a time-course of serum-induced differentiation.
805Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
80672 hours) following serum switch using the Fluidigm C1 microfluidic system.
807RNA from each cell was isolated and used to construct mRNA-Seq libraries,
808which were then sequenced to a depth of ~4 million reads per library,
809resulting in a complete gene expression profile for each cell.")
810 (license license:artistic2.0)))
811
812\f
813;;; Packages
814
14bba460
RW		 815(define-public r-biocgenerics
816 (package
817 (name "r-biocgenerics")
818 (version "0.28.0")
819 (source (origin
820 (method url-fetch)
821 (uri (bioconductor-uri "BiocGenerics" version))
822 (sha256
823 (base32
824 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
825 (properties
826 `((upstream-name . "BiocGenerics")))
827 (build-system r-build-system)
828 (home-page "https://bioconductor.org/packages/BiocGenerics")
829 (synopsis "S4 generic functions for Bioconductor")
830 (description
831 "This package provides S4 generic functions needed by many Bioconductor
832packages.")
833 (license license:artistic2.0)))
834
7097c700
RW		 835(define-public r-annotate
836 (package
837 (name "r-annotate")
877fd189 838 (version "1.60.1")
7097c700
RW		 839 (source
840 (origin
841 (method url-fetch)
842 (uri (bioconductor-uri "annotate" version))
843 (sha256
844 (base32
877fd189 845 "0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"))))
7097c700
RW		 846 (build-system r-build-system)
847 (propagated-inputs
848 `(("r-annotationdbi" ,r-annotationdbi)
849 ("r-biobase" ,r-biobase)
850 ("r-biocgenerics" ,r-biocgenerics)
851 ("r-dbi" ,r-dbi)
852 ("r-rcurl" ,r-rcurl)
853 ("r-xml" ,r-xml)
854 ("r-xtable" ,r-xtable)))
855 (home-page
856 "https://bioconductor.org/packages/annotate")
857 (synopsis "Annotation for microarrays")
858 (description "This package provides R environments for the annotation of
859microarrays.")
860 (license license:artistic2.0)))
861
fa596599
RW		 862(define-public r-hpar
863 (package
864 (name "r-hpar")
61686921 865 (version "1.24.0")
fa596599
RW		 866 (source
867 (origin
868 (method url-fetch)
869 (uri (bioconductor-uri "hpar" version))
870 (sha256
871 (base32
61686921 872 "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
fa596599
RW		 873 (build-system r-build-system)
874 (home-page "https://bioconductor.org/packages/hpar/")
875 (synopsis "Human Protein Atlas in R")
876 (description "This package provides a simple interface to and data from
877the Human Protein Atlas project.")
878 (license license:artistic2.0)))
183ce988
RJ		 879
880(define-public r-regioner
881 (package
882 (name "r-regioner")
d639d888 883 (version "1.14.0")
183ce988
RJ		 884 (source
885 (origin
886 (method url-fetch)
887 (uri (bioconductor-uri "regioneR" version))
888 (sha256
889 (base32
d639d888 890 "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
183ce988
RJ		 891 (properties `((upstream-name . "regioneR")))
892 (build-system r-build-system)
893 (propagated-inputs
d639d888 894 `(("r-biostrings" ,r-biostrings)
183ce988 895 ("r-bsgenome" ,r-bsgenome)
183ce988 896 ("r-genomeinfodb" ,r-genomeinfodb)
d639d888 897 ("r-genomicranges" ,r-genomicranges)
72427c72 898 ("r-iranges" ,r-iranges)
d639d888
RW		 899 ("r-memoise" ,r-memoise)
900 ("r-rtracklayer" ,r-rtracklayer)
72427c72 901 ("r-s4vectors" ,r-s4vectors)))
183ce988
RJ		 902 (home-page "https://bioconductor.org/packages/regioneR/")
903 (synopsis "Association analysis of genomic regions")
904 (description "This package offers a statistical framework based on
905customizable permutation tests to assess the association between genomic
906region sets and other genomic features.")
907 (license license:artistic2.0)))
a5b56a53 908
bfb93b48
RW		 909(define-public r-geneplotter
910 (package
911 (name "r-geneplotter")
912 (version "1.60.0")
913 (source
914 (origin
915 (method url-fetch)
916 (uri (bioconductor-uri "geneplotter" version))
917 (sha256
918 (base32
919 "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
920 (build-system r-build-system)
921 (propagated-inputs
922 `(("r-annotate" ,r-annotate)
923 ("r-annotationdbi" ,r-annotationdbi)
924 ("r-biobase" ,r-biobase)
925 ("r-biocgenerics" ,r-biocgenerics)
926 ("r-lattice" ,r-lattice)
927 ("r-rcolorbrewer" ,r-rcolorbrewer)))
928 (home-page "https://bioconductor.org/packages/geneplotter")
929 (synopsis "Graphics functions for genomic data")
930 (description
931 "This package provides functions for plotting genomic data.")
932 (license license:artistic2.0)))
933
4dc2ecc2
RW		 934(define-public r-qvalue
935 (package
936 (name "r-qvalue")
937 (version "2.14.1")
938 (source
939 (origin
940 (method url-fetch)
941 (uri (bioconductor-uri "qvalue" version))
942 (sha256
943 (base32
944 "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
945 (build-system r-build-system)
946 (propagated-inputs
947 `(("r-ggplot2" ,r-ggplot2)
948 ("r-reshape2" ,r-reshape2)))
949 (home-page "http://github.com/jdstorey/qvalue")
950 (synopsis "Q-value estimation for false discovery rate control")
951 (description
952 "This package takes a list of p-values resulting from the simultaneous
953testing of many hypotheses and estimates their q-values and local @dfn{false
954discovery rate} (FDR) values. The q-value of a test measures the proportion
955of false positives incurred when that particular test is called significant.
956The local FDR measures the posterior probability the null hypothesis is true
957given the test's p-value. Various plots are automatically generated, allowing
958one to make sensible significance cut-offs. The software can be applied to
959problems in genomics, brain imaging, astrophysics, and data mining.")
960 ;; Any version of the LGPL.
961 (license license:lgpl3+)))
962
a5b56a53
RJ		 963(define-public r-diffbind
964 (package
965 (name "r-diffbind")
98652568 966 (version "2.10.0")
a5b56a53
RJ		 967 (source
968 (origin
969 (method url-fetch)
970 (uri (bioconductor-uri "DiffBind" version))
971 (sha256
972 (base32
98652568 973 "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
a5b56a53
RJ		 974 (properties `((upstream-name . "DiffBind")))
975 (build-system r-build-system)
976 (inputs
977 `(("zlib" ,zlib)))
978 (propagated-inputs
979 `(("r-amap" ,r-amap)
980 ("r-biocparallel" ,r-biocparallel)
981 ("r-deseq2" ,r-deseq2)
982 ("r-dplyr" ,r-dplyr)
983 ("r-edger" ,r-edger)
984 ("r-genomicalignments" ,r-genomicalignments)
45bbccf4
RW		 985 ("r-genomicranges" ,r-genomicranges)
986 ("r-ggplot2" ,r-ggplot2)
a5b56a53
RJ		 987 ("r-ggrepel" ,r-ggrepel)
988 ("r-gplots" ,r-gplots)
989 ("r-iranges" ,r-iranges)
990 ("r-lattice" ,r-lattice)
991 ("r-limma" ,r-limma)
992 ("r-locfit" ,r-locfit)
993 ("r-rcolorbrewer" , r-rcolorbrewer)
994 ("r-rcpp" ,r-rcpp)
995 ("r-rsamtools" ,r-rsamtools)
996 ("r-s4vectors" ,r-s4vectors)
45bbccf4 997 ("r-summarizedexperiment" ,r-summarizedexperiment)
a5b56a53
RJ		 998 ("r-systempiper" ,r-systempiper)
999 ("r-zlibbioc" ,r-zlibbioc)))
1000 (home-page "http://bioconductor.org/packages/DiffBind")
1001 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1002 (description
1003 "This package computes differentially bound sites from multiple
1004ChIP-seq experiments using affinity (quantitative) data. Also enables
1005occupancy (overlap) analysis and plotting functions.")
1006 (license license:artistic2.0)))
6d94bf6b
RJ		 1007
1008(define-public r-ripseeker
1009 (package
1010 (name "r-ripseeker")
e9427b2c 1011 (version "1.22.0")
6d94bf6b
RJ		 1012 (source
1013 (origin
1014 (method url-fetch)
1015 (uri (bioconductor-uri "RIPSeeker" version))
1016 (sha256
1017 (base32
e9427b2c 1018 "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
6d94bf6b
RJ		 1019 (properties `((upstream-name . "RIPSeeker")))
1020 (build-system r-build-system)
1021 (propagated-inputs
1022 `(("r-s4vectors" ,r-s4vectors)
1023 ("r-iranges" ,r-iranges)
1024 ("r-genomicranges" ,r-genomicranges)
1025 ("r-summarizedexperiment" ,r-summarizedexperiment)
1026 ("r-rsamtools" ,r-rsamtools)
1027 ("r-genomicalignments" ,r-genomicalignments)
1028 ("r-rtracklayer" ,r-rtracklayer)))
1029 (home-page "http://bioconductor.org/packages/RIPSeeker")
1030 (synopsis
1031 "Identifying protein-associated transcripts from RIP-seq experiments")
1032 (description
1033 "This package infers and discriminates RIP peaks from RIP-seq alignments
1034using two-state HMM with negative binomial emission probability. While
1035RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1036a suite of bioinformatics tools integrated within this self-contained software
1037package comprehensively addressing issues ranging from post-alignments
1038processing to visualization and annotation.")
1039 (license license:gpl2)))
a6ae9ffd
RJ		 1040
1041(define-public r-multtest
1042 (package
1043 (name "r-multtest")
95ee4a46 1044 (version "2.38.0")
a6ae9ffd
RJ		 1045 (source
1046 (origin
1047 (method url-fetch)
1048 (uri (bioconductor-uri "multtest" version))
1049 (sha256
1050 (base32
95ee4a46 1051 "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
a6ae9ffd
RJ		 1052 (build-system r-build-system)
1053 (propagated-inputs
1054 `(("r-survival" ,r-survival)
1055 ("r-biocgenerics" ,r-biocgenerics)
1056 ("r-biobase" ,r-biobase)
1057 ("r-mass" ,r-mass)))
1058 (home-page "http://bioconductor.org/packages/multtest")
1059 (synopsis "Resampling-based multiple hypothesis testing")
1060 (description
1061 "This package can do non-parametric bootstrap and permutation
1062resampling-based multiple testing procedures (including empirical Bayes
1063methods) for controlling the family-wise error rate (FWER), generalized
1064family-wise error rate (gFWER), tail probability of the proportion of
1065false positives (TPPFP), and false discovery rate (FDR). Several choices
1066of bootstrap-based null distribution are implemented (centered, centered
1067and scaled, quantile-transformed). Single-step and step-wise methods are
1068available. Tests based on a variety of T- and F-statistics (including
1069T-statistics based on regression parameters from linear and survival models
1070as well as those based on correlation parameters) are included. When probing
1071hypotheses with T-statistics, users may also select a potentially faster null
1072distribution which is multivariate normal with mean zero and variance
1073covariance matrix derived from the vector influence function. Results are
1074reported in terms of adjusted P-values, confidence regions and test statistic
1075cutoffs. The procedures are directly applicable to identifying differentially
1076expressed genes in DNA microarray experiments.")
1077 (license license:lgpl3)))
793f83ef 1078
5dfe4912
RW		 1079(define-public r-graph
1080 (package
1081 (name "r-graph")
14520b64 1082 (version "1.60.0")
5dfe4912
RW		 1083 (source (origin
1084 (method url-fetch)
1085 (uri (bioconductor-uri "graph" version))
1086 (sha256
1087 (base32
14520b64 1088 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
5dfe4912
RW		 1089 (build-system r-build-system)
1090 (propagated-inputs
1091 `(("r-biocgenerics" ,r-biocgenerics)))
1092 (home-page "https://bioconductor.org/packages/graph")
1093 (synopsis "Handle graph data structures in R")
1094 (description
1095 "This package implements some simple graph handling capabilities for R.")
1096 (license license:artistic2.0)))
1097
a207bca2
RW		 1098(define-public r-codedepends
1099 (package
1100 (name "r-codedepends")
1101 (version "0.6.5")
1102 (source
1103 (origin
1104 (method url-fetch)
1105 (uri (cran-uri "CodeDepends" version))
1106 (sha256
1107 (base32
1108 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1109 (properties `((upstream-name . "CodeDepends")))
1110 (build-system r-build-system)
1111 (propagated-inputs
1112 `(("r-codetools" ,r-codetools)
1113 ("r-graph" ,r-graph)
1114 ("r-xml" ,r-xml)))
1115 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1116 (synopsis "Analysis of R code for reproducible research and code comprehension")
1117 (description
1118 "This package provides tools for analyzing R expressions or blocks of
1119code and determining the dependencies between them. It focuses on R scripts,
1120but can be used on the bodies of functions. There are many facilities
1121including the ability to summarize or get a high-level view of code,
1122determining dependencies between variables, code improvement suggestions.")
1123 ;; Any version of the GPL
1124 (license (list license:gpl2+ license:gpl3+))))
1125
793f83ef
RJ		 1126(define-public r-chippeakanno
1127 (package
1128 (name "r-chippeakanno")
add2b195 1129 (version "3.16.1")
793f83ef
RJ		 1130 (source
1131 (origin
1132 (method url-fetch)
1133 (uri (bioconductor-uri "ChIPpeakAnno" version))
1134 (sha256
1135 (base32
add2b195 1136 "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
793f83ef
RJ		 1137 (properties `((upstream-name . "ChIPpeakAnno")))
1138 (build-system r-build-system)
1139 (propagated-inputs
1140 `(("r-biocgenerics" ,r-biocgenerics)
57d2fcd9 1141 ("r-biocmanager" ,r-biocmanager)
f794e85d
RW		 1142 ("r-biostrings" ,r-biostrings)
1143 ("r-delayedarray" ,r-delayedarray)
793f83ef
RJ		 1144 ("r-go-db" ,r-go-db)
1145 ("r-biomart" ,r-biomart)
1146 ("r-bsgenome" ,r-bsgenome)
1147 ("r-genomicfeatures" ,r-genomicfeatures)
f794e85d 1148 ("r-genomicranges" ,r-genomicranges)
793f83ef 1149 ("r-genomeinfodb" ,r-genomeinfodb)
f794e85d 1150 ("r-iranges" ,r-iranges)
793f83ef
RJ		 1151 ("r-matrixstats" ,r-matrixstats)
1152 ("r-annotationdbi" ,r-annotationdbi)
1153 ("r-limma" ,r-limma)
1154 ("r-multtest" ,r-multtest)
1155 ("r-rbgl" ,r-rbgl)
1156 ("r-graph" ,r-graph)
793f83ef
RJ		 1157 ("r-regioner" ,r-regioner)
1158 ("r-dbi" ,r-dbi)
1159 ("r-ensembldb" ,r-ensembldb)
1160 ("r-biobase" ,r-biobase)
f794e85d 1161 ("r-s4vectors" ,r-s4vectors)
793f83ef
RJ		 1162 ("r-seqinr" ,r-seqinr)
1163 ("r-idr" ,r-idr)
1164 ("r-genomicalignments" ,r-genomicalignments)
1165 ("r-summarizedexperiment" ,r-summarizedexperiment)
1166 ("r-rsamtools" ,r-rsamtools)
1167 ("r-venndiagram" ,r-venndiagram)))
1168 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1169 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1170 (description
1171 "The package includes functions to retrieve the sequences around the peak,
1172obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1173custom features such as most conserved elements and other transcription factor
1174binding sites supplied by users. Starting 2.0.5, new functions have been added
1175for finding the peaks with bi-directional promoters with summary statistics
1176(peaksNearBDP), for summarizing the occurrence of motifs in peaks
1177(summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1178enrichedGO (addGeneIDs).")
1179 (license license:gpl2+)))
164502d8
RJ		 1180
1181(define-public r-marray
1182 (package
1183 (name "r-marray")
f1c606ce 1184 (version "1.60.0")
164502d8
RJ		 1185 (source (origin
1186 (method url-fetch)
1187 (uri (bioconductor-uri "marray" version))
1188 (sha256
f1c606ce 1189 (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
164502d8
RJ		 1190 (build-system r-build-system)
1191 (propagated-inputs
67487088 1192 `(("r-limma" ,r-limma)))
164502d8
RJ		 1193 (home-page "http://bioconductor.org/packages/marray")
1194 (synopsis "Exploratory analysis for two-color spotted microarray data")
1195 (description "This package contains class definitions for two-color spotted
1196microarray data. It also includes fuctions for data input, diagnostic plots,
1197normalization and quality checking.")
1198 (license license:lgpl2.0+)))
0416a0d4
RJ		 1199
1200(define-public r-cghbase
1201 (package
1202 (name "r-cghbase")
46cdceef 1203 (version "1.42.0")
0416a0d4
RJ		 1204 (source (origin
1205 (method url-fetch)
1206 (uri (bioconductor-uri "CGHbase" version))
1207 (sha256
46cdceef 1208 (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
0416a0d4
RJ		 1209 (properties `((upstream-name . "CGHbase")))
1210 (build-system r-build-system)
1211 (propagated-inputs
1212 `(("r-biobase" ,r-biobase)
1213 ("r-marray" ,r-marray)))
1214 (home-page "http://bioconductor.org/packages/CGHbase")
1215 (synopsis "Base functions and classes for arrayCGH data analysis")
1216 (description "This package contains functions and classes that are needed by
1217the @code{arrayCGH} packages.")
1218 (license license:gpl2+)))
67ee83d6
RJ		 1219
1220(define-public r-cghcall
1221 (package
1222 (name "r-cghcall")
9add0933 1223 (version "2.44.0")
67ee83d6
RJ		 1224 (source (origin
1225 (method url-fetch)
1226 (uri (bioconductor-uri "CGHcall" version))
1227 (sha256
9add0933 1228 (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
67ee83d6
RJ		 1229 (properties `((upstream-name . "CGHcall")))
1230 (build-system r-build-system)
1231 (propagated-inputs
1232 `(("r-biobase" ,r-biobase)
1233 ("r-cghbase" ,r-cghbase)
1234 ("r-impute" ,r-impute)
1235 ("r-dnacopy" ,r-dnacopy)
1236 ("r-snowfall" ,r-snowfall)))
1237 (home-page "http://bioconductor.org/packages/CGHcall")
1238 (synopsis "Base functions and classes for arrayCGH data analysis")
1239 (description "This package contains functions and classes that are needed by
1240@code{arrayCGH} packages.")
1241 (license license:gpl2+)))
0ef8cc9c
RJ		 1242
1243(define-public r-qdnaseq
1244 (package
1245 (name "r-qdnaseq")
a92f5230 1246 (version "1.18.0")
0ef8cc9c
RJ		 1247 (source (origin
1248 (method url-fetch)
1249 (uri (bioconductor-uri "QDNAseq" version))
1250 (sha256
a92f5230 1251 (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
0ef8cc9c
RJ		 1252 (properties `((upstream-name . "QDNAseq")))
1253 (build-system r-build-system)
1254 (propagated-inputs
1255 `(("r-biobase" ,r-biobase)
81b0181b 1256 ("r-biocparallel" ,r-biocparallel)
0ef8cc9c
RJ		 1257 ("r-cghbase" ,r-cghbase)
1258 ("r-cghcall" ,r-cghcall)
1259 ("r-dnacopy" ,r-dnacopy)
1260 ("r-genomicranges" ,r-genomicranges)
1261 ("r-iranges" ,r-iranges)
1262 ("r-matrixstats" ,r-matrixstats)
1263 ("r-r-utils" ,r-r-utils)
1264 ("r-rsamtools" ,r-rsamtools)))
1265 (home-page "http://bioconductor.org/packages/QDNAseq")
1266 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1267 (description "The genome is divided into non-overlapping fixed-sized bins,
1268number of sequence reads in each counted, adjusted with a simultaneous
1269two-dimensional loess correction for sequence mappability and GC content, and
1270filtered to remove spurious regions in the genome. Downstream steps of
1271segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1272respectively.")
1273 (license license:gpl2+)))
bb15b581
RW		 1274
1275(define-public r-bayseq
1276 (package
1277 (name "r-bayseq")
4728e275 1278 (version "2.16.0")
bb15b581
RW		 1279 (source
1280 (origin
1281 (method url-fetch)
1282 (uri (bioconductor-uri "baySeq" version))
1283 (sha256
1284 (base32
4728e275 1285 "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
bb15b581
RW		 1286 (properties `((upstream-name . "baySeq")))
1287 (build-system r-build-system)
1288 (propagated-inputs
1289 `(("r-abind" ,r-abind)
1290 ("r-edger" ,r-edger)
1291 ("r-genomicranges" ,r-genomicranges)))
1292 (home-page "https://bioconductor.org/packages/baySeq/")
1293 (synopsis "Bayesian analysis of differential expression patterns in count data")
1294 (description
1295 "This package identifies differential expression in high-throughput count
1296data, such as that derived from next-generation sequencing machines,
1297calculating estimated posterior likelihoods of differential expression (or
1298more complex hypotheses) via empirical Bayesian methods.")
1299 (license license:gpl3)))
609f4ad1
RW		 1300
1301(define-public r-chipcomp
1302 (package
1303 (name "r-chipcomp")
aa802eaf 1304 (version "1.12.0")
609f4ad1
RW		 1305 (source
1306 (origin
1307 (method url-fetch)
1308 (uri (bioconductor-uri "ChIPComp" version))
1309 (sha256
1310 (base32
aa802eaf 1311 "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
609f4ad1
RW		 1312 (properties `((upstream-name . "ChIPComp")))
1313 (build-system r-build-system)
1314 (propagated-inputs
1315 `(("r-biocgenerics" ,r-biocgenerics)
1316 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1317 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1318 ("r-genomeinfodb" ,r-genomeinfodb)
1319 ("r-genomicranges" ,r-genomicranges)
1320 ("r-iranges" ,r-iranges)
1321 ("r-limma" ,r-limma)
1322 ("r-rsamtools" ,r-rsamtools)
1323 ("r-rtracklayer" ,r-rtracklayer)
1324 ("r-s4vectors" ,r-s4vectors)))
1325 (home-page "https://bioconductor.org/packages/ChIPComp")
1326 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1327 (description
1328 "ChIPComp implements a statistical method for quantitative comparison of
1329multiple ChIP-seq datasets. It detects differentially bound sharp binding
1330sites across multiple conditions considering matching control in ChIP-seq
1331datasets.")
1332 ;; Any version of the GPL.
1333 (license license:gpl3+)))
0490f9de
RW		 1334
1335(define-public r-riboprofiling
1336 (package
1337 (name "r-riboprofiling")
e22e462b 1338 (version "1.12.0")
0490f9de
RW		 1339 (source
1340 (origin
1341 (method url-fetch)
1342 (uri (bioconductor-uri "RiboProfiling" version))
1343 (sha256
1344 (base32
e22e462b 1345 "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
0490f9de
RW		 1346 (properties `((upstream-name . "RiboProfiling")))
1347 (build-system r-build-system)
1348 (propagated-inputs
1349 `(("r-biocgenerics" ,r-biocgenerics)
1350 ("r-biostrings" ,r-biostrings)
1351 ("r-data-table" ,r-data-table)
1352 ("r-genomeinfodb" ,r-genomeinfodb)
1353 ("r-genomicalignments" ,r-genomicalignments)
1354 ("r-genomicfeatures" ,r-genomicfeatures)
1355 ("r-genomicranges" ,r-genomicranges)
1356 ("r-ggbio" ,r-ggbio)
1357 ("r-ggplot2" ,r-ggplot2)
1358 ("r-iranges" ,r-iranges)
1359 ("r-plyr" ,r-plyr)
1360 ("r-reshape2" ,r-reshape2)
1361 ("r-rsamtools" ,r-rsamtools)
1362 ("r-rtracklayer" ,r-rtracklayer)
1363 ("r-s4vectors" ,r-s4vectors)
1364 ("r-sqldf" ,r-sqldf)))
1365 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1366 (synopsis "Ribosome profiling data analysis")
1367 (description "Starting with a BAM file, this package provides the
1368necessary functions for quality assessment, read start position recalibration,
1369the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1370of count data: pairs, log fold-change, codon frequency and coverage
1371assessment, principal component analysis on codon coverage.")
1372 (license license:gpl3)))
6ffdfe6a
RW		 1373
1374(define-public r-riboseqr
1375 (package
1376 (name "r-riboseqr")
c4fed658 1377 (version "1.16.0")
6ffdfe6a
RW		 1378 (source
1379 (origin
1380 (method url-fetch)
1381 (uri (bioconductor-uri "riboSeqR" version))
1382 (sha256
1383 (base32
c4fed658 1384 "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
6ffdfe6a
RW		 1385 (properties `((upstream-name . "riboSeqR")))
1386 (build-system r-build-system)
1387 (propagated-inputs
1388 `(("r-abind" ,r-abind)
1389 ("r-bayseq" ,r-bayseq)
1390 ("r-genomeinfodb" ,r-genomeinfodb)
1391 ("r-genomicranges" ,r-genomicranges)
1392 ("r-iranges" ,r-iranges)
1393 ("r-rsamtools" ,r-rsamtools)
1394 ("r-seqlogo" ,r-seqlogo)))
1395 (home-page "https://bioconductor.org/packages/riboSeqR/")
1396 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1397 (description
1398 "This package provides plotting functions, frameshift detection and
1399parsing of genetic sequencing data from ribosome profiling experiments.")
1400 (license license:gpl3)))
a32279ff
RW		 1401
1402(define-public r-interactionset
1403 (package
1404 (name "r-interactionset")
bbc4787c 1405 (version "1.10.0")
a32279ff
RW		 1406 (source
1407 (origin
1408 (method url-fetch)
1409 (uri (bioconductor-uri "InteractionSet" version))
1410 (sha256
1411 (base32
bbc4787c 1412 "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
a32279ff
RW		 1413 (properties
1414 `((upstream-name . "InteractionSet")))
1415 (build-system r-build-system)
1416 (propagated-inputs
1417 `(("r-biocgenerics" ,r-biocgenerics)
1418 ("r-genomeinfodb" ,r-genomeinfodb)
1419 ("r-genomicranges" ,r-genomicranges)
1420 ("r-iranges" ,r-iranges)
1421 ("r-matrix" ,r-matrix)
1422 ("r-rcpp" ,r-rcpp)
1423 ("r-s4vectors" ,r-s4vectors)
1424 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1425 (home-page "https://bioconductor.org/packages/InteractionSet")
1426 (synopsis "Base classes for storing genomic interaction data")
1427 (description
1428 "This packages provides the @code{GInteractions},
1429@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1430for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1431experiments.")
1432 (license license:gpl3)))
cf9a29b2
RW		 1433
1434(define-public r-genomicinteractions
1435 (package
1436 (name "r-genomicinteractions")
5f2d0e63 1437 (version "1.16.0")
cf9a29b2
RW		 1438 (source
1439 (origin
1440 (method url-fetch)
1441 (uri (bioconductor-uri "GenomicInteractions" version))
1442 (sha256
1443 (base32
5f2d0e63 1444 "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
cf9a29b2
RW		 1445 (properties
1446 `((upstream-name . "GenomicInteractions")))
1447 (build-system r-build-system)
1448 (propagated-inputs
1449 `(("r-biobase" ,r-biobase)
1450 ("r-biocgenerics" ,r-biocgenerics)
1451 ("r-data-table" ,r-data-table)
1452 ("r-dplyr" ,r-dplyr)
1453 ("r-genomeinfodb" ,r-genomeinfodb)
1454 ("r-genomicranges" ,r-genomicranges)
1455 ("r-ggplot2" ,r-ggplot2)
1456 ("r-gridextra" ,r-gridextra)
1457 ("r-gviz" ,r-gviz)
1458 ("r-igraph" ,r-igraph)
1459 ("r-interactionset" ,r-interactionset)
1460 ("r-iranges" ,r-iranges)
1461 ("r-rsamtools" ,r-rsamtools)
1462 ("r-rtracklayer" ,r-rtracklayer)
1463 ("r-s4vectors" ,r-s4vectors)
1464 ("r-stringr" ,r-stringr)))
1465 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1466 (synopsis "R package for handling genomic interaction data")
1467 (description
1468 "This R package provides tools for handling genomic interaction data,
1469such as ChIA-PET/Hi-C, annotating genomic features with interaction
1470information and producing various plots and statistics.")
1471 (license license:gpl3)))
27c51606
RW		 1472
1473(define-public r-ctc
1474 (package
1475 (name "r-ctc")
b858338c 1476 (version "1.56.0")
27c51606
RW		 1477 (source
1478 (origin
1479 (method url-fetch)
1480 (uri (bioconductor-uri "ctc" version))
1481 (sha256
1482 (base32
b858338c 1483 "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
27c51606
RW		 1484 (build-system r-build-system)
1485 (propagated-inputs `(("r-amap" ,r-amap)))
1486 (home-page "https://bioconductor.org/packages/ctc/")
1487 (synopsis "Cluster and tree conversion")
1488 (description
1489 "This package provides tools for exporting and importing classification
1490trees and clusters to other programs.")
1491 (license license:gpl2)))
5da0e142
RW		 1492
1493(define-public r-goseq
1494 (package
1495 (name "r-goseq")
7f2b1c4a 1496 (version "1.34.1")
5da0e142
RW		 1497 (source
1498 (origin
1499 (method url-fetch)
1500 (uri (bioconductor-uri "goseq" version))
1501 (sha256
1502 (base32
7f2b1c4a 1503 "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
5da0e142
RW		 1504 (build-system r-build-system)
1505 (propagated-inputs
1506 `(("r-annotationdbi" ,r-annotationdbi)
1507 ("r-biasedurn" ,r-biasedurn)
1508 ("r-biocgenerics" ,r-biocgenerics)
1509 ("r-genelendatabase" ,r-genelendatabase)
1510 ("r-go-db" ,r-go-db)
1511 ("r-mgcv" ,r-mgcv)))
1512 (home-page "https://bioconductor.org/packages/goseq/")
1513 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1514 (description
1515 "This package provides tools to detect Gene Ontology and/or other user
1516defined categories which are over/under represented in RNA-seq data.")
1517 (license license:lgpl2.0+)))
f4235c0e
RW		 1518
1519(define-public r-glimma
1520 (package
1521 (name "r-glimma")
0b469ee2 1522 (version "1.10.1")
f4235c0e
RW		 1523 (source
1524 (origin
1525 (method url-fetch)
1526 (uri (bioconductor-uri "Glimma" version))
1527 (sha256
1528 (base32
0b469ee2 1529 "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
f4235c0e
RW		 1530 (properties `((upstream-name . "Glimma")))
1531 (build-system r-build-system)
1532 (propagated-inputs
1533 `(("r-edger" ,r-edger)
1534 ("r-jsonlite" ,r-jsonlite)
1535 ("r-s4vectors" ,r-s4vectors)))
1536 (home-page "https://github.com/Shians/Glimma")
1537 (synopsis "Interactive HTML graphics")
1538 (description
1539 "This package generates interactive visualisations for analysis of
1540RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1541HTML page. The interactions are built on top of the popular static
1542representations of analysis results in order to provide additional
1543information.")
1544 (license license:lgpl3)))
aa388dc7
RW		 1545
1546(define-public r-rots
1547 (package
1548 (name "r-rots")
45dcd7dc 1549 (version "1.10.1")
aa388dc7
RW		 1550 (source
1551 (origin
1552 (method url-fetch)
1553 (uri (bioconductor-uri "ROTS" version))
1554 (sha256
1555 (base32
45dcd7dc 1556 "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
aa388dc7
RW		 1557 (properties `((upstream-name . "ROTS")))
1558 (build-system r-build-system)
1559 (propagated-inputs
1560 `(("r-biobase" ,r-biobase)
1561 ("r-rcpp" ,r-rcpp)))
1562 (home-page "https://bioconductor.org/packages/ROTS/")
1563 (synopsis "Reproducibility-Optimized Test Statistic")
1564 (description
1565 "This package provides tools for calculating the
1566@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1567in omics data.")
1568 (license license:gpl2+)))
b64ce4b7 1569
cad6fb2d
RW		 1570(define-public r-plgem
1571 (package
1572 (name "r-plgem")
1573 (version "1.54.1")
1574 (source
1575 (origin
1576 (method url-fetch)
1577 (uri (bioconductor-uri "plgem" version))
1578 (sha256
1579 (base32
1580 "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
1581 (build-system r-build-system)
1582 (propagated-inputs
1583 `(("r-biobase" ,r-biobase)
1584 ("r-mass" ,r-mass)))
1585 (home-page "http://www.genopolis.it")
1586 (synopsis "Detect differential expression in microarray and proteomics datasets")
1587 (description
1588 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1589model the variance-versus-mean dependence that exists in a variety of
1590genome-wide datasets, including microarray and proteomics data. The use of
1591PLGEM has been shown to improve the detection of differentially expressed
1592genes or proteins in these datasets.")
1593 (license license:gpl2)))
1594
b64ce4b7
RW		 1595(define-public r-inspect
1596 (package
1597 (name "r-inspect")
c86fc969 1598 (version "1.12.1")
b64ce4b7
RW		 1599 (source
1600 (origin
1601 (method url-fetch)
1602 (uri (bioconductor-uri "INSPEcT" version))
1603 (sha256
1604 (base32
c86fc969 1605 "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
b64ce4b7
RW		 1606 (properties `((upstream-name . "INSPEcT")))
1607 (build-system r-build-system)
1608 (propagated-inputs
1609 `(("r-biobase" ,r-biobase)
1610 ("r-biocgenerics" ,r-biocgenerics)
1611 ("r-biocparallel" ,r-biocparallel)
c86fc969 1612 ("r-deseq2" ,r-deseq2)
b64ce4b7
RW		 1613 ("r-desolve" ,r-desolve)
1614 ("r-genomicalignments" ,r-genomicalignments)
1615 ("r-genomicfeatures" ,r-genomicfeatures)
1616 ("r-genomicranges" ,r-genomicranges)
1617 ("r-iranges" ,r-iranges)
c86fc969 1618 ("r-plgem" ,r-plgem)
b64ce4b7
RW		 1619 ("r-preprocesscore" ,r-preprocesscore)
1620 ("r-proc" ,r-proc)
1621 ("r-rootsolve" ,r-rootsolve)
1622 ("r-rsamtools" ,r-rsamtools)
c86fc969
RW		 1623 ("r-s4vectors" ,r-s4vectors)
1624 ("r-shiny" ,r-shiny)
1625 ("r-summarizedexperiment" ,r-summarizedexperiment)
1626 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1627 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
b64ce4b7
RW		 1628 (home-page "https://bioconductor.org/packages/INSPEcT")
1629 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1630 (description
1631 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1632Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1633order to evaluate synthesis, processing and degradation rates and assess via
1634modeling the rates that determines changes in mature mRNA levels.")
1635 (license license:gpl2)))
f6e99763
RW		 1636
1637(define-public r-dnabarcodes
1638 (package
1639 (name "r-dnabarcodes")
318bcbc4 1640 (version "1.12.0")
f6e99763
RW		 1641 (source
1642 (origin
1643 (method url-fetch)
1644 (uri (bioconductor-uri "DNABarcodes" version))
1645 (sha256
1646 (base32
318bcbc4 1647 "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
f6e99763
RW		 1648 (properties `((upstream-name . "DNABarcodes")))
1649 (build-system r-build-system)
1650 (propagated-inputs
1651 `(("r-bh" ,r-bh)
1652 ("r-matrix" ,r-matrix)
1653 ("r-rcpp" ,r-rcpp)))
1654 (home-page "https://bioconductor.org/packages/DNABarcodes")
1655 (synopsis "Create and analyze DNA barcodes")
1656 (description
1657 "This package offers tools to create DNA barcode sets capable of
1658correcting insertion, deletion, and substitution errors. Existing barcodes
1659can be analyzed regarding their minimal, maximal and average distances between
1660barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1661demultiplexed, i.e. assigned to their original reference barcode.")
1662 (license license:gpl2)))
09aa3d06
RW		 1663
1664(define-public r-ruvseq
1665 (package
1666 (name "r-ruvseq")
c6e9b494 1667 (version "1.16.1")
09aa3d06
RW		 1668 (source
1669 (origin
1670 (method url-fetch)
1671 (uri (bioconductor-uri "RUVSeq" version))
1672 (sha256
1673 (base32
c6e9b494 1674 "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
09aa3d06
RW		 1675 (properties `((upstream-name . "RUVSeq")))
1676 (build-system r-build-system)
1677 (propagated-inputs
1678 `(("r-biobase" ,r-biobase)
1679 ("r-edaseq" ,r-edaseq)
1680 ("r-edger" ,r-edger)
1681 ("r-mass" ,r-mass)))
1682 (home-page "https://github.com/drisso/RUVSeq")
1683 (synopsis "Remove unwanted variation from RNA-Seq data")
1684 (description
1685 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1686of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1687samples.")
1688 (license license:artistic2.0)))
286157dc
RW		 1689
1690(define-public r-biocneighbors
1691 (package
1692 (name "r-biocneighbors")
1693 (version "1.0.0")
1694 (source
1695 (origin
1696 (method url-fetch)
1697 (uri (bioconductor-uri "BiocNeighbors" version))
1698 (sha256
1699 (base32
1700 "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
1701 (properties `((upstream-name . "BiocNeighbors")))
1702 (build-system r-build-system)
1703 (propagated-inputs
1704 `(("r-biocparallel" ,r-biocparallel)
1705 ("r-rcpp" ,r-rcpp)
1706 ("r-rcppannoy" ,r-rcppannoy)
1707 ("r-s4vectors" ,r-s4vectors)))
1708 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1709 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1710 (description
1711 "This package implements exact and approximate methods for nearest
1712neighbor detection, in a framework that allows them to be easily switched
1713within Bioconductor packages or workflows. The exact algorithm is implemented
1714using pre-clustering with the k-means algorithm. Functions are also provided
1715to search for all neighbors within a given distance. Parallelization is
1716achieved for all methods using the BiocParallel framework.")
1717 (license license:gpl3)))
8a587c89 1718
a961ae46
RW		 1719(define-public r-destiny
1720 (package
1721 (name "r-destiny")
1722 (version "2.12.0")
1723 (source
1724 (origin
1725 (method url-fetch)
1726 (uri (bioconductor-uri "destiny" version))
1727 (sha256
1728 (base32
1729 "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
1730 (build-system r-build-system)
1731 (propagated-inputs
1732 `(("r-biobase" ,r-biobase)
1733 ("r-biocgenerics" ,r-biocgenerics)
1734 ("r-fnn" ,r-fnn)
1735 ("r-ggthemes" ,r-ggthemes)
1736 ("r-hmisc" ,r-hmisc)
1737 ("r-igraph" ,r-igraph)
1738 ("r-matrix" ,r-matrix)
1739 ("r-proxy" ,r-proxy)
1740 ("r-rcpp" ,r-rcpp)
1741 ("r-rcppeigen" ,r-rcppeigen)
1742 ("r-scales" ,r-scales)
1743 ("r-scatterplot3d" ,r-scatterplot3d)
1744 ("r-smoother" ,r-smoother)
1745 ("r-summarizedexperiment" ,r-summarizedexperiment)
1746 ("r-vim" ,r-vim)))
1747 (home-page "https://bioconductor.org/packages/destiny/")
1748 (synopsis "Create and plot diffusion maps")
1749 (description "This package provides tools to create and plot diffusion
1750maps.")
1751 ;; Any version of the GPL
1752 (license license:gpl3+)))
1753
8a587c89
RW		 1754(define-public r-savr
1755 (package
1756 (name "r-savr")
1757 (version "1.20.0")
1758 (source
1759 (origin
1760 (method url-fetch)
1761 (uri (bioconductor-uri "savR" version))
1762 (sha256
1763 (base32
1764 "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
1765 (properties `((upstream-name . "savR")))
1766 (build-system r-build-system)
1767 (propagated-inputs
1768 `(("r-ggplot2" ,r-ggplot2)
1769 ("r-gridextra" ,r-gridextra)
1770 ("r-reshape2" ,r-reshape2)
1771 ("r-scales" ,r-scales)
1772 ("r-xml" ,r-xml)))
1773 (home-page "https://github.com/bcalder/savR")
1774 (synopsis "Parse and analyze Illumina SAV files")
1775 (description
1776 "This package provides tools to parse Illumina Sequence Analysis
1777Viewer (SAV) files, access data, and generate QC plots.")
1778 (license license:agpl3+)))
41ffc214
RW		 1779
1780(define-public r-chipexoqual
1781 (package
1782 (name "r-chipexoqual")
1783 (version "1.6.0")
1784 (source
1785 (origin
1786 (method url-fetch)
1787 (uri (bioconductor-uri "ChIPexoQual" version))
1788 (sha256
1789 (base32
1790 "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
1791 (properties `((upstream-name . "ChIPexoQual")))
1792 (build-system r-build-system)
1793 (propagated-inputs
1794 `(("r-biocparallel" ,r-biocparallel)
1795 ("r-biovizbase" ,r-biovizbase)
1796 ("r-broom" ,r-broom)
1797 ("r-data-table" ,r-data-table)
1798 ("r-dplyr" ,r-dplyr)
1799 ("r-genomeinfodb" ,r-genomeinfodb)
1800 ("r-genomicalignments" ,r-genomicalignments)
1801 ("r-genomicranges" ,r-genomicranges)
1802 ("r-ggplot2" ,r-ggplot2)
1803 ("r-hexbin" ,r-hexbin)
1804 ("r-iranges" ,r-iranges)
1805 ("r-rcolorbrewer" ,r-rcolorbrewer)
1806 ("r-rmarkdown" ,r-rmarkdown)
1807 ("r-rsamtools" ,r-rsamtools)
1808 ("r-s4vectors" ,r-s4vectors)
1809 ("r-scales" ,r-scales)
1810 ("r-viridis" ,r-viridis)))
1811 (home-page "https://github.com/keleslab/ChIPexoQual")
1812 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1813 (description
1814 "This package provides a quality control pipeline for ChIP-exo/nexus
1815sequencing data.")
1816 (license license:gpl2+)))
c18dccff 1817
3d13b448
RW		 1818(define-public r-copynumber
1819 (package
1820 (name "r-copynumber")
1821 (version "1.22.0")
1822 (source (origin
1823 (method url-fetch)
1824 (uri (bioconductor-uri "copynumber" version))
1825 (sha256
1826 (base32
1827 "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
1828 (build-system r-build-system)
1829 (propagated-inputs
1830 `(("r-s4vectors" ,r-s4vectors)
1831 ("r-iranges" ,r-iranges)
1832 ("r-genomicranges" ,r-genomicranges)
1833 ("r-biocgenerics" ,r-biocgenerics)))
1834 (home-page "https://bioconductor.org/packages/copynumber")
1835 (synopsis "Segmentation of single- and multi-track copy number data")
1836 (description
1837 "This package segments single- and multi-track copy number data by a
1838penalized least squares regression method.")
1839 (license license:artistic2.0)))
1840
c18dccff
RW		 1841(define-public r-dnacopy
1842 (package
1843 (name "r-dnacopy")
1844 (version "1.56.0")
1845 (source
1846 (origin
1847 (method url-fetch)
1848 (uri (bioconductor-uri "DNAcopy" version))
1849 (sha256
1850 (base32
1851 "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
1852 (properties `((upstream-name . "DNAcopy")))
1853 (build-system r-build-system)
1854 (native-inputs `(("gfortran" ,gfortran)))
1855 (home-page "https://bioconductor.org/packages/DNAcopy")
1856 (synopsis "DNA copy number data analysis")
1857 (description
1858 "This package implements the @dfn{circular binary segmentation} (CBS)
1859algorithm to segment DNA copy number data and identify genomic regions with
1860abnormal copy number.")
1861 (license license:gpl2+)))
3a0babac
RW		 1862
1863;; This is a CRAN package, but it uncharacteristically depends on a
1864;; Bioconductor package.
1865(define-public r-htscluster
1866 (package
1867 (name "r-htscluster")
1868 (version "2.0.8")
1869 (source
1870 (origin
1871 (method url-fetch)
1872 (uri (cran-uri "HTSCluster" version))
1873 (sha256
1874 (base32
1875 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1876 (properties `((upstream-name . "HTSCluster")))
1877 (build-system r-build-system)
1878 (propagated-inputs
1879 `(("r-capushe" ,r-capushe)
1880 ("r-edger" ,r-edger)
1881 ("r-plotrix" ,r-plotrix)))
1882 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1883 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1884 (description
1885 "This package provides a Poisson mixture model is implemented to cluster
1886genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
1887estimation is performed using either the EM or CEM algorithm, and the slope
1888heuristics are used for model selection (i.e., to choose the number of
1889clusters).")
1890 (license license:gpl3+)))
173c9960
RW		 1891
1892(define-public r-deds
1893 (package
1894 (name "r-deds")
1895 (version "1.56.0")
1896 (source
1897 (origin
1898 (method url-fetch)
1899 (uri (bioconductor-uri "DEDS" version))
1900 (sha256
1901 (base32
1902 "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
1903 (properties `((upstream-name . "DEDS")))
1904 (build-system r-build-system)
1905 (home-page "https://bioconductor.org/packages/DEDS/")
1906 (synopsis "Differential expression via distance summary for microarray data")
1907 (description
1908 "This library contains functions that calculate various statistics of
1909differential expression for microarray data, including t statistics, fold
1910change, F statistics, SAM, moderated t and F statistics and B statistics. It
1911also implements a new methodology called DEDS (Differential Expression via
1912Distance Summary), which selects differentially expressed genes by integrating
1913and summarizing a set of statistics using a weighted distance approach.")
1914 ;; Any version of the LGPL.
1915 (license license:lgpl3+)))
7ed869f7
RW		 1916
1917;; This is a CRAN package, but since it depends on a Bioconductor package we
1918;; put it here.
1919(define-public r-nbpseq
1920 (package
1921 (name "r-nbpseq")
1922 (version "0.3.0")
1923 (source
1924 (origin
1925 (method url-fetch)
1926 (uri (cran-uri "NBPSeq" version))
1927 (sha256
1928 (base32
1929 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
1930 (properties `((upstream-name . "NBPSeq")))
1931 (build-system r-build-system)
1932 (propagated-inputs
1933 `(("r-qvalue" ,r-qvalue)))
1934 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
1935 (synopsis "Negative binomial models for RNA-Seq data")
1936 (description
1937 "This package provides negative binomial models for two-group comparisons
1938and regression inferences from RNA-sequencing data.")
1939 (license license:gpl2)))
3087a2f3
RW		 1940
1941(define-public r-ebseq
1942 (package
1943 (name "r-ebseq")
1944 (version "1.22.1")
1945 (source
1946 (origin
1947 (method url-fetch)
1948 (uri (bioconductor-uri "EBSeq" version))
1949 (sha256
1950 (base32
1951 "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
1952 (properties `((upstream-name . "EBSeq")))
1953 (build-system r-build-system)
1954 (propagated-inputs
1955 `(("r-blockmodeling" ,r-blockmodeling)
1956 ("r-gplots" ,r-gplots)
1957 ("r-testthat" ,r-testthat)))
1958 (home-page "https://bioconductor.org/packages/EBSeq")
1959 (synopsis "Differential expression analysis of RNA-seq data")
1960 (description
1961 "This package provides tools for differential expression analysis at both
1962gene and isoform level using RNA-seq data")
1963 (license license:artistic2.0)))
2cb71d81
RW		 1964
1965(define-public r-lpsymphony
1966 (package
1967 (name "r-lpsymphony")
1968 (version "1.10.0")
1969 (source
1970 (origin
1971 (method url-fetch)
1972 (uri (bioconductor-uri "lpsymphony" version))
1973 (sha256
1974 (base32
1975 "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
1976 (build-system r-build-system)
1977 (inputs
1978 `(("gfortran" ,gfortran)
1979 ("zlib" ,zlib)))
1980 (native-inputs
1981 `(("pkg-config" ,pkg-config)))
1982 (home-page "http://r-forge.r-project.org/projects/rsymphony")
1983 (synopsis "Symphony integer linear programming solver in R")
1984 (description
1985 "This package was derived from Rsymphony. The package provides an R
1986interface to SYMPHONY, a linear programming solver written in C++. The main
1987difference between this package and Rsymphony is that it includes the solver
1988source code, while Rsymphony expects to find header and library files on the
1989users' system. Thus the intention of @code{lpsymphony} is to provide an easy
1990to install interface to SYMPHONY.")
1991 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
1992 ;; lpsimphony is released under the same terms.
1993 (license license:epl1.0)))
704de8f5
RW		 1994
1995(define-public r-ihw
1996 (package
1997 (name "r-ihw")
1998 (version "1.10.1")
1999 (source
2000 (origin
2001 (method url-fetch)
2002 (uri (bioconductor-uri "IHW" version))
2003 (sha256
2004 (base32
2005 "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
2006 (properties `((upstream-name . "IHW")))
2007 (build-system r-build-system)
2008 (propagated-inputs
2009 `(("r-biocgenerics" ,r-biocgenerics)
2010 ("r-fdrtool" ,r-fdrtool)
2011 ("r-lpsymphony" ,r-lpsymphony)
2012 ("r-slam" ,r-slam)))
2013 (home-page "https://bioconductor.org/packages/IHW")
2014 (synopsis "Independent hypothesis weighting")
2015 (description
2016 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2017procedure that increases power compared to the method of Benjamini and
2018Hochberg by assigning data-driven weights to each hypothesis. The input to
2019IHW is a two-column table of p-values and covariates. The covariate can be
2020any continuous-valued or categorical variable that is thought to be
2021informative on the statistical properties of each hypothesis test, while it is
2022independent of the p-value under the null hypothesis.")
2023 (license license:artistic2.0)))
251e0830
RW		 2024
2025(define-public r-icobra
2026 (package
2027 (name "r-icobra")
2028 (version "1.10.0")
2029 (source
2030 (origin
2031 (method url-fetch)
2032 (uri (bioconductor-uri "iCOBRA" version))
2033 (sha256
2034 (base32
2035 "0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"))))
2036 (properties `((upstream-name . "iCOBRA")))
2037 (build-system r-build-system)
2038 (propagated-inputs
2039 `(("r-dplyr" ,r-dplyr)
2040 ("r-dt" ,r-dt)
2041 ("r-ggplot2" ,r-ggplot2)
2042 ("r-limma" ,r-limma)
2043 ("r-reshape2" ,r-reshape2)
2044 ("r-rocr" ,r-rocr)
2045 ("r-scales" ,r-scales)
2046 ("r-shiny" ,r-shiny)
2047 ("r-shinybs" ,r-shinybs)
2048 ("r-shinydashboard" ,r-shinydashboard)
2049 ("r-upsetr" ,r-upsetr)))
2050 (home-page "https://bioconductor.org/packages/iCOBRA")
2051 (synopsis "Comparison and visualization of ranking and assignment methods")
2052 (description
2053 "This package provides functions for calculation and visualization of
2054performance metrics for evaluation of ranking and binary
2055classification (assignment) methods. It also contains a Shiny application for
2056interactive exploration of results.")
2057 (license license:gpl2+)))
925fcdbb
RW		 2058
2059(define-public r-mast
2060 (package
2061 (name "r-mast")
2062 (version "1.8.2")
2063 (source
2064 (origin
2065 (method url-fetch)
2066 (uri (bioconductor-uri "MAST" version))
2067 (sha256
2068 (base32
2069 "0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"))))
2070 (properties `((upstream-name . "MAST")))
2071 (build-system r-build-system)
2072 (propagated-inputs
2073 `(("r-abind" ,r-abind)
2074 ("r-biobase" ,r-biobase)
2075 ("r-biocgenerics" ,r-biocgenerics)
2076 ("r-data-table" ,r-data-table)
2077 ("r-ggplot2" ,r-ggplot2)
2078 ("r-plyr" ,r-plyr)
2079 ("r-progress" ,r-progress)
2080 ("r-reshape2" ,r-reshape2)
2081 ("r-s4vectors" ,r-s4vectors)
2082 ("r-singlecellexperiment" ,r-singlecellexperiment)
2083 ("r-stringr" ,r-stringr)
2084 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2085 (home-page "https://github.com/RGLab/MAST/")
2086 (synopsis "Model-based analysis of single cell transcriptomics")
2087 (description
2088 "This package provides methods and models for handling zero-inflated
2089single cell assay data.")
2090 (license license:gpl2+)))
2d7627cf
RW		 2091
2092(define-public r-monocle
2093 (package
2094 (name "r-monocle")
2095 (version "2.10.1")
2096 (source
2097 (origin
2098 (method url-fetch)
2099 (uri (bioconductor-uri "monocle" version))
2100 (sha256
2101 (base32
2102 "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
2103 (build-system r-build-system)
2104 (propagated-inputs
2105 `(("r-biobase" ,r-biobase)
2106 ("r-biocgenerics" ,r-biocgenerics)
2107 ("r-biocviews" ,r-biocviews)
2108 ("r-cluster" ,r-cluster)
2109 ("r-combinat" ,r-combinat)
2110 ("r-ddrtree" ,r-ddrtree)
2111 ("r-densityclust" ,r-densityclust)
2112 ("r-dplyr" ,r-dplyr)
2113 ("r-fastica" ,r-fastica)
2114 ("r-ggplot2" ,r-ggplot2)
2115 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2116 ("r-igraph" ,r-igraph)
2117 ("r-irlba" ,r-irlba)
2118 ("r-limma" ,r-limma)
2119 ("r-mass" ,r-mass)
2120 ("r-matrix" ,r-matrix)
2121 ("r-matrixstats" ,r-matrixstats)
2122 ("r-pheatmap" ,r-pheatmap)
2123 ("r-plyr" ,r-plyr)
2124 ("r-proxy" ,r-proxy)
2125 ("r-qlcmatrix" ,r-qlcmatrix)
2126 ("r-rann" ,r-rann)
2127 ("r-rcpp" ,r-rcpp)
2128 ("r-reshape2" ,r-reshape2)
2129 ("r-rtsne" ,r-rtsne)
2130 ("r-slam" ,r-slam)
2131 ("r-stringr" ,r-stringr)
2132 ("r-tibble" ,r-tibble)
2133 ("r-vgam" ,r-vgam)
2134 ("r-viridis" ,r-viridis)))
2135 (home-page "https://bioconductor.org/packages/monocle")
2136 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2137 (description
2138 "Monocle performs differential expression and time-series analysis for
2139single-cell expression experiments. It orders individual cells according to
2140progress through a biological process, without knowing ahead of time which
2141genes define progress through that process. Monocle also performs
2142differential expression analysis, clustering, visualization, and other useful
2143tasks on single cell expression data. It is designed to work with RNA-Seq and
2144qPCR data, but could be used with other types as well.")
2145 (license license:artistic2.0)))
6213e441
RW		 2146
2147(define-public r-noiseq
2148 (package
2149 (name "r-noiseq")
2150 (version "2.26.1")
2151 (source
2152 (origin
2153 (method url-fetch)
2154 (uri (bioconductor-uri "NOISeq" version))
2155 (sha256
2156 (base32
2157 "1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"))))
2158 (properties `((upstream-name . "NOISeq")))
2159 (build-system r-build-system)
2160 (propagated-inputs
2161 `(("r-biobase" ,r-biobase)
2162 ("r-matrix" ,r-matrix)))
2163 (home-page "https://bioconductor.org/packages/NOISeq")
2164 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2165 (description
2166 "This package provides tools to support the analysis of RNA-seq
2167expression data or other similar kind of data. It provides exploratory plots
2168to evaluate saturation, count distribution, expression per chromosome, type of
2169detected features, features length, etc. It also supports the analysis of
2170differential expression between two experimental conditions with no parametric
2171assumptions.")
2172 (license license:artistic2.0)))
b409c357
RW		 2173
2174(define-public r-scdd
2175 (package
2176 (name "r-scdd")
2177 (version "1.6.1")
2178 (source
2179 (origin
2180 (method url-fetch)
2181 (uri (bioconductor-uri "scDD" version))
2182 (sha256
2183 (base32
2184 "0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"))))
2185 (properties `((upstream-name . "scDD")))
2186 (build-system r-build-system)
2187 (propagated-inputs
2188 `(("r-arm" ,r-arm)
2189 ("r-biocparallel" ,r-biocparallel)
2190 ("r-ebseq" ,r-ebseq)
2191 ("r-fields" ,r-fields)
2192 ("r-ggplot2" ,r-ggplot2)
2193 ("r-mclust" ,r-mclust)
2194 ("r-outliers" ,r-outliers)
2195 ("r-s4vectors" ,r-s4vectors)
2196 ("r-scran" ,r-scran)
2197 ("r-singlecellexperiment" ,r-singlecellexperiment)
2198 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2199 (home-page "https://github.com/kdkorthauer/scDD")
2200 (synopsis "Mixture modeling of single-cell RNA-seq data")
2201 (description
2202 "This package implements a method to analyze single-cell RNA-seq data
2203utilizing flexible Dirichlet Process mixture models. Genes with differential
2204distributions of expression are classified into several interesting patterns
2205of differences between two conditions. The package also includes functions
2206for simulating data with these patterns from negative binomial
2207distributions.")
2208 (license license:gpl2)))
f0887757
RW		 2209
2210(define-public r-scone
2211 (package
2212 (name "r-scone")
2213 (version "1.6.1")
2214 (source
2215 (origin
2216 (method url-fetch)
2217 (uri (bioconductor-uri "scone" version))
2218 (sha256
2219 (base32
2220 "0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"))))
2221 (build-system r-build-system)
2222 (propagated-inputs
2223 `(("r-aroma-light" ,r-aroma-light)
2224 ("r-biocparallel" ,r-biocparallel)
2225 ("r-boot" ,r-boot)
2226 ("r-class" ,r-class)
2227 ("r-cluster" ,r-cluster)
2228 ("r-compositions" ,r-compositions)
2229 ("r-diptest" ,r-diptest)
2230 ("r-edger" ,r-edger)
2231 ("r-fpc" ,r-fpc)
2232 ("r-gplots" ,r-gplots)
2233 ("r-hexbin" ,r-hexbin)
2234 ("r-limma" ,r-limma)
2235 ("r-matrixstats" ,r-matrixstats)
2236 ("r-mixtools" ,r-mixtools)
2237 ("r-rarpack" ,r-rarpack)
2238 ("r-rcolorbrewer" ,r-rcolorbrewer)
2239 ("r-rhdf5" ,r-rhdf5)
2240 ("r-ruvseq" ,r-ruvseq)
2241 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2242 (home-page "https://bioconductor.org/packages/scone")
2243 (synopsis "Single cell overview of normalized expression data")
2244 (description
2245 "SCONE is an R package for comparing and ranking the performance of
2246different normalization schemes for single-cell RNA-seq and other
2247high-throughput analyses.")
2248 (license license:artistic2.0)))
f9201d67
RW		 2249
2250(define-public r-geoquery
2251 (package
2252 (name "r-geoquery")
2253 (version "2.50.5")
2254 (source
2255 (origin
2256 (method url-fetch)
2257 (uri (bioconductor-uri "GEOquery" version))
2258 (sha256
2259 (base32
2260 "074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"))))
2261 (properties `((upstream-name . "GEOquery")))
2262 (build-system r-build-system)
2263 (propagated-inputs
2264 `(("r-biobase" ,r-biobase)
2265 ("r-dplyr" ,r-dplyr)
2266 ("r-httr" ,r-httr)
2267 ("r-limma" ,r-limma)
2268 ("r-magrittr" ,r-magrittr)
2269 ("r-readr" ,r-readr)
2270 ("r-tidyr" ,r-tidyr)
2271 ("r-xml2" ,r-xml2)))
2272 (home-page "https://github.com/seandavi/GEOquery/")
2273 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2274 (description
2275 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2276microarray data. Given the rich and varied nature of this resource, it is
2277only natural to want to apply BioConductor tools to these data. GEOquery is
2278the bridge between GEO and BioConductor.")
2279 (license license:gpl2)))
eed6ff03
RW		 2280
2281(define-public r-illuminaio
2282 (package
2283 (name "r-illuminaio")
2284 (version "0.24.0")
2285 (source
2286 (origin
2287 (method url-fetch)
2288 (uri (bioconductor-uri "illuminaio" version))
2289 (sha256
2290 (base32
2291 "1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"))))
2292 (build-system r-build-system)
2293 (propagated-inputs
2294 `(("r-base64" ,r-base64)))
2295 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2296 (synopsis "Parse Illumina microarray output files")
2297 (description
2298 "This package provides tools for parsing Illumina's microarray output
2299files, including IDAT.")
2300 (license license:gpl2)))
f4eac096
RW		 2301
2302(define-public r-siggenes
2303 (package
2304 (name "r-siggenes")
2305 (version "1.56.0")
2306 (source
2307 (origin
2308 (method url-fetch)
2309 (uri (bioconductor-uri "siggenes" version))
2310 (sha256
2311 (base32
2312 "0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"))))
2313 (build-system r-build-system)
2314 (propagated-inputs
2315 `(("r-biobase" ,r-biobase)
2316 ("r-multtest" ,r-multtest)))
2317 (home-page "https://bioconductor.org/packages/siggenes/")
2318 (synopsis
2319 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2320 (description
2321 "This package provides tools for the identification of differentially
2322expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2323both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2324Bayes Analyses of Microarrays} (EBAM).")
2325 (license license:lgpl2.0+)))
34a24f95
RW		 2326
2327(define-public r-bumphunter
2328 (package
2329 (name "r-bumphunter")
2330 (version "1.24.5")
2331 (source
2332 (origin
2333 (method url-fetch)
2334 (uri (bioconductor-uri "bumphunter" version))
2335 (sha256
2336 (base32
2337 "1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"))))
2338 (build-system r-build-system)
2339 (propagated-inputs
2340 `(("r-annotationdbi" ,r-annotationdbi)
2341 ("r-biocgenerics" ,r-biocgenerics)
2342 ("r-dorng" ,r-dorng)
2343 ("r-foreach" ,r-foreach)
2344 ("r-genomeinfodb" ,r-genomeinfodb)
2345 ("r-genomicfeatures" ,r-genomicfeatures)
2346 ("r-genomicranges" ,r-genomicranges)
2347 ("r-iranges" ,r-iranges)
2348 ("r-iterators" ,r-iterators)
2349 ("r-limma" ,r-limma)
2350 ("r-locfit" ,r-locfit)
2351 ("r-matrixstats" ,r-matrixstats)
2352 ("r-s4vectors" ,r-s4vectors)))
2353 (home-page "https://github.com/ririzarr/bumphunter")
2354 (synopsis "Find bumps in genomic data")
2355 (description
2356 "This package provides tools for finding bumps in genomic data in order
2357to identify differentially methylated regions in epigenetic epidemiology
2358studies.")
2359 (license license:artistic2.0)))
0fbaf195
RW		 2360
2361(define-public r-minfi
2362 (package
2363 (name "r-minfi")
2364 (version "1.28.4")
2365 (source
2366 (origin
2367 (method url-fetch)
2368 (uri (bioconductor-uri "minfi" version))
2369 (sha256
2370 (base32
2371 "1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"))))
2372 (build-system r-build-system)
2373 (propagated-inputs
2374 `(("r-beanplot" ,r-beanplot)
2375 ("r-biobase" ,r-biobase)
2376 ("r-biocgenerics" ,r-biocgenerics)
2377 ("r-biocparallel" ,r-biocparallel)
2378 ("r-biostrings" ,r-biostrings)
2379 ("r-bumphunter" ,r-bumphunter)
2380 ("r-data-table" ,r-data-table)
2381 ("r-delayedarray" ,r-delayedarray)
2382 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2383 ("r-genefilter" ,r-genefilter)
2384 ("r-genomeinfodb" ,r-genomeinfodb)
2385 ("r-genomicranges" ,r-genomicranges)
2386 ("r-geoquery" ,r-geoquery)
2387 ("r-hdf5array" ,r-hdf5array)
2388 ("r-illuminaio" ,r-illuminaio)
2389 ("r-iranges" ,r-iranges)
2390 ("r-lattice" ,r-lattice)
2391 ("r-limma" ,r-limma)
2392 ("r-mass" ,r-mass)
2393 ("r-mclust" ,r-mclust)
2394 ("r-nlme" ,r-nlme)
2395 ("r-nor1mix" ,r-nor1mix)
2396 ("r-preprocesscore" ,r-preprocesscore)
2397 ("r-quadprog" ,r-quadprog)
2398 ("r-rcolorbrewer" ,r-rcolorbrewer)
2399 ("r-reshape" ,r-reshape)
2400 ("r-s4vectors" ,r-s4vectors)
2401 ("r-siggenes" ,r-siggenes)
2402 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2403 (home-page "https://github.com/hansenlab/minfi")
2404 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2405 (description
2406 "This package provides tools to analyze and visualize Illumina Infinium
2407methylation arrays.")
2408 (license license:artistic2.0)))
5ec5ba02
RW		 2409
2410(define-public r-methylumi
2411 (package
2412 (name "r-methylumi")
2413 (version "2.28.0")
2414 (source
2415 (origin
2416 (method url-fetch)
2417 (uri (bioconductor-uri "methylumi" version))
2418 (sha256
2419 (base32
2420 "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"))))
2421 (build-system r-build-system)
2422 (propagated-inputs
2423 `(("r-annotate" ,r-annotate)
2424 ("r-annotationdbi" ,r-annotationdbi)
2425 ("r-biobase" ,r-biobase)
2426 ("r-biocgenerics" ,r-biocgenerics)
2427 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2428 ("r-genefilter" ,r-genefilter)
2429 ("r-genomeinfodb" ,r-genomeinfodb)
2430 ("r-genomicranges" ,r-genomicranges)
2431 ("r-ggplot2" ,r-ggplot2)
2432 ("r-illuminaio" ,r-illuminaio)
2433 ("r-iranges" ,r-iranges)
2434 ("r-lattice" ,r-lattice)
2435 ("r-matrixstats" ,r-matrixstats)
2436 ("r-minfi" ,r-minfi)
2437 ("r-reshape2" ,r-reshape2)
2438 ("r-s4vectors" ,r-s4vectors)
2439 ("r-scales" ,r-scales)
2440 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2441 (home-page "https://bioconductor.org/packages/methylumi")
2442 (synopsis "Handle Illumina methylation data")
2443 (description
2444 "This package provides classes for holding and manipulating Illumina
2445methylation data. Based on eSet, it can contain MIAME information, sample
2446information, feature information, and multiple matrices of data. An
2447\"intelligent\" import function, methylumiR can read the Illumina text files
2448and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2449HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2450background correction, and quality control features for GoldenGate, Infinium,
2451and Infinium HD arrays are also included.")
2452 (license license:gpl2)))
09605cb2
RW		 2453
2454(define-public r-lumi
2455 (package
2456 (name "r-lumi")
2457 (version "2.34.0")
2458 (source
2459 (origin
2460 (method url-fetch)
2461 (uri (bioconductor-uri "lumi" version))
2462 (sha256
2463 (base32
2464 "1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"))))
2465 (build-system r-build-system)
2466 (propagated-inputs
2467 `(("r-affy" ,r-affy)
2468 ("r-annotate" ,r-annotate)
2469 ("r-annotationdbi" ,r-annotationdbi)
2470 ("r-biobase" ,r-biobase)
2471 ("r-dbi" ,r-dbi)
2472 ("r-genomicfeatures" ,r-genomicfeatures)
2473 ("r-genomicranges" ,r-genomicranges)
2474 ("r-kernsmooth" ,r-kernsmooth)
2475 ("r-lattice" ,r-lattice)
2476 ("r-mass" ,r-mass)
2477 ("r-methylumi" ,r-methylumi)
2478 ("r-mgcv" ,r-mgcv)
2479 ("r-nleqslv" ,r-nleqslv)
2480 ("r-preprocesscore" ,r-preprocesscore)
2481 ("r-rsqlite" ,r-rsqlite)))
2482 (home-page "https://bioconductor.org/packages/lumi")
2483 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2484 (description
2485 "The lumi package provides an integrated solution for the Illumina
2486microarray data analysis. It includes functions of Illumina
2487BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2488variance stabilization, normalization and gene annotation at the probe level.
2489It also includes the functions of processing Illumina methylation microarrays,
2490especially Illumina Infinium methylation microarrays.")
2491 (license license:lgpl2.0+)))
4291f36a
RW		 2492
2493(define-public r-linnorm
2494 (package
2495 (name "r-linnorm")
2496 (version "2.6.1")
2497 (source
2498 (origin
2499 (method url-fetch)
2500 (uri (bioconductor-uri "Linnorm" version))
2501 (sha256
2502 (base32
2503 "1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"))))
2504 (properties `((upstream-name . "Linnorm")))
2505 (build-system r-build-system)
2506 (propagated-inputs
2507 `(("r-amap" ,r-amap)
2508 ("r-apcluster" ,r-apcluster)
2509 ("r-ellipse" ,r-ellipse)
2510 ("r-fastcluster" ,r-fastcluster)
2511 ("r-fpc" ,r-fpc)
2512 ("r-ggdendro" ,r-ggdendro)
2513 ("r-ggplot2" ,r-ggplot2)
2514 ("r-gmodels" ,r-gmodels)
2515 ("r-igraph" ,r-igraph)
2516 ("r-limma" ,r-limma)
2517 ("r-mass" ,r-mass)
2518 ("r-mclust" ,r-mclust)
2519 ("r-rcpp" ,r-rcpp)
2520 ("r-rcpparmadillo" ,r-rcpparmadillo)
2521 ("r-rtsne" ,r-rtsne)
2522 ("r-statmod" ,r-statmod)
2523 ("r-vegan" ,r-vegan)
2524 ("r-zoo" ,r-zoo)))
2525 (home-page "http://www.jjwanglab.org/Linnorm/")
2526 (synopsis "Linear model and normality based transformation method")
2527 (description
2528 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2529count data or any large scale count data. It transforms such datasets for
2530parametric tests. In addition to the transformtion function (@code{Linnorm}),
2531the following pipelines are implemented:
2532
2533@enumerate
2534@item Library size/batch effect normalization (@code{Linnorm.Norm})
2535@item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2536 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2537 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2538@item Differential expression analysis or differential peak detection using
2539 limma (@code{Linnorm.limma})
2540@item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2541@item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2542@item Stable gene selection for scRNA-seq data; for users without or who do
2543 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2544@item Data imputation (@code{Linnorm.DataImput}).
2545@end enumerate
2546
2547Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2548@code{RnaXSim} function is included for simulating RNA-seq data for the
2549evaluation of DEG analysis methods.")
2550 (license license:expat)))
e4a17532
RW		 2551
2552(define-public r-ioniser
2553 (package
2554 (name "r-ioniser")
2555 (version "2.6.0")
2556 (source
2557 (origin
2558 (method url-fetch)
2559 (uri (bioconductor-uri "IONiseR" version))
2560 (sha256
2561 (base32
2562 "01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"))))
2563 (properties `((upstream-name . "IONiseR")))
2564 (build-system r-build-system)
2565 (propagated-inputs
2566 `(("r-biocgenerics" ,r-biocgenerics)
2567 ("r-biocparallel" ,r-biocparallel)
2568 ("r-biostrings" ,r-biostrings)
2569 ("r-bit64" ,r-bit64)
2570 ("r-dplyr" ,r-dplyr)
2571 ("r-ggplot2" ,r-ggplot2)
2572 ("r-magrittr" ,r-magrittr)
2573 ("r-rhdf5" ,r-rhdf5)
2574 ("r-shortread" ,r-shortread)
2575 ("r-stringr" ,r-stringr)
2576 ("r-tibble" ,r-tibble)
2577 ("r-tidyr" ,r-tidyr)
2578 ("r-xvector" ,r-xvector)))
2579 (home-page "https://bioconductor.org/packages/IONiseR/")
2580 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2581 (description
2582 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2583MinION data. It extracts summary statistics from a set of fast5 files and can
2584be used either before or after base calling. In addition to standard
2585summaries of the read-types produced, it provides a number of plots for
2586visualising metrics relative to experiment run time or spatially over the
2587surface of a flowcell.")
2588 (license license:expat)))
80eb01c7
RW		 2589
2590;; This is a CRAN package, but it depends on packages from Bioconductor.
2591(define-public r-gkmsvm
2592 (package
2593 (name "r-gkmsvm")
2594 (version "0.79.0")
2595 (source
2596 (origin
2597 (method url-fetch)
2598 (uri (cran-uri "gkmSVM" version))
2599 (sha256
2600 (base32
2601 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2602 (properties `((upstream-name . "gkmSVM")))
2603 (build-system r-build-system)
2604 (propagated-inputs
2605 `(("r-biocgenerics" ,r-biocgenerics)
2606 ("r-biostrings" ,r-biostrings)
2607 ("r-genomeinfodb" ,r-genomeinfodb)
2608 ("r-genomicranges" ,r-genomicranges)
2609 ("r-iranges" ,r-iranges)
2610 ("r-kernlab" ,r-kernlab)
2611 ("r-rcpp" ,r-rcpp)
2612 ("r-rocr" ,r-rocr)
2613 ("r-rtracklayer" ,r-rtracklayer)
2614 ("r-s4vectors" ,r-s4vectors)
2615 ("r-seqinr" ,r-seqinr)))
2616 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2617 (synopsis "Gapped-kmer support vector machine")
2618 (description
2619 "This R package provides tools for training gapped-kmer SVM classifiers
2620for DNA and protein sequences. This package supports several sequence
2621kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2622 (license license:gpl2+)))
8a5460b4
RW		 2623
2624(define-public r-triform
2625 (package
2626 (name "r-triform")
2627 (version "1.24.0")
2628 (source
2629 (origin
2630 (method url-fetch)
2631 (uri (bioconductor-uri "triform" version))
2632 (sha256
2633 (base32
2634 "12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s"))))
2635 (build-system r-build-system)
2636 (propagated-inputs
2637 `(("r-biocgenerics" ,r-biocgenerics)
2638 ("r-iranges" ,r-iranges)
2639 ("r-yaml" ,r-yaml)))
2640 (home-page "https://bioconductor.org/packages/triform/")
2641 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2642 (description
2643 "The Triform algorithm uses model-free statistics to identify peak-like
2644distributions of TF ChIP sequencing reads, taking advantage of an improved
2645peak definition in combination with known profile characteristics.")
2646 (license license:gpl2)))
c538bcdd
RW		 2647
2648(define-public r-varianttools
2649 (package
2650 (name "r-varianttools")
2651 (version "1.24.0")
2652 (source
2653 (origin
2654 (method url-fetch)
2655 (uri (bioconductor-uri "VariantTools" version))
2656 (sha256
2657 (base32
2658 "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
2659 (properties `((upstream-name . "VariantTools")))
2660 (build-system r-build-system)
2661 (propagated-inputs
2662 `(("r-biobase" ,r-biobase)
2663 ("r-biocgenerics" ,r-biocgenerics)
2664 ("r-biocparallel" ,r-biocparallel)
2665 ("r-biostrings" ,r-biostrings)
2666 ("r-bsgenome" ,r-bsgenome)
2667 ("r-genomeinfodb" ,r-genomeinfodb)
2668 ("r-genomicfeatures" ,r-genomicfeatures)
2669 ("r-genomicranges" ,r-genomicranges)
2670 ("r-iranges" ,r-iranges)
2671 ("r-matrix" ,r-matrix)
2672 ("r-rsamtools" ,r-rsamtools)
2673 ("r-rtracklayer" ,r-rtracklayer)
2674 ("r-s4vectors" ,r-s4vectors)
2675 ("r-variantannotation" ,r-variantannotation)))
2676 (home-page "https://bioconductor.org/packages/VariantTools/")
2677 (synopsis "Tools for exploratory analysis of variant calls")
2678 (description
2679 "Explore, diagnose, and compare variant calls using filters. The
2680VariantTools package supports a workflow for loading data, calling single
2681sample variants and tumor-specific somatic mutations or other sample-specific
2682variant types (e.g., RNA editing). Most of the functions operate on
2683alignments (BAM files) or datasets of called variants. The user is expected
2684to have already aligned the reads with a separate tool, e.g., GSNAP via
2685gmapR.")
2686 (license license:artistic2.0)))
3e41919d
RW		 2687
2688(define-public r-heatplus
2689 (package
2690 (name "r-heatplus")
2691 (version "2.28.0")
2692 (source
2693 (origin
2694 (method url-fetch)
2695 (uri (bioconductor-uri "Heatplus" version))
2696 (sha256
2697 (base32
2698 "0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48"))))
2699 (properties `((upstream-name . "Heatplus")))
2700 (build-system r-build-system)
2701 (propagated-inputs
2702 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2703 (home-page "https://github.com/alexploner/Heatplus")
2704 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2705 (description
2706 "This package provides tools to display a rectangular heatmap (intensity
2707plot) of a data matrix. By default, both samples (columns) and features (row)
2708of the matrix are sorted according to a hierarchical clustering, and the
2709corresponding dendrogram is plotted. Optionally, panels with additional
2710information about samples and features can be added to the plot.")
2711 (license license:gpl2+)))
c04f230e
RW		 2712
2713(define-public r-gosemsim
2714 (package
2715 (name "r-gosemsim")
2716 (version "2.8.0")
2717 (source
2718 (origin
2719 (method url-fetch)
2720 (uri (bioconductor-uri "GOSemSim" version))
2721 (sha256
2722 (base32
2723 "0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib"))))
2724 (properties `((upstream-name . "GOSemSim")))
2725 (build-system r-build-system)
2726 (propagated-inputs
2727 `(("r-annotationdbi" ,r-annotationdbi)
2728 ("r-go-db" ,r-go-db)
2729 ("r-rcpp" ,r-rcpp)))
2730 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2731 (synopsis "GO-terms semantic similarity measures")
2732 (description
2733 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2734quantitative ways to compute similarities between genes and gene groups, and
2735have became important basis for many bioinformatics analysis approaches.
2736GOSemSim is an R package for semantic similarity computation among GO terms,
2737sets of GO terms, gene products and gene clusters.")
2738 (license license:artistic2.0)))
9d0f7942
RW		 2739
2740(define-public r-anota
2741 (package
2742 (name "r-anota")
2743 (version "1.30.0")
2744 (source
2745 (origin
2746 (method url-fetch)
2747 (uri (bioconductor-uri "anota" version))
2748 (sha256
2749 (base32
2750 "182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"))))
2751 (build-system r-build-system)
2752 (propagated-inputs
2753 `(("r-multtest" ,r-multtest)
2754 ("r-qvalue" ,r-qvalue)))
2755 (home-page "https://bioconductor.org/packages/anota/")
2756 (synopsis "Analysis of translational activity")
2757 (description
2758 "Genome wide studies of translational control is emerging as a tool to
2759study verious biological conditions. The output from such analysis is both
2760the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2761involved in translation (the actively translating mRNA level) for each mRNA.
2762The standard analysis of such data strives towards identifying differential
2763translational between two or more sample classes - i.e. differences in
2764actively translated mRNA levels that are independent of underlying differences
2765in cytosolic mRNA levels. This package allows for such analysis using partial
2766variances and the random variance model. As 10s of thousands of mRNAs are
2767analyzed in parallell the library performs a number of tests to assure that
2768the data set is suitable for such analysis.")
2769 (license license:gpl3)))
a6d867fe
RW		 2770
2771(define-public r-sigpathway
2772 (package
2773 (name "r-sigpathway")
2774 (version "1.50.0")
2775 (source
2776 (origin
2777 (method url-fetch)
2778 (uri (bioconductor-uri "sigPathway" version))
2779 (sha256
2780 (base32
2781 "0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3"))))
2782 (properties `((upstream-name . "sigPathway")))
2783 (build-system r-build-system)
2784 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
2785 (synopsis "Pathway analysis")
2786 (description
2787 "This package is used to conduct pathway analysis by calculating the NT_k
2788and NE_k statistics in a statistical framework for determining whether a
2789specified group of genes for a pathway has a coordinated association with a
2790phenotype of interest.")
2791 (license license:gpl2)))
af26c7ae
RW		 2792
2793(define-public r-fgsea
2794 (package
2795 (name "r-fgsea")
2796 (version "1.8.0")
2797 (source
2798 (origin
2799 (method url-fetch)
2800 (uri (bioconductor-uri "fgsea" version))
2801 (sha256
2802 (base32
2803 "0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"))))
2804 (build-system r-build-system)
2805 (propagated-inputs
2806 `(("r-biocparallel" ,r-biocparallel)
2807 ("r-data-table" ,r-data-table)
2808 ("r-fastmatch" ,r-fastmatch)
2809 ("r-ggplot2" ,r-ggplot2)
2810 ("r-gridextra" ,r-gridextra)
2811 ("r-matrix" ,r-matrix)
2812 ("r-rcpp" ,r-rcpp)))
2813 (home-page "https://github.com/ctlab/fgsea/")
2814 (synopsis "Fast gene set enrichment analysis")
2815 (description
2816 "The package implements an algorithm for fast gene set enrichment
2817analysis. Using the fast algorithm allows to make more permutations and get
2818more fine grained p-values, which allows to use accurate stantard approaches
2819to multiple hypothesis correction.")
2820 (license license:expat)))
305050b5
RW		 2821
2822(define-public r-dose
2823 (package
2824 (name "r-dose")
2825 (version "3.8.2")
2826 (source
2827 (origin
2828 (method url-fetch)
2829 (uri (bioconductor-uri "DOSE" version))
2830 (sha256
2831 (base32
2832 "1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa"))))
2833 (properties `((upstream-name . "DOSE")))
2834 (build-system r-build-system)
2835 (propagated-inputs
2836 `(("r-annotationdbi" ,r-annotationdbi)
2837 ("r-biocparallel" ,r-biocparallel)
2838 ("r-do-db" ,r-do-db)
2839 ("r-fgsea" ,r-fgsea)
2840 ("r-ggplot2" ,r-ggplot2)
2841 ("r-gosemsim" ,r-gosemsim)
2842 ("r-qvalue" ,r-qvalue)
2843 ("r-reshape2" ,r-reshape2)
2844 ("r-s4vectors" ,r-s4vectors)))
2845 (home-page "https://guangchuangyu.github.io/software/DOSE/")
2846 (synopsis "Disease ontology semantic and enrichment analysis")
2847 (description
2848 "This package implements five methods proposed by Resnik, Schlicker,
2849Jiang, Lin and Wang, respectively, for measuring semantic similarities among
2850@dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
2851including hypergeometric model and gene set enrichment analysis are also
2852implemented for discovering disease associations of high-throughput biological
2853data.")
2854 (license license:artistic2.0)))
9c30cf65
RW		 2855
2856(define-public r-enrichplot
2857 (package
2858 (name "r-enrichplot")
2859 (version "1.2.0")
2860 (source
2861 (origin
2862 (method url-fetch)
2863 (uri (bioconductor-uri "enrichplot" version))
2864 (sha256
2865 (base32
2866 "0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"))))
2867 (build-system r-build-system)
2868 (propagated-inputs
2869 `(("r-annotationdbi" ,r-annotationdbi)
2870 ("r-cowplot" ,r-cowplot)
2871 ("r-dose" ,r-dose)
2872 ("r-europepmc" ,r-europepmc)
2873 ("r-ggplot2" ,r-ggplot2)
2874 ("r-ggplotify" ,r-ggplotify)
2875 ("r-ggraph" ,r-ggraph)
2876 ("r-ggridges" ,r-ggridges)
2877 ("r-gosemsim" ,r-gosemsim)
2878 ("r-gridextra" ,r-gridextra)
2879 ("r-igraph" ,r-igraph)
2880 ("r-purrr" ,r-purrr)
2881 ("r-rcolorbrewer" ,r-rcolorbrewer)
2882 ("r-reshape2" ,r-reshape2)
2883 ("r-upsetr" ,r-upsetr)))
2884 (home-page "https://github.com/GuangchuangYu/enrichplot")
2885 (synopsis "Visualization of functional enrichment result")
2886 (description
2887 "The enrichplot package implements several visualization methods for
2888interpreting functional enrichment results obtained from ORA or GSEA analyses.
2889All the visualization methods are developed based on ggplot2 graphics.")
2890 (license license:artistic2.0)))
f8295ee6
RW		 2891
2892(define-public r-clusterprofiler
2893 (package
2894 (name "r-clusterprofiler")
2895 (version "3.10.1")
2896 (source
2897 (origin
2898 (method url-fetch)
2899 (uri (bioconductor-uri "clusterProfiler" version))
2900 (sha256
2901 (base32
2902 "1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm"))))
2903 (properties
2904 `((upstream-name . "clusterProfiler")))
2905 (build-system r-build-system)
2906 (propagated-inputs
2907 `(("r-annotationdbi" ,r-annotationdbi)
2908 ("r-dose" ,r-dose)
2909 ("r-enrichplot" ,r-enrichplot)
2910 ("r-ggplot2" ,r-ggplot2)
2911 ("r-go-db" ,r-go-db)
2912 ("r-gosemsim" ,r-gosemsim)
2913 ("r-magrittr" ,r-magrittr)
2914 ("r-plyr" ,r-plyr)
2915 ("r-qvalue" ,r-qvalue)
2916 ("r-rvcheck" ,r-rvcheck)
2917 ("r-tidyr" ,r-tidyr)))
2918 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
2919 (synopsis "Analysis and visualization of functional profiles for gene clusters")
2920 (description
2921 "This package implements methods to analyze and visualize functional
2922profiles (GO and KEGG) of gene and gene clusters.")
2923 (license license:artistic2.0)))
ce77562a
RW		 2924
2925(define-public r-mlinterfaces
2926 (package
2927 (name "r-mlinterfaces")
2928 (version "1.62.0")
2929 (source
2930 (origin
2931 (method url-fetch)
2932 (uri (bioconductor-uri "MLInterfaces" version))
2933 (sha256
2934 (base32
2935 "12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8"))))
2936 (properties `((upstream-name . "MLInterfaces")))
2937 (build-system r-build-system)
2938 (propagated-inputs
2939 `(("r-annotate" ,r-annotate)
2940 ("r-biobase" ,r-biobase)
2941 ("r-biocgenerics" ,r-biocgenerics)
2942 ("r-cluster" ,r-cluster)
2943 ("r-fpc" ,r-fpc)
2944 ("r-gbm" ,r-gbm)
2945 ("r-gdata" ,r-gdata)
2946 ("r-genefilter" ,r-genefilter)
2947 ("r-ggvis" ,r-ggvis)
2948 ("r-hwriter" ,r-hwriter)
2949 ("r-mass" ,r-mass)
2950 ("r-mlbench" ,r-mlbench)
2951 ("r-pls" ,r-pls)
2952 ("r-rcolorbrewer" ,r-rcolorbrewer)
2953 ("r-rda" ,r-rda)
2954 ("r-rpart" ,r-rpart)
2955 ("r-sfsmisc" ,r-sfsmisc)
2956 ("r-shiny" ,r-shiny)
2957 ("r-threejs" ,r-threejs)))
2958 (home-page "https://bioconductor.org/packages/MLInterfaces/")
2959 (synopsis "Interfaces to R machine learning procedures")
2960 (description
2961 "This package provides uniform interfaces to machine learning code for
2962data in R and Bioconductor containers.")
2963 ;; Any version of the LGPL.
2964 (license license:lgpl2.1+)))
a793e88c
RW		 2965
2966(define-public r-annaffy
2967 (package
2968 (name "r-annaffy")
2969 (version "1.54.0")
2970 (source
2971 (origin
2972 (method url-fetch)
2973 (uri (bioconductor-uri "annaffy" version))
2974 (sha256
2975 (base32
2976 "16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5"))))
2977 (build-system r-build-system)
2978 (arguments
2979 `(#:phases
2980 (modify-phases %standard-phases
2981 (add-after 'unpack 'remove-reference-to-non-free-data
2982 (lambda _
2983 (substitute* "DESCRIPTION"
2984 ((", KEGG.db") ""))
2985 #t)))))
2986 (propagated-inputs
2987 `(("r-annotationdbi" ,r-annotationdbi)
2988 ("r-biobase" ,r-biobase)
2989 ("r-dbi" ,r-dbi)
2990 ("r-go-db" ,r-go-db)))
2991 (home-page "https://bioconductor.org/packages/annaffy/")
2992 (synopsis "Annotation tools for Affymetrix biological metadata")
2993 (description
2994 "This package provides functions for handling data from Bioconductor
2995Affymetrix annotation data packages. It produces compact HTML and text
2996reports including experimental data and URL links to many online databases.
2997It allows searching of biological metadata using various criteria.")
2998 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
2999 ;; the LGPL 2.1 is included.
3000 (license license:lgpl2.1+)))
0ec0a5ec
RW		 3001
3002(define-public r-a4core
3003 (package
3004 (name "r-a4core")
3005 (version "1.30.0")
3006 (source
3007 (origin
3008 (method url-fetch)
3009 (uri (bioconductor-uri "a4Core" version))
3010 (sha256
3011 (base32
3012 "1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr"))))
3013 (properties `((upstream-name . "a4Core")))
3014 (build-system r-build-system)
3015 (propagated-inputs
3016 `(("r-biobase" ,r-biobase)
3017 ("r-glmnet" ,r-glmnet)))
3018 (home-page "https://bioconductor.org/packages/a4Core")
3019 (synopsis "Automated Affymetrix array analysis core package")
3020 (description
3021 "This is the core package for the automated analysis of Affymetrix
3022arrays.")
3023 (license license:gpl3)))
9ae37581
RW		 3024
3025(define-public r-a4classif
3026 (package
3027 (name "r-a4classif")
3028 (version "1.30.0")
3029 (source
3030 (origin
3031 (method url-fetch)
3032 (uri (bioconductor-uri "a4Classif" version))
3033 (sha256
3034 (base32
3035 "02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j"))))
3036 (properties `((upstream-name . "a4Classif")))
3037 (build-system r-build-system)
3038 (propagated-inputs
3039 `(("r-a4core" ,r-a4core)
3040 ("r-a4preproc" ,r-a4preproc)
3041 ("r-glmnet" ,r-glmnet)
3042 ("r-mlinterfaces" ,r-mlinterfaces)
3043 ("r-pamr" ,r-pamr)
3044 ("r-rocr" ,r-rocr)
3045 ("r-varselrf" ,r-varselrf)))
3046 (home-page "https://bioconductor.org/packages/a4Classif/")
3047 (synopsis "Automated Affymetrix array analysis classification package")
3048 (description
3049 "This is the classification package for the automated analysis of
3050Affymetrix arrays.")
3051 (license license:gpl3)))
b8d13e2c
RW		 3052
3053(define-public r-a4preproc
3054 (package
3055 (name "r-a4preproc")
3056 (version "1.30.0")
3057 (source
3058 (origin
3059 (method url-fetch)
3060 (uri (bioconductor-uri "a4Preproc" version))
3061 (sha256
3062 (base32
3063 "1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp"))))
3064 (properties `((upstream-name . "a4Preproc")))
3065 (build-system r-build-system)
3066 (propagated-inputs
3067 `(("r-annotationdbi" ,r-annotationdbi)))
3068 (home-page "https://bioconductor.org/packages/a4Preproc/")
3069 (synopsis "Automated Affymetrix array analysis preprocessing package")
3070 (description
3071 "This is a package for the automated analysis of Affymetrix arrays. It
3072is used for preprocessing the arrays.")
3073 (license license:gpl3)))
8e15f861
RW		 3074
3075(define-public r-a4reporting
3076 (package
3077 (name "r-a4reporting")
3078 (version "1.30.0")
3079 (source
3080 (origin
3081 (method url-fetch)
3082 (uri (bioconductor-uri "a4Reporting" version))
3083 (sha256
3084 (base32
3085 "124774z3bfdjgxx2ad40795h92aam21yfx0rw0n01nk2wf6k7xc4"))))
3086 (properties `((upstream-name . "a4Reporting")))
3087 (build-system r-build-system)
3088 (propagated-inputs
3089 `(("r-annaffy" ,r-annaffy)
3090 ("r-xtable" ,r-xtable)))
3091 (home-page "https://bioconductor.org/packages/a4Reporting/")
3092 (synopsis "Automated Affymetrix array analysis reporting package")
3093 (description
3094 "This is a package for the automated analysis of Affymetrix arrays. It
3095provides reporting features.")
3096 (license license:gpl3)))
dbfe3375
RW		 3097
3098(define-public r-a4base
3099 (package
3100 (name "r-a4base")
3101 (version "1.30.0")
3102 (source
3103 (origin
3104 (method url-fetch)
3105 (uri (bioconductor-uri "a4Base" version))
3106 (sha256
3107 (base32
3108 "0k9k3bv99msbwf2y416cz316ssaha2dxvmaddbl7z9037p8mjr70"))))
3109 (properties `((upstream-name . "a4Base")))
3110 (build-system r-build-system)
3111 (propagated-inputs
3112 `(("r-a4core" ,r-a4core)
3113 ("r-a4preproc" ,r-a4preproc)
3114 ("r-annaffy" ,r-annaffy)
3115 ("r-annotationdbi" ,r-annotationdbi)
3116 ("r-biobase" ,r-biobase)
3117 ("r-genefilter" ,r-genefilter)
3118 ("r-glmnet" ,r-glmnet)
3119 ("r-gplots" ,r-gplots)
3120 ("r-limma" ,r-limma)
3121 ("r-mpm" ,r-mpm)
3122 ("r-multtest" ,r-multtest)))
3123 (home-page "https://bioconductor.org/packages/a4Base/")
3124 (synopsis "Automated Affymetrix array analysis base package")
3125 (description
3126 "This package provides basic features for the automated analysis of
3127Affymetrix arrays.")
3128 (license license:gpl3)))
84ad024e
RW		 3129
3130(define-public r-a4
3131 (package
3132 (name "r-a4")
3133 (version "1.30.0")
3134 (source
3135 (origin
3136 (method url-fetch)
3137 (uri (bioconductor-uri "a4" version))
3138 (sha256
3139 (base32
3140 "1iqjy35rqx3m2y0dm2bk4cnzdm1qvbi608bfmrid88w6wmwz3qlk"))))
3141 (build-system r-build-system)
3142 (propagated-inputs
3143 `(("r-a4base" ,r-a4base)
3144 ("r-a4classif" ,r-a4classif)
3145 ("r-a4core" ,r-a4core)
3146 ("r-a4preproc" ,r-a4preproc)
3147 ("r-a4reporting" ,r-a4reporting)))
3148 (home-page "https://bioconductor.org/packages/a4/")
3149 (synopsis "Automated Affymetrix array analysis umbrella package")
3150 (description
3151 "This package provides a software suite for the automated analysis of
3152Affymetrix arrays.")
3153 (license license:gpl3)))
59d331f1
RW		 3154
3155(define-public r-abseqr
3156 (package
3157 (name "r-abseqr")
3158 (version "1.0.0")
3159 (source
3160 (origin
3161 (method url-fetch)
3162 (uri (bioconductor-uri "abseqR" version))
3163 (sha256
3164 (base32
3165 "0w0ngxnilcrxlixsz7ls3zm99gyabxwn7w1r3r45n96d4aj075ry"))))
3166 (properties `((upstream-name . "abseqR")))
3167 (build-system r-build-system)
3168 (inputs
3169 `(("pandoc" ,ghc-pandoc)))
3170 (propagated-inputs
3171 `(("r-biocparallel" ,r-biocparallel)
3172 ("r-biocstyle" ,r-biocstyle)
3173 ("r-circlize" ,r-circlize)
3174 ("r-flexdashboard" ,r-flexdashboard)
3175 ("r-ggcorrplot" ,r-ggcorrplot)
3176 ("r-ggdendro" ,r-ggdendro)
3177 ("r-ggplot2" ,r-ggplot2)
3178 ("r-gridextra" ,r-gridextra)
3179 ("r-knitr" ,r-knitr)
3180 ("r-plotly" ,r-plotly)
3181 ("r-plyr" ,r-plyr)
3182 ("r-png" ,r-png)
3183 ("r-rcolorbrewer" ,r-rcolorbrewer)
3184 ("r-reshape2" ,r-reshape2)
3185 ("r-rmarkdown" ,r-rmarkdown)
3186 ("r-stringr" ,r-stringr)
3187 ("r-vegan" ,r-vegan)
3188 ("r-venndiagram" ,r-venndiagram)))
3189 (home-page "https://github.com/malhamdoosh/abseqR")
3190 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3191 (description
3192 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3193sequencing datasets generated from antibody libraries and abseqR is one of its
3194packages. AbseqR empowers the users of abseqPy with plotting and reporting
3195capabilities and allows them to generate interactive HTML reports for the
3196convenience of viewing and sharing with other researchers. Additionally,
3197abseqR extends abseqPy to compare multiple repertoire analyses and perform
3198further downstream analysis on its output.")
3199 (license license:gpl3)))
41aab7d1
RW		 3200
3201(define-public r-bacon
3202 (package
3203 (name "r-bacon")
3204 (version "1.10.1")
3205 (source
3206 (origin
3207 (method url-fetch)
3208 (uri (bioconductor-uri "bacon" version))
3209 (sha256
3210 (base32
3211 "1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df"))))
3212 (build-system r-build-system)
3213 (propagated-inputs
3214 `(("r-biocparallel" ,r-biocparallel)
3215 ("r-ellipse" ,r-ellipse)
3216 ("r-ggplot2" ,r-ggplot2)))
3217 (home-page "https://bioconductor.org/packages/bacon/")
3218 (synopsis "Controlling bias and inflation in association studies")
3219 (description
3220 "Bacon can be used to remove inflation and bias often observed in
3221epigenome- and transcriptome-wide association studies. To this end bacon
3222constructs an empirical null distribution using a Gibbs Sampling algorithm by
3223fitting a three-component normal mixture on z-scores.")
3224 (license license:gpl2+)))
051e8e1a
RW		 3225
3226(define-public r-rgadem
3227 (package
3228 (name "r-rgadem")
3229 (version "2.30.0")
3230 (source
3231 (origin
3232 (method url-fetch)
3233 (uri (bioconductor-uri "rGADEM" version))
3234 (sha256
3235 (base32
3236 "1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2"))))
3237 (properties `((upstream-name . "rGADEM")))
3238 (build-system r-build-system)
3239 (propagated-inputs
3240 `(("r-biostrings" ,r-biostrings)
3241 ("r-bsgenome" ,r-bsgenome)
3242 ("r-iranges" ,r-iranges)
3243 ("r-seqlogo" ,r-seqlogo)))
3244 (home-page "https://bioconductor.org/packages/rGADEM/")
3245 (synopsis "De novo sequence motif discovery")
3246 (description
3247 "rGADEM is an efficient de novo motif discovery tool for large-scale
3248genomic sequence data.")
3249 (license license:artistic2.0)))
229f97c3
RW		 3250
3251(define-public r-motiv
3252 (package
3253 (name "r-motiv")
3254 (version "1.38.0")
3255 (source
3256 (origin
3257 (method url-fetch)
3258 (uri (bioconductor-uri "MotIV" version))
3259 (sha256
3260 (base32
3261 "1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8"))))
3262 (properties `((upstream-name . "MotIV")))
3263 (build-system r-build-system)
3264 (inputs
3265 `(("gsl" ,gsl)))
3266 (propagated-inputs
3267 `(("r-biocgenerics" ,r-biocgenerics)
3268 ("r-biostrings" ,r-biostrings)
3269 ("r-iranges" ,r-iranges)
3270 ("r-lattice" ,r-lattice)
3271 ("r-rgadem" ,r-rgadem)
3272 ("r-s4vectors" ,r-s4vectors)))
3273 (home-page "https://bioconductor.org/packages/MotIV/")
3274 (synopsis "Motif identification and validation")
3275 (description
3276 "This package is used for the identification and validation of sequence
3277motifs. It makes use of STAMP for comparing a set of motifs to a given
3278database (e.g. JASPAR). It can also be used to visualize motifs, motif
3279distributions, modules and filter motifs.")
3280 (license license:gpl2)))
2a72ef56
RW		 3281
3282(define-public r-motifstack
3283 (package
3284 (name "r-motifstack")
3285 (version "1.26.0")
3286 (source
3287 (origin
3288 (method url-fetch)
3289 (uri (bioconductor-uri "motifStack" version))
3290 (sha256
3291 (base32
3292 "1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf"))))
3293 (properties `((upstream-name . "motifStack")))
3294 (build-system r-build-system)
3295 (propagated-inputs
3296 `(("r-ade4" ,r-ade4)
3297 ("r-biostrings" ,r-biostrings)
3298 ("r-grimport" ,r-grimport)
3299 ("r-htmlwidgets" ,r-htmlwidgets)
3300 ("r-motiv" ,r-motiv)
3301 ("r-scales" ,r-scales)
3302 ("r-xml" ,r-xml)))
3303 (home-page "https://bioconductor.org/packages/motifStack/")
3304 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3305 (description
3306 "The motifStack package is designed for graphic representation of
3307multiple motifs with different similarity scores. It works with both DNA/RNA
3308sequence motifs and amino acid sequence motifs. In addition, it provides the
3309flexibility for users to customize the graphic parameters such as the font
3310type and symbol colors.")
3311 (license license:gpl2+)))
e5bff307
RW		 3312
3313(define-public r-genomicscores
3314 (package
3315 (name "r-genomicscores")
3316 (version "1.6.0")
3317 (source
3318 (origin
3319 (method url-fetch)
3320 (uri (bioconductor-uri "GenomicScores" version))
3321 (sha256
3322 (base32
3323 "0lrhkcblvnki6kncwpavs01gbcz22yza6ma8zvfmbrrkfaxqzh8n"))))
3324 (properties `((upstream-name . "GenomicScores")))
3325 (build-system r-build-system)
3326 (propagated-inputs
3327 `(("r-annotationhub" ,r-annotationhub)
3328 ("r-biobase" ,r-biobase)
3329 ("r-biocgenerics" ,r-biocgenerics)
3330 ("r-biostrings" ,r-biostrings)
3331 ("r-bsgenome" ,r-bsgenome)
3332 ("r-genomeinfodb" ,r-genomeinfodb)
3333 ("r-genomicranges" ,r-genomicranges)
3334 ("r-iranges" ,r-iranges)
3335 ("r-s4vectors" ,r-s4vectors)
3336 ("r-xml" ,r-xml)))
3337 (home-page "https://github.com/rcastelo/GenomicScores/")
3338 (synopsis "Work with genome-wide position-specific scores")
3339 (description
3340 "This package provides infrastructure to store and access genome-wide
3341position-specific scores within R and Bioconductor.")
3342 (license license:artistic2.0)))
32e0f906
RW		 3343
3344(define-public r-atacseqqc
3345 (package
3346 (name "r-atacseqqc")
3347 (version "1.6.4")
3348 (source
3349 (origin
3350 (method url-fetch)
3351 (uri (bioconductor-uri "ATACseqQC" version))
3352 (sha256
3353 (base32
3354 "1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn"))))
3355 (properties `((upstream-name . "ATACseqQC")))
3356 (build-system r-build-system)
3357 (propagated-inputs
3358 `(("r-biocgenerics" ,r-biocgenerics)
3359 ("r-biostrings" ,r-biostrings)
3360 ("r-bsgenome" ,r-bsgenome)
3361 ("r-chippeakanno" ,r-chippeakanno)
3362 ("r-genomeinfodb" ,r-genomeinfodb)
3363 ("r-genomicalignments" ,r-genomicalignments)
3364 ("r-genomicranges" ,r-genomicranges)
3365 ("r-genomicscores" ,r-genomicscores)
3366 ("r-iranges" ,r-iranges)
3367 ("r-kernsmooth" ,r-kernsmooth)
3368 ("r-limma" ,r-limma)
3369 ("r-motifstack" ,r-motifstack)
3370 ("r-preseqr" ,r-preseqr)
3371 ("r-randomforest" ,r-randomforest)
3372 ("r-rsamtools" ,r-rsamtools)
3373 ("r-rtracklayer" ,r-rtracklayer)
3374 ("r-s4vectors" ,r-s4vectors)))
3375 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3376 (synopsis "ATAC-seq quality control")
3377 (description
3378 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3379sequencing, is a rapid and sensitive method for chromatin accessibility
3380analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3381and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3382assess whether their ATAC-seq experiment is successful. It includes
3383diagnostic plots of fragment size distribution, proportion of mitochondria
3384reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3385footprints.")
3386 (license license:gpl2+)))
3972cfce
RW		 3387
3388(define-public r-gofuncr
3389 (package
3390 (name "r-gofuncr")
3391 (version "1.2.0")
3392 (source
3393 (origin
3394 (method url-fetch)
3395 (uri (bioconductor-uri "GOfuncR" version))
3396 (sha256
3397 (base32
3398 "021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk"))))
3399 (properties `((upstream-name . "GOfuncR")))
3400 (build-system r-build-system)
3401 (propagated-inputs
3402 `(("r-annotationdbi" ,r-annotationdbi)
3403 ("r-genomicranges" ,r-genomicranges)
3404 ("r-gtools" ,r-gtools)
3405 ("r-iranges" ,r-iranges)
3406 ("r-mapplots" ,r-mapplots)
3407 ("r-rcpp" ,r-rcpp)
3408 ("r-vioplot" ,r-vioplot)))
3409 (home-page "https://bioconductor.org/packages/GOfuncR/")
3410 (synopsis "Gene ontology enrichment using FUNC")
3411 (description
3412 "GOfuncR performs a gene ontology enrichment analysis based on the
3413ontology enrichment software FUNC. GO-annotations are obtained from
3414OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3415included in the package and updated regularly. GOfuncR provides the standard
3416candidate vs background enrichment analysis using the hypergeometric test, as
3417well as three additional tests:
3418
3419@enumerate
3420@item the Wilcoxon rank-sum test that is used when genes are ranked,
3421@item a binomial test that is used when genes are associated with two counts,
3422 and
3423@item a Chi-square or Fisher's exact test that is used in cases when genes are
3424associated with four counts.
3425@end enumerate
3426
3427To correct for multiple testing and interdependency of the tests, family-wise
3428error rates are computed based on random permutations of the gene-associated
3429variables. GOfuncR also provides tools for exploring the ontology graph and
3430the annotations, and options to take gene-length or spatial clustering of
3431genes into account. It is also possible to provide custom gene coordinates,
3432annotations and ontologies.")
3433 (license license:gpl2+)))
9bf4bb19
RW		 3434
3435(define-public r-abaenrichment
3436 (package
3437 (name "r-abaenrichment")
3438 (version "1.12.0")
3439 (source
3440 (origin
3441 (method url-fetch)
3442 (uri (bioconductor-uri "ABAEnrichment" version))
3443 (sha256
3444 (base32
3445 "0bvanqmg1smyckh16m2qn7d68zq4j7n74sgsnbgms5jngbp9158v"))))
3446 (properties `((upstream-name . "ABAEnrichment")))
3447 (build-system r-build-system)
3448 (propagated-inputs
3449 `(("r-abadata" ,r-abadata)
3450 ("r-data-table" ,r-data-table)
3451 ("r-gofuncr" ,r-gofuncr)
3452 ("r-gplots" ,r-gplots)
3453 ("r-gtools" ,r-gtools)
3454 ("r-rcpp" ,r-rcpp)))
3455 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3456 (synopsis "Gene expression enrichment in human brain regions")
3457 (description
3458 "The package ABAEnrichment is designed to test for enrichment of user
3459defined candidate genes in the set of expressed genes in different human brain
3460regions. The core function @code{aba_enrich} integrates the expression of the
3461candidate gene set (averaged across donors) and the structural information of
3462the brain using an ontology, both provided by the Allen Brain Atlas project.")
3463 (license license:gpl2+)))
0b91b7b9
RW		 3464
3465(define-public r-annotationfuncs
3466 (package
3467 (name "r-annotationfuncs")
3468 (version "1.32.0")
3469 (source
3470 (origin
3471 (method url-fetch)
3472 (uri (bioconductor-uri "AnnotationFuncs" version))
3473 (sha256
3474 (base32
3475 "1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss"))))
3476 (properties
3477 `((upstream-name . "AnnotationFuncs")))
3478 (build-system r-build-system)
3479 (propagated-inputs
3480 `(("r-annotationdbi" ,r-annotationdbi)
3481 ("r-dbi" ,r-dbi)))
3482 (home-page "https://www.iysik.com/r/annotationfuncs")
3483 (synopsis "Annotation translation functions")
3484 (description
3485 "This package provides functions for handling translating between
3486different identifieres using the Biocore Data Team data-packages (e.g.
3487@code{org.Bt.eg.db}).")
3488 (license license:gpl2)))
adf7d813
RW		 3489
3490(define-public r-annotationtools
3491 (package
3492 (name "r-annotationtools")
3493 (version "1.56.0")
3494 (source
3495 (origin
3496 (method url-fetch)
3497 (uri (bioconductor-uri "annotationTools" version))
3498 (sha256
3499 (base32
3500 "0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z"))))
3501 (properties
3502 `((upstream-name . "annotationTools")))
3503 (build-system r-build-system)
3504 (propagated-inputs `(("r-biobase" ,r-biobase)))
3505 (home-page "https://bioconductor.org/packages/annotationTools/")
3506 (synopsis "Annotate microarrays and perform gene expression analyses")
3507 (description
3508 "This package provides functions to annotate microarrays, find orthologs,
3509and integrate heterogeneous gene expression profiles using annotation and
3510other molecular biology information available as flat file database (plain
3511text files).")
3512 ;; Any version of the GPL.
3513 (license (list license:gpl2+))))
f31e10f8
RW		 3514
3515(define-public r-allelicimbalance
3516 (package
3517 (name "r-allelicimbalance")
3518 (version "1.20.0")
3519 (source
3520 (origin
3521 (method url-fetch)
3522 (uri (bioconductor-uri "AllelicImbalance" version))
3523 (sha256
3524 (base32
3525 "03524lj6aw9cskbpxzjmi9g708x6p94mf26yz4j941g1d0mc3z91"))))
3526 (properties
3527 `((upstream-name . "AllelicImbalance")))
3528 (build-system r-build-system)
3529 (propagated-inputs
3530 `(("r-annotationdbi" ,r-annotationdbi)
3531 ("r-biocgenerics" ,r-biocgenerics)
3532 ("r-biostrings" ,r-biostrings)
3533 ("r-bsgenome" ,r-bsgenome)
3534 ("r-genomeinfodb" ,r-genomeinfodb)
3535 ("r-genomicalignments" ,r-genomicalignments)
3536 ("r-genomicfeatures" ,r-genomicfeatures)
3537 ("r-genomicranges" ,r-genomicranges)
3538 ("r-gridextra" ,r-gridextra)
3539 ("r-gviz" ,r-gviz)
3540 ("r-iranges" ,r-iranges)
3541 ("r-lattice" ,r-lattice)
3542 ("r-latticeextra" ,r-latticeextra)
3543 ("r-nlme" ,r-nlme)
3544 ("r-rsamtools" ,r-rsamtools)
3545 ("r-s4vectors" ,r-s4vectors)
3546 ("r-seqinr" ,r-seqinr)
3547 ("r-summarizedexperiment" ,r-summarizedexperiment)
3548 ("r-variantannotation" ,r-variantannotation)))
3549 (home-page "https://github.com/pappewaio/AllelicImbalance")
3550 (synopsis "Investigate allele-specific expression")
3551 (description
3552 "This package provides a framework for allele-specific expression
3553investigation using RNA-seq data.")
3554 (license license:gpl3)))
ffe7029b
RW		 3555
3556(define-public r-aucell
3557 (package
3558 (name "r-aucell")
3559 (version "1.4.1")
3560 (source
3561 (origin
3562 (method url-fetch)
3563 (uri (bioconductor-uri "AUCell" version))
3564 (sha256
3565 (base32
3566 "1kdrs0521cyb8wlc4i3idfprrcy2f9w6kl56hfa94n0brmx62ya9"))))
3567 (properties `((upstream-name . "AUCell")))
3568 (build-system r-build-system)
3569 (propagated-inputs
3570 `(("r-data-table" ,r-data-table)
3571 ("r-gseabase" ,r-gseabase)
3572 ("r-mixtools" ,r-mixtools)
3573 ("r-r-utils" ,r-r-utils)
3574 ("r-shiny" ,r-shiny)
3575 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3576 (home-page "https://bioconductor.org/packages/AUCell/")
3577 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
3578 (description
3579 "AUCell allows to identify cells with active gene sets (e.g. signatures,
3580gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
3581Under the Curve} (AUC) to calculate whether a critical subset of the input
3582gene set is enriched within the expressed genes for each cell. The
3583distribution of AUC scores across all the cells allows exploring the relative
3584expression of the signature. Since the scoring method is ranking-based,
3585AUCell is independent of the gene expression units and the normalization
3586procedure. In addition, since the cells are evaluated individually, it can
3587easily be applied to bigger datasets, subsetting the expression matrix if
3588needed.")
3589 (license license:gpl3)))
5cfa4bff
RW		 3590
3591(define-public r-ebimage
3592 (package
3593 (name "r-ebimage")
3594 (version "4.24.0")
3595 (source
3596 (origin
3597 (method url-fetch)
3598 (uri (bioconductor-uri "EBImage" version))
3599 (sha256
3600 (base32
3601 "18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx"))))
3602 (properties `((upstream-name . "EBImage")))
3603 (build-system r-build-system)
3604 (propagated-inputs
3605 `(("r-abind" ,r-abind)
3606 ("r-biocgenerics" ,r-biocgenerics)
3607 ("r-fftwtools" ,r-fftwtools)
3608 ("r-htmltools" ,r-htmltools)
3609 ("r-htmlwidgets" ,r-htmlwidgets)
3610 ("r-jpeg" ,r-jpeg)
3611 ("r-locfit" ,r-locfit)
3612 ("r-png" ,r-png)
3613 ("r-rcurl" ,r-rcurl)
3614 ("r-tiff" ,r-tiff)))
3615 (native-inputs
3616 `(("r-knitr" ,r-knitr))) ; for vignettes
3617 (home-page "https://github.com/aoles/EBImage")
3618 (synopsis "Image processing and analysis toolbox for R")
3619 (description
3620 "EBImage provides general purpose functionality for image processing and
3621analysis. In the context of (high-throughput) microscopy-based cellular
3622assays, EBImage offers tools to segment cells and extract quantitative
3623cellular descriptors. This allows the automation of such tasks using the R
3624programming language and facilitates the use of other tools in the R
3625environment for signal processing, statistical modeling, machine learning and
3626visualization with image data.")
3627 ;; Any version of the LGPL.
3628 (license license:lgpl2.1+)))
51e98f7e
RW		 3629
3630(define-public r-yamss
3631 (package
3632 (name "r-yamss")
3633 (version "1.8.1")
3634 (source
3635 (origin
3636 (method url-fetch)
3637 (uri (bioconductor-uri "yamss" version))
3638 (sha256
3639 (base32
3640 "13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9"))))
3641 (build-system r-build-system)
3642 (propagated-inputs
3643 `(("r-biocgenerics" ,r-biocgenerics)
3644 ("r-data-table" ,r-data-table)
3645 ("r-ebimage" ,r-ebimage)
3646 ("r-iranges" ,r-iranges)
3647 ("r-limma" ,r-limma)
3648 ("r-matrix" ,r-matrix)
3649 ("r-mzr" ,r-mzr)
3650 ("r-s4vectors" ,r-s4vectors)
3651 ("r-summarizedexperiment"
3652 ,r-summarizedexperiment)))
3653 (home-page "https://github.com/hansenlab/yamss")
3654 (synopsis "Tools for high-throughput metabolomics")
3655 (description
3656 "This package provides tools to analyze and visualize high-throughput
3657metabolomics data aquired using chromatography-mass spectrometry. These tools
3658preprocess data in a way that enables reliable and powerful differential
3659analysis.")
3660 (license license:artistic2.0)))
398c4a93
RW		 3661
3662(define-public r-gtrellis
3663 (package
3664 (name "r-gtrellis")
3665 (version "1.14.0")
3666 (source
3667 (origin
3668 (method url-fetch)
3669 (uri (bioconductor-uri "gtrellis" version))
3670 (sha256
3671 (base32
3672 "17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v"))))
3673 (build-system r-build-system)
3674 (propagated-inputs
3675 `(("r-circlize" ,r-circlize)
3676 ("r-genomicranges" ,r-genomicranges)
3677 ("r-getoptlong" ,r-getoptlong)
3678 ("r-iranges" ,r-iranges)))
3679 (home-page "https://github.com/jokergoo/gtrellis")
3680 (synopsis "Genome level Trellis layout")
3681 (description
3682 "Genome level Trellis graph visualizes genomic data conditioned by
3683genomic categories (e.g. chromosomes). For each genomic category, multiple
3684dimensional data which are represented as tracks describe different features
3685from different aspects. This package provides high flexibility to arrange
3686genomic categories and to add self-defined graphics in the plot.")
3687 (license license:expat)))
28098414
RW		 3688
3689(define-public r-somaticsignatures
3690 (package
3691 (name "r-somaticsignatures")
3692 (version "2.18.0")
3693 (source
3694 (origin
3695 (method url-fetch)
3696 (uri (bioconductor-uri "SomaticSignatures" version))
3697 (sha256
3698 (base32
3699 "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02"))))
3700 (properties
3701 `((upstream-name . "SomaticSignatures")))
3702 (build-system r-build-system)
3703 (propagated-inputs
3704 `(("r-biobase" ,r-biobase)
3705 ("r-biostrings" ,r-biostrings)
3706 ("r-genomeinfodb" ,r-genomeinfodb)
3707 ("r-genomicranges" ,r-genomicranges)
3708 ("r-ggbio" ,r-ggbio)
3709 ("r-ggplot2" ,r-ggplot2)
3710 ("r-iranges" ,r-iranges)
3711 ("r-nmf" ,r-nmf)
3712 ("r-pcamethods" ,r-pcamethods)
3713 ("r-proxy" ,r-proxy)
3714 ("r-reshape2" ,r-reshape2)
3715 ("r-s4vectors" ,r-s4vectors)
3716 ("r-variantannotation" ,r-variantannotation)))
3717 (home-page "https://github.com/juliangehring/SomaticSignatures")
3718 (synopsis "Somatic signatures")
3719 (description
3720 "This package identifies mutational signatures of @dfn{single nucleotide
3721variants} (SNVs). It provides a infrastructure related to the methodology
3722described in Nik-Zainal (2012, Cell), with flexibility in the matrix
3723decomposition algorithms.")
3724 (license license:expat)))
303f2ed1
RW		 3725
3726(define-public r-yapsa
3727 (package
3728 (name "r-yapsa")
3729 (version "1.8.0")
3730 (source
3731 (origin
3732 (method url-fetch)
3733 (uri (bioconductor-uri "YAPSA" version))
3734 (sha256
3735 (base32
3736 "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j"))))
3737 (properties `((upstream-name . "YAPSA")))
3738 (build-system r-build-system)
3739 (propagated-inputs
3740 `(("r-circlize" ,r-circlize)
3741 ("r-complexheatmap" ,r-complexheatmap)
3742 ("r-corrplot" ,r-corrplot)
3743 ("r-dendextend" ,r-dendextend)
3744 ("r-genomeinfodb" ,r-genomeinfodb)
3745 ("r-genomicranges" ,r-genomicranges)
3746 ("r-getoptlong" ,r-getoptlong)
3747 ("r-ggplot2" ,r-ggplot2)
3748 ("r-gridextra" ,r-gridextra)
3749 ("r-gtrellis" ,r-gtrellis)
3750 ("r-keggrest" ,r-keggrest)
3751 ("r-lsei" ,r-lsei)
3752 ("r-pmcmr" ,r-pmcmr)
3753 ("r-reshape2" ,r-reshape2)
3754 ("r-somaticsignatures" ,r-somaticsignatures)
3755 ("r-variantannotation" ,r-variantannotation)))
3756 (home-page "https://bioconductor.org/packages/YAPSA/")
3757 (synopsis "Yet another package for signature analysis")
3758 (description
3759 "This package provides functions and routines useful in the analysis of
3760somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
3761functions to perform a signature analysis with known signatures and a
3762signature analysis on @dfn{stratified mutational catalogue} (SMC) are
3763provided.")
3764 (license license:gpl3)))
e99380d6
RW		 3765
3766(define-public r-gcrma
3767 (package
3768 (name "r-gcrma")
3769 (version "2.54.0")
3770 (source
3771 (origin
3772 (method url-fetch)
3773 (uri (bioconductor-uri "gcrma" version))
3774 (sha256
3775 (base32
3776 "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim"))))
3777 (build-system r-build-system)
3778 (propagated-inputs
3779 `(("r-affy" ,r-affy)
3780 ("r-affyio" ,r-affyio)
3781 ("r-biobase" ,r-biobase)
3782 ("r-biocmanager" ,r-biocmanager)
3783 ("r-biostrings" ,r-biostrings)
3784 ("r-xvector" ,r-xvector)))
3785 (home-page "https://bioconductor.org/packages/gcrma/")
3786 (synopsis "Background adjustment using sequence information")
3787 (description
3788 "Gcrma adjusts for background intensities in Affymetrix array data which
3789include optical noise and @dfn{non-specific binding} (NSB). The main function
3790@code{gcrma} converts background adjusted probe intensities to expression
3791measures using the same normalization and summarization methods as a
3792@dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
3793to estimate probe affinity to NSB. The sequence information is summarized in
3794a more complex way than the simple GC content. Instead, the base types (A, T,
3795G or C) at each position along the probe determine the affinity of each probe.
3796The parameters of the position-specific base contributions to the probe
3797affinity is estimated in an NSB experiment in which only NSB but no
3798gene-specific bidning is expected.")
3799 ;; Any version of the LGPL
3800 (license license:lgpl2.1+)))
jackhill's copy of GNU Guix: https://guix.gnu.org/