Commit | Line | Data |
---|---|---|
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) |
b64ce4b7 | 32 | #:use-module (gnu packages maths) |
f4235c0e RW |
33 | #:use-module (gnu packages statistics) |
34 | #:use-module (gnu packages web)) | |
fa596599 | 35 | |
557a1089 RW |
36 | \f |
37 | ;;; Annotations | |
38 | ||
b7d93cf5 RW |
39 | (define-public r-bsgenome-celegans-ucsc-ce6 |
40 | (package | |
41 | (name "r-bsgenome-celegans-ucsc-ce6") | |
42 | (version "1.4.0") | |
43 | (source (origin | |
44 | (method url-fetch) | |
45 | ;; We cannot use bioconductor-uri here because this tarball is | |
46 | ;; located under "data/annotation/" instead of "bioc/". | |
47 | (uri (string-append "https://www.bioconductor.org/packages/" | |
48 | "release/data/annotation/src/contrib/" | |
49 | "BSgenome.Celegans.UCSC.ce6_" | |
50 | version ".tar.gz")) | |
51 | (sha256 | |
52 | (base32 | |
53 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
54 | (properties | |
55 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
56 | (build-system r-build-system) | |
57 | ;; As this package provides little more than a very large data file it | |
58 | ;; doesn't make sense to build substitutes. | |
59 | (arguments `(#:substitutable? #f)) | |
60 | (propagated-inputs | |
61 | `(("r-bsgenome" ,r-bsgenome))) | |
62 | (home-page | |
63 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
64 | (synopsis "Full genome sequences for Worm") | |
65 | (description | |
66 | "This package provides full genome sequences for Caenorhabditis | |
67 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
0c792ffb RW |
68 | objects.") |
69 | (license license:artistic2.0))) | |
70 | ||
71 | (define-public r-bsgenome-celegans-ucsc-ce10 | |
72 | (package | |
73 | (name "r-bsgenome-celegans-ucsc-ce10") | |
74 | (version "1.4.0") | |
75 | (source (origin | |
76 | (method url-fetch) | |
77 | ;; We cannot use bioconductor-uri here because this tarball is | |
78 | ;; located under "data/annotation/" instead of "bioc/". | |
79 | (uri (string-append "https://www.bioconductor.org/packages/" | |
80 | "release/data/annotation/src/contrib/" | |
81 | "BSgenome.Celegans.UCSC.ce10_" | |
82 | version ".tar.gz")) | |
83 | (sha256 | |
84 | (base32 | |
85 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
86 | (properties | |
87 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
88 | (build-system r-build-system) | |
89 | ;; As this package provides little more than a very large data file it | |
90 | ;; doesn't make sense to build substitutes. | |
91 | (arguments `(#:substitutable? #f)) | |
92 | (propagated-inputs | |
93 | `(("r-bsgenome" ,r-bsgenome))) | |
94 | (home-page | |
95 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
96 | (synopsis "Full genome sequences for Worm") | |
97 | (description | |
98 | "This package provides full genome sequences for Caenorhabditis | |
99 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
b7d93cf5 RW |
100 | objects.") |
101 | (license license:artistic2.0))) | |
102 | ||
183db725 RW |
103 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
104 | (package | |
105 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
106 | (version "1.4.1") | |
107 | (source (origin | |
108 | (method url-fetch) | |
109 | ;; We cannot use bioconductor-uri here because this tarball is | |
110 | ;; located under "data/annotation/" instead of "bioc/". | |
111 | (uri (string-append "https://www.bioconductor.org/packages/" | |
112 | "release/data/annotation/src/contrib/" | |
113 | "BSgenome.Dmelanogaster.UCSC.dm6_" | |
114 | version ".tar.gz")) | |
115 | (sha256 | |
116 | (base32 | |
117 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
118 | (properties | |
119 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
120 | (build-system r-build-system) | |
121 | ;; As this package provides little more than a very large data file it | |
122 | ;; doesn't make sense to build substitutes. | |
123 | (arguments `(#:substitutable? #f)) | |
124 | (propagated-inputs | |
125 | `(("r-bsgenome" ,r-bsgenome))) | |
126 | (home-page | |
127 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
128 | (synopsis "Full genome sequences for Fly") | |
129 | (description | |
130 | "This package provides full genome sequences for Drosophila | |
131 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
132 | objects.") | |
133 | (license license:artistic2.0))) | |
134 | ||
13dabd69 RW |
135 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
136 | (package | |
137 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
138 | (version "1.4.0") | |
139 | (source (origin | |
140 | (method url-fetch) | |
141 | ;; We cannot use bioconductor-uri here because this tarball is | |
142 | ;; located under "data/annotation/" instead of "bioc/". | |
143 | (uri (string-append "https://www.bioconductor.org/packages/" | |
144 | "release/data/annotation/src/contrib/" | |
145 | "BSgenome.Dmelanogaster.UCSC.dm3_" | |
146 | version ".tar.gz")) | |
147 | (sha256 | |
148 | (base32 | |
149 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
150 | (properties | |
151 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
152 | (build-system r-build-system) | |
153 | ;; As this package provides little more than a very large data file it | |
154 | ;; doesn't make sense to build substitutes. | |
155 | (arguments `(#:substitutable? #f)) | |
156 | (propagated-inputs | |
157 | `(("r-bsgenome" ,r-bsgenome))) | |
158 | (home-page | |
159 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
160 | (synopsis "Full genome sequences for Fly") | |
161 | (description | |
162 | "This package provides full genome sequences for Drosophila | |
163 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
164 | Biostrings objects.") | |
165 | (license license:artistic2.0))) | |
166 | ||
dfac7eb9 RW |
167 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
168 | (package | |
169 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
170 | (version "1.3.99") | |
171 | (source (origin | |
172 | (method url-fetch) | |
173 | ;; We cannot use bioconductor-uri here because this tarball is | |
174 | ;; located under "data/annotation/" instead of "bioc/". | |
175 | (uri (string-append "http://www.bioconductor.org/packages/" | |
176 | "release/data/annotation/src/contrib/" | |
177 | "BSgenome.Dmelanogaster.UCSC.dm3.masked_" | |
178 | version ".tar.gz")) | |
179 | (sha256 | |
180 | (base32 | |
181 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
182 | (properties | |
183 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
184 | (build-system r-build-system) | |
185 | (propagated-inputs | |
186 | `(("r-bsgenome" ,r-bsgenome) | |
187 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
188 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
189 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
190 | (synopsis "Full masked genome sequences for Fly") | |
191 | (description | |
192 | "This package provides full masked genome sequences for Drosophila | |
193 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
194 | Biostrings objects. The sequences are the same as in | |
195 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
196 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
197 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
198 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
199 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
200 | (license license:artistic2.0))) | |
201 | ||
40a65057 RW |
202 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
203 | (package | |
204 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
205 | (version "0.99.1") | |
206 | (source (origin | |
207 | (method url-fetch) | |
208 | ;; We cannot use bioconductor-uri here because this tarball is | |
209 | ;; located under "data/annotation/" instead of "bioc/". | |
210 | (uri (string-append "https://www.bioconductor.org/packages/" | |
211 | "release/data/annotation/src/contrib/" | |
212 | "BSgenome.Hsapiens.1000genomes.hs37d5_" | |
213 | version ".tar.gz")) | |
214 | (sha256 | |
215 | (base32 | |
216 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
217 | (properties | |
218 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
219 | (build-system r-build-system) | |
220 | ;; As this package provides little more than a very large data file it | |
221 | ;; doesn't make sense to build substitutes. | |
222 | (arguments `(#:substitutable? #f)) | |
223 | (propagated-inputs | |
224 | `(("r-bsgenome" ,r-bsgenome))) | |
225 | (home-page | |
226 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
227 | (synopsis "Full genome sequences for Homo sapiens") | |
228 | (description | |
229 | "This package provides full genome sequences for Homo sapiens from | |
230 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
231 | (license license:artistic2.0))) | |
232 | ||
6fbd759b RW |
233 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
234 | (package | |
235 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
236 | (version "1.3.99") | |
237 | (source (origin | |
238 | (method url-fetch) | |
239 | ;; We cannot use bioconductor-uri here because this tarball is | |
240 | ;; located under "data/annotation/" instead of "bioc/". | |
241 | (uri (string-append "http://www.bioconductor.org/packages/" | |
242 | "release/data/annotation/src/contrib/" | |
243 | "BSgenome.Hsapiens.UCSC.hg19.masked_" | |
244 | version ".tar.gz")) | |
245 | (sha256 | |
246 | (base32 | |
247 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
248 | (properties | |
249 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
250 | (build-system r-build-system) | |
251 | (propagated-inputs | |
252 | `(("r-bsgenome" ,r-bsgenome) | |
253 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
254 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
255 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
256 | (synopsis "Full masked genome sequences for Homo sapiens") | |
257 | (description | |
258 | "This package provides full genome sequences for Homo sapiens (Human) as | |
259 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
260 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
261 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
262 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
263 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
264 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
265 | default.") | |
266 | (license license:artistic2.0))) | |
267 | ||
5acb9052 RW |
268 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
269 | (package | |
270 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
271 | (version "1.4.0") | |
272 | (source (origin | |
273 | (method url-fetch) | |
274 | ;; We cannot use bioconductor-uri here because this tarball is | |
275 | ;; located under "data/annotation/" instead of "bioc/". | |
276 | (uri (string-append "https://www.bioconductor.org/packages/" | |
277 | "release/data/annotation/src/contrib/" | |
278 | "BSgenome.Mmusculus.UCSC.mm9_" | |
279 | version ".tar.gz")) | |
280 | (sha256 | |
281 | (base32 | |
282 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
283 | (properties | |
284 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
285 | (build-system r-build-system) | |
286 | ;; As this package provides little more than a very large data file it | |
287 | ;; doesn't make sense to build substitutes. | |
288 | (arguments `(#:substitutable? #f)) | |
289 | (propagated-inputs | |
290 | `(("r-bsgenome" ,r-bsgenome))) | |
291 | (home-page | |
292 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
293 | (synopsis "Full genome sequences for Mouse") | |
294 | (description | |
295 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
296 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
297 | (license license:artistic2.0))) | |
298 | ||
2bece692 RW |
299 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
300 | (package | |
301 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
302 | (version "1.3.99") | |
303 | (source (origin | |
304 | (method url-fetch) | |
305 | ;; We cannot use bioconductor-uri here because this tarball is | |
306 | ;; located under "data/annotation/" instead of "bioc/". | |
307 | (uri (string-append "http://www.bioconductor.org/packages/" | |
308 | "release/data/annotation/src/contrib/" | |
309 | "BSgenome.Mmusculus.UCSC.mm9.masked_" | |
310 | version ".tar.gz")) | |
311 | (sha256 | |
312 | (base32 | |
313 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
314 | (properties | |
315 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
316 | (build-system r-build-system) | |
317 | (propagated-inputs | |
318 | `(("r-bsgenome" ,r-bsgenome) | |
319 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
320 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
321 | (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") | |
322 | (synopsis "Full masked genome sequences for Mouse") | |
323 | (description | |
324 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
325 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
326 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
327 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
328 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
329 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
330 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
331 | default." ) | |
332 | (license license:artistic2.0))) | |
333 | ||
c3adc830 RW |
334 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
335 | (package | |
336 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
337 | (version "1.4.0") | |
338 | (source (origin | |
339 | (method url-fetch) | |
340 | ;; We cannot use bioconductor-uri here because this tarball is | |
341 | ;; located under "data/annotation/" instead of "bioc/". | |
342 | (uri (string-append "https://www.bioconductor.org/packages/" | |
343 | "release/data/annotation/src/contrib/" | |
344 | "BSgenome.Mmusculus.UCSC.mm10_" | |
345 | version ".tar.gz")) | |
346 | (sha256 | |
347 | (base32 | |
348 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
349 | (properties | |
350 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
351 | (build-system r-build-system) | |
352 | ;; As this package provides little more than a very large data file it | |
353 | ;; doesn't make sense to build substitutes. | |
354 | (arguments `(#:substitutable? #f)) | |
355 | (propagated-inputs | |
356 | `(("r-bsgenome" ,r-bsgenome))) | |
357 | (home-page | |
358 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
359 | (synopsis "Full genome sequences for Mouse") | |
360 | (description | |
361 | "This package provides full genome sequences for Mus | |
362 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
363 | in Biostrings objects.") | |
364 | (license license:artistic2.0))) | |
365 | ||
3a08940e RW |
366 | (define-public r-org-ce-eg-db |
367 | (package | |
368 | (name "r-org-ce-eg-db") | |
369 | (version "3.7.0") | |
370 | (source (origin | |
371 | (method url-fetch) | |
372 | ;; We cannot use bioconductor-uri here because this tarball is | |
373 | ;; located under "data/annotation/" instead of "bioc/". | |
374 | (uri (string-append "https://www.bioconductor.org/packages/" | |
375 | "release/data/annotation/src/contrib/" | |
376 | "org.Ce.eg.db_" version ".tar.gz")) | |
377 | (sha256 | |
378 | (base32 | |
379 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) | |
380 | (properties | |
381 | `((upstream-name . "org.Ce.eg.db"))) | |
382 | (build-system r-build-system) | |
383 | (propagated-inputs | |
384 | `(("r-annotationdbi" ,r-annotationdbi))) | |
385 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") | |
386 | (synopsis "Genome wide annotation for Worm") | |
387 | (description | |
388 | "This package provides mappings from Entrez gene identifiers to various | |
389 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
390 | (license license:artistic2.0))) | |
391 | ||
f8780e96 RW |
392 | (define-public r-org-dm-eg-db |
393 | (package | |
394 | (name "r-org-dm-eg-db") | |
395 | (version "3.7.0") | |
396 | (source (origin | |
397 | (method url-fetch) | |
398 | ;; We cannot use bioconductor-uri here because this tarball is | |
399 | ;; located under "data/annotation/" instead of "bioc/". | |
400 | (uri (string-append "https://www.bioconductor.org/packages/" | |
401 | "release/data/annotation/src/contrib/" | |
402 | "org.Dm.eg.db_" version ".tar.gz")) | |
403 | (sha256 | |
404 | (base32 | |
405 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) | |
406 | (properties | |
407 | `((upstream-name . "org.Dm.eg.db"))) | |
408 | (build-system r-build-system) | |
409 | (propagated-inputs | |
410 | `(("r-annotationdbi" ,r-annotationdbi))) | |
411 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") | |
412 | (synopsis "Genome wide annotation for Fly") | |
413 | (description | |
414 | "This package provides mappings from Entrez gene identifiers to various | |
415 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
416 | (license license:artistic2.0))) | |
417 | ||
3dad6087 RW |
418 | (define-public r-org-dr-eg-db |
419 | (package | |
420 | (name "r-org-dr-eg-db") | |
421 | (version "3.7.0") | |
422 | (source (origin | |
423 | (method url-fetch) | |
424 | ;; We cannot use bioconductor-uri here because this tarball is | |
425 | ;; located under "data/annotation/" instead of "bioc/". | |
426 | (uri (string-append "https://www.bioconductor.org/packages/" | |
427 | "release/data/annotation/src/contrib/" | |
428 | "org.Dr.eg.db_" version ".tar.gz")) | |
429 | (sha256 | |
430 | (base32 | |
431 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) | |
432 | (properties | |
433 | `((upstream-name . "org.Dr.eg.db"))) | |
434 | (build-system r-build-system) | |
435 | (propagated-inputs | |
436 | `(("r-annotationdbi" ,r-annotationdbi))) | |
437 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") | |
438 | (synopsis "Annotation for Zebrafish") | |
439 | (description | |
440 | "This package provides genome wide annotations for Zebrafish, primarily | |
441 | based on mapping using Entrez Gene identifiers.") | |
442 | (license license:artistic2.0))) | |
443 | ||
d56df35a RW |
444 | (define-public r-org-hs-eg-db |
445 | (package | |
446 | (name "r-org-hs-eg-db") | |
447 | (version "3.7.0") | |
448 | (source (origin | |
449 | (method url-fetch) | |
450 | ;; We cannot use bioconductor-uri here because this tarball is | |
451 | ;; located under "data/annotation/" instead of "bioc/". | |
452 | (uri (string-append "https://www.bioconductor.org/packages/" | |
453 | "release/data/annotation/src/contrib/" | |
454 | "org.Hs.eg.db_" version ".tar.gz")) | |
455 | (sha256 | |
456 | (base32 | |
457 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) | |
458 | (properties | |
459 | `((upstream-name . "org.Hs.eg.db"))) | |
460 | (build-system r-build-system) | |
461 | (propagated-inputs | |
462 | `(("r-annotationdbi" ,r-annotationdbi))) | |
463 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") | |
464 | (synopsis "Genome wide annotation for Human") | |
465 | (description | |
466 | "This package contains genome-wide annotations for Human, primarily based | |
467 | on mapping using Entrez Gene identifiers.") | |
468 | (license license:artistic2.0))) | |
469 | ||
8035819f RW |
470 | (define-public r-org-mm-eg-db |
471 | (package | |
472 | (name "r-org-mm-eg-db") | |
473 | (version "3.7.0") | |
474 | (source (origin | |
475 | (method url-fetch) | |
476 | ;; We cannot use bioconductor-uri here because this tarball is | |
477 | ;; located under "data/annotation/" instead of "bioc/". | |
478 | (uri (string-append "https://www.bioconductor.org/packages/" | |
479 | "release/data/annotation/src/contrib/" | |
480 | "org.Mm.eg.db_" version ".tar.gz")) | |
481 | (sha256 | |
482 | (base32 | |
483 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) | |
484 | (properties | |
485 | `((upstream-name . "org.Mm.eg.db"))) | |
486 | (build-system r-build-system) | |
487 | (propagated-inputs | |
488 | `(("r-annotationdbi" ,r-annotationdbi))) | |
489 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") | |
490 | (synopsis "Genome wide annotation for Mouse") | |
491 | (description | |
492 | "This package provides mappings from Entrez gene identifiers to various | |
493 | annotations for the genome of the model mouse Mus musculus.") | |
494 | (license license:artistic2.0))) | |
495 | ||
fe0b76e2 RW |
496 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
497 | (package | |
498 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
499 | (version "1.4.0") | |
500 | (source (origin | |
501 | (method url-fetch) | |
502 | ;; We cannot use bioconductor-uri here because this tarball is | |
503 | ;; located under "data/annotation/" instead of "bioc/". | |
504 | (uri (string-append "https://www.bioconductor.org/packages/" | |
505 | "release/data/annotation/src/contrib/" | |
506 | "BSgenome.Hsapiens.UCSC.hg19_" | |
507 | version ".tar.gz")) | |
508 | (sha256 | |
509 | (base32 | |
510 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) | |
511 | (properties | |
512 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
513 | (build-system r-build-system) | |
514 | ;; As this package provides little more than a very large data file it | |
515 | ;; doesn't make sense to build substitutes. | |
516 | (arguments `(#:substitutable? #f)) | |
517 | (propagated-inputs | |
518 | `(("r-bsgenome" ,r-bsgenome))) | |
519 | (home-page | |
520 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
521 | (synopsis "Full genome sequences for Homo sapiens") | |
522 | (description | |
523 | "This package provides full genome sequences for Homo sapiens as provided | |
524 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
525 | (license license:artistic2.0))) | |
526 | ||
2cc51108 RW |
527 | (define-public r-genelendatabase |
528 | (package | |
529 | (name "r-genelendatabase") | |
daeb3cd9 | 530 | (version "1.18.0") |
2cc51108 RW |
531 | (source |
532 | (origin | |
533 | (method url-fetch) | |
534 | ;; We cannot use bioconductor-uri here because this tarball is | |
535 | ;; located under "data/experiment/" instead of "bioc/". | |
536 | (uri (string-append "https://bioconductor.org/packages/" | |
537 | "release/data/experiment/src/contrib" | |
538 | "/geneLenDataBase_" version ".tar.gz")) | |
539 | (sha256 | |
540 | (base32 | |
daeb3cd9 | 541 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
2cc51108 RW |
542 | (properties |
543 | `((upstream-name . "geneLenDataBase"))) | |
544 | (build-system r-build-system) | |
545 | (propagated-inputs | |
546 | `(("r-rtracklayer" ,r-rtracklayer) | |
547 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
548 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
549 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
550 | (description | |
551 | "This package provides the lengths of mRNA transcripts for a number of | |
552 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
553 | (license license:lgpl2.0+))) | |
554 | ||
66e35ce6 RW |
555 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
556 | (package | |
557 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
558 | (version "3.2.2") | |
559 | (source (origin | |
560 | (method url-fetch) | |
561 | ;; We cannot use bioconductor-uri here because this tarball is | |
562 | ;; located under "data/annotation/" instead of "bioc/". | |
563 | (uri (string-append "https://bioconductor.org/packages/" | |
564 | "release/data/annotation/src/contrib" | |
565 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" | |
566 | version ".tar.gz")) | |
567 | (sha256 | |
568 | (base32 | |
569 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
570 | (properties | |
571 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
572 | (build-system r-build-system) | |
573 | ;; As this package provides little more than a very large data file it | |
574 | ;; doesn't make sense to build substitutes. | |
575 | (arguments `(#:substitutable? #f)) | |
576 | (propagated-inputs | |
577 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
578 | (home-page | |
579 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
580 | (synopsis "Annotation package for human genome in TxDb format") | |
581 | (description | |
582 | "This package provides an annotation database of Homo sapiens genome | |
583 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
584 | track. The database is exposed as a @code{TxDb} object.") | |
585 | (license license:artistic2.0))) | |
586 | ||
d220babf RW |
587 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
588 | (package | |
589 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
590 | (version "3.2.2") | |
591 | (source (origin | |
592 | (method url-fetch) | |
593 | ;; We cannot use bioconductor-uri here because this tarball is | |
594 | ;; located under "data/annotation/" instead of "bioc/". | |
595 | (uri (string-append "https://bioconductor.org/packages/" | |
596 | "release/data/annotation/src/contrib" | |
597 | "/TxDb.Mmusculus.UCSC.mm9.knownGene_" | |
598 | version ".tar.gz")) | |
599 | (sha256 | |
600 | (base32 | |
601 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
602 | (properties | |
603 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
604 | (build-system r-build-system) | |
605 | (propagated-inputs | |
606 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
607 | ("r-annotationdbi" ,r-annotationdbi))) | |
608 | (home-page | |
609 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
610 | (synopsis "Annotation package for mouse genome in TxDb format") | |
611 | (description | |
612 | "This package provides an annotation database of Mouse genome data. It | |
613 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
614 | database is exposed as a @code{TxDb} object.") | |
615 | (license license:artistic2.0))) | |
616 | ||
7bc5d1b0 RW |
617 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
618 | (package | |
619 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
620 | (version "3.4.4") | |
621 | (source (origin | |
622 | (method url-fetch) | |
623 | ;; We cannot use bioconductor-uri here because this tarball is | |
624 | ;; located under "data/annotation/" instead of "bioc/". | |
625 | (uri (string-append "https://www.bioconductor.org/packages/" | |
626 | "release/data/annotation/src/contrib/" | |
627 | "TxDb.Mmusculus.UCSC.mm10.knownGene_" | |
628 | version ".tar.gz")) | |
629 | (sha256 | |
630 | (base32 | |
631 | "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39")))) | |
632 | (properties | |
633 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
634 | (build-system r-build-system) | |
635 | ;; As this package provides little more than a very large data file it | |
636 | ;; doesn't make sense to build substitutes. | |
637 | (arguments `(#:substitutable? #f)) | |
638 | (propagated-inputs | |
639 | `(("r-bsgenome" ,r-bsgenome) | |
640 | ("r-genomicfeatures" ,r-genomicfeatures) | |
641 | ("r-annotationdbi" ,r-annotationdbi))) | |
642 | (home-page | |
643 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
644 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
645 | (description | |
646 | "This package loads a TxDb object, which is an R interface to | |
647 | prefabricated databases contained in this package. This package provides | |
648 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
649 | based on the knownGene track.") | |
650 | (license license:artistic2.0))) | |
651 | ||
2cc51108 | 652 | \f |
557a1089 RW |
653 | ;;; Experiment data |
654 | ||
655 | (define-public r-hsmmsinglecell | |
656 | (package | |
657 | (name "r-hsmmsinglecell") | |
658 | (version "1.2.0") | |
659 | (source (origin | |
660 | (method url-fetch) | |
661 | ;; We cannot use bioconductor-uri here because this tarball is | |
662 | ;; located under "data/experiment/" instead of "bioc/". | |
663 | (uri (string-append "https://www.bioconductor.org/packages/" | |
664 | "release/data/experiment/src/contrib/" | |
665 | "HSMMSingleCell_" version ".tar.gz")) | |
666 | (sha256 | |
667 | (base32 | |
668 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) | |
669 | (properties | |
670 | `((upstream-name . "HSMMSingleCell"))) | |
671 | (build-system r-build-system) | |
672 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") | |
673 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") | |
674 | (description | |
675 | "Skeletal myoblasts undergo a well-characterized sequence of | |
676 | morphological and transcriptional changes during differentiation. In this | |
677 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded | |
678 | under high mitogen conditions (GM) and then differentiated by switching to | |
679 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several | |
680 | hundred cells taken over a time-course of serum-induced differentiation. | |
681 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, | |
682 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. | |
683 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, | |
684 | which were then sequenced to a depth of ~4 million reads per library, | |
685 | resulting in a complete gene expression profile for each cell.") | |
686 | (license license:artistic2.0))) | |
687 | ||
688 | \f | |
689 | ;;; Packages | |
690 | ||
14bba460 RW |
691 | (define-public r-biocgenerics |
692 | (package | |
693 | (name "r-biocgenerics") | |
694 | (version "0.28.0") | |
695 | (source (origin | |
696 | (method url-fetch) | |
697 | (uri (bioconductor-uri "BiocGenerics" version)) | |
698 | (sha256 | |
699 | (base32 | |
700 | "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8")))) | |
701 | (properties | |
702 | `((upstream-name . "BiocGenerics"))) | |
703 | (build-system r-build-system) | |
704 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
705 | (synopsis "S4 generic functions for Bioconductor") | |
706 | (description | |
707 | "This package provides S4 generic functions needed by many Bioconductor | |
708 | packages.") | |
709 | (license license:artistic2.0))) | |
710 | ||
7097c700 RW |
711 | (define-public r-annotate |
712 | (package | |
713 | (name "r-annotate") | |
714 | (version "1.60.0") | |
715 | (source | |
716 | (origin | |
717 | (method url-fetch) | |
718 | (uri (bioconductor-uri "annotate" version)) | |
719 | (sha256 | |
720 | (base32 | |
721 | "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n")))) | |
722 | (build-system r-build-system) | |
723 | (propagated-inputs | |
724 | `(("r-annotationdbi" ,r-annotationdbi) | |
725 | ("r-biobase" ,r-biobase) | |
726 | ("r-biocgenerics" ,r-biocgenerics) | |
727 | ("r-dbi" ,r-dbi) | |
728 | ("r-rcurl" ,r-rcurl) | |
729 | ("r-xml" ,r-xml) | |
730 | ("r-xtable" ,r-xtable))) | |
731 | (home-page | |
732 | "https://bioconductor.org/packages/annotate") | |
733 | (synopsis "Annotation for microarrays") | |
734 | (description "This package provides R environments for the annotation of | |
735 | microarrays.") | |
736 | (license license:artistic2.0))) | |
737 | ||
fa596599 RW |
738 | (define-public r-hpar |
739 | (package | |
740 | (name "r-hpar") | |
61686921 | 741 | (version "1.24.0") |
fa596599 RW |
742 | (source |
743 | (origin | |
744 | (method url-fetch) | |
745 | (uri (bioconductor-uri "hpar" version)) | |
746 | (sha256 | |
747 | (base32 | |
61686921 | 748 | "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn")))) |
fa596599 RW |
749 | (build-system r-build-system) |
750 | (home-page "https://bioconductor.org/packages/hpar/") | |
751 | (synopsis "Human Protein Atlas in R") | |
752 | (description "This package provides a simple interface to and data from | |
753 | the Human Protein Atlas project.") | |
754 | (license license:artistic2.0))) | |
183ce988 RJ |
755 | |
756 | (define-public r-regioner | |
757 | (package | |
758 | (name "r-regioner") | |
d639d888 | 759 | (version "1.14.0") |
183ce988 RJ |
760 | (source |
761 | (origin | |
762 | (method url-fetch) | |
763 | (uri (bioconductor-uri "regioneR" version)) | |
764 | (sha256 | |
765 | (base32 | |
d639d888 | 766 | "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd")))) |
183ce988 RJ |
767 | (properties `((upstream-name . "regioneR"))) |
768 | (build-system r-build-system) | |
769 | (propagated-inputs | |
d639d888 | 770 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 771 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 772 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 773 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 774 | ("r-iranges" ,r-iranges) |
d639d888 RW |
775 | ("r-memoise" ,r-memoise) |
776 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 777 | ("r-s4vectors" ,r-s4vectors))) |
183ce988 RJ |
778 | (home-page "https://bioconductor.org/packages/regioneR/") |
779 | (synopsis "Association analysis of genomic regions") | |
780 | (description "This package offers a statistical framework based on | |
781 | customizable permutation tests to assess the association between genomic | |
782 | region sets and other genomic features.") | |
783 | (license license:artistic2.0))) | |
a5b56a53 | 784 | |
bfb93b48 RW |
785 | (define-public r-geneplotter |
786 | (package | |
787 | (name "r-geneplotter") | |
788 | (version "1.60.0") | |
789 | (source | |
790 | (origin | |
791 | (method url-fetch) | |
792 | (uri (bioconductor-uri "geneplotter" version)) | |
793 | (sha256 | |
794 | (base32 | |
795 | "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz")))) | |
796 | (build-system r-build-system) | |
797 | (propagated-inputs | |
798 | `(("r-annotate" ,r-annotate) | |
799 | ("r-annotationdbi" ,r-annotationdbi) | |
800 | ("r-biobase" ,r-biobase) | |
801 | ("r-biocgenerics" ,r-biocgenerics) | |
802 | ("r-lattice" ,r-lattice) | |
803 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
804 | (home-page "https://bioconductor.org/packages/geneplotter") | |
805 | (synopsis "Graphics functions for genomic data") | |
806 | (description | |
807 | "This package provides functions for plotting genomic data.") | |
808 | (license license:artistic2.0))) | |
809 | ||
4dc2ecc2 RW |
810 | (define-public r-qvalue |
811 | (package | |
812 | (name "r-qvalue") | |
813 | (version "2.14.1") | |
814 | (source | |
815 | (origin | |
816 | (method url-fetch) | |
817 | (uri (bioconductor-uri "qvalue" version)) | |
818 | (sha256 | |
819 | (base32 | |
820 | "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc")))) | |
821 | (build-system r-build-system) | |
822 | (propagated-inputs | |
823 | `(("r-ggplot2" ,r-ggplot2) | |
824 | ("r-reshape2" ,r-reshape2))) | |
825 | (home-page "http://github.com/jdstorey/qvalue") | |
826 | (synopsis "Q-value estimation for false discovery rate control") | |
827 | (description | |
828 | "This package takes a list of p-values resulting from the simultaneous | |
829 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
830 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
831 | of false positives incurred when that particular test is called significant. | |
832 | The local FDR measures the posterior probability the null hypothesis is true | |
833 | given the test's p-value. Various plots are automatically generated, allowing | |
834 | one to make sensible significance cut-offs. The software can be applied to | |
835 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
836 | ;; Any version of the LGPL. | |
837 | (license license:lgpl3+))) | |
838 | ||
a5b56a53 RJ |
839 | (define-public r-diffbind |
840 | (package | |
841 | (name "r-diffbind") | |
98652568 | 842 | (version "2.10.0") |
a5b56a53 RJ |
843 | (source |
844 | (origin | |
845 | (method url-fetch) | |
846 | (uri (bioconductor-uri "DiffBind" version)) | |
847 | (sha256 | |
848 | (base32 | |
98652568 | 849 | "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5")))) |
a5b56a53 RJ |
850 | (properties `((upstream-name . "DiffBind"))) |
851 | (build-system r-build-system) | |
852 | (inputs | |
853 | `(("zlib" ,zlib))) | |
854 | (propagated-inputs | |
855 | `(("r-amap" ,r-amap) | |
856 | ("r-biocparallel" ,r-biocparallel) | |
857 | ("r-deseq2" ,r-deseq2) | |
858 | ("r-dplyr" ,r-dplyr) | |
859 | ("r-edger" ,r-edger) | |
860 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
861 | ("r-genomicranges" ,r-genomicranges) |
862 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
863 | ("r-ggrepel" ,r-ggrepel) |
864 | ("r-gplots" ,r-gplots) | |
865 | ("r-iranges" ,r-iranges) | |
866 | ("r-lattice" ,r-lattice) | |
867 | ("r-limma" ,r-limma) | |
868 | ("r-locfit" ,r-locfit) | |
869 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
870 | ("r-rcpp" ,r-rcpp) | |
871 | ("r-rsamtools" ,r-rsamtools) | |
872 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 873 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
a5b56a53 RJ |
874 | ("r-systempiper" ,r-systempiper) |
875 | ("r-zlibbioc" ,r-zlibbioc))) | |
876 | (home-page "http://bioconductor.org/packages/DiffBind") | |
877 | (synopsis "Differential binding analysis of ChIP-Seq peak data") | |
878 | (description | |
879 | "This package computes differentially bound sites from multiple | |
880 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
881 | occupancy (overlap) analysis and plotting functions.") | |
882 | (license license:artistic2.0))) | |
6d94bf6b RJ |
883 | |
884 | (define-public r-ripseeker | |
885 | (package | |
886 | (name "r-ripseeker") | |
e9427b2c | 887 | (version "1.22.0") |
6d94bf6b RJ |
888 | (source |
889 | (origin | |
890 | (method url-fetch) | |
891 | (uri (bioconductor-uri "RIPSeeker" version)) | |
892 | (sha256 | |
893 | (base32 | |
e9427b2c | 894 | "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i")))) |
6d94bf6b RJ |
895 | (properties `((upstream-name . "RIPSeeker"))) |
896 | (build-system r-build-system) | |
897 | (propagated-inputs | |
898 | `(("r-s4vectors" ,r-s4vectors) | |
899 | ("r-iranges" ,r-iranges) | |
900 | ("r-genomicranges" ,r-genomicranges) | |
901 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
902 | ("r-rsamtools" ,r-rsamtools) | |
903 | ("r-genomicalignments" ,r-genomicalignments) | |
904 | ("r-rtracklayer" ,r-rtracklayer))) | |
905 | (home-page "http://bioconductor.org/packages/RIPSeeker") | |
906 | (synopsis | |
907 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
908 | (description | |
909 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
910 | using two-state HMM with negative binomial emission probability. While | |
911 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
912 | a suite of bioinformatics tools integrated within this self-contained software | |
913 | package comprehensively addressing issues ranging from post-alignments | |
914 | processing to visualization and annotation.") | |
915 | (license license:gpl2))) | |
a6ae9ffd RJ |
916 | |
917 | (define-public r-multtest | |
918 | (package | |
919 | (name "r-multtest") | |
95ee4a46 | 920 | (version "2.38.0") |
a6ae9ffd RJ |
921 | (source |
922 | (origin | |
923 | (method url-fetch) | |
924 | (uri (bioconductor-uri "multtest" version)) | |
925 | (sha256 | |
926 | (base32 | |
95ee4a46 | 927 | "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k")))) |
a6ae9ffd RJ |
928 | (build-system r-build-system) |
929 | (propagated-inputs | |
930 | `(("r-survival" ,r-survival) | |
931 | ("r-biocgenerics" ,r-biocgenerics) | |
932 | ("r-biobase" ,r-biobase) | |
933 | ("r-mass" ,r-mass))) | |
934 | (home-page "http://bioconductor.org/packages/multtest") | |
935 | (synopsis "Resampling-based multiple hypothesis testing") | |
936 | (description | |
937 | "This package can do non-parametric bootstrap and permutation | |
938 | resampling-based multiple testing procedures (including empirical Bayes | |
939 | methods) for controlling the family-wise error rate (FWER), generalized | |
940 | family-wise error rate (gFWER), tail probability of the proportion of | |
941 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
942 | of bootstrap-based null distribution are implemented (centered, centered | |
943 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
944 | available. Tests based on a variety of T- and F-statistics (including | |
945 | T-statistics based on regression parameters from linear and survival models | |
946 | as well as those based on correlation parameters) are included. When probing | |
947 | hypotheses with T-statistics, users may also select a potentially faster null | |
948 | distribution which is multivariate normal with mean zero and variance | |
949 | covariance matrix derived from the vector influence function. Results are | |
950 | reported in terms of adjusted P-values, confidence regions and test statistic | |
951 | cutoffs. The procedures are directly applicable to identifying differentially | |
952 | expressed genes in DNA microarray experiments.") | |
953 | (license license:lgpl3))) | |
793f83ef | 954 | |
5dfe4912 RW |
955 | (define-public r-graph |
956 | (package | |
957 | (name "r-graph") | |
14520b64 | 958 | (version "1.60.0") |
5dfe4912 RW |
959 | (source (origin |
960 | (method url-fetch) | |
961 | (uri (bioconductor-uri "graph" version)) | |
962 | (sha256 | |
963 | (base32 | |
14520b64 | 964 | "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i")))) |
5dfe4912 RW |
965 | (build-system r-build-system) |
966 | (propagated-inputs | |
967 | `(("r-biocgenerics" ,r-biocgenerics))) | |
968 | (home-page "https://bioconductor.org/packages/graph") | |
969 | (synopsis "Handle graph data structures in R") | |
970 | (description | |
971 | "This package implements some simple graph handling capabilities for R.") | |
972 | (license license:artistic2.0))) | |
973 | ||
a207bca2 RW |
974 | (define-public r-codedepends |
975 | (package | |
976 | (name "r-codedepends") | |
977 | (version "0.6.5") | |
978 | (source | |
979 | (origin | |
980 | (method url-fetch) | |
981 | (uri (cran-uri "CodeDepends" version)) | |
982 | (sha256 | |
983 | (base32 | |
984 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
985 | (properties `((upstream-name . "CodeDepends"))) | |
986 | (build-system r-build-system) | |
987 | (propagated-inputs | |
988 | `(("r-codetools" ,r-codetools) | |
989 | ("r-graph" ,r-graph) | |
990 | ("r-xml" ,r-xml))) | |
991 | (home-page "http://cran.r-project.org/web/packages/CodeDepends") | |
992 | (synopsis "Analysis of R code for reproducible research and code comprehension") | |
993 | (description | |
994 | "This package provides tools for analyzing R expressions or blocks of | |
995 | code and determining the dependencies between them. It focuses on R scripts, | |
996 | but can be used on the bodies of functions. There are many facilities | |
997 | including the ability to summarize or get a high-level view of code, | |
998 | determining dependencies between variables, code improvement suggestions.") | |
999 | ;; Any version of the GPL | |
1000 | (license (list license:gpl2+ license:gpl3+)))) | |
1001 | ||
793f83ef RJ |
1002 | (define-public r-chippeakanno |
1003 | (package | |
1004 | (name "r-chippeakanno") | |
add2b195 | 1005 | (version "3.16.1") |
793f83ef RJ |
1006 | (source |
1007 | (origin | |
1008 | (method url-fetch) | |
1009 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
1010 | (sha256 | |
1011 | (base32 | |
add2b195 | 1012 | "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3")))) |
793f83ef RJ |
1013 | (properties `((upstream-name . "ChIPpeakAnno"))) |
1014 | (build-system r-build-system) | |
1015 | (propagated-inputs | |
1016 | `(("r-biocgenerics" ,r-biocgenerics) | |
57d2fcd9 | 1017 | ("r-biocmanager" ,r-biocmanager) |
f794e85d RW |
1018 | ("r-biostrings" ,r-biostrings) |
1019 | ("r-delayedarray" ,r-delayedarray) | |
793f83ef RJ |
1020 | ("r-go-db" ,r-go-db) |
1021 | ("r-biomart" ,r-biomart) | |
1022 | ("r-bsgenome" ,r-bsgenome) | |
1023 | ("r-genomicfeatures" ,r-genomicfeatures) | |
f794e85d | 1024 | ("r-genomicranges" ,r-genomicranges) |
793f83ef | 1025 | ("r-genomeinfodb" ,r-genomeinfodb) |
f794e85d | 1026 | ("r-iranges" ,r-iranges) |
793f83ef RJ |
1027 | ("r-matrixstats" ,r-matrixstats) |
1028 | ("r-annotationdbi" ,r-annotationdbi) | |
1029 | ("r-limma" ,r-limma) | |
1030 | ("r-multtest" ,r-multtest) | |
1031 | ("r-rbgl" ,r-rbgl) | |
1032 | ("r-graph" ,r-graph) | |
793f83ef RJ |
1033 | ("r-regioner" ,r-regioner) |
1034 | ("r-dbi" ,r-dbi) | |
1035 | ("r-ensembldb" ,r-ensembldb) | |
1036 | ("r-biobase" ,r-biobase) | |
f794e85d | 1037 | ("r-s4vectors" ,r-s4vectors) |
793f83ef RJ |
1038 | ("r-seqinr" ,r-seqinr) |
1039 | ("r-idr" ,r-idr) | |
1040 | ("r-genomicalignments" ,r-genomicalignments) | |
1041 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1042 | ("r-rsamtools" ,r-rsamtools) | |
1043 | ("r-venndiagram" ,r-venndiagram))) | |
1044 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") | |
1045 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") | |
1046 | (description | |
1047 | "The package includes functions to retrieve the sequences around the peak, | |
1048 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
1049 | custom features such as most conserved elements and other transcription factor | |
1050 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
1051 | for finding the peaks with bi-directional promoters with summary statistics | |
1052 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
1053 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
1054 | enrichedGO (addGeneIDs).") | |
1055 | (license license:gpl2+))) | |
164502d8 RJ |
1056 | |
1057 | (define-public r-marray | |
1058 | (package | |
1059 | (name "r-marray") | |
f1c606ce | 1060 | (version "1.60.0") |
164502d8 RJ |
1061 | (source (origin |
1062 | (method url-fetch) | |
1063 | (uri (bioconductor-uri "marray" version)) | |
1064 | (sha256 | |
f1c606ce | 1065 | (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky")))) |
164502d8 RJ |
1066 | (build-system r-build-system) |
1067 | (propagated-inputs | |
67487088 | 1068 | `(("r-limma" ,r-limma))) |
164502d8 RJ |
1069 | (home-page "http://bioconductor.org/packages/marray") |
1070 | (synopsis "Exploratory analysis for two-color spotted microarray data") | |
1071 | (description "This package contains class definitions for two-color spotted | |
1072 | microarray data. It also includes fuctions for data input, diagnostic plots, | |
1073 | normalization and quality checking.") | |
1074 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
1075 | |
1076 | (define-public r-cghbase | |
1077 | (package | |
1078 | (name "r-cghbase") | |
46cdceef | 1079 | (version "1.42.0") |
0416a0d4 RJ |
1080 | (source (origin |
1081 | (method url-fetch) | |
1082 | (uri (bioconductor-uri "CGHbase" version)) | |
1083 | (sha256 | |
46cdceef | 1084 | (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc")))) |
0416a0d4 RJ |
1085 | (properties `((upstream-name . "CGHbase"))) |
1086 | (build-system r-build-system) | |
1087 | (propagated-inputs | |
1088 | `(("r-biobase" ,r-biobase) | |
1089 | ("r-marray" ,r-marray))) | |
1090 | (home-page "http://bioconductor.org/packages/CGHbase") | |
1091 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
1092 | (description "This package contains functions and classes that are needed by | |
1093 | the @code{arrayCGH} packages.") | |
1094 | (license license:gpl2+))) | |
67ee83d6 RJ |
1095 | |
1096 | (define-public r-cghcall | |
1097 | (package | |
1098 | (name "r-cghcall") | |
9add0933 | 1099 | (version "2.44.0") |
67ee83d6 RJ |
1100 | (source (origin |
1101 | (method url-fetch) | |
1102 | (uri (bioconductor-uri "CGHcall" version)) | |
1103 | (sha256 | |
9add0933 | 1104 | (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi")))) |
67ee83d6 RJ |
1105 | (properties `((upstream-name . "CGHcall"))) |
1106 | (build-system r-build-system) | |
1107 | (propagated-inputs | |
1108 | `(("r-biobase" ,r-biobase) | |
1109 | ("r-cghbase" ,r-cghbase) | |
1110 | ("r-impute" ,r-impute) | |
1111 | ("r-dnacopy" ,r-dnacopy) | |
1112 | ("r-snowfall" ,r-snowfall))) | |
1113 | (home-page "http://bioconductor.org/packages/CGHcall") | |
1114 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
1115 | (description "This package contains functions and classes that are needed by | |
1116 | @code{arrayCGH} packages.") | |
1117 | (license license:gpl2+))) | |
0ef8cc9c RJ |
1118 | |
1119 | (define-public r-qdnaseq | |
1120 | (package | |
1121 | (name "r-qdnaseq") | |
a92f5230 | 1122 | (version "1.18.0") |
0ef8cc9c RJ |
1123 | (source (origin |
1124 | (method url-fetch) | |
1125 | (uri (bioconductor-uri "QDNAseq" version)) | |
1126 | (sha256 | |
a92f5230 | 1127 | (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2")))) |
0ef8cc9c RJ |
1128 | (properties `((upstream-name . "QDNAseq"))) |
1129 | (build-system r-build-system) | |
1130 | (propagated-inputs | |
1131 | `(("r-biobase" ,r-biobase) | |
81b0181b | 1132 | ("r-biocparallel" ,r-biocparallel) |
0ef8cc9c RJ |
1133 | ("r-cghbase" ,r-cghbase) |
1134 | ("r-cghcall" ,r-cghcall) | |
1135 | ("r-dnacopy" ,r-dnacopy) | |
1136 | ("r-genomicranges" ,r-genomicranges) | |
1137 | ("r-iranges" ,r-iranges) | |
1138 | ("r-matrixstats" ,r-matrixstats) | |
1139 | ("r-r-utils" ,r-r-utils) | |
1140 | ("r-rsamtools" ,r-rsamtools))) | |
1141 | (home-page "http://bioconductor.org/packages/QDNAseq") | |
1142 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") | |
1143 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
1144 | number of sequence reads in each counted, adjusted with a simultaneous | |
1145 | two-dimensional loess correction for sequence mappability and GC content, and | |
1146 | filtered to remove spurious regions in the genome. Downstream steps of | |
1147 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
1148 | respectively.") | |
1149 | (license license:gpl2+))) | |
bb15b581 RW |
1150 | |
1151 | (define-public r-bayseq | |
1152 | (package | |
1153 | (name "r-bayseq") | |
4728e275 | 1154 | (version "2.16.0") |
bb15b581 RW |
1155 | (source |
1156 | (origin | |
1157 | (method url-fetch) | |
1158 | (uri (bioconductor-uri "baySeq" version)) | |
1159 | (sha256 | |
1160 | (base32 | |
4728e275 | 1161 | "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5")))) |
bb15b581 RW |
1162 | (properties `((upstream-name . "baySeq"))) |
1163 | (build-system r-build-system) | |
1164 | (propagated-inputs | |
1165 | `(("r-abind" ,r-abind) | |
1166 | ("r-edger" ,r-edger) | |
1167 | ("r-genomicranges" ,r-genomicranges))) | |
1168 | (home-page "https://bioconductor.org/packages/baySeq/") | |
1169 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
1170 | (description | |
1171 | "This package identifies differential expression in high-throughput count | |
1172 | data, such as that derived from next-generation sequencing machines, | |
1173 | calculating estimated posterior likelihoods of differential expression (or | |
1174 | more complex hypotheses) via empirical Bayesian methods.") | |
1175 | (license license:gpl3))) | |
609f4ad1 RW |
1176 | |
1177 | (define-public r-chipcomp | |
1178 | (package | |
1179 | (name "r-chipcomp") | |
aa802eaf | 1180 | (version "1.12.0") |
609f4ad1 RW |
1181 | (source |
1182 | (origin | |
1183 | (method url-fetch) | |
1184 | (uri (bioconductor-uri "ChIPComp" version)) | |
1185 | (sha256 | |
1186 | (base32 | |
aa802eaf | 1187 | "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85")))) |
609f4ad1 RW |
1188 | (properties `((upstream-name . "ChIPComp"))) |
1189 | (build-system r-build-system) | |
1190 | (propagated-inputs | |
1191 | `(("r-biocgenerics" ,r-biocgenerics) | |
1192 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
1193 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
1194 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1195 | ("r-genomicranges" ,r-genomicranges) | |
1196 | ("r-iranges" ,r-iranges) | |
1197 | ("r-limma" ,r-limma) | |
1198 | ("r-rsamtools" ,r-rsamtools) | |
1199 | ("r-rtracklayer" ,r-rtracklayer) | |
1200 | ("r-s4vectors" ,r-s4vectors))) | |
1201 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
1202 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
1203 | (description | |
1204 | "ChIPComp implements a statistical method for quantitative comparison of | |
1205 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
1206 | sites across multiple conditions considering matching control in ChIP-seq | |
1207 | datasets.") | |
1208 | ;; Any version of the GPL. | |
1209 | (license license:gpl3+))) | |
0490f9de RW |
1210 | |
1211 | (define-public r-riboprofiling | |
1212 | (package | |
1213 | (name "r-riboprofiling") | |
e22e462b | 1214 | (version "1.12.0") |
0490f9de RW |
1215 | (source |
1216 | (origin | |
1217 | (method url-fetch) | |
1218 | (uri (bioconductor-uri "RiboProfiling" version)) | |
1219 | (sha256 | |
1220 | (base32 | |
e22e462b | 1221 | "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z")))) |
0490f9de RW |
1222 | (properties `((upstream-name . "RiboProfiling"))) |
1223 | (build-system r-build-system) | |
1224 | (propagated-inputs | |
1225 | `(("r-biocgenerics" ,r-biocgenerics) | |
1226 | ("r-biostrings" ,r-biostrings) | |
1227 | ("r-data-table" ,r-data-table) | |
1228 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1229 | ("r-genomicalignments" ,r-genomicalignments) | |
1230 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1231 | ("r-genomicranges" ,r-genomicranges) | |
1232 | ("r-ggbio" ,r-ggbio) | |
1233 | ("r-ggplot2" ,r-ggplot2) | |
1234 | ("r-iranges" ,r-iranges) | |
1235 | ("r-plyr" ,r-plyr) | |
1236 | ("r-reshape2" ,r-reshape2) | |
1237 | ("r-rsamtools" ,r-rsamtools) | |
1238 | ("r-rtracklayer" ,r-rtracklayer) | |
1239 | ("r-s4vectors" ,r-s4vectors) | |
1240 | ("r-sqldf" ,r-sqldf))) | |
1241 | (home-page "https://bioconductor.org/packages/RiboProfiling/") | |
1242 | (synopsis "Ribosome profiling data analysis") | |
1243 | (description "Starting with a BAM file, this package provides the | |
1244 | necessary functions for quality assessment, read start position recalibration, | |
1245 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
1246 | of count data: pairs, log fold-change, codon frequency and coverage | |
1247 | assessment, principal component analysis on codon coverage.") | |
1248 | (license license:gpl3))) | |
6ffdfe6a RW |
1249 | |
1250 | (define-public r-riboseqr | |
1251 | (package | |
1252 | (name "r-riboseqr") | |
c4fed658 | 1253 | (version "1.16.0") |
6ffdfe6a RW |
1254 | (source |
1255 | (origin | |
1256 | (method url-fetch) | |
1257 | (uri (bioconductor-uri "riboSeqR" version)) | |
1258 | (sha256 | |
1259 | (base32 | |
c4fed658 | 1260 | "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb")))) |
6ffdfe6a RW |
1261 | (properties `((upstream-name . "riboSeqR"))) |
1262 | (build-system r-build-system) | |
1263 | (propagated-inputs | |
1264 | `(("r-abind" ,r-abind) | |
1265 | ("r-bayseq" ,r-bayseq) | |
1266 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1267 | ("r-genomicranges" ,r-genomicranges) | |
1268 | ("r-iranges" ,r-iranges) | |
1269 | ("r-rsamtools" ,r-rsamtools) | |
1270 | ("r-seqlogo" ,r-seqlogo))) | |
1271 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
1272 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
1273 | (description | |
1274 | "This package provides plotting functions, frameshift detection and | |
1275 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
1276 | (license license:gpl3))) | |
a32279ff RW |
1277 | |
1278 | (define-public r-interactionset | |
1279 | (package | |
1280 | (name "r-interactionset") | |
bbc4787c | 1281 | (version "1.10.0") |
a32279ff RW |
1282 | (source |
1283 | (origin | |
1284 | (method url-fetch) | |
1285 | (uri (bioconductor-uri "InteractionSet" version)) | |
1286 | (sha256 | |
1287 | (base32 | |
bbc4787c | 1288 | "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb")))) |
a32279ff RW |
1289 | (properties |
1290 | `((upstream-name . "InteractionSet"))) | |
1291 | (build-system r-build-system) | |
1292 | (propagated-inputs | |
1293 | `(("r-biocgenerics" ,r-biocgenerics) | |
1294 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1295 | ("r-genomicranges" ,r-genomicranges) | |
1296 | ("r-iranges" ,r-iranges) | |
1297 | ("r-matrix" ,r-matrix) | |
1298 | ("r-rcpp" ,r-rcpp) | |
1299 | ("r-s4vectors" ,r-s4vectors) | |
1300 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1301 | (home-page "https://bioconductor.org/packages/InteractionSet") | |
1302 | (synopsis "Base classes for storing genomic interaction data") | |
1303 | (description | |
1304 | "This packages provides the @code{GInteractions}, | |
1305 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods | |
1306 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
1307 | experiments.") | |
1308 | (license license:gpl3))) | |
cf9a29b2 RW |
1309 | |
1310 | (define-public r-genomicinteractions | |
1311 | (package | |
1312 | (name "r-genomicinteractions") | |
5f2d0e63 | 1313 | (version "1.16.0") |
cf9a29b2 RW |
1314 | (source |
1315 | (origin | |
1316 | (method url-fetch) | |
1317 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
1318 | (sha256 | |
1319 | (base32 | |
5f2d0e63 | 1320 | "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q")))) |
cf9a29b2 RW |
1321 | (properties |
1322 | `((upstream-name . "GenomicInteractions"))) | |
1323 | (build-system r-build-system) | |
1324 | (propagated-inputs | |
1325 | `(("r-biobase" ,r-biobase) | |
1326 | ("r-biocgenerics" ,r-biocgenerics) | |
1327 | ("r-data-table" ,r-data-table) | |
1328 | ("r-dplyr" ,r-dplyr) | |
1329 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1330 | ("r-genomicranges" ,r-genomicranges) | |
1331 | ("r-ggplot2" ,r-ggplot2) | |
1332 | ("r-gridextra" ,r-gridextra) | |
1333 | ("r-gviz" ,r-gviz) | |
1334 | ("r-igraph" ,r-igraph) | |
1335 | ("r-interactionset" ,r-interactionset) | |
1336 | ("r-iranges" ,r-iranges) | |
1337 | ("r-rsamtools" ,r-rsamtools) | |
1338 | ("r-rtracklayer" ,r-rtracklayer) | |
1339 | ("r-s4vectors" ,r-s4vectors) | |
1340 | ("r-stringr" ,r-stringr))) | |
1341 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") | |
1342 | (synopsis "R package for handling genomic interaction data") | |
1343 | (description | |
1344 | "This R package provides tools for handling genomic interaction data, | |
1345 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
1346 | information and producing various plots and statistics.") | |
1347 | (license license:gpl3))) | |
27c51606 RW |
1348 | |
1349 | (define-public r-ctc | |
1350 | (package | |
1351 | (name "r-ctc") | |
b858338c | 1352 | (version "1.56.0") |
27c51606 RW |
1353 | (source |
1354 | (origin | |
1355 | (method url-fetch) | |
1356 | (uri (bioconductor-uri "ctc" version)) | |
1357 | (sha256 | |
1358 | (base32 | |
b858338c | 1359 | "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2")))) |
27c51606 RW |
1360 | (build-system r-build-system) |
1361 | (propagated-inputs `(("r-amap" ,r-amap))) | |
1362 | (home-page "https://bioconductor.org/packages/ctc/") | |
1363 | (synopsis "Cluster and tree conversion") | |
1364 | (description | |
1365 | "This package provides tools for exporting and importing classification | |
1366 | trees and clusters to other programs.") | |
1367 | (license license:gpl2))) | |
5da0e142 RW |
1368 | |
1369 | (define-public r-goseq | |
1370 | (package | |
1371 | (name "r-goseq") | |
7f2b1c4a | 1372 | (version "1.34.1") |
5da0e142 RW |
1373 | (source |
1374 | (origin | |
1375 | (method url-fetch) | |
1376 | (uri (bioconductor-uri "goseq" version)) | |
1377 | (sha256 | |
1378 | (base32 | |
7f2b1c4a | 1379 | "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn")))) |
5da0e142 RW |
1380 | (build-system r-build-system) |
1381 | (propagated-inputs | |
1382 | `(("r-annotationdbi" ,r-annotationdbi) | |
1383 | ("r-biasedurn" ,r-biasedurn) | |
1384 | ("r-biocgenerics" ,r-biocgenerics) | |
1385 | ("r-genelendatabase" ,r-genelendatabase) | |
1386 | ("r-go-db" ,r-go-db) | |
1387 | ("r-mgcv" ,r-mgcv))) | |
1388 | (home-page "https://bioconductor.org/packages/goseq/") | |
1389 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
1390 | (description | |
1391 | "This package provides tools to detect Gene Ontology and/or other user | |
1392 | defined categories which are over/under represented in RNA-seq data.") | |
1393 | (license license:lgpl2.0+))) | |
f4235c0e RW |
1394 | |
1395 | (define-public r-glimma | |
1396 | (package | |
1397 | (name "r-glimma") | |
0b469ee2 | 1398 | (version "1.10.1") |
f4235c0e RW |
1399 | (source |
1400 | (origin | |
1401 | (method url-fetch) | |
1402 | (uri (bioconductor-uri "Glimma" version)) | |
1403 | (sha256 | |
1404 | (base32 | |
0b469ee2 | 1405 | "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv")))) |
f4235c0e RW |
1406 | (properties `((upstream-name . "Glimma"))) |
1407 | (build-system r-build-system) | |
1408 | (propagated-inputs | |
1409 | `(("r-edger" ,r-edger) | |
1410 | ("r-jsonlite" ,r-jsonlite) | |
1411 | ("r-s4vectors" ,r-s4vectors))) | |
1412 | (home-page "https://github.com/Shians/Glimma") | |
1413 | (synopsis "Interactive HTML graphics") | |
1414 | (description | |
1415 | "This package generates interactive visualisations for analysis of | |
1416 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
1417 | HTML page. The interactions are built on top of the popular static | |
1418 | representations of analysis results in order to provide additional | |
1419 | information.") | |
1420 | (license license:lgpl3))) | |
aa388dc7 RW |
1421 | |
1422 | (define-public r-rots | |
1423 | (package | |
1424 | (name "r-rots") | |
45dcd7dc | 1425 | (version "1.10.1") |
aa388dc7 RW |
1426 | (source |
1427 | (origin | |
1428 | (method url-fetch) | |
1429 | (uri (bioconductor-uri "ROTS" version)) | |
1430 | (sha256 | |
1431 | (base32 | |
45dcd7dc | 1432 | "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6")))) |
aa388dc7 RW |
1433 | (properties `((upstream-name . "ROTS"))) |
1434 | (build-system r-build-system) | |
1435 | (propagated-inputs | |
1436 | `(("r-biobase" ,r-biobase) | |
1437 | ("r-rcpp" ,r-rcpp))) | |
1438 | (home-page "https://bioconductor.org/packages/ROTS/") | |
1439 | (synopsis "Reproducibility-Optimized Test Statistic") | |
1440 | (description | |
1441 | "This package provides tools for calculating the | |
1442 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
1443 | in omics data.") | |
1444 | (license license:gpl2+))) | |
b64ce4b7 | 1445 | |
cad6fb2d RW |
1446 | (define-public r-plgem |
1447 | (package | |
1448 | (name "r-plgem") | |
1449 | (version "1.54.1") | |
1450 | (source | |
1451 | (origin | |
1452 | (method url-fetch) | |
1453 | (uri (bioconductor-uri "plgem" version)) | |
1454 | (sha256 | |
1455 | (base32 | |
1456 | "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg")))) | |
1457 | (build-system r-build-system) | |
1458 | (propagated-inputs | |
1459 | `(("r-biobase" ,r-biobase) | |
1460 | ("r-mass" ,r-mass))) | |
1461 | (home-page "http://www.genopolis.it") | |
1462 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
1463 | (description | |
1464 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
1465 | model the variance-versus-mean dependence that exists in a variety of | |
1466 | genome-wide datasets, including microarray and proteomics data. The use of | |
1467 | PLGEM has been shown to improve the detection of differentially expressed | |
1468 | genes or proteins in these datasets.") | |
1469 | (license license:gpl2))) | |
1470 | ||
b64ce4b7 RW |
1471 | (define-public r-inspect |
1472 | (package | |
1473 | (name "r-inspect") | |
c86fc969 | 1474 | (version "1.12.1") |
b64ce4b7 RW |
1475 | (source |
1476 | (origin | |
1477 | (method url-fetch) | |
1478 | (uri (bioconductor-uri "INSPEcT" version)) | |
1479 | (sha256 | |
1480 | (base32 | |
c86fc969 | 1481 | "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp")))) |
b64ce4b7 RW |
1482 | (properties `((upstream-name . "INSPEcT"))) |
1483 | (build-system r-build-system) | |
1484 | (propagated-inputs | |
1485 | `(("r-biobase" ,r-biobase) | |
1486 | ("r-biocgenerics" ,r-biocgenerics) | |
1487 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 1488 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 RW |
1489 | ("r-desolve" ,r-desolve) |
1490 | ("r-genomicalignments" ,r-genomicalignments) | |
1491 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1492 | ("r-genomicranges" ,r-genomicranges) | |
1493 | ("r-iranges" ,r-iranges) | |
c86fc969 | 1494 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
1495 | ("r-preprocesscore" ,r-preprocesscore) |
1496 | ("r-proc" ,r-proc) | |
1497 | ("r-rootsolve" ,r-rootsolve) | |
1498 | ("r-rsamtools" ,r-rsamtools) | |
c86fc969 RW |
1499 | ("r-s4vectors" ,r-s4vectors) |
1500 | ("r-shiny" ,r-shiny) | |
1501 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1502 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
1503 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
b64ce4b7 RW |
1504 | (home-page "https://bioconductor.org/packages/INSPEcT") |
1505 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
1506 | (description | |
1507 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
1508 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
1509 | order to evaluate synthesis, processing and degradation rates and assess via | |
1510 | modeling the rates that determines changes in mature mRNA levels.") | |
1511 | (license license:gpl2))) | |
f6e99763 RW |
1512 | |
1513 | (define-public r-dnabarcodes | |
1514 | (package | |
1515 | (name "r-dnabarcodes") | |
318bcbc4 | 1516 | (version "1.12.0") |
f6e99763 RW |
1517 | (source |
1518 | (origin | |
1519 | (method url-fetch) | |
1520 | (uri (bioconductor-uri "DNABarcodes" version)) | |
1521 | (sha256 | |
1522 | (base32 | |
318bcbc4 | 1523 | "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0")))) |
f6e99763 RW |
1524 | (properties `((upstream-name . "DNABarcodes"))) |
1525 | (build-system r-build-system) | |
1526 | (propagated-inputs | |
1527 | `(("r-bh" ,r-bh) | |
1528 | ("r-matrix" ,r-matrix) | |
1529 | ("r-rcpp" ,r-rcpp))) | |
1530 | (home-page "https://bioconductor.org/packages/DNABarcodes") | |
1531 | (synopsis "Create and analyze DNA barcodes") | |
1532 | (description | |
1533 | "This package offers tools to create DNA barcode sets capable of | |
1534 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
1535 | can be analyzed regarding their minimal, maximal and average distances between | |
1536 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
1537 | demultiplexed, i.e. assigned to their original reference barcode.") | |
1538 | (license license:gpl2))) | |
09aa3d06 RW |
1539 | |
1540 | (define-public r-ruvseq | |
1541 | (package | |
1542 | (name "r-ruvseq") | |
c6e9b494 | 1543 | (version "1.16.1") |
09aa3d06 RW |
1544 | (source |
1545 | (origin | |
1546 | (method url-fetch) | |
1547 | (uri (bioconductor-uri "RUVSeq" version)) | |
1548 | (sha256 | |
1549 | (base32 | |
c6e9b494 | 1550 | "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv")))) |
09aa3d06 RW |
1551 | (properties `((upstream-name . "RUVSeq"))) |
1552 | (build-system r-build-system) | |
1553 | (propagated-inputs | |
1554 | `(("r-biobase" ,r-biobase) | |
1555 | ("r-edaseq" ,r-edaseq) | |
1556 | ("r-edger" ,r-edger) | |
1557 | ("r-mass" ,r-mass))) | |
1558 | (home-page "https://github.com/drisso/RUVSeq") | |
1559 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
1560 | (description | |
1561 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
1562 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
1563 | samples.") | |
1564 | (license license:artistic2.0))) | |
286157dc RW |
1565 | |
1566 | (define-public r-biocneighbors | |
1567 | (package | |
1568 | (name "r-biocneighbors") | |
1569 | (version "1.0.0") | |
1570 | (source | |
1571 | (origin | |
1572 | (method url-fetch) | |
1573 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
1574 | (sha256 | |
1575 | (base32 | |
1576 | "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll")))) | |
1577 | (properties `((upstream-name . "BiocNeighbors"))) | |
1578 | (build-system r-build-system) | |
1579 | (propagated-inputs | |
1580 | `(("r-biocparallel" ,r-biocparallel) | |
1581 | ("r-rcpp" ,r-rcpp) | |
1582 | ("r-rcppannoy" ,r-rcppannoy) | |
1583 | ("r-s4vectors" ,r-s4vectors))) | |
1584 | (home-page "https://bioconductor.org/packages/BiocNeighbors") | |
1585 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
1586 | (description | |
1587 | "This package implements exact and approximate methods for nearest | |
1588 | neighbor detection, in a framework that allows them to be easily switched | |
1589 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
1590 | using pre-clustering with the k-means algorithm. Functions are also provided | |
1591 | to search for all neighbors within a given distance. Parallelization is | |
1592 | achieved for all methods using the BiocParallel framework.") | |
1593 | (license license:gpl3))) | |
8a587c89 | 1594 | |
a961ae46 RW |
1595 | (define-public r-destiny |
1596 | (package | |
1597 | (name "r-destiny") | |
1598 | (version "2.12.0") | |
1599 | (source | |
1600 | (origin | |
1601 | (method url-fetch) | |
1602 | (uri (bioconductor-uri "destiny" version)) | |
1603 | (sha256 | |
1604 | (base32 | |
1605 | "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67")))) | |
1606 | (build-system r-build-system) | |
1607 | (propagated-inputs | |
1608 | `(("r-biobase" ,r-biobase) | |
1609 | ("r-biocgenerics" ,r-biocgenerics) | |
1610 | ("r-fnn" ,r-fnn) | |
1611 | ("r-ggthemes" ,r-ggthemes) | |
1612 | ("r-hmisc" ,r-hmisc) | |
1613 | ("r-igraph" ,r-igraph) | |
1614 | ("r-matrix" ,r-matrix) | |
1615 | ("r-proxy" ,r-proxy) | |
1616 | ("r-rcpp" ,r-rcpp) | |
1617 | ("r-rcppeigen" ,r-rcppeigen) | |
1618 | ("r-scales" ,r-scales) | |
1619 | ("r-scatterplot3d" ,r-scatterplot3d) | |
1620 | ("r-smoother" ,r-smoother) | |
1621 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1622 | ("r-vim" ,r-vim))) | |
1623 | (home-page "https://bioconductor.org/packages/destiny/") | |
1624 | (synopsis "Create and plot diffusion maps") | |
1625 | (description "This package provides tools to create and plot diffusion | |
1626 | maps.") | |
1627 | ;; Any version of the GPL | |
1628 | (license license:gpl3+))) | |
1629 | ||
8a587c89 RW |
1630 | (define-public r-savr |
1631 | (package | |
1632 | (name "r-savr") | |
1633 | (version "1.20.0") | |
1634 | (source | |
1635 | (origin | |
1636 | (method url-fetch) | |
1637 | (uri (bioconductor-uri "savR" version)) | |
1638 | (sha256 | |
1639 | (base32 | |
1640 | "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7")))) | |
1641 | (properties `((upstream-name . "savR"))) | |
1642 | (build-system r-build-system) | |
1643 | (propagated-inputs | |
1644 | `(("r-ggplot2" ,r-ggplot2) | |
1645 | ("r-gridextra" ,r-gridextra) | |
1646 | ("r-reshape2" ,r-reshape2) | |
1647 | ("r-scales" ,r-scales) | |
1648 | ("r-xml" ,r-xml))) | |
1649 | (home-page "https://github.com/bcalder/savR") | |
1650 | (synopsis "Parse and analyze Illumina SAV files") | |
1651 | (description | |
1652 | "This package provides tools to parse Illumina Sequence Analysis | |
1653 | Viewer (SAV) files, access data, and generate QC plots.") | |
1654 | (license license:agpl3+))) | |
41ffc214 RW |
1655 | |
1656 | (define-public r-chipexoqual | |
1657 | (package | |
1658 | (name "r-chipexoqual") | |
1659 | (version "1.6.0") | |
1660 | (source | |
1661 | (origin | |
1662 | (method url-fetch) | |
1663 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
1664 | (sha256 | |
1665 | (base32 | |
1666 | "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp")))) | |
1667 | (properties `((upstream-name . "ChIPexoQual"))) | |
1668 | (build-system r-build-system) | |
1669 | (propagated-inputs | |
1670 | `(("r-biocparallel" ,r-biocparallel) | |
1671 | ("r-biovizbase" ,r-biovizbase) | |
1672 | ("r-broom" ,r-broom) | |
1673 | ("r-data-table" ,r-data-table) | |
1674 | ("r-dplyr" ,r-dplyr) | |
1675 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1676 | ("r-genomicalignments" ,r-genomicalignments) | |
1677 | ("r-genomicranges" ,r-genomicranges) | |
1678 | ("r-ggplot2" ,r-ggplot2) | |
1679 | ("r-hexbin" ,r-hexbin) | |
1680 | ("r-iranges" ,r-iranges) | |
1681 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
1682 | ("r-rmarkdown" ,r-rmarkdown) | |
1683 | ("r-rsamtools" ,r-rsamtools) | |
1684 | ("r-s4vectors" ,r-s4vectors) | |
1685 | ("r-scales" ,r-scales) | |
1686 | ("r-viridis" ,r-viridis))) | |
1687 | (home-page "https://github.com/keleslab/ChIPexoQual") | |
1688 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
1689 | (description | |
1690 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
1691 | sequencing data.") | |
1692 | (license license:gpl2+))) | |
c18dccff | 1693 | |
3d13b448 RW |
1694 | (define-public r-copynumber |
1695 | (package | |
1696 | (name "r-copynumber") | |
1697 | (version "1.22.0") | |
1698 | (source (origin | |
1699 | (method url-fetch) | |
1700 | (uri (bioconductor-uri "copynumber" version)) | |
1701 | (sha256 | |
1702 | (base32 | |
1703 | "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3")))) | |
1704 | (build-system r-build-system) | |
1705 | (propagated-inputs | |
1706 | `(("r-s4vectors" ,r-s4vectors) | |
1707 | ("r-iranges" ,r-iranges) | |
1708 | ("r-genomicranges" ,r-genomicranges) | |
1709 | ("r-biocgenerics" ,r-biocgenerics))) | |
1710 | (home-page "https://bioconductor.org/packages/copynumber") | |
1711 | (synopsis "Segmentation of single- and multi-track copy number data") | |
1712 | (description | |
1713 | "This package segments single- and multi-track copy number data by a | |
1714 | penalized least squares regression method.") | |
1715 | (license license:artistic2.0))) | |
1716 | ||
c18dccff RW |
1717 | (define-public r-dnacopy |
1718 | (package | |
1719 | (name "r-dnacopy") | |
1720 | (version "1.56.0") | |
1721 | (source | |
1722 | (origin | |
1723 | (method url-fetch) | |
1724 | (uri (bioconductor-uri "DNAcopy" version)) | |
1725 | (sha256 | |
1726 | (base32 | |
1727 | "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82")))) | |
1728 | (properties `((upstream-name . "DNAcopy"))) | |
1729 | (build-system r-build-system) | |
1730 | (native-inputs `(("gfortran" ,gfortran))) | |
1731 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
1732 | (synopsis "DNA copy number data analysis") | |
1733 | (description | |
1734 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
1735 | algorithm to segment DNA copy number data and identify genomic regions with | |
1736 | abnormal copy number.") | |
1737 | (license license:gpl2+))) | |
3a0babac RW |
1738 | |
1739 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
1740 | ;; Bioconductor package. | |
1741 | (define-public r-htscluster | |
1742 | (package | |
1743 | (name "r-htscluster") | |
1744 | (version "2.0.8") | |
1745 | (source | |
1746 | (origin | |
1747 | (method url-fetch) | |
1748 | (uri (cran-uri "HTSCluster" version)) | |
1749 | (sha256 | |
1750 | (base32 | |
1751 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
1752 | (properties `((upstream-name . "HTSCluster"))) | |
1753 | (build-system r-build-system) | |
1754 | (propagated-inputs | |
1755 | `(("r-capushe" ,r-capushe) | |
1756 | ("r-edger" ,r-edger) | |
1757 | ("r-plotrix" ,r-plotrix))) | |
1758 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
1759 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
1760 | (description | |
1761 | "This package provides a Poisson mixture model is implemented to cluster | |
1762 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
1763 | estimation is performed using either the EM or CEM algorithm, and the slope | |
1764 | heuristics are used for model selection (i.e., to choose the number of | |
1765 | clusters).") | |
1766 | (license license:gpl3+))) |