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