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fa596599 | 1 | ;;; GNU Guix --- Functional package management for GNU |
6aa896d8 RW |
2 | ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> |
3 | ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> | |
bfb93b48 | 4 | ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> |
fa596599 RW |
5 | ;;; |
6 | ;;; This file is part of GNU Guix. | |
7 | ;;; | |
8 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
9 | ;;; under the terms of the GNU General Public License as published by | |
10 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
11 | ;;; your option) any later version. | |
12 | ;;; | |
13 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
14 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
16 | ;;; GNU General Public License for more details. | |
17 | ;;; | |
18 | ;;; You should have received a copy of the GNU General Public License | |
19 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
20 | ||
21 | (define-module (gnu packages bioconductor) | |
22 | #:use-module ((guix licenses) #:prefix license:) | |
23 | #:use-module (guix packages) | |
24 | #:use-module (guix download) | |
25 | #:use-module (guix build-system r) | |
183ce988 | 26 | #:use-module (gnu packages) |
cf9a29b2 | 27 | #:use-module (gnu packages bioinformatics) |
a5b56a53 RJ |
28 | #:use-module (gnu packages cran) |
29 | #:use-module (gnu packages compression) | |
c18dccff | 30 | #:use-module (gnu packages gcc) |
cf9a29b2 | 31 | #:use-module (gnu packages graph) |
59d331f1 | 32 | #:use-module (gnu packages haskell) |
5cfa4bff | 33 | #:use-module (gnu packages image) |
b64ce4b7 | 34 | #:use-module (gnu packages maths) |
6b12f213 RW |
35 | #:use-module (gnu packages netpbm) |
36 | #:use-module (gnu packages perl) | |
2cb71d81 | 37 | #:use-module (gnu packages pkg-config) |
f4235c0e RW |
38 | #:use-module (gnu packages statistics) |
39 | #:use-module (gnu packages web)) | |
fa596599 | 40 | |
557a1089 RW |
41 | \f |
42 | ;;; Annotations | |
43 | ||
b7d93cf5 RW |
44 | (define-public r-bsgenome-celegans-ucsc-ce6 |
45 | (package | |
46 | (name "r-bsgenome-celegans-ucsc-ce6") | |
47 | (version "1.4.0") | |
48 | (source (origin | |
49 | (method url-fetch) | |
50 | ;; We cannot use bioconductor-uri here because this tarball is | |
51 | ;; located under "data/annotation/" instead of "bioc/". | |
52 | (uri (string-append "https://www.bioconductor.org/packages/" | |
53 | "release/data/annotation/src/contrib/" | |
54 | "BSgenome.Celegans.UCSC.ce6_" | |
55 | version ".tar.gz")) | |
56 | (sha256 | |
57 | (base32 | |
58 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
59 | (properties | |
60 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
61 | (build-system r-build-system) | |
62 | ;; As this package provides little more than a very large data file it | |
63 | ;; doesn't make sense to build substitutes. | |
64 | (arguments `(#:substitutable? #f)) | |
65 | (propagated-inputs | |
66 | `(("r-bsgenome" ,r-bsgenome))) | |
67 | (home-page | |
68 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
69 | (synopsis "Full genome sequences for Worm") | |
70 | (description | |
71 | "This package provides full genome sequences for Caenorhabditis | |
72 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
0c792ffb RW |
73 | objects.") |
74 | (license license:artistic2.0))) | |
75 | ||
76 | (define-public r-bsgenome-celegans-ucsc-ce10 | |
77 | (package | |
78 | (name "r-bsgenome-celegans-ucsc-ce10") | |
79 | (version "1.4.0") | |
80 | (source (origin | |
81 | (method url-fetch) | |
82 | ;; We cannot use bioconductor-uri here because this tarball is | |
83 | ;; located under "data/annotation/" instead of "bioc/". | |
84 | (uri (string-append "https://www.bioconductor.org/packages/" | |
85 | "release/data/annotation/src/contrib/" | |
86 | "BSgenome.Celegans.UCSC.ce10_" | |
87 | version ".tar.gz")) | |
88 | (sha256 | |
89 | (base32 | |
90 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
91 | (properties | |
92 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
93 | (build-system r-build-system) | |
94 | ;; As this package provides little more than a very large data file it | |
95 | ;; doesn't make sense to build substitutes. | |
96 | (arguments `(#:substitutable? #f)) | |
97 | (propagated-inputs | |
98 | `(("r-bsgenome" ,r-bsgenome))) | |
99 | (home-page | |
100 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
101 | (synopsis "Full genome sequences for Worm") | |
102 | (description | |
103 | "This package provides full genome sequences for Caenorhabditis | |
104 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
b7d93cf5 RW |
105 | objects.") |
106 | (license license:artistic2.0))) | |
107 | ||
183db725 RW |
108 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
109 | (package | |
110 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
111 | (version "1.4.1") | |
112 | (source (origin | |
113 | (method url-fetch) | |
114 | ;; We cannot use bioconductor-uri here because this tarball is | |
115 | ;; located under "data/annotation/" instead of "bioc/". | |
116 | (uri (string-append "https://www.bioconductor.org/packages/" | |
117 | "release/data/annotation/src/contrib/" | |
118 | "BSgenome.Dmelanogaster.UCSC.dm6_" | |
119 | version ".tar.gz")) | |
120 | (sha256 | |
121 | (base32 | |
122 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
123 | (properties | |
124 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
125 | (build-system r-build-system) | |
126 | ;; As this package provides little more than a very large data file it | |
127 | ;; doesn't make sense to build substitutes. | |
128 | (arguments `(#:substitutable? #f)) | |
129 | (propagated-inputs | |
130 | `(("r-bsgenome" ,r-bsgenome))) | |
131 | (home-page | |
132 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
133 | (synopsis "Full genome sequences for Fly") | |
134 | (description | |
135 | "This package provides full genome sequences for Drosophila | |
136 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
137 | objects.") | |
138 | (license license:artistic2.0))) | |
139 | ||
13dabd69 RW |
140 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
141 | (package | |
142 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
143 | (version "1.4.0") | |
144 | (source (origin | |
145 | (method url-fetch) | |
146 | ;; We cannot use bioconductor-uri here because this tarball is | |
147 | ;; located under "data/annotation/" instead of "bioc/". | |
148 | (uri (string-append "https://www.bioconductor.org/packages/" | |
149 | "release/data/annotation/src/contrib/" | |
150 | "BSgenome.Dmelanogaster.UCSC.dm3_" | |
151 | version ".tar.gz")) | |
152 | (sha256 | |
153 | (base32 | |
154 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
155 | (properties | |
156 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
157 | (build-system r-build-system) | |
158 | ;; As this package provides little more than a very large data file it | |
159 | ;; doesn't make sense to build substitutes. | |
160 | (arguments `(#:substitutable? #f)) | |
161 | (propagated-inputs | |
162 | `(("r-bsgenome" ,r-bsgenome))) | |
163 | (home-page | |
164 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
165 | (synopsis "Full genome sequences for Fly") | |
166 | (description | |
167 | "This package provides full genome sequences for Drosophila | |
168 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
169 | Biostrings objects.") | |
170 | (license license:artistic2.0))) | |
171 | ||
dfac7eb9 RW |
172 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
173 | (package | |
174 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
175 | (version "1.3.99") | |
176 | (source (origin | |
177 | (method url-fetch) | |
178 | ;; We cannot use bioconductor-uri here because this tarball is | |
179 | ;; located under "data/annotation/" instead of "bioc/". | |
180 | (uri (string-append "http://www.bioconductor.org/packages/" | |
181 | "release/data/annotation/src/contrib/" | |
182 | "BSgenome.Dmelanogaster.UCSC.dm3.masked_" | |
183 | version ".tar.gz")) | |
184 | (sha256 | |
185 | (base32 | |
186 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
187 | (properties | |
188 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
189 | (build-system r-build-system) | |
190 | (propagated-inputs | |
191 | `(("r-bsgenome" ,r-bsgenome) | |
192 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
193 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
194 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
195 | (synopsis "Full masked genome sequences for Fly") | |
196 | (description | |
197 | "This package provides full masked genome sequences for Drosophila | |
198 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
199 | Biostrings objects. The sequences are the same as in | |
200 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
201 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
202 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
203 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
204 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
205 | (license license:artistic2.0))) | |
206 | ||
40a65057 RW |
207 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
208 | (package | |
209 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
210 | (version "0.99.1") | |
211 | (source (origin | |
212 | (method url-fetch) | |
213 | ;; We cannot use bioconductor-uri here because this tarball is | |
214 | ;; located under "data/annotation/" instead of "bioc/". | |
215 | (uri (string-append "https://www.bioconductor.org/packages/" | |
216 | "release/data/annotation/src/contrib/" | |
217 | "BSgenome.Hsapiens.1000genomes.hs37d5_" | |
218 | version ".tar.gz")) | |
219 | (sha256 | |
220 | (base32 | |
221 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
222 | (properties | |
223 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
224 | (build-system r-build-system) | |
225 | ;; As this package provides little more than a very large data file it | |
226 | ;; doesn't make sense to build substitutes. | |
227 | (arguments `(#:substitutable? #f)) | |
228 | (propagated-inputs | |
229 | `(("r-bsgenome" ,r-bsgenome))) | |
230 | (home-page | |
231 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
232 | (synopsis "Full genome sequences for Homo sapiens") | |
233 | (description | |
234 | "This package provides full genome sequences for Homo sapiens from | |
235 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
236 | (license license:artistic2.0))) | |
237 | ||
6fbd759b RW |
238 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
239 | (package | |
240 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
241 | (version "1.3.99") | |
242 | (source (origin | |
243 | (method url-fetch) | |
244 | ;; We cannot use bioconductor-uri here because this tarball is | |
245 | ;; located under "data/annotation/" instead of "bioc/". | |
246 | (uri (string-append "http://www.bioconductor.org/packages/" | |
247 | "release/data/annotation/src/contrib/" | |
248 | "BSgenome.Hsapiens.UCSC.hg19.masked_" | |
249 | version ".tar.gz")) | |
250 | (sha256 | |
251 | (base32 | |
252 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
253 | (properties | |
254 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
255 | (build-system r-build-system) | |
256 | (propagated-inputs | |
257 | `(("r-bsgenome" ,r-bsgenome) | |
258 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
259 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
260 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
261 | (synopsis "Full masked genome sequences for Homo sapiens") | |
262 | (description | |
263 | "This package provides full genome sequences for Homo sapiens (Human) as | |
264 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
265 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
266 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
267 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
268 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
269 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
270 | default.") | |
271 | (license license:artistic2.0))) | |
272 | ||
5acb9052 RW |
273 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
274 | (package | |
275 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
276 | (version "1.4.0") | |
277 | (source (origin | |
278 | (method url-fetch) | |
279 | ;; We cannot use bioconductor-uri here because this tarball is | |
280 | ;; located under "data/annotation/" instead of "bioc/". | |
281 | (uri (string-append "https://www.bioconductor.org/packages/" | |
282 | "release/data/annotation/src/contrib/" | |
283 | "BSgenome.Mmusculus.UCSC.mm9_" | |
284 | version ".tar.gz")) | |
285 | (sha256 | |
286 | (base32 | |
287 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
288 | (properties | |
289 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
290 | (build-system r-build-system) | |
291 | ;; As this package provides little more than a very large data file it | |
292 | ;; doesn't make sense to build substitutes. | |
293 | (arguments `(#:substitutable? #f)) | |
294 | (propagated-inputs | |
295 | `(("r-bsgenome" ,r-bsgenome))) | |
296 | (home-page | |
297 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
298 | (synopsis "Full genome sequences for Mouse") | |
299 | (description | |
300 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
301 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
302 | (license license:artistic2.0))) | |
303 | ||
2bece692 RW |
304 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
305 | (package | |
306 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
307 | (version "1.3.99") | |
308 | (source (origin | |
309 | (method url-fetch) | |
310 | ;; We cannot use bioconductor-uri here because this tarball is | |
311 | ;; located under "data/annotation/" instead of "bioc/". | |
312 | (uri (string-append "http://www.bioconductor.org/packages/" | |
313 | "release/data/annotation/src/contrib/" | |
314 | "BSgenome.Mmusculus.UCSC.mm9.masked_" | |
315 | version ".tar.gz")) | |
316 | (sha256 | |
317 | (base32 | |
318 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
319 | (properties | |
320 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
321 | (build-system r-build-system) | |
322 | (propagated-inputs | |
323 | `(("r-bsgenome" ,r-bsgenome) | |
324 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
325 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
326 | (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") | |
327 | (synopsis "Full masked genome sequences for Mouse") | |
328 | (description | |
329 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
330 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
331 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
332 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
333 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
334 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
335 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
336 | default." ) | |
337 | (license license:artistic2.0))) | |
338 | ||
c3adc830 RW |
339 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
340 | (package | |
341 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
342 | (version "1.4.0") | |
343 | (source (origin | |
344 | (method url-fetch) | |
345 | ;; We cannot use bioconductor-uri here because this tarball is | |
346 | ;; located under "data/annotation/" instead of "bioc/". | |
347 | (uri (string-append "https://www.bioconductor.org/packages/" | |
348 | "release/data/annotation/src/contrib/" | |
349 | "BSgenome.Mmusculus.UCSC.mm10_" | |
350 | version ".tar.gz")) | |
351 | (sha256 | |
352 | (base32 | |
353 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
354 | (properties | |
355 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
356 | (build-system r-build-system) | |
357 | ;; As this package provides little more than a very large data file it | |
358 | ;; doesn't make sense to build substitutes. | |
359 | (arguments `(#:substitutable? #f)) | |
360 | (propagated-inputs | |
361 | `(("r-bsgenome" ,r-bsgenome))) | |
362 | (home-page | |
363 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
364 | (synopsis "Full genome sequences for Mouse") | |
365 | (description | |
366 | "This package provides full genome sequences for Mus | |
367 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
368 | in Biostrings objects.") | |
369 | (license license:artistic2.0))) | |
370 | ||
3a08940e RW |
371 | (define-public r-org-ce-eg-db |
372 | (package | |
373 | (name "r-org-ce-eg-db") | |
374 | (version "3.7.0") | |
375 | (source (origin | |
376 | (method url-fetch) | |
377 | ;; We cannot use bioconductor-uri here because this tarball is | |
378 | ;; located under "data/annotation/" instead of "bioc/". | |
379 | (uri (string-append "https://www.bioconductor.org/packages/" | |
380 | "release/data/annotation/src/contrib/" | |
381 | "org.Ce.eg.db_" version ".tar.gz")) | |
382 | (sha256 | |
383 | (base32 | |
384 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) | |
385 | (properties | |
386 | `((upstream-name . "org.Ce.eg.db"))) | |
387 | (build-system r-build-system) | |
388 | (propagated-inputs | |
389 | `(("r-annotationdbi" ,r-annotationdbi))) | |
390 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") | |
391 | (synopsis "Genome wide annotation for Worm") | |
392 | (description | |
393 | "This package provides mappings from Entrez gene identifiers to various | |
394 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
395 | (license license:artistic2.0))) | |
396 | ||
f8780e96 RW |
397 | (define-public r-org-dm-eg-db |
398 | (package | |
399 | (name "r-org-dm-eg-db") | |
400 | (version "3.7.0") | |
401 | (source (origin | |
402 | (method url-fetch) | |
403 | ;; We cannot use bioconductor-uri here because this tarball is | |
404 | ;; located under "data/annotation/" instead of "bioc/". | |
405 | (uri (string-append "https://www.bioconductor.org/packages/" | |
406 | "release/data/annotation/src/contrib/" | |
407 | "org.Dm.eg.db_" version ".tar.gz")) | |
408 | (sha256 | |
409 | (base32 | |
410 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) | |
411 | (properties | |
412 | `((upstream-name . "org.Dm.eg.db"))) | |
413 | (build-system r-build-system) | |
414 | (propagated-inputs | |
415 | `(("r-annotationdbi" ,r-annotationdbi))) | |
416 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") | |
417 | (synopsis "Genome wide annotation for Fly") | |
418 | (description | |
419 | "This package provides mappings from Entrez gene identifiers to various | |
420 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
421 | (license license:artistic2.0))) | |
422 | ||
3dad6087 RW |
423 | (define-public r-org-dr-eg-db |
424 | (package | |
425 | (name "r-org-dr-eg-db") | |
426 | (version "3.7.0") | |
427 | (source (origin | |
428 | (method url-fetch) | |
429 | ;; We cannot use bioconductor-uri here because this tarball is | |
430 | ;; located under "data/annotation/" instead of "bioc/". | |
431 | (uri (string-append "https://www.bioconductor.org/packages/" | |
432 | "release/data/annotation/src/contrib/" | |
433 | "org.Dr.eg.db_" version ".tar.gz")) | |
434 | (sha256 | |
435 | (base32 | |
436 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) | |
437 | (properties | |
438 | `((upstream-name . "org.Dr.eg.db"))) | |
439 | (build-system r-build-system) | |
440 | (propagated-inputs | |
441 | `(("r-annotationdbi" ,r-annotationdbi))) | |
442 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") | |
443 | (synopsis "Annotation for Zebrafish") | |
444 | (description | |
445 | "This package provides genome wide annotations for Zebrafish, primarily | |
446 | based on mapping using Entrez Gene identifiers.") | |
447 | (license license:artistic2.0))) | |
448 | ||
d56df35a RW |
449 | (define-public r-org-hs-eg-db |
450 | (package | |
451 | (name "r-org-hs-eg-db") | |
452 | (version "3.7.0") | |
453 | (source (origin | |
454 | (method url-fetch) | |
455 | ;; We cannot use bioconductor-uri here because this tarball is | |
456 | ;; located under "data/annotation/" instead of "bioc/". | |
457 | (uri (string-append "https://www.bioconductor.org/packages/" | |
458 | "release/data/annotation/src/contrib/" | |
459 | "org.Hs.eg.db_" version ".tar.gz")) | |
460 | (sha256 | |
461 | (base32 | |
462 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) | |
463 | (properties | |
464 | `((upstream-name . "org.Hs.eg.db"))) | |
465 | (build-system r-build-system) | |
466 | (propagated-inputs | |
467 | `(("r-annotationdbi" ,r-annotationdbi))) | |
468 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") | |
469 | (synopsis "Genome wide annotation for Human") | |
470 | (description | |
471 | "This package contains genome-wide annotations for Human, primarily based | |
472 | on mapping using Entrez Gene identifiers.") | |
473 | (license license:artistic2.0))) | |
474 | ||
8035819f RW |
475 | (define-public r-org-mm-eg-db |
476 | (package | |
477 | (name "r-org-mm-eg-db") | |
478 | (version "3.7.0") | |
479 | (source (origin | |
480 | (method url-fetch) | |
481 | ;; We cannot use bioconductor-uri here because this tarball is | |
482 | ;; located under "data/annotation/" instead of "bioc/". | |
483 | (uri (string-append "https://www.bioconductor.org/packages/" | |
484 | "release/data/annotation/src/contrib/" | |
485 | "org.Mm.eg.db_" version ".tar.gz")) | |
486 | (sha256 | |
487 | (base32 | |
488 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) | |
489 | (properties | |
490 | `((upstream-name . "org.Mm.eg.db"))) | |
491 | (build-system r-build-system) | |
492 | (propagated-inputs | |
493 | `(("r-annotationdbi" ,r-annotationdbi))) | |
494 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") | |
495 | (synopsis "Genome wide annotation for Mouse") | |
496 | (description | |
497 | "This package provides mappings from Entrez gene identifiers to various | |
498 | annotations for the genome of the model mouse Mus musculus.") | |
499 | (license license:artistic2.0))) | |
500 | ||
fe0b76e2 RW |
501 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
502 | (package | |
503 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
504 | (version "1.4.0") | |
505 | (source (origin | |
506 | (method url-fetch) | |
507 | ;; We cannot use bioconductor-uri here because this tarball is | |
508 | ;; located under "data/annotation/" instead of "bioc/". | |
509 | (uri (string-append "https://www.bioconductor.org/packages/" | |
510 | "release/data/annotation/src/contrib/" | |
511 | "BSgenome.Hsapiens.UCSC.hg19_" | |
512 | version ".tar.gz")) | |
513 | (sha256 | |
514 | (base32 | |
515 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) | |
516 | (properties | |
517 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
518 | (build-system r-build-system) | |
519 | ;; As this package provides little more than a very large data file it | |
520 | ;; doesn't make sense to build substitutes. | |
521 | (arguments `(#:substitutable? #f)) | |
522 | (propagated-inputs | |
523 | `(("r-bsgenome" ,r-bsgenome))) | |
524 | (home-page | |
525 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
526 | (synopsis "Full genome sequences for Homo sapiens") | |
527 | (description | |
528 | "This package provides full genome sequences for Homo sapiens as provided | |
529 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
530 | (license license:artistic2.0))) | |
531 | ||
2cc51108 RW |
532 | (define-public r-genelendatabase |
533 | (package | |
534 | (name "r-genelendatabase") | |
daeb3cd9 | 535 | (version "1.18.0") |
2cc51108 RW |
536 | (source |
537 | (origin | |
538 | (method url-fetch) | |
539 | ;; We cannot use bioconductor-uri here because this tarball is | |
540 | ;; located under "data/experiment/" instead of "bioc/". | |
541 | (uri (string-append "https://bioconductor.org/packages/" | |
542 | "release/data/experiment/src/contrib" | |
543 | "/geneLenDataBase_" version ".tar.gz")) | |
544 | (sha256 | |
545 | (base32 | |
daeb3cd9 | 546 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
2cc51108 RW |
547 | (properties |
548 | `((upstream-name . "geneLenDataBase"))) | |
549 | (build-system r-build-system) | |
550 | (propagated-inputs | |
551 | `(("r-rtracklayer" ,r-rtracklayer) | |
552 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
553 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
554 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
555 | (description | |
556 | "This package provides the lengths of mRNA transcripts for a number of | |
557 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
558 | (license license:lgpl2.0+))) | |
559 | ||
66e35ce6 RW |
560 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
561 | (package | |
562 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
563 | (version "3.2.2") | |
564 | (source (origin | |
565 | (method url-fetch) | |
566 | ;; We cannot use bioconductor-uri here because this tarball is | |
567 | ;; located under "data/annotation/" instead of "bioc/". | |
568 | (uri (string-append "https://bioconductor.org/packages/" | |
569 | "release/data/annotation/src/contrib" | |
570 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" | |
571 | version ".tar.gz")) | |
572 | (sha256 | |
573 | (base32 | |
574 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
575 | (properties | |
576 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
577 | (build-system r-build-system) | |
578 | ;; As this package provides little more than a very large data file it | |
579 | ;; doesn't make sense to build substitutes. | |
580 | (arguments `(#:substitutable? #f)) | |
581 | (propagated-inputs | |
582 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
583 | (home-page | |
584 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
585 | (synopsis "Annotation package for human genome in TxDb format") | |
586 | (description | |
587 | "This package provides an annotation database of Homo sapiens genome | |
588 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
589 | track. The database is exposed as a @code{TxDb} object.") | |
590 | (license license:artistic2.0))) | |
591 | ||
d220babf RW |
592 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
593 | (package | |
594 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
595 | (version "3.2.2") | |
596 | (source (origin | |
597 | (method url-fetch) | |
598 | ;; We cannot use bioconductor-uri here because this tarball is | |
599 | ;; located under "data/annotation/" instead of "bioc/". | |
600 | (uri (string-append "https://bioconductor.org/packages/" | |
601 | "release/data/annotation/src/contrib" | |
602 | "/TxDb.Mmusculus.UCSC.mm9.knownGene_" | |
603 | version ".tar.gz")) | |
604 | (sha256 | |
605 | (base32 | |
606 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
607 | (properties | |
608 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
609 | (build-system r-build-system) | |
610 | (propagated-inputs | |
611 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
612 | ("r-annotationdbi" ,r-annotationdbi))) | |
613 | (home-page | |
614 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
615 | (synopsis "Annotation package for mouse genome in TxDb format") | |
616 | (description | |
617 | "This package provides an annotation database of Mouse genome data. It | |
618 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
619 | database is exposed as a @code{TxDb} object.") | |
620 | (license license:artistic2.0))) | |
621 | ||
7bc5d1b0 RW |
622 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
623 | (package | |
624 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
625 | (version "3.4.4") | |
626 | (source (origin | |
627 | (method url-fetch) | |
628 | ;; We cannot use bioconductor-uri here because this tarball is | |
629 | ;; located under "data/annotation/" instead of "bioc/". | |
630 | (uri (string-append "https://www.bioconductor.org/packages/" | |
631 | "release/data/annotation/src/contrib/" | |
632 | "TxDb.Mmusculus.UCSC.mm10.knownGene_" | |
633 | version ".tar.gz")) | |
634 | (sha256 | |
635 | (base32 | |
636 | "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39")))) | |
637 | (properties | |
638 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
639 | (build-system r-build-system) | |
640 | ;; As this package provides little more than a very large data file it | |
641 | ;; doesn't make sense to build substitutes. | |
642 | (arguments `(#:substitutable? #f)) | |
643 | (propagated-inputs | |
644 | `(("r-bsgenome" ,r-bsgenome) | |
645 | ("r-genomicfeatures" ,r-genomicfeatures) | |
646 | ("r-annotationdbi" ,r-annotationdbi))) | |
647 | (home-page | |
648 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
649 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
650 | (description | |
651 | "This package loads a TxDb object, which is an R interface to | |
652 | prefabricated databases contained in this package. This package provides | |
653 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
654 | based on the knownGene track.") | |
655 | (license license:artistic2.0))) | |
656 | ||
0f5c9cec RW |
657 | (define-public r-fdb-infiniummethylation-hg19 |
658 | (package | |
659 | (name "r-fdb-infiniummethylation-hg19") | |
660 | (version "2.2.0") | |
661 | (source (origin | |
662 | (method url-fetch) | |
663 | ;; We cannot use bioconductor-uri here because this tarball is | |
664 | ;; located under "data/annotation/" instead of "bioc/". | |
665 | (uri (string-append "https://www.bioconductor.org/packages/" | |
666 | "release/data/annotation/src/contrib/" | |
667 | "FDb.InfiniumMethylation.hg19_" | |
668 | version ".tar.gz")) | |
669 | (sha256 | |
670 | (base32 | |
671 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) | |
672 | (properties | |
673 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) | |
674 | (build-system r-build-system) | |
675 | (propagated-inputs | |
676 | `(("r-biostrings" ,r-biostrings) | |
677 | ("r-genomicfeatures" ,r-genomicfeatures) | |
678 | ("r-annotationdbi" ,r-annotationdbi) | |
679 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
680 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) | |
681 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") | |
682 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") | |
683 | (description | |
684 | "This is an annotation package for Illumina Infinium DNA methylation | |
685 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 | |
686 | annotations.") | |
687 | (license license:artistic2.0))) | |
688 | ||
9475a248 RW |
689 | (define-public r-illuminahumanmethylationepicmanifest |
690 | (package | |
691 | (name "r-illuminahumanmethylationepicmanifest") | |
692 | (version "0.3.0") | |
693 | (source (origin | |
694 | (method url-fetch) | |
695 | ;; We cannot use bioconductor-uri here because this tarball is | |
696 | ;; located under "data/annotation/" instead of "bioc/". | |
697 | (uri (string-append "https://www.bioconductor.org/packages/" | |
698 | "release/data/annotation/src/contrib/" | |
699 | "IlluminaHumanMethylationEPICmanifest_" | |
700 | version ".tar.gz")) | |
701 | (sha256 | |
702 | (base32 | |
703 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) | |
704 | (properties | |
705 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) | |
706 | (build-system r-build-system) | |
707 | (propagated-inputs | |
708 | `(("r-minfi" ,r-minfi))) | |
709 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") | |
710 | (synopsis "Manifest for Illumina's EPIC methylation arrays") | |
711 | (description | |
712 | "This is a manifest package for Illumina's EPIC methylation arrays.") | |
713 | (license license:artistic2.0))) | |
714 | ||
f8a5af46 RW |
715 | (define-public r-do-db |
716 | (package | |
717 | (name "r-do-db") | |
718 | (version "2.9") | |
719 | (source (origin | |
720 | (method url-fetch) | |
721 | ;; We cannot use bioconductor-uri here because this tarball is | |
722 | ;; located under "data/annotation/" instead of "bioc/". | |
723 | (uri (string-append "https://www.bioconductor.org/packages/" | |
724 | "release/data/annotation/src/contrib/" | |
725 | "DO.db_" version ".tar.gz")) | |
726 | (sha256 | |
727 | (base32 | |
728 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) | |
729 | (properties | |
730 | `((upstream-name . "DO.db"))) | |
731 | (build-system r-build-system) | |
732 | (propagated-inputs | |
733 | `(("r-annotationdbi" ,r-annotationdbi))) | |
734 | (home-page "https://www.bioconductor.org/packages/DO.db/") | |
735 | (synopsis "Annotation maps describing the entire Disease Ontology") | |
736 | (description | |
737 | "This package provides a set of annotation maps describing the entire | |
738 | Disease Ontology.") | |
739 | (license license:artistic2.0))) | |
740 | ||
2cc51108 | 741 | \f |
557a1089 RW |
742 | ;;; Experiment data |
743 | ||
692bce15 RW |
744 | (define-public r-abadata |
745 | (package | |
746 | (name "r-abadata") | |
747 | (version "1.12.0") | |
748 | (source (origin | |
749 | (method url-fetch) | |
750 | ;; We cannot use bioconductor-uri here because this tarball is | |
751 | ;; located under "data/experiment/" instead of "bioc/". | |
752 | (uri (string-append "https://www.bioconductor.org/packages/" | |
753 | "release/data/experiment/src/contrib/" | |
754 | "ABAData_" version ".tar.gz")) | |
755 | (sha256 | |
756 | (base32 | |
757 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) | |
758 | (properties | |
759 | `((upstream-name . "ABAData"))) | |
760 | (build-system r-build-system) | |
761 | (propagated-inputs | |
762 | `(("r-annotationdbi" ,r-annotationdbi))) | |
763 | (home-page "https://www.bioconductor.org/packages/ABAData/") | |
764 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") | |
765 | (description | |
766 | "This package provides the data for the gene expression enrichment | |
767 | analysis conducted in the package ABAEnrichment. The package includes three | |
768 | datasets which are derived from the Allen Brain Atlas: | |
769 | ||
770 | @enumerate | |
771 | @item Gene expression data from Human Brain (adults) averaged across donors, | |
772 | @item Gene expression data from the Developing Human Brain pooled into five | |
773 | age categories and averaged across donors, and | |
774 | @item a developmental effect score based on the Developing Human Brain | |
775 | expression data. | |
776 | @end enumerate | |
777 | ||
778 | All datasets are restricted to protein coding genes.") | |
779 | (license license:gpl2+))) | |
780 | ||
b50c9660 RW |
781 | (define-public r-arrmdata |
782 | (package | |
783 | (name "r-arrmdata") | |
784 | (version "1.18.0") | |
785 | (source (origin | |
786 | (method url-fetch) | |
787 | ;; We cannot use bioconductor-uri here because this tarball is | |
788 | ;; located under "data/experiment/" instead of "bioc/". | |
789 | (uri (string-append "https://www.bioconductor.org/packages/" | |
790 | "release/data/experiment/src/contrib/" | |
791 | "ARRmData_" version ".tar.gz")) | |
792 | (sha256 | |
793 | (base32 | |
794 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) | |
795 | (properties | |
796 | `((upstream-name . "ARRmData"))) | |
797 | (build-system r-build-system) | |
798 | (home-page "https://www.bioconductor.org/packages/ARRmData/") | |
799 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") | |
800 | (description | |
801 | "This package provides raw beta values from 36 samples across 3 groups | |
802 | from Illumina 450k methylation arrays.") | |
803 | (license license:artistic2.0))) | |
804 | ||
557a1089 RW |
805 | (define-public r-hsmmsinglecell |
806 | (package | |
807 | (name "r-hsmmsinglecell") | |
808 | (version "1.2.0") | |
809 | (source (origin | |
810 | (method url-fetch) | |
811 | ;; We cannot use bioconductor-uri here because this tarball is | |
812 | ;; located under "data/experiment/" instead of "bioc/". | |
813 | (uri (string-append "https://www.bioconductor.org/packages/" | |
814 | "release/data/experiment/src/contrib/" | |
815 | "HSMMSingleCell_" version ".tar.gz")) | |
816 | (sha256 | |
817 | (base32 | |
818 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) | |
819 | (properties | |
820 | `((upstream-name . "HSMMSingleCell"))) | |
821 | (build-system r-build-system) | |
822 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") | |
823 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") | |
824 | (description | |
825 | "Skeletal myoblasts undergo a well-characterized sequence of | |
826 | morphological and transcriptional changes during differentiation. In this | |
827 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded | |
828 | under high mitogen conditions (GM) and then differentiated by switching to | |
829 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several | |
830 | hundred cells taken over a time-course of serum-induced differentiation. | |
831 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, | |
832 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. | |
833 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, | |
834 | which were then sequenced to a depth of ~4 million reads per library, | |
835 | resulting in a complete gene expression profile for each cell.") | |
836 | (license license:artistic2.0))) | |
837 | ||
838 | \f | |
839 | ;;; Packages | |
840 | ||
14bba460 RW |
841 | (define-public r-biocgenerics |
842 | (package | |
843 | (name "r-biocgenerics") | |
81a1c45d | 844 | (version "0.30.0") |
14bba460 RW |
845 | (source (origin |
846 | (method url-fetch) | |
847 | (uri (bioconductor-uri "BiocGenerics" version)) | |
848 | (sha256 | |
849 | (base32 | |
81a1c45d | 850 | "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f")))) |
14bba460 RW |
851 | (properties |
852 | `((upstream-name . "BiocGenerics"))) | |
853 | (build-system r-build-system) | |
854 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
855 | (synopsis "S4 generic functions for Bioconductor") | |
856 | (description | |
857 | "This package provides S4 generic functions needed by many Bioconductor | |
858 | packages.") | |
859 | (license license:artistic2.0))) | |
860 | ||
7097c700 RW |
861 | (define-public r-annotate |
862 | (package | |
863 | (name "r-annotate") | |
0c53332a | 864 | (version "1.62.0") |
7097c700 RW |
865 | (source |
866 | (origin | |
867 | (method url-fetch) | |
868 | (uri (bioconductor-uri "annotate" version)) | |
869 | (sha256 | |
870 | (base32 | |
0c53332a | 871 | "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs")))) |
7097c700 RW |
872 | (build-system r-build-system) |
873 | (propagated-inputs | |
874 | `(("r-annotationdbi" ,r-annotationdbi) | |
875 | ("r-biobase" ,r-biobase) | |
876 | ("r-biocgenerics" ,r-biocgenerics) | |
877 | ("r-dbi" ,r-dbi) | |
878 | ("r-rcurl" ,r-rcurl) | |
879 | ("r-xml" ,r-xml) | |
880 | ("r-xtable" ,r-xtable))) | |
881 | (home-page | |
882 | "https://bioconductor.org/packages/annotate") | |
883 | (synopsis "Annotation for microarrays") | |
884 | (description "This package provides R environments for the annotation of | |
885 | microarrays.") | |
886 | (license license:artistic2.0))) | |
887 | ||
fa596599 RW |
888 | (define-public r-hpar |
889 | (package | |
890 | (name "r-hpar") | |
43a23a07 | 891 | (version "1.26.0") |
fa596599 RW |
892 | (source |
893 | (origin | |
894 | (method url-fetch) | |
895 | (uri (bioconductor-uri "hpar" version)) | |
896 | (sha256 | |
897 | (base32 | |
43a23a07 | 898 | "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5")))) |
fa596599 RW |
899 | (build-system r-build-system) |
900 | (home-page "https://bioconductor.org/packages/hpar/") | |
901 | (synopsis "Human Protein Atlas in R") | |
902 | (description "This package provides a simple interface to and data from | |
903 | the Human Protein Atlas project.") | |
904 | (license license:artistic2.0))) | |
183ce988 RJ |
905 | |
906 | (define-public r-regioner | |
907 | (package | |
908 | (name "r-regioner") | |
4b53d55e | 909 | (version "1.16.0") |
183ce988 RJ |
910 | (source |
911 | (origin | |
912 | (method url-fetch) | |
913 | (uri (bioconductor-uri "regioneR" version)) | |
914 | (sha256 | |
915 | (base32 | |
4b53d55e | 916 | "014h2q346ynfdbpavh4p69cyv4j65hk934liq5892zznjzl73z7p")))) |
183ce988 RJ |
917 | (properties `((upstream-name . "regioneR"))) |
918 | (build-system r-build-system) | |
919 | (propagated-inputs | |
d639d888 | 920 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 921 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 922 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 923 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 924 | ("r-iranges" ,r-iranges) |
d639d888 RW |
925 | ("r-memoise" ,r-memoise) |
926 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 927 | ("r-s4vectors" ,r-s4vectors))) |
183ce988 RJ |
928 | (home-page "https://bioconductor.org/packages/regioneR/") |
929 | (synopsis "Association analysis of genomic regions") | |
930 | (description "This package offers a statistical framework based on | |
931 | customizable permutation tests to assess the association between genomic | |
932 | region sets and other genomic features.") | |
933 | (license license:artistic2.0))) | |
a5b56a53 | 934 | |
bfb93b48 RW |
935 | (define-public r-geneplotter |
936 | (package | |
937 | (name "r-geneplotter") | |
3e1bc88c | 938 | (version "1.62.0") |
bfb93b48 RW |
939 | (source |
940 | (origin | |
941 | (method url-fetch) | |
942 | (uri (bioconductor-uri "geneplotter" version)) | |
943 | (sha256 | |
944 | (base32 | |
3e1bc88c | 945 | "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb")))) |
bfb93b48 RW |
946 | (build-system r-build-system) |
947 | (propagated-inputs | |
948 | `(("r-annotate" ,r-annotate) | |
949 | ("r-annotationdbi" ,r-annotationdbi) | |
950 | ("r-biobase" ,r-biobase) | |
951 | ("r-biocgenerics" ,r-biocgenerics) | |
952 | ("r-lattice" ,r-lattice) | |
953 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
954 | (home-page "https://bioconductor.org/packages/geneplotter") | |
955 | (synopsis "Graphics functions for genomic data") | |
956 | (description | |
957 | "This package provides functions for plotting genomic data.") | |
958 | (license license:artistic2.0))) | |
959 | ||
4dc2ecc2 RW |
960 | (define-public r-qvalue |
961 | (package | |
962 | (name "r-qvalue") | |
e02162f7 | 963 | (version "2.16.0") |
4dc2ecc2 RW |
964 | (source |
965 | (origin | |
966 | (method url-fetch) | |
967 | (uri (bioconductor-uri "qvalue" version)) | |
968 | (sha256 | |
969 | (base32 | |
e02162f7 | 970 | "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5")))) |
4dc2ecc2 RW |
971 | (build-system r-build-system) |
972 | (propagated-inputs | |
973 | `(("r-ggplot2" ,r-ggplot2) | |
974 | ("r-reshape2" ,r-reshape2))) | |
975 | (home-page "http://github.com/jdstorey/qvalue") | |
976 | (synopsis "Q-value estimation for false discovery rate control") | |
977 | (description | |
978 | "This package takes a list of p-values resulting from the simultaneous | |
979 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
980 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
981 | of false positives incurred when that particular test is called significant. | |
982 | The local FDR measures the posterior probability the null hypothesis is true | |
983 | given the test's p-value. Various plots are automatically generated, allowing | |
984 | one to make sensible significance cut-offs. The software can be applied to | |
985 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
986 | ;; Any version of the LGPL. | |
987 | (license license:lgpl3+))) | |
988 | ||
a5b56a53 RJ |
989 | (define-public r-diffbind |
990 | (package | |
991 | (name "r-diffbind") | |
4c221b3b | 992 | (version "2.12.0") |
a5b56a53 RJ |
993 | (source |
994 | (origin | |
995 | (method url-fetch) | |
996 | (uri (bioconductor-uri "DiffBind" version)) | |
997 | (sha256 | |
998 | (base32 | |
4c221b3b | 999 | "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich")))) |
a5b56a53 RJ |
1000 | (properties `((upstream-name . "DiffBind"))) |
1001 | (build-system r-build-system) | |
1002 | (inputs | |
1003 | `(("zlib" ,zlib))) | |
1004 | (propagated-inputs | |
1005 | `(("r-amap" ,r-amap) | |
1006 | ("r-biocparallel" ,r-biocparallel) | |
1007 | ("r-deseq2" ,r-deseq2) | |
1008 | ("r-dplyr" ,r-dplyr) | |
1009 | ("r-edger" ,r-edger) | |
1010 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
1011 | ("r-genomicranges" ,r-genomicranges) |
1012 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
1013 | ("r-ggrepel" ,r-ggrepel) |
1014 | ("r-gplots" ,r-gplots) | |
1015 | ("r-iranges" ,r-iranges) | |
1016 | ("r-lattice" ,r-lattice) | |
1017 | ("r-limma" ,r-limma) | |
1018 | ("r-locfit" ,r-locfit) | |
1019 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
1020 | ("r-rcpp" ,r-rcpp) | |
4c221b3b | 1021 | ("r-rhtslib" ,r-rhtslib) |
a5b56a53 RJ |
1022 | ("r-rsamtools" ,r-rsamtools) |
1023 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 1024 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
4c221b3b | 1025 | ("r-systempiper" ,r-systempiper))) |
a5b56a53 RJ |
1026 | (home-page "http://bioconductor.org/packages/DiffBind") |
1027 | (synopsis "Differential binding analysis of ChIP-Seq peak data") | |
1028 | (description | |
1029 | "This package computes differentially bound sites from multiple | |
1030 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
1031 | occupancy (overlap) analysis and plotting functions.") | |
1032 | (license license:artistic2.0))) | |
6d94bf6b RJ |
1033 | |
1034 | (define-public r-ripseeker | |
1035 | (package | |
1036 | (name "r-ripseeker") | |
0968a448 | 1037 | (version "1.24.0") |
6d94bf6b RJ |
1038 | (source |
1039 | (origin | |
1040 | (method url-fetch) | |
1041 | (uri (bioconductor-uri "RIPSeeker" version)) | |
1042 | (sha256 | |
1043 | (base32 | |
0968a448 | 1044 | "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43")))) |
6d94bf6b RJ |
1045 | (properties `((upstream-name . "RIPSeeker"))) |
1046 | (build-system r-build-system) | |
1047 | (propagated-inputs | |
1048 | `(("r-s4vectors" ,r-s4vectors) | |
1049 | ("r-iranges" ,r-iranges) | |
1050 | ("r-genomicranges" ,r-genomicranges) | |
1051 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1052 | ("r-rsamtools" ,r-rsamtools) | |
1053 | ("r-genomicalignments" ,r-genomicalignments) | |
1054 | ("r-rtracklayer" ,r-rtracklayer))) | |
1055 | (home-page "http://bioconductor.org/packages/RIPSeeker") | |
1056 | (synopsis | |
1057 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
1058 | (description | |
1059 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
1060 | using two-state HMM with negative binomial emission probability. While | |
1061 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
1062 | a suite of bioinformatics tools integrated within this self-contained software | |
1063 | package comprehensively addressing issues ranging from post-alignments | |
1064 | processing to visualization and annotation.") | |
1065 | (license license:gpl2))) | |
a6ae9ffd RJ |
1066 | |
1067 | (define-public r-multtest | |
1068 | (package | |
1069 | (name "r-multtest") | |
588b63c2 | 1070 | (version "2.40.0") |
a6ae9ffd RJ |
1071 | (source |
1072 | (origin | |
1073 | (method url-fetch) | |
1074 | (uri (bioconductor-uri "multtest" version)) | |
1075 | (sha256 | |
1076 | (base32 | |
588b63c2 | 1077 | "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv")))) |
a6ae9ffd RJ |
1078 | (build-system r-build-system) |
1079 | (propagated-inputs | |
1080 | `(("r-survival" ,r-survival) | |
1081 | ("r-biocgenerics" ,r-biocgenerics) | |
1082 | ("r-biobase" ,r-biobase) | |
1083 | ("r-mass" ,r-mass))) | |
1084 | (home-page "http://bioconductor.org/packages/multtest") | |
1085 | (synopsis "Resampling-based multiple hypothesis testing") | |
1086 | (description | |
1087 | "This package can do non-parametric bootstrap and permutation | |
1088 | resampling-based multiple testing procedures (including empirical Bayes | |
1089 | methods) for controlling the family-wise error rate (FWER), generalized | |
1090 | family-wise error rate (gFWER), tail probability of the proportion of | |
1091 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
1092 | of bootstrap-based null distribution are implemented (centered, centered | |
1093 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
1094 | available. Tests based on a variety of T- and F-statistics (including | |
1095 | T-statistics based on regression parameters from linear and survival models | |
1096 | as well as those based on correlation parameters) are included. When probing | |
1097 | hypotheses with T-statistics, users may also select a potentially faster null | |
1098 | distribution which is multivariate normal with mean zero and variance | |
1099 | covariance matrix derived from the vector influence function. Results are | |
1100 | reported in terms of adjusted P-values, confidence regions and test statistic | |
1101 | cutoffs. The procedures are directly applicable to identifying differentially | |
1102 | expressed genes in DNA microarray experiments.") | |
1103 | (license license:lgpl3))) | |
793f83ef | 1104 | |
5dfe4912 RW |
1105 | (define-public r-graph |
1106 | (package | |
1107 | (name "r-graph") | |
a61bcb28 | 1108 | (version "1.62.0") |
5dfe4912 RW |
1109 | (source (origin |
1110 | (method url-fetch) | |
1111 | (uri (bioconductor-uri "graph" version)) | |
1112 | (sha256 | |
1113 | (base32 | |
a61bcb28 | 1114 | "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w")))) |
5dfe4912 RW |
1115 | (build-system r-build-system) |
1116 | (propagated-inputs | |
1117 | `(("r-biocgenerics" ,r-biocgenerics))) | |
1118 | (home-page "https://bioconductor.org/packages/graph") | |
1119 | (synopsis "Handle graph data structures in R") | |
1120 | (description | |
1121 | "This package implements some simple graph handling capabilities for R.") | |
1122 | (license license:artistic2.0))) | |
1123 | ||
a207bca2 RW |
1124 | (define-public r-codedepends |
1125 | (package | |
1126 | (name "r-codedepends") | |
1127 | (version "0.6.5") | |
1128 | (source | |
1129 | (origin | |
1130 | (method url-fetch) | |
1131 | (uri (cran-uri "CodeDepends" version)) | |
1132 | (sha256 | |
1133 | (base32 | |
1134 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
1135 | (properties `((upstream-name . "CodeDepends"))) | |
1136 | (build-system r-build-system) | |
1137 | (propagated-inputs | |
1138 | `(("r-codetools" ,r-codetools) | |
1139 | ("r-graph" ,r-graph) | |
1140 | ("r-xml" ,r-xml))) | |
1141 | (home-page "http://cran.r-project.org/web/packages/CodeDepends") | |
1142 | (synopsis "Analysis of R code for reproducible research and code comprehension") | |
1143 | (description | |
1144 | "This package provides tools for analyzing R expressions or blocks of | |
1145 | code and determining the dependencies between them. It focuses on R scripts, | |
1146 | but can be used on the bodies of functions. There are many facilities | |
1147 | including the ability to summarize or get a high-level view of code, | |
1148 | determining dependencies between variables, code improvement suggestions.") | |
1149 | ;; Any version of the GPL | |
1150 | (license (list license:gpl2+ license:gpl3+)))) | |
1151 | ||
793f83ef RJ |
1152 | (define-public r-chippeakanno |
1153 | (package | |
1154 | (name "r-chippeakanno") | |
add2b195 | 1155 | (version "3.16.1") |
793f83ef RJ |
1156 | (source |
1157 | (origin | |
1158 | (method url-fetch) | |
1159 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
1160 | (sha256 | |
1161 | (base32 | |
add2b195 | 1162 | "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3")))) |
793f83ef RJ |
1163 | (properties `((upstream-name . "ChIPpeakAnno"))) |
1164 | (build-system r-build-system) | |
1165 | (propagated-inputs | |
1166 | `(("r-biocgenerics" ,r-biocgenerics) | |
57d2fcd9 | 1167 | ("r-biocmanager" ,r-biocmanager) |
f794e85d RW |
1168 | ("r-biostrings" ,r-biostrings) |
1169 | ("r-delayedarray" ,r-delayedarray) | |
793f83ef RJ |
1170 | ("r-go-db" ,r-go-db) |
1171 | ("r-biomart" ,r-biomart) | |
1172 | ("r-bsgenome" ,r-bsgenome) | |
1173 | ("r-genomicfeatures" ,r-genomicfeatures) | |
f794e85d | 1174 | ("r-genomicranges" ,r-genomicranges) |
793f83ef | 1175 | ("r-genomeinfodb" ,r-genomeinfodb) |
f794e85d | 1176 | ("r-iranges" ,r-iranges) |
793f83ef RJ |
1177 | ("r-matrixstats" ,r-matrixstats) |
1178 | ("r-annotationdbi" ,r-annotationdbi) | |
1179 | ("r-limma" ,r-limma) | |
1180 | ("r-multtest" ,r-multtest) | |
1181 | ("r-rbgl" ,r-rbgl) | |
1182 | ("r-graph" ,r-graph) | |
793f83ef RJ |
1183 | ("r-regioner" ,r-regioner) |
1184 | ("r-dbi" ,r-dbi) | |
1185 | ("r-ensembldb" ,r-ensembldb) | |
1186 | ("r-biobase" ,r-biobase) | |
f794e85d | 1187 | ("r-s4vectors" ,r-s4vectors) |
793f83ef RJ |
1188 | ("r-seqinr" ,r-seqinr) |
1189 | ("r-idr" ,r-idr) | |
1190 | ("r-genomicalignments" ,r-genomicalignments) | |
1191 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1192 | ("r-rsamtools" ,r-rsamtools) | |
1193 | ("r-venndiagram" ,r-venndiagram))) | |
1194 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") | |
1195 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") | |
1196 | (description | |
1197 | "The package includes functions to retrieve the sequences around the peak, | |
1198 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
1199 | custom features such as most conserved elements and other transcription factor | |
1200 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
1201 | for finding the peaks with bi-directional promoters with summary statistics | |
1202 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
1203 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
1204 | enrichedGO (addGeneIDs).") | |
1205 | (license license:gpl2+))) | |
164502d8 RJ |
1206 | |
1207 | (define-public r-marray | |
1208 | (package | |
1209 | (name "r-marray") | |
bcb95b7a | 1210 | (version "1.62.0") |
164502d8 RJ |
1211 | (source (origin |
1212 | (method url-fetch) | |
1213 | (uri (bioconductor-uri "marray" version)) | |
1214 | (sha256 | |
bcb95b7a | 1215 | (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz")))) |
164502d8 RJ |
1216 | (build-system r-build-system) |
1217 | (propagated-inputs | |
67487088 | 1218 | `(("r-limma" ,r-limma))) |
164502d8 RJ |
1219 | (home-page "http://bioconductor.org/packages/marray") |
1220 | (synopsis "Exploratory analysis for two-color spotted microarray data") | |
1221 | (description "This package contains class definitions for two-color spotted | |
1222 | microarray data. It also includes fuctions for data input, diagnostic plots, | |
1223 | normalization and quality checking.") | |
1224 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
1225 | |
1226 | (define-public r-cghbase | |
1227 | (package | |
1228 | (name "r-cghbase") | |
8efb842f | 1229 | (version "1.44.0") |
0416a0d4 RJ |
1230 | (source (origin |
1231 | (method url-fetch) | |
1232 | (uri (bioconductor-uri "CGHbase" version)) | |
1233 | (sha256 | |
8efb842f | 1234 | (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm")))) |
0416a0d4 RJ |
1235 | (properties `((upstream-name . "CGHbase"))) |
1236 | (build-system r-build-system) | |
1237 | (propagated-inputs | |
1238 | `(("r-biobase" ,r-biobase) | |
1239 | ("r-marray" ,r-marray))) | |
1240 | (home-page "http://bioconductor.org/packages/CGHbase") | |
1241 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
1242 | (description "This package contains functions and classes that are needed by | |
1243 | the @code{arrayCGH} packages.") | |
1244 | (license license:gpl2+))) | |
67ee83d6 RJ |
1245 | |
1246 | (define-public r-cghcall | |
1247 | (package | |
1248 | (name "r-cghcall") | |
23177309 | 1249 | (version "2.46.0") |
67ee83d6 RJ |
1250 | (source (origin |
1251 | (method url-fetch) | |
1252 | (uri (bioconductor-uri "CGHcall" version)) | |
1253 | (sha256 | |
23177309 | 1254 | (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93")))) |
67ee83d6 RJ |
1255 | (properties `((upstream-name . "CGHcall"))) |
1256 | (build-system r-build-system) | |
1257 | (propagated-inputs | |
1258 | `(("r-biobase" ,r-biobase) | |
1259 | ("r-cghbase" ,r-cghbase) | |
1260 | ("r-impute" ,r-impute) | |
1261 | ("r-dnacopy" ,r-dnacopy) | |
1262 | ("r-snowfall" ,r-snowfall))) | |
1263 | (home-page "http://bioconductor.org/packages/CGHcall") | |
1264 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
1265 | (description "This package contains functions and classes that are needed by | |
1266 | @code{arrayCGH} packages.") | |
1267 | (license license:gpl2+))) | |
0ef8cc9c RJ |
1268 | |
1269 | (define-public r-qdnaseq | |
1270 | (package | |
1271 | (name "r-qdnaseq") | |
4f4bed7d | 1272 | (version "1.20.0") |
0ef8cc9c RJ |
1273 | (source (origin |
1274 | (method url-fetch) | |
1275 | (uri (bioconductor-uri "QDNAseq" version)) | |
1276 | (sha256 | |
4f4bed7d | 1277 | (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz")))) |
0ef8cc9c RJ |
1278 | (properties `((upstream-name . "QDNAseq"))) |
1279 | (build-system r-build-system) | |
1280 | (propagated-inputs | |
1281 | `(("r-biobase" ,r-biobase) | |
81b0181b | 1282 | ("r-biocparallel" ,r-biocparallel) |
0ef8cc9c RJ |
1283 | ("r-cghbase" ,r-cghbase) |
1284 | ("r-cghcall" ,r-cghcall) | |
1285 | ("r-dnacopy" ,r-dnacopy) | |
1286 | ("r-genomicranges" ,r-genomicranges) | |
1287 | ("r-iranges" ,r-iranges) | |
1288 | ("r-matrixstats" ,r-matrixstats) | |
1289 | ("r-r-utils" ,r-r-utils) | |
1290 | ("r-rsamtools" ,r-rsamtools))) | |
1291 | (home-page "http://bioconductor.org/packages/QDNAseq") | |
1292 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") | |
1293 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
1294 | number of sequence reads in each counted, adjusted with a simultaneous | |
1295 | two-dimensional loess correction for sequence mappability and GC content, and | |
1296 | filtered to remove spurious regions in the genome. Downstream steps of | |
1297 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
1298 | respectively.") | |
1299 | (license license:gpl2+))) | |
bb15b581 RW |
1300 | |
1301 | (define-public r-bayseq | |
1302 | (package | |
1303 | (name "r-bayseq") | |
c38de815 | 1304 | (version "2.18.0") |
bb15b581 RW |
1305 | (source |
1306 | (origin | |
1307 | (method url-fetch) | |
1308 | (uri (bioconductor-uri "baySeq" version)) | |
1309 | (sha256 | |
1310 | (base32 | |
c38de815 | 1311 | "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w")))) |
bb15b581 RW |
1312 | (properties `((upstream-name . "baySeq"))) |
1313 | (build-system r-build-system) | |
1314 | (propagated-inputs | |
1315 | `(("r-abind" ,r-abind) | |
1316 | ("r-edger" ,r-edger) | |
1317 | ("r-genomicranges" ,r-genomicranges))) | |
1318 | (home-page "https://bioconductor.org/packages/baySeq/") | |
1319 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
1320 | (description | |
1321 | "This package identifies differential expression in high-throughput count | |
1322 | data, such as that derived from next-generation sequencing machines, | |
1323 | calculating estimated posterior likelihoods of differential expression (or | |
1324 | more complex hypotheses) via empirical Bayesian methods.") | |
1325 | (license license:gpl3))) | |
609f4ad1 RW |
1326 | |
1327 | (define-public r-chipcomp | |
1328 | (package | |
1329 | (name "r-chipcomp") | |
1ddd4af5 | 1330 | (version "1.14.0") |
609f4ad1 RW |
1331 | (source |
1332 | (origin | |
1333 | (method url-fetch) | |
1334 | (uri (bioconductor-uri "ChIPComp" version)) | |
1335 | (sha256 | |
1336 | (base32 | |
1ddd4af5 | 1337 | "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y")))) |
609f4ad1 RW |
1338 | (properties `((upstream-name . "ChIPComp"))) |
1339 | (build-system r-build-system) | |
1340 | (propagated-inputs | |
1341 | `(("r-biocgenerics" ,r-biocgenerics) | |
1342 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
1343 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
1344 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1345 | ("r-genomicranges" ,r-genomicranges) | |
1346 | ("r-iranges" ,r-iranges) | |
1347 | ("r-limma" ,r-limma) | |
1348 | ("r-rsamtools" ,r-rsamtools) | |
1349 | ("r-rtracklayer" ,r-rtracklayer) | |
1350 | ("r-s4vectors" ,r-s4vectors))) | |
1351 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
1352 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
1353 | (description | |
1354 | "ChIPComp implements a statistical method for quantitative comparison of | |
1355 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
1356 | sites across multiple conditions considering matching control in ChIP-seq | |
1357 | datasets.") | |
1358 | ;; Any version of the GPL. | |
1359 | (license license:gpl3+))) | |
0490f9de RW |
1360 | |
1361 | (define-public r-riboprofiling | |
1362 | (package | |
1363 | (name "r-riboprofiling") | |
7d5acf7a | 1364 | (version "1.14.0") |
0490f9de RW |
1365 | (source |
1366 | (origin | |
1367 | (method url-fetch) | |
1368 | (uri (bioconductor-uri "RiboProfiling" version)) | |
1369 | (sha256 | |
1370 | (base32 | |
7d5acf7a | 1371 | "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9")))) |
0490f9de RW |
1372 | (properties `((upstream-name . "RiboProfiling"))) |
1373 | (build-system r-build-system) | |
1374 | (propagated-inputs | |
1375 | `(("r-biocgenerics" ,r-biocgenerics) | |
1376 | ("r-biostrings" ,r-biostrings) | |
1377 | ("r-data-table" ,r-data-table) | |
1378 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1379 | ("r-genomicalignments" ,r-genomicalignments) | |
1380 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1381 | ("r-genomicranges" ,r-genomicranges) | |
1382 | ("r-ggbio" ,r-ggbio) | |
1383 | ("r-ggplot2" ,r-ggplot2) | |
1384 | ("r-iranges" ,r-iranges) | |
1385 | ("r-plyr" ,r-plyr) | |
1386 | ("r-reshape2" ,r-reshape2) | |
1387 | ("r-rsamtools" ,r-rsamtools) | |
1388 | ("r-rtracklayer" ,r-rtracklayer) | |
1389 | ("r-s4vectors" ,r-s4vectors) | |
1390 | ("r-sqldf" ,r-sqldf))) | |
1391 | (home-page "https://bioconductor.org/packages/RiboProfiling/") | |
1392 | (synopsis "Ribosome profiling data analysis") | |
1393 | (description "Starting with a BAM file, this package provides the | |
1394 | necessary functions for quality assessment, read start position recalibration, | |
1395 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
1396 | of count data: pairs, log fold-change, codon frequency and coverage | |
1397 | assessment, principal component analysis on codon coverage.") | |
1398 | (license license:gpl3))) | |
6ffdfe6a RW |
1399 | |
1400 | (define-public r-riboseqr | |
1401 | (package | |
1402 | (name "r-riboseqr") | |
eff6b2eb | 1403 | (version "1.18.0") |
6ffdfe6a RW |
1404 | (source |
1405 | (origin | |
1406 | (method url-fetch) | |
1407 | (uri (bioconductor-uri "riboSeqR" version)) | |
1408 | (sha256 | |
1409 | (base32 | |
eff6b2eb | 1410 | "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga")))) |
6ffdfe6a RW |
1411 | (properties `((upstream-name . "riboSeqR"))) |
1412 | (build-system r-build-system) | |
1413 | (propagated-inputs | |
1414 | `(("r-abind" ,r-abind) | |
1415 | ("r-bayseq" ,r-bayseq) | |
1416 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1417 | ("r-genomicranges" ,r-genomicranges) | |
1418 | ("r-iranges" ,r-iranges) | |
1419 | ("r-rsamtools" ,r-rsamtools) | |
1420 | ("r-seqlogo" ,r-seqlogo))) | |
1421 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
1422 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
1423 | (description | |
1424 | "This package provides plotting functions, frameshift detection and | |
1425 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
1426 | (license license:gpl3))) | |
a32279ff RW |
1427 | |
1428 | (define-public r-interactionset | |
1429 | (package | |
1430 | (name "r-interactionset") | |
176a264c | 1431 | (version "1.12.0") |
a32279ff RW |
1432 | (source |
1433 | (origin | |
1434 | (method url-fetch) | |
1435 | (uri (bioconductor-uri "InteractionSet" version)) | |
1436 | (sha256 | |
1437 | (base32 | |
176a264c | 1438 | "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6")))) |
a32279ff RW |
1439 | (properties |
1440 | `((upstream-name . "InteractionSet"))) | |
1441 | (build-system r-build-system) | |
1442 | (propagated-inputs | |
1443 | `(("r-biocgenerics" ,r-biocgenerics) | |
1444 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1445 | ("r-genomicranges" ,r-genomicranges) | |
1446 | ("r-iranges" ,r-iranges) | |
1447 | ("r-matrix" ,r-matrix) | |
1448 | ("r-rcpp" ,r-rcpp) | |
1449 | ("r-s4vectors" ,r-s4vectors) | |
1450 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1451 | (home-page "https://bioconductor.org/packages/InteractionSet") | |
1452 | (synopsis "Base classes for storing genomic interaction data") | |
1453 | (description | |
1454 | "This packages provides the @code{GInteractions}, | |
1455 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods | |
1456 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
1457 | experiments.") | |
1458 | (license license:gpl3))) | |
cf9a29b2 RW |
1459 | |
1460 | (define-public r-genomicinteractions | |
1461 | (package | |
1462 | (name "r-genomicinteractions") | |
1236ce8e | 1463 | (version "1.18.0") |
cf9a29b2 RW |
1464 | (source |
1465 | (origin | |
1466 | (method url-fetch) | |
1467 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
1468 | (sha256 | |
1469 | (base32 | |
1236ce8e | 1470 | "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b")))) |
cf9a29b2 RW |
1471 | (properties |
1472 | `((upstream-name . "GenomicInteractions"))) | |
1473 | (build-system r-build-system) | |
1474 | (propagated-inputs | |
1475 | `(("r-biobase" ,r-biobase) | |
1476 | ("r-biocgenerics" ,r-biocgenerics) | |
1477 | ("r-data-table" ,r-data-table) | |
1478 | ("r-dplyr" ,r-dplyr) | |
1479 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1480 | ("r-genomicranges" ,r-genomicranges) | |
1481 | ("r-ggplot2" ,r-ggplot2) | |
1482 | ("r-gridextra" ,r-gridextra) | |
1483 | ("r-gviz" ,r-gviz) | |
1484 | ("r-igraph" ,r-igraph) | |
1485 | ("r-interactionset" ,r-interactionset) | |
1486 | ("r-iranges" ,r-iranges) | |
1487 | ("r-rsamtools" ,r-rsamtools) | |
1488 | ("r-rtracklayer" ,r-rtracklayer) | |
1489 | ("r-s4vectors" ,r-s4vectors) | |
1490 | ("r-stringr" ,r-stringr))) | |
1491 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") | |
1492 | (synopsis "R package for handling genomic interaction data") | |
1493 | (description | |
1494 | "This R package provides tools for handling genomic interaction data, | |
1495 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
1496 | information and producing various plots and statistics.") | |
1497 | (license license:gpl3))) | |
27c51606 RW |
1498 | |
1499 | (define-public r-ctc | |
1500 | (package | |
1501 | (name "r-ctc") | |
7a5d729a | 1502 | (version "1.58.0") |
27c51606 RW |
1503 | (source |
1504 | (origin | |
1505 | (method url-fetch) | |
1506 | (uri (bioconductor-uri "ctc" version)) | |
1507 | (sha256 | |
1508 | (base32 | |
7a5d729a | 1509 | "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am")))) |
27c51606 RW |
1510 | (build-system r-build-system) |
1511 | (propagated-inputs `(("r-amap" ,r-amap))) | |
1512 | (home-page "https://bioconductor.org/packages/ctc/") | |
1513 | (synopsis "Cluster and tree conversion") | |
1514 | (description | |
1515 | "This package provides tools for exporting and importing classification | |
1516 | trees and clusters to other programs.") | |
1517 | (license license:gpl2))) | |
5da0e142 RW |
1518 | |
1519 | (define-public r-goseq | |
1520 | (package | |
1521 | (name "r-goseq") | |
40f0ee43 | 1522 | (version "1.36.0") |
5da0e142 RW |
1523 | (source |
1524 | (origin | |
1525 | (method url-fetch) | |
1526 | (uri (bioconductor-uri "goseq" version)) | |
1527 | (sha256 | |
1528 | (base32 | |
40f0ee43 | 1529 | "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw")))) |
5da0e142 RW |
1530 | (build-system r-build-system) |
1531 | (propagated-inputs | |
1532 | `(("r-annotationdbi" ,r-annotationdbi) | |
1533 | ("r-biasedurn" ,r-biasedurn) | |
1534 | ("r-biocgenerics" ,r-biocgenerics) | |
1535 | ("r-genelendatabase" ,r-genelendatabase) | |
1536 | ("r-go-db" ,r-go-db) | |
1537 | ("r-mgcv" ,r-mgcv))) | |
1538 | (home-page "https://bioconductor.org/packages/goseq/") | |
1539 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
1540 | (description | |
1541 | "This package provides tools to detect Gene Ontology and/or other user | |
1542 | defined categories which are over/under represented in RNA-seq data.") | |
1543 | (license license:lgpl2.0+))) | |
f4235c0e RW |
1544 | |
1545 | (define-public r-glimma | |
1546 | (package | |
1547 | (name "r-glimma") | |
07252952 | 1548 | (version "1.12.0") |
f4235c0e RW |
1549 | (source |
1550 | (origin | |
1551 | (method url-fetch) | |
1552 | (uri (bioconductor-uri "Glimma" version)) | |
1553 | (sha256 | |
1554 | (base32 | |
07252952 | 1555 | "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x")))) |
f4235c0e RW |
1556 | (properties `((upstream-name . "Glimma"))) |
1557 | (build-system r-build-system) | |
1558 | (propagated-inputs | |
1559 | `(("r-edger" ,r-edger) | |
1560 | ("r-jsonlite" ,r-jsonlite) | |
1561 | ("r-s4vectors" ,r-s4vectors))) | |
1562 | (home-page "https://github.com/Shians/Glimma") | |
1563 | (synopsis "Interactive HTML graphics") | |
1564 | (description | |
1565 | "This package generates interactive visualisations for analysis of | |
1566 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
1567 | HTML page. The interactions are built on top of the popular static | |
1568 | representations of analysis results in order to provide additional | |
1569 | information.") | |
1570 | (license license:lgpl3))) | |
aa388dc7 RW |
1571 | |
1572 | (define-public r-rots | |
1573 | (package | |
1574 | (name "r-rots") | |
5bf7eb49 | 1575 | (version "1.12.0") |
aa388dc7 RW |
1576 | (source |
1577 | (origin | |
1578 | (method url-fetch) | |
1579 | (uri (bioconductor-uri "ROTS" version)) | |
1580 | (sha256 | |
1581 | (base32 | |
5bf7eb49 | 1582 | "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77")))) |
aa388dc7 RW |
1583 | (properties `((upstream-name . "ROTS"))) |
1584 | (build-system r-build-system) | |
1585 | (propagated-inputs | |
1586 | `(("r-biobase" ,r-biobase) | |
1587 | ("r-rcpp" ,r-rcpp))) | |
1588 | (home-page "https://bioconductor.org/packages/ROTS/") | |
1589 | (synopsis "Reproducibility-Optimized Test Statistic") | |
1590 | (description | |
1591 | "This package provides tools for calculating the | |
1592 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
1593 | in omics data.") | |
1594 | (license license:gpl2+))) | |
b64ce4b7 | 1595 | |
cad6fb2d RW |
1596 | (define-public r-plgem |
1597 | (package | |
1598 | (name "r-plgem") | |
5dce7153 | 1599 | (version "1.56.0") |
cad6fb2d RW |
1600 | (source |
1601 | (origin | |
1602 | (method url-fetch) | |
1603 | (uri (bioconductor-uri "plgem" version)) | |
1604 | (sha256 | |
1605 | (base32 | |
5dce7153 | 1606 | "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp")))) |
cad6fb2d RW |
1607 | (build-system r-build-system) |
1608 | (propagated-inputs | |
1609 | `(("r-biobase" ,r-biobase) | |
1610 | ("r-mass" ,r-mass))) | |
1611 | (home-page "http://www.genopolis.it") | |
1612 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
1613 | (description | |
1614 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
1615 | model the variance-versus-mean dependence that exists in a variety of | |
1616 | genome-wide datasets, including microarray and proteomics data. The use of | |
1617 | PLGEM has been shown to improve the detection of differentially expressed | |
1618 | genes or proteins in these datasets.") | |
1619 | (license license:gpl2))) | |
1620 | ||
b64ce4b7 RW |
1621 | (define-public r-inspect |
1622 | (package | |
1623 | (name "r-inspect") | |
3649d046 | 1624 | (version "1.14.0") |
b64ce4b7 RW |
1625 | (source |
1626 | (origin | |
1627 | (method url-fetch) | |
1628 | (uri (bioconductor-uri "INSPEcT" version)) | |
1629 | (sha256 | |
1630 | (base32 | |
3649d046 | 1631 | "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r")))) |
b64ce4b7 RW |
1632 | (properties `((upstream-name . "INSPEcT"))) |
1633 | (build-system r-build-system) | |
1634 | (propagated-inputs | |
1635 | `(("r-biobase" ,r-biobase) | |
1636 | ("r-biocgenerics" ,r-biocgenerics) | |
1637 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 1638 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 RW |
1639 | ("r-desolve" ,r-desolve) |
1640 | ("r-genomicalignments" ,r-genomicalignments) | |
1641 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1642 | ("r-genomicranges" ,r-genomicranges) | |
1643 | ("r-iranges" ,r-iranges) | |
c86fc969 | 1644 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
1645 | ("r-preprocesscore" ,r-preprocesscore) |
1646 | ("r-proc" ,r-proc) | |
1647 | ("r-rootsolve" ,r-rootsolve) | |
1648 | ("r-rsamtools" ,r-rsamtools) | |
c86fc969 RW |
1649 | ("r-s4vectors" ,r-s4vectors) |
1650 | ("r-shiny" ,r-shiny) | |
1651 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1652 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
1653 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
b64ce4b7 RW |
1654 | (home-page "https://bioconductor.org/packages/INSPEcT") |
1655 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
1656 | (description | |
1657 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
1658 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
1659 | order to evaluate synthesis, processing and degradation rates and assess via | |
1660 | modeling the rates that determines changes in mature mRNA levels.") | |
1661 | (license license:gpl2))) | |
f6e99763 RW |
1662 | |
1663 | (define-public r-dnabarcodes | |
1664 | (package | |
1665 | (name "r-dnabarcodes") | |
774e499c | 1666 | (version "1.14.0") |
f6e99763 RW |
1667 | (source |
1668 | (origin | |
1669 | (method url-fetch) | |
1670 | (uri (bioconductor-uri "DNABarcodes" version)) | |
1671 | (sha256 | |
1672 | (base32 | |
774e499c | 1673 | "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0")))) |
f6e99763 RW |
1674 | (properties `((upstream-name . "DNABarcodes"))) |
1675 | (build-system r-build-system) | |
1676 | (propagated-inputs | |
1677 | `(("r-bh" ,r-bh) | |
1678 | ("r-matrix" ,r-matrix) | |
1679 | ("r-rcpp" ,r-rcpp))) | |
1680 | (home-page "https://bioconductor.org/packages/DNABarcodes") | |
1681 | (synopsis "Create and analyze DNA barcodes") | |
1682 | (description | |
1683 | "This package offers tools to create DNA barcode sets capable of | |
1684 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
1685 | can be analyzed regarding their minimal, maximal and average distances between | |
1686 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
1687 | demultiplexed, i.e. assigned to their original reference barcode.") | |
1688 | (license license:gpl2))) | |
09aa3d06 RW |
1689 | |
1690 | (define-public r-ruvseq | |
1691 | (package | |
1692 | (name "r-ruvseq") | |
d8771f5f | 1693 | (version "1.18.0") |
09aa3d06 RW |
1694 | (source |
1695 | (origin | |
1696 | (method url-fetch) | |
1697 | (uri (bioconductor-uri "RUVSeq" version)) | |
1698 | (sha256 | |
1699 | (base32 | |
d8771f5f | 1700 | "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33")))) |
09aa3d06 RW |
1701 | (properties `((upstream-name . "RUVSeq"))) |
1702 | (build-system r-build-system) | |
1703 | (propagated-inputs | |
1704 | `(("r-biobase" ,r-biobase) | |
1705 | ("r-edaseq" ,r-edaseq) | |
1706 | ("r-edger" ,r-edger) | |
1707 | ("r-mass" ,r-mass))) | |
1708 | (home-page "https://github.com/drisso/RUVSeq") | |
1709 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
1710 | (description | |
1711 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
1712 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
1713 | samples.") | |
1714 | (license license:artistic2.0))) | |
286157dc RW |
1715 | |
1716 | (define-public r-biocneighbors | |
1717 | (package | |
1718 | (name "r-biocneighbors") | |
6fc161fc | 1719 | (version "1.2.0") |
286157dc RW |
1720 | (source |
1721 | (origin | |
1722 | (method url-fetch) | |
1723 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
1724 | (sha256 | |
1725 | (base32 | |
6fc161fc | 1726 | "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg")))) |
286157dc RW |
1727 | (properties `((upstream-name . "BiocNeighbors"))) |
1728 | (build-system r-build-system) | |
1729 | (propagated-inputs | |
6fc161fc RW |
1730 | `(("r-biocgenerics" ,r-biocgenerics) |
1731 | ("r-biocparallel" ,r-biocparallel) | |
286157dc RW |
1732 | ("r-rcpp" ,r-rcpp) |
1733 | ("r-rcppannoy" ,r-rcppannoy) | |
6fc161fc | 1734 | ("r-rcpphnsw" ,r-rcpphnsw) |
286157dc RW |
1735 | ("r-s4vectors" ,r-s4vectors))) |
1736 | (home-page "https://bioconductor.org/packages/BiocNeighbors") | |
1737 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
1738 | (description | |
1739 | "This package implements exact and approximate methods for nearest | |
1740 | neighbor detection, in a framework that allows them to be easily switched | |
1741 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
1742 | using pre-clustering with the k-means algorithm. Functions are also provided | |
1743 | to search for all neighbors within a given distance. Parallelization is | |
1744 | achieved for all methods using the BiocParallel framework.") | |
1745 | (license license:gpl3))) | |
8a587c89 | 1746 | |
99391290 RW |
1747 | (define-public r-biocsingular |
1748 | (package | |
1749 | (name "r-biocsingular") | |
1750 | (version "1.0.0") | |
1751 | (source | |
1752 | (origin | |
1753 | (method url-fetch) | |
1754 | (uri (bioconductor-uri "BiocSingular" version)) | |
1755 | (sha256 | |
1756 | (base32 | |
1757 | "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5")))) | |
1758 | (properties `((upstream-name . "BiocSingular"))) | |
1759 | (build-system r-build-system) | |
1760 | (propagated-inputs | |
1761 | `(("r-beachmat" ,r-beachmat) | |
1762 | ("r-biocgenerics" ,r-biocgenerics) | |
1763 | ("r-biocparallel" ,r-biocparallel) | |
1764 | ("r-delayedarray" ,r-delayedarray) | |
1765 | ("r-irlba" ,r-irlba) | |
1766 | ("r-matrix" ,r-matrix) | |
1767 | ("r-rcpp" ,r-rcpp) | |
1768 | ("r-rsvd" ,r-rsvd) | |
1769 | ("r-s4vectors" ,r-s4vectors))) | |
1770 | (home-page "https://github.com/LTLA/BiocSingular") | |
1771 | (synopsis "Singular value decomposition for Bioconductor packages") | |
1772 | (description | |
1773 | "This package implements exact and approximate methods for singular value | |
1774 | decomposition and principal components analysis, in a framework that allows | |
1775 | them to be easily switched within Bioconductor packages or workflows. Where | |
1776 | possible, parallelization is achieved using the BiocParallel framework.") | |
1777 | (license license:gpl3))) | |
1778 | ||
a961ae46 RW |
1779 | (define-public r-destiny |
1780 | (package | |
1781 | (name "r-destiny") | |
0aa72f2d | 1782 | (version "2.14.0") |
a961ae46 RW |
1783 | (source |
1784 | (origin | |
1785 | (method url-fetch) | |
1786 | (uri (bioconductor-uri "destiny" version)) | |
1787 | (sha256 | |
1788 | (base32 | |
0aa72f2d | 1789 | "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3")))) |
a961ae46 RW |
1790 | (build-system r-build-system) |
1791 | (propagated-inputs | |
1792 | `(("r-biobase" ,r-biobase) | |
1793 | ("r-biocgenerics" ,r-biocgenerics) | |
0aa72f2d | 1794 | ("r-ggplot2" ,r-ggplot2) |
a961ae46 | 1795 | ("r-ggthemes" ,r-ggthemes) |
a961ae46 RW |
1796 | ("r-igraph" ,r-igraph) |
1797 | ("r-matrix" ,r-matrix) | |
1798 | ("r-proxy" ,r-proxy) | |
1799 | ("r-rcpp" ,r-rcpp) | |
1800 | ("r-rcppeigen" ,r-rcppeigen) | |
1801 | ("r-scales" ,r-scales) | |
1802 | ("r-scatterplot3d" ,r-scatterplot3d) | |
1803 | ("r-smoother" ,r-smoother) | |
1804 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1805 | ("r-vim" ,r-vim))) | |
1806 | (home-page "https://bioconductor.org/packages/destiny/") | |
1807 | (synopsis "Create and plot diffusion maps") | |
1808 | (description "This package provides tools to create and plot diffusion | |
1809 | maps.") | |
1810 | ;; Any version of the GPL | |
1811 | (license license:gpl3+))) | |
1812 | ||
8a587c89 RW |
1813 | (define-public r-savr |
1814 | (package | |
1815 | (name "r-savr") | |
8d3d0c3a | 1816 | (version "1.22.0") |
8a587c89 RW |
1817 | (source |
1818 | (origin | |
1819 | (method url-fetch) | |
1820 | (uri (bioconductor-uri "savR" version)) | |
1821 | (sha256 | |
1822 | (base32 | |
8d3d0c3a | 1823 | "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h")))) |
8a587c89 RW |
1824 | (properties `((upstream-name . "savR"))) |
1825 | (build-system r-build-system) | |
1826 | (propagated-inputs | |
1827 | `(("r-ggplot2" ,r-ggplot2) | |
1828 | ("r-gridextra" ,r-gridextra) | |
1829 | ("r-reshape2" ,r-reshape2) | |
1830 | ("r-scales" ,r-scales) | |
1831 | ("r-xml" ,r-xml))) | |
1832 | (home-page "https://github.com/bcalder/savR") | |
1833 | (synopsis "Parse and analyze Illumina SAV files") | |
1834 | (description | |
1835 | "This package provides tools to parse Illumina Sequence Analysis | |
1836 | Viewer (SAV) files, access data, and generate QC plots.") | |
1837 | (license license:agpl3+))) | |
41ffc214 RW |
1838 | |
1839 | (define-public r-chipexoqual | |
1840 | (package | |
1841 | (name "r-chipexoqual") | |
58a43fc2 | 1842 | (version "1.8.0") |
41ffc214 RW |
1843 | (source |
1844 | (origin | |
1845 | (method url-fetch) | |
1846 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
1847 | (sha256 | |
1848 | (base32 | |
58a43fc2 | 1849 | "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj")))) |
41ffc214 RW |
1850 | (properties `((upstream-name . "ChIPexoQual"))) |
1851 | (build-system r-build-system) | |
1852 | (propagated-inputs | |
1853 | `(("r-biocparallel" ,r-biocparallel) | |
1854 | ("r-biovizbase" ,r-biovizbase) | |
1855 | ("r-broom" ,r-broom) | |
1856 | ("r-data-table" ,r-data-table) | |
1857 | ("r-dplyr" ,r-dplyr) | |
1858 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1859 | ("r-genomicalignments" ,r-genomicalignments) | |
1860 | ("r-genomicranges" ,r-genomicranges) | |
1861 | ("r-ggplot2" ,r-ggplot2) | |
1862 | ("r-hexbin" ,r-hexbin) | |
1863 | ("r-iranges" ,r-iranges) | |
1864 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
1865 | ("r-rmarkdown" ,r-rmarkdown) | |
1866 | ("r-rsamtools" ,r-rsamtools) | |
1867 | ("r-s4vectors" ,r-s4vectors) | |
1868 | ("r-scales" ,r-scales) | |
1869 | ("r-viridis" ,r-viridis))) | |
1870 | (home-page "https://github.com/keleslab/ChIPexoQual") | |
1871 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
1872 | (description | |
1873 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
1874 | sequencing data.") | |
1875 | (license license:gpl2+))) | |
c18dccff | 1876 | |
3d13b448 RW |
1877 | (define-public r-copynumber |
1878 | (package | |
1879 | (name "r-copynumber") | |
d9419185 | 1880 | (version "1.24.0") |
3d13b448 RW |
1881 | (source (origin |
1882 | (method url-fetch) | |
1883 | (uri (bioconductor-uri "copynumber" version)) | |
1884 | (sha256 | |
1885 | (base32 | |
d9419185 | 1886 | "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp")))) |
3d13b448 RW |
1887 | (build-system r-build-system) |
1888 | (propagated-inputs | |
1889 | `(("r-s4vectors" ,r-s4vectors) | |
1890 | ("r-iranges" ,r-iranges) | |
1891 | ("r-genomicranges" ,r-genomicranges) | |
1892 | ("r-biocgenerics" ,r-biocgenerics))) | |
1893 | (home-page "https://bioconductor.org/packages/copynumber") | |
1894 | (synopsis "Segmentation of single- and multi-track copy number data") | |
1895 | (description | |
1896 | "This package segments single- and multi-track copy number data by a | |
1897 | penalized least squares regression method.") | |
1898 | (license license:artistic2.0))) | |
1899 | ||
c18dccff RW |
1900 | (define-public r-dnacopy |
1901 | (package | |
1902 | (name "r-dnacopy") | |
d5f3c0d0 | 1903 | (version "1.58.0") |
c18dccff RW |
1904 | (source |
1905 | (origin | |
1906 | (method url-fetch) | |
1907 | (uri (bioconductor-uri "DNAcopy" version)) | |
1908 | (sha256 | |
1909 | (base32 | |
d5f3c0d0 | 1910 | "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa")))) |
c18dccff RW |
1911 | (properties `((upstream-name . "DNAcopy"))) |
1912 | (build-system r-build-system) | |
1913 | (native-inputs `(("gfortran" ,gfortran))) | |
1914 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
1915 | (synopsis "DNA copy number data analysis") | |
1916 | (description | |
1917 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
1918 | algorithm to segment DNA copy number data and identify genomic regions with | |
1919 | abnormal copy number.") | |
1920 | (license license:gpl2+))) | |
3a0babac RW |
1921 | |
1922 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
1923 | ;; Bioconductor package. | |
1924 | (define-public r-htscluster | |
1925 | (package | |
1926 | (name "r-htscluster") | |
1927 | (version "2.0.8") | |
1928 | (source | |
1929 | (origin | |
1930 | (method url-fetch) | |
1931 | (uri (cran-uri "HTSCluster" version)) | |
1932 | (sha256 | |
1933 | (base32 | |
1934 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
1935 | (properties `((upstream-name . "HTSCluster"))) | |
1936 | (build-system r-build-system) | |
1937 | (propagated-inputs | |
1938 | `(("r-capushe" ,r-capushe) | |
1939 | ("r-edger" ,r-edger) | |
1940 | ("r-plotrix" ,r-plotrix))) | |
1941 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
1942 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
1943 | (description | |
1944 | "This package provides a Poisson mixture model is implemented to cluster | |
1945 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
1946 | estimation is performed using either the EM or CEM algorithm, and the slope | |
1947 | heuristics are used for model selection (i.e., to choose the number of | |
1948 | clusters).") | |
1949 | (license license:gpl3+))) | |
173c9960 RW |
1950 | |
1951 | (define-public r-deds | |
1952 | (package | |
1953 | (name "r-deds") | |
301c4ff1 | 1954 | (version "1.58.0") |
173c9960 RW |
1955 | (source |
1956 | (origin | |
1957 | (method url-fetch) | |
1958 | (uri (bioconductor-uri "DEDS" version)) | |
1959 | (sha256 | |
1960 | (base32 | |
301c4ff1 | 1961 | "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs")))) |
173c9960 RW |
1962 | (properties `((upstream-name . "DEDS"))) |
1963 | (build-system r-build-system) | |
1964 | (home-page "https://bioconductor.org/packages/DEDS/") | |
1965 | (synopsis "Differential expression via distance summary for microarray data") | |
1966 | (description | |
1967 | "This library contains functions that calculate various statistics of | |
1968 | differential expression for microarray data, including t statistics, fold | |
1969 | change, F statistics, SAM, moderated t and F statistics and B statistics. It | |
1970 | also implements a new methodology called DEDS (Differential Expression via | |
1971 | Distance Summary), which selects differentially expressed genes by integrating | |
1972 | and summarizing a set of statistics using a weighted distance approach.") | |
1973 | ;; Any version of the LGPL. | |
1974 | (license license:lgpl3+))) | |
7ed869f7 RW |
1975 | |
1976 | ;; This is a CRAN package, but since it depends on a Bioconductor package we | |
1977 | ;; put it here. | |
1978 | (define-public r-nbpseq | |
1979 | (package | |
1980 | (name "r-nbpseq") | |
1981 | (version "0.3.0") | |
1982 | (source | |
1983 | (origin | |
1984 | (method url-fetch) | |
1985 | (uri (cran-uri "NBPSeq" version)) | |
1986 | (sha256 | |
1987 | (base32 | |
1988 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) | |
1989 | (properties `((upstream-name . "NBPSeq"))) | |
1990 | (build-system r-build-system) | |
1991 | (propagated-inputs | |
1992 | `(("r-qvalue" ,r-qvalue))) | |
1993 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") | |
1994 | (synopsis "Negative binomial models for RNA-Seq data") | |
1995 | (description | |
1996 | "This package provides negative binomial models for two-group comparisons | |
1997 | and regression inferences from RNA-sequencing data.") | |
1998 | (license license:gpl2))) | |
3087a2f3 RW |
1999 | |
2000 | (define-public r-ebseq | |
2001 | (package | |
2002 | (name "r-ebseq") | |
4a3c47e9 | 2003 | (version "1.24.0") |
3087a2f3 RW |
2004 | (source |
2005 | (origin | |
2006 | (method url-fetch) | |
2007 | (uri (bioconductor-uri "EBSeq" version)) | |
2008 | (sha256 | |
2009 | (base32 | |
4a3c47e9 | 2010 | "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83")))) |
3087a2f3 RW |
2011 | (properties `((upstream-name . "EBSeq"))) |
2012 | (build-system r-build-system) | |
2013 | (propagated-inputs | |
2014 | `(("r-blockmodeling" ,r-blockmodeling) | |
2015 | ("r-gplots" ,r-gplots) | |
2016 | ("r-testthat" ,r-testthat))) | |
2017 | (home-page "https://bioconductor.org/packages/EBSeq") | |
2018 | (synopsis "Differential expression analysis of RNA-seq data") | |
2019 | (description | |
2020 | "This package provides tools for differential expression analysis at both | |
2021 | gene and isoform level using RNA-seq data") | |
2022 | (license license:artistic2.0))) | |
2cb71d81 RW |
2023 | |
2024 | (define-public r-lpsymphony | |
2025 | (package | |
2026 | (name "r-lpsymphony") | |
61c79d55 | 2027 | (version "1.12.0") |
2cb71d81 RW |
2028 | (source |
2029 | (origin | |
2030 | (method url-fetch) | |
2031 | (uri (bioconductor-uri "lpsymphony" version)) | |
2032 | (sha256 | |
2033 | (base32 | |
61c79d55 | 2034 | "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv")))) |
2cb71d81 RW |
2035 | (build-system r-build-system) |
2036 | (inputs | |
2037 | `(("gfortran" ,gfortran) | |
2038 | ("zlib" ,zlib))) | |
2039 | (native-inputs | |
2040 | `(("pkg-config" ,pkg-config))) | |
2041 | (home-page "http://r-forge.r-project.org/projects/rsymphony") | |
2042 | (synopsis "Symphony integer linear programming solver in R") | |
2043 | (description | |
2044 | "This package was derived from Rsymphony. The package provides an R | |
2045 | interface to SYMPHONY, a linear programming solver written in C++. The main | |
2046 | difference between this package and Rsymphony is that it includes the solver | |
2047 | source code, while Rsymphony expects to find header and library files on the | |
2048 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy | |
2049 | to install interface to SYMPHONY.") | |
2050 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. | |
2051 | ;; lpsimphony is released under the same terms. | |
2052 | (license license:epl1.0))) | |
704de8f5 RW |
2053 | |
2054 | (define-public r-ihw | |
2055 | (package | |
2056 | (name "r-ihw") | |
bcd8b7a9 | 2057 | (version "1.12.0") |
704de8f5 RW |
2058 | (source |
2059 | (origin | |
2060 | (method url-fetch) | |
2061 | (uri (bioconductor-uri "IHW" version)) | |
2062 | (sha256 | |
2063 | (base32 | |
bcd8b7a9 | 2064 | "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz")))) |
704de8f5 RW |
2065 | (properties `((upstream-name . "IHW"))) |
2066 | (build-system r-build-system) | |
2067 | (propagated-inputs | |
2068 | `(("r-biocgenerics" ,r-biocgenerics) | |
2069 | ("r-fdrtool" ,r-fdrtool) | |
2070 | ("r-lpsymphony" ,r-lpsymphony) | |
2071 | ("r-slam" ,r-slam))) | |
2072 | (home-page "https://bioconductor.org/packages/IHW") | |
2073 | (synopsis "Independent hypothesis weighting") | |
2074 | (description | |
2075 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing | |
2076 | procedure that increases power compared to the method of Benjamini and | |
2077 | Hochberg by assigning data-driven weights to each hypothesis. The input to | |
2078 | IHW is a two-column table of p-values and covariates. The covariate can be | |
2079 | any continuous-valued or categorical variable that is thought to be | |
2080 | informative on the statistical properties of each hypothesis test, while it is | |
2081 | independent of the p-value under the null hypothesis.") | |
2082 | (license license:artistic2.0))) | |
251e0830 RW |
2083 | |
2084 | (define-public r-icobra | |
2085 | (package | |
2086 | (name "r-icobra") | |
3fd2ea88 | 2087 | (version "1.12.0") |
251e0830 RW |
2088 | (source |
2089 | (origin | |
2090 | (method url-fetch) | |
2091 | (uri (bioconductor-uri "iCOBRA" version)) | |
2092 | (sha256 | |
2093 | (base32 | |
3fd2ea88 | 2094 | "1w9frnczgypzc2czbwrvlizqcqhbp6cdpyws7vkmnn9k0ggzxvfc")))) |
251e0830 RW |
2095 | (properties `((upstream-name . "iCOBRA"))) |
2096 | (build-system r-build-system) | |
2097 | (propagated-inputs | |
2098 | `(("r-dplyr" ,r-dplyr) | |
2099 | ("r-dt" ,r-dt) | |
2100 | ("r-ggplot2" ,r-ggplot2) | |
2101 | ("r-limma" ,r-limma) | |
2102 | ("r-reshape2" ,r-reshape2) | |
2103 | ("r-rocr" ,r-rocr) | |
2104 | ("r-scales" ,r-scales) | |
2105 | ("r-shiny" ,r-shiny) | |
2106 | ("r-shinybs" ,r-shinybs) | |
2107 | ("r-shinydashboard" ,r-shinydashboard) | |
2108 | ("r-upsetr" ,r-upsetr))) | |
2109 | (home-page "https://bioconductor.org/packages/iCOBRA") | |
2110 | (synopsis "Comparison and visualization of ranking and assignment methods") | |
2111 | (description | |
2112 | "This package provides functions for calculation and visualization of | |
2113 | performance metrics for evaluation of ranking and binary | |
2114 | classification (assignment) methods. It also contains a Shiny application for | |
2115 | interactive exploration of results.") | |
2116 | (license license:gpl2+))) | |
925fcdbb RW |
2117 | |
2118 | (define-public r-mast | |
2119 | (package | |
2120 | (name "r-mast") | |
a0ff725d | 2121 | (version "1.10.0") |
925fcdbb RW |
2122 | (source |
2123 | (origin | |
2124 | (method url-fetch) | |
2125 | (uri (bioconductor-uri "MAST" version)) | |
2126 | (sha256 | |
2127 | (base32 | |
a0ff725d | 2128 | "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx")))) |
925fcdbb RW |
2129 | (properties `((upstream-name . "MAST"))) |
2130 | (build-system r-build-system) | |
2131 | (propagated-inputs | |
2132 | `(("r-abind" ,r-abind) | |
a0ff725d | 2133 | ("r-blme" ,r-blme) |
925fcdbb RW |
2134 | ("r-biobase" ,r-biobase) |
2135 | ("r-biocgenerics" ,r-biocgenerics) | |
2136 | ("r-data-table" ,r-data-table) | |
2137 | ("r-ggplot2" ,r-ggplot2) | |
2138 | ("r-plyr" ,r-plyr) | |
2139 | ("r-progress" ,r-progress) | |
2140 | ("r-reshape2" ,r-reshape2) | |
2141 | ("r-s4vectors" ,r-s4vectors) | |
2142 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2143 | ("r-stringr" ,r-stringr) | |
2144 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2145 | (home-page "https://github.com/RGLab/MAST/") | |
2146 | (synopsis "Model-based analysis of single cell transcriptomics") | |
2147 | (description | |
2148 | "This package provides methods and models for handling zero-inflated | |
2149 | single cell assay data.") | |
2150 | (license license:gpl2+))) | |
2d7627cf RW |
2151 | |
2152 | (define-public r-monocle | |
2153 | (package | |
2154 | (name "r-monocle") | |
78b63267 | 2155 | (version "2.12.0") |
2d7627cf RW |
2156 | (source |
2157 | (origin | |
2158 | (method url-fetch) | |
2159 | (uri (bioconductor-uri "monocle" version)) | |
2160 | (sha256 | |
2161 | (base32 | |
78b63267 | 2162 | "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z")))) |
2d7627cf RW |
2163 | (build-system r-build-system) |
2164 | (propagated-inputs | |
2165 | `(("r-biobase" ,r-biobase) | |
2166 | ("r-biocgenerics" ,r-biocgenerics) | |
2167 | ("r-biocviews" ,r-biocviews) | |
2168 | ("r-cluster" ,r-cluster) | |
2169 | ("r-combinat" ,r-combinat) | |
2170 | ("r-ddrtree" ,r-ddrtree) | |
2171 | ("r-densityclust" ,r-densityclust) | |
2172 | ("r-dplyr" ,r-dplyr) | |
2173 | ("r-fastica" ,r-fastica) | |
2174 | ("r-ggplot2" ,r-ggplot2) | |
2175 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) | |
2176 | ("r-igraph" ,r-igraph) | |
2177 | ("r-irlba" ,r-irlba) | |
2178 | ("r-limma" ,r-limma) | |
2179 | ("r-mass" ,r-mass) | |
2180 | ("r-matrix" ,r-matrix) | |
2181 | ("r-matrixstats" ,r-matrixstats) | |
2182 | ("r-pheatmap" ,r-pheatmap) | |
2183 | ("r-plyr" ,r-plyr) | |
2184 | ("r-proxy" ,r-proxy) | |
2185 | ("r-qlcmatrix" ,r-qlcmatrix) | |
2186 | ("r-rann" ,r-rann) | |
2187 | ("r-rcpp" ,r-rcpp) | |
2188 | ("r-reshape2" ,r-reshape2) | |
2189 | ("r-rtsne" ,r-rtsne) | |
2190 | ("r-slam" ,r-slam) | |
2191 | ("r-stringr" ,r-stringr) | |
2192 | ("r-tibble" ,r-tibble) | |
2193 | ("r-vgam" ,r-vgam) | |
2194 | ("r-viridis" ,r-viridis))) | |
2195 | (home-page "https://bioconductor.org/packages/monocle") | |
2196 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") | |
2197 | (description | |
2198 | "Monocle performs differential expression and time-series analysis for | |
2199 | single-cell expression experiments. It orders individual cells according to | |
2200 | progress through a biological process, without knowing ahead of time which | |
2201 | genes define progress through that process. Monocle also performs | |
2202 | differential expression analysis, clustering, visualization, and other useful | |
2203 | tasks on single cell expression data. It is designed to work with RNA-Seq and | |
2204 | qPCR data, but could be used with other types as well.") | |
2205 | (license license:artistic2.0))) | |
6213e441 RW |
2206 | |
2207 | (define-public r-noiseq | |
2208 | (package | |
2209 | (name "r-noiseq") | |
6a2c58b7 | 2210 | (version "2.28.0") |
6213e441 RW |
2211 | (source |
2212 | (origin | |
2213 | (method url-fetch) | |
2214 | (uri (bioconductor-uri "NOISeq" version)) | |
2215 | (sha256 | |
2216 | (base32 | |
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6213e441 RW |
2218 | (properties `((upstream-name . "NOISeq"))) |
2219 | (build-system r-build-system) | |
2220 | (propagated-inputs | |
2221 | `(("r-biobase" ,r-biobase) | |
2222 | ("r-matrix" ,r-matrix))) | |
2223 | (home-page "https://bioconductor.org/packages/NOISeq") | |
2224 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") | |
2225 | (description | |
2226 | "This package provides tools to support the analysis of RNA-seq | |
2227 | expression data or other similar kind of data. It provides exploratory plots | |
2228 | to evaluate saturation, count distribution, expression per chromosome, type of | |
2229 | detected features, features length, etc. It also supports the analysis of | |
2230 | differential expression between two experimental conditions with no parametric | |
2231 | assumptions.") | |
2232 | (license license:artistic2.0))) | |
b409c357 RW |
2233 | |
2234 | (define-public r-scdd | |
2235 | (package | |
2236 | (name "r-scdd") | |
7baa59ed | 2237 | (version "1.8.0") |
b409c357 RW |
2238 | (source |
2239 | (origin | |
2240 | (method url-fetch) | |
2241 | (uri (bioconductor-uri "scDD" version)) | |
2242 | (sha256 | |
2243 | (base32 | |
7baa59ed | 2244 | "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf")))) |
b409c357 RW |
2245 | (properties `((upstream-name . "scDD"))) |
2246 | (build-system r-build-system) | |
2247 | (propagated-inputs | |
2248 | `(("r-arm" ,r-arm) | |
2249 | ("r-biocparallel" ,r-biocparallel) | |
2250 | ("r-ebseq" ,r-ebseq) | |
2251 | ("r-fields" ,r-fields) | |
2252 | ("r-ggplot2" ,r-ggplot2) | |
2253 | ("r-mclust" ,r-mclust) | |
2254 | ("r-outliers" ,r-outliers) | |
2255 | ("r-s4vectors" ,r-s4vectors) | |
2256 | ("r-scran" ,r-scran) | |
2257 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2258 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2259 | (home-page "https://github.com/kdkorthauer/scDD") | |
2260 | (synopsis "Mixture modeling of single-cell RNA-seq data") | |
2261 | (description | |
2262 | "This package implements a method to analyze single-cell RNA-seq data | |
2263 | utilizing flexible Dirichlet Process mixture models. Genes with differential | |
2264 | distributions of expression are classified into several interesting patterns | |
2265 | of differences between two conditions. The package also includes functions | |
2266 | for simulating data with these patterns from negative binomial | |
2267 | distributions.") | |
2268 | (license license:gpl2))) | |
f0887757 RW |
2269 | |
2270 | (define-public r-scone | |
2271 | (package | |
2272 | (name "r-scone") | |
26c72fff | 2273 | (version "1.8.0") |
f0887757 RW |
2274 | (source |
2275 | (origin | |
2276 | (method url-fetch) | |
2277 | (uri (bioconductor-uri "scone" version)) | |
2278 | (sha256 | |
2279 | (base32 | |
26c72fff | 2280 | "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck")))) |
f0887757 RW |
2281 | (build-system r-build-system) |
2282 | (propagated-inputs | |
2283 | `(("r-aroma-light" ,r-aroma-light) | |
2284 | ("r-biocparallel" ,r-biocparallel) | |
2285 | ("r-boot" ,r-boot) | |
2286 | ("r-class" ,r-class) | |
2287 | ("r-cluster" ,r-cluster) | |
2288 | ("r-compositions" ,r-compositions) | |
2289 | ("r-diptest" ,r-diptest) | |
2290 | ("r-edger" ,r-edger) | |
2291 | ("r-fpc" ,r-fpc) | |
2292 | ("r-gplots" ,r-gplots) | |
2293 | ("r-hexbin" ,r-hexbin) | |
2294 | ("r-limma" ,r-limma) | |
2295 | ("r-matrixstats" ,r-matrixstats) | |
2296 | ("r-mixtools" ,r-mixtools) | |
2297 | ("r-rarpack" ,r-rarpack) | |
2298 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2299 | ("r-rhdf5" ,r-rhdf5) | |
2300 | ("r-ruvseq" ,r-ruvseq) | |
2301 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2302 | (home-page "https://bioconductor.org/packages/scone") | |
2303 | (synopsis "Single cell overview of normalized expression data") | |
2304 | (description | |
2305 | "SCONE is an R package for comparing and ranking the performance of | |
2306 | different normalization schemes for single-cell RNA-seq and other | |
2307 | high-throughput analyses.") | |
2308 | (license license:artistic2.0))) | |
f9201d67 RW |
2309 | |
2310 | (define-public r-geoquery | |
2311 | (package | |
2312 | (name "r-geoquery") | |
2d443087 | 2313 | (version "2.52.0") |
f9201d67 RW |
2314 | (source |
2315 | (origin | |
2316 | (method url-fetch) | |
2317 | (uri (bioconductor-uri "GEOquery" version)) | |
2318 | (sha256 | |
2319 | (base32 | |
2d443087 | 2320 | "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr")))) |
f9201d67 RW |
2321 | (properties `((upstream-name . "GEOquery"))) |
2322 | (build-system r-build-system) | |
2323 | (propagated-inputs | |
2324 | `(("r-biobase" ,r-biobase) | |
2325 | ("r-dplyr" ,r-dplyr) | |
2326 | ("r-httr" ,r-httr) | |
2327 | ("r-limma" ,r-limma) | |
2328 | ("r-magrittr" ,r-magrittr) | |
2329 | ("r-readr" ,r-readr) | |
2330 | ("r-tidyr" ,r-tidyr) | |
2331 | ("r-xml2" ,r-xml2))) | |
2332 | (home-page "https://github.com/seandavi/GEOquery/") | |
2333 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") | |
2334 | (description | |
2335 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of | |
2336 | microarray data. Given the rich and varied nature of this resource, it is | |
2337 | only natural to want to apply BioConductor tools to these data. GEOquery is | |
2338 | the bridge between GEO and BioConductor.") | |
2339 | (license license:gpl2))) | |
eed6ff03 RW |
2340 | |
2341 | (define-public r-illuminaio | |
2342 | (package | |
2343 | (name "r-illuminaio") | |
fadc6db8 | 2344 | (version "0.26.0") |
eed6ff03 RW |
2345 | (source |
2346 | (origin | |
2347 | (method url-fetch) | |
2348 | (uri (bioconductor-uri "illuminaio" version)) | |
2349 | (sha256 | |
2350 | (base32 | |
fadc6db8 | 2351 | "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8")))) |
eed6ff03 RW |
2352 | (build-system r-build-system) |
2353 | (propagated-inputs | |
2354 | `(("r-base64" ,r-base64))) | |
2355 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") | |
2356 | (synopsis "Parse Illumina microarray output files") | |
2357 | (description | |
2358 | "This package provides tools for parsing Illumina's microarray output | |
2359 | files, including IDAT.") | |
2360 | (license license:gpl2))) | |
f4eac096 RW |
2361 | |
2362 | (define-public r-siggenes | |
2363 | (package | |
2364 | (name "r-siggenes") | |
409f4dd6 | 2365 | (version "1.58.0") |
f4eac096 RW |
2366 | (source |
2367 | (origin | |
2368 | (method url-fetch) | |
2369 | (uri (bioconductor-uri "siggenes" version)) | |
2370 | (sha256 | |
2371 | (base32 | |
409f4dd6 | 2372 | "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib")))) |
f4eac096 RW |
2373 | (build-system r-build-system) |
2374 | (propagated-inputs | |
2375 | `(("r-biobase" ,r-biobase) | |
409f4dd6 RW |
2376 | ("r-multtest" ,r-multtest) |
2377 | ("r-scrime" ,r-scrime))) | |
f4eac096 RW |
2378 | (home-page "https://bioconductor.org/packages/siggenes/") |
2379 | (synopsis | |
2380 | "Multiple testing using SAM and Efron's empirical Bayes approaches") | |
2381 | (description | |
2382 | "This package provides tools for the identification of differentially | |
2383 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using | |
2384 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical | |
2385 | Bayes Analyses of Microarrays} (EBAM).") | |
2386 | (license license:lgpl2.0+))) | |
34a24f95 RW |
2387 | |
2388 | (define-public r-bumphunter | |
2389 | (package | |
2390 | (name "r-bumphunter") | |
693a9805 | 2391 | (version "1.26.0") |
34a24f95 RW |
2392 | (source |
2393 | (origin | |
2394 | (method url-fetch) | |
2395 | (uri (bioconductor-uri "bumphunter" version)) | |
2396 | (sha256 | |
2397 | (base32 | |
693a9805 | 2398 | "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx")))) |
34a24f95 RW |
2399 | (build-system r-build-system) |
2400 | (propagated-inputs | |
2401 | `(("r-annotationdbi" ,r-annotationdbi) | |
2402 | ("r-biocgenerics" ,r-biocgenerics) | |
2403 | ("r-dorng" ,r-dorng) | |
2404 | ("r-foreach" ,r-foreach) | |
2405 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2406 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2407 | ("r-genomicranges" ,r-genomicranges) | |
2408 | ("r-iranges" ,r-iranges) | |
2409 | ("r-iterators" ,r-iterators) | |
2410 | ("r-limma" ,r-limma) | |
2411 | ("r-locfit" ,r-locfit) | |
2412 | ("r-matrixstats" ,r-matrixstats) | |
2413 | ("r-s4vectors" ,r-s4vectors))) | |
2414 | (home-page "https://github.com/ririzarr/bumphunter") | |
2415 | (synopsis "Find bumps in genomic data") | |
2416 | (description | |
2417 | "This package provides tools for finding bumps in genomic data in order | |
2418 | to identify differentially methylated regions in epigenetic epidemiology | |
2419 | studies.") | |
2420 | (license license:artistic2.0))) | |
0fbaf195 RW |
2421 | |
2422 | (define-public r-minfi | |
2423 | (package | |
2424 | (name "r-minfi") | |
8c0fae3c | 2425 | (version "1.30.0") |
0fbaf195 RW |
2426 | (source |
2427 | (origin | |
2428 | (method url-fetch) | |
2429 | (uri (bioconductor-uri "minfi" version)) | |
2430 | (sha256 | |
2431 | (base32 | |
8c0fae3c | 2432 | "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd")))) |
0fbaf195 RW |
2433 | (build-system r-build-system) |
2434 | (propagated-inputs | |
2435 | `(("r-beanplot" ,r-beanplot) | |
2436 | ("r-biobase" ,r-biobase) | |
2437 | ("r-biocgenerics" ,r-biocgenerics) | |
2438 | ("r-biocparallel" ,r-biocparallel) | |
2439 | ("r-biostrings" ,r-biostrings) | |
2440 | ("r-bumphunter" ,r-bumphunter) | |
2441 | ("r-data-table" ,r-data-table) | |
2442 | ("r-delayedarray" ,r-delayedarray) | |
2443 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
2444 | ("r-genefilter" ,r-genefilter) | |
2445 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2446 | ("r-genomicranges" ,r-genomicranges) | |
2447 | ("r-geoquery" ,r-geoquery) | |
2448 | ("r-hdf5array" ,r-hdf5array) | |
2449 | ("r-illuminaio" ,r-illuminaio) | |
2450 | ("r-iranges" ,r-iranges) | |
2451 | ("r-lattice" ,r-lattice) | |
2452 | ("r-limma" ,r-limma) | |
2453 | ("r-mass" ,r-mass) | |
2454 | ("r-mclust" ,r-mclust) | |
2455 | ("r-nlme" ,r-nlme) | |
2456 | ("r-nor1mix" ,r-nor1mix) | |
2457 | ("r-preprocesscore" ,r-preprocesscore) | |
2458 | ("r-quadprog" ,r-quadprog) | |
2459 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2460 | ("r-reshape" ,r-reshape) | |
2461 | ("r-s4vectors" ,r-s4vectors) | |
2462 | ("r-siggenes" ,r-siggenes) | |
2463 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2464 | (home-page "https://github.com/hansenlab/minfi") | |
2465 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") | |
2466 | (description | |
2467 | "This package provides tools to analyze and visualize Illumina Infinium | |
2468 | methylation arrays.") | |
2469 | (license license:artistic2.0))) | |
5ec5ba02 RW |
2470 | |
2471 | (define-public r-methylumi | |
2472 | (package | |
2473 | (name "r-methylumi") | |
2986b51f | 2474 | (version "2.30.0") |
5ec5ba02 RW |
2475 | (source |
2476 | (origin | |
2477 | (method url-fetch) | |
2478 | (uri (bioconductor-uri "methylumi" version)) | |
2479 | (sha256 | |
2480 | (base32 | |
2986b51f | 2481 | "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f")))) |
5ec5ba02 RW |
2482 | (build-system r-build-system) |
2483 | (propagated-inputs | |
2484 | `(("r-annotate" ,r-annotate) | |
2485 | ("r-annotationdbi" ,r-annotationdbi) | |
2486 | ("r-biobase" ,r-biobase) | |
2487 | ("r-biocgenerics" ,r-biocgenerics) | |
2488 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) | |
2489 | ("r-genefilter" ,r-genefilter) | |
2490 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2491 | ("r-genomicranges" ,r-genomicranges) | |
2492 | ("r-ggplot2" ,r-ggplot2) | |
2493 | ("r-illuminaio" ,r-illuminaio) | |
2494 | ("r-iranges" ,r-iranges) | |
2495 | ("r-lattice" ,r-lattice) | |
2496 | ("r-matrixstats" ,r-matrixstats) | |
2497 | ("r-minfi" ,r-minfi) | |
2498 | ("r-reshape2" ,r-reshape2) | |
2499 | ("r-s4vectors" ,r-s4vectors) | |
2500 | ("r-scales" ,r-scales) | |
2501 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2502 | (home-page "https://bioconductor.org/packages/methylumi") | |
2503 | (synopsis "Handle Illumina methylation data") | |
2504 | (description | |
2505 | "This package provides classes for holding and manipulating Illumina | |
2506 | methylation data. Based on eSet, it can contain MIAME information, sample | |
2507 | information, feature information, and multiple matrices of data. An | |
2508 | \"intelligent\" import function, methylumiR can read the Illumina text files | |
2509 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from | |
2510 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, | |
2511 | background correction, and quality control features for GoldenGate, Infinium, | |
2512 | and Infinium HD arrays are also included.") | |
2513 | (license license:gpl2))) | |
09605cb2 RW |
2514 | |
2515 | (define-public r-lumi | |
2516 | (package | |
2517 | (name "r-lumi") | |
5551b07c | 2518 | (version "2.36.0") |
09605cb2 RW |
2519 | (source |
2520 | (origin | |
2521 | (method url-fetch) | |
2522 | (uri (bioconductor-uri "lumi" version)) | |
2523 | (sha256 | |
2524 | (base32 | |
5551b07c | 2525 | "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba")))) |
09605cb2 RW |
2526 | (build-system r-build-system) |
2527 | (propagated-inputs | |
2528 | `(("r-affy" ,r-affy) | |
2529 | ("r-annotate" ,r-annotate) | |
2530 | ("r-annotationdbi" ,r-annotationdbi) | |
2531 | ("r-biobase" ,r-biobase) | |
2532 | ("r-dbi" ,r-dbi) | |
2533 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2534 | ("r-genomicranges" ,r-genomicranges) | |
2535 | ("r-kernsmooth" ,r-kernsmooth) | |
2536 | ("r-lattice" ,r-lattice) | |
2537 | ("r-mass" ,r-mass) | |
2538 | ("r-methylumi" ,r-methylumi) | |
2539 | ("r-mgcv" ,r-mgcv) | |
2540 | ("r-nleqslv" ,r-nleqslv) | |
2541 | ("r-preprocesscore" ,r-preprocesscore) | |
2542 | ("r-rsqlite" ,r-rsqlite))) | |
2543 | (home-page "https://bioconductor.org/packages/lumi") | |
2544 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") | |
2545 | (description | |
2546 | "The lumi package provides an integrated solution for the Illumina | |
2547 | microarray data analysis. It includes functions of Illumina | |
2548 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific | |
2549 | variance stabilization, normalization and gene annotation at the probe level. | |
2550 | It also includes the functions of processing Illumina methylation microarrays, | |
2551 | especially Illumina Infinium methylation microarrays.") | |
2552 | (license license:lgpl2.0+))) | |
4291f36a RW |
2553 | |
2554 | (define-public r-linnorm | |
2555 | (package | |
2556 | (name "r-linnorm") | |
48c2a7eb | 2557 | (version "2.8.0") |
4291f36a RW |
2558 | (source |
2559 | (origin | |
2560 | (method url-fetch) | |
2561 | (uri (bioconductor-uri "Linnorm" version)) | |
2562 | (sha256 | |
2563 | (base32 | |
48c2a7eb | 2564 | "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5")))) |
4291f36a RW |
2565 | (properties `((upstream-name . "Linnorm"))) |
2566 | (build-system r-build-system) | |
2567 | (propagated-inputs | |
2568 | `(("r-amap" ,r-amap) | |
2569 | ("r-apcluster" ,r-apcluster) | |
2570 | ("r-ellipse" ,r-ellipse) | |
2571 | ("r-fastcluster" ,r-fastcluster) | |
2572 | ("r-fpc" ,r-fpc) | |
2573 | ("r-ggdendro" ,r-ggdendro) | |
2574 | ("r-ggplot2" ,r-ggplot2) | |
2575 | ("r-gmodels" ,r-gmodels) | |
2576 | ("r-igraph" ,r-igraph) | |
2577 | ("r-limma" ,r-limma) | |
2578 | ("r-mass" ,r-mass) | |
2579 | ("r-mclust" ,r-mclust) | |
2580 | ("r-rcpp" ,r-rcpp) | |
2581 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
2582 | ("r-rtsne" ,r-rtsne) | |
2583 | ("r-statmod" ,r-statmod) | |
2584 | ("r-vegan" ,r-vegan) | |
2585 | ("r-zoo" ,r-zoo))) | |
2586 | (home-page "http://www.jjwanglab.org/Linnorm/") | |
2587 | (synopsis "Linear model and normality based transformation method") | |
2588 | (description | |
2589 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq | |
2590 | count data or any large scale count data. It transforms such datasets for | |
2591 | parametric tests. In addition to the transformtion function (@code{Linnorm}), | |
2592 | the following pipelines are implemented: | |
2593 | ||
2594 | @enumerate | |
2595 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) | |
2596 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means | |
2597 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, | |
2598 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) | |
2599 | @item Differential expression analysis or differential peak detection using | |
2600 | limma (@code{Linnorm.limma}) | |
2601 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) | |
2602 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) | |
2603 | @item Stable gene selection for scRNA-seq data; for users without or who do | |
2604 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) | |
2605 | @item Data imputation (@code{Linnorm.DataImput}). | |
2606 | @end enumerate | |
2607 | ||
2608 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the | |
2609 | @code{RnaXSim} function is included for simulating RNA-seq data for the | |
2610 | evaluation of DEG analysis methods.") | |
2611 | (license license:expat))) | |
e4a17532 RW |
2612 | |
2613 | (define-public r-ioniser | |
2614 | (package | |
2615 | (name "r-ioniser") | |
2ee91179 | 2616 | (version "2.8.0") |
e4a17532 RW |
2617 | (source |
2618 | (origin | |
2619 | (method url-fetch) | |
2620 | (uri (bioconductor-uri "IONiseR" version)) | |
2621 | (sha256 | |
2622 | (base32 | |
2ee91179 | 2623 | "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y")))) |
e4a17532 RW |
2624 | (properties `((upstream-name . "IONiseR"))) |
2625 | (build-system r-build-system) | |
2626 | (propagated-inputs | |
2627 | `(("r-biocgenerics" ,r-biocgenerics) | |
2628 | ("r-biocparallel" ,r-biocparallel) | |
2629 | ("r-biostrings" ,r-biostrings) | |
2630 | ("r-bit64" ,r-bit64) | |
2631 | ("r-dplyr" ,r-dplyr) | |
2632 | ("r-ggplot2" ,r-ggplot2) | |
2633 | ("r-magrittr" ,r-magrittr) | |
2634 | ("r-rhdf5" ,r-rhdf5) | |
2635 | ("r-shortread" ,r-shortread) | |
2636 | ("r-stringr" ,r-stringr) | |
2637 | ("r-tibble" ,r-tibble) | |
2638 | ("r-tidyr" ,r-tidyr) | |
2639 | ("r-xvector" ,r-xvector))) | |
2640 | (home-page "https://bioconductor.org/packages/IONiseR/") | |
2641 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") | |
2642 | (description | |
2643 | "IONiseR provides tools for the quality assessment of Oxford Nanopore | |
2644 | MinION data. It extracts summary statistics from a set of fast5 files and can | |
2645 | be used either before or after base calling. In addition to standard | |
2646 | summaries of the read-types produced, it provides a number of plots for | |
2647 | visualising metrics relative to experiment run time or spatially over the | |
2648 | surface of a flowcell.") | |
2649 | (license license:expat))) | |
80eb01c7 RW |
2650 | |
2651 | ;; This is a CRAN package, but it depends on packages from Bioconductor. | |
2652 | (define-public r-gkmsvm | |
2653 | (package | |
2654 | (name "r-gkmsvm") | |
2655 | (version "0.79.0") | |
2656 | (source | |
2657 | (origin | |
2658 | (method url-fetch) | |
2659 | (uri (cran-uri "gkmSVM" version)) | |
2660 | (sha256 | |
2661 | (base32 | |
2662 | "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) | |
2663 | (properties `((upstream-name . "gkmSVM"))) | |
2664 | (build-system r-build-system) | |
2665 | (propagated-inputs | |
2666 | `(("r-biocgenerics" ,r-biocgenerics) | |
2667 | ("r-biostrings" ,r-biostrings) | |
2668 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2669 | ("r-genomicranges" ,r-genomicranges) | |
2670 | ("r-iranges" ,r-iranges) | |
2671 | ("r-kernlab" ,r-kernlab) | |
2672 | ("r-rcpp" ,r-rcpp) | |
2673 | ("r-rocr" ,r-rocr) | |
2674 | ("r-rtracklayer" ,r-rtracklayer) | |
2675 | ("r-s4vectors" ,r-s4vectors) | |
2676 | ("r-seqinr" ,r-seqinr))) | |
2677 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") | |
2678 | (synopsis "Gapped-kmer support vector machine") | |
2679 | (description | |
2680 | "This R package provides tools for training gapped-kmer SVM classifiers | |
2681 | for DNA and protein sequences. This package supports several sequence | |
2682 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
2683 | (license license:gpl2+))) | |
8a5460b4 RW |
2684 | |
2685 | (define-public r-triform | |
2686 | (package | |
2687 | (name "r-triform") | |
bc083eca | 2688 | (version "1.26.0") |
8a5460b4 RW |
2689 | (source |
2690 | (origin | |
2691 | (method url-fetch) | |
2692 | (uri (bioconductor-uri "triform" version)) | |
2693 | (sha256 | |
2694 | (base32 | |
bc083eca | 2695 | "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya")))) |
8a5460b4 RW |
2696 | (build-system r-build-system) |
2697 | (propagated-inputs | |
2698 | `(("r-biocgenerics" ,r-biocgenerics) | |
2699 | ("r-iranges" ,r-iranges) | |
2700 | ("r-yaml" ,r-yaml))) | |
2701 | (home-page "https://bioconductor.org/packages/triform/") | |
2702 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") | |
2703 | (description | |
2704 | "The Triform algorithm uses model-free statistics to identify peak-like | |
2705 | distributions of TF ChIP sequencing reads, taking advantage of an improved | |
2706 | peak definition in combination with known profile characteristics.") | |
2707 | (license license:gpl2))) | |
c538bcdd RW |
2708 | |
2709 | (define-public r-varianttools | |
2710 | (package | |
2711 | (name "r-varianttools") | |
c2effded | 2712 | (version "1.26.0") |
c538bcdd RW |
2713 | (source |
2714 | (origin | |
2715 | (method url-fetch) | |
2716 | (uri (bioconductor-uri "VariantTools" version)) | |
2717 | (sha256 | |
2718 | (base32 | |
c2effded | 2719 | "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql")))) |
c538bcdd RW |
2720 | (properties `((upstream-name . "VariantTools"))) |
2721 | (build-system r-build-system) | |
2722 | (propagated-inputs | |
2723 | `(("r-biobase" ,r-biobase) | |
2724 | ("r-biocgenerics" ,r-biocgenerics) | |
2725 | ("r-biocparallel" ,r-biocparallel) | |
2726 | ("r-biostrings" ,r-biostrings) | |
2727 | ("r-bsgenome" ,r-bsgenome) | |
2728 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2729 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2730 | ("r-genomicranges" ,r-genomicranges) | |
2731 | ("r-iranges" ,r-iranges) | |
2732 | ("r-matrix" ,r-matrix) | |
2733 | ("r-rsamtools" ,r-rsamtools) | |
2734 | ("r-rtracklayer" ,r-rtracklayer) | |
2735 | ("r-s4vectors" ,r-s4vectors) | |
2736 | ("r-variantannotation" ,r-variantannotation))) | |
2737 | (home-page "https://bioconductor.org/packages/VariantTools/") | |
2738 | (synopsis "Tools for exploratory analysis of variant calls") | |
2739 | (description | |
2740 | "Explore, diagnose, and compare variant calls using filters. The | |
2741 | VariantTools package supports a workflow for loading data, calling single | |
2742 | sample variants and tumor-specific somatic mutations or other sample-specific | |
2743 | variant types (e.g., RNA editing). Most of the functions operate on | |
2744 | alignments (BAM files) or datasets of called variants. The user is expected | |
2745 | to have already aligned the reads with a separate tool, e.g., GSNAP via | |
2746 | gmapR.") | |
2747 | (license license:artistic2.0))) | |
3e41919d RW |
2748 | |
2749 | (define-public r-heatplus | |
2750 | (package | |
2751 | (name "r-heatplus") | |
376d1fe7 | 2752 | (version "2.30.0") |
3e41919d RW |
2753 | (source |
2754 | (origin | |
2755 | (method url-fetch) | |
2756 | (uri (bioconductor-uri "Heatplus" version)) | |
2757 | (sha256 | |
2758 | (base32 | |
376d1fe7 | 2759 | "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6")))) |
3e41919d RW |
2760 | (properties `((upstream-name . "Heatplus"))) |
2761 | (build-system r-build-system) | |
2762 | (propagated-inputs | |
2763 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) | |
2764 | (home-page "https://github.com/alexploner/Heatplus") | |
2765 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") | |
2766 | (description | |
2767 | "This package provides tools to display a rectangular heatmap (intensity | |
2768 | plot) of a data matrix. By default, both samples (columns) and features (row) | |
2769 | of the matrix are sorted according to a hierarchical clustering, and the | |
2770 | corresponding dendrogram is plotted. Optionally, panels with additional | |
2771 | information about samples and features can be added to the plot.") | |
2772 | (license license:gpl2+))) | |
c04f230e RW |
2773 | |
2774 | (define-public r-gosemsim | |
2775 | (package | |
2776 | (name "r-gosemsim") | |
24cf7bad | 2777 | (version "2.10.0") |
c04f230e RW |
2778 | (source |
2779 | (origin | |
2780 | (method url-fetch) | |
2781 | (uri (bioconductor-uri "GOSemSim" version)) | |
2782 | (sha256 | |
2783 | (base32 | |
24cf7bad | 2784 | "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg")))) |
c04f230e RW |
2785 | (properties `((upstream-name . "GOSemSim"))) |
2786 | (build-system r-build-system) | |
2787 | (propagated-inputs | |
2788 | `(("r-annotationdbi" ,r-annotationdbi) | |
2789 | ("r-go-db" ,r-go-db) | |
2790 | ("r-rcpp" ,r-rcpp))) | |
2791 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") | |
2792 | (synopsis "GO-terms semantic similarity measures") | |
2793 | (description | |
2794 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide | |
2795 | quantitative ways to compute similarities between genes and gene groups, and | |
2796 | have became important basis for many bioinformatics analysis approaches. | |
2797 | GOSemSim is an R package for semantic similarity computation among GO terms, | |
2798 | sets of GO terms, gene products and gene clusters.") | |
2799 | (license license:artistic2.0))) | |
9d0f7942 RW |
2800 | |
2801 | (define-public r-anota | |
2802 | (package | |
2803 | (name "r-anota") | |
0a41b5db | 2804 | (version "1.32.0") |
9d0f7942 RW |
2805 | (source |
2806 | (origin | |
2807 | (method url-fetch) | |
2808 | (uri (bioconductor-uri "anota" version)) | |
2809 | (sha256 | |
2810 | (base32 | |
0a41b5db | 2811 | "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c")))) |
9d0f7942 RW |
2812 | (build-system r-build-system) |
2813 | (propagated-inputs | |
2814 | `(("r-multtest" ,r-multtest) | |
2815 | ("r-qvalue" ,r-qvalue))) | |
2816 | (home-page "https://bioconductor.org/packages/anota/") | |
2817 | (synopsis "Analysis of translational activity") | |
2818 | (description | |
2819 | "Genome wide studies of translational control is emerging as a tool to | |
2820 | study verious biological conditions. The output from such analysis is both | |
2821 | the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively | |
2822 | involved in translation (the actively translating mRNA level) for each mRNA. | |
2823 | The standard analysis of such data strives towards identifying differential | |
2824 | translational between two or more sample classes - i.e. differences in | |
2825 | actively translated mRNA levels that are independent of underlying differences | |
2826 | in cytosolic mRNA levels. This package allows for such analysis using partial | |
2827 | variances and the random variance model. As 10s of thousands of mRNAs are | |
2828 | analyzed in parallell the library performs a number of tests to assure that | |
2829 | the data set is suitable for such analysis.") | |
2830 | (license license:gpl3))) | |
a6d867fe RW |
2831 | |
2832 | (define-public r-sigpathway | |
2833 | (package | |
2834 | (name "r-sigpathway") | |
3e5ee6f6 | 2835 | (version "1.52.0") |
a6d867fe RW |
2836 | (source |
2837 | (origin | |
2838 | (method url-fetch) | |
2839 | (uri (bioconductor-uri "sigPathway" version)) | |
2840 | (sha256 | |
2841 | (base32 | |
3e5ee6f6 | 2842 | "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7")))) |
a6d867fe RW |
2843 | (properties `((upstream-name . "sigPathway"))) |
2844 | (build-system r-build-system) | |
2845 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") | |
2846 | (synopsis "Pathway analysis") | |
2847 | (description | |
2848 | "This package is used to conduct pathway analysis by calculating the NT_k | |
2849 | and NE_k statistics in a statistical framework for determining whether a | |
2850 | specified group of genes for a pathway has a coordinated association with a | |
2851 | phenotype of interest.") | |
2852 | (license license:gpl2))) | |
af26c7ae RW |
2853 | |
2854 | (define-public r-fgsea | |
2855 | (package | |
2856 | (name "r-fgsea") | |
ebffd24c | 2857 | (version "1.10.0") |
af26c7ae RW |
2858 | (source |
2859 | (origin | |
2860 | (method url-fetch) | |
2861 | (uri (bioconductor-uri "fgsea" version)) | |
2862 | (sha256 | |
2863 | (base32 | |
ebffd24c | 2864 | "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c")))) |
af26c7ae RW |
2865 | (build-system r-build-system) |
2866 | (propagated-inputs | |
ebffd24c RW |
2867 | `(("r-bh" ,r-bh) |
2868 | ("r-biocparallel" ,r-biocparallel) | |
af26c7ae RW |
2869 | ("r-data-table" ,r-data-table) |
2870 | ("r-fastmatch" ,r-fastmatch) | |
2871 | ("r-ggplot2" ,r-ggplot2) | |
2872 | ("r-gridextra" ,r-gridextra) | |
2873 | ("r-matrix" ,r-matrix) | |
2874 | ("r-rcpp" ,r-rcpp))) | |
2875 | (home-page "https://github.com/ctlab/fgsea/") | |
2876 | (synopsis "Fast gene set enrichment analysis") | |
2877 | (description | |
2878 | "The package implements an algorithm for fast gene set enrichment | |
2879 | analysis. Using the fast algorithm allows to make more permutations and get | |
2880 | more fine grained p-values, which allows to use accurate stantard approaches | |
2881 | to multiple hypothesis correction.") | |
2882 | (license license:expat))) | |
305050b5 RW |
2883 | |
2884 | (define-public r-dose | |
2885 | (package | |
2886 | (name "r-dose") | |
1990ff9d | 2887 | (version "3.10.0") |
305050b5 RW |
2888 | (source |
2889 | (origin | |
2890 | (method url-fetch) | |
2891 | (uri (bioconductor-uri "DOSE" version)) | |
2892 | (sha256 | |
2893 | (base32 | |
1990ff9d | 2894 | "0dvhnfhzhhzcxm8zhdwrkif7sak4p888sjqfd3a0p77h0hs6g8pv")))) |
305050b5 RW |
2895 | (properties `((upstream-name . "DOSE"))) |
2896 | (build-system r-build-system) | |
2897 | (propagated-inputs | |
2898 | `(("r-annotationdbi" ,r-annotationdbi) | |
2899 | ("r-biocparallel" ,r-biocparallel) | |
2900 | ("r-do-db" ,r-do-db) | |
2901 | ("r-fgsea" ,r-fgsea) | |
2902 | ("r-ggplot2" ,r-ggplot2) | |
2903 | ("r-gosemsim" ,r-gosemsim) | |
2904 | ("r-qvalue" ,r-qvalue) | |
2905 | ("r-reshape2" ,r-reshape2) | |
2906 | ("r-s4vectors" ,r-s4vectors))) | |
2907 | (home-page "https://guangchuangyu.github.io/software/DOSE/") | |
2908 | (synopsis "Disease ontology semantic and enrichment analysis") | |
2909 | (description | |
2910 | "This package implements five methods proposed by Resnik, Schlicker, | |
2911 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among | |
2912 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses | |
2913 | including hypergeometric model and gene set enrichment analysis are also | |
2914 | implemented for discovering disease associations of high-throughput biological | |
2915 | data.") | |
2916 | (license license:artistic2.0))) | |
9c30cf65 RW |
2917 | |
2918 | (define-public r-enrichplot | |
2919 | (package | |
2920 | (name "r-enrichplot") | |
77d28d66 | 2921 | (version "1.4.0") |
9c30cf65 RW |
2922 | (source |
2923 | (origin | |
2924 | (method url-fetch) | |
2925 | (uri (bioconductor-uri "enrichplot" version)) | |
2926 | (sha256 | |
2927 | (base32 | |
77d28d66 | 2928 | "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h")))) |
9c30cf65 RW |
2929 | (build-system r-build-system) |
2930 | (propagated-inputs | |
2931 | `(("r-annotationdbi" ,r-annotationdbi) | |
2932 | ("r-cowplot" ,r-cowplot) | |
2933 | ("r-dose" ,r-dose) | |
2934 | ("r-europepmc" ,r-europepmc) | |
2935 | ("r-ggplot2" ,r-ggplot2) | |
2936 | ("r-ggplotify" ,r-ggplotify) | |
2937 | ("r-ggraph" ,r-ggraph) | |
2938 | ("r-ggridges" ,r-ggridges) | |
2939 | ("r-gosemsim" ,r-gosemsim) | |
2940 | ("r-gridextra" ,r-gridextra) | |
2941 | ("r-igraph" ,r-igraph) | |
2942 | ("r-purrr" ,r-purrr) | |
2943 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2944 | ("r-reshape2" ,r-reshape2) | |
2945 | ("r-upsetr" ,r-upsetr))) | |
2946 | (home-page "https://github.com/GuangchuangYu/enrichplot") | |
2947 | (synopsis "Visualization of functional enrichment result") | |
2948 | (description | |
2949 | "The enrichplot package implements several visualization methods for | |
2950 | interpreting functional enrichment results obtained from ORA or GSEA analyses. | |
2951 | All the visualization methods are developed based on ggplot2 graphics.") | |
2952 | (license license:artistic2.0))) | |
f8295ee6 RW |
2953 | |
2954 | (define-public r-clusterprofiler | |
2955 | (package | |
2956 | (name "r-clusterprofiler") | |
1a3e33be | 2957 | (version "3.12.0") |
f8295ee6 RW |
2958 | (source |
2959 | (origin | |
2960 | (method url-fetch) | |
2961 | (uri (bioconductor-uri "clusterProfiler" version)) | |
2962 | (sha256 | |
2963 | (base32 | |
1a3e33be | 2964 | "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq")))) |
f8295ee6 RW |
2965 | (properties |
2966 | `((upstream-name . "clusterProfiler"))) | |
2967 | (build-system r-build-system) | |
2968 | (propagated-inputs | |
2969 | `(("r-annotationdbi" ,r-annotationdbi) | |
2970 | ("r-dose" ,r-dose) | |
2971 | ("r-enrichplot" ,r-enrichplot) | |
2972 | ("r-ggplot2" ,r-ggplot2) | |
2973 | ("r-go-db" ,r-go-db) | |
2974 | ("r-gosemsim" ,r-gosemsim) | |
2975 | ("r-magrittr" ,r-magrittr) | |
2976 | ("r-plyr" ,r-plyr) | |
2977 | ("r-qvalue" ,r-qvalue) | |
2978 | ("r-rvcheck" ,r-rvcheck) | |
2979 | ("r-tidyr" ,r-tidyr))) | |
2980 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") | |
2981 | (synopsis "Analysis and visualization of functional profiles for gene clusters") | |
2982 | (description | |
2983 | "This package implements methods to analyze and visualize functional | |
2984 | profiles (GO and KEGG) of gene and gene clusters.") | |
2985 | (license license:artistic2.0))) | |
ce77562a RW |
2986 | |
2987 | (define-public r-mlinterfaces | |
2988 | (package | |
2989 | (name "r-mlinterfaces") | |
8265a111 | 2990 | (version "1.64.0") |
ce77562a RW |
2991 | (source |
2992 | (origin | |
2993 | (method url-fetch) | |
2994 | (uri (bioconductor-uri "MLInterfaces" version)) | |
2995 | (sha256 | |
2996 | (base32 | |
8265a111 | 2997 | "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j")))) |
ce77562a RW |
2998 | (properties `((upstream-name . "MLInterfaces"))) |
2999 | (build-system r-build-system) | |
3000 | (propagated-inputs | |
3001 | `(("r-annotate" ,r-annotate) | |
3002 | ("r-biobase" ,r-biobase) | |
3003 | ("r-biocgenerics" ,r-biocgenerics) | |
3004 | ("r-cluster" ,r-cluster) | |
3005 | ("r-fpc" ,r-fpc) | |
3006 | ("r-gbm" ,r-gbm) | |
3007 | ("r-gdata" ,r-gdata) | |
3008 | ("r-genefilter" ,r-genefilter) | |
3009 | ("r-ggvis" ,r-ggvis) | |
3010 | ("r-hwriter" ,r-hwriter) | |
3011 | ("r-mass" ,r-mass) | |
3012 | ("r-mlbench" ,r-mlbench) | |
3013 | ("r-pls" ,r-pls) | |
3014 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3015 | ("r-rda" ,r-rda) | |
3016 | ("r-rpart" ,r-rpart) | |
3017 | ("r-sfsmisc" ,r-sfsmisc) | |
3018 | ("r-shiny" ,r-shiny) | |
3019 | ("r-threejs" ,r-threejs))) | |
3020 | (home-page "https://bioconductor.org/packages/MLInterfaces/") | |
3021 | (synopsis "Interfaces to R machine learning procedures") | |
3022 | (description | |
3023 | "This package provides uniform interfaces to machine learning code for | |
3024 | data in R and Bioconductor containers.") | |
3025 | ;; Any version of the LGPL. | |
3026 | (license license:lgpl2.1+))) | |
a793e88c RW |
3027 | |
3028 | (define-public r-annaffy | |
3029 | (package | |
3030 | (name "r-annaffy") | |
8bef9df4 | 3031 | (version "1.56.0") |
a793e88c RW |
3032 | (source |
3033 | (origin | |
3034 | (method url-fetch) | |
3035 | (uri (bioconductor-uri "annaffy" version)) | |
3036 | (sha256 | |
3037 | (base32 | |
8bef9df4 | 3038 | "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9")))) |
a793e88c RW |
3039 | (build-system r-build-system) |
3040 | (arguments | |
3041 | `(#:phases | |
3042 | (modify-phases %standard-phases | |
3043 | (add-after 'unpack 'remove-reference-to-non-free-data | |
3044 | (lambda _ | |
3045 | (substitute* "DESCRIPTION" | |
3046 | ((", KEGG.db") "")) | |
3047 | #t))))) | |
3048 | (propagated-inputs | |
3049 | `(("r-annotationdbi" ,r-annotationdbi) | |
3050 | ("r-biobase" ,r-biobase) | |
3051 | ("r-dbi" ,r-dbi) | |
3052 | ("r-go-db" ,r-go-db))) | |
3053 | (home-page "https://bioconductor.org/packages/annaffy/") | |
3054 | (synopsis "Annotation tools for Affymetrix biological metadata") | |
3055 | (description | |
3056 | "This package provides functions for handling data from Bioconductor | |
3057 | Affymetrix annotation data packages. It produces compact HTML and text | |
3058 | reports including experimental data and URL links to many online databases. | |
3059 | It allows searching of biological metadata using various criteria.") | |
3060 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of | |
3061 | ;; the LGPL 2.1 is included. | |
3062 | (license license:lgpl2.1+))) | |
0ec0a5ec RW |
3063 | |
3064 | (define-public r-a4core | |
3065 | (package | |
3066 | (name "r-a4core") | |
b077e3db | 3067 | (version "1.32.0") |
0ec0a5ec RW |
3068 | (source |
3069 | (origin | |
3070 | (method url-fetch) | |
3071 | (uri (bioconductor-uri "a4Core" version)) | |
3072 | (sha256 | |
3073 | (base32 | |
b077e3db | 3074 | "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7")))) |
0ec0a5ec RW |
3075 | (properties `((upstream-name . "a4Core"))) |
3076 | (build-system r-build-system) | |
3077 | (propagated-inputs | |
3078 | `(("r-biobase" ,r-biobase) | |
3079 | ("r-glmnet" ,r-glmnet))) | |
3080 | (home-page "https://bioconductor.org/packages/a4Core") | |
3081 | (synopsis "Automated Affymetrix array analysis core package") | |
3082 | (description | |
3083 | "This is the core package for the automated analysis of Affymetrix | |
3084 | arrays.") | |
3085 | (license license:gpl3))) | |
9ae37581 RW |
3086 | |
3087 | (define-public r-a4classif | |
3088 | (package | |
3089 | (name "r-a4classif") | |
82de77da | 3090 | (version "1.32.0") |
9ae37581 RW |
3091 | (source |
3092 | (origin | |
3093 | (method url-fetch) | |
3094 | (uri (bioconductor-uri "a4Classif" version)) | |
3095 | (sha256 | |
3096 | (base32 | |
82de77da | 3097 | "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0")))) |
9ae37581 RW |
3098 | (properties `((upstream-name . "a4Classif"))) |
3099 | (build-system r-build-system) | |
3100 | (propagated-inputs | |
3101 | `(("r-a4core" ,r-a4core) | |
3102 | ("r-a4preproc" ,r-a4preproc) | |
3103 | ("r-glmnet" ,r-glmnet) | |
3104 | ("r-mlinterfaces" ,r-mlinterfaces) | |
3105 | ("r-pamr" ,r-pamr) | |
3106 | ("r-rocr" ,r-rocr) | |
3107 | ("r-varselrf" ,r-varselrf))) | |
3108 | (home-page "https://bioconductor.org/packages/a4Classif/") | |
3109 | (synopsis "Automated Affymetrix array analysis classification package") | |
3110 | (description | |
3111 | "This is the classification package for the automated analysis of | |
3112 | Affymetrix arrays.") | |
3113 | (license license:gpl3))) | |
b8d13e2c RW |
3114 | |
3115 | (define-public r-a4preproc | |
3116 | (package | |
3117 | (name "r-a4preproc") | |
0b609162 | 3118 | (version "1.32.0") |
b8d13e2c RW |
3119 | (source |
3120 | (origin | |
3121 | (method url-fetch) | |
3122 | (uri (bioconductor-uri "a4Preproc" version)) | |
3123 | (sha256 | |
3124 | (base32 | |
0b609162 | 3125 | "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr")))) |
b8d13e2c RW |
3126 | (properties `((upstream-name . "a4Preproc"))) |
3127 | (build-system r-build-system) | |
3128 | (propagated-inputs | |
3129 | `(("r-annotationdbi" ,r-annotationdbi))) | |
3130 | (home-page "https://bioconductor.org/packages/a4Preproc/") | |
3131 | (synopsis "Automated Affymetrix array analysis preprocessing package") | |
3132 | (description | |
3133 | "This is a package for the automated analysis of Affymetrix arrays. It | |
3134 | is used for preprocessing the arrays.") | |
3135 | (license license:gpl3))) | |
8e15f861 RW |
3136 | |
3137 | (define-public r-a4reporting | |
3138 | (package | |
3139 | (name "r-a4reporting") | |
e5a36543 | 3140 | (version "1.32.0") |
8e15f861 RW |
3141 | (source |
3142 | (origin | |
3143 | (method url-fetch) | |
3144 | (uri (bioconductor-uri "a4Reporting" version)) | |
3145 | (sha256 | |
3146 | (base32 | |
e5a36543 | 3147 | "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj")))) |
8e15f861 RW |
3148 | (properties `((upstream-name . "a4Reporting"))) |
3149 | (build-system r-build-system) | |
3150 | (propagated-inputs | |
3151 | `(("r-annaffy" ,r-annaffy) | |
3152 | ("r-xtable" ,r-xtable))) | |
3153 | (home-page "https://bioconductor.org/packages/a4Reporting/") | |
3154 | (synopsis "Automated Affymetrix array analysis reporting package") | |
3155 | (description | |
3156 | "This is a package for the automated analysis of Affymetrix arrays. It | |
3157 | provides reporting features.") | |
3158 | (license license:gpl3))) | |
dbfe3375 RW |
3159 | |
3160 | (define-public r-a4base | |
3161 | (package | |
3162 | (name "r-a4base") | |
ae1730ae | 3163 | (version "1.32.0") |
dbfe3375 RW |
3164 | (source |
3165 | (origin | |
3166 | (method url-fetch) | |
3167 | (uri (bioconductor-uri "a4Base" version)) | |
3168 | (sha256 | |
3169 | (base32 | |
ae1730ae | 3170 | "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1")))) |
dbfe3375 RW |
3171 | (properties `((upstream-name . "a4Base"))) |
3172 | (build-system r-build-system) | |
3173 | (propagated-inputs | |
3174 | `(("r-a4core" ,r-a4core) | |
3175 | ("r-a4preproc" ,r-a4preproc) | |
3176 | ("r-annaffy" ,r-annaffy) | |
3177 | ("r-annotationdbi" ,r-annotationdbi) | |
3178 | ("r-biobase" ,r-biobase) | |
3179 | ("r-genefilter" ,r-genefilter) | |
3180 | ("r-glmnet" ,r-glmnet) | |
3181 | ("r-gplots" ,r-gplots) | |
3182 | ("r-limma" ,r-limma) | |
3183 | ("r-mpm" ,r-mpm) | |
3184 | ("r-multtest" ,r-multtest))) | |
3185 | (home-page "https://bioconductor.org/packages/a4Base/") | |
3186 | (synopsis "Automated Affymetrix array analysis base package") | |
3187 | (description | |
3188 | "This package provides basic features for the automated analysis of | |
3189 | Affymetrix arrays.") | |
3190 | (license license:gpl3))) | |
84ad024e RW |
3191 | |
3192 | (define-public r-a4 | |
3193 | (package | |
3194 | (name "r-a4") | |
1aadddea | 3195 | (version "1.32.0") |
84ad024e RW |
3196 | (source |
3197 | (origin | |
3198 | (method url-fetch) | |
3199 | (uri (bioconductor-uri "a4" version)) | |
3200 | (sha256 | |
3201 | (base32 | |
1aadddea | 3202 | "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy")))) |
84ad024e RW |
3203 | (build-system r-build-system) |
3204 | (propagated-inputs | |
3205 | `(("r-a4base" ,r-a4base) | |
3206 | ("r-a4classif" ,r-a4classif) | |
3207 | ("r-a4core" ,r-a4core) | |
3208 | ("r-a4preproc" ,r-a4preproc) | |
3209 | ("r-a4reporting" ,r-a4reporting))) | |
3210 | (home-page "https://bioconductor.org/packages/a4/") | |
3211 | (synopsis "Automated Affymetrix array analysis umbrella package") | |
3212 | (description | |
3213 | "This package provides a software suite for the automated analysis of | |
3214 | Affymetrix arrays.") | |
3215 | (license license:gpl3))) | |
59d331f1 RW |
3216 | |
3217 | (define-public r-abseqr | |
3218 | (package | |
3219 | (name "r-abseqr") | |
b7ddf0f0 | 3220 | (version "1.2.0") |
59d331f1 RW |
3221 | (source |
3222 | (origin | |
3223 | (method url-fetch) | |
3224 | (uri (bioconductor-uri "abseqR" version)) | |
3225 | (sha256 | |
3226 | (base32 | |
b7ddf0f0 | 3227 | "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r")))) |
59d331f1 RW |
3228 | (properties `((upstream-name . "abseqR"))) |
3229 | (build-system r-build-system) | |
3230 | (inputs | |
3231 | `(("pandoc" ,ghc-pandoc))) | |
3232 | (propagated-inputs | |
3233 | `(("r-biocparallel" ,r-biocparallel) | |
3234 | ("r-biocstyle" ,r-biocstyle) | |
3235 | ("r-circlize" ,r-circlize) | |
3236 | ("r-flexdashboard" ,r-flexdashboard) | |
3237 | ("r-ggcorrplot" ,r-ggcorrplot) | |
3238 | ("r-ggdendro" ,r-ggdendro) | |
3239 | ("r-ggplot2" ,r-ggplot2) | |
3240 | ("r-gridextra" ,r-gridextra) | |
3241 | ("r-knitr" ,r-knitr) | |
3242 | ("r-plotly" ,r-plotly) | |
3243 | ("r-plyr" ,r-plyr) | |
3244 | ("r-png" ,r-png) | |
3245 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3246 | ("r-reshape2" ,r-reshape2) | |
3247 | ("r-rmarkdown" ,r-rmarkdown) | |
3248 | ("r-stringr" ,r-stringr) | |
3249 | ("r-vegan" ,r-vegan) | |
3250 | ("r-venndiagram" ,r-venndiagram))) | |
3251 | (home-page "https://github.com/malhamdoosh/abseqR") | |
3252 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") | |
3253 | (description | |
3254 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of | |
3255 | sequencing datasets generated from antibody libraries and abseqR is one of its | |
3256 | packages. AbseqR empowers the users of abseqPy with plotting and reporting | |
3257 | capabilities and allows them to generate interactive HTML reports for the | |
3258 | convenience of viewing and sharing with other researchers. Additionally, | |
3259 | abseqR extends abseqPy to compare multiple repertoire analyses and perform | |
3260 | further downstream analysis on its output.") | |
3261 | (license license:gpl3))) | |
41aab7d1 RW |
3262 | |
3263 | (define-public r-bacon | |
3264 | (package | |
3265 | (name "r-bacon") | |
e33c25ff | 3266 | (version "1.12.0") |
41aab7d1 RW |
3267 | (source |
3268 | (origin | |
3269 | (method url-fetch) | |
3270 | (uri (bioconductor-uri "bacon" version)) | |
3271 | (sha256 | |
3272 | (base32 | |
e33c25ff | 3273 | "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q")))) |
41aab7d1 RW |
3274 | (build-system r-build-system) |
3275 | (propagated-inputs | |
3276 | `(("r-biocparallel" ,r-biocparallel) | |
3277 | ("r-ellipse" ,r-ellipse) | |
3278 | ("r-ggplot2" ,r-ggplot2))) | |
3279 | (home-page "https://bioconductor.org/packages/bacon/") | |
3280 | (synopsis "Controlling bias and inflation in association studies") | |
3281 | (description | |
3282 | "Bacon can be used to remove inflation and bias often observed in | |
3283 | epigenome- and transcriptome-wide association studies. To this end bacon | |
3284 | constructs an empirical null distribution using a Gibbs Sampling algorithm by | |
3285 | fitting a three-component normal mixture on z-scores.") | |
3286 | (license license:gpl2+))) | |
051e8e1a RW |
3287 | |
3288 | (define-public r-rgadem | |
3289 | (package | |
3290 | (name "r-rgadem") | |
a5860ebe | 3291 | (version "2.31.0") |
051e8e1a RW |
3292 | (source |
3293 | (origin | |
3294 | (method url-fetch) | |
3295 | (uri (bioconductor-uri "rGADEM" version)) | |
3296 | (sha256 | |
3297 | (base32 | |
a5860ebe | 3298 | "0mck3dsxzjxszfs1cl96kd83q7n85p3763s0y3gwws69jn7p6w5j")))) |
051e8e1a RW |
3299 | (properties `((upstream-name . "rGADEM"))) |
3300 | (build-system r-build-system) | |
3301 | (propagated-inputs | |
3302 | `(("r-biostrings" ,r-biostrings) | |
3303 | ("r-bsgenome" ,r-bsgenome) | |
3304 | ("r-iranges" ,r-iranges) | |
3305 | ("r-seqlogo" ,r-seqlogo))) | |
3306 | (home-page "https://bioconductor.org/packages/rGADEM/") | |
3307 | (synopsis "De novo sequence motif discovery") | |
3308 | (description | |
3309 | "rGADEM is an efficient de novo motif discovery tool for large-scale | |
3310 | genomic sequence data.") | |
3311 | (license license:artistic2.0))) | |
229f97c3 RW |
3312 | |
3313 | (define-public r-motiv | |
3314 | (package | |
3315 | (name "r-motiv") | |
f7a495b1 | 3316 | (version "1.40.0") |
229f97c3 RW |
3317 | (source |
3318 | (origin | |
3319 | (method url-fetch) | |
3320 | (uri (bioconductor-uri "MotIV" version)) | |
3321 | (sha256 | |
3322 | (base32 | |
f7a495b1 | 3323 | "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf")))) |
229f97c3 RW |
3324 | (properties `((upstream-name . "MotIV"))) |
3325 | (build-system r-build-system) | |
3326 | (inputs | |
3327 | `(("gsl" ,gsl))) | |
3328 | (propagated-inputs | |
3329 | `(("r-biocgenerics" ,r-biocgenerics) | |
3330 | ("r-biostrings" ,r-biostrings) | |
3331 | ("r-iranges" ,r-iranges) | |
3332 | ("r-lattice" ,r-lattice) | |
3333 | ("r-rgadem" ,r-rgadem) | |
3334 | ("r-s4vectors" ,r-s4vectors))) | |
3335 | (home-page "https://bioconductor.org/packages/MotIV/") | |
3336 | (synopsis "Motif identification and validation") | |
3337 | (description | |
3338 | "This package is used for the identification and validation of sequence | |
3339 | motifs. It makes use of STAMP for comparing a set of motifs to a given | |
3340 | database (e.g. JASPAR). It can also be used to visualize motifs, motif | |
3341 | distributions, modules and filter motifs.") | |
3342 | (license license:gpl2))) | |
2a72ef56 RW |
3343 | |
3344 | (define-public r-motifstack | |
3345 | (package | |
3346 | (name "r-motifstack") | |
aa0ebfd2 | 3347 | (version "1.28.0") |
2a72ef56 RW |
3348 | (source |
3349 | (origin | |
3350 | (method url-fetch) | |
3351 | (uri (bioconductor-uri "motifStack" version)) | |
3352 | (sha256 | |
3353 | (base32 | |
aa0ebfd2 | 3354 | "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f")))) |
2a72ef56 RW |
3355 | (properties `((upstream-name . "motifStack"))) |
3356 | (build-system r-build-system) | |
3357 | (propagated-inputs | |
3358 | `(("r-ade4" ,r-ade4) | |
3359 | ("r-biostrings" ,r-biostrings) | |
aa0ebfd2 | 3360 | ("r-grimport2" ,r-grimport2) |
2a72ef56 RW |
3361 | ("r-htmlwidgets" ,r-htmlwidgets) |
3362 | ("r-motiv" ,r-motiv) | |
3363 | ("r-scales" ,r-scales) | |
3364 | ("r-xml" ,r-xml))) | |
3365 | (home-page "https://bioconductor.org/packages/motifStack/") | |
3366 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") | |
3367 | (description | |
3368 | "The motifStack package is designed for graphic representation of | |
3369 | multiple motifs with different similarity scores. It works with both DNA/RNA | |
3370 | sequence motifs and amino acid sequence motifs. In addition, it provides the | |
3371 | flexibility for users to customize the graphic parameters such as the font | |
3372 | type and symbol colors.") | |
3373 | (license license:gpl2+))) | |
e5bff307 RW |
3374 | |
3375 | (define-public r-genomicscores | |
3376 | (package | |
3377 | (name "r-genomicscores") | |
19ee7637 | 3378 | (version "1.8.0") |
e5bff307 RW |
3379 | (source |
3380 | (origin | |
3381 | (method url-fetch) | |
3382 | (uri (bioconductor-uri "GenomicScores" version)) | |
3383 | (sha256 | |
3384 | (base32 | |
19ee7637 | 3385 | "17bd61icfycc61b5dij1968h026w7vfd9miwdcbppak1j6s08idq")))) |
e5bff307 RW |
3386 | (properties `((upstream-name . "GenomicScores"))) |
3387 | (build-system r-build-system) | |
3388 | (propagated-inputs | |
3389 | `(("r-annotationhub" ,r-annotationhub) | |
3390 | ("r-biobase" ,r-biobase) | |
3391 | ("r-biocgenerics" ,r-biocgenerics) | |
3392 | ("r-biostrings" ,r-biostrings) | |
3393 | ("r-bsgenome" ,r-bsgenome) | |
3394 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3395 | ("r-genomicranges" ,r-genomicranges) | |
3396 | ("r-iranges" ,r-iranges) | |
3397 | ("r-s4vectors" ,r-s4vectors) | |
3398 | ("r-xml" ,r-xml))) | |
3399 | (home-page "https://github.com/rcastelo/GenomicScores/") | |
3400 | (synopsis "Work with genome-wide position-specific scores") | |
3401 | (description | |
3402 | "This package provides infrastructure to store and access genome-wide | |
3403 | position-specific scores within R and Bioconductor.") | |
3404 | (license license:artistic2.0))) | |
32e0f906 RW |
3405 | |
3406 | (define-public r-atacseqqc | |
3407 | (package | |
3408 | (name "r-atacseqqc") | |
bcc233c1 | 3409 | (version "1.8.0") |
32e0f906 RW |
3410 | (source |
3411 | (origin | |
3412 | (method url-fetch) | |
3413 | (uri (bioconductor-uri "ATACseqQC" version)) | |
3414 | (sha256 | |
3415 | (base32 | |
bcc233c1 | 3416 | "03f130vcd6hd3fv2pg60id0ddd6qkwsyx73gm907xaayf42ar2pj")))) |
32e0f906 RW |
3417 | (properties `((upstream-name . "ATACseqQC"))) |
3418 | (build-system r-build-system) | |
3419 | (propagated-inputs | |
3420 | `(("r-biocgenerics" ,r-biocgenerics) | |
3421 | ("r-biostrings" ,r-biostrings) | |
3422 | ("r-bsgenome" ,r-bsgenome) | |
3423 | ("r-chippeakanno" ,r-chippeakanno) | |
bcc233c1 | 3424 | ("r-edger" ,r-edger) |
32e0f906 RW |
3425 | ("r-genomeinfodb" ,r-genomeinfodb) |
3426 | ("r-genomicalignments" ,r-genomicalignments) | |
3427 | ("r-genomicranges" ,r-genomicranges) | |
3428 | ("r-genomicscores" ,r-genomicscores) | |
3429 | ("r-iranges" ,r-iranges) | |
3430 | ("r-kernsmooth" ,r-kernsmooth) | |
3431 | ("r-limma" ,r-limma) | |
3432 | ("r-motifstack" ,r-motifstack) | |
3433 | ("r-preseqr" ,r-preseqr) | |
3434 | ("r-randomforest" ,r-randomforest) | |
3435 | ("r-rsamtools" ,r-rsamtools) | |
3436 | ("r-rtracklayer" ,r-rtracklayer) | |
3437 | ("r-s4vectors" ,r-s4vectors))) | |
3438 | (home-page "https://bioconductor.org/packages/ATACseqQC/") | |
3439 | (synopsis "ATAC-seq quality control") | |
3440 | (description | |
3441 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using | |
3442 | sequencing, is a rapid and sensitive method for chromatin accessibility | |
3443 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq | |
3444 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly | |
3445 | assess whether their ATAC-seq experiment is successful. It includes | |
3446 | diagnostic plots of fragment size distribution, proportion of mitochondria | |
3447 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor | |
3448 | footprints.") | |
3449 | (license license:gpl2+))) | |
3972cfce RW |
3450 | |
3451 | (define-public r-gofuncr | |
3452 | (package | |
3453 | (name "r-gofuncr") | |
bab06a6f | 3454 | (version "1.4.0") |
3972cfce RW |
3455 | (source |
3456 | (origin | |
3457 | (method url-fetch) | |
3458 | (uri (bioconductor-uri "GOfuncR" version)) | |
3459 | (sha256 | |
3460 | (base32 | |
bab06a6f | 3461 | "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm")))) |
3972cfce RW |
3462 | (properties `((upstream-name . "GOfuncR"))) |
3463 | (build-system r-build-system) | |
3464 | (propagated-inputs | |
3465 | `(("r-annotationdbi" ,r-annotationdbi) | |
3466 | ("r-genomicranges" ,r-genomicranges) | |
3467 | ("r-gtools" ,r-gtools) | |
3468 | ("r-iranges" ,r-iranges) | |
3469 | ("r-mapplots" ,r-mapplots) | |
3470 | ("r-rcpp" ,r-rcpp) | |
3471 | ("r-vioplot" ,r-vioplot))) | |
3472 | (home-page "https://bioconductor.org/packages/GOfuncR/") | |
3473 | (synopsis "Gene ontology enrichment using FUNC") | |
3474 | (description | |
3475 | "GOfuncR performs a gene ontology enrichment analysis based on the | |
3476 | ontology enrichment software FUNC. GO-annotations are obtained from | |
3477 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is | |
3478 | included in the package and updated regularly. GOfuncR provides the standard | |
3479 | candidate vs background enrichment analysis using the hypergeometric test, as | |
3480 | well as three additional tests: | |
3481 | ||
3482 | @enumerate | |
3483 | @item the Wilcoxon rank-sum test that is used when genes are ranked, | |
3484 | @item a binomial test that is used when genes are associated with two counts, | |
3485 | and | |
3486 | @item a Chi-square or Fisher's exact test that is used in cases when genes are | |
3487 | associated with four counts. | |
3488 | @end enumerate | |
3489 | ||
3490 | To correct for multiple testing and interdependency of the tests, family-wise | |
3491 | error rates are computed based on random permutations of the gene-associated | |
3492 | variables. GOfuncR also provides tools for exploring the ontology graph and | |
3493 | the annotations, and options to take gene-length or spatial clustering of | |
3494 | genes into account. It is also possible to provide custom gene coordinates, | |
3495 | annotations and ontologies.") | |
3496 | (license license:gpl2+))) | |
9bf4bb19 RW |
3497 | |
3498 | (define-public r-abaenrichment | |
3499 | (package | |
3500 | (name "r-abaenrichment") | |
e2e1dea2 | 3501 | (version "1.14.0") |
9bf4bb19 RW |
3502 | (source |
3503 | (origin | |
3504 | (method url-fetch) | |
3505 | (uri (bioconductor-uri "ABAEnrichment" version)) | |
3506 | (sha256 | |
3507 | (base32 | |
e2e1dea2 | 3508 | "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2")))) |
9bf4bb19 RW |
3509 | (properties `((upstream-name . "ABAEnrichment"))) |
3510 | (build-system r-build-system) | |
3511 | (propagated-inputs | |
3512 | `(("r-abadata" ,r-abadata) | |
3513 | ("r-data-table" ,r-data-table) | |
3514 | ("r-gofuncr" ,r-gofuncr) | |
3515 | ("r-gplots" ,r-gplots) | |
3516 | ("r-gtools" ,r-gtools) | |
3517 | ("r-rcpp" ,r-rcpp))) | |
3518 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") | |
3519 | (synopsis "Gene expression enrichment in human brain regions") | |
3520 | (description | |
3521 | "The package ABAEnrichment is designed to test for enrichment of user | |
3522 | defined candidate genes in the set of expressed genes in different human brain | |
3523 | regions. The core function @code{aba_enrich} integrates the expression of the | |
3524 | candidate gene set (averaged across donors) and the structural information of | |
3525 | the brain using an ontology, both provided by the Allen Brain Atlas project.") | |
3526 | (license license:gpl2+))) | |
0b91b7b9 RW |
3527 | |
3528 | (define-public r-annotationfuncs | |
3529 | (package | |
3530 | (name "r-annotationfuncs") | |
69a2ec54 | 3531 | (version "1.34.0") |
0b91b7b9 RW |
3532 | (source |
3533 | (origin | |
3534 | (method url-fetch) | |
3535 | (uri (bioconductor-uri "AnnotationFuncs" version)) | |
3536 | (sha256 | |
3537 | (base32 | |
69a2ec54 | 3538 | "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3")))) |
0b91b7b9 RW |
3539 | (properties |
3540 | `((upstream-name . "AnnotationFuncs"))) | |
3541 | (build-system r-build-system) | |
3542 | (propagated-inputs | |
3543 | `(("r-annotationdbi" ,r-annotationdbi) | |
3544 | ("r-dbi" ,r-dbi))) | |
3545 | (home-page "https://www.iysik.com/r/annotationfuncs") | |
3546 | (synopsis "Annotation translation functions") | |
3547 | (description | |
3548 | "This package provides functions for handling translating between | |
3549 | different identifieres using the Biocore Data Team data-packages (e.g. | |
3550 | @code{org.Bt.eg.db}).") | |
3551 | (license license:gpl2))) | |
adf7d813 RW |
3552 | |
3553 | (define-public r-annotationtools | |
3554 | (package | |
3555 | (name "r-annotationtools") | |
ee1a45d7 | 3556 | (version "1.58.0") |
adf7d813 RW |
3557 | (source |
3558 | (origin | |
3559 | (method url-fetch) | |
3560 | (uri (bioconductor-uri "annotationTools" version)) | |
3561 | (sha256 | |
3562 | (base32 | |
ee1a45d7 | 3563 | "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1")))) |
adf7d813 RW |
3564 | (properties |
3565 | `((upstream-name . "annotationTools"))) | |
3566 | (build-system r-build-system) | |
3567 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
3568 | (home-page "https://bioconductor.org/packages/annotationTools/") | |
3569 | (synopsis "Annotate microarrays and perform gene expression analyses") | |
3570 | (description | |
3571 | "This package provides functions to annotate microarrays, find orthologs, | |
3572 | and integrate heterogeneous gene expression profiles using annotation and | |
3573 | other molecular biology information available as flat file database (plain | |
3574 | text files).") | |
3575 | ;; Any version of the GPL. | |
3576 | (license (list license:gpl2+)))) | |
f31e10f8 RW |
3577 | |
3578 | (define-public r-allelicimbalance | |
3579 | (package | |
3580 | (name "r-allelicimbalance") | |
9da2021f | 3581 | (version "1.22.0") |
f31e10f8 RW |
3582 | (source |
3583 | (origin | |
3584 | (method url-fetch) | |
3585 | (uri (bioconductor-uri "AllelicImbalance" version)) | |
3586 | (sha256 | |
3587 | (base32 | |
9da2021f | 3588 | "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng")))) |
f31e10f8 RW |
3589 | (properties |
3590 | `((upstream-name . "AllelicImbalance"))) | |
3591 | (build-system r-build-system) | |
3592 | (propagated-inputs | |
3593 | `(("r-annotationdbi" ,r-annotationdbi) | |
3594 | ("r-biocgenerics" ,r-biocgenerics) | |
3595 | ("r-biostrings" ,r-biostrings) | |
3596 | ("r-bsgenome" ,r-bsgenome) | |
3597 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3598 | ("r-genomicalignments" ,r-genomicalignments) | |
3599 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3600 | ("r-genomicranges" ,r-genomicranges) | |
3601 | ("r-gridextra" ,r-gridextra) | |
3602 | ("r-gviz" ,r-gviz) | |
3603 | ("r-iranges" ,r-iranges) | |
3604 | ("r-lattice" ,r-lattice) | |
3605 | ("r-latticeextra" ,r-latticeextra) | |
3606 | ("r-nlme" ,r-nlme) | |
3607 | ("r-rsamtools" ,r-rsamtools) | |
3608 | ("r-s4vectors" ,r-s4vectors) | |
3609 | ("r-seqinr" ,r-seqinr) | |
3610 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
3611 | ("r-variantannotation" ,r-variantannotation))) | |
3612 | (home-page "https://github.com/pappewaio/AllelicImbalance") | |
3613 | (synopsis "Investigate allele-specific expression") | |
3614 | (description | |
3615 | "This package provides a framework for allele-specific expression | |
3616 | investigation using RNA-seq data.") | |
3617 | (license license:gpl3))) | |
ffe7029b RW |
3618 | |
3619 | (define-public r-aucell | |
3620 | (package | |
3621 | (name "r-aucell") | |
b68a9e80 | 3622 | (version "1.6.0") |
ffe7029b RW |
3623 | (source |
3624 | (origin | |
3625 | (method url-fetch) | |
3626 | (uri (bioconductor-uri "AUCell" version)) | |
3627 | (sha256 | |
3628 | (base32 | |
b68a9e80 | 3629 | "025q1as9pifbxa7hidlz634q6d7l73zx8mqy4rjbfrk7d5615xvm")))) |
ffe7029b RW |
3630 | (properties `((upstream-name . "AUCell"))) |
3631 | (build-system r-build-system) | |
3632 | (propagated-inputs | |
3633 | `(("r-data-table" ,r-data-table) | |
3634 | ("r-gseabase" ,r-gseabase) | |
3635 | ("r-mixtools" ,r-mixtools) | |
3636 | ("r-r-utils" ,r-r-utils) | |
3637 | ("r-shiny" ,r-shiny) | |
3638 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
3639 | (home-page "https://bioconductor.org/packages/AUCell/") | |
3640 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") | |
3641 | (description | |
3642 | "AUCell allows to identify cells with active gene sets (e.g. signatures, | |
3643 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area | |
3644 | Under the Curve} (AUC) to calculate whether a critical subset of the input | |
3645 | gene set is enriched within the expressed genes for each cell. The | |
3646 | distribution of AUC scores across all the cells allows exploring the relative | |
3647 | expression of the signature. Since the scoring method is ranking-based, | |
3648 | AUCell is independent of the gene expression units and the normalization | |
3649 | procedure. In addition, since the cells are evaluated individually, it can | |
3650 | easily be applied to bigger datasets, subsetting the expression matrix if | |
3651 | needed.") | |
3652 | (license license:gpl3))) | |
5cfa4bff RW |
3653 | |
3654 | (define-public r-ebimage | |
3655 | (package | |
3656 | (name "r-ebimage") | |
3657 | (version "4.24.0") | |
3658 | (source | |
3659 | (origin | |
3660 | (method url-fetch) | |
3661 | (uri (bioconductor-uri "EBImage" version)) | |
3662 | (sha256 | |
3663 | (base32 | |
3664 | "18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx")))) | |
3665 | (properties `((upstream-name . "EBImage"))) | |
3666 | (build-system r-build-system) | |
3667 | (propagated-inputs | |
3668 | `(("r-abind" ,r-abind) | |
3669 | ("r-biocgenerics" ,r-biocgenerics) | |
3670 | ("r-fftwtools" ,r-fftwtools) | |
3671 | ("r-htmltools" ,r-htmltools) | |
3672 | ("r-htmlwidgets" ,r-htmlwidgets) | |
3673 | ("r-jpeg" ,r-jpeg) | |
3674 | ("r-locfit" ,r-locfit) | |
3675 | ("r-png" ,r-png) | |
3676 | ("r-rcurl" ,r-rcurl) | |
3677 | ("r-tiff" ,r-tiff))) | |
3678 | (native-inputs | |
3679 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
3680 | (home-page "https://github.com/aoles/EBImage") | |
3681 | (synopsis "Image processing and analysis toolbox for R") | |
3682 | (description | |
3683 | "EBImage provides general purpose functionality for image processing and | |
3684 | analysis. In the context of (high-throughput) microscopy-based cellular | |
3685 | assays, EBImage offers tools to segment cells and extract quantitative | |
3686 | cellular descriptors. This allows the automation of such tasks using the R | |
3687 | programming language and facilitates the use of other tools in the R | |
3688 | environment for signal processing, statistical modeling, machine learning and | |
3689 | visualization with image data.") | |
3690 | ;; Any version of the LGPL. | |
3691 | (license license:lgpl2.1+))) | |
51e98f7e RW |
3692 | |
3693 | (define-public r-yamss | |
3694 | (package | |
3695 | (name "r-yamss") | |
3696 | (version "1.8.1") | |
3697 | (source | |
3698 | (origin | |
3699 | (method url-fetch) | |
3700 | (uri (bioconductor-uri "yamss" version)) | |
3701 | (sha256 | |
3702 | (base32 | |
3703 | "13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9")))) | |
3704 | (build-system r-build-system) | |
3705 | (propagated-inputs | |
3706 | `(("r-biocgenerics" ,r-biocgenerics) | |
3707 | ("r-data-table" ,r-data-table) | |
3708 | ("r-ebimage" ,r-ebimage) | |
3709 | ("r-iranges" ,r-iranges) | |
3710 | ("r-limma" ,r-limma) | |
3711 | ("r-matrix" ,r-matrix) | |
3712 | ("r-mzr" ,r-mzr) | |
3713 | ("r-s4vectors" ,r-s4vectors) | |
3714 | ("r-summarizedexperiment" | |
3715 | ,r-summarizedexperiment))) | |
3716 | (home-page "https://github.com/hansenlab/yamss") | |
3717 | (synopsis "Tools for high-throughput metabolomics") | |
3718 | (description | |
3719 | "This package provides tools to analyze and visualize high-throughput | |
9b19734c | 3720 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
51e98f7e RW |
3721 | preprocess data in a way that enables reliable and powerful differential |
3722 | analysis.") | |
3723 | (license license:artistic2.0))) | |
398c4a93 RW |
3724 | |
3725 | (define-public r-gtrellis | |
3726 | (package | |
3727 | (name "r-gtrellis") | |
3728 | (version "1.14.0") | |
3729 | (source | |
3730 | (origin | |
3731 | (method url-fetch) | |
3732 | (uri (bioconductor-uri "gtrellis" version)) | |
3733 | (sha256 | |
3734 | (base32 | |
3735 | "17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v")))) | |
3736 | (build-system r-build-system) | |
3737 | (propagated-inputs | |
3738 | `(("r-circlize" ,r-circlize) | |
3739 | ("r-genomicranges" ,r-genomicranges) | |
3740 | ("r-getoptlong" ,r-getoptlong) | |
3741 | ("r-iranges" ,r-iranges))) | |
3742 | (home-page "https://github.com/jokergoo/gtrellis") | |
3743 | (synopsis "Genome level Trellis layout") | |
3744 | (description | |
3745 | "Genome level Trellis graph visualizes genomic data conditioned by | |
3746 | genomic categories (e.g. chromosomes). For each genomic category, multiple | |
3747 | dimensional data which are represented as tracks describe different features | |
3748 | from different aspects. This package provides high flexibility to arrange | |
3749 | genomic categories and to add self-defined graphics in the plot.") | |
3750 | (license license:expat))) | |
28098414 RW |
3751 | |
3752 | (define-public r-somaticsignatures | |
3753 | (package | |
3754 | (name "r-somaticsignatures") | |
3755 | (version "2.18.0") | |
3756 | (source | |
3757 | (origin | |
3758 | (method url-fetch) | |
3759 | (uri (bioconductor-uri "SomaticSignatures" version)) | |
3760 | (sha256 | |
3761 | (base32 | |
3762 | "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02")))) | |
3763 | (properties | |
3764 | `((upstream-name . "SomaticSignatures"))) | |
3765 | (build-system r-build-system) | |
3766 | (propagated-inputs | |
3767 | `(("r-biobase" ,r-biobase) | |
3768 | ("r-biostrings" ,r-biostrings) | |
3769 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3770 | ("r-genomicranges" ,r-genomicranges) | |
3771 | ("r-ggbio" ,r-ggbio) | |
3772 | ("r-ggplot2" ,r-ggplot2) | |
3773 | ("r-iranges" ,r-iranges) | |
3774 | ("r-nmf" ,r-nmf) | |
3775 | ("r-pcamethods" ,r-pcamethods) | |
3776 | ("r-proxy" ,r-proxy) | |
3777 | ("r-reshape2" ,r-reshape2) | |
3778 | ("r-s4vectors" ,r-s4vectors) | |
3779 | ("r-variantannotation" ,r-variantannotation))) | |
3780 | (home-page "https://github.com/juliangehring/SomaticSignatures") | |
3781 | (synopsis "Somatic signatures") | |
3782 | (description | |
3783 | "This package identifies mutational signatures of @dfn{single nucleotide | |
3784 | variants} (SNVs). It provides a infrastructure related to the methodology | |
3785 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix | |
3786 | decomposition algorithms.") | |
3787 | (license license:expat))) | |
303f2ed1 RW |
3788 | |
3789 | (define-public r-yapsa | |
3790 | (package | |
3791 | (name "r-yapsa") | |
3792 | (version "1.8.0") | |
3793 | (source | |
3794 | (origin | |
3795 | (method url-fetch) | |
3796 | (uri (bioconductor-uri "YAPSA" version)) | |
3797 | (sha256 | |
3798 | (base32 | |
3799 | "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j")))) | |
3800 | (properties `((upstream-name . "YAPSA"))) | |
3801 | (build-system r-build-system) | |
3802 | (propagated-inputs | |
3803 | `(("r-circlize" ,r-circlize) | |
3804 | ("r-complexheatmap" ,r-complexheatmap) | |
3805 | ("r-corrplot" ,r-corrplot) | |
3806 | ("r-dendextend" ,r-dendextend) | |
3807 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3808 | ("r-genomicranges" ,r-genomicranges) | |
3809 | ("r-getoptlong" ,r-getoptlong) | |
3810 | ("r-ggplot2" ,r-ggplot2) | |
3811 | ("r-gridextra" ,r-gridextra) | |
3812 | ("r-gtrellis" ,r-gtrellis) | |
3813 | ("r-keggrest" ,r-keggrest) | |
3814 | ("r-lsei" ,r-lsei) | |
3815 | ("r-pmcmr" ,r-pmcmr) | |
3816 | ("r-reshape2" ,r-reshape2) | |
3817 | ("r-somaticsignatures" ,r-somaticsignatures) | |
3818 | ("r-variantannotation" ,r-variantannotation))) | |
3819 | (home-page "https://bioconductor.org/packages/YAPSA/") | |
3820 | (synopsis "Yet another package for signature analysis") | |
3821 | (description | |
3822 | "This package provides functions and routines useful in the analysis of | |
3823 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, | |
3824 | functions to perform a signature analysis with known signatures and a | |
3825 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are | |
3826 | provided.") | |
3827 | (license license:gpl3))) | |
e99380d6 RW |
3828 | |
3829 | (define-public r-gcrma | |
3830 | (package | |
3831 | (name "r-gcrma") | |
3832 | (version "2.54.0") | |
3833 | (source | |
3834 | (origin | |
3835 | (method url-fetch) | |
3836 | (uri (bioconductor-uri "gcrma" version)) | |
3837 | (sha256 | |
3838 | (base32 | |
3839 | "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim")))) | |
3840 | (build-system r-build-system) | |
3841 | (propagated-inputs | |
3842 | `(("r-affy" ,r-affy) | |
3843 | ("r-affyio" ,r-affyio) | |
3844 | ("r-biobase" ,r-biobase) | |
3845 | ("r-biocmanager" ,r-biocmanager) | |
3846 | ("r-biostrings" ,r-biostrings) | |
3847 | ("r-xvector" ,r-xvector))) | |
3848 | (home-page "https://bioconductor.org/packages/gcrma/") | |
3849 | (synopsis "Background adjustment using sequence information") | |
3850 | (description | |
3851 | "Gcrma adjusts for background intensities in Affymetrix array data which | |
3852 | include optical noise and @dfn{non-specific binding} (NSB). The main function | |
3853 | @code{gcrma} converts background adjusted probe intensities to expression | |
3854 | measures using the same normalization and summarization methods as a | |
3855 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information | |
3856 | to estimate probe affinity to NSB. The sequence information is summarized in | |
3857 | a more complex way than the simple GC content. Instead, the base types (A, T, | |
3858 | G or C) at each position along the probe determine the affinity of each probe. | |
3859 | The parameters of the position-specific base contributions to the probe | |
3860 | affinity is estimated in an NSB experiment in which only NSB but no | |
3861 | gene-specific bidning is expected.") | |
3862 | ;; Any version of the LGPL | |
3863 | (license license:lgpl2.1+))) | |
4675b3cf RW |
3864 | |
3865 | (define-public r-simpleaffy | |
3866 | (package | |
3867 | (name "r-simpleaffy") | |
3868 | (version "2.58.0") | |
3869 | (source | |
3870 | (origin | |
3871 | (method url-fetch) | |
3872 | (uri (bioconductor-uri "simpleaffy" version)) | |
3873 | (sha256 | |
3874 | (base32 | |
3875 | "0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s")))) | |
3876 | (build-system r-build-system) | |
3877 | (propagated-inputs | |
3878 | `(("r-affy" ,r-affy) | |
3879 | ("r-biobase" ,r-biobase) | |
3880 | ("r-biocgenerics" ,r-biocgenerics) | |
3881 | ("r-gcrma" ,r-gcrma) | |
3882 | ("r-genefilter" ,r-genefilter))) | |
3883 | (home-page "https://bioconductor.org/packages/simpleaffy/") | |
3884 | (synopsis "Very simple high level analysis of Affymetrix data") | |
3885 | (description | |
3886 | "This package provides high level functions for reading Affy @file{.CEL} | |
3887 | files, phenotypic data, and then computing simple things with it, such as | |
3888 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} | |
3889 | library. It also has some basic scatter plot functions and mechanisms for | |
3890 | generating high resolution journal figures.") | |
3891 | (license license:gpl2+))) | |
f562c90a RW |
3892 | |
3893 | (define-public r-yaqcaffy | |
3894 | (package | |
3895 | (name "r-yaqcaffy") | |
3896 | (version "1.42.0") | |
3897 | (source | |
3898 | (origin | |
3899 | (method url-fetch) | |
3900 | (uri (bioconductor-uri "yaqcaffy" version)) | |
3901 | (sha256 | |
3902 | (base32 | |
3903 | "192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk")))) | |
3904 | (build-system r-build-system) | |
3905 | (propagated-inputs | |
3906 | `(("r-simpleaffy" ,r-simpleaffy))) | |
3907 | (home-page "https://bioconductor.org/packages/yaqcaffy/") | |
3908 | (synopsis "Affymetrix quality control and reproducibility analysis") | |
3909 | (description | |
3910 | "This is a package that can be used for quality control of Affymetrix | |
3911 | GeneChip expression data and reproducibility analysis of human whole genome | |
3912 | chips with the MAQC reference datasets.") | |
3913 | (license license:artistic2.0))) | |
59cf2629 RW |
3914 | |
3915 | (define-public r-quantro | |
3916 | (package | |
3917 | (name "r-quantro") | |
3918 | (version "1.16.0") | |
3919 | (source | |
3920 | (origin | |
3921 | (method url-fetch) | |
3922 | (uri (bioconductor-uri "quantro" version)) | |
3923 | (sha256 | |
3924 | (base32 | |
3925 | "1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib")))) | |
3926 | (build-system r-build-system) | |
3927 | (propagated-inputs | |
3928 | `(("r-biobase" ,r-biobase) | |
3929 | ("r-doparallel" ,r-doparallel) | |
3930 | ("r-foreach" ,r-foreach) | |
3931 | ("r-ggplot2" ,r-ggplot2) | |
3932 | ("r-iterators" ,r-iterators) | |
3933 | ("r-minfi" ,r-minfi) | |
3934 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
3935 | (home-page "https://bioconductor.org/packages/quantro/") | |
3936 | (synopsis "Test for when to use quantile normalization") | |
3937 | (description | |
3938 | "This package provides a data-driven test for the assumptions of quantile | |
3939 | normalization using raw data such as objects that inherit eSets (e.g. | |
3940 | ExpressionSet, MethylSet). Group level information about each sample (such as | |
3941 | Tumor / Normal status) must also be provided because the test assesses if | |
3942 | there are global differences in the distributions between the user-defined | |
3943 | groups.") | |
3944 | (license license:gpl3+))) | |
98a2af31 RW |
3945 | |
3946 | (define-public r-yarn | |
3947 | (package | |
3948 | (name "r-yarn") | |
3949 | (version "1.8.1") | |
3950 | (source | |
3951 | (origin | |
3952 | (method url-fetch) | |
3953 | (uri (bioconductor-uri "yarn" version)) | |
3954 | (sha256 | |
3955 | (base32 | |
3956 | "0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s")))) | |
3957 | (build-system r-build-system) | |
3958 | (propagated-inputs | |
3959 | `(("r-biobase" ,r-biobase) | |
3960 | ("r-biomart" ,r-biomart) | |
3961 | ("r-downloader" ,r-downloader) | |
3962 | ("r-edger" ,r-edger) | |
3963 | ("r-gplots" ,r-gplots) | |
3964 | ("r-limma" ,r-limma) | |
3965 | ("r-matrixstats" ,r-matrixstats) | |
3966 | ("r-preprocesscore" ,r-preprocesscore) | |
3967 | ("r-quantro" ,r-quantro) | |
3968 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3969 | ("r-readr" ,r-readr))) | |
3970 | (home-page "https://bioconductor.org/packages/yarn/") | |
3971 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") | |
3972 | (description | |
3973 | "Expedite large RNA-Seq analyses using a combination of previously | |
3974 | developed tools. YARN is meant to make it easier for the user in performing | |
3975 | basic mis-annotation quality control, filtering, and condition-aware | |
3976 | normalization. YARN leverages many Bioconductor tools and statistical | |
3977 | techniques to account for the large heterogeneity and sparsity found in very | |
3978 | large RNA-seq experiments.") | |
3979 | (license license:artistic2.0))) | |
a6e1eb1a RW |
3980 | |
3981 | (define-public r-roar | |
3982 | (package | |
3983 | (name "r-roar") | |
3984 | (version "1.18.0") | |
3985 | (source | |
3986 | (origin | |
3987 | (method url-fetch) | |
3988 | (uri (bioconductor-uri "roar" version)) | |
3989 | (sha256 | |
3990 | (base32 | |
3991 | "15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw")))) | |
3992 | (build-system r-build-system) | |
3993 | (propagated-inputs | |
3994 | `(("r-biocgenerics" ,r-biocgenerics) | |
3995 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3996 | ("r-genomicalignments" ,r-genomicalignments) | |
3997 | ("r-genomicranges" ,r-genomicranges) | |
3998 | ("r-iranges" ,r-iranges) | |
3999 | ("r-rtracklayer" ,r-rtracklayer) | |
4000 | ("r-s4vectors" ,r-s4vectors) | |
4001 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4002 | (home-page "https://github.com/vodkatad/roar/") | |
4003 | (synopsis "Identify differential APA usage from RNA-seq alignments") | |
4004 | (description | |
4005 | "This package provides tools for identifying preferential usage of APA | |
4006 | sites, comparing two biological conditions, starting from known alternative | |
4007 | sites and alignments obtained from standard RNA-seq experiments.") | |
4008 | (license license:gpl3))) | |
50d91770 RW |
4009 | |
4010 | (define-public r-xbseq | |
4011 | (package | |
4012 | (name "r-xbseq") | |
4013 | (version "1.14.1") | |
4014 | (source | |
4015 | (origin | |
4016 | (method url-fetch) | |
4017 | (uri (bioconductor-uri "XBSeq" version)) | |
4018 | (sha256 | |
4019 | (base32 | |
4020 | "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph")))) | |
4021 | (properties `((upstream-name . "XBSeq"))) | |
4022 | (build-system r-build-system) | |
4023 | (propagated-inputs | |
4024 | `(("r-biobase" ,r-biobase) | |
4025 | ("r-deseq2" ,r-deseq2) | |
4026 | ("r-dplyr" ,r-dplyr) | |
4027 | ("r-ggplot2" ,r-ggplot2) | |
4028 | ("r-locfit" ,r-locfit) | |
4029 | ("r-magrittr" ,r-magrittr) | |
4030 | ("r-matrixstats" ,r-matrixstats) | |
4031 | ("r-pracma" ,r-pracma) | |
4032 | ("r-roar" ,r-roar))) | |
4033 | (home-page "https://github.com/Liuy12/XBSeq") | |
4034 | (synopsis "Test for differential expression for RNA-seq data") | |
4035 | (description | |
4036 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential | |
4037 | expression} (DE), where a statistical model was established based on the | |
4038 | assumption that observed signals are the convolution of true expression | |
4039 | signals and sequencing noises. The mapped reads in non-exonic regions are | |
4040 | considered as sequencing noises, which follows a Poisson distribution. Given | |
4041 | measurable observed signal and background noise from RNA-seq data, true | |
4042 | expression signals, assuming governed by the negative binomial distribution, | |
4043 | can be delineated and thus the accurate detection of differential expressed | |
4044 | genes.") | |
4045 | (license license:gpl3+))) | |
c8310056 RW |
4046 | |
4047 | (define-public r-massspecwavelet | |
4048 | (package | |
4049 | (name "r-massspecwavelet") | |
4050 | (version "1.48.1") | |
4051 | (source | |
4052 | (origin | |
4053 | (method url-fetch) | |
4054 | (uri (bioconductor-uri "MassSpecWavelet" version)) | |
4055 | (sha256 | |
4056 | (base32 | |
4057 | "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz")))) | |
4058 | (properties | |
4059 | `((upstream-name . "MassSpecWavelet"))) | |
4060 | (build-system r-build-system) | |
4061 | (propagated-inputs | |
4062 | `(("r-waveslim" ,r-waveslim))) | |
4063 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") | |
4064 | (synopsis "Mass spectrum processing by wavelet-based algorithms") | |
4065 | (description | |
4066 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) | |
4067 | data mainly through the use of wavelet transforms. It supports peak detection | |
4068 | based on @dfn{Continuous Wavelet Transform} (CWT).") | |
4069 | (license license:lgpl2.0+))) | |
ec12e537 RW |
4070 | |
4071 | (define-public r-xcms | |
4072 | (package | |
4073 | (name "r-xcms") | |
4074 | (version "3.4.4") | |
4075 | (source | |
4076 | (origin | |
4077 | (method url-fetch) | |
4078 | (uri (bioconductor-uri "xcms" version)) | |
4079 | (sha256 | |
4080 | (base32 | |
4081 | "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww")))) | |
4082 | (build-system r-build-system) | |
4083 | (propagated-inputs | |
4084 | `(("r-biobase" ,r-biobase) | |
4085 | ("r-biocgenerics" ,r-biocgenerics) | |
4086 | ("r-biocparallel" ,r-biocparallel) | |
4087 | ("r-lattice" ,r-lattice) | |
4088 | ("r-massspecwavelet" ,r-massspecwavelet) | |
4089 | ("r-msnbase" ,r-msnbase) | |
4090 | ("r-multtest" ,r-multtest) | |
4091 | ("r-mzr" ,r-mzr) | |
4092 | ("r-plyr" ,r-plyr) | |
4093 | ("r-protgenerics" ,r-protgenerics) | |
4094 | ("r-rann" ,r-rann) | |
4095 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4096 | ("r-robustbase" ,r-robustbase) | |
4097 | ("r-s4vectors" ,r-s4vectors))) | |
4098 | (home-page "https://bioconductor.org/packages/xcms/") | |
4099 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") | |
4100 | (description | |
4101 | "This package provides a framework for processing and visualization of | |
4102 | chromatographically separated and single-spectra mass spectral data. It | |
4103 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses | |
4104 | data for high-throughput, untargeted analyte profiling.") | |
4105 | (license license:gpl2+))) | |
8830664d RW |
4106 | |
4107 | (define-public r-wrench | |
4108 | (package | |
4109 | (name "r-wrench") | |
4110 | (version "1.0.0") | |
4111 | (source | |
4112 | (origin | |
4113 | (method url-fetch) | |
4114 | (uri (bioconductor-uri "Wrench" version)) | |
4115 | (sha256 | |
4116 | (base32 | |
4117 | "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg")))) | |
4118 | (properties `((upstream-name . "Wrench"))) | |
4119 | (build-system r-build-system) | |
4120 | (propagated-inputs | |
4121 | `(("r-limma" ,r-limma) | |
4122 | ("r-locfit" ,r-locfit) | |
4123 | ("r-matrixstats" ,r-matrixstats))) | |
4124 | (home-page "https://github.com/HCBravoLab/Wrench") | |
4125 | (synopsis "Wrench normalization for sparse count data") | |
4126 | (description | |
4127 | "Wrench is a package for normalization sparse genomic count data, like | |
4128 | that arising from 16s metagenomic surveys.") | |
4129 | (license license:artistic2.0))) | |
b9b8b447 RW |
4130 | |
4131 | (define-public r-wiggleplotr | |
4132 | (package | |
4133 | (name "r-wiggleplotr") | |
4134 | (version "1.6.1") | |
4135 | (source | |
4136 | (origin | |
4137 | (method url-fetch) | |
4138 | (uri (bioconductor-uri "wiggleplotr" version)) | |
4139 | (sha256 | |
4140 | (base32 | |
4141 | "12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3")))) | |
4142 | (build-system r-build-system) | |
4143 | (propagated-inputs | |
4144 | `(("r-assertthat" ,r-assertthat) | |
4145 | ("r-cowplot" ,r-cowplot) | |
4146 | ("r-dplyr" ,r-dplyr) | |
4147 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4148 | ("r-genomicranges" ,r-genomicranges) | |
4149 | ("r-ggplot2" ,r-ggplot2) | |
4150 | ("r-iranges" ,r-iranges) | |
4151 | ("r-purrr" ,r-purrr) | |
4152 | ("r-rtracklayer" ,r-rtracklayer) | |
4153 | ("r-s4vectors" ,r-s4vectors))) | |
4154 | (home-page "https://bioconductor.org/packages/wiggleplotr/") | |
4155 | (synopsis "Make read coverage plots from BigWig files") | |
4156 | (description | |
4157 | "This package provides tools to visualize read coverage from sequencing | |
4158 | experiments together with genomic annotations (genes, transcripts, peaks). | |
4159 | Introns of long transcripts can be rescaled to a fixed length for better | |
4160 | visualization of exonic read coverage.") | |
4161 | (license license:asl2.0))) | |
7b5101c5 RW |
4162 | |
4163 | (define-public r-widgettools | |
4164 | (package | |
4165 | (name "r-widgettools") | |
4166 | (version "1.60.0") | |
4167 | (source | |
4168 | (origin | |
4169 | (method url-fetch) | |
4170 | (uri (bioconductor-uri "widgetTools" version)) | |
4171 | (sha256 | |
4172 | (base32 | |
4173 | "0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf")))) | |
4174 | (properties `((upstream-name . "widgetTools"))) | |
4175 | (build-system r-build-system) | |
4176 | (home-page "https://bioconductor.org/packages/widgetTools/") | |
4177 | (synopsis "Tools for creating interactive tcltk widgets") | |
4178 | (description | |
4179 | "This packages contains tools to support the construction of tcltk | |
4180 | widgets in R.") | |
4181 | ;; Any version of the LGPL. | |
4182 | (license license:lgpl3+))) | |
6b12f213 RW |
4183 | |
4184 | (define-public r-webbioc | |
4185 | (package | |
4186 | (name "r-webbioc") | |
4187 | (version "1.54.0") | |
4188 | (source | |
4189 | (origin | |
4190 | (method url-fetch) | |
4191 | (uri (bioconductor-uri "webbioc" version)) | |
4192 | (sha256 | |
4193 | (base32 | |
4194 | "16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi")))) | |
4195 | (build-system r-build-system) | |
4196 | (inputs | |
4197 | `(("netpbm" ,netpbm) | |
4198 | ("perl" ,perl))) | |
4199 | (propagated-inputs | |
4200 | `(("r-affy" ,r-affy) | |
4201 | ("r-annaffy" ,r-annaffy) | |
4202 | ("r-biobase" ,r-biobase) | |
4203 | ("r-biocmanager" ,r-biocmanager) | |
4204 | ("r-gcrma" ,r-gcrma) | |
4205 | ("r-multtest" ,r-multtest) | |
4206 | ("r-qvalue" ,r-qvalue) | |
4207 | ("r-vsn" ,r-vsn))) | |
4208 | (home-page "https://www.bioconductor.org/") | |
4209 | (synopsis "Bioconductor web interface") | |
4210 | (description | |
4211 | "This package provides an integrated web interface for doing microarray | |
4212 | analysis using several of the Bioconductor packages. It is intended to be | |
4213 | deployed as a centralized bioinformatics resource for use by many users. | |
4214 | Currently only Affymetrix oligonucleotide analysis is supported.") | |
4215 | (license license:gpl2+))) | |
9800d859 RW |
4216 | |
4217 | (define-public r-zfpkm | |
4218 | (package | |
4219 | (name "r-zfpkm") | |
4220 | (version "1.4.1") | |
4221 | (source | |
4222 | (origin | |
4223 | (method url-fetch) | |
4224 | (uri (bioconductor-uri "zFPKM" version)) | |
4225 | (sha256 | |
4226 | (base32 | |
4227 | "0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5")))) | |
4228 | (properties `((upstream-name . "zFPKM"))) | |
4229 | (build-system r-build-system) | |
4230 | (propagated-inputs | |
4231 | `(("r-checkmate" ,r-checkmate) | |
4232 | ("r-dplyr" ,r-dplyr) | |
4233 | ("r-ggplot2" ,r-ggplot2) | |
4234 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
4235 | ("r-tidyr" ,r-tidyr))) | |
4236 | (home-page "https://github.com/ronammar/zFPKM/") | |
4237 | (synopsis "Functions to facilitate zFPKM transformations") | |
4238 | (description | |
4239 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. | |
4240 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID | |
4241 | 24215113).") | |
4242 | (license license:gpl3))) | |
2bdc88fc RW |
4243 | |
4244 | (define-public r-rbowtie2 | |
4245 | (package | |
4246 | (name "r-rbowtie2") | |
4247 | (version "1.4.0") | |
4248 | (source | |
4249 | (origin | |
4250 | (method url-fetch) | |
4251 | (uri (bioconductor-uri "Rbowtie2" version)) | |
4252 | (sha256 | |
4253 | (base32 | |
4254 | "045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr")))) | |
4255 | (properties `((upstream-name . "Rbowtie2"))) | |
4256 | (build-system r-build-system) | |
4257 | (inputs | |
4258 | `(("zlib" ,zlib))) | |
4259 | (home-page "https://bioconductor.org/packages/Rbowtie2/") | |
4260 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") | |
4261 | (description | |
4262 | "This package provides an R wrapper of the popular @code{bowtie2} | |
4263 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for | |
4264 | rapid adapter trimming, identification, and read merging.") | |
4265 | (license license:gpl3+))) | |
5622628f RW |
4266 | |
4267 | (define-public r-progeny | |
4268 | (package | |
4269 | (name "r-progeny") | |
4270 | (version "1.4.1") | |
4271 | (source | |
4272 | (origin | |
4273 | (method url-fetch) | |
4274 | (uri (bioconductor-uri "progeny" version)) | |
4275 | (sha256 | |
4276 | (base32 | |
4277 | "02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7")))) | |
4278 | (build-system r-build-system) | |
4279 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4280 | (home-page "https://github.com/saezlab/progeny") | |
4281 | (synopsis "Pathway responsive gene activity inference") | |
4282 | (description | |
4283 | "This package provides a function to infer pathway activity from gene | |
4284 | expression. It contains the linear model inferred in the publication | |
4285 | \"Perturbation-response genes reveal signaling footprints in cancer gene | |
4286 | expression\".") | |
4287 | (license license:asl2.0))) | |
307586c1 RW |
4288 | |
4289 | (define-public r-arrmnormalization | |
4290 | (package | |
4291 | (name "r-arrmnormalization") | |
4292 | (version "1.22.0") | |
4293 | (source | |
4294 | (origin | |
4295 | (method url-fetch) | |
4296 | (uri (bioconductor-uri "ARRmNormalization" version)) | |
4297 | (sha256 | |
4298 | (base32 | |
4299 | "09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd")))) | |
4300 | (properties | |
4301 | `((upstream-name . "ARRmNormalization"))) | |
4302 | (build-system r-build-system) | |
4303 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) | |
4304 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") | |
4305 | (synopsis "Adaptive robust regression normalization for methylation data") | |
4306 | (description | |
4307 | "This is a package to perform the @dfn{Adaptive Robust Regression | |
4308 | method} (ARRm) for the normalization of methylation data from the Illumina | |
4309 | Infinium HumanMethylation 450k assay.") | |
4310 | (license license:artistic2.0))) | |
fbf34949 RW |
4311 | |
4312 | (define-public r-biocfilecache | |
4313 | (package | |
4314 | (name "r-biocfilecache") | |
4315 | (version "1.8.0") | |
4316 | (source | |
4317 | (origin | |
4318 | (method url-fetch) | |
4319 | (uri (bioconductor-uri "BiocFileCache" version)) | |
4320 | (sha256 | |
4321 | (base32 | |
4322 | "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb")))) | |
4323 | (properties `((upstream-name . "BiocFileCache"))) | |
4324 | (build-system r-build-system) | |
4325 | (propagated-inputs | |
4326 | `(("r-curl" ,r-curl) | |
4327 | ("r-dbi" ,r-dbi) | |
4328 | ("r-dbplyr" ,r-dbplyr) | |
4329 | ("r-dplyr" ,r-dplyr) | |
4330 | ("r-httr" ,r-httr) | |
4331 | ("r-rappdirs" ,r-rappdirs) | |
4332 | ("r-rsqlite" ,r-rsqlite))) | |
4333 | (home-page "https://bioconductor.org/packages/BiocFileCache/") | |
4334 | (synopsis "Manage files across sessions") | |
4335 | (description | |
4336 | "This package creates a persistent on-disk cache of files that the user | |
4337 | can add, update, and retrieve. It is useful for managing resources (such as | |
4338 | custom Txdb objects) that are costly or difficult to create, web resources, | |
4339 | and data files used across sessions.") | |
4340 | (license license:artistic2.0))) |