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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> | |
61242625 | 4 | ;;; Copyright © 2017, 2018, 2019 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) |
58656064 | 27 | #:use-module (gnu packages base) |
cf9a29b2 | 28 | #:use-module (gnu packages bioinformatics) |
a5b56a53 RJ |
29 | #:use-module (gnu packages cran) |
30 | #:use-module (gnu packages compression) | |
c18dccff | 31 | #:use-module (gnu packages gcc) |
cf9a29b2 | 32 | #:use-module (gnu packages graph) |
59d331f1 | 33 | #:use-module (gnu packages haskell) |
5cfa4bff | 34 | #:use-module (gnu packages image) |
b64ce4b7 | 35 | #:use-module (gnu packages maths) |
6b12f213 RW |
36 | #:use-module (gnu packages netpbm) |
37 | #:use-module (gnu packages perl) | |
2cb71d81 | 38 | #:use-module (gnu packages pkg-config) |
f4235c0e RW |
39 | #:use-module (gnu packages statistics) |
40 | #:use-module (gnu packages web)) | |
fa596599 | 41 | |
557a1089 RW |
42 | \f |
43 | ;;; Annotations | |
44 | ||
b7d93cf5 RW |
45 | (define-public r-bsgenome-celegans-ucsc-ce6 |
46 | (package | |
47 | (name "r-bsgenome-celegans-ucsc-ce6") | |
48 | (version "1.4.0") | |
49 | (source (origin | |
50 | (method url-fetch) | |
51 | ;; We cannot use bioconductor-uri here because this tarball is | |
52 | ;; located under "data/annotation/" instead of "bioc/". | |
53 | (uri (string-append "https://www.bioconductor.org/packages/" | |
54 | "release/data/annotation/src/contrib/" | |
55 | "BSgenome.Celegans.UCSC.ce6_" | |
56 | version ".tar.gz")) | |
57 | (sha256 | |
58 | (base32 | |
59 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
60 | (properties | |
61 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
62 | (build-system r-build-system) | |
63 | ;; As this package provides little more than a very large data file it | |
64 | ;; doesn't make sense to build substitutes. | |
65 | (arguments `(#:substitutable? #f)) | |
66 | (propagated-inputs | |
67 | `(("r-bsgenome" ,r-bsgenome))) | |
68 | (home-page | |
69 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
70 | (synopsis "Full genome sequences for Worm") | |
71 | (description | |
72 | "This package provides full genome sequences for Caenorhabditis | |
73 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
0c792ffb RW |
74 | objects.") |
75 | (license license:artistic2.0))) | |
76 | ||
77 | (define-public r-bsgenome-celegans-ucsc-ce10 | |
78 | (package | |
79 | (name "r-bsgenome-celegans-ucsc-ce10") | |
80 | (version "1.4.0") | |
81 | (source (origin | |
82 | (method url-fetch) | |
83 | ;; We cannot use bioconductor-uri here because this tarball is | |
84 | ;; located under "data/annotation/" instead of "bioc/". | |
85 | (uri (string-append "https://www.bioconductor.org/packages/" | |
86 | "release/data/annotation/src/contrib/" | |
87 | "BSgenome.Celegans.UCSC.ce10_" | |
88 | version ".tar.gz")) | |
89 | (sha256 | |
90 | (base32 | |
91 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
92 | (properties | |
93 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
94 | (build-system r-build-system) | |
95 | ;; As this package provides little more than a very large data file it | |
96 | ;; doesn't make sense to build substitutes. | |
97 | (arguments `(#:substitutable? #f)) | |
98 | (propagated-inputs | |
99 | `(("r-bsgenome" ,r-bsgenome))) | |
100 | (home-page | |
101 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
102 | (synopsis "Full genome sequences for Worm") | |
103 | (description | |
104 | "This package provides full genome sequences for Caenorhabditis | |
105 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
b7d93cf5 RW |
106 | objects.") |
107 | (license license:artistic2.0))) | |
108 | ||
183db725 RW |
109 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
110 | (package | |
111 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
112 | (version "1.4.1") | |
113 | (source (origin | |
114 | (method url-fetch) | |
115 | ;; We cannot use bioconductor-uri here because this tarball is | |
116 | ;; located under "data/annotation/" instead of "bioc/". | |
117 | (uri (string-append "https://www.bioconductor.org/packages/" | |
118 | "release/data/annotation/src/contrib/" | |
119 | "BSgenome.Dmelanogaster.UCSC.dm6_" | |
120 | version ".tar.gz")) | |
121 | (sha256 | |
122 | (base32 | |
123 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
124 | (properties | |
125 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
126 | (build-system r-build-system) | |
127 | ;; As this package provides little more than a very large data file it | |
128 | ;; doesn't make sense to build substitutes. | |
129 | (arguments `(#:substitutable? #f)) | |
130 | (propagated-inputs | |
131 | `(("r-bsgenome" ,r-bsgenome))) | |
132 | (home-page | |
133 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
134 | (synopsis "Full genome sequences for Fly") | |
135 | (description | |
136 | "This package provides full genome sequences for Drosophila | |
137 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
138 | objects.") | |
139 | (license license:artistic2.0))) | |
140 | ||
13dabd69 RW |
141 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
142 | (package | |
143 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
144 | (version "1.4.0") | |
145 | (source (origin | |
146 | (method url-fetch) | |
147 | ;; We cannot use bioconductor-uri here because this tarball is | |
148 | ;; located under "data/annotation/" instead of "bioc/". | |
149 | (uri (string-append "https://www.bioconductor.org/packages/" | |
150 | "release/data/annotation/src/contrib/" | |
151 | "BSgenome.Dmelanogaster.UCSC.dm3_" | |
152 | version ".tar.gz")) | |
153 | (sha256 | |
154 | (base32 | |
155 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
156 | (properties | |
157 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
158 | (build-system r-build-system) | |
159 | ;; As this package provides little more than a very large data file it | |
160 | ;; doesn't make sense to build substitutes. | |
161 | (arguments `(#:substitutable? #f)) | |
162 | (propagated-inputs | |
163 | `(("r-bsgenome" ,r-bsgenome))) | |
164 | (home-page | |
165 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
166 | (synopsis "Full genome sequences for Fly") | |
167 | (description | |
168 | "This package provides full genome sequences for Drosophila | |
169 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
170 | Biostrings objects.") | |
171 | (license license:artistic2.0))) | |
172 | ||
dfac7eb9 RW |
173 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
174 | (package | |
175 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
176 | (version "1.3.99") | |
177 | (source (origin | |
178 | (method url-fetch) | |
179 | ;; We cannot use bioconductor-uri here because this tarball is | |
180 | ;; located under "data/annotation/" instead of "bioc/". | |
181 | (uri (string-append "http://www.bioconductor.org/packages/" | |
182 | "release/data/annotation/src/contrib/" | |
183 | "BSgenome.Dmelanogaster.UCSC.dm3.masked_" | |
184 | version ".tar.gz")) | |
185 | (sha256 | |
186 | (base32 | |
187 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
188 | (properties | |
189 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
190 | (build-system r-build-system) | |
191 | (propagated-inputs | |
192 | `(("r-bsgenome" ,r-bsgenome) | |
193 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
194 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
195 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
196 | (synopsis "Full masked genome sequences for Fly") | |
197 | (description | |
198 | "This package provides full masked genome sequences for Drosophila | |
199 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
200 | Biostrings objects. The sequences are the same as in | |
201 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
202 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
203 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
204 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
205 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
206 | (license license:artistic2.0))) | |
207 | ||
40a65057 RW |
208 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
209 | (package | |
210 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
211 | (version "0.99.1") | |
212 | (source (origin | |
213 | (method url-fetch) | |
214 | ;; We cannot use bioconductor-uri here because this tarball is | |
215 | ;; located under "data/annotation/" instead of "bioc/". | |
216 | (uri (string-append "https://www.bioconductor.org/packages/" | |
217 | "release/data/annotation/src/contrib/" | |
218 | "BSgenome.Hsapiens.1000genomes.hs37d5_" | |
219 | version ".tar.gz")) | |
220 | (sha256 | |
221 | (base32 | |
222 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
223 | (properties | |
224 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
225 | (build-system r-build-system) | |
226 | ;; As this package provides little more than a very large data file it | |
227 | ;; doesn't make sense to build substitutes. | |
228 | (arguments `(#:substitutable? #f)) | |
229 | (propagated-inputs | |
230 | `(("r-bsgenome" ,r-bsgenome))) | |
231 | (home-page | |
232 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
233 | (synopsis "Full genome sequences for Homo sapiens") | |
234 | (description | |
235 | "This package provides full genome sequences for Homo sapiens from | |
236 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
237 | (license license:artistic2.0))) | |
238 | ||
6fbd759b RW |
239 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
240 | (package | |
241 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
242 | (version "1.3.99") | |
243 | (source (origin | |
244 | (method url-fetch) | |
245 | ;; We cannot use bioconductor-uri here because this tarball is | |
246 | ;; located under "data/annotation/" instead of "bioc/". | |
247 | (uri (string-append "http://www.bioconductor.org/packages/" | |
248 | "release/data/annotation/src/contrib/" | |
249 | "BSgenome.Hsapiens.UCSC.hg19.masked_" | |
250 | version ".tar.gz")) | |
251 | (sha256 | |
252 | (base32 | |
253 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
254 | (properties | |
255 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
256 | (build-system r-build-system) | |
257 | (propagated-inputs | |
258 | `(("r-bsgenome" ,r-bsgenome) | |
259 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
260 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
261 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
262 | (synopsis "Full masked genome sequences for Homo sapiens") | |
263 | (description | |
264 | "This package provides full genome sequences for Homo sapiens (Human) as | |
265 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
266 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
267 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
268 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
269 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
270 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
271 | default.") | |
272 | (license license:artistic2.0))) | |
273 | ||
5acb9052 RW |
274 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
275 | (package | |
276 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
277 | (version "1.4.0") | |
278 | (source (origin | |
279 | (method url-fetch) | |
280 | ;; We cannot use bioconductor-uri here because this tarball is | |
281 | ;; located under "data/annotation/" instead of "bioc/". | |
282 | (uri (string-append "https://www.bioconductor.org/packages/" | |
283 | "release/data/annotation/src/contrib/" | |
284 | "BSgenome.Mmusculus.UCSC.mm9_" | |
285 | version ".tar.gz")) | |
286 | (sha256 | |
287 | (base32 | |
288 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
289 | (properties | |
290 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
291 | (build-system r-build-system) | |
292 | ;; As this package provides little more than a very large data file it | |
293 | ;; doesn't make sense to build substitutes. | |
294 | (arguments `(#:substitutable? #f)) | |
295 | (propagated-inputs | |
296 | `(("r-bsgenome" ,r-bsgenome))) | |
297 | (home-page | |
298 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
299 | (synopsis "Full genome sequences for Mouse") | |
300 | (description | |
301 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
302 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
303 | (license license:artistic2.0))) | |
304 | ||
2bece692 RW |
305 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
306 | (package | |
307 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
308 | (version "1.3.99") | |
309 | (source (origin | |
310 | (method url-fetch) | |
311 | ;; We cannot use bioconductor-uri here because this tarball is | |
312 | ;; located under "data/annotation/" instead of "bioc/". | |
313 | (uri (string-append "http://www.bioconductor.org/packages/" | |
314 | "release/data/annotation/src/contrib/" | |
315 | "BSgenome.Mmusculus.UCSC.mm9.masked_" | |
316 | version ".tar.gz")) | |
317 | (sha256 | |
318 | (base32 | |
319 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
320 | (properties | |
321 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
322 | (build-system r-build-system) | |
323 | (propagated-inputs | |
324 | `(("r-bsgenome" ,r-bsgenome) | |
325 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
326 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
327 | (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") | |
328 | (synopsis "Full masked genome sequences for Mouse") | |
329 | (description | |
330 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
331 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
332 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
333 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
334 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
335 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
336 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
337 | default." ) | |
338 | (license license:artistic2.0))) | |
339 | ||
c3adc830 RW |
340 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
341 | (package | |
342 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
343 | (version "1.4.0") | |
344 | (source (origin | |
345 | (method url-fetch) | |
346 | ;; We cannot use bioconductor-uri here because this tarball is | |
347 | ;; located under "data/annotation/" instead of "bioc/". | |
348 | (uri (string-append "https://www.bioconductor.org/packages/" | |
349 | "release/data/annotation/src/contrib/" | |
350 | "BSgenome.Mmusculus.UCSC.mm10_" | |
351 | version ".tar.gz")) | |
352 | (sha256 | |
353 | (base32 | |
354 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
355 | (properties | |
356 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
357 | (build-system r-build-system) | |
358 | ;; As this package provides little more than a very large data file it | |
359 | ;; doesn't make sense to build substitutes. | |
360 | (arguments `(#:substitutable? #f)) | |
361 | (propagated-inputs | |
362 | `(("r-bsgenome" ,r-bsgenome))) | |
363 | (home-page | |
364 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
365 | (synopsis "Full genome sequences for Mouse") | |
366 | (description | |
367 | "This package provides full genome sequences for Mus | |
368 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
369 | in Biostrings objects.") | |
370 | (license license:artistic2.0))) | |
371 | ||
3a08940e RW |
372 | (define-public r-org-ce-eg-db |
373 | (package | |
374 | (name "r-org-ce-eg-db") | |
375 | (version "3.7.0") | |
376 | (source (origin | |
377 | (method url-fetch) | |
378 | ;; We cannot use bioconductor-uri here because this tarball is | |
379 | ;; located under "data/annotation/" instead of "bioc/". | |
380 | (uri (string-append "https://www.bioconductor.org/packages/" | |
381 | "release/data/annotation/src/contrib/" | |
382 | "org.Ce.eg.db_" version ".tar.gz")) | |
383 | (sha256 | |
384 | (base32 | |
385 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) | |
386 | (properties | |
387 | `((upstream-name . "org.Ce.eg.db"))) | |
388 | (build-system r-build-system) | |
389 | (propagated-inputs | |
390 | `(("r-annotationdbi" ,r-annotationdbi))) | |
391 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") | |
392 | (synopsis "Genome wide annotation for Worm") | |
393 | (description | |
394 | "This package provides mappings from Entrez gene identifiers to various | |
395 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
396 | (license license:artistic2.0))) | |
397 | ||
f8780e96 RW |
398 | (define-public r-org-dm-eg-db |
399 | (package | |
400 | (name "r-org-dm-eg-db") | |
401 | (version "3.7.0") | |
402 | (source (origin | |
403 | (method url-fetch) | |
404 | ;; We cannot use bioconductor-uri here because this tarball is | |
405 | ;; located under "data/annotation/" instead of "bioc/". | |
406 | (uri (string-append "https://www.bioconductor.org/packages/" | |
407 | "release/data/annotation/src/contrib/" | |
408 | "org.Dm.eg.db_" version ".tar.gz")) | |
409 | (sha256 | |
410 | (base32 | |
411 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) | |
412 | (properties | |
413 | `((upstream-name . "org.Dm.eg.db"))) | |
414 | (build-system r-build-system) | |
415 | (propagated-inputs | |
416 | `(("r-annotationdbi" ,r-annotationdbi))) | |
417 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") | |
418 | (synopsis "Genome wide annotation for Fly") | |
419 | (description | |
420 | "This package provides mappings from Entrez gene identifiers to various | |
421 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
422 | (license license:artistic2.0))) | |
423 | ||
3dad6087 RW |
424 | (define-public r-org-dr-eg-db |
425 | (package | |
426 | (name "r-org-dr-eg-db") | |
427 | (version "3.7.0") | |
428 | (source (origin | |
429 | (method url-fetch) | |
430 | ;; We cannot use bioconductor-uri here because this tarball is | |
431 | ;; located under "data/annotation/" instead of "bioc/". | |
432 | (uri (string-append "https://www.bioconductor.org/packages/" | |
433 | "release/data/annotation/src/contrib/" | |
434 | "org.Dr.eg.db_" version ".tar.gz")) | |
435 | (sha256 | |
436 | (base32 | |
437 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) | |
438 | (properties | |
439 | `((upstream-name . "org.Dr.eg.db"))) | |
440 | (build-system r-build-system) | |
441 | (propagated-inputs | |
442 | `(("r-annotationdbi" ,r-annotationdbi))) | |
443 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") | |
444 | (synopsis "Annotation for Zebrafish") | |
445 | (description | |
446 | "This package provides genome wide annotations for Zebrafish, primarily | |
447 | based on mapping using Entrez Gene identifiers.") | |
448 | (license license:artistic2.0))) | |
449 | ||
d56df35a RW |
450 | (define-public r-org-hs-eg-db |
451 | (package | |
452 | (name "r-org-hs-eg-db") | |
453 | (version "3.7.0") | |
454 | (source (origin | |
455 | (method url-fetch) | |
456 | ;; We cannot use bioconductor-uri here because this tarball is | |
457 | ;; located under "data/annotation/" instead of "bioc/". | |
458 | (uri (string-append "https://www.bioconductor.org/packages/" | |
459 | "release/data/annotation/src/contrib/" | |
460 | "org.Hs.eg.db_" version ".tar.gz")) | |
461 | (sha256 | |
462 | (base32 | |
463 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) | |
464 | (properties | |
465 | `((upstream-name . "org.Hs.eg.db"))) | |
466 | (build-system r-build-system) | |
467 | (propagated-inputs | |
468 | `(("r-annotationdbi" ,r-annotationdbi))) | |
469 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") | |
470 | (synopsis "Genome wide annotation for Human") | |
471 | (description | |
472 | "This package contains genome-wide annotations for Human, primarily based | |
473 | on mapping using Entrez Gene identifiers.") | |
474 | (license license:artistic2.0))) | |
475 | ||
8035819f RW |
476 | (define-public r-org-mm-eg-db |
477 | (package | |
478 | (name "r-org-mm-eg-db") | |
479 | (version "3.7.0") | |
480 | (source (origin | |
481 | (method url-fetch) | |
482 | ;; We cannot use bioconductor-uri here because this tarball is | |
483 | ;; located under "data/annotation/" instead of "bioc/". | |
484 | (uri (string-append "https://www.bioconductor.org/packages/" | |
485 | "release/data/annotation/src/contrib/" | |
486 | "org.Mm.eg.db_" version ".tar.gz")) | |
487 | (sha256 | |
488 | (base32 | |
489 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) | |
490 | (properties | |
491 | `((upstream-name . "org.Mm.eg.db"))) | |
492 | (build-system r-build-system) | |
493 | (propagated-inputs | |
494 | `(("r-annotationdbi" ,r-annotationdbi))) | |
495 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") | |
496 | (synopsis "Genome wide annotation for Mouse") | |
497 | (description | |
498 | "This package provides mappings from Entrez gene identifiers to various | |
499 | annotations for the genome of the model mouse Mus musculus.") | |
500 | (license license:artistic2.0))) | |
501 | ||
fe0b76e2 RW |
502 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
503 | (package | |
504 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
505 | (version "1.4.0") | |
506 | (source (origin | |
507 | (method url-fetch) | |
508 | ;; We cannot use bioconductor-uri here because this tarball is | |
509 | ;; located under "data/annotation/" instead of "bioc/". | |
510 | (uri (string-append "https://www.bioconductor.org/packages/" | |
511 | "release/data/annotation/src/contrib/" | |
512 | "BSgenome.Hsapiens.UCSC.hg19_" | |
513 | version ".tar.gz")) | |
514 | (sha256 | |
515 | (base32 | |
516 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) | |
517 | (properties | |
518 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
519 | (build-system r-build-system) | |
520 | ;; As this package provides little more than a very large data file it | |
521 | ;; doesn't make sense to build substitutes. | |
522 | (arguments `(#:substitutable? #f)) | |
523 | (propagated-inputs | |
524 | `(("r-bsgenome" ,r-bsgenome))) | |
525 | (home-page | |
526 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
527 | (synopsis "Full genome sequences for Homo sapiens") | |
528 | (description | |
529 | "This package provides full genome sequences for Homo sapiens as provided | |
530 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
531 | (license license:artistic2.0))) | |
532 | ||
2cc51108 RW |
533 | (define-public r-genelendatabase |
534 | (package | |
535 | (name "r-genelendatabase") | |
daeb3cd9 | 536 | (version "1.18.0") |
2cc51108 RW |
537 | (source |
538 | (origin | |
539 | (method url-fetch) | |
540 | ;; We cannot use bioconductor-uri here because this tarball is | |
541 | ;; located under "data/experiment/" instead of "bioc/". | |
542 | (uri (string-append "https://bioconductor.org/packages/" | |
543 | "release/data/experiment/src/contrib" | |
544 | "/geneLenDataBase_" version ".tar.gz")) | |
545 | (sha256 | |
546 | (base32 | |
daeb3cd9 | 547 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
2cc51108 RW |
548 | (properties |
549 | `((upstream-name . "geneLenDataBase"))) | |
550 | (build-system r-build-system) | |
551 | (propagated-inputs | |
552 | `(("r-rtracklayer" ,r-rtracklayer) | |
553 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
554 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
555 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
556 | (description | |
557 | "This package provides the lengths of mRNA transcripts for a number of | |
558 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
559 | (license license:lgpl2.0+))) | |
560 | ||
66e35ce6 RW |
561 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
562 | (package | |
563 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
564 | (version "3.2.2") | |
565 | (source (origin | |
566 | (method url-fetch) | |
567 | ;; We cannot use bioconductor-uri here because this tarball is | |
568 | ;; located under "data/annotation/" instead of "bioc/". | |
569 | (uri (string-append "https://bioconductor.org/packages/" | |
570 | "release/data/annotation/src/contrib" | |
571 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" | |
572 | version ".tar.gz")) | |
573 | (sha256 | |
574 | (base32 | |
575 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
576 | (properties | |
577 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
578 | (build-system r-build-system) | |
579 | ;; As this package provides little more than a very large data file it | |
580 | ;; doesn't make sense to build substitutes. | |
581 | (arguments `(#:substitutable? #f)) | |
582 | (propagated-inputs | |
583 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
584 | (home-page | |
585 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
586 | (synopsis "Annotation package for human genome in TxDb format") | |
587 | (description | |
588 | "This package provides an annotation database of Homo sapiens genome | |
589 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
798b80ce RW |
590 | track. The database is exposed as a @code{TxDb} object.") |
591 | (license license:artistic2.0))) | |
592 | ||
593 | (define-public r-txdb-hsapiens-ucsc-hg38-knowngene | |
594 | (package | |
595 | (name "r-txdb-hsapiens-ucsc-hg38-knowngene") | |
596 | (version "3.4.6") | |
597 | (source (origin | |
598 | (method url-fetch) | |
599 | ;; We cannot use bioconductor-uri here because this tarball is | |
600 | ;; located under "data/annotation/" instead of "bioc/". | |
601 | (uri (string-append "https://bioconductor.org/packages/" | |
602 | "release/data/annotation/src/contrib" | |
603 | "/TxDb.Hsapiens.UCSC.hg38.knownGene_" | |
604 | version ".tar.gz")) | |
605 | (sha256 | |
606 | (base32 | |
607 | "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) | |
608 | (properties | |
609 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) | |
610 | (build-system r-build-system) | |
611 | (propagated-inputs | |
612 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
613 | (home-page | |
614 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") | |
615 | (synopsis "Annotation package for human genome in TxDb format") | |
616 | (description | |
617 | "This package provides an annotation database of Homo sapiens genome | |
618 | data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" | |
66e35ce6 RW |
619 | track. The database is exposed as a @code{TxDb} object.") |
620 | (license license:artistic2.0))) | |
621 | ||
d220babf RW |
622 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
623 | (package | |
624 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
625 | (version "3.2.2") | |
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://bioconductor.org/packages/" | |
631 | "release/data/annotation/src/contrib" | |
632 | "/TxDb.Mmusculus.UCSC.mm9.knownGene_" | |
633 | version ".tar.gz")) | |
634 | (sha256 | |
635 | (base32 | |
636 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
637 | (properties | |
638 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
639 | (build-system r-build-system) | |
640 | (propagated-inputs | |
641 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
642 | ("r-annotationdbi" ,r-annotationdbi))) | |
643 | (home-page | |
644 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
645 | (synopsis "Annotation package for mouse genome in TxDb format") | |
646 | (description | |
647 | "This package provides an annotation database of Mouse genome data. It | |
648 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
649 | database is exposed as a @code{TxDb} object.") | |
650 | (license license:artistic2.0))) | |
651 | ||
7bc5d1b0 RW |
652 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
653 | (package | |
654 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
61242625 | 655 | (version "3.4.7") |
7bc5d1b0 RW |
656 | (source (origin |
657 | (method url-fetch) | |
658 | ;; We cannot use bioconductor-uri here because this tarball is | |
659 | ;; located under "data/annotation/" instead of "bioc/". | |
660 | (uri (string-append "https://www.bioconductor.org/packages/" | |
661 | "release/data/annotation/src/contrib/" | |
662 | "TxDb.Mmusculus.UCSC.mm10.knownGene_" | |
663 | version ".tar.gz")) | |
664 | (sha256 | |
665 | (base32 | |
61242625 | 666 | "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b")))) |
7bc5d1b0 RW |
667 | (properties |
668 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
669 | (build-system r-build-system) | |
670 | ;; As this package provides little more than a very large data file it | |
671 | ;; doesn't make sense to build substitutes. | |
672 | (arguments `(#:substitutable? #f)) | |
673 | (propagated-inputs | |
674 | `(("r-bsgenome" ,r-bsgenome) | |
675 | ("r-genomicfeatures" ,r-genomicfeatures) | |
676 | ("r-annotationdbi" ,r-annotationdbi))) | |
677 | (home-page | |
678 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
679 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
680 | (description | |
681 | "This package loads a TxDb object, which is an R interface to | |
682 | prefabricated databases contained in this package. This package provides | |
683 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
684 | based on the knownGene track.") | |
685 | (license license:artistic2.0))) | |
686 | ||
0f5c9cec RW |
687 | (define-public r-fdb-infiniummethylation-hg19 |
688 | (package | |
689 | (name "r-fdb-infiniummethylation-hg19") | |
690 | (version "2.2.0") | |
691 | (source (origin | |
692 | (method url-fetch) | |
693 | ;; We cannot use bioconductor-uri here because this tarball is | |
694 | ;; located under "data/annotation/" instead of "bioc/". | |
695 | (uri (string-append "https://www.bioconductor.org/packages/" | |
696 | "release/data/annotation/src/contrib/" | |
697 | "FDb.InfiniumMethylation.hg19_" | |
698 | version ".tar.gz")) | |
699 | (sha256 | |
700 | (base32 | |
701 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) | |
702 | (properties | |
703 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) | |
704 | (build-system r-build-system) | |
705 | (propagated-inputs | |
706 | `(("r-biostrings" ,r-biostrings) | |
707 | ("r-genomicfeatures" ,r-genomicfeatures) | |
708 | ("r-annotationdbi" ,r-annotationdbi) | |
709 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
710 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) | |
711 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") | |
712 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") | |
713 | (description | |
714 | "This is an annotation package for Illumina Infinium DNA methylation | |
715 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 | |
716 | annotations.") | |
717 | (license license:artistic2.0))) | |
718 | ||
9475a248 RW |
719 | (define-public r-illuminahumanmethylationepicmanifest |
720 | (package | |
721 | (name "r-illuminahumanmethylationepicmanifest") | |
722 | (version "0.3.0") | |
723 | (source (origin | |
724 | (method url-fetch) | |
725 | ;; We cannot use bioconductor-uri here because this tarball is | |
726 | ;; located under "data/annotation/" instead of "bioc/". | |
727 | (uri (string-append "https://www.bioconductor.org/packages/" | |
728 | "release/data/annotation/src/contrib/" | |
729 | "IlluminaHumanMethylationEPICmanifest_" | |
730 | version ".tar.gz")) | |
731 | (sha256 | |
732 | (base32 | |
733 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) | |
734 | (properties | |
735 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) | |
736 | (build-system r-build-system) | |
737 | (propagated-inputs | |
738 | `(("r-minfi" ,r-minfi))) | |
739 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") | |
740 | (synopsis "Manifest for Illumina's EPIC methylation arrays") | |
741 | (description | |
742 | "This is a manifest package for Illumina's EPIC methylation arrays.") | |
743 | (license license:artistic2.0))) | |
744 | ||
f8a5af46 RW |
745 | (define-public r-do-db |
746 | (package | |
747 | (name "r-do-db") | |
748 | (version "2.9") | |
749 | (source (origin | |
750 | (method url-fetch) | |
751 | ;; We cannot use bioconductor-uri here because this tarball is | |
752 | ;; located under "data/annotation/" instead of "bioc/". | |
753 | (uri (string-append "https://www.bioconductor.org/packages/" | |
754 | "release/data/annotation/src/contrib/" | |
755 | "DO.db_" version ".tar.gz")) | |
756 | (sha256 | |
757 | (base32 | |
758 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) | |
759 | (properties | |
760 | `((upstream-name . "DO.db"))) | |
761 | (build-system r-build-system) | |
762 | (propagated-inputs | |
763 | `(("r-annotationdbi" ,r-annotationdbi))) | |
764 | (home-page "https://www.bioconductor.org/packages/DO.db/") | |
765 | (synopsis "Annotation maps describing the entire Disease Ontology") | |
766 | (description | |
767 | "This package provides a set of annotation maps describing the entire | |
768 | Disease Ontology.") | |
769 | (license license:artistic2.0))) | |
770 | ||
2cc51108 | 771 | \f |
557a1089 RW |
772 | ;;; Experiment data |
773 | ||
692bce15 RW |
774 | (define-public r-abadata |
775 | (package | |
776 | (name "r-abadata") | |
777 | (version "1.12.0") | |
778 | (source (origin | |
779 | (method url-fetch) | |
780 | ;; We cannot use bioconductor-uri here because this tarball is | |
781 | ;; located under "data/experiment/" instead of "bioc/". | |
782 | (uri (string-append "https://www.bioconductor.org/packages/" | |
783 | "release/data/experiment/src/contrib/" | |
784 | "ABAData_" version ".tar.gz")) | |
785 | (sha256 | |
786 | (base32 | |
787 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) | |
788 | (properties | |
789 | `((upstream-name . "ABAData"))) | |
790 | (build-system r-build-system) | |
791 | (propagated-inputs | |
792 | `(("r-annotationdbi" ,r-annotationdbi))) | |
793 | (home-page "https://www.bioconductor.org/packages/ABAData/") | |
794 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") | |
795 | (description | |
796 | "This package provides the data for the gene expression enrichment | |
797 | analysis conducted in the package ABAEnrichment. The package includes three | |
798 | datasets which are derived from the Allen Brain Atlas: | |
799 | ||
800 | @enumerate | |
801 | @item Gene expression data from Human Brain (adults) averaged across donors, | |
802 | @item Gene expression data from the Developing Human Brain pooled into five | |
803 | age categories and averaged across donors, and | |
804 | @item a developmental effect score based on the Developing Human Brain | |
805 | expression data. | |
806 | @end enumerate | |
807 | ||
808 | All datasets are restricted to protein coding genes.") | |
809 | (license license:gpl2+))) | |
810 | ||
b50c9660 RW |
811 | (define-public r-arrmdata |
812 | (package | |
813 | (name "r-arrmdata") | |
814 | (version "1.18.0") | |
815 | (source (origin | |
816 | (method url-fetch) | |
817 | ;; We cannot use bioconductor-uri here because this tarball is | |
818 | ;; located under "data/experiment/" instead of "bioc/". | |
819 | (uri (string-append "https://www.bioconductor.org/packages/" | |
820 | "release/data/experiment/src/contrib/" | |
821 | "ARRmData_" version ".tar.gz")) | |
822 | (sha256 | |
823 | (base32 | |
824 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) | |
825 | (properties | |
826 | `((upstream-name . "ARRmData"))) | |
827 | (build-system r-build-system) | |
828 | (home-page "https://www.bioconductor.org/packages/ARRmData/") | |
829 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") | |
830 | (description | |
831 | "This package provides raw beta values from 36 samples across 3 groups | |
832 | from Illumina 450k methylation arrays.") | |
833 | (license license:artistic2.0))) | |
834 | ||
557a1089 RW |
835 | (define-public r-hsmmsinglecell |
836 | (package | |
837 | (name "r-hsmmsinglecell") | |
838 | (version "1.2.0") | |
839 | (source (origin | |
840 | (method url-fetch) | |
841 | ;; We cannot use bioconductor-uri here because this tarball is | |
842 | ;; located under "data/experiment/" instead of "bioc/". | |
843 | (uri (string-append "https://www.bioconductor.org/packages/" | |
844 | "release/data/experiment/src/contrib/" | |
845 | "HSMMSingleCell_" version ".tar.gz")) | |
846 | (sha256 | |
847 | (base32 | |
848 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) | |
849 | (properties | |
850 | `((upstream-name . "HSMMSingleCell"))) | |
851 | (build-system r-build-system) | |
852 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") | |
853 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") | |
854 | (description | |
855 | "Skeletal myoblasts undergo a well-characterized sequence of | |
856 | morphological and transcriptional changes during differentiation. In this | |
857 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded | |
858 | under high mitogen conditions (GM) and then differentiated by switching to | |
859 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several | |
860 | hundred cells taken over a time-course of serum-induced differentiation. | |
861 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, | |
862 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. | |
863 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, | |
864 | which were then sequenced to a depth of ~4 million reads per library, | |
865 | resulting in a complete gene expression profile for each cell.") | |
866 | (license license:artistic2.0))) | |
ad8f46c6 | 867 | |
868 | (define-public r-all | |
869 | (package | |
870 | (name "r-all") | |
871 | (version "1.26.0") | |
872 | (source (origin | |
873 | (method url-fetch) | |
874 | ;; We cannot use bioconductor-uri here because this tarball is | |
875 | ;; located under "data/experiment/" instead of "bioc/". | |
876 | (uri (string-append "https://www.bioconductor.org/packages/" | |
877 | "release/data/experiment/src/contrib/" | |
878 | "ALL_" version ".tar.gz")) | |
879 | (sha256 | |
880 | (base32 | |
881 | "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) | |
882 | (properties `((upstream-name . "ALL"))) | |
883 | (build-system r-build-system) | |
884 | (propagated-inputs | |
885 | `(("r-biobase" ,r-biobase))) | |
886 | (home-page "https://bioconductor.org/packages/ALL") | |
887 | (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") | |
888 | (description | |
889 | "The data consist of microarrays from 128 different individuals with | |
890 | @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates | |
891 | are available. The data have been normalized (using rma) and it is the | |
892 | jointly normalized data that are available here. The data are presented in | |
893 | the form of an @code{exprSet} object.") | |
894 | (license license:artistic2.0))) | |
557a1089 RW |
895 | |
896 | \f | |
897 | ;;; Packages | |
898 | ||
14bba460 RW |
899 | (define-public r-biocgenerics |
900 | (package | |
901 | (name "r-biocgenerics") | |
81a1c45d | 902 | (version "0.30.0") |
14bba460 RW |
903 | (source (origin |
904 | (method url-fetch) | |
905 | (uri (bioconductor-uri "BiocGenerics" version)) | |
906 | (sha256 | |
907 | (base32 | |
81a1c45d | 908 | "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f")))) |
14bba460 RW |
909 | (properties |
910 | `((upstream-name . "BiocGenerics"))) | |
911 | (build-system r-build-system) | |
912 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
913 | (synopsis "S4 generic functions for Bioconductor") | |
914 | (description | |
915 | "This package provides S4 generic functions needed by many Bioconductor | |
916 | packages.") | |
917 | (license license:artistic2.0))) | |
918 | ||
7097c700 RW |
919 | (define-public r-annotate |
920 | (package | |
921 | (name "r-annotate") | |
0c53332a | 922 | (version "1.62.0") |
7097c700 RW |
923 | (source |
924 | (origin | |
925 | (method url-fetch) | |
926 | (uri (bioconductor-uri "annotate" version)) | |
927 | (sha256 | |
928 | (base32 | |
0c53332a | 929 | "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs")))) |
7097c700 RW |
930 | (build-system r-build-system) |
931 | (propagated-inputs | |
932 | `(("r-annotationdbi" ,r-annotationdbi) | |
933 | ("r-biobase" ,r-biobase) | |
934 | ("r-biocgenerics" ,r-biocgenerics) | |
935 | ("r-dbi" ,r-dbi) | |
936 | ("r-rcurl" ,r-rcurl) | |
937 | ("r-xml" ,r-xml) | |
938 | ("r-xtable" ,r-xtable))) | |
939 | (home-page | |
940 | "https://bioconductor.org/packages/annotate") | |
941 | (synopsis "Annotation for microarrays") | |
942 | (description "This package provides R environments for the annotation of | |
943 | microarrays.") | |
944 | (license license:artistic2.0))) | |
945 | ||
fa596599 RW |
946 | (define-public r-hpar |
947 | (package | |
948 | (name "r-hpar") | |
43a23a07 | 949 | (version "1.26.0") |
fa596599 RW |
950 | (source |
951 | (origin | |
952 | (method url-fetch) | |
953 | (uri (bioconductor-uri "hpar" version)) | |
954 | (sha256 | |
955 | (base32 | |
43a23a07 | 956 | "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5")))) |
fa596599 RW |
957 | (build-system r-build-system) |
958 | (home-page "https://bioconductor.org/packages/hpar/") | |
959 | (synopsis "Human Protein Atlas in R") | |
960 | (description "This package provides a simple interface to and data from | |
961 | the Human Protein Atlas project.") | |
962 | (license license:artistic2.0))) | |
183ce988 RJ |
963 | |
964 | (define-public r-regioner | |
965 | (package | |
966 | (name "r-regioner") | |
b8f6b813 | 967 | (version "1.16.2") |
183ce988 RJ |
968 | (source |
969 | (origin | |
970 | (method url-fetch) | |
971 | (uri (bioconductor-uri "regioneR" version)) | |
972 | (sha256 | |
973 | (base32 | |
b8f6b813 | 974 | "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q")))) |
183ce988 RJ |
975 | (properties `((upstream-name . "regioneR"))) |
976 | (build-system r-build-system) | |
977 | (propagated-inputs | |
d639d888 | 978 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 979 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 980 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 981 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 982 | ("r-iranges" ,r-iranges) |
d639d888 RW |
983 | ("r-memoise" ,r-memoise) |
984 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 985 | ("r-s4vectors" ,r-s4vectors))) |
183ce988 RJ |
986 | (home-page "https://bioconductor.org/packages/regioneR/") |
987 | (synopsis "Association analysis of genomic regions") | |
988 | (description "This package offers a statistical framework based on | |
989 | customizable permutation tests to assess the association between genomic | |
990 | region sets and other genomic features.") | |
991 | (license license:artistic2.0))) | |
a5b56a53 | 992 | |
bfb93b48 RW |
993 | (define-public r-geneplotter |
994 | (package | |
995 | (name "r-geneplotter") | |
3e1bc88c | 996 | (version "1.62.0") |
bfb93b48 RW |
997 | (source |
998 | (origin | |
999 | (method url-fetch) | |
1000 | (uri (bioconductor-uri "geneplotter" version)) | |
1001 | (sha256 | |
1002 | (base32 | |
3e1bc88c | 1003 | "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb")))) |
bfb93b48 RW |
1004 | (build-system r-build-system) |
1005 | (propagated-inputs | |
1006 | `(("r-annotate" ,r-annotate) | |
1007 | ("r-annotationdbi" ,r-annotationdbi) | |
1008 | ("r-biobase" ,r-biobase) | |
1009 | ("r-biocgenerics" ,r-biocgenerics) | |
1010 | ("r-lattice" ,r-lattice) | |
1011 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
1012 | (home-page "https://bioconductor.org/packages/geneplotter") | |
1013 | (synopsis "Graphics functions for genomic data") | |
1014 | (description | |
1015 | "This package provides functions for plotting genomic data.") | |
1016 | (license license:artistic2.0))) | |
1017 | ||
4dc2ecc2 RW |
1018 | (define-public r-qvalue |
1019 | (package | |
1020 | (name "r-qvalue") | |
e02162f7 | 1021 | (version "2.16.0") |
4dc2ecc2 RW |
1022 | (source |
1023 | (origin | |
1024 | (method url-fetch) | |
1025 | (uri (bioconductor-uri "qvalue" version)) | |
1026 | (sha256 | |
1027 | (base32 | |
e02162f7 | 1028 | "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5")))) |
4dc2ecc2 RW |
1029 | (build-system r-build-system) |
1030 | (propagated-inputs | |
1031 | `(("r-ggplot2" ,r-ggplot2) | |
1032 | ("r-reshape2" ,r-reshape2))) | |
1033 | (home-page "http://github.com/jdstorey/qvalue") | |
1034 | (synopsis "Q-value estimation for false discovery rate control") | |
1035 | (description | |
1036 | "This package takes a list of p-values resulting from the simultaneous | |
1037 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
1038 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
1039 | of false positives incurred when that particular test is called significant. | |
1040 | The local FDR measures the posterior probability the null hypothesis is true | |
1041 | given the test's p-value. Various plots are automatically generated, allowing | |
1042 | one to make sensible significance cut-offs. The software can be applied to | |
1043 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
1044 | ;; Any version of the LGPL. | |
1045 | (license license:lgpl3+))) | |
1046 | ||
a5b56a53 RJ |
1047 | (define-public r-diffbind |
1048 | (package | |
1049 | (name "r-diffbind") | |
4c221b3b | 1050 | (version "2.12.0") |
a5b56a53 RJ |
1051 | (source |
1052 | (origin | |
1053 | (method url-fetch) | |
1054 | (uri (bioconductor-uri "DiffBind" version)) | |
1055 | (sha256 | |
1056 | (base32 | |
4c221b3b | 1057 | "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich")))) |
a5b56a53 RJ |
1058 | (properties `((upstream-name . "DiffBind"))) |
1059 | (build-system r-build-system) | |
1060 | (inputs | |
1061 | `(("zlib" ,zlib))) | |
1062 | (propagated-inputs | |
1063 | `(("r-amap" ,r-amap) | |
1064 | ("r-biocparallel" ,r-biocparallel) | |
1065 | ("r-deseq2" ,r-deseq2) | |
1066 | ("r-dplyr" ,r-dplyr) | |
1067 | ("r-edger" ,r-edger) | |
1068 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
1069 | ("r-genomicranges" ,r-genomicranges) |
1070 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
1071 | ("r-ggrepel" ,r-ggrepel) |
1072 | ("r-gplots" ,r-gplots) | |
1073 | ("r-iranges" ,r-iranges) | |
1074 | ("r-lattice" ,r-lattice) | |
1075 | ("r-limma" ,r-limma) | |
1076 | ("r-locfit" ,r-locfit) | |
1077 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
1078 | ("r-rcpp" ,r-rcpp) | |
4c221b3b | 1079 | ("r-rhtslib" ,r-rhtslib) |
a5b56a53 RJ |
1080 | ("r-rsamtools" ,r-rsamtools) |
1081 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 1082 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
4c221b3b | 1083 | ("r-systempiper" ,r-systempiper))) |
a5b56a53 RJ |
1084 | (home-page "http://bioconductor.org/packages/DiffBind") |
1085 | (synopsis "Differential binding analysis of ChIP-Seq peak data") | |
1086 | (description | |
1087 | "This package computes differentially bound sites from multiple | |
1088 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
1089 | occupancy (overlap) analysis and plotting functions.") | |
1090 | (license license:artistic2.0))) | |
6d94bf6b RJ |
1091 | |
1092 | (define-public r-ripseeker | |
1093 | (package | |
1094 | (name "r-ripseeker") | |
0968a448 | 1095 | (version "1.24.0") |
6d94bf6b RJ |
1096 | (source |
1097 | (origin | |
1098 | (method url-fetch) | |
1099 | (uri (bioconductor-uri "RIPSeeker" version)) | |
1100 | (sha256 | |
1101 | (base32 | |
0968a448 | 1102 | "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43")))) |
6d94bf6b RJ |
1103 | (properties `((upstream-name . "RIPSeeker"))) |
1104 | (build-system r-build-system) | |
1105 | (propagated-inputs | |
1106 | `(("r-s4vectors" ,r-s4vectors) | |
1107 | ("r-iranges" ,r-iranges) | |
1108 | ("r-genomicranges" ,r-genomicranges) | |
1109 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1110 | ("r-rsamtools" ,r-rsamtools) | |
1111 | ("r-genomicalignments" ,r-genomicalignments) | |
1112 | ("r-rtracklayer" ,r-rtracklayer))) | |
1113 | (home-page "http://bioconductor.org/packages/RIPSeeker") | |
1114 | (synopsis | |
1115 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
1116 | (description | |
1117 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
1118 | using two-state HMM with negative binomial emission probability. While | |
1119 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
1120 | a suite of bioinformatics tools integrated within this self-contained software | |
1121 | package comprehensively addressing issues ranging from post-alignments | |
1122 | processing to visualization and annotation.") | |
1123 | (license license:gpl2))) | |
a6ae9ffd RJ |
1124 | |
1125 | (define-public r-multtest | |
1126 | (package | |
1127 | (name "r-multtest") | |
588b63c2 | 1128 | (version "2.40.0") |
a6ae9ffd RJ |
1129 | (source |
1130 | (origin | |
1131 | (method url-fetch) | |
1132 | (uri (bioconductor-uri "multtest" version)) | |
1133 | (sha256 | |
1134 | (base32 | |
588b63c2 | 1135 | "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv")))) |
a6ae9ffd RJ |
1136 | (build-system r-build-system) |
1137 | (propagated-inputs | |
1138 | `(("r-survival" ,r-survival) | |
1139 | ("r-biocgenerics" ,r-biocgenerics) | |
1140 | ("r-biobase" ,r-biobase) | |
1141 | ("r-mass" ,r-mass))) | |
1142 | (home-page "http://bioconductor.org/packages/multtest") | |
1143 | (synopsis "Resampling-based multiple hypothesis testing") | |
1144 | (description | |
1145 | "This package can do non-parametric bootstrap and permutation | |
1146 | resampling-based multiple testing procedures (including empirical Bayes | |
1147 | methods) for controlling the family-wise error rate (FWER), generalized | |
1148 | family-wise error rate (gFWER), tail probability of the proportion of | |
1149 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
1150 | of bootstrap-based null distribution are implemented (centered, centered | |
1151 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
1152 | available. Tests based on a variety of T- and F-statistics (including | |
1153 | T-statistics based on regression parameters from linear and survival models | |
1154 | as well as those based on correlation parameters) are included. When probing | |
1155 | hypotheses with T-statistics, users may also select a potentially faster null | |
1156 | distribution which is multivariate normal with mean zero and variance | |
1157 | covariance matrix derived from the vector influence function. Results are | |
1158 | reported in terms of adjusted P-values, confidence regions and test statistic | |
1159 | cutoffs. The procedures are directly applicable to identifying differentially | |
1160 | expressed genes in DNA microarray experiments.") | |
1161 | (license license:lgpl3))) | |
793f83ef | 1162 | |
5dfe4912 RW |
1163 | (define-public r-graph |
1164 | (package | |
1165 | (name "r-graph") | |
a61bcb28 | 1166 | (version "1.62.0") |
5dfe4912 RW |
1167 | (source (origin |
1168 | (method url-fetch) | |
1169 | (uri (bioconductor-uri "graph" version)) | |
1170 | (sha256 | |
1171 | (base32 | |
a61bcb28 | 1172 | "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w")))) |
5dfe4912 RW |
1173 | (build-system r-build-system) |
1174 | (propagated-inputs | |
1175 | `(("r-biocgenerics" ,r-biocgenerics))) | |
1176 | (home-page "https://bioconductor.org/packages/graph") | |
1177 | (synopsis "Handle graph data structures in R") | |
1178 | (description | |
1179 | "This package implements some simple graph handling capabilities for R.") | |
1180 | (license license:artistic2.0))) | |
1181 | ||
a207bca2 RW |
1182 | (define-public r-codedepends |
1183 | (package | |
1184 | (name "r-codedepends") | |
1185 | (version "0.6.5") | |
1186 | (source | |
1187 | (origin | |
1188 | (method url-fetch) | |
1189 | (uri (cran-uri "CodeDepends" version)) | |
1190 | (sha256 | |
1191 | (base32 | |
1192 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
1193 | (properties `((upstream-name . "CodeDepends"))) | |
1194 | (build-system r-build-system) | |
1195 | (propagated-inputs | |
1196 | `(("r-codetools" ,r-codetools) | |
1197 | ("r-graph" ,r-graph) | |
1198 | ("r-xml" ,r-xml))) | |
1199 | (home-page "http://cran.r-project.org/web/packages/CodeDepends") | |
1200 | (synopsis "Analysis of R code for reproducible research and code comprehension") | |
1201 | (description | |
1202 | "This package provides tools for analyzing R expressions or blocks of | |
1203 | code and determining the dependencies between them. It focuses on R scripts, | |
1204 | but can be used on the bodies of functions. There are many facilities | |
1205 | including the ability to summarize or get a high-level view of code, | |
1206 | determining dependencies between variables, code improvement suggestions.") | |
1207 | ;; Any version of the GPL | |
1208 | (license (list license:gpl2+ license:gpl3+)))) | |
1209 | ||
793f83ef RJ |
1210 | (define-public r-chippeakanno |
1211 | (package | |
1212 | (name "r-chippeakanno") | |
85d0bd53 | 1213 | (version "3.18.1") |
793f83ef RJ |
1214 | (source |
1215 | (origin | |
1216 | (method url-fetch) | |
1217 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
1218 | (sha256 | |
1219 | (base32 | |
85d0bd53 | 1220 | "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji")))) |
793f83ef RJ |
1221 | (properties `((upstream-name . "ChIPpeakAnno"))) |
1222 | (build-system r-build-system) | |
1223 | (propagated-inputs | |
85c1d20f RW |
1224 | `(("r-annotationdbi" ,r-annotationdbi) |
1225 | ("r-biobase" ,r-biobase) | |
1226 | ("r-biocgenerics" ,r-biocgenerics) | |
57d2fcd9 | 1227 | ("r-biocmanager" ,r-biocmanager) |
793f83ef | 1228 | ("r-biomart" ,r-biomart) |
85c1d20f | 1229 | ("r-biostrings" ,r-biostrings) |
793f83ef | 1230 | ("r-bsgenome" ,r-bsgenome) |
85c1d20f RW |
1231 | ("r-dbi" ,r-dbi) |
1232 | ("r-delayedarray" ,r-delayedarray) | |
1233 | ("r-ensembldb" ,r-ensembldb) | |
1234 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1235 | ("r-genomicalignments" ,r-genomicalignments) | |
793f83ef | 1236 | ("r-genomicfeatures" ,r-genomicfeatures) |
f794e85d | 1237 | ("r-genomicranges" ,r-genomicranges) |
85c1d20f RW |
1238 | ("r-go-db" ,r-go-db) |
1239 | ("r-graph" ,r-graph) | |
1240 | ("r-idr" ,r-idr) | |
f794e85d | 1241 | ("r-iranges" ,r-iranges) |
793f83ef | 1242 | ("r-limma" ,r-limma) |
85c1d20f | 1243 | ("r-matrixstats" ,r-matrixstats) |
793f83ef RJ |
1244 | ("r-multtest" ,r-multtest) |
1245 | ("r-rbgl" ,r-rbgl) | |
793f83ef | 1246 | ("r-regioner" ,r-regioner) |
85c1d20f RW |
1247 | ("r-rsamtools" ,r-rsamtools) |
1248 | ("r-rtracklayer" ,r-rtracklayer) | |
f794e85d | 1249 | ("r-s4vectors" ,r-s4vectors) |
793f83ef | 1250 | ("r-seqinr" ,r-seqinr) |
793f83ef | 1251 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
793f83ef RJ |
1252 | ("r-venndiagram" ,r-venndiagram))) |
1253 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") | |
1254 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") | |
1255 | (description | |
1256 | "The package includes functions to retrieve the sequences around the peak, | |
1257 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
1258 | custom features such as most conserved elements and other transcription factor | |
1259 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
1260 | for finding the peaks with bi-directional promoters with summary statistics | |
1261 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
1262 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
1263 | enrichedGO (addGeneIDs).") | |
1264 | (license license:gpl2+))) | |
164502d8 RJ |
1265 | |
1266 | (define-public r-marray | |
1267 | (package | |
1268 | (name "r-marray") | |
bcb95b7a | 1269 | (version "1.62.0") |
164502d8 RJ |
1270 | (source (origin |
1271 | (method url-fetch) | |
1272 | (uri (bioconductor-uri "marray" version)) | |
1273 | (sha256 | |
bcb95b7a | 1274 | (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz")))) |
164502d8 RJ |
1275 | (build-system r-build-system) |
1276 | (propagated-inputs | |
67487088 | 1277 | `(("r-limma" ,r-limma))) |
164502d8 RJ |
1278 | (home-page "http://bioconductor.org/packages/marray") |
1279 | (synopsis "Exploratory analysis for two-color spotted microarray data") | |
1280 | (description "This package contains class definitions for two-color spotted | |
ab8979fc | 1281 | microarray data. It also includes functions for data input, diagnostic plots, |
164502d8 RJ |
1282 | normalization and quality checking.") |
1283 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
1284 | |
1285 | (define-public r-cghbase | |
1286 | (package | |
1287 | (name "r-cghbase") | |
8efb842f | 1288 | (version "1.44.0") |
0416a0d4 RJ |
1289 | (source (origin |
1290 | (method url-fetch) | |
1291 | (uri (bioconductor-uri "CGHbase" version)) | |
1292 | (sha256 | |
8efb842f | 1293 | (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm")))) |
0416a0d4 RJ |
1294 | (properties `((upstream-name . "CGHbase"))) |
1295 | (build-system r-build-system) | |
1296 | (propagated-inputs | |
1297 | `(("r-biobase" ,r-biobase) | |
1298 | ("r-marray" ,r-marray))) | |
1299 | (home-page "http://bioconductor.org/packages/CGHbase") | |
1300 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
1301 | (description "This package contains functions and classes that are needed by | |
1302 | the @code{arrayCGH} packages.") | |
1303 | (license license:gpl2+))) | |
67ee83d6 RJ |
1304 | |
1305 | (define-public r-cghcall | |
1306 | (package | |
1307 | (name "r-cghcall") | |
23177309 | 1308 | (version "2.46.0") |
67ee83d6 RJ |
1309 | (source (origin |
1310 | (method url-fetch) | |
1311 | (uri (bioconductor-uri "CGHcall" version)) | |
1312 | (sha256 | |
23177309 | 1313 | (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93")))) |
67ee83d6 RJ |
1314 | (properties `((upstream-name . "CGHcall"))) |
1315 | (build-system r-build-system) | |
1316 | (propagated-inputs | |
1317 | `(("r-biobase" ,r-biobase) | |
1318 | ("r-cghbase" ,r-cghbase) | |
1319 | ("r-impute" ,r-impute) | |
1320 | ("r-dnacopy" ,r-dnacopy) | |
1321 | ("r-snowfall" ,r-snowfall))) | |
1322 | (home-page "http://bioconductor.org/packages/CGHcall") | |
1323 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
1324 | (description "This package contains functions and classes that are needed by | |
1325 | @code{arrayCGH} packages.") | |
1326 | (license license:gpl2+))) | |
0ef8cc9c RJ |
1327 | |
1328 | (define-public r-qdnaseq | |
1329 | (package | |
1330 | (name "r-qdnaseq") | |
4f4bed7d | 1331 | (version "1.20.0") |
0ef8cc9c RJ |
1332 | (source (origin |
1333 | (method url-fetch) | |
1334 | (uri (bioconductor-uri "QDNAseq" version)) | |
1335 | (sha256 | |
4f4bed7d | 1336 | (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz")))) |
0ef8cc9c RJ |
1337 | (properties `((upstream-name . "QDNAseq"))) |
1338 | (build-system r-build-system) | |
1339 | (propagated-inputs | |
1340 | `(("r-biobase" ,r-biobase) | |
81b0181b | 1341 | ("r-biocparallel" ,r-biocparallel) |
0ef8cc9c RJ |
1342 | ("r-cghbase" ,r-cghbase) |
1343 | ("r-cghcall" ,r-cghcall) | |
1344 | ("r-dnacopy" ,r-dnacopy) | |
1345 | ("r-genomicranges" ,r-genomicranges) | |
1346 | ("r-iranges" ,r-iranges) | |
1347 | ("r-matrixstats" ,r-matrixstats) | |
1348 | ("r-r-utils" ,r-r-utils) | |
1349 | ("r-rsamtools" ,r-rsamtools))) | |
1350 | (home-page "http://bioconductor.org/packages/QDNAseq") | |
1351 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") | |
1352 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
1353 | number of sequence reads in each counted, adjusted with a simultaneous | |
1354 | two-dimensional loess correction for sequence mappability and GC content, and | |
1355 | filtered to remove spurious regions in the genome. Downstream steps of | |
1356 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
1357 | respectively.") | |
1358 | (license license:gpl2+))) | |
bb15b581 RW |
1359 | |
1360 | (define-public r-bayseq | |
1361 | (package | |
1362 | (name "r-bayseq") | |
c38de815 | 1363 | (version "2.18.0") |
bb15b581 RW |
1364 | (source |
1365 | (origin | |
1366 | (method url-fetch) | |
1367 | (uri (bioconductor-uri "baySeq" version)) | |
1368 | (sha256 | |
1369 | (base32 | |
c38de815 | 1370 | "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w")))) |
bb15b581 RW |
1371 | (properties `((upstream-name . "baySeq"))) |
1372 | (build-system r-build-system) | |
1373 | (propagated-inputs | |
1374 | `(("r-abind" ,r-abind) | |
1375 | ("r-edger" ,r-edger) | |
1376 | ("r-genomicranges" ,r-genomicranges))) | |
1377 | (home-page "https://bioconductor.org/packages/baySeq/") | |
1378 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
1379 | (description | |
1380 | "This package identifies differential expression in high-throughput count | |
1381 | data, such as that derived from next-generation sequencing machines, | |
1382 | calculating estimated posterior likelihoods of differential expression (or | |
1383 | more complex hypotheses) via empirical Bayesian methods.") | |
1384 | (license license:gpl3))) | |
609f4ad1 RW |
1385 | |
1386 | (define-public r-chipcomp | |
1387 | (package | |
1388 | (name "r-chipcomp") | |
1ddd4af5 | 1389 | (version "1.14.0") |
609f4ad1 RW |
1390 | (source |
1391 | (origin | |
1392 | (method url-fetch) | |
1393 | (uri (bioconductor-uri "ChIPComp" version)) | |
1394 | (sha256 | |
1395 | (base32 | |
1ddd4af5 | 1396 | "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y")))) |
609f4ad1 RW |
1397 | (properties `((upstream-name . "ChIPComp"))) |
1398 | (build-system r-build-system) | |
1399 | (propagated-inputs | |
1400 | `(("r-biocgenerics" ,r-biocgenerics) | |
1401 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
1402 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
1403 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1404 | ("r-genomicranges" ,r-genomicranges) | |
1405 | ("r-iranges" ,r-iranges) | |
1406 | ("r-limma" ,r-limma) | |
1407 | ("r-rsamtools" ,r-rsamtools) | |
1408 | ("r-rtracklayer" ,r-rtracklayer) | |
1409 | ("r-s4vectors" ,r-s4vectors))) | |
1410 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
1411 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
1412 | (description | |
1413 | "ChIPComp implements a statistical method for quantitative comparison of | |
1414 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
1415 | sites across multiple conditions considering matching control in ChIP-seq | |
1416 | datasets.") | |
1417 | ;; Any version of the GPL. | |
1418 | (license license:gpl3+))) | |
0490f9de RW |
1419 | |
1420 | (define-public r-riboprofiling | |
1421 | (package | |
1422 | (name "r-riboprofiling") | |
7d5acf7a | 1423 | (version "1.14.0") |
0490f9de RW |
1424 | (source |
1425 | (origin | |
1426 | (method url-fetch) | |
1427 | (uri (bioconductor-uri "RiboProfiling" version)) | |
1428 | (sha256 | |
1429 | (base32 | |
7d5acf7a | 1430 | "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9")))) |
0490f9de RW |
1431 | (properties `((upstream-name . "RiboProfiling"))) |
1432 | (build-system r-build-system) | |
1433 | (propagated-inputs | |
1434 | `(("r-biocgenerics" ,r-biocgenerics) | |
1435 | ("r-biostrings" ,r-biostrings) | |
1436 | ("r-data-table" ,r-data-table) | |
1437 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1438 | ("r-genomicalignments" ,r-genomicalignments) | |
1439 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1440 | ("r-genomicranges" ,r-genomicranges) | |
1441 | ("r-ggbio" ,r-ggbio) | |
1442 | ("r-ggplot2" ,r-ggplot2) | |
1443 | ("r-iranges" ,r-iranges) | |
1444 | ("r-plyr" ,r-plyr) | |
1445 | ("r-reshape2" ,r-reshape2) | |
1446 | ("r-rsamtools" ,r-rsamtools) | |
1447 | ("r-rtracklayer" ,r-rtracklayer) | |
1448 | ("r-s4vectors" ,r-s4vectors) | |
1449 | ("r-sqldf" ,r-sqldf))) | |
1450 | (home-page "https://bioconductor.org/packages/RiboProfiling/") | |
1451 | (synopsis "Ribosome profiling data analysis") | |
1452 | (description "Starting with a BAM file, this package provides the | |
1453 | necessary functions for quality assessment, read start position recalibration, | |
1454 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
1455 | of count data: pairs, log fold-change, codon frequency and coverage | |
1456 | assessment, principal component analysis on codon coverage.") | |
1457 | (license license:gpl3))) | |
6ffdfe6a RW |
1458 | |
1459 | (define-public r-riboseqr | |
1460 | (package | |
1461 | (name "r-riboseqr") | |
eff6b2eb | 1462 | (version "1.18.0") |
6ffdfe6a RW |
1463 | (source |
1464 | (origin | |
1465 | (method url-fetch) | |
1466 | (uri (bioconductor-uri "riboSeqR" version)) | |
1467 | (sha256 | |
1468 | (base32 | |
eff6b2eb | 1469 | "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga")))) |
6ffdfe6a RW |
1470 | (properties `((upstream-name . "riboSeqR"))) |
1471 | (build-system r-build-system) | |
1472 | (propagated-inputs | |
1473 | `(("r-abind" ,r-abind) | |
1474 | ("r-bayseq" ,r-bayseq) | |
1475 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1476 | ("r-genomicranges" ,r-genomicranges) | |
1477 | ("r-iranges" ,r-iranges) | |
1478 | ("r-rsamtools" ,r-rsamtools) | |
1479 | ("r-seqlogo" ,r-seqlogo))) | |
1480 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
1481 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
1482 | (description | |
1483 | "This package provides plotting functions, frameshift detection and | |
1484 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
1485 | (license license:gpl3))) | |
a32279ff RW |
1486 | |
1487 | (define-public r-interactionset | |
1488 | (package | |
1489 | (name "r-interactionset") | |
176a264c | 1490 | (version "1.12.0") |
a32279ff RW |
1491 | (source |
1492 | (origin | |
1493 | (method url-fetch) | |
1494 | (uri (bioconductor-uri "InteractionSet" version)) | |
1495 | (sha256 | |
1496 | (base32 | |
176a264c | 1497 | "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6")))) |
a32279ff RW |
1498 | (properties |
1499 | `((upstream-name . "InteractionSet"))) | |
1500 | (build-system r-build-system) | |
1501 | (propagated-inputs | |
1502 | `(("r-biocgenerics" ,r-biocgenerics) | |
1503 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1504 | ("r-genomicranges" ,r-genomicranges) | |
1505 | ("r-iranges" ,r-iranges) | |
1506 | ("r-matrix" ,r-matrix) | |
1507 | ("r-rcpp" ,r-rcpp) | |
1508 | ("r-s4vectors" ,r-s4vectors) | |
1509 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1510 | (home-page "https://bioconductor.org/packages/InteractionSet") | |
1511 | (synopsis "Base classes for storing genomic interaction data") | |
1512 | (description | |
02fe0976 | 1513 | "This package provides the @code{GInteractions}, |
a32279ff RW |
1514 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
1515 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
1516 | experiments.") | |
1517 | (license license:gpl3))) | |
cf9a29b2 RW |
1518 | |
1519 | (define-public r-genomicinteractions | |
1520 | (package | |
1521 | (name "r-genomicinteractions") | |
1236ce8e | 1522 | (version "1.18.0") |
cf9a29b2 RW |
1523 | (source |
1524 | (origin | |
1525 | (method url-fetch) | |
1526 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
1527 | (sha256 | |
1528 | (base32 | |
1236ce8e | 1529 | "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b")))) |
cf9a29b2 RW |
1530 | (properties |
1531 | `((upstream-name . "GenomicInteractions"))) | |
1532 | (build-system r-build-system) | |
1533 | (propagated-inputs | |
1534 | `(("r-biobase" ,r-biobase) | |
1535 | ("r-biocgenerics" ,r-biocgenerics) | |
1536 | ("r-data-table" ,r-data-table) | |
1537 | ("r-dplyr" ,r-dplyr) | |
1538 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1539 | ("r-genomicranges" ,r-genomicranges) | |
1540 | ("r-ggplot2" ,r-ggplot2) | |
1541 | ("r-gridextra" ,r-gridextra) | |
1542 | ("r-gviz" ,r-gviz) | |
1543 | ("r-igraph" ,r-igraph) | |
1544 | ("r-interactionset" ,r-interactionset) | |
1545 | ("r-iranges" ,r-iranges) | |
1546 | ("r-rsamtools" ,r-rsamtools) | |
1547 | ("r-rtracklayer" ,r-rtracklayer) | |
1548 | ("r-s4vectors" ,r-s4vectors) | |
1549 | ("r-stringr" ,r-stringr))) | |
1550 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") | |
1551 | (synopsis "R package for handling genomic interaction data") | |
1552 | (description | |
1553 | "This R package provides tools for handling genomic interaction data, | |
1554 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
1555 | information and producing various plots and statistics.") | |
1556 | (license license:gpl3))) | |
27c51606 RW |
1557 | |
1558 | (define-public r-ctc | |
1559 | (package | |
1560 | (name "r-ctc") | |
7a5d729a | 1561 | (version "1.58.0") |
27c51606 RW |
1562 | (source |
1563 | (origin | |
1564 | (method url-fetch) | |
1565 | (uri (bioconductor-uri "ctc" version)) | |
1566 | (sha256 | |
1567 | (base32 | |
7a5d729a | 1568 | "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am")))) |
27c51606 RW |
1569 | (build-system r-build-system) |
1570 | (propagated-inputs `(("r-amap" ,r-amap))) | |
1571 | (home-page "https://bioconductor.org/packages/ctc/") | |
1572 | (synopsis "Cluster and tree conversion") | |
1573 | (description | |
1574 | "This package provides tools for exporting and importing classification | |
1575 | trees and clusters to other programs.") | |
1576 | (license license:gpl2))) | |
5da0e142 RW |
1577 | |
1578 | (define-public r-goseq | |
1579 | (package | |
1580 | (name "r-goseq") | |
40f0ee43 | 1581 | (version "1.36.0") |
5da0e142 RW |
1582 | (source |
1583 | (origin | |
1584 | (method url-fetch) | |
1585 | (uri (bioconductor-uri "goseq" version)) | |
1586 | (sha256 | |
1587 | (base32 | |
40f0ee43 | 1588 | "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw")))) |
5da0e142 RW |
1589 | (build-system r-build-system) |
1590 | (propagated-inputs | |
1591 | `(("r-annotationdbi" ,r-annotationdbi) | |
1592 | ("r-biasedurn" ,r-biasedurn) | |
1593 | ("r-biocgenerics" ,r-biocgenerics) | |
1594 | ("r-genelendatabase" ,r-genelendatabase) | |
1595 | ("r-go-db" ,r-go-db) | |
1596 | ("r-mgcv" ,r-mgcv))) | |
1597 | (home-page "https://bioconductor.org/packages/goseq/") | |
1598 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
1599 | (description | |
1600 | "This package provides tools to detect Gene Ontology and/or other user | |
1601 | defined categories which are over/under represented in RNA-seq data.") | |
1602 | (license license:lgpl2.0+))) | |
f4235c0e RW |
1603 | |
1604 | (define-public r-glimma | |
1605 | (package | |
1606 | (name "r-glimma") | |
07252952 | 1607 | (version "1.12.0") |
f4235c0e RW |
1608 | (source |
1609 | (origin | |
1610 | (method url-fetch) | |
1611 | (uri (bioconductor-uri "Glimma" version)) | |
1612 | (sha256 | |
1613 | (base32 | |
07252952 | 1614 | "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x")))) |
f4235c0e RW |
1615 | (properties `((upstream-name . "Glimma"))) |
1616 | (build-system r-build-system) | |
1617 | (propagated-inputs | |
1618 | `(("r-edger" ,r-edger) | |
1619 | ("r-jsonlite" ,r-jsonlite) | |
1620 | ("r-s4vectors" ,r-s4vectors))) | |
1621 | (home-page "https://github.com/Shians/Glimma") | |
1622 | (synopsis "Interactive HTML graphics") | |
1623 | (description | |
1624 | "This package generates interactive visualisations for analysis of | |
1625 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
1626 | HTML page. The interactions are built on top of the popular static | |
1627 | representations of analysis results in order to provide additional | |
1628 | information.") | |
1629 | (license license:lgpl3))) | |
aa388dc7 RW |
1630 | |
1631 | (define-public r-rots | |
1632 | (package | |
1633 | (name "r-rots") | |
5bf7eb49 | 1634 | (version "1.12.0") |
aa388dc7 RW |
1635 | (source |
1636 | (origin | |
1637 | (method url-fetch) | |
1638 | (uri (bioconductor-uri "ROTS" version)) | |
1639 | (sha256 | |
1640 | (base32 | |
5bf7eb49 | 1641 | "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77")))) |
aa388dc7 RW |
1642 | (properties `((upstream-name . "ROTS"))) |
1643 | (build-system r-build-system) | |
1644 | (propagated-inputs | |
1645 | `(("r-biobase" ,r-biobase) | |
1646 | ("r-rcpp" ,r-rcpp))) | |
1647 | (home-page "https://bioconductor.org/packages/ROTS/") | |
1648 | (synopsis "Reproducibility-Optimized Test Statistic") | |
1649 | (description | |
1650 | "This package provides tools for calculating the | |
1651 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
1652 | in omics data.") | |
1653 | (license license:gpl2+))) | |
b64ce4b7 | 1654 | |
cad6fb2d RW |
1655 | (define-public r-plgem |
1656 | (package | |
1657 | (name "r-plgem") | |
5dce7153 | 1658 | (version "1.56.0") |
cad6fb2d RW |
1659 | (source |
1660 | (origin | |
1661 | (method url-fetch) | |
1662 | (uri (bioconductor-uri "plgem" version)) | |
1663 | (sha256 | |
1664 | (base32 | |
5dce7153 | 1665 | "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp")))) |
cad6fb2d RW |
1666 | (build-system r-build-system) |
1667 | (propagated-inputs | |
1668 | `(("r-biobase" ,r-biobase) | |
1669 | ("r-mass" ,r-mass))) | |
1670 | (home-page "http://www.genopolis.it") | |
1671 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
1672 | (description | |
1673 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
1674 | model the variance-versus-mean dependence that exists in a variety of | |
1675 | genome-wide datasets, including microarray and proteomics data. The use of | |
1676 | PLGEM has been shown to improve the detection of differentially expressed | |
1677 | genes or proteins in these datasets.") | |
1678 | (license license:gpl2))) | |
1679 | ||
b64ce4b7 RW |
1680 | (define-public r-inspect |
1681 | (package | |
1682 | (name "r-inspect") | |
3649d046 | 1683 | (version "1.14.0") |
b64ce4b7 RW |
1684 | (source |
1685 | (origin | |
1686 | (method url-fetch) | |
1687 | (uri (bioconductor-uri "INSPEcT" version)) | |
1688 | (sha256 | |
1689 | (base32 | |
3649d046 | 1690 | "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r")))) |
b64ce4b7 RW |
1691 | (properties `((upstream-name . "INSPEcT"))) |
1692 | (build-system r-build-system) | |
1693 | (propagated-inputs | |
1694 | `(("r-biobase" ,r-biobase) | |
1695 | ("r-biocgenerics" ,r-biocgenerics) | |
1696 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 1697 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 RW |
1698 | ("r-desolve" ,r-desolve) |
1699 | ("r-genomicalignments" ,r-genomicalignments) | |
1700 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1701 | ("r-genomicranges" ,r-genomicranges) | |
1702 | ("r-iranges" ,r-iranges) | |
c86fc969 | 1703 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
1704 | ("r-preprocesscore" ,r-preprocesscore) |
1705 | ("r-proc" ,r-proc) | |
1706 | ("r-rootsolve" ,r-rootsolve) | |
1707 | ("r-rsamtools" ,r-rsamtools) | |
c86fc969 RW |
1708 | ("r-s4vectors" ,r-s4vectors) |
1709 | ("r-shiny" ,r-shiny) | |
1710 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1711 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
1712 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
b64ce4b7 RW |
1713 | (home-page "https://bioconductor.org/packages/INSPEcT") |
1714 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
1715 | (description | |
1716 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
1717 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
1718 | order to evaluate synthesis, processing and degradation rates and assess via | |
1719 | modeling the rates that determines changes in mature mRNA levels.") | |
1720 | (license license:gpl2))) | |
f6e99763 RW |
1721 | |
1722 | (define-public r-dnabarcodes | |
1723 | (package | |
1724 | (name "r-dnabarcodes") | |
774e499c | 1725 | (version "1.14.0") |
f6e99763 RW |
1726 | (source |
1727 | (origin | |
1728 | (method url-fetch) | |
1729 | (uri (bioconductor-uri "DNABarcodes" version)) | |
1730 | (sha256 | |
1731 | (base32 | |
774e499c | 1732 | "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0")))) |
f6e99763 RW |
1733 | (properties `((upstream-name . "DNABarcodes"))) |
1734 | (build-system r-build-system) | |
1735 | (propagated-inputs | |
1736 | `(("r-bh" ,r-bh) | |
1737 | ("r-matrix" ,r-matrix) | |
1738 | ("r-rcpp" ,r-rcpp))) | |
1739 | (home-page "https://bioconductor.org/packages/DNABarcodes") | |
1740 | (synopsis "Create and analyze DNA barcodes") | |
1741 | (description | |
1742 | "This package offers tools to create DNA barcode sets capable of | |
1743 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
1744 | can be analyzed regarding their minimal, maximal and average distances between | |
1745 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
1746 | demultiplexed, i.e. assigned to their original reference barcode.") | |
1747 | (license license:gpl2))) | |
09aa3d06 RW |
1748 | |
1749 | (define-public r-ruvseq | |
1750 | (package | |
1751 | (name "r-ruvseq") | |
d8771f5f | 1752 | (version "1.18.0") |
09aa3d06 RW |
1753 | (source |
1754 | (origin | |
1755 | (method url-fetch) | |
1756 | (uri (bioconductor-uri "RUVSeq" version)) | |
1757 | (sha256 | |
1758 | (base32 | |
d8771f5f | 1759 | "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33")))) |
09aa3d06 RW |
1760 | (properties `((upstream-name . "RUVSeq"))) |
1761 | (build-system r-build-system) | |
1762 | (propagated-inputs | |
1763 | `(("r-biobase" ,r-biobase) | |
1764 | ("r-edaseq" ,r-edaseq) | |
1765 | ("r-edger" ,r-edger) | |
1766 | ("r-mass" ,r-mass))) | |
1767 | (home-page "https://github.com/drisso/RUVSeq") | |
1768 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
1769 | (description | |
1770 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
1771 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
1772 | samples.") | |
1773 | (license license:artistic2.0))) | |
286157dc RW |
1774 | |
1775 | (define-public r-biocneighbors | |
1776 | (package | |
1777 | (name "r-biocneighbors") | |
6fc161fc | 1778 | (version "1.2.0") |
286157dc RW |
1779 | (source |
1780 | (origin | |
1781 | (method url-fetch) | |
1782 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
1783 | (sha256 | |
1784 | (base32 | |
6fc161fc | 1785 | "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg")))) |
286157dc RW |
1786 | (properties `((upstream-name . "BiocNeighbors"))) |
1787 | (build-system r-build-system) | |
1788 | (propagated-inputs | |
6fc161fc RW |
1789 | `(("r-biocgenerics" ,r-biocgenerics) |
1790 | ("r-biocparallel" ,r-biocparallel) | |
286157dc RW |
1791 | ("r-rcpp" ,r-rcpp) |
1792 | ("r-rcppannoy" ,r-rcppannoy) | |
6fc161fc | 1793 | ("r-rcpphnsw" ,r-rcpphnsw) |
286157dc RW |
1794 | ("r-s4vectors" ,r-s4vectors))) |
1795 | (home-page "https://bioconductor.org/packages/BiocNeighbors") | |
1796 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
1797 | (description | |
1798 | "This package implements exact and approximate methods for nearest | |
1799 | neighbor detection, in a framework that allows them to be easily switched | |
1800 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
1801 | using pre-clustering with the k-means algorithm. Functions are also provided | |
1802 | to search for all neighbors within a given distance. Parallelization is | |
1803 | achieved for all methods using the BiocParallel framework.") | |
1804 | (license license:gpl3))) | |
8a587c89 | 1805 | |
99391290 RW |
1806 | (define-public r-biocsingular |
1807 | (package | |
1808 | (name "r-biocsingular") | |
1809 | (version "1.0.0") | |
1810 | (source | |
1811 | (origin | |
1812 | (method url-fetch) | |
1813 | (uri (bioconductor-uri "BiocSingular" version)) | |
1814 | (sha256 | |
1815 | (base32 | |
1816 | "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5")))) | |
1817 | (properties `((upstream-name . "BiocSingular"))) | |
1818 | (build-system r-build-system) | |
1819 | (propagated-inputs | |
1820 | `(("r-beachmat" ,r-beachmat) | |
1821 | ("r-biocgenerics" ,r-biocgenerics) | |
1822 | ("r-biocparallel" ,r-biocparallel) | |
1823 | ("r-delayedarray" ,r-delayedarray) | |
1824 | ("r-irlba" ,r-irlba) | |
1825 | ("r-matrix" ,r-matrix) | |
1826 | ("r-rcpp" ,r-rcpp) | |
1827 | ("r-rsvd" ,r-rsvd) | |
1828 | ("r-s4vectors" ,r-s4vectors))) | |
1829 | (home-page "https://github.com/LTLA/BiocSingular") | |
1830 | (synopsis "Singular value decomposition for Bioconductor packages") | |
1831 | (description | |
1832 | "This package implements exact and approximate methods for singular value | |
1833 | decomposition and principal components analysis, in a framework that allows | |
1834 | them to be easily switched within Bioconductor packages or workflows. Where | |
1835 | possible, parallelization is achieved using the BiocParallel framework.") | |
1836 | (license license:gpl3))) | |
1837 | ||
a961ae46 RW |
1838 | (define-public r-destiny |
1839 | (package | |
1840 | (name "r-destiny") | |
0aa72f2d | 1841 | (version "2.14.0") |
a961ae46 RW |
1842 | (source |
1843 | (origin | |
1844 | (method url-fetch) | |
1845 | (uri (bioconductor-uri "destiny" version)) | |
1846 | (sha256 | |
1847 | (base32 | |
0aa72f2d | 1848 | "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3")))) |
a961ae46 RW |
1849 | (build-system r-build-system) |
1850 | (propagated-inputs | |
1851 | `(("r-biobase" ,r-biobase) | |
1852 | ("r-biocgenerics" ,r-biocgenerics) | |
0aa72f2d | 1853 | ("r-ggplot2" ,r-ggplot2) |
a961ae46 | 1854 | ("r-ggthemes" ,r-ggthemes) |
a961ae46 RW |
1855 | ("r-igraph" ,r-igraph) |
1856 | ("r-matrix" ,r-matrix) | |
1857 | ("r-proxy" ,r-proxy) | |
1858 | ("r-rcpp" ,r-rcpp) | |
1859 | ("r-rcppeigen" ,r-rcppeigen) | |
1860 | ("r-scales" ,r-scales) | |
1861 | ("r-scatterplot3d" ,r-scatterplot3d) | |
1862 | ("r-smoother" ,r-smoother) | |
1863 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1864 | ("r-vim" ,r-vim))) | |
1865 | (home-page "https://bioconductor.org/packages/destiny/") | |
1866 | (synopsis "Create and plot diffusion maps") | |
1867 | (description "This package provides tools to create and plot diffusion | |
1868 | maps.") | |
1869 | ;; Any version of the GPL | |
1870 | (license license:gpl3+))) | |
1871 | ||
8a587c89 RW |
1872 | (define-public r-savr |
1873 | (package | |
1874 | (name "r-savr") | |
8d3d0c3a | 1875 | (version "1.22.0") |
8a587c89 RW |
1876 | (source |
1877 | (origin | |
1878 | (method url-fetch) | |
1879 | (uri (bioconductor-uri "savR" version)) | |
1880 | (sha256 | |
1881 | (base32 | |
8d3d0c3a | 1882 | "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h")))) |
8a587c89 RW |
1883 | (properties `((upstream-name . "savR"))) |
1884 | (build-system r-build-system) | |
1885 | (propagated-inputs | |
1886 | `(("r-ggplot2" ,r-ggplot2) | |
1887 | ("r-gridextra" ,r-gridextra) | |
1888 | ("r-reshape2" ,r-reshape2) | |
1889 | ("r-scales" ,r-scales) | |
1890 | ("r-xml" ,r-xml))) | |
1891 | (home-page "https://github.com/bcalder/savR") | |
1892 | (synopsis "Parse and analyze Illumina SAV files") | |
1893 | (description | |
1894 | "This package provides tools to parse Illumina Sequence Analysis | |
1895 | Viewer (SAV) files, access data, and generate QC plots.") | |
1896 | (license license:agpl3+))) | |
41ffc214 RW |
1897 | |
1898 | (define-public r-chipexoqual | |
1899 | (package | |
1900 | (name "r-chipexoqual") | |
58a43fc2 | 1901 | (version "1.8.0") |
41ffc214 RW |
1902 | (source |
1903 | (origin | |
1904 | (method url-fetch) | |
1905 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
1906 | (sha256 | |
1907 | (base32 | |
58a43fc2 | 1908 | "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj")))) |
41ffc214 RW |
1909 | (properties `((upstream-name . "ChIPexoQual"))) |
1910 | (build-system r-build-system) | |
1911 | (propagated-inputs | |
1912 | `(("r-biocparallel" ,r-biocparallel) | |
1913 | ("r-biovizbase" ,r-biovizbase) | |
1914 | ("r-broom" ,r-broom) | |
1915 | ("r-data-table" ,r-data-table) | |
1916 | ("r-dplyr" ,r-dplyr) | |
1917 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1918 | ("r-genomicalignments" ,r-genomicalignments) | |
1919 | ("r-genomicranges" ,r-genomicranges) | |
1920 | ("r-ggplot2" ,r-ggplot2) | |
1921 | ("r-hexbin" ,r-hexbin) | |
1922 | ("r-iranges" ,r-iranges) | |
1923 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
1924 | ("r-rmarkdown" ,r-rmarkdown) | |
1925 | ("r-rsamtools" ,r-rsamtools) | |
1926 | ("r-s4vectors" ,r-s4vectors) | |
1927 | ("r-scales" ,r-scales) | |
1928 | ("r-viridis" ,r-viridis))) | |
1929 | (home-page "https://github.com/keleslab/ChIPexoQual") | |
1930 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
1931 | (description | |
1932 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
1933 | sequencing data.") | |
1934 | (license license:gpl2+))) | |
c18dccff | 1935 | |
3d13b448 RW |
1936 | (define-public r-copynumber |
1937 | (package | |
1938 | (name "r-copynumber") | |
d9419185 | 1939 | (version "1.24.0") |
3d13b448 RW |
1940 | (source (origin |
1941 | (method url-fetch) | |
1942 | (uri (bioconductor-uri "copynumber" version)) | |
1943 | (sha256 | |
1944 | (base32 | |
d9419185 | 1945 | "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp")))) |
3d13b448 RW |
1946 | (build-system r-build-system) |
1947 | (propagated-inputs | |
1948 | `(("r-s4vectors" ,r-s4vectors) | |
1949 | ("r-iranges" ,r-iranges) | |
1950 | ("r-genomicranges" ,r-genomicranges) | |
1951 | ("r-biocgenerics" ,r-biocgenerics))) | |
1952 | (home-page "https://bioconductor.org/packages/copynumber") | |
1953 | (synopsis "Segmentation of single- and multi-track copy number data") | |
1954 | (description | |
1955 | "This package segments single- and multi-track copy number data by a | |
1956 | penalized least squares regression method.") | |
1957 | (license license:artistic2.0))) | |
1958 | ||
c18dccff RW |
1959 | (define-public r-dnacopy |
1960 | (package | |
1961 | (name "r-dnacopy") | |
d5f3c0d0 | 1962 | (version "1.58.0") |
c18dccff RW |
1963 | (source |
1964 | (origin | |
1965 | (method url-fetch) | |
1966 | (uri (bioconductor-uri "DNAcopy" version)) | |
1967 | (sha256 | |
1968 | (base32 | |
d5f3c0d0 | 1969 | "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa")))) |
c18dccff RW |
1970 | (properties `((upstream-name . "DNAcopy"))) |
1971 | (build-system r-build-system) | |
1972 | (native-inputs `(("gfortran" ,gfortran))) | |
1973 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
1974 | (synopsis "DNA copy number data analysis") | |
1975 | (description | |
1976 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
1977 | algorithm to segment DNA copy number data and identify genomic regions with | |
1978 | abnormal copy number.") | |
1979 | (license license:gpl2+))) | |
3a0babac RW |
1980 | |
1981 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
1982 | ;; Bioconductor package. | |
1983 | (define-public r-htscluster | |
1984 | (package | |
1985 | (name "r-htscluster") | |
1986 | (version "2.0.8") | |
1987 | (source | |
1988 | (origin | |
1989 | (method url-fetch) | |
1990 | (uri (cran-uri "HTSCluster" version)) | |
1991 | (sha256 | |
1992 | (base32 | |
1993 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
1994 | (properties `((upstream-name . "HTSCluster"))) | |
1995 | (build-system r-build-system) | |
1996 | (propagated-inputs | |
1997 | `(("r-capushe" ,r-capushe) | |
1998 | ("r-edger" ,r-edger) | |
1999 | ("r-plotrix" ,r-plotrix))) | |
2000 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
2001 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
2002 | (description | |
2003 | "This package provides a Poisson mixture model is implemented to cluster | |
2004 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
2005 | estimation is performed using either the EM or CEM algorithm, and the slope | |
2006 | heuristics are used for model selection (i.e., to choose the number of | |
2007 | clusters).") | |
2008 | (license license:gpl3+))) | |
173c9960 RW |
2009 | |
2010 | (define-public r-deds | |
2011 | (package | |
2012 | (name "r-deds") | |
301c4ff1 | 2013 | (version "1.58.0") |
173c9960 RW |
2014 | (source |
2015 | (origin | |
2016 | (method url-fetch) | |
2017 | (uri (bioconductor-uri "DEDS" version)) | |
2018 | (sha256 | |
2019 | (base32 | |
301c4ff1 | 2020 | "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs")))) |
173c9960 RW |
2021 | (properties `((upstream-name . "DEDS"))) |
2022 | (build-system r-build-system) | |
2023 | (home-page "https://bioconductor.org/packages/DEDS/") | |
2024 | (synopsis "Differential expression via distance summary for microarray data") | |
2025 | (description | |
2026 | "This library contains functions that calculate various statistics of | |
2027 | differential expression for microarray data, including t statistics, fold | |
2028 | change, F statistics, SAM, moderated t and F statistics and B statistics. It | |
2029 | also implements a new methodology called DEDS (Differential Expression via | |
2030 | Distance Summary), which selects differentially expressed genes by integrating | |
2031 | and summarizing a set of statistics using a weighted distance approach.") | |
2032 | ;; Any version of the LGPL. | |
2033 | (license license:lgpl3+))) | |
7ed869f7 RW |
2034 | |
2035 | ;; This is a CRAN package, but since it depends on a Bioconductor package we | |
2036 | ;; put it here. | |
2037 | (define-public r-nbpseq | |
2038 | (package | |
2039 | (name "r-nbpseq") | |
2040 | (version "0.3.0") | |
2041 | (source | |
2042 | (origin | |
2043 | (method url-fetch) | |
2044 | (uri (cran-uri "NBPSeq" version)) | |
2045 | (sha256 | |
2046 | (base32 | |
2047 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) | |
2048 | (properties `((upstream-name . "NBPSeq"))) | |
2049 | (build-system r-build-system) | |
2050 | (propagated-inputs | |
2051 | `(("r-qvalue" ,r-qvalue))) | |
2052 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") | |
2053 | (synopsis "Negative binomial models for RNA-Seq data") | |
2054 | (description | |
2055 | "This package provides negative binomial models for two-group comparisons | |
2056 | and regression inferences from RNA-sequencing data.") | |
2057 | (license license:gpl2))) | |
3087a2f3 RW |
2058 | |
2059 | (define-public r-ebseq | |
2060 | (package | |
2061 | (name "r-ebseq") | |
4a3c47e9 | 2062 | (version "1.24.0") |
3087a2f3 RW |
2063 | (source |
2064 | (origin | |
2065 | (method url-fetch) | |
2066 | (uri (bioconductor-uri "EBSeq" version)) | |
2067 | (sha256 | |
2068 | (base32 | |
4a3c47e9 | 2069 | "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83")))) |
3087a2f3 RW |
2070 | (properties `((upstream-name . "EBSeq"))) |
2071 | (build-system r-build-system) | |
2072 | (propagated-inputs | |
2073 | `(("r-blockmodeling" ,r-blockmodeling) | |
2074 | ("r-gplots" ,r-gplots) | |
2075 | ("r-testthat" ,r-testthat))) | |
2076 | (home-page "https://bioconductor.org/packages/EBSeq") | |
2077 | (synopsis "Differential expression analysis of RNA-seq data") | |
2078 | (description | |
2079 | "This package provides tools for differential expression analysis at both | |
2080 | gene and isoform level using RNA-seq data") | |
2081 | (license license:artistic2.0))) | |
2cb71d81 RW |
2082 | |
2083 | (define-public r-lpsymphony | |
2084 | (package | |
2085 | (name "r-lpsymphony") | |
61c79d55 | 2086 | (version "1.12.0") |
2cb71d81 RW |
2087 | (source |
2088 | (origin | |
2089 | (method url-fetch) | |
2090 | (uri (bioconductor-uri "lpsymphony" version)) | |
2091 | (sha256 | |
2092 | (base32 | |
61c79d55 | 2093 | "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv")))) |
2cb71d81 RW |
2094 | (build-system r-build-system) |
2095 | (inputs | |
2096 | `(("gfortran" ,gfortran) | |
2097 | ("zlib" ,zlib))) | |
2098 | (native-inputs | |
2099 | `(("pkg-config" ,pkg-config))) | |
2100 | (home-page "http://r-forge.r-project.org/projects/rsymphony") | |
2101 | (synopsis "Symphony integer linear programming solver in R") | |
2102 | (description | |
2103 | "This package was derived from Rsymphony. The package provides an R | |
2104 | interface to SYMPHONY, a linear programming solver written in C++. The main | |
2105 | difference between this package and Rsymphony is that it includes the solver | |
2106 | source code, while Rsymphony expects to find header and library files on the | |
2107 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy | |
2108 | to install interface to SYMPHONY.") | |
2109 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. | |
2110 | ;; lpsimphony is released under the same terms. | |
2111 | (license license:epl1.0))) | |
704de8f5 RW |
2112 | |
2113 | (define-public r-ihw | |
2114 | (package | |
2115 | (name "r-ihw") | |
bcd8b7a9 | 2116 | (version "1.12.0") |
704de8f5 RW |
2117 | (source |
2118 | (origin | |
2119 | (method url-fetch) | |
2120 | (uri (bioconductor-uri "IHW" version)) | |
2121 | (sha256 | |
2122 | (base32 | |
bcd8b7a9 | 2123 | "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz")))) |
704de8f5 RW |
2124 | (properties `((upstream-name . "IHW"))) |
2125 | (build-system r-build-system) | |
2126 | (propagated-inputs | |
2127 | `(("r-biocgenerics" ,r-biocgenerics) | |
2128 | ("r-fdrtool" ,r-fdrtool) | |
2129 | ("r-lpsymphony" ,r-lpsymphony) | |
2130 | ("r-slam" ,r-slam))) | |
2131 | (home-page "https://bioconductor.org/packages/IHW") | |
2132 | (synopsis "Independent hypothesis weighting") | |
2133 | (description | |
2134 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing | |
2135 | procedure that increases power compared to the method of Benjamini and | |
2136 | Hochberg by assigning data-driven weights to each hypothesis. The input to | |
2137 | IHW is a two-column table of p-values and covariates. The covariate can be | |
2138 | any continuous-valued or categorical variable that is thought to be | |
2139 | informative on the statistical properties of each hypothesis test, while it is | |
2140 | independent of the p-value under the null hypothesis.") | |
2141 | (license license:artistic2.0))) | |
251e0830 RW |
2142 | |
2143 | (define-public r-icobra | |
2144 | (package | |
2145 | (name "r-icobra") | |
13b49976 | 2146 | (version "1.12.1") |
251e0830 RW |
2147 | (source |
2148 | (origin | |
2149 | (method url-fetch) | |
2150 | (uri (bioconductor-uri "iCOBRA" version)) | |
2151 | (sha256 | |
2152 | (base32 | |
13b49976 | 2153 | "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q")))) |
251e0830 RW |
2154 | (properties `((upstream-name . "iCOBRA"))) |
2155 | (build-system r-build-system) | |
2156 | (propagated-inputs | |
2157 | `(("r-dplyr" ,r-dplyr) | |
2158 | ("r-dt" ,r-dt) | |
2159 | ("r-ggplot2" ,r-ggplot2) | |
2160 | ("r-limma" ,r-limma) | |
2161 | ("r-reshape2" ,r-reshape2) | |
2162 | ("r-rocr" ,r-rocr) | |
2163 | ("r-scales" ,r-scales) | |
2164 | ("r-shiny" ,r-shiny) | |
2165 | ("r-shinybs" ,r-shinybs) | |
2166 | ("r-shinydashboard" ,r-shinydashboard) | |
2167 | ("r-upsetr" ,r-upsetr))) | |
2168 | (home-page "https://bioconductor.org/packages/iCOBRA") | |
2169 | (synopsis "Comparison and visualization of ranking and assignment methods") | |
2170 | (description | |
2171 | "This package provides functions for calculation and visualization of | |
2172 | performance metrics for evaluation of ranking and binary | |
2173 | classification (assignment) methods. It also contains a Shiny application for | |
2174 | interactive exploration of results.") | |
2175 | (license license:gpl2+))) | |
925fcdbb RW |
2176 | |
2177 | (define-public r-mast | |
2178 | (package | |
2179 | (name "r-mast") | |
a0ff725d | 2180 | (version "1.10.0") |
925fcdbb RW |
2181 | (source |
2182 | (origin | |
2183 | (method url-fetch) | |
2184 | (uri (bioconductor-uri "MAST" version)) | |
2185 | (sha256 | |
2186 | (base32 | |
a0ff725d | 2187 | "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx")))) |
925fcdbb RW |
2188 | (properties `((upstream-name . "MAST"))) |
2189 | (build-system r-build-system) | |
2190 | (propagated-inputs | |
2191 | `(("r-abind" ,r-abind) | |
a0ff725d | 2192 | ("r-blme" ,r-blme) |
925fcdbb RW |
2193 | ("r-biobase" ,r-biobase) |
2194 | ("r-biocgenerics" ,r-biocgenerics) | |
2195 | ("r-data-table" ,r-data-table) | |
2196 | ("r-ggplot2" ,r-ggplot2) | |
2197 | ("r-plyr" ,r-plyr) | |
2198 | ("r-progress" ,r-progress) | |
2199 | ("r-reshape2" ,r-reshape2) | |
2200 | ("r-s4vectors" ,r-s4vectors) | |
2201 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2202 | ("r-stringr" ,r-stringr) | |
2203 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2204 | (home-page "https://github.com/RGLab/MAST/") | |
2205 | (synopsis "Model-based analysis of single cell transcriptomics") | |
2206 | (description | |
2207 | "This package provides methods and models for handling zero-inflated | |
2208 | single cell assay data.") | |
2209 | (license license:gpl2+))) | |
2d7627cf RW |
2210 | |
2211 | (define-public r-monocle | |
2212 | (package | |
2213 | (name "r-monocle") | |
78b63267 | 2214 | (version "2.12.0") |
2d7627cf RW |
2215 | (source |
2216 | (origin | |
2217 | (method url-fetch) | |
2218 | (uri (bioconductor-uri "monocle" version)) | |
2219 | (sha256 | |
2220 | (base32 | |
78b63267 | 2221 | "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z")))) |
2d7627cf RW |
2222 | (build-system r-build-system) |
2223 | (propagated-inputs | |
2224 | `(("r-biobase" ,r-biobase) | |
2225 | ("r-biocgenerics" ,r-biocgenerics) | |
2226 | ("r-biocviews" ,r-biocviews) | |
2227 | ("r-cluster" ,r-cluster) | |
2228 | ("r-combinat" ,r-combinat) | |
2229 | ("r-ddrtree" ,r-ddrtree) | |
2230 | ("r-densityclust" ,r-densityclust) | |
2231 | ("r-dplyr" ,r-dplyr) | |
2232 | ("r-fastica" ,r-fastica) | |
2233 | ("r-ggplot2" ,r-ggplot2) | |
2234 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) | |
2235 | ("r-igraph" ,r-igraph) | |
2236 | ("r-irlba" ,r-irlba) | |
2237 | ("r-limma" ,r-limma) | |
2238 | ("r-mass" ,r-mass) | |
2239 | ("r-matrix" ,r-matrix) | |
2240 | ("r-matrixstats" ,r-matrixstats) | |
2241 | ("r-pheatmap" ,r-pheatmap) | |
2242 | ("r-plyr" ,r-plyr) | |
2243 | ("r-proxy" ,r-proxy) | |
2244 | ("r-qlcmatrix" ,r-qlcmatrix) | |
2245 | ("r-rann" ,r-rann) | |
2246 | ("r-rcpp" ,r-rcpp) | |
2247 | ("r-reshape2" ,r-reshape2) | |
2248 | ("r-rtsne" ,r-rtsne) | |
2249 | ("r-slam" ,r-slam) | |
2250 | ("r-stringr" ,r-stringr) | |
2251 | ("r-tibble" ,r-tibble) | |
2252 | ("r-vgam" ,r-vgam) | |
2253 | ("r-viridis" ,r-viridis))) | |
2254 | (home-page "https://bioconductor.org/packages/monocle") | |
2255 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") | |
2256 | (description | |
2257 | "Monocle performs differential expression and time-series analysis for | |
2258 | single-cell expression experiments. It orders individual cells according to | |
2259 | progress through a biological process, without knowing ahead of time which | |
2260 | genes define progress through that process. Monocle also performs | |
2261 | differential expression analysis, clustering, visualization, and other useful | |
2262 | tasks on single cell expression data. It is designed to work with RNA-Seq and | |
2263 | qPCR data, but could be used with other types as well.") | |
2264 | (license license:artistic2.0))) | |
6213e441 RW |
2265 | |
2266 | (define-public r-noiseq | |
2267 | (package | |
2268 | (name "r-noiseq") | |
6a2c58b7 | 2269 | (version "2.28.0") |
6213e441 RW |
2270 | (source |
2271 | (origin | |
2272 | (method url-fetch) | |
2273 | (uri (bioconductor-uri "NOISeq" version)) | |
2274 | (sha256 | |
2275 | (base32 | |
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6213e441 RW |
2277 | (properties `((upstream-name . "NOISeq"))) |
2278 | (build-system r-build-system) | |
2279 | (propagated-inputs | |
2280 | `(("r-biobase" ,r-biobase) | |
2281 | ("r-matrix" ,r-matrix))) | |
2282 | (home-page "https://bioconductor.org/packages/NOISeq") | |
2283 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") | |
2284 | (description | |
2285 | "This package provides tools to support the analysis of RNA-seq | |
2286 | expression data or other similar kind of data. It provides exploratory plots | |
2287 | to evaluate saturation, count distribution, expression per chromosome, type of | |
2288 | detected features, features length, etc. It also supports the analysis of | |
2289 | differential expression between two experimental conditions with no parametric | |
2290 | assumptions.") | |
2291 | (license license:artistic2.0))) | |
b409c357 RW |
2292 | |
2293 | (define-public r-scdd | |
2294 | (package | |
2295 | (name "r-scdd") | |
7baa59ed | 2296 | (version "1.8.0") |
b409c357 RW |
2297 | (source |
2298 | (origin | |
2299 | (method url-fetch) | |
2300 | (uri (bioconductor-uri "scDD" version)) | |
2301 | (sha256 | |
2302 | (base32 | |
7baa59ed | 2303 | "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf")))) |
b409c357 RW |
2304 | (properties `((upstream-name . "scDD"))) |
2305 | (build-system r-build-system) | |
2306 | (propagated-inputs | |
2307 | `(("r-arm" ,r-arm) | |
2308 | ("r-biocparallel" ,r-biocparallel) | |
2309 | ("r-ebseq" ,r-ebseq) | |
2310 | ("r-fields" ,r-fields) | |
2311 | ("r-ggplot2" ,r-ggplot2) | |
2312 | ("r-mclust" ,r-mclust) | |
2313 | ("r-outliers" ,r-outliers) | |
2314 | ("r-s4vectors" ,r-s4vectors) | |
2315 | ("r-scran" ,r-scran) | |
2316 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2317 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2318 | (home-page "https://github.com/kdkorthauer/scDD") | |
2319 | (synopsis "Mixture modeling of single-cell RNA-seq data") | |
2320 | (description | |
2321 | "This package implements a method to analyze single-cell RNA-seq data | |
2322 | utilizing flexible Dirichlet Process mixture models. Genes with differential | |
2323 | distributions of expression are classified into several interesting patterns | |
2324 | of differences between two conditions. The package also includes functions | |
2325 | for simulating data with these patterns from negative binomial | |
2326 | distributions.") | |
2327 | (license license:gpl2))) | |
f0887757 RW |
2328 | |
2329 | (define-public r-scone | |
2330 | (package | |
2331 | (name "r-scone") | |
26c72fff | 2332 | (version "1.8.0") |
f0887757 RW |
2333 | (source |
2334 | (origin | |
2335 | (method url-fetch) | |
2336 | (uri (bioconductor-uri "scone" version)) | |
2337 | (sha256 | |
2338 | (base32 | |
26c72fff | 2339 | "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck")))) |
f0887757 RW |
2340 | (build-system r-build-system) |
2341 | (propagated-inputs | |
2342 | `(("r-aroma-light" ,r-aroma-light) | |
2343 | ("r-biocparallel" ,r-biocparallel) | |
2344 | ("r-boot" ,r-boot) | |
2345 | ("r-class" ,r-class) | |
2346 | ("r-cluster" ,r-cluster) | |
2347 | ("r-compositions" ,r-compositions) | |
2348 | ("r-diptest" ,r-diptest) | |
2349 | ("r-edger" ,r-edger) | |
2350 | ("r-fpc" ,r-fpc) | |
2351 | ("r-gplots" ,r-gplots) | |
2352 | ("r-hexbin" ,r-hexbin) | |
2353 | ("r-limma" ,r-limma) | |
2354 | ("r-matrixstats" ,r-matrixstats) | |
2355 | ("r-mixtools" ,r-mixtools) | |
2356 | ("r-rarpack" ,r-rarpack) | |
2357 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2358 | ("r-rhdf5" ,r-rhdf5) | |
2359 | ("r-ruvseq" ,r-ruvseq) | |
2360 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2361 | (home-page "https://bioconductor.org/packages/scone") | |
2362 | (synopsis "Single cell overview of normalized expression data") | |
2363 | (description | |
2364 | "SCONE is an R package for comparing and ranking the performance of | |
2365 | different normalization schemes for single-cell RNA-seq and other | |
2366 | high-throughput analyses.") | |
2367 | (license license:artistic2.0))) | |
f9201d67 RW |
2368 | |
2369 | (define-public r-geoquery | |
2370 | (package | |
2371 | (name "r-geoquery") | |
2d443087 | 2372 | (version "2.52.0") |
f9201d67 RW |
2373 | (source |
2374 | (origin | |
2375 | (method url-fetch) | |
2376 | (uri (bioconductor-uri "GEOquery" version)) | |
2377 | (sha256 | |
2378 | (base32 | |
2d443087 | 2379 | "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr")))) |
f9201d67 RW |
2380 | (properties `((upstream-name . "GEOquery"))) |
2381 | (build-system r-build-system) | |
2382 | (propagated-inputs | |
2383 | `(("r-biobase" ,r-biobase) | |
2384 | ("r-dplyr" ,r-dplyr) | |
2385 | ("r-httr" ,r-httr) | |
2386 | ("r-limma" ,r-limma) | |
2387 | ("r-magrittr" ,r-magrittr) | |
2388 | ("r-readr" ,r-readr) | |
2389 | ("r-tidyr" ,r-tidyr) | |
2390 | ("r-xml2" ,r-xml2))) | |
2391 | (home-page "https://github.com/seandavi/GEOquery/") | |
2392 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") | |
2393 | (description | |
2394 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of | |
2395 | microarray data. Given the rich and varied nature of this resource, it is | |
2396 | only natural to want to apply BioConductor tools to these data. GEOquery is | |
2397 | the bridge between GEO and BioConductor.") | |
2398 | (license license:gpl2))) | |
eed6ff03 RW |
2399 | |
2400 | (define-public r-illuminaio | |
2401 | (package | |
2402 | (name "r-illuminaio") | |
fadc6db8 | 2403 | (version "0.26.0") |
eed6ff03 RW |
2404 | (source |
2405 | (origin | |
2406 | (method url-fetch) | |
2407 | (uri (bioconductor-uri "illuminaio" version)) | |
2408 | (sha256 | |
2409 | (base32 | |
fadc6db8 | 2410 | "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8")))) |
eed6ff03 RW |
2411 | (build-system r-build-system) |
2412 | (propagated-inputs | |
2413 | `(("r-base64" ,r-base64))) | |
2414 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") | |
2415 | (synopsis "Parse Illumina microarray output files") | |
2416 | (description | |
2417 | "This package provides tools for parsing Illumina's microarray output | |
2418 | files, including IDAT.") | |
2419 | (license license:gpl2))) | |
f4eac096 RW |
2420 | |
2421 | (define-public r-siggenes | |
2422 | (package | |
2423 | (name "r-siggenes") | |
409f4dd6 | 2424 | (version "1.58.0") |
f4eac096 RW |
2425 | (source |
2426 | (origin | |
2427 | (method url-fetch) | |
2428 | (uri (bioconductor-uri "siggenes" version)) | |
2429 | (sha256 | |
2430 | (base32 | |
409f4dd6 | 2431 | "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib")))) |
f4eac096 RW |
2432 | (build-system r-build-system) |
2433 | (propagated-inputs | |
2434 | `(("r-biobase" ,r-biobase) | |
409f4dd6 RW |
2435 | ("r-multtest" ,r-multtest) |
2436 | ("r-scrime" ,r-scrime))) | |
f4eac096 RW |
2437 | (home-page "https://bioconductor.org/packages/siggenes/") |
2438 | (synopsis | |
2439 | "Multiple testing using SAM and Efron's empirical Bayes approaches") | |
2440 | (description | |
2441 | "This package provides tools for the identification of differentially | |
2442 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using | |
2443 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical | |
2444 | Bayes Analyses of Microarrays} (EBAM).") | |
2445 | (license license:lgpl2.0+))) | |
34a24f95 RW |
2446 | |
2447 | (define-public r-bumphunter | |
2448 | (package | |
2449 | (name "r-bumphunter") | |
693a9805 | 2450 | (version "1.26.0") |
34a24f95 RW |
2451 | (source |
2452 | (origin | |
2453 | (method url-fetch) | |
2454 | (uri (bioconductor-uri "bumphunter" version)) | |
2455 | (sha256 | |
2456 | (base32 | |
693a9805 | 2457 | "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx")))) |
34a24f95 RW |
2458 | (build-system r-build-system) |
2459 | (propagated-inputs | |
2460 | `(("r-annotationdbi" ,r-annotationdbi) | |
2461 | ("r-biocgenerics" ,r-biocgenerics) | |
2462 | ("r-dorng" ,r-dorng) | |
2463 | ("r-foreach" ,r-foreach) | |
2464 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2465 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2466 | ("r-genomicranges" ,r-genomicranges) | |
2467 | ("r-iranges" ,r-iranges) | |
2468 | ("r-iterators" ,r-iterators) | |
2469 | ("r-limma" ,r-limma) | |
2470 | ("r-locfit" ,r-locfit) | |
2471 | ("r-matrixstats" ,r-matrixstats) | |
2472 | ("r-s4vectors" ,r-s4vectors))) | |
2473 | (home-page "https://github.com/ririzarr/bumphunter") | |
2474 | (synopsis "Find bumps in genomic data") | |
2475 | (description | |
2476 | "This package provides tools for finding bumps in genomic data in order | |
2477 | to identify differentially methylated regions in epigenetic epidemiology | |
2478 | studies.") | |
2479 | (license license:artistic2.0))) | |
0fbaf195 RW |
2480 | |
2481 | (define-public r-minfi | |
2482 | (package | |
2483 | (name "r-minfi") | |
8c0fae3c | 2484 | (version "1.30.0") |
0fbaf195 RW |
2485 | (source |
2486 | (origin | |
2487 | (method url-fetch) | |
2488 | (uri (bioconductor-uri "minfi" version)) | |
2489 | (sha256 | |
2490 | (base32 | |
8c0fae3c | 2491 | "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd")))) |
0fbaf195 RW |
2492 | (build-system r-build-system) |
2493 | (propagated-inputs | |
2494 | `(("r-beanplot" ,r-beanplot) | |
2495 | ("r-biobase" ,r-biobase) | |
2496 | ("r-biocgenerics" ,r-biocgenerics) | |
2497 | ("r-biocparallel" ,r-biocparallel) | |
2498 | ("r-biostrings" ,r-biostrings) | |
2499 | ("r-bumphunter" ,r-bumphunter) | |
2500 | ("r-data-table" ,r-data-table) | |
2501 | ("r-delayedarray" ,r-delayedarray) | |
2502 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
2503 | ("r-genefilter" ,r-genefilter) | |
2504 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2505 | ("r-genomicranges" ,r-genomicranges) | |
2506 | ("r-geoquery" ,r-geoquery) | |
2507 | ("r-hdf5array" ,r-hdf5array) | |
2508 | ("r-illuminaio" ,r-illuminaio) | |
2509 | ("r-iranges" ,r-iranges) | |
2510 | ("r-lattice" ,r-lattice) | |
2511 | ("r-limma" ,r-limma) | |
2512 | ("r-mass" ,r-mass) | |
2513 | ("r-mclust" ,r-mclust) | |
2514 | ("r-nlme" ,r-nlme) | |
2515 | ("r-nor1mix" ,r-nor1mix) | |
2516 | ("r-preprocesscore" ,r-preprocesscore) | |
2517 | ("r-quadprog" ,r-quadprog) | |
2518 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2519 | ("r-reshape" ,r-reshape) | |
2520 | ("r-s4vectors" ,r-s4vectors) | |
2521 | ("r-siggenes" ,r-siggenes) | |
2522 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2523 | (home-page "https://github.com/hansenlab/minfi") | |
2524 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") | |
2525 | (description | |
2526 | "This package provides tools to analyze and visualize Illumina Infinium | |
2527 | methylation arrays.") | |
2528 | (license license:artistic2.0))) | |
5ec5ba02 RW |
2529 | |
2530 | (define-public r-methylumi | |
2531 | (package | |
2532 | (name "r-methylumi") | |
2986b51f | 2533 | (version "2.30.0") |
5ec5ba02 RW |
2534 | (source |
2535 | (origin | |
2536 | (method url-fetch) | |
2537 | (uri (bioconductor-uri "methylumi" version)) | |
2538 | (sha256 | |
2539 | (base32 | |
2986b51f | 2540 | "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f")))) |
5ec5ba02 RW |
2541 | (build-system r-build-system) |
2542 | (propagated-inputs | |
2543 | `(("r-annotate" ,r-annotate) | |
2544 | ("r-annotationdbi" ,r-annotationdbi) | |
2545 | ("r-biobase" ,r-biobase) | |
2546 | ("r-biocgenerics" ,r-biocgenerics) | |
2547 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) | |
2548 | ("r-genefilter" ,r-genefilter) | |
2549 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2550 | ("r-genomicranges" ,r-genomicranges) | |
2551 | ("r-ggplot2" ,r-ggplot2) | |
2552 | ("r-illuminaio" ,r-illuminaio) | |
2553 | ("r-iranges" ,r-iranges) | |
2554 | ("r-lattice" ,r-lattice) | |
2555 | ("r-matrixstats" ,r-matrixstats) | |
2556 | ("r-minfi" ,r-minfi) | |
2557 | ("r-reshape2" ,r-reshape2) | |
2558 | ("r-s4vectors" ,r-s4vectors) | |
2559 | ("r-scales" ,r-scales) | |
2560 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2561 | (home-page "https://bioconductor.org/packages/methylumi") | |
2562 | (synopsis "Handle Illumina methylation data") | |
2563 | (description | |
2564 | "This package provides classes for holding and manipulating Illumina | |
2565 | methylation data. Based on eSet, it can contain MIAME information, sample | |
2566 | information, feature information, and multiple matrices of data. An | |
2567 | \"intelligent\" import function, methylumiR can read the Illumina text files | |
2568 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from | |
2569 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, | |
2570 | background correction, and quality control features for GoldenGate, Infinium, | |
2571 | and Infinium HD arrays are also included.") | |
2572 | (license license:gpl2))) | |
09605cb2 RW |
2573 | |
2574 | (define-public r-lumi | |
2575 | (package | |
2576 | (name "r-lumi") | |
5551b07c | 2577 | (version "2.36.0") |
09605cb2 RW |
2578 | (source |
2579 | (origin | |
2580 | (method url-fetch) | |
2581 | (uri (bioconductor-uri "lumi" version)) | |
2582 | (sha256 | |
2583 | (base32 | |
5551b07c | 2584 | "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba")))) |
09605cb2 RW |
2585 | (build-system r-build-system) |
2586 | (propagated-inputs | |
2587 | `(("r-affy" ,r-affy) | |
2588 | ("r-annotate" ,r-annotate) | |
2589 | ("r-annotationdbi" ,r-annotationdbi) | |
2590 | ("r-biobase" ,r-biobase) | |
2591 | ("r-dbi" ,r-dbi) | |
2592 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2593 | ("r-genomicranges" ,r-genomicranges) | |
2594 | ("r-kernsmooth" ,r-kernsmooth) | |
2595 | ("r-lattice" ,r-lattice) | |
2596 | ("r-mass" ,r-mass) | |
2597 | ("r-methylumi" ,r-methylumi) | |
2598 | ("r-mgcv" ,r-mgcv) | |
2599 | ("r-nleqslv" ,r-nleqslv) | |
2600 | ("r-preprocesscore" ,r-preprocesscore) | |
2601 | ("r-rsqlite" ,r-rsqlite))) | |
2602 | (home-page "https://bioconductor.org/packages/lumi") | |
2603 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") | |
2604 | (description | |
2605 | "The lumi package provides an integrated solution for the Illumina | |
2606 | microarray data analysis. It includes functions of Illumina | |
2607 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific | |
2608 | variance stabilization, normalization and gene annotation at the probe level. | |
2609 | It also includes the functions of processing Illumina methylation microarrays, | |
2610 | especially Illumina Infinium methylation microarrays.") | |
2611 | (license license:lgpl2.0+))) | |
4291f36a RW |
2612 | |
2613 | (define-public r-linnorm | |
2614 | (package | |
2615 | (name "r-linnorm") | |
48c2a7eb | 2616 | (version "2.8.0") |
4291f36a RW |
2617 | (source |
2618 | (origin | |
2619 | (method url-fetch) | |
2620 | (uri (bioconductor-uri "Linnorm" version)) | |
2621 | (sha256 | |
2622 | (base32 | |
48c2a7eb | 2623 | "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5")))) |
4291f36a RW |
2624 | (properties `((upstream-name . "Linnorm"))) |
2625 | (build-system r-build-system) | |
2626 | (propagated-inputs | |
2627 | `(("r-amap" ,r-amap) | |
2628 | ("r-apcluster" ,r-apcluster) | |
2629 | ("r-ellipse" ,r-ellipse) | |
2630 | ("r-fastcluster" ,r-fastcluster) | |
2631 | ("r-fpc" ,r-fpc) | |
2632 | ("r-ggdendro" ,r-ggdendro) | |
2633 | ("r-ggplot2" ,r-ggplot2) | |
2634 | ("r-gmodels" ,r-gmodels) | |
2635 | ("r-igraph" ,r-igraph) | |
2636 | ("r-limma" ,r-limma) | |
2637 | ("r-mass" ,r-mass) | |
2638 | ("r-mclust" ,r-mclust) | |
2639 | ("r-rcpp" ,r-rcpp) | |
2640 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
2641 | ("r-rtsne" ,r-rtsne) | |
2642 | ("r-statmod" ,r-statmod) | |
2643 | ("r-vegan" ,r-vegan) | |
2644 | ("r-zoo" ,r-zoo))) | |
2645 | (home-page "http://www.jjwanglab.org/Linnorm/") | |
2646 | (synopsis "Linear model and normality based transformation method") | |
2647 | (description | |
2648 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq | |
2649 | count data or any large scale count data. It transforms such datasets for | |
2650 | parametric tests. In addition to the transformtion function (@code{Linnorm}), | |
2651 | the following pipelines are implemented: | |
2652 | ||
2653 | @enumerate | |
2654 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) | |
2655 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means | |
2656 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, | |
2657 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) | |
2658 | @item Differential expression analysis or differential peak detection using | |
2659 | limma (@code{Linnorm.limma}) | |
2660 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) | |
2661 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) | |
2662 | @item Stable gene selection for scRNA-seq data; for users without or who do | |
2663 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) | |
2664 | @item Data imputation (@code{Linnorm.DataImput}). | |
2665 | @end enumerate | |
2666 | ||
2667 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the | |
2668 | @code{RnaXSim} function is included for simulating RNA-seq data for the | |
2669 | evaluation of DEG analysis methods.") | |
2670 | (license license:expat))) | |
e4a17532 RW |
2671 | |
2672 | (define-public r-ioniser | |
2673 | (package | |
2674 | (name "r-ioniser") | |
2ee91179 | 2675 | (version "2.8.0") |
e4a17532 RW |
2676 | (source |
2677 | (origin | |
2678 | (method url-fetch) | |
2679 | (uri (bioconductor-uri "IONiseR" version)) | |
2680 | (sha256 | |
2681 | (base32 | |
2ee91179 | 2682 | "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y")))) |
e4a17532 RW |
2683 | (properties `((upstream-name . "IONiseR"))) |
2684 | (build-system r-build-system) | |
2685 | (propagated-inputs | |
2686 | `(("r-biocgenerics" ,r-biocgenerics) | |
2687 | ("r-biocparallel" ,r-biocparallel) | |
2688 | ("r-biostrings" ,r-biostrings) | |
2689 | ("r-bit64" ,r-bit64) | |
2690 | ("r-dplyr" ,r-dplyr) | |
2691 | ("r-ggplot2" ,r-ggplot2) | |
2692 | ("r-magrittr" ,r-magrittr) | |
2693 | ("r-rhdf5" ,r-rhdf5) | |
2694 | ("r-shortread" ,r-shortread) | |
2695 | ("r-stringr" ,r-stringr) | |
2696 | ("r-tibble" ,r-tibble) | |
2697 | ("r-tidyr" ,r-tidyr) | |
2698 | ("r-xvector" ,r-xvector))) | |
2699 | (home-page "https://bioconductor.org/packages/IONiseR/") | |
2700 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") | |
2701 | (description | |
2702 | "IONiseR provides tools for the quality assessment of Oxford Nanopore | |
2703 | MinION data. It extracts summary statistics from a set of fast5 files and can | |
2704 | be used either before or after base calling. In addition to standard | |
2705 | summaries of the read-types produced, it provides a number of plots for | |
2706 | visualising metrics relative to experiment run time or spatially over the | |
2707 | surface of a flowcell.") | |
2708 | (license license:expat))) | |
80eb01c7 RW |
2709 | |
2710 | ;; This is a CRAN package, but it depends on packages from Bioconductor. | |
2711 | (define-public r-gkmsvm | |
2712 | (package | |
2713 | (name "r-gkmsvm") | |
2714 | (version "0.79.0") | |
2715 | (source | |
2716 | (origin | |
2717 | (method url-fetch) | |
2718 | (uri (cran-uri "gkmSVM" version)) | |
2719 | (sha256 | |
2720 | (base32 | |
2721 | "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) | |
2722 | (properties `((upstream-name . "gkmSVM"))) | |
2723 | (build-system r-build-system) | |
2724 | (propagated-inputs | |
2725 | `(("r-biocgenerics" ,r-biocgenerics) | |
2726 | ("r-biostrings" ,r-biostrings) | |
2727 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2728 | ("r-genomicranges" ,r-genomicranges) | |
2729 | ("r-iranges" ,r-iranges) | |
2730 | ("r-kernlab" ,r-kernlab) | |
2731 | ("r-rcpp" ,r-rcpp) | |
2732 | ("r-rocr" ,r-rocr) | |
2733 | ("r-rtracklayer" ,r-rtracklayer) | |
2734 | ("r-s4vectors" ,r-s4vectors) | |
2735 | ("r-seqinr" ,r-seqinr))) | |
2736 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") | |
2737 | (synopsis "Gapped-kmer support vector machine") | |
2738 | (description | |
2739 | "This R package provides tools for training gapped-kmer SVM classifiers | |
2740 | for DNA and protein sequences. This package supports several sequence | |
2741 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
2742 | (license license:gpl2+))) | |
8a5460b4 RW |
2743 | |
2744 | (define-public r-triform | |
2745 | (package | |
2746 | (name "r-triform") | |
bc083eca | 2747 | (version "1.26.0") |
8a5460b4 RW |
2748 | (source |
2749 | (origin | |
2750 | (method url-fetch) | |
2751 | (uri (bioconductor-uri "triform" version)) | |
2752 | (sha256 | |
2753 | (base32 | |
bc083eca | 2754 | "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya")))) |
8a5460b4 RW |
2755 | (build-system r-build-system) |
2756 | (propagated-inputs | |
2757 | `(("r-biocgenerics" ,r-biocgenerics) | |
2758 | ("r-iranges" ,r-iranges) | |
2759 | ("r-yaml" ,r-yaml))) | |
2760 | (home-page "https://bioconductor.org/packages/triform/") | |
2761 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") | |
2762 | (description | |
2763 | "The Triform algorithm uses model-free statistics to identify peak-like | |
2764 | distributions of TF ChIP sequencing reads, taking advantage of an improved | |
2765 | peak definition in combination with known profile characteristics.") | |
2766 | (license license:gpl2))) | |
c538bcdd RW |
2767 | |
2768 | (define-public r-varianttools | |
2769 | (package | |
2770 | (name "r-varianttools") | |
c2effded | 2771 | (version "1.26.0") |
c538bcdd RW |
2772 | (source |
2773 | (origin | |
2774 | (method url-fetch) | |
2775 | (uri (bioconductor-uri "VariantTools" version)) | |
2776 | (sha256 | |
2777 | (base32 | |
c2effded | 2778 | "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql")))) |
c538bcdd RW |
2779 | (properties `((upstream-name . "VariantTools"))) |
2780 | (build-system r-build-system) | |
2781 | (propagated-inputs | |
2782 | `(("r-biobase" ,r-biobase) | |
2783 | ("r-biocgenerics" ,r-biocgenerics) | |
2784 | ("r-biocparallel" ,r-biocparallel) | |
2785 | ("r-biostrings" ,r-biostrings) | |
2786 | ("r-bsgenome" ,r-bsgenome) | |
2787 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2788 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2789 | ("r-genomicranges" ,r-genomicranges) | |
2790 | ("r-iranges" ,r-iranges) | |
2791 | ("r-matrix" ,r-matrix) | |
2792 | ("r-rsamtools" ,r-rsamtools) | |
2793 | ("r-rtracklayer" ,r-rtracklayer) | |
2794 | ("r-s4vectors" ,r-s4vectors) | |
2795 | ("r-variantannotation" ,r-variantannotation))) | |
2796 | (home-page "https://bioconductor.org/packages/VariantTools/") | |
2797 | (synopsis "Tools for exploratory analysis of variant calls") | |
2798 | (description | |
2799 | "Explore, diagnose, and compare variant calls using filters. The | |
2800 | VariantTools package supports a workflow for loading data, calling single | |
2801 | sample variants and tumor-specific somatic mutations or other sample-specific | |
2802 | variant types (e.g., RNA editing). Most of the functions operate on | |
2803 | alignments (BAM files) or datasets of called variants. The user is expected | |
2804 | to have already aligned the reads with a separate tool, e.g., GSNAP via | |
2805 | gmapR.") | |
2806 | (license license:artistic2.0))) | |
3e41919d RW |
2807 | |
2808 | (define-public r-heatplus | |
2809 | (package | |
2810 | (name "r-heatplus") | |
376d1fe7 | 2811 | (version "2.30.0") |
3e41919d RW |
2812 | (source |
2813 | (origin | |
2814 | (method url-fetch) | |
2815 | (uri (bioconductor-uri "Heatplus" version)) | |
2816 | (sha256 | |
2817 | (base32 | |
376d1fe7 | 2818 | "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6")))) |
3e41919d RW |
2819 | (properties `((upstream-name . "Heatplus"))) |
2820 | (build-system r-build-system) | |
2821 | (propagated-inputs | |
2822 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) | |
2823 | (home-page "https://github.com/alexploner/Heatplus") | |
2824 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") | |
2825 | (description | |
2826 | "This package provides tools to display a rectangular heatmap (intensity | |
2827 | plot) of a data matrix. By default, both samples (columns) and features (row) | |
2828 | of the matrix are sorted according to a hierarchical clustering, and the | |
2829 | corresponding dendrogram is plotted. Optionally, panels with additional | |
2830 | information about samples and features can be added to the plot.") | |
2831 | (license license:gpl2+))) | |
c04f230e RW |
2832 | |
2833 | (define-public r-gosemsim | |
2834 | (package | |
2835 | (name "r-gosemsim") | |
24cf7bad | 2836 | (version "2.10.0") |
c04f230e RW |
2837 | (source |
2838 | (origin | |
2839 | (method url-fetch) | |
2840 | (uri (bioconductor-uri "GOSemSim" version)) | |
2841 | (sha256 | |
2842 | (base32 | |
24cf7bad | 2843 | "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg")))) |
c04f230e RW |
2844 | (properties `((upstream-name . "GOSemSim"))) |
2845 | (build-system r-build-system) | |
2846 | (propagated-inputs | |
2847 | `(("r-annotationdbi" ,r-annotationdbi) | |
2848 | ("r-go-db" ,r-go-db) | |
2849 | ("r-rcpp" ,r-rcpp))) | |
2850 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") | |
2851 | (synopsis "GO-terms semantic similarity measures") | |
2852 | (description | |
2853 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide | |
2854 | quantitative ways to compute similarities between genes and gene groups, and | |
2855 | have became important basis for many bioinformatics analysis approaches. | |
2856 | GOSemSim is an R package for semantic similarity computation among GO terms, | |
2857 | sets of GO terms, gene products and gene clusters.") | |
2858 | (license license:artistic2.0))) | |
9d0f7942 RW |
2859 | |
2860 | (define-public r-anota | |
2861 | (package | |
2862 | (name "r-anota") | |
0a41b5db | 2863 | (version "1.32.0") |
9d0f7942 RW |
2864 | (source |
2865 | (origin | |
2866 | (method url-fetch) | |
2867 | (uri (bioconductor-uri "anota" version)) | |
2868 | (sha256 | |
2869 | (base32 | |
0a41b5db | 2870 | "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c")))) |
9d0f7942 RW |
2871 | (build-system r-build-system) |
2872 | (propagated-inputs | |
2873 | `(("r-multtest" ,r-multtest) | |
2874 | ("r-qvalue" ,r-qvalue))) | |
2875 | (home-page "https://bioconductor.org/packages/anota/") | |
2876 | (synopsis "Analysis of translational activity") | |
2877 | (description | |
2878 | "Genome wide studies of translational control is emerging as a tool to | |
0cea26bd | 2879 | study various biological conditions. The output from such analysis is both |
9d0f7942 RW |
2880 | the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively |
2881 | involved in translation (the actively translating mRNA level) for each mRNA. | |
2882 | The standard analysis of such data strives towards identifying differential | |
2883 | translational between two or more sample classes - i.e. differences in | |
2884 | actively translated mRNA levels that are independent of underlying differences | |
2885 | in cytosolic mRNA levels. This package allows for such analysis using partial | |
2886 | variances and the random variance model. As 10s of thousands of mRNAs are | |
4f664004 | 2887 | analyzed in parallel the library performs a number of tests to assure that |
9d0f7942 RW |
2888 | the data set is suitable for such analysis.") |
2889 | (license license:gpl3))) | |
a6d867fe RW |
2890 | |
2891 | (define-public r-sigpathway | |
2892 | (package | |
2893 | (name "r-sigpathway") | |
3e5ee6f6 | 2894 | (version "1.52.0") |
a6d867fe RW |
2895 | (source |
2896 | (origin | |
2897 | (method url-fetch) | |
2898 | (uri (bioconductor-uri "sigPathway" version)) | |
2899 | (sha256 | |
2900 | (base32 | |
3e5ee6f6 | 2901 | "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7")))) |
a6d867fe RW |
2902 | (properties `((upstream-name . "sigPathway"))) |
2903 | (build-system r-build-system) | |
2904 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") | |
2905 | (synopsis "Pathway analysis") | |
2906 | (description | |
2907 | "This package is used to conduct pathway analysis by calculating the NT_k | |
2908 | and NE_k statistics in a statistical framework for determining whether a | |
2909 | specified group of genes for a pathway has a coordinated association with a | |
2910 | phenotype of interest.") | |
2911 | (license license:gpl2))) | |
af26c7ae RW |
2912 | |
2913 | (define-public r-fgsea | |
2914 | (package | |
2915 | (name "r-fgsea") | |
ebffd24c | 2916 | (version "1.10.0") |
af26c7ae RW |
2917 | (source |
2918 | (origin | |
2919 | (method url-fetch) | |
2920 | (uri (bioconductor-uri "fgsea" version)) | |
2921 | (sha256 | |
2922 | (base32 | |
ebffd24c | 2923 | "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c")))) |
af26c7ae RW |
2924 | (build-system r-build-system) |
2925 | (propagated-inputs | |
ebffd24c RW |
2926 | `(("r-bh" ,r-bh) |
2927 | ("r-biocparallel" ,r-biocparallel) | |
af26c7ae RW |
2928 | ("r-data-table" ,r-data-table) |
2929 | ("r-fastmatch" ,r-fastmatch) | |
2930 | ("r-ggplot2" ,r-ggplot2) | |
2931 | ("r-gridextra" ,r-gridextra) | |
2932 | ("r-matrix" ,r-matrix) | |
2933 | ("r-rcpp" ,r-rcpp))) | |
2934 | (home-page "https://github.com/ctlab/fgsea/") | |
2935 | (synopsis "Fast gene set enrichment analysis") | |
2936 | (description | |
2937 | "The package implements an algorithm for fast gene set enrichment | |
2938 | analysis. Using the fast algorithm allows to make more permutations and get | |
2939 | more fine grained p-values, which allows to use accurate stantard approaches | |
2940 | to multiple hypothesis correction.") | |
2941 | (license license:expat))) | |
305050b5 RW |
2942 | |
2943 | (define-public r-dose | |
2944 | (package | |
2945 | (name "r-dose") | |
aff3ecbf | 2946 | (version "3.10.2") |
305050b5 RW |
2947 | (source |
2948 | (origin | |
2949 | (method url-fetch) | |
2950 | (uri (bioconductor-uri "DOSE" version)) | |
2951 | (sha256 | |
2952 | (base32 | |
aff3ecbf | 2953 | "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj")))) |
305050b5 RW |
2954 | (properties `((upstream-name . "DOSE"))) |
2955 | (build-system r-build-system) | |
2956 | (propagated-inputs | |
2957 | `(("r-annotationdbi" ,r-annotationdbi) | |
2958 | ("r-biocparallel" ,r-biocparallel) | |
2959 | ("r-do-db" ,r-do-db) | |
2960 | ("r-fgsea" ,r-fgsea) | |
2961 | ("r-ggplot2" ,r-ggplot2) | |
2962 | ("r-gosemsim" ,r-gosemsim) | |
2963 | ("r-qvalue" ,r-qvalue) | |
2964 | ("r-reshape2" ,r-reshape2) | |
2965 | ("r-s4vectors" ,r-s4vectors))) | |
2966 | (home-page "https://guangchuangyu.github.io/software/DOSE/") | |
2967 | (synopsis "Disease ontology semantic and enrichment analysis") | |
2968 | (description | |
2969 | "This package implements five methods proposed by Resnik, Schlicker, | |
2970 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among | |
2971 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses | |
2972 | including hypergeometric model and gene set enrichment analysis are also | |
2973 | implemented for discovering disease associations of high-throughput biological | |
2974 | data.") | |
2975 | (license license:artistic2.0))) | |
9c30cf65 RW |
2976 | |
2977 | (define-public r-enrichplot | |
2978 | (package | |
2979 | (name "r-enrichplot") | |
77d28d66 | 2980 | (version "1.4.0") |
9c30cf65 RW |
2981 | (source |
2982 | (origin | |
2983 | (method url-fetch) | |
2984 | (uri (bioconductor-uri "enrichplot" version)) | |
2985 | (sha256 | |
2986 | (base32 | |
77d28d66 | 2987 | "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h")))) |
9c30cf65 RW |
2988 | (build-system r-build-system) |
2989 | (propagated-inputs | |
2990 | `(("r-annotationdbi" ,r-annotationdbi) | |
2991 | ("r-cowplot" ,r-cowplot) | |
2992 | ("r-dose" ,r-dose) | |
2993 | ("r-europepmc" ,r-europepmc) | |
2994 | ("r-ggplot2" ,r-ggplot2) | |
2995 | ("r-ggplotify" ,r-ggplotify) | |
2996 | ("r-ggraph" ,r-ggraph) | |
2997 | ("r-ggridges" ,r-ggridges) | |
2998 | ("r-gosemsim" ,r-gosemsim) | |
2999 | ("r-gridextra" ,r-gridextra) | |
3000 | ("r-igraph" ,r-igraph) | |
3001 | ("r-purrr" ,r-purrr) | |
3002 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3003 | ("r-reshape2" ,r-reshape2) | |
3004 | ("r-upsetr" ,r-upsetr))) | |
3005 | (home-page "https://github.com/GuangchuangYu/enrichplot") | |
3006 | (synopsis "Visualization of functional enrichment result") | |
3007 | (description | |
3008 | "The enrichplot package implements several visualization methods for | |
3009 | interpreting functional enrichment results obtained from ORA or GSEA analyses. | |
3010 | All the visualization methods are developed based on ggplot2 graphics.") | |
3011 | (license license:artistic2.0))) | |
f8295ee6 RW |
3012 | |
3013 | (define-public r-clusterprofiler | |
3014 | (package | |
3015 | (name "r-clusterprofiler") | |
1a3e33be | 3016 | (version "3.12.0") |
f8295ee6 RW |
3017 | (source |
3018 | (origin | |
3019 | (method url-fetch) | |
3020 | (uri (bioconductor-uri "clusterProfiler" version)) | |
3021 | (sha256 | |
3022 | (base32 | |
1a3e33be | 3023 | "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq")))) |
f8295ee6 RW |
3024 | (properties |
3025 | `((upstream-name . "clusterProfiler"))) | |
3026 | (build-system r-build-system) | |
3027 | (propagated-inputs | |
3028 | `(("r-annotationdbi" ,r-annotationdbi) | |
3029 | ("r-dose" ,r-dose) | |
3030 | ("r-enrichplot" ,r-enrichplot) | |
3031 | ("r-ggplot2" ,r-ggplot2) | |
3032 | ("r-go-db" ,r-go-db) | |
3033 | ("r-gosemsim" ,r-gosemsim) | |
3034 | ("r-magrittr" ,r-magrittr) | |
3035 | ("r-plyr" ,r-plyr) | |
3036 | ("r-qvalue" ,r-qvalue) | |
3037 | ("r-rvcheck" ,r-rvcheck) | |
3038 | ("r-tidyr" ,r-tidyr))) | |
3039 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") | |
3040 | (synopsis "Analysis and visualization of functional profiles for gene clusters") | |
3041 | (description | |
3042 | "This package implements methods to analyze and visualize functional | |
3043 | profiles (GO and KEGG) of gene and gene clusters.") | |
3044 | (license license:artistic2.0))) | |
ce77562a RW |
3045 | |
3046 | (define-public r-mlinterfaces | |
3047 | (package | |
3048 | (name "r-mlinterfaces") | |
8265a111 | 3049 | (version "1.64.0") |
ce77562a RW |
3050 | (source |
3051 | (origin | |
3052 | (method url-fetch) | |
3053 | (uri (bioconductor-uri "MLInterfaces" version)) | |
3054 | (sha256 | |
3055 | (base32 | |
8265a111 | 3056 | "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j")))) |
ce77562a RW |
3057 | (properties `((upstream-name . "MLInterfaces"))) |
3058 | (build-system r-build-system) | |
3059 | (propagated-inputs | |
3060 | `(("r-annotate" ,r-annotate) | |
3061 | ("r-biobase" ,r-biobase) | |
3062 | ("r-biocgenerics" ,r-biocgenerics) | |
3063 | ("r-cluster" ,r-cluster) | |
3064 | ("r-fpc" ,r-fpc) | |
3065 | ("r-gbm" ,r-gbm) | |
3066 | ("r-gdata" ,r-gdata) | |
3067 | ("r-genefilter" ,r-genefilter) | |
3068 | ("r-ggvis" ,r-ggvis) | |
3069 | ("r-hwriter" ,r-hwriter) | |
3070 | ("r-mass" ,r-mass) | |
3071 | ("r-mlbench" ,r-mlbench) | |
3072 | ("r-pls" ,r-pls) | |
3073 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3074 | ("r-rda" ,r-rda) | |
3075 | ("r-rpart" ,r-rpart) | |
3076 | ("r-sfsmisc" ,r-sfsmisc) | |
3077 | ("r-shiny" ,r-shiny) | |
3078 | ("r-threejs" ,r-threejs))) | |
3079 | (home-page "https://bioconductor.org/packages/MLInterfaces/") | |
3080 | (synopsis "Interfaces to R machine learning procedures") | |
3081 | (description | |
3082 | "This package provides uniform interfaces to machine learning code for | |
3083 | data in R and Bioconductor containers.") | |
3084 | ;; Any version of the LGPL. | |
3085 | (license license:lgpl2.1+))) | |
a793e88c RW |
3086 | |
3087 | (define-public r-annaffy | |
3088 | (package | |
3089 | (name "r-annaffy") | |
8bef9df4 | 3090 | (version "1.56.0") |
a793e88c RW |
3091 | (source |
3092 | (origin | |
3093 | (method url-fetch) | |
3094 | (uri (bioconductor-uri "annaffy" version)) | |
3095 | (sha256 | |
3096 | (base32 | |
8bef9df4 | 3097 | "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9")))) |
a793e88c RW |
3098 | (build-system r-build-system) |
3099 | (arguments | |
3100 | `(#:phases | |
3101 | (modify-phases %standard-phases | |
3102 | (add-after 'unpack 'remove-reference-to-non-free-data | |
3103 | (lambda _ | |
3104 | (substitute* "DESCRIPTION" | |
3105 | ((", KEGG.db") "")) | |
3106 | #t))))) | |
3107 | (propagated-inputs | |
3108 | `(("r-annotationdbi" ,r-annotationdbi) | |
3109 | ("r-biobase" ,r-biobase) | |
3110 | ("r-dbi" ,r-dbi) | |
3111 | ("r-go-db" ,r-go-db))) | |
3112 | (home-page "https://bioconductor.org/packages/annaffy/") | |
3113 | (synopsis "Annotation tools for Affymetrix biological metadata") | |
3114 | (description | |
3115 | "This package provides functions for handling data from Bioconductor | |
3116 | Affymetrix annotation data packages. It produces compact HTML and text | |
3117 | reports including experimental data and URL links to many online databases. | |
3118 | It allows searching of biological metadata using various criteria.") | |
3119 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of | |
3120 | ;; the LGPL 2.1 is included. | |
3121 | (license license:lgpl2.1+))) | |
0ec0a5ec RW |
3122 | |
3123 | (define-public r-a4core | |
3124 | (package | |
3125 | (name "r-a4core") | |
b077e3db | 3126 | (version "1.32.0") |
0ec0a5ec RW |
3127 | (source |
3128 | (origin | |
3129 | (method url-fetch) | |
3130 | (uri (bioconductor-uri "a4Core" version)) | |
3131 | (sha256 | |
3132 | (base32 | |
b077e3db | 3133 | "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7")))) |
0ec0a5ec RW |
3134 | (properties `((upstream-name . "a4Core"))) |
3135 | (build-system r-build-system) | |
3136 | (propagated-inputs | |
3137 | `(("r-biobase" ,r-biobase) | |
3138 | ("r-glmnet" ,r-glmnet))) | |
3139 | (home-page "https://bioconductor.org/packages/a4Core") | |
3140 | (synopsis "Automated Affymetrix array analysis core package") | |
3141 | (description | |
3142 | "This is the core package for the automated analysis of Affymetrix | |
3143 | arrays.") | |
3144 | (license license:gpl3))) | |
9ae37581 RW |
3145 | |
3146 | (define-public r-a4classif | |
3147 | (package | |
3148 | (name "r-a4classif") | |
82de77da | 3149 | (version "1.32.0") |
9ae37581 RW |
3150 | (source |
3151 | (origin | |
3152 | (method url-fetch) | |
3153 | (uri (bioconductor-uri "a4Classif" version)) | |
3154 | (sha256 | |
3155 | (base32 | |
82de77da | 3156 | "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0")))) |
9ae37581 RW |
3157 | (properties `((upstream-name . "a4Classif"))) |
3158 | (build-system r-build-system) | |
3159 | (propagated-inputs | |
3160 | `(("r-a4core" ,r-a4core) | |
3161 | ("r-a4preproc" ,r-a4preproc) | |
3162 | ("r-glmnet" ,r-glmnet) | |
3163 | ("r-mlinterfaces" ,r-mlinterfaces) | |
3164 | ("r-pamr" ,r-pamr) | |
3165 | ("r-rocr" ,r-rocr) | |
3166 | ("r-varselrf" ,r-varselrf))) | |
3167 | (home-page "https://bioconductor.org/packages/a4Classif/") | |
3168 | (synopsis "Automated Affymetrix array analysis classification package") | |
3169 | (description | |
3170 | "This is the classification package for the automated analysis of | |
3171 | Affymetrix arrays.") | |
3172 | (license license:gpl3))) | |
b8d13e2c RW |
3173 | |
3174 | (define-public r-a4preproc | |
3175 | (package | |
3176 | (name "r-a4preproc") | |
0b609162 | 3177 | (version "1.32.0") |
b8d13e2c RW |
3178 | (source |
3179 | (origin | |
3180 | (method url-fetch) | |
3181 | (uri (bioconductor-uri "a4Preproc" version)) | |
3182 | (sha256 | |
3183 | (base32 | |
0b609162 | 3184 | "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr")))) |
b8d13e2c RW |
3185 | (properties `((upstream-name . "a4Preproc"))) |
3186 | (build-system r-build-system) | |
3187 | (propagated-inputs | |
3188 | `(("r-annotationdbi" ,r-annotationdbi))) | |
3189 | (home-page "https://bioconductor.org/packages/a4Preproc/") | |
3190 | (synopsis "Automated Affymetrix array analysis preprocessing package") | |
3191 | (description | |
3192 | "This is a package for the automated analysis of Affymetrix arrays. It | |
3193 | is used for preprocessing the arrays.") | |
3194 | (license license:gpl3))) | |
8e15f861 RW |
3195 | |
3196 | (define-public r-a4reporting | |
3197 | (package | |
3198 | (name "r-a4reporting") | |
e5a36543 | 3199 | (version "1.32.0") |
8e15f861 RW |
3200 | (source |
3201 | (origin | |
3202 | (method url-fetch) | |
3203 | (uri (bioconductor-uri "a4Reporting" version)) | |
3204 | (sha256 | |
3205 | (base32 | |
e5a36543 | 3206 | "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj")))) |
8e15f861 RW |
3207 | (properties `((upstream-name . "a4Reporting"))) |
3208 | (build-system r-build-system) | |
3209 | (propagated-inputs | |
3210 | `(("r-annaffy" ,r-annaffy) | |
3211 | ("r-xtable" ,r-xtable))) | |
3212 | (home-page "https://bioconductor.org/packages/a4Reporting/") | |
3213 | (synopsis "Automated Affymetrix array analysis reporting package") | |
3214 | (description | |
3215 | "This is a package for the automated analysis of Affymetrix arrays. It | |
3216 | provides reporting features.") | |
3217 | (license license:gpl3))) | |
dbfe3375 RW |
3218 | |
3219 | (define-public r-a4base | |
3220 | (package | |
3221 | (name "r-a4base") | |
ae1730ae | 3222 | (version "1.32.0") |
dbfe3375 RW |
3223 | (source |
3224 | (origin | |
3225 | (method url-fetch) | |
3226 | (uri (bioconductor-uri "a4Base" version)) | |
3227 | (sha256 | |
3228 | (base32 | |
ae1730ae | 3229 | "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1")))) |
dbfe3375 RW |
3230 | (properties `((upstream-name . "a4Base"))) |
3231 | (build-system r-build-system) | |
3232 | (propagated-inputs | |
3233 | `(("r-a4core" ,r-a4core) | |
3234 | ("r-a4preproc" ,r-a4preproc) | |
3235 | ("r-annaffy" ,r-annaffy) | |
3236 | ("r-annotationdbi" ,r-annotationdbi) | |
3237 | ("r-biobase" ,r-biobase) | |
3238 | ("r-genefilter" ,r-genefilter) | |
3239 | ("r-glmnet" ,r-glmnet) | |
3240 | ("r-gplots" ,r-gplots) | |
3241 | ("r-limma" ,r-limma) | |
3242 | ("r-mpm" ,r-mpm) | |
3243 | ("r-multtest" ,r-multtest))) | |
3244 | (home-page "https://bioconductor.org/packages/a4Base/") | |
3245 | (synopsis "Automated Affymetrix array analysis base package") | |
3246 | (description | |
3247 | "This package provides basic features for the automated analysis of | |
3248 | Affymetrix arrays.") | |
3249 | (license license:gpl3))) | |
84ad024e RW |
3250 | |
3251 | (define-public r-a4 | |
3252 | (package | |
3253 | (name "r-a4") | |
1aadddea | 3254 | (version "1.32.0") |
84ad024e RW |
3255 | (source |
3256 | (origin | |
3257 | (method url-fetch) | |
3258 | (uri (bioconductor-uri "a4" version)) | |
3259 | (sha256 | |
3260 | (base32 | |
1aadddea | 3261 | "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy")))) |
84ad024e RW |
3262 | (build-system r-build-system) |
3263 | (propagated-inputs | |
3264 | `(("r-a4base" ,r-a4base) | |
3265 | ("r-a4classif" ,r-a4classif) | |
3266 | ("r-a4core" ,r-a4core) | |
3267 | ("r-a4preproc" ,r-a4preproc) | |
3268 | ("r-a4reporting" ,r-a4reporting))) | |
3269 | (home-page "https://bioconductor.org/packages/a4/") | |
3270 | (synopsis "Automated Affymetrix array analysis umbrella package") | |
3271 | (description | |
3272 | "This package provides a software suite for the automated analysis of | |
3273 | Affymetrix arrays.") | |
3274 | (license license:gpl3))) | |
59d331f1 RW |
3275 | |
3276 | (define-public r-abseqr | |
3277 | (package | |
3278 | (name "r-abseqr") | |
b7ddf0f0 | 3279 | (version "1.2.0") |
59d331f1 RW |
3280 | (source |
3281 | (origin | |
3282 | (method url-fetch) | |
3283 | (uri (bioconductor-uri "abseqR" version)) | |
3284 | (sha256 | |
3285 | (base32 | |
b7ddf0f0 | 3286 | "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r")))) |
59d331f1 RW |
3287 | (properties `((upstream-name . "abseqR"))) |
3288 | (build-system r-build-system) | |
3289 | (inputs | |
3290 | `(("pandoc" ,ghc-pandoc))) | |
3291 | (propagated-inputs | |
3292 | `(("r-biocparallel" ,r-biocparallel) | |
3293 | ("r-biocstyle" ,r-biocstyle) | |
3294 | ("r-circlize" ,r-circlize) | |
3295 | ("r-flexdashboard" ,r-flexdashboard) | |
3296 | ("r-ggcorrplot" ,r-ggcorrplot) | |
3297 | ("r-ggdendro" ,r-ggdendro) | |
3298 | ("r-ggplot2" ,r-ggplot2) | |
3299 | ("r-gridextra" ,r-gridextra) | |
3300 | ("r-knitr" ,r-knitr) | |
3301 | ("r-plotly" ,r-plotly) | |
3302 | ("r-plyr" ,r-plyr) | |
3303 | ("r-png" ,r-png) | |
3304 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3305 | ("r-reshape2" ,r-reshape2) | |
3306 | ("r-rmarkdown" ,r-rmarkdown) | |
3307 | ("r-stringr" ,r-stringr) | |
3308 | ("r-vegan" ,r-vegan) | |
3309 | ("r-venndiagram" ,r-venndiagram))) | |
3310 | (home-page "https://github.com/malhamdoosh/abseqR") | |
3311 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") | |
3312 | (description | |
3313 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of | |
3314 | sequencing datasets generated from antibody libraries and abseqR is one of its | |
3315 | packages. AbseqR empowers the users of abseqPy with plotting and reporting | |
3316 | capabilities and allows them to generate interactive HTML reports for the | |
3317 | convenience of viewing and sharing with other researchers. Additionally, | |
3318 | abseqR extends abseqPy to compare multiple repertoire analyses and perform | |
3319 | further downstream analysis on its output.") | |
3320 | (license license:gpl3))) | |
41aab7d1 RW |
3321 | |
3322 | (define-public r-bacon | |
3323 | (package | |
3324 | (name "r-bacon") | |
e33c25ff | 3325 | (version "1.12.0") |
41aab7d1 RW |
3326 | (source |
3327 | (origin | |
3328 | (method url-fetch) | |
3329 | (uri (bioconductor-uri "bacon" version)) | |
3330 | (sha256 | |
3331 | (base32 | |
e33c25ff | 3332 | "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q")))) |
41aab7d1 RW |
3333 | (build-system r-build-system) |
3334 | (propagated-inputs | |
3335 | `(("r-biocparallel" ,r-biocparallel) | |
3336 | ("r-ellipse" ,r-ellipse) | |
3337 | ("r-ggplot2" ,r-ggplot2))) | |
3338 | (home-page "https://bioconductor.org/packages/bacon/") | |
3339 | (synopsis "Controlling bias and inflation in association studies") | |
3340 | (description | |
3341 | "Bacon can be used to remove inflation and bias often observed in | |
3342 | epigenome- and transcriptome-wide association studies. To this end bacon | |
3343 | constructs an empirical null distribution using a Gibbs Sampling algorithm by | |
3344 | fitting a three-component normal mixture on z-scores.") | |
3345 | (license license:gpl2+))) | |
051e8e1a RW |
3346 | |
3347 | (define-public r-rgadem | |
3348 | (package | |
3349 | (name "r-rgadem") | |
93f8a009 | 3350 | (version "2.32.0") |
051e8e1a RW |
3351 | (source |
3352 | (origin | |
3353 | (method url-fetch) | |
3354 | (uri (bioconductor-uri "rGADEM" version)) | |
3355 | (sha256 | |
3356 | (base32 | |
93f8a009 | 3357 | "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18")))) |
051e8e1a RW |
3358 | (properties `((upstream-name . "rGADEM"))) |
3359 | (build-system r-build-system) | |
3360 | (propagated-inputs | |
3361 | `(("r-biostrings" ,r-biostrings) | |
3362 | ("r-bsgenome" ,r-bsgenome) | |
3363 | ("r-iranges" ,r-iranges) | |
3364 | ("r-seqlogo" ,r-seqlogo))) | |
3365 | (home-page "https://bioconductor.org/packages/rGADEM/") | |
3366 | (synopsis "De novo sequence motif discovery") | |
3367 | (description | |
3368 | "rGADEM is an efficient de novo motif discovery tool for large-scale | |
3369 | genomic sequence data.") | |
3370 | (license license:artistic2.0))) | |
229f97c3 RW |
3371 | |
3372 | (define-public r-motiv | |
3373 | (package | |
3374 | (name "r-motiv") | |
f7a495b1 | 3375 | (version "1.40.0") |
229f97c3 RW |
3376 | (source |
3377 | (origin | |
3378 | (method url-fetch) | |
3379 | (uri (bioconductor-uri "MotIV" version)) | |
3380 | (sha256 | |
3381 | (base32 | |
f7a495b1 | 3382 | "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf")))) |
229f97c3 RW |
3383 | (properties `((upstream-name . "MotIV"))) |
3384 | (build-system r-build-system) | |
3385 | (inputs | |
3386 | `(("gsl" ,gsl))) | |
3387 | (propagated-inputs | |
3388 | `(("r-biocgenerics" ,r-biocgenerics) | |
3389 | ("r-biostrings" ,r-biostrings) | |
3390 | ("r-iranges" ,r-iranges) | |
3391 | ("r-lattice" ,r-lattice) | |
3392 | ("r-rgadem" ,r-rgadem) | |
3393 | ("r-s4vectors" ,r-s4vectors))) | |
3394 | (home-page "https://bioconductor.org/packages/MotIV/") | |
3395 | (synopsis "Motif identification and validation") | |
3396 | (description | |
3397 | "This package is used for the identification and validation of sequence | |
3398 | motifs. It makes use of STAMP for comparing a set of motifs to a given | |
3399 | database (e.g. JASPAR). It can also be used to visualize motifs, motif | |
3400 | distributions, modules and filter motifs.") | |
3401 | (license license:gpl2))) | |
2a72ef56 RW |
3402 | |
3403 | (define-public r-motifstack | |
3404 | (package | |
3405 | (name "r-motifstack") | |
aa0ebfd2 | 3406 | (version "1.28.0") |
2a72ef56 RW |
3407 | (source |
3408 | (origin | |
3409 | (method url-fetch) | |
3410 | (uri (bioconductor-uri "motifStack" version)) | |
3411 | (sha256 | |
3412 | (base32 | |
aa0ebfd2 | 3413 | "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f")))) |
2a72ef56 RW |
3414 | (properties `((upstream-name . "motifStack"))) |
3415 | (build-system r-build-system) | |
3416 | (propagated-inputs | |
3417 | `(("r-ade4" ,r-ade4) | |
3418 | ("r-biostrings" ,r-biostrings) | |
aa0ebfd2 | 3419 | ("r-grimport2" ,r-grimport2) |
2a72ef56 RW |
3420 | ("r-htmlwidgets" ,r-htmlwidgets) |
3421 | ("r-motiv" ,r-motiv) | |
3422 | ("r-scales" ,r-scales) | |
3423 | ("r-xml" ,r-xml))) | |
3424 | (home-page "https://bioconductor.org/packages/motifStack/") | |
3425 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") | |
3426 | (description | |
3427 | "The motifStack package is designed for graphic representation of | |
3428 | multiple motifs with different similarity scores. It works with both DNA/RNA | |
3429 | sequence motifs and amino acid sequence motifs. In addition, it provides the | |
3430 | flexibility for users to customize the graphic parameters such as the font | |
3431 | type and symbol colors.") | |
3432 | (license license:gpl2+))) | |
e5bff307 RW |
3433 | |
3434 | (define-public r-genomicscores | |
3435 | (package | |
3436 | (name "r-genomicscores") | |
3c944fda | 3437 | (version "1.8.1") |
e5bff307 RW |
3438 | (source |
3439 | (origin | |
3440 | (method url-fetch) | |
3441 | (uri (bioconductor-uri "GenomicScores" version)) | |
3442 | (sha256 | |
3443 | (base32 | |
3c944fda | 3444 | "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy")))) |
e5bff307 RW |
3445 | (properties `((upstream-name . "GenomicScores"))) |
3446 | (build-system r-build-system) | |
3447 | (propagated-inputs | |
3448 | `(("r-annotationhub" ,r-annotationhub) | |
3449 | ("r-biobase" ,r-biobase) | |
3450 | ("r-biocgenerics" ,r-biocgenerics) | |
3451 | ("r-biostrings" ,r-biostrings) | |
3452 | ("r-bsgenome" ,r-bsgenome) | |
3453 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3454 | ("r-genomicranges" ,r-genomicranges) | |
3455 | ("r-iranges" ,r-iranges) | |
3456 | ("r-s4vectors" ,r-s4vectors) | |
3457 | ("r-xml" ,r-xml))) | |
3458 | (home-page "https://github.com/rcastelo/GenomicScores/") | |
3459 | (synopsis "Work with genome-wide position-specific scores") | |
3460 | (description | |
3461 | "This package provides infrastructure to store and access genome-wide | |
3462 | position-specific scores within R and Bioconductor.") | |
3463 | (license license:artistic2.0))) | |
32e0f906 RW |
3464 | |
3465 | (define-public r-atacseqqc | |
3466 | (package | |
3467 | (name "r-atacseqqc") | |
e4519ee7 | 3468 | (version "1.8.1") |
32e0f906 RW |
3469 | (source |
3470 | (origin | |
3471 | (method url-fetch) | |
3472 | (uri (bioconductor-uri "ATACseqQC" version)) | |
3473 | (sha256 | |
3474 | (base32 | |
e4519ee7 | 3475 | "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69")))) |
32e0f906 RW |
3476 | (properties `((upstream-name . "ATACseqQC"))) |
3477 | (build-system r-build-system) | |
3478 | (propagated-inputs | |
3479 | `(("r-biocgenerics" ,r-biocgenerics) | |
3480 | ("r-biostrings" ,r-biostrings) | |
3481 | ("r-bsgenome" ,r-bsgenome) | |
3482 | ("r-chippeakanno" ,r-chippeakanno) | |
bcc233c1 | 3483 | ("r-edger" ,r-edger) |
32e0f906 RW |
3484 | ("r-genomeinfodb" ,r-genomeinfodb) |
3485 | ("r-genomicalignments" ,r-genomicalignments) | |
3486 | ("r-genomicranges" ,r-genomicranges) | |
3487 | ("r-genomicscores" ,r-genomicscores) | |
3488 | ("r-iranges" ,r-iranges) | |
3489 | ("r-kernsmooth" ,r-kernsmooth) | |
3490 | ("r-limma" ,r-limma) | |
3491 | ("r-motifstack" ,r-motifstack) | |
3492 | ("r-preseqr" ,r-preseqr) | |
3493 | ("r-randomforest" ,r-randomforest) | |
3494 | ("r-rsamtools" ,r-rsamtools) | |
3495 | ("r-rtracklayer" ,r-rtracklayer) | |
3496 | ("r-s4vectors" ,r-s4vectors))) | |
3497 | (home-page "https://bioconductor.org/packages/ATACseqQC/") | |
3498 | (synopsis "ATAC-seq quality control") | |
3499 | (description | |
3500 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using | |
3501 | sequencing, is a rapid and sensitive method for chromatin accessibility | |
3502 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq | |
3503 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly | |
3504 | assess whether their ATAC-seq experiment is successful. It includes | |
3505 | diagnostic plots of fragment size distribution, proportion of mitochondria | |
3506 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor | |
3507 | footprints.") | |
3508 | (license license:gpl2+))) | |
3972cfce RW |
3509 | |
3510 | (define-public r-gofuncr | |
3511 | (package | |
3512 | (name "r-gofuncr") | |
bab06a6f | 3513 | (version "1.4.0") |
3972cfce RW |
3514 | (source |
3515 | (origin | |
3516 | (method url-fetch) | |
3517 | (uri (bioconductor-uri "GOfuncR" version)) | |
3518 | (sha256 | |
3519 | (base32 | |
bab06a6f | 3520 | "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm")))) |
3972cfce RW |
3521 | (properties `((upstream-name . "GOfuncR"))) |
3522 | (build-system r-build-system) | |
3523 | (propagated-inputs | |
3524 | `(("r-annotationdbi" ,r-annotationdbi) | |
3525 | ("r-genomicranges" ,r-genomicranges) | |
3526 | ("r-gtools" ,r-gtools) | |
3527 | ("r-iranges" ,r-iranges) | |
3528 | ("r-mapplots" ,r-mapplots) | |
3529 | ("r-rcpp" ,r-rcpp) | |
3530 | ("r-vioplot" ,r-vioplot))) | |
3531 | (home-page "https://bioconductor.org/packages/GOfuncR/") | |
3532 | (synopsis "Gene ontology enrichment using FUNC") | |
3533 | (description | |
3534 | "GOfuncR performs a gene ontology enrichment analysis based on the | |
3535 | ontology enrichment software FUNC. GO-annotations are obtained from | |
3536 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is | |
3537 | included in the package and updated regularly. GOfuncR provides the standard | |
3538 | candidate vs background enrichment analysis using the hypergeometric test, as | |
3539 | well as three additional tests: | |
3540 | ||
3541 | @enumerate | |
3542 | @item the Wilcoxon rank-sum test that is used when genes are ranked, | |
3543 | @item a binomial test that is used when genes are associated with two counts, | |
3544 | and | |
3545 | @item a Chi-square or Fisher's exact test that is used in cases when genes are | |
3546 | associated with four counts. | |
3547 | @end enumerate | |
3548 | ||
3549 | To correct for multiple testing and interdependency of the tests, family-wise | |
3550 | error rates are computed based on random permutations of the gene-associated | |
3551 | variables. GOfuncR also provides tools for exploring the ontology graph and | |
3552 | the annotations, and options to take gene-length or spatial clustering of | |
3553 | genes into account. It is also possible to provide custom gene coordinates, | |
3554 | annotations and ontologies.") | |
3555 | (license license:gpl2+))) | |
9bf4bb19 RW |
3556 | |
3557 | (define-public r-abaenrichment | |
3558 | (package | |
3559 | (name "r-abaenrichment") | |
e2e1dea2 | 3560 | (version "1.14.0") |
9bf4bb19 RW |
3561 | (source |
3562 | (origin | |
3563 | (method url-fetch) | |
3564 | (uri (bioconductor-uri "ABAEnrichment" version)) | |
3565 | (sha256 | |
3566 | (base32 | |
e2e1dea2 | 3567 | "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2")))) |
9bf4bb19 RW |
3568 | (properties `((upstream-name . "ABAEnrichment"))) |
3569 | (build-system r-build-system) | |
3570 | (propagated-inputs | |
3571 | `(("r-abadata" ,r-abadata) | |
3572 | ("r-data-table" ,r-data-table) | |
3573 | ("r-gofuncr" ,r-gofuncr) | |
3574 | ("r-gplots" ,r-gplots) | |
3575 | ("r-gtools" ,r-gtools) | |
3576 | ("r-rcpp" ,r-rcpp))) | |
3577 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") | |
3578 | (synopsis "Gene expression enrichment in human brain regions") | |
3579 | (description | |
3580 | "The package ABAEnrichment is designed to test for enrichment of user | |
3581 | defined candidate genes in the set of expressed genes in different human brain | |
3582 | regions. The core function @code{aba_enrich} integrates the expression of the | |
3583 | candidate gene set (averaged across donors) and the structural information of | |
3584 | the brain using an ontology, both provided by the Allen Brain Atlas project.") | |
3585 | (license license:gpl2+))) | |
0b91b7b9 RW |
3586 | |
3587 | (define-public r-annotationfuncs | |
3588 | (package | |
3589 | (name "r-annotationfuncs") | |
69a2ec54 | 3590 | (version "1.34.0") |
0b91b7b9 RW |
3591 | (source |
3592 | (origin | |
3593 | (method url-fetch) | |
3594 | (uri (bioconductor-uri "AnnotationFuncs" version)) | |
3595 | (sha256 | |
3596 | (base32 | |
69a2ec54 | 3597 | "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3")))) |
0b91b7b9 RW |
3598 | (properties |
3599 | `((upstream-name . "AnnotationFuncs"))) | |
3600 | (build-system r-build-system) | |
3601 | (propagated-inputs | |
3602 | `(("r-annotationdbi" ,r-annotationdbi) | |
3603 | ("r-dbi" ,r-dbi))) | |
3604 | (home-page "https://www.iysik.com/r/annotationfuncs") | |
3605 | (synopsis "Annotation translation functions") | |
3606 | (description | |
3607 | "This package provides functions for handling translating between | |
3608 | different identifieres using the Biocore Data Team data-packages (e.g. | |
3609 | @code{org.Bt.eg.db}).") | |
3610 | (license license:gpl2))) | |
adf7d813 RW |
3611 | |
3612 | (define-public r-annotationtools | |
3613 | (package | |
3614 | (name "r-annotationtools") | |
ee1a45d7 | 3615 | (version "1.58.0") |
adf7d813 RW |
3616 | (source |
3617 | (origin | |
3618 | (method url-fetch) | |
3619 | (uri (bioconductor-uri "annotationTools" version)) | |
3620 | (sha256 | |
3621 | (base32 | |
ee1a45d7 | 3622 | "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1")))) |
adf7d813 RW |
3623 | (properties |
3624 | `((upstream-name . "annotationTools"))) | |
3625 | (build-system r-build-system) | |
3626 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
3627 | (home-page "https://bioconductor.org/packages/annotationTools/") | |
3628 | (synopsis "Annotate microarrays and perform gene expression analyses") | |
3629 | (description | |
3630 | "This package provides functions to annotate microarrays, find orthologs, | |
3631 | and integrate heterogeneous gene expression profiles using annotation and | |
3632 | other molecular biology information available as flat file database (plain | |
3633 | text files).") | |
3634 | ;; Any version of the GPL. | |
3635 | (license (list license:gpl2+)))) | |
f31e10f8 RW |
3636 | |
3637 | (define-public r-allelicimbalance | |
3638 | (package | |
3639 | (name "r-allelicimbalance") | |
9da2021f | 3640 | (version "1.22.0") |
f31e10f8 RW |
3641 | (source |
3642 | (origin | |
3643 | (method url-fetch) | |
3644 | (uri (bioconductor-uri "AllelicImbalance" version)) | |
3645 | (sha256 | |
3646 | (base32 | |
9da2021f | 3647 | "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng")))) |
f31e10f8 RW |
3648 | (properties |
3649 | `((upstream-name . "AllelicImbalance"))) | |
3650 | (build-system r-build-system) | |
3651 | (propagated-inputs | |
3652 | `(("r-annotationdbi" ,r-annotationdbi) | |
3653 | ("r-biocgenerics" ,r-biocgenerics) | |
3654 | ("r-biostrings" ,r-biostrings) | |
3655 | ("r-bsgenome" ,r-bsgenome) | |
3656 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3657 | ("r-genomicalignments" ,r-genomicalignments) | |
3658 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3659 | ("r-genomicranges" ,r-genomicranges) | |
3660 | ("r-gridextra" ,r-gridextra) | |
3661 | ("r-gviz" ,r-gviz) | |
3662 | ("r-iranges" ,r-iranges) | |
3663 | ("r-lattice" ,r-lattice) | |
3664 | ("r-latticeextra" ,r-latticeextra) | |
3665 | ("r-nlme" ,r-nlme) | |
3666 | ("r-rsamtools" ,r-rsamtools) | |
3667 | ("r-s4vectors" ,r-s4vectors) | |
3668 | ("r-seqinr" ,r-seqinr) | |
3669 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
3670 | ("r-variantannotation" ,r-variantannotation))) | |
3671 | (home-page "https://github.com/pappewaio/AllelicImbalance") | |
3672 | (synopsis "Investigate allele-specific expression") | |
3673 | (description | |
3674 | "This package provides a framework for allele-specific expression | |
3675 | investigation using RNA-seq data.") | |
3676 | (license license:gpl3))) | |
ffe7029b RW |
3677 | |
3678 | (define-public r-aucell | |
3679 | (package | |
3680 | (name "r-aucell") | |
61730c3d | 3681 | (version "1.6.1") |
ffe7029b RW |
3682 | (source |
3683 | (origin | |
3684 | (method url-fetch) | |
3685 | (uri (bioconductor-uri "AUCell" version)) | |
3686 | (sha256 | |
3687 | (base32 | |
61730c3d | 3688 | "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b")))) |
ffe7029b RW |
3689 | (properties `((upstream-name . "AUCell"))) |
3690 | (build-system r-build-system) | |
3691 | (propagated-inputs | |
3692 | `(("r-data-table" ,r-data-table) | |
3693 | ("r-gseabase" ,r-gseabase) | |
3694 | ("r-mixtools" ,r-mixtools) | |
3695 | ("r-r-utils" ,r-r-utils) | |
3696 | ("r-shiny" ,r-shiny) | |
3697 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
3698 | (home-page "https://bioconductor.org/packages/AUCell/") | |
3699 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") | |
3700 | (description | |
3701 | "AUCell allows to identify cells with active gene sets (e.g. signatures, | |
3702 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area | |
3703 | Under the Curve} (AUC) to calculate whether a critical subset of the input | |
3704 | gene set is enriched within the expressed genes for each cell. The | |
3705 | distribution of AUC scores across all the cells allows exploring the relative | |
3706 | expression of the signature. Since the scoring method is ranking-based, | |
3707 | AUCell is independent of the gene expression units and the normalization | |
3708 | procedure. In addition, since the cells are evaluated individually, it can | |
3709 | easily be applied to bigger datasets, subsetting the expression matrix if | |
3710 | needed.") | |
3711 | (license license:gpl3))) | |
5cfa4bff RW |
3712 | |
3713 | (define-public r-ebimage | |
3714 | (package | |
3715 | (name "r-ebimage") | |
2a6d8383 | 3716 | (version "4.26.0") |
5cfa4bff RW |
3717 | (source |
3718 | (origin | |
3719 | (method url-fetch) | |
3720 | (uri (bioconductor-uri "EBImage" version)) | |
3721 | (sha256 | |
3722 | (base32 | |
2a6d8383 | 3723 | "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq")))) |
5cfa4bff RW |
3724 | (properties `((upstream-name . "EBImage"))) |
3725 | (build-system r-build-system) | |
3726 | (propagated-inputs | |
3727 | `(("r-abind" ,r-abind) | |
3728 | ("r-biocgenerics" ,r-biocgenerics) | |
3729 | ("r-fftwtools" ,r-fftwtools) | |
3730 | ("r-htmltools" ,r-htmltools) | |
3731 | ("r-htmlwidgets" ,r-htmlwidgets) | |
3732 | ("r-jpeg" ,r-jpeg) | |
3733 | ("r-locfit" ,r-locfit) | |
3734 | ("r-png" ,r-png) | |
3735 | ("r-rcurl" ,r-rcurl) | |
3736 | ("r-tiff" ,r-tiff))) | |
3737 | (native-inputs | |
3738 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
3739 | (home-page "https://github.com/aoles/EBImage") | |
3740 | (synopsis "Image processing and analysis toolbox for R") | |
3741 | (description | |
3742 | "EBImage provides general purpose functionality for image processing and | |
3743 | analysis. In the context of (high-throughput) microscopy-based cellular | |
3744 | assays, EBImage offers tools to segment cells and extract quantitative | |
3745 | cellular descriptors. This allows the automation of such tasks using the R | |
3746 | programming language and facilitates the use of other tools in the R | |
3747 | environment for signal processing, statistical modeling, machine learning and | |
3748 | visualization with image data.") | |
3749 | ;; Any version of the LGPL. | |
3750 | (license license:lgpl2.1+))) | |
51e98f7e RW |
3751 | |
3752 | (define-public r-yamss | |
3753 | (package | |
3754 | (name "r-yamss") | |
1269a926 | 3755 | (version "1.10.0") |
51e98f7e RW |
3756 | (source |
3757 | (origin | |
3758 | (method url-fetch) | |
3759 | (uri (bioconductor-uri "yamss" version)) | |
3760 | (sha256 | |
3761 | (base32 | |
1269a926 | 3762 | "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23")))) |
51e98f7e RW |
3763 | (build-system r-build-system) |
3764 | (propagated-inputs | |
3765 | `(("r-biocgenerics" ,r-biocgenerics) | |
3766 | ("r-data-table" ,r-data-table) | |
3767 | ("r-ebimage" ,r-ebimage) | |
3768 | ("r-iranges" ,r-iranges) | |
3769 | ("r-limma" ,r-limma) | |
3770 | ("r-matrix" ,r-matrix) | |
3771 | ("r-mzr" ,r-mzr) | |
3772 | ("r-s4vectors" ,r-s4vectors) | |
3773 | ("r-summarizedexperiment" | |
3774 | ,r-summarizedexperiment))) | |
3775 | (home-page "https://github.com/hansenlab/yamss") | |
3776 | (synopsis "Tools for high-throughput metabolomics") | |
3777 | (description | |
3778 | "This package provides tools to analyze and visualize high-throughput | |
9b19734c | 3779 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
51e98f7e RW |
3780 | preprocess data in a way that enables reliable and powerful differential |
3781 | analysis.") | |
3782 | (license license:artistic2.0))) | |
398c4a93 RW |
3783 | |
3784 | (define-public r-gtrellis | |
3785 | (package | |
3786 | (name "r-gtrellis") | |
128c6d59 | 3787 | (version "1.16.0") |
398c4a93 RW |
3788 | (source |
3789 | (origin | |
3790 | (method url-fetch) | |
3791 | (uri (bioconductor-uri "gtrellis" version)) | |
3792 | (sha256 | |
3793 | (base32 | |
128c6d59 | 3794 | "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y")))) |
398c4a93 RW |
3795 | (build-system r-build-system) |
3796 | (propagated-inputs | |
3797 | `(("r-circlize" ,r-circlize) | |
3798 | ("r-genomicranges" ,r-genomicranges) | |
3799 | ("r-getoptlong" ,r-getoptlong) | |
3800 | ("r-iranges" ,r-iranges))) | |
3801 | (home-page "https://github.com/jokergoo/gtrellis") | |
3802 | (synopsis "Genome level Trellis layout") | |
3803 | (description | |
3804 | "Genome level Trellis graph visualizes genomic data conditioned by | |
3805 | genomic categories (e.g. chromosomes). For each genomic category, multiple | |
3806 | dimensional data which are represented as tracks describe different features | |
3807 | from different aspects. This package provides high flexibility to arrange | |
3808 | genomic categories and to add self-defined graphics in the plot.") | |
3809 | (license license:expat))) | |
28098414 RW |
3810 | |
3811 | (define-public r-somaticsignatures | |
3812 | (package | |
3813 | (name "r-somaticsignatures") | |
3cdc5d1a | 3814 | (version "2.20.0") |
28098414 RW |
3815 | (source |
3816 | (origin | |
3817 | (method url-fetch) | |
3818 | (uri (bioconductor-uri "SomaticSignatures" version)) | |
3819 | (sha256 | |
3820 | (base32 | |
3cdc5d1a | 3821 | "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx")))) |
28098414 RW |
3822 | (properties |
3823 | `((upstream-name . "SomaticSignatures"))) | |
3824 | (build-system r-build-system) | |
3825 | (propagated-inputs | |
3826 | `(("r-biobase" ,r-biobase) | |
3827 | ("r-biostrings" ,r-biostrings) | |
3828 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3829 | ("r-genomicranges" ,r-genomicranges) | |
3830 | ("r-ggbio" ,r-ggbio) | |
3831 | ("r-ggplot2" ,r-ggplot2) | |
3832 | ("r-iranges" ,r-iranges) | |
3833 | ("r-nmf" ,r-nmf) | |
3834 | ("r-pcamethods" ,r-pcamethods) | |
3835 | ("r-proxy" ,r-proxy) | |
3836 | ("r-reshape2" ,r-reshape2) | |
3837 | ("r-s4vectors" ,r-s4vectors) | |
3838 | ("r-variantannotation" ,r-variantannotation))) | |
3839 | (home-page "https://github.com/juliangehring/SomaticSignatures") | |
3840 | (synopsis "Somatic signatures") | |
3841 | (description | |
3842 | "This package identifies mutational signatures of @dfn{single nucleotide | |
3843 | variants} (SNVs). It provides a infrastructure related to the methodology | |
3844 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix | |
3845 | decomposition algorithms.") | |
3846 | (license license:expat))) | |
303f2ed1 RW |
3847 | |
3848 | (define-public r-yapsa | |
3849 | (package | |
3850 | (name "r-yapsa") | |
edba69b2 | 3851 | (version "1.10.0") |
303f2ed1 RW |
3852 | (source |
3853 | (origin | |
3854 | (method url-fetch) | |
3855 | (uri (bioconductor-uri "YAPSA" version)) | |
3856 | (sha256 | |
3857 | (base32 | |
edba69b2 | 3858 | "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q")))) |
303f2ed1 RW |
3859 | (properties `((upstream-name . "YAPSA"))) |
3860 | (build-system r-build-system) | |
3861 | (propagated-inputs | |
3862 | `(("r-circlize" ,r-circlize) | |
3863 | ("r-complexheatmap" ,r-complexheatmap) | |
3864 | ("r-corrplot" ,r-corrplot) | |
3865 | ("r-dendextend" ,r-dendextend) | |
3866 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3867 | ("r-genomicranges" ,r-genomicranges) | |
3868 | ("r-getoptlong" ,r-getoptlong) | |
3869 | ("r-ggplot2" ,r-ggplot2) | |
3870 | ("r-gridextra" ,r-gridextra) | |
3871 | ("r-gtrellis" ,r-gtrellis) | |
3872 | ("r-keggrest" ,r-keggrest) | |
3873 | ("r-lsei" ,r-lsei) | |
3874 | ("r-pmcmr" ,r-pmcmr) | |
3875 | ("r-reshape2" ,r-reshape2) | |
3876 | ("r-somaticsignatures" ,r-somaticsignatures) | |
3877 | ("r-variantannotation" ,r-variantannotation))) | |
3878 | (home-page "https://bioconductor.org/packages/YAPSA/") | |
3879 | (synopsis "Yet another package for signature analysis") | |
3880 | (description | |
3881 | "This package provides functions and routines useful in the analysis of | |
3882 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, | |
3883 | functions to perform a signature analysis with known signatures and a | |
3884 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are | |
3885 | provided.") | |
3886 | (license license:gpl3))) | |
e99380d6 RW |
3887 | |
3888 | (define-public r-gcrma | |
3889 | (package | |
3890 | (name "r-gcrma") | |
56576bea | 3891 | (version "2.56.0") |
e99380d6 RW |
3892 | (source |
3893 | (origin | |
3894 | (method url-fetch) | |
3895 | (uri (bioconductor-uri "gcrma" version)) | |
3896 | (sha256 | |
3897 | (base32 | |
56576bea | 3898 | "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4")))) |
e99380d6 RW |
3899 | (build-system r-build-system) |
3900 | (propagated-inputs | |
3901 | `(("r-affy" ,r-affy) | |
3902 | ("r-affyio" ,r-affyio) | |
3903 | ("r-biobase" ,r-biobase) | |
3904 | ("r-biocmanager" ,r-biocmanager) | |
3905 | ("r-biostrings" ,r-biostrings) | |
3906 | ("r-xvector" ,r-xvector))) | |
3907 | (home-page "https://bioconductor.org/packages/gcrma/") | |
3908 | (synopsis "Background adjustment using sequence information") | |
3909 | (description | |
3910 | "Gcrma adjusts for background intensities in Affymetrix array data which | |
3911 | include optical noise and @dfn{non-specific binding} (NSB). The main function | |
3912 | @code{gcrma} converts background adjusted probe intensities to expression | |
3913 | measures using the same normalization and summarization methods as a | |
3914 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information | |
3915 | to estimate probe affinity to NSB. The sequence information is summarized in | |
3916 | a more complex way than the simple GC content. Instead, the base types (A, T, | |
3917 | G or C) at each position along the probe determine the affinity of each probe. | |
3918 | The parameters of the position-specific base contributions to the probe | |
3919 | affinity is estimated in an NSB experiment in which only NSB but no | |
3920 | gene-specific bidning is expected.") | |
3921 | ;; Any version of the LGPL | |
3922 | (license license:lgpl2.1+))) | |
4675b3cf RW |
3923 | |
3924 | (define-public r-simpleaffy | |
3925 | (package | |
3926 | (name "r-simpleaffy") | |
38c5d13a | 3927 | (version "2.60.0") |
4675b3cf RW |
3928 | (source |
3929 | (origin | |
3930 | (method url-fetch) | |
3931 | (uri (bioconductor-uri "simpleaffy" version)) | |
3932 | (sha256 | |
3933 | (base32 | |
38c5d13a | 3934 | "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a")))) |
4675b3cf RW |
3935 | (build-system r-build-system) |
3936 | (propagated-inputs | |
3937 | `(("r-affy" ,r-affy) | |
3938 | ("r-biobase" ,r-biobase) | |
3939 | ("r-biocgenerics" ,r-biocgenerics) | |
3940 | ("r-gcrma" ,r-gcrma) | |
3941 | ("r-genefilter" ,r-genefilter))) | |
3942 | (home-page "https://bioconductor.org/packages/simpleaffy/") | |
3943 | (synopsis "Very simple high level analysis of Affymetrix data") | |
3944 | (description | |
3945 | "This package provides high level functions for reading Affy @file{.CEL} | |
3946 | files, phenotypic data, and then computing simple things with it, such as | |
3947 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} | |
3948 | library. It also has some basic scatter plot functions and mechanisms for | |
3949 | generating high resolution journal figures.") | |
3950 | (license license:gpl2+))) | |
f562c90a RW |
3951 | |
3952 | (define-public r-yaqcaffy | |
3953 | (package | |
3954 | (name "r-yaqcaffy") | |
f48e29da | 3955 | (version "1.44.0") |
f562c90a RW |
3956 | (source |
3957 | (origin | |
3958 | (method url-fetch) | |
3959 | (uri (bioconductor-uri "yaqcaffy" version)) | |
3960 | (sha256 | |
3961 | (base32 | |
f48e29da | 3962 | "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670")))) |
f562c90a RW |
3963 | (build-system r-build-system) |
3964 | (propagated-inputs | |
3965 | `(("r-simpleaffy" ,r-simpleaffy))) | |
3966 | (home-page "https://bioconductor.org/packages/yaqcaffy/") | |
3967 | (synopsis "Affymetrix quality control and reproducibility analysis") | |
3968 | (description | |
3969 | "This is a package that can be used for quality control of Affymetrix | |
3970 | GeneChip expression data and reproducibility analysis of human whole genome | |
3971 | chips with the MAQC reference datasets.") | |
3972 | (license license:artistic2.0))) | |
59cf2629 RW |
3973 | |
3974 | (define-public r-quantro | |
3975 | (package | |
3976 | (name "r-quantro") | |
2feea2d2 | 3977 | (version "1.18.0") |
59cf2629 RW |
3978 | (source |
3979 | (origin | |
3980 | (method url-fetch) | |
3981 | (uri (bioconductor-uri "quantro" version)) | |
3982 | (sha256 | |
3983 | (base32 | |
2feea2d2 | 3984 | "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab")))) |
59cf2629 RW |
3985 | (build-system r-build-system) |
3986 | (propagated-inputs | |
3987 | `(("r-biobase" ,r-biobase) | |
3988 | ("r-doparallel" ,r-doparallel) | |
3989 | ("r-foreach" ,r-foreach) | |
3990 | ("r-ggplot2" ,r-ggplot2) | |
3991 | ("r-iterators" ,r-iterators) | |
3992 | ("r-minfi" ,r-minfi) | |
3993 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
3994 | (home-page "https://bioconductor.org/packages/quantro/") | |
3995 | (synopsis "Test for when to use quantile normalization") | |
3996 | (description | |
3997 | "This package provides a data-driven test for the assumptions of quantile | |
3998 | normalization using raw data such as objects that inherit eSets (e.g. | |
3999 | ExpressionSet, MethylSet). Group level information about each sample (such as | |
4000 | Tumor / Normal status) must also be provided because the test assesses if | |
4001 | there are global differences in the distributions between the user-defined | |
4002 | groups.") | |
4003 | (license license:gpl3+))) | |
98a2af31 RW |
4004 | |
4005 | (define-public r-yarn | |
4006 | (package | |
4007 | (name "r-yarn") | |
7f4957b2 | 4008 | (version "1.10.0") |
98a2af31 RW |
4009 | (source |
4010 | (origin | |
4011 | (method url-fetch) | |
4012 | (uri (bioconductor-uri "yarn" version)) | |
4013 | (sha256 | |
4014 | (base32 | |
7f4957b2 | 4015 | "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6")))) |
98a2af31 RW |
4016 | (build-system r-build-system) |
4017 | (propagated-inputs | |
4018 | `(("r-biobase" ,r-biobase) | |
4019 | ("r-biomart" ,r-biomart) | |
4020 | ("r-downloader" ,r-downloader) | |
4021 | ("r-edger" ,r-edger) | |
4022 | ("r-gplots" ,r-gplots) | |
4023 | ("r-limma" ,r-limma) | |
4024 | ("r-matrixstats" ,r-matrixstats) | |
4025 | ("r-preprocesscore" ,r-preprocesscore) | |
4026 | ("r-quantro" ,r-quantro) | |
4027 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4028 | ("r-readr" ,r-readr))) | |
4029 | (home-page "https://bioconductor.org/packages/yarn/") | |
4030 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") | |
4031 | (description | |
4032 | "Expedite large RNA-Seq analyses using a combination of previously | |
4033 | developed tools. YARN is meant to make it easier for the user in performing | |
4034 | basic mis-annotation quality control, filtering, and condition-aware | |
4035 | normalization. YARN leverages many Bioconductor tools and statistical | |
4036 | techniques to account for the large heterogeneity and sparsity found in very | |
4037 | large RNA-seq experiments.") | |
4038 | (license license:artistic2.0))) | |
a6e1eb1a RW |
4039 | |
4040 | (define-public r-roar | |
4041 | (package | |
4042 | (name "r-roar") | |
0334b203 | 4043 | (version "1.20.0") |
a6e1eb1a RW |
4044 | (source |
4045 | (origin | |
4046 | (method url-fetch) | |
4047 | (uri (bioconductor-uri "roar" version)) | |
4048 | (sha256 | |
4049 | (base32 | |
0334b203 | 4050 | "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7")))) |
a6e1eb1a RW |
4051 | (build-system r-build-system) |
4052 | (propagated-inputs | |
4053 | `(("r-biocgenerics" ,r-biocgenerics) | |
4054 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4055 | ("r-genomicalignments" ,r-genomicalignments) | |
4056 | ("r-genomicranges" ,r-genomicranges) | |
4057 | ("r-iranges" ,r-iranges) | |
4058 | ("r-rtracklayer" ,r-rtracklayer) | |
4059 | ("r-s4vectors" ,r-s4vectors) | |
4060 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4061 | (home-page "https://github.com/vodkatad/roar/") | |
4062 | (synopsis "Identify differential APA usage from RNA-seq alignments") | |
4063 | (description | |
4064 | "This package provides tools for identifying preferential usage of APA | |
4065 | sites, comparing two biological conditions, starting from known alternative | |
4066 | sites and alignments obtained from standard RNA-seq experiments.") | |
4067 | (license license:gpl3))) | |
50d91770 RW |
4068 | |
4069 | (define-public r-xbseq | |
4070 | (package | |
4071 | (name "r-xbseq") | |
88469def | 4072 | (version "1.16.0") |
50d91770 RW |
4073 | (source |
4074 | (origin | |
4075 | (method url-fetch) | |
4076 | (uri (bioconductor-uri "XBSeq" version)) | |
4077 | (sha256 | |
4078 | (base32 | |
88469def | 4079 | "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy")))) |
50d91770 RW |
4080 | (properties `((upstream-name . "XBSeq"))) |
4081 | (build-system r-build-system) | |
4082 | (propagated-inputs | |
4083 | `(("r-biobase" ,r-biobase) | |
4084 | ("r-deseq2" ,r-deseq2) | |
4085 | ("r-dplyr" ,r-dplyr) | |
4086 | ("r-ggplot2" ,r-ggplot2) | |
4087 | ("r-locfit" ,r-locfit) | |
4088 | ("r-magrittr" ,r-magrittr) | |
4089 | ("r-matrixstats" ,r-matrixstats) | |
4090 | ("r-pracma" ,r-pracma) | |
4091 | ("r-roar" ,r-roar))) | |
4092 | (home-page "https://github.com/Liuy12/XBSeq") | |
4093 | (synopsis "Test for differential expression for RNA-seq data") | |
4094 | (description | |
4095 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential | |
4096 | expression} (DE), where a statistical model was established based on the | |
4097 | assumption that observed signals are the convolution of true expression | |
4098 | signals and sequencing noises. The mapped reads in non-exonic regions are | |
4099 | considered as sequencing noises, which follows a Poisson distribution. Given | |
4100 | measurable observed signal and background noise from RNA-seq data, true | |
4101 | expression signals, assuming governed by the negative binomial distribution, | |
4102 | can be delineated and thus the accurate detection of differential expressed | |
4103 | genes.") | |
4104 | (license license:gpl3+))) | |
c8310056 RW |
4105 | |
4106 | (define-public r-massspecwavelet | |
4107 | (package | |
4108 | (name "r-massspecwavelet") | |
7c888138 | 4109 | (version "1.50.0") |
c8310056 RW |
4110 | (source |
4111 | (origin | |
4112 | (method url-fetch) | |
4113 | (uri (bioconductor-uri "MassSpecWavelet" version)) | |
4114 | (sha256 | |
4115 | (base32 | |
7c888138 | 4116 | "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72")))) |
c8310056 RW |
4117 | (properties |
4118 | `((upstream-name . "MassSpecWavelet"))) | |
4119 | (build-system r-build-system) | |
4120 | (propagated-inputs | |
4121 | `(("r-waveslim" ,r-waveslim))) | |
4122 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") | |
4123 | (synopsis "Mass spectrum processing by wavelet-based algorithms") | |
4124 | (description | |
4125 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) | |
4126 | data mainly through the use of wavelet transforms. It supports peak detection | |
4127 | based on @dfn{Continuous Wavelet Transform} (CWT).") | |
4128 | (license license:lgpl2.0+))) | |
ec12e537 RW |
4129 | |
4130 | (define-public r-xcms | |
4131 | (package | |
4132 | (name "r-xcms") | |
40b2f7bc | 4133 | (version "3.6.1") |
ec12e537 RW |
4134 | (source |
4135 | (origin | |
4136 | (method url-fetch) | |
4137 | (uri (bioconductor-uri "xcms" version)) | |
4138 | (sha256 | |
4139 | (base32 | |
40b2f7bc | 4140 | "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g")))) |
ec12e537 RW |
4141 | (build-system r-build-system) |
4142 | (propagated-inputs | |
4143 | `(("r-biobase" ,r-biobase) | |
4144 | ("r-biocgenerics" ,r-biocgenerics) | |
4145 | ("r-biocparallel" ,r-biocparallel) | |
4146 | ("r-lattice" ,r-lattice) | |
4147 | ("r-massspecwavelet" ,r-massspecwavelet) | |
4148 | ("r-msnbase" ,r-msnbase) | |
4149 | ("r-multtest" ,r-multtest) | |
4150 | ("r-mzr" ,r-mzr) | |
4151 | ("r-plyr" ,r-plyr) | |
4152 | ("r-protgenerics" ,r-protgenerics) | |
4153 | ("r-rann" ,r-rann) | |
4154 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4155 | ("r-robustbase" ,r-robustbase) | |
4156 | ("r-s4vectors" ,r-s4vectors))) | |
4157 | (home-page "https://bioconductor.org/packages/xcms/") | |
4158 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") | |
4159 | (description | |
4160 | "This package provides a framework for processing and visualization of | |
4161 | chromatographically separated and single-spectra mass spectral data. It | |
4162 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses | |
4163 | data for high-throughput, untargeted analyte profiling.") | |
4164 | (license license:gpl2+))) | |
8830664d RW |
4165 | |
4166 | (define-public r-wrench | |
4167 | (package | |
4168 | (name "r-wrench") | |
07597c85 | 4169 | (version "1.2.0") |
8830664d RW |
4170 | (source |
4171 | (origin | |
4172 | (method url-fetch) | |
4173 | (uri (bioconductor-uri "Wrench" version)) | |
4174 | (sha256 | |
4175 | (base32 | |
07597c85 | 4176 | "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i")))) |
8830664d RW |
4177 | (properties `((upstream-name . "Wrench"))) |
4178 | (build-system r-build-system) | |
4179 | (propagated-inputs | |
4180 | `(("r-limma" ,r-limma) | |
4181 | ("r-locfit" ,r-locfit) | |
4182 | ("r-matrixstats" ,r-matrixstats))) | |
4183 | (home-page "https://github.com/HCBravoLab/Wrench") | |
4184 | (synopsis "Wrench normalization for sparse count data") | |
4185 | (description | |
4186 | "Wrench is a package for normalization sparse genomic count data, like | |
4187 | that arising from 16s metagenomic surveys.") | |
4188 | (license license:artistic2.0))) | |
b9b8b447 RW |
4189 | |
4190 | (define-public r-wiggleplotr | |
4191 | (package | |
4192 | (name "r-wiggleplotr") | |
a6edf335 | 4193 | (version "1.8.0") |
b9b8b447 RW |
4194 | (source |
4195 | (origin | |
4196 | (method url-fetch) | |
4197 | (uri (bioconductor-uri "wiggleplotr" version)) | |
4198 | (sha256 | |
4199 | (base32 | |
a6edf335 | 4200 | "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0")))) |
b9b8b447 RW |
4201 | (build-system r-build-system) |
4202 | (propagated-inputs | |
4203 | `(("r-assertthat" ,r-assertthat) | |
4204 | ("r-cowplot" ,r-cowplot) | |
4205 | ("r-dplyr" ,r-dplyr) | |
4206 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4207 | ("r-genomicranges" ,r-genomicranges) | |
4208 | ("r-ggplot2" ,r-ggplot2) | |
4209 | ("r-iranges" ,r-iranges) | |
4210 | ("r-purrr" ,r-purrr) | |
4211 | ("r-rtracklayer" ,r-rtracklayer) | |
4212 | ("r-s4vectors" ,r-s4vectors))) | |
4213 | (home-page "https://bioconductor.org/packages/wiggleplotr/") | |
4214 | (synopsis "Make read coverage plots from BigWig files") | |
4215 | (description | |
4216 | "This package provides tools to visualize read coverage from sequencing | |
4217 | experiments together with genomic annotations (genes, transcripts, peaks). | |
4218 | Introns of long transcripts can be rescaled to a fixed length for better | |
4219 | visualization of exonic read coverage.") | |
4220 | (license license:asl2.0))) | |
7b5101c5 RW |
4221 | |
4222 | (define-public r-widgettools | |
4223 | (package | |
4224 | (name "r-widgettools") | |
c881b9ef | 4225 | (version "1.62.0") |
7b5101c5 RW |
4226 | (source |
4227 | (origin | |
4228 | (method url-fetch) | |
4229 | (uri (bioconductor-uri "widgetTools" version)) | |
4230 | (sha256 | |
4231 | (base32 | |
c881b9ef | 4232 | "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a")))) |
7b5101c5 RW |
4233 | (properties `((upstream-name . "widgetTools"))) |
4234 | (build-system r-build-system) | |
4235 | (home-page "https://bioconductor.org/packages/widgetTools/") | |
4236 | (synopsis "Tools for creating interactive tcltk widgets") | |
4237 | (description | |
337bdc17 | 4238 | "This package contains tools to support the construction of tcltk |
7b5101c5 RW |
4239 | widgets in R.") |
4240 | ;; Any version of the LGPL. | |
4241 | (license license:lgpl3+))) | |
6b12f213 RW |
4242 | |
4243 | (define-public r-webbioc | |
4244 | (package | |
4245 | (name "r-webbioc") | |
67bc9255 | 4246 | (version "1.56.0") |
6b12f213 RW |
4247 | (source |
4248 | (origin | |
4249 | (method url-fetch) | |
4250 | (uri (bioconductor-uri "webbioc" version)) | |
4251 | (sha256 | |
4252 | (base32 | |
67bc9255 | 4253 | "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz")))) |
6b12f213 RW |
4254 | (build-system r-build-system) |
4255 | (inputs | |
4256 | `(("netpbm" ,netpbm) | |
4257 | ("perl" ,perl))) | |
4258 | (propagated-inputs | |
4259 | `(("r-affy" ,r-affy) | |
4260 | ("r-annaffy" ,r-annaffy) | |
4261 | ("r-biobase" ,r-biobase) | |
4262 | ("r-biocmanager" ,r-biocmanager) | |
4263 | ("r-gcrma" ,r-gcrma) | |
4264 | ("r-multtest" ,r-multtest) | |
4265 | ("r-qvalue" ,r-qvalue) | |
4266 | ("r-vsn" ,r-vsn))) | |
4267 | (home-page "https://www.bioconductor.org/") | |
4268 | (synopsis "Bioconductor web interface") | |
4269 | (description | |
4270 | "This package provides an integrated web interface for doing microarray | |
4271 | analysis using several of the Bioconductor packages. It is intended to be | |
4272 | deployed as a centralized bioinformatics resource for use by many users. | |
4273 | Currently only Affymetrix oligonucleotide analysis is supported.") | |
4274 | (license license:gpl2+))) | |
9800d859 RW |
4275 | |
4276 | (define-public r-zfpkm | |
4277 | (package | |
4278 | (name "r-zfpkm") | |
02530c28 | 4279 | (version "1.6.0") |
9800d859 RW |
4280 | (source |
4281 | (origin | |
4282 | (method url-fetch) | |
4283 | (uri (bioconductor-uri "zFPKM" version)) | |
4284 | (sha256 | |
4285 | (base32 | |
02530c28 | 4286 | "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz")))) |
9800d859 RW |
4287 | (properties `((upstream-name . "zFPKM"))) |
4288 | (build-system r-build-system) | |
4289 | (propagated-inputs | |
4290 | `(("r-checkmate" ,r-checkmate) | |
4291 | ("r-dplyr" ,r-dplyr) | |
4292 | ("r-ggplot2" ,r-ggplot2) | |
4293 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
4294 | ("r-tidyr" ,r-tidyr))) | |
4295 | (home-page "https://github.com/ronammar/zFPKM/") | |
4296 | (synopsis "Functions to facilitate zFPKM transformations") | |
4297 | (description | |
4298 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. | |
4299 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID | |
4300 | 24215113).") | |
4301 | (license license:gpl3))) | |
2bdc88fc RW |
4302 | |
4303 | (define-public r-rbowtie2 | |
4304 | (package | |
4305 | (name "r-rbowtie2") | |
7d33d36c | 4306 | (version "1.6.0") |
2bdc88fc RW |
4307 | (source |
4308 | (origin | |
4309 | (method url-fetch) | |
4310 | (uri (bioconductor-uri "Rbowtie2" version)) | |
4311 | (sha256 | |
4312 | (base32 | |
7d33d36c | 4313 | "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4")))) |
2bdc88fc RW |
4314 | (properties `((upstream-name . "Rbowtie2"))) |
4315 | (build-system r-build-system) | |
4316 | (inputs | |
4317 | `(("zlib" ,zlib))) | |
4318 | (home-page "https://bioconductor.org/packages/Rbowtie2/") | |
4319 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") | |
4320 | (description | |
4321 | "This package provides an R wrapper of the popular @code{bowtie2} | |
4322 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for | |
4323 | rapid adapter trimming, identification, and read merging.") | |
4324 | (license license:gpl3+))) | |
5622628f RW |
4325 | |
4326 | (define-public r-progeny | |
4327 | (package | |
4328 | (name "r-progeny") | |
c2bfb978 | 4329 | (version "1.6.0") |
5622628f RW |
4330 | (source |
4331 | (origin | |
4332 | (method url-fetch) | |
4333 | (uri (bioconductor-uri "progeny" version)) | |
4334 | (sha256 | |
4335 | (base32 | |
c2bfb978 | 4336 | "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw")))) |
5622628f RW |
4337 | (build-system r-build-system) |
4338 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4339 | (home-page "https://github.com/saezlab/progeny") | |
4340 | (synopsis "Pathway responsive gene activity inference") | |
4341 | (description | |
4342 | "This package provides a function to infer pathway activity from gene | |
4343 | expression. It contains the linear model inferred in the publication | |
4344 | \"Perturbation-response genes reveal signaling footprints in cancer gene | |
4345 | expression\".") | |
4346 | (license license:asl2.0))) | |
307586c1 RW |
4347 | |
4348 | (define-public r-arrmnormalization | |
4349 | (package | |
4350 | (name "r-arrmnormalization") | |
c24adbbf | 4351 | (version "1.24.0") |
307586c1 RW |
4352 | (source |
4353 | (origin | |
4354 | (method url-fetch) | |
4355 | (uri (bioconductor-uri "ARRmNormalization" version)) | |
4356 | (sha256 | |
4357 | (base32 | |
c24adbbf | 4358 | "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1")))) |
307586c1 RW |
4359 | (properties |
4360 | `((upstream-name . "ARRmNormalization"))) | |
4361 | (build-system r-build-system) | |
4362 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) | |
4363 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") | |
4364 | (synopsis "Adaptive robust regression normalization for methylation data") | |
4365 | (description | |
4366 | "This is a package to perform the @dfn{Adaptive Robust Regression | |
4367 | method} (ARRm) for the normalization of methylation data from the Illumina | |
4368 | Infinium HumanMethylation 450k assay.") | |
4369 | (license license:artistic2.0))) | |
fbf34949 RW |
4370 | |
4371 | (define-public r-biocfilecache | |
4372 | (package | |
4373 | (name "r-biocfilecache") | |
4374 | (version "1.8.0") | |
4375 | (source | |
4376 | (origin | |
4377 | (method url-fetch) | |
4378 | (uri (bioconductor-uri "BiocFileCache" version)) | |
4379 | (sha256 | |
4380 | (base32 | |
4381 | "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb")))) | |
4382 | (properties `((upstream-name . "BiocFileCache"))) | |
4383 | (build-system r-build-system) | |
4384 | (propagated-inputs | |
4385 | `(("r-curl" ,r-curl) | |
4386 | ("r-dbi" ,r-dbi) | |
4387 | ("r-dbplyr" ,r-dbplyr) | |
4388 | ("r-dplyr" ,r-dplyr) | |
4389 | ("r-httr" ,r-httr) | |
4390 | ("r-rappdirs" ,r-rappdirs) | |
4391 | ("r-rsqlite" ,r-rsqlite))) | |
4392 | (home-page "https://bioconductor.org/packages/BiocFileCache/") | |
4393 | (synopsis "Manage files across sessions") | |
4394 | (description | |
4395 | "This package creates a persistent on-disk cache of files that the user | |
4396 | can add, update, and retrieve. It is useful for managing resources (such as | |
4397 | custom Txdb objects) that are costly or difficult to create, web resources, | |
4398 | and data files used across sessions.") | |
4399 | (license license:artistic2.0))) | |
8c42f8f6 RW |
4400 | |
4401 | (define-public r-iclusterplus | |
4402 | (package | |
4403 | (name "r-iclusterplus") | |
4404 | (version "1.20.0") | |
4405 | (source | |
4406 | (origin | |
4407 | (method url-fetch) | |
4408 | (uri (bioconductor-uri "iClusterPlus" version)) | |
4409 | (sha256 | |
4410 | (base32 | |
4411 | "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq")))) | |
4412 | (properties `((upstream-name . "iClusterPlus"))) | |
4413 | (build-system r-build-system) | |
4414 | (native-inputs `(("gfortran" ,gfortran))) | |
4415 | (home-page "https://bioconductor.org/packages/iClusterPlus/") | |
4416 | (synopsis "Integrative clustering of multi-type genomic data") | |
4417 | (description | |
4418 | "iClusterPlus is developed for integrative clustering analysis of | |
4419 | multi-type genomic data and is an enhanced version of iCluster proposed and | |
4420 | developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise | |
4421 | from the experiments where biological samples (e.g. tumor samples) are | |
4422 | analyzed by multiple techniques, for instance, @dfn{array comparative genomic | |
4423 | hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so | |
4424 | on. In the iClusterPlus model, binary observations such as somatic mutation | |
4425 | are modeled as Binomial processes; categorical observations such as copy | |
4426 | number states are realizations of Multinomial random variables; counts are | |
4427 | modeled as Poisson random processes; and continuous measures are modeled by | |
4428 | Gaussian distributions.") | |
4429 | (license license:gpl2+))) | |
4d06ef4b RW |
4430 | |
4431 | (define-public r-rbowtie | |
4432 | (package | |
4433 | (name "r-rbowtie") | |
4434 | (version "1.24.0") | |
4435 | (source | |
4436 | (origin | |
4437 | (method url-fetch) | |
4438 | (uri (bioconductor-uri "Rbowtie" version)) | |
4439 | (sha256 | |
4440 | (base32 | |
4441 | "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f")))) | |
4442 | (properties `((upstream-name . "Rbowtie"))) | |
4443 | (build-system r-build-system) | |
4444 | (inputs | |
4445 | `(("zlib" ,zlib))) | |
4446 | (home-page "https://bioconductor.org/packages/Rbowtie/") | |
4447 | (synopsis "R bowtie wrapper") | |
4448 | (description | |
4449 | "This package provides an R wrapper around the popular bowtie short read | |
4450 | aligner and around SpliceMap, a de novo splice junction discovery and | |
4451 | alignment tool.") | |
4452 | (license license:artistic2.0))) | |
14441539 RW |
4453 | |
4454 | (define-public r-sgseq | |
4455 | (package | |
4456 | (name "r-sgseq") | |
4457 | (version "1.18.0") | |
4458 | (source | |
4459 | (origin | |
4460 | (method url-fetch) | |
4461 | (uri (bioconductor-uri "SGSeq" version)) | |
4462 | (sha256 | |
4463 | (base32 | |
4464 | "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s")))) | |
4465 | (properties `((upstream-name . "SGSeq"))) | |
4466 | (build-system r-build-system) | |
4467 | (propagated-inputs | |
4468 | `(("r-annotationdbi" ,r-annotationdbi) | |
4469 | ("r-biocgenerics" ,r-biocgenerics) | |
4470 | ("r-biostrings" ,r-biostrings) | |
4471 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4472 | ("r-genomicalignments" ,r-genomicalignments) | |
4473 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4474 | ("r-genomicranges" ,r-genomicranges) | |
4475 | ("r-igraph" ,r-igraph) | |
4476 | ("r-iranges" ,r-iranges) | |
4477 | ("r-rsamtools" ,r-rsamtools) | |
4478 | ("r-rtracklayer" ,r-rtracklayer) | |
4479 | ("r-runit" ,r-runit) | |
4480 | ("r-s4vectors" ,r-s4vectors) | |
4481 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4482 | (home-page "https://bioconductor.org/packages/SGSeq/") | |
4483 | (synopsis "Splice event prediction and quantification from RNA-seq data") | |
4484 | (description | |
4485 | "SGSeq is a package for analyzing splice events from RNA-seq data. Input | |
4486 | data are RNA-seq reads mapped to a reference genome in BAM format. Genes are | |
4487 | represented as a splice graph, which can be obtained from existing annotation | |
4488 | or predicted from the mapped sequence reads. Splice events are identified | |
4489 | from the graph and are quantified locally using structurally compatible reads | |
4490 | at the start or end of each splice variant. The software includes functions | |
4491 | for splice event prediction, quantification, visualization and | |
4492 | interpretation.") | |
4493 | (license license:artistic2.0))) | |
58656064 RW |
4494 | |
4495 | (define-public r-rhisat2 | |
4496 | (package | |
4497 | (name "r-rhisat2") | |
932a6c42 | 4498 | (version "1.0.3") |
58656064 RW |
4499 | (source |
4500 | (origin | |
4501 | (method url-fetch) | |
4502 | (uri (bioconductor-uri "Rhisat2" version)) | |
4503 | (sha256 | |
4504 | (base32 | |
932a6c42 | 4505 | "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5")))) |
58656064 RW |
4506 | (properties `((upstream-name . "Rhisat2"))) |
4507 | (build-system r-build-system) | |
4508 | (native-inputs | |
4509 | `(("which" ,which))) | |
4510 | (propagated-inputs | |
4511 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
4512 | ("r-genomicranges" ,r-genomicranges) | |
4513 | ("r-sgseq" ,r-sgseq))) | |
4514 | (home-page "https://github.com/fmicompbio/Rhisat2") | |
4515 | (synopsis "R Wrapper for HISAT2 sequence aligner") | |
4516 | (description | |
4517 | "This package provides an R interface to the HISAT2 spliced short-read | |
4518 | aligner by Kim et al. (2015). The package contains wrapper functions to | |
4519 | create a genome index and to perform the read alignment to the generated | |
4520 | index.") | |
4521 | (license license:gpl3))) | |
5e0241db RW |
4522 | |
4523 | (define-public r-quasr | |
4524 | (package | |
4525 | (name "r-quasr") | |
b3319f4c | 4526 | (version "1.24.2") |
5e0241db RW |
4527 | (source |
4528 | (origin | |
4529 | (method url-fetch) | |
4530 | (uri (bioconductor-uri "QuasR" version)) | |
4531 | (sha256 | |
4532 | (base32 | |
b3319f4c | 4533 | "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx")))) |
5e0241db RW |
4534 | (properties `((upstream-name . "QuasR"))) |
4535 | (build-system r-build-system) | |
4536 | (inputs | |
4537 | `(("zlib" ,zlib))) | |
4538 | (propagated-inputs | |
4539 | `(("r-annotationdbi" ,r-annotationdbi) | |
4540 | ("r-biobase" ,r-biobase) | |
4541 | ("r-biocgenerics" ,r-biocgenerics) | |
4542 | ("r-biocmanager" ,r-biocmanager) | |
4543 | ("r-biocparallel" ,r-biocparallel) | |
4544 | ("r-biostrings" ,r-biostrings) | |
4545 | ("r-bsgenome" ,r-bsgenome) | |
4546 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4547 | ("r-genomicalignments" ,r-genomicalignments) | |
4548 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4549 | ("r-genomicfiles" ,r-genomicfiles) | |
4550 | ("r-genomicranges" ,r-genomicranges) | |
4551 | ("r-iranges" ,r-iranges) | |
4552 | ("r-rbowtie" ,r-rbowtie) | |
4553 | ("r-rhisat2" ,r-rhisat2) | |
4554 | ("r-rhtslib" ,r-rhtslib) | |
4555 | ("r-rsamtools" ,r-rsamtools) | |
4556 | ("r-rtracklayer" ,r-rtracklayer) | |
4557 | ("r-s4vectors" ,r-s4vectors) | |
4558 | ("r-shortread" ,r-shortread))) | |
4559 | (home-page "https://bioconductor.org/packages/QuasR/") | |
4560 | (synopsis "Quantify and annotate short reads in R") | |
4561 | (description | |
4562 | "This package provides a framework for the quantification and analysis of | |
4563 | short genomic reads. It covers a complete workflow starting from raw sequence | |
4564 | reads, over creation of alignments and quality control plots, to the | |
4565 | quantification of genomic regions of interest.") | |
4566 | (license license:gpl2))) | |
496b024f RW |
4567 | |
4568 | (define-public r-rqc | |
4569 | (package | |
4570 | (name "r-rqc") | |
4571 | (version "1.18.0") | |
4572 | (source | |
4573 | (origin | |
4574 | (method url-fetch) | |
4575 | (uri (bioconductor-uri "Rqc" version)) | |
4576 | (sha256 | |
4577 | (base32 | |
4578 | "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g")))) | |
4579 | (properties `((upstream-name . "Rqc"))) | |
4580 | (build-system r-build-system) | |
4581 | (propagated-inputs | |
4582 | `(("r-biocgenerics" ,r-biocgenerics) | |
4583 | ("r-biocparallel" ,r-biocparallel) | |
4584 | ("r-biocstyle" ,r-biocstyle) | |
4585 | ("r-biostrings" ,r-biostrings) | |
4586 | ("r-biovizbase" ,r-biovizbase) | |
4587 | ("r-genomicalignments" ,r-genomicalignments) | |
4588 | ("r-genomicfiles" ,r-genomicfiles) | |
4589 | ("r-ggplot2" ,r-ggplot2) | |
4590 | ("r-iranges" ,r-iranges) | |
4591 | ("r-knitr" ,r-knitr) | |
4592 | ("r-markdown" ,r-markdown) | |
4593 | ("r-plyr" ,r-plyr) | |
4594 | ("r-rcpp" ,r-rcpp) | |
4595 | ("r-reshape2" ,r-reshape2) | |
4596 | ("r-rsamtools" ,r-rsamtools) | |
4597 | ("r-s4vectors" ,r-s4vectors) | |
4598 | ("r-shiny" ,r-shiny) | |
4599 | ("r-shortread" ,r-shortread))) | |
4600 | (home-page "https://github.com/labbcb/Rqc") | |
4601 | (synopsis "Quality control tool for high-throughput sequencing data") | |
4602 | (description | |
4603 | "Rqc is an optimized tool designed for quality control and assessment of | |
4604 | high-throughput sequencing data. It performs parallel processing of entire | |
4605 | files and produces a report which contains a set of high-resolution | |
4606 | graphics.") | |
4607 | (license license:gpl2+))) | |
81e3de01 RW |
4608 | |
4609 | (define-public r-birewire | |
4610 | (package | |
4611 | (name "r-birewire") | |
4612 | (version "3.16.0") | |
4613 | (source | |
4614 | (origin | |
4615 | (method url-fetch) | |
4616 | (uri (bioconductor-uri "BiRewire" version)) | |
4617 | (sha256 | |
4618 | (base32 | |
4619 | "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518")))) | |
4620 | (properties `((upstream-name . "BiRewire"))) | |
4621 | (build-system r-build-system) | |
4622 | (propagated-inputs | |
4623 | `(("r-igraph" ,r-igraph) | |
4624 | ("r-matrix" ,r-matrix) | |
4625 | ("r-slam" ,r-slam) | |
4626 | ("r-tsne" ,r-tsne))) | |
4627 | (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") | |
4628 | (synopsis "Tools for randomization of bipartite graphs") | |
4629 | (description | |
4630 | "This package provides functions for bipartite network rewiring through N | |
4631 | consecutive switching steps and for the computation of the minimal number of | |
4632 | switching steps to be performed in order to maximise the dissimilarity with | |
4633 | respect to the original network. It includes functions for the analysis of | |
4634 | the introduced randomness across the switching steps and several other | |
4635 | routines to analyse the resulting networks and their natural projections.") | |
4636 | (license license:gpl3))) | |
1a24f855 RW |
4637 | |
4638 | (define-public r-birta | |
4639 | (package | |
4640 | (name "r-birta") | |
4641 | (version "1.28.0") | |
4642 | (source | |
4643 | (origin | |
4644 | (method url-fetch) | |
4645 | (uri (bioconductor-uri "birta" version)) | |
4646 | (sha256 | |
4647 | (base32 | |
4648 | "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2")))) | |
4649 | (build-system r-build-system) | |
4650 | (propagated-inputs | |
4651 | `(("r-biobase" ,r-biobase) | |
4652 | ("r-limma" ,r-limma) | |
4653 | ("r-mass" ,r-mass))) | |
4654 | (home-page "https://bioconductor.org/packages/birta") | |
4655 | (synopsis "Bayesian inference of regulation of transcriptional activity") | |
4656 | (description | |
4657 | "Expression levels of mRNA molecules are regulated by different | |
4658 | processes, comprising inhibition or activation by transcription factors and | |
4659 | post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian | |
4660 | Inference of Regulation of Transcriptional Activity) uses the regulatory | |
4661 | networks of transcription factors and miRNAs together with mRNA and miRNA | |
4662 | expression data to predict switches in regulatory activity between two | |
4663 | conditions. A Bayesian network is used to model the regulatory structure and | |
4664 | Markov-Chain-Monte-Carlo is applied to sample the activity states.") | |
4665 | (license license:gpl2+))) | |
a9fac3f4 RW |
4666 | |
4667 | (define-public r-ropls | |
4668 | (package | |
4669 | (name "r-ropls") | |
4670 | (version "1.16.0") | |
4671 | (source | |
4672 | (origin | |
4673 | (method url-fetch) | |
4674 | (uri (bioconductor-uri "ropls" version)) | |
4675 | (sha256 | |
4676 | (base32 | |
4677 | "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2")))) | |
4678 | (build-system r-build-system) | |
4679 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4680 | (native-inputs | |
4681 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
4682 | (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") | |
4683 | (synopsis "Multivariate analysis and feature selection of omics data") | |
4684 | (description | |
4685 | "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) | |
4686 | and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, | |
4687 | regression, classification, and feature selection of omics data where the | |
4688 | number of variables exceeds the number of samples and with multicollinearity | |
4689 | among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to | |
4690 | separately model the variation correlated (predictive) to the factor of | |
4691 | interest and the uncorrelated (orthogonal) variation. While performing | |
4692 | similarly to PLS, OPLS facilitates interpretation. | |
4693 | ||
4694 | This package provides imlementations of PCA, PLS, and OPLS for multivariate | |
4695 | analysis and feature selection of omics data. In addition to scores, loadings | |
4696 | and weights plots, the package provides metrics and graphics to determine the | |
4697 | optimal number of components (e.g. with the R2 and Q2 coefficients), check the | |
4698 | validity of the model by permutation testing, detect outliers, and perform | |
4699 | feature selection (e.g. with Variable Importance in Projection or regression | |
4700 | coefficients).") | |
4701 | (license license:cecill))) | |
075a9094 RW |
4702 | |
4703 | (define-public r-biosigner | |
4704 | (package | |
4705 | (name "r-biosigner") | |
4706 | (version "1.12.0") | |
4707 | (source | |
4708 | (origin | |
4709 | (method url-fetch) | |
4710 | (uri (bioconductor-uri "biosigner" version)) | |
4711 | (sha256 | |
4712 | (base32 | |
4713 | "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b")))) | |
4714 | (build-system r-build-system) | |
4715 | (propagated-inputs | |
4716 | `(("r-biobase" ,r-biobase) | |
4717 | ("r-e1071" ,r-e1071) | |
4718 | ("r-randomforest" ,r-randomforest) | |
4719 | ("r-ropls" ,r-ropls))) | |
4720 | (native-inputs | |
4721 | `(("r-knitr" ,r-knitr) | |
4722 | ("r-rmarkdown" ,r-rmarkdown) | |
4723 | ("pandoc" ,ghc-pandoc) | |
4724 | ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes | |
4725 | (home-page "https://bioconductor.org/packages/biosigner/") | |
4726 | (synopsis "Signature discovery from omics data") | |
4727 | (description | |
4728 | "Feature selection is critical in omics data analysis to extract | |
4729 | restricted and meaningful molecular signatures from complex and high-dimension | |
4730 | data, and to build robust classifiers. This package implements a method to | |
4731 | assess the relevance of the variables for the prediction performances of the | |
4732 | classifier. The approach can be run in parallel with the PLS-DA, Random | |
4733 | Forest, and SVM binary classifiers. The signatures and the corresponding | |
4734 | 'restricted' models are returned, enabling future predictions on new | |
4735 | datasets.") | |
4736 | (license license:cecill))) | |
ae6fa185 RW |
4737 | |
4738 | (define-public r-annotatr | |
4739 | (package | |
4740 | (name "r-annotatr") | |
4741 | (version "1.10.0") | |
4742 | (source | |
4743 | (origin | |
4744 | (method url-fetch) | |
4745 | (uri (bioconductor-uri "annotatr" version)) | |
4746 | (sha256 | |
4747 | (base32 | |
4748 | "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f")))) | |
4749 | (build-system r-build-system) | |
4750 | (propagated-inputs | |
4751 | `(("r-annotationdbi" ,r-annotationdbi) | |
4752 | ("r-annotationhub" ,r-annotationhub) | |
4753 | ("r-dplyr" ,r-dplyr) | |
4754 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4755 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4756 | ("r-genomicranges" ,r-genomicranges) | |
4757 | ("r-ggplot2" ,r-ggplot2) | |
4758 | ("r-iranges" ,r-iranges) | |
4759 | ("r-readr" ,r-readr) | |
4760 | ("r-regioner" ,r-regioner) | |
4761 | ("r-reshape2" ,r-reshape2) | |
4762 | ("r-rtracklayer" ,r-rtracklayer) | |
4763 | ("r-s4vectors" ,r-s4vectors))) | |
4764 | (home-page "https://bioconductor.org/packages/annotatr/") | |
4765 | (synopsis "Annotation of genomic regions to genomic annotations") | |
4766 | (description | |
4767 | "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, | |
4768 | differentially methylated CpGs or regions, SNPs, etc.) it is often of interest | |
4769 | to investigate the intersecting genomic annotations. Such annotations include | |
4770 | those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), | |
4771 | CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as | |
4772 | enhancers. The annotatr package provides an easy way to summarize and | |
4773 | visualize the intersection of genomic sites/regions with genomic | |
4774 | annotations.") | |
4775 | (license license:gpl3))) | |
2cb738a6 RW |
4776 | |
4777 | (define-public r-rsubread | |
4778 | (package | |
4779 | (name "r-rsubread") | |
3e265d96 | 4780 | (version "1.34.4") |
2cb738a6 RW |
4781 | (source |
4782 | (origin | |
4783 | (method url-fetch) | |
4784 | (uri (bioconductor-uri "Rsubread" version)) | |
4785 | (sha256 | |
4786 | (base32 | |
3e265d96 | 4787 | "1230p8nsakifmpsqfiaj8rpm7npa8ab903mfjmayfa71n6yzvcbs")))) |
2cb738a6 RW |
4788 | (properties `((upstream-name . "Rsubread"))) |
4789 | (build-system r-build-system) | |
4790 | (inputs `(("zlib" ,zlib))) | |
4791 | (home-page "https://bioconductor.org/packages/Rsubread/") | |
4792 | (synopsis "Subread sequence alignment and counting for R") | |
4793 | (description | |
4794 | "This package provides tools for alignment, quantification and analysis | |
4795 | of second and third generation sequencing data. It includes functionality for | |
4796 | read mapping, read counting, SNP calling, structural variant detection and | |
4797 | gene fusion discovery. It can be applied to all major sequencing techologies | |
4798 | and to both short and long sequence reads.") | |
4799 | (license license:gpl3))) | |
a6fedf1f | 4800 | |
a0422d18 | 4801 | (define-public r-flowutils |
4802 | (package | |
4803 | (name "r-flowutils") | |
4804 | (version "1.48.0") | |
4805 | (source | |
4806 | (origin | |
4807 | (method url-fetch) | |
4808 | (uri (bioconductor-uri "flowUtils" version)) | |
4809 | (sha256 | |
4810 | (base32 | |
4811 | "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm")))) | |
4812 | (properties `((upstream-name . "flowUtils"))) | |
4813 | (build-system r-build-system) | |
4814 | (propagated-inputs | |
4815 | `(("r-biobase" ,r-biobase) | |
4816 | ("r-corpcor" ,r-corpcor) | |
4817 | ("r-flowcore" ,r-flowcore) | |
4818 | ("r-graph" ,r-graph) | |
4819 | ("r-runit" ,r-runit) | |
4820 | ("r-xml" ,r-xml))) | |
4821 | (home-page "https://github.com/jspidlen/flowUtils") | |
4822 | (synopsis "Utilities for flow cytometry") | |
4823 | (description | |
4824 | "This package provides utilities for flow cytometry data.") | |
4825 | (license license:artistic2.0))) | |
4826 | ||
a6fedf1f | 4827 | (define-public r-flowcore |
4828 | (package | |
4829 | (name "r-flowcore") | |
4830 | (version "1.50.0") | |
4831 | (source | |
4832 | (origin | |
4833 | (method url-fetch) | |
4834 | (uri (bioconductor-uri "flowCore" version)) | |
4835 | (sha256 | |
4836 | (base32 | |
4837 | "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan")))) | |
4838 | (properties `((upstream-name . "flowCore"))) | |
4839 | (build-system r-build-system) | |
4840 | (propagated-inputs | |
4841 | `(("r-bh" ,r-bh) | |
4842 | ("r-biobase" ,r-biobase) | |
4843 | ("r-biocgenerics" ,r-biocgenerics) | |
4844 | ("r-corpcor" ,r-corpcor) | |
4845 | ("r-graph" ,r-graph) | |
4846 | ("r-mass" ,r-mass) | |
4847 | ("r-matrixstats" ,r-matrixstats) | |
4848 | ("r-rcpp" ,r-rcpp) | |
4849 | ("r-rrcov" ,r-rrcov))) | |
4850 | (home-page "https://bioconductor.org/packages/flowCore") | |
4851 | (synopsis "Basic structures for flow cytometry data") | |
4852 | (description | |
4853 | "This package provides S4 data structures and basic functions to deal | |
4854 | with flow cytometry data.") | |
4855 | (license license:artistic2.0))) |