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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> |
16e2e4f2 | 5 | ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com> |
fa596599 RW |
6 | ;;; |
7 | ;;; This file is part of GNU Guix. | |
8 | ;;; | |
9 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
10 | ;;; under the terms of the GNU General Public License as published by | |
11 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
12 | ;;; your option) any later version. | |
13 | ;;; | |
14 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
15 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
16 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
17 | ;;; GNU General Public License for more details. | |
18 | ;;; | |
19 | ;;; You should have received a copy of the GNU General Public License | |
20 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
21 | ||
22 | (define-module (gnu packages bioconductor) | |
23 | #:use-module ((guix licenses) #:prefix license:) | |
24 | #:use-module (guix packages) | |
25 | #:use-module (guix download) | |
b2dce6b5 | 26 | #:use-module (guix git-download) |
fa596599 | 27 | #:use-module (guix build-system r) |
183ce988 | 28 | #:use-module (gnu packages) |
58656064 | 29 | #:use-module (gnu packages base) |
cf9a29b2 | 30 | #:use-module (gnu packages bioinformatics) |
a5b56a53 RJ |
31 | #:use-module (gnu packages cran) |
32 | #:use-module (gnu packages compression) | |
c18dccff | 33 | #:use-module (gnu packages gcc) |
cf9a29b2 | 34 | #:use-module (gnu packages graph) |
dddbc90c | 35 | #:use-module (gnu packages haskell-xyz) |
5cfa4bff | 36 | #:use-module (gnu packages image) |
b64ce4b7 | 37 | #:use-module (gnu packages maths) |
6b12f213 RW |
38 | #:use-module (gnu packages netpbm) |
39 | #:use-module (gnu packages perl) | |
2cb71d81 | 40 | #:use-module (gnu packages pkg-config) |
f4235c0e | 41 | #:use-module (gnu packages statistics) |
14bb1c48 RW |
42 | #:use-module (gnu packages web) |
43 | #:use-module (srfi srfi-1)) | |
fa596599 | 44 | |
557a1089 RW |
45 | \f |
46 | ;;; Annotations | |
47 | ||
b7d93cf5 RW |
48 | (define-public r-bsgenome-celegans-ucsc-ce6 |
49 | (package | |
50 | (name "r-bsgenome-celegans-ucsc-ce6") | |
51 | (version "1.4.0") | |
52 | (source (origin | |
53 | (method url-fetch) | |
86ced7b2 RW |
54 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6" |
55 | version 'annotation)) | |
b7d93cf5 RW |
56 | (sha256 |
57 | (base32 | |
58 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
59 | (properties | |
60 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
61 | (build-system r-build-system) | |
b7d93cf5 RW |
62 | (propagated-inputs |
63 | `(("r-bsgenome" ,r-bsgenome))) | |
64 | (home-page | |
65 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
66 | (synopsis "Full genome sequences for Worm") | |
67 | (description | |
68 | "This package provides full genome sequences for Caenorhabditis | |
69 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
0c792ffb RW |
70 | objects.") |
71 | (license license:artistic2.0))) | |
72 | ||
73 | (define-public r-bsgenome-celegans-ucsc-ce10 | |
74 | (package | |
75 | (name "r-bsgenome-celegans-ucsc-ce10") | |
76 | (version "1.4.0") | |
77 | (source (origin | |
78 | (method url-fetch) | |
79 | ;; We cannot use bioconductor-uri here because this tarball is | |
80 | ;; located under "data/annotation/" instead of "bioc/". | |
81 | (uri (string-append "https://www.bioconductor.org/packages/" | |
82 | "release/data/annotation/src/contrib/" | |
83 | "BSgenome.Celegans.UCSC.ce10_" | |
84 | version ".tar.gz")) | |
85 | (sha256 | |
86 | (base32 | |
87 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
88 | (properties | |
89 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
90 | (build-system r-build-system) | |
91 | ;; As this package provides little more than a very large data file it | |
92 | ;; doesn't make sense to build substitutes. | |
93 | (arguments `(#:substitutable? #f)) | |
94 | (propagated-inputs | |
95 | `(("r-bsgenome" ,r-bsgenome))) | |
96 | (home-page | |
97 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
98 | (synopsis "Full genome sequences for Worm") | |
99 | (description | |
100 | "This package provides full genome sequences for Caenorhabditis | |
101 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
b7d93cf5 RW |
102 | objects.") |
103 | (license license:artistic2.0))) | |
104 | ||
183db725 RW |
105 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
106 | (package | |
107 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
108 | (version "1.4.1") | |
109 | (source (origin | |
110 | (method url-fetch) | |
111 | ;; We cannot use bioconductor-uri here because this tarball is | |
112 | ;; located under "data/annotation/" instead of "bioc/". | |
113 | (uri (string-append "https://www.bioconductor.org/packages/" | |
114 | "release/data/annotation/src/contrib/" | |
115 | "BSgenome.Dmelanogaster.UCSC.dm6_" | |
116 | version ".tar.gz")) | |
117 | (sha256 | |
118 | (base32 | |
119 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
120 | (properties | |
121 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
122 | (build-system r-build-system) | |
123 | ;; As this package provides little more than a very large data file it | |
124 | ;; doesn't make sense to build substitutes. | |
125 | (arguments `(#:substitutable? #f)) | |
126 | (propagated-inputs | |
127 | `(("r-bsgenome" ,r-bsgenome))) | |
128 | (home-page | |
129 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
130 | (synopsis "Full genome sequences for Fly") | |
131 | (description | |
132 | "This package provides full genome sequences for Drosophila | |
133 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
134 | objects.") | |
135 | (license license:artistic2.0))) | |
136 | ||
13dabd69 RW |
137 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
138 | (package | |
139 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
140 | (version "1.4.0") | |
141 | (source (origin | |
142 | (method url-fetch) | |
143 | ;; We cannot use bioconductor-uri here because this tarball is | |
144 | ;; located under "data/annotation/" instead of "bioc/". | |
145 | (uri (string-append "https://www.bioconductor.org/packages/" | |
146 | "release/data/annotation/src/contrib/" | |
147 | "BSgenome.Dmelanogaster.UCSC.dm3_" | |
148 | version ".tar.gz")) | |
149 | (sha256 | |
150 | (base32 | |
151 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
152 | (properties | |
153 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
154 | (build-system r-build-system) | |
155 | ;; As this package provides little more than a very large data file it | |
156 | ;; doesn't make sense to build substitutes. | |
157 | (arguments `(#:substitutable? #f)) | |
158 | (propagated-inputs | |
159 | `(("r-bsgenome" ,r-bsgenome))) | |
160 | (home-page | |
161 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
162 | (synopsis "Full genome sequences for Fly") | |
163 | (description | |
164 | "This package provides full genome sequences for Drosophila | |
165 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
166 | Biostrings objects.") | |
167 | (license license:artistic2.0))) | |
168 | ||
dfac7eb9 RW |
169 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
170 | (package | |
171 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
172 | (version "1.3.99") | |
173 | (source (origin | |
174 | (method url-fetch) | |
175 | ;; We cannot use bioconductor-uri here because this tarball is | |
176 | ;; located under "data/annotation/" instead of "bioc/". | |
177 | (uri (string-append "http://www.bioconductor.org/packages/" | |
178 | "release/data/annotation/src/contrib/" | |
179 | "BSgenome.Dmelanogaster.UCSC.dm3.masked_" | |
180 | version ".tar.gz")) | |
181 | (sha256 | |
182 | (base32 | |
183 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
184 | (properties | |
185 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
186 | (build-system r-build-system) | |
187 | (propagated-inputs | |
188 | `(("r-bsgenome" ,r-bsgenome) | |
189 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
190 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
191 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
192 | (synopsis "Full masked genome sequences for Fly") | |
193 | (description | |
194 | "This package provides full masked genome sequences for Drosophila | |
195 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
196 | Biostrings objects. The sequences are the same as in | |
197 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
198 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
199 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
200 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
201 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
202 | (license license:artistic2.0))) | |
203 | ||
40a65057 RW |
204 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
205 | (package | |
206 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
207 | (version "0.99.1") | |
208 | (source (origin | |
209 | (method url-fetch) | |
210 | ;; We cannot use bioconductor-uri here because this tarball is | |
211 | ;; located under "data/annotation/" instead of "bioc/". | |
212 | (uri (string-append "https://www.bioconductor.org/packages/" | |
213 | "release/data/annotation/src/contrib/" | |
214 | "BSgenome.Hsapiens.1000genomes.hs37d5_" | |
215 | version ".tar.gz")) | |
216 | (sha256 | |
217 | (base32 | |
218 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
219 | (properties | |
220 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
221 | (build-system r-build-system) | |
222 | ;; As this package provides little more than a very large data file it | |
223 | ;; doesn't make sense to build substitutes. | |
224 | (arguments `(#:substitutable? #f)) | |
225 | (propagated-inputs | |
226 | `(("r-bsgenome" ,r-bsgenome))) | |
227 | (home-page | |
228 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
229 | (synopsis "Full genome sequences for Homo sapiens") | |
230 | (description | |
231 | "This package provides full genome sequences for Homo sapiens from | |
232 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
233 | (license license:artistic2.0))) | |
234 | ||
6fbd759b RW |
235 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
236 | (package | |
237 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
238 | (version "1.3.99") | |
239 | (source (origin | |
240 | (method url-fetch) | |
241 | ;; We cannot use bioconductor-uri here because this tarball is | |
242 | ;; located under "data/annotation/" instead of "bioc/". | |
243 | (uri (string-append "http://www.bioconductor.org/packages/" | |
244 | "release/data/annotation/src/contrib/" | |
245 | "BSgenome.Hsapiens.UCSC.hg19.masked_" | |
246 | version ".tar.gz")) | |
247 | (sha256 | |
248 | (base32 | |
249 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
250 | (properties | |
251 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
252 | (build-system r-build-system) | |
253 | (propagated-inputs | |
254 | `(("r-bsgenome" ,r-bsgenome) | |
255 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
256 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
257 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
258 | (synopsis "Full masked genome sequences for Homo sapiens") | |
259 | (description | |
260 | "This package provides full genome sequences for Homo sapiens (Human) as | |
261 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
262 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
263 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
264 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
265 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
266 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
267 | default.") | |
268 | (license license:artistic2.0))) | |
269 | ||
5acb9052 RW |
270 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
271 | (package | |
272 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
273 | (version "1.4.0") | |
274 | (source (origin | |
275 | (method url-fetch) | |
276 | ;; We cannot use bioconductor-uri here because this tarball is | |
277 | ;; located under "data/annotation/" instead of "bioc/". | |
278 | (uri (string-append "https://www.bioconductor.org/packages/" | |
279 | "release/data/annotation/src/contrib/" | |
280 | "BSgenome.Mmusculus.UCSC.mm9_" | |
281 | version ".tar.gz")) | |
282 | (sha256 | |
283 | (base32 | |
284 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
285 | (properties | |
286 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
287 | (build-system r-build-system) | |
288 | ;; As this package provides little more than a very large data file it | |
289 | ;; doesn't make sense to build substitutes. | |
290 | (arguments `(#:substitutable? #f)) | |
291 | (propagated-inputs | |
292 | `(("r-bsgenome" ,r-bsgenome))) | |
293 | (home-page | |
294 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
295 | (synopsis "Full genome sequences for Mouse") | |
296 | (description | |
297 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
298 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
299 | (license license:artistic2.0))) | |
300 | ||
2bece692 RW |
301 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
302 | (package | |
303 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
304 | (version "1.3.99") | |
305 | (source (origin | |
306 | (method url-fetch) | |
307 | ;; We cannot use bioconductor-uri here because this tarball is | |
308 | ;; located under "data/annotation/" instead of "bioc/". | |
309 | (uri (string-append "http://www.bioconductor.org/packages/" | |
310 | "release/data/annotation/src/contrib/" | |
311 | "BSgenome.Mmusculus.UCSC.mm9.masked_" | |
312 | version ".tar.gz")) | |
313 | (sha256 | |
314 | (base32 | |
315 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
316 | (properties | |
317 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
318 | (build-system r-build-system) | |
319 | (propagated-inputs | |
320 | `(("r-bsgenome" ,r-bsgenome) | |
321 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
322 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
323 | (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") | |
324 | (synopsis "Full masked genome sequences for Mouse") | |
325 | (description | |
326 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
327 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
328 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
329 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
330 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
331 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
332 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
333 | default." ) | |
334 | (license license:artistic2.0))) | |
335 | ||
c3adc830 RW |
336 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
337 | (package | |
338 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
339 | (version "1.4.0") | |
340 | (source (origin | |
341 | (method url-fetch) | |
342 | ;; We cannot use bioconductor-uri here because this tarball is | |
343 | ;; located under "data/annotation/" instead of "bioc/". | |
344 | (uri (string-append "https://www.bioconductor.org/packages/" | |
345 | "release/data/annotation/src/contrib/" | |
346 | "BSgenome.Mmusculus.UCSC.mm10_" | |
347 | version ".tar.gz")) | |
348 | (sha256 | |
349 | (base32 | |
350 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
351 | (properties | |
352 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
353 | (build-system r-build-system) | |
354 | ;; As this package provides little more than a very large data file it | |
355 | ;; doesn't make sense to build substitutes. | |
356 | (arguments `(#:substitutable? #f)) | |
357 | (propagated-inputs | |
358 | `(("r-bsgenome" ,r-bsgenome))) | |
359 | (home-page | |
360 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
361 | (synopsis "Full genome sequences for Mouse") | |
362 | (description | |
363 | "This package provides full genome sequences for Mus | |
364 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
365 | in Biostrings objects.") | |
366 | (license license:artistic2.0))) | |
367 | ||
3a08940e RW |
368 | (define-public r-org-ce-eg-db |
369 | (package | |
370 | (name "r-org-ce-eg-db") | |
371 | (version "3.7.0") | |
372 | (source (origin | |
373 | (method url-fetch) | |
374 | ;; We cannot use bioconductor-uri here because this tarball is | |
375 | ;; located under "data/annotation/" instead of "bioc/". | |
376 | (uri (string-append "https://www.bioconductor.org/packages/" | |
377 | "release/data/annotation/src/contrib/" | |
378 | "org.Ce.eg.db_" version ".tar.gz")) | |
379 | (sha256 | |
380 | (base32 | |
381 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) | |
382 | (properties | |
383 | `((upstream-name . "org.Ce.eg.db"))) | |
384 | (build-system r-build-system) | |
385 | (propagated-inputs | |
386 | `(("r-annotationdbi" ,r-annotationdbi))) | |
387 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") | |
388 | (synopsis "Genome wide annotation for Worm") | |
389 | (description | |
390 | "This package provides mappings from Entrez gene identifiers to various | |
391 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
392 | (license license:artistic2.0))) | |
393 | ||
f8780e96 RW |
394 | (define-public r-org-dm-eg-db |
395 | (package | |
396 | (name "r-org-dm-eg-db") | |
397 | (version "3.7.0") | |
398 | (source (origin | |
399 | (method url-fetch) | |
400 | ;; We cannot use bioconductor-uri here because this tarball is | |
401 | ;; located under "data/annotation/" instead of "bioc/". | |
402 | (uri (string-append "https://www.bioconductor.org/packages/" | |
403 | "release/data/annotation/src/contrib/" | |
404 | "org.Dm.eg.db_" version ".tar.gz")) | |
405 | (sha256 | |
406 | (base32 | |
407 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) | |
408 | (properties | |
409 | `((upstream-name . "org.Dm.eg.db"))) | |
410 | (build-system r-build-system) | |
411 | (propagated-inputs | |
412 | `(("r-annotationdbi" ,r-annotationdbi))) | |
413 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") | |
414 | (synopsis "Genome wide annotation for Fly") | |
415 | (description | |
416 | "This package provides mappings from Entrez gene identifiers to various | |
417 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
418 | (license license:artistic2.0))) | |
419 | ||
3dad6087 RW |
420 | (define-public r-org-dr-eg-db |
421 | (package | |
422 | (name "r-org-dr-eg-db") | |
423 | (version "3.7.0") | |
424 | (source (origin | |
425 | (method url-fetch) | |
426 | ;; We cannot use bioconductor-uri here because this tarball is | |
427 | ;; located under "data/annotation/" instead of "bioc/". | |
428 | (uri (string-append "https://www.bioconductor.org/packages/" | |
429 | "release/data/annotation/src/contrib/" | |
430 | "org.Dr.eg.db_" version ".tar.gz")) | |
431 | (sha256 | |
432 | (base32 | |
433 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) | |
434 | (properties | |
435 | `((upstream-name . "org.Dr.eg.db"))) | |
436 | (build-system r-build-system) | |
437 | (propagated-inputs | |
438 | `(("r-annotationdbi" ,r-annotationdbi))) | |
439 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") | |
440 | (synopsis "Annotation for Zebrafish") | |
441 | (description | |
442 | "This package provides genome wide annotations for Zebrafish, primarily | |
443 | based on mapping using Entrez Gene identifiers.") | |
444 | (license license:artistic2.0))) | |
445 | ||
d56df35a RW |
446 | (define-public r-org-hs-eg-db |
447 | (package | |
448 | (name "r-org-hs-eg-db") | |
449 | (version "3.7.0") | |
450 | (source (origin | |
451 | (method url-fetch) | |
452 | ;; We cannot use bioconductor-uri here because this tarball is | |
453 | ;; located under "data/annotation/" instead of "bioc/". | |
454 | (uri (string-append "https://www.bioconductor.org/packages/" | |
455 | "release/data/annotation/src/contrib/" | |
456 | "org.Hs.eg.db_" version ".tar.gz")) | |
457 | (sha256 | |
458 | (base32 | |
459 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) | |
460 | (properties | |
461 | `((upstream-name . "org.Hs.eg.db"))) | |
462 | (build-system r-build-system) | |
463 | (propagated-inputs | |
464 | `(("r-annotationdbi" ,r-annotationdbi))) | |
465 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") | |
466 | (synopsis "Genome wide annotation for Human") | |
467 | (description | |
468 | "This package contains genome-wide annotations for Human, primarily based | |
469 | on mapping using Entrez Gene identifiers.") | |
470 | (license license:artistic2.0))) | |
471 | ||
8035819f RW |
472 | (define-public r-org-mm-eg-db |
473 | (package | |
474 | (name "r-org-mm-eg-db") | |
475 | (version "3.7.0") | |
476 | (source (origin | |
477 | (method url-fetch) | |
478 | ;; We cannot use bioconductor-uri here because this tarball is | |
479 | ;; located under "data/annotation/" instead of "bioc/". | |
480 | (uri (string-append "https://www.bioconductor.org/packages/" | |
481 | "release/data/annotation/src/contrib/" | |
482 | "org.Mm.eg.db_" version ".tar.gz")) | |
483 | (sha256 | |
484 | (base32 | |
485 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) | |
486 | (properties | |
487 | `((upstream-name . "org.Mm.eg.db"))) | |
488 | (build-system r-build-system) | |
489 | (propagated-inputs | |
490 | `(("r-annotationdbi" ,r-annotationdbi))) | |
491 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") | |
492 | (synopsis "Genome wide annotation for Mouse") | |
493 | (description | |
494 | "This package provides mappings from Entrez gene identifiers to various | |
495 | annotations for the genome of the model mouse Mus musculus.") | |
496 | (license license:artistic2.0))) | |
497 | ||
fe0b76e2 RW |
498 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
499 | (package | |
500 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
501 | (version "1.4.0") | |
502 | (source (origin | |
503 | (method url-fetch) | |
504 | ;; We cannot use bioconductor-uri here because this tarball is | |
505 | ;; located under "data/annotation/" instead of "bioc/". | |
506 | (uri (string-append "https://www.bioconductor.org/packages/" | |
507 | "release/data/annotation/src/contrib/" | |
508 | "BSgenome.Hsapiens.UCSC.hg19_" | |
509 | version ".tar.gz")) | |
510 | (sha256 | |
511 | (base32 | |
512 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) | |
513 | (properties | |
514 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
515 | (build-system r-build-system) | |
516 | ;; As this package provides little more than a very large data file it | |
517 | ;; doesn't make sense to build substitutes. | |
518 | (arguments `(#:substitutable? #f)) | |
519 | (propagated-inputs | |
520 | `(("r-bsgenome" ,r-bsgenome))) | |
521 | (home-page | |
522 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
523 | (synopsis "Full genome sequences for Homo sapiens") | |
524 | (description | |
525 | "This package provides full genome sequences for Homo sapiens as provided | |
526 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
527 | (license license:artistic2.0))) | |
528 | ||
8324e64c RW |
529 | (define-public r-ensdb-hsapiens-v75 |
530 | (package | |
531 | (name "r-ensdb-hsapiens-v75") | |
532 | (version "2.99.0") | |
533 | (source | |
534 | (origin | |
535 | (method url-fetch) | |
536 | (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) | |
537 | (sha256 | |
538 | (base32 | |
539 | "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) | |
540 | (properties | |
541 | `((upstream-name . "EnsDb.Hsapiens.v75"))) | |
542 | (build-system r-build-system) | |
543 | (propagated-inputs | |
544 | `(("r-ensembldb" ,r-ensembldb))) | |
545 | (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") | |
546 | (synopsis "Ensembl based annotation package") | |
547 | (description | |
548 | "This package exposes an annotation database generated from Ensembl.") | |
549 | (license license:artistic2.0))) | |
550 | ||
2cc51108 RW |
551 | (define-public r-genelendatabase |
552 | (package | |
553 | (name "r-genelendatabase") | |
daeb3cd9 | 554 | (version "1.18.0") |
2cc51108 RW |
555 | (source |
556 | (origin | |
557 | (method url-fetch) | |
558 | ;; We cannot use bioconductor-uri here because this tarball is | |
559 | ;; located under "data/experiment/" instead of "bioc/". | |
560 | (uri (string-append "https://bioconductor.org/packages/" | |
561 | "release/data/experiment/src/contrib" | |
562 | "/geneLenDataBase_" version ".tar.gz")) | |
563 | (sha256 | |
564 | (base32 | |
daeb3cd9 | 565 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
2cc51108 RW |
566 | (properties |
567 | `((upstream-name . "geneLenDataBase"))) | |
568 | (build-system r-build-system) | |
569 | (propagated-inputs | |
570 | `(("r-rtracklayer" ,r-rtracklayer) | |
571 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
572 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
573 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
574 | (description | |
575 | "This package provides the lengths of mRNA transcripts for a number of | |
576 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
577 | (license license:lgpl2.0+))) | |
578 | ||
66e35ce6 RW |
579 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
580 | (package | |
581 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
582 | (version "3.2.2") | |
583 | (source (origin | |
584 | (method url-fetch) | |
585 | ;; We cannot use bioconductor-uri here because this tarball is | |
586 | ;; located under "data/annotation/" instead of "bioc/". | |
587 | (uri (string-append "https://bioconductor.org/packages/" | |
588 | "release/data/annotation/src/contrib" | |
589 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" | |
590 | version ".tar.gz")) | |
591 | (sha256 | |
592 | (base32 | |
593 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
594 | (properties | |
595 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
596 | (build-system r-build-system) | |
597 | ;; As this package provides little more than a very large data file it | |
598 | ;; doesn't make sense to build substitutes. | |
599 | (arguments `(#:substitutable? #f)) | |
600 | (propagated-inputs | |
601 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
602 | (home-page | |
603 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
604 | (synopsis "Annotation package for human genome in TxDb format") | |
605 | (description | |
606 | "This package provides an annotation database of Homo sapiens genome | |
607 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
798b80ce RW |
608 | track. The database is exposed as a @code{TxDb} object.") |
609 | (license license:artistic2.0))) | |
610 | ||
611 | (define-public r-txdb-hsapiens-ucsc-hg38-knowngene | |
612 | (package | |
613 | (name "r-txdb-hsapiens-ucsc-hg38-knowngene") | |
614 | (version "3.4.6") | |
615 | (source (origin | |
616 | (method url-fetch) | |
617 | ;; We cannot use bioconductor-uri here because this tarball is | |
618 | ;; located under "data/annotation/" instead of "bioc/". | |
619 | (uri (string-append "https://bioconductor.org/packages/" | |
620 | "release/data/annotation/src/contrib" | |
621 | "/TxDb.Hsapiens.UCSC.hg38.knownGene_" | |
622 | version ".tar.gz")) | |
623 | (sha256 | |
624 | (base32 | |
625 | "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) | |
626 | (properties | |
627 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) | |
628 | (build-system r-build-system) | |
629 | (propagated-inputs | |
630 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
631 | (home-page | |
632 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") | |
633 | (synopsis "Annotation package for human genome in TxDb format") | |
634 | (description | |
635 | "This package provides an annotation database of Homo sapiens genome | |
636 | data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" | |
66e35ce6 RW |
637 | track. The database is exposed as a @code{TxDb} object.") |
638 | (license license:artistic2.0))) | |
639 | ||
d220babf RW |
640 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
641 | (package | |
642 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
643 | (version "3.2.2") | |
644 | (source (origin | |
645 | (method url-fetch) | |
646 | ;; We cannot use bioconductor-uri here because this tarball is | |
647 | ;; located under "data/annotation/" instead of "bioc/". | |
648 | (uri (string-append "https://bioconductor.org/packages/" | |
649 | "release/data/annotation/src/contrib" | |
650 | "/TxDb.Mmusculus.UCSC.mm9.knownGene_" | |
651 | version ".tar.gz")) | |
652 | (sha256 | |
653 | (base32 | |
654 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
655 | (properties | |
656 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
657 | (build-system r-build-system) | |
658 | (propagated-inputs | |
659 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
660 | ("r-annotationdbi" ,r-annotationdbi))) | |
661 | (home-page | |
662 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
663 | (synopsis "Annotation package for mouse genome in TxDb format") | |
664 | (description | |
665 | "This package provides an annotation database of Mouse genome data. It | |
666 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
667 | database is exposed as a @code{TxDb} object.") | |
668 | (license license:artistic2.0))) | |
669 | ||
7bc5d1b0 RW |
670 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
671 | (package | |
672 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
61242625 | 673 | (version "3.4.7") |
7bc5d1b0 RW |
674 | (source (origin |
675 | (method url-fetch) | |
676 | ;; We cannot use bioconductor-uri here because this tarball is | |
677 | ;; located under "data/annotation/" instead of "bioc/". | |
678 | (uri (string-append "https://www.bioconductor.org/packages/" | |
679 | "release/data/annotation/src/contrib/" | |
680 | "TxDb.Mmusculus.UCSC.mm10.knownGene_" | |
681 | version ".tar.gz")) | |
682 | (sha256 | |
683 | (base32 | |
61242625 | 684 | "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b")))) |
7bc5d1b0 RW |
685 | (properties |
686 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
687 | (build-system r-build-system) | |
688 | ;; As this package provides little more than a very large data file it | |
689 | ;; doesn't make sense to build substitutes. | |
690 | (arguments `(#:substitutable? #f)) | |
691 | (propagated-inputs | |
692 | `(("r-bsgenome" ,r-bsgenome) | |
693 | ("r-genomicfeatures" ,r-genomicfeatures) | |
694 | ("r-annotationdbi" ,r-annotationdbi))) | |
695 | (home-page | |
696 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
697 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
698 | (description | |
699 | "This package loads a TxDb object, which is an R interface to | |
700 | prefabricated databases contained in this package. This package provides | |
701 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
702 | based on the knownGene track.") | |
703 | (license license:artistic2.0))) | |
704 | ||
7cd446fd RW |
705 | (define-public r-txdb-celegans-ucsc-ce6-ensgene |
706 | (package | |
707 | (name "r-txdb-celegans-ucsc-ce6-ensgene") | |
708 | (version "3.2.2") | |
709 | (source | |
710 | (origin | |
711 | (method url-fetch) | |
712 | (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene" | |
713 | version 'annotation)) | |
714 | (sha256 | |
715 | (base32 | |
716 | "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90")))) | |
717 | (properties | |
718 | `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) | |
719 | (build-system r-build-system) | |
720 | (propagated-inputs | |
721 | `(("r-annotationdbi" ,r-annotationdbi) | |
722 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
723 | (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") | |
724 | (synopsis "Annotation package for C elegans TxDb objects") | |
725 | (description | |
726 | "This package exposes a C elegans annotation database generated from UCSC | |
727 | by exposing these as TxDb objects.") | |
728 | (license license:artistic2.0))) | |
729 | ||
0f5c9cec RW |
730 | (define-public r-fdb-infiniummethylation-hg19 |
731 | (package | |
732 | (name "r-fdb-infiniummethylation-hg19") | |
733 | (version "2.2.0") | |
734 | (source (origin | |
735 | (method url-fetch) | |
736 | ;; We cannot use bioconductor-uri here because this tarball is | |
737 | ;; located under "data/annotation/" instead of "bioc/". | |
738 | (uri (string-append "https://www.bioconductor.org/packages/" | |
739 | "release/data/annotation/src/contrib/" | |
740 | "FDb.InfiniumMethylation.hg19_" | |
741 | version ".tar.gz")) | |
742 | (sha256 | |
743 | (base32 | |
744 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) | |
745 | (properties | |
746 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) | |
747 | (build-system r-build-system) | |
748 | (propagated-inputs | |
749 | `(("r-biostrings" ,r-biostrings) | |
750 | ("r-genomicfeatures" ,r-genomicfeatures) | |
751 | ("r-annotationdbi" ,r-annotationdbi) | |
752 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
753 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) | |
754 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") | |
755 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") | |
756 | (description | |
757 | "This is an annotation package for Illumina Infinium DNA methylation | |
758 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 | |
759 | annotations.") | |
760 | (license license:artistic2.0))) | |
761 | ||
9475a248 RW |
762 | (define-public r-illuminahumanmethylationepicmanifest |
763 | (package | |
764 | (name "r-illuminahumanmethylationepicmanifest") | |
765 | (version "0.3.0") | |
766 | (source (origin | |
767 | (method url-fetch) | |
768 | ;; We cannot use bioconductor-uri here because this tarball is | |
769 | ;; located under "data/annotation/" instead of "bioc/". | |
770 | (uri (string-append "https://www.bioconductor.org/packages/" | |
771 | "release/data/annotation/src/contrib/" | |
772 | "IlluminaHumanMethylationEPICmanifest_" | |
773 | version ".tar.gz")) | |
774 | (sha256 | |
775 | (base32 | |
776 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) | |
777 | (properties | |
778 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) | |
779 | (build-system r-build-system) | |
780 | (propagated-inputs | |
781 | `(("r-minfi" ,r-minfi))) | |
782 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") | |
783 | (synopsis "Manifest for Illumina's EPIC methylation arrays") | |
784 | (description | |
785 | "This is a manifest package for Illumina's EPIC methylation arrays.") | |
786 | (license license:artistic2.0))) | |
787 | ||
f8a5af46 RW |
788 | (define-public r-do-db |
789 | (package | |
790 | (name "r-do-db") | |
791 | (version "2.9") | |
792 | (source (origin | |
793 | (method url-fetch) | |
794 | ;; We cannot use bioconductor-uri here because this tarball is | |
795 | ;; located under "data/annotation/" instead of "bioc/". | |
796 | (uri (string-append "https://www.bioconductor.org/packages/" | |
797 | "release/data/annotation/src/contrib/" | |
798 | "DO.db_" version ".tar.gz")) | |
799 | (sha256 | |
800 | (base32 | |
801 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) | |
802 | (properties | |
803 | `((upstream-name . "DO.db"))) | |
804 | (build-system r-build-system) | |
805 | (propagated-inputs | |
806 | `(("r-annotationdbi" ,r-annotationdbi))) | |
807 | (home-page "https://www.bioconductor.org/packages/DO.db/") | |
808 | (synopsis "Annotation maps describing the entire Disease Ontology") | |
809 | (description | |
810 | "This package provides a set of annotation maps describing the entire | |
811 | Disease Ontology.") | |
812 | (license license:artistic2.0))) | |
813 | ||
83b42091 RW |
814 | (define-public r-pfam-db |
815 | (package | |
816 | (name "r-pfam-db") | |
817 | (version "3.8.2") | |
818 | (source | |
819 | (origin | |
820 | (method url-fetch) | |
821 | (uri (bioconductor-uri "PFAM.db" version 'annotation)) | |
822 | (sha256 | |
823 | (base32 | |
824 | "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) | |
825 | (properties `((upstream-name . "PFAM.db"))) | |
826 | (build-system r-build-system) | |
827 | (propagated-inputs | |
828 | `(("r-annotationdbi" ,r-annotationdbi))) | |
829 | (home-page "https://bioconductor.org/packages/PFAM.db") | |
830 | (synopsis "Set of protein ID mappings for PFAM") | |
831 | (description | |
832 | "This package provides a set of protein ID mappings for PFAM, assembled | |
833 | using data from public repositories.") | |
834 | (license license:artistic2.0))) | |
835 | ||
40be965e RW |
836 | (define-public r-phastcons100way-ucsc-hg19 |
837 | (package | |
838 | (name "r-phastcons100way-ucsc-hg19") | |
839 | (version "3.7.2") | |
840 | (source | |
841 | (origin | |
842 | (method url-fetch) | |
843 | (uri (bioconductor-uri "phastCons100way.UCSC.hg19" | |
844 | version 'annotation)) | |
845 | (sha256 | |
846 | (base32 | |
847 | "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa")))) | |
848 | (properties | |
849 | `((upstream-name . "phastCons100way.UCSC.hg19"))) | |
850 | (build-system r-build-system) | |
851 | (propagated-inputs | |
852 | `(("r-bsgenome" ,r-bsgenome) | |
853 | ("r-genomeinfodb" ,r-genomeinfodb) | |
854 | ("r-genomicranges" ,r-genomicranges) | |
855 | ("r-genomicscores" ,r-genomicscores) | |
856 | ("r-iranges" ,r-iranges) | |
857 | ("r-s4vectors" ,r-s4vectors))) | |
858 | (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") | |
859 | (synopsis "UCSC phastCons conservation scores for hg19") | |
860 | (description | |
861 | "This package provides UCSC phastCons conservation scores for the human | |
862 | genome (hg19) calculated from multiple alignments with other 99 vertebrate | |
863 | species.") | |
864 | (license license:artistic2.0))) | |
865 | ||
2cc51108 | 866 | \f |
557a1089 RW |
867 | ;;; Experiment data |
868 | ||
692bce15 RW |
869 | (define-public r-abadata |
870 | (package | |
871 | (name "r-abadata") | |
872 | (version "1.12.0") | |
873 | (source (origin | |
874 | (method url-fetch) | |
875 | ;; We cannot use bioconductor-uri here because this tarball is | |
876 | ;; located under "data/experiment/" instead of "bioc/". | |
877 | (uri (string-append "https://www.bioconductor.org/packages/" | |
878 | "release/data/experiment/src/contrib/" | |
879 | "ABAData_" version ".tar.gz")) | |
880 | (sha256 | |
881 | (base32 | |
882 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) | |
883 | (properties | |
884 | `((upstream-name . "ABAData"))) | |
885 | (build-system r-build-system) | |
886 | (propagated-inputs | |
887 | `(("r-annotationdbi" ,r-annotationdbi))) | |
888 | (home-page "https://www.bioconductor.org/packages/ABAData/") | |
889 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") | |
890 | (description | |
891 | "This package provides the data for the gene expression enrichment | |
892 | analysis conducted in the package ABAEnrichment. The package includes three | |
893 | datasets which are derived from the Allen Brain Atlas: | |
894 | ||
895 | @enumerate | |
896 | @item Gene expression data from Human Brain (adults) averaged across donors, | |
897 | @item Gene expression data from the Developing Human Brain pooled into five | |
898 | age categories and averaged across donors, and | |
899 | @item a developmental effect score based on the Developing Human Brain | |
900 | expression data. | |
901 | @end enumerate | |
902 | ||
903 | All datasets are restricted to protein coding genes.") | |
904 | (license license:gpl2+))) | |
905 | ||
b50c9660 RW |
906 | (define-public r-arrmdata |
907 | (package | |
908 | (name "r-arrmdata") | |
909 | (version "1.18.0") | |
910 | (source (origin | |
911 | (method url-fetch) | |
912 | ;; We cannot use bioconductor-uri here because this tarball is | |
913 | ;; located under "data/experiment/" instead of "bioc/". | |
914 | (uri (string-append "https://www.bioconductor.org/packages/" | |
915 | "release/data/experiment/src/contrib/" | |
916 | "ARRmData_" version ".tar.gz")) | |
917 | (sha256 | |
918 | (base32 | |
919 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) | |
920 | (properties | |
921 | `((upstream-name . "ARRmData"))) | |
922 | (build-system r-build-system) | |
923 | (home-page "https://www.bioconductor.org/packages/ARRmData/") | |
924 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") | |
925 | (description | |
926 | "This package provides raw beta values from 36 samples across 3 groups | |
927 | from Illumina 450k methylation arrays.") | |
928 | (license license:artistic2.0))) | |
929 | ||
557a1089 RW |
930 | (define-public r-hsmmsinglecell |
931 | (package | |
932 | (name "r-hsmmsinglecell") | |
933 | (version "1.2.0") | |
934 | (source (origin | |
935 | (method url-fetch) | |
936 | ;; We cannot use bioconductor-uri here because this tarball is | |
937 | ;; located under "data/experiment/" instead of "bioc/". | |
938 | (uri (string-append "https://www.bioconductor.org/packages/" | |
939 | "release/data/experiment/src/contrib/" | |
940 | "HSMMSingleCell_" version ".tar.gz")) | |
941 | (sha256 | |
942 | (base32 | |
943 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) | |
944 | (properties | |
945 | `((upstream-name . "HSMMSingleCell"))) | |
946 | (build-system r-build-system) | |
947 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") | |
948 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") | |
949 | (description | |
950 | "Skeletal myoblasts undergo a well-characterized sequence of | |
951 | morphological and transcriptional changes during differentiation. In this | |
952 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded | |
953 | under high mitogen conditions (GM) and then differentiated by switching to | |
954 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several | |
955 | hundred cells taken over a time-course of serum-induced differentiation. | |
956 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, | |
957 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. | |
958 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, | |
959 | which were then sequenced to a depth of ~4 million reads per library, | |
960 | resulting in a complete gene expression profile for each cell.") | |
961 | (license license:artistic2.0))) | |
ad8f46c6 | 962 | |
963 | (define-public r-all | |
964 | (package | |
965 | (name "r-all") | |
966 | (version "1.26.0") | |
967 | (source (origin | |
968 | (method url-fetch) | |
969 | ;; We cannot use bioconductor-uri here because this tarball is | |
970 | ;; located under "data/experiment/" instead of "bioc/". | |
971 | (uri (string-append "https://www.bioconductor.org/packages/" | |
972 | "release/data/experiment/src/contrib/" | |
973 | "ALL_" version ".tar.gz")) | |
974 | (sha256 | |
975 | (base32 | |
976 | "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) | |
977 | (properties `((upstream-name . "ALL"))) | |
978 | (build-system r-build-system) | |
979 | (propagated-inputs | |
980 | `(("r-biobase" ,r-biobase))) | |
981 | (home-page "https://bioconductor.org/packages/ALL") | |
982 | (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") | |
983 | (description | |
984 | "The data consist of microarrays from 128 different individuals with | |
985 | @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates | |
986 | are available. The data have been normalized (using rma) and it is the | |
987 | jointly normalized data that are available here. The data are presented in | |
988 | the form of an @code{exprSet} object.") | |
989 | (license license:artistic2.0))) | |
557a1089 | 990 | |
53b1e10f RW |
991 | (define-public r-affydata |
992 | (package | |
993 | (name "r-affydata") | |
994 | (version "1.32.0") | |
995 | (source | |
996 | (origin | |
997 | (method url-fetch) | |
998 | (uri (bioconductor-uri "affydata" version 'experiment)) | |
999 | (sha256 | |
1000 | (base32 | |
1001 | "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) | |
1002 | (properties `((upstream-name . "affydata"))) | |
1003 | (build-system r-build-system) | |
1004 | (propagated-inputs | |
1005 | `(("r-affy" ,r-affy))) | |
1006 | (home-page "https://bioconductor.org/packages/affydata/") | |
1007 | (synopsis "Affymetrix data for demonstration purposes") | |
1008 | (description | |
1009 | "This package provides example datasets that represent 'real world | |
1010 | examples' of Affymetrix data, unlike the artificial examples included in the | |
1011 | package @code{affy}.") | |
1012 | (license license:gpl2+))) | |
1013 | ||
557a1089 RW |
1014 | \f |
1015 | ;;; Packages | |
1016 | ||
14bba460 RW |
1017 | (define-public r-biocgenerics |
1018 | (package | |
1019 | (name "r-biocgenerics") | |
81a1c45d | 1020 | (version "0.30.0") |
14bba460 RW |
1021 | (source (origin |
1022 | (method url-fetch) | |
1023 | (uri (bioconductor-uri "BiocGenerics" version)) | |
1024 | (sha256 | |
1025 | (base32 | |
81a1c45d | 1026 | "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f")))) |
14bba460 RW |
1027 | (properties |
1028 | `((upstream-name . "BiocGenerics"))) | |
1029 | (build-system r-build-system) | |
1030 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
1031 | (synopsis "S4 generic functions for Bioconductor") | |
1032 | (description | |
1033 | "This package provides S4 generic functions needed by many Bioconductor | |
1034 | packages.") | |
1035 | (license license:artistic2.0))) | |
1036 | ||
5cf940de RW |
1037 | (define-public r-affycomp |
1038 | (package | |
1039 | (name "r-affycomp") | |
1040 | (version "1.60.0") | |
1041 | (source | |
1042 | (origin | |
1043 | (method url-fetch) | |
1044 | (uri (bioconductor-uri "affycomp" version)) | |
1045 | (sha256 | |
1046 | (base32 | |
1047 | "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n")))) | |
1048 | (properties `((upstream-name . "affycomp"))) | |
1049 | (build-system r-build-system) | |
1050 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
1051 | (home-page "https://bioconductor.org/packages/affycomp/") | |
1052 | (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") | |
1053 | (description | |
1054 | "The package contains functions that can be used to compare expression | |
1055 | measures for Affymetrix Oligonucleotide Arrays.") | |
1056 | (license license:gpl2+))) | |
1057 | ||
5094aa94 RW |
1058 | (define-public r-affycompatible |
1059 | (package | |
1060 | (name "r-affycompatible") | |
1061 | (version "1.44.0") | |
1062 | (source | |
1063 | (origin | |
1064 | (method url-fetch) | |
1065 | (uri (bioconductor-uri "AffyCompatible" version)) | |
1066 | (sha256 | |
1067 | (base32 | |
1068 | "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs")))) | |
1069 | (properties | |
1070 | `((upstream-name . "AffyCompatible"))) | |
1071 | (build-system r-build-system) | |
1072 | (propagated-inputs | |
1073 | `(("r-biostrings" ,r-biostrings) | |
1074 | ("r-rcurl" ,r-rcurl) | |
1075 | ("r-xml" ,r-xml))) | |
1076 | (home-page "https://bioconductor.org/packages/AffyCompatible/") | |
1077 | (synopsis "Work with Affymetrix GeneChip files") | |
1078 | (description | |
1079 | "This package provides an interface to Affymetrix chip annotation and | |
1080 | sample attribute files. The package allows an easy way for users to download | |
1081 | and manage local data bases of Affynmetrix NetAffx annotation files. It also | |
1082 | provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip | |
1083 | Command Console} (AGCC)-compatible sample annotation files.") | |
1084 | (license license:artistic2.0))) | |
1085 | ||
4ca2d6c1 RW |
1086 | (define-public r-affycontam |
1087 | (package | |
1088 | (name "r-affycontam") | |
1089 | (version "1.42.0") | |
1090 | (source | |
1091 | (origin | |
1092 | (method url-fetch) | |
1093 | (uri (bioconductor-uri "affyContam" version)) | |
1094 | (sha256 | |
1095 | (base32 | |
1096 | "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp")))) | |
1097 | (properties `((upstream-name . "affyContam"))) | |
1098 | (build-system r-build-system) | |
1099 | (propagated-inputs | |
1100 | `(("r-affy" ,r-affy) | |
1101 | ("r-affydata" ,r-affydata) | |
1102 | ("r-biobase" ,r-biobase))) | |
1103 | (home-page "https://bioconductor.org/packages/affyContam/") | |
1104 | (synopsis "Structured corruption of Affymetrix CEL file data") | |
1105 | (description | |
1106 | "Microarray quality assessment is a major concern of microarray analysts. | |
1107 | This package provides some simple approaches to in silico creation of quality | |
1108 | problems in CEL-level data to help evaluate performance of quality metrics.") | |
1109 | (license license:artistic2.0))) | |
1110 | ||
12105c6c RW |
1111 | (define-public r-affycoretools |
1112 | (package | |
1113 | (name "r-affycoretools") | |
1114 | (version "1.56.0") | |
1115 | (source | |
1116 | (origin | |
1117 | (method url-fetch) | |
1118 | (uri (bioconductor-uri "affycoretools" version)) | |
1119 | (sha256 | |
1120 | (base32 | |
1121 | "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s")))) | |
1122 | (properties `((upstream-name . "affycoretools"))) | |
1123 | (build-system r-build-system) | |
1124 | (propagated-inputs | |
1125 | `(("r-affy" ,r-affy) | |
1126 | ("r-annotationdbi" ,r-annotationdbi) | |
1127 | ("r-biobase" ,r-biobase) | |
1128 | ("r-biocgenerics" ,r-biocgenerics) | |
1129 | ("r-dbi" ,r-dbi) | |
1130 | ("r-edger" ,r-edger) | |
1131 | ("r-gcrma" ,r-gcrma) | |
1132 | ("r-ggplot2" ,r-ggplot2) | |
1133 | ("r-gostats" ,r-gostats) | |
1134 | ("r-gplots" ,r-gplots) | |
1135 | ("r-hwriter" ,r-hwriter) | |
1136 | ("r-lattice" ,r-lattice) | |
1137 | ("r-limma" ,r-limma) | |
1138 | ("r-oligoclasses" ,r-oligoclasses) | |
1139 | ("r-reportingtools" ,r-reportingtools) | |
1140 | ("r-rsqlite" ,r-rsqlite) | |
1141 | ("r-s4vectors" ,r-s4vectors) | |
1142 | ("r-xtable" ,r-xtable))) | |
1143 | (home-page "https://bioconductor.org/packages/affycoretools/") | |
1144 | (synopsis "Functions for analyses with Affymetrix GeneChips") | |
1145 | (description | |
1146 | "This package provides various wrapper functions that have been written | |
1147 | to streamline the more common analyses that a Biostatistician might see.") | |
1148 | (license license:artistic2.0))) | |
1149 | ||
d6a5d9b2 RW |
1150 | (define-public r-affxparser |
1151 | (package | |
1152 | (name "r-affxparser") | |
1153 | (version "1.56.0") | |
1154 | (source | |
1155 | (origin | |
1156 | (method url-fetch) | |
1157 | (uri (bioconductor-uri "affxparser" version)) | |
1158 | (sha256 | |
1159 | (base32 | |
1160 | "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33")))) | |
1161 | (properties `((upstream-name . "affxparser"))) | |
1162 | (build-system r-build-system) | |
1163 | (home-page "https://github.com/HenrikBengtsson/affxparser") | |
1164 | (synopsis "Affymetrix File Parsing SDK") | |
1165 | (description | |
1166 | "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, | |
1167 | BAR). It provides methods for fast and memory efficient parsing of Affymetrix | |
1168 | files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files | |
1169 | are supported. Currently, there are methods for reading @dfn{chip definition | |
1170 | file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read | |
1171 | either in full or in part. For example, probe signals from a few probesets | |
1172 | can be extracted very quickly from a set of CEL files into a convenient list | |
1173 | structure.") | |
1174 | ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is | |
1175 | ;; under LGPLv2+. | |
1176 | (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2)))) | |
1177 | ||
7097c700 RW |
1178 | (define-public r-annotate |
1179 | (package | |
1180 | (name "r-annotate") | |
0c53332a | 1181 | (version "1.62.0") |
7097c700 RW |
1182 | (source |
1183 | (origin | |
1184 | (method url-fetch) | |
1185 | (uri (bioconductor-uri "annotate" version)) | |
1186 | (sha256 | |
1187 | (base32 | |
0c53332a | 1188 | "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs")))) |
7097c700 RW |
1189 | (build-system r-build-system) |
1190 | (propagated-inputs | |
1191 | `(("r-annotationdbi" ,r-annotationdbi) | |
1192 | ("r-biobase" ,r-biobase) | |
1193 | ("r-biocgenerics" ,r-biocgenerics) | |
1194 | ("r-dbi" ,r-dbi) | |
1195 | ("r-rcurl" ,r-rcurl) | |
1196 | ("r-xml" ,r-xml) | |
1197 | ("r-xtable" ,r-xtable))) | |
1198 | (home-page | |
1199 | "https://bioconductor.org/packages/annotate") | |
1200 | (synopsis "Annotation for microarrays") | |
1201 | (description "This package provides R environments for the annotation of | |
1202 | microarrays.") | |
1203 | (license license:artistic2.0))) | |
1204 | ||
fa596599 RW |
1205 | (define-public r-hpar |
1206 | (package | |
1207 | (name "r-hpar") | |
43a23a07 | 1208 | (version "1.26.0") |
fa596599 RW |
1209 | (source |
1210 | (origin | |
1211 | (method url-fetch) | |
1212 | (uri (bioconductor-uri "hpar" version)) | |
1213 | (sha256 | |
1214 | (base32 | |
43a23a07 | 1215 | "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5")))) |
fa596599 RW |
1216 | (build-system r-build-system) |
1217 | (home-page "https://bioconductor.org/packages/hpar/") | |
1218 | (synopsis "Human Protein Atlas in R") | |
1219 | (description "This package provides a simple interface to and data from | |
1220 | the Human Protein Atlas project.") | |
1221 | (license license:artistic2.0))) | |
183ce988 RJ |
1222 | |
1223 | (define-public r-regioner | |
1224 | (package | |
1225 | (name "r-regioner") | |
1c2e5733 | 1226 | (version "1.16.5") |
183ce988 RJ |
1227 | (source |
1228 | (origin | |
1229 | (method url-fetch) | |
1230 | (uri (bioconductor-uri "regioneR" version)) | |
1231 | (sha256 | |
1232 | (base32 | |
1c2e5733 | 1233 | "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h")))) |
183ce988 RJ |
1234 | (properties `((upstream-name . "regioneR"))) |
1235 | (build-system r-build-system) | |
1236 | (propagated-inputs | |
d639d888 | 1237 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 1238 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 1239 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 1240 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 1241 | ("r-iranges" ,r-iranges) |
d639d888 RW |
1242 | ("r-memoise" ,r-memoise) |
1243 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 1244 | ("r-s4vectors" ,r-s4vectors))) |
183ce988 RJ |
1245 | (home-page "https://bioconductor.org/packages/regioneR/") |
1246 | (synopsis "Association analysis of genomic regions") | |
1247 | (description "This package offers a statistical framework based on | |
1248 | customizable permutation tests to assess the association between genomic | |
1249 | region sets and other genomic features.") | |
1250 | (license license:artistic2.0))) | |
a5b56a53 | 1251 | |
15184fb3 RW |
1252 | (define-public r-reportingtools |
1253 | (package | |
1254 | (name "r-reportingtools") | |
1255 | (version "2.24.0") | |
1256 | (source | |
1257 | (origin | |
1258 | (method url-fetch) | |
1259 | (uri (bioconductor-uri "ReportingTools" version)) | |
1260 | (sha256 | |
1261 | (base32 | |
1262 | "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc")))) | |
1263 | (properties | |
1264 | `((upstream-name . "ReportingTools"))) | |
1265 | (build-system r-build-system) | |
1266 | (propagated-inputs | |
1267 | `(("r-annotate" ,r-annotate) | |
1268 | ("r-annotationdbi" ,r-annotationdbi) | |
1269 | ("r-biobase" ,r-biobase) | |
1270 | ("r-biocgenerics" ,r-biocgenerics) | |
1271 | ("r-category" ,r-category) | |
1272 | ("r-deseq2" ,r-deseq2) | |
1273 | ("r-edger" ,r-edger) | |
1274 | ("r-ggbio" ,r-ggbio) | |
1275 | ("r-ggplot2" ,r-ggplot2) | |
1276 | ("r-gostats" ,r-gostats) | |
1277 | ("r-gseabase" ,r-gseabase) | |
1278 | ("r-hwriter" ,r-hwriter) | |
1279 | ("r-iranges" ,r-iranges) | |
1280 | ("r-knitr" ,r-knitr) | |
1281 | ("r-lattice" ,r-lattice) | |
1282 | ("r-limma" ,r-limma) | |
1283 | ("r-pfam-db" ,r-pfam-db) | |
1284 | ("r-r-utils" ,r-r-utils) | |
1285 | ("r-xml" ,r-xml))) | |
1286 | (home-page "https://bioconductor.org/packages/ReportingTools/") | |
1287 | (synopsis "Tools for making reports in various formats") | |
1288 | (description | |
1289 | "The ReportingTools package enables users to easily display reports of | |
1290 | analysis results generated from sources such as microarray and sequencing | |
1291 | data. The package allows users to create HTML pages that may be viewed on a | |
1292 | web browser, or in other formats. Users can generate tables with sortable and | |
1293 | filterable columns, make and display plots, and link table entries to other | |
1294 | data sources such as NCBI or larger plots within the HTML page. Using the | |
1295 | package, users can also produce a table of contents page to link various | |
1296 | reports together for a particular project that can be viewed in a web | |
1297 | browser.") | |
1298 | (license license:artistic2.0))) | |
1299 | ||
bfb93b48 RW |
1300 | (define-public r-geneplotter |
1301 | (package | |
1302 | (name "r-geneplotter") | |
3e1bc88c | 1303 | (version "1.62.0") |
bfb93b48 RW |
1304 | (source |
1305 | (origin | |
1306 | (method url-fetch) | |
1307 | (uri (bioconductor-uri "geneplotter" version)) | |
1308 | (sha256 | |
1309 | (base32 | |
3e1bc88c | 1310 | "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb")))) |
bfb93b48 RW |
1311 | (build-system r-build-system) |
1312 | (propagated-inputs | |
1313 | `(("r-annotate" ,r-annotate) | |
1314 | ("r-annotationdbi" ,r-annotationdbi) | |
1315 | ("r-biobase" ,r-biobase) | |
1316 | ("r-biocgenerics" ,r-biocgenerics) | |
1317 | ("r-lattice" ,r-lattice) | |
1318 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
1319 | (home-page "https://bioconductor.org/packages/geneplotter") | |
1320 | (synopsis "Graphics functions for genomic data") | |
1321 | (description | |
1322 | "This package provides functions for plotting genomic data.") | |
1323 | (license license:artistic2.0))) | |
1324 | ||
01c7ba99 RW |
1325 | (define-public r-oligoclasses |
1326 | (package | |
1327 | (name "r-oligoclasses") | |
1328 | (version "1.46.0") | |
1329 | (source | |
1330 | (origin | |
1331 | (method url-fetch) | |
1332 | (uri (bioconductor-uri "oligoClasses" version)) | |
1333 | (sha256 | |
1334 | (base32 | |
1335 | "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72")))) | |
1336 | (properties `((upstream-name . "oligoClasses"))) | |
1337 | (build-system r-build-system) | |
1338 | (propagated-inputs | |
1339 | `(("r-affyio" ,r-affyio) | |
1340 | ("r-biobase" ,r-biobase) | |
1341 | ("r-biocgenerics" ,r-biocgenerics) | |
1342 | ("r-biocmanager" ,r-biocmanager) | |
1343 | ("r-biostrings" ,r-biostrings) | |
1344 | ("r-dbi" ,r-dbi) | |
1345 | ("r-ff" ,r-ff) | |
1346 | ("r-foreach" ,r-foreach) | |
1347 | ("r-genomicranges" ,r-genomicranges) | |
1348 | ("r-iranges" ,r-iranges) | |
1349 | ("r-rsqlite" ,r-rsqlite) | |
1350 | ("r-s4vectors" ,r-s4vectors) | |
1351 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1352 | (home-page "https://bioconductor.org/packages/oligoClasses/") | |
1353 | (synopsis "Classes for high-throughput arrays") | |
1354 | (description | |
1355 | "This package contains class definitions, validity checks, and | |
1356 | initialization methods for classes used by the @code{oligo} and @code{crlmm} | |
1357 | packages.") | |
1358 | (license license:gpl2+))) | |
1359 | ||
4c63eeb8 RW |
1360 | (define-public r-oligo |
1361 | (package | |
1362 | (name "r-oligo") | |
1363 | (version "1.48.0") | |
1364 | (source | |
1365 | (origin | |
1366 | (method url-fetch) | |
1367 | (uri (bioconductor-uri "oligo" version)) | |
1368 | (sha256 | |
1369 | (base32 | |
1370 | "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df")))) | |
1371 | (properties `((upstream-name . "oligo"))) | |
1372 | (build-system r-build-system) | |
1373 | (inputs `(("zlib" ,zlib))) | |
1374 | (propagated-inputs | |
1375 | `(("r-affxparser" ,r-affxparser) | |
1376 | ("r-affyio" ,r-affyio) | |
1377 | ("r-biobase" ,r-biobase) | |
1378 | ("r-biocgenerics" ,r-biocgenerics) | |
1379 | ("r-biostrings" ,r-biostrings) | |
1380 | ("r-dbi" ,r-dbi) | |
1381 | ("r-ff" ,r-ff) | |
1382 | ("r-oligoclasses" ,r-oligoclasses) | |
1383 | ("r-preprocesscore" ,r-preprocesscore) | |
1384 | ("r-rsqlite" ,r-rsqlite) | |
1385 | ("r-zlibbioc" ,r-zlibbioc))) | |
1386 | (home-page "https://bioconductor.org/packages/oligo/") | |
1387 | (synopsis "Preprocessing tools for oligonucleotide arrays") | |
1388 | (description | |
1389 | "This package provides a package to analyze oligonucleotide | |
1390 | arrays (expression/SNP/tiling/exon) at probe-level. It currently supports | |
1391 | Affymetrix (CEL files) and NimbleGen arrays (XYS files).") | |
1392 | (license license:lgpl2.0+))) | |
1393 | ||
4dc2ecc2 RW |
1394 | (define-public r-qvalue |
1395 | (package | |
1396 | (name "r-qvalue") | |
e02162f7 | 1397 | (version "2.16.0") |
4dc2ecc2 RW |
1398 | (source |
1399 | (origin | |
1400 | (method url-fetch) | |
1401 | (uri (bioconductor-uri "qvalue" version)) | |
1402 | (sha256 | |
1403 | (base32 | |
e02162f7 | 1404 | "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5")))) |
4dc2ecc2 RW |
1405 | (build-system r-build-system) |
1406 | (propagated-inputs | |
1407 | `(("r-ggplot2" ,r-ggplot2) | |
1408 | ("r-reshape2" ,r-reshape2))) | |
1409 | (home-page "http://github.com/jdstorey/qvalue") | |
1410 | (synopsis "Q-value estimation for false discovery rate control") | |
1411 | (description | |
1412 | "This package takes a list of p-values resulting from the simultaneous | |
1413 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
1414 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
1415 | of false positives incurred when that particular test is called significant. | |
1416 | The local FDR measures the posterior probability the null hypothesis is true | |
1417 | given the test's p-value. Various plots are automatically generated, allowing | |
1418 | one to make sensible significance cut-offs. The software can be applied to | |
1419 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
1420 | ;; Any version of the LGPL. | |
1421 | (license license:lgpl3+))) | |
1422 | ||
a5b56a53 RJ |
1423 | (define-public r-diffbind |
1424 | (package | |
1425 | (name "r-diffbind") | |
4c221b3b | 1426 | (version "2.12.0") |
a5b56a53 RJ |
1427 | (source |
1428 | (origin | |
1429 | (method url-fetch) | |
1430 | (uri (bioconductor-uri "DiffBind" version)) | |
1431 | (sha256 | |
1432 | (base32 | |
4c221b3b | 1433 | "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich")))) |
a5b56a53 RJ |
1434 | (properties `((upstream-name . "DiffBind"))) |
1435 | (build-system r-build-system) | |
1436 | (inputs | |
1437 | `(("zlib" ,zlib))) | |
1438 | (propagated-inputs | |
1439 | `(("r-amap" ,r-amap) | |
1440 | ("r-biocparallel" ,r-biocparallel) | |
1441 | ("r-deseq2" ,r-deseq2) | |
1442 | ("r-dplyr" ,r-dplyr) | |
1443 | ("r-edger" ,r-edger) | |
1444 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
1445 | ("r-genomicranges" ,r-genomicranges) |
1446 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
1447 | ("r-ggrepel" ,r-ggrepel) |
1448 | ("r-gplots" ,r-gplots) | |
1449 | ("r-iranges" ,r-iranges) | |
1450 | ("r-lattice" ,r-lattice) | |
1451 | ("r-limma" ,r-limma) | |
1452 | ("r-locfit" ,r-locfit) | |
1453 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
1454 | ("r-rcpp" ,r-rcpp) | |
4c221b3b | 1455 | ("r-rhtslib" ,r-rhtslib) |
a5b56a53 RJ |
1456 | ("r-rsamtools" ,r-rsamtools) |
1457 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 1458 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
4c221b3b | 1459 | ("r-systempiper" ,r-systempiper))) |
a5b56a53 RJ |
1460 | (home-page "http://bioconductor.org/packages/DiffBind") |
1461 | (synopsis "Differential binding analysis of ChIP-Seq peak data") | |
1462 | (description | |
1463 | "This package computes differentially bound sites from multiple | |
1464 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
1465 | occupancy (overlap) analysis and plotting functions.") | |
1466 | (license license:artistic2.0))) | |
6d94bf6b RJ |
1467 | |
1468 | (define-public r-ripseeker | |
1469 | (package | |
1470 | (name "r-ripseeker") | |
0968a448 | 1471 | (version "1.24.0") |
6d94bf6b RJ |
1472 | (source |
1473 | (origin | |
1474 | (method url-fetch) | |
1475 | (uri (bioconductor-uri "RIPSeeker" version)) | |
1476 | (sha256 | |
1477 | (base32 | |
0968a448 | 1478 | "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43")))) |
6d94bf6b RJ |
1479 | (properties `((upstream-name . "RIPSeeker"))) |
1480 | (build-system r-build-system) | |
1481 | (propagated-inputs | |
1482 | `(("r-s4vectors" ,r-s4vectors) | |
1483 | ("r-iranges" ,r-iranges) | |
1484 | ("r-genomicranges" ,r-genomicranges) | |
1485 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1486 | ("r-rsamtools" ,r-rsamtools) | |
1487 | ("r-genomicalignments" ,r-genomicalignments) | |
1488 | ("r-rtracklayer" ,r-rtracklayer))) | |
1489 | (home-page "http://bioconductor.org/packages/RIPSeeker") | |
1490 | (synopsis | |
1491 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
1492 | (description | |
1493 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
1494 | using two-state HMM with negative binomial emission probability. While | |
1495 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
1496 | a suite of bioinformatics tools integrated within this self-contained software | |
1497 | package comprehensively addressing issues ranging from post-alignments | |
1498 | processing to visualization and annotation.") | |
1499 | (license license:gpl2))) | |
a6ae9ffd RJ |
1500 | |
1501 | (define-public r-multtest | |
1502 | (package | |
1503 | (name "r-multtest") | |
588b63c2 | 1504 | (version "2.40.0") |
a6ae9ffd RJ |
1505 | (source |
1506 | (origin | |
1507 | (method url-fetch) | |
1508 | (uri (bioconductor-uri "multtest" version)) | |
1509 | (sha256 | |
1510 | (base32 | |
588b63c2 | 1511 | "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv")))) |
a6ae9ffd RJ |
1512 | (build-system r-build-system) |
1513 | (propagated-inputs | |
1514 | `(("r-survival" ,r-survival) | |
1515 | ("r-biocgenerics" ,r-biocgenerics) | |
1516 | ("r-biobase" ,r-biobase) | |
1517 | ("r-mass" ,r-mass))) | |
1518 | (home-page "http://bioconductor.org/packages/multtest") | |
1519 | (synopsis "Resampling-based multiple hypothesis testing") | |
1520 | (description | |
1521 | "This package can do non-parametric bootstrap and permutation | |
1522 | resampling-based multiple testing procedures (including empirical Bayes | |
1523 | methods) for controlling the family-wise error rate (FWER), generalized | |
1524 | family-wise error rate (gFWER), tail probability of the proportion of | |
1525 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
1526 | of bootstrap-based null distribution are implemented (centered, centered | |
1527 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
1528 | available. Tests based on a variety of T- and F-statistics (including | |
1529 | T-statistics based on regression parameters from linear and survival models | |
1530 | as well as those based on correlation parameters) are included. When probing | |
1531 | hypotheses with T-statistics, users may also select a potentially faster null | |
1532 | distribution which is multivariate normal with mean zero and variance | |
1533 | covariance matrix derived from the vector influence function. Results are | |
1534 | reported in terms of adjusted P-values, confidence regions and test statistic | |
1535 | cutoffs. The procedures are directly applicable to identifying differentially | |
1536 | expressed genes in DNA microarray experiments.") | |
1537 | (license license:lgpl3))) | |
793f83ef | 1538 | |
5dfe4912 RW |
1539 | (define-public r-graph |
1540 | (package | |
1541 | (name "r-graph") | |
a61bcb28 | 1542 | (version "1.62.0") |
5dfe4912 RW |
1543 | (source (origin |
1544 | (method url-fetch) | |
1545 | (uri (bioconductor-uri "graph" version)) | |
1546 | (sha256 | |
1547 | (base32 | |
a61bcb28 | 1548 | "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w")))) |
5dfe4912 RW |
1549 | (build-system r-build-system) |
1550 | (propagated-inputs | |
1551 | `(("r-biocgenerics" ,r-biocgenerics))) | |
1552 | (home-page "https://bioconductor.org/packages/graph") | |
1553 | (synopsis "Handle graph data structures in R") | |
1554 | (description | |
1555 | "This package implements some simple graph handling capabilities for R.") | |
1556 | (license license:artistic2.0))) | |
1557 | ||
a207bca2 RW |
1558 | (define-public r-codedepends |
1559 | (package | |
1560 | (name "r-codedepends") | |
1561 | (version "0.6.5") | |
1562 | (source | |
1563 | (origin | |
1564 | (method url-fetch) | |
1565 | (uri (cran-uri "CodeDepends" version)) | |
1566 | (sha256 | |
1567 | (base32 | |
1568 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
1569 | (properties `((upstream-name . "CodeDepends"))) | |
1570 | (build-system r-build-system) | |
1571 | (propagated-inputs | |
1572 | `(("r-codetools" ,r-codetools) | |
1573 | ("r-graph" ,r-graph) | |
1574 | ("r-xml" ,r-xml))) | |
1575 | (home-page "http://cran.r-project.org/web/packages/CodeDepends") | |
1576 | (synopsis "Analysis of R code for reproducible research and code comprehension") | |
1577 | (description | |
1578 | "This package provides tools for analyzing R expressions or blocks of | |
1579 | code and determining the dependencies between them. It focuses on R scripts, | |
1580 | but can be used on the bodies of functions. There are many facilities | |
1581 | including the ability to summarize or get a high-level view of code, | |
1582 | determining dependencies between variables, code improvement suggestions.") | |
1583 | ;; Any version of the GPL | |
1584 | (license (list license:gpl2+ license:gpl3+)))) | |
1585 | ||
793f83ef RJ |
1586 | (define-public r-chippeakanno |
1587 | (package | |
1588 | (name "r-chippeakanno") | |
109b8ad5 | 1589 | (version "3.18.2") |
793f83ef RJ |
1590 | (source |
1591 | (origin | |
1592 | (method url-fetch) | |
1593 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
1594 | (sha256 | |
1595 | (base32 | |
109b8ad5 | 1596 | "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779")))) |
793f83ef RJ |
1597 | (properties `((upstream-name . "ChIPpeakAnno"))) |
1598 | (build-system r-build-system) | |
1599 | (propagated-inputs | |
85c1d20f RW |
1600 | `(("r-annotationdbi" ,r-annotationdbi) |
1601 | ("r-biobase" ,r-biobase) | |
1602 | ("r-biocgenerics" ,r-biocgenerics) | |
57d2fcd9 | 1603 | ("r-biocmanager" ,r-biocmanager) |
793f83ef | 1604 | ("r-biomart" ,r-biomart) |
85c1d20f | 1605 | ("r-biostrings" ,r-biostrings) |
793f83ef | 1606 | ("r-bsgenome" ,r-bsgenome) |
85c1d20f RW |
1607 | ("r-dbi" ,r-dbi) |
1608 | ("r-delayedarray" ,r-delayedarray) | |
1609 | ("r-ensembldb" ,r-ensembldb) | |
1610 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1611 | ("r-genomicalignments" ,r-genomicalignments) | |
793f83ef | 1612 | ("r-genomicfeatures" ,r-genomicfeatures) |
f794e85d | 1613 | ("r-genomicranges" ,r-genomicranges) |
85c1d20f RW |
1614 | ("r-go-db" ,r-go-db) |
1615 | ("r-graph" ,r-graph) | |
1616 | ("r-idr" ,r-idr) | |
f794e85d | 1617 | ("r-iranges" ,r-iranges) |
793f83ef | 1618 | ("r-limma" ,r-limma) |
85c1d20f | 1619 | ("r-matrixstats" ,r-matrixstats) |
793f83ef RJ |
1620 | ("r-multtest" ,r-multtest) |
1621 | ("r-rbgl" ,r-rbgl) | |
793f83ef | 1622 | ("r-regioner" ,r-regioner) |
85c1d20f RW |
1623 | ("r-rsamtools" ,r-rsamtools) |
1624 | ("r-rtracklayer" ,r-rtracklayer) | |
f794e85d | 1625 | ("r-s4vectors" ,r-s4vectors) |
793f83ef | 1626 | ("r-seqinr" ,r-seqinr) |
793f83ef | 1627 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
793f83ef RJ |
1628 | ("r-venndiagram" ,r-venndiagram))) |
1629 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") | |
1630 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") | |
1631 | (description | |
1632 | "The package includes functions to retrieve the sequences around the peak, | |
1633 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
1634 | custom features such as most conserved elements and other transcription factor | |
1635 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
1636 | for finding the peaks with bi-directional promoters with summary statistics | |
1637 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
1638 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
1639 | enrichedGO (addGeneIDs).") | |
1640 | (license license:gpl2+))) | |
164502d8 RJ |
1641 | |
1642 | (define-public r-marray | |
1643 | (package | |
1644 | (name "r-marray") | |
bcb95b7a | 1645 | (version "1.62.0") |
164502d8 RJ |
1646 | (source (origin |
1647 | (method url-fetch) | |
1648 | (uri (bioconductor-uri "marray" version)) | |
1649 | (sha256 | |
bcb95b7a | 1650 | (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz")))) |
164502d8 RJ |
1651 | (build-system r-build-system) |
1652 | (propagated-inputs | |
67487088 | 1653 | `(("r-limma" ,r-limma))) |
164502d8 RJ |
1654 | (home-page "http://bioconductor.org/packages/marray") |
1655 | (synopsis "Exploratory analysis for two-color spotted microarray data") | |
1656 | (description "This package contains class definitions for two-color spotted | |
ab8979fc | 1657 | microarray data. It also includes functions for data input, diagnostic plots, |
164502d8 RJ |
1658 | normalization and quality checking.") |
1659 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
1660 | |
1661 | (define-public r-cghbase | |
1662 | (package | |
1663 | (name "r-cghbase") | |
8efb842f | 1664 | (version "1.44.0") |
0416a0d4 RJ |
1665 | (source (origin |
1666 | (method url-fetch) | |
1667 | (uri (bioconductor-uri "CGHbase" version)) | |
1668 | (sha256 | |
8efb842f | 1669 | (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm")))) |
0416a0d4 RJ |
1670 | (properties `((upstream-name . "CGHbase"))) |
1671 | (build-system r-build-system) | |
1672 | (propagated-inputs | |
1673 | `(("r-biobase" ,r-biobase) | |
1674 | ("r-marray" ,r-marray))) | |
1675 | (home-page "http://bioconductor.org/packages/CGHbase") | |
1676 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
1677 | (description "This package contains functions and classes that are needed by | |
1678 | the @code{arrayCGH} packages.") | |
1679 | (license license:gpl2+))) | |
67ee83d6 RJ |
1680 | |
1681 | (define-public r-cghcall | |
1682 | (package | |
1683 | (name "r-cghcall") | |
23177309 | 1684 | (version "2.46.0") |
67ee83d6 RJ |
1685 | (source (origin |
1686 | (method url-fetch) | |
1687 | (uri (bioconductor-uri "CGHcall" version)) | |
1688 | (sha256 | |
23177309 | 1689 | (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93")))) |
67ee83d6 RJ |
1690 | (properties `((upstream-name . "CGHcall"))) |
1691 | (build-system r-build-system) | |
1692 | (propagated-inputs | |
1693 | `(("r-biobase" ,r-biobase) | |
1694 | ("r-cghbase" ,r-cghbase) | |
1695 | ("r-impute" ,r-impute) | |
1696 | ("r-dnacopy" ,r-dnacopy) | |
1697 | ("r-snowfall" ,r-snowfall))) | |
1698 | (home-page "http://bioconductor.org/packages/CGHcall") | |
1699 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
1700 | (description "This package contains functions and classes that are needed by | |
1701 | @code{arrayCGH} packages.") | |
1702 | (license license:gpl2+))) | |
0ef8cc9c RJ |
1703 | |
1704 | (define-public r-qdnaseq | |
1705 | (package | |
1706 | (name "r-qdnaseq") | |
4f4bed7d | 1707 | (version "1.20.0") |
0ef8cc9c RJ |
1708 | (source (origin |
1709 | (method url-fetch) | |
1710 | (uri (bioconductor-uri "QDNAseq" version)) | |
1711 | (sha256 | |
4f4bed7d | 1712 | (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz")))) |
0ef8cc9c RJ |
1713 | (properties `((upstream-name . "QDNAseq"))) |
1714 | (build-system r-build-system) | |
1715 | (propagated-inputs | |
1716 | `(("r-biobase" ,r-biobase) | |
81b0181b | 1717 | ("r-biocparallel" ,r-biocparallel) |
0ef8cc9c RJ |
1718 | ("r-cghbase" ,r-cghbase) |
1719 | ("r-cghcall" ,r-cghcall) | |
1720 | ("r-dnacopy" ,r-dnacopy) | |
1721 | ("r-genomicranges" ,r-genomicranges) | |
1722 | ("r-iranges" ,r-iranges) | |
1723 | ("r-matrixstats" ,r-matrixstats) | |
1724 | ("r-r-utils" ,r-r-utils) | |
1725 | ("r-rsamtools" ,r-rsamtools))) | |
1726 | (home-page "http://bioconductor.org/packages/QDNAseq") | |
1727 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") | |
1728 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
1729 | number of sequence reads in each counted, adjusted with a simultaneous | |
1730 | two-dimensional loess correction for sequence mappability and GC content, and | |
1731 | filtered to remove spurious regions in the genome. Downstream steps of | |
1732 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
1733 | respectively.") | |
1734 | (license license:gpl2+))) | |
bb15b581 RW |
1735 | |
1736 | (define-public r-bayseq | |
1737 | (package | |
1738 | (name "r-bayseq") | |
c38de815 | 1739 | (version "2.18.0") |
bb15b581 RW |
1740 | (source |
1741 | (origin | |
1742 | (method url-fetch) | |
1743 | (uri (bioconductor-uri "baySeq" version)) | |
1744 | (sha256 | |
1745 | (base32 | |
c38de815 | 1746 | "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w")))) |
bb15b581 RW |
1747 | (properties `((upstream-name . "baySeq"))) |
1748 | (build-system r-build-system) | |
1749 | (propagated-inputs | |
1750 | `(("r-abind" ,r-abind) | |
1751 | ("r-edger" ,r-edger) | |
1752 | ("r-genomicranges" ,r-genomicranges))) | |
1753 | (home-page "https://bioconductor.org/packages/baySeq/") | |
1754 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
1755 | (description | |
1756 | "This package identifies differential expression in high-throughput count | |
1757 | data, such as that derived from next-generation sequencing machines, | |
1758 | calculating estimated posterior likelihoods of differential expression (or | |
1759 | more complex hypotheses) via empirical Bayesian methods.") | |
1760 | (license license:gpl3))) | |
609f4ad1 RW |
1761 | |
1762 | (define-public r-chipcomp | |
1763 | (package | |
1764 | (name "r-chipcomp") | |
1ddd4af5 | 1765 | (version "1.14.0") |
609f4ad1 RW |
1766 | (source |
1767 | (origin | |
1768 | (method url-fetch) | |
1769 | (uri (bioconductor-uri "ChIPComp" version)) | |
1770 | (sha256 | |
1771 | (base32 | |
1ddd4af5 | 1772 | "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y")))) |
609f4ad1 RW |
1773 | (properties `((upstream-name . "ChIPComp"))) |
1774 | (build-system r-build-system) | |
1775 | (propagated-inputs | |
1776 | `(("r-biocgenerics" ,r-biocgenerics) | |
1777 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
1778 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
1779 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1780 | ("r-genomicranges" ,r-genomicranges) | |
1781 | ("r-iranges" ,r-iranges) | |
1782 | ("r-limma" ,r-limma) | |
1783 | ("r-rsamtools" ,r-rsamtools) | |
1784 | ("r-rtracklayer" ,r-rtracklayer) | |
1785 | ("r-s4vectors" ,r-s4vectors))) | |
1786 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
1787 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
1788 | (description | |
1789 | "ChIPComp implements a statistical method for quantitative comparison of | |
1790 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
1791 | sites across multiple conditions considering matching control in ChIP-seq | |
1792 | datasets.") | |
1793 | ;; Any version of the GPL. | |
1794 | (license license:gpl3+))) | |
0490f9de RW |
1795 | |
1796 | (define-public r-riboprofiling | |
1797 | (package | |
1798 | (name "r-riboprofiling") | |
7d5acf7a | 1799 | (version "1.14.0") |
0490f9de RW |
1800 | (source |
1801 | (origin | |
1802 | (method url-fetch) | |
1803 | (uri (bioconductor-uri "RiboProfiling" version)) | |
1804 | (sha256 | |
1805 | (base32 | |
7d5acf7a | 1806 | "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9")))) |
0490f9de RW |
1807 | (properties `((upstream-name . "RiboProfiling"))) |
1808 | (build-system r-build-system) | |
1809 | (propagated-inputs | |
1810 | `(("r-biocgenerics" ,r-biocgenerics) | |
1811 | ("r-biostrings" ,r-biostrings) | |
1812 | ("r-data-table" ,r-data-table) | |
1813 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1814 | ("r-genomicalignments" ,r-genomicalignments) | |
1815 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1816 | ("r-genomicranges" ,r-genomicranges) | |
1817 | ("r-ggbio" ,r-ggbio) | |
1818 | ("r-ggplot2" ,r-ggplot2) | |
1819 | ("r-iranges" ,r-iranges) | |
1820 | ("r-plyr" ,r-plyr) | |
1821 | ("r-reshape2" ,r-reshape2) | |
1822 | ("r-rsamtools" ,r-rsamtools) | |
1823 | ("r-rtracklayer" ,r-rtracklayer) | |
1824 | ("r-s4vectors" ,r-s4vectors) | |
1825 | ("r-sqldf" ,r-sqldf))) | |
1826 | (home-page "https://bioconductor.org/packages/RiboProfiling/") | |
1827 | (synopsis "Ribosome profiling data analysis") | |
1828 | (description "Starting with a BAM file, this package provides the | |
1829 | necessary functions for quality assessment, read start position recalibration, | |
1830 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
1831 | of count data: pairs, log fold-change, codon frequency and coverage | |
1832 | assessment, principal component analysis on codon coverage.") | |
1833 | (license license:gpl3))) | |
6ffdfe6a RW |
1834 | |
1835 | (define-public r-riboseqr | |
1836 | (package | |
1837 | (name "r-riboseqr") | |
eff6b2eb | 1838 | (version "1.18.0") |
6ffdfe6a RW |
1839 | (source |
1840 | (origin | |
1841 | (method url-fetch) | |
1842 | (uri (bioconductor-uri "riboSeqR" version)) | |
1843 | (sha256 | |
1844 | (base32 | |
eff6b2eb | 1845 | "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga")))) |
6ffdfe6a RW |
1846 | (properties `((upstream-name . "riboSeqR"))) |
1847 | (build-system r-build-system) | |
1848 | (propagated-inputs | |
1849 | `(("r-abind" ,r-abind) | |
1850 | ("r-bayseq" ,r-bayseq) | |
1851 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1852 | ("r-genomicranges" ,r-genomicranges) | |
1853 | ("r-iranges" ,r-iranges) | |
1854 | ("r-rsamtools" ,r-rsamtools) | |
1855 | ("r-seqlogo" ,r-seqlogo))) | |
1856 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
1857 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
1858 | (description | |
1859 | "This package provides plotting functions, frameshift detection and | |
1860 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
1861 | (license license:gpl3))) | |
a32279ff RW |
1862 | |
1863 | (define-public r-interactionset | |
1864 | (package | |
1865 | (name "r-interactionset") | |
176a264c | 1866 | (version "1.12.0") |
a32279ff RW |
1867 | (source |
1868 | (origin | |
1869 | (method url-fetch) | |
1870 | (uri (bioconductor-uri "InteractionSet" version)) | |
1871 | (sha256 | |
1872 | (base32 | |
176a264c | 1873 | "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6")))) |
a32279ff RW |
1874 | (properties |
1875 | `((upstream-name . "InteractionSet"))) | |
1876 | (build-system r-build-system) | |
1877 | (propagated-inputs | |
1878 | `(("r-biocgenerics" ,r-biocgenerics) | |
1879 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1880 | ("r-genomicranges" ,r-genomicranges) | |
1881 | ("r-iranges" ,r-iranges) | |
1882 | ("r-matrix" ,r-matrix) | |
1883 | ("r-rcpp" ,r-rcpp) | |
1884 | ("r-s4vectors" ,r-s4vectors) | |
1885 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1886 | (home-page "https://bioconductor.org/packages/InteractionSet") | |
1887 | (synopsis "Base classes for storing genomic interaction data") | |
1888 | (description | |
02fe0976 | 1889 | "This package provides the @code{GInteractions}, |
a32279ff RW |
1890 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
1891 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
1892 | experiments.") | |
1893 | (license license:gpl3))) | |
cf9a29b2 RW |
1894 | |
1895 | (define-public r-genomicinteractions | |
1896 | (package | |
1897 | (name "r-genomicinteractions") | |
fcbd8960 | 1898 | (version "1.18.1") |
cf9a29b2 RW |
1899 | (source |
1900 | (origin | |
1901 | (method url-fetch) | |
1902 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
1903 | (sha256 | |
1904 | (base32 | |
fcbd8960 | 1905 | "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p")))) |
cf9a29b2 RW |
1906 | (properties |
1907 | `((upstream-name . "GenomicInteractions"))) | |
1908 | (build-system r-build-system) | |
1909 | (propagated-inputs | |
1910 | `(("r-biobase" ,r-biobase) | |
1911 | ("r-biocgenerics" ,r-biocgenerics) | |
1912 | ("r-data-table" ,r-data-table) | |
1913 | ("r-dplyr" ,r-dplyr) | |
1914 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1915 | ("r-genomicranges" ,r-genomicranges) | |
1916 | ("r-ggplot2" ,r-ggplot2) | |
1917 | ("r-gridextra" ,r-gridextra) | |
1918 | ("r-gviz" ,r-gviz) | |
1919 | ("r-igraph" ,r-igraph) | |
1920 | ("r-interactionset" ,r-interactionset) | |
1921 | ("r-iranges" ,r-iranges) | |
1922 | ("r-rsamtools" ,r-rsamtools) | |
1923 | ("r-rtracklayer" ,r-rtracklayer) | |
1924 | ("r-s4vectors" ,r-s4vectors) | |
1925 | ("r-stringr" ,r-stringr))) | |
1926 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") | |
1927 | (synopsis "R package for handling genomic interaction data") | |
1928 | (description | |
1929 | "This R package provides tools for handling genomic interaction data, | |
1930 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
1931 | information and producing various plots and statistics.") | |
1932 | (license license:gpl3))) | |
27c51606 RW |
1933 | |
1934 | (define-public r-ctc | |
1935 | (package | |
1936 | (name "r-ctc") | |
7a5d729a | 1937 | (version "1.58.0") |
27c51606 RW |
1938 | (source |
1939 | (origin | |
1940 | (method url-fetch) | |
1941 | (uri (bioconductor-uri "ctc" version)) | |
1942 | (sha256 | |
1943 | (base32 | |
7a5d729a | 1944 | "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am")))) |
27c51606 RW |
1945 | (build-system r-build-system) |
1946 | (propagated-inputs `(("r-amap" ,r-amap))) | |
1947 | (home-page "https://bioconductor.org/packages/ctc/") | |
1948 | (synopsis "Cluster and tree conversion") | |
1949 | (description | |
1950 | "This package provides tools for exporting and importing classification | |
1951 | trees and clusters to other programs.") | |
1952 | (license license:gpl2))) | |
5da0e142 RW |
1953 | |
1954 | (define-public r-goseq | |
1955 | (package | |
1956 | (name "r-goseq") | |
40f0ee43 | 1957 | (version "1.36.0") |
5da0e142 RW |
1958 | (source |
1959 | (origin | |
1960 | (method url-fetch) | |
1961 | (uri (bioconductor-uri "goseq" version)) | |
1962 | (sha256 | |
1963 | (base32 | |
40f0ee43 | 1964 | "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw")))) |
5da0e142 RW |
1965 | (build-system r-build-system) |
1966 | (propagated-inputs | |
1967 | `(("r-annotationdbi" ,r-annotationdbi) | |
1968 | ("r-biasedurn" ,r-biasedurn) | |
1969 | ("r-biocgenerics" ,r-biocgenerics) | |
1970 | ("r-genelendatabase" ,r-genelendatabase) | |
1971 | ("r-go-db" ,r-go-db) | |
1972 | ("r-mgcv" ,r-mgcv))) | |
1973 | (home-page "https://bioconductor.org/packages/goseq/") | |
1974 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
1975 | (description | |
1976 | "This package provides tools to detect Gene Ontology and/or other user | |
1977 | defined categories which are over/under represented in RNA-seq data.") | |
1978 | (license license:lgpl2.0+))) | |
f4235c0e RW |
1979 | |
1980 | (define-public r-glimma | |
1981 | (package | |
1982 | (name "r-glimma") | |
07252952 | 1983 | (version "1.12.0") |
f4235c0e RW |
1984 | (source |
1985 | (origin | |
1986 | (method url-fetch) | |
1987 | (uri (bioconductor-uri "Glimma" version)) | |
1988 | (sha256 | |
1989 | (base32 | |
07252952 | 1990 | "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x")))) |
f4235c0e RW |
1991 | (properties `((upstream-name . "Glimma"))) |
1992 | (build-system r-build-system) | |
1993 | (propagated-inputs | |
1994 | `(("r-edger" ,r-edger) | |
1995 | ("r-jsonlite" ,r-jsonlite) | |
1996 | ("r-s4vectors" ,r-s4vectors))) | |
1997 | (home-page "https://github.com/Shians/Glimma") | |
1998 | (synopsis "Interactive HTML graphics") | |
1999 | (description | |
2000 | "This package generates interactive visualisations for analysis of | |
2001 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
2002 | HTML page. The interactions are built on top of the popular static | |
2003 | representations of analysis results in order to provide additional | |
2004 | information.") | |
2005 | (license license:lgpl3))) | |
aa388dc7 RW |
2006 | |
2007 | (define-public r-rots | |
2008 | (package | |
2009 | (name "r-rots") | |
5bf7eb49 | 2010 | (version "1.12.0") |
aa388dc7 RW |
2011 | (source |
2012 | (origin | |
2013 | (method url-fetch) | |
2014 | (uri (bioconductor-uri "ROTS" version)) | |
2015 | (sha256 | |
2016 | (base32 | |
5bf7eb49 | 2017 | "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77")))) |
aa388dc7 RW |
2018 | (properties `((upstream-name . "ROTS"))) |
2019 | (build-system r-build-system) | |
2020 | (propagated-inputs | |
2021 | `(("r-biobase" ,r-biobase) | |
2022 | ("r-rcpp" ,r-rcpp))) | |
2023 | (home-page "https://bioconductor.org/packages/ROTS/") | |
2024 | (synopsis "Reproducibility-Optimized Test Statistic") | |
2025 | (description | |
2026 | "This package provides tools for calculating the | |
2027 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
2028 | in omics data.") | |
2029 | (license license:gpl2+))) | |
b64ce4b7 | 2030 | |
cad6fb2d RW |
2031 | (define-public r-plgem |
2032 | (package | |
2033 | (name "r-plgem") | |
5dce7153 | 2034 | (version "1.56.0") |
cad6fb2d RW |
2035 | (source |
2036 | (origin | |
2037 | (method url-fetch) | |
2038 | (uri (bioconductor-uri "plgem" version)) | |
2039 | (sha256 | |
2040 | (base32 | |
5dce7153 | 2041 | "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp")))) |
cad6fb2d RW |
2042 | (build-system r-build-system) |
2043 | (propagated-inputs | |
2044 | `(("r-biobase" ,r-biobase) | |
2045 | ("r-mass" ,r-mass))) | |
2046 | (home-page "http://www.genopolis.it") | |
2047 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
2048 | (description | |
2049 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
2050 | model the variance-versus-mean dependence that exists in a variety of | |
2051 | genome-wide datasets, including microarray and proteomics data. The use of | |
2052 | PLGEM has been shown to improve the detection of differentially expressed | |
2053 | genes or proteins in these datasets.") | |
2054 | (license license:gpl2))) | |
2055 | ||
b64ce4b7 RW |
2056 | (define-public r-inspect |
2057 | (package | |
2058 | (name "r-inspect") | |
3649d046 | 2059 | (version "1.14.0") |
b64ce4b7 RW |
2060 | (source |
2061 | (origin | |
2062 | (method url-fetch) | |
2063 | (uri (bioconductor-uri "INSPEcT" version)) | |
2064 | (sha256 | |
2065 | (base32 | |
3649d046 | 2066 | "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r")))) |
b64ce4b7 RW |
2067 | (properties `((upstream-name . "INSPEcT"))) |
2068 | (build-system r-build-system) | |
2069 | (propagated-inputs | |
2070 | `(("r-biobase" ,r-biobase) | |
2071 | ("r-biocgenerics" ,r-biocgenerics) | |
2072 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 2073 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 RW |
2074 | ("r-desolve" ,r-desolve) |
2075 | ("r-genomicalignments" ,r-genomicalignments) | |
2076 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2077 | ("r-genomicranges" ,r-genomicranges) | |
2078 | ("r-iranges" ,r-iranges) | |
c86fc969 | 2079 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
2080 | ("r-preprocesscore" ,r-preprocesscore) |
2081 | ("r-proc" ,r-proc) | |
2082 | ("r-rootsolve" ,r-rootsolve) | |
2083 | ("r-rsamtools" ,r-rsamtools) | |
c86fc969 RW |
2084 | ("r-s4vectors" ,r-s4vectors) |
2085 | ("r-shiny" ,r-shiny) | |
2086 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
2087 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
2088 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
b64ce4b7 RW |
2089 | (home-page "https://bioconductor.org/packages/INSPEcT") |
2090 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
2091 | (description | |
2092 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
2093 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
2094 | order to evaluate synthesis, processing and degradation rates and assess via | |
2095 | modeling the rates that determines changes in mature mRNA levels.") | |
2096 | (license license:gpl2))) | |
f6e99763 RW |
2097 | |
2098 | (define-public r-dnabarcodes | |
2099 | (package | |
2100 | (name "r-dnabarcodes") | |
774e499c | 2101 | (version "1.14.0") |
f6e99763 RW |
2102 | (source |
2103 | (origin | |
2104 | (method url-fetch) | |
2105 | (uri (bioconductor-uri "DNABarcodes" version)) | |
2106 | (sha256 | |
2107 | (base32 | |
774e499c | 2108 | "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0")))) |
f6e99763 RW |
2109 | (properties `((upstream-name . "DNABarcodes"))) |
2110 | (build-system r-build-system) | |
2111 | (propagated-inputs | |
2112 | `(("r-bh" ,r-bh) | |
2113 | ("r-matrix" ,r-matrix) | |
2114 | ("r-rcpp" ,r-rcpp))) | |
2115 | (home-page "https://bioconductor.org/packages/DNABarcodes") | |
2116 | (synopsis "Create and analyze DNA barcodes") | |
2117 | (description | |
2118 | "This package offers tools to create DNA barcode sets capable of | |
2119 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
2120 | can be analyzed regarding their minimal, maximal and average distances between | |
2121 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
2122 | demultiplexed, i.e. assigned to their original reference barcode.") | |
2123 | (license license:gpl2))) | |
09aa3d06 RW |
2124 | |
2125 | (define-public r-ruvseq | |
2126 | (package | |
2127 | (name "r-ruvseq") | |
d8771f5f | 2128 | (version "1.18.0") |
09aa3d06 RW |
2129 | (source |
2130 | (origin | |
2131 | (method url-fetch) | |
2132 | (uri (bioconductor-uri "RUVSeq" version)) | |
2133 | (sha256 | |
2134 | (base32 | |
d8771f5f | 2135 | "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33")))) |
09aa3d06 RW |
2136 | (properties `((upstream-name . "RUVSeq"))) |
2137 | (build-system r-build-system) | |
2138 | (propagated-inputs | |
2139 | `(("r-biobase" ,r-biobase) | |
2140 | ("r-edaseq" ,r-edaseq) | |
2141 | ("r-edger" ,r-edger) | |
2142 | ("r-mass" ,r-mass))) | |
2143 | (home-page "https://github.com/drisso/RUVSeq") | |
2144 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
2145 | (description | |
2146 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
2147 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
2148 | samples.") | |
2149 | (license license:artistic2.0))) | |
286157dc RW |
2150 | |
2151 | (define-public r-biocneighbors | |
2152 | (package | |
2153 | (name "r-biocneighbors") | |
6fc161fc | 2154 | (version "1.2.0") |
286157dc RW |
2155 | (source |
2156 | (origin | |
2157 | (method url-fetch) | |
2158 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
2159 | (sha256 | |
2160 | (base32 | |
6fc161fc | 2161 | "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg")))) |
286157dc RW |
2162 | (properties `((upstream-name . "BiocNeighbors"))) |
2163 | (build-system r-build-system) | |
2164 | (propagated-inputs | |
6fc161fc RW |
2165 | `(("r-biocgenerics" ,r-biocgenerics) |
2166 | ("r-biocparallel" ,r-biocparallel) | |
286157dc RW |
2167 | ("r-rcpp" ,r-rcpp) |
2168 | ("r-rcppannoy" ,r-rcppannoy) | |
6fc161fc | 2169 | ("r-rcpphnsw" ,r-rcpphnsw) |
286157dc RW |
2170 | ("r-s4vectors" ,r-s4vectors))) |
2171 | (home-page "https://bioconductor.org/packages/BiocNeighbors") | |
2172 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
2173 | (description | |
2174 | "This package implements exact and approximate methods for nearest | |
2175 | neighbor detection, in a framework that allows them to be easily switched | |
2176 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
2177 | using pre-clustering with the k-means algorithm. Functions are also provided | |
2178 | to search for all neighbors within a given distance. Parallelization is | |
2179 | achieved for all methods using the BiocParallel framework.") | |
2180 | (license license:gpl3))) | |
8a587c89 | 2181 | |
99391290 RW |
2182 | (define-public r-biocsingular |
2183 | (package | |
2184 | (name "r-biocsingular") | |
2185 | (version "1.0.0") | |
2186 | (source | |
2187 | (origin | |
2188 | (method url-fetch) | |
2189 | (uri (bioconductor-uri "BiocSingular" version)) | |
2190 | (sha256 | |
2191 | (base32 | |
2192 | "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5")))) | |
2193 | (properties `((upstream-name . "BiocSingular"))) | |
2194 | (build-system r-build-system) | |
2195 | (propagated-inputs | |
2196 | `(("r-beachmat" ,r-beachmat) | |
2197 | ("r-biocgenerics" ,r-biocgenerics) | |
2198 | ("r-biocparallel" ,r-biocparallel) | |
2199 | ("r-delayedarray" ,r-delayedarray) | |
2200 | ("r-irlba" ,r-irlba) | |
2201 | ("r-matrix" ,r-matrix) | |
2202 | ("r-rcpp" ,r-rcpp) | |
2203 | ("r-rsvd" ,r-rsvd) | |
2204 | ("r-s4vectors" ,r-s4vectors))) | |
2205 | (home-page "https://github.com/LTLA/BiocSingular") | |
2206 | (synopsis "Singular value decomposition for Bioconductor packages") | |
2207 | (description | |
2208 | "This package implements exact and approximate methods for singular value | |
2209 | decomposition and principal components analysis, in a framework that allows | |
2210 | them to be easily switched within Bioconductor packages or workflows. Where | |
2211 | possible, parallelization is achieved using the BiocParallel framework.") | |
2212 | (license license:gpl3))) | |
2213 | ||
a961ae46 RW |
2214 | (define-public r-destiny |
2215 | (package | |
2216 | (name "r-destiny") | |
0aa72f2d | 2217 | (version "2.14.0") |
a961ae46 RW |
2218 | (source |
2219 | (origin | |
2220 | (method url-fetch) | |
2221 | (uri (bioconductor-uri "destiny" version)) | |
2222 | (sha256 | |
2223 | (base32 | |
0aa72f2d | 2224 | "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3")))) |
a961ae46 RW |
2225 | (build-system r-build-system) |
2226 | (propagated-inputs | |
2227 | `(("r-biobase" ,r-biobase) | |
2228 | ("r-biocgenerics" ,r-biocgenerics) | |
0aa72f2d | 2229 | ("r-ggplot2" ,r-ggplot2) |
a961ae46 | 2230 | ("r-ggthemes" ,r-ggthemes) |
a961ae46 RW |
2231 | ("r-igraph" ,r-igraph) |
2232 | ("r-matrix" ,r-matrix) | |
2233 | ("r-proxy" ,r-proxy) | |
2234 | ("r-rcpp" ,r-rcpp) | |
2235 | ("r-rcppeigen" ,r-rcppeigen) | |
2236 | ("r-scales" ,r-scales) | |
2237 | ("r-scatterplot3d" ,r-scatterplot3d) | |
2238 | ("r-smoother" ,r-smoother) | |
2239 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
2240 | ("r-vim" ,r-vim))) | |
2241 | (home-page "https://bioconductor.org/packages/destiny/") | |
2242 | (synopsis "Create and plot diffusion maps") | |
2243 | (description "This package provides tools to create and plot diffusion | |
2244 | maps.") | |
2245 | ;; Any version of the GPL | |
2246 | (license license:gpl3+))) | |
2247 | ||
8a587c89 RW |
2248 | (define-public r-savr |
2249 | (package | |
2250 | (name "r-savr") | |
8d3d0c3a | 2251 | (version "1.22.0") |
8a587c89 RW |
2252 | (source |
2253 | (origin | |
2254 | (method url-fetch) | |
2255 | (uri (bioconductor-uri "savR" version)) | |
2256 | (sha256 | |
2257 | (base32 | |
8d3d0c3a | 2258 | "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h")))) |
8a587c89 RW |
2259 | (properties `((upstream-name . "savR"))) |
2260 | (build-system r-build-system) | |
2261 | (propagated-inputs | |
2262 | `(("r-ggplot2" ,r-ggplot2) | |
2263 | ("r-gridextra" ,r-gridextra) | |
2264 | ("r-reshape2" ,r-reshape2) | |
2265 | ("r-scales" ,r-scales) | |
2266 | ("r-xml" ,r-xml))) | |
2267 | (home-page "https://github.com/bcalder/savR") | |
2268 | (synopsis "Parse and analyze Illumina SAV files") | |
2269 | (description | |
2270 | "This package provides tools to parse Illumina Sequence Analysis | |
2271 | Viewer (SAV) files, access data, and generate QC plots.") | |
2272 | (license license:agpl3+))) | |
41ffc214 RW |
2273 | |
2274 | (define-public r-chipexoqual | |
2275 | (package | |
2276 | (name "r-chipexoqual") | |
58a43fc2 | 2277 | (version "1.8.0") |
41ffc214 RW |
2278 | (source |
2279 | (origin | |
2280 | (method url-fetch) | |
2281 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
2282 | (sha256 | |
2283 | (base32 | |
58a43fc2 | 2284 | "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj")))) |
41ffc214 RW |
2285 | (properties `((upstream-name . "ChIPexoQual"))) |
2286 | (build-system r-build-system) | |
2287 | (propagated-inputs | |
2288 | `(("r-biocparallel" ,r-biocparallel) | |
2289 | ("r-biovizbase" ,r-biovizbase) | |
2290 | ("r-broom" ,r-broom) | |
2291 | ("r-data-table" ,r-data-table) | |
2292 | ("r-dplyr" ,r-dplyr) | |
2293 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2294 | ("r-genomicalignments" ,r-genomicalignments) | |
2295 | ("r-genomicranges" ,r-genomicranges) | |
2296 | ("r-ggplot2" ,r-ggplot2) | |
2297 | ("r-hexbin" ,r-hexbin) | |
2298 | ("r-iranges" ,r-iranges) | |
2299 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2300 | ("r-rmarkdown" ,r-rmarkdown) | |
2301 | ("r-rsamtools" ,r-rsamtools) | |
2302 | ("r-s4vectors" ,r-s4vectors) | |
2303 | ("r-scales" ,r-scales) | |
2304 | ("r-viridis" ,r-viridis))) | |
2305 | (home-page "https://github.com/keleslab/ChIPexoQual") | |
2306 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
2307 | (description | |
2308 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
2309 | sequencing data.") | |
2310 | (license license:gpl2+))) | |
c18dccff | 2311 | |
3d13b448 RW |
2312 | (define-public r-copynumber |
2313 | (package | |
2314 | (name "r-copynumber") | |
d9419185 | 2315 | (version "1.24.0") |
3d13b448 RW |
2316 | (source (origin |
2317 | (method url-fetch) | |
2318 | (uri (bioconductor-uri "copynumber" version)) | |
2319 | (sha256 | |
2320 | (base32 | |
d9419185 | 2321 | "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp")))) |
3d13b448 RW |
2322 | (build-system r-build-system) |
2323 | (propagated-inputs | |
2324 | `(("r-s4vectors" ,r-s4vectors) | |
2325 | ("r-iranges" ,r-iranges) | |
2326 | ("r-genomicranges" ,r-genomicranges) | |
2327 | ("r-biocgenerics" ,r-biocgenerics))) | |
2328 | (home-page "https://bioconductor.org/packages/copynumber") | |
2329 | (synopsis "Segmentation of single- and multi-track copy number data") | |
2330 | (description | |
2331 | "This package segments single- and multi-track copy number data by a | |
2332 | penalized least squares regression method.") | |
2333 | (license license:artistic2.0))) | |
2334 | ||
c18dccff RW |
2335 | (define-public r-dnacopy |
2336 | (package | |
2337 | (name "r-dnacopy") | |
d5f3c0d0 | 2338 | (version "1.58.0") |
c18dccff RW |
2339 | (source |
2340 | (origin | |
2341 | (method url-fetch) | |
2342 | (uri (bioconductor-uri "DNAcopy" version)) | |
2343 | (sha256 | |
2344 | (base32 | |
d5f3c0d0 | 2345 | "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa")))) |
c18dccff RW |
2346 | (properties `((upstream-name . "DNAcopy"))) |
2347 | (build-system r-build-system) | |
2348 | (native-inputs `(("gfortran" ,gfortran))) | |
2349 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
2350 | (synopsis "DNA copy number data analysis") | |
2351 | (description | |
2352 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
2353 | algorithm to segment DNA copy number data and identify genomic regions with | |
2354 | abnormal copy number.") | |
2355 | (license license:gpl2+))) | |
3a0babac RW |
2356 | |
2357 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
2358 | ;; Bioconductor package. | |
2359 | (define-public r-htscluster | |
2360 | (package | |
2361 | (name "r-htscluster") | |
2362 | (version "2.0.8") | |
2363 | (source | |
2364 | (origin | |
2365 | (method url-fetch) | |
2366 | (uri (cran-uri "HTSCluster" version)) | |
2367 | (sha256 | |
2368 | (base32 | |
2369 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
2370 | (properties `((upstream-name . "HTSCluster"))) | |
2371 | (build-system r-build-system) | |
2372 | (propagated-inputs | |
2373 | `(("r-capushe" ,r-capushe) | |
2374 | ("r-edger" ,r-edger) | |
2375 | ("r-plotrix" ,r-plotrix))) | |
2376 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
2377 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
2378 | (description | |
2379 | "This package provides a Poisson mixture model is implemented to cluster | |
2380 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
2381 | estimation is performed using either the EM or CEM algorithm, and the slope | |
2382 | heuristics are used for model selection (i.e., to choose the number of | |
2383 | clusters).") | |
2384 | (license license:gpl3+))) | |
173c9960 RW |
2385 | |
2386 | (define-public r-deds | |
2387 | (package | |
2388 | (name "r-deds") | |
301c4ff1 | 2389 | (version "1.58.0") |
173c9960 RW |
2390 | (source |
2391 | (origin | |
2392 | (method url-fetch) | |
2393 | (uri (bioconductor-uri "DEDS" version)) | |
2394 | (sha256 | |
2395 | (base32 | |
301c4ff1 | 2396 | "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs")))) |
173c9960 RW |
2397 | (properties `((upstream-name . "DEDS"))) |
2398 | (build-system r-build-system) | |
2399 | (home-page "https://bioconductor.org/packages/DEDS/") | |
2400 | (synopsis "Differential expression via distance summary for microarray data") | |
2401 | (description | |
2402 | "This library contains functions that calculate various statistics of | |
2403 | differential expression for microarray data, including t statistics, fold | |
2404 | change, F statistics, SAM, moderated t and F statistics and B statistics. It | |
2405 | also implements a new methodology called DEDS (Differential Expression via | |
2406 | Distance Summary), which selects differentially expressed genes by integrating | |
2407 | and summarizing a set of statistics using a weighted distance approach.") | |
2408 | ;; Any version of the LGPL. | |
2409 | (license license:lgpl3+))) | |
7ed869f7 RW |
2410 | |
2411 | ;; This is a CRAN package, but since it depends on a Bioconductor package we | |
2412 | ;; put it here. | |
2413 | (define-public r-nbpseq | |
2414 | (package | |
2415 | (name "r-nbpseq") | |
2416 | (version "0.3.0") | |
2417 | (source | |
2418 | (origin | |
2419 | (method url-fetch) | |
2420 | (uri (cran-uri "NBPSeq" version)) | |
2421 | (sha256 | |
2422 | (base32 | |
2423 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) | |
2424 | (properties `((upstream-name . "NBPSeq"))) | |
2425 | (build-system r-build-system) | |
2426 | (propagated-inputs | |
2427 | `(("r-qvalue" ,r-qvalue))) | |
2428 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") | |
2429 | (synopsis "Negative binomial models for RNA-Seq data") | |
2430 | (description | |
2431 | "This package provides negative binomial models for two-group comparisons | |
2432 | and regression inferences from RNA-sequencing data.") | |
2433 | (license license:gpl2))) | |
3087a2f3 RW |
2434 | |
2435 | (define-public r-ebseq | |
2436 | (package | |
2437 | (name "r-ebseq") | |
4a3c47e9 | 2438 | (version "1.24.0") |
3087a2f3 RW |
2439 | (source |
2440 | (origin | |
2441 | (method url-fetch) | |
2442 | (uri (bioconductor-uri "EBSeq" version)) | |
2443 | (sha256 | |
2444 | (base32 | |
4a3c47e9 | 2445 | "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83")))) |
3087a2f3 RW |
2446 | (properties `((upstream-name . "EBSeq"))) |
2447 | (build-system r-build-system) | |
2448 | (propagated-inputs | |
2449 | `(("r-blockmodeling" ,r-blockmodeling) | |
2450 | ("r-gplots" ,r-gplots) | |
2451 | ("r-testthat" ,r-testthat))) | |
2452 | (home-page "https://bioconductor.org/packages/EBSeq") | |
2453 | (synopsis "Differential expression analysis of RNA-seq data") | |
2454 | (description | |
2455 | "This package provides tools for differential expression analysis at both | |
2456 | gene and isoform level using RNA-seq data") | |
2457 | (license license:artistic2.0))) | |
2cb71d81 RW |
2458 | |
2459 | (define-public r-lpsymphony | |
2460 | (package | |
2461 | (name "r-lpsymphony") | |
61c79d55 | 2462 | (version "1.12.0") |
2cb71d81 RW |
2463 | (source |
2464 | (origin | |
2465 | (method url-fetch) | |
2466 | (uri (bioconductor-uri "lpsymphony" version)) | |
2467 | (sha256 | |
2468 | (base32 | |
61c79d55 | 2469 | "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv")))) |
2cb71d81 RW |
2470 | (build-system r-build-system) |
2471 | (inputs | |
2472 | `(("gfortran" ,gfortran) | |
2473 | ("zlib" ,zlib))) | |
2474 | (native-inputs | |
2475 | `(("pkg-config" ,pkg-config))) | |
2476 | (home-page "http://r-forge.r-project.org/projects/rsymphony") | |
2477 | (synopsis "Symphony integer linear programming solver in R") | |
2478 | (description | |
2479 | "This package was derived from Rsymphony. The package provides an R | |
2480 | interface to SYMPHONY, a linear programming solver written in C++. The main | |
2481 | difference between this package and Rsymphony is that it includes the solver | |
2482 | source code, while Rsymphony expects to find header and library files on the | |
2483 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy | |
2484 | to install interface to SYMPHONY.") | |
2485 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. | |
2486 | ;; lpsimphony is released under the same terms. | |
2487 | (license license:epl1.0))) | |
704de8f5 RW |
2488 | |
2489 | (define-public r-ihw | |
2490 | (package | |
2491 | (name "r-ihw") | |
bcd8b7a9 | 2492 | (version "1.12.0") |
704de8f5 RW |
2493 | (source |
2494 | (origin | |
2495 | (method url-fetch) | |
2496 | (uri (bioconductor-uri "IHW" version)) | |
2497 | (sha256 | |
2498 | (base32 | |
bcd8b7a9 | 2499 | "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz")))) |
704de8f5 RW |
2500 | (properties `((upstream-name . "IHW"))) |
2501 | (build-system r-build-system) | |
2502 | (propagated-inputs | |
2503 | `(("r-biocgenerics" ,r-biocgenerics) | |
2504 | ("r-fdrtool" ,r-fdrtool) | |
2505 | ("r-lpsymphony" ,r-lpsymphony) | |
2506 | ("r-slam" ,r-slam))) | |
2507 | (home-page "https://bioconductor.org/packages/IHW") | |
2508 | (synopsis "Independent hypothesis weighting") | |
2509 | (description | |
2510 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing | |
2511 | procedure that increases power compared to the method of Benjamini and | |
2512 | Hochberg by assigning data-driven weights to each hypothesis. The input to | |
2513 | IHW is a two-column table of p-values and covariates. The covariate can be | |
2514 | any continuous-valued or categorical variable that is thought to be | |
2515 | informative on the statistical properties of each hypothesis test, while it is | |
2516 | independent of the p-value under the null hypothesis.") | |
2517 | (license license:artistic2.0))) | |
251e0830 RW |
2518 | |
2519 | (define-public r-icobra | |
2520 | (package | |
2521 | (name "r-icobra") | |
13b49976 | 2522 | (version "1.12.1") |
251e0830 RW |
2523 | (source |
2524 | (origin | |
2525 | (method url-fetch) | |
2526 | (uri (bioconductor-uri "iCOBRA" version)) | |
2527 | (sha256 | |
2528 | (base32 | |
13b49976 | 2529 | "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q")))) |
251e0830 RW |
2530 | (properties `((upstream-name . "iCOBRA"))) |
2531 | (build-system r-build-system) | |
2532 | (propagated-inputs | |
2533 | `(("r-dplyr" ,r-dplyr) | |
2534 | ("r-dt" ,r-dt) | |
2535 | ("r-ggplot2" ,r-ggplot2) | |
2536 | ("r-limma" ,r-limma) | |
2537 | ("r-reshape2" ,r-reshape2) | |
2538 | ("r-rocr" ,r-rocr) | |
2539 | ("r-scales" ,r-scales) | |
2540 | ("r-shiny" ,r-shiny) | |
2541 | ("r-shinybs" ,r-shinybs) | |
2542 | ("r-shinydashboard" ,r-shinydashboard) | |
2543 | ("r-upsetr" ,r-upsetr))) | |
2544 | (home-page "https://bioconductor.org/packages/iCOBRA") | |
2545 | (synopsis "Comparison and visualization of ranking and assignment methods") | |
2546 | (description | |
2547 | "This package provides functions for calculation and visualization of | |
2548 | performance metrics for evaluation of ranking and binary | |
2549 | classification (assignment) methods. It also contains a Shiny application for | |
2550 | interactive exploration of results.") | |
2551 | (license license:gpl2+))) | |
925fcdbb RW |
2552 | |
2553 | (define-public r-mast | |
2554 | (package | |
2555 | (name "r-mast") | |
a0ff725d | 2556 | (version "1.10.0") |
925fcdbb RW |
2557 | (source |
2558 | (origin | |
2559 | (method url-fetch) | |
2560 | (uri (bioconductor-uri "MAST" version)) | |
2561 | (sha256 | |
2562 | (base32 | |
a0ff725d | 2563 | "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx")))) |
925fcdbb RW |
2564 | (properties `((upstream-name . "MAST"))) |
2565 | (build-system r-build-system) | |
2566 | (propagated-inputs | |
2567 | `(("r-abind" ,r-abind) | |
a0ff725d | 2568 | ("r-blme" ,r-blme) |
925fcdbb RW |
2569 | ("r-biobase" ,r-biobase) |
2570 | ("r-biocgenerics" ,r-biocgenerics) | |
2571 | ("r-data-table" ,r-data-table) | |
2572 | ("r-ggplot2" ,r-ggplot2) | |
2573 | ("r-plyr" ,r-plyr) | |
2574 | ("r-progress" ,r-progress) | |
2575 | ("r-reshape2" ,r-reshape2) | |
2576 | ("r-s4vectors" ,r-s4vectors) | |
2577 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2578 | ("r-stringr" ,r-stringr) | |
2579 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2580 | (home-page "https://github.com/RGLab/MAST/") | |
2581 | (synopsis "Model-based analysis of single cell transcriptomics") | |
2582 | (description | |
2583 | "This package provides methods and models for handling zero-inflated | |
2584 | single cell assay data.") | |
2585 | (license license:gpl2+))) | |
2d7627cf RW |
2586 | |
2587 | (define-public r-monocle | |
2588 | (package | |
2589 | (name "r-monocle") | |
78b63267 | 2590 | (version "2.12.0") |
2d7627cf RW |
2591 | (source |
2592 | (origin | |
2593 | (method url-fetch) | |
2594 | (uri (bioconductor-uri "monocle" version)) | |
2595 | (sha256 | |
2596 | (base32 | |
78b63267 | 2597 | "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z")))) |
2d7627cf RW |
2598 | (build-system r-build-system) |
2599 | (propagated-inputs | |
2600 | `(("r-biobase" ,r-biobase) | |
2601 | ("r-biocgenerics" ,r-biocgenerics) | |
2602 | ("r-biocviews" ,r-biocviews) | |
2603 | ("r-cluster" ,r-cluster) | |
2604 | ("r-combinat" ,r-combinat) | |
2605 | ("r-ddrtree" ,r-ddrtree) | |
2606 | ("r-densityclust" ,r-densityclust) | |
2607 | ("r-dplyr" ,r-dplyr) | |
2608 | ("r-fastica" ,r-fastica) | |
2609 | ("r-ggplot2" ,r-ggplot2) | |
2610 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) | |
2611 | ("r-igraph" ,r-igraph) | |
2612 | ("r-irlba" ,r-irlba) | |
2613 | ("r-limma" ,r-limma) | |
2614 | ("r-mass" ,r-mass) | |
2615 | ("r-matrix" ,r-matrix) | |
2616 | ("r-matrixstats" ,r-matrixstats) | |
2617 | ("r-pheatmap" ,r-pheatmap) | |
2618 | ("r-plyr" ,r-plyr) | |
2619 | ("r-proxy" ,r-proxy) | |
2620 | ("r-qlcmatrix" ,r-qlcmatrix) | |
2621 | ("r-rann" ,r-rann) | |
2622 | ("r-rcpp" ,r-rcpp) | |
2623 | ("r-reshape2" ,r-reshape2) | |
2624 | ("r-rtsne" ,r-rtsne) | |
2625 | ("r-slam" ,r-slam) | |
2626 | ("r-stringr" ,r-stringr) | |
2627 | ("r-tibble" ,r-tibble) | |
2628 | ("r-vgam" ,r-vgam) | |
2629 | ("r-viridis" ,r-viridis))) | |
2630 | (home-page "https://bioconductor.org/packages/monocle") | |
2631 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") | |
2632 | (description | |
2633 | "Monocle performs differential expression and time-series analysis for | |
2634 | single-cell expression experiments. It orders individual cells according to | |
2635 | progress through a biological process, without knowing ahead of time which | |
2636 | genes define progress through that process. Monocle also performs | |
2637 | differential expression analysis, clustering, visualization, and other useful | |
2638 | tasks on single cell expression data. It is designed to work with RNA-Seq and | |
2639 | qPCR data, but could be used with other types as well.") | |
2640 | (license license:artistic2.0))) | |
6213e441 | 2641 | |
b2dce6b5 RW |
2642 | (define-public r-monocle3 |
2643 | (package | |
2644 | (name "r-monocle3") | |
2645 | (version "0.1.2") | |
2646 | (source | |
2647 | (origin | |
2648 | (method git-fetch) | |
2649 | (uri (git-reference | |
2650 | (url "https://github.com/cole-trapnell-lab/monocle3.git") | |
2651 | (commit version))) | |
2652 | (file-name (git-file-name name version)) | |
2653 | (sha256 | |
2654 | (base32 | |
2655 | "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) | |
2656 | (build-system r-build-system) | |
2657 | (propagated-inputs | |
2658 | `(("r-biobase" ,r-biobase) | |
2659 | ("r-biocgenerics" ,r-biocgenerics) | |
2660 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
2661 | ("r-dplyr" ,r-dplyr) | |
2662 | ("r-ggplot2" ,r-ggplot2) | |
2663 | ("r-ggrepel" ,r-ggrepel) | |
2664 | ("r-grr" ,r-grr) | |
2665 | ("r-htmlwidgets" ,r-htmlwidgets) | |
2666 | ("r-igraph" ,r-igraph) | |
2667 | ("r-irlba" ,r-irlba) | |
2668 | ("r-limma" ,r-limma) | |
2669 | ("r-lmtest" ,r-lmtest) | |
2670 | ("r-mass" ,r-mass) | |
2671 | ("r-matrix" ,r-matrix) | |
2672 | ("r-matrix-utils" ,r-matrix-utils) | |
2673 | ("r-pbapply" ,r-pbapply) | |
2674 | ("r-pbmcapply" ,r-pbmcapply) | |
2675 | ("r-pheatmap" ,r-pheatmap) | |
2676 | ("r-plotly" ,r-plotly) | |
2677 | ("r-pryr" ,r-pryr) | |
2678 | ("r-proxy" ,r-proxy) | |
2679 | ("r-pscl" ,r-pscl) | |
2680 | ("r-purrr" ,r-purrr) | |
2681 | ("r-rann" ,r-rann) | |
2682 | ("r-rcpp" ,r-rcpp) | |
2683 | ("r-rcppparallel" ,r-rcppparallel) | |
2684 | ("r-reshape2" ,r-reshape2) | |
2685 | ("r-reticulate" ,r-reticulate) | |
2686 | ("r-rhpcblasctl" ,r-rhpcblasctl) | |
2687 | ("r-rtsne" ,r-rtsne) | |
2688 | ("r-shiny" ,r-shiny) | |
2689 | ("r-slam" ,r-slam) | |
2690 | ("r-spdep" ,r-spdep) | |
2691 | ("r-speedglm" ,r-speedglm) | |
2692 | ("r-stringr" ,r-stringr) | |
2693 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2694 | ("r-tibble" ,r-tibble) | |
2695 | ("r-tidyr" ,r-tidyr) | |
2696 | ("r-uwot" ,r-uwot) | |
2697 | ("r-viridis" ,r-viridis))) | |
2698 | (home-page "https://github.com/cole-trapnell-lab/monocle3") | |
2699 | (synopsis "Analysis toolkit for single-cell RNA-Seq data") | |
2700 | (description | |
2701 | "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") | |
2702 | (license license:expat))) | |
2703 | ||
6213e441 RW |
2704 | (define-public r-noiseq |
2705 | (package | |
2706 | (name "r-noiseq") | |
6a2c58b7 | 2707 | (version "2.28.0") |
6213e441 RW |
2708 | (source |
2709 | (origin | |
2710 | (method url-fetch) | |
2711 | (uri (bioconductor-uri "NOISeq" version)) | |
2712 | (sha256 | |
2713 | (base32 | |
6a2c58b7 | 2714 | "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j")))) |
6213e441 RW |
2715 | (properties `((upstream-name . "NOISeq"))) |
2716 | (build-system r-build-system) | |
2717 | (propagated-inputs | |
2718 | `(("r-biobase" ,r-biobase) | |
2719 | ("r-matrix" ,r-matrix))) | |
2720 | (home-page "https://bioconductor.org/packages/NOISeq") | |
2721 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") | |
2722 | (description | |
2723 | "This package provides tools to support the analysis of RNA-seq | |
2724 | expression data or other similar kind of data. It provides exploratory plots | |
2725 | to evaluate saturation, count distribution, expression per chromosome, type of | |
2726 | detected features, features length, etc. It also supports the analysis of | |
2727 | differential expression between two experimental conditions with no parametric | |
2728 | assumptions.") | |
2729 | (license license:artistic2.0))) | |
b409c357 RW |
2730 | |
2731 | (define-public r-scdd | |
2732 | (package | |
2733 | (name "r-scdd") | |
7baa59ed | 2734 | (version "1.8.0") |
b409c357 RW |
2735 | (source |
2736 | (origin | |
2737 | (method url-fetch) | |
2738 | (uri (bioconductor-uri "scDD" version)) | |
2739 | (sha256 | |
2740 | (base32 | |
7baa59ed | 2741 | "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf")))) |
b409c357 RW |
2742 | (properties `((upstream-name . "scDD"))) |
2743 | (build-system r-build-system) | |
2744 | (propagated-inputs | |
2745 | `(("r-arm" ,r-arm) | |
2746 | ("r-biocparallel" ,r-biocparallel) | |
2747 | ("r-ebseq" ,r-ebseq) | |
2748 | ("r-fields" ,r-fields) | |
2749 | ("r-ggplot2" ,r-ggplot2) | |
2750 | ("r-mclust" ,r-mclust) | |
2751 | ("r-outliers" ,r-outliers) | |
2752 | ("r-s4vectors" ,r-s4vectors) | |
2753 | ("r-scran" ,r-scran) | |
2754 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2755 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2756 | (home-page "https://github.com/kdkorthauer/scDD") | |
2757 | (synopsis "Mixture modeling of single-cell RNA-seq data") | |
2758 | (description | |
2759 | "This package implements a method to analyze single-cell RNA-seq data | |
2760 | utilizing flexible Dirichlet Process mixture models. Genes with differential | |
2761 | distributions of expression are classified into several interesting patterns | |
2762 | of differences between two conditions. The package also includes functions | |
2763 | for simulating data with these patterns from negative binomial | |
2764 | distributions.") | |
2765 | (license license:gpl2))) | |
f0887757 RW |
2766 | |
2767 | (define-public r-scone | |
2768 | (package | |
2769 | (name "r-scone") | |
26c72fff | 2770 | (version "1.8.0") |
f0887757 RW |
2771 | (source |
2772 | (origin | |
2773 | (method url-fetch) | |
2774 | (uri (bioconductor-uri "scone" version)) | |
2775 | (sha256 | |
2776 | (base32 | |
26c72fff | 2777 | "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck")))) |
f0887757 RW |
2778 | (build-system r-build-system) |
2779 | (propagated-inputs | |
2780 | `(("r-aroma-light" ,r-aroma-light) | |
2781 | ("r-biocparallel" ,r-biocparallel) | |
2782 | ("r-boot" ,r-boot) | |
2783 | ("r-class" ,r-class) | |
2784 | ("r-cluster" ,r-cluster) | |
2785 | ("r-compositions" ,r-compositions) | |
2786 | ("r-diptest" ,r-diptest) | |
2787 | ("r-edger" ,r-edger) | |
2788 | ("r-fpc" ,r-fpc) | |
2789 | ("r-gplots" ,r-gplots) | |
2790 | ("r-hexbin" ,r-hexbin) | |
2791 | ("r-limma" ,r-limma) | |
2792 | ("r-matrixstats" ,r-matrixstats) | |
2793 | ("r-mixtools" ,r-mixtools) | |
2794 | ("r-rarpack" ,r-rarpack) | |
2795 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2796 | ("r-rhdf5" ,r-rhdf5) | |
2797 | ("r-ruvseq" ,r-ruvseq) | |
2798 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2799 | (home-page "https://bioconductor.org/packages/scone") | |
2800 | (synopsis "Single cell overview of normalized expression data") | |
2801 | (description | |
2802 | "SCONE is an R package for comparing and ranking the performance of | |
2803 | different normalization schemes for single-cell RNA-seq and other | |
2804 | high-throughput analyses.") | |
2805 | (license license:artistic2.0))) | |
f9201d67 RW |
2806 | |
2807 | (define-public r-geoquery | |
2808 | (package | |
2809 | (name "r-geoquery") | |
2d443087 | 2810 | (version "2.52.0") |
f9201d67 RW |
2811 | (source |
2812 | (origin | |
2813 | (method url-fetch) | |
2814 | (uri (bioconductor-uri "GEOquery" version)) | |
2815 | (sha256 | |
2816 | (base32 | |
2d443087 | 2817 | "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr")))) |
f9201d67 RW |
2818 | (properties `((upstream-name . "GEOquery"))) |
2819 | (build-system r-build-system) | |
2820 | (propagated-inputs | |
2821 | `(("r-biobase" ,r-biobase) | |
2822 | ("r-dplyr" ,r-dplyr) | |
2823 | ("r-httr" ,r-httr) | |
2824 | ("r-limma" ,r-limma) | |
2825 | ("r-magrittr" ,r-magrittr) | |
2826 | ("r-readr" ,r-readr) | |
2827 | ("r-tidyr" ,r-tidyr) | |
2828 | ("r-xml2" ,r-xml2))) | |
2829 | (home-page "https://github.com/seandavi/GEOquery/") | |
2830 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") | |
2831 | (description | |
2832 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of | |
2833 | microarray data. Given the rich and varied nature of this resource, it is | |
2834 | only natural to want to apply BioConductor tools to these data. GEOquery is | |
2835 | the bridge between GEO and BioConductor.") | |
2836 | (license license:gpl2))) | |
eed6ff03 RW |
2837 | |
2838 | (define-public r-illuminaio | |
2839 | (package | |
2840 | (name "r-illuminaio") | |
fadc6db8 | 2841 | (version "0.26.0") |
eed6ff03 RW |
2842 | (source |
2843 | (origin | |
2844 | (method url-fetch) | |
2845 | (uri (bioconductor-uri "illuminaio" version)) | |
2846 | (sha256 | |
2847 | (base32 | |
fadc6db8 | 2848 | "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8")))) |
eed6ff03 RW |
2849 | (build-system r-build-system) |
2850 | (propagated-inputs | |
2851 | `(("r-base64" ,r-base64))) | |
2852 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") | |
2853 | (synopsis "Parse Illumina microarray output files") | |
2854 | (description | |
2855 | "This package provides tools for parsing Illumina's microarray output | |
2856 | files, including IDAT.") | |
2857 | (license license:gpl2))) | |
f4eac096 RW |
2858 | |
2859 | (define-public r-siggenes | |
2860 | (package | |
2861 | (name "r-siggenes") | |
409f4dd6 | 2862 | (version "1.58.0") |
f4eac096 RW |
2863 | (source |
2864 | (origin | |
2865 | (method url-fetch) | |
2866 | (uri (bioconductor-uri "siggenes" version)) | |
2867 | (sha256 | |
2868 | (base32 | |
409f4dd6 | 2869 | "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib")))) |
f4eac096 RW |
2870 | (build-system r-build-system) |
2871 | (propagated-inputs | |
2872 | `(("r-biobase" ,r-biobase) | |
409f4dd6 RW |
2873 | ("r-multtest" ,r-multtest) |
2874 | ("r-scrime" ,r-scrime))) | |
f4eac096 RW |
2875 | (home-page "https://bioconductor.org/packages/siggenes/") |
2876 | (synopsis | |
2877 | "Multiple testing using SAM and Efron's empirical Bayes approaches") | |
2878 | (description | |
2879 | "This package provides tools for the identification of differentially | |
2880 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using | |
2881 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical | |
2882 | Bayes Analyses of Microarrays} (EBAM).") | |
2883 | (license license:lgpl2.0+))) | |
34a24f95 RW |
2884 | |
2885 | (define-public r-bumphunter | |
2886 | (package | |
2887 | (name "r-bumphunter") | |
693a9805 | 2888 | (version "1.26.0") |
34a24f95 RW |
2889 | (source |
2890 | (origin | |
2891 | (method url-fetch) | |
2892 | (uri (bioconductor-uri "bumphunter" version)) | |
2893 | (sha256 | |
2894 | (base32 | |
693a9805 | 2895 | "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx")))) |
34a24f95 RW |
2896 | (build-system r-build-system) |
2897 | (propagated-inputs | |
2898 | `(("r-annotationdbi" ,r-annotationdbi) | |
2899 | ("r-biocgenerics" ,r-biocgenerics) | |
2900 | ("r-dorng" ,r-dorng) | |
2901 | ("r-foreach" ,r-foreach) | |
2902 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2903 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2904 | ("r-genomicranges" ,r-genomicranges) | |
2905 | ("r-iranges" ,r-iranges) | |
2906 | ("r-iterators" ,r-iterators) | |
2907 | ("r-limma" ,r-limma) | |
2908 | ("r-locfit" ,r-locfit) | |
2909 | ("r-matrixstats" ,r-matrixstats) | |
2910 | ("r-s4vectors" ,r-s4vectors))) | |
2911 | (home-page "https://github.com/ririzarr/bumphunter") | |
2912 | (synopsis "Find bumps in genomic data") | |
2913 | (description | |
2914 | "This package provides tools for finding bumps in genomic data in order | |
2915 | to identify differentially methylated regions in epigenetic epidemiology | |
2916 | studies.") | |
2917 | (license license:artistic2.0))) | |
0fbaf195 RW |
2918 | |
2919 | (define-public r-minfi | |
2920 | (package | |
2921 | (name "r-minfi") | |
8c0fae3c | 2922 | (version "1.30.0") |
0fbaf195 RW |
2923 | (source |
2924 | (origin | |
2925 | (method url-fetch) | |
2926 | (uri (bioconductor-uri "minfi" version)) | |
2927 | (sha256 | |
2928 | (base32 | |
8c0fae3c | 2929 | "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd")))) |
0fbaf195 RW |
2930 | (build-system r-build-system) |
2931 | (propagated-inputs | |
2932 | `(("r-beanplot" ,r-beanplot) | |
2933 | ("r-biobase" ,r-biobase) | |
2934 | ("r-biocgenerics" ,r-biocgenerics) | |
2935 | ("r-biocparallel" ,r-biocparallel) | |
2936 | ("r-biostrings" ,r-biostrings) | |
2937 | ("r-bumphunter" ,r-bumphunter) | |
2938 | ("r-data-table" ,r-data-table) | |
2939 | ("r-delayedarray" ,r-delayedarray) | |
2940 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
2941 | ("r-genefilter" ,r-genefilter) | |
2942 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2943 | ("r-genomicranges" ,r-genomicranges) | |
2944 | ("r-geoquery" ,r-geoquery) | |
2945 | ("r-hdf5array" ,r-hdf5array) | |
2946 | ("r-illuminaio" ,r-illuminaio) | |
2947 | ("r-iranges" ,r-iranges) | |
2948 | ("r-lattice" ,r-lattice) | |
2949 | ("r-limma" ,r-limma) | |
2950 | ("r-mass" ,r-mass) | |
2951 | ("r-mclust" ,r-mclust) | |
2952 | ("r-nlme" ,r-nlme) | |
2953 | ("r-nor1mix" ,r-nor1mix) | |
2954 | ("r-preprocesscore" ,r-preprocesscore) | |
2955 | ("r-quadprog" ,r-quadprog) | |
2956 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2957 | ("r-reshape" ,r-reshape) | |
2958 | ("r-s4vectors" ,r-s4vectors) | |
2959 | ("r-siggenes" ,r-siggenes) | |
2960 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2961 | (home-page "https://github.com/hansenlab/minfi") | |
2962 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") | |
2963 | (description | |
2964 | "This package provides tools to analyze and visualize Illumina Infinium | |
2965 | methylation arrays.") | |
2966 | (license license:artistic2.0))) | |
5ec5ba02 RW |
2967 | |
2968 | (define-public r-methylumi | |
2969 | (package | |
2970 | (name "r-methylumi") | |
2986b51f | 2971 | (version "2.30.0") |
5ec5ba02 RW |
2972 | (source |
2973 | (origin | |
2974 | (method url-fetch) | |
2975 | (uri (bioconductor-uri "methylumi" version)) | |
2976 | (sha256 | |
2977 | (base32 | |
2986b51f | 2978 | "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f")))) |
5ec5ba02 RW |
2979 | (build-system r-build-system) |
2980 | (propagated-inputs | |
2981 | `(("r-annotate" ,r-annotate) | |
2982 | ("r-annotationdbi" ,r-annotationdbi) | |
2983 | ("r-biobase" ,r-biobase) | |
2984 | ("r-biocgenerics" ,r-biocgenerics) | |
2985 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) | |
2986 | ("r-genefilter" ,r-genefilter) | |
2987 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2988 | ("r-genomicranges" ,r-genomicranges) | |
2989 | ("r-ggplot2" ,r-ggplot2) | |
2990 | ("r-illuminaio" ,r-illuminaio) | |
2991 | ("r-iranges" ,r-iranges) | |
2992 | ("r-lattice" ,r-lattice) | |
2993 | ("r-matrixstats" ,r-matrixstats) | |
2994 | ("r-minfi" ,r-minfi) | |
2995 | ("r-reshape2" ,r-reshape2) | |
2996 | ("r-s4vectors" ,r-s4vectors) | |
2997 | ("r-scales" ,r-scales) | |
2998 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2999 | (home-page "https://bioconductor.org/packages/methylumi") | |
3000 | (synopsis "Handle Illumina methylation data") | |
3001 | (description | |
3002 | "This package provides classes for holding and manipulating Illumina | |
3003 | methylation data. Based on eSet, it can contain MIAME information, sample | |
3004 | information, feature information, and multiple matrices of data. An | |
3005 | \"intelligent\" import function, methylumiR can read the Illumina text files | |
3006 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from | |
3007 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, | |
3008 | background correction, and quality control features for GoldenGate, Infinium, | |
3009 | and Infinium HD arrays are also included.") | |
3010 | (license license:gpl2))) | |
09605cb2 RW |
3011 | |
3012 | (define-public r-lumi | |
3013 | (package | |
3014 | (name "r-lumi") | |
5551b07c | 3015 | (version "2.36.0") |
09605cb2 RW |
3016 | (source |
3017 | (origin | |
3018 | (method url-fetch) | |
3019 | (uri (bioconductor-uri "lumi" version)) | |
3020 | (sha256 | |
3021 | (base32 | |
5551b07c | 3022 | "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba")))) |
09605cb2 RW |
3023 | (build-system r-build-system) |
3024 | (propagated-inputs | |
3025 | `(("r-affy" ,r-affy) | |
3026 | ("r-annotate" ,r-annotate) | |
3027 | ("r-annotationdbi" ,r-annotationdbi) | |
3028 | ("r-biobase" ,r-biobase) | |
3029 | ("r-dbi" ,r-dbi) | |
3030 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3031 | ("r-genomicranges" ,r-genomicranges) | |
3032 | ("r-kernsmooth" ,r-kernsmooth) | |
3033 | ("r-lattice" ,r-lattice) | |
3034 | ("r-mass" ,r-mass) | |
3035 | ("r-methylumi" ,r-methylumi) | |
3036 | ("r-mgcv" ,r-mgcv) | |
3037 | ("r-nleqslv" ,r-nleqslv) | |
3038 | ("r-preprocesscore" ,r-preprocesscore) | |
3039 | ("r-rsqlite" ,r-rsqlite))) | |
3040 | (home-page "https://bioconductor.org/packages/lumi") | |
3041 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") | |
3042 | (description | |
3043 | "The lumi package provides an integrated solution for the Illumina | |
3044 | microarray data analysis. It includes functions of Illumina | |
3045 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific | |
3046 | variance stabilization, normalization and gene annotation at the probe level. | |
3047 | It also includes the functions of processing Illumina methylation microarrays, | |
3048 | especially Illumina Infinium methylation microarrays.") | |
3049 | (license license:lgpl2.0+))) | |
4291f36a RW |
3050 | |
3051 | (define-public r-linnorm | |
3052 | (package | |
3053 | (name "r-linnorm") | |
48c2a7eb | 3054 | (version "2.8.0") |
4291f36a RW |
3055 | (source |
3056 | (origin | |
3057 | (method url-fetch) | |
3058 | (uri (bioconductor-uri "Linnorm" version)) | |
3059 | (sha256 | |
3060 | (base32 | |
48c2a7eb | 3061 | "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5")))) |
4291f36a RW |
3062 | (properties `((upstream-name . "Linnorm"))) |
3063 | (build-system r-build-system) | |
3064 | (propagated-inputs | |
3065 | `(("r-amap" ,r-amap) | |
3066 | ("r-apcluster" ,r-apcluster) | |
3067 | ("r-ellipse" ,r-ellipse) | |
3068 | ("r-fastcluster" ,r-fastcluster) | |
3069 | ("r-fpc" ,r-fpc) | |
3070 | ("r-ggdendro" ,r-ggdendro) | |
3071 | ("r-ggplot2" ,r-ggplot2) | |
3072 | ("r-gmodels" ,r-gmodels) | |
3073 | ("r-igraph" ,r-igraph) | |
3074 | ("r-limma" ,r-limma) | |
3075 | ("r-mass" ,r-mass) | |
3076 | ("r-mclust" ,r-mclust) | |
3077 | ("r-rcpp" ,r-rcpp) | |
3078 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
3079 | ("r-rtsne" ,r-rtsne) | |
3080 | ("r-statmod" ,r-statmod) | |
3081 | ("r-vegan" ,r-vegan) | |
3082 | ("r-zoo" ,r-zoo))) | |
3083 | (home-page "http://www.jjwanglab.org/Linnorm/") | |
3084 | (synopsis "Linear model and normality based transformation method") | |
3085 | (description | |
3086 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq | |
3087 | count data or any large scale count data. It transforms such datasets for | |
3088 | parametric tests. In addition to the transformtion function (@code{Linnorm}), | |
3089 | the following pipelines are implemented: | |
3090 | ||
3091 | @enumerate | |
3092 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) | |
3093 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means | |
3094 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, | |
3095 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) | |
3096 | @item Differential expression analysis or differential peak detection using | |
3097 | limma (@code{Linnorm.limma}) | |
3098 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) | |
3099 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) | |
3100 | @item Stable gene selection for scRNA-seq data; for users without or who do | |
3101 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) | |
3102 | @item Data imputation (@code{Linnorm.DataImput}). | |
3103 | @end enumerate | |
3104 | ||
3105 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the | |
3106 | @code{RnaXSim} function is included for simulating RNA-seq data for the | |
3107 | evaluation of DEG analysis methods.") | |
3108 | (license license:expat))) | |
e4a17532 RW |
3109 | |
3110 | (define-public r-ioniser | |
3111 | (package | |
3112 | (name "r-ioniser") | |
2ee91179 | 3113 | (version "2.8.0") |
e4a17532 RW |
3114 | (source |
3115 | (origin | |
3116 | (method url-fetch) | |
3117 | (uri (bioconductor-uri "IONiseR" version)) | |
3118 | (sha256 | |
3119 | (base32 | |
2ee91179 | 3120 | "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y")))) |
e4a17532 RW |
3121 | (properties `((upstream-name . "IONiseR"))) |
3122 | (build-system r-build-system) | |
3123 | (propagated-inputs | |
3124 | `(("r-biocgenerics" ,r-biocgenerics) | |
3125 | ("r-biocparallel" ,r-biocparallel) | |
3126 | ("r-biostrings" ,r-biostrings) | |
3127 | ("r-bit64" ,r-bit64) | |
3128 | ("r-dplyr" ,r-dplyr) | |
3129 | ("r-ggplot2" ,r-ggplot2) | |
3130 | ("r-magrittr" ,r-magrittr) | |
3131 | ("r-rhdf5" ,r-rhdf5) | |
3132 | ("r-shortread" ,r-shortread) | |
3133 | ("r-stringr" ,r-stringr) | |
3134 | ("r-tibble" ,r-tibble) | |
3135 | ("r-tidyr" ,r-tidyr) | |
3136 | ("r-xvector" ,r-xvector))) | |
3137 | (home-page "https://bioconductor.org/packages/IONiseR/") | |
3138 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") | |
3139 | (description | |
3140 | "IONiseR provides tools for the quality assessment of Oxford Nanopore | |
3141 | MinION data. It extracts summary statistics from a set of fast5 files and can | |
3142 | be used either before or after base calling. In addition to standard | |
3143 | summaries of the read-types produced, it provides a number of plots for | |
3144 | visualising metrics relative to experiment run time or spatially over the | |
3145 | surface of a flowcell.") | |
3146 | (license license:expat))) | |
80eb01c7 RW |
3147 | |
3148 | ;; This is a CRAN package, but it depends on packages from Bioconductor. | |
3149 | (define-public r-gkmsvm | |
3150 | (package | |
3151 | (name "r-gkmsvm") | |
3152 | (version "0.79.0") | |
3153 | (source | |
3154 | (origin | |
3155 | (method url-fetch) | |
3156 | (uri (cran-uri "gkmSVM" version)) | |
3157 | (sha256 | |
3158 | (base32 | |
3159 | "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) | |
3160 | (properties `((upstream-name . "gkmSVM"))) | |
3161 | (build-system r-build-system) | |
3162 | (propagated-inputs | |
3163 | `(("r-biocgenerics" ,r-biocgenerics) | |
3164 | ("r-biostrings" ,r-biostrings) | |
3165 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3166 | ("r-genomicranges" ,r-genomicranges) | |
3167 | ("r-iranges" ,r-iranges) | |
3168 | ("r-kernlab" ,r-kernlab) | |
3169 | ("r-rcpp" ,r-rcpp) | |
3170 | ("r-rocr" ,r-rocr) | |
3171 | ("r-rtracklayer" ,r-rtracklayer) | |
3172 | ("r-s4vectors" ,r-s4vectors) | |
3173 | ("r-seqinr" ,r-seqinr))) | |
3174 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") | |
3175 | (synopsis "Gapped-kmer support vector machine") | |
3176 | (description | |
3177 | "This R package provides tools for training gapped-kmer SVM classifiers | |
3178 | for DNA and protein sequences. This package supports several sequence | |
3179 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
3180 | (license license:gpl2+))) | |
8a5460b4 RW |
3181 | |
3182 | (define-public r-triform | |
3183 | (package | |
3184 | (name "r-triform") | |
bc083eca | 3185 | (version "1.26.0") |
8a5460b4 RW |
3186 | (source |
3187 | (origin | |
3188 | (method url-fetch) | |
3189 | (uri (bioconductor-uri "triform" version)) | |
3190 | (sha256 | |
3191 | (base32 | |
bc083eca | 3192 | "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya")))) |
8a5460b4 RW |
3193 | (build-system r-build-system) |
3194 | (propagated-inputs | |
3195 | `(("r-biocgenerics" ,r-biocgenerics) | |
3196 | ("r-iranges" ,r-iranges) | |
3197 | ("r-yaml" ,r-yaml))) | |
3198 | (home-page "https://bioconductor.org/packages/triform/") | |
3199 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") | |
3200 | (description | |
3201 | "The Triform algorithm uses model-free statistics to identify peak-like | |
3202 | distributions of TF ChIP sequencing reads, taking advantage of an improved | |
3203 | peak definition in combination with known profile characteristics.") | |
3204 | (license license:gpl2))) | |
c538bcdd RW |
3205 | |
3206 | (define-public r-varianttools | |
3207 | (package | |
3208 | (name "r-varianttools") | |
c2effded | 3209 | (version "1.26.0") |
c538bcdd RW |
3210 | (source |
3211 | (origin | |
3212 | (method url-fetch) | |
3213 | (uri (bioconductor-uri "VariantTools" version)) | |
3214 | (sha256 | |
3215 | (base32 | |
c2effded | 3216 | "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql")))) |
c538bcdd RW |
3217 | (properties `((upstream-name . "VariantTools"))) |
3218 | (build-system r-build-system) | |
3219 | (propagated-inputs | |
3220 | `(("r-biobase" ,r-biobase) | |
3221 | ("r-biocgenerics" ,r-biocgenerics) | |
3222 | ("r-biocparallel" ,r-biocparallel) | |
3223 | ("r-biostrings" ,r-biostrings) | |
3224 | ("r-bsgenome" ,r-bsgenome) | |
3225 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3226 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3227 | ("r-genomicranges" ,r-genomicranges) | |
3228 | ("r-iranges" ,r-iranges) | |
3229 | ("r-matrix" ,r-matrix) | |
3230 | ("r-rsamtools" ,r-rsamtools) | |
3231 | ("r-rtracklayer" ,r-rtracklayer) | |
3232 | ("r-s4vectors" ,r-s4vectors) | |
3233 | ("r-variantannotation" ,r-variantannotation))) | |
3234 | (home-page "https://bioconductor.org/packages/VariantTools/") | |
3235 | (synopsis "Tools for exploratory analysis of variant calls") | |
3236 | (description | |
3237 | "Explore, diagnose, and compare variant calls using filters. The | |
3238 | VariantTools package supports a workflow for loading data, calling single | |
3239 | sample variants and tumor-specific somatic mutations or other sample-specific | |
3240 | variant types (e.g., RNA editing). Most of the functions operate on | |
3241 | alignments (BAM files) or datasets of called variants. The user is expected | |
3242 | to have already aligned the reads with a separate tool, e.g., GSNAP via | |
3243 | gmapR.") | |
3244 | (license license:artistic2.0))) | |
3e41919d RW |
3245 | |
3246 | (define-public r-heatplus | |
3247 | (package | |
3248 | (name "r-heatplus") | |
376d1fe7 | 3249 | (version "2.30.0") |
3e41919d RW |
3250 | (source |
3251 | (origin | |
3252 | (method url-fetch) | |
3253 | (uri (bioconductor-uri "Heatplus" version)) | |
3254 | (sha256 | |
3255 | (base32 | |
376d1fe7 | 3256 | "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6")))) |
3e41919d RW |
3257 | (properties `((upstream-name . "Heatplus"))) |
3258 | (build-system r-build-system) | |
3259 | (propagated-inputs | |
3260 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) | |
3261 | (home-page "https://github.com/alexploner/Heatplus") | |
3262 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") | |
3263 | (description | |
3264 | "This package provides tools to display a rectangular heatmap (intensity | |
3265 | plot) of a data matrix. By default, both samples (columns) and features (row) | |
3266 | of the matrix are sorted according to a hierarchical clustering, and the | |
3267 | corresponding dendrogram is plotted. Optionally, panels with additional | |
3268 | information about samples and features can be added to the plot.") | |
3269 | (license license:gpl2+))) | |
c04f230e RW |
3270 | |
3271 | (define-public r-gosemsim | |
3272 | (package | |
3273 | (name "r-gosemsim") | |
24cf7bad | 3274 | (version "2.10.0") |
c04f230e RW |
3275 | (source |
3276 | (origin | |
3277 | (method url-fetch) | |
3278 | (uri (bioconductor-uri "GOSemSim" version)) | |
3279 | (sha256 | |
3280 | (base32 | |
24cf7bad | 3281 | "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg")))) |
c04f230e RW |
3282 | (properties `((upstream-name . "GOSemSim"))) |
3283 | (build-system r-build-system) | |
3284 | (propagated-inputs | |
3285 | `(("r-annotationdbi" ,r-annotationdbi) | |
3286 | ("r-go-db" ,r-go-db) | |
3287 | ("r-rcpp" ,r-rcpp))) | |
3288 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") | |
3289 | (synopsis "GO-terms semantic similarity measures") | |
3290 | (description | |
3291 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide | |
3292 | quantitative ways to compute similarities between genes and gene groups, and | |
3293 | have became important basis for many bioinformatics analysis approaches. | |
3294 | GOSemSim is an R package for semantic similarity computation among GO terms, | |
3295 | sets of GO terms, gene products and gene clusters.") | |
3296 | (license license:artistic2.0))) | |
9d0f7942 RW |
3297 | |
3298 | (define-public r-anota | |
3299 | (package | |
3300 | (name "r-anota") | |
0a41b5db | 3301 | (version "1.32.0") |
9d0f7942 RW |
3302 | (source |
3303 | (origin | |
3304 | (method url-fetch) | |
3305 | (uri (bioconductor-uri "anota" version)) | |
3306 | (sha256 | |
3307 | (base32 | |
0a41b5db | 3308 | "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c")))) |
9d0f7942 RW |
3309 | (build-system r-build-system) |
3310 | (propagated-inputs | |
3311 | `(("r-multtest" ,r-multtest) | |
3312 | ("r-qvalue" ,r-qvalue))) | |
3313 | (home-page "https://bioconductor.org/packages/anota/") | |
3314 | (synopsis "Analysis of translational activity") | |
3315 | (description | |
3316 | "Genome wide studies of translational control is emerging as a tool to | |
0cea26bd | 3317 | study various biological conditions. The output from such analysis is both |
9d0f7942 RW |
3318 | the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively |
3319 | involved in translation (the actively translating mRNA level) for each mRNA. | |
3320 | The standard analysis of such data strives towards identifying differential | |
3321 | translational between two or more sample classes - i.e. differences in | |
3322 | actively translated mRNA levels that are independent of underlying differences | |
3323 | in cytosolic mRNA levels. This package allows for such analysis using partial | |
3324 | variances and the random variance model. As 10s of thousands of mRNAs are | |
4f664004 | 3325 | analyzed in parallel the library performs a number of tests to assure that |
9d0f7942 RW |
3326 | the data set is suitable for such analysis.") |
3327 | (license license:gpl3))) | |
a6d867fe RW |
3328 | |
3329 | (define-public r-sigpathway | |
3330 | (package | |
3331 | (name "r-sigpathway") | |
3e5ee6f6 | 3332 | (version "1.52.0") |
a6d867fe RW |
3333 | (source |
3334 | (origin | |
3335 | (method url-fetch) | |
3336 | (uri (bioconductor-uri "sigPathway" version)) | |
3337 | (sha256 | |
3338 | (base32 | |
3e5ee6f6 | 3339 | "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7")))) |
a6d867fe RW |
3340 | (properties `((upstream-name . "sigPathway"))) |
3341 | (build-system r-build-system) | |
3342 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") | |
3343 | (synopsis "Pathway analysis") | |
3344 | (description | |
3345 | "This package is used to conduct pathway analysis by calculating the NT_k | |
3346 | and NE_k statistics in a statistical framework for determining whether a | |
3347 | specified group of genes for a pathway has a coordinated association with a | |
3348 | phenotype of interest.") | |
3349 | (license license:gpl2))) | |
af26c7ae RW |
3350 | |
3351 | (define-public r-fgsea | |
3352 | (package | |
3353 | (name "r-fgsea") | |
9b275285 | 3354 | (version "1.10.1") |
af26c7ae RW |
3355 | (source |
3356 | (origin | |
3357 | (method url-fetch) | |
3358 | (uri (bioconductor-uri "fgsea" version)) | |
3359 | (sha256 | |
3360 | (base32 | |
9b275285 | 3361 | "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6")))) |
af26c7ae RW |
3362 | (build-system r-build-system) |
3363 | (propagated-inputs | |
ebffd24c RW |
3364 | `(("r-bh" ,r-bh) |
3365 | ("r-biocparallel" ,r-biocparallel) | |
af26c7ae RW |
3366 | ("r-data-table" ,r-data-table) |
3367 | ("r-fastmatch" ,r-fastmatch) | |
3368 | ("r-ggplot2" ,r-ggplot2) | |
3369 | ("r-gridextra" ,r-gridextra) | |
3370 | ("r-matrix" ,r-matrix) | |
3371 | ("r-rcpp" ,r-rcpp))) | |
3372 | (home-page "https://github.com/ctlab/fgsea/") | |
3373 | (synopsis "Fast gene set enrichment analysis") | |
3374 | (description | |
3375 | "The package implements an algorithm for fast gene set enrichment | |
3376 | analysis. Using the fast algorithm allows to make more permutations and get | |
3377 | more fine grained p-values, which allows to use accurate stantard approaches | |
3378 | to multiple hypothesis correction.") | |
3379 | (license license:expat))) | |
305050b5 RW |
3380 | |
3381 | (define-public r-dose | |
3382 | (package | |
3383 | (name "r-dose") | |
aff3ecbf | 3384 | (version "3.10.2") |
305050b5 RW |
3385 | (source |
3386 | (origin | |
3387 | (method url-fetch) | |
3388 | (uri (bioconductor-uri "DOSE" version)) | |
3389 | (sha256 | |
3390 | (base32 | |
aff3ecbf | 3391 | "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj")))) |
305050b5 RW |
3392 | (properties `((upstream-name . "DOSE"))) |
3393 | (build-system r-build-system) | |
3394 | (propagated-inputs | |
3395 | `(("r-annotationdbi" ,r-annotationdbi) | |
3396 | ("r-biocparallel" ,r-biocparallel) | |
3397 | ("r-do-db" ,r-do-db) | |
3398 | ("r-fgsea" ,r-fgsea) | |
3399 | ("r-ggplot2" ,r-ggplot2) | |
3400 | ("r-gosemsim" ,r-gosemsim) | |
3401 | ("r-qvalue" ,r-qvalue) | |
3402 | ("r-reshape2" ,r-reshape2) | |
3403 | ("r-s4vectors" ,r-s4vectors))) | |
3404 | (home-page "https://guangchuangyu.github.io/software/DOSE/") | |
3405 | (synopsis "Disease ontology semantic and enrichment analysis") | |
3406 | (description | |
3407 | "This package implements five methods proposed by Resnik, Schlicker, | |
3408 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among | |
3409 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses | |
3410 | including hypergeometric model and gene set enrichment analysis are also | |
3411 | implemented for discovering disease associations of high-throughput biological | |
3412 | data.") | |
3413 | (license license:artistic2.0))) | |
9c30cf65 RW |
3414 | |
3415 | (define-public r-enrichplot | |
3416 | (package | |
3417 | (name "r-enrichplot") | |
77d28d66 | 3418 | (version "1.4.0") |
9c30cf65 RW |
3419 | (source |
3420 | (origin | |
3421 | (method url-fetch) | |
3422 | (uri (bioconductor-uri "enrichplot" version)) | |
3423 | (sha256 | |
3424 | (base32 | |
77d28d66 | 3425 | "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h")))) |
9c30cf65 RW |
3426 | (build-system r-build-system) |
3427 | (propagated-inputs | |
3428 | `(("r-annotationdbi" ,r-annotationdbi) | |
3429 | ("r-cowplot" ,r-cowplot) | |
3430 | ("r-dose" ,r-dose) | |
3431 | ("r-europepmc" ,r-europepmc) | |
3432 | ("r-ggplot2" ,r-ggplot2) | |
3433 | ("r-ggplotify" ,r-ggplotify) | |
3434 | ("r-ggraph" ,r-ggraph) | |
3435 | ("r-ggridges" ,r-ggridges) | |
3436 | ("r-gosemsim" ,r-gosemsim) | |
3437 | ("r-gridextra" ,r-gridextra) | |
3438 | ("r-igraph" ,r-igraph) | |
3439 | ("r-purrr" ,r-purrr) | |
3440 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3441 | ("r-reshape2" ,r-reshape2) | |
3442 | ("r-upsetr" ,r-upsetr))) | |
3443 | (home-page "https://github.com/GuangchuangYu/enrichplot") | |
3444 | (synopsis "Visualization of functional enrichment result") | |
3445 | (description | |
3446 | "The enrichplot package implements several visualization methods for | |
3447 | interpreting functional enrichment results obtained from ORA or GSEA analyses. | |
3448 | All the visualization methods are developed based on ggplot2 graphics.") | |
3449 | (license license:artistic2.0))) | |
f8295ee6 RW |
3450 | |
3451 | (define-public r-clusterprofiler | |
3452 | (package | |
3453 | (name "r-clusterprofiler") | |
1a3e33be | 3454 | (version "3.12.0") |
f8295ee6 RW |
3455 | (source |
3456 | (origin | |
3457 | (method url-fetch) | |
3458 | (uri (bioconductor-uri "clusterProfiler" version)) | |
3459 | (sha256 | |
3460 | (base32 | |
1a3e33be | 3461 | "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq")))) |
f8295ee6 RW |
3462 | (properties |
3463 | `((upstream-name . "clusterProfiler"))) | |
3464 | (build-system r-build-system) | |
3465 | (propagated-inputs | |
3466 | `(("r-annotationdbi" ,r-annotationdbi) | |
3467 | ("r-dose" ,r-dose) | |
3468 | ("r-enrichplot" ,r-enrichplot) | |
3469 | ("r-ggplot2" ,r-ggplot2) | |
3470 | ("r-go-db" ,r-go-db) | |
3471 | ("r-gosemsim" ,r-gosemsim) | |
3472 | ("r-magrittr" ,r-magrittr) | |
3473 | ("r-plyr" ,r-plyr) | |
3474 | ("r-qvalue" ,r-qvalue) | |
3475 | ("r-rvcheck" ,r-rvcheck) | |
3476 | ("r-tidyr" ,r-tidyr))) | |
3477 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") | |
3478 | (synopsis "Analysis and visualization of functional profiles for gene clusters") | |
3479 | (description | |
3480 | "This package implements methods to analyze and visualize functional | |
3481 | profiles (GO and KEGG) of gene and gene clusters.") | |
3482 | (license license:artistic2.0))) | |
ce77562a RW |
3483 | |
3484 | (define-public r-mlinterfaces | |
3485 | (package | |
3486 | (name "r-mlinterfaces") | |
8265a111 | 3487 | (version "1.64.0") |
ce77562a RW |
3488 | (source |
3489 | (origin | |
3490 | (method url-fetch) | |
3491 | (uri (bioconductor-uri "MLInterfaces" version)) | |
3492 | (sha256 | |
3493 | (base32 | |
8265a111 | 3494 | "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j")))) |
ce77562a RW |
3495 | (properties `((upstream-name . "MLInterfaces"))) |
3496 | (build-system r-build-system) | |
3497 | (propagated-inputs | |
3498 | `(("r-annotate" ,r-annotate) | |
3499 | ("r-biobase" ,r-biobase) | |
3500 | ("r-biocgenerics" ,r-biocgenerics) | |
3501 | ("r-cluster" ,r-cluster) | |
3502 | ("r-fpc" ,r-fpc) | |
3503 | ("r-gbm" ,r-gbm) | |
3504 | ("r-gdata" ,r-gdata) | |
3505 | ("r-genefilter" ,r-genefilter) | |
3506 | ("r-ggvis" ,r-ggvis) | |
3507 | ("r-hwriter" ,r-hwriter) | |
3508 | ("r-mass" ,r-mass) | |
3509 | ("r-mlbench" ,r-mlbench) | |
3510 | ("r-pls" ,r-pls) | |
3511 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3512 | ("r-rda" ,r-rda) | |
3513 | ("r-rpart" ,r-rpart) | |
3514 | ("r-sfsmisc" ,r-sfsmisc) | |
3515 | ("r-shiny" ,r-shiny) | |
3516 | ("r-threejs" ,r-threejs))) | |
3517 | (home-page "https://bioconductor.org/packages/MLInterfaces/") | |
3518 | (synopsis "Interfaces to R machine learning procedures") | |
3519 | (description | |
3520 | "This package provides uniform interfaces to machine learning code for | |
3521 | data in R and Bioconductor containers.") | |
3522 | ;; Any version of the LGPL. | |
3523 | (license license:lgpl2.1+))) | |
a793e88c RW |
3524 | |
3525 | (define-public r-annaffy | |
3526 | (package | |
3527 | (name "r-annaffy") | |
8bef9df4 | 3528 | (version "1.56.0") |
a793e88c RW |
3529 | (source |
3530 | (origin | |
3531 | (method url-fetch) | |
3532 | (uri (bioconductor-uri "annaffy" version)) | |
3533 | (sha256 | |
3534 | (base32 | |
8bef9df4 | 3535 | "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9")))) |
a793e88c RW |
3536 | (build-system r-build-system) |
3537 | (arguments | |
3538 | `(#:phases | |
3539 | (modify-phases %standard-phases | |
3540 | (add-after 'unpack 'remove-reference-to-non-free-data | |
3541 | (lambda _ | |
3542 | (substitute* "DESCRIPTION" | |
3543 | ((", KEGG.db") "")) | |
3544 | #t))))) | |
3545 | (propagated-inputs | |
3546 | `(("r-annotationdbi" ,r-annotationdbi) | |
3547 | ("r-biobase" ,r-biobase) | |
3548 | ("r-dbi" ,r-dbi) | |
3549 | ("r-go-db" ,r-go-db))) | |
3550 | (home-page "https://bioconductor.org/packages/annaffy/") | |
3551 | (synopsis "Annotation tools for Affymetrix biological metadata") | |
3552 | (description | |
3553 | "This package provides functions for handling data from Bioconductor | |
3554 | Affymetrix annotation data packages. It produces compact HTML and text | |
3555 | reports including experimental data and URL links to many online databases. | |
3556 | It allows searching of biological metadata using various criteria.") | |
3557 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of | |
3558 | ;; the LGPL 2.1 is included. | |
3559 | (license license:lgpl2.1+))) | |
0ec0a5ec RW |
3560 | |
3561 | (define-public r-a4core | |
3562 | (package | |
3563 | (name "r-a4core") | |
b077e3db | 3564 | (version "1.32.0") |
0ec0a5ec RW |
3565 | (source |
3566 | (origin | |
3567 | (method url-fetch) | |
3568 | (uri (bioconductor-uri "a4Core" version)) | |
3569 | (sha256 | |
3570 | (base32 | |
b077e3db | 3571 | "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7")))) |
0ec0a5ec RW |
3572 | (properties `((upstream-name . "a4Core"))) |
3573 | (build-system r-build-system) | |
3574 | (propagated-inputs | |
3575 | `(("r-biobase" ,r-biobase) | |
3576 | ("r-glmnet" ,r-glmnet))) | |
3577 | (home-page "https://bioconductor.org/packages/a4Core") | |
3578 | (synopsis "Automated Affymetrix array analysis core package") | |
3579 | (description | |
3580 | "This is the core package for the automated analysis of Affymetrix | |
3581 | arrays.") | |
3582 | (license license:gpl3))) | |
9ae37581 RW |
3583 | |
3584 | (define-public r-a4classif | |
3585 | (package | |
3586 | (name "r-a4classif") | |
82de77da | 3587 | (version "1.32.0") |
9ae37581 RW |
3588 | (source |
3589 | (origin | |
3590 | (method url-fetch) | |
3591 | (uri (bioconductor-uri "a4Classif" version)) | |
3592 | (sha256 | |
3593 | (base32 | |
82de77da | 3594 | "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0")))) |
9ae37581 RW |
3595 | (properties `((upstream-name . "a4Classif"))) |
3596 | (build-system r-build-system) | |
3597 | (propagated-inputs | |
3598 | `(("r-a4core" ,r-a4core) | |
3599 | ("r-a4preproc" ,r-a4preproc) | |
3600 | ("r-glmnet" ,r-glmnet) | |
3601 | ("r-mlinterfaces" ,r-mlinterfaces) | |
3602 | ("r-pamr" ,r-pamr) | |
3603 | ("r-rocr" ,r-rocr) | |
3604 | ("r-varselrf" ,r-varselrf))) | |
3605 | (home-page "https://bioconductor.org/packages/a4Classif/") | |
3606 | (synopsis "Automated Affymetrix array analysis classification package") | |
3607 | (description | |
3608 | "This is the classification package for the automated analysis of | |
3609 | Affymetrix arrays.") | |
3610 | (license license:gpl3))) | |
b8d13e2c RW |
3611 | |
3612 | (define-public r-a4preproc | |
3613 | (package | |
3614 | (name "r-a4preproc") | |
0b609162 | 3615 | (version "1.32.0") |
b8d13e2c RW |
3616 | (source |
3617 | (origin | |
3618 | (method url-fetch) | |
3619 | (uri (bioconductor-uri "a4Preproc" version)) | |
3620 | (sha256 | |
3621 | (base32 | |
0b609162 | 3622 | "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr")))) |
b8d13e2c RW |
3623 | (properties `((upstream-name . "a4Preproc"))) |
3624 | (build-system r-build-system) | |
3625 | (propagated-inputs | |
3626 | `(("r-annotationdbi" ,r-annotationdbi))) | |
3627 | (home-page "https://bioconductor.org/packages/a4Preproc/") | |
3628 | (synopsis "Automated Affymetrix array analysis preprocessing package") | |
3629 | (description | |
3630 | "This is a package for the automated analysis of Affymetrix arrays. It | |
3631 | is used for preprocessing the arrays.") | |
3632 | (license license:gpl3))) | |
8e15f861 RW |
3633 | |
3634 | (define-public r-a4reporting | |
3635 | (package | |
3636 | (name "r-a4reporting") | |
e5a36543 | 3637 | (version "1.32.0") |
8e15f861 RW |
3638 | (source |
3639 | (origin | |
3640 | (method url-fetch) | |
3641 | (uri (bioconductor-uri "a4Reporting" version)) | |
3642 | (sha256 | |
3643 | (base32 | |
e5a36543 | 3644 | "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj")))) |
8e15f861 RW |
3645 | (properties `((upstream-name . "a4Reporting"))) |
3646 | (build-system r-build-system) | |
3647 | (propagated-inputs | |
3648 | `(("r-annaffy" ,r-annaffy) | |
3649 | ("r-xtable" ,r-xtable))) | |
3650 | (home-page "https://bioconductor.org/packages/a4Reporting/") | |
3651 | (synopsis "Automated Affymetrix array analysis reporting package") | |
3652 | (description | |
3653 | "This is a package for the automated analysis of Affymetrix arrays. It | |
3654 | provides reporting features.") | |
3655 | (license license:gpl3))) | |
dbfe3375 RW |
3656 | |
3657 | (define-public r-a4base | |
3658 | (package | |
3659 | (name "r-a4base") | |
ae1730ae | 3660 | (version "1.32.0") |
dbfe3375 RW |
3661 | (source |
3662 | (origin | |
3663 | (method url-fetch) | |
3664 | (uri (bioconductor-uri "a4Base" version)) | |
3665 | (sha256 | |
3666 | (base32 | |
ae1730ae | 3667 | "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1")))) |
dbfe3375 RW |
3668 | (properties `((upstream-name . "a4Base"))) |
3669 | (build-system r-build-system) | |
3670 | (propagated-inputs | |
3671 | `(("r-a4core" ,r-a4core) | |
3672 | ("r-a4preproc" ,r-a4preproc) | |
3673 | ("r-annaffy" ,r-annaffy) | |
3674 | ("r-annotationdbi" ,r-annotationdbi) | |
3675 | ("r-biobase" ,r-biobase) | |
3676 | ("r-genefilter" ,r-genefilter) | |
3677 | ("r-glmnet" ,r-glmnet) | |
3678 | ("r-gplots" ,r-gplots) | |
3679 | ("r-limma" ,r-limma) | |
3680 | ("r-mpm" ,r-mpm) | |
3681 | ("r-multtest" ,r-multtest))) | |
3682 | (home-page "https://bioconductor.org/packages/a4Base/") | |
3683 | (synopsis "Automated Affymetrix array analysis base package") | |
3684 | (description | |
3685 | "This package provides basic features for the automated analysis of | |
3686 | Affymetrix arrays.") | |
3687 | (license license:gpl3))) | |
84ad024e RW |
3688 | |
3689 | (define-public r-a4 | |
3690 | (package | |
3691 | (name "r-a4") | |
1aadddea | 3692 | (version "1.32.0") |
84ad024e RW |
3693 | (source |
3694 | (origin | |
3695 | (method url-fetch) | |
3696 | (uri (bioconductor-uri "a4" version)) | |
3697 | (sha256 | |
3698 | (base32 | |
1aadddea | 3699 | "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy")))) |
84ad024e RW |
3700 | (build-system r-build-system) |
3701 | (propagated-inputs | |
3702 | `(("r-a4base" ,r-a4base) | |
3703 | ("r-a4classif" ,r-a4classif) | |
3704 | ("r-a4core" ,r-a4core) | |
3705 | ("r-a4preproc" ,r-a4preproc) | |
3706 | ("r-a4reporting" ,r-a4reporting))) | |
3707 | (home-page "https://bioconductor.org/packages/a4/") | |
3708 | (synopsis "Automated Affymetrix array analysis umbrella package") | |
3709 | (description | |
3710 | "This package provides a software suite for the automated analysis of | |
3711 | Affymetrix arrays.") | |
3712 | (license license:gpl3))) | |
59d331f1 RW |
3713 | |
3714 | (define-public r-abseqr | |
3715 | (package | |
3716 | (name "r-abseqr") | |
b7ddf0f0 | 3717 | (version "1.2.0") |
59d331f1 RW |
3718 | (source |
3719 | (origin | |
3720 | (method url-fetch) | |
3721 | (uri (bioconductor-uri "abseqR" version)) | |
3722 | (sha256 | |
3723 | (base32 | |
b7ddf0f0 | 3724 | "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r")))) |
59d331f1 RW |
3725 | (properties `((upstream-name . "abseqR"))) |
3726 | (build-system r-build-system) | |
3727 | (inputs | |
3728 | `(("pandoc" ,ghc-pandoc))) | |
3729 | (propagated-inputs | |
3730 | `(("r-biocparallel" ,r-biocparallel) | |
3731 | ("r-biocstyle" ,r-biocstyle) | |
3732 | ("r-circlize" ,r-circlize) | |
3733 | ("r-flexdashboard" ,r-flexdashboard) | |
3734 | ("r-ggcorrplot" ,r-ggcorrplot) | |
3735 | ("r-ggdendro" ,r-ggdendro) | |
3736 | ("r-ggplot2" ,r-ggplot2) | |
3737 | ("r-gridextra" ,r-gridextra) | |
3738 | ("r-knitr" ,r-knitr) | |
3739 | ("r-plotly" ,r-plotly) | |
3740 | ("r-plyr" ,r-plyr) | |
3741 | ("r-png" ,r-png) | |
3742 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3743 | ("r-reshape2" ,r-reshape2) | |
3744 | ("r-rmarkdown" ,r-rmarkdown) | |
3745 | ("r-stringr" ,r-stringr) | |
3746 | ("r-vegan" ,r-vegan) | |
3747 | ("r-venndiagram" ,r-venndiagram))) | |
3748 | (home-page "https://github.com/malhamdoosh/abseqR") | |
3749 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") | |
3750 | (description | |
3751 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of | |
3752 | sequencing datasets generated from antibody libraries and abseqR is one of its | |
3753 | packages. AbseqR empowers the users of abseqPy with plotting and reporting | |
3754 | capabilities and allows them to generate interactive HTML reports for the | |
3755 | convenience of viewing and sharing with other researchers. Additionally, | |
3756 | abseqR extends abseqPy to compare multiple repertoire analyses and perform | |
3757 | further downstream analysis on its output.") | |
3758 | (license license:gpl3))) | |
41aab7d1 RW |
3759 | |
3760 | (define-public r-bacon | |
3761 | (package | |
3762 | (name "r-bacon") | |
e33c25ff | 3763 | (version "1.12.0") |
41aab7d1 RW |
3764 | (source |
3765 | (origin | |
3766 | (method url-fetch) | |
3767 | (uri (bioconductor-uri "bacon" version)) | |
3768 | (sha256 | |
3769 | (base32 | |
e33c25ff | 3770 | "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q")))) |
41aab7d1 RW |
3771 | (build-system r-build-system) |
3772 | (propagated-inputs | |
3773 | `(("r-biocparallel" ,r-biocparallel) | |
3774 | ("r-ellipse" ,r-ellipse) | |
3775 | ("r-ggplot2" ,r-ggplot2))) | |
3776 | (home-page "https://bioconductor.org/packages/bacon/") | |
3777 | (synopsis "Controlling bias and inflation in association studies") | |
3778 | (description | |
3779 | "Bacon can be used to remove inflation and bias often observed in | |
3780 | epigenome- and transcriptome-wide association studies. To this end bacon | |
3781 | constructs an empirical null distribution using a Gibbs Sampling algorithm by | |
3782 | fitting a three-component normal mixture on z-scores.") | |
3783 | (license license:gpl2+))) | |
051e8e1a RW |
3784 | |
3785 | (define-public r-rgadem | |
3786 | (package | |
3787 | (name "r-rgadem") | |
93f8a009 | 3788 | (version "2.32.0") |
051e8e1a RW |
3789 | (source |
3790 | (origin | |
3791 | (method url-fetch) | |
3792 | (uri (bioconductor-uri "rGADEM" version)) | |
3793 | (sha256 | |
3794 | (base32 | |
93f8a009 | 3795 | "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18")))) |
051e8e1a RW |
3796 | (properties `((upstream-name . "rGADEM"))) |
3797 | (build-system r-build-system) | |
3798 | (propagated-inputs | |
3799 | `(("r-biostrings" ,r-biostrings) | |
3800 | ("r-bsgenome" ,r-bsgenome) | |
3801 | ("r-iranges" ,r-iranges) | |
3802 | ("r-seqlogo" ,r-seqlogo))) | |
3803 | (home-page "https://bioconductor.org/packages/rGADEM/") | |
3804 | (synopsis "De novo sequence motif discovery") | |
3805 | (description | |
3806 | "rGADEM is an efficient de novo motif discovery tool for large-scale | |
3807 | genomic sequence data.") | |
3808 | (license license:artistic2.0))) | |
229f97c3 RW |
3809 | |
3810 | (define-public r-motiv | |
3811 | (package | |
3812 | (name "r-motiv") | |
f7a495b1 | 3813 | (version "1.40.0") |
229f97c3 RW |
3814 | (source |
3815 | (origin | |
3816 | (method url-fetch) | |
3817 | (uri (bioconductor-uri "MotIV" version)) | |
3818 | (sha256 | |
3819 | (base32 | |
f7a495b1 | 3820 | "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf")))) |
229f97c3 RW |
3821 | (properties `((upstream-name . "MotIV"))) |
3822 | (build-system r-build-system) | |
3823 | (inputs | |
3824 | `(("gsl" ,gsl))) | |
3825 | (propagated-inputs | |
3826 | `(("r-biocgenerics" ,r-biocgenerics) | |
3827 | ("r-biostrings" ,r-biostrings) | |
3828 | ("r-iranges" ,r-iranges) | |
3829 | ("r-lattice" ,r-lattice) | |
3830 | ("r-rgadem" ,r-rgadem) | |
3831 | ("r-s4vectors" ,r-s4vectors))) | |
3832 | (home-page "https://bioconductor.org/packages/MotIV/") | |
3833 | (synopsis "Motif identification and validation") | |
3834 | (description | |
3835 | "This package is used for the identification and validation of sequence | |
3836 | motifs. It makes use of STAMP for comparing a set of motifs to a given | |
3837 | database (e.g. JASPAR). It can also be used to visualize motifs, motif | |
3838 | distributions, modules and filter motifs.") | |
3839 | (license license:gpl2))) | |
2a72ef56 RW |
3840 | |
3841 | (define-public r-motifstack | |
3842 | (package | |
3843 | (name "r-motifstack") | |
aa0ebfd2 | 3844 | (version "1.28.0") |
2a72ef56 RW |
3845 | (source |
3846 | (origin | |
3847 | (method url-fetch) | |
3848 | (uri (bioconductor-uri "motifStack" version)) | |
3849 | (sha256 | |
3850 | (base32 | |
aa0ebfd2 | 3851 | "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f")))) |
2a72ef56 RW |
3852 | (properties `((upstream-name . "motifStack"))) |
3853 | (build-system r-build-system) | |
3854 | (propagated-inputs | |
3855 | `(("r-ade4" ,r-ade4) | |
3856 | ("r-biostrings" ,r-biostrings) | |
aa0ebfd2 | 3857 | ("r-grimport2" ,r-grimport2) |
2a72ef56 RW |
3858 | ("r-htmlwidgets" ,r-htmlwidgets) |
3859 | ("r-motiv" ,r-motiv) | |
3860 | ("r-scales" ,r-scales) | |
3861 | ("r-xml" ,r-xml))) | |
3862 | (home-page "https://bioconductor.org/packages/motifStack/") | |
3863 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") | |
3864 | (description | |
3865 | "The motifStack package is designed for graphic representation of | |
3866 | multiple motifs with different similarity scores. It works with both DNA/RNA | |
3867 | sequence motifs and amino acid sequence motifs. In addition, it provides the | |
3868 | flexibility for users to customize the graphic parameters such as the font | |
3869 | type and symbol colors.") | |
3870 | (license license:gpl2+))) | |
e5bff307 RW |
3871 | |
3872 | (define-public r-genomicscores | |
3873 | (package | |
3874 | (name "r-genomicscores") | |
3c944fda | 3875 | (version "1.8.1") |
e5bff307 RW |
3876 | (source |
3877 | (origin | |
3878 | (method url-fetch) | |
3879 | (uri (bioconductor-uri "GenomicScores" version)) | |
3880 | (sha256 | |
3881 | (base32 | |
3c944fda | 3882 | "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy")))) |
e5bff307 RW |
3883 | (properties `((upstream-name . "GenomicScores"))) |
3884 | (build-system r-build-system) | |
3885 | (propagated-inputs | |
3886 | `(("r-annotationhub" ,r-annotationhub) | |
3887 | ("r-biobase" ,r-biobase) | |
3888 | ("r-biocgenerics" ,r-biocgenerics) | |
3889 | ("r-biostrings" ,r-biostrings) | |
3890 | ("r-bsgenome" ,r-bsgenome) | |
3891 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3892 | ("r-genomicranges" ,r-genomicranges) | |
3893 | ("r-iranges" ,r-iranges) | |
3894 | ("r-s4vectors" ,r-s4vectors) | |
3895 | ("r-xml" ,r-xml))) | |
3896 | (home-page "https://github.com/rcastelo/GenomicScores/") | |
3897 | (synopsis "Work with genome-wide position-specific scores") | |
3898 | (description | |
3899 | "This package provides infrastructure to store and access genome-wide | |
3900 | position-specific scores within R and Bioconductor.") | |
3901 | (license license:artistic2.0))) | |
32e0f906 RW |
3902 | |
3903 | (define-public r-atacseqqc | |
3904 | (package | |
3905 | (name "r-atacseqqc") | |
fbe5a087 | 3906 | (version "1.8.5") |
32e0f906 RW |
3907 | (source |
3908 | (origin | |
3909 | (method url-fetch) | |
3910 | (uri (bioconductor-uri "ATACseqQC" version)) | |
3911 | (sha256 | |
3912 | (base32 | |
fbe5a087 | 3913 | "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp")))) |
32e0f906 RW |
3914 | (properties `((upstream-name . "ATACseqQC"))) |
3915 | (build-system r-build-system) | |
3916 | (propagated-inputs | |
3917 | `(("r-biocgenerics" ,r-biocgenerics) | |
3918 | ("r-biostrings" ,r-biostrings) | |
3919 | ("r-bsgenome" ,r-bsgenome) | |
3920 | ("r-chippeakanno" ,r-chippeakanno) | |
bcc233c1 | 3921 | ("r-edger" ,r-edger) |
32e0f906 RW |
3922 | ("r-genomeinfodb" ,r-genomeinfodb) |
3923 | ("r-genomicalignments" ,r-genomicalignments) | |
3924 | ("r-genomicranges" ,r-genomicranges) | |
3925 | ("r-genomicscores" ,r-genomicscores) | |
3926 | ("r-iranges" ,r-iranges) | |
3927 | ("r-kernsmooth" ,r-kernsmooth) | |
3928 | ("r-limma" ,r-limma) | |
3929 | ("r-motifstack" ,r-motifstack) | |
3930 | ("r-preseqr" ,r-preseqr) | |
3931 | ("r-randomforest" ,r-randomforest) | |
3932 | ("r-rsamtools" ,r-rsamtools) | |
3933 | ("r-rtracklayer" ,r-rtracklayer) | |
3934 | ("r-s4vectors" ,r-s4vectors))) | |
3935 | (home-page "https://bioconductor.org/packages/ATACseqQC/") | |
3936 | (synopsis "ATAC-seq quality control") | |
3937 | (description | |
3938 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using | |
3939 | sequencing, is a rapid and sensitive method for chromatin accessibility | |
3940 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq | |
3941 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly | |
3942 | assess whether their ATAC-seq experiment is successful. It includes | |
3943 | diagnostic plots of fragment size distribution, proportion of mitochondria | |
3944 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor | |
3945 | footprints.") | |
3946 | (license license:gpl2+))) | |
3972cfce RW |
3947 | |
3948 | (define-public r-gofuncr | |
3949 | (package | |
3950 | (name "r-gofuncr") | |
bab06a6f | 3951 | (version "1.4.0") |
3972cfce RW |
3952 | (source |
3953 | (origin | |
3954 | (method url-fetch) | |
3955 | (uri (bioconductor-uri "GOfuncR" version)) | |
3956 | (sha256 | |
3957 | (base32 | |
bab06a6f | 3958 | "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm")))) |
3972cfce RW |
3959 | (properties `((upstream-name . "GOfuncR"))) |
3960 | (build-system r-build-system) | |
3961 | (propagated-inputs | |
3962 | `(("r-annotationdbi" ,r-annotationdbi) | |
3963 | ("r-genomicranges" ,r-genomicranges) | |
3964 | ("r-gtools" ,r-gtools) | |
3965 | ("r-iranges" ,r-iranges) | |
3966 | ("r-mapplots" ,r-mapplots) | |
3967 | ("r-rcpp" ,r-rcpp) | |
3968 | ("r-vioplot" ,r-vioplot))) | |
3969 | (home-page "https://bioconductor.org/packages/GOfuncR/") | |
3970 | (synopsis "Gene ontology enrichment using FUNC") | |
3971 | (description | |
3972 | "GOfuncR performs a gene ontology enrichment analysis based on the | |
3973 | ontology enrichment software FUNC. GO-annotations are obtained from | |
3974 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is | |
3975 | included in the package and updated regularly. GOfuncR provides the standard | |
3976 | candidate vs background enrichment analysis using the hypergeometric test, as | |
3977 | well as three additional tests: | |
3978 | ||
3979 | @enumerate | |
3980 | @item the Wilcoxon rank-sum test that is used when genes are ranked, | |
3981 | @item a binomial test that is used when genes are associated with two counts, | |
3982 | and | |
3983 | @item a Chi-square or Fisher's exact test that is used in cases when genes are | |
3984 | associated with four counts. | |
3985 | @end enumerate | |
3986 | ||
3987 | To correct for multiple testing and interdependency of the tests, family-wise | |
3988 | error rates are computed based on random permutations of the gene-associated | |
3989 | variables. GOfuncR also provides tools for exploring the ontology graph and | |
3990 | the annotations, and options to take gene-length or spatial clustering of | |
3991 | genes into account. It is also possible to provide custom gene coordinates, | |
3992 | annotations and ontologies.") | |
3993 | (license license:gpl2+))) | |
9bf4bb19 RW |
3994 | |
3995 | (define-public r-abaenrichment | |
3996 | (package | |
3997 | (name "r-abaenrichment") | |
d6158ecb | 3998 | (version "1.14.1") |
9bf4bb19 RW |
3999 | (source |
4000 | (origin | |
4001 | (method url-fetch) | |
4002 | (uri (bioconductor-uri "ABAEnrichment" version)) | |
4003 | (sha256 | |
4004 | (base32 | |
d6158ecb | 4005 | "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48")))) |
9bf4bb19 RW |
4006 | (properties `((upstream-name . "ABAEnrichment"))) |
4007 | (build-system r-build-system) | |
4008 | (propagated-inputs | |
4009 | `(("r-abadata" ,r-abadata) | |
4010 | ("r-data-table" ,r-data-table) | |
4011 | ("r-gofuncr" ,r-gofuncr) | |
4012 | ("r-gplots" ,r-gplots) | |
4013 | ("r-gtools" ,r-gtools) | |
4014 | ("r-rcpp" ,r-rcpp))) | |
4015 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") | |
4016 | (synopsis "Gene expression enrichment in human brain regions") | |
4017 | (description | |
4018 | "The package ABAEnrichment is designed to test for enrichment of user | |
4019 | defined candidate genes in the set of expressed genes in different human brain | |
4020 | regions. The core function @code{aba_enrich} integrates the expression of the | |
4021 | candidate gene set (averaged across donors) and the structural information of | |
4022 | the brain using an ontology, both provided by the Allen Brain Atlas project.") | |
4023 | (license license:gpl2+))) | |
0b91b7b9 RW |
4024 | |
4025 | (define-public r-annotationfuncs | |
4026 | (package | |
4027 | (name "r-annotationfuncs") | |
69a2ec54 | 4028 | (version "1.34.0") |
0b91b7b9 RW |
4029 | (source |
4030 | (origin | |
4031 | (method url-fetch) | |
4032 | (uri (bioconductor-uri "AnnotationFuncs" version)) | |
4033 | (sha256 | |
4034 | (base32 | |
69a2ec54 | 4035 | "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3")))) |
0b91b7b9 RW |
4036 | (properties |
4037 | `((upstream-name . "AnnotationFuncs"))) | |
4038 | (build-system r-build-system) | |
4039 | (propagated-inputs | |
4040 | `(("r-annotationdbi" ,r-annotationdbi) | |
4041 | ("r-dbi" ,r-dbi))) | |
4042 | (home-page "https://www.iysik.com/r/annotationfuncs") | |
4043 | (synopsis "Annotation translation functions") | |
4044 | (description | |
4045 | "This package provides functions for handling translating between | |
4046 | different identifieres using the Biocore Data Team data-packages (e.g. | |
4047 | @code{org.Bt.eg.db}).") | |
4048 | (license license:gpl2))) | |
adf7d813 RW |
4049 | |
4050 | (define-public r-annotationtools | |
4051 | (package | |
4052 | (name "r-annotationtools") | |
ee1a45d7 | 4053 | (version "1.58.0") |
adf7d813 RW |
4054 | (source |
4055 | (origin | |
4056 | (method url-fetch) | |
4057 | (uri (bioconductor-uri "annotationTools" version)) | |
4058 | (sha256 | |
4059 | (base32 | |
ee1a45d7 | 4060 | "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1")))) |
adf7d813 RW |
4061 | (properties |
4062 | `((upstream-name . "annotationTools"))) | |
4063 | (build-system r-build-system) | |
4064 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4065 | (home-page "https://bioconductor.org/packages/annotationTools/") | |
4066 | (synopsis "Annotate microarrays and perform gene expression analyses") | |
4067 | (description | |
4068 | "This package provides functions to annotate microarrays, find orthologs, | |
4069 | and integrate heterogeneous gene expression profiles using annotation and | |
4070 | other molecular biology information available as flat file database (plain | |
4071 | text files).") | |
4072 | ;; Any version of the GPL. | |
4073 | (license (list license:gpl2+)))) | |
f31e10f8 RW |
4074 | |
4075 | (define-public r-allelicimbalance | |
4076 | (package | |
4077 | (name "r-allelicimbalance") | |
9da2021f | 4078 | (version "1.22.0") |
f31e10f8 RW |
4079 | (source |
4080 | (origin | |
4081 | (method url-fetch) | |
4082 | (uri (bioconductor-uri "AllelicImbalance" version)) | |
4083 | (sha256 | |
4084 | (base32 | |
9da2021f | 4085 | "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng")))) |
f31e10f8 RW |
4086 | (properties |
4087 | `((upstream-name . "AllelicImbalance"))) | |
4088 | (build-system r-build-system) | |
4089 | (propagated-inputs | |
4090 | `(("r-annotationdbi" ,r-annotationdbi) | |
4091 | ("r-biocgenerics" ,r-biocgenerics) | |
4092 | ("r-biostrings" ,r-biostrings) | |
4093 | ("r-bsgenome" ,r-bsgenome) | |
4094 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4095 | ("r-genomicalignments" ,r-genomicalignments) | |
4096 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4097 | ("r-genomicranges" ,r-genomicranges) | |
4098 | ("r-gridextra" ,r-gridextra) | |
4099 | ("r-gviz" ,r-gviz) | |
4100 | ("r-iranges" ,r-iranges) | |
4101 | ("r-lattice" ,r-lattice) | |
4102 | ("r-latticeextra" ,r-latticeextra) | |
4103 | ("r-nlme" ,r-nlme) | |
4104 | ("r-rsamtools" ,r-rsamtools) | |
4105 | ("r-s4vectors" ,r-s4vectors) | |
4106 | ("r-seqinr" ,r-seqinr) | |
4107 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
4108 | ("r-variantannotation" ,r-variantannotation))) | |
4109 | (home-page "https://github.com/pappewaio/AllelicImbalance") | |
4110 | (synopsis "Investigate allele-specific expression") | |
4111 | (description | |
4112 | "This package provides a framework for allele-specific expression | |
4113 | investigation using RNA-seq data.") | |
4114 | (license license:gpl3))) | |
ffe7029b RW |
4115 | |
4116 | (define-public r-aucell | |
4117 | (package | |
4118 | (name "r-aucell") | |
61730c3d | 4119 | (version "1.6.1") |
ffe7029b RW |
4120 | (source |
4121 | (origin | |
4122 | (method url-fetch) | |
4123 | (uri (bioconductor-uri "AUCell" version)) | |
4124 | (sha256 | |
4125 | (base32 | |
61730c3d | 4126 | "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b")))) |
ffe7029b RW |
4127 | (properties `((upstream-name . "AUCell"))) |
4128 | (build-system r-build-system) | |
4129 | (propagated-inputs | |
4130 | `(("r-data-table" ,r-data-table) | |
4131 | ("r-gseabase" ,r-gseabase) | |
4132 | ("r-mixtools" ,r-mixtools) | |
4133 | ("r-r-utils" ,r-r-utils) | |
4134 | ("r-shiny" ,r-shiny) | |
4135 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4136 | (home-page "https://bioconductor.org/packages/AUCell/") | |
4137 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") | |
4138 | (description | |
4139 | "AUCell allows to identify cells with active gene sets (e.g. signatures, | |
4140 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area | |
4141 | Under the Curve} (AUC) to calculate whether a critical subset of the input | |
4142 | gene set is enriched within the expressed genes for each cell. The | |
4143 | distribution of AUC scores across all the cells allows exploring the relative | |
4144 | expression of the signature. Since the scoring method is ranking-based, | |
4145 | AUCell is independent of the gene expression units and the normalization | |
4146 | procedure. In addition, since the cells are evaluated individually, it can | |
4147 | easily be applied to bigger datasets, subsetting the expression matrix if | |
4148 | needed.") | |
4149 | (license license:gpl3))) | |
5cfa4bff RW |
4150 | |
4151 | (define-public r-ebimage | |
4152 | (package | |
4153 | (name "r-ebimage") | |
2a6d8383 | 4154 | (version "4.26.0") |
5cfa4bff RW |
4155 | (source |
4156 | (origin | |
4157 | (method url-fetch) | |
4158 | (uri (bioconductor-uri "EBImage" version)) | |
4159 | (sha256 | |
4160 | (base32 | |
2a6d8383 | 4161 | "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq")))) |
5cfa4bff RW |
4162 | (properties `((upstream-name . "EBImage"))) |
4163 | (build-system r-build-system) | |
4164 | (propagated-inputs | |
4165 | `(("r-abind" ,r-abind) | |
4166 | ("r-biocgenerics" ,r-biocgenerics) | |
4167 | ("r-fftwtools" ,r-fftwtools) | |
4168 | ("r-htmltools" ,r-htmltools) | |
4169 | ("r-htmlwidgets" ,r-htmlwidgets) | |
4170 | ("r-jpeg" ,r-jpeg) | |
4171 | ("r-locfit" ,r-locfit) | |
4172 | ("r-png" ,r-png) | |
4173 | ("r-rcurl" ,r-rcurl) | |
4174 | ("r-tiff" ,r-tiff))) | |
4175 | (native-inputs | |
4176 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
4177 | (home-page "https://github.com/aoles/EBImage") | |
4178 | (synopsis "Image processing and analysis toolbox for R") | |
4179 | (description | |
4180 | "EBImage provides general purpose functionality for image processing and | |
4181 | analysis. In the context of (high-throughput) microscopy-based cellular | |
4182 | assays, EBImage offers tools to segment cells and extract quantitative | |
4183 | cellular descriptors. This allows the automation of such tasks using the R | |
4184 | programming language and facilitates the use of other tools in the R | |
4185 | environment for signal processing, statistical modeling, machine learning and | |
4186 | visualization with image data.") | |
4187 | ;; Any version of the LGPL. | |
4188 | (license license:lgpl2.1+))) | |
51e98f7e RW |
4189 | |
4190 | (define-public r-yamss | |
4191 | (package | |
4192 | (name "r-yamss") | |
1269a926 | 4193 | (version "1.10.0") |
51e98f7e RW |
4194 | (source |
4195 | (origin | |
4196 | (method url-fetch) | |
4197 | (uri (bioconductor-uri "yamss" version)) | |
4198 | (sha256 | |
4199 | (base32 | |
1269a926 | 4200 | "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23")))) |
51e98f7e RW |
4201 | (build-system r-build-system) |
4202 | (propagated-inputs | |
4203 | `(("r-biocgenerics" ,r-biocgenerics) | |
4204 | ("r-data-table" ,r-data-table) | |
4205 | ("r-ebimage" ,r-ebimage) | |
4206 | ("r-iranges" ,r-iranges) | |
4207 | ("r-limma" ,r-limma) | |
4208 | ("r-matrix" ,r-matrix) | |
4209 | ("r-mzr" ,r-mzr) | |
4210 | ("r-s4vectors" ,r-s4vectors) | |
4211 | ("r-summarizedexperiment" | |
4212 | ,r-summarizedexperiment))) | |
4213 | (home-page "https://github.com/hansenlab/yamss") | |
4214 | (synopsis "Tools for high-throughput metabolomics") | |
4215 | (description | |
4216 | "This package provides tools to analyze and visualize high-throughput | |
9b19734c | 4217 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
51e98f7e RW |
4218 | preprocess data in a way that enables reliable and powerful differential |
4219 | analysis.") | |
4220 | (license license:artistic2.0))) | |
398c4a93 RW |
4221 | |
4222 | (define-public r-gtrellis | |
4223 | (package | |
4224 | (name "r-gtrellis") | |
f8fb5b75 | 4225 | (version "1.16.1") |
398c4a93 RW |
4226 | (source |
4227 | (origin | |
4228 | (method url-fetch) | |
4229 | (uri (bioconductor-uri "gtrellis" version)) | |
4230 | (sha256 | |
4231 | (base32 | |
f8fb5b75 | 4232 | "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix")))) |
398c4a93 RW |
4233 | (build-system r-build-system) |
4234 | (propagated-inputs | |
4235 | `(("r-circlize" ,r-circlize) | |
4236 | ("r-genomicranges" ,r-genomicranges) | |
4237 | ("r-getoptlong" ,r-getoptlong) | |
4238 | ("r-iranges" ,r-iranges))) | |
4239 | (home-page "https://github.com/jokergoo/gtrellis") | |
4240 | (synopsis "Genome level Trellis layout") | |
4241 | (description | |
4242 | "Genome level Trellis graph visualizes genomic data conditioned by | |
4243 | genomic categories (e.g. chromosomes). For each genomic category, multiple | |
4244 | dimensional data which are represented as tracks describe different features | |
4245 | from different aspects. This package provides high flexibility to arrange | |
4246 | genomic categories and to add self-defined graphics in the plot.") | |
4247 | (license license:expat))) | |
28098414 RW |
4248 | |
4249 | (define-public r-somaticsignatures | |
4250 | (package | |
4251 | (name "r-somaticsignatures") | |
3cdc5d1a | 4252 | (version "2.20.0") |
28098414 RW |
4253 | (source |
4254 | (origin | |
4255 | (method url-fetch) | |
4256 | (uri (bioconductor-uri "SomaticSignatures" version)) | |
4257 | (sha256 | |
4258 | (base32 | |
3cdc5d1a | 4259 | "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx")))) |
28098414 RW |
4260 | (properties |
4261 | `((upstream-name . "SomaticSignatures"))) | |
4262 | (build-system r-build-system) | |
4263 | (propagated-inputs | |
4264 | `(("r-biobase" ,r-biobase) | |
4265 | ("r-biostrings" ,r-biostrings) | |
4266 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4267 | ("r-genomicranges" ,r-genomicranges) | |
4268 | ("r-ggbio" ,r-ggbio) | |
4269 | ("r-ggplot2" ,r-ggplot2) | |
4270 | ("r-iranges" ,r-iranges) | |
4271 | ("r-nmf" ,r-nmf) | |
4272 | ("r-pcamethods" ,r-pcamethods) | |
4273 | ("r-proxy" ,r-proxy) | |
4274 | ("r-reshape2" ,r-reshape2) | |
4275 | ("r-s4vectors" ,r-s4vectors) | |
4276 | ("r-variantannotation" ,r-variantannotation))) | |
4277 | (home-page "https://github.com/juliangehring/SomaticSignatures") | |
4278 | (synopsis "Somatic signatures") | |
4279 | (description | |
4280 | "This package identifies mutational signatures of @dfn{single nucleotide | |
4281 | variants} (SNVs). It provides a infrastructure related to the methodology | |
4282 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix | |
4283 | decomposition algorithms.") | |
4284 | (license license:expat))) | |
303f2ed1 RW |
4285 | |
4286 | (define-public r-yapsa | |
4287 | (package | |
4288 | (name "r-yapsa") | |
edba69b2 | 4289 | (version "1.10.0") |
303f2ed1 RW |
4290 | (source |
4291 | (origin | |
4292 | (method url-fetch) | |
4293 | (uri (bioconductor-uri "YAPSA" version)) | |
4294 | (sha256 | |
4295 | (base32 | |
edba69b2 | 4296 | "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q")))) |
303f2ed1 RW |
4297 | (properties `((upstream-name . "YAPSA"))) |
4298 | (build-system r-build-system) | |
4299 | (propagated-inputs | |
4300 | `(("r-circlize" ,r-circlize) | |
4301 | ("r-complexheatmap" ,r-complexheatmap) | |
4302 | ("r-corrplot" ,r-corrplot) | |
4303 | ("r-dendextend" ,r-dendextend) | |
4304 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4305 | ("r-genomicranges" ,r-genomicranges) | |
4306 | ("r-getoptlong" ,r-getoptlong) | |
4307 | ("r-ggplot2" ,r-ggplot2) | |
4308 | ("r-gridextra" ,r-gridextra) | |
4309 | ("r-gtrellis" ,r-gtrellis) | |
4310 | ("r-keggrest" ,r-keggrest) | |
4311 | ("r-lsei" ,r-lsei) | |
4312 | ("r-pmcmr" ,r-pmcmr) | |
4313 | ("r-reshape2" ,r-reshape2) | |
4314 | ("r-somaticsignatures" ,r-somaticsignatures) | |
4315 | ("r-variantannotation" ,r-variantannotation))) | |
4316 | (home-page "https://bioconductor.org/packages/YAPSA/") | |
4317 | (synopsis "Yet another package for signature analysis") | |
4318 | (description | |
4319 | "This package provides functions and routines useful in the analysis of | |
4320 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, | |
4321 | functions to perform a signature analysis with known signatures and a | |
4322 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are | |
4323 | provided.") | |
4324 | (license license:gpl3))) | |
e99380d6 RW |
4325 | |
4326 | (define-public r-gcrma | |
4327 | (package | |
4328 | (name "r-gcrma") | |
56576bea | 4329 | (version "2.56.0") |
e99380d6 RW |
4330 | (source |
4331 | (origin | |
4332 | (method url-fetch) | |
4333 | (uri (bioconductor-uri "gcrma" version)) | |
4334 | (sha256 | |
4335 | (base32 | |
56576bea | 4336 | "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4")))) |
e99380d6 RW |
4337 | (build-system r-build-system) |
4338 | (propagated-inputs | |
4339 | `(("r-affy" ,r-affy) | |
4340 | ("r-affyio" ,r-affyio) | |
4341 | ("r-biobase" ,r-biobase) | |
4342 | ("r-biocmanager" ,r-biocmanager) | |
4343 | ("r-biostrings" ,r-biostrings) | |
4344 | ("r-xvector" ,r-xvector))) | |
4345 | (home-page "https://bioconductor.org/packages/gcrma/") | |
4346 | (synopsis "Background adjustment using sequence information") | |
4347 | (description | |
4348 | "Gcrma adjusts for background intensities in Affymetrix array data which | |
4349 | include optical noise and @dfn{non-specific binding} (NSB). The main function | |
4350 | @code{gcrma} converts background adjusted probe intensities to expression | |
4351 | measures using the same normalization and summarization methods as a | |
4352 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information | |
4353 | to estimate probe affinity to NSB. The sequence information is summarized in | |
4354 | a more complex way than the simple GC content. Instead, the base types (A, T, | |
4355 | G or C) at each position along the probe determine the affinity of each probe. | |
4356 | The parameters of the position-specific base contributions to the probe | |
4357 | affinity is estimated in an NSB experiment in which only NSB but no | |
4358 | gene-specific bidning is expected.") | |
4359 | ;; Any version of the LGPL | |
4360 | (license license:lgpl2.1+))) | |
4675b3cf RW |
4361 | |
4362 | (define-public r-simpleaffy | |
4363 | (package | |
4364 | (name "r-simpleaffy") | |
38c5d13a | 4365 | (version "2.60.0") |
4675b3cf RW |
4366 | (source |
4367 | (origin | |
4368 | (method url-fetch) | |
4369 | (uri (bioconductor-uri "simpleaffy" version)) | |
4370 | (sha256 | |
4371 | (base32 | |
38c5d13a | 4372 | "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a")))) |
4675b3cf RW |
4373 | (build-system r-build-system) |
4374 | (propagated-inputs | |
4375 | `(("r-affy" ,r-affy) | |
4376 | ("r-biobase" ,r-biobase) | |
4377 | ("r-biocgenerics" ,r-biocgenerics) | |
4378 | ("r-gcrma" ,r-gcrma) | |
4379 | ("r-genefilter" ,r-genefilter))) | |
4380 | (home-page "https://bioconductor.org/packages/simpleaffy/") | |
4381 | (synopsis "Very simple high level analysis of Affymetrix data") | |
4382 | (description | |
4383 | "This package provides high level functions for reading Affy @file{.CEL} | |
4384 | files, phenotypic data, and then computing simple things with it, such as | |
4385 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} | |
4386 | library. It also has some basic scatter plot functions and mechanisms for | |
4387 | generating high resolution journal figures.") | |
4388 | (license license:gpl2+))) | |
f562c90a RW |
4389 | |
4390 | (define-public r-yaqcaffy | |
4391 | (package | |
4392 | (name "r-yaqcaffy") | |
f48e29da | 4393 | (version "1.44.0") |
f562c90a RW |
4394 | (source |
4395 | (origin | |
4396 | (method url-fetch) | |
4397 | (uri (bioconductor-uri "yaqcaffy" version)) | |
4398 | (sha256 | |
4399 | (base32 | |
f48e29da | 4400 | "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670")))) |
f562c90a RW |
4401 | (build-system r-build-system) |
4402 | (propagated-inputs | |
4403 | `(("r-simpleaffy" ,r-simpleaffy))) | |
4404 | (home-page "https://bioconductor.org/packages/yaqcaffy/") | |
4405 | (synopsis "Affymetrix quality control and reproducibility analysis") | |
4406 | (description | |
4407 | "This is a package that can be used for quality control of Affymetrix | |
4408 | GeneChip expression data and reproducibility analysis of human whole genome | |
4409 | chips with the MAQC reference datasets.") | |
4410 | (license license:artistic2.0))) | |
59cf2629 RW |
4411 | |
4412 | (define-public r-quantro | |
4413 | (package | |
4414 | (name "r-quantro") | |
2feea2d2 | 4415 | (version "1.18.0") |
59cf2629 RW |
4416 | (source |
4417 | (origin | |
4418 | (method url-fetch) | |
4419 | (uri (bioconductor-uri "quantro" version)) | |
4420 | (sha256 | |
4421 | (base32 | |
2feea2d2 | 4422 | "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab")))) |
59cf2629 RW |
4423 | (build-system r-build-system) |
4424 | (propagated-inputs | |
4425 | `(("r-biobase" ,r-biobase) | |
4426 | ("r-doparallel" ,r-doparallel) | |
4427 | ("r-foreach" ,r-foreach) | |
4428 | ("r-ggplot2" ,r-ggplot2) | |
4429 | ("r-iterators" ,r-iterators) | |
4430 | ("r-minfi" ,r-minfi) | |
4431 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
4432 | (home-page "https://bioconductor.org/packages/quantro/") | |
4433 | (synopsis "Test for when to use quantile normalization") | |
4434 | (description | |
4435 | "This package provides a data-driven test for the assumptions of quantile | |
4436 | normalization using raw data such as objects that inherit eSets (e.g. | |
4437 | ExpressionSet, MethylSet). Group level information about each sample (such as | |
4438 | Tumor / Normal status) must also be provided because the test assesses if | |
4439 | there are global differences in the distributions between the user-defined | |
4440 | groups.") | |
4441 | (license license:gpl3+))) | |
98a2af31 RW |
4442 | |
4443 | (define-public r-yarn | |
4444 | (package | |
4445 | (name "r-yarn") | |
7f4957b2 | 4446 | (version "1.10.0") |
98a2af31 RW |
4447 | (source |
4448 | (origin | |
4449 | (method url-fetch) | |
4450 | (uri (bioconductor-uri "yarn" version)) | |
4451 | (sha256 | |
4452 | (base32 | |
7f4957b2 | 4453 | "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6")))) |
98a2af31 RW |
4454 | (build-system r-build-system) |
4455 | (propagated-inputs | |
4456 | `(("r-biobase" ,r-biobase) | |
4457 | ("r-biomart" ,r-biomart) | |
4458 | ("r-downloader" ,r-downloader) | |
4459 | ("r-edger" ,r-edger) | |
4460 | ("r-gplots" ,r-gplots) | |
4461 | ("r-limma" ,r-limma) | |
4462 | ("r-matrixstats" ,r-matrixstats) | |
4463 | ("r-preprocesscore" ,r-preprocesscore) | |
4464 | ("r-quantro" ,r-quantro) | |
4465 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4466 | ("r-readr" ,r-readr))) | |
4467 | (home-page "https://bioconductor.org/packages/yarn/") | |
4468 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") | |
4469 | (description | |
4470 | "Expedite large RNA-Seq analyses using a combination of previously | |
4471 | developed tools. YARN is meant to make it easier for the user in performing | |
4472 | basic mis-annotation quality control, filtering, and condition-aware | |
4473 | normalization. YARN leverages many Bioconductor tools and statistical | |
4474 | techniques to account for the large heterogeneity and sparsity found in very | |
4475 | large RNA-seq experiments.") | |
4476 | (license license:artistic2.0))) | |
a6e1eb1a RW |
4477 | |
4478 | (define-public r-roar | |
4479 | (package | |
4480 | (name "r-roar") | |
0334b203 | 4481 | (version "1.20.0") |
a6e1eb1a RW |
4482 | (source |
4483 | (origin | |
4484 | (method url-fetch) | |
4485 | (uri (bioconductor-uri "roar" version)) | |
4486 | (sha256 | |
4487 | (base32 | |
0334b203 | 4488 | "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7")))) |
a6e1eb1a RW |
4489 | (build-system r-build-system) |
4490 | (propagated-inputs | |
4491 | `(("r-biocgenerics" ,r-biocgenerics) | |
4492 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4493 | ("r-genomicalignments" ,r-genomicalignments) | |
4494 | ("r-genomicranges" ,r-genomicranges) | |
4495 | ("r-iranges" ,r-iranges) | |
4496 | ("r-rtracklayer" ,r-rtracklayer) | |
4497 | ("r-s4vectors" ,r-s4vectors) | |
4498 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4499 | (home-page "https://github.com/vodkatad/roar/") | |
4500 | (synopsis "Identify differential APA usage from RNA-seq alignments") | |
4501 | (description | |
4502 | "This package provides tools for identifying preferential usage of APA | |
4503 | sites, comparing two biological conditions, starting from known alternative | |
4504 | sites and alignments obtained from standard RNA-seq experiments.") | |
4505 | (license license:gpl3))) | |
50d91770 RW |
4506 | |
4507 | (define-public r-xbseq | |
4508 | (package | |
4509 | (name "r-xbseq") | |
88469def | 4510 | (version "1.16.0") |
50d91770 RW |
4511 | (source |
4512 | (origin | |
4513 | (method url-fetch) | |
4514 | (uri (bioconductor-uri "XBSeq" version)) | |
4515 | (sha256 | |
4516 | (base32 | |
88469def | 4517 | "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy")))) |
50d91770 RW |
4518 | (properties `((upstream-name . "XBSeq"))) |
4519 | (build-system r-build-system) | |
4520 | (propagated-inputs | |
4521 | `(("r-biobase" ,r-biobase) | |
4522 | ("r-deseq2" ,r-deseq2) | |
4523 | ("r-dplyr" ,r-dplyr) | |
4524 | ("r-ggplot2" ,r-ggplot2) | |
4525 | ("r-locfit" ,r-locfit) | |
4526 | ("r-magrittr" ,r-magrittr) | |
4527 | ("r-matrixstats" ,r-matrixstats) | |
4528 | ("r-pracma" ,r-pracma) | |
4529 | ("r-roar" ,r-roar))) | |
4530 | (home-page "https://github.com/Liuy12/XBSeq") | |
4531 | (synopsis "Test for differential expression for RNA-seq data") | |
4532 | (description | |
4533 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential | |
4534 | expression} (DE), where a statistical model was established based on the | |
4535 | assumption that observed signals are the convolution of true expression | |
4536 | signals and sequencing noises. The mapped reads in non-exonic regions are | |
4537 | considered as sequencing noises, which follows a Poisson distribution. Given | |
4538 | measurable observed signal and background noise from RNA-seq data, true | |
4539 | expression signals, assuming governed by the negative binomial distribution, | |
4540 | can be delineated and thus the accurate detection of differential expressed | |
4541 | genes.") | |
4542 | (license license:gpl3+))) | |
c8310056 RW |
4543 | |
4544 | (define-public r-massspecwavelet | |
4545 | (package | |
4546 | (name "r-massspecwavelet") | |
7c888138 | 4547 | (version "1.50.0") |
c8310056 RW |
4548 | (source |
4549 | (origin | |
4550 | (method url-fetch) | |
4551 | (uri (bioconductor-uri "MassSpecWavelet" version)) | |
4552 | (sha256 | |
4553 | (base32 | |
7c888138 | 4554 | "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72")))) |
c8310056 RW |
4555 | (properties |
4556 | `((upstream-name . "MassSpecWavelet"))) | |
4557 | (build-system r-build-system) | |
4558 | (propagated-inputs | |
4559 | `(("r-waveslim" ,r-waveslim))) | |
4560 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") | |
4561 | (synopsis "Mass spectrum processing by wavelet-based algorithms") | |
4562 | (description | |
4563 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) | |
4564 | data mainly through the use of wavelet transforms. It supports peak detection | |
4565 | based on @dfn{Continuous Wavelet Transform} (CWT).") | |
4566 | (license license:lgpl2.0+))) | |
ec12e537 RW |
4567 | |
4568 | (define-public r-xcms | |
4569 | (package | |
4570 | (name "r-xcms") | |
40b2f7bc | 4571 | (version "3.6.1") |
ec12e537 RW |
4572 | (source |
4573 | (origin | |
4574 | (method url-fetch) | |
4575 | (uri (bioconductor-uri "xcms" version)) | |
4576 | (sha256 | |
4577 | (base32 | |
40b2f7bc | 4578 | "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g")))) |
ec12e537 RW |
4579 | (build-system r-build-system) |
4580 | (propagated-inputs | |
4581 | `(("r-biobase" ,r-biobase) | |
4582 | ("r-biocgenerics" ,r-biocgenerics) | |
4583 | ("r-biocparallel" ,r-biocparallel) | |
4584 | ("r-lattice" ,r-lattice) | |
4585 | ("r-massspecwavelet" ,r-massspecwavelet) | |
4586 | ("r-msnbase" ,r-msnbase) | |
4587 | ("r-multtest" ,r-multtest) | |
4588 | ("r-mzr" ,r-mzr) | |
4589 | ("r-plyr" ,r-plyr) | |
4590 | ("r-protgenerics" ,r-protgenerics) | |
4591 | ("r-rann" ,r-rann) | |
4592 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4593 | ("r-robustbase" ,r-robustbase) | |
4594 | ("r-s4vectors" ,r-s4vectors))) | |
4595 | (home-page "https://bioconductor.org/packages/xcms/") | |
4596 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") | |
4597 | (description | |
4598 | "This package provides a framework for processing and visualization of | |
4599 | chromatographically separated and single-spectra mass spectral data. It | |
4600 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses | |
4601 | data for high-throughput, untargeted analyte profiling.") | |
4602 | (license license:gpl2+))) | |
8830664d RW |
4603 | |
4604 | (define-public r-wrench | |
4605 | (package | |
4606 | (name "r-wrench") | |
07597c85 | 4607 | (version "1.2.0") |
8830664d RW |
4608 | (source |
4609 | (origin | |
4610 | (method url-fetch) | |
4611 | (uri (bioconductor-uri "Wrench" version)) | |
4612 | (sha256 | |
4613 | (base32 | |
07597c85 | 4614 | "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i")))) |
8830664d RW |
4615 | (properties `((upstream-name . "Wrench"))) |
4616 | (build-system r-build-system) | |
4617 | (propagated-inputs | |
4618 | `(("r-limma" ,r-limma) | |
4619 | ("r-locfit" ,r-locfit) | |
4620 | ("r-matrixstats" ,r-matrixstats))) | |
4621 | (home-page "https://github.com/HCBravoLab/Wrench") | |
4622 | (synopsis "Wrench normalization for sparse count data") | |
4623 | (description | |
4624 | "Wrench is a package for normalization sparse genomic count data, like | |
4625 | that arising from 16s metagenomic surveys.") | |
4626 | (license license:artistic2.0))) | |
b9b8b447 RW |
4627 | |
4628 | (define-public r-wiggleplotr | |
4629 | (package | |
4630 | (name "r-wiggleplotr") | |
a6edf335 | 4631 | (version "1.8.0") |
b9b8b447 RW |
4632 | (source |
4633 | (origin | |
4634 | (method url-fetch) | |
4635 | (uri (bioconductor-uri "wiggleplotr" version)) | |
4636 | (sha256 | |
4637 | (base32 | |
a6edf335 | 4638 | "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0")))) |
b9b8b447 RW |
4639 | (build-system r-build-system) |
4640 | (propagated-inputs | |
4641 | `(("r-assertthat" ,r-assertthat) | |
4642 | ("r-cowplot" ,r-cowplot) | |
4643 | ("r-dplyr" ,r-dplyr) | |
4644 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4645 | ("r-genomicranges" ,r-genomicranges) | |
4646 | ("r-ggplot2" ,r-ggplot2) | |
4647 | ("r-iranges" ,r-iranges) | |
4648 | ("r-purrr" ,r-purrr) | |
4649 | ("r-rtracklayer" ,r-rtracklayer) | |
4650 | ("r-s4vectors" ,r-s4vectors))) | |
4651 | (home-page "https://bioconductor.org/packages/wiggleplotr/") | |
4652 | (synopsis "Make read coverage plots from BigWig files") | |
4653 | (description | |
4654 | "This package provides tools to visualize read coverage from sequencing | |
4655 | experiments together with genomic annotations (genes, transcripts, peaks). | |
4656 | Introns of long transcripts can be rescaled to a fixed length for better | |
4657 | visualization of exonic read coverage.") | |
4658 | (license license:asl2.0))) | |
7b5101c5 RW |
4659 | |
4660 | (define-public r-widgettools | |
4661 | (package | |
4662 | (name "r-widgettools") | |
c881b9ef | 4663 | (version "1.62.0") |
7b5101c5 RW |
4664 | (source |
4665 | (origin | |
4666 | (method url-fetch) | |
4667 | (uri (bioconductor-uri "widgetTools" version)) | |
4668 | (sha256 | |
4669 | (base32 | |
c881b9ef | 4670 | "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a")))) |
7b5101c5 RW |
4671 | (properties `((upstream-name . "widgetTools"))) |
4672 | (build-system r-build-system) | |
4673 | (home-page "https://bioconductor.org/packages/widgetTools/") | |
4674 | (synopsis "Tools for creating interactive tcltk widgets") | |
4675 | (description | |
337bdc17 | 4676 | "This package contains tools to support the construction of tcltk |
7b5101c5 RW |
4677 | widgets in R.") |
4678 | ;; Any version of the LGPL. | |
4679 | (license license:lgpl3+))) | |
6b12f213 RW |
4680 | |
4681 | (define-public r-webbioc | |
4682 | (package | |
4683 | (name "r-webbioc") | |
67bc9255 | 4684 | (version "1.56.0") |
6b12f213 RW |
4685 | (source |
4686 | (origin | |
4687 | (method url-fetch) | |
4688 | (uri (bioconductor-uri "webbioc" version)) | |
4689 | (sha256 | |
4690 | (base32 | |
67bc9255 | 4691 | "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz")))) |
6b12f213 RW |
4692 | (build-system r-build-system) |
4693 | (inputs | |
4694 | `(("netpbm" ,netpbm) | |
4695 | ("perl" ,perl))) | |
4696 | (propagated-inputs | |
4697 | `(("r-affy" ,r-affy) | |
4698 | ("r-annaffy" ,r-annaffy) | |
4699 | ("r-biobase" ,r-biobase) | |
4700 | ("r-biocmanager" ,r-biocmanager) | |
4701 | ("r-gcrma" ,r-gcrma) | |
4702 | ("r-multtest" ,r-multtest) | |
4703 | ("r-qvalue" ,r-qvalue) | |
4704 | ("r-vsn" ,r-vsn))) | |
4705 | (home-page "https://www.bioconductor.org/") | |
4706 | (synopsis "Bioconductor web interface") | |
4707 | (description | |
4708 | "This package provides an integrated web interface for doing microarray | |
4709 | analysis using several of the Bioconductor packages. It is intended to be | |
4710 | deployed as a centralized bioinformatics resource for use by many users. | |
4711 | Currently only Affymetrix oligonucleotide analysis is supported.") | |
4712 | (license license:gpl2+))) | |
9800d859 RW |
4713 | |
4714 | (define-public r-zfpkm | |
4715 | (package | |
4716 | (name "r-zfpkm") | |
02530c28 | 4717 | (version "1.6.0") |
9800d859 RW |
4718 | (source |
4719 | (origin | |
4720 | (method url-fetch) | |
4721 | (uri (bioconductor-uri "zFPKM" version)) | |
4722 | (sha256 | |
4723 | (base32 | |
02530c28 | 4724 | "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz")))) |
9800d859 RW |
4725 | (properties `((upstream-name . "zFPKM"))) |
4726 | (build-system r-build-system) | |
4727 | (propagated-inputs | |
4728 | `(("r-checkmate" ,r-checkmate) | |
4729 | ("r-dplyr" ,r-dplyr) | |
4730 | ("r-ggplot2" ,r-ggplot2) | |
4731 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
4732 | ("r-tidyr" ,r-tidyr))) | |
4733 | (home-page "https://github.com/ronammar/zFPKM/") | |
4734 | (synopsis "Functions to facilitate zFPKM transformations") | |
4735 | (description | |
4736 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. | |
4737 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID | |
4738 | 24215113).") | |
4739 | (license license:gpl3))) | |
2bdc88fc RW |
4740 | |
4741 | (define-public r-rbowtie2 | |
4742 | (package | |
4743 | (name "r-rbowtie2") | |
7d33d36c | 4744 | (version "1.6.0") |
2bdc88fc RW |
4745 | (source |
4746 | (origin | |
4747 | (method url-fetch) | |
4748 | (uri (bioconductor-uri "Rbowtie2" version)) | |
4749 | (sha256 | |
4750 | (base32 | |
7d33d36c | 4751 | "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4")))) |
2bdc88fc RW |
4752 | (properties `((upstream-name . "Rbowtie2"))) |
4753 | (build-system r-build-system) | |
4754 | (inputs | |
4755 | `(("zlib" ,zlib))) | |
4756 | (home-page "https://bioconductor.org/packages/Rbowtie2/") | |
4757 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") | |
4758 | (description | |
4759 | "This package provides an R wrapper of the popular @code{bowtie2} | |
4760 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for | |
4761 | rapid adapter trimming, identification, and read merging.") | |
4762 | (license license:gpl3+))) | |
5622628f RW |
4763 | |
4764 | (define-public r-progeny | |
4765 | (package | |
4766 | (name "r-progeny") | |
c2bfb978 | 4767 | (version "1.6.0") |
5622628f RW |
4768 | (source |
4769 | (origin | |
4770 | (method url-fetch) | |
4771 | (uri (bioconductor-uri "progeny" version)) | |
4772 | (sha256 | |
4773 | (base32 | |
c2bfb978 | 4774 | "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw")))) |
5622628f RW |
4775 | (build-system r-build-system) |
4776 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4777 | (home-page "https://github.com/saezlab/progeny") | |
4778 | (synopsis "Pathway responsive gene activity inference") | |
4779 | (description | |
4780 | "This package provides a function to infer pathway activity from gene | |
4781 | expression. It contains the linear model inferred in the publication | |
4782 | \"Perturbation-response genes reveal signaling footprints in cancer gene | |
4783 | expression\".") | |
4784 | (license license:asl2.0))) | |
307586c1 RW |
4785 | |
4786 | (define-public r-arrmnormalization | |
4787 | (package | |
4788 | (name "r-arrmnormalization") | |
c24adbbf | 4789 | (version "1.24.0") |
307586c1 RW |
4790 | (source |
4791 | (origin | |
4792 | (method url-fetch) | |
4793 | (uri (bioconductor-uri "ARRmNormalization" version)) | |
4794 | (sha256 | |
4795 | (base32 | |
c24adbbf | 4796 | "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1")))) |
307586c1 RW |
4797 | (properties |
4798 | `((upstream-name . "ARRmNormalization"))) | |
4799 | (build-system r-build-system) | |
4800 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) | |
4801 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") | |
4802 | (synopsis "Adaptive robust regression normalization for methylation data") | |
4803 | (description | |
4804 | "This is a package to perform the @dfn{Adaptive Robust Regression | |
4805 | method} (ARRm) for the normalization of methylation data from the Illumina | |
4806 | Infinium HumanMethylation 450k assay.") | |
4807 | (license license:artistic2.0))) | |
fbf34949 RW |
4808 | |
4809 | (define-public r-biocfilecache | |
4810 | (package | |
4811 | (name "r-biocfilecache") | |
4812 | (version "1.8.0") | |
4813 | (source | |
4814 | (origin | |
4815 | (method url-fetch) | |
4816 | (uri (bioconductor-uri "BiocFileCache" version)) | |
4817 | (sha256 | |
4818 | (base32 | |
4819 | "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb")))) | |
4820 | (properties `((upstream-name . "BiocFileCache"))) | |
4821 | (build-system r-build-system) | |
4822 | (propagated-inputs | |
4823 | `(("r-curl" ,r-curl) | |
4824 | ("r-dbi" ,r-dbi) | |
4825 | ("r-dbplyr" ,r-dbplyr) | |
4826 | ("r-dplyr" ,r-dplyr) | |
4827 | ("r-httr" ,r-httr) | |
4828 | ("r-rappdirs" ,r-rappdirs) | |
4829 | ("r-rsqlite" ,r-rsqlite))) | |
4830 | (home-page "https://bioconductor.org/packages/BiocFileCache/") | |
4831 | (synopsis "Manage files across sessions") | |
4832 | (description | |
4833 | "This package creates a persistent on-disk cache of files that the user | |
4834 | can add, update, and retrieve. It is useful for managing resources (such as | |
4835 | custom Txdb objects) that are costly or difficult to create, web resources, | |
4836 | and data files used across sessions.") | |
4837 | (license license:artistic2.0))) | |
8c42f8f6 RW |
4838 | |
4839 | (define-public r-iclusterplus | |
4840 | (package | |
4841 | (name "r-iclusterplus") | |
4842 | (version "1.20.0") | |
4843 | (source | |
4844 | (origin | |
4845 | (method url-fetch) | |
4846 | (uri (bioconductor-uri "iClusterPlus" version)) | |
4847 | (sha256 | |
4848 | (base32 | |
4849 | "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq")))) | |
4850 | (properties `((upstream-name . "iClusterPlus"))) | |
4851 | (build-system r-build-system) | |
4852 | (native-inputs `(("gfortran" ,gfortran))) | |
4853 | (home-page "https://bioconductor.org/packages/iClusterPlus/") | |
4854 | (synopsis "Integrative clustering of multi-type genomic data") | |
4855 | (description | |
4856 | "iClusterPlus is developed for integrative clustering analysis of | |
4857 | multi-type genomic data and is an enhanced version of iCluster proposed and | |
4858 | developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise | |
4859 | from the experiments where biological samples (e.g. tumor samples) are | |
4860 | analyzed by multiple techniques, for instance, @dfn{array comparative genomic | |
4861 | hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so | |
4862 | on. In the iClusterPlus model, binary observations such as somatic mutation | |
4863 | are modeled as Binomial processes; categorical observations such as copy | |
4864 | number states are realizations of Multinomial random variables; counts are | |
4865 | modeled as Poisson random processes; and continuous measures are modeled by | |
4866 | Gaussian distributions.") | |
4867 | (license license:gpl2+))) | |
4d06ef4b RW |
4868 | |
4869 | (define-public r-rbowtie | |
4870 | (package | |
4871 | (name "r-rbowtie") | |
4872 | (version "1.24.0") | |
4873 | (source | |
4874 | (origin | |
4875 | (method url-fetch) | |
4876 | (uri (bioconductor-uri "Rbowtie" version)) | |
4877 | (sha256 | |
4878 | (base32 | |
4879 | "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f")))) | |
4880 | (properties `((upstream-name . "Rbowtie"))) | |
4881 | (build-system r-build-system) | |
4882 | (inputs | |
4883 | `(("zlib" ,zlib))) | |
4884 | (home-page "https://bioconductor.org/packages/Rbowtie/") | |
4885 | (synopsis "R bowtie wrapper") | |
4886 | (description | |
4887 | "This package provides an R wrapper around the popular bowtie short read | |
4888 | aligner and around SpliceMap, a de novo splice junction discovery and | |
4889 | alignment tool.") | |
4890 | (license license:artistic2.0))) | |
14441539 RW |
4891 | |
4892 | (define-public r-sgseq | |
4893 | (package | |
4894 | (name "r-sgseq") | |
4895 | (version "1.18.0") | |
4896 | (source | |
4897 | (origin | |
4898 | (method url-fetch) | |
4899 | (uri (bioconductor-uri "SGSeq" version)) | |
4900 | (sha256 | |
4901 | (base32 | |
4902 | "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s")))) | |
4903 | (properties `((upstream-name . "SGSeq"))) | |
4904 | (build-system r-build-system) | |
4905 | (propagated-inputs | |
4906 | `(("r-annotationdbi" ,r-annotationdbi) | |
4907 | ("r-biocgenerics" ,r-biocgenerics) | |
4908 | ("r-biostrings" ,r-biostrings) | |
4909 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4910 | ("r-genomicalignments" ,r-genomicalignments) | |
4911 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4912 | ("r-genomicranges" ,r-genomicranges) | |
4913 | ("r-igraph" ,r-igraph) | |
4914 | ("r-iranges" ,r-iranges) | |
4915 | ("r-rsamtools" ,r-rsamtools) | |
4916 | ("r-rtracklayer" ,r-rtracklayer) | |
4917 | ("r-runit" ,r-runit) | |
4918 | ("r-s4vectors" ,r-s4vectors) | |
4919 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4920 | (home-page "https://bioconductor.org/packages/SGSeq/") | |
4921 | (synopsis "Splice event prediction and quantification from RNA-seq data") | |
4922 | (description | |
4923 | "SGSeq is a package for analyzing splice events from RNA-seq data. Input | |
4924 | data are RNA-seq reads mapped to a reference genome in BAM format. Genes are | |
4925 | represented as a splice graph, which can be obtained from existing annotation | |
4926 | or predicted from the mapped sequence reads. Splice events are identified | |
4927 | from the graph and are quantified locally using structurally compatible reads | |
4928 | at the start or end of each splice variant. The software includes functions | |
4929 | for splice event prediction, quantification, visualization and | |
4930 | interpretation.") | |
4931 | (license license:artistic2.0))) | |
58656064 RW |
4932 | |
4933 | (define-public r-rhisat2 | |
4934 | (package | |
4935 | (name "r-rhisat2") | |
932a6c42 | 4936 | (version "1.0.3") |
58656064 RW |
4937 | (source |
4938 | (origin | |
4939 | (method url-fetch) | |
4940 | (uri (bioconductor-uri "Rhisat2" version)) | |
4941 | (sha256 | |
4942 | (base32 | |
932a6c42 | 4943 | "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5")))) |
58656064 RW |
4944 | (properties `((upstream-name . "Rhisat2"))) |
4945 | (build-system r-build-system) | |
4946 | (native-inputs | |
4947 | `(("which" ,which))) | |
4948 | (propagated-inputs | |
4949 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
4950 | ("r-genomicranges" ,r-genomicranges) | |
4951 | ("r-sgseq" ,r-sgseq))) | |
4952 | (home-page "https://github.com/fmicompbio/Rhisat2") | |
4953 | (synopsis "R Wrapper for HISAT2 sequence aligner") | |
4954 | (description | |
4955 | "This package provides an R interface to the HISAT2 spliced short-read | |
4956 | aligner by Kim et al. (2015). The package contains wrapper functions to | |
4957 | create a genome index and to perform the read alignment to the generated | |
4958 | index.") | |
4959 | (license license:gpl3))) | |
5e0241db RW |
4960 | |
4961 | (define-public r-quasr | |
4962 | (package | |
4963 | (name "r-quasr") | |
b3319f4c | 4964 | (version "1.24.2") |
5e0241db RW |
4965 | (source |
4966 | (origin | |
4967 | (method url-fetch) | |
4968 | (uri (bioconductor-uri "QuasR" version)) | |
4969 | (sha256 | |
4970 | (base32 | |
b3319f4c | 4971 | "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx")))) |
5e0241db RW |
4972 | (properties `((upstream-name . "QuasR"))) |
4973 | (build-system r-build-system) | |
4974 | (inputs | |
4975 | `(("zlib" ,zlib))) | |
4976 | (propagated-inputs | |
4977 | `(("r-annotationdbi" ,r-annotationdbi) | |
4978 | ("r-biobase" ,r-biobase) | |
4979 | ("r-biocgenerics" ,r-biocgenerics) | |
4980 | ("r-biocmanager" ,r-biocmanager) | |
4981 | ("r-biocparallel" ,r-biocparallel) | |
4982 | ("r-biostrings" ,r-biostrings) | |
4983 | ("r-bsgenome" ,r-bsgenome) | |
4984 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4985 | ("r-genomicalignments" ,r-genomicalignments) | |
4986 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4987 | ("r-genomicfiles" ,r-genomicfiles) | |
4988 | ("r-genomicranges" ,r-genomicranges) | |
4989 | ("r-iranges" ,r-iranges) | |
4990 | ("r-rbowtie" ,r-rbowtie) | |
4991 | ("r-rhisat2" ,r-rhisat2) | |
4992 | ("r-rhtslib" ,r-rhtslib) | |
4993 | ("r-rsamtools" ,r-rsamtools) | |
4994 | ("r-rtracklayer" ,r-rtracklayer) | |
4995 | ("r-s4vectors" ,r-s4vectors) | |
4996 | ("r-shortread" ,r-shortread))) | |
4997 | (home-page "https://bioconductor.org/packages/QuasR/") | |
4998 | (synopsis "Quantify and annotate short reads in R") | |
4999 | (description | |
5000 | "This package provides a framework for the quantification and analysis of | |
5001 | short genomic reads. It covers a complete workflow starting from raw sequence | |
5002 | reads, over creation of alignments and quality control plots, to the | |
5003 | quantification of genomic regions of interest.") | |
5004 | (license license:gpl2))) | |
496b024f RW |
5005 | |
5006 | (define-public r-rqc | |
5007 | (package | |
5008 | (name "r-rqc") | |
5009 | (version "1.18.0") | |
5010 | (source | |
5011 | (origin | |
5012 | (method url-fetch) | |
5013 | (uri (bioconductor-uri "Rqc" version)) | |
5014 | (sha256 | |
5015 | (base32 | |
5016 | "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g")))) | |
5017 | (properties `((upstream-name . "Rqc"))) | |
5018 | (build-system r-build-system) | |
5019 | (propagated-inputs | |
5020 | `(("r-biocgenerics" ,r-biocgenerics) | |
5021 | ("r-biocparallel" ,r-biocparallel) | |
5022 | ("r-biocstyle" ,r-biocstyle) | |
5023 | ("r-biostrings" ,r-biostrings) | |
5024 | ("r-biovizbase" ,r-biovizbase) | |
5025 | ("r-genomicalignments" ,r-genomicalignments) | |
5026 | ("r-genomicfiles" ,r-genomicfiles) | |
5027 | ("r-ggplot2" ,r-ggplot2) | |
5028 | ("r-iranges" ,r-iranges) | |
5029 | ("r-knitr" ,r-knitr) | |
5030 | ("r-markdown" ,r-markdown) | |
5031 | ("r-plyr" ,r-plyr) | |
5032 | ("r-rcpp" ,r-rcpp) | |
5033 | ("r-reshape2" ,r-reshape2) | |
5034 | ("r-rsamtools" ,r-rsamtools) | |
5035 | ("r-s4vectors" ,r-s4vectors) | |
5036 | ("r-shiny" ,r-shiny) | |
5037 | ("r-shortread" ,r-shortread))) | |
5038 | (home-page "https://github.com/labbcb/Rqc") | |
5039 | (synopsis "Quality control tool for high-throughput sequencing data") | |
5040 | (description | |
5041 | "Rqc is an optimized tool designed for quality control and assessment of | |
5042 | high-throughput sequencing data. It performs parallel processing of entire | |
5043 | files and produces a report which contains a set of high-resolution | |
5044 | graphics.") | |
5045 | (license license:gpl2+))) | |
81e3de01 RW |
5046 | |
5047 | (define-public r-birewire | |
5048 | (package | |
5049 | (name "r-birewire") | |
5050 | (version "3.16.0") | |
5051 | (source | |
5052 | (origin | |
5053 | (method url-fetch) | |
5054 | (uri (bioconductor-uri "BiRewire" version)) | |
5055 | (sha256 | |
5056 | (base32 | |
5057 | "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518")))) | |
5058 | (properties `((upstream-name . "BiRewire"))) | |
5059 | (build-system r-build-system) | |
5060 | (propagated-inputs | |
5061 | `(("r-igraph" ,r-igraph) | |
5062 | ("r-matrix" ,r-matrix) | |
5063 | ("r-slam" ,r-slam) | |
5064 | ("r-tsne" ,r-tsne))) | |
5065 | (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") | |
5066 | (synopsis "Tools for randomization of bipartite graphs") | |
5067 | (description | |
5068 | "This package provides functions for bipartite network rewiring through N | |
5069 | consecutive switching steps and for the computation of the minimal number of | |
5070 | switching steps to be performed in order to maximise the dissimilarity with | |
5071 | respect to the original network. It includes functions for the analysis of | |
5072 | the introduced randomness across the switching steps and several other | |
5073 | routines to analyse the resulting networks and their natural projections.") | |
5074 | (license license:gpl3))) | |
1a24f855 RW |
5075 | |
5076 | (define-public r-birta | |
5077 | (package | |
5078 | (name "r-birta") | |
5079 | (version "1.28.0") | |
5080 | (source | |
5081 | (origin | |
5082 | (method url-fetch) | |
5083 | (uri (bioconductor-uri "birta" version)) | |
5084 | (sha256 | |
5085 | (base32 | |
5086 | "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2")))) | |
5087 | (build-system r-build-system) | |
5088 | (propagated-inputs | |
5089 | `(("r-biobase" ,r-biobase) | |
5090 | ("r-limma" ,r-limma) | |
5091 | ("r-mass" ,r-mass))) | |
5092 | (home-page "https://bioconductor.org/packages/birta") | |
5093 | (synopsis "Bayesian inference of regulation of transcriptional activity") | |
5094 | (description | |
5095 | "Expression levels of mRNA molecules are regulated by different | |
5096 | processes, comprising inhibition or activation by transcription factors and | |
5097 | post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian | |
5098 | Inference of Regulation of Transcriptional Activity) uses the regulatory | |
5099 | networks of transcription factors and miRNAs together with mRNA and miRNA | |
5100 | expression data to predict switches in regulatory activity between two | |
5101 | conditions. A Bayesian network is used to model the regulatory structure and | |
5102 | Markov-Chain-Monte-Carlo is applied to sample the activity states.") | |
5103 | (license license:gpl2+))) | |
a9fac3f4 RW |
5104 | |
5105 | (define-public r-ropls | |
5106 | (package | |
5107 | (name "r-ropls") | |
5108 | (version "1.16.0") | |
5109 | (source | |
5110 | (origin | |
5111 | (method url-fetch) | |
5112 | (uri (bioconductor-uri "ropls" version)) | |
5113 | (sha256 | |
5114 | (base32 | |
5115 | "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2")))) | |
5116 | (build-system r-build-system) | |
5117 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
5118 | (native-inputs | |
5119 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
5120 | (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") | |
5121 | (synopsis "Multivariate analysis and feature selection of omics data") | |
5122 | (description | |
5123 | "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) | |
5124 | and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, | |
5125 | regression, classification, and feature selection of omics data where the | |
5126 | number of variables exceeds the number of samples and with multicollinearity | |
5127 | among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to | |
5128 | separately model the variation correlated (predictive) to the factor of | |
5129 | interest and the uncorrelated (orthogonal) variation. While performing | |
5130 | similarly to PLS, OPLS facilitates interpretation. | |
5131 | ||
5132 | This package provides imlementations of PCA, PLS, and OPLS for multivariate | |
5133 | analysis and feature selection of omics data. In addition to scores, loadings | |
5134 | and weights plots, the package provides metrics and graphics to determine the | |
5135 | optimal number of components (e.g. with the R2 and Q2 coefficients), check the | |
5136 | validity of the model by permutation testing, detect outliers, and perform | |
5137 | feature selection (e.g. with Variable Importance in Projection or regression | |
5138 | coefficients).") | |
5139 | (license license:cecill))) | |
075a9094 RW |
5140 | |
5141 | (define-public r-biosigner | |
5142 | (package | |
5143 | (name "r-biosigner") | |
5144 | (version "1.12.0") | |
5145 | (source | |
5146 | (origin | |
5147 | (method url-fetch) | |
5148 | (uri (bioconductor-uri "biosigner" version)) | |
5149 | (sha256 | |
5150 | (base32 | |
5151 | "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b")))) | |
5152 | (build-system r-build-system) | |
5153 | (propagated-inputs | |
5154 | `(("r-biobase" ,r-biobase) | |
5155 | ("r-e1071" ,r-e1071) | |
5156 | ("r-randomforest" ,r-randomforest) | |
5157 | ("r-ropls" ,r-ropls))) | |
5158 | (native-inputs | |
5159 | `(("r-knitr" ,r-knitr) | |
5160 | ("r-rmarkdown" ,r-rmarkdown) | |
5161 | ("pandoc" ,ghc-pandoc) | |
5162 | ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes | |
5163 | (home-page "https://bioconductor.org/packages/biosigner/") | |
5164 | (synopsis "Signature discovery from omics data") | |
5165 | (description | |
5166 | "Feature selection is critical in omics data analysis to extract | |
5167 | restricted and meaningful molecular signatures from complex and high-dimension | |
5168 | data, and to build robust classifiers. This package implements a method to | |
5169 | assess the relevance of the variables for the prediction performances of the | |
5170 | classifier. The approach can be run in parallel with the PLS-DA, Random | |
5171 | Forest, and SVM binary classifiers. The signatures and the corresponding | |
5172 | 'restricted' models are returned, enabling future predictions on new | |
5173 | datasets.") | |
5174 | (license license:cecill))) | |
ae6fa185 RW |
5175 | |
5176 | (define-public r-annotatr | |
5177 | (package | |
5178 | (name "r-annotatr") | |
5179 | (version "1.10.0") | |
5180 | (source | |
5181 | (origin | |
5182 | (method url-fetch) | |
5183 | (uri (bioconductor-uri "annotatr" version)) | |
5184 | (sha256 | |
5185 | (base32 | |
5186 | "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f")))) | |
5187 | (build-system r-build-system) | |
5188 | (propagated-inputs | |
5189 | `(("r-annotationdbi" ,r-annotationdbi) | |
5190 | ("r-annotationhub" ,r-annotationhub) | |
5191 | ("r-dplyr" ,r-dplyr) | |
5192 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5193 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5194 | ("r-genomicranges" ,r-genomicranges) | |
5195 | ("r-ggplot2" ,r-ggplot2) | |
5196 | ("r-iranges" ,r-iranges) | |
5197 | ("r-readr" ,r-readr) | |
5198 | ("r-regioner" ,r-regioner) | |
5199 | ("r-reshape2" ,r-reshape2) | |
5200 | ("r-rtracklayer" ,r-rtracklayer) | |
5201 | ("r-s4vectors" ,r-s4vectors))) | |
5202 | (home-page "https://bioconductor.org/packages/annotatr/") | |
5203 | (synopsis "Annotation of genomic regions to genomic annotations") | |
5204 | (description | |
5205 | "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, | |
5206 | differentially methylated CpGs or regions, SNPs, etc.) it is often of interest | |
5207 | to investigate the intersecting genomic annotations. Such annotations include | |
5208 | those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), | |
5209 | CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as | |
5210 | enhancers. The annotatr package provides an easy way to summarize and | |
5211 | visualize the intersection of genomic sites/regions with genomic | |
5212 | annotations.") | |
5213 | (license license:gpl3))) | |
2cb738a6 RW |
5214 | |
5215 | (define-public r-rsubread | |
5216 | (package | |
5217 | (name "r-rsubread") | |
f791b1ee | 5218 | (version "1.34.7") |
2cb738a6 RW |
5219 | (source |
5220 | (origin | |
5221 | (method url-fetch) | |
5222 | (uri (bioconductor-uri "Rsubread" version)) | |
5223 | (sha256 | |
5224 | (base32 | |
f791b1ee | 5225 | "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y")))) |
2cb738a6 RW |
5226 | (properties `((upstream-name . "Rsubread"))) |
5227 | (build-system r-build-system) | |
5228 | (inputs `(("zlib" ,zlib))) | |
5229 | (home-page "https://bioconductor.org/packages/Rsubread/") | |
5230 | (synopsis "Subread sequence alignment and counting for R") | |
5231 | (description | |
5232 | "This package provides tools for alignment, quantification and analysis | |
5233 | of second and third generation sequencing data. It includes functionality for | |
5234 | read mapping, read counting, SNP calling, structural variant detection and | |
5235 | gene fusion discovery. It can be applied to all major sequencing techologies | |
5236 | and to both short and long sequence reads.") | |
5237 | (license license:gpl3))) | |
a6fedf1f | 5238 | |
a0422d18 | 5239 | (define-public r-flowutils |
5240 | (package | |
5241 | (name "r-flowutils") | |
5242 | (version "1.48.0") | |
5243 | (source | |
5244 | (origin | |
5245 | (method url-fetch) | |
5246 | (uri (bioconductor-uri "flowUtils" version)) | |
5247 | (sha256 | |
5248 | (base32 | |
5249 | "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm")))) | |
5250 | (properties `((upstream-name . "flowUtils"))) | |
5251 | (build-system r-build-system) | |
5252 | (propagated-inputs | |
5253 | `(("r-biobase" ,r-biobase) | |
5254 | ("r-corpcor" ,r-corpcor) | |
5255 | ("r-flowcore" ,r-flowcore) | |
5256 | ("r-graph" ,r-graph) | |
5257 | ("r-runit" ,r-runit) | |
5258 | ("r-xml" ,r-xml))) | |
5259 | (home-page "https://github.com/jspidlen/flowUtils") | |
5260 | (synopsis "Utilities for flow cytometry") | |
5261 | (description | |
5262 | "This package provides utilities for flow cytometry data.") | |
5263 | (license license:artistic2.0))) | |
5264 | ||
ed6f49fc | 5265 | (define-public r-consensusclusterplus |
5266 | (package | |
5267 | (name "r-consensusclusterplus") | |
5268 | (version "1.48.0") | |
5269 | (source | |
5270 | (origin | |
5271 | (method url-fetch) | |
5272 | (uri (bioconductor-uri "ConsensusClusterPlus" version)) | |
5273 | (sha256 | |
5274 | (base32 | |
5275 | "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8")))) | |
5276 | (properties | |
5277 | `((upstream-name . "ConsensusClusterPlus"))) | |
5278 | (build-system r-build-system) | |
5279 | (propagated-inputs | |
5280 | `(("r-all" ,r-all) | |
5281 | ("r-biobase" ,r-biobase) | |
5282 | ("r-cluster" ,r-cluster))) | |
5283 | (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") | |
5284 | (synopsis "Clustering algorithm") | |
5285 | (description | |
5286 | "This package provides an implementation of an algorithm for determining | |
5287 | cluster count and membership by stability evidence in unsupervised analysis.") | |
5288 | (license license:gpl2))) | |
5289 | ||
a6fedf1f | 5290 | (define-public r-flowcore |
5291 | (package | |
5292 | (name "r-flowcore") | |
5293 | (version "1.50.0") | |
5294 | (source | |
5295 | (origin | |
5296 | (method url-fetch) | |
5297 | (uri (bioconductor-uri "flowCore" version)) | |
5298 | (sha256 | |
5299 | (base32 | |
5300 | "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan")))) | |
5301 | (properties `((upstream-name . "flowCore"))) | |
5302 | (build-system r-build-system) | |
5303 | (propagated-inputs | |
5304 | `(("r-bh" ,r-bh) | |
5305 | ("r-biobase" ,r-biobase) | |
5306 | ("r-biocgenerics" ,r-biocgenerics) | |
5307 | ("r-corpcor" ,r-corpcor) | |
5308 | ("r-graph" ,r-graph) | |
5309 | ("r-mass" ,r-mass) | |
5310 | ("r-matrixstats" ,r-matrixstats) | |
5311 | ("r-rcpp" ,r-rcpp) | |
5312 | ("r-rrcov" ,r-rrcov))) | |
5313 | (home-page "https://bioconductor.org/packages/flowCore") | |
5314 | (synopsis "Basic structures for flow cytometry data") | |
5315 | (description | |
5316 | "This package provides S4 data structures and basic functions to deal | |
5317 | with flow cytometry data.") | |
5318 | (license license:artistic2.0))) | |
e0cb053e | 5319 | |
5320 | (define-public r-flowmeans | |
5321 | (package | |
5322 | (name "r-flowmeans") | |
5323 | (version "1.44.0") | |
5324 | (source | |
5325 | (origin | |
5326 | (method url-fetch) | |
5327 | (uri (bioconductor-uri "flowMeans" version)) | |
5328 | (sha256 | |
5329 | (base32 | |
5330 | "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2")))) | |
5331 | (properties `((upstream-name . "flowMeans"))) | |
5332 | (build-system r-build-system) | |
5333 | (propagated-inputs | |
5334 | `(("r-biobase" ,r-biobase) | |
5335 | ("r-feature" ,r-feature) | |
5336 | ("r-flowcore" ,r-flowcore) | |
5337 | ("r-rrcov" ,r-rrcov))) | |
5338 | (home-page "https://bioconductor.org/packages/flowMeans") | |
5339 | (synopsis "Non-parametric flow cytometry data gating") | |
5340 | (description | |
5341 | "This package provides tools to identify cell populations in Flow | |
5342 | Cytometry data using non-parametric clustering and segmented-regression-based | |
5343 | change point detection.") | |
5344 | (license license:artistic2.0))) | |
1502751b | 5345 | |
5346 | (define-public r-flowsom | |
5347 | (package | |
5348 | (name "r-flowsom") | |
5349 | (version "1.16.0") | |
5350 | (source | |
5351 | (origin | |
5352 | (method url-fetch) | |
5353 | (uri (bioconductor-uri "FlowSOM" version)) | |
5354 | (sha256 | |
5355 | (base32 | |
5356 | "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l")))) | |
5357 | (properties `((upstream-name . "FlowSOM"))) | |
5358 | (build-system r-build-system) | |
5359 | (propagated-inputs | |
5360 | `(("r-biocgenerics" ,r-biocgenerics) | |
5361 | ("r-consensusclusterplus" ,r-consensusclusterplus) | |
5362 | ("r-flowcore" ,r-flowcore) | |
5363 | ("r-flowutils" ,r-flowutils) | |
5364 | ("r-igraph" ,r-igraph) | |
5365 | ("r-tsne" ,r-tsne) | |
5366 | ("r-xml" ,r-xml))) | |
5367 | (home-page "https://bioconductor.org/packages/FlowSOM/") | |
5368 | (synopsis "Visualize and interpret cytometry data") | |
5369 | (description | |
5370 | "FlowSOM offers visualization options for cytometry data, by using | |
5371 | self-organizing map clustering and minimal spanning trees.") | |
5372 | (license license:gpl2+))) | |
1adb9cbc | 5373 | |
5374 | (define-public r-mixomics | |
5375 | (package | |
5376 | (name "r-mixomics") | |
eb796f53 | 5377 | (version "6.8.5") |
1adb9cbc | 5378 | (source |
5379 | (origin | |
5380 | (method url-fetch) | |
5381 | (uri (bioconductor-uri "mixOmics" version)) | |
5382 | (sha256 | |
5383 | (base32 | |
eb796f53 | 5384 | "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7")))) |
1adb9cbc | 5385 | (properties `((upstream-name . "mixOmics"))) |
5386 | (build-system r-build-system) | |
5387 | (propagated-inputs | |
5388 | `(("r-corpcor" ,r-corpcor) | |
5389 | ("r-dplyr" ,r-dplyr) | |
5390 | ("r-ellipse" ,r-ellipse) | |
5391 | ("r-ggplot2" ,r-ggplot2) | |
5392 | ("r-gridextra" ,r-gridextra) | |
5393 | ("r-igraph" ,r-igraph) | |
5394 | ("r-lattice" ,r-lattice) | |
5395 | ("r-mass" ,r-mass) | |
5396 | ("r-matrixstats" ,r-matrixstats) | |
5397 | ("r-rarpack" ,r-rarpack) | |
5398 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5399 | ("r-reshape2" ,r-reshape2) | |
5400 | ("r-tidyr" ,r-tidyr))) | |
5401 | (home-page "http://www.mixOmics.org") | |
5402 | (synopsis "Multivariate methods for exploration of biological datasets") | |
5403 | (description | |
5404 | "mixOmics offers a wide range of multivariate methods for the exploration | |
5405 | and integration of biological datasets with a particular focus on variable | |
5406 | selection. The package proposes several sparse multivariate models we have | |
5407 | developed to identify the key variables that are highly correlated, and/or | |
5408 | explain the biological outcome of interest. The data that can be analysed | |
5409 | with mixOmics may come from high throughput sequencing technologies, such as | |
5410 | omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but | |
5411 | also beyond the realm of omics (e.g. spectral imaging). The methods | |
5412 | implemented in mixOmics can also handle missing values without having to | |
5413 | delete entire rows with missing data.") | |
5414 | (license license:gpl2+))) | |
a0efa069 | 5415 | |
5416 | (define-public r-depecher | |
5417 | (package | |
5418 | (name "r-depecher") | |
5419 | (version "1.0.3") | |
5420 | (source | |
5421 | (origin | |
5422 | (method url-fetch) | |
5423 | (uri (bioconductor-uri "DepecheR" version)) | |
5424 | (sha256 | |
5425 | (base32 | |
5426 | "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h")))) | |
5427 | (properties `((upstream-name . "DepecheR"))) | |
5428 | (build-system r-build-system) | |
5429 | (arguments | |
5430 | `(#:phases | |
5431 | (modify-phases %standard-phases | |
5432 | (add-after 'unpack 'fix-syntax-error | |
5433 | (lambda _ | |
5434 | (substitute* "src/Makevars" | |
5435 | ((" & ") " && ")) | |
5436 | #t))))) | |
5437 | (propagated-inputs | |
5438 | `(("r-beanplot" ,r-beanplot) | |
5439 | ("r-biocparallel" ,r-biocparallel) | |
5440 | ("r-dosnow" ,r-dosnow) | |
5441 | ("r-dplyr" ,r-dplyr) | |
5442 | ("r-foreach" ,r-foreach) | |
5443 | ("r-ggplot2" ,r-ggplot2) | |
5444 | ("r-gplots" ,r-gplots) | |
5445 | ("r-mass" ,r-mass) | |
5446 | ("r-matrixstats" ,r-matrixstats) | |
5447 | ("r-mixomics" ,r-mixomics) | |
5448 | ("r-moments" ,r-moments) | |
5449 | ("r-rcpp" ,r-rcpp) | |
5450 | ("r-rcppeigen" ,r-rcppeigen) | |
5451 | ("r-reshape2" ,r-reshape2) | |
5452 | ("r-viridis" ,r-viridis))) | |
5453 | (home-page "https://bioconductor.org/packages/DepecheR/") | |
5454 | (synopsis "Identify traits of clusters in high-dimensional entities") | |
5455 | (description | |
5456 | "The purpose of this package is to identify traits in a dataset that can | |
5457 | separate groups. This is done on two levels. First, clustering is performed, | |
5458 | using an implementation of sparse K-means. Secondly, the generated clusters | |
5459 | are used to predict outcomes of groups of individuals based on their | |
5460 | distribution of observations in the different clusters. As certain clusters | |
5461 | with separating information will be identified, and these clusters are defined | |
5462 | by a sparse number of variables, this method can reduce the complexity of | |
5463 | data, to only emphasize the data that actually matters.") | |
5464 | (license license:expat))) | |
b46a0ee7 | 5465 | |
bb88417f RW |
5466 | (define-public r-rcistarget |
5467 | (package | |
5468 | (name "r-rcistarget") | |
5469 | (version "1.4.0") | |
5470 | (source | |
5471 | (origin | |
5472 | (method url-fetch) | |
5473 | (uri (bioconductor-uri "RcisTarget" version)) | |
5474 | (sha256 | |
5475 | (base32 | |
5476 | "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd")))) | |
5477 | (properties `((upstream-name . "RcisTarget"))) | |
5478 | (build-system r-build-system) | |
5479 | (propagated-inputs | |
5480 | `(("r-aucell" ,r-aucell) | |
5481 | ("r-biocgenerics" ,r-biocgenerics) | |
5482 | ("r-data-table" ,r-data-table) | |
5483 | ("r-feather" ,r-feather) | |
5484 | ("r-gseabase" ,r-gseabase) | |
5485 | ("r-r-utils" ,r-r-utils) | |
5486 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5487 | (home-page "https://aertslab.org/#scenic") | |
5488 | (synopsis "Identify transcription factor binding motifs enriched on a gene list") | |
5489 | (description | |
5490 | "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) | |
5491 | over-represented on a gene list. In a first step, RcisTarget selects DNA | |
5492 | motifs that are significantly over-represented in the surroundings of the | |
5493 | @dfn{transcription start site} (TSS) of the genes in the gene-set. This is | |
5494 | achieved by using a database that contains genome-wide cross-species rankings | |
5495 | for each motif. The motifs that are then annotated to TFs and those that have | |
5496 | a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for | |
5497 | each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. | |
5498 | genes in the gene-set that are ranked above the leading edge).") | |
5499 | (license license:gpl3))) | |
5500 | ||
b46a0ee7 RW |
5501 | (define-public r-cicero |
5502 | (package | |
5503 | (name "r-cicero") | |
5504 | (version "1.2.0") | |
5505 | (source | |
5506 | (origin | |
5507 | (method url-fetch) | |
5508 | (uri (bioconductor-uri "cicero" version)) | |
5509 | (sha256 | |
5510 | (base32 | |
5511 | "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr")))) | |
5512 | (build-system r-build-system) | |
5513 | (propagated-inputs | |
5514 | `(("r-assertthat" ,r-assertthat) | |
5515 | ("r-biobase" ,r-biobase) | |
5516 | ("r-biocgenerics" ,r-biocgenerics) | |
5517 | ("r-data-table" ,r-data-table) | |
5518 | ("r-dplyr" ,r-dplyr) | |
5519 | ("r-fnn" ,r-fnn) | |
5520 | ("r-genomicranges" ,r-genomicranges) | |
5521 | ("r-ggplot2" ,r-ggplot2) | |
5522 | ("r-glasso" ,r-glasso) | |
5523 | ("r-gviz" ,r-gviz) | |
5524 | ("r-igraph" ,r-igraph) | |
5525 | ("r-iranges" ,r-iranges) | |
5526 | ("r-matrix" ,r-matrix) | |
5527 | ("r-monocle" ,r-monocle) | |
5528 | ("r-plyr" ,r-plyr) | |
5529 | ("r-reshape2" ,r-reshape2) | |
5530 | ("r-s4vectors" ,r-s4vectors) | |
5531 | ("r-stringr" ,r-stringr) | |
5532 | ("r-tibble" ,r-tibble) | |
5533 | ("r-vgam" ,r-vgam))) | |
5534 | (home-page "https://bioconductor.org/packages/cicero/") | |
5535 | (synopsis "Predict cis-co-accessibility from single-cell data") | |
5536 | (description | |
5537 | "Cicero computes putative cis-regulatory maps from single-cell chromatin | |
5538 | accessibility data. It also extends the monocle package for use in chromatin | |
5539 | accessibility data.") | |
5540 | (license license:expat))) | |
14bb1c48 RW |
5541 | |
5542 | ;; This is the latest commit on the "monocle3" branch. | |
5543 | (define-public r-cicero-monocle3 | |
5544 | (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") | |
5545 | (revision "1")) | |
5546 | (package (inherit r-cicero) | |
5547 | (name "r-cicero-monocle3") | |
5548 | (version (git-version "1.3.2" revision commit)) | |
5549 | (source | |
5550 | (origin | |
5551 | (method git-fetch) | |
5552 | (uri (git-reference | |
5553 | (url "https://github.com/cole-trapnell-lab/cicero-release.git") | |
5554 | (commit commit))) | |
5555 | (file-name (git-file-name name version)) | |
5556 | (sha256 | |
5557 | (base32 | |
5558 | "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) | |
5559 | (propagated-inputs | |
5560 | `(("r-monocle3" ,r-monocle3) | |
5561 | ,@(alist-delete "r-monocle" | |
5562 | (package-propagated-inputs r-cicero))))))) | |
a9815a6c RW |
5563 | |
5564 | (define-public r-cistopic | |
5565 | (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") | |
5566 | (revision "0")) | |
5567 | (package | |
5568 | (name "r-cistopic") | |
5569 | (version (git-version "0.2.1" revision commit)) | |
5570 | (source | |
5571 | (origin | |
5572 | (method git-fetch) | |
5573 | (uri (git-reference | |
5574 | (url "https://github.com/aertslab/cisTopic.git") | |
5575 | (commit commit))) | |
5576 | (file-name (git-file-name name version)) | |
5577 | (sha256 | |
5578 | (base32 | |
5579 | "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) | |
5580 | (build-system r-build-system) | |
5581 | (propagated-inputs | |
5582 | `(("r-aucell" ,r-aucell) | |
5583 | ("r-data-table" ,r-data-table) | |
5584 | ("r-dplyr" ,r-dplyr) | |
5585 | ("r-dosnow" ,r-dosnow) | |
5586 | ("r-dt" ,r-dt) | |
5587 | ("r-feather" ,r-feather) | |
5588 | ("r-fitdistrplus" ,r-fitdistrplus) | |
5589 | ("r-genomicranges" ,r-genomicranges) | |
5590 | ("r-ggplot2" ,r-ggplot2) | |
5591 | ("r-lda" ,r-lda) | |
5592 | ("r-matrix" ,r-matrix) | |
5593 | ("r-plyr" ,r-plyr) | |
5594 | ("r-rcistarget" ,r-rcistarget) | |
5595 | ("r-rtracklayer" ,r-rtracklayer) | |
5596 | ("r-s4vectors" ,r-s4vectors))) | |
5597 | (home-page "https://github.com/aertslab/cisTopic") | |
5598 | (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") | |
5599 | (description | |
5600 | "The sparse nature of single cell epigenomics data can be overruled using | |
5601 | probabilistic modelling methods such as @dfn{Latent Dirichlet | |
5602 | Allocation} (LDA). This package allows the probabilistic modelling of | |
5603 | cis-regulatory topics (cisTopics) from single cell epigenomics data, and | |
5604 | includes functionalities to identify cell states based on the contribution of | |
5605 | cisTopics and explore the nature and regulatory proteins driving them.") | |
5606 | (license license:gpl3)))) | |
d85c0f98 RW |
5607 | |
5608 | (define-public r-genie3 | |
5609 | (package | |
5610 | (name "r-genie3") | |
5611 | (version "1.6.0") | |
5612 | (source | |
5613 | (origin | |
5614 | (method url-fetch) | |
5615 | (uri (bioconductor-uri "GENIE3" version)) | |
5616 | (sha256 | |
5617 | (base32 | |
5618 | "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx")))) | |
5619 | (properties `((upstream-name . "GENIE3"))) | |
5620 | (build-system r-build-system) | |
5621 | (propagated-inputs `(("r-reshape2" ,r-reshape2))) | |
5622 | (home-page "https://bioconductor.org/packages/GENIE3") | |
5623 | (synopsis "Gene network inference with ensemble of trees") | |
5624 | (description | |
5625 | "This package implements the GENIE3 algorithm for inferring gene | |
5626 | regulatory networks from expression data.") | |
5627 | (license license:gpl2+))) | |
db316d73 RW |
5628 | |
5629 | (define-public r-roc | |
5630 | (package | |
5631 | (name "r-roc") | |
5632 | (version "1.60.0") | |
5633 | (source | |
5634 | (origin | |
5635 | (method url-fetch) | |
5636 | (uri (bioconductor-uri "ROC" version)) | |
5637 | (sha256 | |
5638 | (base32 | |
5639 | "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c")))) | |
5640 | (properties `((upstream-name . "ROC"))) | |
5641 | (build-system r-build-system) | |
5642 | (home-page "https://www.bioconductor.org/packages/ROC/") | |
5643 | (synopsis "Utilities for ROC curves") | |
5644 | (description | |
5645 | "This package provides utilities for @dfn{Receiver Operating | |
5646 | Characteristic} (ROC) curves, with a focus on micro arrays.") | |
5647 | (license license:artistic2.0))) | |
46721dea RW |
5648 | |
5649 | (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 | |
5650 | (package | |
5651 | (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") | |
5652 | (version "0.6.0") | |
5653 | (source | |
5654 | (origin | |
5655 | (method url-fetch) | |
5656 | (uri (bioconductor-uri | |
5657 | "IlluminaHumanMethylation450kanno.ilmn12.hg19" | |
5658 | version 'annotation)) | |
5659 | (sha256 | |
5660 | (base32 | |
5661 | "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) | |
5662 | (properties | |
5663 | `((upstream-name | |
5664 | . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) | |
5665 | (build-system r-build-system) | |
5666 | (propagated-inputs `(("r-minfi" ,r-minfi))) | |
5667 | (home-page | |
5668 | "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") | |
5669 | (synopsis "Annotation for Illumina's 450k methylation arrays") | |
5670 | (description | |
5671 | "This package provides manifests and annotation for Illumina's 450k array | |
5672 | data.") | |
5673 | (license license:artistic2.0))) | |
38babeaa RW |
5674 | |
5675 | (define-public r-watermelon | |
5676 | (package | |
5677 | (name "r-watermelon") | |
5678 | (version "1.28.0") | |
5679 | (source | |
5680 | (origin | |
5681 | (method url-fetch) | |
5682 | (uri (bioconductor-uri "wateRmelon" version)) | |
5683 | (sha256 | |
5684 | (base32 | |
5685 | "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z")))) | |
5686 | (properties `((upstream-name . "wateRmelon"))) | |
5687 | (build-system r-build-system) | |
5688 | (propagated-inputs | |
5689 | `(("r-biobase" ,r-biobase) | |
5690 | ("r-illuminahumanmethylation450kanno-ilmn12-hg19" | |
5691 | ,r-illuminahumanmethylation450kanno-ilmn12-hg19) | |
5692 | ("r-illuminaio" ,r-illuminaio) | |
5693 | ("r-limma" ,r-limma) | |
5694 | ("r-lumi" ,r-lumi) | |
5695 | ("r-matrixstats" ,r-matrixstats) | |
5696 | ("r-methylumi" ,r-methylumi) | |
5697 | ("r-roc" ,r-roc))) | |
5698 | (home-page "https://bioconductor.org/packages/wateRmelon/") | |
5699 | (synopsis "Illumina 450 methylation array normalization and metrics") | |
5700 | (description | |
5701 | "The standard index of DNA methylation (beta) is computed from methylated | |
5702 | and unmethylated signal intensities. Betas calculated from raw signal | |
5703 | intensities perform well, but using 11 methylomic datasets we demonstrate that | |
5704 | quantile normalization methods produce marked improvement. The commonly used | |
5705 | procedure of normalizing betas is inferior to the separate normalization of M | |
5706 | and U, and it is also advantageous to normalize Type I and Type II assays | |
5707 | separately. This package provides 15 flavours of betas and three performance | |
5708 | metrics, with methods for objects produced by the @code{methylumi} and | |
5709 | @code{minfi} packages.") | |
5710 | (license license:gpl3))) | |
7d2cb646 RW |
5711 | |
5712 | (define-public r-gdsfmt | |
5713 | (package | |
5714 | (name "r-gdsfmt") | |
5715 | (version "1.20.0") | |
5716 | (source | |
5717 | (origin | |
5718 | (method url-fetch) | |
5719 | (uri (bioconductor-uri "gdsfmt" version)) | |
5720 | (sha256 | |
5721 | (base32 | |
5722 | "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy")) | |
5723 | (modules '((guix build utils))) | |
5724 | ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build | |
5725 | ;; them and link with system libraries instead. | |
5726 | (snippet | |
5727 | '(begin | |
5728 | (for-each delete-file-recursively | |
5729 | '("src/LZ4" | |
5730 | "src/XZ" | |
5731 | "src/ZLIB")) | |
5732 | (substitute* "src/Makevars" | |
5733 | (("all: \\$\\(SHLIB\\)") "all:") | |
5734 | (("\\$\\(SHLIB\\): liblzma.a") "") | |
5735 | (("(ZLIB|LZ4)/.*") "") | |
5736 | (("CoreArray/dVLIntGDS.cpp.*") | |
5737 | "CoreArray/dVLIntGDS.cpp") | |
5738 | (("CoreArray/dVLIntGDS.o.*") | |
5739 | "CoreArray/dVLIntGDS.o") | |
5740 | (("PKG_LIBS = ./liblzma.a") | |
5741 | "PKG_LIBS = -llz4")) | |
5742 | (substitute* "src/CoreArray/dStream.h" | |
5743 | (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) | |
5744 | (string-append "include <" header ">"))) | |
5745 | #t)))) | |
5746 | (properties `((upstream-name . "gdsfmt"))) | |
5747 | (build-system r-build-system) | |
5748 | (inputs | |
5749 | `(("lz4" ,lz4) | |
5750 | ("xz" ,xz) | |
5751 | ("zlib" ,zlib))) | |
5752 | (home-page "http://corearray.sourceforge.net/") | |
5753 | (synopsis | |
5754 | "R Interface to CoreArray Genomic Data Structure (GDS) Files") | |
5755 | (description | |
5756 | "This package provides a high-level R interface to CoreArray @dfn{Genomic | |
5757 | Data Structure} (GDS) data files, which are portable across platforms with | |
5758 | hierarchical structure to store multiple scalable array-oriented data sets | |
5759 | with metadata information. It is suited for large-scale datasets, especially | |
5760 | for data which are much larger than the available random-access memory. The | |
5761 | @code{gdsfmt} package offers efficient operations specifically designed for | |
5762 | integers of less than 8 bits, since a diploid genotype, like | |
5763 | @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a | |
5764 | byte. Data compression and decompression are available with relatively | |
5765 | efficient random access. It is also allowed to read a GDS file in parallel | |
5766 | with multiple R processes supported by the package @code{parallel}.") | |
5767 | (license license:lgpl3))) | |
6b5f59c7 RW |
5768 | |
5769 | (define-public r-bigmelon | |
5770 | (package | |
5771 | (name "r-bigmelon") | |
5772 | (version "1.10.0") | |
5773 | (source | |
5774 | (origin | |
5775 | (method url-fetch) | |
5776 | (uri (bioconductor-uri "bigmelon" version)) | |
5777 | (sha256 | |
5778 | (base32 | |
5779 | "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9")))) | |
5780 | (properties `((upstream-name . "bigmelon"))) | |
5781 | (build-system r-build-system) | |
5782 | (propagated-inputs | |
5783 | `(("r-biobase" ,r-biobase) | |
5784 | ("r-biocgenerics" ,r-biocgenerics) | |
5785 | ("r-gdsfmt" ,r-gdsfmt) | |
5786 | ("r-geoquery" ,r-geoquery) | |
5787 | ("r-methylumi" ,r-methylumi) | |
5788 | ("r-minfi" ,r-minfi) | |
5789 | ("r-watermelon" ,r-watermelon))) | |
5790 | (home-page "https://bioconductor.org/packages/bigmelon/") | |
5791 | (synopsis "Illumina methylation array analysis for large experiments") | |
5792 | (description | |
5793 | "This package provides methods for working with Illumina arrays using the | |
5794 | @code{gdsfmt} package.") | |
5795 | (license license:gpl3))) | |
739b2d10 | 5796 | |
e5dfcd8e RW |
5797 | (define-public r-seqbias |
5798 | (package | |
5799 | (name "r-seqbias") | |
5800 | (version "1.32.0") | |
5801 | (source | |
5802 | (origin | |
5803 | (method url-fetch) | |
5804 | (uri (bioconductor-uri "seqbias" version)) | |
5805 | (sha256 | |
5806 | (base32 | |
5807 | "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw")))) | |
5808 | (properties `((upstream-name . "seqbias"))) | |
5809 | (build-system r-build-system) | |
5810 | (propagated-inputs | |
5811 | `(("r-biostrings" ,r-biostrings) | |
5812 | ("r-genomicranges" ,r-genomicranges) | |
5813 | ("r-rhtslib" ,r-rhtslib))) | |
5814 | (inputs | |
5815 | `(("zlib" ,zlib))) ; This comes from rhtslib. | |
5816 | (home-page "https://bioconductor.org/packages/seqbias/") | |
5817 | (synopsis "Estimation of per-position bias in high-throughput sequencing data") | |
5818 | (description | |
5819 | "This package implements a model of per-position sequencing bias in | |
5820 | high-throughput sequencing data using a simple Bayesian network, the structure | |
5821 | and parameters of which are trained on a set of aligned reads and a reference | |
5822 | genome sequence.") | |
5823 | (license license:lgpl3))) | |
5824 | ||
bb0024dc RW |
5825 | (define-public r-reqon |
5826 | (package | |
5827 | (name "r-reqon") | |
5828 | (version "1.30.0") | |
5829 | (source | |
5830 | (origin | |
5831 | (method url-fetch) | |
5832 | (uri (bioconductor-uri "ReQON" version)) | |
5833 | (sha256 | |
5834 | (base32 | |
5835 | "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a")))) | |
5836 | (properties `((upstream-name . "ReQON"))) | |
5837 | (build-system r-build-system) | |
5838 | (propagated-inputs | |
5839 | `(("r-rjava" ,r-rjava) | |
5840 | ("r-rsamtools" ,r-rsamtools) | |
5841 | ("r-seqbias" ,r-seqbias))) | |
5842 | (home-page "https://bioconductor.org/packages/ReQON/") | |
5843 | (synopsis "Recalibrating quality of nucleotides") | |
5844 | (description | |
5845 | "This package provides an implementation of an algorithm for | |
5846 | recalibrating the base quality scores for aligned sequencing data in BAM | |
5847 | format.") | |
5848 | (license license:gpl2))) | |
5849 | ||
739b2d10 RW |
5850 | (define-public r-wavcluster |
5851 | (package | |
5852 | (name "r-wavcluster") | |
5853 | (version "2.18.0") | |
5854 | (source | |
5855 | (origin | |
5856 | (method url-fetch) | |
5857 | (uri (bioconductor-uri "wavClusteR" version)) | |
5858 | (sha256 | |
5859 | (base32 | |
5860 | "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2")))) | |
5861 | (properties `((upstream-name . "wavClusteR"))) | |
5862 | (build-system r-build-system) | |
5863 | (propagated-inputs | |
5864 | `(("r-biocgenerics" ,r-biocgenerics) | |
5865 | ("r-biostrings" ,r-biostrings) | |
5866 | ("r-foreach" ,r-foreach) | |
5867 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5868 | ("r-genomicranges" ,r-genomicranges) | |
5869 | ("r-ggplot2" ,r-ggplot2) | |
5870 | ("r-hmisc" ,r-hmisc) | |
5871 | ("r-iranges" ,r-iranges) | |
5872 | ("r-mclust" ,r-mclust) | |
5873 | ("r-rsamtools" ,r-rsamtools) | |
5874 | ("r-rtracklayer" ,r-rtracklayer) | |
5875 | ("r-s4vectors" ,r-s4vectors) | |
5876 | ("r-seqinr" ,r-seqinr) | |
5877 | ("r-stringr" ,r-stringr) | |
5878 | ("r-wmtsa" ,r-wmtsa))) | |
5879 | (home-page "https://bioconductor.org/packages/wavClusteR/") | |
5880 | (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") | |
5881 | (description | |
5882 | "This package provides an integrated pipeline for the analysis of | |
5883 | PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from | |
5884 | sequencing errors, SNPs and additional non-experimental sources by a non- | |
5885 | parametric mixture model. The protein binding sites (clusters) are then | |
5886 | resolved at high resolution and cluster statistics are estimated using a | |
5887 | rigorous Bayesian framework. Post-processing of the results, data export for | |
5888 | UCSC genome browser visualization and motif search analysis are provided. In | |
5889 | addition, the package allows to integrate RNA-Seq data to estimate the False | |
5890 | Discovery Rate of cluster detection. Key functions support parallel multicore | |
5891 | computing. While wavClusteR was designed for PAR-CLIP data analysis, it can | |
5892 | be applied to the analysis of other NGS data obtained from experimental | |
5893 | procedures that induce nucleotide substitutions (e.g. BisSeq).") | |
5894 | (license license:gpl2))) | |
853211a5 RW |
5895 | |
5896 | (define-public r-timeseriesexperiment | |
5897 | (package | |
5898 | (name "r-timeseriesexperiment") | |
5899 | (version "1.2.0") | |
5900 | (source | |
5901 | (origin | |
5902 | (method url-fetch) | |
5903 | (uri (bioconductor-uri "TimeSeriesExperiment" version)) | |
5904 | (sha256 | |
5905 | (base32 | |
5906 | "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y")))) | |
5907 | (properties | |
5908 | `((upstream-name . "TimeSeriesExperiment"))) | |
5909 | (build-system r-build-system) | |
5910 | (propagated-inputs | |
5911 | `(("r-deseq2" ,r-deseq2) | |
5912 | ("r-dplyr" ,r-dplyr) | |
5913 | ("r-dynamictreecut" ,r-dynamictreecut) | |
5914 | ("r-edger" ,r-edger) | |
5915 | ("r-ggplot2" ,r-ggplot2) | |
5916 | ("r-hmisc" ,r-hmisc) | |
5917 | ("r-limma" ,r-limma) | |
5918 | ("r-magrittr" ,r-magrittr) | |
5919 | ("r-proxy" ,r-proxy) | |
5920 | ("r-s4vectors" ,r-s4vectors) | |
5921 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
5922 | ("r-tibble" ,r-tibble) | |
5923 | ("r-tidyr" ,r-tidyr) | |
5924 | ("r-vegan" ,r-vegan) | |
5925 | ("r-viridis" ,r-viridis))) | |
5926 | (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") | |
5927 | (synopsis "Analysis for short time-series data") | |
5928 | (description | |
5929 | "This package is a visualization and analysis toolbox for short time | |
5930 | course data which includes dimensionality reduction, clustering, two-sample | |
5931 | differential expression testing and gene ranking techniques. The package also | |
5932 | provides methods for retrieving enriched pathways.") | |
5933 | (license license:lgpl3+))) | |
df8576e5 RW |
5934 | |
5935 | (define-public r-variantfiltering | |
5936 | (package | |
5937 | (name "r-variantfiltering") | |
5938 | (version "1.20.0") | |
5939 | (source | |
5940 | (origin | |
5941 | (method url-fetch) | |
5942 | (uri (bioconductor-uri "VariantFiltering" version)) | |
5943 | (sha256 | |
5944 | (base32 | |
5945 | "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17")))) | |
5946 | (properties | |
5947 | `((upstream-name . "VariantFiltering"))) | |
5948 | (build-system r-build-system) | |
5949 | (propagated-inputs | |
5950 | `(("r-annotationdbi" ,r-annotationdbi) | |
5951 | ("r-biobase" ,r-biobase) | |
5952 | ("r-biocgenerics" ,r-biocgenerics) | |
5953 | ("r-biocparallel" ,r-biocparallel) | |
5954 | ("r-biostrings" ,r-biostrings) | |
5955 | ("r-bsgenome" ,r-bsgenome) | |
5956 | ("r-dt" ,r-dt) | |
5957 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5958 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5959 | ("r-genomicranges" ,r-genomicranges) | |
5960 | ("r-genomicscores" ,r-genomicscores) | |
5961 | ("r-graph" ,r-graph) | |
5962 | ("r-gviz" ,r-gviz) | |
5963 | ("r-iranges" ,r-iranges) | |
5964 | ("r-rbgl" ,r-rbgl) | |
5965 | ("r-rsamtools" ,r-rsamtools) | |
5966 | ("r-s4vectors" ,r-s4vectors) | |
5967 | ("r-shiny" ,r-shiny) | |
5968 | ("r-shinyjs" ,r-shinyjs) | |
5969 | ("r-shinythemes" ,r-shinythemes) | |
5970 | ("r-shinytree" ,r-shinytree) | |
5971 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
5972 | ("r-variantannotation" ,r-variantannotation) | |
5973 | ("r-xvector" ,r-xvector))) | |
5974 | (home-page "https://github.com/rcastelo/VariantFiltering") | |
5975 | (synopsis "Filtering of coding and non-coding genetic variants") | |
5976 | (description | |
5977 | "Filter genetic variants using different criteria such as inheritance | |
5978 | model, amino acid change consequence, minor allele frequencies across human | |
5979 | populations, splice site strength, conservation, etc.") | |
5980 | (license license:artistic2.0))) | |
f5349b4d RW |
5981 | |
5982 | (define-public r-genomegraphs | |
5983 | (package | |
5984 | (name "r-genomegraphs") | |
5985 | (version "1.44.0") | |
5986 | (source | |
5987 | (origin | |
5988 | (method url-fetch) | |
5989 | (uri (bioconductor-uri "GenomeGraphs" version)) | |
5990 | (sha256 | |
5991 | (base32 | |
5992 | "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd")))) | |
5993 | (properties `((upstream-name . "GenomeGraphs"))) | |
5994 | (build-system r-build-system) | |
5995 | (propagated-inputs | |
5996 | `(("r-biomart" ,r-biomart))) | |
5997 | (home-page "https://bioconductor.org/packages/GenomeGraphs/") | |
5998 | (synopsis "Plotting genomic information from Ensembl") | |
5999 | (description | |
6000 | "Genomic data analyses requires integrated visualization of known genomic | |
6001 | information and new experimental data. GenomeGraphs uses the biomaRt package | |
6002 | to perform live annotation queries to Ensembl and translates this to e.g. | |
6003 | gene/transcript structures in viewports of the grid graphics package. This | |
6004 | results in genomic information plotted together with your data. Another | |
6005 | strength of GenomeGraphs is to plot different data types such as array CGH, | |
6006 | gene expression, sequencing and other data, together in one plot using the | |
6007 | same genome coordinate system.") | |
6008 | (license license:artistic2.0))) | |
2a360cf6 RW |
6009 | |
6010 | (define-public r-wavetiling | |
6011 | (package | |
6012 | (name "r-wavetiling") | |
6013 | (version "1.26.0") | |
6014 | (source | |
6015 | (origin | |
6016 | (method url-fetch) | |
6017 | (uri (bioconductor-uri "waveTiling" version)) | |
6018 | (sha256 | |
6019 | (base32 | |
6020 | "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir")))) | |
6021 | (properties `((upstream-name . "waveTiling"))) | |
6022 | (build-system r-build-system) | |
6023 | (propagated-inputs | |
6024 | `(("r-affy" ,r-affy) | |
6025 | ("r-biobase" ,r-biobase) | |
6026 | ("r-biostrings" ,r-biostrings) | |
6027 | ("r-genomegraphs" ,r-genomegraphs) | |
6028 | ("r-genomicranges" ,r-genomicranges) | |
6029 | ("r-iranges" ,r-iranges) | |
6030 | ("r-oligo" ,r-oligo) | |
6031 | ("r-oligoclasses" ,r-oligoclasses) | |
6032 | ("r-preprocesscore" ,r-preprocesscore) | |
6033 | ("r-waveslim" ,r-waveslim))) | |
6034 | (home-page "https://r-forge.r-project.org/projects/wavetiling/") | |
6035 | (synopsis "Wavelet-based models for tiling array transcriptome analysis") | |
6036 | (description | |
6037 | "This package is designed to conduct transcriptome analysis for tiling | |
6038 | arrays based on fast wavelet-based functional models.") | |
6039 | (license license:gpl2+))) | |
d80a1569 RW |
6040 | |
6041 | (define-public r-variancepartition | |
6042 | (package | |
6043 | (name "r-variancepartition") | |
326746e1 | 6044 | (version "1.14.1") |
d80a1569 RW |
6045 | (source |
6046 | (origin | |
6047 | (method url-fetch) | |
6048 | (uri (bioconductor-uri "variancePartition" version)) | |
6049 | (sha256 | |
6050 | (base32 | |
326746e1 | 6051 | "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd")))) |
d80a1569 RW |
6052 | (properties |
6053 | `((upstream-name . "variancePartition"))) | |
6054 | (build-system r-build-system) | |
6055 | (propagated-inputs | |
6056 | `(("r-biobase" ,r-biobase) | |
326746e1 | 6057 | ("r-biocparallel" ,r-biocparallel) |
d80a1569 RW |
6058 | ("r-colorramps" ,r-colorramps) |
6059 | ("r-doparallel" ,r-doparallel) | |
6060 | ("r-foreach" ,r-foreach) | |
6061 | ("r-ggplot2" ,r-ggplot2) | |
6062 | ("r-gplots" ,r-gplots) | |
6063 | ("r-iterators" ,r-iterators) | |
6064 | ("r-limma" ,r-limma) | |
6065 | ("r-lme4" ,r-lme4) | |
6066 | ("r-lmertest" ,r-lmertest) | |
6067 | ("r-mass" ,r-mass) | |
6068 | ("r-pbkrtest" ,r-pbkrtest) | |
6069 | ("r-progress" ,r-progress) | |
6070 | ("r-reshape2" ,r-reshape2) | |
6071 | ("r-scales" ,r-scales))) | |
6072 | (home-page "https://bioconductor.org/packages/variancePartition/") | |
6073 | (synopsis "Analyze variation in gene expression experiments") | |
6074 | (description | |
6075 | "This is a package providing tools to quantify and interpret multiple | |
6076 | sources of biological and technical variation in gene expression experiments. | |
6077 | It uses a linear mixed model to quantify variation in gene expression | |
6078 | attributable to individual, tissue, time point, or technical variables. The | |
6079 | package includes dream differential expression analysis for repeated | |
6080 | measures.") | |
6081 | (license license:gpl2+))) | |
16e2e4f2 | 6082 | |
6083 | (define-public r-htqpcr | |
6084 | (package | |
6085 | (name "r-htqpcr") | |
6086 | (version "1.38.0") | |
6087 | (source | |
6088 | (origin | |
6089 | (method url-fetch) | |
6090 | (uri (bioconductor-uri "HTqPCR" version)) | |
6091 | (sha256 | |
6092 | (base32 | |
6093 | "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7")))) | |
6094 | (properties `((upstream-name . "HTqPCR"))) | |
6095 | (build-system r-build-system) | |
6096 | (propagated-inputs | |
6097 | `(("r-affy" ,r-affy) | |
6098 | ("r-biobase" ,r-biobase) | |
6099 | ("r-gplots" ,r-gplots) | |
6100 | ("r-limma" ,r-limma) | |
6101 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
6102 | (home-page "http://www.ebi.ac.uk/bertone/software") | |
6103 | (synopsis "Automated analysis of high-throughput qPCR data") | |
6104 | (description | |
6105 | "Analysis of Ct values from high throughput quantitative real-time | |
6106 | PCR (qPCR) assays across multiple conditions or replicates. The input data | |
6107 | can be from spatially-defined formats such ABI TaqMan Low Density Arrays or | |
6108 | OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad | |
6109 | Laboratories; conventional 96- or 384-well plates; or microfluidic devices | |
6110 | such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data | |
6111 | loading, quality assessment, normalization, visualization and parametric or | |
6112 | non-parametric testing for statistical significance in Ct values between | |
6113 | features (e.g. genes, microRNAs).") | |
6114 | (license license:artistic2.0))) | |
86fb2c63 | 6115 | |
6116 | (define-public r-unifiedwmwqpcr | |
6117 | (package | |
6118 | (name "r-unifiedwmwqpcr") | |
6119 | (version "1.20.0") | |
6120 | (source | |
6121 | (origin | |
6122 | (method url-fetch) | |
6123 | (uri (bioconductor-uri "unifiedWMWqPCR" version)) | |
6124 | (sha256 | |
6125 | (base32 | |
6126 | "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a")))) | |
6127 | (properties | |
6128 | `((upstream-name . "unifiedWMWqPCR"))) | |
6129 | (build-system r-build-system) | |
6130 | (propagated-inputs | |
6131 | `(("r-biocgenerics" ,r-biocgenerics) | |
6132 | ("r-htqpcr" ,r-htqpcr))) | |
6133 | (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") | |
6134 | (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") | |
6135 | (description | |
6136 | "This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR | |
6137 | data. This modified test allows for testing differential expression in qPCR | |
6138 | data.") | |
6139 | (license license:gpl2+))) |