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fa596599 | 1 | ;;; GNU Guix --- Functional package management for GNU |
6aa896d8 RW |
2 | ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> |
3 | ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> | |
61242625 | 4 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
fa596599 RW |
5 | ;;; |
6 | ;;; This file is part of GNU Guix. | |
7 | ;;; | |
8 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
9 | ;;; under the terms of the GNU General Public License as published by | |
10 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
11 | ;;; your option) any later version. | |
12 | ;;; | |
13 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
14 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
16 | ;;; GNU General Public License for more details. | |
17 | ;;; | |
18 | ;;; You should have received a copy of the GNU General Public License | |
19 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
20 | ||
21 | (define-module (gnu packages bioconductor) | |
22 | #:use-module ((guix licenses) #:prefix license:) | |
23 | #:use-module (guix packages) | |
24 | #:use-module (guix download) | |
b2dce6b5 | 25 | #:use-module (guix git-download) |
fa596599 | 26 | #:use-module (guix build-system r) |
183ce988 | 27 | #:use-module (gnu packages) |
58656064 | 28 | #:use-module (gnu packages base) |
cf9a29b2 | 29 | #:use-module (gnu packages bioinformatics) |
a5b56a53 RJ |
30 | #:use-module (gnu packages cran) |
31 | #:use-module (gnu packages compression) | |
c18dccff | 32 | #:use-module (gnu packages gcc) |
cf9a29b2 | 33 | #:use-module (gnu packages graph) |
dddbc90c | 34 | #:use-module (gnu packages haskell-xyz) |
5cfa4bff | 35 | #:use-module (gnu packages image) |
b64ce4b7 | 36 | #:use-module (gnu packages maths) |
6b12f213 RW |
37 | #:use-module (gnu packages netpbm) |
38 | #:use-module (gnu packages perl) | |
2cb71d81 | 39 | #:use-module (gnu packages pkg-config) |
f4235c0e | 40 | #:use-module (gnu packages statistics) |
14bb1c48 RW |
41 | #:use-module (gnu packages web) |
42 | #:use-module (srfi srfi-1)) | |
fa596599 | 43 | |
557a1089 RW |
44 | \f |
45 | ;;; Annotations | |
46 | ||
b7d93cf5 RW |
47 | (define-public r-bsgenome-celegans-ucsc-ce6 |
48 | (package | |
49 | (name "r-bsgenome-celegans-ucsc-ce6") | |
50 | (version "1.4.0") | |
51 | (source (origin | |
52 | (method url-fetch) | |
53 | ;; We cannot use bioconductor-uri here because this tarball is | |
54 | ;; located under "data/annotation/" instead of "bioc/". | |
55 | (uri (string-append "https://www.bioconductor.org/packages/" | |
56 | "release/data/annotation/src/contrib/" | |
57 | "BSgenome.Celegans.UCSC.ce6_" | |
58 | version ".tar.gz")) | |
59 | (sha256 | |
60 | (base32 | |
61 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
62 | (properties | |
63 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
64 | (build-system r-build-system) | |
65 | ;; As this package provides little more than a very large data file it | |
66 | ;; doesn't make sense to build substitutes. | |
67 | (arguments `(#:substitutable? #f)) | |
68 | (propagated-inputs | |
69 | `(("r-bsgenome" ,r-bsgenome))) | |
70 | (home-page | |
71 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
72 | (synopsis "Full genome sequences for Worm") | |
73 | (description | |
74 | "This package provides full genome sequences for Caenorhabditis | |
75 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
0c792ffb RW |
76 | objects.") |
77 | (license license:artistic2.0))) | |
78 | ||
79 | (define-public r-bsgenome-celegans-ucsc-ce10 | |
80 | (package | |
81 | (name "r-bsgenome-celegans-ucsc-ce10") | |
82 | (version "1.4.0") | |
83 | (source (origin | |
84 | (method url-fetch) | |
85 | ;; We cannot use bioconductor-uri here because this tarball is | |
86 | ;; located under "data/annotation/" instead of "bioc/". | |
87 | (uri (string-append "https://www.bioconductor.org/packages/" | |
88 | "release/data/annotation/src/contrib/" | |
89 | "BSgenome.Celegans.UCSC.ce10_" | |
90 | version ".tar.gz")) | |
91 | (sha256 | |
92 | (base32 | |
93 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
94 | (properties | |
95 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
96 | (build-system r-build-system) | |
97 | ;; As this package provides little more than a very large data file it | |
98 | ;; doesn't make sense to build substitutes. | |
99 | (arguments `(#:substitutable? #f)) | |
100 | (propagated-inputs | |
101 | `(("r-bsgenome" ,r-bsgenome))) | |
102 | (home-page | |
103 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
104 | (synopsis "Full genome sequences for Worm") | |
105 | (description | |
106 | "This package provides full genome sequences for Caenorhabditis | |
107 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
b7d93cf5 RW |
108 | objects.") |
109 | (license license:artistic2.0))) | |
110 | ||
183db725 RW |
111 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
112 | (package | |
113 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
114 | (version "1.4.1") | |
115 | (source (origin | |
116 | (method url-fetch) | |
117 | ;; We cannot use bioconductor-uri here because this tarball is | |
118 | ;; located under "data/annotation/" instead of "bioc/". | |
119 | (uri (string-append "https://www.bioconductor.org/packages/" | |
120 | "release/data/annotation/src/contrib/" | |
121 | "BSgenome.Dmelanogaster.UCSC.dm6_" | |
122 | version ".tar.gz")) | |
123 | (sha256 | |
124 | (base32 | |
125 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
126 | (properties | |
127 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
128 | (build-system r-build-system) | |
129 | ;; As this package provides little more than a very large data file it | |
130 | ;; doesn't make sense to build substitutes. | |
131 | (arguments `(#:substitutable? #f)) | |
132 | (propagated-inputs | |
133 | `(("r-bsgenome" ,r-bsgenome))) | |
134 | (home-page | |
135 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
136 | (synopsis "Full genome sequences for Fly") | |
137 | (description | |
138 | "This package provides full genome sequences for Drosophila | |
139 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
140 | objects.") | |
141 | (license license:artistic2.0))) | |
142 | ||
13dabd69 RW |
143 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
144 | (package | |
145 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
146 | (version "1.4.0") | |
147 | (source (origin | |
148 | (method url-fetch) | |
149 | ;; We cannot use bioconductor-uri here because this tarball is | |
150 | ;; located under "data/annotation/" instead of "bioc/". | |
151 | (uri (string-append "https://www.bioconductor.org/packages/" | |
152 | "release/data/annotation/src/contrib/" | |
153 | "BSgenome.Dmelanogaster.UCSC.dm3_" | |
154 | version ".tar.gz")) | |
155 | (sha256 | |
156 | (base32 | |
157 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
158 | (properties | |
159 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
160 | (build-system r-build-system) | |
161 | ;; As this package provides little more than a very large data file it | |
162 | ;; doesn't make sense to build substitutes. | |
163 | (arguments `(#:substitutable? #f)) | |
164 | (propagated-inputs | |
165 | `(("r-bsgenome" ,r-bsgenome))) | |
166 | (home-page | |
167 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
168 | (synopsis "Full genome sequences for Fly") | |
169 | (description | |
170 | "This package provides full genome sequences for Drosophila | |
171 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
172 | Biostrings objects.") | |
173 | (license license:artistic2.0))) | |
174 | ||
dfac7eb9 RW |
175 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
176 | (package | |
177 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
178 | (version "1.3.99") | |
179 | (source (origin | |
180 | (method url-fetch) | |
181 | ;; We cannot use bioconductor-uri here because this tarball is | |
182 | ;; located under "data/annotation/" instead of "bioc/". | |
183 | (uri (string-append "http://www.bioconductor.org/packages/" | |
184 | "release/data/annotation/src/contrib/" | |
185 | "BSgenome.Dmelanogaster.UCSC.dm3.masked_" | |
186 | version ".tar.gz")) | |
187 | (sha256 | |
188 | (base32 | |
189 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
190 | (properties | |
191 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
192 | (build-system r-build-system) | |
193 | (propagated-inputs | |
194 | `(("r-bsgenome" ,r-bsgenome) | |
195 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
196 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
197 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
198 | (synopsis "Full masked genome sequences for Fly") | |
199 | (description | |
200 | "This package provides full masked genome sequences for Drosophila | |
201 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
202 | Biostrings objects. The sequences are the same as in | |
203 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
204 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
205 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
206 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
207 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
208 | (license license:artistic2.0))) | |
209 | ||
40a65057 RW |
210 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
211 | (package | |
212 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
213 | (version "0.99.1") | |
214 | (source (origin | |
215 | (method url-fetch) | |
216 | ;; We cannot use bioconductor-uri here because this tarball is | |
217 | ;; located under "data/annotation/" instead of "bioc/". | |
218 | (uri (string-append "https://www.bioconductor.org/packages/" | |
219 | "release/data/annotation/src/contrib/" | |
220 | "BSgenome.Hsapiens.1000genomes.hs37d5_" | |
221 | version ".tar.gz")) | |
222 | (sha256 | |
223 | (base32 | |
224 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
225 | (properties | |
226 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
227 | (build-system r-build-system) | |
228 | ;; As this package provides little more than a very large data file it | |
229 | ;; doesn't make sense to build substitutes. | |
230 | (arguments `(#:substitutable? #f)) | |
231 | (propagated-inputs | |
232 | `(("r-bsgenome" ,r-bsgenome))) | |
233 | (home-page | |
234 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
235 | (synopsis "Full genome sequences for Homo sapiens") | |
236 | (description | |
237 | "This package provides full genome sequences for Homo sapiens from | |
238 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
239 | (license license:artistic2.0))) | |
240 | ||
6fbd759b RW |
241 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
242 | (package | |
243 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
244 | (version "1.3.99") | |
245 | (source (origin | |
246 | (method url-fetch) | |
247 | ;; We cannot use bioconductor-uri here because this tarball is | |
248 | ;; located under "data/annotation/" instead of "bioc/". | |
249 | (uri (string-append "http://www.bioconductor.org/packages/" | |
250 | "release/data/annotation/src/contrib/" | |
251 | "BSgenome.Hsapiens.UCSC.hg19.masked_" | |
252 | version ".tar.gz")) | |
253 | (sha256 | |
254 | (base32 | |
255 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
256 | (properties | |
257 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
258 | (build-system r-build-system) | |
259 | (propagated-inputs | |
260 | `(("r-bsgenome" ,r-bsgenome) | |
261 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
262 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
263 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
264 | (synopsis "Full masked genome sequences for Homo sapiens") | |
265 | (description | |
266 | "This package provides full genome sequences for Homo sapiens (Human) as | |
267 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
268 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
269 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
270 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
271 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
272 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
273 | default.") | |
274 | (license license:artistic2.0))) | |
275 | ||
5acb9052 RW |
276 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
277 | (package | |
278 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
279 | (version "1.4.0") | |
280 | (source (origin | |
281 | (method url-fetch) | |
282 | ;; We cannot use bioconductor-uri here because this tarball is | |
283 | ;; located under "data/annotation/" instead of "bioc/". | |
284 | (uri (string-append "https://www.bioconductor.org/packages/" | |
285 | "release/data/annotation/src/contrib/" | |
286 | "BSgenome.Mmusculus.UCSC.mm9_" | |
287 | version ".tar.gz")) | |
288 | (sha256 | |
289 | (base32 | |
290 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
291 | (properties | |
292 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
293 | (build-system r-build-system) | |
294 | ;; As this package provides little more than a very large data file it | |
295 | ;; doesn't make sense to build substitutes. | |
296 | (arguments `(#:substitutable? #f)) | |
297 | (propagated-inputs | |
298 | `(("r-bsgenome" ,r-bsgenome))) | |
299 | (home-page | |
300 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
301 | (synopsis "Full genome sequences for Mouse") | |
302 | (description | |
303 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
304 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
305 | (license license:artistic2.0))) | |
306 | ||
2bece692 RW |
307 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
308 | (package | |
309 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
310 | (version "1.3.99") | |
311 | (source (origin | |
312 | (method url-fetch) | |
313 | ;; We cannot use bioconductor-uri here because this tarball is | |
314 | ;; located under "data/annotation/" instead of "bioc/". | |
315 | (uri (string-append "http://www.bioconductor.org/packages/" | |
316 | "release/data/annotation/src/contrib/" | |
317 | "BSgenome.Mmusculus.UCSC.mm9.masked_" | |
318 | version ".tar.gz")) | |
319 | (sha256 | |
320 | (base32 | |
321 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
322 | (properties | |
323 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
324 | (build-system r-build-system) | |
325 | (propagated-inputs | |
326 | `(("r-bsgenome" ,r-bsgenome) | |
327 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
328 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
329 | (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") | |
330 | (synopsis "Full masked genome sequences for Mouse") | |
331 | (description | |
332 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
333 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
334 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
335 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
336 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
337 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
338 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
339 | default." ) | |
340 | (license license:artistic2.0))) | |
341 | ||
c3adc830 RW |
342 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
343 | (package | |
344 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
345 | (version "1.4.0") | |
346 | (source (origin | |
347 | (method url-fetch) | |
348 | ;; We cannot use bioconductor-uri here because this tarball is | |
349 | ;; located under "data/annotation/" instead of "bioc/". | |
350 | (uri (string-append "https://www.bioconductor.org/packages/" | |
351 | "release/data/annotation/src/contrib/" | |
352 | "BSgenome.Mmusculus.UCSC.mm10_" | |
353 | version ".tar.gz")) | |
354 | (sha256 | |
355 | (base32 | |
356 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
357 | (properties | |
358 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
359 | (build-system r-build-system) | |
360 | ;; As this package provides little more than a very large data file it | |
361 | ;; doesn't make sense to build substitutes. | |
362 | (arguments `(#:substitutable? #f)) | |
363 | (propagated-inputs | |
364 | `(("r-bsgenome" ,r-bsgenome))) | |
365 | (home-page | |
366 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
367 | (synopsis "Full genome sequences for Mouse") | |
368 | (description | |
369 | "This package provides full genome sequences for Mus | |
370 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
371 | in Biostrings objects.") | |
372 | (license license:artistic2.0))) | |
373 | ||
3a08940e RW |
374 | (define-public r-org-ce-eg-db |
375 | (package | |
376 | (name "r-org-ce-eg-db") | |
377 | (version "3.7.0") | |
378 | (source (origin | |
379 | (method url-fetch) | |
380 | ;; We cannot use bioconductor-uri here because this tarball is | |
381 | ;; located under "data/annotation/" instead of "bioc/". | |
382 | (uri (string-append "https://www.bioconductor.org/packages/" | |
383 | "release/data/annotation/src/contrib/" | |
384 | "org.Ce.eg.db_" version ".tar.gz")) | |
385 | (sha256 | |
386 | (base32 | |
387 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) | |
388 | (properties | |
389 | `((upstream-name . "org.Ce.eg.db"))) | |
390 | (build-system r-build-system) | |
391 | (propagated-inputs | |
392 | `(("r-annotationdbi" ,r-annotationdbi))) | |
393 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") | |
394 | (synopsis "Genome wide annotation for Worm") | |
395 | (description | |
396 | "This package provides mappings from Entrez gene identifiers to various | |
397 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
398 | (license license:artistic2.0))) | |
399 | ||
f8780e96 RW |
400 | (define-public r-org-dm-eg-db |
401 | (package | |
402 | (name "r-org-dm-eg-db") | |
403 | (version "3.7.0") | |
404 | (source (origin | |
405 | (method url-fetch) | |
406 | ;; We cannot use bioconductor-uri here because this tarball is | |
407 | ;; located under "data/annotation/" instead of "bioc/". | |
408 | (uri (string-append "https://www.bioconductor.org/packages/" | |
409 | "release/data/annotation/src/contrib/" | |
410 | "org.Dm.eg.db_" version ".tar.gz")) | |
411 | (sha256 | |
412 | (base32 | |
413 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) | |
414 | (properties | |
415 | `((upstream-name . "org.Dm.eg.db"))) | |
416 | (build-system r-build-system) | |
417 | (propagated-inputs | |
418 | `(("r-annotationdbi" ,r-annotationdbi))) | |
419 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") | |
420 | (synopsis "Genome wide annotation for Fly") | |
421 | (description | |
422 | "This package provides mappings from Entrez gene identifiers to various | |
423 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
424 | (license license:artistic2.0))) | |
425 | ||
3dad6087 RW |
426 | (define-public r-org-dr-eg-db |
427 | (package | |
428 | (name "r-org-dr-eg-db") | |
429 | (version "3.7.0") | |
430 | (source (origin | |
431 | (method url-fetch) | |
432 | ;; We cannot use bioconductor-uri here because this tarball is | |
433 | ;; located under "data/annotation/" instead of "bioc/". | |
434 | (uri (string-append "https://www.bioconductor.org/packages/" | |
435 | "release/data/annotation/src/contrib/" | |
436 | "org.Dr.eg.db_" version ".tar.gz")) | |
437 | (sha256 | |
438 | (base32 | |
439 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) | |
440 | (properties | |
441 | `((upstream-name . "org.Dr.eg.db"))) | |
442 | (build-system r-build-system) | |
443 | (propagated-inputs | |
444 | `(("r-annotationdbi" ,r-annotationdbi))) | |
445 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") | |
446 | (synopsis "Annotation for Zebrafish") | |
447 | (description | |
448 | "This package provides genome wide annotations for Zebrafish, primarily | |
449 | based on mapping using Entrez Gene identifiers.") | |
450 | (license license:artistic2.0))) | |
451 | ||
d56df35a RW |
452 | (define-public r-org-hs-eg-db |
453 | (package | |
454 | (name "r-org-hs-eg-db") | |
455 | (version "3.7.0") | |
456 | (source (origin | |
457 | (method url-fetch) | |
458 | ;; We cannot use bioconductor-uri here because this tarball is | |
459 | ;; located under "data/annotation/" instead of "bioc/". | |
460 | (uri (string-append "https://www.bioconductor.org/packages/" | |
461 | "release/data/annotation/src/contrib/" | |
462 | "org.Hs.eg.db_" version ".tar.gz")) | |
463 | (sha256 | |
464 | (base32 | |
465 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) | |
466 | (properties | |
467 | `((upstream-name . "org.Hs.eg.db"))) | |
468 | (build-system r-build-system) | |
469 | (propagated-inputs | |
470 | `(("r-annotationdbi" ,r-annotationdbi))) | |
471 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") | |
472 | (synopsis "Genome wide annotation for Human") | |
473 | (description | |
474 | "This package contains genome-wide annotations for Human, primarily based | |
475 | on mapping using Entrez Gene identifiers.") | |
476 | (license license:artistic2.0))) | |
477 | ||
8035819f RW |
478 | (define-public r-org-mm-eg-db |
479 | (package | |
480 | (name "r-org-mm-eg-db") | |
481 | (version "3.7.0") | |
482 | (source (origin | |
483 | (method url-fetch) | |
484 | ;; We cannot use bioconductor-uri here because this tarball is | |
485 | ;; located under "data/annotation/" instead of "bioc/". | |
486 | (uri (string-append "https://www.bioconductor.org/packages/" | |
487 | "release/data/annotation/src/contrib/" | |
488 | "org.Mm.eg.db_" version ".tar.gz")) | |
489 | (sha256 | |
490 | (base32 | |
491 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) | |
492 | (properties | |
493 | `((upstream-name . "org.Mm.eg.db"))) | |
494 | (build-system r-build-system) | |
495 | (propagated-inputs | |
496 | `(("r-annotationdbi" ,r-annotationdbi))) | |
497 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") | |
498 | (synopsis "Genome wide annotation for Mouse") | |
499 | (description | |
500 | "This package provides mappings from Entrez gene identifiers to various | |
501 | annotations for the genome of the model mouse Mus musculus.") | |
502 | (license license:artistic2.0))) | |
503 | ||
fe0b76e2 RW |
504 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
505 | (package | |
506 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
507 | (version "1.4.0") | |
508 | (source (origin | |
509 | (method url-fetch) | |
510 | ;; We cannot use bioconductor-uri here because this tarball is | |
511 | ;; located under "data/annotation/" instead of "bioc/". | |
512 | (uri (string-append "https://www.bioconductor.org/packages/" | |
513 | "release/data/annotation/src/contrib/" | |
514 | "BSgenome.Hsapiens.UCSC.hg19_" | |
515 | version ".tar.gz")) | |
516 | (sha256 | |
517 | (base32 | |
518 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) | |
519 | (properties | |
520 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
521 | (build-system r-build-system) | |
522 | ;; As this package provides little more than a very large data file it | |
523 | ;; doesn't make sense to build substitutes. | |
524 | (arguments `(#:substitutable? #f)) | |
525 | (propagated-inputs | |
526 | `(("r-bsgenome" ,r-bsgenome))) | |
527 | (home-page | |
528 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
529 | (synopsis "Full genome sequences for Homo sapiens") | |
530 | (description | |
531 | "This package provides full genome sequences for Homo sapiens as provided | |
532 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
533 | (license license:artistic2.0))) | |
534 | ||
8324e64c RW |
535 | (define-public r-ensdb-hsapiens-v75 |
536 | (package | |
537 | (name "r-ensdb-hsapiens-v75") | |
538 | (version "2.99.0") | |
539 | (source | |
540 | (origin | |
541 | (method url-fetch) | |
542 | (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) | |
543 | (sha256 | |
544 | (base32 | |
545 | "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) | |
546 | (properties | |
547 | `((upstream-name . "EnsDb.Hsapiens.v75"))) | |
548 | (build-system r-build-system) | |
549 | (propagated-inputs | |
550 | `(("r-ensembldb" ,r-ensembldb))) | |
551 | (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") | |
552 | (synopsis "Ensembl based annotation package") | |
553 | (description | |
554 | "This package exposes an annotation database generated from Ensembl.") | |
555 | (license license:artistic2.0))) | |
556 | ||
2cc51108 RW |
557 | (define-public r-genelendatabase |
558 | (package | |
559 | (name "r-genelendatabase") | |
daeb3cd9 | 560 | (version "1.18.0") |
2cc51108 RW |
561 | (source |
562 | (origin | |
563 | (method url-fetch) | |
564 | ;; We cannot use bioconductor-uri here because this tarball is | |
565 | ;; located under "data/experiment/" instead of "bioc/". | |
566 | (uri (string-append "https://bioconductor.org/packages/" | |
567 | "release/data/experiment/src/contrib" | |
568 | "/geneLenDataBase_" version ".tar.gz")) | |
569 | (sha256 | |
570 | (base32 | |
daeb3cd9 | 571 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
2cc51108 RW |
572 | (properties |
573 | `((upstream-name . "geneLenDataBase"))) | |
574 | (build-system r-build-system) | |
575 | (propagated-inputs | |
576 | `(("r-rtracklayer" ,r-rtracklayer) | |
577 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
578 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
579 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
580 | (description | |
581 | "This package provides the lengths of mRNA transcripts for a number of | |
582 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
583 | (license license:lgpl2.0+))) | |
584 | ||
66e35ce6 RW |
585 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
586 | (package | |
587 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
588 | (version "3.2.2") | |
589 | (source (origin | |
590 | (method url-fetch) | |
591 | ;; We cannot use bioconductor-uri here because this tarball is | |
592 | ;; located under "data/annotation/" instead of "bioc/". | |
593 | (uri (string-append "https://bioconductor.org/packages/" | |
594 | "release/data/annotation/src/contrib" | |
595 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" | |
596 | version ".tar.gz")) | |
597 | (sha256 | |
598 | (base32 | |
599 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
600 | (properties | |
601 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
602 | (build-system r-build-system) | |
603 | ;; As this package provides little more than a very large data file it | |
604 | ;; doesn't make sense to build substitutes. | |
605 | (arguments `(#:substitutable? #f)) | |
606 | (propagated-inputs | |
607 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
608 | (home-page | |
609 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
610 | (synopsis "Annotation package for human genome in TxDb format") | |
611 | (description | |
612 | "This package provides an annotation database of Homo sapiens genome | |
613 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
798b80ce RW |
614 | track. The database is exposed as a @code{TxDb} object.") |
615 | (license license:artistic2.0))) | |
616 | ||
617 | (define-public r-txdb-hsapiens-ucsc-hg38-knowngene | |
618 | (package | |
619 | (name "r-txdb-hsapiens-ucsc-hg38-knowngene") | |
620 | (version "3.4.6") | |
621 | (source (origin | |
622 | (method url-fetch) | |
623 | ;; We cannot use bioconductor-uri here because this tarball is | |
624 | ;; located under "data/annotation/" instead of "bioc/". | |
625 | (uri (string-append "https://bioconductor.org/packages/" | |
626 | "release/data/annotation/src/contrib" | |
627 | "/TxDb.Hsapiens.UCSC.hg38.knownGene_" | |
628 | version ".tar.gz")) | |
629 | (sha256 | |
630 | (base32 | |
631 | "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) | |
632 | (properties | |
633 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) | |
634 | (build-system r-build-system) | |
635 | (propagated-inputs | |
636 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
637 | (home-page | |
638 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") | |
639 | (synopsis "Annotation package for human genome in TxDb format") | |
640 | (description | |
641 | "This package provides an annotation database of Homo sapiens genome | |
642 | data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" | |
66e35ce6 RW |
643 | track. The database is exposed as a @code{TxDb} object.") |
644 | (license license:artistic2.0))) | |
645 | ||
d220babf RW |
646 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
647 | (package | |
648 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
649 | (version "3.2.2") | |
650 | (source (origin | |
651 | (method url-fetch) | |
652 | ;; We cannot use bioconductor-uri here because this tarball is | |
653 | ;; located under "data/annotation/" instead of "bioc/". | |
654 | (uri (string-append "https://bioconductor.org/packages/" | |
655 | "release/data/annotation/src/contrib" | |
656 | "/TxDb.Mmusculus.UCSC.mm9.knownGene_" | |
657 | version ".tar.gz")) | |
658 | (sha256 | |
659 | (base32 | |
660 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
661 | (properties | |
662 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
663 | (build-system r-build-system) | |
664 | (propagated-inputs | |
665 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
666 | ("r-annotationdbi" ,r-annotationdbi))) | |
667 | (home-page | |
668 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
669 | (synopsis "Annotation package for mouse genome in TxDb format") | |
670 | (description | |
671 | "This package provides an annotation database of Mouse genome data. It | |
672 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
673 | database is exposed as a @code{TxDb} object.") | |
674 | (license license:artistic2.0))) | |
675 | ||
7bc5d1b0 RW |
676 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
677 | (package | |
678 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
61242625 | 679 | (version "3.4.7") |
7bc5d1b0 RW |
680 | (source (origin |
681 | (method url-fetch) | |
682 | ;; We cannot use bioconductor-uri here because this tarball is | |
683 | ;; located under "data/annotation/" instead of "bioc/". | |
684 | (uri (string-append "https://www.bioconductor.org/packages/" | |
685 | "release/data/annotation/src/contrib/" | |
686 | "TxDb.Mmusculus.UCSC.mm10.knownGene_" | |
687 | version ".tar.gz")) | |
688 | (sha256 | |
689 | (base32 | |
61242625 | 690 | "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b")))) |
7bc5d1b0 RW |
691 | (properties |
692 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
693 | (build-system r-build-system) | |
694 | ;; As this package provides little more than a very large data file it | |
695 | ;; doesn't make sense to build substitutes. | |
696 | (arguments `(#:substitutable? #f)) | |
697 | (propagated-inputs | |
698 | `(("r-bsgenome" ,r-bsgenome) | |
699 | ("r-genomicfeatures" ,r-genomicfeatures) | |
700 | ("r-annotationdbi" ,r-annotationdbi))) | |
701 | (home-page | |
702 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
703 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
704 | (description | |
705 | "This package loads a TxDb object, which is an R interface to | |
706 | prefabricated databases contained in this package. This package provides | |
707 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
708 | based on the knownGene track.") | |
709 | (license license:artistic2.0))) | |
710 | ||
0f5c9cec RW |
711 | (define-public r-fdb-infiniummethylation-hg19 |
712 | (package | |
713 | (name "r-fdb-infiniummethylation-hg19") | |
714 | (version "2.2.0") | |
715 | (source (origin | |
716 | (method url-fetch) | |
717 | ;; We cannot use bioconductor-uri here because this tarball is | |
718 | ;; located under "data/annotation/" instead of "bioc/". | |
719 | (uri (string-append "https://www.bioconductor.org/packages/" | |
720 | "release/data/annotation/src/contrib/" | |
721 | "FDb.InfiniumMethylation.hg19_" | |
722 | version ".tar.gz")) | |
723 | (sha256 | |
724 | (base32 | |
725 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) | |
726 | (properties | |
727 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) | |
728 | (build-system r-build-system) | |
729 | (propagated-inputs | |
730 | `(("r-biostrings" ,r-biostrings) | |
731 | ("r-genomicfeatures" ,r-genomicfeatures) | |
732 | ("r-annotationdbi" ,r-annotationdbi) | |
733 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
734 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) | |
735 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") | |
736 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") | |
737 | (description | |
738 | "This is an annotation package for Illumina Infinium DNA methylation | |
739 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 | |
740 | annotations.") | |
741 | (license license:artistic2.0))) | |
742 | ||
9475a248 RW |
743 | (define-public r-illuminahumanmethylationepicmanifest |
744 | (package | |
745 | (name "r-illuminahumanmethylationepicmanifest") | |
746 | (version "0.3.0") | |
747 | (source (origin | |
748 | (method url-fetch) | |
749 | ;; We cannot use bioconductor-uri here because this tarball is | |
750 | ;; located under "data/annotation/" instead of "bioc/". | |
751 | (uri (string-append "https://www.bioconductor.org/packages/" | |
752 | "release/data/annotation/src/contrib/" | |
753 | "IlluminaHumanMethylationEPICmanifest_" | |
754 | version ".tar.gz")) | |
755 | (sha256 | |
756 | (base32 | |
757 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) | |
758 | (properties | |
759 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) | |
760 | (build-system r-build-system) | |
761 | (propagated-inputs | |
762 | `(("r-minfi" ,r-minfi))) | |
763 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") | |
764 | (synopsis "Manifest for Illumina's EPIC methylation arrays") | |
765 | (description | |
766 | "This is a manifest package for Illumina's EPIC methylation arrays.") | |
767 | (license license:artistic2.0))) | |
768 | ||
f8a5af46 RW |
769 | (define-public r-do-db |
770 | (package | |
771 | (name "r-do-db") | |
772 | (version "2.9") | |
773 | (source (origin | |
774 | (method url-fetch) | |
775 | ;; We cannot use bioconductor-uri here because this tarball is | |
776 | ;; located under "data/annotation/" instead of "bioc/". | |
777 | (uri (string-append "https://www.bioconductor.org/packages/" | |
778 | "release/data/annotation/src/contrib/" | |
779 | "DO.db_" version ".tar.gz")) | |
780 | (sha256 | |
781 | (base32 | |
782 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) | |
783 | (properties | |
784 | `((upstream-name . "DO.db"))) | |
785 | (build-system r-build-system) | |
786 | (propagated-inputs | |
787 | `(("r-annotationdbi" ,r-annotationdbi))) | |
788 | (home-page "https://www.bioconductor.org/packages/DO.db/") | |
789 | (synopsis "Annotation maps describing the entire Disease Ontology") | |
790 | (description | |
791 | "This package provides a set of annotation maps describing the entire | |
792 | Disease Ontology.") | |
793 | (license license:artistic2.0))) | |
794 | ||
2cc51108 | 795 | \f |
557a1089 RW |
796 | ;;; Experiment data |
797 | ||
692bce15 RW |
798 | (define-public r-abadata |
799 | (package | |
800 | (name "r-abadata") | |
801 | (version "1.12.0") | |
802 | (source (origin | |
803 | (method url-fetch) | |
804 | ;; We cannot use bioconductor-uri here because this tarball is | |
805 | ;; located under "data/experiment/" instead of "bioc/". | |
806 | (uri (string-append "https://www.bioconductor.org/packages/" | |
807 | "release/data/experiment/src/contrib/" | |
808 | "ABAData_" version ".tar.gz")) | |
809 | (sha256 | |
810 | (base32 | |
811 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) | |
812 | (properties | |
813 | `((upstream-name . "ABAData"))) | |
814 | (build-system r-build-system) | |
815 | (propagated-inputs | |
816 | `(("r-annotationdbi" ,r-annotationdbi))) | |
817 | (home-page "https://www.bioconductor.org/packages/ABAData/") | |
818 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") | |
819 | (description | |
820 | "This package provides the data for the gene expression enrichment | |
821 | analysis conducted in the package ABAEnrichment. The package includes three | |
822 | datasets which are derived from the Allen Brain Atlas: | |
823 | ||
824 | @enumerate | |
825 | @item Gene expression data from Human Brain (adults) averaged across donors, | |
826 | @item Gene expression data from the Developing Human Brain pooled into five | |
827 | age categories and averaged across donors, and | |
828 | @item a developmental effect score based on the Developing Human Brain | |
829 | expression data. | |
830 | @end enumerate | |
831 | ||
832 | All datasets are restricted to protein coding genes.") | |
833 | (license license:gpl2+))) | |
834 | ||
b50c9660 RW |
835 | (define-public r-arrmdata |
836 | (package | |
837 | (name "r-arrmdata") | |
838 | (version "1.18.0") | |
839 | (source (origin | |
840 | (method url-fetch) | |
841 | ;; We cannot use bioconductor-uri here because this tarball is | |
842 | ;; located under "data/experiment/" instead of "bioc/". | |
843 | (uri (string-append "https://www.bioconductor.org/packages/" | |
844 | "release/data/experiment/src/contrib/" | |
845 | "ARRmData_" version ".tar.gz")) | |
846 | (sha256 | |
847 | (base32 | |
848 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) | |
849 | (properties | |
850 | `((upstream-name . "ARRmData"))) | |
851 | (build-system r-build-system) | |
852 | (home-page "https://www.bioconductor.org/packages/ARRmData/") | |
853 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") | |
854 | (description | |
855 | "This package provides raw beta values from 36 samples across 3 groups | |
856 | from Illumina 450k methylation arrays.") | |
857 | (license license:artistic2.0))) | |
858 | ||
557a1089 RW |
859 | (define-public r-hsmmsinglecell |
860 | (package | |
861 | (name "r-hsmmsinglecell") | |
862 | (version "1.2.0") | |
863 | (source (origin | |
864 | (method url-fetch) | |
865 | ;; We cannot use bioconductor-uri here because this tarball is | |
866 | ;; located under "data/experiment/" instead of "bioc/". | |
867 | (uri (string-append "https://www.bioconductor.org/packages/" | |
868 | "release/data/experiment/src/contrib/" | |
869 | "HSMMSingleCell_" version ".tar.gz")) | |
870 | (sha256 | |
871 | (base32 | |
872 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) | |
873 | (properties | |
874 | `((upstream-name . "HSMMSingleCell"))) | |
875 | (build-system r-build-system) | |
876 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") | |
877 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") | |
878 | (description | |
879 | "Skeletal myoblasts undergo a well-characterized sequence of | |
880 | morphological and transcriptional changes during differentiation. In this | |
881 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded | |
882 | under high mitogen conditions (GM) and then differentiated by switching to | |
883 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several | |
884 | hundred cells taken over a time-course of serum-induced differentiation. | |
885 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, | |
886 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. | |
887 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, | |
888 | which were then sequenced to a depth of ~4 million reads per library, | |
889 | resulting in a complete gene expression profile for each cell.") | |
890 | (license license:artistic2.0))) | |
ad8f46c6 | 891 | |
892 | (define-public r-all | |
893 | (package | |
894 | (name "r-all") | |
895 | (version "1.26.0") | |
896 | (source (origin | |
897 | (method url-fetch) | |
898 | ;; We cannot use bioconductor-uri here because this tarball is | |
899 | ;; located under "data/experiment/" instead of "bioc/". | |
900 | (uri (string-append "https://www.bioconductor.org/packages/" | |
901 | "release/data/experiment/src/contrib/" | |
902 | "ALL_" version ".tar.gz")) | |
903 | (sha256 | |
904 | (base32 | |
905 | "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) | |
906 | (properties `((upstream-name . "ALL"))) | |
907 | (build-system r-build-system) | |
908 | (propagated-inputs | |
909 | `(("r-biobase" ,r-biobase))) | |
910 | (home-page "https://bioconductor.org/packages/ALL") | |
911 | (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") | |
912 | (description | |
913 | "The data consist of microarrays from 128 different individuals with | |
914 | @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates | |
915 | are available. The data have been normalized (using rma) and it is the | |
916 | jointly normalized data that are available here. The data are presented in | |
917 | the form of an @code{exprSet} object.") | |
918 | (license license:artistic2.0))) | |
557a1089 RW |
919 | |
920 | \f | |
921 | ;;; Packages | |
922 | ||
14bba460 RW |
923 | (define-public r-biocgenerics |
924 | (package | |
925 | (name "r-biocgenerics") | |
81a1c45d | 926 | (version "0.30.0") |
14bba460 RW |
927 | (source (origin |
928 | (method url-fetch) | |
929 | (uri (bioconductor-uri "BiocGenerics" version)) | |
930 | (sha256 | |
931 | (base32 | |
81a1c45d | 932 | "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f")))) |
14bba460 RW |
933 | (properties |
934 | `((upstream-name . "BiocGenerics"))) | |
935 | (build-system r-build-system) | |
936 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
937 | (synopsis "S4 generic functions for Bioconductor") | |
938 | (description | |
939 | "This package provides S4 generic functions needed by many Bioconductor | |
940 | packages.") | |
941 | (license license:artistic2.0))) | |
942 | ||
7097c700 RW |
943 | (define-public r-annotate |
944 | (package | |
945 | (name "r-annotate") | |
0c53332a | 946 | (version "1.62.0") |
7097c700 RW |
947 | (source |
948 | (origin | |
949 | (method url-fetch) | |
950 | (uri (bioconductor-uri "annotate" version)) | |
951 | (sha256 | |
952 | (base32 | |
0c53332a | 953 | "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs")))) |
7097c700 RW |
954 | (build-system r-build-system) |
955 | (propagated-inputs | |
956 | `(("r-annotationdbi" ,r-annotationdbi) | |
957 | ("r-biobase" ,r-biobase) | |
958 | ("r-biocgenerics" ,r-biocgenerics) | |
959 | ("r-dbi" ,r-dbi) | |
960 | ("r-rcurl" ,r-rcurl) | |
961 | ("r-xml" ,r-xml) | |
962 | ("r-xtable" ,r-xtable))) | |
963 | (home-page | |
964 | "https://bioconductor.org/packages/annotate") | |
965 | (synopsis "Annotation for microarrays") | |
966 | (description "This package provides R environments for the annotation of | |
967 | microarrays.") | |
968 | (license license:artistic2.0))) | |
969 | ||
fa596599 RW |
970 | (define-public r-hpar |
971 | (package | |
972 | (name "r-hpar") | |
43a23a07 | 973 | (version "1.26.0") |
fa596599 RW |
974 | (source |
975 | (origin | |
976 | (method url-fetch) | |
977 | (uri (bioconductor-uri "hpar" version)) | |
978 | (sha256 | |
979 | (base32 | |
43a23a07 | 980 | "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5")))) |
fa596599 RW |
981 | (build-system r-build-system) |
982 | (home-page "https://bioconductor.org/packages/hpar/") | |
983 | (synopsis "Human Protein Atlas in R") | |
984 | (description "This package provides a simple interface to and data from | |
985 | the Human Protein Atlas project.") | |
986 | (license license:artistic2.0))) | |
183ce988 RJ |
987 | |
988 | (define-public r-regioner | |
989 | (package | |
990 | (name "r-regioner") | |
b8f6b813 | 991 | (version "1.16.2") |
183ce988 RJ |
992 | (source |
993 | (origin | |
994 | (method url-fetch) | |
995 | (uri (bioconductor-uri "regioneR" version)) | |
996 | (sha256 | |
997 | (base32 | |
b8f6b813 | 998 | "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q")))) |
183ce988 RJ |
999 | (properties `((upstream-name . "regioneR"))) |
1000 | (build-system r-build-system) | |
1001 | (propagated-inputs | |
d639d888 | 1002 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 1003 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 1004 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 1005 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 1006 | ("r-iranges" ,r-iranges) |
d639d888 RW |
1007 | ("r-memoise" ,r-memoise) |
1008 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 1009 | ("r-s4vectors" ,r-s4vectors))) |
183ce988 RJ |
1010 | (home-page "https://bioconductor.org/packages/regioneR/") |
1011 | (synopsis "Association analysis of genomic regions") | |
1012 | (description "This package offers a statistical framework based on | |
1013 | customizable permutation tests to assess the association between genomic | |
1014 | region sets and other genomic features.") | |
1015 | (license license:artistic2.0))) | |
a5b56a53 | 1016 | |
bfb93b48 RW |
1017 | (define-public r-geneplotter |
1018 | (package | |
1019 | (name "r-geneplotter") | |
3e1bc88c | 1020 | (version "1.62.0") |
bfb93b48 RW |
1021 | (source |
1022 | (origin | |
1023 | (method url-fetch) | |
1024 | (uri (bioconductor-uri "geneplotter" version)) | |
1025 | (sha256 | |
1026 | (base32 | |
3e1bc88c | 1027 | "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb")))) |
bfb93b48 RW |
1028 | (build-system r-build-system) |
1029 | (propagated-inputs | |
1030 | `(("r-annotate" ,r-annotate) | |
1031 | ("r-annotationdbi" ,r-annotationdbi) | |
1032 | ("r-biobase" ,r-biobase) | |
1033 | ("r-biocgenerics" ,r-biocgenerics) | |
1034 | ("r-lattice" ,r-lattice) | |
1035 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
1036 | (home-page "https://bioconductor.org/packages/geneplotter") | |
1037 | (synopsis "Graphics functions for genomic data") | |
1038 | (description | |
1039 | "This package provides functions for plotting genomic data.") | |
1040 | (license license:artistic2.0))) | |
1041 | ||
4dc2ecc2 RW |
1042 | (define-public r-qvalue |
1043 | (package | |
1044 | (name "r-qvalue") | |
e02162f7 | 1045 | (version "2.16.0") |
4dc2ecc2 RW |
1046 | (source |
1047 | (origin | |
1048 | (method url-fetch) | |
1049 | (uri (bioconductor-uri "qvalue" version)) | |
1050 | (sha256 | |
1051 | (base32 | |
e02162f7 | 1052 | "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5")))) |
4dc2ecc2 RW |
1053 | (build-system r-build-system) |
1054 | (propagated-inputs | |
1055 | `(("r-ggplot2" ,r-ggplot2) | |
1056 | ("r-reshape2" ,r-reshape2))) | |
1057 | (home-page "http://github.com/jdstorey/qvalue") | |
1058 | (synopsis "Q-value estimation for false discovery rate control") | |
1059 | (description | |
1060 | "This package takes a list of p-values resulting from the simultaneous | |
1061 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
1062 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
1063 | of false positives incurred when that particular test is called significant. | |
1064 | The local FDR measures the posterior probability the null hypothesis is true | |
1065 | given the test's p-value. Various plots are automatically generated, allowing | |
1066 | one to make sensible significance cut-offs. The software can be applied to | |
1067 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
1068 | ;; Any version of the LGPL. | |
1069 | (license license:lgpl3+))) | |
1070 | ||
a5b56a53 RJ |
1071 | (define-public r-diffbind |
1072 | (package | |
1073 | (name "r-diffbind") | |
4c221b3b | 1074 | (version "2.12.0") |
a5b56a53 RJ |
1075 | (source |
1076 | (origin | |
1077 | (method url-fetch) | |
1078 | (uri (bioconductor-uri "DiffBind" version)) | |
1079 | (sha256 | |
1080 | (base32 | |
4c221b3b | 1081 | "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich")))) |
a5b56a53 RJ |
1082 | (properties `((upstream-name . "DiffBind"))) |
1083 | (build-system r-build-system) | |
1084 | (inputs | |
1085 | `(("zlib" ,zlib))) | |
1086 | (propagated-inputs | |
1087 | `(("r-amap" ,r-amap) | |
1088 | ("r-biocparallel" ,r-biocparallel) | |
1089 | ("r-deseq2" ,r-deseq2) | |
1090 | ("r-dplyr" ,r-dplyr) | |
1091 | ("r-edger" ,r-edger) | |
1092 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
1093 | ("r-genomicranges" ,r-genomicranges) |
1094 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
1095 | ("r-ggrepel" ,r-ggrepel) |
1096 | ("r-gplots" ,r-gplots) | |
1097 | ("r-iranges" ,r-iranges) | |
1098 | ("r-lattice" ,r-lattice) | |
1099 | ("r-limma" ,r-limma) | |
1100 | ("r-locfit" ,r-locfit) | |
1101 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
1102 | ("r-rcpp" ,r-rcpp) | |
4c221b3b | 1103 | ("r-rhtslib" ,r-rhtslib) |
a5b56a53 RJ |
1104 | ("r-rsamtools" ,r-rsamtools) |
1105 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 1106 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
4c221b3b | 1107 | ("r-systempiper" ,r-systempiper))) |
a5b56a53 RJ |
1108 | (home-page "http://bioconductor.org/packages/DiffBind") |
1109 | (synopsis "Differential binding analysis of ChIP-Seq peak data") | |
1110 | (description | |
1111 | "This package computes differentially bound sites from multiple | |
1112 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
1113 | occupancy (overlap) analysis and plotting functions.") | |
1114 | (license license:artistic2.0))) | |
6d94bf6b RJ |
1115 | |
1116 | (define-public r-ripseeker | |
1117 | (package | |
1118 | (name "r-ripseeker") | |
0968a448 | 1119 | (version "1.24.0") |
6d94bf6b RJ |
1120 | (source |
1121 | (origin | |
1122 | (method url-fetch) | |
1123 | (uri (bioconductor-uri "RIPSeeker" version)) | |
1124 | (sha256 | |
1125 | (base32 | |
0968a448 | 1126 | "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43")))) |
6d94bf6b RJ |
1127 | (properties `((upstream-name . "RIPSeeker"))) |
1128 | (build-system r-build-system) | |
1129 | (propagated-inputs | |
1130 | `(("r-s4vectors" ,r-s4vectors) | |
1131 | ("r-iranges" ,r-iranges) | |
1132 | ("r-genomicranges" ,r-genomicranges) | |
1133 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1134 | ("r-rsamtools" ,r-rsamtools) | |
1135 | ("r-genomicalignments" ,r-genomicalignments) | |
1136 | ("r-rtracklayer" ,r-rtracklayer))) | |
1137 | (home-page "http://bioconductor.org/packages/RIPSeeker") | |
1138 | (synopsis | |
1139 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
1140 | (description | |
1141 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
1142 | using two-state HMM with negative binomial emission probability. While | |
1143 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
1144 | a suite of bioinformatics tools integrated within this self-contained software | |
1145 | package comprehensively addressing issues ranging from post-alignments | |
1146 | processing to visualization and annotation.") | |
1147 | (license license:gpl2))) | |
a6ae9ffd RJ |
1148 | |
1149 | (define-public r-multtest | |
1150 | (package | |
1151 | (name "r-multtest") | |
588b63c2 | 1152 | (version "2.40.0") |
a6ae9ffd RJ |
1153 | (source |
1154 | (origin | |
1155 | (method url-fetch) | |
1156 | (uri (bioconductor-uri "multtest" version)) | |
1157 | (sha256 | |
1158 | (base32 | |
588b63c2 | 1159 | "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv")))) |
a6ae9ffd RJ |
1160 | (build-system r-build-system) |
1161 | (propagated-inputs | |
1162 | `(("r-survival" ,r-survival) | |
1163 | ("r-biocgenerics" ,r-biocgenerics) | |
1164 | ("r-biobase" ,r-biobase) | |
1165 | ("r-mass" ,r-mass))) | |
1166 | (home-page "http://bioconductor.org/packages/multtest") | |
1167 | (synopsis "Resampling-based multiple hypothesis testing") | |
1168 | (description | |
1169 | "This package can do non-parametric bootstrap and permutation | |
1170 | resampling-based multiple testing procedures (including empirical Bayes | |
1171 | methods) for controlling the family-wise error rate (FWER), generalized | |
1172 | family-wise error rate (gFWER), tail probability of the proportion of | |
1173 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
1174 | of bootstrap-based null distribution are implemented (centered, centered | |
1175 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
1176 | available. Tests based on a variety of T- and F-statistics (including | |
1177 | T-statistics based on regression parameters from linear and survival models | |
1178 | as well as those based on correlation parameters) are included. When probing | |
1179 | hypotheses with T-statistics, users may also select a potentially faster null | |
1180 | distribution which is multivariate normal with mean zero and variance | |
1181 | covariance matrix derived from the vector influence function. Results are | |
1182 | reported in terms of adjusted P-values, confidence regions and test statistic | |
1183 | cutoffs. The procedures are directly applicable to identifying differentially | |
1184 | expressed genes in DNA microarray experiments.") | |
1185 | (license license:lgpl3))) | |
793f83ef | 1186 | |
5dfe4912 RW |
1187 | (define-public r-graph |
1188 | (package | |
1189 | (name "r-graph") | |
a61bcb28 | 1190 | (version "1.62.0") |
5dfe4912 RW |
1191 | (source (origin |
1192 | (method url-fetch) | |
1193 | (uri (bioconductor-uri "graph" version)) | |
1194 | (sha256 | |
1195 | (base32 | |
a61bcb28 | 1196 | "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w")))) |
5dfe4912 RW |
1197 | (build-system r-build-system) |
1198 | (propagated-inputs | |
1199 | `(("r-biocgenerics" ,r-biocgenerics))) | |
1200 | (home-page "https://bioconductor.org/packages/graph") | |
1201 | (synopsis "Handle graph data structures in R") | |
1202 | (description | |
1203 | "This package implements some simple graph handling capabilities for R.") | |
1204 | (license license:artistic2.0))) | |
1205 | ||
a207bca2 RW |
1206 | (define-public r-codedepends |
1207 | (package | |
1208 | (name "r-codedepends") | |
1209 | (version "0.6.5") | |
1210 | (source | |
1211 | (origin | |
1212 | (method url-fetch) | |
1213 | (uri (cran-uri "CodeDepends" version)) | |
1214 | (sha256 | |
1215 | (base32 | |
1216 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
1217 | (properties `((upstream-name . "CodeDepends"))) | |
1218 | (build-system r-build-system) | |
1219 | (propagated-inputs | |
1220 | `(("r-codetools" ,r-codetools) | |
1221 | ("r-graph" ,r-graph) | |
1222 | ("r-xml" ,r-xml))) | |
1223 | (home-page "http://cran.r-project.org/web/packages/CodeDepends") | |
1224 | (synopsis "Analysis of R code for reproducible research and code comprehension") | |
1225 | (description | |
1226 | "This package provides tools for analyzing R expressions or blocks of | |
1227 | code and determining the dependencies between them. It focuses on R scripts, | |
1228 | but can be used on the bodies of functions. There are many facilities | |
1229 | including the ability to summarize or get a high-level view of code, | |
1230 | determining dependencies between variables, code improvement suggestions.") | |
1231 | ;; Any version of the GPL | |
1232 | (license (list license:gpl2+ license:gpl3+)))) | |
1233 | ||
793f83ef RJ |
1234 | (define-public r-chippeakanno |
1235 | (package | |
1236 | (name "r-chippeakanno") | |
109b8ad5 | 1237 | (version "3.18.2") |
793f83ef RJ |
1238 | (source |
1239 | (origin | |
1240 | (method url-fetch) | |
1241 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
1242 | (sha256 | |
1243 | (base32 | |
109b8ad5 | 1244 | "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779")))) |
793f83ef RJ |
1245 | (properties `((upstream-name . "ChIPpeakAnno"))) |
1246 | (build-system r-build-system) | |
1247 | (propagated-inputs | |
85c1d20f RW |
1248 | `(("r-annotationdbi" ,r-annotationdbi) |
1249 | ("r-biobase" ,r-biobase) | |
1250 | ("r-biocgenerics" ,r-biocgenerics) | |
57d2fcd9 | 1251 | ("r-biocmanager" ,r-biocmanager) |
793f83ef | 1252 | ("r-biomart" ,r-biomart) |
85c1d20f | 1253 | ("r-biostrings" ,r-biostrings) |
793f83ef | 1254 | ("r-bsgenome" ,r-bsgenome) |
85c1d20f RW |
1255 | ("r-dbi" ,r-dbi) |
1256 | ("r-delayedarray" ,r-delayedarray) | |
1257 | ("r-ensembldb" ,r-ensembldb) | |
1258 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1259 | ("r-genomicalignments" ,r-genomicalignments) | |
793f83ef | 1260 | ("r-genomicfeatures" ,r-genomicfeatures) |
f794e85d | 1261 | ("r-genomicranges" ,r-genomicranges) |
85c1d20f RW |
1262 | ("r-go-db" ,r-go-db) |
1263 | ("r-graph" ,r-graph) | |
1264 | ("r-idr" ,r-idr) | |
f794e85d | 1265 | ("r-iranges" ,r-iranges) |
793f83ef | 1266 | ("r-limma" ,r-limma) |
85c1d20f | 1267 | ("r-matrixstats" ,r-matrixstats) |
793f83ef RJ |
1268 | ("r-multtest" ,r-multtest) |
1269 | ("r-rbgl" ,r-rbgl) | |
793f83ef | 1270 | ("r-regioner" ,r-regioner) |
85c1d20f RW |
1271 | ("r-rsamtools" ,r-rsamtools) |
1272 | ("r-rtracklayer" ,r-rtracklayer) | |
f794e85d | 1273 | ("r-s4vectors" ,r-s4vectors) |
793f83ef | 1274 | ("r-seqinr" ,r-seqinr) |
793f83ef | 1275 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
793f83ef RJ |
1276 | ("r-venndiagram" ,r-venndiagram))) |
1277 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") | |
1278 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") | |
1279 | (description | |
1280 | "The package includes functions to retrieve the sequences around the peak, | |
1281 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
1282 | custom features such as most conserved elements and other transcription factor | |
1283 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
1284 | for finding the peaks with bi-directional promoters with summary statistics | |
1285 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
1286 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
1287 | enrichedGO (addGeneIDs).") | |
1288 | (license license:gpl2+))) | |
164502d8 RJ |
1289 | |
1290 | (define-public r-marray | |
1291 | (package | |
1292 | (name "r-marray") | |
bcb95b7a | 1293 | (version "1.62.0") |
164502d8 RJ |
1294 | (source (origin |
1295 | (method url-fetch) | |
1296 | (uri (bioconductor-uri "marray" version)) | |
1297 | (sha256 | |
bcb95b7a | 1298 | (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz")))) |
164502d8 RJ |
1299 | (build-system r-build-system) |
1300 | (propagated-inputs | |
67487088 | 1301 | `(("r-limma" ,r-limma))) |
164502d8 RJ |
1302 | (home-page "http://bioconductor.org/packages/marray") |
1303 | (synopsis "Exploratory analysis for two-color spotted microarray data") | |
1304 | (description "This package contains class definitions for two-color spotted | |
ab8979fc | 1305 | microarray data. It also includes functions for data input, diagnostic plots, |
164502d8 RJ |
1306 | normalization and quality checking.") |
1307 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
1308 | |
1309 | (define-public r-cghbase | |
1310 | (package | |
1311 | (name "r-cghbase") | |
8efb842f | 1312 | (version "1.44.0") |
0416a0d4 RJ |
1313 | (source (origin |
1314 | (method url-fetch) | |
1315 | (uri (bioconductor-uri "CGHbase" version)) | |
1316 | (sha256 | |
8efb842f | 1317 | (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm")))) |
0416a0d4 RJ |
1318 | (properties `((upstream-name . "CGHbase"))) |
1319 | (build-system r-build-system) | |
1320 | (propagated-inputs | |
1321 | `(("r-biobase" ,r-biobase) | |
1322 | ("r-marray" ,r-marray))) | |
1323 | (home-page "http://bioconductor.org/packages/CGHbase") | |
1324 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
1325 | (description "This package contains functions and classes that are needed by | |
1326 | the @code{arrayCGH} packages.") | |
1327 | (license license:gpl2+))) | |
67ee83d6 RJ |
1328 | |
1329 | (define-public r-cghcall | |
1330 | (package | |
1331 | (name "r-cghcall") | |
23177309 | 1332 | (version "2.46.0") |
67ee83d6 RJ |
1333 | (source (origin |
1334 | (method url-fetch) | |
1335 | (uri (bioconductor-uri "CGHcall" version)) | |
1336 | (sha256 | |
23177309 | 1337 | (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93")))) |
67ee83d6 RJ |
1338 | (properties `((upstream-name . "CGHcall"))) |
1339 | (build-system r-build-system) | |
1340 | (propagated-inputs | |
1341 | `(("r-biobase" ,r-biobase) | |
1342 | ("r-cghbase" ,r-cghbase) | |
1343 | ("r-impute" ,r-impute) | |
1344 | ("r-dnacopy" ,r-dnacopy) | |
1345 | ("r-snowfall" ,r-snowfall))) | |
1346 | (home-page "http://bioconductor.org/packages/CGHcall") | |
1347 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
1348 | (description "This package contains functions and classes that are needed by | |
1349 | @code{arrayCGH} packages.") | |
1350 | (license license:gpl2+))) | |
0ef8cc9c RJ |
1351 | |
1352 | (define-public r-qdnaseq | |
1353 | (package | |
1354 | (name "r-qdnaseq") | |
4f4bed7d | 1355 | (version "1.20.0") |
0ef8cc9c RJ |
1356 | (source (origin |
1357 | (method url-fetch) | |
1358 | (uri (bioconductor-uri "QDNAseq" version)) | |
1359 | (sha256 | |
4f4bed7d | 1360 | (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz")))) |
0ef8cc9c RJ |
1361 | (properties `((upstream-name . "QDNAseq"))) |
1362 | (build-system r-build-system) | |
1363 | (propagated-inputs | |
1364 | `(("r-biobase" ,r-biobase) | |
81b0181b | 1365 | ("r-biocparallel" ,r-biocparallel) |
0ef8cc9c RJ |
1366 | ("r-cghbase" ,r-cghbase) |
1367 | ("r-cghcall" ,r-cghcall) | |
1368 | ("r-dnacopy" ,r-dnacopy) | |
1369 | ("r-genomicranges" ,r-genomicranges) | |
1370 | ("r-iranges" ,r-iranges) | |
1371 | ("r-matrixstats" ,r-matrixstats) | |
1372 | ("r-r-utils" ,r-r-utils) | |
1373 | ("r-rsamtools" ,r-rsamtools))) | |
1374 | (home-page "http://bioconductor.org/packages/QDNAseq") | |
1375 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") | |
1376 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
1377 | number of sequence reads in each counted, adjusted with a simultaneous | |
1378 | two-dimensional loess correction for sequence mappability and GC content, and | |
1379 | filtered to remove spurious regions in the genome. Downstream steps of | |
1380 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
1381 | respectively.") | |
1382 | (license license:gpl2+))) | |
bb15b581 RW |
1383 | |
1384 | (define-public r-bayseq | |
1385 | (package | |
1386 | (name "r-bayseq") | |
c38de815 | 1387 | (version "2.18.0") |
bb15b581 RW |
1388 | (source |
1389 | (origin | |
1390 | (method url-fetch) | |
1391 | (uri (bioconductor-uri "baySeq" version)) | |
1392 | (sha256 | |
1393 | (base32 | |
c38de815 | 1394 | "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w")))) |
bb15b581 RW |
1395 | (properties `((upstream-name . "baySeq"))) |
1396 | (build-system r-build-system) | |
1397 | (propagated-inputs | |
1398 | `(("r-abind" ,r-abind) | |
1399 | ("r-edger" ,r-edger) | |
1400 | ("r-genomicranges" ,r-genomicranges))) | |
1401 | (home-page "https://bioconductor.org/packages/baySeq/") | |
1402 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
1403 | (description | |
1404 | "This package identifies differential expression in high-throughput count | |
1405 | data, such as that derived from next-generation sequencing machines, | |
1406 | calculating estimated posterior likelihoods of differential expression (or | |
1407 | more complex hypotheses) via empirical Bayesian methods.") | |
1408 | (license license:gpl3))) | |
609f4ad1 RW |
1409 | |
1410 | (define-public r-chipcomp | |
1411 | (package | |
1412 | (name "r-chipcomp") | |
1ddd4af5 | 1413 | (version "1.14.0") |
609f4ad1 RW |
1414 | (source |
1415 | (origin | |
1416 | (method url-fetch) | |
1417 | (uri (bioconductor-uri "ChIPComp" version)) | |
1418 | (sha256 | |
1419 | (base32 | |
1ddd4af5 | 1420 | "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y")))) |
609f4ad1 RW |
1421 | (properties `((upstream-name . "ChIPComp"))) |
1422 | (build-system r-build-system) | |
1423 | (propagated-inputs | |
1424 | `(("r-biocgenerics" ,r-biocgenerics) | |
1425 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
1426 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
1427 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1428 | ("r-genomicranges" ,r-genomicranges) | |
1429 | ("r-iranges" ,r-iranges) | |
1430 | ("r-limma" ,r-limma) | |
1431 | ("r-rsamtools" ,r-rsamtools) | |
1432 | ("r-rtracklayer" ,r-rtracklayer) | |
1433 | ("r-s4vectors" ,r-s4vectors))) | |
1434 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
1435 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
1436 | (description | |
1437 | "ChIPComp implements a statistical method for quantitative comparison of | |
1438 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
1439 | sites across multiple conditions considering matching control in ChIP-seq | |
1440 | datasets.") | |
1441 | ;; Any version of the GPL. | |
1442 | (license license:gpl3+))) | |
0490f9de RW |
1443 | |
1444 | (define-public r-riboprofiling | |
1445 | (package | |
1446 | (name "r-riboprofiling") | |
7d5acf7a | 1447 | (version "1.14.0") |
0490f9de RW |
1448 | (source |
1449 | (origin | |
1450 | (method url-fetch) | |
1451 | (uri (bioconductor-uri "RiboProfiling" version)) | |
1452 | (sha256 | |
1453 | (base32 | |
7d5acf7a | 1454 | "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9")))) |
0490f9de RW |
1455 | (properties `((upstream-name . "RiboProfiling"))) |
1456 | (build-system r-build-system) | |
1457 | (propagated-inputs | |
1458 | `(("r-biocgenerics" ,r-biocgenerics) | |
1459 | ("r-biostrings" ,r-biostrings) | |
1460 | ("r-data-table" ,r-data-table) | |
1461 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1462 | ("r-genomicalignments" ,r-genomicalignments) | |
1463 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1464 | ("r-genomicranges" ,r-genomicranges) | |
1465 | ("r-ggbio" ,r-ggbio) | |
1466 | ("r-ggplot2" ,r-ggplot2) | |
1467 | ("r-iranges" ,r-iranges) | |
1468 | ("r-plyr" ,r-plyr) | |
1469 | ("r-reshape2" ,r-reshape2) | |
1470 | ("r-rsamtools" ,r-rsamtools) | |
1471 | ("r-rtracklayer" ,r-rtracklayer) | |
1472 | ("r-s4vectors" ,r-s4vectors) | |
1473 | ("r-sqldf" ,r-sqldf))) | |
1474 | (home-page "https://bioconductor.org/packages/RiboProfiling/") | |
1475 | (synopsis "Ribosome profiling data analysis") | |
1476 | (description "Starting with a BAM file, this package provides the | |
1477 | necessary functions for quality assessment, read start position recalibration, | |
1478 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
1479 | of count data: pairs, log fold-change, codon frequency and coverage | |
1480 | assessment, principal component analysis on codon coverage.") | |
1481 | (license license:gpl3))) | |
6ffdfe6a RW |
1482 | |
1483 | (define-public r-riboseqr | |
1484 | (package | |
1485 | (name "r-riboseqr") | |
eff6b2eb | 1486 | (version "1.18.0") |
6ffdfe6a RW |
1487 | (source |
1488 | (origin | |
1489 | (method url-fetch) | |
1490 | (uri (bioconductor-uri "riboSeqR" version)) | |
1491 | (sha256 | |
1492 | (base32 | |
eff6b2eb | 1493 | "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga")))) |
6ffdfe6a RW |
1494 | (properties `((upstream-name . "riboSeqR"))) |
1495 | (build-system r-build-system) | |
1496 | (propagated-inputs | |
1497 | `(("r-abind" ,r-abind) | |
1498 | ("r-bayseq" ,r-bayseq) | |
1499 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1500 | ("r-genomicranges" ,r-genomicranges) | |
1501 | ("r-iranges" ,r-iranges) | |
1502 | ("r-rsamtools" ,r-rsamtools) | |
1503 | ("r-seqlogo" ,r-seqlogo))) | |
1504 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
1505 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
1506 | (description | |
1507 | "This package provides plotting functions, frameshift detection and | |
1508 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
1509 | (license license:gpl3))) | |
a32279ff RW |
1510 | |
1511 | (define-public r-interactionset | |
1512 | (package | |
1513 | (name "r-interactionset") | |
176a264c | 1514 | (version "1.12.0") |
a32279ff RW |
1515 | (source |
1516 | (origin | |
1517 | (method url-fetch) | |
1518 | (uri (bioconductor-uri "InteractionSet" version)) | |
1519 | (sha256 | |
1520 | (base32 | |
176a264c | 1521 | "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6")))) |
a32279ff RW |
1522 | (properties |
1523 | `((upstream-name . "InteractionSet"))) | |
1524 | (build-system r-build-system) | |
1525 | (propagated-inputs | |
1526 | `(("r-biocgenerics" ,r-biocgenerics) | |
1527 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1528 | ("r-genomicranges" ,r-genomicranges) | |
1529 | ("r-iranges" ,r-iranges) | |
1530 | ("r-matrix" ,r-matrix) | |
1531 | ("r-rcpp" ,r-rcpp) | |
1532 | ("r-s4vectors" ,r-s4vectors) | |
1533 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1534 | (home-page "https://bioconductor.org/packages/InteractionSet") | |
1535 | (synopsis "Base classes for storing genomic interaction data") | |
1536 | (description | |
02fe0976 | 1537 | "This package provides the @code{GInteractions}, |
a32279ff RW |
1538 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
1539 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
1540 | experiments.") | |
1541 | (license license:gpl3))) | |
cf9a29b2 RW |
1542 | |
1543 | (define-public r-genomicinteractions | |
1544 | (package | |
1545 | (name "r-genomicinteractions") | |
fcbd8960 | 1546 | (version "1.18.1") |
cf9a29b2 RW |
1547 | (source |
1548 | (origin | |
1549 | (method url-fetch) | |
1550 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
1551 | (sha256 | |
1552 | (base32 | |
fcbd8960 | 1553 | "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p")))) |
cf9a29b2 RW |
1554 | (properties |
1555 | `((upstream-name . "GenomicInteractions"))) | |
1556 | (build-system r-build-system) | |
1557 | (propagated-inputs | |
1558 | `(("r-biobase" ,r-biobase) | |
1559 | ("r-biocgenerics" ,r-biocgenerics) | |
1560 | ("r-data-table" ,r-data-table) | |
1561 | ("r-dplyr" ,r-dplyr) | |
1562 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1563 | ("r-genomicranges" ,r-genomicranges) | |
1564 | ("r-ggplot2" ,r-ggplot2) | |
1565 | ("r-gridextra" ,r-gridextra) | |
1566 | ("r-gviz" ,r-gviz) | |
1567 | ("r-igraph" ,r-igraph) | |
1568 | ("r-interactionset" ,r-interactionset) | |
1569 | ("r-iranges" ,r-iranges) | |
1570 | ("r-rsamtools" ,r-rsamtools) | |
1571 | ("r-rtracklayer" ,r-rtracklayer) | |
1572 | ("r-s4vectors" ,r-s4vectors) | |
1573 | ("r-stringr" ,r-stringr))) | |
1574 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") | |
1575 | (synopsis "R package for handling genomic interaction data") | |
1576 | (description | |
1577 | "This R package provides tools for handling genomic interaction data, | |
1578 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
1579 | information and producing various plots and statistics.") | |
1580 | (license license:gpl3))) | |
27c51606 RW |
1581 | |
1582 | (define-public r-ctc | |
1583 | (package | |
1584 | (name "r-ctc") | |
7a5d729a | 1585 | (version "1.58.0") |
27c51606 RW |
1586 | (source |
1587 | (origin | |
1588 | (method url-fetch) | |
1589 | (uri (bioconductor-uri "ctc" version)) | |
1590 | (sha256 | |
1591 | (base32 | |
7a5d729a | 1592 | "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am")))) |
27c51606 RW |
1593 | (build-system r-build-system) |
1594 | (propagated-inputs `(("r-amap" ,r-amap))) | |
1595 | (home-page "https://bioconductor.org/packages/ctc/") | |
1596 | (synopsis "Cluster and tree conversion") | |
1597 | (description | |
1598 | "This package provides tools for exporting and importing classification | |
1599 | trees and clusters to other programs.") | |
1600 | (license license:gpl2))) | |
5da0e142 RW |
1601 | |
1602 | (define-public r-goseq | |
1603 | (package | |
1604 | (name "r-goseq") | |
40f0ee43 | 1605 | (version "1.36.0") |
5da0e142 RW |
1606 | (source |
1607 | (origin | |
1608 | (method url-fetch) | |
1609 | (uri (bioconductor-uri "goseq" version)) | |
1610 | (sha256 | |
1611 | (base32 | |
40f0ee43 | 1612 | "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw")))) |
5da0e142 RW |
1613 | (build-system r-build-system) |
1614 | (propagated-inputs | |
1615 | `(("r-annotationdbi" ,r-annotationdbi) | |
1616 | ("r-biasedurn" ,r-biasedurn) | |
1617 | ("r-biocgenerics" ,r-biocgenerics) | |
1618 | ("r-genelendatabase" ,r-genelendatabase) | |
1619 | ("r-go-db" ,r-go-db) | |
1620 | ("r-mgcv" ,r-mgcv))) | |
1621 | (home-page "https://bioconductor.org/packages/goseq/") | |
1622 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
1623 | (description | |
1624 | "This package provides tools to detect Gene Ontology and/or other user | |
1625 | defined categories which are over/under represented in RNA-seq data.") | |
1626 | (license license:lgpl2.0+))) | |
f4235c0e RW |
1627 | |
1628 | (define-public r-glimma | |
1629 | (package | |
1630 | (name "r-glimma") | |
07252952 | 1631 | (version "1.12.0") |
f4235c0e RW |
1632 | (source |
1633 | (origin | |
1634 | (method url-fetch) | |
1635 | (uri (bioconductor-uri "Glimma" version)) | |
1636 | (sha256 | |
1637 | (base32 | |
07252952 | 1638 | "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x")))) |
f4235c0e RW |
1639 | (properties `((upstream-name . "Glimma"))) |
1640 | (build-system r-build-system) | |
1641 | (propagated-inputs | |
1642 | `(("r-edger" ,r-edger) | |
1643 | ("r-jsonlite" ,r-jsonlite) | |
1644 | ("r-s4vectors" ,r-s4vectors))) | |
1645 | (home-page "https://github.com/Shians/Glimma") | |
1646 | (synopsis "Interactive HTML graphics") | |
1647 | (description | |
1648 | "This package generates interactive visualisations for analysis of | |
1649 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
1650 | HTML page. The interactions are built on top of the popular static | |
1651 | representations of analysis results in order to provide additional | |
1652 | information.") | |
1653 | (license license:lgpl3))) | |
aa388dc7 RW |
1654 | |
1655 | (define-public r-rots | |
1656 | (package | |
1657 | (name "r-rots") | |
5bf7eb49 | 1658 | (version "1.12.0") |
aa388dc7 RW |
1659 | (source |
1660 | (origin | |
1661 | (method url-fetch) | |
1662 | (uri (bioconductor-uri "ROTS" version)) | |
1663 | (sha256 | |
1664 | (base32 | |
5bf7eb49 | 1665 | "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77")))) |
aa388dc7 RW |
1666 | (properties `((upstream-name . "ROTS"))) |
1667 | (build-system r-build-system) | |
1668 | (propagated-inputs | |
1669 | `(("r-biobase" ,r-biobase) | |
1670 | ("r-rcpp" ,r-rcpp))) | |
1671 | (home-page "https://bioconductor.org/packages/ROTS/") | |
1672 | (synopsis "Reproducibility-Optimized Test Statistic") | |
1673 | (description | |
1674 | "This package provides tools for calculating the | |
1675 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
1676 | in omics data.") | |
1677 | (license license:gpl2+))) | |
b64ce4b7 | 1678 | |
cad6fb2d RW |
1679 | (define-public r-plgem |
1680 | (package | |
1681 | (name "r-plgem") | |
5dce7153 | 1682 | (version "1.56.0") |
cad6fb2d RW |
1683 | (source |
1684 | (origin | |
1685 | (method url-fetch) | |
1686 | (uri (bioconductor-uri "plgem" version)) | |
1687 | (sha256 | |
1688 | (base32 | |
5dce7153 | 1689 | "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp")))) |
cad6fb2d RW |
1690 | (build-system r-build-system) |
1691 | (propagated-inputs | |
1692 | `(("r-biobase" ,r-biobase) | |
1693 | ("r-mass" ,r-mass))) | |
1694 | (home-page "http://www.genopolis.it") | |
1695 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
1696 | (description | |
1697 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
1698 | model the variance-versus-mean dependence that exists in a variety of | |
1699 | genome-wide datasets, including microarray and proteomics data. The use of | |
1700 | PLGEM has been shown to improve the detection of differentially expressed | |
1701 | genes or proteins in these datasets.") | |
1702 | (license license:gpl2))) | |
1703 | ||
b64ce4b7 RW |
1704 | (define-public r-inspect |
1705 | (package | |
1706 | (name "r-inspect") | |
3649d046 | 1707 | (version "1.14.0") |
b64ce4b7 RW |
1708 | (source |
1709 | (origin | |
1710 | (method url-fetch) | |
1711 | (uri (bioconductor-uri "INSPEcT" version)) | |
1712 | (sha256 | |
1713 | (base32 | |
3649d046 | 1714 | "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r")))) |
b64ce4b7 RW |
1715 | (properties `((upstream-name . "INSPEcT"))) |
1716 | (build-system r-build-system) | |
1717 | (propagated-inputs | |
1718 | `(("r-biobase" ,r-biobase) | |
1719 | ("r-biocgenerics" ,r-biocgenerics) | |
1720 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 1721 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 RW |
1722 | ("r-desolve" ,r-desolve) |
1723 | ("r-genomicalignments" ,r-genomicalignments) | |
1724 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1725 | ("r-genomicranges" ,r-genomicranges) | |
1726 | ("r-iranges" ,r-iranges) | |
c86fc969 | 1727 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
1728 | ("r-preprocesscore" ,r-preprocesscore) |
1729 | ("r-proc" ,r-proc) | |
1730 | ("r-rootsolve" ,r-rootsolve) | |
1731 | ("r-rsamtools" ,r-rsamtools) | |
c86fc969 RW |
1732 | ("r-s4vectors" ,r-s4vectors) |
1733 | ("r-shiny" ,r-shiny) | |
1734 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1735 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
1736 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
b64ce4b7 RW |
1737 | (home-page "https://bioconductor.org/packages/INSPEcT") |
1738 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
1739 | (description | |
1740 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
1741 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
1742 | order to evaluate synthesis, processing and degradation rates and assess via | |
1743 | modeling the rates that determines changes in mature mRNA levels.") | |
1744 | (license license:gpl2))) | |
f6e99763 RW |
1745 | |
1746 | (define-public r-dnabarcodes | |
1747 | (package | |
1748 | (name "r-dnabarcodes") | |
774e499c | 1749 | (version "1.14.0") |
f6e99763 RW |
1750 | (source |
1751 | (origin | |
1752 | (method url-fetch) | |
1753 | (uri (bioconductor-uri "DNABarcodes" version)) | |
1754 | (sha256 | |
1755 | (base32 | |
774e499c | 1756 | "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0")))) |
f6e99763 RW |
1757 | (properties `((upstream-name . "DNABarcodes"))) |
1758 | (build-system r-build-system) | |
1759 | (propagated-inputs | |
1760 | `(("r-bh" ,r-bh) | |
1761 | ("r-matrix" ,r-matrix) | |
1762 | ("r-rcpp" ,r-rcpp))) | |
1763 | (home-page "https://bioconductor.org/packages/DNABarcodes") | |
1764 | (synopsis "Create and analyze DNA barcodes") | |
1765 | (description | |
1766 | "This package offers tools to create DNA barcode sets capable of | |
1767 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
1768 | can be analyzed regarding their minimal, maximal and average distances between | |
1769 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
1770 | demultiplexed, i.e. assigned to their original reference barcode.") | |
1771 | (license license:gpl2))) | |
09aa3d06 RW |
1772 | |
1773 | (define-public r-ruvseq | |
1774 | (package | |
1775 | (name "r-ruvseq") | |
d8771f5f | 1776 | (version "1.18.0") |
09aa3d06 RW |
1777 | (source |
1778 | (origin | |
1779 | (method url-fetch) | |
1780 | (uri (bioconductor-uri "RUVSeq" version)) | |
1781 | (sha256 | |
1782 | (base32 | |
d8771f5f | 1783 | "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33")))) |
09aa3d06 RW |
1784 | (properties `((upstream-name . "RUVSeq"))) |
1785 | (build-system r-build-system) | |
1786 | (propagated-inputs | |
1787 | `(("r-biobase" ,r-biobase) | |
1788 | ("r-edaseq" ,r-edaseq) | |
1789 | ("r-edger" ,r-edger) | |
1790 | ("r-mass" ,r-mass))) | |
1791 | (home-page "https://github.com/drisso/RUVSeq") | |
1792 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
1793 | (description | |
1794 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
1795 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
1796 | samples.") | |
1797 | (license license:artistic2.0))) | |
286157dc RW |
1798 | |
1799 | (define-public r-biocneighbors | |
1800 | (package | |
1801 | (name "r-biocneighbors") | |
6fc161fc | 1802 | (version "1.2.0") |
286157dc RW |
1803 | (source |
1804 | (origin | |
1805 | (method url-fetch) | |
1806 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
1807 | (sha256 | |
1808 | (base32 | |
6fc161fc | 1809 | "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg")))) |
286157dc RW |
1810 | (properties `((upstream-name . "BiocNeighbors"))) |
1811 | (build-system r-build-system) | |
1812 | (propagated-inputs | |
6fc161fc RW |
1813 | `(("r-biocgenerics" ,r-biocgenerics) |
1814 | ("r-biocparallel" ,r-biocparallel) | |
286157dc RW |
1815 | ("r-rcpp" ,r-rcpp) |
1816 | ("r-rcppannoy" ,r-rcppannoy) | |
6fc161fc | 1817 | ("r-rcpphnsw" ,r-rcpphnsw) |
286157dc RW |
1818 | ("r-s4vectors" ,r-s4vectors))) |
1819 | (home-page "https://bioconductor.org/packages/BiocNeighbors") | |
1820 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
1821 | (description | |
1822 | "This package implements exact and approximate methods for nearest | |
1823 | neighbor detection, in a framework that allows them to be easily switched | |
1824 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
1825 | using pre-clustering with the k-means algorithm. Functions are also provided | |
1826 | to search for all neighbors within a given distance. Parallelization is | |
1827 | achieved for all methods using the BiocParallel framework.") | |
1828 | (license license:gpl3))) | |
8a587c89 | 1829 | |
99391290 RW |
1830 | (define-public r-biocsingular |
1831 | (package | |
1832 | (name "r-biocsingular") | |
1833 | (version "1.0.0") | |
1834 | (source | |
1835 | (origin | |
1836 | (method url-fetch) | |
1837 | (uri (bioconductor-uri "BiocSingular" version)) | |
1838 | (sha256 | |
1839 | (base32 | |
1840 | "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5")))) | |
1841 | (properties `((upstream-name . "BiocSingular"))) | |
1842 | (build-system r-build-system) | |
1843 | (propagated-inputs | |
1844 | `(("r-beachmat" ,r-beachmat) | |
1845 | ("r-biocgenerics" ,r-biocgenerics) | |
1846 | ("r-biocparallel" ,r-biocparallel) | |
1847 | ("r-delayedarray" ,r-delayedarray) | |
1848 | ("r-irlba" ,r-irlba) | |
1849 | ("r-matrix" ,r-matrix) | |
1850 | ("r-rcpp" ,r-rcpp) | |
1851 | ("r-rsvd" ,r-rsvd) | |
1852 | ("r-s4vectors" ,r-s4vectors))) | |
1853 | (home-page "https://github.com/LTLA/BiocSingular") | |
1854 | (synopsis "Singular value decomposition for Bioconductor packages") | |
1855 | (description | |
1856 | "This package implements exact and approximate methods for singular value | |
1857 | decomposition and principal components analysis, in a framework that allows | |
1858 | them to be easily switched within Bioconductor packages or workflows. Where | |
1859 | possible, parallelization is achieved using the BiocParallel framework.") | |
1860 | (license license:gpl3))) | |
1861 | ||
a961ae46 RW |
1862 | (define-public r-destiny |
1863 | (package | |
1864 | (name "r-destiny") | |
0aa72f2d | 1865 | (version "2.14.0") |
a961ae46 RW |
1866 | (source |
1867 | (origin | |
1868 | (method url-fetch) | |
1869 | (uri (bioconductor-uri "destiny" version)) | |
1870 | (sha256 | |
1871 | (base32 | |
0aa72f2d | 1872 | "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3")))) |
a961ae46 RW |
1873 | (build-system r-build-system) |
1874 | (propagated-inputs | |
1875 | `(("r-biobase" ,r-biobase) | |
1876 | ("r-biocgenerics" ,r-biocgenerics) | |
0aa72f2d | 1877 | ("r-ggplot2" ,r-ggplot2) |
a961ae46 | 1878 | ("r-ggthemes" ,r-ggthemes) |
a961ae46 RW |
1879 | ("r-igraph" ,r-igraph) |
1880 | ("r-matrix" ,r-matrix) | |
1881 | ("r-proxy" ,r-proxy) | |
1882 | ("r-rcpp" ,r-rcpp) | |
1883 | ("r-rcppeigen" ,r-rcppeigen) | |
1884 | ("r-scales" ,r-scales) | |
1885 | ("r-scatterplot3d" ,r-scatterplot3d) | |
1886 | ("r-smoother" ,r-smoother) | |
1887 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1888 | ("r-vim" ,r-vim))) | |
1889 | (home-page "https://bioconductor.org/packages/destiny/") | |
1890 | (synopsis "Create and plot diffusion maps") | |
1891 | (description "This package provides tools to create and plot diffusion | |
1892 | maps.") | |
1893 | ;; Any version of the GPL | |
1894 | (license license:gpl3+))) | |
1895 | ||
8a587c89 RW |
1896 | (define-public r-savr |
1897 | (package | |
1898 | (name "r-savr") | |
8d3d0c3a | 1899 | (version "1.22.0") |
8a587c89 RW |
1900 | (source |
1901 | (origin | |
1902 | (method url-fetch) | |
1903 | (uri (bioconductor-uri "savR" version)) | |
1904 | (sha256 | |
1905 | (base32 | |
8d3d0c3a | 1906 | "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h")))) |
8a587c89 RW |
1907 | (properties `((upstream-name . "savR"))) |
1908 | (build-system r-build-system) | |
1909 | (propagated-inputs | |
1910 | `(("r-ggplot2" ,r-ggplot2) | |
1911 | ("r-gridextra" ,r-gridextra) | |
1912 | ("r-reshape2" ,r-reshape2) | |
1913 | ("r-scales" ,r-scales) | |
1914 | ("r-xml" ,r-xml))) | |
1915 | (home-page "https://github.com/bcalder/savR") | |
1916 | (synopsis "Parse and analyze Illumina SAV files") | |
1917 | (description | |
1918 | "This package provides tools to parse Illumina Sequence Analysis | |
1919 | Viewer (SAV) files, access data, and generate QC plots.") | |
1920 | (license license:agpl3+))) | |
41ffc214 RW |
1921 | |
1922 | (define-public r-chipexoqual | |
1923 | (package | |
1924 | (name "r-chipexoqual") | |
58a43fc2 | 1925 | (version "1.8.0") |
41ffc214 RW |
1926 | (source |
1927 | (origin | |
1928 | (method url-fetch) | |
1929 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
1930 | (sha256 | |
1931 | (base32 | |
58a43fc2 | 1932 | "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj")))) |
41ffc214 RW |
1933 | (properties `((upstream-name . "ChIPexoQual"))) |
1934 | (build-system r-build-system) | |
1935 | (propagated-inputs | |
1936 | `(("r-biocparallel" ,r-biocparallel) | |
1937 | ("r-biovizbase" ,r-biovizbase) | |
1938 | ("r-broom" ,r-broom) | |
1939 | ("r-data-table" ,r-data-table) | |
1940 | ("r-dplyr" ,r-dplyr) | |
1941 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1942 | ("r-genomicalignments" ,r-genomicalignments) | |
1943 | ("r-genomicranges" ,r-genomicranges) | |
1944 | ("r-ggplot2" ,r-ggplot2) | |
1945 | ("r-hexbin" ,r-hexbin) | |
1946 | ("r-iranges" ,r-iranges) | |
1947 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
1948 | ("r-rmarkdown" ,r-rmarkdown) | |
1949 | ("r-rsamtools" ,r-rsamtools) | |
1950 | ("r-s4vectors" ,r-s4vectors) | |
1951 | ("r-scales" ,r-scales) | |
1952 | ("r-viridis" ,r-viridis))) | |
1953 | (home-page "https://github.com/keleslab/ChIPexoQual") | |
1954 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
1955 | (description | |
1956 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
1957 | sequencing data.") | |
1958 | (license license:gpl2+))) | |
c18dccff | 1959 | |
3d13b448 RW |
1960 | (define-public r-copynumber |
1961 | (package | |
1962 | (name "r-copynumber") | |
d9419185 | 1963 | (version "1.24.0") |
3d13b448 RW |
1964 | (source (origin |
1965 | (method url-fetch) | |
1966 | (uri (bioconductor-uri "copynumber" version)) | |
1967 | (sha256 | |
1968 | (base32 | |
d9419185 | 1969 | "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp")))) |
3d13b448 RW |
1970 | (build-system r-build-system) |
1971 | (propagated-inputs | |
1972 | `(("r-s4vectors" ,r-s4vectors) | |
1973 | ("r-iranges" ,r-iranges) | |
1974 | ("r-genomicranges" ,r-genomicranges) | |
1975 | ("r-biocgenerics" ,r-biocgenerics))) | |
1976 | (home-page "https://bioconductor.org/packages/copynumber") | |
1977 | (synopsis "Segmentation of single- and multi-track copy number data") | |
1978 | (description | |
1979 | "This package segments single- and multi-track copy number data by a | |
1980 | penalized least squares regression method.") | |
1981 | (license license:artistic2.0))) | |
1982 | ||
c18dccff RW |
1983 | (define-public r-dnacopy |
1984 | (package | |
1985 | (name "r-dnacopy") | |
d5f3c0d0 | 1986 | (version "1.58.0") |
c18dccff RW |
1987 | (source |
1988 | (origin | |
1989 | (method url-fetch) | |
1990 | (uri (bioconductor-uri "DNAcopy" version)) | |
1991 | (sha256 | |
1992 | (base32 | |
d5f3c0d0 | 1993 | "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa")))) |
c18dccff RW |
1994 | (properties `((upstream-name . "DNAcopy"))) |
1995 | (build-system r-build-system) | |
1996 | (native-inputs `(("gfortran" ,gfortran))) | |
1997 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
1998 | (synopsis "DNA copy number data analysis") | |
1999 | (description | |
2000 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
2001 | algorithm to segment DNA copy number data and identify genomic regions with | |
2002 | abnormal copy number.") | |
2003 | (license license:gpl2+))) | |
3a0babac RW |
2004 | |
2005 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
2006 | ;; Bioconductor package. | |
2007 | (define-public r-htscluster | |
2008 | (package | |
2009 | (name "r-htscluster") | |
2010 | (version "2.0.8") | |
2011 | (source | |
2012 | (origin | |
2013 | (method url-fetch) | |
2014 | (uri (cran-uri "HTSCluster" version)) | |
2015 | (sha256 | |
2016 | (base32 | |
2017 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
2018 | (properties `((upstream-name . "HTSCluster"))) | |
2019 | (build-system r-build-system) | |
2020 | (propagated-inputs | |
2021 | `(("r-capushe" ,r-capushe) | |
2022 | ("r-edger" ,r-edger) | |
2023 | ("r-plotrix" ,r-plotrix))) | |
2024 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
2025 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
2026 | (description | |
2027 | "This package provides a Poisson mixture model is implemented to cluster | |
2028 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
2029 | estimation is performed using either the EM or CEM algorithm, and the slope | |
2030 | heuristics are used for model selection (i.e., to choose the number of | |
2031 | clusters).") | |
2032 | (license license:gpl3+))) | |
173c9960 RW |
2033 | |
2034 | (define-public r-deds | |
2035 | (package | |
2036 | (name "r-deds") | |
301c4ff1 | 2037 | (version "1.58.0") |
173c9960 RW |
2038 | (source |
2039 | (origin | |
2040 | (method url-fetch) | |
2041 | (uri (bioconductor-uri "DEDS" version)) | |
2042 | (sha256 | |
2043 | (base32 | |
301c4ff1 | 2044 | "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs")))) |
173c9960 RW |
2045 | (properties `((upstream-name . "DEDS"))) |
2046 | (build-system r-build-system) | |
2047 | (home-page "https://bioconductor.org/packages/DEDS/") | |
2048 | (synopsis "Differential expression via distance summary for microarray data") | |
2049 | (description | |
2050 | "This library contains functions that calculate various statistics of | |
2051 | differential expression for microarray data, including t statistics, fold | |
2052 | change, F statistics, SAM, moderated t and F statistics and B statistics. It | |
2053 | also implements a new methodology called DEDS (Differential Expression via | |
2054 | Distance Summary), which selects differentially expressed genes by integrating | |
2055 | and summarizing a set of statistics using a weighted distance approach.") | |
2056 | ;; Any version of the LGPL. | |
2057 | (license license:lgpl3+))) | |
7ed869f7 RW |
2058 | |
2059 | ;; This is a CRAN package, but since it depends on a Bioconductor package we | |
2060 | ;; put it here. | |
2061 | (define-public r-nbpseq | |
2062 | (package | |
2063 | (name "r-nbpseq") | |
2064 | (version "0.3.0") | |
2065 | (source | |
2066 | (origin | |
2067 | (method url-fetch) | |
2068 | (uri (cran-uri "NBPSeq" version)) | |
2069 | (sha256 | |
2070 | (base32 | |
2071 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) | |
2072 | (properties `((upstream-name . "NBPSeq"))) | |
2073 | (build-system r-build-system) | |
2074 | (propagated-inputs | |
2075 | `(("r-qvalue" ,r-qvalue))) | |
2076 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") | |
2077 | (synopsis "Negative binomial models for RNA-Seq data") | |
2078 | (description | |
2079 | "This package provides negative binomial models for two-group comparisons | |
2080 | and regression inferences from RNA-sequencing data.") | |
2081 | (license license:gpl2))) | |
3087a2f3 RW |
2082 | |
2083 | (define-public r-ebseq | |
2084 | (package | |
2085 | (name "r-ebseq") | |
4a3c47e9 | 2086 | (version "1.24.0") |
3087a2f3 RW |
2087 | (source |
2088 | (origin | |
2089 | (method url-fetch) | |
2090 | (uri (bioconductor-uri "EBSeq" version)) | |
2091 | (sha256 | |
2092 | (base32 | |
4a3c47e9 | 2093 | "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83")))) |
3087a2f3 RW |
2094 | (properties `((upstream-name . "EBSeq"))) |
2095 | (build-system r-build-system) | |
2096 | (propagated-inputs | |
2097 | `(("r-blockmodeling" ,r-blockmodeling) | |
2098 | ("r-gplots" ,r-gplots) | |
2099 | ("r-testthat" ,r-testthat))) | |
2100 | (home-page "https://bioconductor.org/packages/EBSeq") | |
2101 | (synopsis "Differential expression analysis of RNA-seq data") | |
2102 | (description | |
2103 | "This package provides tools for differential expression analysis at both | |
2104 | gene and isoform level using RNA-seq data") | |
2105 | (license license:artistic2.0))) | |
2cb71d81 RW |
2106 | |
2107 | (define-public r-lpsymphony | |
2108 | (package | |
2109 | (name "r-lpsymphony") | |
61c79d55 | 2110 | (version "1.12.0") |
2cb71d81 RW |
2111 | (source |
2112 | (origin | |
2113 | (method url-fetch) | |
2114 | (uri (bioconductor-uri "lpsymphony" version)) | |
2115 | (sha256 | |
2116 | (base32 | |
61c79d55 | 2117 | "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv")))) |
2cb71d81 RW |
2118 | (build-system r-build-system) |
2119 | (inputs | |
2120 | `(("gfortran" ,gfortran) | |
2121 | ("zlib" ,zlib))) | |
2122 | (native-inputs | |
2123 | `(("pkg-config" ,pkg-config))) | |
2124 | (home-page "http://r-forge.r-project.org/projects/rsymphony") | |
2125 | (synopsis "Symphony integer linear programming solver in R") | |
2126 | (description | |
2127 | "This package was derived from Rsymphony. The package provides an R | |
2128 | interface to SYMPHONY, a linear programming solver written in C++. The main | |
2129 | difference between this package and Rsymphony is that it includes the solver | |
2130 | source code, while Rsymphony expects to find header and library files on the | |
2131 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy | |
2132 | to install interface to SYMPHONY.") | |
2133 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. | |
2134 | ;; lpsimphony is released under the same terms. | |
2135 | (license license:epl1.0))) | |
704de8f5 RW |
2136 | |
2137 | (define-public r-ihw | |
2138 | (package | |
2139 | (name "r-ihw") | |
bcd8b7a9 | 2140 | (version "1.12.0") |
704de8f5 RW |
2141 | (source |
2142 | (origin | |
2143 | (method url-fetch) | |
2144 | (uri (bioconductor-uri "IHW" version)) | |
2145 | (sha256 | |
2146 | (base32 | |
bcd8b7a9 | 2147 | "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz")))) |
704de8f5 RW |
2148 | (properties `((upstream-name . "IHW"))) |
2149 | (build-system r-build-system) | |
2150 | (propagated-inputs | |
2151 | `(("r-biocgenerics" ,r-biocgenerics) | |
2152 | ("r-fdrtool" ,r-fdrtool) | |
2153 | ("r-lpsymphony" ,r-lpsymphony) | |
2154 | ("r-slam" ,r-slam))) | |
2155 | (home-page "https://bioconductor.org/packages/IHW") | |
2156 | (synopsis "Independent hypothesis weighting") | |
2157 | (description | |
2158 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing | |
2159 | procedure that increases power compared to the method of Benjamini and | |
2160 | Hochberg by assigning data-driven weights to each hypothesis. The input to | |
2161 | IHW is a two-column table of p-values and covariates. The covariate can be | |
2162 | any continuous-valued or categorical variable that is thought to be | |
2163 | informative on the statistical properties of each hypothesis test, while it is | |
2164 | independent of the p-value under the null hypothesis.") | |
2165 | (license license:artistic2.0))) | |
251e0830 RW |
2166 | |
2167 | (define-public r-icobra | |
2168 | (package | |
2169 | (name "r-icobra") | |
13b49976 | 2170 | (version "1.12.1") |
251e0830 RW |
2171 | (source |
2172 | (origin | |
2173 | (method url-fetch) | |
2174 | (uri (bioconductor-uri "iCOBRA" version)) | |
2175 | (sha256 | |
2176 | (base32 | |
13b49976 | 2177 | "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q")))) |
251e0830 RW |
2178 | (properties `((upstream-name . "iCOBRA"))) |
2179 | (build-system r-build-system) | |
2180 | (propagated-inputs | |
2181 | `(("r-dplyr" ,r-dplyr) | |
2182 | ("r-dt" ,r-dt) | |
2183 | ("r-ggplot2" ,r-ggplot2) | |
2184 | ("r-limma" ,r-limma) | |
2185 | ("r-reshape2" ,r-reshape2) | |
2186 | ("r-rocr" ,r-rocr) | |
2187 | ("r-scales" ,r-scales) | |
2188 | ("r-shiny" ,r-shiny) | |
2189 | ("r-shinybs" ,r-shinybs) | |
2190 | ("r-shinydashboard" ,r-shinydashboard) | |
2191 | ("r-upsetr" ,r-upsetr))) | |
2192 | (home-page "https://bioconductor.org/packages/iCOBRA") | |
2193 | (synopsis "Comparison and visualization of ranking and assignment methods") | |
2194 | (description | |
2195 | "This package provides functions for calculation and visualization of | |
2196 | performance metrics for evaluation of ranking and binary | |
2197 | classification (assignment) methods. It also contains a Shiny application for | |
2198 | interactive exploration of results.") | |
2199 | (license license:gpl2+))) | |
925fcdbb RW |
2200 | |
2201 | (define-public r-mast | |
2202 | (package | |
2203 | (name "r-mast") | |
a0ff725d | 2204 | (version "1.10.0") |
925fcdbb RW |
2205 | (source |
2206 | (origin | |
2207 | (method url-fetch) | |
2208 | (uri (bioconductor-uri "MAST" version)) | |
2209 | (sha256 | |
2210 | (base32 | |
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925fcdbb RW |
2212 | (properties `((upstream-name . "MAST"))) |
2213 | (build-system r-build-system) | |
2214 | (propagated-inputs | |
2215 | `(("r-abind" ,r-abind) | |
a0ff725d | 2216 | ("r-blme" ,r-blme) |
925fcdbb RW |
2217 | ("r-biobase" ,r-biobase) |
2218 | ("r-biocgenerics" ,r-biocgenerics) | |
2219 | ("r-data-table" ,r-data-table) | |
2220 | ("r-ggplot2" ,r-ggplot2) | |
2221 | ("r-plyr" ,r-plyr) | |
2222 | ("r-progress" ,r-progress) | |
2223 | ("r-reshape2" ,r-reshape2) | |
2224 | ("r-s4vectors" ,r-s4vectors) | |
2225 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2226 | ("r-stringr" ,r-stringr) | |
2227 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2228 | (home-page "https://github.com/RGLab/MAST/") | |
2229 | (synopsis "Model-based analysis of single cell transcriptomics") | |
2230 | (description | |
2231 | "This package provides methods and models for handling zero-inflated | |
2232 | single cell assay data.") | |
2233 | (license license:gpl2+))) | |
2d7627cf RW |
2234 | |
2235 | (define-public r-monocle | |
2236 | (package | |
2237 | (name "r-monocle") | |
78b63267 | 2238 | (version "2.12.0") |
2d7627cf RW |
2239 | (source |
2240 | (origin | |
2241 | (method url-fetch) | |
2242 | (uri (bioconductor-uri "monocle" version)) | |
2243 | (sha256 | |
2244 | (base32 | |
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2d7627cf RW |
2246 | (build-system r-build-system) |
2247 | (propagated-inputs | |
2248 | `(("r-biobase" ,r-biobase) | |
2249 | ("r-biocgenerics" ,r-biocgenerics) | |
2250 | ("r-biocviews" ,r-biocviews) | |
2251 | ("r-cluster" ,r-cluster) | |
2252 | ("r-combinat" ,r-combinat) | |
2253 | ("r-ddrtree" ,r-ddrtree) | |
2254 | ("r-densityclust" ,r-densityclust) | |
2255 | ("r-dplyr" ,r-dplyr) | |
2256 | ("r-fastica" ,r-fastica) | |
2257 | ("r-ggplot2" ,r-ggplot2) | |
2258 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) | |
2259 | ("r-igraph" ,r-igraph) | |
2260 | ("r-irlba" ,r-irlba) | |
2261 | ("r-limma" ,r-limma) | |
2262 | ("r-mass" ,r-mass) | |
2263 | ("r-matrix" ,r-matrix) | |
2264 | ("r-matrixstats" ,r-matrixstats) | |
2265 | ("r-pheatmap" ,r-pheatmap) | |
2266 | ("r-plyr" ,r-plyr) | |
2267 | ("r-proxy" ,r-proxy) | |
2268 | ("r-qlcmatrix" ,r-qlcmatrix) | |
2269 | ("r-rann" ,r-rann) | |
2270 | ("r-rcpp" ,r-rcpp) | |
2271 | ("r-reshape2" ,r-reshape2) | |
2272 | ("r-rtsne" ,r-rtsne) | |
2273 | ("r-slam" ,r-slam) | |
2274 | ("r-stringr" ,r-stringr) | |
2275 | ("r-tibble" ,r-tibble) | |
2276 | ("r-vgam" ,r-vgam) | |
2277 | ("r-viridis" ,r-viridis))) | |
2278 | (home-page "https://bioconductor.org/packages/monocle") | |
2279 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") | |
2280 | (description | |
2281 | "Monocle performs differential expression and time-series analysis for | |
2282 | single-cell expression experiments. It orders individual cells according to | |
2283 | progress through a biological process, without knowing ahead of time which | |
2284 | genes define progress through that process. Monocle also performs | |
2285 | differential expression analysis, clustering, visualization, and other useful | |
2286 | tasks on single cell expression data. It is designed to work with RNA-Seq and | |
2287 | qPCR data, but could be used with other types as well.") | |
2288 | (license license:artistic2.0))) | |
6213e441 | 2289 | |
b2dce6b5 RW |
2290 | (define-public r-monocle3 |
2291 | (package | |
2292 | (name "r-monocle3") | |
2293 | (version "0.1.2") | |
2294 | (source | |
2295 | (origin | |
2296 | (method git-fetch) | |
2297 | (uri (git-reference | |
2298 | (url "https://github.com/cole-trapnell-lab/monocle3.git") | |
2299 | (commit version))) | |
2300 | (file-name (git-file-name name version)) | |
2301 | (sha256 | |
2302 | (base32 | |
2303 | "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) | |
2304 | (build-system r-build-system) | |
2305 | (propagated-inputs | |
2306 | `(("r-biobase" ,r-biobase) | |
2307 | ("r-biocgenerics" ,r-biocgenerics) | |
2308 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
2309 | ("r-dplyr" ,r-dplyr) | |
2310 | ("r-ggplot2" ,r-ggplot2) | |
2311 | ("r-ggrepel" ,r-ggrepel) | |
2312 | ("r-grr" ,r-grr) | |
2313 | ("r-htmlwidgets" ,r-htmlwidgets) | |
2314 | ("r-igraph" ,r-igraph) | |
2315 | ("r-irlba" ,r-irlba) | |
2316 | ("r-limma" ,r-limma) | |
2317 | ("r-lmtest" ,r-lmtest) | |
2318 | ("r-mass" ,r-mass) | |
2319 | ("r-matrix" ,r-matrix) | |
2320 | ("r-matrix-utils" ,r-matrix-utils) | |
2321 | ("r-pbapply" ,r-pbapply) | |
2322 | ("r-pbmcapply" ,r-pbmcapply) | |
2323 | ("r-pheatmap" ,r-pheatmap) | |
2324 | ("r-plotly" ,r-plotly) | |
2325 | ("r-pryr" ,r-pryr) | |
2326 | ("r-proxy" ,r-proxy) | |
2327 | ("r-pscl" ,r-pscl) | |
2328 | ("r-purrr" ,r-purrr) | |
2329 | ("r-rann" ,r-rann) | |
2330 | ("r-rcpp" ,r-rcpp) | |
2331 | ("r-rcppparallel" ,r-rcppparallel) | |
2332 | ("r-reshape2" ,r-reshape2) | |
2333 | ("r-reticulate" ,r-reticulate) | |
2334 | ("r-rhpcblasctl" ,r-rhpcblasctl) | |
2335 | ("r-rtsne" ,r-rtsne) | |
2336 | ("r-shiny" ,r-shiny) | |
2337 | ("r-slam" ,r-slam) | |
2338 | ("r-spdep" ,r-spdep) | |
2339 | ("r-speedglm" ,r-speedglm) | |
2340 | ("r-stringr" ,r-stringr) | |
2341 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2342 | ("r-tibble" ,r-tibble) | |
2343 | ("r-tidyr" ,r-tidyr) | |
2344 | ("r-uwot" ,r-uwot) | |
2345 | ("r-viridis" ,r-viridis))) | |
2346 | (home-page "https://github.com/cole-trapnell-lab/monocle3") | |
2347 | (synopsis "Analysis toolkit for single-cell RNA-Seq data") | |
2348 | (description | |
2349 | "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") | |
2350 | (license license:expat))) | |
2351 | ||
6213e441 RW |
2352 | (define-public r-noiseq |
2353 | (package | |
2354 | (name "r-noiseq") | |
6a2c58b7 | 2355 | (version "2.28.0") |
6213e441 RW |
2356 | (source |
2357 | (origin | |
2358 | (method url-fetch) | |
2359 | (uri (bioconductor-uri "NOISeq" version)) | |
2360 | (sha256 | |
2361 | (base32 | |
6a2c58b7 | 2362 | "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j")))) |
6213e441 RW |
2363 | (properties `((upstream-name . "NOISeq"))) |
2364 | (build-system r-build-system) | |
2365 | (propagated-inputs | |
2366 | `(("r-biobase" ,r-biobase) | |
2367 | ("r-matrix" ,r-matrix))) | |
2368 | (home-page "https://bioconductor.org/packages/NOISeq") | |
2369 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") | |
2370 | (description | |
2371 | "This package provides tools to support the analysis of RNA-seq | |
2372 | expression data or other similar kind of data. It provides exploratory plots | |
2373 | to evaluate saturation, count distribution, expression per chromosome, type of | |
2374 | detected features, features length, etc. It also supports the analysis of | |
2375 | differential expression between two experimental conditions with no parametric | |
2376 | assumptions.") | |
2377 | (license license:artistic2.0))) | |
b409c357 RW |
2378 | |
2379 | (define-public r-scdd | |
2380 | (package | |
2381 | (name "r-scdd") | |
7baa59ed | 2382 | (version "1.8.0") |
b409c357 RW |
2383 | (source |
2384 | (origin | |
2385 | (method url-fetch) | |
2386 | (uri (bioconductor-uri "scDD" version)) | |
2387 | (sha256 | |
2388 | (base32 | |
7baa59ed | 2389 | "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf")))) |
b409c357 RW |
2390 | (properties `((upstream-name . "scDD"))) |
2391 | (build-system r-build-system) | |
2392 | (propagated-inputs | |
2393 | `(("r-arm" ,r-arm) | |
2394 | ("r-biocparallel" ,r-biocparallel) | |
2395 | ("r-ebseq" ,r-ebseq) | |
2396 | ("r-fields" ,r-fields) | |
2397 | ("r-ggplot2" ,r-ggplot2) | |
2398 | ("r-mclust" ,r-mclust) | |
2399 | ("r-outliers" ,r-outliers) | |
2400 | ("r-s4vectors" ,r-s4vectors) | |
2401 | ("r-scran" ,r-scran) | |
2402 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2403 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2404 | (home-page "https://github.com/kdkorthauer/scDD") | |
2405 | (synopsis "Mixture modeling of single-cell RNA-seq data") | |
2406 | (description | |
2407 | "This package implements a method to analyze single-cell RNA-seq data | |
2408 | utilizing flexible Dirichlet Process mixture models. Genes with differential | |
2409 | distributions of expression are classified into several interesting patterns | |
2410 | of differences between two conditions. The package also includes functions | |
2411 | for simulating data with these patterns from negative binomial | |
2412 | distributions.") | |
2413 | (license license:gpl2))) | |
f0887757 RW |
2414 | |
2415 | (define-public r-scone | |
2416 | (package | |
2417 | (name "r-scone") | |
26c72fff | 2418 | (version "1.8.0") |
f0887757 RW |
2419 | (source |
2420 | (origin | |
2421 | (method url-fetch) | |
2422 | (uri (bioconductor-uri "scone" version)) | |
2423 | (sha256 | |
2424 | (base32 | |
26c72fff | 2425 | "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck")))) |
f0887757 RW |
2426 | (build-system r-build-system) |
2427 | (propagated-inputs | |
2428 | `(("r-aroma-light" ,r-aroma-light) | |
2429 | ("r-biocparallel" ,r-biocparallel) | |
2430 | ("r-boot" ,r-boot) | |
2431 | ("r-class" ,r-class) | |
2432 | ("r-cluster" ,r-cluster) | |
2433 | ("r-compositions" ,r-compositions) | |
2434 | ("r-diptest" ,r-diptest) | |
2435 | ("r-edger" ,r-edger) | |
2436 | ("r-fpc" ,r-fpc) | |
2437 | ("r-gplots" ,r-gplots) | |
2438 | ("r-hexbin" ,r-hexbin) | |
2439 | ("r-limma" ,r-limma) | |
2440 | ("r-matrixstats" ,r-matrixstats) | |
2441 | ("r-mixtools" ,r-mixtools) | |
2442 | ("r-rarpack" ,r-rarpack) | |
2443 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2444 | ("r-rhdf5" ,r-rhdf5) | |
2445 | ("r-ruvseq" ,r-ruvseq) | |
2446 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2447 | (home-page "https://bioconductor.org/packages/scone") | |
2448 | (synopsis "Single cell overview of normalized expression data") | |
2449 | (description | |
2450 | "SCONE is an R package for comparing and ranking the performance of | |
2451 | different normalization schemes for single-cell RNA-seq and other | |
2452 | high-throughput analyses.") | |
2453 | (license license:artistic2.0))) | |
f9201d67 RW |
2454 | |
2455 | (define-public r-geoquery | |
2456 | (package | |
2457 | (name "r-geoquery") | |
2d443087 | 2458 | (version "2.52.0") |
f9201d67 RW |
2459 | (source |
2460 | (origin | |
2461 | (method url-fetch) | |
2462 | (uri (bioconductor-uri "GEOquery" version)) | |
2463 | (sha256 | |
2464 | (base32 | |
2d443087 | 2465 | "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr")))) |
f9201d67 RW |
2466 | (properties `((upstream-name . "GEOquery"))) |
2467 | (build-system r-build-system) | |
2468 | (propagated-inputs | |
2469 | `(("r-biobase" ,r-biobase) | |
2470 | ("r-dplyr" ,r-dplyr) | |
2471 | ("r-httr" ,r-httr) | |
2472 | ("r-limma" ,r-limma) | |
2473 | ("r-magrittr" ,r-magrittr) | |
2474 | ("r-readr" ,r-readr) | |
2475 | ("r-tidyr" ,r-tidyr) | |
2476 | ("r-xml2" ,r-xml2))) | |
2477 | (home-page "https://github.com/seandavi/GEOquery/") | |
2478 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") | |
2479 | (description | |
2480 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of | |
2481 | microarray data. Given the rich and varied nature of this resource, it is | |
2482 | only natural to want to apply BioConductor tools to these data. GEOquery is | |
2483 | the bridge between GEO and BioConductor.") | |
2484 | (license license:gpl2))) | |
eed6ff03 RW |
2485 | |
2486 | (define-public r-illuminaio | |
2487 | (package | |
2488 | (name "r-illuminaio") | |
fadc6db8 | 2489 | (version "0.26.0") |
eed6ff03 RW |
2490 | (source |
2491 | (origin | |
2492 | (method url-fetch) | |
2493 | (uri (bioconductor-uri "illuminaio" version)) | |
2494 | (sha256 | |
2495 | (base32 | |
fadc6db8 | 2496 | "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8")))) |
eed6ff03 RW |
2497 | (build-system r-build-system) |
2498 | (propagated-inputs | |
2499 | `(("r-base64" ,r-base64))) | |
2500 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") | |
2501 | (synopsis "Parse Illumina microarray output files") | |
2502 | (description | |
2503 | "This package provides tools for parsing Illumina's microarray output | |
2504 | files, including IDAT.") | |
2505 | (license license:gpl2))) | |
f4eac096 RW |
2506 | |
2507 | (define-public r-siggenes | |
2508 | (package | |
2509 | (name "r-siggenes") | |
409f4dd6 | 2510 | (version "1.58.0") |
f4eac096 RW |
2511 | (source |
2512 | (origin | |
2513 | (method url-fetch) | |
2514 | (uri (bioconductor-uri "siggenes" version)) | |
2515 | (sha256 | |
2516 | (base32 | |
409f4dd6 | 2517 | "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib")))) |
f4eac096 RW |
2518 | (build-system r-build-system) |
2519 | (propagated-inputs | |
2520 | `(("r-biobase" ,r-biobase) | |
409f4dd6 RW |
2521 | ("r-multtest" ,r-multtest) |
2522 | ("r-scrime" ,r-scrime))) | |
f4eac096 RW |
2523 | (home-page "https://bioconductor.org/packages/siggenes/") |
2524 | (synopsis | |
2525 | "Multiple testing using SAM and Efron's empirical Bayes approaches") | |
2526 | (description | |
2527 | "This package provides tools for the identification of differentially | |
2528 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using | |
2529 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical | |
2530 | Bayes Analyses of Microarrays} (EBAM).") | |
2531 | (license license:lgpl2.0+))) | |
34a24f95 RW |
2532 | |
2533 | (define-public r-bumphunter | |
2534 | (package | |
2535 | (name "r-bumphunter") | |
693a9805 | 2536 | (version "1.26.0") |
34a24f95 RW |
2537 | (source |
2538 | (origin | |
2539 | (method url-fetch) | |
2540 | (uri (bioconductor-uri "bumphunter" version)) | |
2541 | (sha256 | |
2542 | (base32 | |
693a9805 | 2543 | "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx")))) |
34a24f95 RW |
2544 | (build-system r-build-system) |
2545 | (propagated-inputs | |
2546 | `(("r-annotationdbi" ,r-annotationdbi) | |
2547 | ("r-biocgenerics" ,r-biocgenerics) | |
2548 | ("r-dorng" ,r-dorng) | |
2549 | ("r-foreach" ,r-foreach) | |
2550 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2551 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2552 | ("r-genomicranges" ,r-genomicranges) | |
2553 | ("r-iranges" ,r-iranges) | |
2554 | ("r-iterators" ,r-iterators) | |
2555 | ("r-limma" ,r-limma) | |
2556 | ("r-locfit" ,r-locfit) | |
2557 | ("r-matrixstats" ,r-matrixstats) | |
2558 | ("r-s4vectors" ,r-s4vectors))) | |
2559 | (home-page "https://github.com/ririzarr/bumphunter") | |
2560 | (synopsis "Find bumps in genomic data") | |
2561 | (description | |
2562 | "This package provides tools for finding bumps in genomic data in order | |
2563 | to identify differentially methylated regions in epigenetic epidemiology | |
2564 | studies.") | |
2565 | (license license:artistic2.0))) | |
0fbaf195 RW |
2566 | |
2567 | (define-public r-minfi | |
2568 | (package | |
2569 | (name "r-minfi") | |
8c0fae3c | 2570 | (version "1.30.0") |
0fbaf195 RW |
2571 | (source |
2572 | (origin | |
2573 | (method url-fetch) | |
2574 | (uri (bioconductor-uri "minfi" version)) | |
2575 | (sha256 | |
2576 | (base32 | |
8c0fae3c | 2577 | "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd")))) |
0fbaf195 RW |
2578 | (build-system r-build-system) |
2579 | (propagated-inputs | |
2580 | `(("r-beanplot" ,r-beanplot) | |
2581 | ("r-biobase" ,r-biobase) | |
2582 | ("r-biocgenerics" ,r-biocgenerics) | |
2583 | ("r-biocparallel" ,r-biocparallel) | |
2584 | ("r-biostrings" ,r-biostrings) | |
2585 | ("r-bumphunter" ,r-bumphunter) | |
2586 | ("r-data-table" ,r-data-table) | |
2587 | ("r-delayedarray" ,r-delayedarray) | |
2588 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
2589 | ("r-genefilter" ,r-genefilter) | |
2590 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2591 | ("r-genomicranges" ,r-genomicranges) | |
2592 | ("r-geoquery" ,r-geoquery) | |
2593 | ("r-hdf5array" ,r-hdf5array) | |
2594 | ("r-illuminaio" ,r-illuminaio) | |
2595 | ("r-iranges" ,r-iranges) | |
2596 | ("r-lattice" ,r-lattice) | |
2597 | ("r-limma" ,r-limma) | |
2598 | ("r-mass" ,r-mass) | |
2599 | ("r-mclust" ,r-mclust) | |
2600 | ("r-nlme" ,r-nlme) | |
2601 | ("r-nor1mix" ,r-nor1mix) | |
2602 | ("r-preprocesscore" ,r-preprocesscore) | |
2603 | ("r-quadprog" ,r-quadprog) | |
2604 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2605 | ("r-reshape" ,r-reshape) | |
2606 | ("r-s4vectors" ,r-s4vectors) | |
2607 | ("r-siggenes" ,r-siggenes) | |
2608 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2609 | (home-page "https://github.com/hansenlab/minfi") | |
2610 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") | |
2611 | (description | |
2612 | "This package provides tools to analyze and visualize Illumina Infinium | |
2613 | methylation arrays.") | |
2614 | (license license:artistic2.0))) | |
5ec5ba02 RW |
2615 | |
2616 | (define-public r-methylumi | |
2617 | (package | |
2618 | (name "r-methylumi") | |
2986b51f | 2619 | (version "2.30.0") |
5ec5ba02 RW |
2620 | (source |
2621 | (origin | |
2622 | (method url-fetch) | |
2623 | (uri (bioconductor-uri "methylumi" version)) | |
2624 | (sha256 | |
2625 | (base32 | |
2986b51f | 2626 | "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f")))) |
5ec5ba02 RW |
2627 | (build-system r-build-system) |
2628 | (propagated-inputs | |
2629 | `(("r-annotate" ,r-annotate) | |
2630 | ("r-annotationdbi" ,r-annotationdbi) | |
2631 | ("r-biobase" ,r-biobase) | |
2632 | ("r-biocgenerics" ,r-biocgenerics) | |
2633 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) | |
2634 | ("r-genefilter" ,r-genefilter) | |
2635 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2636 | ("r-genomicranges" ,r-genomicranges) | |
2637 | ("r-ggplot2" ,r-ggplot2) | |
2638 | ("r-illuminaio" ,r-illuminaio) | |
2639 | ("r-iranges" ,r-iranges) | |
2640 | ("r-lattice" ,r-lattice) | |
2641 | ("r-matrixstats" ,r-matrixstats) | |
2642 | ("r-minfi" ,r-minfi) | |
2643 | ("r-reshape2" ,r-reshape2) | |
2644 | ("r-s4vectors" ,r-s4vectors) | |
2645 | ("r-scales" ,r-scales) | |
2646 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2647 | (home-page "https://bioconductor.org/packages/methylumi") | |
2648 | (synopsis "Handle Illumina methylation data") | |
2649 | (description | |
2650 | "This package provides classes for holding and manipulating Illumina | |
2651 | methylation data. Based on eSet, it can contain MIAME information, sample | |
2652 | information, feature information, and multiple matrices of data. An | |
2653 | \"intelligent\" import function, methylumiR can read the Illumina text files | |
2654 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from | |
2655 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, | |
2656 | background correction, and quality control features for GoldenGate, Infinium, | |
2657 | and Infinium HD arrays are also included.") | |
2658 | (license license:gpl2))) | |
09605cb2 RW |
2659 | |
2660 | (define-public r-lumi | |
2661 | (package | |
2662 | (name "r-lumi") | |
5551b07c | 2663 | (version "2.36.0") |
09605cb2 RW |
2664 | (source |
2665 | (origin | |
2666 | (method url-fetch) | |
2667 | (uri (bioconductor-uri "lumi" version)) | |
2668 | (sha256 | |
2669 | (base32 | |
5551b07c | 2670 | "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba")))) |
09605cb2 RW |
2671 | (build-system r-build-system) |
2672 | (propagated-inputs | |
2673 | `(("r-affy" ,r-affy) | |
2674 | ("r-annotate" ,r-annotate) | |
2675 | ("r-annotationdbi" ,r-annotationdbi) | |
2676 | ("r-biobase" ,r-biobase) | |
2677 | ("r-dbi" ,r-dbi) | |
2678 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2679 | ("r-genomicranges" ,r-genomicranges) | |
2680 | ("r-kernsmooth" ,r-kernsmooth) | |
2681 | ("r-lattice" ,r-lattice) | |
2682 | ("r-mass" ,r-mass) | |
2683 | ("r-methylumi" ,r-methylumi) | |
2684 | ("r-mgcv" ,r-mgcv) | |
2685 | ("r-nleqslv" ,r-nleqslv) | |
2686 | ("r-preprocesscore" ,r-preprocesscore) | |
2687 | ("r-rsqlite" ,r-rsqlite))) | |
2688 | (home-page "https://bioconductor.org/packages/lumi") | |
2689 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") | |
2690 | (description | |
2691 | "The lumi package provides an integrated solution for the Illumina | |
2692 | microarray data analysis. It includes functions of Illumina | |
2693 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific | |
2694 | variance stabilization, normalization and gene annotation at the probe level. | |
2695 | It also includes the functions of processing Illumina methylation microarrays, | |
2696 | especially Illumina Infinium methylation microarrays.") | |
2697 | (license license:lgpl2.0+))) | |
4291f36a RW |
2698 | |
2699 | (define-public r-linnorm | |
2700 | (package | |
2701 | (name "r-linnorm") | |
48c2a7eb | 2702 | (version "2.8.0") |
4291f36a RW |
2703 | (source |
2704 | (origin | |
2705 | (method url-fetch) | |
2706 | (uri (bioconductor-uri "Linnorm" version)) | |
2707 | (sha256 | |
2708 | (base32 | |
48c2a7eb | 2709 | "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5")))) |
4291f36a RW |
2710 | (properties `((upstream-name . "Linnorm"))) |
2711 | (build-system r-build-system) | |
2712 | (propagated-inputs | |
2713 | `(("r-amap" ,r-amap) | |
2714 | ("r-apcluster" ,r-apcluster) | |
2715 | ("r-ellipse" ,r-ellipse) | |
2716 | ("r-fastcluster" ,r-fastcluster) | |
2717 | ("r-fpc" ,r-fpc) | |
2718 | ("r-ggdendro" ,r-ggdendro) | |
2719 | ("r-ggplot2" ,r-ggplot2) | |
2720 | ("r-gmodels" ,r-gmodels) | |
2721 | ("r-igraph" ,r-igraph) | |
2722 | ("r-limma" ,r-limma) | |
2723 | ("r-mass" ,r-mass) | |
2724 | ("r-mclust" ,r-mclust) | |
2725 | ("r-rcpp" ,r-rcpp) | |
2726 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
2727 | ("r-rtsne" ,r-rtsne) | |
2728 | ("r-statmod" ,r-statmod) | |
2729 | ("r-vegan" ,r-vegan) | |
2730 | ("r-zoo" ,r-zoo))) | |
2731 | (home-page "http://www.jjwanglab.org/Linnorm/") | |
2732 | (synopsis "Linear model and normality based transformation method") | |
2733 | (description | |
2734 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq | |
2735 | count data or any large scale count data. It transforms such datasets for | |
2736 | parametric tests. In addition to the transformtion function (@code{Linnorm}), | |
2737 | the following pipelines are implemented: | |
2738 | ||
2739 | @enumerate | |
2740 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) | |
2741 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means | |
2742 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, | |
2743 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) | |
2744 | @item Differential expression analysis or differential peak detection using | |
2745 | limma (@code{Linnorm.limma}) | |
2746 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) | |
2747 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) | |
2748 | @item Stable gene selection for scRNA-seq data; for users without or who do | |
2749 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) | |
2750 | @item Data imputation (@code{Linnorm.DataImput}). | |
2751 | @end enumerate | |
2752 | ||
2753 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the | |
2754 | @code{RnaXSim} function is included for simulating RNA-seq data for the | |
2755 | evaluation of DEG analysis methods.") | |
2756 | (license license:expat))) | |
e4a17532 RW |
2757 | |
2758 | (define-public r-ioniser | |
2759 | (package | |
2760 | (name "r-ioniser") | |
2ee91179 | 2761 | (version "2.8.0") |
e4a17532 RW |
2762 | (source |
2763 | (origin | |
2764 | (method url-fetch) | |
2765 | (uri (bioconductor-uri "IONiseR" version)) | |
2766 | (sha256 | |
2767 | (base32 | |
2ee91179 | 2768 | "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y")))) |
e4a17532 RW |
2769 | (properties `((upstream-name . "IONiseR"))) |
2770 | (build-system r-build-system) | |
2771 | (propagated-inputs | |
2772 | `(("r-biocgenerics" ,r-biocgenerics) | |
2773 | ("r-biocparallel" ,r-biocparallel) | |
2774 | ("r-biostrings" ,r-biostrings) | |
2775 | ("r-bit64" ,r-bit64) | |
2776 | ("r-dplyr" ,r-dplyr) | |
2777 | ("r-ggplot2" ,r-ggplot2) | |
2778 | ("r-magrittr" ,r-magrittr) | |
2779 | ("r-rhdf5" ,r-rhdf5) | |
2780 | ("r-shortread" ,r-shortread) | |
2781 | ("r-stringr" ,r-stringr) | |
2782 | ("r-tibble" ,r-tibble) | |
2783 | ("r-tidyr" ,r-tidyr) | |
2784 | ("r-xvector" ,r-xvector))) | |
2785 | (home-page "https://bioconductor.org/packages/IONiseR/") | |
2786 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") | |
2787 | (description | |
2788 | "IONiseR provides tools for the quality assessment of Oxford Nanopore | |
2789 | MinION data. It extracts summary statistics from a set of fast5 files and can | |
2790 | be used either before or after base calling. In addition to standard | |
2791 | summaries of the read-types produced, it provides a number of plots for | |
2792 | visualising metrics relative to experiment run time or spatially over the | |
2793 | surface of a flowcell.") | |
2794 | (license license:expat))) | |
80eb01c7 RW |
2795 | |
2796 | ;; This is a CRAN package, but it depends on packages from Bioconductor. | |
2797 | (define-public r-gkmsvm | |
2798 | (package | |
2799 | (name "r-gkmsvm") | |
2800 | (version "0.79.0") | |
2801 | (source | |
2802 | (origin | |
2803 | (method url-fetch) | |
2804 | (uri (cran-uri "gkmSVM" version)) | |
2805 | (sha256 | |
2806 | (base32 | |
2807 | "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) | |
2808 | (properties `((upstream-name . "gkmSVM"))) | |
2809 | (build-system r-build-system) | |
2810 | (propagated-inputs | |
2811 | `(("r-biocgenerics" ,r-biocgenerics) | |
2812 | ("r-biostrings" ,r-biostrings) | |
2813 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2814 | ("r-genomicranges" ,r-genomicranges) | |
2815 | ("r-iranges" ,r-iranges) | |
2816 | ("r-kernlab" ,r-kernlab) | |
2817 | ("r-rcpp" ,r-rcpp) | |
2818 | ("r-rocr" ,r-rocr) | |
2819 | ("r-rtracklayer" ,r-rtracklayer) | |
2820 | ("r-s4vectors" ,r-s4vectors) | |
2821 | ("r-seqinr" ,r-seqinr))) | |
2822 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") | |
2823 | (synopsis "Gapped-kmer support vector machine") | |
2824 | (description | |
2825 | "This R package provides tools for training gapped-kmer SVM classifiers | |
2826 | for DNA and protein sequences. This package supports several sequence | |
2827 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
2828 | (license license:gpl2+))) | |
8a5460b4 RW |
2829 | |
2830 | (define-public r-triform | |
2831 | (package | |
2832 | (name "r-triform") | |
bc083eca | 2833 | (version "1.26.0") |
8a5460b4 RW |
2834 | (source |
2835 | (origin | |
2836 | (method url-fetch) | |
2837 | (uri (bioconductor-uri "triform" version)) | |
2838 | (sha256 | |
2839 | (base32 | |
bc083eca | 2840 | "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya")))) |
8a5460b4 RW |
2841 | (build-system r-build-system) |
2842 | (propagated-inputs | |
2843 | `(("r-biocgenerics" ,r-biocgenerics) | |
2844 | ("r-iranges" ,r-iranges) | |
2845 | ("r-yaml" ,r-yaml))) | |
2846 | (home-page "https://bioconductor.org/packages/triform/") | |
2847 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") | |
2848 | (description | |
2849 | "The Triform algorithm uses model-free statistics to identify peak-like | |
2850 | distributions of TF ChIP sequencing reads, taking advantage of an improved | |
2851 | peak definition in combination with known profile characteristics.") | |
2852 | (license license:gpl2))) | |
c538bcdd RW |
2853 | |
2854 | (define-public r-varianttools | |
2855 | (package | |
2856 | (name "r-varianttools") | |
c2effded | 2857 | (version "1.26.0") |
c538bcdd RW |
2858 | (source |
2859 | (origin | |
2860 | (method url-fetch) | |
2861 | (uri (bioconductor-uri "VariantTools" version)) | |
2862 | (sha256 | |
2863 | (base32 | |
c2effded | 2864 | "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql")))) |
c538bcdd RW |
2865 | (properties `((upstream-name . "VariantTools"))) |
2866 | (build-system r-build-system) | |
2867 | (propagated-inputs | |
2868 | `(("r-biobase" ,r-biobase) | |
2869 | ("r-biocgenerics" ,r-biocgenerics) | |
2870 | ("r-biocparallel" ,r-biocparallel) | |
2871 | ("r-biostrings" ,r-biostrings) | |
2872 | ("r-bsgenome" ,r-bsgenome) | |
2873 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2874 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2875 | ("r-genomicranges" ,r-genomicranges) | |
2876 | ("r-iranges" ,r-iranges) | |
2877 | ("r-matrix" ,r-matrix) | |
2878 | ("r-rsamtools" ,r-rsamtools) | |
2879 | ("r-rtracklayer" ,r-rtracklayer) | |
2880 | ("r-s4vectors" ,r-s4vectors) | |
2881 | ("r-variantannotation" ,r-variantannotation))) | |
2882 | (home-page "https://bioconductor.org/packages/VariantTools/") | |
2883 | (synopsis "Tools for exploratory analysis of variant calls") | |
2884 | (description | |
2885 | "Explore, diagnose, and compare variant calls using filters. The | |
2886 | VariantTools package supports a workflow for loading data, calling single | |
2887 | sample variants and tumor-specific somatic mutations or other sample-specific | |
2888 | variant types (e.g., RNA editing). Most of the functions operate on | |
2889 | alignments (BAM files) or datasets of called variants. The user is expected | |
2890 | to have already aligned the reads with a separate tool, e.g., GSNAP via | |
2891 | gmapR.") | |
2892 | (license license:artistic2.0))) | |
3e41919d RW |
2893 | |
2894 | (define-public r-heatplus | |
2895 | (package | |
2896 | (name "r-heatplus") | |
376d1fe7 | 2897 | (version "2.30.0") |
3e41919d RW |
2898 | (source |
2899 | (origin | |
2900 | (method url-fetch) | |
2901 | (uri (bioconductor-uri "Heatplus" version)) | |
2902 | (sha256 | |
2903 | (base32 | |
376d1fe7 | 2904 | "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6")))) |
3e41919d RW |
2905 | (properties `((upstream-name . "Heatplus"))) |
2906 | (build-system r-build-system) | |
2907 | (propagated-inputs | |
2908 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) | |
2909 | (home-page "https://github.com/alexploner/Heatplus") | |
2910 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") | |
2911 | (description | |
2912 | "This package provides tools to display a rectangular heatmap (intensity | |
2913 | plot) of a data matrix. By default, both samples (columns) and features (row) | |
2914 | of the matrix are sorted according to a hierarchical clustering, and the | |
2915 | corresponding dendrogram is plotted. Optionally, panels with additional | |
2916 | information about samples and features can be added to the plot.") | |
2917 | (license license:gpl2+))) | |
c04f230e RW |
2918 | |
2919 | (define-public r-gosemsim | |
2920 | (package | |
2921 | (name "r-gosemsim") | |
24cf7bad | 2922 | (version "2.10.0") |
c04f230e RW |
2923 | (source |
2924 | (origin | |
2925 | (method url-fetch) | |
2926 | (uri (bioconductor-uri "GOSemSim" version)) | |
2927 | (sha256 | |
2928 | (base32 | |
24cf7bad | 2929 | "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg")))) |
c04f230e RW |
2930 | (properties `((upstream-name . "GOSemSim"))) |
2931 | (build-system r-build-system) | |
2932 | (propagated-inputs | |
2933 | `(("r-annotationdbi" ,r-annotationdbi) | |
2934 | ("r-go-db" ,r-go-db) | |
2935 | ("r-rcpp" ,r-rcpp))) | |
2936 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") | |
2937 | (synopsis "GO-terms semantic similarity measures") | |
2938 | (description | |
2939 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide | |
2940 | quantitative ways to compute similarities between genes and gene groups, and | |
2941 | have became important basis for many bioinformatics analysis approaches. | |
2942 | GOSemSim is an R package for semantic similarity computation among GO terms, | |
2943 | sets of GO terms, gene products and gene clusters.") | |
2944 | (license license:artistic2.0))) | |
9d0f7942 RW |
2945 | |
2946 | (define-public r-anota | |
2947 | (package | |
2948 | (name "r-anota") | |
0a41b5db | 2949 | (version "1.32.0") |
9d0f7942 RW |
2950 | (source |
2951 | (origin | |
2952 | (method url-fetch) | |
2953 | (uri (bioconductor-uri "anota" version)) | |
2954 | (sha256 | |
2955 | (base32 | |
0a41b5db | 2956 | "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c")))) |
9d0f7942 RW |
2957 | (build-system r-build-system) |
2958 | (propagated-inputs | |
2959 | `(("r-multtest" ,r-multtest) | |
2960 | ("r-qvalue" ,r-qvalue))) | |
2961 | (home-page "https://bioconductor.org/packages/anota/") | |
2962 | (synopsis "Analysis of translational activity") | |
2963 | (description | |
2964 | "Genome wide studies of translational control is emerging as a tool to | |
0cea26bd | 2965 | study various biological conditions. The output from such analysis is both |
9d0f7942 RW |
2966 | the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively |
2967 | involved in translation (the actively translating mRNA level) for each mRNA. | |
2968 | The standard analysis of such data strives towards identifying differential | |
2969 | translational between two or more sample classes - i.e. differences in | |
2970 | actively translated mRNA levels that are independent of underlying differences | |
2971 | in cytosolic mRNA levels. This package allows for such analysis using partial | |
2972 | variances and the random variance model. As 10s of thousands of mRNAs are | |
4f664004 | 2973 | analyzed in parallel the library performs a number of tests to assure that |
9d0f7942 RW |
2974 | the data set is suitable for such analysis.") |
2975 | (license license:gpl3))) | |
a6d867fe RW |
2976 | |
2977 | (define-public r-sigpathway | |
2978 | (package | |
2979 | (name "r-sigpathway") | |
3e5ee6f6 | 2980 | (version "1.52.0") |
a6d867fe RW |
2981 | (source |
2982 | (origin | |
2983 | (method url-fetch) | |
2984 | (uri (bioconductor-uri "sigPathway" version)) | |
2985 | (sha256 | |
2986 | (base32 | |
3e5ee6f6 | 2987 | "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7")))) |
a6d867fe RW |
2988 | (properties `((upstream-name . "sigPathway"))) |
2989 | (build-system r-build-system) | |
2990 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") | |
2991 | (synopsis "Pathway analysis") | |
2992 | (description | |
2993 | "This package is used to conduct pathway analysis by calculating the NT_k | |
2994 | and NE_k statistics in a statistical framework for determining whether a | |
2995 | specified group of genes for a pathway has a coordinated association with a | |
2996 | phenotype of interest.") | |
2997 | (license license:gpl2))) | |
af26c7ae RW |
2998 | |
2999 | (define-public r-fgsea | |
3000 | (package | |
3001 | (name "r-fgsea") | |
9b275285 | 3002 | (version "1.10.1") |
af26c7ae RW |
3003 | (source |
3004 | (origin | |
3005 | (method url-fetch) | |
3006 | (uri (bioconductor-uri "fgsea" version)) | |
3007 | (sha256 | |
3008 | (base32 | |
9b275285 | 3009 | "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6")))) |
af26c7ae RW |
3010 | (build-system r-build-system) |
3011 | (propagated-inputs | |
ebffd24c RW |
3012 | `(("r-bh" ,r-bh) |
3013 | ("r-biocparallel" ,r-biocparallel) | |
af26c7ae RW |
3014 | ("r-data-table" ,r-data-table) |
3015 | ("r-fastmatch" ,r-fastmatch) | |
3016 | ("r-ggplot2" ,r-ggplot2) | |
3017 | ("r-gridextra" ,r-gridextra) | |
3018 | ("r-matrix" ,r-matrix) | |
3019 | ("r-rcpp" ,r-rcpp))) | |
3020 | (home-page "https://github.com/ctlab/fgsea/") | |
3021 | (synopsis "Fast gene set enrichment analysis") | |
3022 | (description | |
3023 | "The package implements an algorithm for fast gene set enrichment | |
3024 | analysis. Using the fast algorithm allows to make more permutations and get | |
3025 | more fine grained p-values, which allows to use accurate stantard approaches | |
3026 | to multiple hypothesis correction.") | |
3027 | (license license:expat))) | |
305050b5 RW |
3028 | |
3029 | (define-public r-dose | |
3030 | (package | |
3031 | (name "r-dose") | |
aff3ecbf | 3032 | (version "3.10.2") |
305050b5 RW |
3033 | (source |
3034 | (origin | |
3035 | (method url-fetch) | |
3036 | (uri (bioconductor-uri "DOSE" version)) | |
3037 | (sha256 | |
3038 | (base32 | |
aff3ecbf | 3039 | "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj")))) |
305050b5 RW |
3040 | (properties `((upstream-name . "DOSE"))) |
3041 | (build-system r-build-system) | |
3042 | (propagated-inputs | |
3043 | `(("r-annotationdbi" ,r-annotationdbi) | |
3044 | ("r-biocparallel" ,r-biocparallel) | |
3045 | ("r-do-db" ,r-do-db) | |
3046 | ("r-fgsea" ,r-fgsea) | |
3047 | ("r-ggplot2" ,r-ggplot2) | |
3048 | ("r-gosemsim" ,r-gosemsim) | |
3049 | ("r-qvalue" ,r-qvalue) | |
3050 | ("r-reshape2" ,r-reshape2) | |
3051 | ("r-s4vectors" ,r-s4vectors))) | |
3052 | (home-page "https://guangchuangyu.github.io/software/DOSE/") | |
3053 | (synopsis "Disease ontology semantic and enrichment analysis") | |
3054 | (description | |
3055 | "This package implements five methods proposed by Resnik, Schlicker, | |
3056 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among | |
3057 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses | |
3058 | including hypergeometric model and gene set enrichment analysis are also | |
3059 | implemented for discovering disease associations of high-throughput biological | |
3060 | data.") | |
3061 | (license license:artistic2.0))) | |
9c30cf65 RW |
3062 | |
3063 | (define-public r-enrichplot | |
3064 | (package | |
3065 | (name "r-enrichplot") | |
77d28d66 | 3066 | (version "1.4.0") |
9c30cf65 RW |
3067 | (source |
3068 | (origin | |
3069 | (method url-fetch) | |
3070 | (uri (bioconductor-uri "enrichplot" version)) | |
3071 | (sha256 | |
3072 | (base32 | |
77d28d66 | 3073 | "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h")))) |
9c30cf65 RW |
3074 | (build-system r-build-system) |
3075 | (propagated-inputs | |
3076 | `(("r-annotationdbi" ,r-annotationdbi) | |
3077 | ("r-cowplot" ,r-cowplot) | |
3078 | ("r-dose" ,r-dose) | |
3079 | ("r-europepmc" ,r-europepmc) | |
3080 | ("r-ggplot2" ,r-ggplot2) | |
3081 | ("r-ggplotify" ,r-ggplotify) | |
3082 | ("r-ggraph" ,r-ggraph) | |
3083 | ("r-ggridges" ,r-ggridges) | |
3084 | ("r-gosemsim" ,r-gosemsim) | |
3085 | ("r-gridextra" ,r-gridextra) | |
3086 | ("r-igraph" ,r-igraph) | |
3087 | ("r-purrr" ,r-purrr) | |
3088 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3089 | ("r-reshape2" ,r-reshape2) | |
3090 | ("r-upsetr" ,r-upsetr))) | |
3091 | (home-page "https://github.com/GuangchuangYu/enrichplot") | |
3092 | (synopsis "Visualization of functional enrichment result") | |
3093 | (description | |
3094 | "The enrichplot package implements several visualization methods for | |
3095 | interpreting functional enrichment results obtained from ORA or GSEA analyses. | |
3096 | All the visualization methods are developed based on ggplot2 graphics.") | |
3097 | (license license:artistic2.0))) | |
f8295ee6 RW |
3098 | |
3099 | (define-public r-clusterprofiler | |
3100 | (package | |
3101 | (name "r-clusterprofiler") | |
1a3e33be | 3102 | (version "3.12.0") |
f8295ee6 RW |
3103 | (source |
3104 | (origin | |
3105 | (method url-fetch) | |
3106 | (uri (bioconductor-uri "clusterProfiler" version)) | |
3107 | (sha256 | |
3108 | (base32 | |
1a3e33be | 3109 | "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq")))) |
f8295ee6 RW |
3110 | (properties |
3111 | `((upstream-name . "clusterProfiler"))) | |
3112 | (build-system r-build-system) | |
3113 | (propagated-inputs | |
3114 | `(("r-annotationdbi" ,r-annotationdbi) | |
3115 | ("r-dose" ,r-dose) | |
3116 | ("r-enrichplot" ,r-enrichplot) | |
3117 | ("r-ggplot2" ,r-ggplot2) | |
3118 | ("r-go-db" ,r-go-db) | |
3119 | ("r-gosemsim" ,r-gosemsim) | |
3120 | ("r-magrittr" ,r-magrittr) | |
3121 | ("r-plyr" ,r-plyr) | |
3122 | ("r-qvalue" ,r-qvalue) | |
3123 | ("r-rvcheck" ,r-rvcheck) | |
3124 | ("r-tidyr" ,r-tidyr))) | |
3125 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") | |
3126 | (synopsis "Analysis and visualization of functional profiles for gene clusters") | |
3127 | (description | |
3128 | "This package implements methods to analyze and visualize functional | |
3129 | profiles (GO and KEGG) of gene and gene clusters.") | |
3130 | (license license:artistic2.0))) | |
ce77562a RW |
3131 | |
3132 | (define-public r-mlinterfaces | |
3133 | (package | |
3134 | (name "r-mlinterfaces") | |
8265a111 | 3135 | (version "1.64.0") |
ce77562a RW |
3136 | (source |
3137 | (origin | |
3138 | (method url-fetch) | |
3139 | (uri (bioconductor-uri "MLInterfaces" version)) | |
3140 | (sha256 | |
3141 | (base32 | |
8265a111 | 3142 | "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j")))) |
ce77562a RW |
3143 | (properties `((upstream-name . "MLInterfaces"))) |
3144 | (build-system r-build-system) | |
3145 | (propagated-inputs | |
3146 | `(("r-annotate" ,r-annotate) | |
3147 | ("r-biobase" ,r-biobase) | |
3148 | ("r-biocgenerics" ,r-biocgenerics) | |
3149 | ("r-cluster" ,r-cluster) | |
3150 | ("r-fpc" ,r-fpc) | |
3151 | ("r-gbm" ,r-gbm) | |
3152 | ("r-gdata" ,r-gdata) | |
3153 | ("r-genefilter" ,r-genefilter) | |
3154 | ("r-ggvis" ,r-ggvis) | |
3155 | ("r-hwriter" ,r-hwriter) | |
3156 | ("r-mass" ,r-mass) | |
3157 | ("r-mlbench" ,r-mlbench) | |
3158 | ("r-pls" ,r-pls) | |
3159 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3160 | ("r-rda" ,r-rda) | |
3161 | ("r-rpart" ,r-rpart) | |
3162 | ("r-sfsmisc" ,r-sfsmisc) | |
3163 | ("r-shiny" ,r-shiny) | |
3164 | ("r-threejs" ,r-threejs))) | |
3165 | (home-page "https://bioconductor.org/packages/MLInterfaces/") | |
3166 | (synopsis "Interfaces to R machine learning procedures") | |
3167 | (description | |
3168 | "This package provides uniform interfaces to machine learning code for | |
3169 | data in R and Bioconductor containers.") | |
3170 | ;; Any version of the LGPL. | |
3171 | (license license:lgpl2.1+))) | |
a793e88c RW |
3172 | |
3173 | (define-public r-annaffy | |
3174 | (package | |
3175 | (name "r-annaffy") | |
8bef9df4 | 3176 | (version "1.56.0") |
a793e88c RW |
3177 | (source |
3178 | (origin | |
3179 | (method url-fetch) | |
3180 | (uri (bioconductor-uri "annaffy" version)) | |
3181 | (sha256 | |
3182 | (base32 | |
8bef9df4 | 3183 | "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9")))) |
a793e88c RW |
3184 | (build-system r-build-system) |
3185 | (arguments | |
3186 | `(#:phases | |
3187 | (modify-phases %standard-phases | |
3188 | (add-after 'unpack 'remove-reference-to-non-free-data | |
3189 | (lambda _ | |
3190 | (substitute* "DESCRIPTION" | |
3191 | ((", KEGG.db") "")) | |
3192 | #t))))) | |
3193 | (propagated-inputs | |
3194 | `(("r-annotationdbi" ,r-annotationdbi) | |
3195 | ("r-biobase" ,r-biobase) | |
3196 | ("r-dbi" ,r-dbi) | |
3197 | ("r-go-db" ,r-go-db))) | |
3198 | (home-page "https://bioconductor.org/packages/annaffy/") | |
3199 | (synopsis "Annotation tools for Affymetrix biological metadata") | |
3200 | (description | |
3201 | "This package provides functions for handling data from Bioconductor | |
3202 | Affymetrix annotation data packages. It produces compact HTML and text | |
3203 | reports including experimental data and URL links to many online databases. | |
3204 | It allows searching of biological metadata using various criteria.") | |
3205 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of | |
3206 | ;; the LGPL 2.1 is included. | |
3207 | (license license:lgpl2.1+))) | |
0ec0a5ec RW |
3208 | |
3209 | (define-public r-a4core | |
3210 | (package | |
3211 | (name "r-a4core") | |
b077e3db | 3212 | (version "1.32.0") |
0ec0a5ec RW |
3213 | (source |
3214 | (origin | |
3215 | (method url-fetch) | |
3216 | (uri (bioconductor-uri "a4Core" version)) | |
3217 | (sha256 | |
3218 | (base32 | |
b077e3db | 3219 | "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7")))) |
0ec0a5ec RW |
3220 | (properties `((upstream-name . "a4Core"))) |
3221 | (build-system r-build-system) | |
3222 | (propagated-inputs | |
3223 | `(("r-biobase" ,r-biobase) | |
3224 | ("r-glmnet" ,r-glmnet))) | |
3225 | (home-page "https://bioconductor.org/packages/a4Core") | |
3226 | (synopsis "Automated Affymetrix array analysis core package") | |
3227 | (description | |
3228 | "This is the core package for the automated analysis of Affymetrix | |
3229 | arrays.") | |
3230 | (license license:gpl3))) | |
9ae37581 RW |
3231 | |
3232 | (define-public r-a4classif | |
3233 | (package | |
3234 | (name "r-a4classif") | |
82de77da | 3235 | (version "1.32.0") |
9ae37581 RW |
3236 | (source |
3237 | (origin | |
3238 | (method url-fetch) | |
3239 | (uri (bioconductor-uri "a4Classif" version)) | |
3240 | (sha256 | |
3241 | (base32 | |
82de77da | 3242 | "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0")))) |
9ae37581 RW |
3243 | (properties `((upstream-name . "a4Classif"))) |
3244 | (build-system r-build-system) | |
3245 | (propagated-inputs | |
3246 | `(("r-a4core" ,r-a4core) | |
3247 | ("r-a4preproc" ,r-a4preproc) | |
3248 | ("r-glmnet" ,r-glmnet) | |
3249 | ("r-mlinterfaces" ,r-mlinterfaces) | |
3250 | ("r-pamr" ,r-pamr) | |
3251 | ("r-rocr" ,r-rocr) | |
3252 | ("r-varselrf" ,r-varselrf))) | |
3253 | (home-page "https://bioconductor.org/packages/a4Classif/") | |
3254 | (synopsis "Automated Affymetrix array analysis classification package") | |
3255 | (description | |
3256 | "This is the classification package for the automated analysis of | |
3257 | Affymetrix arrays.") | |
3258 | (license license:gpl3))) | |
b8d13e2c RW |
3259 | |
3260 | (define-public r-a4preproc | |
3261 | (package | |
3262 | (name "r-a4preproc") | |
0b609162 | 3263 | (version "1.32.0") |
b8d13e2c RW |
3264 | (source |
3265 | (origin | |
3266 | (method url-fetch) | |
3267 | (uri (bioconductor-uri "a4Preproc" version)) | |
3268 | (sha256 | |
3269 | (base32 | |
0b609162 | 3270 | "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr")))) |
b8d13e2c RW |
3271 | (properties `((upstream-name . "a4Preproc"))) |
3272 | (build-system r-build-system) | |
3273 | (propagated-inputs | |
3274 | `(("r-annotationdbi" ,r-annotationdbi))) | |
3275 | (home-page "https://bioconductor.org/packages/a4Preproc/") | |
3276 | (synopsis "Automated Affymetrix array analysis preprocessing package") | |
3277 | (description | |
3278 | "This is a package for the automated analysis of Affymetrix arrays. It | |
3279 | is used for preprocessing the arrays.") | |
3280 | (license license:gpl3))) | |
8e15f861 RW |
3281 | |
3282 | (define-public r-a4reporting | |
3283 | (package | |
3284 | (name "r-a4reporting") | |
e5a36543 | 3285 | (version "1.32.0") |
8e15f861 RW |
3286 | (source |
3287 | (origin | |
3288 | (method url-fetch) | |
3289 | (uri (bioconductor-uri "a4Reporting" version)) | |
3290 | (sha256 | |
3291 | (base32 | |
e5a36543 | 3292 | "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj")))) |
8e15f861 RW |
3293 | (properties `((upstream-name . "a4Reporting"))) |
3294 | (build-system r-build-system) | |
3295 | (propagated-inputs | |
3296 | `(("r-annaffy" ,r-annaffy) | |
3297 | ("r-xtable" ,r-xtable))) | |
3298 | (home-page "https://bioconductor.org/packages/a4Reporting/") | |
3299 | (synopsis "Automated Affymetrix array analysis reporting package") | |
3300 | (description | |
3301 | "This is a package for the automated analysis of Affymetrix arrays. It | |
3302 | provides reporting features.") | |
3303 | (license license:gpl3))) | |
dbfe3375 RW |
3304 | |
3305 | (define-public r-a4base | |
3306 | (package | |
3307 | (name "r-a4base") | |
ae1730ae | 3308 | (version "1.32.0") |
dbfe3375 RW |
3309 | (source |
3310 | (origin | |
3311 | (method url-fetch) | |
3312 | (uri (bioconductor-uri "a4Base" version)) | |
3313 | (sha256 | |
3314 | (base32 | |
ae1730ae | 3315 | "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1")))) |
dbfe3375 RW |
3316 | (properties `((upstream-name . "a4Base"))) |
3317 | (build-system r-build-system) | |
3318 | (propagated-inputs | |
3319 | `(("r-a4core" ,r-a4core) | |
3320 | ("r-a4preproc" ,r-a4preproc) | |
3321 | ("r-annaffy" ,r-annaffy) | |
3322 | ("r-annotationdbi" ,r-annotationdbi) | |
3323 | ("r-biobase" ,r-biobase) | |
3324 | ("r-genefilter" ,r-genefilter) | |
3325 | ("r-glmnet" ,r-glmnet) | |
3326 | ("r-gplots" ,r-gplots) | |
3327 | ("r-limma" ,r-limma) | |
3328 | ("r-mpm" ,r-mpm) | |
3329 | ("r-multtest" ,r-multtest))) | |
3330 | (home-page "https://bioconductor.org/packages/a4Base/") | |
3331 | (synopsis "Automated Affymetrix array analysis base package") | |
3332 | (description | |
3333 | "This package provides basic features for the automated analysis of | |
3334 | Affymetrix arrays.") | |
3335 | (license license:gpl3))) | |
84ad024e RW |
3336 | |
3337 | (define-public r-a4 | |
3338 | (package | |
3339 | (name "r-a4") | |
1aadddea | 3340 | (version "1.32.0") |
84ad024e RW |
3341 | (source |
3342 | (origin | |
3343 | (method url-fetch) | |
3344 | (uri (bioconductor-uri "a4" version)) | |
3345 | (sha256 | |
3346 | (base32 | |
1aadddea | 3347 | "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy")))) |
84ad024e RW |
3348 | (build-system r-build-system) |
3349 | (propagated-inputs | |
3350 | `(("r-a4base" ,r-a4base) | |
3351 | ("r-a4classif" ,r-a4classif) | |
3352 | ("r-a4core" ,r-a4core) | |
3353 | ("r-a4preproc" ,r-a4preproc) | |
3354 | ("r-a4reporting" ,r-a4reporting))) | |
3355 | (home-page "https://bioconductor.org/packages/a4/") | |
3356 | (synopsis "Automated Affymetrix array analysis umbrella package") | |
3357 | (description | |
3358 | "This package provides a software suite for the automated analysis of | |
3359 | Affymetrix arrays.") | |
3360 | (license license:gpl3))) | |
59d331f1 RW |
3361 | |
3362 | (define-public r-abseqr | |
3363 | (package | |
3364 | (name "r-abseqr") | |
b7ddf0f0 | 3365 | (version "1.2.0") |
59d331f1 RW |
3366 | (source |
3367 | (origin | |
3368 | (method url-fetch) | |
3369 | (uri (bioconductor-uri "abseqR" version)) | |
3370 | (sha256 | |
3371 | (base32 | |
b7ddf0f0 | 3372 | "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r")))) |
59d331f1 RW |
3373 | (properties `((upstream-name . "abseqR"))) |
3374 | (build-system r-build-system) | |
3375 | (inputs | |
3376 | `(("pandoc" ,ghc-pandoc))) | |
3377 | (propagated-inputs | |
3378 | `(("r-biocparallel" ,r-biocparallel) | |
3379 | ("r-biocstyle" ,r-biocstyle) | |
3380 | ("r-circlize" ,r-circlize) | |
3381 | ("r-flexdashboard" ,r-flexdashboard) | |
3382 | ("r-ggcorrplot" ,r-ggcorrplot) | |
3383 | ("r-ggdendro" ,r-ggdendro) | |
3384 | ("r-ggplot2" ,r-ggplot2) | |
3385 | ("r-gridextra" ,r-gridextra) | |
3386 | ("r-knitr" ,r-knitr) | |
3387 | ("r-plotly" ,r-plotly) | |
3388 | ("r-plyr" ,r-plyr) | |
3389 | ("r-png" ,r-png) | |
3390 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3391 | ("r-reshape2" ,r-reshape2) | |
3392 | ("r-rmarkdown" ,r-rmarkdown) | |
3393 | ("r-stringr" ,r-stringr) | |
3394 | ("r-vegan" ,r-vegan) | |
3395 | ("r-venndiagram" ,r-venndiagram))) | |
3396 | (home-page "https://github.com/malhamdoosh/abseqR") | |
3397 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") | |
3398 | (description | |
3399 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of | |
3400 | sequencing datasets generated from antibody libraries and abseqR is one of its | |
3401 | packages. AbseqR empowers the users of abseqPy with plotting and reporting | |
3402 | capabilities and allows them to generate interactive HTML reports for the | |
3403 | convenience of viewing and sharing with other researchers. Additionally, | |
3404 | abseqR extends abseqPy to compare multiple repertoire analyses and perform | |
3405 | further downstream analysis on its output.") | |
3406 | (license license:gpl3))) | |
41aab7d1 RW |
3407 | |
3408 | (define-public r-bacon | |
3409 | (package | |
3410 | (name "r-bacon") | |
e33c25ff | 3411 | (version "1.12.0") |
41aab7d1 RW |
3412 | (source |
3413 | (origin | |
3414 | (method url-fetch) | |
3415 | (uri (bioconductor-uri "bacon" version)) | |
3416 | (sha256 | |
3417 | (base32 | |
e33c25ff | 3418 | "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q")))) |
41aab7d1 RW |
3419 | (build-system r-build-system) |
3420 | (propagated-inputs | |
3421 | `(("r-biocparallel" ,r-biocparallel) | |
3422 | ("r-ellipse" ,r-ellipse) | |
3423 | ("r-ggplot2" ,r-ggplot2))) | |
3424 | (home-page "https://bioconductor.org/packages/bacon/") | |
3425 | (synopsis "Controlling bias and inflation in association studies") | |
3426 | (description | |
3427 | "Bacon can be used to remove inflation and bias often observed in | |
3428 | epigenome- and transcriptome-wide association studies. To this end bacon | |
3429 | constructs an empirical null distribution using a Gibbs Sampling algorithm by | |
3430 | fitting a three-component normal mixture on z-scores.") | |
3431 | (license license:gpl2+))) | |
051e8e1a RW |
3432 | |
3433 | (define-public r-rgadem | |
3434 | (package | |
3435 | (name "r-rgadem") | |
93f8a009 | 3436 | (version "2.32.0") |
051e8e1a RW |
3437 | (source |
3438 | (origin | |
3439 | (method url-fetch) | |
3440 | (uri (bioconductor-uri "rGADEM" version)) | |
3441 | (sha256 | |
3442 | (base32 | |
93f8a009 | 3443 | "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18")))) |
051e8e1a RW |
3444 | (properties `((upstream-name . "rGADEM"))) |
3445 | (build-system r-build-system) | |
3446 | (propagated-inputs | |
3447 | `(("r-biostrings" ,r-biostrings) | |
3448 | ("r-bsgenome" ,r-bsgenome) | |
3449 | ("r-iranges" ,r-iranges) | |
3450 | ("r-seqlogo" ,r-seqlogo))) | |
3451 | (home-page "https://bioconductor.org/packages/rGADEM/") | |
3452 | (synopsis "De novo sequence motif discovery") | |
3453 | (description | |
3454 | "rGADEM is an efficient de novo motif discovery tool for large-scale | |
3455 | genomic sequence data.") | |
3456 | (license license:artistic2.0))) | |
229f97c3 RW |
3457 | |
3458 | (define-public r-motiv | |
3459 | (package | |
3460 | (name "r-motiv") | |
f7a495b1 | 3461 | (version "1.40.0") |
229f97c3 RW |
3462 | (source |
3463 | (origin | |
3464 | (method url-fetch) | |
3465 | (uri (bioconductor-uri "MotIV" version)) | |
3466 | (sha256 | |
3467 | (base32 | |
f7a495b1 | 3468 | "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf")))) |
229f97c3 RW |
3469 | (properties `((upstream-name . "MotIV"))) |
3470 | (build-system r-build-system) | |
3471 | (inputs | |
3472 | `(("gsl" ,gsl))) | |
3473 | (propagated-inputs | |
3474 | `(("r-biocgenerics" ,r-biocgenerics) | |
3475 | ("r-biostrings" ,r-biostrings) | |
3476 | ("r-iranges" ,r-iranges) | |
3477 | ("r-lattice" ,r-lattice) | |
3478 | ("r-rgadem" ,r-rgadem) | |
3479 | ("r-s4vectors" ,r-s4vectors))) | |
3480 | (home-page "https://bioconductor.org/packages/MotIV/") | |
3481 | (synopsis "Motif identification and validation") | |
3482 | (description | |
3483 | "This package is used for the identification and validation of sequence | |
3484 | motifs. It makes use of STAMP for comparing a set of motifs to a given | |
3485 | database (e.g. JASPAR). It can also be used to visualize motifs, motif | |
3486 | distributions, modules and filter motifs.") | |
3487 | (license license:gpl2))) | |
2a72ef56 RW |
3488 | |
3489 | (define-public r-motifstack | |
3490 | (package | |
3491 | (name "r-motifstack") | |
aa0ebfd2 | 3492 | (version "1.28.0") |
2a72ef56 RW |
3493 | (source |
3494 | (origin | |
3495 | (method url-fetch) | |
3496 | (uri (bioconductor-uri "motifStack" version)) | |
3497 | (sha256 | |
3498 | (base32 | |
aa0ebfd2 | 3499 | "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f")))) |
2a72ef56 RW |
3500 | (properties `((upstream-name . "motifStack"))) |
3501 | (build-system r-build-system) | |
3502 | (propagated-inputs | |
3503 | `(("r-ade4" ,r-ade4) | |
3504 | ("r-biostrings" ,r-biostrings) | |
aa0ebfd2 | 3505 | ("r-grimport2" ,r-grimport2) |
2a72ef56 RW |
3506 | ("r-htmlwidgets" ,r-htmlwidgets) |
3507 | ("r-motiv" ,r-motiv) | |
3508 | ("r-scales" ,r-scales) | |
3509 | ("r-xml" ,r-xml))) | |
3510 | (home-page "https://bioconductor.org/packages/motifStack/") | |
3511 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") | |
3512 | (description | |
3513 | "The motifStack package is designed for graphic representation of | |
3514 | multiple motifs with different similarity scores. It works with both DNA/RNA | |
3515 | sequence motifs and amino acid sequence motifs. In addition, it provides the | |
3516 | flexibility for users to customize the graphic parameters such as the font | |
3517 | type and symbol colors.") | |
3518 | (license license:gpl2+))) | |
e5bff307 RW |
3519 | |
3520 | (define-public r-genomicscores | |
3521 | (package | |
3522 | (name "r-genomicscores") | |
3c944fda | 3523 | (version "1.8.1") |
e5bff307 RW |
3524 | (source |
3525 | (origin | |
3526 | (method url-fetch) | |
3527 | (uri (bioconductor-uri "GenomicScores" version)) | |
3528 | (sha256 | |
3529 | (base32 | |
3c944fda | 3530 | "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy")))) |
e5bff307 RW |
3531 | (properties `((upstream-name . "GenomicScores"))) |
3532 | (build-system r-build-system) | |
3533 | (propagated-inputs | |
3534 | `(("r-annotationhub" ,r-annotationhub) | |
3535 | ("r-biobase" ,r-biobase) | |
3536 | ("r-biocgenerics" ,r-biocgenerics) | |
3537 | ("r-biostrings" ,r-biostrings) | |
3538 | ("r-bsgenome" ,r-bsgenome) | |
3539 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3540 | ("r-genomicranges" ,r-genomicranges) | |
3541 | ("r-iranges" ,r-iranges) | |
3542 | ("r-s4vectors" ,r-s4vectors) | |
3543 | ("r-xml" ,r-xml))) | |
3544 | (home-page "https://github.com/rcastelo/GenomicScores/") | |
3545 | (synopsis "Work with genome-wide position-specific scores") | |
3546 | (description | |
3547 | "This package provides infrastructure to store and access genome-wide | |
3548 | position-specific scores within R and Bioconductor.") | |
3549 | (license license:artistic2.0))) | |
32e0f906 RW |
3550 | |
3551 | (define-public r-atacseqqc | |
3552 | (package | |
3553 | (name "r-atacseqqc") | |
fbe5a087 | 3554 | (version "1.8.5") |
32e0f906 RW |
3555 | (source |
3556 | (origin | |
3557 | (method url-fetch) | |
3558 | (uri (bioconductor-uri "ATACseqQC" version)) | |
3559 | (sha256 | |
3560 | (base32 | |
fbe5a087 | 3561 | "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp")))) |
32e0f906 RW |
3562 | (properties `((upstream-name . "ATACseqQC"))) |
3563 | (build-system r-build-system) | |
3564 | (propagated-inputs | |
3565 | `(("r-biocgenerics" ,r-biocgenerics) | |
3566 | ("r-biostrings" ,r-biostrings) | |
3567 | ("r-bsgenome" ,r-bsgenome) | |
3568 | ("r-chippeakanno" ,r-chippeakanno) | |
bcc233c1 | 3569 | ("r-edger" ,r-edger) |
32e0f906 RW |
3570 | ("r-genomeinfodb" ,r-genomeinfodb) |
3571 | ("r-genomicalignments" ,r-genomicalignments) | |
3572 | ("r-genomicranges" ,r-genomicranges) | |
3573 | ("r-genomicscores" ,r-genomicscores) | |
3574 | ("r-iranges" ,r-iranges) | |
3575 | ("r-kernsmooth" ,r-kernsmooth) | |
3576 | ("r-limma" ,r-limma) | |
3577 | ("r-motifstack" ,r-motifstack) | |
3578 | ("r-preseqr" ,r-preseqr) | |
3579 | ("r-randomforest" ,r-randomforest) | |
3580 | ("r-rsamtools" ,r-rsamtools) | |
3581 | ("r-rtracklayer" ,r-rtracklayer) | |
3582 | ("r-s4vectors" ,r-s4vectors))) | |
3583 | (home-page "https://bioconductor.org/packages/ATACseqQC/") | |
3584 | (synopsis "ATAC-seq quality control") | |
3585 | (description | |
3586 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using | |
3587 | sequencing, is a rapid and sensitive method for chromatin accessibility | |
3588 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq | |
3589 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly | |
3590 | assess whether their ATAC-seq experiment is successful. It includes | |
3591 | diagnostic plots of fragment size distribution, proportion of mitochondria | |
3592 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor | |
3593 | footprints.") | |
3594 | (license license:gpl2+))) | |
3972cfce RW |
3595 | |
3596 | (define-public r-gofuncr | |
3597 | (package | |
3598 | (name "r-gofuncr") | |
bab06a6f | 3599 | (version "1.4.0") |
3972cfce RW |
3600 | (source |
3601 | (origin | |
3602 | (method url-fetch) | |
3603 | (uri (bioconductor-uri "GOfuncR" version)) | |
3604 | (sha256 | |
3605 | (base32 | |
bab06a6f | 3606 | "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm")))) |
3972cfce RW |
3607 | (properties `((upstream-name . "GOfuncR"))) |
3608 | (build-system r-build-system) | |
3609 | (propagated-inputs | |
3610 | `(("r-annotationdbi" ,r-annotationdbi) | |
3611 | ("r-genomicranges" ,r-genomicranges) | |
3612 | ("r-gtools" ,r-gtools) | |
3613 | ("r-iranges" ,r-iranges) | |
3614 | ("r-mapplots" ,r-mapplots) | |
3615 | ("r-rcpp" ,r-rcpp) | |
3616 | ("r-vioplot" ,r-vioplot))) | |
3617 | (home-page "https://bioconductor.org/packages/GOfuncR/") | |
3618 | (synopsis "Gene ontology enrichment using FUNC") | |
3619 | (description | |
3620 | "GOfuncR performs a gene ontology enrichment analysis based on the | |
3621 | ontology enrichment software FUNC. GO-annotations are obtained from | |
3622 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is | |
3623 | included in the package and updated regularly. GOfuncR provides the standard | |
3624 | candidate vs background enrichment analysis using the hypergeometric test, as | |
3625 | well as three additional tests: | |
3626 | ||
3627 | @enumerate | |
3628 | @item the Wilcoxon rank-sum test that is used when genes are ranked, | |
3629 | @item a binomial test that is used when genes are associated with two counts, | |
3630 | and | |
3631 | @item a Chi-square or Fisher's exact test that is used in cases when genes are | |
3632 | associated with four counts. | |
3633 | @end enumerate | |
3634 | ||
3635 | To correct for multiple testing and interdependency of the tests, family-wise | |
3636 | error rates are computed based on random permutations of the gene-associated | |
3637 | variables. GOfuncR also provides tools for exploring the ontology graph and | |
3638 | the annotations, and options to take gene-length or spatial clustering of | |
3639 | genes into account. It is also possible to provide custom gene coordinates, | |
3640 | annotations and ontologies.") | |
3641 | (license license:gpl2+))) | |
9bf4bb19 RW |
3642 | |
3643 | (define-public r-abaenrichment | |
3644 | (package | |
3645 | (name "r-abaenrichment") | |
d6158ecb | 3646 | (version "1.14.1") |
9bf4bb19 RW |
3647 | (source |
3648 | (origin | |
3649 | (method url-fetch) | |
3650 | (uri (bioconductor-uri "ABAEnrichment" version)) | |
3651 | (sha256 | |
3652 | (base32 | |
d6158ecb | 3653 | "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48")))) |
9bf4bb19 RW |
3654 | (properties `((upstream-name . "ABAEnrichment"))) |
3655 | (build-system r-build-system) | |
3656 | (propagated-inputs | |
3657 | `(("r-abadata" ,r-abadata) | |
3658 | ("r-data-table" ,r-data-table) | |
3659 | ("r-gofuncr" ,r-gofuncr) | |
3660 | ("r-gplots" ,r-gplots) | |
3661 | ("r-gtools" ,r-gtools) | |
3662 | ("r-rcpp" ,r-rcpp))) | |
3663 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") | |
3664 | (synopsis "Gene expression enrichment in human brain regions") | |
3665 | (description | |
3666 | "The package ABAEnrichment is designed to test for enrichment of user | |
3667 | defined candidate genes in the set of expressed genes in different human brain | |
3668 | regions. The core function @code{aba_enrich} integrates the expression of the | |
3669 | candidate gene set (averaged across donors) and the structural information of | |
3670 | the brain using an ontology, both provided by the Allen Brain Atlas project.") | |
3671 | (license license:gpl2+))) | |
0b91b7b9 RW |
3672 | |
3673 | (define-public r-annotationfuncs | |
3674 | (package | |
3675 | (name "r-annotationfuncs") | |
69a2ec54 | 3676 | (version "1.34.0") |
0b91b7b9 RW |
3677 | (source |
3678 | (origin | |
3679 | (method url-fetch) | |
3680 | (uri (bioconductor-uri "AnnotationFuncs" version)) | |
3681 | (sha256 | |
3682 | (base32 | |
69a2ec54 | 3683 | "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3")))) |
0b91b7b9 RW |
3684 | (properties |
3685 | `((upstream-name . "AnnotationFuncs"))) | |
3686 | (build-system r-build-system) | |
3687 | (propagated-inputs | |
3688 | `(("r-annotationdbi" ,r-annotationdbi) | |
3689 | ("r-dbi" ,r-dbi))) | |
3690 | (home-page "https://www.iysik.com/r/annotationfuncs") | |
3691 | (synopsis "Annotation translation functions") | |
3692 | (description | |
3693 | "This package provides functions for handling translating between | |
3694 | different identifieres using the Biocore Data Team data-packages (e.g. | |
3695 | @code{org.Bt.eg.db}).") | |
3696 | (license license:gpl2))) | |
adf7d813 RW |
3697 | |
3698 | (define-public r-annotationtools | |
3699 | (package | |
3700 | (name "r-annotationtools") | |
ee1a45d7 | 3701 | (version "1.58.0") |
adf7d813 RW |
3702 | (source |
3703 | (origin | |
3704 | (method url-fetch) | |
3705 | (uri (bioconductor-uri "annotationTools" version)) | |
3706 | (sha256 | |
3707 | (base32 | |
ee1a45d7 | 3708 | "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1")))) |
adf7d813 RW |
3709 | (properties |
3710 | `((upstream-name . "annotationTools"))) | |
3711 | (build-system r-build-system) | |
3712 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
3713 | (home-page "https://bioconductor.org/packages/annotationTools/") | |
3714 | (synopsis "Annotate microarrays and perform gene expression analyses") | |
3715 | (description | |
3716 | "This package provides functions to annotate microarrays, find orthologs, | |
3717 | and integrate heterogeneous gene expression profiles using annotation and | |
3718 | other molecular biology information available as flat file database (plain | |
3719 | text files).") | |
3720 | ;; Any version of the GPL. | |
3721 | (license (list license:gpl2+)))) | |
f31e10f8 RW |
3722 | |
3723 | (define-public r-allelicimbalance | |
3724 | (package | |
3725 | (name "r-allelicimbalance") | |
9da2021f | 3726 | (version "1.22.0") |
f31e10f8 RW |
3727 | (source |
3728 | (origin | |
3729 | (method url-fetch) | |
3730 | (uri (bioconductor-uri "AllelicImbalance" version)) | |
3731 | (sha256 | |
3732 | (base32 | |
9da2021f | 3733 | "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng")))) |
f31e10f8 RW |
3734 | (properties |
3735 | `((upstream-name . "AllelicImbalance"))) | |
3736 | (build-system r-build-system) | |
3737 | (propagated-inputs | |
3738 | `(("r-annotationdbi" ,r-annotationdbi) | |
3739 | ("r-biocgenerics" ,r-biocgenerics) | |
3740 | ("r-biostrings" ,r-biostrings) | |
3741 | ("r-bsgenome" ,r-bsgenome) | |
3742 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3743 | ("r-genomicalignments" ,r-genomicalignments) | |
3744 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3745 | ("r-genomicranges" ,r-genomicranges) | |
3746 | ("r-gridextra" ,r-gridextra) | |
3747 | ("r-gviz" ,r-gviz) | |
3748 | ("r-iranges" ,r-iranges) | |
3749 | ("r-lattice" ,r-lattice) | |
3750 | ("r-latticeextra" ,r-latticeextra) | |
3751 | ("r-nlme" ,r-nlme) | |
3752 | ("r-rsamtools" ,r-rsamtools) | |
3753 | ("r-s4vectors" ,r-s4vectors) | |
3754 | ("r-seqinr" ,r-seqinr) | |
3755 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
3756 | ("r-variantannotation" ,r-variantannotation))) | |
3757 | (home-page "https://github.com/pappewaio/AllelicImbalance") | |
3758 | (synopsis "Investigate allele-specific expression") | |
3759 | (description | |
3760 | "This package provides a framework for allele-specific expression | |
3761 | investigation using RNA-seq data.") | |
3762 | (license license:gpl3))) | |
ffe7029b RW |
3763 | |
3764 | (define-public r-aucell | |
3765 | (package | |
3766 | (name "r-aucell") | |
61730c3d | 3767 | (version "1.6.1") |
ffe7029b RW |
3768 | (source |
3769 | (origin | |
3770 | (method url-fetch) | |
3771 | (uri (bioconductor-uri "AUCell" version)) | |
3772 | (sha256 | |
3773 | (base32 | |
61730c3d | 3774 | "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b")))) |
ffe7029b RW |
3775 | (properties `((upstream-name . "AUCell"))) |
3776 | (build-system r-build-system) | |
3777 | (propagated-inputs | |
3778 | `(("r-data-table" ,r-data-table) | |
3779 | ("r-gseabase" ,r-gseabase) | |
3780 | ("r-mixtools" ,r-mixtools) | |
3781 | ("r-r-utils" ,r-r-utils) | |
3782 | ("r-shiny" ,r-shiny) | |
3783 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
3784 | (home-page "https://bioconductor.org/packages/AUCell/") | |
3785 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") | |
3786 | (description | |
3787 | "AUCell allows to identify cells with active gene sets (e.g. signatures, | |
3788 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area | |
3789 | Under the Curve} (AUC) to calculate whether a critical subset of the input | |
3790 | gene set is enriched within the expressed genes for each cell. The | |
3791 | distribution of AUC scores across all the cells allows exploring the relative | |
3792 | expression of the signature. Since the scoring method is ranking-based, | |
3793 | AUCell is independent of the gene expression units and the normalization | |
3794 | procedure. In addition, since the cells are evaluated individually, it can | |
3795 | easily be applied to bigger datasets, subsetting the expression matrix if | |
3796 | needed.") | |
3797 | (license license:gpl3))) | |
5cfa4bff RW |
3798 | |
3799 | (define-public r-ebimage | |
3800 | (package | |
3801 | (name "r-ebimage") | |
2a6d8383 | 3802 | (version "4.26.0") |
5cfa4bff RW |
3803 | (source |
3804 | (origin | |
3805 | (method url-fetch) | |
3806 | (uri (bioconductor-uri "EBImage" version)) | |
3807 | (sha256 | |
3808 | (base32 | |
2a6d8383 | 3809 | "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq")))) |
5cfa4bff RW |
3810 | (properties `((upstream-name . "EBImage"))) |
3811 | (build-system r-build-system) | |
3812 | (propagated-inputs | |
3813 | `(("r-abind" ,r-abind) | |
3814 | ("r-biocgenerics" ,r-biocgenerics) | |
3815 | ("r-fftwtools" ,r-fftwtools) | |
3816 | ("r-htmltools" ,r-htmltools) | |
3817 | ("r-htmlwidgets" ,r-htmlwidgets) | |
3818 | ("r-jpeg" ,r-jpeg) | |
3819 | ("r-locfit" ,r-locfit) | |
3820 | ("r-png" ,r-png) | |
3821 | ("r-rcurl" ,r-rcurl) | |
3822 | ("r-tiff" ,r-tiff))) | |
3823 | (native-inputs | |
3824 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
3825 | (home-page "https://github.com/aoles/EBImage") | |
3826 | (synopsis "Image processing and analysis toolbox for R") | |
3827 | (description | |
3828 | "EBImage provides general purpose functionality for image processing and | |
3829 | analysis. In the context of (high-throughput) microscopy-based cellular | |
3830 | assays, EBImage offers tools to segment cells and extract quantitative | |
3831 | cellular descriptors. This allows the automation of such tasks using the R | |
3832 | programming language and facilitates the use of other tools in the R | |
3833 | environment for signal processing, statistical modeling, machine learning and | |
3834 | visualization with image data.") | |
3835 | ;; Any version of the LGPL. | |
3836 | (license license:lgpl2.1+))) | |
51e98f7e RW |
3837 | |
3838 | (define-public r-yamss | |
3839 | (package | |
3840 | (name "r-yamss") | |
1269a926 | 3841 | (version "1.10.0") |
51e98f7e RW |
3842 | (source |
3843 | (origin | |
3844 | (method url-fetch) | |
3845 | (uri (bioconductor-uri "yamss" version)) | |
3846 | (sha256 | |
3847 | (base32 | |
1269a926 | 3848 | "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23")))) |
51e98f7e RW |
3849 | (build-system r-build-system) |
3850 | (propagated-inputs | |
3851 | `(("r-biocgenerics" ,r-biocgenerics) | |
3852 | ("r-data-table" ,r-data-table) | |
3853 | ("r-ebimage" ,r-ebimage) | |
3854 | ("r-iranges" ,r-iranges) | |
3855 | ("r-limma" ,r-limma) | |
3856 | ("r-matrix" ,r-matrix) | |
3857 | ("r-mzr" ,r-mzr) | |
3858 | ("r-s4vectors" ,r-s4vectors) | |
3859 | ("r-summarizedexperiment" | |
3860 | ,r-summarizedexperiment))) | |
3861 | (home-page "https://github.com/hansenlab/yamss") | |
3862 | (synopsis "Tools for high-throughput metabolomics") | |
3863 | (description | |
3864 | "This package provides tools to analyze and visualize high-throughput | |
9b19734c | 3865 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
51e98f7e RW |
3866 | preprocess data in a way that enables reliable and powerful differential |
3867 | analysis.") | |
3868 | (license license:artistic2.0))) | |
398c4a93 RW |
3869 | |
3870 | (define-public r-gtrellis | |
3871 | (package | |
3872 | (name "r-gtrellis") | |
128c6d59 | 3873 | (version "1.16.0") |
398c4a93 RW |
3874 | (source |
3875 | (origin | |
3876 | (method url-fetch) | |
3877 | (uri (bioconductor-uri "gtrellis" version)) | |
3878 | (sha256 | |
3879 | (base32 | |
128c6d59 | 3880 | "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y")))) |
398c4a93 RW |
3881 | (build-system r-build-system) |
3882 | (propagated-inputs | |
3883 | `(("r-circlize" ,r-circlize) | |
3884 | ("r-genomicranges" ,r-genomicranges) | |
3885 | ("r-getoptlong" ,r-getoptlong) | |
3886 | ("r-iranges" ,r-iranges))) | |
3887 | (home-page "https://github.com/jokergoo/gtrellis") | |
3888 | (synopsis "Genome level Trellis layout") | |
3889 | (description | |
3890 | "Genome level Trellis graph visualizes genomic data conditioned by | |
3891 | genomic categories (e.g. chromosomes). For each genomic category, multiple | |
3892 | dimensional data which are represented as tracks describe different features | |
3893 | from different aspects. This package provides high flexibility to arrange | |
3894 | genomic categories and to add self-defined graphics in the plot.") | |
3895 | (license license:expat))) | |
28098414 RW |
3896 | |
3897 | (define-public r-somaticsignatures | |
3898 | (package | |
3899 | (name "r-somaticsignatures") | |
3cdc5d1a | 3900 | (version "2.20.0") |
28098414 RW |
3901 | (source |
3902 | (origin | |
3903 | (method url-fetch) | |
3904 | (uri (bioconductor-uri "SomaticSignatures" version)) | |
3905 | (sha256 | |
3906 | (base32 | |
3cdc5d1a | 3907 | "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx")))) |
28098414 RW |
3908 | (properties |
3909 | `((upstream-name . "SomaticSignatures"))) | |
3910 | (build-system r-build-system) | |
3911 | (propagated-inputs | |
3912 | `(("r-biobase" ,r-biobase) | |
3913 | ("r-biostrings" ,r-biostrings) | |
3914 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3915 | ("r-genomicranges" ,r-genomicranges) | |
3916 | ("r-ggbio" ,r-ggbio) | |
3917 | ("r-ggplot2" ,r-ggplot2) | |
3918 | ("r-iranges" ,r-iranges) | |
3919 | ("r-nmf" ,r-nmf) | |
3920 | ("r-pcamethods" ,r-pcamethods) | |
3921 | ("r-proxy" ,r-proxy) | |
3922 | ("r-reshape2" ,r-reshape2) | |
3923 | ("r-s4vectors" ,r-s4vectors) | |
3924 | ("r-variantannotation" ,r-variantannotation))) | |
3925 | (home-page "https://github.com/juliangehring/SomaticSignatures") | |
3926 | (synopsis "Somatic signatures") | |
3927 | (description | |
3928 | "This package identifies mutational signatures of @dfn{single nucleotide | |
3929 | variants} (SNVs). It provides a infrastructure related to the methodology | |
3930 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix | |
3931 | decomposition algorithms.") | |
3932 | (license license:expat))) | |
303f2ed1 RW |
3933 | |
3934 | (define-public r-yapsa | |
3935 | (package | |
3936 | (name "r-yapsa") | |
edba69b2 | 3937 | (version "1.10.0") |
303f2ed1 RW |
3938 | (source |
3939 | (origin | |
3940 | (method url-fetch) | |
3941 | (uri (bioconductor-uri "YAPSA" version)) | |
3942 | (sha256 | |
3943 | (base32 | |
edba69b2 | 3944 | "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q")))) |
303f2ed1 RW |
3945 | (properties `((upstream-name . "YAPSA"))) |
3946 | (build-system r-build-system) | |
3947 | (propagated-inputs | |
3948 | `(("r-circlize" ,r-circlize) | |
3949 | ("r-complexheatmap" ,r-complexheatmap) | |
3950 | ("r-corrplot" ,r-corrplot) | |
3951 | ("r-dendextend" ,r-dendextend) | |
3952 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3953 | ("r-genomicranges" ,r-genomicranges) | |
3954 | ("r-getoptlong" ,r-getoptlong) | |
3955 | ("r-ggplot2" ,r-ggplot2) | |
3956 | ("r-gridextra" ,r-gridextra) | |
3957 | ("r-gtrellis" ,r-gtrellis) | |
3958 | ("r-keggrest" ,r-keggrest) | |
3959 | ("r-lsei" ,r-lsei) | |
3960 | ("r-pmcmr" ,r-pmcmr) | |
3961 | ("r-reshape2" ,r-reshape2) | |
3962 | ("r-somaticsignatures" ,r-somaticsignatures) | |
3963 | ("r-variantannotation" ,r-variantannotation))) | |
3964 | (home-page "https://bioconductor.org/packages/YAPSA/") | |
3965 | (synopsis "Yet another package for signature analysis") | |
3966 | (description | |
3967 | "This package provides functions and routines useful in the analysis of | |
3968 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, | |
3969 | functions to perform a signature analysis with known signatures and a | |
3970 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are | |
3971 | provided.") | |
3972 | (license license:gpl3))) | |
e99380d6 RW |
3973 | |
3974 | (define-public r-gcrma | |
3975 | (package | |
3976 | (name "r-gcrma") | |
56576bea | 3977 | (version "2.56.0") |
e99380d6 RW |
3978 | (source |
3979 | (origin | |
3980 | (method url-fetch) | |
3981 | (uri (bioconductor-uri "gcrma" version)) | |
3982 | (sha256 | |
3983 | (base32 | |
56576bea | 3984 | "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4")))) |
e99380d6 RW |
3985 | (build-system r-build-system) |
3986 | (propagated-inputs | |
3987 | `(("r-affy" ,r-affy) | |
3988 | ("r-affyio" ,r-affyio) | |
3989 | ("r-biobase" ,r-biobase) | |
3990 | ("r-biocmanager" ,r-biocmanager) | |
3991 | ("r-biostrings" ,r-biostrings) | |
3992 | ("r-xvector" ,r-xvector))) | |
3993 | (home-page "https://bioconductor.org/packages/gcrma/") | |
3994 | (synopsis "Background adjustment using sequence information") | |
3995 | (description | |
3996 | "Gcrma adjusts for background intensities in Affymetrix array data which | |
3997 | include optical noise and @dfn{non-specific binding} (NSB). The main function | |
3998 | @code{gcrma} converts background adjusted probe intensities to expression | |
3999 | measures using the same normalization and summarization methods as a | |
4000 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information | |
4001 | to estimate probe affinity to NSB. The sequence information is summarized in | |
4002 | a more complex way than the simple GC content. Instead, the base types (A, T, | |
4003 | G or C) at each position along the probe determine the affinity of each probe. | |
4004 | The parameters of the position-specific base contributions to the probe | |
4005 | affinity is estimated in an NSB experiment in which only NSB but no | |
4006 | gene-specific bidning is expected.") | |
4007 | ;; Any version of the LGPL | |
4008 | (license license:lgpl2.1+))) | |
4675b3cf RW |
4009 | |
4010 | (define-public r-simpleaffy | |
4011 | (package | |
4012 | (name "r-simpleaffy") | |
38c5d13a | 4013 | (version "2.60.0") |
4675b3cf RW |
4014 | (source |
4015 | (origin | |
4016 | (method url-fetch) | |
4017 | (uri (bioconductor-uri "simpleaffy" version)) | |
4018 | (sha256 | |
4019 | (base32 | |
38c5d13a | 4020 | "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a")))) |
4675b3cf RW |
4021 | (build-system r-build-system) |
4022 | (propagated-inputs | |
4023 | `(("r-affy" ,r-affy) | |
4024 | ("r-biobase" ,r-biobase) | |
4025 | ("r-biocgenerics" ,r-biocgenerics) | |
4026 | ("r-gcrma" ,r-gcrma) | |
4027 | ("r-genefilter" ,r-genefilter))) | |
4028 | (home-page "https://bioconductor.org/packages/simpleaffy/") | |
4029 | (synopsis "Very simple high level analysis of Affymetrix data") | |
4030 | (description | |
4031 | "This package provides high level functions for reading Affy @file{.CEL} | |
4032 | files, phenotypic data, and then computing simple things with it, such as | |
4033 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} | |
4034 | library. It also has some basic scatter plot functions and mechanisms for | |
4035 | generating high resolution journal figures.") | |
4036 | (license license:gpl2+))) | |
f562c90a RW |
4037 | |
4038 | (define-public r-yaqcaffy | |
4039 | (package | |
4040 | (name "r-yaqcaffy") | |
f48e29da | 4041 | (version "1.44.0") |
f562c90a RW |
4042 | (source |
4043 | (origin | |
4044 | (method url-fetch) | |
4045 | (uri (bioconductor-uri "yaqcaffy" version)) | |
4046 | (sha256 | |
4047 | (base32 | |
f48e29da | 4048 | "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670")))) |
f562c90a RW |
4049 | (build-system r-build-system) |
4050 | (propagated-inputs | |
4051 | `(("r-simpleaffy" ,r-simpleaffy))) | |
4052 | (home-page "https://bioconductor.org/packages/yaqcaffy/") | |
4053 | (synopsis "Affymetrix quality control and reproducibility analysis") | |
4054 | (description | |
4055 | "This is a package that can be used for quality control of Affymetrix | |
4056 | GeneChip expression data and reproducibility analysis of human whole genome | |
4057 | chips with the MAQC reference datasets.") | |
4058 | (license license:artistic2.0))) | |
59cf2629 RW |
4059 | |
4060 | (define-public r-quantro | |
4061 | (package | |
4062 | (name "r-quantro") | |
2feea2d2 | 4063 | (version "1.18.0") |
59cf2629 RW |
4064 | (source |
4065 | (origin | |
4066 | (method url-fetch) | |
4067 | (uri (bioconductor-uri "quantro" version)) | |
4068 | (sha256 | |
4069 | (base32 | |
2feea2d2 | 4070 | "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab")))) |
59cf2629 RW |
4071 | (build-system r-build-system) |
4072 | (propagated-inputs | |
4073 | `(("r-biobase" ,r-biobase) | |
4074 | ("r-doparallel" ,r-doparallel) | |
4075 | ("r-foreach" ,r-foreach) | |
4076 | ("r-ggplot2" ,r-ggplot2) | |
4077 | ("r-iterators" ,r-iterators) | |
4078 | ("r-minfi" ,r-minfi) | |
4079 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
4080 | (home-page "https://bioconductor.org/packages/quantro/") | |
4081 | (synopsis "Test for when to use quantile normalization") | |
4082 | (description | |
4083 | "This package provides a data-driven test for the assumptions of quantile | |
4084 | normalization using raw data such as objects that inherit eSets (e.g. | |
4085 | ExpressionSet, MethylSet). Group level information about each sample (such as | |
4086 | Tumor / Normal status) must also be provided because the test assesses if | |
4087 | there are global differences in the distributions between the user-defined | |
4088 | groups.") | |
4089 | (license license:gpl3+))) | |
98a2af31 RW |
4090 | |
4091 | (define-public r-yarn | |
4092 | (package | |
4093 | (name "r-yarn") | |
7f4957b2 | 4094 | (version "1.10.0") |
98a2af31 RW |
4095 | (source |
4096 | (origin | |
4097 | (method url-fetch) | |
4098 | (uri (bioconductor-uri "yarn" version)) | |
4099 | (sha256 | |
4100 | (base32 | |
7f4957b2 | 4101 | "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6")))) |
98a2af31 RW |
4102 | (build-system r-build-system) |
4103 | (propagated-inputs | |
4104 | `(("r-biobase" ,r-biobase) | |
4105 | ("r-biomart" ,r-biomart) | |
4106 | ("r-downloader" ,r-downloader) | |
4107 | ("r-edger" ,r-edger) | |
4108 | ("r-gplots" ,r-gplots) | |
4109 | ("r-limma" ,r-limma) | |
4110 | ("r-matrixstats" ,r-matrixstats) | |
4111 | ("r-preprocesscore" ,r-preprocesscore) | |
4112 | ("r-quantro" ,r-quantro) | |
4113 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4114 | ("r-readr" ,r-readr))) | |
4115 | (home-page "https://bioconductor.org/packages/yarn/") | |
4116 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") | |
4117 | (description | |
4118 | "Expedite large RNA-Seq analyses using a combination of previously | |
4119 | developed tools. YARN is meant to make it easier for the user in performing | |
4120 | basic mis-annotation quality control, filtering, and condition-aware | |
4121 | normalization. YARN leverages many Bioconductor tools and statistical | |
4122 | techniques to account for the large heterogeneity and sparsity found in very | |
4123 | large RNA-seq experiments.") | |
4124 | (license license:artistic2.0))) | |
a6e1eb1a RW |
4125 | |
4126 | (define-public r-roar | |
4127 | (package | |
4128 | (name "r-roar") | |
0334b203 | 4129 | (version "1.20.0") |
a6e1eb1a RW |
4130 | (source |
4131 | (origin | |
4132 | (method url-fetch) | |
4133 | (uri (bioconductor-uri "roar" version)) | |
4134 | (sha256 | |
4135 | (base32 | |
0334b203 | 4136 | "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7")))) |
a6e1eb1a RW |
4137 | (build-system r-build-system) |
4138 | (propagated-inputs | |
4139 | `(("r-biocgenerics" ,r-biocgenerics) | |
4140 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4141 | ("r-genomicalignments" ,r-genomicalignments) | |
4142 | ("r-genomicranges" ,r-genomicranges) | |
4143 | ("r-iranges" ,r-iranges) | |
4144 | ("r-rtracklayer" ,r-rtracklayer) | |
4145 | ("r-s4vectors" ,r-s4vectors) | |
4146 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4147 | (home-page "https://github.com/vodkatad/roar/") | |
4148 | (synopsis "Identify differential APA usage from RNA-seq alignments") | |
4149 | (description | |
4150 | "This package provides tools for identifying preferential usage of APA | |
4151 | sites, comparing two biological conditions, starting from known alternative | |
4152 | sites and alignments obtained from standard RNA-seq experiments.") | |
4153 | (license license:gpl3))) | |
50d91770 RW |
4154 | |
4155 | (define-public r-xbseq | |
4156 | (package | |
4157 | (name "r-xbseq") | |
88469def | 4158 | (version "1.16.0") |
50d91770 RW |
4159 | (source |
4160 | (origin | |
4161 | (method url-fetch) | |
4162 | (uri (bioconductor-uri "XBSeq" version)) | |
4163 | (sha256 | |
4164 | (base32 | |
88469def | 4165 | "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy")))) |
50d91770 RW |
4166 | (properties `((upstream-name . "XBSeq"))) |
4167 | (build-system r-build-system) | |
4168 | (propagated-inputs | |
4169 | `(("r-biobase" ,r-biobase) | |
4170 | ("r-deseq2" ,r-deseq2) | |
4171 | ("r-dplyr" ,r-dplyr) | |
4172 | ("r-ggplot2" ,r-ggplot2) | |
4173 | ("r-locfit" ,r-locfit) | |
4174 | ("r-magrittr" ,r-magrittr) | |
4175 | ("r-matrixstats" ,r-matrixstats) | |
4176 | ("r-pracma" ,r-pracma) | |
4177 | ("r-roar" ,r-roar))) | |
4178 | (home-page "https://github.com/Liuy12/XBSeq") | |
4179 | (synopsis "Test for differential expression for RNA-seq data") | |
4180 | (description | |
4181 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential | |
4182 | expression} (DE), where a statistical model was established based on the | |
4183 | assumption that observed signals are the convolution of true expression | |
4184 | signals and sequencing noises. The mapped reads in non-exonic regions are | |
4185 | considered as sequencing noises, which follows a Poisson distribution. Given | |
4186 | measurable observed signal and background noise from RNA-seq data, true | |
4187 | expression signals, assuming governed by the negative binomial distribution, | |
4188 | can be delineated and thus the accurate detection of differential expressed | |
4189 | genes.") | |
4190 | (license license:gpl3+))) | |
c8310056 RW |
4191 | |
4192 | (define-public r-massspecwavelet | |
4193 | (package | |
4194 | (name "r-massspecwavelet") | |
7c888138 | 4195 | (version "1.50.0") |
c8310056 RW |
4196 | (source |
4197 | (origin | |
4198 | (method url-fetch) | |
4199 | (uri (bioconductor-uri "MassSpecWavelet" version)) | |
4200 | (sha256 | |
4201 | (base32 | |
7c888138 | 4202 | "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72")))) |
c8310056 RW |
4203 | (properties |
4204 | `((upstream-name . "MassSpecWavelet"))) | |
4205 | (build-system r-build-system) | |
4206 | (propagated-inputs | |
4207 | `(("r-waveslim" ,r-waveslim))) | |
4208 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") | |
4209 | (synopsis "Mass spectrum processing by wavelet-based algorithms") | |
4210 | (description | |
4211 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) | |
4212 | data mainly through the use of wavelet transforms. It supports peak detection | |
4213 | based on @dfn{Continuous Wavelet Transform} (CWT).") | |
4214 | (license license:lgpl2.0+))) | |
ec12e537 RW |
4215 | |
4216 | (define-public r-xcms | |
4217 | (package | |
4218 | (name "r-xcms") | |
40b2f7bc | 4219 | (version "3.6.1") |
ec12e537 RW |
4220 | (source |
4221 | (origin | |
4222 | (method url-fetch) | |
4223 | (uri (bioconductor-uri "xcms" version)) | |
4224 | (sha256 | |
4225 | (base32 | |
40b2f7bc | 4226 | "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g")))) |
ec12e537 RW |
4227 | (build-system r-build-system) |
4228 | (propagated-inputs | |
4229 | `(("r-biobase" ,r-biobase) | |
4230 | ("r-biocgenerics" ,r-biocgenerics) | |
4231 | ("r-biocparallel" ,r-biocparallel) | |
4232 | ("r-lattice" ,r-lattice) | |
4233 | ("r-massspecwavelet" ,r-massspecwavelet) | |
4234 | ("r-msnbase" ,r-msnbase) | |
4235 | ("r-multtest" ,r-multtest) | |
4236 | ("r-mzr" ,r-mzr) | |
4237 | ("r-plyr" ,r-plyr) | |
4238 | ("r-protgenerics" ,r-protgenerics) | |
4239 | ("r-rann" ,r-rann) | |
4240 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4241 | ("r-robustbase" ,r-robustbase) | |
4242 | ("r-s4vectors" ,r-s4vectors))) | |
4243 | (home-page "https://bioconductor.org/packages/xcms/") | |
4244 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") | |
4245 | (description | |
4246 | "This package provides a framework for processing and visualization of | |
4247 | chromatographically separated and single-spectra mass spectral data. It | |
4248 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses | |
4249 | data for high-throughput, untargeted analyte profiling.") | |
4250 | (license license:gpl2+))) | |
8830664d RW |
4251 | |
4252 | (define-public r-wrench | |
4253 | (package | |
4254 | (name "r-wrench") | |
07597c85 | 4255 | (version "1.2.0") |
8830664d RW |
4256 | (source |
4257 | (origin | |
4258 | (method url-fetch) | |
4259 | (uri (bioconductor-uri "Wrench" version)) | |
4260 | (sha256 | |
4261 | (base32 | |
07597c85 | 4262 | "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i")))) |
8830664d RW |
4263 | (properties `((upstream-name . "Wrench"))) |
4264 | (build-system r-build-system) | |
4265 | (propagated-inputs | |
4266 | `(("r-limma" ,r-limma) | |
4267 | ("r-locfit" ,r-locfit) | |
4268 | ("r-matrixstats" ,r-matrixstats))) | |
4269 | (home-page "https://github.com/HCBravoLab/Wrench") | |
4270 | (synopsis "Wrench normalization for sparse count data") | |
4271 | (description | |
4272 | "Wrench is a package for normalization sparse genomic count data, like | |
4273 | that arising from 16s metagenomic surveys.") | |
4274 | (license license:artistic2.0))) | |
b9b8b447 RW |
4275 | |
4276 | (define-public r-wiggleplotr | |
4277 | (package | |
4278 | (name "r-wiggleplotr") | |
a6edf335 | 4279 | (version "1.8.0") |
b9b8b447 RW |
4280 | (source |
4281 | (origin | |
4282 | (method url-fetch) | |
4283 | (uri (bioconductor-uri "wiggleplotr" version)) | |
4284 | (sha256 | |
4285 | (base32 | |
a6edf335 | 4286 | "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0")))) |
b9b8b447 RW |
4287 | (build-system r-build-system) |
4288 | (propagated-inputs | |
4289 | `(("r-assertthat" ,r-assertthat) | |
4290 | ("r-cowplot" ,r-cowplot) | |
4291 | ("r-dplyr" ,r-dplyr) | |
4292 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4293 | ("r-genomicranges" ,r-genomicranges) | |
4294 | ("r-ggplot2" ,r-ggplot2) | |
4295 | ("r-iranges" ,r-iranges) | |
4296 | ("r-purrr" ,r-purrr) | |
4297 | ("r-rtracklayer" ,r-rtracklayer) | |
4298 | ("r-s4vectors" ,r-s4vectors))) | |
4299 | (home-page "https://bioconductor.org/packages/wiggleplotr/") | |
4300 | (synopsis "Make read coverage plots from BigWig files") | |
4301 | (description | |
4302 | "This package provides tools to visualize read coverage from sequencing | |
4303 | experiments together with genomic annotations (genes, transcripts, peaks). | |
4304 | Introns of long transcripts can be rescaled to a fixed length for better | |
4305 | visualization of exonic read coverage.") | |
4306 | (license license:asl2.0))) | |
7b5101c5 RW |
4307 | |
4308 | (define-public r-widgettools | |
4309 | (package | |
4310 | (name "r-widgettools") | |
c881b9ef | 4311 | (version "1.62.0") |
7b5101c5 RW |
4312 | (source |
4313 | (origin | |
4314 | (method url-fetch) | |
4315 | (uri (bioconductor-uri "widgetTools" version)) | |
4316 | (sha256 | |
4317 | (base32 | |
c881b9ef | 4318 | "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a")))) |
7b5101c5 RW |
4319 | (properties `((upstream-name . "widgetTools"))) |
4320 | (build-system r-build-system) | |
4321 | (home-page "https://bioconductor.org/packages/widgetTools/") | |
4322 | (synopsis "Tools for creating interactive tcltk widgets") | |
4323 | (description | |
337bdc17 | 4324 | "This package contains tools to support the construction of tcltk |
7b5101c5 RW |
4325 | widgets in R.") |
4326 | ;; Any version of the LGPL. | |
4327 | (license license:lgpl3+))) | |
6b12f213 RW |
4328 | |
4329 | (define-public r-webbioc | |
4330 | (package | |
4331 | (name "r-webbioc") | |
67bc9255 | 4332 | (version "1.56.0") |
6b12f213 RW |
4333 | (source |
4334 | (origin | |
4335 | (method url-fetch) | |
4336 | (uri (bioconductor-uri "webbioc" version)) | |
4337 | (sha256 | |
4338 | (base32 | |
67bc9255 | 4339 | "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz")))) |
6b12f213 RW |
4340 | (build-system r-build-system) |
4341 | (inputs | |
4342 | `(("netpbm" ,netpbm) | |
4343 | ("perl" ,perl))) | |
4344 | (propagated-inputs | |
4345 | `(("r-affy" ,r-affy) | |
4346 | ("r-annaffy" ,r-annaffy) | |
4347 | ("r-biobase" ,r-biobase) | |
4348 | ("r-biocmanager" ,r-biocmanager) | |
4349 | ("r-gcrma" ,r-gcrma) | |
4350 | ("r-multtest" ,r-multtest) | |
4351 | ("r-qvalue" ,r-qvalue) | |
4352 | ("r-vsn" ,r-vsn))) | |
4353 | (home-page "https://www.bioconductor.org/") | |
4354 | (synopsis "Bioconductor web interface") | |
4355 | (description | |
4356 | "This package provides an integrated web interface for doing microarray | |
4357 | analysis using several of the Bioconductor packages. It is intended to be | |
4358 | deployed as a centralized bioinformatics resource for use by many users. | |
4359 | Currently only Affymetrix oligonucleotide analysis is supported.") | |
4360 | (license license:gpl2+))) | |
9800d859 RW |
4361 | |
4362 | (define-public r-zfpkm | |
4363 | (package | |
4364 | (name "r-zfpkm") | |
02530c28 | 4365 | (version "1.6.0") |
9800d859 RW |
4366 | (source |
4367 | (origin | |
4368 | (method url-fetch) | |
4369 | (uri (bioconductor-uri "zFPKM" version)) | |
4370 | (sha256 | |
4371 | (base32 | |
02530c28 | 4372 | "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz")))) |
9800d859 RW |
4373 | (properties `((upstream-name . "zFPKM"))) |
4374 | (build-system r-build-system) | |
4375 | (propagated-inputs | |
4376 | `(("r-checkmate" ,r-checkmate) | |
4377 | ("r-dplyr" ,r-dplyr) | |
4378 | ("r-ggplot2" ,r-ggplot2) | |
4379 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
4380 | ("r-tidyr" ,r-tidyr))) | |
4381 | (home-page "https://github.com/ronammar/zFPKM/") | |
4382 | (synopsis "Functions to facilitate zFPKM transformations") | |
4383 | (description | |
4384 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. | |
4385 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID | |
4386 | 24215113).") | |
4387 | (license license:gpl3))) | |
2bdc88fc RW |
4388 | |
4389 | (define-public r-rbowtie2 | |
4390 | (package | |
4391 | (name "r-rbowtie2") | |
7d33d36c | 4392 | (version "1.6.0") |
2bdc88fc RW |
4393 | (source |
4394 | (origin | |
4395 | (method url-fetch) | |
4396 | (uri (bioconductor-uri "Rbowtie2" version)) | |
4397 | (sha256 | |
4398 | (base32 | |
7d33d36c | 4399 | "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4")))) |
2bdc88fc RW |
4400 | (properties `((upstream-name . "Rbowtie2"))) |
4401 | (build-system r-build-system) | |
4402 | (inputs | |
4403 | `(("zlib" ,zlib))) | |
4404 | (home-page "https://bioconductor.org/packages/Rbowtie2/") | |
4405 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") | |
4406 | (description | |
4407 | "This package provides an R wrapper of the popular @code{bowtie2} | |
4408 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for | |
4409 | rapid adapter trimming, identification, and read merging.") | |
4410 | (license license:gpl3+))) | |
5622628f RW |
4411 | |
4412 | (define-public r-progeny | |
4413 | (package | |
4414 | (name "r-progeny") | |
c2bfb978 | 4415 | (version "1.6.0") |
5622628f RW |
4416 | (source |
4417 | (origin | |
4418 | (method url-fetch) | |
4419 | (uri (bioconductor-uri "progeny" version)) | |
4420 | (sha256 | |
4421 | (base32 | |
c2bfb978 | 4422 | "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw")))) |
5622628f RW |
4423 | (build-system r-build-system) |
4424 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4425 | (home-page "https://github.com/saezlab/progeny") | |
4426 | (synopsis "Pathway responsive gene activity inference") | |
4427 | (description | |
4428 | "This package provides a function to infer pathway activity from gene | |
4429 | expression. It contains the linear model inferred in the publication | |
4430 | \"Perturbation-response genes reveal signaling footprints in cancer gene | |
4431 | expression\".") | |
4432 | (license license:asl2.0))) | |
307586c1 RW |
4433 | |
4434 | (define-public r-arrmnormalization | |
4435 | (package | |
4436 | (name "r-arrmnormalization") | |
c24adbbf | 4437 | (version "1.24.0") |
307586c1 RW |
4438 | (source |
4439 | (origin | |
4440 | (method url-fetch) | |
4441 | (uri (bioconductor-uri "ARRmNormalization" version)) | |
4442 | (sha256 | |
4443 | (base32 | |
c24adbbf | 4444 | "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1")))) |
307586c1 RW |
4445 | (properties |
4446 | `((upstream-name . "ARRmNormalization"))) | |
4447 | (build-system r-build-system) | |
4448 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) | |
4449 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") | |
4450 | (synopsis "Adaptive robust regression normalization for methylation data") | |
4451 | (description | |
4452 | "This is a package to perform the @dfn{Adaptive Robust Regression | |
4453 | method} (ARRm) for the normalization of methylation data from the Illumina | |
4454 | Infinium HumanMethylation 450k assay.") | |
4455 | (license license:artistic2.0))) | |
fbf34949 RW |
4456 | |
4457 | (define-public r-biocfilecache | |
4458 | (package | |
4459 | (name "r-biocfilecache") | |
4460 | (version "1.8.0") | |
4461 | (source | |
4462 | (origin | |
4463 | (method url-fetch) | |
4464 | (uri (bioconductor-uri "BiocFileCache" version)) | |
4465 | (sha256 | |
4466 | (base32 | |
4467 | "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb")))) | |
4468 | (properties `((upstream-name . "BiocFileCache"))) | |
4469 | (build-system r-build-system) | |
4470 | (propagated-inputs | |
4471 | `(("r-curl" ,r-curl) | |
4472 | ("r-dbi" ,r-dbi) | |
4473 | ("r-dbplyr" ,r-dbplyr) | |
4474 | ("r-dplyr" ,r-dplyr) | |
4475 | ("r-httr" ,r-httr) | |
4476 | ("r-rappdirs" ,r-rappdirs) | |
4477 | ("r-rsqlite" ,r-rsqlite))) | |
4478 | (home-page "https://bioconductor.org/packages/BiocFileCache/") | |
4479 | (synopsis "Manage files across sessions") | |
4480 | (description | |
4481 | "This package creates a persistent on-disk cache of files that the user | |
4482 | can add, update, and retrieve. It is useful for managing resources (such as | |
4483 | custom Txdb objects) that are costly or difficult to create, web resources, | |
4484 | and data files used across sessions.") | |
4485 | (license license:artistic2.0))) | |
8c42f8f6 RW |
4486 | |
4487 | (define-public r-iclusterplus | |
4488 | (package | |
4489 | (name "r-iclusterplus") | |
4490 | (version "1.20.0") | |
4491 | (source | |
4492 | (origin | |
4493 | (method url-fetch) | |
4494 | (uri (bioconductor-uri "iClusterPlus" version)) | |
4495 | (sha256 | |
4496 | (base32 | |
4497 | "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq")))) | |
4498 | (properties `((upstream-name . "iClusterPlus"))) | |
4499 | (build-system r-build-system) | |
4500 | (native-inputs `(("gfortran" ,gfortran))) | |
4501 | (home-page "https://bioconductor.org/packages/iClusterPlus/") | |
4502 | (synopsis "Integrative clustering of multi-type genomic data") | |
4503 | (description | |
4504 | "iClusterPlus is developed for integrative clustering analysis of | |
4505 | multi-type genomic data and is an enhanced version of iCluster proposed and | |
4506 | developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise | |
4507 | from the experiments where biological samples (e.g. tumor samples) are | |
4508 | analyzed by multiple techniques, for instance, @dfn{array comparative genomic | |
4509 | hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so | |
4510 | on. In the iClusterPlus model, binary observations such as somatic mutation | |
4511 | are modeled as Binomial processes; categorical observations such as copy | |
4512 | number states are realizations of Multinomial random variables; counts are | |
4513 | modeled as Poisson random processes; and continuous measures are modeled by | |
4514 | Gaussian distributions.") | |
4515 | (license license:gpl2+))) | |
4d06ef4b RW |
4516 | |
4517 | (define-public r-rbowtie | |
4518 | (package | |
4519 | (name "r-rbowtie") | |
4520 | (version "1.24.0") | |
4521 | (source | |
4522 | (origin | |
4523 | (method url-fetch) | |
4524 | (uri (bioconductor-uri "Rbowtie" version)) | |
4525 | (sha256 | |
4526 | (base32 | |
4527 | "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f")))) | |
4528 | (properties `((upstream-name . "Rbowtie"))) | |
4529 | (build-system r-build-system) | |
4530 | (inputs | |
4531 | `(("zlib" ,zlib))) | |
4532 | (home-page "https://bioconductor.org/packages/Rbowtie/") | |
4533 | (synopsis "R bowtie wrapper") | |
4534 | (description | |
4535 | "This package provides an R wrapper around the popular bowtie short read | |
4536 | aligner and around SpliceMap, a de novo splice junction discovery and | |
4537 | alignment tool.") | |
4538 | (license license:artistic2.0))) | |
14441539 RW |
4539 | |
4540 | (define-public r-sgseq | |
4541 | (package | |
4542 | (name "r-sgseq") | |
4543 | (version "1.18.0") | |
4544 | (source | |
4545 | (origin | |
4546 | (method url-fetch) | |
4547 | (uri (bioconductor-uri "SGSeq" version)) | |
4548 | (sha256 | |
4549 | (base32 | |
4550 | "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s")))) | |
4551 | (properties `((upstream-name . "SGSeq"))) | |
4552 | (build-system r-build-system) | |
4553 | (propagated-inputs | |
4554 | `(("r-annotationdbi" ,r-annotationdbi) | |
4555 | ("r-biocgenerics" ,r-biocgenerics) | |
4556 | ("r-biostrings" ,r-biostrings) | |
4557 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4558 | ("r-genomicalignments" ,r-genomicalignments) | |
4559 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4560 | ("r-genomicranges" ,r-genomicranges) | |
4561 | ("r-igraph" ,r-igraph) | |
4562 | ("r-iranges" ,r-iranges) | |
4563 | ("r-rsamtools" ,r-rsamtools) | |
4564 | ("r-rtracklayer" ,r-rtracklayer) | |
4565 | ("r-runit" ,r-runit) | |
4566 | ("r-s4vectors" ,r-s4vectors) | |
4567 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4568 | (home-page "https://bioconductor.org/packages/SGSeq/") | |
4569 | (synopsis "Splice event prediction and quantification from RNA-seq data") | |
4570 | (description | |
4571 | "SGSeq is a package for analyzing splice events from RNA-seq data. Input | |
4572 | data are RNA-seq reads mapped to a reference genome in BAM format. Genes are | |
4573 | represented as a splice graph, which can be obtained from existing annotation | |
4574 | or predicted from the mapped sequence reads. Splice events are identified | |
4575 | from the graph and are quantified locally using structurally compatible reads | |
4576 | at the start or end of each splice variant. The software includes functions | |
4577 | for splice event prediction, quantification, visualization and | |
4578 | interpretation.") | |
4579 | (license license:artistic2.0))) | |
58656064 RW |
4580 | |
4581 | (define-public r-rhisat2 | |
4582 | (package | |
4583 | (name "r-rhisat2") | |
932a6c42 | 4584 | (version "1.0.3") |
58656064 RW |
4585 | (source |
4586 | (origin | |
4587 | (method url-fetch) | |
4588 | (uri (bioconductor-uri "Rhisat2" version)) | |
4589 | (sha256 | |
4590 | (base32 | |
932a6c42 | 4591 | "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5")))) |
58656064 RW |
4592 | (properties `((upstream-name . "Rhisat2"))) |
4593 | (build-system r-build-system) | |
4594 | (native-inputs | |
4595 | `(("which" ,which))) | |
4596 | (propagated-inputs | |
4597 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
4598 | ("r-genomicranges" ,r-genomicranges) | |
4599 | ("r-sgseq" ,r-sgseq))) | |
4600 | (home-page "https://github.com/fmicompbio/Rhisat2") | |
4601 | (synopsis "R Wrapper for HISAT2 sequence aligner") | |
4602 | (description | |
4603 | "This package provides an R interface to the HISAT2 spliced short-read | |
4604 | aligner by Kim et al. (2015). The package contains wrapper functions to | |
4605 | create a genome index and to perform the read alignment to the generated | |
4606 | index.") | |
4607 | (license license:gpl3))) | |
5e0241db RW |
4608 | |
4609 | (define-public r-quasr | |
4610 | (package | |
4611 | (name "r-quasr") | |
b3319f4c | 4612 | (version "1.24.2") |
5e0241db RW |
4613 | (source |
4614 | (origin | |
4615 | (method url-fetch) | |
4616 | (uri (bioconductor-uri "QuasR" version)) | |
4617 | (sha256 | |
4618 | (base32 | |
b3319f4c | 4619 | "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx")))) |
5e0241db RW |
4620 | (properties `((upstream-name . "QuasR"))) |
4621 | (build-system r-build-system) | |
4622 | (inputs | |
4623 | `(("zlib" ,zlib))) | |
4624 | (propagated-inputs | |
4625 | `(("r-annotationdbi" ,r-annotationdbi) | |
4626 | ("r-biobase" ,r-biobase) | |
4627 | ("r-biocgenerics" ,r-biocgenerics) | |
4628 | ("r-biocmanager" ,r-biocmanager) | |
4629 | ("r-biocparallel" ,r-biocparallel) | |
4630 | ("r-biostrings" ,r-biostrings) | |
4631 | ("r-bsgenome" ,r-bsgenome) | |
4632 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4633 | ("r-genomicalignments" ,r-genomicalignments) | |
4634 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4635 | ("r-genomicfiles" ,r-genomicfiles) | |
4636 | ("r-genomicranges" ,r-genomicranges) | |
4637 | ("r-iranges" ,r-iranges) | |
4638 | ("r-rbowtie" ,r-rbowtie) | |
4639 | ("r-rhisat2" ,r-rhisat2) | |
4640 | ("r-rhtslib" ,r-rhtslib) | |
4641 | ("r-rsamtools" ,r-rsamtools) | |
4642 | ("r-rtracklayer" ,r-rtracklayer) | |
4643 | ("r-s4vectors" ,r-s4vectors) | |
4644 | ("r-shortread" ,r-shortread))) | |
4645 | (home-page "https://bioconductor.org/packages/QuasR/") | |
4646 | (synopsis "Quantify and annotate short reads in R") | |
4647 | (description | |
4648 | "This package provides a framework for the quantification and analysis of | |
4649 | short genomic reads. It covers a complete workflow starting from raw sequence | |
4650 | reads, over creation of alignments and quality control plots, to the | |
4651 | quantification of genomic regions of interest.") | |
4652 | (license license:gpl2))) | |
496b024f RW |
4653 | |
4654 | (define-public r-rqc | |
4655 | (package | |
4656 | (name "r-rqc") | |
4657 | (version "1.18.0") | |
4658 | (source | |
4659 | (origin | |
4660 | (method url-fetch) | |
4661 | (uri (bioconductor-uri "Rqc" version)) | |
4662 | (sha256 | |
4663 | (base32 | |
4664 | "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g")))) | |
4665 | (properties `((upstream-name . "Rqc"))) | |
4666 | (build-system r-build-system) | |
4667 | (propagated-inputs | |
4668 | `(("r-biocgenerics" ,r-biocgenerics) | |
4669 | ("r-biocparallel" ,r-biocparallel) | |
4670 | ("r-biocstyle" ,r-biocstyle) | |
4671 | ("r-biostrings" ,r-biostrings) | |
4672 | ("r-biovizbase" ,r-biovizbase) | |
4673 | ("r-genomicalignments" ,r-genomicalignments) | |
4674 | ("r-genomicfiles" ,r-genomicfiles) | |
4675 | ("r-ggplot2" ,r-ggplot2) | |
4676 | ("r-iranges" ,r-iranges) | |
4677 | ("r-knitr" ,r-knitr) | |
4678 | ("r-markdown" ,r-markdown) | |
4679 | ("r-plyr" ,r-plyr) | |
4680 | ("r-rcpp" ,r-rcpp) | |
4681 | ("r-reshape2" ,r-reshape2) | |
4682 | ("r-rsamtools" ,r-rsamtools) | |
4683 | ("r-s4vectors" ,r-s4vectors) | |
4684 | ("r-shiny" ,r-shiny) | |
4685 | ("r-shortread" ,r-shortread))) | |
4686 | (home-page "https://github.com/labbcb/Rqc") | |
4687 | (synopsis "Quality control tool for high-throughput sequencing data") | |
4688 | (description | |
4689 | "Rqc is an optimized tool designed for quality control and assessment of | |
4690 | high-throughput sequencing data. It performs parallel processing of entire | |
4691 | files and produces a report which contains a set of high-resolution | |
4692 | graphics.") | |
4693 | (license license:gpl2+))) | |
81e3de01 RW |
4694 | |
4695 | (define-public r-birewire | |
4696 | (package | |
4697 | (name "r-birewire") | |
4698 | (version "3.16.0") | |
4699 | (source | |
4700 | (origin | |
4701 | (method url-fetch) | |
4702 | (uri (bioconductor-uri "BiRewire" version)) | |
4703 | (sha256 | |
4704 | (base32 | |
4705 | "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518")))) | |
4706 | (properties `((upstream-name . "BiRewire"))) | |
4707 | (build-system r-build-system) | |
4708 | (propagated-inputs | |
4709 | `(("r-igraph" ,r-igraph) | |
4710 | ("r-matrix" ,r-matrix) | |
4711 | ("r-slam" ,r-slam) | |
4712 | ("r-tsne" ,r-tsne))) | |
4713 | (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") | |
4714 | (synopsis "Tools for randomization of bipartite graphs") | |
4715 | (description | |
4716 | "This package provides functions for bipartite network rewiring through N | |
4717 | consecutive switching steps and for the computation of the minimal number of | |
4718 | switching steps to be performed in order to maximise the dissimilarity with | |
4719 | respect to the original network. It includes functions for the analysis of | |
4720 | the introduced randomness across the switching steps and several other | |
4721 | routines to analyse the resulting networks and their natural projections.") | |
4722 | (license license:gpl3))) | |
1a24f855 RW |
4723 | |
4724 | (define-public r-birta | |
4725 | (package | |
4726 | (name "r-birta") | |
4727 | (version "1.28.0") | |
4728 | (source | |
4729 | (origin | |
4730 | (method url-fetch) | |
4731 | (uri (bioconductor-uri "birta" version)) | |
4732 | (sha256 | |
4733 | (base32 | |
4734 | "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2")))) | |
4735 | (build-system r-build-system) | |
4736 | (propagated-inputs | |
4737 | `(("r-biobase" ,r-biobase) | |
4738 | ("r-limma" ,r-limma) | |
4739 | ("r-mass" ,r-mass))) | |
4740 | (home-page "https://bioconductor.org/packages/birta") | |
4741 | (synopsis "Bayesian inference of regulation of transcriptional activity") | |
4742 | (description | |
4743 | "Expression levels of mRNA molecules are regulated by different | |
4744 | processes, comprising inhibition or activation by transcription factors and | |
4745 | post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian | |
4746 | Inference of Regulation of Transcriptional Activity) uses the regulatory | |
4747 | networks of transcription factors and miRNAs together with mRNA and miRNA | |
4748 | expression data to predict switches in regulatory activity between two | |
4749 | conditions. A Bayesian network is used to model the regulatory structure and | |
4750 | Markov-Chain-Monte-Carlo is applied to sample the activity states.") | |
4751 | (license license:gpl2+))) | |
a9fac3f4 RW |
4752 | |
4753 | (define-public r-ropls | |
4754 | (package | |
4755 | (name "r-ropls") | |
4756 | (version "1.16.0") | |
4757 | (source | |
4758 | (origin | |
4759 | (method url-fetch) | |
4760 | (uri (bioconductor-uri "ropls" version)) | |
4761 | (sha256 | |
4762 | (base32 | |
4763 | "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2")))) | |
4764 | (build-system r-build-system) | |
4765 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4766 | (native-inputs | |
4767 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
4768 | (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") | |
4769 | (synopsis "Multivariate analysis and feature selection of omics data") | |
4770 | (description | |
4771 | "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) | |
4772 | and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, | |
4773 | regression, classification, and feature selection of omics data where the | |
4774 | number of variables exceeds the number of samples and with multicollinearity | |
4775 | among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to | |
4776 | separately model the variation correlated (predictive) to the factor of | |
4777 | interest and the uncorrelated (orthogonal) variation. While performing | |
4778 | similarly to PLS, OPLS facilitates interpretation. | |
4779 | ||
4780 | This package provides imlementations of PCA, PLS, and OPLS for multivariate | |
4781 | analysis and feature selection of omics data. In addition to scores, loadings | |
4782 | and weights plots, the package provides metrics and graphics to determine the | |
4783 | optimal number of components (e.g. with the R2 and Q2 coefficients), check the | |
4784 | validity of the model by permutation testing, detect outliers, and perform | |
4785 | feature selection (e.g. with Variable Importance in Projection or regression | |
4786 | coefficients).") | |
4787 | (license license:cecill))) | |
075a9094 RW |
4788 | |
4789 | (define-public r-biosigner | |
4790 | (package | |
4791 | (name "r-biosigner") | |
4792 | (version "1.12.0") | |
4793 | (source | |
4794 | (origin | |
4795 | (method url-fetch) | |
4796 | (uri (bioconductor-uri "biosigner" version)) | |
4797 | (sha256 | |
4798 | (base32 | |
4799 | "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b")))) | |
4800 | (build-system r-build-system) | |
4801 | (propagated-inputs | |
4802 | `(("r-biobase" ,r-biobase) | |
4803 | ("r-e1071" ,r-e1071) | |
4804 | ("r-randomforest" ,r-randomforest) | |
4805 | ("r-ropls" ,r-ropls))) | |
4806 | (native-inputs | |
4807 | `(("r-knitr" ,r-knitr) | |
4808 | ("r-rmarkdown" ,r-rmarkdown) | |
4809 | ("pandoc" ,ghc-pandoc) | |
4810 | ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes | |
4811 | (home-page "https://bioconductor.org/packages/biosigner/") | |
4812 | (synopsis "Signature discovery from omics data") | |
4813 | (description | |
4814 | "Feature selection is critical in omics data analysis to extract | |
4815 | restricted and meaningful molecular signatures from complex and high-dimension | |
4816 | data, and to build robust classifiers. This package implements a method to | |
4817 | assess the relevance of the variables for the prediction performances of the | |
4818 | classifier. The approach can be run in parallel with the PLS-DA, Random | |
4819 | Forest, and SVM binary classifiers. The signatures and the corresponding | |
4820 | 'restricted' models are returned, enabling future predictions on new | |
4821 | datasets.") | |
4822 | (license license:cecill))) | |
ae6fa185 RW |
4823 | |
4824 | (define-public r-annotatr | |
4825 | (package | |
4826 | (name "r-annotatr") | |
4827 | (version "1.10.0") | |
4828 | (source | |
4829 | (origin | |
4830 | (method url-fetch) | |
4831 | (uri (bioconductor-uri "annotatr" version)) | |
4832 | (sha256 | |
4833 | (base32 | |
4834 | "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f")))) | |
4835 | (build-system r-build-system) | |
4836 | (propagated-inputs | |
4837 | `(("r-annotationdbi" ,r-annotationdbi) | |
4838 | ("r-annotationhub" ,r-annotationhub) | |
4839 | ("r-dplyr" ,r-dplyr) | |
4840 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4841 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4842 | ("r-genomicranges" ,r-genomicranges) | |
4843 | ("r-ggplot2" ,r-ggplot2) | |
4844 | ("r-iranges" ,r-iranges) | |
4845 | ("r-readr" ,r-readr) | |
4846 | ("r-regioner" ,r-regioner) | |
4847 | ("r-reshape2" ,r-reshape2) | |
4848 | ("r-rtracklayer" ,r-rtracklayer) | |
4849 | ("r-s4vectors" ,r-s4vectors))) | |
4850 | (home-page "https://bioconductor.org/packages/annotatr/") | |
4851 | (synopsis "Annotation of genomic regions to genomic annotations") | |
4852 | (description | |
4853 | "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, | |
4854 | differentially methylated CpGs or regions, SNPs, etc.) it is often of interest | |
4855 | to investigate the intersecting genomic annotations. Such annotations include | |
4856 | those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), | |
4857 | CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as | |
4858 | enhancers. The annotatr package provides an easy way to summarize and | |
4859 | visualize the intersection of genomic sites/regions with genomic | |
4860 | annotations.") | |
4861 | (license license:gpl3))) | |
2cb738a6 RW |
4862 | |
4863 | (define-public r-rsubread | |
4864 | (package | |
4865 | (name "r-rsubread") | |
b1207891 | 4866 | (version "1.34.6") |
2cb738a6 RW |
4867 | (source |
4868 | (origin | |
4869 | (method url-fetch) | |
4870 | (uri (bioconductor-uri "Rsubread" version)) | |
4871 | (sha256 | |
4872 | (base32 | |
b1207891 | 4873 | "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550")))) |
2cb738a6 RW |
4874 | (properties `((upstream-name . "Rsubread"))) |
4875 | (build-system r-build-system) | |
4876 | (inputs `(("zlib" ,zlib))) | |
4877 | (home-page "https://bioconductor.org/packages/Rsubread/") | |
4878 | (synopsis "Subread sequence alignment and counting for R") | |
4879 | (description | |
4880 | "This package provides tools for alignment, quantification and analysis | |
4881 | of second and third generation sequencing data. It includes functionality for | |
4882 | read mapping, read counting, SNP calling, structural variant detection and | |
4883 | gene fusion discovery. It can be applied to all major sequencing techologies | |
4884 | and to both short and long sequence reads.") | |
4885 | (license license:gpl3))) | |
a6fedf1f | 4886 | |
a0422d18 | 4887 | (define-public r-flowutils |
4888 | (package | |
4889 | (name "r-flowutils") | |
4890 | (version "1.48.0") | |
4891 | (source | |
4892 | (origin | |
4893 | (method url-fetch) | |
4894 | (uri (bioconductor-uri "flowUtils" version)) | |
4895 | (sha256 | |
4896 | (base32 | |
4897 | "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm")))) | |
4898 | (properties `((upstream-name . "flowUtils"))) | |
4899 | (build-system r-build-system) | |
4900 | (propagated-inputs | |
4901 | `(("r-biobase" ,r-biobase) | |
4902 | ("r-corpcor" ,r-corpcor) | |
4903 | ("r-flowcore" ,r-flowcore) | |
4904 | ("r-graph" ,r-graph) | |
4905 | ("r-runit" ,r-runit) | |
4906 | ("r-xml" ,r-xml))) | |
4907 | (home-page "https://github.com/jspidlen/flowUtils") | |
4908 | (synopsis "Utilities for flow cytometry") | |
4909 | (description | |
4910 | "This package provides utilities for flow cytometry data.") | |
4911 | (license license:artistic2.0))) | |
4912 | ||
ed6f49fc | 4913 | (define-public r-consensusclusterplus |
4914 | (package | |
4915 | (name "r-consensusclusterplus") | |
4916 | (version "1.48.0") | |
4917 | (source | |
4918 | (origin | |
4919 | (method url-fetch) | |
4920 | (uri (bioconductor-uri "ConsensusClusterPlus" version)) | |
4921 | (sha256 | |
4922 | (base32 | |
4923 | "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8")))) | |
4924 | (properties | |
4925 | `((upstream-name . "ConsensusClusterPlus"))) | |
4926 | (build-system r-build-system) | |
4927 | (propagated-inputs | |
4928 | `(("r-all" ,r-all) | |
4929 | ("r-biobase" ,r-biobase) | |
4930 | ("r-cluster" ,r-cluster))) | |
4931 | (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") | |
4932 | (synopsis "Clustering algorithm") | |
4933 | (description | |
4934 | "This package provides an implementation of an algorithm for determining | |
4935 | cluster count and membership by stability evidence in unsupervised analysis.") | |
4936 | (license license:gpl2))) | |
4937 | ||
a6fedf1f | 4938 | (define-public r-flowcore |
4939 | (package | |
4940 | (name "r-flowcore") | |
4941 | (version "1.50.0") | |
4942 | (source | |
4943 | (origin | |
4944 | (method url-fetch) | |
4945 | (uri (bioconductor-uri "flowCore" version)) | |
4946 | (sha256 | |
4947 | (base32 | |
4948 | "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan")))) | |
4949 | (properties `((upstream-name . "flowCore"))) | |
4950 | (build-system r-build-system) | |
4951 | (propagated-inputs | |
4952 | `(("r-bh" ,r-bh) | |
4953 | ("r-biobase" ,r-biobase) | |
4954 | ("r-biocgenerics" ,r-biocgenerics) | |
4955 | ("r-corpcor" ,r-corpcor) | |
4956 | ("r-graph" ,r-graph) | |
4957 | ("r-mass" ,r-mass) | |
4958 | ("r-matrixstats" ,r-matrixstats) | |
4959 | ("r-rcpp" ,r-rcpp) | |
4960 | ("r-rrcov" ,r-rrcov))) | |
4961 | (home-page "https://bioconductor.org/packages/flowCore") | |
4962 | (synopsis "Basic structures for flow cytometry data") | |
4963 | (description | |
4964 | "This package provides S4 data structures and basic functions to deal | |
4965 | with flow cytometry data.") | |
4966 | (license license:artistic2.0))) | |
e0cb053e | 4967 | |
4968 | (define-public r-flowmeans | |
4969 | (package | |
4970 | (name "r-flowmeans") | |
4971 | (version "1.44.0") | |
4972 | (source | |
4973 | (origin | |
4974 | (method url-fetch) | |
4975 | (uri (bioconductor-uri "flowMeans" version)) | |
4976 | (sha256 | |
4977 | (base32 | |
4978 | "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2")))) | |
4979 | (properties `((upstream-name . "flowMeans"))) | |
4980 | (build-system r-build-system) | |
4981 | (propagated-inputs | |
4982 | `(("r-biobase" ,r-biobase) | |
4983 | ("r-feature" ,r-feature) | |
4984 | ("r-flowcore" ,r-flowcore) | |
4985 | ("r-rrcov" ,r-rrcov))) | |
4986 | (home-page "https://bioconductor.org/packages/flowMeans") | |
4987 | (synopsis "Non-parametric flow cytometry data gating") | |
4988 | (description | |
4989 | "This package provides tools to identify cell populations in Flow | |
4990 | Cytometry data using non-parametric clustering and segmented-regression-based | |
4991 | change point detection.") | |
4992 | (license license:artistic2.0))) | |
1502751b | 4993 | |
4994 | (define-public r-flowsom | |
4995 | (package | |
4996 | (name "r-flowsom") | |
4997 | (version "1.16.0") | |
4998 | (source | |
4999 | (origin | |
5000 | (method url-fetch) | |
5001 | (uri (bioconductor-uri "FlowSOM" version)) | |
5002 | (sha256 | |
5003 | (base32 | |
5004 | "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l")))) | |
5005 | (properties `((upstream-name . "FlowSOM"))) | |
5006 | (build-system r-build-system) | |
5007 | (propagated-inputs | |
5008 | `(("r-biocgenerics" ,r-biocgenerics) | |
5009 | ("r-consensusclusterplus" ,r-consensusclusterplus) | |
5010 | ("r-flowcore" ,r-flowcore) | |
5011 | ("r-flowutils" ,r-flowutils) | |
5012 | ("r-igraph" ,r-igraph) | |
5013 | ("r-tsne" ,r-tsne) | |
5014 | ("r-xml" ,r-xml))) | |
5015 | (home-page "https://bioconductor.org/packages/FlowSOM/") | |
5016 | (synopsis "Visualize and interpret cytometry data") | |
5017 | (description | |
5018 | "FlowSOM offers visualization options for cytometry data, by using | |
5019 | self-organizing map clustering and minimal spanning trees.") | |
5020 | (license license:gpl2+))) | |
1adb9cbc | 5021 | |
5022 | (define-public r-mixomics | |
5023 | (package | |
5024 | (name "r-mixomics") | |
b58b4410 | 5025 | (version "6.8.2") |
1adb9cbc | 5026 | (source |
5027 | (origin | |
5028 | (method url-fetch) | |
5029 | (uri (bioconductor-uri "mixOmics" version)) | |
5030 | (sha256 | |
5031 | (base32 | |
b58b4410 | 5032 | "0issfrhsgc102sr33q9v6w6jrrd32plig7szd1nm0n4r3yn4y2fc")))) |
1adb9cbc | 5033 | (properties `((upstream-name . "mixOmics"))) |
5034 | (build-system r-build-system) | |
5035 | (propagated-inputs | |
5036 | `(("r-corpcor" ,r-corpcor) | |
5037 | ("r-dplyr" ,r-dplyr) | |
5038 | ("r-ellipse" ,r-ellipse) | |
5039 | ("r-ggplot2" ,r-ggplot2) | |
5040 | ("r-gridextra" ,r-gridextra) | |
5041 | ("r-igraph" ,r-igraph) | |
5042 | ("r-lattice" ,r-lattice) | |
5043 | ("r-mass" ,r-mass) | |
5044 | ("r-matrixstats" ,r-matrixstats) | |
5045 | ("r-rarpack" ,r-rarpack) | |
5046 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5047 | ("r-reshape2" ,r-reshape2) | |
5048 | ("r-tidyr" ,r-tidyr))) | |
5049 | (home-page "http://www.mixOmics.org") | |
5050 | (synopsis "Multivariate methods for exploration of biological datasets") | |
5051 | (description | |
5052 | "mixOmics offers a wide range of multivariate methods for the exploration | |
5053 | and integration of biological datasets with a particular focus on variable | |
5054 | selection. The package proposes several sparse multivariate models we have | |
5055 | developed to identify the key variables that are highly correlated, and/or | |
5056 | explain the biological outcome of interest. The data that can be analysed | |
5057 | with mixOmics may come from high throughput sequencing technologies, such as | |
5058 | omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but | |
5059 | also beyond the realm of omics (e.g. spectral imaging). The methods | |
5060 | implemented in mixOmics can also handle missing values without having to | |
5061 | delete entire rows with missing data.") | |
5062 | (license license:gpl2+))) | |
a0efa069 | 5063 | |
5064 | (define-public r-depecher | |
5065 | (package | |
5066 | (name "r-depecher") | |
5067 | (version "1.0.3") | |
5068 | (source | |
5069 | (origin | |
5070 | (method url-fetch) | |
5071 | (uri (bioconductor-uri "DepecheR" version)) | |
5072 | (sha256 | |
5073 | (base32 | |
5074 | "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h")))) | |
5075 | (properties `((upstream-name . "DepecheR"))) | |
5076 | (build-system r-build-system) | |
5077 | (arguments | |
5078 | `(#:phases | |
5079 | (modify-phases %standard-phases | |
5080 | (add-after 'unpack 'fix-syntax-error | |
5081 | (lambda _ | |
5082 | (substitute* "src/Makevars" | |
5083 | ((" & ") " && ")) | |
5084 | #t))))) | |
5085 | (propagated-inputs | |
5086 | `(("r-beanplot" ,r-beanplot) | |
5087 | ("r-biocparallel" ,r-biocparallel) | |
5088 | ("r-dosnow" ,r-dosnow) | |
5089 | ("r-dplyr" ,r-dplyr) | |
5090 | ("r-foreach" ,r-foreach) | |
5091 | ("r-ggplot2" ,r-ggplot2) | |
5092 | ("r-gplots" ,r-gplots) | |
5093 | ("r-mass" ,r-mass) | |
5094 | ("r-matrixstats" ,r-matrixstats) | |
5095 | ("r-mixomics" ,r-mixomics) | |
5096 | ("r-moments" ,r-moments) | |
5097 | ("r-rcpp" ,r-rcpp) | |
5098 | ("r-rcppeigen" ,r-rcppeigen) | |
5099 | ("r-reshape2" ,r-reshape2) | |
5100 | ("r-viridis" ,r-viridis))) | |
5101 | (home-page "https://bioconductor.org/packages/DepecheR/") | |
5102 | (synopsis "Identify traits of clusters in high-dimensional entities") | |
5103 | (description | |
5104 | "The purpose of this package is to identify traits in a dataset that can | |
5105 | separate groups. This is done on two levels. First, clustering is performed, | |
5106 | using an implementation of sparse K-means. Secondly, the generated clusters | |
5107 | are used to predict outcomes of groups of individuals based on their | |
5108 | distribution of observations in the different clusters. As certain clusters | |
5109 | with separating information will be identified, and these clusters are defined | |
5110 | by a sparse number of variables, this method can reduce the complexity of | |
5111 | data, to only emphasize the data that actually matters.") | |
5112 | (license license:expat))) | |
b46a0ee7 | 5113 | |
bb88417f RW |
5114 | (define-public r-rcistarget |
5115 | (package | |
5116 | (name "r-rcistarget") | |
5117 | (version "1.4.0") | |
5118 | (source | |
5119 | (origin | |
5120 | (method url-fetch) | |
5121 | (uri (bioconductor-uri "RcisTarget" version)) | |
5122 | (sha256 | |
5123 | (base32 | |
5124 | "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd")))) | |
5125 | (properties `((upstream-name . "RcisTarget"))) | |
5126 | (build-system r-build-system) | |
5127 | (propagated-inputs | |
5128 | `(("r-aucell" ,r-aucell) | |
5129 | ("r-biocgenerics" ,r-biocgenerics) | |
5130 | ("r-data-table" ,r-data-table) | |
5131 | ("r-feather" ,r-feather) | |
5132 | ("r-gseabase" ,r-gseabase) | |
5133 | ("r-r-utils" ,r-r-utils) | |
5134 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5135 | (home-page "https://aertslab.org/#scenic") | |
5136 | (synopsis "Identify transcription factor binding motifs enriched on a gene list") | |
5137 | (description | |
5138 | "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) | |
5139 | over-represented on a gene list. In a first step, RcisTarget selects DNA | |
5140 | motifs that are significantly over-represented in the surroundings of the | |
5141 | @dfn{transcription start site} (TSS) of the genes in the gene-set. This is | |
5142 | achieved by using a database that contains genome-wide cross-species rankings | |
5143 | for each motif. The motifs that are then annotated to TFs and those that have | |
5144 | a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for | |
5145 | each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. | |
5146 | genes in the gene-set that are ranked above the leading edge).") | |
5147 | (license license:gpl3))) | |
5148 | ||
b46a0ee7 RW |
5149 | (define-public r-cicero |
5150 | (package | |
5151 | (name "r-cicero") | |
5152 | (version "1.2.0") | |
5153 | (source | |
5154 | (origin | |
5155 | (method url-fetch) | |
5156 | (uri (bioconductor-uri "cicero" version)) | |
5157 | (sha256 | |
5158 | (base32 | |
5159 | "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr")))) | |
5160 | (build-system r-build-system) | |
5161 | (propagated-inputs | |
5162 | `(("r-assertthat" ,r-assertthat) | |
5163 | ("r-biobase" ,r-biobase) | |
5164 | ("r-biocgenerics" ,r-biocgenerics) | |
5165 | ("r-data-table" ,r-data-table) | |
5166 | ("r-dplyr" ,r-dplyr) | |
5167 | ("r-fnn" ,r-fnn) | |
5168 | ("r-genomicranges" ,r-genomicranges) | |
5169 | ("r-ggplot2" ,r-ggplot2) | |
5170 | ("r-glasso" ,r-glasso) | |
5171 | ("r-gviz" ,r-gviz) | |
5172 | ("r-igraph" ,r-igraph) | |
5173 | ("r-iranges" ,r-iranges) | |
5174 | ("r-matrix" ,r-matrix) | |
5175 | ("r-monocle" ,r-monocle) | |
5176 | ("r-plyr" ,r-plyr) | |
5177 | ("r-reshape2" ,r-reshape2) | |
5178 | ("r-s4vectors" ,r-s4vectors) | |
5179 | ("r-stringr" ,r-stringr) | |
5180 | ("r-tibble" ,r-tibble) | |
5181 | ("r-vgam" ,r-vgam))) | |
5182 | (home-page "https://bioconductor.org/packages/cicero/") | |
5183 | (synopsis "Predict cis-co-accessibility from single-cell data") | |
5184 | (description | |
5185 | "Cicero computes putative cis-regulatory maps from single-cell chromatin | |
5186 | accessibility data. It also extends the monocle package for use in chromatin | |
5187 | accessibility data.") | |
5188 | (license license:expat))) | |
14bb1c48 RW |
5189 | |
5190 | ;; This is the latest commit on the "monocle3" branch. | |
5191 | (define-public r-cicero-monocle3 | |
5192 | (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") | |
5193 | (revision "1")) | |
5194 | (package (inherit r-cicero) | |
5195 | (name "r-cicero-monocle3") | |
5196 | (version (git-version "1.3.2" revision commit)) | |
5197 | (source | |
5198 | (origin | |
5199 | (method git-fetch) | |
5200 | (uri (git-reference | |
5201 | (url "https://github.com/cole-trapnell-lab/cicero-release.git") | |
5202 | (commit commit))) | |
5203 | (file-name (git-file-name name version)) | |
5204 | (sha256 | |
5205 | (base32 | |
5206 | "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) | |
5207 | (propagated-inputs | |
5208 | `(("r-monocle3" ,r-monocle3) | |
5209 | ,@(alist-delete "r-monocle" | |
5210 | (package-propagated-inputs r-cicero))))))) | |
a9815a6c RW |
5211 | |
5212 | (define-public r-cistopic | |
5213 | (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") | |
5214 | (revision "0")) | |
5215 | (package | |
5216 | (name "r-cistopic") | |
5217 | (version (git-version "0.2.1" revision commit)) | |
5218 | (source | |
5219 | (origin | |
5220 | (method git-fetch) | |
5221 | (uri (git-reference | |
5222 | (url "https://github.com/aertslab/cisTopic.git") | |
5223 | (commit commit))) | |
5224 | (file-name (git-file-name name version)) | |
5225 | (sha256 | |
5226 | (base32 | |
5227 | "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) | |
5228 | (build-system r-build-system) | |
5229 | (propagated-inputs | |
5230 | `(("r-aucell" ,r-aucell) | |
5231 | ("r-data-table" ,r-data-table) | |
5232 | ("r-dplyr" ,r-dplyr) | |
5233 | ("r-dosnow" ,r-dosnow) | |
5234 | ("r-dt" ,r-dt) | |
5235 | ("r-feather" ,r-feather) | |
5236 | ("r-fitdistrplus" ,r-fitdistrplus) | |
5237 | ("r-genomicranges" ,r-genomicranges) | |
5238 | ("r-ggplot2" ,r-ggplot2) | |
5239 | ("r-lda" ,r-lda) | |
5240 | ("r-matrix" ,r-matrix) | |
5241 | ("r-plyr" ,r-plyr) | |
5242 | ("r-rcistarget" ,r-rcistarget) | |
5243 | ("r-rtracklayer" ,r-rtracklayer) | |
5244 | ("r-s4vectors" ,r-s4vectors))) | |
5245 | (home-page "https://github.com/aertslab/cisTopic") | |
5246 | (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") | |
5247 | (description | |
5248 | "The sparse nature of single cell epigenomics data can be overruled using | |
5249 | probabilistic modelling methods such as @dfn{Latent Dirichlet | |
5250 | Allocation} (LDA). This package allows the probabilistic modelling of | |
5251 | cis-regulatory topics (cisTopics) from single cell epigenomics data, and | |
5252 | includes functionalities to identify cell states based on the contribution of | |
5253 | cisTopics and explore the nature and regulatory proteins driving them.") | |
5254 | (license license:gpl3)))) | |
d85c0f98 RW |
5255 | |
5256 | (define-public r-genie3 | |
5257 | (package | |
5258 | (name "r-genie3") | |
5259 | (version "1.6.0") | |
5260 | (source | |
5261 | (origin | |
5262 | (method url-fetch) | |
5263 | (uri (bioconductor-uri "GENIE3" version)) | |
5264 | (sha256 | |
5265 | (base32 | |
5266 | "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx")))) | |
5267 | (properties `((upstream-name . "GENIE3"))) | |
5268 | (build-system r-build-system) | |
5269 | (propagated-inputs `(("r-reshape2" ,r-reshape2))) | |
5270 | (home-page "https://bioconductor.org/packages/GENIE3") | |
5271 | (synopsis "Gene network inference with ensemble of trees") | |
5272 | (description | |
5273 | "This package implements the GENIE3 algorithm for inferring gene | |
5274 | regulatory networks from expression data.") | |
5275 | (license license:gpl2+))) | |
db316d73 RW |
5276 | |
5277 | (define-public r-roc | |
5278 | (package | |
5279 | (name "r-roc") | |
5280 | (version "1.60.0") | |
5281 | (source | |
5282 | (origin | |
5283 | (method url-fetch) | |
5284 | (uri (bioconductor-uri "ROC" version)) | |
5285 | (sha256 | |
5286 | (base32 | |
5287 | "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c")))) | |
5288 | (properties `((upstream-name . "ROC"))) | |
5289 | (build-system r-build-system) | |
5290 | (home-page "https://www.bioconductor.org/packages/ROC/") | |
5291 | (synopsis "Utilities for ROC curves") | |
5292 | (description | |
5293 | "This package provides utilities for @dfn{Receiver Operating | |
5294 | Characteristic} (ROC) curves, with a focus on micro arrays.") | |
5295 | (license license:artistic2.0))) | |
46721dea RW |
5296 | |
5297 | (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 | |
5298 | (package | |
5299 | (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") | |
5300 | (version "0.6.0") | |
5301 | (source | |
5302 | (origin | |
5303 | (method url-fetch) | |
5304 | (uri (bioconductor-uri | |
5305 | "IlluminaHumanMethylation450kanno.ilmn12.hg19" | |
5306 | version 'annotation)) | |
5307 | (sha256 | |
5308 | (base32 | |
5309 | "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) | |
5310 | (properties | |
5311 | `((upstream-name | |
5312 | . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) | |
5313 | (build-system r-build-system) | |
5314 | (propagated-inputs `(("r-minfi" ,r-minfi))) | |
5315 | (home-page | |
5316 | "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") | |
5317 | (synopsis "Annotation for Illumina's 450k methylation arrays") | |
5318 | (description | |
5319 | "This package provides manifests and annotation for Illumina's 450k array | |
5320 | data.") | |
5321 | (license license:artistic2.0))) | |
38babeaa RW |
5322 | |
5323 | (define-public r-watermelon | |
5324 | (package | |
5325 | (name "r-watermelon") | |
5326 | (version "1.28.0") | |
5327 | (source | |
5328 | (origin | |
5329 | (method url-fetch) | |
5330 | (uri (bioconductor-uri "wateRmelon" version)) | |
5331 | (sha256 | |
5332 | (base32 | |
5333 | "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z")))) | |
5334 | (properties `((upstream-name . "wateRmelon"))) | |
5335 | (build-system r-build-system) | |
5336 | (propagated-inputs | |
5337 | `(("r-biobase" ,r-biobase) | |
5338 | ("r-illuminahumanmethylation450kanno-ilmn12-hg19" | |
5339 | ,r-illuminahumanmethylation450kanno-ilmn12-hg19) | |
5340 | ("r-illuminaio" ,r-illuminaio) | |
5341 | ("r-limma" ,r-limma) | |
5342 | ("r-lumi" ,r-lumi) | |
5343 | ("r-matrixstats" ,r-matrixstats) | |
5344 | ("r-methylumi" ,r-methylumi) | |
5345 | ("r-roc" ,r-roc))) | |
5346 | (home-page "https://bioconductor.org/packages/wateRmelon/") | |
5347 | (synopsis "Illumina 450 methylation array normalization and metrics") | |
5348 | (description | |
5349 | "The standard index of DNA methylation (beta) is computed from methylated | |
5350 | and unmethylated signal intensities. Betas calculated from raw signal | |
5351 | intensities perform well, but using 11 methylomic datasets we demonstrate that | |
5352 | quantile normalization methods produce marked improvement. The commonly used | |
5353 | procedure of normalizing betas is inferior to the separate normalization of M | |
5354 | and U, and it is also advantageous to normalize Type I and Type II assays | |
5355 | separately. This package provides 15 flavours of betas and three performance | |
5356 | metrics, with methods for objects produced by the @code{methylumi} and | |
5357 | @code{minfi} packages.") | |
5358 | (license license:gpl3))) | |
7d2cb646 RW |
5359 | |
5360 | (define-public r-gdsfmt | |
5361 | (package | |
5362 | (name "r-gdsfmt") | |
5363 | (version "1.20.0") | |
5364 | (source | |
5365 | (origin | |
5366 | (method url-fetch) | |
5367 | (uri (bioconductor-uri "gdsfmt" version)) | |
5368 | (sha256 | |
5369 | (base32 | |
5370 | "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy")) | |
5371 | (modules '((guix build utils))) | |
5372 | ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build | |
5373 | ;; them and link with system libraries instead. | |
5374 | (snippet | |
5375 | '(begin | |
5376 | (for-each delete-file-recursively | |
5377 | '("src/LZ4" | |
5378 | "src/XZ" | |
5379 | "src/ZLIB")) | |
5380 | (substitute* "src/Makevars" | |
5381 | (("all: \\$\\(SHLIB\\)") "all:") | |
5382 | (("\\$\\(SHLIB\\): liblzma.a") "") | |
5383 | (("(ZLIB|LZ4)/.*") "") | |
5384 | (("CoreArray/dVLIntGDS.cpp.*") | |
5385 | "CoreArray/dVLIntGDS.cpp") | |
5386 | (("CoreArray/dVLIntGDS.o.*") | |
5387 | "CoreArray/dVLIntGDS.o") | |
5388 | (("PKG_LIBS = ./liblzma.a") | |
5389 | "PKG_LIBS = -llz4")) | |
5390 | (substitute* "src/CoreArray/dStream.h" | |
5391 | (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) | |
5392 | (string-append "include <" header ">"))) | |
5393 | #t)))) | |
5394 | (properties `((upstream-name . "gdsfmt"))) | |
5395 | (build-system r-build-system) | |
5396 | (inputs | |
5397 | `(("lz4" ,lz4) | |
5398 | ("xz" ,xz) | |
5399 | ("zlib" ,zlib))) | |
5400 | (home-page "http://corearray.sourceforge.net/") | |
5401 | (synopsis | |
5402 | "R Interface to CoreArray Genomic Data Structure (GDS) Files") | |
5403 | (description | |
5404 | "This package provides a high-level R interface to CoreArray @dfn{Genomic | |
5405 | Data Structure} (GDS) data files, which are portable across platforms with | |
5406 | hierarchical structure to store multiple scalable array-oriented data sets | |
5407 | with metadata information. It is suited for large-scale datasets, especially | |
5408 | for data which are much larger than the available random-access memory. The | |
5409 | @code{gdsfmt} package offers efficient operations specifically designed for | |
5410 | integers of less than 8 bits, since a diploid genotype, like | |
5411 | @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a | |
5412 | byte. Data compression and decompression are available with relatively | |
5413 | efficient random access. It is also allowed to read a GDS file in parallel | |
5414 | with multiple R processes supported by the package @code{parallel}.") | |
5415 | (license license:lgpl3))) | |
6b5f59c7 RW |
5416 | |
5417 | (define-public r-bigmelon | |
5418 | (package | |
5419 | (name "r-bigmelon") | |
5420 | (version "1.10.0") | |
5421 | (source | |
5422 | (origin | |
5423 | (method url-fetch) | |
5424 | (uri (bioconductor-uri "bigmelon" version)) | |
5425 | (sha256 | |
5426 | (base32 | |
5427 | "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9")))) | |
5428 | (properties `((upstream-name . "bigmelon"))) | |
5429 | (build-system r-build-system) | |
5430 | (propagated-inputs | |
5431 | `(("r-biobase" ,r-biobase) | |
5432 | ("r-biocgenerics" ,r-biocgenerics) | |
5433 | ("r-gdsfmt" ,r-gdsfmt) | |
5434 | ("r-geoquery" ,r-geoquery) | |
5435 | ("r-methylumi" ,r-methylumi) | |
5436 | ("r-minfi" ,r-minfi) | |
5437 | ("r-watermelon" ,r-watermelon))) | |
5438 | (home-page "https://bioconductor.org/packages/bigmelon/") | |
5439 | (synopsis "Illumina methylation array analysis for large experiments") | |
5440 | (description | |
5441 | "This package provides methods for working with Illumina arrays using the | |
5442 | @code{gdsfmt} package.") | |
5443 | (license license:gpl3))) |