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fa596599 | 1 | ;;; GNU Guix --- Functional package management for GNU |
f8f181ae | 2 | ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> |
e8d435f7 | 3 | ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> |
61242625 | 4 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
16e2e4f2 | 5 | ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com> |
fa596599 RW |
6 | ;;; |
7 | ;;; This file is part of GNU Guix. | |
8 | ;;; | |
9 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
10 | ;;; under the terms of the GNU General Public License as published by | |
11 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
12 | ;;; your option) any later version. | |
13 | ;;; | |
14 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
15 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
16 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
17 | ;;; GNU General Public License for more details. | |
18 | ;;; | |
19 | ;;; You should have received a copy of the GNU General Public License | |
20 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
21 | ||
22 | (define-module (gnu packages bioconductor) | |
23 | #:use-module ((guix licenses) #:prefix license:) | |
24 | #:use-module (guix packages) | |
25 | #:use-module (guix download) | |
b2dce6b5 | 26 | #:use-module (guix git-download) |
fa596599 | 27 | #:use-module (guix build-system r) |
183ce988 | 28 | #:use-module (gnu packages) |
58656064 | 29 | #:use-module (gnu packages base) |
cf9a29b2 | 30 | #:use-module (gnu packages bioinformatics) |
a5b56a53 RJ |
31 | #:use-module (gnu packages cran) |
32 | #:use-module (gnu packages compression) | |
c18dccff | 33 | #:use-module (gnu packages gcc) |
cf9a29b2 | 34 | #:use-module (gnu packages graph) |
5aef09bd | 35 | #:use-module (gnu packages graphviz) |
dddbc90c | 36 | #:use-module (gnu packages haskell-xyz) |
5cfa4bff | 37 | #:use-module (gnu packages image) |
b64ce4b7 | 38 | #:use-module (gnu packages maths) |
6b12f213 RW |
39 | #:use-module (gnu packages netpbm) |
40 | #:use-module (gnu packages perl) | |
2cb71d81 | 41 | #:use-module (gnu packages pkg-config) |
f4235c0e | 42 | #:use-module (gnu packages statistics) |
14bb1c48 | 43 | #:use-module (gnu packages web) |
7a62d5e0 | 44 | #:use-module (gnu packages xml) |
14bb1c48 | 45 | #:use-module (srfi srfi-1)) |
fa596599 | 46 | |
557a1089 RW |
47 | \f |
48 | ;;; Annotations | |
49 | ||
6f15ea24 RW |
50 | (define-public r-reactome-db |
51 | (package | |
52 | (name "r-reactome-db") | |
53 | (version "1.70.0") | |
54 | (source | |
55 | (origin | |
56 | (method url-fetch) | |
57 | (uri (bioconductor-uri "reactome.db" version 'annotation)) | |
58 | (sha256 | |
59 | (base32 | |
60 | "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg")))) | |
61 | (properties `((upstream-name . "reactome.db"))) | |
62 | (build-system r-build-system) | |
63 | (propagated-inputs | |
64 | `(("r-annotationdbi" ,r-annotationdbi))) | |
65 | (home-page "https://bioconductor.org/packages/reactome.db/") | |
66 | (synopsis "Annotation maps for reactome") | |
67 | (description | |
68 | "This package provides a set of annotation maps for the REACTOME | |
69 | database, assembled using data from REACTOME.") | |
70 | (license license:cc-by4.0))) | |
71 | ||
b7d93cf5 RW |
72 | (define-public r-bsgenome-celegans-ucsc-ce6 |
73 | (package | |
74 | (name "r-bsgenome-celegans-ucsc-ce6") | |
75 | (version "1.4.0") | |
76 | (source (origin | |
77 | (method url-fetch) | |
86ced7b2 RW |
78 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6" |
79 | version 'annotation)) | |
b7d93cf5 RW |
80 | (sha256 |
81 | (base32 | |
82 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
83 | (properties | |
84 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
85 | (build-system r-build-system) | |
b7d93cf5 RW |
86 | (propagated-inputs |
87 | `(("r-bsgenome" ,r-bsgenome))) | |
88 | (home-page | |
89 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
90 | (synopsis "Full genome sequences for Worm") | |
91 | (description | |
92 | "This package provides full genome sequences for Caenorhabditis | |
93 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
0c792ffb RW |
94 | objects.") |
95 | (license license:artistic2.0))) | |
96 | ||
97 | (define-public r-bsgenome-celegans-ucsc-ce10 | |
98 | (package | |
99 | (name "r-bsgenome-celegans-ucsc-ce10") | |
100 | (version "1.4.0") | |
101 | (source (origin | |
102 | (method url-fetch) | |
6998ecba RW |
103 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10" |
104 | version 'annotation)) | |
0c792ffb RW |
105 | (sha256 |
106 | (base32 | |
107 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
108 | (properties | |
109 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
110 | (build-system r-build-system) | |
0c792ffb RW |
111 | (propagated-inputs |
112 | `(("r-bsgenome" ,r-bsgenome))) | |
113 | (home-page | |
114 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
115 | (synopsis "Full genome sequences for Worm") | |
116 | (description | |
117 | "This package provides full genome sequences for Caenorhabditis | |
118 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
b7d93cf5 RW |
119 | objects.") |
120 | (license license:artistic2.0))) | |
121 | ||
183db725 RW |
122 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
123 | (package | |
124 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
125 | (version "1.4.1") | |
126 | (source (origin | |
127 | (method url-fetch) | |
149f351f RW |
128 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6" |
129 | version 'annotation)) | |
183db725 RW |
130 | (sha256 |
131 | (base32 | |
132 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
133 | (properties | |
134 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
135 | (build-system r-build-system) | |
183db725 RW |
136 | (propagated-inputs |
137 | `(("r-bsgenome" ,r-bsgenome))) | |
138 | (home-page | |
139 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
140 | (synopsis "Full genome sequences for Fly") | |
141 | (description | |
142 | "This package provides full genome sequences for Drosophila | |
143 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
144 | objects.") | |
145 | (license license:artistic2.0))) | |
146 | ||
13dabd69 RW |
147 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
148 | (package | |
149 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
150 | (version "1.4.0") | |
151 | (source (origin | |
152 | (method url-fetch) | |
87073b7e RW |
153 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3" |
154 | version 'annotation)) | |
13dabd69 RW |
155 | (sha256 |
156 | (base32 | |
157 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
158 | (properties | |
159 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
160 | (build-system r-build-system) | |
13dabd69 RW |
161 | (propagated-inputs |
162 | `(("r-bsgenome" ,r-bsgenome))) | |
163 | (home-page | |
164 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
165 | (synopsis "Full genome sequences for Fly") | |
166 | (description | |
167 | "This package provides full genome sequences for Drosophila | |
168 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
169 | Biostrings objects.") | |
170 | (license license:artistic2.0))) | |
171 | ||
dfac7eb9 RW |
172 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
173 | (package | |
174 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
175 | (version "1.3.99") | |
176 | (source (origin | |
177 | (method url-fetch) | |
bf05ece1 RW |
178 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked" |
179 | version 'annotation)) | |
dfac7eb9 RW |
180 | (sha256 |
181 | (base32 | |
182 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
183 | (properties | |
184 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
185 | (build-system r-build-system) | |
186 | (propagated-inputs | |
187 | `(("r-bsgenome" ,r-bsgenome) | |
188 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
189 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
190 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
191 | (synopsis "Full masked genome sequences for Fly") | |
192 | (description | |
193 | "This package provides full masked genome sequences for Drosophila | |
194 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
195 | Biostrings objects. The sequences are the same as in | |
196 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
197 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
198 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
199 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
200 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
201 | (license license:artistic2.0))) | |
202 | ||
40a65057 RW |
203 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
204 | (package | |
205 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
206 | (version "0.99.1") | |
207 | (source (origin | |
208 | (method url-fetch) | |
88e7c7db RW |
209 | (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5" |
210 | version 'annotation)) | |
40a65057 RW |
211 | (sha256 |
212 | (base32 | |
213 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
214 | (properties | |
215 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
216 | (build-system r-build-system) | |
40a65057 RW |
217 | (propagated-inputs |
218 | `(("r-bsgenome" ,r-bsgenome))) | |
219 | (home-page | |
220 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
221 | (synopsis "Full genome sequences for Homo sapiens") | |
222 | (description | |
223 | "This package provides full genome sequences for Homo sapiens from | |
224 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
225 | (license license:artistic2.0))) | |
226 | ||
c51c0033 MIP |
227 | (define-public r-bsgenome-hsapiens-ncbi-grch38 |
228 | (package | |
229 | (name "r-bsgenome-hsapiens-ncbi-grch38") | |
230 | (version "1.3.1000") | |
231 | (source | |
232 | (origin | |
233 | (method url-fetch) | |
234 | (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38" | |
235 | version 'annotation)) | |
236 | (sha256 | |
237 | (base32 | |
238 | "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) | |
239 | (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) | |
240 | (build-system r-build-system) | |
241 | (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) | |
242 | (home-page | |
243 | "https://bioconductor.org/packages/release/data/annotation/html/\ | |
244 | BSgenome.Hsapiens.NCBI.GRCh38.html") | |
245 | (synopsis "Full genome sequences for Homo sapiens (GRCh38)") | |
246 | (description | |
247 | "This package provides full genome sequences for Homo sapiens (Human) as | |
248 | provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") | |
249 | (license license:artistic2.0))) | |
250 | ||
6fbd759b RW |
251 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
252 | (package | |
253 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
254 | (version "1.3.99") | |
255 | (source (origin | |
256 | (method url-fetch) | |
a47646bd RW |
257 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" |
258 | version 'annotation)) | |
6fbd759b RW |
259 | (sha256 |
260 | (base32 | |
261 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
262 | (properties | |
263 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
264 | (build-system r-build-system) | |
265 | (propagated-inputs | |
266 | `(("r-bsgenome" ,r-bsgenome) | |
267 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
268 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
269 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
270 | (synopsis "Full masked genome sequences for Homo sapiens") | |
271 | (description | |
272 | "This package provides full genome sequences for Homo sapiens (Human) as | |
273 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
274 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
275 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
276 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
277 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
278 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
279 | default.") | |
280 | (license license:artistic2.0))) | |
281 | ||
5acb9052 RW |
282 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
283 | (package | |
284 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
285 | (version "1.4.0") | |
286 | (source (origin | |
287 | (method url-fetch) | |
21f6dae7 RW |
288 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9" |
289 | version 'annotation)) | |
5acb9052 RW |
290 | (sha256 |
291 | (base32 | |
292 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
293 | (properties | |
294 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
295 | (build-system r-build-system) | |
5acb9052 RW |
296 | (propagated-inputs |
297 | `(("r-bsgenome" ,r-bsgenome))) | |
298 | (home-page | |
299 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
300 | (synopsis "Full genome sequences for Mouse") | |
301 | (description | |
302 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
303 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
304 | (license license:artistic2.0))) | |
305 | ||
2bece692 RW |
306 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
307 | (package | |
308 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
309 | (version "1.3.99") | |
310 | (source (origin | |
311 | (method url-fetch) | |
51dc4a2d RW |
312 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked" |
313 | version 'annotation)) | |
2bece692 RW |
314 | (sha256 |
315 | (base32 | |
316 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
317 | (properties | |
318 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
319 | (build-system r-build-system) | |
320 | (propagated-inputs | |
321 | `(("r-bsgenome" ,r-bsgenome) | |
322 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
323 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
99db6db7 | 324 | (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") |
2bece692 RW |
325 | (synopsis "Full masked genome sequences for Mouse") |
326 | (description | |
327 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
328 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
329 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
330 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
331 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
332 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
333 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
334 | default." ) | |
335 | (license license:artistic2.0))) | |
336 | ||
c3adc830 RW |
337 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
338 | (package | |
339 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
340 | (version "1.4.0") | |
341 | (source (origin | |
342 | (method url-fetch) | |
f83404bc RW |
343 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10" |
344 | version 'annotation)) | |
c3adc830 RW |
345 | (sha256 |
346 | (base32 | |
347 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
348 | (properties | |
349 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
350 | (build-system r-build-system) | |
c3adc830 RW |
351 | (propagated-inputs |
352 | `(("r-bsgenome" ,r-bsgenome))) | |
353 | (home-page | |
354 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
355 | (synopsis "Full genome sequences for Mouse") | |
356 | (description | |
357 | "This package provides full genome sequences for Mus | |
358 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
359 | in Biostrings objects.") | |
360 | (license license:artistic2.0))) | |
361 | ||
3a08940e RW |
362 | (define-public r-org-ce-eg-db |
363 | (package | |
364 | (name "r-org-ce-eg-db") | |
365 | (version "3.7.0") | |
366 | (source (origin | |
367 | (method url-fetch) | |
1c05e637 | 368 | (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation)) |
3a08940e RW |
369 | (sha256 |
370 | (base32 | |
371 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) | |
372 | (properties | |
373 | `((upstream-name . "org.Ce.eg.db"))) | |
374 | (build-system r-build-system) | |
375 | (propagated-inputs | |
376 | `(("r-annotationdbi" ,r-annotationdbi))) | |
377 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") | |
378 | (synopsis "Genome wide annotation for Worm") | |
379 | (description | |
380 | "This package provides mappings from Entrez gene identifiers to various | |
381 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
382 | (license license:artistic2.0))) | |
383 | ||
f8780e96 RW |
384 | (define-public r-org-dm-eg-db |
385 | (package | |
386 | (name "r-org-dm-eg-db") | |
387 | (version "3.7.0") | |
388 | (source (origin | |
389 | (method url-fetch) | |
b0dfc79b | 390 | (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation)) |
f8780e96 RW |
391 | (sha256 |
392 | (base32 | |
393 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) | |
394 | (properties | |
395 | `((upstream-name . "org.Dm.eg.db"))) | |
396 | (build-system r-build-system) | |
397 | (propagated-inputs | |
398 | `(("r-annotationdbi" ,r-annotationdbi))) | |
399 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") | |
400 | (synopsis "Genome wide annotation for Fly") | |
401 | (description | |
402 | "This package provides mappings from Entrez gene identifiers to various | |
403 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
404 | (license license:artistic2.0))) | |
405 | ||
3dad6087 RW |
406 | (define-public r-org-dr-eg-db |
407 | (package | |
408 | (name "r-org-dr-eg-db") | |
409 | (version "3.7.0") | |
410 | (source (origin | |
411 | (method url-fetch) | |
7bb65a22 | 412 | (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation)) |
3dad6087 RW |
413 | (sha256 |
414 | (base32 | |
415 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) | |
416 | (properties | |
417 | `((upstream-name . "org.Dr.eg.db"))) | |
418 | (build-system r-build-system) | |
419 | (propagated-inputs | |
420 | `(("r-annotationdbi" ,r-annotationdbi))) | |
421 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") | |
422 | (synopsis "Annotation for Zebrafish") | |
423 | (description | |
424 | "This package provides genome wide annotations for Zebrafish, primarily | |
425 | based on mapping using Entrez Gene identifiers.") | |
426 | (license license:artistic2.0))) | |
427 | ||
d56df35a RW |
428 | (define-public r-org-hs-eg-db |
429 | (package | |
430 | (name "r-org-hs-eg-db") | |
431 | (version "3.7.0") | |
432 | (source (origin | |
433 | (method url-fetch) | |
f53becc6 | 434 | (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) |
d56df35a RW |
435 | (sha256 |
436 | (base32 | |
437 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) | |
438 | (properties | |
439 | `((upstream-name . "org.Hs.eg.db"))) | |
440 | (build-system r-build-system) | |
441 | (propagated-inputs | |
442 | `(("r-annotationdbi" ,r-annotationdbi))) | |
443 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") | |
444 | (synopsis "Genome wide annotation for Human") | |
445 | (description | |
446 | "This package contains genome-wide annotations for Human, primarily based | |
447 | on mapping using Entrez Gene identifiers.") | |
448 | (license license:artistic2.0))) | |
449 | ||
8035819f RW |
450 | (define-public r-org-mm-eg-db |
451 | (package | |
452 | (name "r-org-mm-eg-db") | |
453 | (version "3.7.0") | |
454 | (source (origin | |
455 | (method url-fetch) | |
411be88b | 456 | (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation)) |
8035819f RW |
457 | (sha256 |
458 | (base32 | |
459 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) | |
460 | (properties | |
461 | `((upstream-name . "org.Mm.eg.db"))) | |
462 | (build-system r-build-system) | |
463 | (propagated-inputs | |
464 | `(("r-annotationdbi" ,r-annotationdbi))) | |
465 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") | |
466 | (synopsis "Genome wide annotation for Mouse") | |
467 | (description | |
468 | "This package provides mappings from Entrez gene identifiers to various | |
469 | annotations for the genome of the model mouse Mus musculus.") | |
470 | (license license:artistic2.0))) | |
471 | ||
fe0b76e2 RW |
472 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
473 | (package | |
474 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
475 | (version "1.4.0") | |
476 | (source (origin | |
477 | (method url-fetch) | |
e7a8cf2e RW |
478 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19" |
479 | version 'annotation)) | |
fe0b76e2 RW |
480 | (sha256 |
481 | (base32 | |
482 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) | |
483 | (properties | |
484 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
485 | (build-system r-build-system) | |
fe0b76e2 RW |
486 | (propagated-inputs |
487 | `(("r-bsgenome" ,r-bsgenome))) | |
488 | (home-page | |
489 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
490 | (synopsis "Full genome sequences for Homo sapiens") | |
491 | (description | |
492 | "This package provides full genome sequences for Homo sapiens as provided | |
493 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
494 | (license license:artistic2.0))) | |
495 | ||
8324e64c RW |
496 | (define-public r-ensdb-hsapiens-v75 |
497 | (package | |
498 | (name "r-ensdb-hsapiens-v75") | |
499 | (version "2.99.0") | |
500 | (source | |
501 | (origin | |
502 | (method url-fetch) | |
503 | (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) | |
504 | (sha256 | |
505 | (base32 | |
506 | "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) | |
507 | (properties | |
508 | `((upstream-name . "EnsDb.Hsapiens.v75"))) | |
509 | (build-system r-build-system) | |
510 | (propagated-inputs | |
511 | `(("r-ensembldb" ,r-ensembldb))) | |
512 | (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") | |
513 | (synopsis "Ensembl based annotation package") | |
514 | (description | |
515 | "This package exposes an annotation database generated from Ensembl.") | |
516 | (license license:artistic2.0))) | |
517 | ||
2cc51108 RW |
518 | (define-public r-genelendatabase |
519 | (package | |
520 | (name "r-genelendatabase") | |
daeb3cd9 | 521 | (version "1.18.0") |
2cc51108 RW |
522 | (source |
523 | (origin | |
524 | (method url-fetch) | |
717d7cda | 525 | (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) |
2cc51108 RW |
526 | (sha256 |
527 | (base32 | |
daeb3cd9 | 528 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
2cc51108 RW |
529 | (properties |
530 | `((upstream-name . "geneLenDataBase"))) | |
531 | (build-system r-build-system) | |
532 | (propagated-inputs | |
533 | `(("r-rtracklayer" ,r-rtracklayer) | |
534 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
535 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
536 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
537 | (description | |
538 | "This package provides the lengths of mRNA transcripts for a number of | |
539 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
540 | (license license:lgpl2.0+))) | |
541 | ||
66e35ce6 RW |
542 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
543 | (package | |
544 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
545 | (version "3.2.2") | |
546 | (source (origin | |
547 | (method url-fetch) | |
f2580a13 RW |
548 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene" |
549 | version 'annotation)) | |
66e35ce6 RW |
550 | (sha256 |
551 | (base32 | |
552 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
553 | (properties | |
554 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
555 | (build-system r-build-system) | |
66e35ce6 RW |
556 | (propagated-inputs |
557 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
558 | (home-page | |
559 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
560 | (synopsis "Annotation package for human genome in TxDb format") | |
561 | (description | |
562 | "This package provides an annotation database of Homo sapiens genome | |
563 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
798b80ce RW |
564 | track. The database is exposed as a @code{TxDb} object.") |
565 | (license license:artistic2.0))) | |
566 | ||
567 | (define-public r-txdb-hsapiens-ucsc-hg38-knowngene | |
568 | (package | |
569 | (name "r-txdb-hsapiens-ucsc-hg38-knowngene") | |
570 | (version "3.4.6") | |
571 | (source (origin | |
572 | (method url-fetch) | |
d78db088 RW |
573 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" |
574 | version 'annotation)) | |
798b80ce RW |
575 | (sha256 |
576 | (base32 | |
577 | "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) | |
578 | (properties | |
579 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) | |
580 | (build-system r-build-system) | |
581 | (propagated-inputs | |
582 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
583 | (home-page | |
584 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") | |
585 | (synopsis "Annotation package for human genome in TxDb format") | |
586 | (description | |
587 | "This package provides an annotation database of Homo sapiens genome | |
588 | data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" | |
66e35ce6 RW |
589 | track. The database is exposed as a @code{TxDb} object.") |
590 | (license license:artistic2.0))) | |
591 | ||
d220babf RW |
592 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
593 | (package | |
594 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
595 | (version "3.2.2") | |
596 | (source (origin | |
597 | (method url-fetch) | |
1afdf41b RW |
598 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene" |
599 | version 'annotation)) | |
d220babf RW |
600 | (sha256 |
601 | (base32 | |
602 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
603 | (properties | |
604 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
605 | (build-system r-build-system) | |
606 | (propagated-inputs | |
607 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
608 | ("r-annotationdbi" ,r-annotationdbi))) | |
609 | (home-page | |
610 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
611 | (synopsis "Annotation package for mouse genome in TxDb format") | |
612 | (description | |
613 | "This package provides an annotation database of Mouse genome data. It | |
614 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
615 | database is exposed as a @code{TxDb} object.") | |
616 | (license license:artistic2.0))) | |
617 | ||
7bc5d1b0 RW |
618 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
619 | (package | |
620 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
b69c7703 | 621 | (version "3.10.0") |
7bc5d1b0 RW |
622 | (source (origin |
623 | (method url-fetch) | |
c271d990 RW |
624 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene" |
625 | version 'annotation)) | |
7bc5d1b0 RW |
626 | (sha256 |
627 | (base32 | |
b69c7703 | 628 | "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9")))) |
7bc5d1b0 RW |
629 | (properties |
630 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
631 | (build-system r-build-system) | |
7bc5d1b0 RW |
632 | (propagated-inputs |
633 | `(("r-bsgenome" ,r-bsgenome) | |
634 | ("r-genomicfeatures" ,r-genomicfeatures) | |
635 | ("r-annotationdbi" ,r-annotationdbi))) | |
636 | (home-page | |
637 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
638 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
639 | (description | |
640 | "This package loads a TxDb object, which is an R interface to | |
641 | prefabricated databases contained in this package. This package provides | |
642 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
643 | based on the knownGene track.") | |
644 | (license license:artistic2.0))) | |
645 | ||
7cd446fd RW |
646 | (define-public r-txdb-celegans-ucsc-ce6-ensgene |
647 | (package | |
648 | (name "r-txdb-celegans-ucsc-ce6-ensgene") | |
649 | (version "3.2.2") | |
650 | (source | |
651 | (origin | |
652 | (method url-fetch) | |
653 | (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene" | |
654 | version 'annotation)) | |
655 | (sha256 | |
656 | (base32 | |
657 | "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90")))) | |
658 | (properties | |
659 | `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) | |
660 | (build-system r-build-system) | |
661 | (propagated-inputs | |
662 | `(("r-annotationdbi" ,r-annotationdbi) | |
663 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
664 | (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") | |
665 | (synopsis "Annotation package for C elegans TxDb objects") | |
666 | (description | |
667 | "This package exposes a C elegans annotation database generated from UCSC | |
668 | by exposing these as TxDb objects.") | |
669 | (license license:artistic2.0))) | |
670 | ||
0f5c9cec RW |
671 | (define-public r-fdb-infiniummethylation-hg19 |
672 | (package | |
673 | (name "r-fdb-infiniummethylation-hg19") | |
674 | (version "2.2.0") | |
675 | (source (origin | |
676 | (method url-fetch) | |
6aca4054 RW |
677 | (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19" |
678 | version 'annotation)) | |
0f5c9cec RW |
679 | (sha256 |
680 | (base32 | |
681 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) | |
682 | (properties | |
683 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) | |
684 | (build-system r-build-system) | |
685 | (propagated-inputs | |
686 | `(("r-biostrings" ,r-biostrings) | |
687 | ("r-genomicfeatures" ,r-genomicfeatures) | |
688 | ("r-annotationdbi" ,r-annotationdbi) | |
689 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
690 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) | |
691 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") | |
692 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") | |
693 | (description | |
694 | "This is an annotation package for Illumina Infinium DNA methylation | |
695 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 | |
696 | annotations.") | |
697 | (license license:artistic2.0))) | |
698 | ||
9475a248 RW |
699 | (define-public r-illuminahumanmethylationepicmanifest |
700 | (package | |
701 | (name "r-illuminahumanmethylationepicmanifest") | |
702 | (version "0.3.0") | |
703 | (source (origin | |
704 | (method url-fetch) | |
25f567a8 RW |
705 | (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest" |
706 | version 'annotation)) | |
9475a248 RW |
707 | (sha256 |
708 | (base32 | |
709 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) | |
710 | (properties | |
711 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) | |
712 | (build-system r-build-system) | |
713 | (propagated-inputs | |
714 | `(("r-minfi" ,r-minfi))) | |
715 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") | |
716 | (synopsis "Manifest for Illumina's EPIC methylation arrays") | |
717 | (description | |
718 | "This is a manifest package for Illumina's EPIC methylation arrays.") | |
719 | (license license:artistic2.0))) | |
e8d435f7 RJ |
720 | |
721 | (define-public r-ideoviz | |
722 | (package | |
723 | (name "r-ideoviz") | |
724 | (version "1.22.0") | |
725 | (source (origin | |
726 | (method url-fetch) | |
727 | (uri (bioconductor-uri "IdeoViz" version)) | |
728 | (sha256 | |
729 | (base32 | |
730 | "0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil")))) | |
731 | (build-system r-build-system) | |
732 | (propagated-inputs | |
733 | `(("r-biobase" ,r-biobase) | |
734 | ("r-iranges" ,r-iranges) | |
735 | ("r-genomicranges" ,r-genomicranges) | |
736 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
737 | ("r-rtracklayer" ,r-rtracklayer) | |
738 | ("r-genomeinfodb" ,r-genomeinfodb))) | |
739 | (home-page "https://bioconductor.org/packages/IdeoViz/") | |
740 | (synopsis "Plots data along a chromosomal ideogram") | |
741 | (description "This package provides functions to plot data associated with | |
742 | arbitrary genomic intervals along chromosomal ideogram.") | |
743 | (license license:gpl2))) | |
9475a248 | 744 | |
a38bf7c8 RJ |
745 | ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 |
746 | ;; from Bioconductor. | |
747 | (define-public r-deconstructsigs | |
748 | (package | |
749 | (name "r-deconstructsigs") | |
750 | (version "1.8.0") | |
751 | (source (origin | |
752 | (method url-fetch) | |
753 | (uri (cran-uri "deconstructSigs" version)) | |
754 | (sha256 | |
755 | (base32 | |
756 | "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) | |
757 | (properties | |
758 | `((upstream-name . "deconstructSigs"))) | |
759 | (build-system r-build-system) | |
760 | (propagated-inputs | |
761 | `(("r-bsgenome" ,r-bsgenome) | |
762 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
763 | ("r-genomeinfodb" ,r-genomeinfodb) | |
764 | ("r-reshape2" ,r-reshape2))) | |
765 | (home-page "https://github.com/raerose01/deconstructSigs") | |
766 | (synopsis "Identifies signatures present in a tumor sample") | |
767 | (description "This package takes sample information in the form of the | |
768 | fraction of mutations in each of 96 trinucleotide contexts and identifies | |
769 | the weighted combination of published signatures that, when summed, most | |
770 | closely reconstructs the mutational profile.") | |
771 | (license license:gpl2+))) | |
772 | ||
7c9d8a5d RW |
773 | ;; This is a CRAN package, but it depends on Bioconductor packages. |
774 | (define-public r-nmf | |
775 | (package | |
776 | (name "r-nmf") | |
be1042b3 | 777 | (version "0.22.0") |
7c9d8a5d RW |
778 | (source |
779 | (origin | |
780 | (method url-fetch) | |
781 | (uri (cran-uri "NMF" version)) | |
782 | (sha256 | |
783 | (base32 | |
be1042b3 | 784 | "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq")))) |
7c9d8a5d RW |
785 | (properties `((upstream-name . "NMF"))) |
786 | (build-system r-build-system) | |
787 | (propagated-inputs | |
788 | `(("r-cluster" ,r-cluster) | |
be1042b3 RW |
789 | ("r-biobase" ,r-biobase) |
790 | ("r-biocmanager" ,r-biocmanager) | |
7c9d8a5d RW |
791 | ("r-bigmemory" ,r-bigmemory) ; suggested |
792 | ("r-synchronicity" ,r-synchronicity) ; suggested | |
793 | ("r-colorspace" ,r-colorspace) | |
794 | ("r-digest" ,r-digest) | |
795 | ("r-doparallel" ,r-doparallel) | |
796 | ("r-foreach" ,r-foreach) | |
797 | ("r-ggplot2" ,r-ggplot2) | |
798 | ("r-gridbase" ,r-gridbase) | |
799 | ("r-pkgmaker" ,r-pkgmaker) | |
800 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
801 | ("r-registry" ,r-registry) | |
802 | ("r-reshape2" ,r-reshape2) | |
803 | ("r-rngtools" ,r-rngtools) | |
804 | ("r-stringr" ,r-stringr))) | |
805 | (home-page "http://renozao.github.io/NMF") | |
806 | (synopsis "Algorithms and framework for nonnegative matrix factorization") | |
807 | (description | |
808 | "This package provides a framework to perform Non-negative Matrix | |
809 | Factorization (NMF). The package implements a set of already published | |
810 | algorithms and seeding methods, and provides a framework to test, develop and | |
811 | plug new or custom algorithms. Most of the built-in algorithms have been | |
812 | optimized in C++, and the main interface function provides an easy way of | |
813 | performing parallel computations on multicore machines.") | |
814 | (license license:gpl2+))) | |
815 | ||
f8a5af46 RW |
816 | (define-public r-do-db |
817 | (package | |
818 | (name "r-do-db") | |
819 | (version "2.9") | |
820 | (source (origin | |
821 | (method url-fetch) | |
eed2766a | 822 | (uri (bioconductor-uri "DO.db" version 'annotation)) |
f8a5af46 RW |
823 | (sha256 |
824 | (base32 | |
825 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) | |
826 | (properties | |
827 | `((upstream-name . "DO.db"))) | |
828 | (build-system r-build-system) | |
829 | (propagated-inputs | |
830 | `(("r-annotationdbi" ,r-annotationdbi))) | |
831 | (home-page "https://www.bioconductor.org/packages/DO.db/") | |
832 | (synopsis "Annotation maps describing the entire Disease Ontology") | |
833 | (description | |
834 | "This package provides a set of annotation maps describing the entire | |
835 | Disease Ontology.") | |
836 | (license license:artistic2.0))) | |
837 | ||
ec20858a RJ |
838 | (define-public r-pasilla |
839 | (package | |
840 | (name "r-pasilla") | |
841 | (version "1.14.0") | |
842 | (source (origin | |
843 | (method url-fetch) | |
844 | (uri (string-append | |
845 | "http://bioconductor.org/packages/release/data/experiment" | |
846 | "/src/contrib/pasilla_" version ".tar.gz")) | |
847 | (sha256 | |
848 | (base32 | |
849 | "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) | |
850 | (build-system r-build-system) | |
851 | (propagated-inputs | |
852 | `(("r-biocstyle" ,r-biocstyle) | |
853 | ("r-dexseq" ,r-dexseq) | |
854 | ("r-knitr" ,r-knitr) | |
855 | ("r-rmarkdown" ,r-rmarkdown))) | |
856 | (home-page "https://www.bioconductor.org/packages/pasilla/") | |
857 | (synopsis "Data package with per-exon and per-gene read counts") | |
858 | (description "This package provides per-exon and per-gene read counts | |
859 | computed for selected genes from RNA-seq data that were presented in the | |
860 | article 'Conservation of an RNA regulatory map between Drosophila and mammals' | |
861 | by Brooks et al., Genome Research 2011.") | |
862 | (license license:lgpl2.1+))) | |
863 | ||
83b42091 RW |
864 | (define-public r-pfam-db |
865 | (package | |
866 | (name "r-pfam-db") | |
867 | (version "3.8.2") | |
868 | (source | |
869 | (origin | |
870 | (method url-fetch) | |
871 | (uri (bioconductor-uri "PFAM.db" version 'annotation)) | |
872 | (sha256 | |
873 | (base32 | |
874 | "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) | |
875 | (properties `((upstream-name . "PFAM.db"))) | |
876 | (build-system r-build-system) | |
877 | (propagated-inputs | |
878 | `(("r-annotationdbi" ,r-annotationdbi))) | |
879 | (home-page "https://bioconductor.org/packages/PFAM.db") | |
880 | (synopsis "Set of protein ID mappings for PFAM") | |
881 | (description | |
882 | "This package provides a set of protein ID mappings for PFAM, assembled | |
883 | using data from public repositories.") | |
884 | (license license:artistic2.0))) | |
885 | ||
40be965e RW |
886 | (define-public r-phastcons100way-ucsc-hg19 |
887 | (package | |
888 | (name "r-phastcons100way-ucsc-hg19") | |
889 | (version "3.7.2") | |
890 | (source | |
891 | (origin | |
892 | (method url-fetch) | |
893 | (uri (bioconductor-uri "phastCons100way.UCSC.hg19" | |
894 | version 'annotation)) | |
895 | (sha256 | |
896 | (base32 | |
897 | "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa")))) | |
898 | (properties | |
899 | `((upstream-name . "phastCons100way.UCSC.hg19"))) | |
900 | (build-system r-build-system) | |
901 | (propagated-inputs | |
902 | `(("r-bsgenome" ,r-bsgenome) | |
903 | ("r-genomeinfodb" ,r-genomeinfodb) | |
904 | ("r-genomicranges" ,r-genomicranges) | |
905 | ("r-genomicscores" ,r-genomicscores) | |
906 | ("r-iranges" ,r-iranges) | |
907 | ("r-s4vectors" ,r-s4vectors))) | |
908 | (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") | |
909 | (synopsis "UCSC phastCons conservation scores for hg19") | |
910 | (description | |
911 | "This package provides UCSC phastCons conservation scores for the human | |
912 | genome (hg19) calculated from multiple alignments with other 99 vertebrate | |
913 | species.") | |
914 | (license license:artistic2.0))) | |
915 | ||
2cc51108 | 916 | \f |
557a1089 RW |
917 | ;;; Experiment data |
918 | ||
692bce15 RW |
919 | (define-public r-abadata |
920 | (package | |
921 | (name "r-abadata") | |
922 | (version "1.12.0") | |
923 | (source (origin | |
924 | (method url-fetch) | |
ced61edf | 925 | (uri (bioconductor-uri "ABAData" version 'experiment)) |
692bce15 RW |
926 | (sha256 |
927 | (base32 | |
928 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) | |
929 | (properties | |
930 | `((upstream-name . "ABAData"))) | |
931 | (build-system r-build-system) | |
932 | (propagated-inputs | |
933 | `(("r-annotationdbi" ,r-annotationdbi))) | |
934 | (home-page "https://www.bioconductor.org/packages/ABAData/") | |
935 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") | |
936 | (description | |
937 | "This package provides the data for the gene expression enrichment | |
938 | analysis conducted in the package ABAEnrichment. The package includes three | |
939 | datasets which are derived from the Allen Brain Atlas: | |
940 | ||
941 | @enumerate | |
942 | @item Gene expression data from Human Brain (adults) averaged across donors, | |
943 | @item Gene expression data from the Developing Human Brain pooled into five | |
944 | age categories and averaged across donors, and | |
945 | @item a developmental effect score based on the Developing Human Brain | |
946 | expression data. | |
947 | @end enumerate | |
948 | ||
949 | All datasets are restricted to protein coding genes.") | |
950 | (license license:gpl2+))) | |
951 | ||
b50c9660 RW |
952 | (define-public r-arrmdata |
953 | (package | |
954 | (name "r-arrmdata") | |
955 | (version "1.18.0") | |
956 | (source (origin | |
957 | (method url-fetch) | |
b86f7746 | 958 | (uri (bioconductor-uri "ARRmData" version 'experiment)) |
b50c9660 RW |
959 | (sha256 |
960 | (base32 | |
961 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) | |
962 | (properties | |
963 | `((upstream-name . "ARRmData"))) | |
964 | (build-system r-build-system) | |
965 | (home-page "https://www.bioconductor.org/packages/ARRmData/") | |
966 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") | |
967 | (description | |
968 | "This package provides raw beta values from 36 samples across 3 groups | |
969 | from Illumina 450k methylation arrays.") | |
970 | (license license:artistic2.0))) | |
971 | ||
557a1089 RW |
972 | (define-public r-hsmmsinglecell |
973 | (package | |
974 | (name "r-hsmmsinglecell") | |
975 | (version "1.2.0") | |
976 | (source (origin | |
977 | (method url-fetch) | |
545e67ac | 978 | (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) |
557a1089 RW |
979 | (sha256 |
980 | (base32 | |
981 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) | |
982 | (properties | |
983 | `((upstream-name . "HSMMSingleCell"))) | |
984 | (build-system r-build-system) | |
985 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") | |
986 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") | |
987 | (description | |
988 | "Skeletal myoblasts undergo a well-characterized sequence of | |
989 | morphological and transcriptional changes during differentiation. In this | |
990 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded | |
991 | under high mitogen conditions (GM) and then differentiated by switching to | |
992 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several | |
993 | hundred cells taken over a time-course of serum-induced differentiation. | |
994 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, | |
995 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. | |
996 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, | |
997 | which were then sequenced to a depth of ~4 million reads per library, | |
998 | resulting in a complete gene expression profile for each cell.") | |
999 | (license license:artistic2.0))) | |
ad8f46c6 | 1000 | |
1001 | (define-public r-all | |
1002 | (package | |
1003 | (name "r-all") | |
1004 | (version "1.26.0") | |
1005 | (source (origin | |
1006 | (method url-fetch) | |
41728d23 | 1007 | (uri (bioconductor-uri "ALL" version 'experiment)) |
ad8f46c6 | 1008 | (sha256 |
1009 | (base32 | |
1010 | "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) | |
1011 | (properties `((upstream-name . "ALL"))) | |
1012 | (build-system r-build-system) | |
1013 | (propagated-inputs | |
1014 | `(("r-biobase" ,r-biobase))) | |
1015 | (home-page "https://bioconductor.org/packages/ALL") | |
1016 | (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") | |
1017 | (description | |
1018 | "The data consist of microarrays from 128 different individuals with | |
1019 | @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates | |
1020 | are available. The data have been normalized (using rma) and it is the | |
1021 | jointly normalized data that are available here. The data are presented in | |
1022 | the form of an @code{exprSet} object.") | |
1023 | (license license:artistic2.0))) | |
557a1089 | 1024 | |
53b1e10f RW |
1025 | (define-public r-affydata |
1026 | (package | |
1027 | (name "r-affydata") | |
1028 | (version "1.32.0") | |
1029 | (source | |
1030 | (origin | |
1031 | (method url-fetch) | |
1032 | (uri (bioconductor-uri "affydata" version 'experiment)) | |
1033 | (sha256 | |
1034 | (base32 | |
1035 | "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) | |
1036 | (properties `((upstream-name . "affydata"))) | |
1037 | (build-system r-build-system) | |
1038 | (propagated-inputs | |
1039 | `(("r-affy" ,r-affy))) | |
1040 | (home-page "https://bioconductor.org/packages/affydata/") | |
1041 | (synopsis "Affymetrix data for demonstration purposes") | |
1042 | (description | |
1043 | "This package provides example datasets that represent 'real world | |
1044 | examples' of Affymetrix data, unlike the artificial examples included in the | |
1045 | package @code{affy}.") | |
1046 | (license license:gpl2+))) | |
1047 | ||
ff1146b9 RW |
1048 | (define-public r-curatedtcgadata |
1049 | (package | |
1050 | (name "r-curatedtcgadata") | |
1051 | (version "1.8.0") | |
1052 | (source | |
1053 | (origin | |
1054 | (method url-fetch) | |
1055 | (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) | |
1056 | (sha256 | |
1057 | (base32 | |
1058 | "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) | |
1059 | (properties | |
1060 | `((upstream-name . "curatedTCGAData"))) | |
1061 | (build-system r-build-system) | |
1062 | (propagated-inputs | |
1063 | `(("r-annotationhub" ,r-annotationhub) | |
1064 | ("r-experimenthub" ,r-experimenthub) | |
1065 | ("r-hdf5array" ,r-hdf5array) | |
1066 | ("r-multiassayexperiment" ,r-multiassayexperiment) | |
1067 | ("r-s4vectors" ,r-s4vectors) | |
1068 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1069 | (home-page "https://bioconductor.org/packages/curatedTCGAData/") | |
1070 | (synopsis "Curated data from The Cancer Genome Atlas") | |
1071 | (description | |
1072 | "This package provides publicly available data from The Cancer Genome | |
1073 | Atlas (TCGA) as @code{MultiAssayExperiment} objects. | |
1074 | @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy | |
1075 | number, mutation, microRNA, protein, and others) with clinical / pathological | |
1076 | data. It also links assay barcodes with patient identifiers, enabling | |
1077 | harmonized subsetting of rows (features) and columns (patients / samples) | |
1078 | across the entire multi-'omics experiment.") | |
1079 | (license license:artistic2.0))) | |
1080 | ||
557a1089 RW |
1081 | \f |
1082 | ;;; Packages | |
1083 | ||
e5d722fb RW |
1084 | (define-public r-biocversion |
1085 | (package | |
1086 | (name "r-biocversion") | |
1087 | (version "3.10.1") | |
1088 | (source | |
1089 | (origin | |
1090 | (method url-fetch) | |
1091 | (uri (bioconductor-uri "BiocVersion" version)) | |
1092 | (sha256 | |
1093 | (base32 | |
1094 | "0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f")))) | |
1095 | (properties `((upstream-name . "BiocVersion"))) | |
1096 | (build-system r-build-system) | |
1097 | (home-page "https://bioconductor.org/packages/BiocVersion/") | |
1098 | (synopsis "Set the appropriate version of Bioconductor packages") | |
1099 | (description | |
1100 | "This package provides repository information for the appropriate version | |
1101 | of Bioconductor.") | |
1102 | (license license:artistic2.0))) | |
1103 | ||
14bba460 RW |
1104 | (define-public r-biocgenerics |
1105 | (package | |
1106 | (name "r-biocgenerics") | |
be5e4e96 | 1107 | (version "0.32.0") |
14bba460 RW |
1108 | (source (origin |
1109 | (method url-fetch) | |
1110 | (uri (bioconductor-uri "BiocGenerics" version)) | |
1111 | (sha256 | |
1112 | (base32 | |
be5e4e96 | 1113 | "1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn")))) |
14bba460 RW |
1114 | (properties |
1115 | `((upstream-name . "BiocGenerics"))) | |
1116 | (build-system r-build-system) | |
1117 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
1118 | (synopsis "S4 generic functions for Bioconductor") | |
1119 | (description | |
1120 | "This package provides S4 generic functions needed by many Bioconductor | |
1121 | packages.") | |
1122 | (license license:artistic2.0))) | |
1123 | ||
5cf940de RW |
1124 | (define-public r-affycomp |
1125 | (package | |
1126 | (name "r-affycomp") | |
5d87f126 | 1127 | (version "1.62.0") |
5cf940de RW |
1128 | (source |
1129 | (origin | |
1130 | (method url-fetch) | |
1131 | (uri (bioconductor-uri "affycomp" version)) | |
1132 | (sha256 | |
1133 | (base32 | |
5d87f126 | 1134 | "0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js")))) |
5cf940de RW |
1135 | (properties `((upstream-name . "affycomp"))) |
1136 | (build-system r-build-system) | |
1137 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
1138 | (home-page "https://bioconductor.org/packages/affycomp/") | |
1139 | (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") | |
1140 | (description | |
1141 | "The package contains functions that can be used to compare expression | |
1142 | measures for Affymetrix Oligonucleotide Arrays.") | |
1143 | (license license:gpl2+))) | |
1144 | ||
5094aa94 RW |
1145 | (define-public r-affycompatible |
1146 | (package | |
1147 | (name "r-affycompatible") | |
c2fa63e9 | 1148 | (version "1.46.0") |
5094aa94 RW |
1149 | (source |
1150 | (origin | |
1151 | (method url-fetch) | |
1152 | (uri (bioconductor-uri "AffyCompatible" version)) | |
1153 | (sha256 | |
1154 | (base32 | |
c2fa63e9 | 1155 | "10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks")))) |
5094aa94 RW |
1156 | (properties |
1157 | `((upstream-name . "AffyCompatible"))) | |
1158 | (build-system r-build-system) | |
1159 | (propagated-inputs | |
1160 | `(("r-biostrings" ,r-biostrings) | |
1161 | ("r-rcurl" ,r-rcurl) | |
1162 | ("r-xml" ,r-xml))) | |
1163 | (home-page "https://bioconductor.org/packages/AffyCompatible/") | |
1164 | (synopsis "Work with Affymetrix GeneChip files") | |
1165 | (description | |
1166 | "This package provides an interface to Affymetrix chip annotation and | |
1167 | sample attribute files. The package allows an easy way for users to download | |
1168 | and manage local data bases of Affynmetrix NetAffx annotation files. It also | |
1169 | provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip | |
1170 | Command Console} (AGCC)-compatible sample annotation files.") | |
1171 | (license license:artistic2.0))) | |
1172 | ||
4ca2d6c1 RW |
1173 | (define-public r-affycontam |
1174 | (package | |
1175 | (name "r-affycontam") | |
f561421d | 1176 | (version "1.44.0") |
4ca2d6c1 RW |
1177 | (source |
1178 | (origin | |
1179 | (method url-fetch) | |
1180 | (uri (bioconductor-uri "affyContam" version)) | |
1181 | (sha256 | |
1182 | (base32 | |
f561421d | 1183 | "0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l")))) |
4ca2d6c1 RW |
1184 | (properties `((upstream-name . "affyContam"))) |
1185 | (build-system r-build-system) | |
1186 | (propagated-inputs | |
1187 | `(("r-affy" ,r-affy) | |
1188 | ("r-affydata" ,r-affydata) | |
1189 | ("r-biobase" ,r-biobase))) | |
1190 | (home-page "https://bioconductor.org/packages/affyContam/") | |
1191 | (synopsis "Structured corruption of Affymetrix CEL file data") | |
1192 | (description | |
1193 | "Microarray quality assessment is a major concern of microarray analysts. | |
1194 | This package provides some simple approaches to in silico creation of quality | |
1195 | problems in CEL-level data to help evaluate performance of quality metrics.") | |
1196 | (license license:artistic2.0))) | |
1197 | ||
12105c6c RW |
1198 | (define-public r-affycoretools |
1199 | (package | |
1200 | (name "r-affycoretools") | |
f8f181ae | 1201 | (version "1.58.4") |
12105c6c RW |
1202 | (source |
1203 | (origin | |
1204 | (method url-fetch) | |
1205 | (uri (bioconductor-uri "affycoretools" version)) | |
1206 | (sha256 | |
1207 | (base32 | |
f8f181ae | 1208 | "1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw")))) |
12105c6c RW |
1209 | (properties `((upstream-name . "affycoretools"))) |
1210 | (build-system r-build-system) | |
1211 | (propagated-inputs | |
1212 | `(("r-affy" ,r-affy) | |
1213 | ("r-annotationdbi" ,r-annotationdbi) | |
1214 | ("r-biobase" ,r-biobase) | |
1215 | ("r-biocgenerics" ,r-biocgenerics) | |
1216 | ("r-dbi" ,r-dbi) | |
1217 | ("r-edger" ,r-edger) | |
1218 | ("r-gcrma" ,r-gcrma) | |
f8f181ae | 1219 | ("r-glimma" ,r-glimma) |
12105c6c RW |
1220 | ("r-ggplot2" ,r-ggplot2) |
1221 | ("r-gostats" ,r-gostats) | |
1222 | ("r-gplots" ,r-gplots) | |
1223 | ("r-hwriter" ,r-hwriter) | |
1224 | ("r-lattice" ,r-lattice) | |
1225 | ("r-limma" ,r-limma) | |
1226 | ("r-oligoclasses" ,r-oligoclasses) | |
1227 | ("r-reportingtools" ,r-reportingtools) | |
1228 | ("r-rsqlite" ,r-rsqlite) | |
1229 | ("r-s4vectors" ,r-s4vectors) | |
1230 | ("r-xtable" ,r-xtable))) | |
1231 | (home-page "https://bioconductor.org/packages/affycoretools/") | |
1232 | (synopsis "Functions for analyses with Affymetrix GeneChips") | |
1233 | (description | |
1234 | "This package provides various wrapper functions that have been written | |
1235 | to streamline the more common analyses that a Biostatistician might see.") | |
1236 | (license license:artistic2.0))) | |
1237 | ||
d6a5d9b2 RW |
1238 | (define-public r-affxparser |
1239 | (package | |
1240 | (name "r-affxparser") | |
ce5162d0 | 1241 | (version "1.58.0") |
d6a5d9b2 RW |
1242 | (source |
1243 | (origin | |
1244 | (method url-fetch) | |
1245 | (uri (bioconductor-uri "affxparser" version)) | |
1246 | (sha256 | |
1247 | (base32 | |
ce5162d0 | 1248 | "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40")))) |
d6a5d9b2 RW |
1249 | (properties `((upstream-name . "affxparser"))) |
1250 | (build-system r-build-system) | |
1251 | (home-page "https://github.com/HenrikBengtsson/affxparser") | |
1252 | (synopsis "Affymetrix File Parsing SDK") | |
1253 | (description | |
1254 | "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, | |
1255 | BAR). It provides methods for fast and memory efficient parsing of Affymetrix | |
1256 | files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files | |
1257 | are supported. Currently, there are methods for reading @dfn{chip definition | |
1258 | file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read | |
1259 | either in full or in part. For example, probe signals from a few probesets | |
1260 | can be extracted very quickly from a set of CEL files into a convenient list | |
1261 | structure.") | |
1262 | ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is | |
1263 | ;; under LGPLv2+. | |
1264 | (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2)))) | |
1265 | ||
7097c700 RW |
1266 | (define-public r-annotate |
1267 | (package | |
1268 | (name "r-annotate") | |
7a111924 | 1269 | (version "1.64.0") |
7097c700 RW |
1270 | (source |
1271 | (origin | |
1272 | (method url-fetch) | |
1273 | (uri (bioconductor-uri "annotate" version)) | |
1274 | (sha256 | |
1275 | (base32 | |
7a111924 | 1276 | "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy")))) |
7097c700 RW |
1277 | (build-system r-build-system) |
1278 | (propagated-inputs | |
1279 | `(("r-annotationdbi" ,r-annotationdbi) | |
1280 | ("r-biobase" ,r-biobase) | |
1281 | ("r-biocgenerics" ,r-biocgenerics) | |
1282 | ("r-dbi" ,r-dbi) | |
1283 | ("r-rcurl" ,r-rcurl) | |
1284 | ("r-xml" ,r-xml) | |
1285 | ("r-xtable" ,r-xtable))) | |
1286 | (home-page | |
1287 | "https://bioconductor.org/packages/annotate") | |
1288 | (synopsis "Annotation for microarrays") | |
1289 | (description "This package provides R environments for the annotation of | |
1290 | microarrays.") | |
1291 | (license license:artistic2.0))) | |
1292 | ||
fa596599 RW |
1293 | (define-public r-hpar |
1294 | (package | |
1295 | (name "r-hpar") | |
ddd36739 | 1296 | (version "1.28.0") |
fa596599 RW |
1297 | (source |
1298 | (origin | |
1299 | (method url-fetch) | |
1300 | (uri (bioconductor-uri "hpar" version)) | |
1301 | (sha256 | |
1302 | (base32 | |
ddd36739 | 1303 | "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m")))) |
fa596599 RW |
1304 | (build-system r-build-system) |
1305 | (home-page "https://bioconductor.org/packages/hpar/") | |
1306 | (synopsis "Human Protein Atlas in R") | |
1307 | (description "This package provides a simple interface to and data from | |
1308 | the Human Protein Atlas project.") | |
1309 | (license license:artistic2.0))) | |
183ce988 RJ |
1310 | |
1311 | (define-public r-regioner | |
1312 | (package | |
1313 | (name "r-regioner") | |
7a8fcdac | 1314 | (version "1.18.1") |
183ce988 RJ |
1315 | (source |
1316 | (origin | |
1317 | (method url-fetch) | |
1318 | (uri (bioconductor-uri "regioneR" version)) | |
1319 | (sha256 | |
1320 | (base32 | |
7a8fcdac | 1321 | "0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9")))) |
183ce988 RJ |
1322 | (properties `((upstream-name . "regioneR"))) |
1323 | (build-system r-build-system) | |
1324 | (propagated-inputs | |
d639d888 | 1325 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 1326 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 1327 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 1328 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 1329 | ("r-iranges" ,r-iranges) |
d639d888 RW |
1330 | ("r-memoise" ,r-memoise) |
1331 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 1332 | ("r-s4vectors" ,r-s4vectors))) |
183ce988 RJ |
1333 | (home-page "https://bioconductor.org/packages/regioneR/") |
1334 | (synopsis "Association analysis of genomic regions") | |
1335 | (description "This package offers a statistical framework based on | |
1336 | customizable permutation tests to assess the association between genomic | |
1337 | region sets and other genomic features.") | |
1338 | (license license:artistic2.0))) | |
a5b56a53 | 1339 | |
15184fb3 RW |
1340 | (define-public r-reportingtools |
1341 | (package | |
1342 | (name "r-reportingtools") | |
7ccbaf1b | 1343 | (version "2.26.0") |
15184fb3 RW |
1344 | (source |
1345 | (origin | |
1346 | (method url-fetch) | |
1347 | (uri (bioconductor-uri "ReportingTools" version)) | |
1348 | (sha256 | |
1349 | (base32 | |
7ccbaf1b | 1350 | "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w")))) |
15184fb3 RW |
1351 | (properties |
1352 | `((upstream-name . "ReportingTools"))) | |
1353 | (build-system r-build-system) | |
1354 | (propagated-inputs | |
1355 | `(("r-annotate" ,r-annotate) | |
1356 | ("r-annotationdbi" ,r-annotationdbi) | |
1357 | ("r-biobase" ,r-biobase) | |
1358 | ("r-biocgenerics" ,r-biocgenerics) | |
1359 | ("r-category" ,r-category) | |
1360 | ("r-deseq2" ,r-deseq2) | |
1361 | ("r-edger" ,r-edger) | |
1362 | ("r-ggbio" ,r-ggbio) | |
1363 | ("r-ggplot2" ,r-ggplot2) | |
1364 | ("r-gostats" ,r-gostats) | |
1365 | ("r-gseabase" ,r-gseabase) | |
1366 | ("r-hwriter" ,r-hwriter) | |
1367 | ("r-iranges" ,r-iranges) | |
1368 | ("r-knitr" ,r-knitr) | |
1369 | ("r-lattice" ,r-lattice) | |
1370 | ("r-limma" ,r-limma) | |
1371 | ("r-pfam-db" ,r-pfam-db) | |
1372 | ("r-r-utils" ,r-r-utils) | |
1373 | ("r-xml" ,r-xml))) | |
1374 | (home-page "https://bioconductor.org/packages/ReportingTools/") | |
1375 | (synopsis "Tools for making reports in various formats") | |
1376 | (description | |
1377 | "The ReportingTools package enables users to easily display reports of | |
1378 | analysis results generated from sources such as microarray and sequencing | |
1379 | data. The package allows users to create HTML pages that may be viewed on a | |
1380 | web browser, or in other formats. Users can generate tables with sortable and | |
1381 | filterable columns, make and display plots, and link table entries to other | |
1382 | data sources such as NCBI or larger plots within the HTML page. Using the | |
1383 | package, users can also produce a table of contents page to link various | |
1384 | reports together for a particular project that can be viewed in a web | |
1385 | browser.") | |
1386 | (license license:artistic2.0))) | |
1387 | ||
bfb93b48 RW |
1388 | (define-public r-geneplotter |
1389 | (package | |
1390 | (name "r-geneplotter") | |
7778e91a | 1391 | (version "1.64.0") |
bfb93b48 RW |
1392 | (source |
1393 | (origin | |
1394 | (method url-fetch) | |
1395 | (uri (bioconductor-uri "geneplotter" version)) | |
1396 | (sha256 | |
1397 | (base32 | |
7778e91a | 1398 | "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx")))) |
bfb93b48 RW |
1399 | (build-system r-build-system) |
1400 | (propagated-inputs | |
1401 | `(("r-annotate" ,r-annotate) | |
1402 | ("r-annotationdbi" ,r-annotationdbi) | |
1403 | ("r-biobase" ,r-biobase) | |
1404 | ("r-biocgenerics" ,r-biocgenerics) | |
1405 | ("r-lattice" ,r-lattice) | |
1406 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
1407 | (home-page "https://bioconductor.org/packages/geneplotter") | |
1408 | (synopsis "Graphics functions for genomic data") | |
1409 | (description | |
1410 | "This package provides functions for plotting genomic data.") | |
1411 | (license license:artistic2.0))) | |
1412 | ||
01c7ba99 RW |
1413 | (define-public r-oligoclasses |
1414 | (package | |
1415 | (name "r-oligoclasses") | |
79820b9f | 1416 | (version "1.48.0") |
01c7ba99 RW |
1417 | (source |
1418 | (origin | |
1419 | (method url-fetch) | |
1420 | (uri (bioconductor-uri "oligoClasses" version)) | |
1421 | (sha256 | |
1422 | (base32 | |
79820b9f | 1423 | "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf")))) |
01c7ba99 RW |
1424 | (properties `((upstream-name . "oligoClasses"))) |
1425 | (build-system r-build-system) | |
1426 | (propagated-inputs | |
1427 | `(("r-affyio" ,r-affyio) | |
1428 | ("r-biobase" ,r-biobase) | |
1429 | ("r-biocgenerics" ,r-biocgenerics) | |
1430 | ("r-biocmanager" ,r-biocmanager) | |
1431 | ("r-biostrings" ,r-biostrings) | |
1432 | ("r-dbi" ,r-dbi) | |
1433 | ("r-ff" ,r-ff) | |
1434 | ("r-foreach" ,r-foreach) | |
1435 | ("r-genomicranges" ,r-genomicranges) | |
1436 | ("r-iranges" ,r-iranges) | |
1437 | ("r-rsqlite" ,r-rsqlite) | |
1438 | ("r-s4vectors" ,r-s4vectors) | |
1439 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1440 | (home-page "https://bioconductor.org/packages/oligoClasses/") | |
1441 | (synopsis "Classes for high-throughput arrays") | |
1442 | (description | |
1443 | "This package contains class definitions, validity checks, and | |
1444 | initialization methods for classes used by the @code{oligo} and @code{crlmm} | |
1445 | packages.") | |
1446 | (license license:gpl2+))) | |
1447 | ||
4c63eeb8 RW |
1448 | (define-public r-oligo |
1449 | (package | |
1450 | (name "r-oligo") | |
084c651c | 1451 | (version "1.50.0") |
4c63eeb8 RW |
1452 | (source |
1453 | (origin | |
1454 | (method url-fetch) | |
1455 | (uri (bioconductor-uri "oligo" version)) | |
1456 | (sha256 | |
1457 | (base32 | |
084c651c | 1458 | "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3")))) |
4c63eeb8 RW |
1459 | (properties `((upstream-name . "oligo"))) |
1460 | (build-system r-build-system) | |
1461 | (inputs `(("zlib" ,zlib))) | |
1462 | (propagated-inputs | |
1463 | `(("r-affxparser" ,r-affxparser) | |
1464 | ("r-affyio" ,r-affyio) | |
1465 | ("r-biobase" ,r-biobase) | |
1466 | ("r-biocgenerics" ,r-biocgenerics) | |
1467 | ("r-biostrings" ,r-biostrings) | |
1468 | ("r-dbi" ,r-dbi) | |
1469 | ("r-ff" ,r-ff) | |
1470 | ("r-oligoclasses" ,r-oligoclasses) | |
1471 | ("r-preprocesscore" ,r-preprocesscore) | |
1472 | ("r-rsqlite" ,r-rsqlite) | |
1473 | ("r-zlibbioc" ,r-zlibbioc))) | |
1474 | (home-page "https://bioconductor.org/packages/oligo/") | |
1475 | (synopsis "Preprocessing tools for oligonucleotide arrays") | |
1476 | (description | |
1477 | "This package provides a package to analyze oligonucleotide | |
1478 | arrays (expression/SNP/tiling/exon) at probe-level. It currently supports | |
1479 | Affymetrix (CEL files) and NimbleGen arrays (XYS files).") | |
1480 | (license license:lgpl2.0+))) | |
1481 | ||
4dc2ecc2 RW |
1482 | (define-public r-qvalue |
1483 | (package | |
1484 | (name "r-qvalue") | |
bcf711b5 | 1485 | (version "2.18.0") |
4dc2ecc2 RW |
1486 | (source |
1487 | (origin | |
1488 | (method url-fetch) | |
1489 | (uri (bioconductor-uri "qvalue" version)) | |
1490 | (sha256 | |
1491 | (base32 | |
bcf711b5 | 1492 | "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j")))) |
4dc2ecc2 RW |
1493 | (build-system r-build-system) |
1494 | (propagated-inputs | |
1495 | `(("r-ggplot2" ,r-ggplot2) | |
1496 | ("r-reshape2" ,r-reshape2))) | |
1497 | (home-page "http://github.com/jdstorey/qvalue") | |
1498 | (synopsis "Q-value estimation for false discovery rate control") | |
1499 | (description | |
1500 | "This package takes a list of p-values resulting from the simultaneous | |
1501 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
1502 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
1503 | of false positives incurred when that particular test is called significant. | |
1504 | The local FDR measures the posterior probability the null hypothesis is true | |
1505 | given the test's p-value. Various plots are automatically generated, allowing | |
1506 | one to make sensible significance cut-offs. The software can be applied to | |
1507 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
1508 | ;; Any version of the LGPL. | |
1509 | (license license:lgpl3+))) | |
1510 | ||
a5b56a53 RJ |
1511 | (define-public r-diffbind |
1512 | (package | |
1513 | (name "r-diffbind") | |
73883f0f | 1514 | (version "2.14.0") |
a5b56a53 RJ |
1515 | (source |
1516 | (origin | |
1517 | (method url-fetch) | |
1518 | (uri (bioconductor-uri "DiffBind" version)) | |
1519 | (sha256 | |
1520 | (base32 | |
73883f0f | 1521 | "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2")))) |
a5b56a53 RJ |
1522 | (properties `((upstream-name . "DiffBind"))) |
1523 | (build-system r-build-system) | |
1524 | (inputs | |
1525 | `(("zlib" ,zlib))) | |
1526 | (propagated-inputs | |
1527 | `(("r-amap" ,r-amap) | |
1528 | ("r-biocparallel" ,r-biocparallel) | |
1529 | ("r-deseq2" ,r-deseq2) | |
1530 | ("r-dplyr" ,r-dplyr) | |
1531 | ("r-edger" ,r-edger) | |
1532 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
1533 | ("r-genomicranges" ,r-genomicranges) |
1534 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
1535 | ("r-ggrepel" ,r-ggrepel) |
1536 | ("r-gplots" ,r-gplots) | |
1537 | ("r-iranges" ,r-iranges) | |
1538 | ("r-lattice" ,r-lattice) | |
1539 | ("r-limma" ,r-limma) | |
1540 | ("r-locfit" ,r-locfit) | |
1541 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
1542 | ("r-rcpp" ,r-rcpp) | |
4c221b3b | 1543 | ("r-rhtslib" ,r-rhtslib) |
a5b56a53 RJ |
1544 | ("r-rsamtools" ,r-rsamtools) |
1545 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 1546 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
4c221b3b | 1547 | ("r-systempiper" ,r-systempiper))) |
99db6db7 | 1548 | (home-page "https://bioconductor.org/packages/DiffBind") |
a5b56a53 RJ |
1549 | (synopsis "Differential binding analysis of ChIP-Seq peak data") |
1550 | (description | |
1551 | "This package computes differentially bound sites from multiple | |
1552 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
1553 | occupancy (overlap) analysis and plotting functions.") | |
1554 | (license license:artistic2.0))) | |
6d94bf6b RJ |
1555 | |
1556 | (define-public r-ripseeker | |
1557 | (package | |
1558 | (name "r-ripseeker") | |
ba74434f | 1559 | (version "1.26.0") |
6d94bf6b RJ |
1560 | (source |
1561 | (origin | |
1562 | (method url-fetch) | |
1563 | (uri (bioconductor-uri "RIPSeeker" version)) | |
1564 | (sha256 | |
1565 | (base32 | |
ba74434f | 1566 | "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) |
6d94bf6b RJ |
1567 | (properties `((upstream-name . "RIPSeeker"))) |
1568 | (build-system r-build-system) | |
1569 | (propagated-inputs | |
1570 | `(("r-s4vectors" ,r-s4vectors) | |
1571 | ("r-iranges" ,r-iranges) | |
1572 | ("r-genomicranges" ,r-genomicranges) | |
1573 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1574 | ("r-rsamtools" ,r-rsamtools) | |
1575 | ("r-genomicalignments" ,r-genomicalignments) | |
1576 | ("r-rtracklayer" ,r-rtracklayer))) | |
99db6db7 | 1577 | (home-page "https://bioconductor.org/packages/RIPSeeker") |
6d94bf6b RJ |
1578 | (synopsis |
1579 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
1580 | (description | |
1581 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
1582 | using two-state HMM with negative binomial emission probability. While | |
1583 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
1584 | a suite of bioinformatics tools integrated within this self-contained software | |
1585 | package comprehensively addressing issues ranging from post-alignments | |
1586 | processing to visualization and annotation.") | |
1587 | (license license:gpl2))) | |
a6ae9ffd RJ |
1588 | |
1589 | (define-public r-multtest | |
1590 | (package | |
1591 | (name "r-multtest") | |
16d49c2a | 1592 | (version "2.42.0") |
a6ae9ffd RJ |
1593 | (source |
1594 | (origin | |
1595 | (method url-fetch) | |
1596 | (uri (bioconductor-uri "multtest" version)) | |
1597 | (sha256 | |
1598 | (base32 | |
16d49c2a | 1599 | "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari")))) |
a6ae9ffd RJ |
1600 | (build-system r-build-system) |
1601 | (propagated-inputs | |
1602 | `(("r-survival" ,r-survival) | |
1603 | ("r-biocgenerics" ,r-biocgenerics) | |
1604 | ("r-biobase" ,r-biobase) | |
1605 | ("r-mass" ,r-mass))) | |
99db6db7 | 1606 | (home-page "https://bioconductor.org/packages/multtest") |
a6ae9ffd RJ |
1607 | (synopsis "Resampling-based multiple hypothesis testing") |
1608 | (description | |
1609 | "This package can do non-parametric bootstrap and permutation | |
1610 | resampling-based multiple testing procedures (including empirical Bayes | |
1611 | methods) for controlling the family-wise error rate (FWER), generalized | |
1612 | family-wise error rate (gFWER), tail probability of the proportion of | |
1613 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
1614 | of bootstrap-based null distribution are implemented (centered, centered | |
1615 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
1616 | available. Tests based on a variety of T- and F-statistics (including | |
1617 | T-statistics based on regression parameters from linear and survival models | |
1618 | as well as those based on correlation parameters) are included. When probing | |
1619 | hypotheses with T-statistics, users may also select a potentially faster null | |
1620 | distribution which is multivariate normal with mean zero and variance | |
1621 | covariance matrix derived from the vector influence function. Results are | |
1622 | reported in terms of adjusted P-values, confidence regions and test statistic | |
1623 | cutoffs. The procedures are directly applicable to identifying differentially | |
1624 | expressed genes in DNA microarray experiments.") | |
1625 | (license license:lgpl3))) | |
793f83ef | 1626 | |
5dfe4912 RW |
1627 | (define-public r-graph |
1628 | (package | |
1629 | (name "r-graph") | |
70eb483a | 1630 | (version "1.64.0") |
5dfe4912 RW |
1631 | (source (origin |
1632 | (method url-fetch) | |
1633 | (uri (bioconductor-uri "graph" version)) | |
1634 | (sha256 | |
1635 | (base32 | |
70eb483a | 1636 | "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc")))) |
5dfe4912 RW |
1637 | (build-system r-build-system) |
1638 | (propagated-inputs | |
1639 | `(("r-biocgenerics" ,r-biocgenerics))) | |
1640 | (home-page "https://bioconductor.org/packages/graph") | |
1641 | (synopsis "Handle graph data structures in R") | |
1642 | (description | |
1643 | "This package implements some simple graph handling capabilities for R.") | |
1644 | (license license:artistic2.0))) | |
1645 | ||
8017eb0a RW |
1646 | ;; This is a CRAN package, but it depends on a Bioconductor package. |
1647 | (define-public r-ggm | |
1648 | (package | |
1649 | (name "r-ggm") | |
1650 | (version "2.5") | |
1651 | (source | |
1652 | (origin | |
1653 | (method url-fetch) | |
1654 | (uri (cran-uri "ggm" version)) | |
1655 | (sha256 | |
1656 | (base32 | |
1657 | "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) | |
1658 | (properties `((upstream-name . "ggm"))) | |
1659 | (build-system r-build-system) | |
1660 | (propagated-inputs | |
1661 | `(("r-graph" ,r-graph) | |
1662 | ("r-igraph" ,r-igraph))) | |
1663 | (home-page "https://cran.r-project.org/package=ggm") | |
1664 | (synopsis "Functions for graphical Markov models") | |
1665 | (description | |
1666 | "This package provides functions and datasets for maximum likelihood | |
1667 | fitting of some classes of graphical Markov models.") | |
1668 | (license license:gpl2+))) | |
1669 | ||
a207bca2 RW |
1670 | (define-public r-codedepends |
1671 | (package | |
1672 | (name "r-codedepends") | |
1673 | (version "0.6.5") | |
1674 | (source | |
1675 | (origin | |
1676 | (method url-fetch) | |
1677 | (uri (cran-uri "CodeDepends" version)) | |
1678 | (sha256 | |
1679 | (base32 | |
1680 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
1681 | (properties `((upstream-name . "CodeDepends"))) | |
1682 | (build-system r-build-system) | |
1683 | (propagated-inputs | |
1684 | `(("r-codetools" ,r-codetools) | |
1685 | ("r-graph" ,r-graph) | |
1686 | ("r-xml" ,r-xml))) | |
5e1f2362 | 1687 | (home-page "https://cran.r-project.org/web/packages/CodeDepends") |
a207bca2 RW |
1688 | (synopsis "Analysis of R code for reproducible research and code comprehension") |
1689 | (description | |
1690 | "This package provides tools for analyzing R expressions or blocks of | |
1691 | code and determining the dependencies between them. It focuses on R scripts, | |
1692 | but can be used on the bodies of functions. There are many facilities | |
1693 | including the ability to summarize or get a high-level view of code, | |
1694 | determining dependencies between variables, code improvement suggestions.") | |
1695 | ;; Any version of the GPL | |
1696 | (license (list license:gpl2+ license:gpl3+)))) | |
1697 | ||
793f83ef RJ |
1698 | (define-public r-chippeakanno |
1699 | (package | |
1700 | (name "r-chippeakanno") | |
8351faae | 1701 | (version "3.20.1") |
793f83ef RJ |
1702 | (source |
1703 | (origin | |
1704 | (method url-fetch) | |
1705 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
1706 | (sha256 | |
1707 | (base32 | |
8351faae | 1708 | "0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc")))) |
793f83ef RJ |
1709 | (properties `((upstream-name . "ChIPpeakAnno"))) |
1710 | (build-system r-build-system) | |
1711 | (propagated-inputs | |
85c1d20f RW |
1712 | `(("r-annotationdbi" ,r-annotationdbi) |
1713 | ("r-biobase" ,r-biobase) | |
1714 | ("r-biocgenerics" ,r-biocgenerics) | |
57d2fcd9 | 1715 | ("r-biocmanager" ,r-biocmanager) |
793f83ef | 1716 | ("r-biomart" ,r-biomart) |
85c1d20f | 1717 | ("r-biostrings" ,r-biostrings) |
793f83ef | 1718 | ("r-bsgenome" ,r-bsgenome) |
85c1d20f RW |
1719 | ("r-dbi" ,r-dbi) |
1720 | ("r-delayedarray" ,r-delayedarray) | |
1721 | ("r-ensembldb" ,r-ensembldb) | |
1722 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1723 | ("r-genomicalignments" ,r-genomicalignments) | |
793f83ef | 1724 | ("r-genomicfeatures" ,r-genomicfeatures) |
f794e85d | 1725 | ("r-genomicranges" ,r-genomicranges) |
85c1d20f RW |
1726 | ("r-go-db" ,r-go-db) |
1727 | ("r-graph" ,r-graph) | |
1728 | ("r-idr" ,r-idr) | |
f794e85d | 1729 | ("r-iranges" ,r-iranges) |
793f83ef | 1730 | ("r-limma" ,r-limma) |
85c1d20f | 1731 | ("r-matrixstats" ,r-matrixstats) |
793f83ef RJ |
1732 | ("r-multtest" ,r-multtest) |
1733 | ("r-rbgl" ,r-rbgl) | |
793f83ef | 1734 | ("r-regioner" ,r-regioner) |
85c1d20f RW |
1735 | ("r-rsamtools" ,r-rsamtools) |
1736 | ("r-rtracklayer" ,r-rtracklayer) | |
f794e85d | 1737 | ("r-s4vectors" ,r-s4vectors) |
793f83ef | 1738 | ("r-seqinr" ,r-seqinr) |
793f83ef | 1739 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
793f83ef | 1740 | ("r-venndiagram" ,r-venndiagram))) |
99db6db7 | 1741 | (home-page "https://bioconductor.org/packages/ChIPpeakAnno") |
793f83ef RJ |
1742 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") |
1743 | (description | |
1744 | "The package includes functions to retrieve the sequences around the peak, | |
1745 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
1746 | custom features such as most conserved elements and other transcription factor | |
1747 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
1748 | for finding the peaks with bi-directional promoters with summary statistics | |
1749 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
1750 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
1751 | enrichedGO (addGeneIDs).") | |
1752 | (license license:gpl2+))) | |
164502d8 RJ |
1753 | |
1754 | (define-public r-marray | |
1755 | (package | |
1756 | (name "r-marray") | |
b6c2f098 | 1757 | (version "1.64.0") |
164502d8 RJ |
1758 | (source (origin |
1759 | (method url-fetch) | |
1760 | (uri (bioconductor-uri "marray" version)) | |
1761 | (sha256 | |
b6c2f098 | 1762 | (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl")))) |
164502d8 RJ |
1763 | (build-system r-build-system) |
1764 | (propagated-inputs | |
67487088 | 1765 | `(("r-limma" ,r-limma))) |
99db6db7 | 1766 | (home-page "https://bioconductor.org/packages/marray") |
164502d8 RJ |
1767 | (synopsis "Exploratory analysis for two-color spotted microarray data") |
1768 | (description "This package contains class definitions for two-color spotted | |
ab8979fc | 1769 | microarray data. It also includes functions for data input, diagnostic plots, |
164502d8 RJ |
1770 | normalization and quality checking.") |
1771 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
1772 | |
1773 | (define-public r-cghbase | |
1774 | (package | |
1775 | (name "r-cghbase") | |
8341f706 | 1776 | (version "1.46.0") |
0416a0d4 RJ |
1777 | (source (origin |
1778 | (method url-fetch) | |
1779 | (uri (bioconductor-uri "CGHbase" version)) | |
1780 | (sha256 | |
8341f706 | 1781 | (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x")))) |
0416a0d4 RJ |
1782 | (properties `((upstream-name . "CGHbase"))) |
1783 | (build-system r-build-system) | |
1784 | (propagated-inputs | |
1785 | `(("r-biobase" ,r-biobase) | |
1786 | ("r-marray" ,r-marray))) | |
99db6db7 | 1787 | (home-page "https://bioconductor.org/packages/CGHbase") |
0416a0d4 RJ |
1788 | (synopsis "Base functions and classes for arrayCGH data analysis") |
1789 | (description "This package contains functions and classes that are needed by | |
1790 | the @code{arrayCGH} packages.") | |
1791 | (license license:gpl2+))) | |
67ee83d6 RJ |
1792 | |
1793 | (define-public r-cghcall | |
1794 | (package | |
1795 | (name "r-cghcall") | |
8f2a4ea1 | 1796 | (version "2.48.0") |
67ee83d6 RJ |
1797 | (source (origin |
1798 | (method url-fetch) | |
1799 | (uri (bioconductor-uri "CGHcall" version)) | |
1800 | (sha256 | |
8f2a4ea1 | 1801 | (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s")))) |
67ee83d6 RJ |
1802 | (properties `((upstream-name . "CGHcall"))) |
1803 | (build-system r-build-system) | |
1804 | (propagated-inputs | |
1805 | `(("r-biobase" ,r-biobase) | |
1806 | ("r-cghbase" ,r-cghbase) | |
1807 | ("r-impute" ,r-impute) | |
1808 | ("r-dnacopy" ,r-dnacopy) | |
1809 | ("r-snowfall" ,r-snowfall))) | |
99db6db7 | 1810 | (home-page "https://bioconductor.org/packages/CGHcall") |
67ee83d6 RJ |
1811 | (synopsis "Base functions and classes for arrayCGH data analysis") |
1812 | (description "This package contains functions and classes that are needed by | |
1813 | @code{arrayCGH} packages.") | |
1814 | (license license:gpl2+))) | |
0ef8cc9c RJ |
1815 | |
1816 | (define-public r-qdnaseq | |
1817 | (package | |
1818 | (name "r-qdnaseq") | |
23ce5ad1 | 1819 | (version "1.22.0") |
0ef8cc9c RJ |
1820 | (source (origin |
1821 | (method url-fetch) | |
1822 | (uri (bioconductor-uri "QDNAseq" version)) | |
1823 | (sha256 | |
23ce5ad1 | 1824 | (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq")))) |
0ef8cc9c RJ |
1825 | (properties `((upstream-name . "QDNAseq"))) |
1826 | (build-system r-build-system) | |
1827 | (propagated-inputs | |
1828 | `(("r-biobase" ,r-biobase) | |
1829 | ("r-cghbase" ,r-cghbase) | |
1830 | ("r-cghcall" ,r-cghcall) | |
1831 | ("r-dnacopy" ,r-dnacopy) | |
23ce5ad1 RW |
1832 | ("r-future" ,r-future) |
1833 | ("r-future-apply" ,r-future-apply) | |
0ef8cc9c RJ |
1834 | ("r-genomicranges" ,r-genomicranges) |
1835 | ("r-iranges" ,r-iranges) | |
1836 | ("r-matrixstats" ,r-matrixstats) | |
1837 | ("r-r-utils" ,r-r-utils) | |
1838 | ("r-rsamtools" ,r-rsamtools))) | |
99db6db7 | 1839 | (home-page "https://bioconductor.org/packages/QDNAseq") |
0ef8cc9c RJ |
1840 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") |
1841 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
1842 | number of sequence reads in each counted, adjusted with a simultaneous | |
1843 | two-dimensional loess correction for sequence mappability and GC content, and | |
1844 | filtered to remove spurious regions in the genome. Downstream steps of | |
1845 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
1846 | respectively.") | |
1847 | (license license:gpl2+))) | |
bb15b581 RW |
1848 | |
1849 | (define-public r-bayseq | |
1850 | (package | |
1851 | (name "r-bayseq") | |
d7722823 | 1852 | (version "2.20.0") |
bb15b581 RW |
1853 | (source |
1854 | (origin | |
1855 | (method url-fetch) | |
1856 | (uri (bioconductor-uri "baySeq" version)) | |
1857 | (sha256 | |
1858 | (base32 | |
d7722823 | 1859 | "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk")))) |
bb15b581 RW |
1860 | (properties `((upstream-name . "baySeq"))) |
1861 | (build-system r-build-system) | |
1862 | (propagated-inputs | |
1863 | `(("r-abind" ,r-abind) | |
1864 | ("r-edger" ,r-edger) | |
1865 | ("r-genomicranges" ,r-genomicranges))) | |
1866 | (home-page "https://bioconductor.org/packages/baySeq/") | |
1867 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
1868 | (description | |
1869 | "This package identifies differential expression in high-throughput count | |
1870 | data, such as that derived from next-generation sequencing machines, | |
1871 | calculating estimated posterior likelihoods of differential expression (or | |
1872 | more complex hypotheses) via empirical Bayesian methods.") | |
1873 | (license license:gpl3))) | |
609f4ad1 RW |
1874 | |
1875 | (define-public r-chipcomp | |
1876 | (package | |
1877 | (name "r-chipcomp") | |
b0897fbf | 1878 | (version "1.16.0") |
609f4ad1 RW |
1879 | (source |
1880 | (origin | |
1881 | (method url-fetch) | |
1882 | (uri (bioconductor-uri "ChIPComp" version)) | |
1883 | (sha256 | |
1884 | (base32 | |
b0897fbf | 1885 | "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg")))) |
609f4ad1 RW |
1886 | (properties `((upstream-name . "ChIPComp"))) |
1887 | (build-system r-build-system) | |
1888 | (propagated-inputs | |
1889 | `(("r-biocgenerics" ,r-biocgenerics) | |
1890 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
1891 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
1892 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1893 | ("r-genomicranges" ,r-genomicranges) | |
1894 | ("r-iranges" ,r-iranges) | |
1895 | ("r-limma" ,r-limma) | |
1896 | ("r-rsamtools" ,r-rsamtools) | |
1897 | ("r-rtracklayer" ,r-rtracklayer) | |
1898 | ("r-s4vectors" ,r-s4vectors))) | |
1899 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
1900 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
1901 | (description | |
1902 | "ChIPComp implements a statistical method for quantitative comparison of | |
1903 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
1904 | sites across multiple conditions considering matching control in ChIP-seq | |
1905 | datasets.") | |
1906 | ;; Any version of the GPL. | |
1907 | (license license:gpl3+))) | |
0490f9de RW |
1908 | |
1909 | (define-public r-riboprofiling | |
1910 | (package | |
1911 | (name "r-riboprofiling") | |
88af7049 | 1912 | (version "1.16.0") |
0490f9de RW |
1913 | (source |
1914 | (origin | |
1915 | (method url-fetch) | |
1916 | (uri (bioconductor-uri "RiboProfiling" version)) | |
1917 | (sha256 | |
1918 | (base32 | |
88af7049 | 1919 | "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx")))) |
0490f9de RW |
1920 | (properties `((upstream-name . "RiboProfiling"))) |
1921 | (build-system r-build-system) | |
1922 | (propagated-inputs | |
1923 | `(("r-biocgenerics" ,r-biocgenerics) | |
1924 | ("r-biostrings" ,r-biostrings) | |
1925 | ("r-data-table" ,r-data-table) | |
1926 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1927 | ("r-genomicalignments" ,r-genomicalignments) | |
1928 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1929 | ("r-genomicranges" ,r-genomicranges) | |
1930 | ("r-ggbio" ,r-ggbio) | |
1931 | ("r-ggplot2" ,r-ggplot2) | |
1932 | ("r-iranges" ,r-iranges) | |
1933 | ("r-plyr" ,r-plyr) | |
1934 | ("r-reshape2" ,r-reshape2) | |
1935 | ("r-rsamtools" ,r-rsamtools) | |
1936 | ("r-rtracklayer" ,r-rtracklayer) | |
1937 | ("r-s4vectors" ,r-s4vectors) | |
1938 | ("r-sqldf" ,r-sqldf))) | |
1939 | (home-page "https://bioconductor.org/packages/RiboProfiling/") | |
1940 | (synopsis "Ribosome profiling data analysis") | |
1941 | (description "Starting with a BAM file, this package provides the | |
1942 | necessary functions for quality assessment, read start position recalibration, | |
1943 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
1944 | of count data: pairs, log fold-change, codon frequency and coverage | |
1945 | assessment, principal component analysis on codon coverage.") | |
1946 | (license license:gpl3))) | |
6ffdfe6a RW |
1947 | |
1948 | (define-public r-riboseqr | |
1949 | (package | |
1950 | (name "r-riboseqr") | |
595b6c9a | 1951 | (version "1.20.0") |
6ffdfe6a RW |
1952 | (source |
1953 | (origin | |
1954 | (method url-fetch) | |
1955 | (uri (bioconductor-uri "riboSeqR" version)) | |
1956 | (sha256 | |
1957 | (base32 | |
595b6c9a | 1958 | "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm")))) |
6ffdfe6a RW |
1959 | (properties `((upstream-name . "riboSeqR"))) |
1960 | (build-system r-build-system) | |
1961 | (propagated-inputs | |
1962 | `(("r-abind" ,r-abind) | |
1963 | ("r-bayseq" ,r-bayseq) | |
1964 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1965 | ("r-genomicranges" ,r-genomicranges) | |
1966 | ("r-iranges" ,r-iranges) | |
1967 | ("r-rsamtools" ,r-rsamtools) | |
1968 | ("r-seqlogo" ,r-seqlogo))) | |
1969 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
1970 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
1971 | (description | |
1972 | "This package provides plotting functions, frameshift detection and | |
1973 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
1974 | (license license:gpl3))) | |
a32279ff RW |
1975 | |
1976 | (define-public r-interactionset | |
1977 | (package | |
1978 | (name "r-interactionset") | |
bb841742 | 1979 | (version "1.14.0") |
a32279ff RW |
1980 | (source |
1981 | (origin | |
1982 | (method url-fetch) | |
1983 | (uri (bioconductor-uri "InteractionSet" version)) | |
1984 | (sha256 | |
1985 | (base32 | |
bb841742 | 1986 | "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh")))) |
a32279ff RW |
1987 | (properties |
1988 | `((upstream-name . "InteractionSet"))) | |
1989 | (build-system r-build-system) | |
1990 | (propagated-inputs | |
1991 | `(("r-biocgenerics" ,r-biocgenerics) | |
1992 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1993 | ("r-genomicranges" ,r-genomicranges) | |
1994 | ("r-iranges" ,r-iranges) | |
1995 | ("r-matrix" ,r-matrix) | |
1996 | ("r-rcpp" ,r-rcpp) | |
1997 | ("r-s4vectors" ,r-s4vectors) | |
1998 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1999 | (home-page "https://bioconductor.org/packages/InteractionSet") | |
2000 | (synopsis "Base classes for storing genomic interaction data") | |
2001 | (description | |
02fe0976 | 2002 | "This package provides the @code{GInteractions}, |
a32279ff RW |
2003 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
2004 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
2005 | experiments.") | |
2006 | (license license:gpl3))) | |
cf9a29b2 RW |
2007 | |
2008 | (define-public r-genomicinteractions | |
2009 | (package | |
2010 | (name "r-genomicinteractions") | |
64cf2ff9 | 2011 | (version "1.20.3") |
cf9a29b2 RW |
2012 | (source |
2013 | (origin | |
2014 | (method url-fetch) | |
2015 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
2016 | (sha256 | |
2017 | (base32 | |
64cf2ff9 | 2018 | "01ps97cs29qvzy5piq2l2k0yyr56rmg5cycfiqhbbvqpjrfvy60g")))) |
cf9a29b2 RW |
2019 | (properties |
2020 | `((upstream-name . "GenomicInteractions"))) | |
2021 | (build-system r-build-system) | |
2022 | (propagated-inputs | |
2023 | `(("r-biobase" ,r-biobase) | |
2024 | ("r-biocgenerics" ,r-biocgenerics) | |
2025 | ("r-data-table" ,r-data-table) | |
2026 | ("r-dplyr" ,r-dplyr) | |
2027 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2028 | ("r-genomicranges" ,r-genomicranges) | |
2029 | ("r-ggplot2" ,r-ggplot2) | |
2030 | ("r-gridextra" ,r-gridextra) | |
2031 | ("r-gviz" ,r-gviz) | |
2032 | ("r-igraph" ,r-igraph) | |
2033 | ("r-interactionset" ,r-interactionset) | |
2034 | ("r-iranges" ,r-iranges) | |
2035 | ("r-rsamtools" ,r-rsamtools) | |
2036 | ("r-rtracklayer" ,r-rtracklayer) | |
2037 | ("r-s4vectors" ,r-s4vectors) | |
2038 | ("r-stringr" ,r-stringr))) | |
81a37891 RW |
2039 | (native-inputs |
2040 | `(("r-knitr" ,r-knitr))) | |
cf9a29b2 RW |
2041 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") |
2042 | (synopsis "R package for handling genomic interaction data") | |
2043 | (description | |
2044 | "This R package provides tools for handling genomic interaction data, | |
2045 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
2046 | information and producing various plots and statistics.") | |
2047 | (license license:gpl3))) | |
27c51606 RW |
2048 | |
2049 | (define-public r-ctc | |
2050 | (package | |
2051 | (name "r-ctc") | |
b2b5b031 | 2052 | (version "1.60.0") |
27c51606 RW |
2053 | (source |
2054 | (origin | |
2055 | (method url-fetch) | |
2056 | (uri (bioconductor-uri "ctc" version)) | |
2057 | (sha256 | |
2058 | (base32 | |
b2b5b031 | 2059 | "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d")))) |
27c51606 RW |
2060 | (build-system r-build-system) |
2061 | (propagated-inputs `(("r-amap" ,r-amap))) | |
2062 | (home-page "https://bioconductor.org/packages/ctc/") | |
2063 | (synopsis "Cluster and tree conversion") | |
2064 | (description | |
2065 | "This package provides tools for exporting and importing classification | |
2066 | trees and clusters to other programs.") | |
2067 | (license license:gpl2))) | |
5da0e142 RW |
2068 | |
2069 | (define-public r-goseq | |
2070 | (package | |
2071 | (name "r-goseq") | |
ab7f3cbb | 2072 | (version "1.38.0") |
5da0e142 RW |
2073 | (source |
2074 | (origin | |
2075 | (method url-fetch) | |
2076 | (uri (bioconductor-uri "goseq" version)) | |
2077 | (sha256 | |
2078 | (base32 | |
ab7f3cbb | 2079 | "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv")))) |
5da0e142 RW |
2080 | (build-system r-build-system) |
2081 | (propagated-inputs | |
2082 | `(("r-annotationdbi" ,r-annotationdbi) | |
2083 | ("r-biasedurn" ,r-biasedurn) | |
2084 | ("r-biocgenerics" ,r-biocgenerics) | |
2085 | ("r-genelendatabase" ,r-genelendatabase) | |
2086 | ("r-go-db" ,r-go-db) | |
2087 | ("r-mgcv" ,r-mgcv))) | |
2088 | (home-page "https://bioconductor.org/packages/goseq/") | |
2089 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
2090 | (description | |
2091 | "This package provides tools to detect Gene Ontology and/or other user | |
2092 | defined categories which are over/under represented in RNA-seq data.") | |
2093 | (license license:lgpl2.0+))) | |
f4235c0e RW |
2094 | |
2095 | (define-public r-glimma | |
2096 | (package | |
2097 | (name "r-glimma") | |
728571fb | 2098 | (version "1.14.0") |
f4235c0e RW |
2099 | (source |
2100 | (origin | |
2101 | (method url-fetch) | |
2102 | (uri (bioconductor-uri "Glimma" version)) | |
2103 | (sha256 | |
2104 | (base32 | |
728571fb | 2105 | "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r")))) |
f4235c0e RW |
2106 | (properties `((upstream-name . "Glimma"))) |
2107 | (build-system r-build-system) | |
2108 | (propagated-inputs | |
2109 | `(("r-edger" ,r-edger) | |
2110 | ("r-jsonlite" ,r-jsonlite) | |
2111 | ("r-s4vectors" ,r-s4vectors))) | |
2112 | (home-page "https://github.com/Shians/Glimma") | |
2113 | (synopsis "Interactive HTML graphics") | |
2114 | (description | |
2115 | "This package generates interactive visualisations for analysis of | |
2116 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
2117 | HTML page. The interactions are built on top of the popular static | |
2118 | representations of analysis results in order to provide additional | |
2119 | information.") | |
2120 | (license license:lgpl3))) | |
aa388dc7 RW |
2121 | |
2122 | (define-public r-rots | |
2123 | (package | |
2124 | (name "r-rots") | |
9c071144 | 2125 | (version "1.14.0") |
aa388dc7 RW |
2126 | (source |
2127 | (origin | |
2128 | (method url-fetch) | |
2129 | (uri (bioconductor-uri "ROTS" version)) | |
2130 | (sha256 | |
2131 | (base32 | |
9c071144 | 2132 | "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm")))) |
aa388dc7 RW |
2133 | (properties `((upstream-name . "ROTS"))) |
2134 | (build-system r-build-system) | |
2135 | (propagated-inputs | |
2136 | `(("r-biobase" ,r-biobase) | |
2137 | ("r-rcpp" ,r-rcpp))) | |
2138 | (home-page "https://bioconductor.org/packages/ROTS/") | |
2139 | (synopsis "Reproducibility-Optimized Test Statistic") | |
2140 | (description | |
2141 | "This package provides tools for calculating the | |
2142 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
2143 | in omics data.") | |
2144 | (license license:gpl2+))) | |
b64ce4b7 | 2145 | |
cad6fb2d RW |
2146 | (define-public r-plgem |
2147 | (package | |
2148 | (name "r-plgem") | |
565bb84b | 2149 | (version "1.58.0") |
cad6fb2d RW |
2150 | (source |
2151 | (origin | |
2152 | (method url-fetch) | |
2153 | (uri (bioconductor-uri "plgem" version)) | |
2154 | (sha256 | |
2155 | (base32 | |
565bb84b | 2156 | "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v")))) |
cad6fb2d RW |
2157 | (build-system r-build-system) |
2158 | (propagated-inputs | |
2159 | `(("r-biobase" ,r-biobase) | |
2160 | ("r-mass" ,r-mass))) | |
2161 | (home-page "http://www.genopolis.it") | |
2162 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
2163 | (description | |
2164 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
2165 | model the variance-versus-mean dependence that exists in a variety of | |
2166 | genome-wide datasets, including microarray and proteomics data. The use of | |
2167 | PLGEM has been shown to improve the detection of differentially expressed | |
2168 | genes or proteins in these datasets.") | |
2169 | (license license:gpl2))) | |
2170 | ||
b64ce4b7 RW |
2171 | (define-public r-inspect |
2172 | (package | |
2173 | (name "r-inspect") | |
b7e86efd | 2174 | (version "1.16.3") |
b64ce4b7 RW |
2175 | (source |
2176 | (origin | |
2177 | (method url-fetch) | |
2178 | (uri (bioconductor-uri "INSPEcT" version)) | |
2179 | (sha256 | |
2180 | (base32 | |
b7e86efd | 2181 | "0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp")))) |
b64ce4b7 RW |
2182 | (properties `((upstream-name . "INSPEcT"))) |
2183 | (build-system r-build-system) | |
2184 | (propagated-inputs | |
2185 | `(("r-biobase" ,r-biobase) | |
2186 | ("r-biocgenerics" ,r-biocgenerics) | |
2187 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 2188 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 | 2189 | ("r-desolve" ,r-desolve) |
bd824de3 | 2190 | ("r-gdata" ,r-gdata) |
74bb4cdf | 2191 | ("r-genomeinfodb" ,r-genomeinfodb) |
b64ce4b7 RW |
2192 | ("r-genomicalignments" ,r-genomicalignments) |
2193 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2194 | ("r-genomicranges" ,r-genomicranges) | |
2195 | ("r-iranges" ,r-iranges) | |
74bb4cdf | 2196 | ("r-kernsmooth" ,r-kernsmooth) |
c86fc969 | 2197 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
2198 | ("r-proc" ,r-proc) |
2199 | ("r-rootsolve" ,r-rootsolve) | |
2200 | ("r-rsamtools" ,r-rsamtools) | |
c86fc969 RW |
2201 | ("r-s4vectors" ,r-s4vectors) |
2202 | ("r-shiny" ,r-shiny) | |
2203 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
2204 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
2205 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
b64ce4b7 RW |
2206 | (home-page "https://bioconductor.org/packages/INSPEcT") |
2207 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
2208 | (description | |
2209 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
2210 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
2211 | order to evaluate synthesis, processing and degradation rates and assess via | |
2212 | modeling the rates that determines changes in mature mRNA levels.") | |
2213 | (license license:gpl2))) | |
f6e99763 RW |
2214 | |
2215 | (define-public r-dnabarcodes | |
2216 | (package | |
2217 | (name "r-dnabarcodes") | |
2d86dc20 | 2218 | (version "1.16.0") |
f6e99763 RW |
2219 | (source |
2220 | (origin | |
2221 | (method url-fetch) | |
2222 | (uri (bioconductor-uri "DNABarcodes" version)) | |
2223 | (sha256 | |
2224 | (base32 | |
2d86dc20 | 2225 | "0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd")))) |
f6e99763 RW |
2226 | (properties `((upstream-name . "DNABarcodes"))) |
2227 | (build-system r-build-system) | |
2228 | (propagated-inputs | |
2229 | `(("r-bh" ,r-bh) | |
2230 | ("r-matrix" ,r-matrix) | |
2231 | ("r-rcpp" ,r-rcpp))) | |
2232 | (home-page "https://bioconductor.org/packages/DNABarcodes") | |
2233 | (synopsis "Create and analyze DNA barcodes") | |
2234 | (description | |
2235 | "This package offers tools to create DNA barcode sets capable of | |
2236 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
2237 | can be analyzed regarding their minimal, maximal and average distances between | |
2238 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
2239 | demultiplexed, i.e. assigned to their original reference barcode.") | |
2240 | (license license:gpl2))) | |
09aa3d06 RW |
2241 | |
2242 | (define-public r-ruvseq | |
2243 | (package | |
2244 | (name "r-ruvseq") | |
efd09347 | 2245 | (version "1.20.0") |
09aa3d06 RW |
2246 | (source |
2247 | (origin | |
2248 | (method url-fetch) | |
2249 | (uri (bioconductor-uri "RUVSeq" version)) | |
2250 | (sha256 | |
2251 | (base32 | |
efd09347 | 2252 | "1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj")))) |
09aa3d06 RW |
2253 | (properties `((upstream-name . "RUVSeq"))) |
2254 | (build-system r-build-system) | |
2255 | (propagated-inputs | |
2256 | `(("r-biobase" ,r-biobase) | |
2257 | ("r-edaseq" ,r-edaseq) | |
2258 | ("r-edger" ,r-edger) | |
2259 | ("r-mass" ,r-mass))) | |
2260 | (home-page "https://github.com/drisso/RUVSeq") | |
2261 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
2262 | (description | |
2263 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
2264 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
2265 | samples.") | |
2266 | (license license:artistic2.0))) | |
286157dc RW |
2267 | |
2268 | (define-public r-biocneighbors | |
2269 | (package | |
2270 | (name "r-biocneighbors") | |
aece78fe | 2271 | (version "1.4.2") |
286157dc RW |
2272 | (source |
2273 | (origin | |
2274 | (method url-fetch) | |
2275 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
2276 | (sha256 | |
2277 | (base32 | |
aece78fe | 2278 | "1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6")))) |
286157dc RW |
2279 | (properties `((upstream-name . "BiocNeighbors"))) |
2280 | (build-system r-build-system) | |
2281 | (propagated-inputs | |
12e2aa96 RW |
2282 | `(("r-biocparallel" ,r-biocparallel) |
2283 | ("r-matrix" ,r-matrix) | |
286157dc RW |
2284 | ("r-rcpp" ,r-rcpp) |
2285 | ("r-rcppannoy" ,r-rcppannoy) | |
6fc161fc | 2286 | ("r-rcpphnsw" ,r-rcpphnsw) |
286157dc RW |
2287 | ("r-s4vectors" ,r-s4vectors))) |
2288 | (home-page "https://bioconductor.org/packages/BiocNeighbors") | |
2289 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
2290 | (description | |
2291 | "This package implements exact and approximate methods for nearest | |
2292 | neighbor detection, in a framework that allows them to be easily switched | |
2293 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
2294 | using pre-clustering with the k-means algorithm. Functions are also provided | |
2295 | to search for all neighbors within a given distance. Parallelization is | |
2296 | achieved for all methods using the BiocParallel framework.") | |
2297 | (license license:gpl3))) | |
8a587c89 | 2298 | |
99391290 RW |
2299 | (define-public r-biocsingular |
2300 | (package | |
2301 | (name "r-biocsingular") | |
effbf7d9 | 2302 | (version "1.2.2") |
99391290 RW |
2303 | (source |
2304 | (origin | |
2305 | (method url-fetch) | |
2306 | (uri (bioconductor-uri "BiocSingular" version)) | |
2307 | (sha256 | |
2308 | (base32 | |
effbf7d9 | 2309 | "1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407")))) |
99391290 RW |
2310 | (properties `((upstream-name . "BiocSingular"))) |
2311 | (build-system r-build-system) | |
2312 | (propagated-inputs | |
2313 | `(("r-beachmat" ,r-beachmat) | |
2314 | ("r-biocgenerics" ,r-biocgenerics) | |
2315 | ("r-biocparallel" ,r-biocparallel) | |
2316 | ("r-delayedarray" ,r-delayedarray) | |
2317 | ("r-irlba" ,r-irlba) | |
2318 | ("r-matrix" ,r-matrix) | |
2319 | ("r-rcpp" ,r-rcpp) | |
2320 | ("r-rsvd" ,r-rsvd) | |
2321 | ("r-s4vectors" ,r-s4vectors))) | |
2322 | (home-page "https://github.com/LTLA/BiocSingular") | |
2323 | (synopsis "Singular value decomposition for Bioconductor packages") | |
2324 | (description | |
2325 | "This package implements exact and approximate methods for singular value | |
2326 | decomposition and principal components analysis, in a framework that allows | |
2327 | them to be easily switched within Bioconductor packages or workflows. Where | |
2328 | possible, parallelization is achieved using the BiocParallel framework.") | |
2329 | (license license:gpl3))) | |
2330 | ||
a961ae46 RW |
2331 | (define-public r-destiny |
2332 | (package | |
2333 | (name "r-destiny") | |
062cbc4f | 2334 | (version "3.0.1") |
a961ae46 RW |
2335 | (source |
2336 | (origin | |
2337 | (method url-fetch) | |
2338 | (uri (bioconductor-uri "destiny" version)) | |
2339 | (sha256 | |
2340 | (base32 | |
062cbc4f | 2341 | "1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi")))) |
a961ae46 RW |
2342 | (build-system r-build-system) |
2343 | (propagated-inputs | |
2344 | `(("r-biobase" ,r-biobase) | |
2345 | ("r-biocgenerics" ,r-biocgenerics) | |
6e10ac07 | 2346 | ("r-ggplot-multistats" ,r-ggplot-multistats) |
0aa72f2d | 2347 | ("r-ggplot2" ,r-ggplot2) |
a961ae46 | 2348 | ("r-ggthemes" ,r-ggthemes) |
6e10ac07 RW |
2349 | ("r-irlba" ,r-irlba) |
2350 | ("r-knn-covertree" ,r-knn-covertree) | |
a961ae46 | 2351 | ("r-matrix" ,r-matrix) |
6e10ac07 | 2352 | ("r-pcamethods" ,r-pcamethods) |
a961ae46 RW |
2353 | ("r-proxy" ,r-proxy) |
2354 | ("r-rcpp" ,r-rcpp) | |
2355 | ("r-rcppeigen" ,r-rcppeigen) | |
6e10ac07 RW |
2356 | ("r-rcpphnsw" ,r-rcpphnsw) |
2357 | ("r-rspectra" ,r-rspectra) | |
a961ae46 RW |
2358 | ("r-scales" ,r-scales) |
2359 | ("r-scatterplot3d" ,r-scatterplot3d) | |
6e10ac07 | 2360 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
a961ae46 RW |
2361 | ("r-smoother" ,r-smoother) |
2362 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6e10ac07 RW |
2363 | ("r-tidyr" ,r-tidyr) |
2364 | ("r-tidyselect" ,r-tidyselect) | |
a961ae46 | 2365 | ("r-vim" ,r-vim))) |
3f782a6d RW |
2366 | (native-inputs |
2367 | `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes | |
a961ae46 RW |
2368 | (home-page "https://bioconductor.org/packages/destiny/") |
2369 | (synopsis "Create and plot diffusion maps") | |
2370 | (description "This package provides tools to create and plot diffusion | |
2371 | maps.") | |
2372 | ;; Any version of the GPL | |
2373 | (license license:gpl3+))) | |
2374 | ||
8a587c89 RW |
2375 | (define-public r-savr |
2376 | (package | |
2377 | (name "r-savr") | |
2e17cbd7 | 2378 | (version "1.24.0") |
8a587c89 RW |
2379 | (source |
2380 | (origin | |
2381 | (method url-fetch) | |
2382 | (uri (bioconductor-uri "savR" version)) | |
2383 | (sha256 | |
2384 | (base32 | |
2e17cbd7 | 2385 | "1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf")))) |
8a587c89 RW |
2386 | (properties `((upstream-name . "savR"))) |
2387 | (build-system r-build-system) | |
2388 | (propagated-inputs | |
2389 | `(("r-ggplot2" ,r-ggplot2) | |
2390 | ("r-gridextra" ,r-gridextra) | |
2391 | ("r-reshape2" ,r-reshape2) | |
2392 | ("r-scales" ,r-scales) | |
2393 | ("r-xml" ,r-xml))) | |
2394 | (home-page "https://github.com/bcalder/savR") | |
2395 | (synopsis "Parse and analyze Illumina SAV files") | |
2396 | (description | |
2397 | "This package provides tools to parse Illumina Sequence Analysis | |
2398 | Viewer (SAV) files, access data, and generate QC plots.") | |
2399 | (license license:agpl3+))) | |
41ffc214 RW |
2400 | |
2401 | (define-public r-chipexoqual | |
2402 | (package | |
2403 | (name "r-chipexoqual") | |
84825e55 | 2404 | (version "1.10.0") |
41ffc214 RW |
2405 | (source |
2406 | (origin | |
2407 | (method url-fetch) | |
2408 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
2409 | (sha256 | |
2410 | (base32 | |
84825e55 | 2411 | "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0")))) |
41ffc214 RW |
2412 | (properties `((upstream-name . "ChIPexoQual"))) |
2413 | (build-system r-build-system) | |
2414 | (propagated-inputs | |
2415 | `(("r-biocparallel" ,r-biocparallel) | |
2416 | ("r-biovizbase" ,r-biovizbase) | |
2417 | ("r-broom" ,r-broom) | |
2418 | ("r-data-table" ,r-data-table) | |
2419 | ("r-dplyr" ,r-dplyr) | |
2420 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2421 | ("r-genomicalignments" ,r-genomicalignments) | |
2422 | ("r-genomicranges" ,r-genomicranges) | |
2423 | ("r-ggplot2" ,r-ggplot2) | |
2424 | ("r-hexbin" ,r-hexbin) | |
2425 | ("r-iranges" ,r-iranges) | |
2426 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2427 | ("r-rmarkdown" ,r-rmarkdown) | |
2428 | ("r-rsamtools" ,r-rsamtools) | |
2429 | ("r-s4vectors" ,r-s4vectors) | |
2430 | ("r-scales" ,r-scales) | |
2431 | ("r-viridis" ,r-viridis))) | |
2432 | (home-page "https://github.com/keleslab/ChIPexoQual") | |
2433 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
2434 | (description | |
2435 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
2436 | sequencing data.") | |
2437 | (license license:gpl2+))) | |
c18dccff | 2438 | |
3d13b448 RW |
2439 | (define-public r-copynumber |
2440 | (package | |
2441 | (name "r-copynumber") | |
eb3fd382 | 2442 | (version "1.26.0") |
3d13b448 RW |
2443 | (source (origin |
2444 | (method url-fetch) | |
2445 | (uri (bioconductor-uri "copynumber" version)) | |
2446 | (sha256 | |
2447 | (base32 | |
eb3fd382 | 2448 | "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj")))) |
3d13b448 RW |
2449 | (build-system r-build-system) |
2450 | (propagated-inputs | |
2451 | `(("r-s4vectors" ,r-s4vectors) | |
2452 | ("r-iranges" ,r-iranges) | |
2453 | ("r-genomicranges" ,r-genomicranges) | |
2454 | ("r-biocgenerics" ,r-biocgenerics))) | |
2455 | (home-page "https://bioconductor.org/packages/copynumber") | |
2456 | (synopsis "Segmentation of single- and multi-track copy number data") | |
2457 | (description | |
2458 | "This package segments single- and multi-track copy number data by a | |
2459 | penalized least squares regression method.") | |
2460 | (license license:artistic2.0))) | |
2461 | ||
c18dccff RW |
2462 | (define-public r-dnacopy |
2463 | (package | |
2464 | (name "r-dnacopy") | |
bba70cda | 2465 | (version "1.60.0") |
c18dccff RW |
2466 | (source |
2467 | (origin | |
2468 | (method url-fetch) | |
2469 | (uri (bioconductor-uri "DNAcopy" version)) | |
2470 | (sha256 | |
2471 | (base32 | |
bba70cda | 2472 | "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw")))) |
c18dccff RW |
2473 | (properties `((upstream-name . "DNAcopy"))) |
2474 | (build-system r-build-system) | |
2475 | (native-inputs `(("gfortran" ,gfortran))) | |
2476 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
2477 | (synopsis "DNA copy number data analysis") | |
2478 | (description | |
2479 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
2480 | algorithm to segment DNA copy number data and identify genomic regions with | |
2481 | abnormal copy number.") | |
2482 | (license license:gpl2+))) | |
3a0babac RW |
2483 | |
2484 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
2485 | ;; Bioconductor package. | |
2486 | (define-public r-htscluster | |
2487 | (package | |
2488 | (name "r-htscluster") | |
2489 | (version "2.0.8") | |
2490 | (source | |
2491 | (origin | |
2492 | (method url-fetch) | |
2493 | (uri (cran-uri "HTSCluster" version)) | |
2494 | (sha256 | |
2495 | (base32 | |
2496 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
2497 | (properties `((upstream-name . "HTSCluster"))) | |
2498 | (build-system r-build-system) | |
2499 | (propagated-inputs | |
2500 | `(("r-capushe" ,r-capushe) | |
2501 | ("r-edger" ,r-edger) | |
2502 | ("r-plotrix" ,r-plotrix))) | |
2503 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
2504 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
2505 | (description | |
2506 | "This package provides a Poisson mixture model is implemented to cluster | |
2507 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
2508 | estimation is performed using either the EM or CEM algorithm, and the slope | |
2509 | heuristics are used for model selection (i.e., to choose the number of | |
2510 | clusters).") | |
2511 | (license license:gpl3+))) | |
173c9960 RW |
2512 | |
2513 | (define-public r-deds | |
2514 | (package | |
2515 | (name "r-deds") | |
96030bf7 | 2516 | (version "1.60.0") |
173c9960 RW |
2517 | (source |
2518 | (origin | |
2519 | (method url-fetch) | |
2520 | (uri (bioconductor-uri "DEDS" version)) | |
2521 | (sha256 | |
2522 | (base32 | |
96030bf7 | 2523 | "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8")))) |
173c9960 RW |
2524 | (properties `((upstream-name . "DEDS"))) |
2525 | (build-system r-build-system) | |
2526 | (home-page "https://bioconductor.org/packages/DEDS/") | |
2527 | (synopsis "Differential expression via distance summary for microarray data") | |
2528 | (description | |
2529 | "This library contains functions that calculate various statistics of | |
2530 | differential expression for microarray data, including t statistics, fold | |
2531 | change, F statistics, SAM, moderated t and F statistics and B statistics. It | |
2532 | also implements a new methodology called DEDS (Differential Expression via | |
2533 | Distance Summary), which selects differentially expressed genes by integrating | |
2534 | and summarizing a set of statistics using a weighted distance approach.") | |
2535 | ;; Any version of the LGPL. | |
2536 | (license license:lgpl3+))) | |
7ed869f7 RW |
2537 | |
2538 | ;; This is a CRAN package, but since it depends on a Bioconductor package we | |
2539 | ;; put it here. | |
2540 | (define-public r-nbpseq | |
2541 | (package | |
2542 | (name "r-nbpseq") | |
2543 | (version "0.3.0") | |
2544 | (source | |
2545 | (origin | |
2546 | (method url-fetch) | |
2547 | (uri (cran-uri "NBPSeq" version)) | |
2548 | (sha256 | |
2549 | (base32 | |
2550 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) | |
2551 | (properties `((upstream-name . "NBPSeq"))) | |
2552 | (build-system r-build-system) | |
2553 | (propagated-inputs | |
2554 | `(("r-qvalue" ,r-qvalue))) | |
2555 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") | |
2556 | (synopsis "Negative binomial models for RNA-Seq data") | |
2557 | (description | |
2558 | "This package provides negative binomial models for two-group comparisons | |
2559 | and regression inferences from RNA-sequencing data.") | |
2560 | (license license:gpl2))) | |
3087a2f3 RW |
2561 | |
2562 | (define-public r-ebseq | |
2563 | (package | |
2564 | (name "r-ebseq") | |
a9649c41 | 2565 | (version "1.26.0") |
3087a2f3 RW |
2566 | (source |
2567 | (origin | |
2568 | (method url-fetch) | |
2569 | (uri (bioconductor-uri "EBSeq" version)) | |
2570 | (sha256 | |
2571 | (base32 | |
a9649c41 | 2572 | "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6")))) |
3087a2f3 RW |
2573 | (properties `((upstream-name . "EBSeq"))) |
2574 | (build-system r-build-system) | |
2575 | (propagated-inputs | |
2576 | `(("r-blockmodeling" ,r-blockmodeling) | |
2577 | ("r-gplots" ,r-gplots) | |
2578 | ("r-testthat" ,r-testthat))) | |
2579 | (home-page "https://bioconductor.org/packages/EBSeq") | |
2580 | (synopsis "Differential expression analysis of RNA-seq data") | |
2581 | (description | |
2582 | "This package provides tools for differential expression analysis at both | |
2583 | gene and isoform level using RNA-seq data") | |
2584 | (license license:artistic2.0))) | |
2cb71d81 RW |
2585 | |
2586 | (define-public r-lpsymphony | |
2587 | (package | |
2588 | (name "r-lpsymphony") | |
153dc51b | 2589 | (version "1.14.0") |
2cb71d81 RW |
2590 | (source |
2591 | (origin | |
2592 | (method url-fetch) | |
2593 | (uri (bioconductor-uri "lpsymphony" version)) | |
2594 | (sha256 | |
2595 | (base32 | |
153dc51b | 2596 | "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv")))) |
2cb71d81 RW |
2597 | (build-system r-build-system) |
2598 | (inputs | |
2599 | `(("gfortran" ,gfortran) | |
2600 | ("zlib" ,zlib))) | |
2601 | (native-inputs | |
2602 | `(("pkg-config" ,pkg-config))) | |
c756328e | 2603 | (home-page "https://r-forge.r-project.org/projects/rsymphony") |
2cb71d81 RW |
2604 | (synopsis "Symphony integer linear programming solver in R") |
2605 | (description | |
2606 | "This package was derived from Rsymphony. The package provides an R | |
2607 | interface to SYMPHONY, a linear programming solver written in C++. The main | |
2608 | difference between this package and Rsymphony is that it includes the solver | |
2609 | source code, while Rsymphony expects to find header and library files on the | |
2610 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy | |
2611 | to install interface to SYMPHONY.") | |
2612 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. | |
2613 | ;; lpsimphony is released under the same terms. | |
2614 | (license license:epl1.0))) | |
704de8f5 RW |
2615 | |
2616 | (define-public r-ihw | |
2617 | (package | |
2618 | (name "r-ihw") | |
0383bd05 | 2619 | (version "1.14.0") |
704de8f5 RW |
2620 | (source |
2621 | (origin | |
2622 | (method url-fetch) | |
2623 | (uri (bioconductor-uri "IHW" version)) | |
2624 | (sha256 | |
2625 | (base32 | |
0383bd05 | 2626 | "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x")))) |
704de8f5 RW |
2627 | (properties `((upstream-name . "IHW"))) |
2628 | (build-system r-build-system) | |
2629 | (propagated-inputs | |
2630 | `(("r-biocgenerics" ,r-biocgenerics) | |
2631 | ("r-fdrtool" ,r-fdrtool) | |
2632 | ("r-lpsymphony" ,r-lpsymphony) | |
2633 | ("r-slam" ,r-slam))) | |
2634 | (home-page "https://bioconductor.org/packages/IHW") | |
2635 | (synopsis "Independent hypothesis weighting") | |
2636 | (description | |
2637 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing | |
2638 | procedure that increases power compared to the method of Benjamini and | |
2639 | Hochberg by assigning data-driven weights to each hypothesis. The input to | |
2640 | IHW is a two-column table of p-values and covariates. The covariate can be | |
2641 | any continuous-valued or categorical variable that is thought to be | |
2642 | informative on the statistical properties of each hypothesis test, while it is | |
2643 | independent of the p-value under the null hypothesis.") | |
2644 | (license license:artistic2.0))) | |
251e0830 RW |
2645 | |
2646 | (define-public r-icobra | |
2647 | (package | |
2648 | (name "r-icobra") | |
a5cc1f10 | 2649 | (version "1.14.0") |
251e0830 RW |
2650 | (source |
2651 | (origin | |
2652 | (method url-fetch) | |
2653 | (uri (bioconductor-uri "iCOBRA" version)) | |
2654 | (sha256 | |
2655 | (base32 | |
a5cc1f10 | 2656 | "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz")))) |
251e0830 RW |
2657 | (properties `((upstream-name . "iCOBRA"))) |
2658 | (build-system r-build-system) | |
2659 | (propagated-inputs | |
2660 | `(("r-dplyr" ,r-dplyr) | |
2661 | ("r-dt" ,r-dt) | |
2662 | ("r-ggplot2" ,r-ggplot2) | |
2663 | ("r-limma" ,r-limma) | |
2664 | ("r-reshape2" ,r-reshape2) | |
2665 | ("r-rocr" ,r-rocr) | |
2666 | ("r-scales" ,r-scales) | |
2667 | ("r-shiny" ,r-shiny) | |
2668 | ("r-shinybs" ,r-shinybs) | |
2669 | ("r-shinydashboard" ,r-shinydashboard) | |
2670 | ("r-upsetr" ,r-upsetr))) | |
2671 | (home-page "https://bioconductor.org/packages/iCOBRA") | |
2672 | (synopsis "Comparison and visualization of ranking and assignment methods") | |
2673 | (description | |
2674 | "This package provides functions for calculation and visualization of | |
2675 | performance metrics for evaluation of ranking and binary | |
2676 | classification (assignment) methods. It also contains a Shiny application for | |
2677 | interactive exploration of results.") | |
2678 | (license license:gpl2+))) | |
925fcdbb RW |
2679 | |
2680 | (define-public r-mast | |
2681 | (package | |
2682 | (name "r-mast") | |
dc5237f8 | 2683 | (version "1.12.0") |
925fcdbb RW |
2684 | (source |
2685 | (origin | |
2686 | (method url-fetch) | |
2687 | (uri (bioconductor-uri "MAST" version)) | |
2688 | (sha256 | |
2689 | (base32 | |
dc5237f8 | 2690 | "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga")))) |
925fcdbb RW |
2691 | (properties `((upstream-name . "MAST"))) |
2692 | (build-system r-build-system) | |
2693 | (propagated-inputs | |
2694 | `(("r-abind" ,r-abind) | |
2695 | ("r-biobase" ,r-biobase) | |
2696 | ("r-biocgenerics" ,r-biocgenerics) | |
2697 | ("r-data-table" ,r-data-table) | |
2698 | ("r-ggplot2" ,r-ggplot2) | |
2699 | ("r-plyr" ,r-plyr) | |
2700 | ("r-progress" ,r-progress) | |
2701 | ("r-reshape2" ,r-reshape2) | |
2702 | ("r-s4vectors" ,r-s4vectors) | |
2703 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2704 | ("r-stringr" ,r-stringr) | |
2705 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
51d1a7a2 RW |
2706 | (native-inputs |
2707 | `(("r-knitr" ,r-knitr))) | |
925fcdbb RW |
2708 | (home-page "https://github.com/RGLab/MAST/") |
2709 | (synopsis "Model-based analysis of single cell transcriptomics") | |
2710 | (description | |
2711 | "This package provides methods and models for handling zero-inflated | |
2712 | single cell assay data.") | |
2713 | (license license:gpl2+))) | |
2d7627cf RW |
2714 | |
2715 | (define-public r-monocle | |
2716 | (package | |
2717 | (name "r-monocle") | |
9732e690 | 2718 | (version "2.14.0") |
2d7627cf RW |
2719 | (source |
2720 | (origin | |
2721 | (method url-fetch) | |
2722 | (uri (bioconductor-uri "monocle" version)) | |
2723 | (sha256 | |
2724 | (base32 | |
9732e690 | 2725 | "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2")))) |
2d7627cf RW |
2726 | (build-system r-build-system) |
2727 | (propagated-inputs | |
2728 | `(("r-biobase" ,r-biobase) | |
2729 | ("r-biocgenerics" ,r-biocgenerics) | |
2730 | ("r-biocviews" ,r-biocviews) | |
2731 | ("r-cluster" ,r-cluster) | |
2732 | ("r-combinat" ,r-combinat) | |
2733 | ("r-ddrtree" ,r-ddrtree) | |
2734 | ("r-densityclust" ,r-densityclust) | |
2735 | ("r-dplyr" ,r-dplyr) | |
2736 | ("r-fastica" ,r-fastica) | |
2737 | ("r-ggplot2" ,r-ggplot2) | |
2738 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) | |
2739 | ("r-igraph" ,r-igraph) | |
2740 | ("r-irlba" ,r-irlba) | |
2741 | ("r-limma" ,r-limma) | |
2742 | ("r-mass" ,r-mass) | |
2743 | ("r-matrix" ,r-matrix) | |
2744 | ("r-matrixstats" ,r-matrixstats) | |
2745 | ("r-pheatmap" ,r-pheatmap) | |
2746 | ("r-plyr" ,r-plyr) | |
2747 | ("r-proxy" ,r-proxy) | |
2748 | ("r-qlcmatrix" ,r-qlcmatrix) | |
2749 | ("r-rann" ,r-rann) | |
2750 | ("r-rcpp" ,r-rcpp) | |
2751 | ("r-reshape2" ,r-reshape2) | |
2752 | ("r-rtsne" ,r-rtsne) | |
2753 | ("r-slam" ,r-slam) | |
2754 | ("r-stringr" ,r-stringr) | |
2755 | ("r-tibble" ,r-tibble) | |
2756 | ("r-vgam" ,r-vgam) | |
2757 | ("r-viridis" ,r-viridis))) | |
2758 | (home-page "https://bioconductor.org/packages/monocle") | |
2759 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") | |
2760 | (description | |
2761 | "Monocle performs differential expression and time-series analysis for | |
2762 | single-cell expression experiments. It orders individual cells according to | |
2763 | progress through a biological process, without knowing ahead of time which | |
2764 | genes define progress through that process. Monocle also performs | |
2765 | differential expression analysis, clustering, visualization, and other useful | |
2766 | tasks on single cell expression data. It is designed to work with RNA-Seq and | |
2767 | qPCR data, but could be used with other types as well.") | |
2768 | (license license:artistic2.0))) | |
6213e441 | 2769 | |
b2dce6b5 RW |
2770 | (define-public r-monocle3 |
2771 | (package | |
2772 | (name "r-monocle3") | |
2773 | (version "0.1.2") | |
2774 | (source | |
2775 | (origin | |
2776 | (method git-fetch) | |
2777 | (uri (git-reference | |
2778 | (url "https://github.com/cole-trapnell-lab/monocle3.git") | |
2779 | (commit version))) | |
2780 | (file-name (git-file-name name version)) | |
2781 | (sha256 | |
2782 | (base32 | |
2783 | "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) | |
2784 | (build-system r-build-system) | |
2785 | (propagated-inputs | |
2786 | `(("r-biobase" ,r-biobase) | |
2787 | ("r-biocgenerics" ,r-biocgenerics) | |
2788 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
2789 | ("r-dplyr" ,r-dplyr) | |
2790 | ("r-ggplot2" ,r-ggplot2) | |
2791 | ("r-ggrepel" ,r-ggrepel) | |
2792 | ("r-grr" ,r-grr) | |
2793 | ("r-htmlwidgets" ,r-htmlwidgets) | |
2794 | ("r-igraph" ,r-igraph) | |
2795 | ("r-irlba" ,r-irlba) | |
2796 | ("r-limma" ,r-limma) | |
2797 | ("r-lmtest" ,r-lmtest) | |
2798 | ("r-mass" ,r-mass) | |
2799 | ("r-matrix" ,r-matrix) | |
2800 | ("r-matrix-utils" ,r-matrix-utils) | |
2801 | ("r-pbapply" ,r-pbapply) | |
2802 | ("r-pbmcapply" ,r-pbmcapply) | |
2803 | ("r-pheatmap" ,r-pheatmap) | |
2804 | ("r-plotly" ,r-plotly) | |
2805 | ("r-pryr" ,r-pryr) | |
2806 | ("r-proxy" ,r-proxy) | |
2807 | ("r-pscl" ,r-pscl) | |
2808 | ("r-purrr" ,r-purrr) | |
2809 | ("r-rann" ,r-rann) | |
2810 | ("r-rcpp" ,r-rcpp) | |
2811 | ("r-rcppparallel" ,r-rcppparallel) | |
2812 | ("r-reshape2" ,r-reshape2) | |
2813 | ("r-reticulate" ,r-reticulate) | |
2814 | ("r-rhpcblasctl" ,r-rhpcblasctl) | |
2815 | ("r-rtsne" ,r-rtsne) | |
2816 | ("r-shiny" ,r-shiny) | |
2817 | ("r-slam" ,r-slam) | |
2818 | ("r-spdep" ,r-spdep) | |
2819 | ("r-speedglm" ,r-speedglm) | |
2820 | ("r-stringr" ,r-stringr) | |
2821 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2822 | ("r-tibble" ,r-tibble) | |
2823 | ("r-tidyr" ,r-tidyr) | |
2824 | ("r-uwot" ,r-uwot) | |
2825 | ("r-viridis" ,r-viridis))) | |
2826 | (home-page "https://github.com/cole-trapnell-lab/monocle3") | |
2827 | (synopsis "Analysis toolkit for single-cell RNA-Seq data") | |
2828 | (description | |
2829 | "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") | |
2830 | (license license:expat))) | |
2831 | ||
6213e441 RW |
2832 | (define-public r-noiseq |
2833 | (package | |
2834 | (name "r-noiseq") | |
81a125cd | 2835 | (version "2.30.0") |
6213e441 RW |
2836 | (source |
2837 | (origin | |
2838 | (method url-fetch) | |
2839 | (uri (bioconductor-uri "NOISeq" version)) | |
2840 | (sha256 | |
2841 | (base32 | |
81a125cd | 2842 | "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4")))) |
6213e441 RW |
2843 | (properties `((upstream-name . "NOISeq"))) |
2844 | (build-system r-build-system) | |
2845 | (propagated-inputs | |
2846 | `(("r-biobase" ,r-biobase) | |
2847 | ("r-matrix" ,r-matrix))) | |
2848 | (home-page "https://bioconductor.org/packages/NOISeq") | |
2849 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") | |
2850 | (description | |
2851 | "This package provides tools to support the analysis of RNA-seq | |
2852 | expression data or other similar kind of data. It provides exploratory plots | |
2853 | to evaluate saturation, count distribution, expression per chromosome, type of | |
2854 | detected features, features length, etc. It also supports the analysis of | |
2855 | differential expression between two experimental conditions with no parametric | |
2856 | assumptions.") | |
2857 | (license license:artistic2.0))) | |
b409c357 RW |
2858 | |
2859 | (define-public r-scdd | |
2860 | (package | |
2861 | (name "r-scdd") | |
2f223b21 | 2862 | (version "1.10.0") |
b409c357 RW |
2863 | (source |
2864 | (origin | |
2865 | (method url-fetch) | |
2866 | (uri (bioconductor-uri "scDD" version)) | |
2867 | (sha256 | |
2868 | (base32 | |
2f223b21 | 2869 | "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4")))) |
b409c357 RW |
2870 | (properties `((upstream-name . "scDD"))) |
2871 | (build-system r-build-system) | |
2872 | (propagated-inputs | |
2873 | `(("r-arm" ,r-arm) | |
2874 | ("r-biocparallel" ,r-biocparallel) | |
2875 | ("r-ebseq" ,r-ebseq) | |
2876 | ("r-fields" ,r-fields) | |
2877 | ("r-ggplot2" ,r-ggplot2) | |
2878 | ("r-mclust" ,r-mclust) | |
2879 | ("r-outliers" ,r-outliers) | |
2880 | ("r-s4vectors" ,r-s4vectors) | |
2881 | ("r-scran" ,r-scran) | |
2882 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2883 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2884 | (home-page "https://github.com/kdkorthauer/scDD") | |
2885 | (synopsis "Mixture modeling of single-cell RNA-seq data") | |
2886 | (description | |
2887 | "This package implements a method to analyze single-cell RNA-seq data | |
2888 | utilizing flexible Dirichlet Process mixture models. Genes with differential | |
2889 | distributions of expression are classified into several interesting patterns | |
2890 | of differences between two conditions. The package also includes functions | |
2891 | for simulating data with these patterns from negative binomial | |
2892 | distributions.") | |
2893 | (license license:gpl2))) | |
f0887757 RW |
2894 | |
2895 | (define-public r-scone | |
2896 | (package | |
2897 | (name "r-scone") | |
048a43d6 | 2898 | (version "1.10.0") |
f0887757 RW |
2899 | (source |
2900 | (origin | |
2901 | (method url-fetch) | |
2902 | (uri (bioconductor-uri "scone" version)) | |
2903 | (sha256 | |
2904 | (base32 | |
048a43d6 | 2905 | "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp")))) |
f0887757 RW |
2906 | (build-system r-build-system) |
2907 | (propagated-inputs | |
2908 | `(("r-aroma-light" ,r-aroma-light) | |
2909 | ("r-biocparallel" ,r-biocparallel) | |
2910 | ("r-boot" ,r-boot) | |
2911 | ("r-class" ,r-class) | |
2912 | ("r-cluster" ,r-cluster) | |
2913 | ("r-compositions" ,r-compositions) | |
2914 | ("r-diptest" ,r-diptest) | |
2915 | ("r-edger" ,r-edger) | |
2916 | ("r-fpc" ,r-fpc) | |
2917 | ("r-gplots" ,r-gplots) | |
2918 | ("r-hexbin" ,r-hexbin) | |
2919 | ("r-limma" ,r-limma) | |
2920 | ("r-matrixstats" ,r-matrixstats) | |
2921 | ("r-mixtools" ,r-mixtools) | |
2922 | ("r-rarpack" ,r-rarpack) | |
2923 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2924 | ("r-rhdf5" ,r-rhdf5) | |
2925 | ("r-ruvseq" ,r-ruvseq) | |
2926 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2927 | (home-page "https://bioconductor.org/packages/scone") | |
2928 | (synopsis "Single cell overview of normalized expression data") | |
2929 | (description | |
2930 | "SCONE is an R package for comparing and ranking the performance of | |
2931 | different normalization schemes for single-cell RNA-seq and other | |
2932 | high-throughput analyses.") | |
2933 | (license license:artistic2.0))) | |
f9201d67 RW |
2934 | |
2935 | (define-public r-geoquery | |
2936 | (package | |
2937 | (name "r-geoquery") | |
db85744e | 2938 | (version "2.54.1") |
f9201d67 RW |
2939 | (source |
2940 | (origin | |
2941 | (method url-fetch) | |
2942 | (uri (bioconductor-uri "GEOquery" version)) | |
2943 | (sha256 | |
2944 | (base32 | |
db85744e | 2945 | "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5")))) |
f9201d67 RW |
2946 | (properties `((upstream-name . "GEOquery"))) |
2947 | (build-system r-build-system) | |
2948 | (propagated-inputs | |
2949 | `(("r-biobase" ,r-biobase) | |
2950 | ("r-dplyr" ,r-dplyr) | |
2951 | ("r-httr" ,r-httr) | |
2952 | ("r-limma" ,r-limma) | |
2953 | ("r-magrittr" ,r-magrittr) | |
2954 | ("r-readr" ,r-readr) | |
2955 | ("r-tidyr" ,r-tidyr) | |
2956 | ("r-xml2" ,r-xml2))) | |
2957 | (home-page "https://github.com/seandavi/GEOquery/") | |
2958 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") | |
2959 | (description | |
2960 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of | |
2961 | microarray data. Given the rich and varied nature of this resource, it is | |
2962 | only natural to want to apply BioConductor tools to these data. GEOquery is | |
2963 | the bridge between GEO and BioConductor.") | |
2964 | (license license:gpl2))) | |
eed6ff03 RW |
2965 | |
2966 | (define-public r-illuminaio | |
2967 | (package | |
2968 | (name "r-illuminaio") | |
418d7214 | 2969 | (version "0.28.0") |
eed6ff03 RW |
2970 | (source |
2971 | (origin | |
2972 | (method url-fetch) | |
2973 | (uri (bioconductor-uri "illuminaio" version)) | |
2974 | (sha256 | |
2975 | (base32 | |
418d7214 | 2976 | "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh")))) |
eed6ff03 RW |
2977 | (build-system r-build-system) |
2978 | (propagated-inputs | |
2979 | `(("r-base64" ,r-base64))) | |
2980 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") | |
2981 | (synopsis "Parse Illumina microarray output files") | |
2982 | (description | |
2983 | "This package provides tools for parsing Illumina's microarray output | |
2984 | files, including IDAT.") | |
2985 | (license license:gpl2))) | |
f4eac096 RW |
2986 | |
2987 | (define-public r-siggenes | |
2988 | (package | |
2989 | (name "r-siggenes") | |
b4ee4148 | 2990 | (version "1.60.0") |
f4eac096 RW |
2991 | (source |
2992 | (origin | |
2993 | (method url-fetch) | |
2994 | (uri (bioconductor-uri "siggenes" version)) | |
2995 | (sha256 | |
2996 | (base32 | |
b4ee4148 | 2997 | "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4")))) |
f4eac096 RW |
2998 | (build-system r-build-system) |
2999 | (propagated-inputs | |
3000 | `(("r-biobase" ,r-biobase) | |
409f4dd6 RW |
3001 | ("r-multtest" ,r-multtest) |
3002 | ("r-scrime" ,r-scrime))) | |
f4eac096 RW |
3003 | (home-page "https://bioconductor.org/packages/siggenes/") |
3004 | (synopsis | |
3005 | "Multiple testing using SAM and Efron's empirical Bayes approaches") | |
3006 | (description | |
3007 | "This package provides tools for the identification of differentially | |
3008 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using | |
3009 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical | |
3010 | Bayes Analyses of Microarrays} (EBAM).") | |
3011 | (license license:lgpl2.0+))) | |
34a24f95 RW |
3012 | |
3013 | (define-public r-bumphunter | |
3014 | (package | |
3015 | (name "r-bumphunter") | |
4efdac56 | 3016 | (version "1.28.0") |
34a24f95 RW |
3017 | (source |
3018 | (origin | |
3019 | (method url-fetch) | |
3020 | (uri (bioconductor-uri "bumphunter" version)) | |
3021 | (sha256 | |
3022 | (base32 | |
4efdac56 | 3023 | "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv")))) |
34a24f95 RW |
3024 | (build-system r-build-system) |
3025 | (propagated-inputs | |
3026 | `(("r-annotationdbi" ,r-annotationdbi) | |
3027 | ("r-biocgenerics" ,r-biocgenerics) | |
3028 | ("r-dorng" ,r-dorng) | |
3029 | ("r-foreach" ,r-foreach) | |
3030 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3031 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3032 | ("r-genomicranges" ,r-genomicranges) | |
3033 | ("r-iranges" ,r-iranges) | |
3034 | ("r-iterators" ,r-iterators) | |
3035 | ("r-limma" ,r-limma) | |
3036 | ("r-locfit" ,r-locfit) | |
3037 | ("r-matrixstats" ,r-matrixstats) | |
3038 | ("r-s4vectors" ,r-s4vectors))) | |
3039 | (home-page "https://github.com/ririzarr/bumphunter") | |
3040 | (synopsis "Find bumps in genomic data") | |
3041 | (description | |
3042 | "This package provides tools for finding bumps in genomic data in order | |
3043 | to identify differentially methylated regions in epigenetic epidemiology | |
3044 | studies.") | |
3045 | (license license:artistic2.0))) | |
0fbaf195 RW |
3046 | |
3047 | (define-public r-minfi | |
3048 | (package | |
3049 | (name "r-minfi") | |
dfd4287c | 3050 | (version "1.32.0") |
0fbaf195 RW |
3051 | (source |
3052 | (origin | |
3053 | (method url-fetch) | |
3054 | (uri (bioconductor-uri "minfi" version)) | |
3055 | (sha256 | |
3056 | (base32 | |
dfd4287c | 3057 | "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3")))) |
0fbaf195 RW |
3058 | (build-system r-build-system) |
3059 | (propagated-inputs | |
3060 | `(("r-beanplot" ,r-beanplot) | |
3061 | ("r-biobase" ,r-biobase) | |
3062 | ("r-biocgenerics" ,r-biocgenerics) | |
3063 | ("r-biocparallel" ,r-biocparallel) | |
3064 | ("r-biostrings" ,r-biostrings) | |
3065 | ("r-bumphunter" ,r-bumphunter) | |
3066 | ("r-data-table" ,r-data-table) | |
3067 | ("r-delayedarray" ,r-delayedarray) | |
3068 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
3069 | ("r-genefilter" ,r-genefilter) | |
3070 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3071 | ("r-genomicranges" ,r-genomicranges) | |
3072 | ("r-geoquery" ,r-geoquery) | |
3073 | ("r-hdf5array" ,r-hdf5array) | |
3074 | ("r-illuminaio" ,r-illuminaio) | |
3075 | ("r-iranges" ,r-iranges) | |
3076 | ("r-lattice" ,r-lattice) | |
3077 | ("r-limma" ,r-limma) | |
3078 | ("r-mass" ,r-mass) | |
3079 | ("r-mclust" ,r-mclust) | |
3080 | ("r-nlme" ,r-nlme) | |
3081 | ("r-nor1mix" ,r-nor1mix) | |
3082 | ("r-preprocesscore" ,r-preprocesscore) | |
3083 | ("r-quadprog" ,r-quadprog) | |
3084 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3085 | ("r-reshape" ,r-reshape) | |
3086 | ("r-s4vectors" ,r-s4vectors) | |
3087 | ("r-siggenes" ,r-siggenes) | |
3088 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
3089 | (home-page "https://github.com/hansenlab/minfi") | |
3090 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") | |
3091 | (description | |
3092 | "This package provides tools to analyze and visualize Illumina Infinium | |
3093 | methylation arrays.") | |
3094 | (license license:artistic2.0))) | |
5ec5ba02 RW |
3095 | |
3096 | (define-public r-methylumi | |
3097 | (package | |
3098 | (name "r-methylumi") | |
b57cffb9 | 3099 | (version "2.32.0") |
5ec5ba02 RW |
3100 | (source |
3101 | (origin | |
3102 | (method url-fetch) | |
3103 | (uri (bioconductor-uri "methylumi" version)) | |
3104 | (sha256 | |
3105 | (base32 | |
b57cffb9 | 3106 | "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w")))) |
5ec5ba02 RW |
3107 | (build-system r-build-system) |
3108 | (propagated-inputs | |
3109 | `(("r-annotate" ,r-annotate) | |
3110 | ("r-annotationdbi" ,r-annotationdbi) | |
3111 | ("r-biobase" ,r-biobase) | |
3112 | ("r-biocgenerics" ,r-biocgenerics) | |
3113 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) | |
3114 | ("r-genefilter" ,r-genefilter) | |
3115 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3116 | ("r-genomicranges" ,r-genomicranges) | |
3117 | ("r-ggplot2" ,r-ggplot2) | |
3118 | ("r-illuminaio" ,r-illuminaio) | |
3119 | ("r-iranges" ,r-iranges) | |
3120 | ("r-lattice" ,r-lattice) | |
3121 | ("r-matrixstats" ,r-matrixstats) | |
3122 | ("r-minfi" ,r-minfi) | |
3123 | ("r-reshape2" ,r-reshape2) | |
3124 | ("r-s4vectors" ,r-s4vectors) | |
3125 | ("r-scales" ,r-scales) | |
3126 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
3127 | (home-page "https://bioconductor.org/packages/methylumi") | |
3128 | (synopsis "Handle Illumina methylation data") | |
3129 | (description | |
3130 | "This package provides classes for holding and manipulating Illumina | |
3131 | methylation data. Based on eSet, it can contain MIAME information, sample | |
3132 | information, feature information, and multiple matrices of data. An | |
3133 | \"intelligent\" import function, methylumiR can read the Illumina text files | |
3134 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from | |
3135 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, | |
3136 | background correction, and quality control features for GoldenGate, Infinium, | |
3137 | and Infinium HD arrays are also included.") | |
3138 | (license license:gpl2))) | |
09605cb2 RW |
3139 | |
3140 | (define-public r-lumi | |
3141 | (package | |
3142 | (name "r-lumi") | |
8f7bc872 | 3143 | (version "2.38.0") |
09605cb2 RW |
3144 | (source |
3145 | (origin | |
3146 | (method url-fetch) | |
3147 | (uri (bioconductor-uri "lumi" version)) | |
3148 | (sha256 | |
3149 | (base32 | |
8f7bc872 | 3150 | "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm")))) |
09605cb2 RW |
3151 | (build-system r-build-system) |
3152 | (propagated-inputs | |
3153 | `(("r-affy" ,r-affy) | |
3154 | ("r-annotate" ,r-annotate) | |
3155 | ("r-annotationdbi" ,r-annotationdbi) | |
3156 | ("r-biobase" ,r-biobase) | |
3157 | ("r-dbi" ,r-dbi) | |
3158 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3159 | ("r-genomicranges" ,r-genomicranges) | |
3160 | ("r-kernsmooth" ,r-kernsmooth) | |
3161 | ("r-lattice" ,r-lattice) | |
3162 | ("r-mass" ,r-mass) | |
3163 | ("r-methylumi" ,r-methylumi) | |
3164 | ("r-mgcv" ,r-mgcv) | |
3165 | ("r-nleqslv" ,r-nleqslv) | |
3166 | ("r-preprocesscore" ,r-preprocesscore) | |
3167 | ("r-rsqlite" ,r-rsqlite))) | |
3168 | (home-page "https://bioconductor.org/packages/lumi") | |
3169 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") | |
3170 | (description | |
3171 | "The lumi package provides an integrated solution for the Illumina | |
3172 | microarray data analysis. It includes functions of Illumina | |
3173 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific | |
3174 | variance stabilization, normalization and gene annotation at the probe level. | |
3175 | It also includes the functions of processing Illumina methylation microarrays, | |
3176 | especially Illumina Infinium methylation microarrays.") | |
3177 | (license license:lgpl2.0+))) | |
4291f36a RW |
3178 | |
3179 | (define-public r-linnorm | |
3180 | (package | |
3181 | (name "r-linnorm") | |
a2877d69 | 3182 | (version "2.10.0") |
4291f36a RW |
3183 | (source |
3184 | (origin | |
3185 | (method url-fetch) | |
3186 | (uri (bioconductor-uri "Linnorm" version)) | |
3187 | (sha256 | |
3188 | (base32 | |
a2877d69 | 3189 | "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67")))) |
4291f36a RW |
3190 | (properties `((upstream-name . "Linnorm"))) |
3191 | (build-system r-build-system) | |
3192 | (propagated-inputs | |
3193 | `(("r-amap" ,r-amap) | |
3194 | ("r-apcluster" ,r-apcluster) | |
3195 | ("r-ellipse" ,r-ellipse) | |
3196 | ("r-fastcluster" ,r-fastcluster) | |
3197 | ("r-fpc" ,r-fpc) | |
3198 | ("r-ggdendro" ,r-ggdendro) | |
3199 | ("r-ggplot2" ,r-ggplot2) | |
3200 | ("r-gmodels" ,r-gmodels) | |
3201 | ("r-igraph" ,r-igraph) | |
3202 | ("r-limma" ,r-limma) | |
3203 | ("r-mass" ,r-mass) | |
3204 | ("r-mclust" ,r-mclust) | |
3205 | ("r-rcpp" ,r-rcpp) | |
3206 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
3207 | ("r-rtsne" ,r-rtsne) | |
3208 | ("r-statmod" ,r-statmod) | |
3209 | ("r-vegan" ,r-vegan) | |
3210 | ("r-zoo" ,r-zoo))) | |
3211 | (home-page "http://www.jjwanglab.org/Linnorm/") | |
3212 | (synopsis "Linear model and normality based transformation method") | |
3213 | (description | |
3214 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq | |
3215 | count data or any large scale count data. It transforms such datasets for | |
3216 | parametric tests. In addition to the transformtion function (@code{Linnorm}), | |
3217 | the following pipelines are implemented: | |
3218 | ||
3219 | @enumerate | |
3220 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) | |
3221 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means | |
3222 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, | |
3223 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) | |
3224 | @item Differential expression analysis or differential peak detection using | |
3225 | limma (@code{Linnorm.limma}) | |
3226 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) | |
3227 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) | |
3228 | @item Stable gene selection for scRNA-seq data; for users without or who do | |
3229 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) | |
3230 | @item Data imputation (@code{Linnorm.DataImput}). | |
3231 | @end enumerate | |
3232 | ||
3233 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the | |
3234 | @code{RnaXSim} function is included for simulating RNA-seq data for the | |
3235 | evaluation of DEG analysis methods.") | |
3236 | (license license:expat))) | |
e4a17532 RW |
3237 | |
3238 | (define-public r-ioniser | |
3239 | (package | |
3240 | (name "r-ioniser") | |
1b890c32 | 3241 | (version "2.10.0") |
e4a17532 RW |
3242 | (source |
3243 | (origin | |
3244 | (method url-fetch) | |
3245 | (uri (bioconductor-uri "IONiseR" version)) | |
3246 | (sha256 | |
3247 | (base32 | |
1b890c32 | 3248 | "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f")))) |
e4a17532 RW |
3249 | (properties `((upstream-name . "IONiseR"))) |
3250 | (build-system r-build-system) | |
3251 | (propagated-inputs | |
3252 | `(("r-biocgenerics" ,r-biocgenerics) | |
3253 | ("r-biocparallel" ,r-biocparallel) | |
3254 | ("r-biostrings" ,r-biostrings) | |
3255 | ("r-bit64" ,r-bit64) | |
3256 | ("r-dplyr" ,r-dplyr) | |
3257 | ("r-ggplot2" ,r-ggplot2) | |
3258 | ("r-magrittr" ,r-magrittr) | |
3259 | ("r-rhdf5" ,r-rhdf5) | |
3260 | ("r-shortread" ,r-shortread) | |
3261 | ("r-stringr" ,r-stringr) | |
3262 | ("r-tibble" ,r-tibble) | |
3263 | ("r-tidyr" ,r-tidyr) | |
3264 | ("r-xvector" ,r-xvector))) | |
3265 | (home-page "https://bioconductor.org/packages/IONiseR/") | |
3266 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") | |
3267 | (description | |
3268 | "IONiseR provides tools for the quality assessment of Oxford Nanopore | |
3269 | MinION data. It extracts summary statistics from a set of fast5 files and can | |
3270 | be used either before or after base calling. In addition to standard | |
3271 | summaries of the read-types produced, it provides a number of plots for | |
3272 | visualising metrics relative to experiment run time or spatially over the | |
3273 | surface of a flowcell.") | |
3274 | (license license:expat))) | |
80eb01c7 RW |
3275 | |
3276 | ;; This is a CRAN package, but it depends on packages from Bioconductor. | |
3277 | (define-public r-gkmsvm | |
3278 | (package | |
3279 | (name "r-gkmsvm") | |
975cfe26 | 3280 | (version "0.80.0") |
80eb01c7 RW |
3281 | (source |
3282 | (origin | |
3283 | (method url-fetch) | |
3284 | (uri (cran-uri "gkmSVM" version)) | |
3285 | (sha256 | |
3286 | (base32 | |
975cfe26 | 3287 | "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p")))) |
80eb01c7 RW |
3288 | (properties `((upstream-name . "gkmSVM"))) |
3289 | (build-system r-build-system) | |
3290 | (propagated-inputs | |
975cfe26 | 3291 | `(("r-kernlab" ,r-kernlab) |
80eb01c7 RW |
3292 | ("r-rcpp" ,r-rcpp) |
3293 | ("r-rocr" ,r-rocr) | |
80eb01c7 RW |
3294 | ("r-seqinr" ,r-seqinr))) |
3295 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") | |
3296 | (synopsis "Gapped-kmer support vector machine") | |
3297 | (description | |
3298 | "This R package provides tools for training gapped-kmer SVM classifiers | |
3299 | for DNA and protein sequences. This package supports several sequence | |
3300 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
3301 | (license license:gpl2+))) | |
8a5460b4 | 3302 | |
f2114762 RW |
3303 | ;; This is a CRAN package, but it depends on multtest from Bioconductor. |
3304 | (define-public r-mutoss | |
3305 | (package | |
3306 | (name "r-mutoss") | |
3307 | (version "0.1-12") | |
3308 | (source | |
3309 | (origin | |
3310 | (method url-fetch) | |
3311 | (uri (cran-uri "mutoss" version)) | |
3312 | (sha256 | |
3313 | (base32 | |
3314 | "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298")))) | |
3315 | (properties `((upstream-name . "mutoss"))) | |
3316 | (build-system r-build-system) | |
3317 | (propagated-inputs | |
3318 | `(("r-multcomp" ,r-multcomp) | |
3319 | ("r-multtest" ,r-multtest) | |
3320 | ("r-mvtnorm" ,r-mvtnorm) | |
3321 | ("r-plotrix" ,r-plotrix))) | |
3322 | (home-page "https://github.com/kornl/mutoss/") | |
3323 | (synopsis "Unified multiple testing procedures") | |
3324 | (description | |
3325 | "This package is designed to ease the application and comparison of | |
3326 | multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods | |
3327 | are standardized and usable by the accompanying mutossGUI package.") | |
3328 | ;; Any version of the GPL. | |
3329 | (license (list license:gpl2+ license:gpl3+)))) | |
3330 | ||
bf770d92 RW |
3331 | ;; This is a CRAN package, but it depends on mutoss, which depends on multtest |
3332 | ;; from Bioconductor, so we put it here. | |
3333 | (define-public r-metap | |
3334 | (package | |
3335 | (name "r-metap") | |
fd6412cd | 3336 | (version "1.3") |
bf770d92 RW |
3337 | (source |
3338 | (origin | |
3339 | (method url-fetch) | |
3340 | (uri (cran-uri "metap" version)) | |
3341 | (sha256 | |
3342 | (base32 | |
fd6412cd | 3343 | "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) |
bf770d92 RW |
3344 | (build-system r-build-system) |
3345 | (propagated-inputs | |
3346 | `(("r-lattice" ,r-lattice) | |
3347 | ("r-mutoss" ,r-mutoss) | |
3348 | ("r-rdpack" ,r-rdpack) | |
3349 | ("r-tfisher" ,r-tfisher))) | |
3350 | (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") | |
3351 | (synopsis "Meta-analysis of significance values") | |
3352 | (description | |
3353 | "The canonical way to perform meta-analysis involves using effect sizes. | |
3354 | When they are not available this package provides a number of methods for | |
3355 | meta-analysis of significance values including the methods of Edgington, | |
3356 | Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate | |
3357 | published results; and a routine for graphical display.") | |
3358 | (license license:gpl2))) | |
3359 | ||
8a5460b4 RW |
3360 | (define-public r-triform |
3361 | (package | |
3362 | (name "r-triform") | |
a18f325e | 3363 | (version "1.28.0") |
8a5460b4 RW |
3364 | (source |
3365 | (origin | |
3366 | (method url-fetch) | |
3367 | (uri (bioconductor-uri "triform" version)) | |
3368 | (sha256 | |
3369 | (base32 | |
a18f325e | 3370 | "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9")))) |
8a5460b4 RW |
3371 | (build-system r-build-system) |
3372 | (propagated-inputs | |
3373 | `(("r-biocgenerics" ,r-biocgenerics) | |
3374 | ("r-iranges" ,r-iranges) | |
3375 | ("r-yaml" ,r-yaml))) | |
3376 | (home-page "https://bioconductor.org/packages/triform/") | |
3377 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") | |
3378 | (description | |
3379 | "The Triform algorithm uses model-free statistics to identify peak-like | |
3380 | distributions of TF ChIP sequencing reads, taking advantage of an improved | |
3381 | peak definition in combination with known profile characteristics.") | |
3382 | (license license:gpl2))) | |
c538bcdd RW |
3383 | |
3384 | (define-public r-varianttools | |
3385 | (package | |
3386 | (name "r-varianttools") | |
851081bf | 3387 | (version "1.28.1") |
c538bcdd RW |
3388 | (source |
3389 | (origin | |
3390 | (method url-fetch) | |
3391 | (uri (bioconductor-uri "VariantTools" version)) | |
3392 | (sha256 | |
3393 | (base32 | |
851081bf | 3394 | "1x57shc3slcbnc807ra1nwnjr37sqjh04n2xfwd469m4hkjb0jzh")))) |
c538bcdd RW |
3395 | (properties `((upstream-name . "VariantTools"))) |
3396 | (build-system r-build-system) | |
3397 | (propagated-inputs | |
3398 | `(("r-biobase" ,r-biobase) | |
3399 | ("r-biocgenerics" ,r-biocgenerics) | |
3400 | ("r-biocparallel" ,r-biocparallel) | |
3401 | ("r-biostrings" ,r-biostrings) | |
3402 | ("r-bsgenome" ,r-bsgenome) | |
3403 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3404 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3405 | ("r-genomicranges" ,r-genomicranges) | |
3406 | ("r-iranges" ,r-iranges) | |
3407 | ("r-matrix" ,r-matrix) | |
3408 | ("r-rsamtools" ,r-rsamtools) | |
3409 | ("r-rtracklayer" ,r-rtracklayer) | |
3410 | ("r-s4vectors" ,r-s4vectors) | |
3411 | ("r-variantannotation" ,r-variantannotation))) | |
3412 | (home-page "https://bioconductor.org/packages/VariantTools/") | |
3413 | (synopsis "Tools for exploratory analysis of variant calls") | |
3414 | (description | |
3415 | "Explore, diagnose, and compare variant calls using filters. The | |
3416 | VariantTools package supports a workflow for loading data, calling single | |
3417 | sample variants and tumor-specific somatic mutations or other sample-specific | |
3418 | variant types (e.g., RNA editing). Most of the functions operate on | |
3419 | alignments (BAM files) or datasets of called variants. The user is expected | |
3420 | to have already aligned the reads with a separate tool, e.g., GSNAP via | |
3421 | gmapR.") | |
3422 | (license license:artistic2.0))) | |
3e41919d RW |
3423 | |
3424 | (define-public r-heatplus | |
3425 | (package | |
3426 | (name "r-heatplus") | |
776e98fe | 3427 | (version "2.32.1") |
3e41919d RW |
3428 | (source |
3429 | (origin | |
3430 | (method url-fetch) | |
3431 | (uri (bioconductor-uri "Heatplus" version)) | |
3432 | (sha256 | |
3433 | (base32 | |
776e98fe | 3434 | "1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1")))) |
3e41919d RW |
3435 | (properties `((upstream-name . "Heatplus"))) |
3436 | (build-system r-build-system) | |
3437 | (propagated-inputs | |
3438 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) | |
3439 | (home-page "https://github.com/alexploner/Heatplus") | |
3440 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") | |
3441 | (description | |
3442 | "This package provides tools to display a rectangular heatmap (intensity | |
3443 | plot) of a data matrix. By default, both samples (columns) and features (row) | |
3444 | of the matrix are sorted according to a hierarchical clustering, and the | |
3445 | corresponding dendrogram is plotted. Optionally, panels with additional | |
3446 | information about samples and features can be added to the plot.") | |
3447 | (license license:gpl2+))) | |
c04f230e RW |
3448 | |
3449 | (define-public r-gosemsim | |
3450 | (package | |
3451 | (name "r-gosemsim") | |
d5951dc4 | 3452 | (version "2.12.1") |
c04f230e RW |
3453 | (source |
3454 | (origin | |
3455 | (method url-fetch) | |
3456 | (uri (bioconductor-uri "GOSemSim" version)) | |
3457 | (sha256 | |
3458 | (base32 | |
d5951dc4 | 3459 | "1r8yx6qw6d6602cp8aspzl3shi1l1zqcrc8fm9d5wg01sw1whs05")))) |
c04f230e RW |
3460 | (properties `((upstream-name . "GOSemSim"))) |
3461 | (build-system r-build-system) | |
3462 | (propagated-inputs | |
3463 | `(("r-annotationdbi" ,r-annotationdbi) | |
3464 | ("r-go-db" ,r-go-db) | |
3465 | ("r-rcpp" ,r-rcpp))) | |
d5951dc4 RW |
3466 | (native-inputs |
3467 | `(("r-knitr" ,r-knitr))) | |
c04f230e RW |
3468 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") |
3469 | (synopsis "GO-terms semantic similarity measures") | |
3470 | (description | |
3471 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide | |
3472 | quantitative ways to compute similarities between genes and gene groups, and | |
3473 | have became important basis for many bioinformatics analysis approaches. | |
3474 | GOSemSim is an R package for semantic similarity computation among GO terms, | |
3475 | sets of GO terms, gene products and gene clusters.") | |
3476 | (license license:artistic2.0))) | |
9d0f7942 RW |
3477 | |
3478 | (define-public r-anota | |
3479 | (package | |
3480 | (name "r-anota") | |
5ed76752 | 3481 | (version "1.34.0") |
9d0f7942 RW |
3482 | (source |
3483 | (origin | |
3484 | (method url-fetch) | |
3485 | (uri (bioconductor-uri "anota" version)) | |
3486 | (sha256 | |
3487 | (base32 | |
5ed76752 | 3488 | "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m")))) |
9d0f7942 RW |
3489 | (build-system r-build-system) |
3490 | (propagated-inputs | |
3491 | `(("r-multtest" ,r-multtest) | |
3492 | ("r-qvalue" ,r-qvalue))) | |
3493 | (home-page "https://bioconductor.org/packages/anota/") | |
3494 | (synopsis "Analysis of translational activity") | |
3495 | (description | |
3496 | "Genome wide studies of translational control is emerging as a tool to | |
0cea26bd | 3497 | study various biological conditions. The output from such analysis is both |
9d0f7942 RW |
3498 | the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively |
3499 | involved in translation (the actively translating mRNA level) for each mRNA. | |
3500 | The standard analysis of such data strives towards identifying differential | |
3501 | translational between two or more sample classes - i.e. differences in | |
3502 | actively translated mRNA levels that are independent of underlying differences | |
3503 | in cytosolic mRNA levels. This package allows for such analysis using partial | |
3504 | variances and the random variance model. As 10s of thousands of mRNAs are | |
4f664004 | 3505 | analyzed in parallel the library performs a number of tests to assure that |
9d0f7942 RW |
3506 | the data set is suitable for such analysis.") |
3507 | (license license:gpl3))) | |
a6d867fe RW |
3508 | |
3509 | (define-public r-sigpathway | |
3510 | (package | |
3511 | (name "r-sigpathway") | |
869965df | 3512 | (version "1.54.0") |
a6d867fe RW |
3513 | (source |
3514 | (origin | |
3515 | (method url-fetch) | |
3516 | (uri (bioconductor-uri "sigPathway" version)) | |
3517 | (sha256 | |
3518 | (base32 | |
869965df | 3519 | "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb")))) |
a6d867fe RW |
3520 | (properties `((upstream-name . "sigPathway"))) |
3521 | (build-system r-build-system) | |
3522 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") | |
3523 | (synopsis "Pathway analysis") | |
3524 | (description | |
3525 | "This package is used to conduct pathway analysis by calculating the NT_k | |
3526 | and NE_k statistics in a statistical framework for determining whether a | |
3527 | specified group of genes for a pathway has a coordinated association with a | |
3528 | phenotype of interest.") | |
3529 | (license license:gpl2))) | |
af26c7ae RW |
3530 | |
3531 | (define-public r-fgsea | |
3532 | (package | |
3533 | (name "r-fgsea") | |
b4e1268c | 3534 | (version "1.12.0") |
af26c7ae RW |
3535 | (source |
3536 | (origin | |
3537 | (method url-fetch) | |
3538 | (uri (bioconductor-uri "fgsea" version)) | |
3539 | (sha256 | |
3540 | (base32 | |
b4e1268c | 3541 | "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1")))) |
af26c7ae RW |
3542 | (build-system r-build-system) |
3543 | (propagated-inputs | |
ebffd24c RW |
3544 | `(("r-bh" ,r-bh) |
3545 | ("r-biocparallel" ,r-biocparallel) | |
af26c7ae RW |
3546 | ("r-data-table" ,r-data-table) |
3547 | ("r-fastmatch" ,r-fastmatch) | |
3548 | ("r-ggplot2" ,r-ggplot2) | |
3549 | ("r-gridextra" ,r-gridextra) | |
3550 | ("r-matrix" ,r-matrix) | |
3551 | ("r-rcpp" ,r-rcpp))) | |
3552 | (home-page "https://github.com/ctlab/fgsea/") | |
3553 | (synopsis "Fast gene set enrichment analysis") | |
3554 | (description | |
3555 | "The package implements an algorithm for fast gene set enrichment | |
23c8ef71 VC |
3556 | analysis. Using the fast algorithm makes more permutations and gets |
3557 | more fine grained p-values, which allows using accurate standard approaches | |
af26c7ae RW |
3558 | to multiple hypothesis correction.") |
3559 | (license license:expat))) | |
305050b5 RW |
3560 | |
3561 | (define-public r-dose | |
3562 | (package | |
3563 | (name "r-dose") | |
166b3c2d | 3564 | (version "3.12.0") |
305050b5 RW |
3565 | (source |
3566 | (origin | |
3567 | (method url-fetch) | |
3568 | (uri (bioconductor-uri "DOSE" version)) | |
3569 | (sha256 | |
3570 | (base32 | |
166b3c2d | 3571 | "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5")))) |
305050b5 RW |
3572 | (properties `((upstream-name . "DOSE"))) |
3573 | (build-system r-build-system) | |
3574 | (propagated-inputs | |
3575 | `(("r-annotationdbi" ,r-annotationdbi) | |
3576 | ("r-biocparallel" ,r-biocparallel) | |
3577 | ("r-do-db" ,r-do-db) | |
3578 | ("r-fgsea" ,r-fgsea) | |
3579 | ("r-ggplot2" ,r-ggplot2) | |
3580 | ("r-gosemsim" ,r-gosemsim) | |
3581 | ("r-qvalue" ,r-qvalue) | |
3582 | ("r-reshape2" ,r-reshape2) | |
3583 | ("r-s4vectors" ,r-s4vectors))) | |
5ef2b749 RW |
3584 | (native-inputs |
3585 | `(("r-knitr" ,r-knitr))) | |
305050b5 RW |
3586 | (home-page "https://guangchuangyu.github.io/software/DOSE/") |
3587 | (synopsis "Disease ontology semantic and enrichment analysis") | |
3588 | (description | |
3589 | "This package implements five methods proposed by Resnik, Schlicker, | |
3590 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among | |
3591 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses | |
3592 | including hypergeometric model and gene set enrichment analysis are also | |
3593 | implemented for discovering disease associations of high-throughput biological | |
3594 | data.") | |
3595 | (license license:artistic2.0))) | |
9c30cf65 RW |
3596 | |
3597 | (define-public r-enrichplot | |
3598 | (package | |
3599 | (name "r-enrichplot") | |
7621bf2d | 3600 | (version "1.6.1") |
9c30cf65 RW |
3601 | (source |
3602 | (origin | |
3603 | (method url-fetch) | |
3604 | (uri (bioconductor-uri "enrichplot" version)) | |
3605 | (sha256 | |
3606 | (base32 | |
7621bf2d | 3607 | "0707f5ll58psh7pr001cmmk5di7dprnbry1cy2mw20vn8p24nf3x")))) |
9c30cf65 RW |
3608 | (build-system r-build-system) |
3609 | (propagated-inputs | |
3610 | `(("r-annotationdbi" ,r-annotationdbi) | |
3611 | ("r-cowplot" ,r-cowplot) | |
3612 | ("r-dose" ,r-dose) | |
3613 | ("r-europepmc" ,r-europepmc) | |
3614 | ("r-ggplot2" ,r-ggplot2) | |
3615 | ("r-ggplotify" ,r-ggplotify) | |
3616 | ("r-ggraph" ,r-ggraph) | |
3617 | ("r-ggridges" ,r-ggridges) | |
3618 | ("r-gosemsim" ,r-gosemsim) | |
3619 | ("r-gridextra" ,r-gridextra) | |
3620 | ("r-igraph" ,r-igraph) | |
3621 | ("r-purrr" ,r-purrr) | |
3622 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
0654a9bc | 3623 | ("r-reshape2" ,r-reshape2))) |
9c30cf65 RW |
3624 | (home-page "https://github.com/GuangchuangYu/enrichplot") |
3625 | (synopsis "Visualization of functional enrichment result") | |
3626 | (description | |
3627 | "The enrichplot package implements several visualization methods for | |
3628 | interpreting functional enrichment results obtained from ORA or GSEA analyses. | |
3629 | All the visualization methods are developed based on ggplot2 graphics.") | |
3630 | (license license:artistic2.0))) | |
f8295ee6 RW |
3631 | |
3632 | (define-public r-clusterprofiler | |
3633 | (package | |
3634 | (name "r-clusterprofiler") | |
ac9a9c37 | 3635 | (version "3.14.3") |
f8295ee6 RW |
3636 | (source |
3637 | (origin | |
3638 | (method url-fetch) | |
3639 | (uri (bioconductor-uri "clusterProfiler" version)) | |
3640 | (sha256 | |
3641 | (base32 | |
ac9a9c37 | 3642 | "08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg")))) |
f8295ee6 RW |
3643 | (properties |
3644 | `((upstream-name . "clusterProfiler"))) | |
3645 | (build-system r-build-system) | |
3646 | (propagated-inputs | |
3647 | `(("r-annotationdbi" ,r-annotationdbi) | |
3648 | ("r-dose" ,r-dose) | |
3649 | ("r-enrichplot" ,r-enrichplot) | |
3650 | ("r-ggplot2" ,r-ggplot2) | |
3651 | ("r-go-db" ,r-go-db) | |
3652 | ("r-gosemsim" ,r-gosemsim) | |
3653 | ("r-magrittr" ,r-magrittr) | |
3654 | ("r-plyr" ,r-plyr) | |
3655 | ("r-qvalue" ,r-qvalue) | |
3656 | ("r-rvcheck" ,r-rvcheck) | |
3657 | ("r-tidyr" ,r-tidyr))) | |
3658 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") | |
3659 | (synopsis "Analysis and visualization of functional profiles for gene clusters") | |
3660 | (description | |
3661 | "This package implements methods to analyze and visualize functional | |
3662 | profiles (GO and KEGG) of gene and gene clusters.") | |
3663 | (license license:artistic2.0))) | |
ce77562a RW |
3664 | |
3665 | (define-public r-mlinterfaces | |
3666 | (package | |
3667 | (name "r-mlinterfaces") | |
e0061f51 | 3668 | (version "1.66.5") |
ce77562a RW |
3669 | (source |
3670 | (origin | |
3671 | (method url-fetch) | |
3672 | (uri (bioconductor-uri "MLInterfaces" version)) | |
3673 | (sha256 | |
3674 | (base32 | |
e0061f51 | 3675 | "05bg7qcrv485m03rkyq3qg5hrr1m3y7zx49bipwaivzqm3s1mbw5")))) |
ce77562a RW |
3676 | (properties `((upstream-name . "MLInterfaces"))) |
3677 | (build-system r-build-system) | |
3678 | (propagated-inputs | |
3679 | `(("r-annotate" ,r-annotate) | |
3680 | ("r-biobase" ,r-biobase) | |
3681 | ("r-biocgenerics" ,r-biocgenerics) | |
3682 | ("r-cluster" ,r-cluster) | |
3683 | ("r-fpc" ,r-fpc) | |
3684 | ("r-gbm" ,r-gbm) | |
3685 | ("r-gdata" ,r-gdata) | |
3686 | ("r-genefilter" ,r-genefilter) | |
3687 | ("r-ggvis" ,r-ggvis) | |
3688 | ("r-hwriter" ,r-hwriter) | |
3689 | ("r-mass" ,r-mass) | |
3690 | ("r-mlbench" ,r-mlbench) | |
3691 | ("r-pls" ,r-pls) | |
3692 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
ce77562a RW |
3693 | ("r-rpart" ,r-rpart) |
3694 | ("r-sfsmisc" ,r-sfsmisc) | |
3695 | ("r-shiny" ,r-shiny) | |
3696 | ("r-threejs" ,r-threejs))) | |
3697 | (home-page "https://bioconductor.org/packages/MLInterfaces/") | |
3698 | (synopsis "Interfaces to R machine learning procedures") | |
3699 | (description | |
3700 | "This package provides uniform interfaces to machine learning code for | |
3701 | data in R and Bioconductor containers.") | |
3702 | ;; Any version of the LGPL. | |
3703 | (license license:lgpl2.1+))) | |
a793e88c RW |
3704 | |
3705 | (define-public r-annaffy | |
3706 | (package | |
3707 | (name "r-annaffy") | |
fc4a9dd5 | 3708 | (version "1.58.0") |
a793e88c RW |
3709 | (source |
3710 | (origin | |
3711 | (method url-fetch) | |
3712 | (uri (bioconductor-uri "annaffy" version)) | |
3713 | (sha256 | |
3714 | (base32 | |
fc4a9dd5 | 3715 | "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16")))) |
a793e88c RW |
3716 | (build-system r-build-system) |
3717 | (arguments | |
3718 | `(#:phases | |
3719 | (modify-phases %standard-phases | |
3720 | (add-after 'unpack 'remove-reference-to-non-free-data | |
3721 | (lambda _ | |
3722 | (substitute* "DESCRIPTION" | |
3723 | ((", KEGG.db") "")) | |
3724 | #t))))) | |
3725 | (propagated-inputs | |
3726 | `(("r-annotationdbi" ,r-annotationdbi) | |
3727 | ("r-biobase" ,r-biobase) | |
3728 | ("r-dbi" ,r-dbi) | |
3729 | ("r-go-db" ,r-go-db))) | |
3730 | (home-page "https://bioconductor.org/packages/annaffy/") | |
3731 | (synopsis "Annotation tools for Affymetrix biological metadata") | |
3732 | (description | |
3733 | "This package provides functions for handling data from Bioconductor | |
3734 | Affymetrix annotation data packages. It produces compact HTML and text | |
3735 | reports including experimental data and URL links to many online databases. | |
3736 | It allows searching of biological metadata using various criteria.") | |
3737 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of | |
3738 | ;; the LGPL 2.1 is included. | |
3739 | (license license:lgpl2.1+))) | |
0ec0a5ec RW |
3740 | |
3741 | (define-public r-a4core | |
3742 | (package | |
3743 | (name "r-a4core") | |
4ed18ddc | 3744 | (version "1.34.0") |
0ec0a5ec RW |
3745 | (source |
3746 | (origin | |
3747 | (method url-fetch) | |
3748 | (uri (bioconductor-uri "a4Core" version)) | |
3749 | (sha256 | |
3750 | (base32 | |
4ed18ddc | 3751 | "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df")))) |
0ec0a5ec RW |
3752 | (properties `((upstream-name . "a4Core"))) |
3753 | (build-system r-build-system) | |
3754 | (propagated-inputs | |
3755 | `(("r-biobase" ,r-biobase) | |
3756 | ("r-glmnet" ,r-glmnet))) | |
3757 | (home-page "https://bioconductor.org/packages/a4Core") | |
3758 | (synopsis "Automated Affymetrix array analysis core package") | |
3759 | (description | |
3760 | "This is the core package for the automated analysis of Affymetrix | |
3761 | arrays.") | |
3762 | (license license:gpl3))) | |
9ae37581 RW |
3763 | |
3764 | (define-public r-a4classif | |
3765 | (package | |
3766 | (name "r-a4classif") | |
102b982c | 3767 | (version "1.34.0") |
9ae37581 RW |
3768 | (source |
3769 | (origin | |
3770 | (method url-fetch) | |
3771 | (uri (bioconductor-uri "a4Classif" version)) | |
3772 | (sha256 | |
3773 | (base32 | |
102b982c | 3774 | "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn")))) |
9ae37581 RW |
3775 | (properties `((upstream-name . "a4Classif"))) |
3776 | (build-system r-build-system) | |
3777 | (propagated-inputs | |
3778 | `(("r-a4core" ,r-a4core) | |
3779 | ("r-a4preproc" ,r-a4preproc) | |
3780 | ("r-glmnet" ,r-glmnet) | |
3781 | ("r-mlinterfaces" ,r-mlinterfaces) | |
3782 | ("r-pamr" ,r-pamr) | |
3783 | ("r-rocr" ,r-rocr) | |
3784 | ("r-varselrf" ,r-varselrf))) | |
3785 | (home-page "https://bioconductor.org/packages/a4Classif/") | |
3786 | (synopsis "Automated Affymetrix array analysis classification package") | |
3787 | (description | |
3788 | "This is the classification package for the automated analysis of | |
3789 | Affymetrix arrays.") | |
3790 | (license license:gpl3))) | |
b8d13e2c RW |
3791 | |
3792 | (define-public r-a4preproc | |
3793 | (package | |
3794 | (name "r-a4preproc") | |
d6859c7c | 3795 | (version "1.34.0") |
b8d13e2c RW |
3796 | (source |
3797 | (origin | |
3798 | (method url-fetch) | |
3799 | (uri (bioconductor-uri "a4Preproc" version)) | |
3800 | (sha256 | |
3801 | (base32 | |
d6859c7c | 3802 | "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd")))) |
b8d13e2c RW |
3803 | (properties `((upstream-name . "a4Preproc"))) |
3804 | (build-system r-build-system) | |
3805 | (propagated-inputs | |
3806 | `(("r-annotationdbi" ,r-annotationdbi))) | |
3807 | (home-page "https://bioconductor.org/packages/a4Preproc/") | |
3808 | (synopsis "Automated Affymetrix array analysis preprocessing package") | |
3809 | (description | |
3810 | "This is a package for the automated analysis of Affymetrix arrays. It | |
3811 | is used for preprocessing the arrays.") | |
3812 | (license license:gpl3))) | |
8e15f861 RW |
3813 | |
3814 | (define-public r-a4reporting | |
3815 | (package | |
3816 | (name "r-a4reporting") | |
977a7802 | 3817 | (version "1.34.0") |
8e15f861 RW |
3818 | (source |
3819 | (origin | |
3820 | (method url-fetch) | |
3821 | (uri (bioconductor-uri "a4Reporting" version)) | |
3822 | (sha256 | |
3823 | (base32 | |
977a7802 | 3824 | "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5")))) |
8e15f861 RW |
3825 | (properties `((upstream-name . "a4Reporting"))) |
3826 | (build-system r-build-system) | |
3827 | (propagated-inputs | |
3828 | `(("r-annaffy" ,r-annaffy) | |
3829 | ("r-xtable" ,r-xtable))) | |
3830 | (home-page "https://bioconductor.org/packages/a4Reporting/") | |
3831 | (synopsis "Automated Affymetrix array analysis reporting package") | |
3832 | (description | |
3833 | "This is a package for the automated analysis of Affymetrix arrays. It | |
3834 | provides reporting features.") | |
3835 | (license license:gpl3))) | |
dbfe3375 RW |
3836 | |
3837 | (define-public r-a4base | |
3838 | (package | |
3839 | (name "r-a4base") | |
f4be4995 | 3840 | (version "1.34.1") |
dbfe3375 RW |
3841 | (source |
3842 | (origin | |
3843 | (method url-fetch) | |
3844 | (uri (bioconductor-uri "a4Base" version)) | |
3845 | (sha256 | |
3846 | (base32 | |
f4be4995 | 3847 | "1a0yk05ikk1hr1vpxynydrb5xb1hj4hdqlh9zd13n83ir89dss83")))) |
dbfe3375 RW |
3848 | (properties `((upstream-name . "a4Base"))) |
3849 | (build-system r-build-system) | |
3850 | (propagated-inputs | |
3851 | `(("r-a4core" ,r-a4core) | |
3852 | ("r-a4preproc" ,r-a4preproc) | |
3853 | ("r-annaffy" ,r-annaffy) | |
3854 | ("r-annotationdbi" ,r-annotationdbi) | |
3855 | ("r-biobase" ,r-biobase) | |
3856 | ("r-genefilter" ,r-genefilter) | |
3857 | ("r-glmnet" ,r-glmnet) | |
3858 | ("r-gplots" ,r-gplots) | |
3859 | ("r-limma" ,r-limma) | |
3860 | ("r-mpm" ,r-mpm) | |
3861 | ("r-multtest" ,r-multtest))) | |
3862 | (home-page "https://bioconductor.org/packages/a4Base/") | |
3863 | (synopsis "Automated Affymetrix array analysis base package") | |
3864 | (description | |
3865 | "This package provides basic features for the automated analysis of | |
3866 | Affymetrix arrays.") | |
3867 | (license license:gpl3))) | |
84ad024e RW |
3868 | |
3869 | (define-public r-a4 | |
3870 | (package | |
3871 | (name "r-a4") | |
344eb4c4 | 3872 | (version "1.34.0") |
84ad024e RW |
3873 | (source |
3874 | (origin | |
3875 | (method url-fetch) | |
3876 | (uri (bioconductor-uri "a4" version)) | |
3877 | (sha256 | |
3878 | (base32 | |
344eb4c4 | 3879 | "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4")))) |
84ad024e RW |
3880 | (build-system r-build-system) |
3881 | (propagated-inputs | |
3882 | `(("r-a4base" ,r-a4base) | |
3883 | ("r-a4classif" ,r-a4classif) | |
3884 | ("r-a4core" ,r-a4core) | |
3885 | ("r-a4preproc" ,r-a4preproc) | |
3886 | ("r-a4reporting" ,r-a4reporting))) | |
3887 | (home-page "https://bioconductor.org/packages/a4/") | |
3888 | (synopsis "Automated Affymetrix array analysis umbrella package") | |
3889 | (description | |
3890 | "This package provides a software suite for the automated analysis of | |
3891 | Affymetrix arrays.") | |
3892 | (license license:gpl3))) | |
59d331f1 RW |
3893 | |
3894 | (define-public r-abseqr | |
3895 | (package | |
3896 | (name "r-abseqr") | |
aef4b346 | 3897 | (version "1.4.0") |
59d331f1 RW |
3898 | (source |
3899 | (origin | |
3900 | (method url-fetch) | |
3901 | (uri (bioconductor-uri "abseqR" version)) | |
3902 | (sha256 | |
3903 | (base32 | |
aef4b346 | 3904 | "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa")))) |
59d331f1 RW |
3905 | (properties `((upstream-name . "abseqR"))) |
3906 | (build-system r-build-system) | |
3907 | (inputs | |
3908 | `(("pandoc" ,ghc-pandoc))) | |
3909 | (propagated-inputs | |
3910 | `(("r-biocparallel" ,r-biocparallel) | |
3911 | ("r-biocstyle" ,r-biocstyle) | |
3912 | ("r-circlize" ,r-circlize) | |
3913 | ("r-flexdashboard" ,r-flexdashboard) | |
3914 | ("r-ggcorrplot" ,r-ggcorrplot) | |
3915 | ("r-ggdendro" ,r-ggdendro) | |
3916 | ("r-ggplot2" ,r-ggplot2) | |
3917 | ("r-gridextra" ,r-gridextra) | |
3918 | ("r-knitr" ,r-knitr) | |
3919 | ("r-plotly" ,r-plotly) | |
3920 | ("r-plyr" ,r-plyr) | |
3921 | ("r-png" ,r-png) | |
3922 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3923 | ("r-reshape2" ,r-reshape2) | |
3924 | ("r-rmarkdown" ,r-rmarkdown) | |
3925 | ("r-stringr" ,r-stringr) | |
3926 | ("r-vegan" ,r-vegan) | |
3927 | ("r-venndiagram" ,r-venndiagram))) | |
3928 | (home-page "https://github.com/malhamdoosh/abseqR") | |
3929 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") | |
3930 | (description | |
3931 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of | |
3932 | sequencing datasets generated from antibody libraries and abseqR is one of its | |
3933 | packages. AbseqR empowers the users of abseqPy with plotting and reporting | |
3934 | capabilities and allows them to generate interactive HTML reports for the | |
3935 | convenience of viewing and sharing with other researchers. Additionally, | |
3936 | abseqR extends abseqPy to compare multiple repertoire analyses and perform | |
3937 | further downstream analysis on its output.") | |
3938 | (license license:gpl3))) | |
41aab7d1 RW |
3939 | |
3940 | (define-public r-bacon | |
3941 | (package | |
3942 | (name "r-bacon") | |
32b471f4 | 3943 | (version "1.14.0") |
41aab7d1 RW |
3944 | (source |
3945 | (origin | |
3946 | (method url-fetch) | |
3947 | (uri (bioconductor-uri "bacon" version)) | |
3948 | (sha256 | |
3949 | (base32 | |
32b471f4 | 3950 | "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86")))) |
41aab7d1 RW |
3951 | (build-system r-build-system) |
3952 | (propagated-inputs | |
3953 | `(("r-biocparallel" ,r-biocparallel) | |
3954 | ("r-ellipse" ,r-ellipse) | |
3955 | ("r-ggplot2" ,r-ggplot2))) | |
506cbeab RW |
3956 | (native-inputs |
3957 | `(("r-knitr" ,r-knitr))) | |
41aab7d1 RW |
3958 | (home-page "https://bioconductor.org/packages/bacon/") |
3959 | (synopsis "Controlling bias and inflation in association studies") | |
3960 | (description | |
3961 | "Bacon can be used to remove inflation and bias often observed in | |
3962 | epigenome- and transcriptome-wide association studies. To this end bacon | |
3963 | constructs an empirical null distribution using a Gibbs Sampling algorithm by | |
3964 | fitting a three-component normal mixture on z-scores.") | |
3965 | (license license:gpl2+))) | |
051e8e1a RW |
3966 | |
3967 | (define-public r-rgadem | |
3968 | (package | |
3969 | (name "r-rgadem") | |
07189489 | 3970 | (version "2.34.1") |
051e8e1a RW |
3971 | (source |
3972 | (origin | |
3973 | (method url-fetch) | |
3974 | (uri (bioconductor-uri "rGADEM" version)) | |
3975 | (sha256 | |
3976 | (base32 | |
07189489 | 3977 | "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h")))) |
051e8e1a RW |
3978 | (properties `((upstream-name . "rGADEM"))) |
3979 | (build-system r-build-system) | |
3980 | (propagated-inputs | |
3981 | `(("r-biostrings" ,r-biostrings) | |
3982 | ("r-bsgenome" ,r-bsgenome) | |
07189489 | 3983 | ("r-genomicranges" ,r-genomicranges) |
051e8e1a RW |
3984 | ("r-iranges" ,r-iranges) |
3985 | ("r-seqlogo" ,r-seqlogo))) | |
3986 | (home-page "https://bioconductor.org/packages/rGADEM/") | |
3987 | (synopsis "De novo sequence motif discovery") | |
3988 | (description | |
3989 | "rGADEM is an efficient de novo motif discovery tool for large-scale | |
3990 | genomic sequence data.") | |
3991 | (license license:artistic2.0))) | |
229f97c3 RW |
3992 | |
3993 | (define-public r-motiv | |
3994 | (package | |
3995 | (name "r-motiv") | |
35a1b3ec | 3996 | (version "1.42.0") |
229f97c3 RW |
3997 | (source |
3998 | (origin | |
3999 | (method url-fetch) | |
4000 | (uri (bioconductor-uri "MotIV" version)) | |
4001 | (sha256 | |
4002 | (base32 | |
35a1b3ec | 4003 | "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k")))) |
229f97c3 RW |
4004 | (properties `((upstream-name . "MotIV"))) |
4005 | (build-system r-build-system) | |
4006 | (inputs | |
4007 | `(("gsl" ,gsl))) | |
4008 | (propagated-inputs | |
4009 | `(("r-biocgenerics" ,r-biocgenerics) | |
4010 | ("r-biostrings" ,r-biostrings) | |
35a1b3ec | 4011 | ("r-genomicranges" ,r-genomicranges) |
229f97c3 RW |
4012 | ("r-iranges" ,r-iranges) |
4013 | ("r-lattice" ,r-lattice) | |
4014 | ("r-rgadem" ,r-rgadem) | |
4015 | ("r-s4vectors" ,r-s4vectors))) | |
4016 | (home-page "https://bioconductor.org/packages/MotIV/") | |
4017 | (synopsis "Motif identification and validation") | |
4018 | (description | |
4019 | "This package is used for the identification and validation of sequence | |
4020 | motifs. It makes use of STAMP for comparing a set of motifs to a given | |
4021 | database (e.g. JASPAR). It can also be used to visualize motifs, motif | |
4022 | distributions, modules and filter motifs.") | |
4023 | (license license:gpl2))) | |
2a72ef56 | 4024 | |
3699bcf5 RJ |
4025 | (define-public r-motifdb |
4026 | (package | |
4027 | (name "r-motifdb") | |
4028 | (version "1.28.0") | |
4029 | (source (origin | |
4030 | (method url-fetch) | |
4031 | (uri (bioconductor-uri "MotifDb" version)) | |
4032 | (sha256 | |
4033 | (base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc")))) | |
4034 | (properties `((upstream-name . "MotifDb"))) | |
4035 | (build-system r-build-system) | |
4036 | (propagated-inputs | |
4037 | `(("r-biocgenerics" ,r-biocgenerics) | |
4038 | ("r-biostrings" ,r-biostrings) | |
4039 | ("r-iranges" ,r-iranges) | |
4040 | ("r-rtracklayer" ,r-rtracklayer) | |
4041 | ("r-s4vectors" ,r-s4vectors) | |
4042 | ("r-splitstackshape" ,r-splitstackshape))) | |
4043 | (home-page "https://www.bioconductor.org/packages/MotifDb/") | |
4044 | (synopsis "Annotated collection of protein-DNA binding sequence motifs") | |
4045 | (description "This package provides more than 2000 annotated position | |
4046 | frequency matrices from nine public sources, for multiple organisms.") | |
4047 | (license license:artistic2.0))) | |
4048 | ||
886125d7 RJ |
4049 | (define-public r-motifbreakr |
4050 | (package | |
4051 | (name "r-motifbreakr") | |
4052 | (version "2.0.0") | |
4053 | (source (origin | |
4054 | (method url-fetch) | |
4055 | (uri (bioconductor-uri "motifbreakR" version)) | |
4056 | (sha256 | |
4057 | (base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n")))) | |
4058 | (properties `((upstream-name . "motifbreakR"))) | |
4059 | (build-system r-build-system) | |
4060 | (propagated-inputs | |
4061 | `(("r-grimport" ,r-grimport) | |
4062 | ("r-stringr" ,r-stringr) | |
4063 | ("r-biocgenerics" ,r-biocgenerics) | |
4064 | ("r-s4vectors" ,r-s4vectors) | |
4065 | ("r-iranges" ,r-iranges) | |
4066 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4067 | ("r-genomicranges" ,r-genomicranges) | |
4068 | ("r-biostrings" ,r-biostrings) | |
4069 | ("r-bsgenome" ,r-bsgenome) | |
4070 | ("r-rtracklayer" ,r-rtracklayer) | |
4071 | ("r-variantannotation" ,r-variantannotation) | |
4072 | ("r-biocparallel" ,r-biocparallel) | |
4073 | ("r-motifstack" ,r-motifstack) | |
4074 | ("r-gviz" ,r-gviz) | |
4075 | ("r-matrixstats" ,r-matrixstats) | |
4076 | ("r-tfmpvalue" ,r-tfmpvalue) | |
4077 | ("r-motifdb" ,r-motifdb))) | |
4078 | (home-page "https://www.bioconductor.org/packages/motifbreakR/") | |
4079 | (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") | |
4080 | (description "This package allows biologists to judge in the first place | |
4081 | whether the sequence surrounding the polymorphism is a good match, and in | |
4082 | the second place how much information is gained or lost in one allele of | |
4083 | the polymorphism relative to another. This package gives a choice of | |
4084 | algorithms for interrogation of genomes with motifs from public sources: | |
4085 | @enumerate | |
4086 | @item a weighted-sum probability matrix; | |
4087 | @item log-probabilities; | |
4088 | @item weighted by relative entropy. | |
4089 | @end enumerate | |
4090 | ||
4091 | This package can predict effects for novel or previously described variants in | |
4092 | public databases, making it suitable for tasks beyond the scope of its original | |
4093 | design. Lastly, it can be used to interrogate any genome curated within | |
4094 | Bioconductor.") | |
4095 | (license license:gpl2+))) | |
4096 | ||
2a72ef56 RW |
4097 | (define-public r-motifstack |
4098 | (package | |
4099 | (name "r-motifstack") | |
dda936ca | 4100 | (version "1.30.0") |
2a72ef56 RW |
4101 | (source |
4102 | (origin | |
4103 | (method url-fetch) | |
4104 | (uri (bioconductor-uri "motifStack" version)) | |
4105 | (sha256 | |
4106 | (base32 | |
dda936ca | 4107 | "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg")))) |
2a72ef56 RW |
4108 | (properties `((upstream-name . "motifStack"))) |
4109 | (build-system r-build-system) | |
4110 | (propagated-inputs | |
4111 | `(("r-ade4" ,r-ade4) | |
4112 | ("r-biostrings" ,r-biostrings) | |
dda936ca | 4113 | ("r-ggplot2" ,r-ggplot2) |
aa0ebfd2 | 4114 | ("r-grimport2" ,r-grimport2) |
2a72ef56 RW |
4115 | ("r-htmlwidgets" ,r-htmlwidgets) |
4116 | ("r-motiv" ,r-motiv) | |
4117 | ("r-scales" ,r-scales) | |
4118 | ("r-xml" ,r-xml))) | |
4119 | (home-page "https://bioconductor.org/packages/motifStack/") | |
4120 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") | |
4121 | (description | |
4122 | "The motifStack package is designed for graphic representation of | |
4123 | multiple motifs with different similarity scores. It works with both DNA/RNA | |
4124 | sequence motifs and amino acid sequence motifs. In addition, it provides the | |
4125 | flexibility for users to customize the graphic parameters such as the font | |
4126 | type and symbol colors.") | |
4127 | (license license:gpl2+))) | |
e5bff307 RW |
4128 | |
4129 | (define-public r-genomicscores | |
4130 | (package | |
4131 | (name "r-genomicscores") | |
e89f16e6 | 4132 | (version "1.10.0") |
e5bff307 RW |
4133 | (source |
4134 | (origin | |
4135 | (method url-fetch) | |
4136 | (uri (bioconductor-uri "GenomicScores" version)) | |
4137 | (sha256 | |
4138 | (base32 | |
e89f16e6 | 4139 | "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj")))) |
e5bff307 RW |
4140 | (properties `((upstream-name . "GenomicScores"))) |
4141 | (build-system r-build-system) | |
4142 | (propagated-inputs | |
4143 | `(("r-annotationhub" ,r-annotationhub) | |
4144 | ("r-biobase" ,r-biobase) | |
4145 | ("r-biocgenerics" ,r-biocgenerics) | |
4146 | ("r-biostrings" ,r-biostrings) | |
4147 | ("r-bsgenome" ,r-bsgenome) | |
4148 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4149 | ("r-genomicranges" ,r-genomicranges) | |
4150 | ("r-iranges" ,r-iranges) | |
4151 | ("r-s4vectors" ,r-s4vectors) | |
4152 | ("r-xml" ,r-xml))) | |
4153 | (home-page "https://github.com/rcastelo/GenomicScores/") | |
4154 | (synopsis "Work with genome-wide position-specific scores") | |
4155 | (description | |
4156 | "This package provides infrastructure to store and access genome-wide | |
4157 | position-specific scores within R and Bioconductor.") | |
4158 | (license license:artistic2.0))) | |
32e0f906 RW |
4159 | |
4160 | (define-public r-atacseqqc | |
4161 | (package | |
4162 | (name "r-atacseqqc") | |
9a6bc4c2 | 4163 | (version "1.10.4") |
32e0f906 RW |
4164 | (source |
4165 | (origin | |
4166 | (method url-fetch) | |
4167 | (uri (bioconductor-uri "ATACseqQC" version)) | |
4168 | (sha256 | |
4169 | (base32 | |
9a6bc4c2 | 4170 | "1g07ni134cyl3jd9y19afip39kxddfgpm1jjm0rhrm7jgssp24in")))) |
32e0f906 RW |
4171 | (properties `((upstream-name . "ATACseqQC"))) |
4172 | (build-system r-build-system) | |
4173 | (propagated-inputs | |
4174 | `(("r-biocgenerics" ,r-biocgenerics) | |
4175 | ("r-biostrings" ,r-biostrings) | |
4176 | ("r-bsgenome" ,r-bsgenome) | |
4177 | ("r-chippeakanno" ,r-chippeakanno) | |
bcc233c1 | 4178 | ("r-edger" ,r-edger) |
32e0f906 RW |
4179 | ("r-genomeinfodb" ,r-genomeinfodb) |
4180 | ("r-genomicalignments" ,r-genomicalignments) | |
4181 | ("r-genomicranges" ,r-genomicranges) | |
4182 | ("r-genomicscores" ,r-genomicscores) | |
4183 | ("r-iranges" ,r-iranges) | |
4184 | ("r-kernsmooth" ,r-kernsmooth) | |
4185 | ("r-limma" ,r-limma) | |
4186 | ("r-motifstack" ,r-motifstack) | |
4187 | ("r-preseqr" ,r-preseqr) | |
4188 | ("r-randomforest" ,r-randomforest) | |
4189 | ("r-rsamtools" ,r-rsamtools) | |
4190 | ("r-rtracklayer" ,r-rtracklayer) | |
4191 | ("r-s4vectors" ,r-s4vectors))) | |
dc30cc03 RW |
4192 | (native-inputs |
4193 | `(("r-knitr" ,r-knitr))) | |
32e0f906 RW |
4194 | (home-page "https://bioconductor.org/packages/ATACseqQC/") |
4195 | (synopsis "ATAC-seq quality control") | |
4196 | (description | |
4197 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using | |
4198 | sequencing, is a rapid and sensitive method for chromatin accessibility | |
4199 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq | |
4200 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly | |
4201 | assess whether their ATAC-seq experiment is successful. It includes | |
4202 | diagnostic plots of fragment size distribution, proportion of mitochondria | |
4203 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor | |
4204 | footprints.") | |
4205 | (license license:gpl2+))) | |
3972cfce RW |
4206 | |
4207 | (define-public r-gofuncr | |
4208 | (package | |
4209 | (name "r-gofuncr") | |
028fd6f7 | 4210 | (version "1.6.1") |
3972cfce RW |
4211 | (source |
4212 | (origin | |
4213 | (method url-fetch) | |
4214 | (uri (bioconductor-uri "GOfuncR" version)) | |
4215 | (sha256 | |
4216 | (base32 | |
028fd6f7 | 4217 | "1wk7ja6f5il8jx8v05ijzcs9pijp3b953h566ya66xp7dz5jg9rb")))) |
3972cfce RW |
4218 | (properties `((upstream-name . "GOfuncR"))) |
4219 | (build-system r-build-system) | |
4220 | (propagated-inputs | |
4221 | `(("r-annotationdbi" ,r-annotationdbi) | |
4222 | ("r-genomicranges" ,r-genomicranges) | |
4223 | ("r-gtools" ,r-gtools) | |
4224 | ("r-iranges" ,r-iranges) | |
4225 | ("r-mapplots" ,r-mapplots) | |
4226 | ("r-rcpp" ,r-rcpp) | |
4227 | ("r-vioplot" ,r-vioplot))) | |
028fd6f7 RW |
4228 | (native-inputs |
4229 | `(("r-knitr" ,r-knitr))) | |
3972cfce RW |
4230 | (home-page "https://bioconductor.org/packages/GOfuncR/") |
4231 | (synopsis "Gene ontology enrichment using FUNC") | |
4232 | (description | |
4233 | "GOfuncR performs a gene ontology enrichment analysis based on the | |
4234 | ontology enrichment software FUNC. GO-annotations are obtained from | |
4235 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is | |
4236 | included in the package and updated regularly. GOfuncR provides the standard | |
4237 | candidate vs background enrichment analysis using the hypergeometric test, as | |
4238 | well as three additional tests: | |
4239 | ||
4240 | @enumerate | |
4241 | @item the Wilcoxon rank-sum test that is used when genes are ranked, | |
4242 | @item a binomial test that is used when genes are associated with two counts, | |
4243 | and | |
4244 | @item a Chi-square or Fisher's exact test that is used in cases when genes are | |
4245 | associated with four counts. | |
4246 | @end enumerate | |
4247 | ||
4248 | To correct for multiple testing and interdependency of the tests, family-wise | |
4249 | error rates are computed based on random permutations of the gene-associated | |
4250 | variables. GOfuncR also provides tools for exploring the ontology graph and | |
4251 | the annotations, and options to take gene-length or spatial clustering of | |
4252 | genes into account. It is also possible to provide custom gene coordinates, | |
4253 | annotations and ontologies.") | |
4254 | (license license:gpl2+))) | |
9bf4bb19 RW |
4255 | |
4256 | (define-public r-abaenrichment | |
4257 | (package | |
4258 | (name "r-abaenrichment") | |
307667c4 | 4259 | (version "1.16.0") |
9bf4bb19 RW |
4260 | (source |
4261 | (origin | |
4262 | (method url-fetch) | |
4263 | (uri (bioconductor-uri "ABAEnrichment" version)) | |
4264 | (sha256 | |
4265 | (base32 | |
307667c4 | 4266 | "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp")))) |
9bf4bb19 RW |
4267 | (properties `((upstream-name . "ABAEnrichment"))) |
4268 | (build-system r-build-system) | |
4269 | (propagated-inputs | |
4270 | `(("r-abadata" ,r-abadata) | |
4271 | ("r-data-table" ,r-data-table) | |
4272 | ("r-gofuncr" ,r-gofuncr) | |
4273 | ("r-gplots" ,r-gplots) | |
4274 | ("r-gtools" ,r-gtools) | |
4275 | ("r-rcpp" ,r-rcpp))) | |
4276 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") | |
4277 | (synopsis "Gene expression enrichment in human brain regions") | |
4278 | (description | |
4279 | "The package ABAEnrichment is designed to test for enrichment of user | |
4280 | defined candidate genes in the set of expressed genes in different human brain | |
4281 | regions. The core function @code{aba_enrich} integrates the expression of the | |
4282 | candidate gene set (averaged across donors) and the structural information of | |
4283 | the brain using an ontology, both provided by the Allen Brain Atlas project.") | |
4284 | (license license:gpl2+))) | |
0b91b7b9 RW |
4285 | |
4286 | (define-public r-annotationfuncs | |
4287 | (package | |
4288 | (name "r-annotationfuncs") | |
3a731c83 | 4289 | (version "1.36.0") |
0b91b7b9 RW |
4290 | (source |
4291 | (origin | |
4292 | (method url-fetch) | |
4293 | (uri (bioconductor-uri "AnnotationFuncs" version)) | |
4294 | (sha256 | |
4295 | (base32 | |
3a731c83 | 4296 | "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq")))) |
0b91b7b9 RW |
4297 | (properties |
4298 | `((upstream-name . "AnnotationFuncs"))) | |
4299 | (build-system r-build-system) | |
4300 | (propagated-inputs | |
4301 | `(("r-annotationdbi" ,r-annotationdbi) | |
4302 | ("r-dbi" ,r-dbi))) | |
4303 | (home-page "https://www.iysik.com/r/annotationfuncs") | |
4304 | (synopsis "Annotation translation functions") | |
4305 | (description | |
4306 | "This package provides functions for handling translating between | |
4307 | different identifieres using the Biocore Data Team data-packages (e.g. | |
4308 | @code{org.Bt.eg.db}).") | |
4309 | (license license:gpl2))) | |
adf7d813 RW |
4310 | |
4311 | (define-public r-annotationtools | |
4312 | (package | |
4313 | (name "r-annotationtools") | |
eda49085 | 4314 | (version "1.60.0") |
adf7d813 RW |
4315 | (source |
4316 | (origin | |
4317 | (method url-fetch) | |
4318 | (uri (bioconductor-uri "annotationTools" version)) | |
4319 | (sha256 | |
4320 | (base32 | |
eda49085 | 4321 | "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i")))) |
adf7d813 RW |
4322 | (properties |
4323 | `((upstream-name . "annotationTools"))) | |
4324 | (build-system r-build-system) | |
4325 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4326 | (home-page "https://bioconductor.org/packages/annotationTools/") | |
4327 | (synopsis "Annotate microarrays and perform gene expression analyses") | |
4328 | (description | |
4329 | "This package provides functions to annotate microarrays, find orthologs, | |
4330 | and integrate heterogeneous gene expression profiles using annotation and | |
4331 | other molecular biology information available as flat file database (plain | |
4332 | text files).") | |
4333 | ;; Any version of the GPL. | |
4334 | (license (list license:gpl2+)))) | |
f31e10f8 RW |
4335 | |
4336 | (define-public r-allelicimbalance | |
4337 | (package | |
4338 | (name "r-allelicimbalance") | |
50e6f762 | 4339 | (version "1.24.0") |
f31e10f8 RW |
4340 | (source |
4341 | (origin | |
4342 | (method url-fetch) | |
4343 | (uri (bioconductor-uri "AllelicImbalance" version)) | |
4344 | (sha256 | |
4345 | (base32 | |
50e6f762 | 4346 | "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc")))) |
f31e10f8 RW |
4347 | (properties |
4348 | `((upstream-name . "AllelicImbalance"))) | |
4349 | (build-system r-build-system) | |
4350 | (propagated-inputs | |
4351 | `(("r-annotationdbi" ,r-annotationdbi) | |
4352 | ("r-biocgenerics" ,r-biocgenerics) | |
4353 | ("r-biostrings" ,r-biostrings) | |
4354 | ("r-bsgenome" ,r-bsgenome) | |
4355 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4356 | ("r-genomicalignments" ,r-genomicalignments) | |
4357 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4358 | ("r-genomicranges" ,r-genomicranges) | |
4359 | ("r-gridextra" ,r-gridextra) | |
4360 | ("r-gviz" ,r-gviz) | |
4361 | ("r-iranges" ,r-iranges) | |
4362 | ("r-lattice" ,r-lattice) | |
4363 | ("r-latticeextra" ,r-latticeextra) | |
4364 | ("r-nlme" ,r-nlme) | |
4365 | ("r-rsamtools" ,r-rsamtools) | |
4366 | ("r-s4vectors" ,r-s4vectors) | |
4367 | ("r-seqinr" ,r-seqinr) | |
4368 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
4369 | ("r-variantannotation" ,r-variantannotation))) | |
4370 | (home-page "https://github.com/pappewaio/AllelicImbalance") | |
4371 | (synopsis "Investigate allele-specific expression") | |
4372 | (description | |
4373 | "This package provides a framework for allele-specific expression | |
4374 | investigation using RNA-seq data.") | |
4375 | (license license:gpl3))) | |
ffe7029b RW |
4376 | |
4377 | (define-public r-aucell | |
4378 | (package | |
4379 | (name "r-aucell") | |
3a35d274 | 4380 | (version "1.8.0") |
ffe7029b RW |
4381 | (source |
4382 | (origin | |
4383 | (method url-fetch) | |
4384 | (uri (bioconductor-uri "AUCell" version)) | |
4385 | (sha256 | |
4386 | (base32 | |
3a35d274 | 4387 | "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky")))) |
ffe7029b RW |
4388 | (properties `((upstream-name . "AUCell"))) |
4389 | (build-system r-build-system) | |
4390 | (propagated-inputs | |
3a35d274 RW |
4391 | `(("r-biocgenerics" ,r-biocgenerics) |
4392 | ("r-data-table" ,r-data-table) | |
ffe7029b RW |
4393 | ("r-gseabase" ,r-gseabase) |
4394 | ("r-mixtools" ,r-mixtools) | |
4395 | ("r-r-utils" ,r-r-utils) | |
3a35d274 | 4396 | ("r-s4vectors" ,r-s4vectors) |
ffe7029b RW |
4397 | ("r-shiny" ,r-shiny) |
4398 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4399 | (home-page "https://bioconductor.org/packages/AUCell/") | |
4400 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") | |
4401 | (description | |
8c4bf6c2 | 4402 | "AUCell identifies cells with active gene sets (e.g. signatures, |
ffe7029b RW |
4403 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area |
4404 | Under the Curve} (AUC) to calculate whether a critical subset of the input | |
4405 | gene set is enriched within the expressed genes for each cell. The | |
4406 | distribution of AUC scores across all the cells allows exploring the relative | |
4407 | expression of the signature. Since the scoring method is ranking-based, | |
4408 | AUCell is independent of the gene expression units and the normalization | |
4409 | procedure. In addition, since the cells are evaluated individually, it can | |
4410 | easily be applied to bigger datasets, subsetting the expression matrix if | |
4411 | needed.") | |
4412 | (license license:gpl3))) | |
5cfa4bff RW |
4413 | |
4414 | (define-public r-ebimage | |
4415 | (package | |
4416 | (name "r-ebimage") | |
ca7192a1 | 4417 | (version "4.28.1") |
5cfa4bff RW |
4418 | (source |
4419 | (origin | |
4420 | (method url-fetch) | |
4421 | (uri (bioconductor-uri "EBImage" version)) | |
4422 | (sha256 | |
4423 | (base32 | |
ca7192a1 | 4424 | "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs")))) |
5cfa4bff RW |
4425 | (properties `((upstream-name . "EBImage"))) |
4426 | (build-system r-build-system) | |
4427 | (propagated-inputs | |
4428 | `(("r-abind" ,r-abind) | |
4429 | ("r-biocgenerics" ,r-biocgenerics) | |
4430 | ("r-fftwtools" ,r-fftwtools) | |
4431 | ("r-htmltools" ,r-htmltools) | |
4432 | ("r-htmlwidgets" ,r-htmlwidgets) | |
4433 | ("r-jpeg" ,r-jpeg) | |
4434 | ("r-locfit" ,r-locfit) | |
4435 | ("r-png" ,r-png) | |
4436 | ("r-rcurl" ,r-rcurl) | |
4437 | ("r-tiff" ,r-tiff))) | |
4438 | (native-inputs | |
4439 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
4440 | (home-page "https://github.com/aoles/EBImage") | |
4441 | (synopsis "Image processing and analysis toolbox for R") | |
4442 | (description | |
4443 | "EBImage provides general purpose functionality for image processing and | |
4444 | analysis. In the context of (high-throughput) microscopy-based cellular | |
4445 | assays, EBImage offers tools to segment cells and extract quantitative | |
4446 | cellular descriptors. This allows the automation of such tasks using the R | |
4447 | programming language and facilitates the use of other tools in the R | |
4448 | environment for signal processing, statistical modeling, machine learning and | |
4449 | visualization with image data.") | |
4450 | ;; Any version of the LGPL. | |
4451 | (license license:lgpl2.1+))) | |
51e98f7e RW |
4452 | |
4453 | (define-public r-yamss | |
4454 | (package | |
4455 | (name "r-yamss") | |
f0aaa448 | 4456 | (version "1.12.1") |
51e98f7e RW |
4457 | (source |
4458 | (origin | |
4459 | (method url-fetch) | |
4460 | (uri (bioconductor-uri "yamss" version)) | |
4461 | (sha256 | |
4462 | (base32 | |
f0aaa448 | 4463 | "12jr7hbrwhb1gfjadj1024hv80ra22miy46dn40nmsrbklkfn3rw")))) |
51e98f7e RW |
4464 | (build-system r-build-system) |
4465 | (propagated-inputs | |
4466 | `(("r-biocgenerics" ,r-biocgenerics) | |
4467 | ("r-data-table" ,r-data-table) | |
4468 | ("r-ebimage" ,r-ebimage) | |
4469 | ("r-iranges" ,r-iranges) | |
4470 | ("r-limma" ,r-limma) | |
4471 | ("r-matrix" ,r-matrix) | |
4472 | ("r-mzr" ,r-mzr) | |
4473 | ("r-s4vectors" ,r-s4vectors) | |
4474 | ("r-summarizedexperiment" | |
4475 | ,r-summarizedexperiment))) | |
4476 | (home-page "https://github.com/hansenlab/yamss") | |
4477 | (synopsis "Tools for high-throughput metabolomics") | |
4478 | (description | |
4479 | "This package provides tools to analyze and visualize high-throughput | |
9b19734c | 4480 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
51e98f7e RW |
4481 | preprocess data in a way that enables reliable and powerful differential |
4482 | analysis.") | |
4483 | (license license:artistic2.0))) | |
398c4a93 RW |
4484 | |
4485 | (define-public r-gtrellis | |
4486 | (package | |
4487 | (name "r-gtrellis") | |
cf0a1cb3 | 4488 | (version "1.18.0") |
398c4a93 RW |
4489 | (source |
4490 | (origin | |
4491 | (method url-fetch) | |
4492 | (uri (bioconductor-uri "gtrellis" version)) | |
4493 | (sha256 | |
4494 | (base32 | |
cf0a1cb3 | 4495 | "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z")))) |
398c4a93 RW |
4496 | (build-system r-build-system) |
4497 | (propagated-inputs | |
4498 | `(("r-circlize" ,r-circlize) | |
4499 | ("r-genomicranges" ,r-genomicranges) | |
4500 | ("r-getoptlong" ,r-getoptlong) | |
4501 | ("r-iranges" ,r-iranges))) | |
4502 | (home-page "https://github.com/jokergoo/gtrellis") | |
4503 | (synopsis "Genome level Trellis layout") | |
4504 | (description | |
4505 | "Genome level Trellis graph visualizes genomic data conditioned by | |
4506 | genomic categories (e.g. chromosomes). For each genomic category, multiple | |
4507 | dimensional data which are represented as tracks describe different features | |
4508 | from different aspects. This package provides high flexibility to arrange | |
4509 | genomic categories and to add self-defined graphics in the plot.") | |
4510 | (license license:expat))) | |
28098414 RW |
4511 | |
4512 | (define-public r-somaticsignatures | |
4513 | (package | |
4514 | (name "r-somaticsignatures") | |
4f8e0487 | 4515 | (version "2.22.0") |
28098414 RW |
4516 | (source |
4517 | (origin | |
4518 | (method url-fetch) | |
4519 | (uri (bioconductor-uri "SomaticSignatures" version)) | |
4520 | (sha256 | |
4521 | (base32 | |
4f8e0487 | 4522 | "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z")))) |
28098414 RW |
4523 | (properties |
4524 | `((upstream-name . "SomaticSignatures"))) | |
4525 | (build-system r-build-system) | |
4526 | (propagated-inputs | |
4527 | `(("r-biobase" ,r-biobase) | |
4528 | ("r-biostrings" ,r-biostrings) | |
4529 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4530 | ("r-genomicranges" ,r-genomicranges) | |
4531 | ("r-ggbio" ,r-ggbio) | |
4532 | ("r-ggplot2" ,r-ggplot2) | |
4533 | ("r-iranges" ,r-iranges) | |
4534 | ("r-nmf" ,r-nmf) | |
4535 | ("r-pcamethods" ,r-pcamethods) | |
4536 | ("r-proxy" ,r-proxy) | |
4537 | ("r-reshape2" ,r-reshape2) | |
4538 | ("r-s4vectors" ,r-s4vectors) | |
4539 | ("r-variantannotation" ,r-variantannotation))) | |
4540 | (home-page "https://github.com/juliangehring/SomaticSignatures") | |
4541 | (synopsis "Somatic signatures") | |
4542 | (description | |
4543 | "This package identifies mutational signatures of @dfn{single nucleotide | |
4544 | variants} (SNVs). It provides a infrastructure related to the methodology | |
4545 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix | |
4546 | decomposition algorithms.") | |
4547 | (license license:expat))) | |
303f2ed1 RW |
4548 | |
4549 | (define-public r-yapsa | |
4550 | (package | |
4551 | (name "r-yapsa") | |
580e4342 | 4552 | (version "1.12.0") |
303f2ed1 RW |
4553 | (source |
4554 | (origin | |
4555 | (method url-fetch) | |
4556 | (uri (bioconductor-uri "YAPSA" version)) | |
4557 | (sha256 | |
4558 | (base32 | |
580e4342 | 4559 | "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926")))) |
303f2ed1 RW |
4560 | (properties `((upstream-name . "YAPSA"))) |
4561 | (build-system r-build-system) | |
4562 | (propagated-inputs | |
4563 | `(("r-circlize" ,r-circlize) | |
4564 | ("r-complexheatmap" ,r-complexheatmap) | |
4565 | ("r-corrplot" ,r-corrplot) | |
4566 | ("r-dendextend" ,r-dendextend) | |
4567 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4568 | ("r-genomicranges" ,r-genomicranges) | |
4569 | ("r-getoptlong" ,r-getoptlong) | |
4570 | ("r-ggplot2" ,r-ggplot2) | |
4571 | ("r-gridextra" ,r-gridextra) | |
4572 | ("r-gtrellis" ,r-gtrellis) | |
4573 | ("r-keggrest" ,r-keggrest) | |
4574 | ("r-lsei" ,r-lsei) | |
4575 | ("r-pmcmr" ,r-pmcmr) | |
4576 | ("r-reshape2" ,r-reshape2) | |
4577 | ("r-somaticsignatures" ,r-somaticsignatures) | |
4578 | ("r-variantannotation" ,r-variantannotation))) | |
4579 | (home-page "https://bioconductor.org/packages/YAPSA/") | |
4580 | (synopsis "Yet another package for signature analysis") | |
4581 | (description | |
4582 | "This package provides functions and routines useful in the analysis of | |
4583 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, | |
4584 | functions to perform a signature analysis with known signatures and a | |
4585 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are | |
4586 | provided.") | |
4587 | (license license:gpl3))) | |
e99380d6 RW |
4588 | |
4589 | (define-public r-gcrma | |
4590 | (package | |
4591 | (name "r-gcrma") | |
2f90bab8 | 4592 | (version "2.58.0") |
e99380d6 RW |
4593 | (source |
4594 | (origin | |
4595 | (method url-fetch) | |
4596 | (uri (bioconductor-uri "gcrma" version)) | |
4597 | (sha256 | |
4598 | (base32 | |
2f90bab8 | 4599 | "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx")))) |
e99380d6 RW |
4600 | (build-system r-build-system) |
4601 | (propagated-inputs | |
4602 | `(("r-affy" ,r-affy) | |
4603 | ("r-affyio" ,r-affyio) | |
4604 | ("r-biobase" ,r-biobase) | |
4605 | ("r-biocmanager" ,r-biocmanager) | |
4606 | ("r-biostrings" ,r-biostrings) | |
4607 | ("r-xvector" ,r-xvector))) | |
4608 | (home-page "https://bioconductor.org/packages/gcrma/") | |
4609 | (synopsis "Background adjustment using sequence information") | |
4610 | (description | |
4611 | "Gcrma adjusts for background intensities in Affymetrix array data which | |
4612 | include optical noise and @dfn{non-specific binding} (NSB). The main function | |
4613 | @code{gcrma} converts background adjusted probe intensities to expression | |
4614 | measures using the same normalization and summarization methods as a | |
4615 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information | |
4616 | to estimate probe affinity to NSB. The sequence information is summarized in | |
4617 | a more complex way than the simple GC content. Instead, the base types (A, T, | |
4618 | G or C) at each position along the probe determine the affinity of each probe. | |
4619 | The parameters of the position-specific base contributions to the probe | |
4620 | affinity is estimated in an NSB experiment in which only NSB but no | |
4621 | gene-specific bidning is expected.") | |
4622 | ;; Any version of the LGPL | |
4623 | (license license:lgpl2.1+))) | |
4675b3cf RW |
4624 | |
4625 | (define-public r-simpleaffy | |
4626 | (package | |
4627 | (name "r-simpleaffy") | |
a87aa2ff | 4628 | (version "2.62.0") |
4675b3cf RW |
4629 | (source |
4630 | (origin | |
4631 | (method url-fetch) | |
4632 | (uri (bioconductor-uri "simpleaffy" version)) | |
4633 | (sha256 | |
4634 | (base32 | |
a87aa2ff | 4635 | "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs")))) |
4675b3cf RW |
4636 | (build-system r-build-system) |
4637 | (propagated-inputs | |
4638 | `(("r-affy" ,r-affy) | |
4639 | ("r-biobase" ,r-biobase) | |
4640 | ("r-biocgenerics" ,r-biocgenerics) | |
4641 | ("r-gcrma" ,r-gcrma) | |
4642 | ("r-genefilter" ,r-genefilter))) | |
4643 | (home-page "https://bioconductor.org/packages/simpleaffy/") | |
4644 | (synopsis "Very simple high level analysis of Affymetrix data") | |
4645 | (description | |
4646 | "This package provides high level functions for reading Affy @file{.CEL} | |
4647 | files, phenotypic data, and then computing simple things with it, such as | |
4648 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} | |
4649 | library. It also has some basic scatter plot functions and mechanisms for | |
4650 | generating high resolution journal figures.") | |
4651 | (license license:gpl2+))) | |
f562c90a RW |
4652 | |
4653 | (define-public r-yaqcaffy | |
4654 | (package | |
4655 | (name "r-yaqcaffy") | |
87942b74 | 4656 | (version "1.46.0") |
f562c90a RW |
4657 | (source |
4658 | (origin | |
4659 | (method url-fetch) | |
4660 | (uri (bioconductor-uri "yaqcaffy" version)) | |
4661 | (sha256 | |
4662 | (base32 | |
87942b74 | 4663 | "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz")))) |
f562c90a RW |
4664 | (build-system r-build-system) |
4665 | (propagated-inputs | |
4666 | `(("r-simpleaffy" ,r-simpleaffy))) | |
4667 | (home-page "https://bioconductor.org/packages/yaqcaffy/") | |
4668 | (synopsis "Affymetrix quality control and reproducibility analysis") | |
4669 | (description | |
4670 | "This is a package that can be used for quality control of Affymetrix | |
4671 | GeneChip expression data and reproducibility analysis of human whole genome | |
4672 | chips with the MAQC reference datasets.") | |
4673 | (license license:artistic2.0))) | |
59cf2629 RW |
4674 | |
4675 | (define-public r-quantro | |
4676 | (package | |
4677 | (name "r-quantro") | |
eb697ff5 | 4678 | (version "1.20.0") |
59cf2629 RW |
4679 | (source |
4680 | (origin | |
4681 | (method url-fetch) | |
4682 | (uri (bioconductor-uri "quantro" version)) | |
4683 | (sha256 | |
4684 | (base32 | |
eb697ff5 | 4685 | "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m")))) |
59cf2629 RW |
4686 | (build-system r-build-system) |
4687 | (propagated-inputs | |
4688 | `(("r-biobase" ,r-biobase) | |
4689 | ("r-doparallel" ,r-doparallel) | |
4690 | ("r-foreach" ,r-foreach) | |
4691 | ("r-ggplot2" ,r-ggplot2) | |
4692 | ("r-iterators" ,r-iterators) | |
4693 | ("r-minfi" ,r-minfi) | |
4694 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
4695 | (home-page "https://bioconductor.org/packages/quantro/") | |
4696 | (synopsis "Test for when to use quantile normalization") | |
4697 | (description | |
4698 | "This package provides a data-driven test for the assumptions of quantile | |
4699 | normalization using raw data such as objects that inherit eSets (e.g. | |
4700 | ExpressionSet, MethylSet). Group level information about each sample (such as | |
4701 | Tumor / Normal status) must also be provided because the test assesses if | |
4702 | there are global differences in the distributions between the user-defined | |
4703 | groups.") | |
4704 | (license license:gpl3+))) | |
98a2af31 RW |
4705 | |
4706 | (define-public r-yarn | |
4707 | (package | |
4708 | (name "r-yarn") | |
94fdea12 | 4709 | (version "1.12.0") |
98a2af31 RW |
4710 | (source |
4711 | (origin | |
4712 | (method url-fetch) | |
4713 | (uri (bioconductor-uri "yarn" version)) | |
4714 | (sha256 | |
4715 | (base32 | |
94fdea12 | 4716 | "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp")))) |
98a2af31 RW |
4717 | (build-system r-build-system) |
4718 | (propagated-inputs | |
4719 | `(("r-biobase" ,r-biobase) | |
4720 | ("r-biomart" ,r-biomart) | |
4721 | ("r-downloader" ,r-downloader) | |
4722 | ("r-edger" ,r-edger) | |
4723 | ("r-gplots" ,r-gplots) | |
4724 | ("r-limma" ,r-limma) | |
4725 | ("r-matrixstats" ,r-matrixstats) | |
4726 | ("r-preprocesscore" ,r-preprocesscore) | |
4727 | ("r-quantro" ,r-quantro) | |
4728 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4729 | ("r-readr" ,r-readr))) | |
4730 | (home-page "https://bioconductor.org/packages/yarn/") | |
4731 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") | |
4732 | (description | |
4733 | "Expedite large RNA-Seq analyses using a combination of previously | |
4734 | developed tools. YARN is meant to make it easier for the user in performing | |
4735 | basic mis-annotation quality control, filtering, and condition-aware | |
4736 | normalization. YARN leverages many Bioconductor tools and statistical | |
4737 | techniques to account for the large heterogeneity and sparsity found in very | |
4738 | large RNA-seq experiments.") | |
4739 | (license license:artistic2.0))) | |
a6e1eb1a RW |
4740 | |
4741 | (define-public r-roar | |
4742 | (package | |
4743 | (name "r-roar") | |
f0dd0fec | 4744 | (version "1.22.0") |
a6e1eb1a RW |
4745 | (source |
4746 | (origin | |
4747 | (method url-fetch) | |
4748 | (uri (bioconductor-uri "roar" version)) | |
4749 | (sha256 | |
4750 | (base32 | |
f0dd0fec | 4751 | "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06")))) |
a6e1eb1a RW |
4752 | (build-system r-build-system) |
4753 | (propagated-inputs | |
4754 | `(("r-biocgenerics" ,r-biocgenerics) | |
4755 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4756 | ("r-genomicalignments" ,r-genomicalignments) | |
4757 | ("r-genomicranges" ,r-genomicranges) | |
4758 | ("r-iranges" ,r-iranges) | |
4759 | ("r-rtracklayer" ,r-rtracklayer) | |
4760 | ("r-s4vectors" ,r-s4vectors) | |
4761 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4762 | (home-page "https://github.com/vodkatad/roar/") | |
4763 | (synopsis "Identify differential APA usage from RNA-seq alignments") | |
4764 | (description | |
4765 | "This package provides tools for identifying preferential usage of APA | |
4766 | sites, comparing two biological conditions, starting from known alternative | |
4767 | sites and alignments obtained from standard RNA-seq experiments.") | |
4768 | (license license:gpl3))) | |
50d91770 RW |
4769 | |
4770 | (define-public r-xbseq | |
4771 | (package | |
4772 | (name "r-xbseq") | |
1f0101ae | 4773 | (version "1.18.0") |
50d91770 RW |
4774 | (source |
4775 | (origin | |
4776 | (method url-fetch) | |
4777 | (uri (bioconductor-uri "XBSeq" version)) | |
4778 | (sha256 | |
4779 | (base32 | |
1f0101ae | 4780 | "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp")))) |
50d91770 RW |
4781 | (properties `((upstream-name . "XBSeq"))) |
4782 | (build-system r-build-system) | |
4783 | (propagated-inputs | |
4784 | `(("r-biobase" ,r-biobase) | |
4785 | ("r-deseq2" ,r-deseq2) | |
4786 | ("r-dplyr" ,r-dplyr) | |
4787 | ("r-ggplot2" ,r-ggplot2) | |
4788 | ("r-locfit" ,r-locfit) | |
4789 | ("r-magrittr" ,r-magrittr) | |
4790 | ("r-matrixstats" ,r-matrixstats) | |
4791 | ("r-pracma" ,r-pracma) | |
4792 | ("r-roar" ,r-roar))) | |
4793 | (home-page "https://github.com/Liuy12/XBSeq") | |
4794 | (synopsis "Test for differential expression for RNA-seq data") | |
4795 | (description | |
4796 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential | |
4797 | expression} (DE), where a statistical model was established based on the | |
4798 | assumption that observed signals are the convolution of true expression | |
4799 | signals and sequencing noises. The mapped reads in non-exonic regions are | |
4800 | considered as sequencing noises, which follows a Poisson distribution. Given | |
4801 | measurable observed signal and background noise from RNA-seq data, true | |
4802 | expression signals, assuming governed by the negative binomial distribution, | |
4803 | can be delineated and thus the accurate detection of differential expressed | |
4804 | genes.") | |
4805 | (license license:gpl3+))) | |
c8310056 RW |
4806 | |
4807 | (define-public r-massspecwavelet | |
4808 | (package | |
4809 | (name "r-massspecwavelet") | |
a07ee258 | 4810 | (version "1.52.0") |
c8310056 RW |
4811 | (source |
4812 | (origin | |
4813 | (method url-fetch) | |
4814 | (uri (bioconductor-uri "MassSpecWavelet" version)) | |
4815 | (sha256 | |
4816 | (base32 | |
a07ee258 | 4817 | "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7")))) |
c8310056 RW |
4818 | (properties |
4819 | `((upstream-name . "MassSpecWavelet"))) | |
4820 | (build-system r-build-system) | |
4821 | (propagated-inputs | |
4822 | `(("r-waveslim" ,r-waveslim))) | |
4823 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") | |
4824 | (synopsis "Mass spectrum processing by wavelet-based algorithms") | |
4825 | (description | |
4826 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) | |
4827 | data mainly through the use of wavelet transforms. It supports peak detection | |
4828 | based on @dfn{Continuous Wavelet Transform} (CWT).") | |
4829 | (license license:lgpl2.0+))) | |
ec12e537 RW |
4830 | |
4831 | (define-public r-xcms | |
4832 | (package | |
4833 | (name "r-xcms") | |
a2512e43 | 4834 | (version "3.8.2") |
ec12e537 RW |
4835 | (source |
4836 | (origin | |
4837 | (method url-fetch) | |
4838 | (uri (bioconductor-uri "xcms" version)) | |
4839 | (sha256 | |
4840 | (base32 | |
a2512e43 | 4841 | "0bfl56v3l6k31i11l09nx1yqfjy6z5yragm6k83z4w0mpgk18y7g")))) |
ec12e537 RW |
4842 | (build-system r-build-system) |
4843 | (propagated-inputs | |
4844 | `(("r-biobase" ,r-biobase) | |
4845 | ("r-biocgenerics" ,r-biocgenerics) | |
4846 | ("r-biocparallel" ,r-biocparallel) | |
4fb52345 | 4847 | ("r-iranges" ,r-iranges) |
ec12e537 RW |
4848 | ("r-lattice" ,r-lattice) |
4849 | ("r-massspecwavelet" ,r-massspecwavelet) | |
4850 | ("r-msnbase" ,r-msnbase) | |
4851 | ("r-multtest" ,r-multtest) | |
4852 | ("r-mzr" ,r-mzr) | |
4853 | ("r-plyr" ,r-plyr) | |
4854 | ("r-protgenerics" ,r-protgenerics) | |
4855 | ("r-rann" ,r-rann) | |
4856 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4857 | ("r-robustbase" ,r-robustbase) | |
4858 | ("r-s4vectors" ,r-s4vectors))) | |
4859 | (home-page "https://bioconductor.org/packages/xcms/") | |
4860 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") | |
4861 | (description | |
4862 | "This package provides a framework for processing and visualization of | |
4863 | chromatographically separated and single-spectra mass spectral data. It | |
4864 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses | |
4865 | data for high-throughput, untargeted analyte profiling.") | |
4866 | (license license:gpl2+))) | |
8830664d RW |
4867 | |
4868 | (define-public r-wrench | |
4869 | (package | |
4870 | (name "r-wrench") | |
92f40538 | 4871 | (version "1.4.0") |
8830664d RW |
4872 | (source |
4873 | (origin | |
4874 | (method url-fetch) | |
4875 | (uri (bioconductor-uri "Wrench" version)) | |
4876 | (sha256 | |
4877 | (base32 | |
92f40538 | 4878 | "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm")))) |
8830664d RW |
4879 | (properties `((upstream-name . "Wrench"))) |
4880 | (build-system r-build-system) | |
4881 | (propagated-inputs | |
4882 | `(("r-limma" ,r-limma) | |
4883 | ("r-locfit" ,r-locfit) | |
4884 | ("r-matrixstats" ,r-matrixstats))) | |
4885 | (home-page "https://github.com/HCBravoLab/Wrench") | |
4886 | (synopsis "Wrench normalization for sparse count data") | |
4887 | (description | |
4888 | "Wrench is a package for normalization sparse genomic count data, like | |
4889 | that arising from 16s metagenomic surveys.") | |
4890 | (license license:artistic2.0))) | |
b9b8b447 RW |
4891 | |
4892 | (define-public r-wiggleplotr | |
4893 | (package | |
4894 | (name "r-wiggleplotr") | |
25db5611 | 4895 | (version "1.10.1") |
b9b8b447 RW |
4896 | (source |
4897 | (origin | |
4898 | (method url-fetch) | |
4899 | (uri (bioconductor-uri "wiggleplotr" version)) | |
4900 | (sha256 | |
4901 | (base32 | |
25db5611 | 4902 | "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m")))) |
b9b8b447 RW |
4903 | (build-system r-build-system) |
4904 | (propagated-inputs | |
4905 | `(("r-assertthat" ,r-assertthat) | |
4906 | ("r-cowplot" ,r-cowplot) | |
4907 | ("r-dplyr" ,r-dplyr) | |
4908 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4909 | ("r-genomicranges" ,r-genomicranges) | |
4910 | ("r-ggplot2" ,r-ggplot2) | |
4911 | ("r-iranges" ,r-iranges) | |
4912 | ("r-purrr" ,r-purrr) | |
4913 | ("r-rtracklayer" ,r-rtracklayer) | |
4914 | ("r-s4vectors" ,r-s4vectors))) | |
4915 | (home-page "https://bioconductor.org/packages/wiggleplotr/") | |
4916 | (synopsis "Make read coverage plots from BigWig files") | |
4917 | (description | |
4918 | "This package provides tools to visualize read coverage from sequencing | |
4919 | experiments together with genomic annotations (genes, transcripts, peaks). | |
4920 | Introns of long transcripts can be rescaled to a fixed length for better | |
4921 | visualization of exonic read coverage.") | |
4922 | (license license:asl2.0))) | |
7b5101c5 RW |
4923 | |
4924 | (define-public r-widgettools | |
4925 | (package | |
4926 | (name "r-widgettools") | |
1a2569e4 | 4927 | (version "1.64.0") |
7b5101c5 RW |
4928 | (source |
4929 | (origin | |
4930 | (method url-fetch) | |
4931 | (uri (bioconductor-uri "widgetTools" version)) | |
4932 | (sha256 | |
4933 | (base32 | |
1a2569e4 | 4934 | "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5")))) |
7b5101c5 RW |
4935 | (properties `((upstream-name . "widgetTools"))) |
4936 | (build-system r-build-system) | |
4937 | (home-page "https://bioconductor.org/packages/widgetTools/") | |
4938 | (synopsis "Tools for creating interactive tcltk widgets") | |
4939 | (description | |
337bdc17 | 4940 | "This package contains tools to support the construction of tcltk |
7b5101c5 RW |
4941 | widgets in R.") |
4942 | ;; Any version of the LGPL. | |
4943 | (license license:lgpl3+))) | |
6b12f213 RW |
4944 | |
4945 | (define-public r-webbioc | |
4946 | (package | |
4947 | (name "r-webbioc") | |
316bcd07 | 4948 | (version "1.58.0") |
6b12f213 RW |
4949 | (source |
4950 | (origin | |
4951 | (method url-fetch) | |
4952 | (uri (bioconductor-uri "webbioc" version)) | |
4953 | (sha256 | |
4954 | (base32 | |
316bcd07 | 4955 | "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62")))) |
6b12f213 RW |
4956 | (build-system r-build-system) |
4957 | (inputs | |
4958 | `(("netpbm" ,netpbm) | |
4959 | ("perl" ,perl))) | |
4960 | (propagated-inputs | |
4961 | `(("r-affy" ,r-affy) | |
4962 | ("r-annaffy" ,r-annaffy) | |
4963 | ("r-biobase" ,r-biobase) | |
4964 | ("r-biocmanager" ,r-biocmanager) | |
4965 | ("r-gcrma" ,r-gcrma) | |
4966 | ("r-multtest" ,r-multtest) | |
4967 | ("r-qvalue" ,r-qvalue) | |
4968 | ("r-vsn" ,r-vsn))) | |
4969 | (home-page "https://www.bioconductor.org/") | |
4970 | (synopsis "Bioconductor web interface") | |
4971 | (description | |
4972 | "This package provides an integrated web interface for doing microarray | |
4973 | analysis using several of the Bioconductor packages. It is intended to be | |
4974 | deployed as a centralized bioinformatics resource for use by many users. | |
4975 | Currently only Affymetrix oligonucleotide analysis is supported.") | |
4976 | (license license:gpl2+))) | |
9800d859 RW |
4977 | |
4978 | (define-public r-zfpkm | |
4979 | (package | |
4980 | (name "r-zfpkm") | |
18b93e03 | 4981 | (version "1.8.0") |
9800d859 RW |
4982 | (source |
4983 | (origin | |
4984 | (method url-fetch) | |
4985 | (uri (bioconductor-uri "zFPKM" version)) | |
4986 | (sha256 | |
4987 | (base32 | |
18b93e03 | 4988 | "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n")))) |
9800d859 RW |
4989 | (properties `((upstream-name . "zFPKM"))) |
4990 | (build-system r-build-system) | |
4991 | (propagated-inputs | |
4992 | `(("r-checkmate" ,r-checkmate) | |
4993 | ("r-dplyr" ,r-dplyr) | |
4994 | ("r-ggplot2" ,r-ggplot2) | |
4995 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
4996 | ("r-tidyr" ,r-tidyr))) | |
4997 | (home-page "https://github.com/ronammar/zFPKM/") | |
4998 | (synopsis "Functions to facilitate zFPKM transformations") | |
4999 | (description | |
5000 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. | |
5001 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID | |
5002 | 24215113).") | |
5003 | (license license:gpl3))) | |
2bdc88fc RW |
5004 | |
5005 | (define-public r-rbowtie2 | |
5006 | (package | |
5007 | (name "r-rbowtie2") | |
c5a4c5a1 | 5008 | (version "1.8.0") |
2bdc88fc RW |
5009 | (source |
5010 | (origin | |
5011 | (method url-fetch) | |
5012 | (uri (bioconductor-uri "Rbowtie2" version)) | |
5013 | (sha256 | |
5014 | (base32 | |
c5a4c5a1 | 5015 | "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5")))) |
2bdc88fc RW |
5016 | (properties `((upstream-name . "Rbowtie2"))) |
5017 | (build-system r-build-system) | |
5018 | (inputs | |
5019 | `(("zlib" ,zlib))) | |
5020 | (home-page "https://bioconductor.org/packages/Rbowtie2/") | |
5021 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") | |
5022 | (description | |
5023 | "This package provides an R wrapper of the popular @code{bowtie2} | |
5024 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for | |
5025 | rapid adapter trimming, identification, and read merging.") | |
5026 | (license license:gpl3+))) | |
5622628f RW |
5027 | |
5028 | (define-public r-progeny | |
5029 | (package | |
5030 | (name "r-progeny") | |
82d87ce0 | 5031 | (version "1.8.0") |
5622628f RW |
5032 | (source |
5033 | (origin | |
5034 | (method url-fetch) | |
5035 | (uri (bioconductor-uri "progeny" version)) | |
5036 | (sha256 | |
5037 | (base32 | |
82d87ce0 | 5038 | "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq")))) |
5622628f RW |
5039 | (build-system r-build-system) |
5040 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
5041 | (home-page "https://github.com/saezlab/progeny") | |
5042 | (synopsis "Pathway responsive gene activity inference") | |
5043 | (description | |
5044 | "This package provides a function to infer pathway activity from gene | |
5045 | expression. It contains the linear model inferred in the publication | |
5046 | \"Perturbation-response genes reveal signaling footprints in cancer gene | |
5047 | expression\".") | |
5048 | (license license:asl2.0))) | |
307586c1 RW |
5049 | |
5050 | (define-public r-arrmnormalization | |
5051 | (package | |
5052 | (name "r-arrmnormalization") | |
4f0d8588 | 5053 | (version "1.26.0") |
307586c1 RW |
5054 | (source |
5055 | (origin | |
5056 | (method url-fetch) | |
5057 | (uri (bioconductor-uri "ARRmNormalization" version)) | |
5058 | (sha256 | |
5059 | (base32 | |
4f0d8588 | 5060 | "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1")))) |
307586c1 RW |
5061 | (properties |
5062 | `((upstream-name . "ARRmNormalization"))) | |
5063 | (build-system r-build-system) | |
5064 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) | |
5065 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") | |
5066 | (synopsis "Adaptive robust regression normalization for methylation data") | |
5067 | (description | |
5068 | "This is a package to perform the @dfn{Adaptive Robust Regression | |
5069 | method} (ARRm) for the normalization of methylation data from the Illumina | |
5070 | Infinium HumanMethylation 450k assay.") | |
5071 | (license license:artistic2.0))) | |
fbf34949 RW |
5072 | |
5073 | (define-public r-biocfilecache | |
5074 | (package | |
5075 | (name "r-biocfilecache") | |
97e31700 | 5076 | (version "1.10.2") |
fbf34949 RW |
5077 | (source |
5078 | (origin | |
5079 | (method url-fetch) | |
5080 | (uri (bioconductor-uri "BiocFileCache" version)) | |
5081 | (sha256 | |
5082 | (base32 | |
97e31700 | 5083 | "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6")))) |
fbf34949 RW |
5084 | (properties `((upstream-name . "BiocFileCache"))) |
5085 | (build-system r-build-system) | |
5086 | (propagated-inputs | |
5087 | `(("r-curl" ,r-curl) | |
5088 | ("r-dbi" ,r-dbi) | |
5089 | ("r-dbplyr" ,r-dbplyr) | |
5090 | ("r-dplyr" ,r-dplyr) | |
5091 | ("r-httr" ,r-httr) | |
5092 | ("r-rappdirs" ,r-rappdirs) | |
5093 | ("r-rsqlite" ,r-rsqlite))) | |
5094 | (home-page "https://bioconductor.org/packages/BiocFileCache/") | |
5095 | (synopsis "Manage files across sessions") | |
5096 | (description | |
5097 | "This package creates a persistent on-disk cache of files that the user | |
5098 | can add, update, and retrieve. It is useful for managing resources (such as | |
5099 | custom Txdb objects) that are costly or difficult to create, web resources, | |
5100 | and data files used across sessions.") | |
5101 | (license license:artistic2.0))) | |
8c42f8f6 RW |
5102 | |
5103 | (define-public r-iclusterplus | |
5104 | (package | |
5105 | (name "r-iclusterplus") | |
049de95d | 5106 | (version "1.22.0") |
8c42f8f6 RW |
5107 | (source |
5108 | (origin | |
5109 | (method url-fetch) | |
5110 | (uri (bioconductor-uri "iClusterPlus" version)) | |
5111 | (sha256 | |
5112 | (base32 | |
049de95d | 5113 | "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37")))) |
8c42f8f6 RW |
5114 | (properties `((upstream-name . "iClusterPlus"))) |
5115 | (build-system r-build-system) | |
5116 | (native-inputs `(("gfortran" ,gfortran))) | |
5117 | (home-page "https://bioconductor.org/packages/iClusterPlus/") | |
5118 | (synopsis "Integrative clustering of multi-type genomic data") | |
5119 | (description | |
5120 | "iClusterPlus is developed for integrative clustering analysis of | |
5121 | multi-type genomic data and is an enhanced version of iCluster proposed and | |
5122 | developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise | |
5123 | from the experiments where biological samples (e.g. tumor samples) are | |
5124 | analyzed by multiple techniques, for instance, @dfn{array comparative genomic | |
5125 | hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so | |
5126 | on. In the iClusterPlus model, binary observations such as somatic mutation | |
5127 | are modeled as Binomial processes; categorical observations such as copy | |
5128 | number states are realizations of Multinomial random variables; counts are | |
5129 | modeled as Poisson random processes; and continuous measures are modeled by | |
5130 | Gaussian distributions.") | |
5131 | (license license:gpl2+))) | |
4d06ef4b RW |
5132 | |
5133 | (define-public r-rbowtie | |
5134 | (package | |
5135 | (name "r-rbowtie") | |
02684bec | 5136 | (version "1.26.0") |
4d06ef4b RW |
5137 | (source |
5138 | (origin | |
5139 | (method url-fetch) | |
5140 | (uri (bioconductor-uri "Rbowtie" version)) | |
5141 | (sha256 | |
5142 | (base32 | |
02684bec | 5143 | "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4")))) |
4d06ef4b RW |
5144 | (properties `((upstream-name . "Rbowtie"))) |
5145 | (build-system r-build-system) | |
5146 | (inputs | |
5147 | `(("zlib" ,zlib))) | |
5148 | (home-page "https://bioconductor.org/packages/Rbowtie/") | |
5149 | (synopsis "R bowtie wrapper") | |
5150 | (description | |
5151 | "This package provides an R wrapper around the popular bowtie short read | |
5152 | aligner and around SpliceMap, a de novo splice junction discovery and | |
5153 | alignment tool.") | |
5154 | (license license:artistic2.0))) | |
14441539 RW |
5155 | |
5156 | (define-public r-sgseq | |
5157 | (package | |
5158 | (name "r-sgseq") | |
2cebc5d1 | 5159 | (version "1.20.0") |
14441539 RW |
5160 | (source |
5161 | (origin | |
5162 | (method url-fetch) | |
5163 | (uri (bioconductor-uri "SGSeq" version)) | |
5164 | (sha256 | |
5165 | (base32 | |
2cebc5d1 | 5166 | "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw")))) |
14441539 RW |
5167 | (properties `((upstream-name . "SGSeq"))) |
5168 | (build-system r-build-system) | |
5169 | (propagated-inputs | |
5170 | `(("r-annotationdbi" ,r-annotationdbi) | |
5171 | ("r-biocgenerics" ,r-biocgenerics) | |
5172 | ("r-biostrings" ,r-biostrings) | |
5173 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5174 | ("r-genomicalignments" ,r-genomicalignments) | |
5175 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5176 | ("r-genomicranges" ,r-genomicranges) | |
5177 | ("r-igraph" ,r-igraph) | |
5178 | ("r-iranges" ,r-iranges) | |
5179 | ("r-rsamtools" ,r-rsamtools) | |
5180 | ("r-rtracklayer" ,r-rtracklayer) | |
5181 | ("r-runit" ,r-runit) | |
5182 | ("r-s4vectors" ,r-s4vectors) | |
5183 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5184 | (home-page "https://bioconductor.org/packages/SGSeq/") | |
5185 | (synopsis "Splice event prediction and quantification from RNA-seq data") | |
5186 | (description | |
5187 | "SGSeq is a package for analyzing splice events from RNA-seq data. Input | |
5188 | data are RNA-seq reads mapped to a reference genome in BAM format. Genes are | |
5189 | represented as a splice graph, which can be obtained from existing annotation | |
5190 | or predicted from the mapped sequence reads. Splice events are identified | |
5191 | from the graph and are quantified locally using structurally compatible reads | |
5192 | at the start or end of each splice variant. The software includes functions | |
5193 | for splice event prediction, quantification, visualization and | |
5194 | interpretation.") | |
5195 | (license license:artistic2.0))) | |
58656064 RW |
5196 | |
5197 | (define-public r-rhisat2 | |
5198 | (package | |
5199 | (name "r-rhisat2") | |
3dd2450e | 5200 | (version "1.2.0") |
58656064 RW |
5201 | (source |
5202 | (origin | |
5203 | (method url-fetch) | |
5204 | (uri (bioconductor-uri "Rhisat2" version)) | |
5205 | (sha256 | |
5206 | (base32 | |
3dd2450e | 5207 | "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49")))) |
58656064 RW |
5208 | (properties `((upstream-name . "Rhisat2"))) |
5209 | (build-system r-build-system) | |
3dd2450e RW |
5210 | (arguments |
5211 | `(#:phases | |
5212 | (modify-phases %standard-phases | |
5213 | (add-after 'unpack 'make-reproducible | |
5214 | (lambda _ | |
5215 | (substitute* "src/Makefile" | |
5216 | (("`hostname`") "guix") | |
5217 | (("`date`") "0") | |
5218 | ;; Avoid shelling out to "which". | |
5219 | (("^CC =.*") (which "gcc")) | |
5220 | (("^CPP =.*") (which "g++"))) | |
5221 | #t))))) | |
58656064 RW |
5222 | (propagated-inputs |
5223 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
5224 | ("r-genomicranges" ,r-genomicranges) | |
5225 | ("r-sgseq" ,r-sgseq))) | |
5226 | (home-page "https://github.com/fmicompbio/Rhisat2") | |
5227 | (synopsis "R Wrapper for HISAT2 sequence aligner") | |
5228 | (description | |
5229 | "This package provides an R interface to the HISAT2 spliced short-read | |
5230 | aligner by Kim et al. (2015). The package contains wrapper functions to | |
5231 | create a genome index and to perform the read alignment to the generated | |
5232 | index.") | |
5233 | (license license:gpl3))) | |
5e0241db RW |
5234 | |
5235 | (define-public r-quasr | |
5236 | (package | |
5237 | (name "r-quasr") | |
a15e52ec | 5238 | (version "1.26.0") |
5e0241db RW |
5239 | (source |
5240 | (origin | |
5241 | (method url-fetch) | |
5242 | (uri (bioconductor-uri "QuasR" version)) | |
5243 | (sha256 | |
5244 | (base32 | |
a15e52ec | 5245 | "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv")))) |
5e0241db RW |
5246 | (properties `((upstream-name . "QuasR"))) |
5247 | (build-system r-build-system) | |
5248 | (inputs | |
5249 | `(("zlib" ,zlib))) | |
5250 | (propagated-inputs | |
5251 | `(("r-annotationdbi" ,r-annotationdbi) | |
5252 | ("r-biobase" ,r-biobase) | |
5253 | ("r-biocgenerics" ,r-biocgenerics) | |
5254 | ("r-biocmanager" ,r-biocmanager) | |
5255 | ("r-biocparallel" ,r-biocparallel) | |
5256 | ("r-biostrings" ,r-biostrings) | |
5257 | ("r-bsgenome" ,r-bsgenome) | |
5258 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5259 | ("r-genomicalignments" ,r-genomicalignments) | |
5260 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5261 | ("r-genomicfiles" ,r-genomicfiles) | |
5262 | ("r-genomicranges" ,r-genomicranges) | |
5263 | ("r-iranges" ,r-iranges) | |
5264 | ("r-rbowtie" ,r-rbowtie) | |
5265 | ("r-rhisat2" ,r-rhisat2) | |
5266 | ("r-rhtslib" ,r-rhtslib) | |
5267 | ("r-rsamtools" ,r-rsamtools) | |
5268 | ("r-rtracklayer" ,r-rtracklayer) | |
5269 | ("r-s4vectors" ,r-s4vectors) | |
5270 | ("r-shortread" ,r-shortread))) | |
5271 | (home-page "https://bioconductor.org/packages/QuasR/") | |
5272 | (synopsis "Quantify and annotate short reads in R") | |
5273 | (description | |
5274 | "This package provides a framework for the quantification and analysis of | |
5275 | short genomic reads. It covers a complete workflow starting from raw sequence | |
5276 | reads, over creation of alignments and quality control plots, to the | |
5277 | quantification of genomic regions of interest.") | |
5278 | (license license:gpl2))) | |
496b024f RW |
5279 | |
5280 | (define-public r-rqc | |
5281 | (package | |
5282 | (name "r-rqc") | |
11db82b0 | 5283 | (version "1.20.0") |
496b024f RW |
5284 | (source |
5285 | (origin | |
5286 | (method url-fetch) | |
5287 | (uri (bioconductor-uri "Rqc" version)) | |
5288 | (sha256 | |
5289 | (base32 | |
11db82b0 | 5290 | "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m")))) |
496b024f RW |
5291 | (properties `((upstream-name . "Rqc"))) |
5292 | (build-system r-build-system) | |
5293 | (propagated-inputs | |
5294 | `(("r-biocgenerics" ,r-biocgenerics) | |
5295 | ("r-biocparallel" ,r-biocparallel) | |
5296 | ("r-biocstyle" ,r-biocstyle) | |
5297 | ("r-biostrings" ,r-biostrings) | |
5298 | ("r-biovizbase" ,r-biovizbase) | |
5299 | ("r-genomicalignments" ,r-genomicalignments) | |
5300 | ("r-genomicfiles" ,r-genomicfiles) | |
5301 | ("r-ggplot2" ,r-ggplot2) | |
5302 | ("r-iranges" ,r-iranges) | |
5303 | ("r-knitr" ,r-knitr) | |
5304 | ("r-markdown" ,r-markdown) | |
5305 | ("r-plyr" ,r-plyr) | |
5306 | ("r-rcpp" ,r-rcpp) | |
5307 | ("r-reshape2" ,r-reshape2) | |
5308 | ("r-rsamtools" ,r-rsamtools) | |
5309 | ("r-s4vectors" ,r-s4vectors) | |
5310 | ("r-shiny" ,r-shiny) | |
5311 | ("r-shortread" ,r-shortread))) | |
5312 | (home-page "https://github.com/labbcb/Rqc") | |
5313 | (synopsis "Quality control tool for high-throughput sequencing data") | |
5314 | (description | |
5315 | "Rqc is an optimized tool designed for quality control and assessment of | |
5316 | high-throughput sequencing data. It performs parallel processing of entire | |
5317 | files and produces a report which contains a set of high-resolution | |
5318 | graphics.") | |
5319 | (license license:gpl2+))) | |
81e3de01 RW |
5320 | |
5321 | (define-public r-birewire | |
5322 | (package | |
5323 | (name "r-birewire") | |
a9e5145c | 5324 | (version "3.18.0") |
81e3de01 RW |
5325 | (source |
5326 | (origin | |
5327 | (method url-fetch) | |
5328 | (uri (bioconductor-uri "BiRewire" version)) | |
5329 | (sha256 | |
5330 | (base32 | |
a9e5145c | 5331 | "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q")))) |
81e3de01 RW |
5332 | (properties `((upstream-name . "BiRewire"))) |
5333 | (build-system r-build-system) | |
5334 | (propagated-inputs | |
5335 | `(("r-igraph" ,r-igraph) | |
5336 | ("r-matrix" ,r-matrix) | |
5337 | ("r-slam" ,r-slam) | |
5338 | ("r-tsne" ,r-tsne))) | |
5339 | (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") | |
5340 | (synopsis "Tools for randomization of bipartite graphs") | |
5341 | (description | |
5342 | "This package provides functions for bipartite network rewiring through N | |
5343 | consecutive switching steps and for the computation of the minimal number of | |
5344 | switching steps to be performed in order to maximise the dissimilarity with | |
5345 | respect to the original network. It includes functions for the analysis of | |
5346 | the introduced randomness across the switching steps and several other | |
5347 | routines to analyse the resulting networks and their natural projections.") | |
5348 | (license license:gpl3))) | |
1a24f855 RW |
5349 | |
5350 | (define-public r-birta | |
5351 | (package | |
5352 | (name "r-birta") | |
8d766270 | 5353 | (version "1.30.0") |
1a24f855 RW |
5354 | (source |
5355 | (origin | |
5356 | (method url-fetch) | |
5357 | (uri (bioconductor-uri "birta" version)) | |
5358 | (sha256 | |
5359 | (base32 | |
8d766270 | 5360 | "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg")))) |
1a24f855 RW |
5361 | (build-system r-build-system) |
5362 | (propagated-inputs | |
5363 | `(("r-biobase" ,r-biobase) | |
5364 | ("r-limma" ,r-limma) | |
5365 | ("r-mass" ,r-mass))) | |
5366 | (home-page "https://bioconductor.org/packages/birta") | |
5367 | (synopsis "Bayesian inference of regulation of transcriptional activity") | |
5368 | (description | |
5369 | "Expression levels of mRNA molecules are regulated by different | |
5370 | processes, comprising inhibition or activation by transcription factors and | |
5371 | post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian | |
5372 | Inference of Regulation of Transcriptional Activity) uses the regulatory | |
5373 | networks of transcription factors and miRNAs together with mRNA and miRNA | |
5374 | expression data to predict switches in regulatory activity between two | |
5375 | conditions. A Bayesian network is used to model the regulatory structure and | |
5376 | Markov-Chain-Monte-Carlo is applied to sample the activity states.") | |
5377 | (license license:gpl2+))) | |
a9fac3f4 | 5378 | |
b4a22cca RW |
5379 | (define-public r-multidataset |
5380 | (package | |
5381 | (name "r-multidataset") | |
5382 | (version "1.14.0") | |
5383 | (source | |
5384 | (origin | |
5385 | (method url-fetch) | |
5386 | (uri (bioconductor-uri "MultiDataSet" version)) | |
5387 | (sha256 | |
5388 | (base32 | |
5389 | "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj")))) | |
5390 | (properties `((upstream-name . "MultiDataSet"))) | |
5391 | (build-system r-build-system) | |
5392 | (propagated-inputs | |
5393 | `(("r-biobase" ,r-biobase) | |
5394 | ("r-biocgenerics" ,r-biocgenerics) | |
5395 | ("r-genomicranges" ,r-genomicranges) | |
5396 | ("r-ggplot2" ,r-ggplot2) | |
5397 | ("r-ggrepel" ,r-ggrepel) | |
5398 | ("r-iranges" ,r-iranges) | |
5399 | ("r-limma" ,r-limma) | |
5400 | ("r-qqman" ,r-qqman) | |
5401 | ("r-s4vectors" ,r-s4vectors) | |
5402 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5403 | (home-page "https://bioconductor.org/packages/MultiDataSet/") | |
5404 | (synopsis "Implementation of MultiDataSet and ResultSet") | |
5405 | (description | |
5406 | "This package provides an implementation of the BRGE's (Bioinformatic | |
5407 | Research Group in Epidemiology from Center for Research in Environmental | |
5408 | Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for | |
5409 | integrating multi omics data sets and ResultSet is a container for omics | |
5410 | results. This package contains base classes for MEAL and rexposome | |
5411 | packages.") | |
5412 | (license license:expat))) | |
5413 | ||
a9fac3f4 RW |
5414 | (define-public r-ropls |
5415 | (package | |
5416 | (name "r-ropls") | |
c5d75df3 | 5417 | (version "1.18.8") |
a9fac3f4 RW |
5418 | (source |
5419 | (origin | |
5420 | (method url-fetch) | |
5421 | (uri (bioconductor-uri "ropls" version)) | |
5422 | (sha256 | |
5423 | (base32 | |
c5d75df3 | 5424 | "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a")))) |
a9fac3f4 | 5425 | (build-system r-build-system) |
643aaf7e RW |
5426 | (propagated-inputs |
5427 | `(("r-biobase" ,r-biobase) | |
5428 | ("r-multidataset" ,r-multidataset))) | |
a9fac3f4 RW |
5429 | (native-inputs |
5430 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
5431 | (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") | |
5432 | (synopsis "Multivariate analysis and feature selection of omics data") | |
5433 | (description | |
5434 | "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) | |
5435 | and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, | |
5436 | regression, classification, and feature selection of omics data where the | |
5437 | number of variables exceeds the number of samples and with multicollinearity | |
5438 | among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to | |
5439 | separately model the variation correlated (predictive) to the factor of | |
5440 | interest and the uncorrelated (orthogonal) variation. While performing | |
5441 | similarly to PLS, OPLS facilitates interpretation. | |
5442 | ||
5443 | This package provides imlementations of PCA, PLS, and OPLS for multivariate | |
5444 | analysis and feature selection of omics data. In addition to scores, loadings | |
5445 | and weights plots, the package provides metrics and graphics to determine the | |
5446 | optimal number of components (e.g. with the R2 and Q2 coefficients), check the | |
5447 | validity of the model by permutation testing, detect outliers, and perform | |
5448 | feature selection (e.g. with Variable Importance in Projection or regression | |
5449 | coefficients).") | |
5450 | (license license:cecill))) | |
075a9094 RW |
5451 | |
5452 | (define-public r-biosigner | |
5453 | (package | |
5454 | (name "r-biosigner") | |
4bcb38c8 | 5455 | (version "1.14.4") |
075a9094 RW |
5456 | (source |
5457 | (origin | |
5458 | (method url-fetch) | |
5459 | (uri (bioconductor-uri "biosigner" version)) | |
5460 | (sha256 | |
5461 | (base32 | |
4bcb38c8 | 5462 | "0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl")))) |
075a9094 RW |
5463 | (build-system r-build-system) |
5464 | (propagated-inputs | |
5465 | `(("r-biobase" ,r-biobase) | |
5466 | ("r-e1071" ,r-e1071) | |
7d29dc9c | 5467 | ("r-multidataset" ,r-multidataset) |
075a9094 RW |
5468 | ("r-randomforest" ,r-randomforest) |
5469 | ("r-ropls" ,r-ropls))) | |
5470 | (native-inputs | |
f7100eda | 5471 | `(("r-knitr" ,r-knitr))) |
075a9094 RW |
5472 | (home-page "https://bioconductor.org/packages/biosigner/") |
5473 | (synopsis "Signature discovery from omics data") | |
5474 | (description | |
5475 | "Feature selection is critical in omics data analysis to extract | |
5476 | restricted and meaningful molecular signatures from complex and high-dimension | |
5477 | data, and to build robust classifiers. This package implements a method to | |
5478 | assess the relevance of the variables for the prediction performances of the | |
5479 | classifier. The approach can be run in parallel with the PLS-DA, Random | |
5480 | Forest, and SVM binary classifiers. The signatures and the corresponding | |
5481 | 'restricted' models are returned, enabling future predictions on new | |
5482 | datasets.") | |
5483 | (license license:cecill))) | |
ae6fa185 RW |
5484 | |
5485 | (define-public r-annotatr | |
5486 | (package | |
5487 | (name "r-annotatr") | |
70007256 | 5488 | (version "1.12.1") |
ae6fa185 RW |
5489 | (source |
5490 | (origin | |
5491 | (method url-fetch) | |
5492 | (uri (bioconductor-uri "annotatr" version)) | |
5493 | (sha256 | |
5494 | (base32 | |
70007256 | 5495 | "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj")))) |
ae6fa185 RW |
5496 | (build-system r-build-system) |
5497 | (propagated-inputs | |
5498 | `(("r-annotationdbi" ,r-annotationdbi) | |
5499 | ("r-annotationhub" ,r-annotationhub) | |
5500 | ("r-dplyr" ,r-dplyr) | |
5501 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5502 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5503 | ("r-genomicranges" ,r-genomicranges) | |
5504 | ("r-ggplot2" ,r-ggplot2) | |
5505 | ("r-iranges" ,r-iranges) | |
5506 | ("r-readr" ,r-readr) | |
5507 | ("r-regioner" ,r-regioner) | |
5508 | ("r-reshape2" ,r-reshape2) | |
5509 | ("r-rtracklayer" ,r-rtracklayer) | |
5510 | ("r-s4vectors" ,r-s4vectors))) | |
5511 | (home-page "https://bioconductor.org/packages/annotatr/") | |
5512 | (synopsis "Annotation of genomic regions to genomic annotations") | |
5513 | (description | |
5514 | "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, | |
5515 | differentially methylated CpGs or regions, SNPs, etc.) it is often of interest | |
5516 | to investigate the intersecting genomic annotations. Such annotations include | |
5517 | those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), | |
5518 | CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as | |
5519 | enhancers. The annotatr package provides an easy way to summarize and | |
5520 | visualize the intersection of genomic sites/regions with genomic | |
5521 | annotations.") | |
5522 | (license license:gpl3))) | |
2cb738a6 RW |
5523 | |
5524 | (define-public r-rsubread | |
5525 | (package | |
5526 | (name "r-rsubread") | |
e01fa33b | 5527 | (version "2.0.1") |
2cb738a6 RW |
5528 | (source |
5529 | (origin | |
5530 | (method url-fetch) | |
5531 | (uri (bioconductor-uri "Rsubread" version)) | |
5532 | (sha256 | |
5533 | (base32 | |
e01fa33b | 5534 | "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy")))) |
2cb738a6 RW |
5535 | (properties `((upstream-name . "Rsubread"))) |
5536 | (build-system r-build-system) | |
5537 | (inputs `(("zlib" ,zlib))) | |
5538 | (home-page "https://bioconductor.org/packages/Rsubread/") | |
5539 | (synopsis "Subread sequence alignment and counting for R") | |
5540 | (description | |
5541 | "This package provides tools for alignment, quantification and analysis | |
5542 | of second and third generation sequencing data. It includes functionality for | |
5543 | read mapping, read counting, SNP calling, structural variant detection and | |
5544 | gene fusion discovery. It can be applied to all major sequencing techologies | |
5545 | and to both short and long sequence reads.") | |
5546 | (license license:gpl3))) | |
a6fedf1f | 5547 | |
a0422d18 | 5548 | (define-public r-flowutils |
5549 | (package | |
5550 | (name "r-flowutils") | |
482ba0b3 | 5551 | (version "1.50.0") |
a0422d18 | 5552 | (source |
5553 | (origin | |
5554 | (method url-fetch) | |
5555 | (uri (bioconductor-uri "flowUtils" version)) | |
5556 | (sha256 | |
5557 | (base32 | |
482ba0b3 | 5558 | "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81")))) |
a0422d18 | 5559 | (properties `((upstream-name . "flowUtils"))) |
5560 | (build-system r-build-system) | |
5561 | (propagated-inputs | |
5562 | `(("r-biobase" ,r-biobase) | |
5563 | ("r-corpcor" ,r-corpcor) | |
5564 | ("r-flowcore" ,r-flowcore) | |
5565 | ("r-graph" ,r-graph) | |
5566 | ("r-runit" ,r-runit) | |
5567 | ("r-xml" ,r-xml))) | |
5568 | (home-page "https://github.com/jspidlen/flowUtils") | |
5569 | (synopsis "Utilities for flow cytometry") | |
5570 | (description | |
5571 | "This package provides utilities for flow cytometry data.") | |
5572 | (license license:artistic2.0))) | |
5573 | ||
ed6f49fc | 5574 | (define-public r-consensusclusterplus |
5575 | (package | |
5576 | (name "r-consensusclusterplus") | |
8ad6b23f | 5577 | (version "1.50.0") |
ed6f49fc | 5578 | (source |
5579 | (origin | |
5580 | (method url-fetch) | |
5581 | (uri (bioconductor-uri "ConsensusClusterPlus" version)) | |
5582 | (sha256 | |
5583 | (base32 | |
8ad6b23f | 5584 | "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4")))) |
ed6f49fc | 5585 | (properties |
5586 | `((upstream-name . "ConsensusClusterPlus"))) | |
5587 | (build-system r-build-system) | |
5588 | (propagated-inputs | |
5589 | `(("r-all" ,r-all) | |
5590 | ("r-biobase" ,r-biobase) | |
5591 | ("r-cluster" ,r-cluster))) | |
5592 | (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") | |
5593 | (synopsis "Clustering algorithm") | |
5594 | (description | |
5595 | "This package provides an implementation of an algorithm for determining | |
5596 | cluster count and membership by stability evidence in unsupervised analysis.") | |
5597 | (license license:gpl2))) | |
5598 | ||
b4aee31d RW |
5599 | (define-public r-cytolib |
5600 | (package | |
5601 | (name "r-cytolib") | |
5602 | (version "1.8.0") | |
5603 | (source | |
5604 | (origin | |
5605 | (method url-fetch) | |
5606 | (uri (bioconductor-uri "cytolib" version)) | |
5607 | (sha256 | |
5608 | (base32 | |
5609 | "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9")))) | |
5610 | (properties `((upstream-name . "cytolib"))) | |
5611 | (build-system r-build-system) | |
5612 | (home-page "https://bioconductor.org/packages/cytolib/") | |
5613 | (synopsis "C++ infrastructure for working with gated cytometry") | |
5614 | (description | |
5615 | "This package provides the core data structure and API to represent and | |
5616 | interact with gated cytometry data.") | |
5617 | (license license:artistic2.0))) | |
5618 | ||
a6fedf1f | 5619 | (define-public r-flowcore |
5620 | (package | |
5621 | (name "r-flowcore") | |
b2a2f321 | 5622 | (version "1.52.1") |
a6fedf1f | 5623 | (source |
5624 | (origin | |
5625 | (method url-fetch) | |
5626 | (uri (bioconductor-uri "flowCore" version)) | |
5627 | (sha256 | |
5628 | (base32 | |
b2a2f321 | 5629 | "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2")))) |
a6fedf1f | 5630 | (properties `((upstream-name . "flowCore"))) |
5631 | (build-system r-build-system) | |
5632 | (propagated-inputs | |
5633 | `(("r-bh" ,r-bh) | |
5634 | ("r-biobase" ,r-biobase) | |
5635 | ("r-biocgenerics" ,r-biocgenerics) | |
b2a2f321 | 5636 | ("r-cytolib" ,r-cytolib) |
a6fedf1f | 5637 | ("r-matrixstats" ,r-matrixstats) |
b2a2f321 | 5638 | ("r-rcpp" ,r-rcpp))) |
a6fedf1f | 5639 | (home-page "https://bioconductor.org/packages/flowCore") |
5640 | (synopsis "Basic structures for flow cytometry data") | |
5641 | (description | |
5642 | "This package provides S4 data structures and basic functions to deal | |
5643 | with flow cytometry data.") | |
5644 | (license license:artistic2.0))) | |
e0cb053e | 5645 | |
5646 | (define-public r-flowmeans | |
5647 | (package | |
5648 | (name "r-flowmeans") | |
80420878 | 5649 | (version "1.46.0") |
e0cb053e | 5650 | (source |
5651 | (origin | |
5652 | (method url-fetch) | |
5653 | (uri (bioconductor-uri "flowMeans" version)) | |
5654 | (sha256 | |
5655 | (base32 | |
80420878 | 5656 | "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h")))) |
e0cb053e | 5657 | (properties `((upstream-name . "flowMeans"))) |
5658 | (build-system r-build-system) | |
5659 | (propagated-inputs | |
5660 | `(("r-biobase" ,r-biobase) | |
5661 | ("r-feature" ,r-feature) | |
5662 | ("r-flowcore" ,r-flowcore) | |
5663 | ("r-rrcov" ,r-rrcov))) | |
5664 | (home-page "https://bioconductor.org/packages/flowMeans") | |
5665 | (synopsis "Non-parametric flow cytometry data gating") | |
5666 | (description | |
5667 | "This package provides tools to identify cell populations in Flow | |
5668 | Cytometry data using non-parametric clustering and segmented-regression-based | |
5669 | change point detection.") | |
5670 | (license license:artistic2.0))) | |
1502751b | 5671 | |
15ac0c19 RW |
5672 | (define-public r-ncdfflow |
5673 | (package | |
5674 | (name "r-ncdfflow") | |
5675 | (version "2.32.0") | |
5676 | (source | |
5677 | (origin | |
5678 | (method url-fetch) | |
5679 | (uri (bioconductor-uri "ncdfFlow" version)) | |
5680 | (sha256 | |
5681 | (base32 | |
5682 | "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i")))) | |
5683 | (properties `((upstream-name . "ncdfFlow"))) | |
5684 | (build-system r-build-system) | |
5685 | (inputs | |
5686 | `(("zlib" ,zlib))) | |
5687 | (propagated-inputs | |
5688 | `(("r-bh" ,r-bh) | |
5689 | ("r-biobase" ,r-biobase) | |
5690 | ("r-biocgenerics" ,r-biocgenerics) | |
5691 | ("r-flowcore" ,r-flowcore) | |
5692 | ("r-rcpp" ,r-rcpp) | |
5693 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
5694 | ("r-rhdf5lib" ,r-rhdf5lib) | |
5695 | ("r-zlibbioc" ,r-zlibbioc))) | |
5696 | (home-page "https://bioconductor.org/packages/ncdfFlow/") | |
5697 | (synopsis "HDF5 based storage for flow cytometry data") | |
5698 | (description | |
5699 | "This package provides HDF5 storage based methods and functions for | |
5700 | manipulation of flow cytometry data.") | |
5701 | (license license:artistic2.0))) | |
5702 | ||
f5f44031 RW |
5703 | (define-public r-ggcyto |
5704 | (package | |
5705 | (name "r-ggcyto") | |
0754fefb | 5706 | (version "1.14.1") |
f5f44031 RW |
5707 | (source |
5708 | (origin | |
5709 | (method url-fetch) | |
5710 | (uri (bioconductor-uri "ggcyto" version)) | |
5711 | (sha256 | |
5712 | (base32 | |
0754fefb | 5713 | "16jwdslhmj1nsa28wmaircy15cq7qn8nsyiawinjv711qiqhgw50")))) |
f5f44031 RW |
5714 | (properties `((upstream-name . "ggcyto"))) |
5715 | (build-system r-build-system) | |
5716 | (propagated-inputs | |
5717 | `(("r-data-table" ,r-data-table) | |
5718 | ("r-flowcore" ,r-flowcore) | |
5719 | ("r-flowworkspace" ,r-flowworkspace) | |
5720 | ("r-ggplot2" ,r-ggplot2) | |
5721 | ("r-gridextra" ,r-gridextra) | |
5722 | ("r-ncdfflow" ,r-ncdfflow) | |
5723 | ("r-plyr" ,r-plyr) | |
5724 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5725 | ("r-rlang" ,r-rlang) | |
5726 | ("r-scales" ,r-scales))) | |
0754fefb RW |
5727 | (native-inputs |
5728 | `(("r-knitr" ,r-knitr))) | |
f5f44031 RW |
5729 | (home-page "https://github.com/RGLab/ggcyto/issues") |
5730 | (synopsis "Visualize Cytometry data with ggplot") | |
5731 | (description | |
5732 | "With the dedicated fortify method implemented for @code{flowSet}, | |
5733 | @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow | |
5734 | cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper | |
5735 | and some custom layers also make it easy to add gates and population | |
5736 | statistics to the plot.") | |
5737 | (license license:artistic2.0))) | |
5738 | ||
0dd4b7d7 RW |
5739 | (define-public r-flowviz |
5740 | (package | |
5741 | (name "r-flowviz") | |
5742 | (version "1.50.0") | |
5743 | (source | |
5744 | (origin | |
5745 | (method url-fetch) | |
5746 | (uri (bioconductor-uri "flowViz" version)) | |
5747 | (sha256 | |
5748 | (base32 | |
5749 | "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7")))) | |
5750 | (properties `((upstream-name . "flowViz"))) | |
5751 | (build-system r-build-system) | |
5752 | (propagated-inputs | |
5753 | `(("r-biobase" ,r-biobase) | |
5754 | ("r-flowcore" ,r-flowcore) | |
5755 | ("r-hexbin" ,r-hexbin) | |
5756 | ("r-idpmisc" ,r-idpmisc) | |
5757 | ("r-kernsmooth" ,r-kernsmooth) | |
5758 | ("r-lattice" ,r-lattice) | |
5759 | ("r-latticeextra" ,r-latticeextra) | |
5760 | ("r-mass" ,r-mass) | |
5761 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
5762 | (home-page "https://bioconductor.org/packages/flowViz/") | |
5763 | (synopsis "Visualization for flow cytometry") | |
5764 | (description | |
5765 | "This package provides visualization tools for flow cytometry data.") | |
5766 | (license license:artistic2.0))) | |
5767 | ||
c8ab9eb1 RW |
5768 | (define-public r-flowclust |
5769 | (package | |
5770 | (name "r-flowclust") | |
5771 | (version "3.24.0") | |
5772 | (source | |
5773 | (origin | |
5774 | (method url-fetch) | |
5775 | (uri (bioconductor-uri "flowClust" version)) | |
5776 | (sha256 | |
5777 | (base32 | |
5778 | "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s")))) | |
5779 | (properties `((upstream-name . "flowClust"))) | |
5780 | (build-system r-build-system) | |
5781 | (arguments | |
5782 | `(#:configure-flags | |
5783 | (list "--configure-args=--enable-bundled-gsl=no"))) | |
5784 | (propagated-inputs | |
5785 | `(("r-biobase" ,r-biobase) | |
5786 | ("r-biocgenerics" ,r-biocgenerics) | |
5787 | ("r-clue" ,r-clue) | |
5788 | ("r-corpcor" ,r-corpcor) | |
5789 | ("r-ellipse" ,r-ellipse) | |
5790 | ("r-flowcore" ,r-flowcore) | |
5791 | ("r-flowviz" ,r-flowviz) | |
5792 | ("r-graph" ,r-graph) | |
5793 | ("r-mnormt" ,r-mnormt))) | |
5794 | (inputs | |
5795 | `(("gsl" ,gsl))) | |
5796 | (native-inputs | |
5797 | `(("pkg-config" ,pkg-config))) | |
5798 | (home-page "https://bioconductor.org/packages/flowClust") | |
5799 | (synopsis "Clustering for flow cytometry") | |
5800 | (description | |
5801 | "This package provides robust model-based clustering using a t-mixture | |
5802 | model with Box-Cox transformation.") | |
5803 | (license license:artistic2.0))) | |
5804 | ||
f1964519 RW |
5805 | ;; TODO: this package bundles an old version of protobuf. It's not easy to |
5806 | ;; make it use our protobuf package instead. | |
5807 | (define-public r-rprotobuflib | |
5808 | (package | |
5809 | (name "r-rprotobuflib") | |
5810 | (version "1.8.0") | |
5811 | (source | |
5812 | (origin | |
5813 | (method url-fetch) | |
5814 | (uri (bioconductor-uri "RProtoBufLib" version)) | |
5815 | (sha256 | |
5816 | (base32 | |
5817 | "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm")))) | |
5818 | (properties `((upstream-name . "RProtoBufLib"))) | |
5819 | (build-system r-build-system) | |
5820 | (arguments | |
5821 | `(#:phases | |
5822 | (modify-phases %standard-phases | |
5823 | (add-after 'unpack 'unpack-bundled-sources | |
5824 | (lambda _ | |
5825 | (with-directory-excursion "src" | |
5826 | (invoke "tar" "xf" "protobuf-2.6.0.tgz")) | |
5827 | #t))))) | |
5828 | (home-page "https://bioconductor.org/packages/RProtoBufLib/") | |
5829 | (synopsis "C++ headers and static libraries of Protocol buffers") | |
5830 | (description | |
5831 | "This package provides the headers and static library of Protocol buffers | |
5832 | for other R packages to compile and link against.") | |
5833 | (license license:bsd-3))) | |
5834 | ||
82c11117 RW |
5835 | (define-public r-flowworkspace |
5836 | (package | |
5837 | (name "r-flowworkspace") | |
e8ccb98a | 5838 | (version "3.34.1") |
82c11117 RW |
5839 | (source |
5840 | (origin | |
5841 | (method url-fetch) | |
5842 | (uri (bioconductor-uri "flowWorkspace" version)) | |
5843 | (sha256 | |
5844 | (base32 | |
e8ccb98a | 5845 | "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn")))) |
82c11117 RW |
5846 | (properties `((upstream-name . "flowWorkspace"))) |
5847 | (build-system r-build-system) | |
5848 | (propagated-inputs | |
5849 | `(("r-bh" ,r-bh) | |
5850 | ("r-biobase" ,r-biobase) | |
5851 | ("r-biocgenerics" ,r-biocgenerics) | |
5852 | ("r-cytolib" ,r-cytolib) | |
5853 | ("r-data-table" ,r-data-table) | |
5854 | ("r-digest" ,r-digest) | |
5855 | ("r-dplyr" ,r-dplyr) | |
5856 | ("r-flowcore" ,r-flowcore) | |
5857 | ("r-flowviz" ,r-flowviz) | |
5858 | ("r-graph" ,r-graph) | |
5859 | ("r-gridextra" ,r-gridextra) | |
5860 | ("r-lattice" ,r-lattice) | |
5861 | ("r-latticeextra" ,r-latticeextra) | |
5862 | ("r-matrixstats" ,r-matrixstats) | |
5863 | ("r-ncdfflow" ,r-ncdfflow) | |
5864 | ("r-rbgl" ,r-rbgl) | |
5865 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5866 | ("r-rcpp" ,r-rcpp) | |
5867 | ("r-rcppparallel" ,r-rcppparallel) | |
5868 | ("r-rgraphviz" ,r-rgraphviz) | |
5869 | ("r-rprotobuflib" ,r-rprotobuflib) | |
5870 | ("r-scales" ,r-scales) | |
5871 | ("r-stringr" ,r-stringr))) | |
5872 | (home-page "https://bioconductor.org/packages/flowWorkspace/") | |
5873 | (synopsis "Infrastructure for working with cytometry data") | |
5874 | (description | |
5875 | "This package is designed to facilitate comparison of automated gating | |
5876 | methods against manual gating done in flowJo. This package allows you to | |
5877 | import basic flowJo workspaces into BioConductor and replicate the gating from | |
5878 | flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of | |
5879 | samples, compensation, and transformation are performed so that the output | |
5880 | matches the flowJo analysis.") | |
5881 | (license license:artistic2.0))) | |
5882 | ||
b700b9ec RW |
5883 | (define-public r-flowstats |
5884 | (package | |
5885 | (name "r-flowstats") | |
5886 | (version "3.44.0") | |
5887 | (source | |
5888 | (origin | |
5889 | (method url-fetch) | |
5890 | (uri (bioconductor-uri "flowStats" version)) | |
5891 | (sha256 | |
5892 | (base32 | |
5893 | "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w")))) | |
5894 | (properties `((upstream-name . "flowStats"))) | |
5895 | (build-system r-build-system) | |
5896 | (propagated-inputs | |
5897 | `(("r-biobase" ,r-biobase) | |
5898 | ("r-biocgenerics" ,r-biocgenerics) | |
5899 | ("r-cluster" ,r-cluster) | |
5900 | ("r-fda" ,r-fda) | |
5901 | ("r-flowcore" ,r-flowcore) | |
5902 | ("r-flowviz" ,r-flowviz) | |
5903 | ("r-flowworkspace" ,r-flowworkspace) | |
5904 | ("r-kernsmooth" ,r-kernsmooth) | |
5905 | ("r-ks" ,r-ks) | |
5906 | ("r-lattice" ,r-lattice) | |
5907 | ("r-mass" ,r-mass) | |
5908 | ("r-ncdfflow" ,r-ncdfflow) | |
5909 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5910 | ("r-rrcov" ,r-rrcov))) | |
5911 | (home-page "http://www.github.com/RGLab/flowStats") | |
5912 | (synopsis "Statistical methods for the analysis of flow cytometry data") | |
5913 | (description | |
5914 | "This package provides methods and functionality to analyze flow data | |
5915 | that is beyond the basic infrastructure provided by the @code{flowCore} | |
5916 | package.") | |
5917 | (license license:artistic2.0))) | |
5918 | ||
6aedc805 RW |
5919 | (define-public r-opencyto |
5920 | (package | |
5921 | (name "r-opencyto") | |
5922 | (version "1.24.0") | |
5923 | (source | |
5924 | (origin | |
5925 | (method url-fetch) | |
5926 | (uri (bioconductor-uri "openCyto" version)) | |
5927 | (sha256 | |
5928 | (base32 | |
5929 | "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb")))) | |
5930 | (properties `((upstream-name . "openCyto"))) | |
5931 | (build-system r-build-system) | |
5932 | (propagated-inputs | |
5933 | `(("r-biobase" ,r-biobase) | |
5934 | ("r-biocgenerics" ,r-biocgenerics) | |
5935 | ("r-clue" ,r-clue) | |
5936 | ("r-data-table" ,r-data-table) | |
5937 | ("r-flowclust" ,r-flowclust) | |
5938 | ("r-flowcore" ,r-flowcore) | |
5939 | ("r-flowstats" ,r-flowstats) | |
5940 | ("r-flowviz" ,r-flowviz) | |
5941 | ("r-flowworkspace" ,r-flowworkspace) | |
5942 | ("r-graph" ,r-graph) | |
5943 | ("r-gtools" ,r-gtools) | |
5944 | ("r-ks" ,r-ks) | |
5945 | ("r-lattice" ,r-lattice) | |
5946 | ("r-mass" ,r-mass) | |
5947 | ("r-ncdfflow" ,r-ncdfflow) | |
5948 | ("r-plyr" ,r-plyr) | |
5949 | ("r-r-utils" ,r-r-utils) | |
5950 | ("r-rbgl" ,r-rbgl) | |
5951 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5952 | ("r-rcpp" ,r-rcpp) | |
5953 | ("r-rrcov" ,r-rrcov))) | |
5954 | (home-page "https://bioconductor.org/packages/openCyto") | |
5955 | (synopsis "Hierarchical gating pipeline for flow cytometry data") | |
5956 | (description | |
5957 | "This package is designed to facilitate the automated gating methods in a | |
5958 | sequential way to mimic the manual gating strategy.") | |
5959 | (license license:artistic2.0))) | |
5960 | ||
7a62d5e0 RW |
5961 | (define-public r-cytoml |
5962 | (package | |
5963 | (name "r-cytoml") | |
d49e3f01 | 5964 | (version "1.12.1") |
7a62d5e0 RW |
5965 | (source |
5966 | (origin | |
5967 | (method url-fetch) | |
5968 | (uri (bioconductor-uri "CytoML" version)) | |
5969 | (sha256 | |
5970 | (base32 | |
d49e3f01 | 5971 | "0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz")))) |
7a62d5e0 RW |
5972 | (properties `((upstream-name . "CytoML"))) |
5973 | (build-system r-build-system) | |
5974 | (inputs | |
5975 | `(("libxml2" ,libxml2))) | |
5976 | (propagated-inputs | |
5977 | `(("r-base64enc" ,r-base64enc) | |
5978 | ("r-bh" ,r-bh) | |
5979 | ("r-biobase" ,r-biobase) | |
5980 | ("r-corpcor" ,r-corpcor) | |
5981 | ("r-cytolib" ,r-cytolib) | |
5982 | ("r-data-table" ,r-data-table) | |
5983 | ("r-dplyr" ,r-dplyr) | |
5984 | ("r-flowcore" ,r-flowcore) | |
5985 | ("r-flowworkspace" ,r-flowworkspace) | |
5986 | ("r-ggcyto" ,r-ggcyto) | |
5987 | ("r-graph" ,r-graph) | |
5988 | ("r-jsonlite" ,r-jsonlite) | |
5989 | ("r-lattice" ,r-lattice) | |
5990 | ("r-ncdfflow" ,r-ncdfflow) | |
5991 | ("r-opencyto" ,r-opencyto) | |
5992 | ("r-plyr" ,r-plyr) | |
5993 | ("r-rbgl" ,r-rbgl) | |
5994 | ("r-rcpp" ,r-rcpp) | |
5995 | ("r-rcppparallel" ,r-rcppparallel) | |
5996 | ("r-rgraphviz" ,r-rgraphviz) | |
5997 | ("r-rprotobuflib" ,r-rprotobuflib) | |
5998 | ("r-runit" ,r-runit) | |
5999 | ("r-xml" ,r-xml) | |
6000 | ("r-yaml" ,r-yaml))) | |
d49e3f01 RW |
6001 | (native-inputs |
6002 | `(("r-knitr" ,r-knitr))) | |
7a62d5e0 RW |
6003 | (home-page "https://github.com/RGLab/CytoML") |
6004 | (synopsis "GatingML interface for cross platform cytometry data sharing") | |
6005 | (description | |
6006 | "This package provides an interface to implementations of the GatingML2.0 | |
6007 | standard to exchange gated cytometry data with other software platforms.") | |
6008 | (license license:artistic2.0))) | |
6009 | ||
1502751b | 6010 | (define-public r-flowsom |
6011 | (package | |
6012 | (name "r-flowsom") | |
ba71567a | 6013 | (version "1.18.0") |
1502751b | 6014 | (source |
6015 | (origin | |
6016 | (method url-fetch) | |
6017 | (uri (bioconductor-uri "FlowSOM" version)) | |
6018 | (sha256 | |
6019 | (base32 | |
ba71567a | 6020 | "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5")))) |
1502751b | 6021 | (properties `((upstream-name . "FlowSOM"))) |
6022 | (build-system r-build-system) | |
6023 | (propagated-inputs | |
6024 | `(("r-biocgenerics" ,r-biocgenerics) | |
6025 | ("r-consensusclusterplus" ,r-consensusclusterplus) | |
ba71567a | 6026 | ("r-cytoml" ,r-cytoml) |
1502751b | 6027 | ("r-flowcore" ,r-flowcore) |
ba71567a | 6028 | ("r-flowworkspace" ,r-flowworkspace) |
1502751b | 6029 | ("r-igraph" ,r-igraph) |
ba71567a | 6030 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
1502751b | 6031 | ("r-tsne" ,r-tsne) |
6032 | ("r-xml" ,r-xml))) | |
6033 | (home-page "https://bioconductor.org/packages/FlowSOM/") | |
6034 | (synopsis "Visualize and interpret cytometry data") | |
6035 | (description | |
6036 | "FlowSOM offers visualization options for cytometry data, by using | |
6037 | self-organizing map clustering and minimal spanning trees.") | |
6038 | (license license:gpl2+))) | |
1adb9cbc | 6039 | |
6040 | (define-public r-mixomics | |
6041 | (package | |
6042 | (name "r-mixomics") | |
9669bc17 | 6043 | (version "6.10.9") |
1adb9cbc | 6044 | (source |
6045 | (origin | |
6046 | (method url-fetch) | |
6047 | (uri (bioconductor-uri "mixOmics" version)) | |
6048 | (sha256 | |
6049 | (base32 | |
9669bc17 | 6050 | "0b457yg8mwqlrn5l344w8qcj8v2ghlj1wdx1ysxbncqvqx7nvgig")))) |
1adb9cbc | 6051 | (properties `((upstream-name . "mixOmics"))) |
6052 | (build-system r-build-system) | |
6053 | (propagated-inputs | |
6054 | `(("r-corpcor" ,r-corpcor) | |
6055 | ("r-dplyr" ,r-dplyr) | |
6056 | ("r-ellipse" ,r-ellipse) | |
6057 | ("r-ggplot2" ,r-ggplot2) | |
6058 | ("r-gridextra" ,r-gridextra) | |
6059 | ("r-igraph" ,r-igraph) | |
6060 | ("r-lattice" ,r-lattice) | |
6061 | ("r-mass" ,r-mass) | |
6062 | ("r-matrixstats" ,r-matrixstats) | |
6063 | ("r-rarpack" ,r-rarpack) | |
6064 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6065 | ("r-reshape2" ,r-reshape2) | |
6066 | ("r-tidyr" ,r-tidyr))) | |
9669bc17 RW |
6067 | (native-inputs |
6068 | `(("r-knitr" ,r-knitr))) | |
1adb9cbc | 6069 | (home-page "http://www.mixOmics.org") |
6070 | (synopsis "Multivariate methods for exploration of biological datasets") | |
6071 | (description | |
6072 | "mixOmics offers a wide range of multivariate methods for the exploration | |
6073 | and integration of biological datasets with a particular focus on variable | |
6074 | selection. The package proposes several sparse multivariate models we have | |
6075 | developed to identify the key variables that are highly correlated, and/or | |
6076 | explain the biological outcome of interest. The data that can be analysed | |
6077 | with mixOmics may come from high throughput sequencing technologies, such as | |
6078 | omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but | |
6079 | also beyond the realm of omics (e.g. spectral imaging). The methods | |
6080 | implemented in mixOmics can also handle missing values without having to | |
6081 | delete entire rows with missing data.") | |
6082 | (license license:gpl2+))) | |
a0efa069 | 6083 | |
6084 | (define-public r-depecher | |
6085 | (package | |
6086 | (name "r-depecher") | |
bf3722f9 | 6087 | (version "1.2.2") |
a0efa069 | 6088 | (source |
6089 | (origin | |
6090 | (method url-fetch) | |
6091 | (uri (bioconductor-uri "DepecheR" version)) | |
6092 | (sha256 | |
6093 | (base32 | |
bf3722f9 | 6094 | "199j2kw0xnw7y4v1gakm2jgyc7zzlj8xh0570f2yjq55gp1kggbm")))) |
a0efa069 | 6095 | (properties `((upstream-name . "DepecheR"))) |
6096 | (build-system r-build-system) | |
a0efa069 | 6097 | (propagated-inputs |
6098 | `(("r-beanplot" ,r-beanplot) | |
a0efa069 | 6099 | ("r-dosnow" ,r-dosnow) |
6100 | ("r-dplyr" ,r-dplyr) | |
2c8433ca | 6101 | ("r-fnn" ,r-fnn) |
a0efa069 | 6102 | ("r-foreach" ,r-foreach) |
6103 | ("r-ggplot2" ,r-ggplot2) | |
6104 | ("r-gplots" ,r-gplots) | |
6105 | ("r-mass" ,r-mass) | |
6106 | ("r-matrixstats" ,r-matrixstats) | |
6107 | ("r-mixomics" ,r-mixomics) | |
6108 | ("r-moments" ,r-moments) | |
6109 | ("r-rcpp" ,r-rcpp) | |
6110 | ("r-rcppeigen" ,r-rcppeigen) | |
6111 | ("r-reshape2" ,r-reshape2) | |
2c8433ca | 6112 | ("r-robustbase" ,r-robustbase) |
a0efa069 | 6113 | ("r-viridis" ,r-viridis))) |
bf3722f9 RW |
6114 | (native-inputs |
6115 | `(("r-knitr" ,r-knitr))) | |
a0efa069 | 6116 | (home-page "https://bioconductor.org/packages/DepecheR/") |
6117 | (synopsis "Identify traits of clusters in high-dimensional entities") | |
6118 | (description | |
6119 | "The purpose of this package is to identify traits in a dataset that can | |
6120 | separate groups. This is done on two levels. First, clustering is performed, | |
6121 | using an implementation of sparse K-means. Secondly, the generated clusters | |
6122 | are used to predict outcomes of groups of individuals based on their | |
6123 | distribution of observations in the different clusters. As certain clusters | |
6124 | with separating information will be identified, and these clusters are defined | |
6125 | by a sparse number of variables, this method can reduce the complexity of | |
6126 | data, to only emphasize the data that actually matters.") | |
6127 | (license license:expat))) | |
b46a0ee7 | 6128 | |
bb88417f RW |
6129 | (define-public r-rcistarget |
6130 | (package | |
6131 | (name "r-rcistarget") | |
51ffac45 | 6132 | (version "1.6.0") |
bb88417f RW |
6133 | (source |
6134 | (origin | |
6135 | (method url-fetch) | |
6136 | (uri (bioconductor-uri "RcisTarget" version)) | |
6137 | (sha256 | |
6138 | (base32 | |
51ffac45 | 6139 | "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw")))) |
bb88417f RW |
6140 | (properties `((upstream-name . "RcisTarget"))) |
6141 | (build-system r-build-system) | |
6142 | (propagated-inputs | |
6143 | `(("r-aucell" ,r-aucell) | |
6144 | ("r-biocgenerics" ,r-biocgenerics) | |
6145 | ("r-data-table" ,r-data-table) | |
6146 | ("r-feather" ,r-feather) | |
6147 | ("r-gseabase" ,r-gseabase) | |
6148 | ("r-r-utils" ,r-r-utils) | |
6149 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
6150 | (home-page "https://aertslab.org/#scenic") | |
6151 | (synopsis "Identify transcription factor binding motifs enriched on a gene list") | |
6152 | (description | |
6153 | "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) | |
6154 | over-represented on a gene list. In a first step, RcisTarget selects DNA | |
6155 | motifs that are significantly over-represented in the surroundings of the | |
6156 | @dfn{transcription start site} (TSS) of the genes in the gene-set. This is | |
6157 | achieved by using a database that contains genome-wide cross-species rankings | |
6158 | for each motif. The motifs that are then annotated to TFs and those that have | |
6159 | a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for | |
6160 | each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. | |
6161 | genes in the gene-set that are ranked above the leading edge).") | |
6162 | (license license:gpl3))) | |
6163 | ||
b46a0ee7 RW |
6164 | (define-public r-cicero |
6165 | (package | |
6166 | (name "r-cicero") | |
6bd6097e | 6167 | (version "1.4.4") |
b46a0ee7 RW |
6168 | (source |
6169 | (origin | |
6170 | (method url-fetch) | |
6171 | (uri (bioconductor-uri "cicero" version)) | |
6172 | (sha256 | |
6173 | (base32 | |
6bd6097e | 6174 | "1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld")))) |
b46a0ee7 RW |
6175 | (build-system r-build-system) |
6176 | (propagated-inputs | |
6177 | `(("r-assertthat" ,r-assertthat) | |
6178 | ("r-biobase" ,r-biobase) | |
6179 | ("r-biocgenerics" ,r-biocgenerics) | |
6180 | ("r-data-table" ,r-data-table) | |
6181 | ("r-dplyr" ,r-dplyr) | |
6182 | ("r-fnn" ,r-fnn) | |
6183 | ("r-genomicranges" ,r-genomicranges) | |
6184 | ("r-ggplot2" ,r-ggplot2) | |
6185 | ("r-glasso" ,r-glasso) | |
6186 | ("r-gviz" ,r-gviz) | |
6187 | ("r-igraph" ,r-igraph) | |
6188 | ("r-iranges" ,r-iranges) | |
6189 | ("r-matrix" ,r-matrix) | |
6190 | ("r-monocle" ,r-monocle) | |
6191 | ("r-plyr" ,r-plyr) | |
6192 | ("r-reshape2" ,r-reshape2) | |
6193 | ("r-s4vectors" ,r-s4vectors) | |
6194 | ("r-stringr" ,r-stringr) | |
6195 | ("r-tibble" ,r-tibble) | |
5ea4f604 | 6196 | ("r-tidyr" ,r-tidyr) |
b46a0ee7 | 6197 | ("r-vgam" ,r-vgam))) |
6bd6097e RW |
6198 | (native-inputs |
6199 | `(("r-knitr" ,r-knitr))) | |
b46a0ee7 RW |
6200 | (home-page "https://bioconductor.org/packages/cicero/") |
6201 | (synopsis "Predict cis-co-accessibility from single-cell data") | |
6202 | (description | |
6203 | "Cicero computes putative cis-regulatory maps from single-cell chromatin | |
6204 | accessibility data. It also extends the monocle package for use in chromatin | |
6205 | accessibility data.") | |
6206 | (license license:expat))) | |
14bb1c48 RW |
6207 | |
6208 | ;; This is the latest commit on the "monocle3" branch. | |
6209 | (define-public r-cicero-monocle3 | |
6210 | (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") | |
6211 | (revision "1")) | |
6212 | (package (inherit r-cicero) | |
6213 | (name "r-cicero-monocle3") | |
6214 | (version (git-version "1.3.2" revision commit)) | |
6215 | (source | |
6216 | (origin | |
6217 | (method git-fetch) | |
6218 | (uri (git-reference | |
6219 | (url "https://github.com/cole-trapnell-lab/cicero-release.git") | |
6220 | (commit commit))) | |
6221 | (file-name (git-file-name name version)) | |
6222 | (sha256 | |
6223 | (base32 | |
6224 | "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) | |
6225 | (propagated-inputs | |
6226 | `(("r-monocle3" ,r-monocle3) | |
6227 | ,@(alist-delete "r-monocle" | |
6228 | (package-propagated-inputs r-cicero))))))) | |
a9815a6c RW |
6229 | |
6230 | (define-public r-cistopic | |
6231 | (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") | |
6232 | (revision "0")) | |
6233 | (package | |
6234 | (name "r-cistopic") | |
6235 | (version (git-version "0.2.1" revision commit)) | |
6236 | (source | |
6237 | (origin | |
6238 | (method git-fetch) | |
6239 | (uri (git-reference | |
6240 | (url "https://github.com/aertslab/cisTopic.git") | |
6241 | (commit commit))) | |
6242 | (file-name (git-file-name name version)) | |
6243 | (sha256 | |
6244 | (base32 | |
6245 | "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) | |
6246 | (build-system r-build-system) | |
6247 | (propagated-inputs | |
6248 | `(("r-aucell" ,r-aucell) | |
6249 | ("r-data-table" ,r-data-table) | |
6250 | ("r-dplyr" ,r-dplyr) | |
6251 | ("r-dosnow" ,r-dosnow) | |
6252 | ("r-dt" ,r-dt) | |
6253 | ("r-feather" ,r-feather) | |
6254 | ("r-fitdistrplus" ,r-fitdistrplus) | |
6255 | ("r-genomicranges" ,r-genomicranges) | |
6256 | ("r-ggplot2" ,r-ggplot2) | |
6257 | ("r-lda" ,r-lda) | |
6258 | ("r-matrix" ,r-matrix) | |
6259 | ("r-plyr" ,r-plyr) | |
6260 | ("r-rcistarget" ,r-rcistarget) | |
6261 | ("r-rtracklayer" ,r-rtracklayer) | |
6262 | ("r-s4vectors" ,r-s4vectors))) | |
6263 | (home-page "https://github.com/aertslab/cisTopic") | |
6264 | (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") | |
6265 | (description | |
6266 | "The sparse nature of single cell epigenomics data can be overruled using | |
6267 | probabilistic modelling methods such as @dfn{Latent Dirichlet | |
6268 | Allocation} (LDA). This package allows the probabilistic modelling of | |
6269 | cis-regulatory topics (cisTopics) from single cell epigenomics data, and | |
6270 | includes functionalities to identify cell states based on the contribution of | |
6271 | cisTopics and explore the nature and regulatory proteins driving them.") | |
6272 | (license license:gpl3)))) | |
d85c0f98 RW |
6273 | |
6274 | (define-public r-genie3 | |
6275 | (package | |
6276 | (name "r-genie3") | |
33ce50e3 | 6277 | (version "1.8.0") |
d85c0f98 RW |
6278 | (source |
6279 | (origin | |
6280 | (method url-fetch) | |
6281 | (uri (bioconductor-uri "GENIE3" version)) | |
6282 | (sha256 | |
6283 | (base32 | |
33ce50e3 | 6284 | "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l")))) |
d85c0f98 RW |
6285 | (properties `((upstream-name . "GENIE3"))) |
6286 | (build-system r-build-system) | |
6287 | (propagated-inputs `(("r-reshape2" ,r-reshape2))) | |
6288 | (home-page "https://bioconductor.org/packages/GENIE3") | |
6289 | (synopsis "Gene network inference with ensemble of trees") | |
6290 | (description | |
6291 | "This package implements the GENIE3 algorithm for inferring gene | |
6292 | regulatory networks from expression data.") | |
6293 | (license license:gpl2+))) | |
db316d73 RW |
6294 | |
6295 | (define-public r-roc | |
6296 | (package | |
6297 | (name "r-roc") | |
3672b74f | 6298 | (version "1.62.0") |
db316d73 RW |
6299 | (source |
6300 | (origin | |
6301 | (method url-fetch) | |
6302 | (uri (bioconductor-uri "ROC" version)) | |
6303 | (sha256 | |
6304 | (base32 | |
3672b74f | 6305 | "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y")))) |
db316d73 RW |
6306 | (properties `((upstream-name . "ROC"))) |
6307 | (build-system r-build-system) | |
3672b74f RW |
6308 | (propagated-inputs |
6309 | `(("r-knitr" ,r-knitr))) | |
db316d73 RW |
6310 | (home-page "https://www.bioconductor.org/packages/ROC/") |
6311 | (synopsis "Utilities for ROC curves") | |
6312 | (description | |
6313 | "This package provides utilities for @dfn{Receiver Operating | |
6314 | Characteristic} (ROC) curves, with a focus on micro arrays.") | |
6315 | (license license:artistic2.0))) | |
46721dea RW |
6316 | |
6317 | (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 | |
6318 | (package | |
6319 | (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") | |
6320 | (version "0.6.0") | |
6321 | (source | |
6322 | (origin | |
6323 | (method url-fetch) | |
6324 | (uri (bioconductor-uri | |
6325 | "IlluminaHumanMethylation450kanno.ilmn12.hg19" | |
6326 | version 'annotation)) | |
6327 | (sha256 | |
6328 | (base32 | |
6329 | "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) | |
6330 | (properties | |
6331 | `((upstream-name | |
6332 | . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) | |
6333 | (build-system r-build-system) | |
6334 | (propagated-inputs `(("r-minfi" ,r-minfi))) | |
6335 | (home-page | |
6336 | "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") | |
6337 | (synopsis "Annotation for Illumina's 450k methylation arrays") | |
6338 | (description | |
6339 | "This package provides manifests and annotation for Illumina's 450k array | |
6340 | data.") | |
6341 | (license license:artistic2.0))) | |
38babeaa RW |
6342 | |
6343 | (define-public r-watermelon | |
6344 | (package | |
6345 | (name "r-watermelon") | |
9eade229 | 6346 | (version "1.30.0") |
38babeaa RW |
6347 | (source |
6348 | (origin | |
6349 | (method url-fetch) | |
6350 | (uri (bioconductor-uri "wateRmelon" version)) | |
6351 | (sha256 | |
6352 | (base32 | |
9eade229 | 6353 | "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0")))) |
38babeaa RW |
6354 | (properties `((upstream-name . "wateRmelon"))) |
6355 | (build-system r-build-system) | |
6356 | (propagated-inputs | |
6357 | `(("r-biobase" ,r-biobase) | |
6358 | ("r-illuminahumanmethylation450kanno-ilmn12-hg19" | |
6359 | ,r-illuminahumanmethylation450kanno-ilmn12-hg19) | |
6360 | ("r-illuminaio" ,r-illuminaio) | |
6361 | ("r-limma" ,r-limma) | |
6362 | ("r-lumi" ,r-lumi) | |
6363 | ("r-matrixstats" ,r-matrixstats) | |
6364 | ("r-methylumi" ,r-methylumi) | |
6365 | ("r-roc" ,r-roc))) | |
6366 | (home-page "https://bioconductor.org/packages/wateRmelon/") | |
6367 | (synopsis "Illumina 450 methylation array normalization and metrics") | |
6368 | (description | |
6369 | "The standard index of DNA methylation (beta) is computed from methylated | |
6370 | and unmethylated signal intensities. Betas calculated from raw signal | |
6371 | intensities perform well, but using 11 methylomic datasets we demonstrate that | |
6372 | quantile normalization methods produce marked improvement. The commonly used | |
6373 | procedure of normalizing betas is inferior to the separate normalization of M | |
6374 | and U, and it is also advantageous to normalize Type I and Type II assays | |
6375 | separately. This package provides 15 flavours of betas and three performance | |
6376 | metrics, with methods for objects produced by the @code{methylumi} and | |
6377 | @code{minfi} packages.") | |
6378 | (license license:gpl3))) | |
7d2cb646 RW |
6379 | |
6380 | (define-public r-gdsfmt | |
6381 | (package | |
6382 | (name "r-gdsfmt") | |
f5ef7dd6 | 6383 | (version "1.22.0") |
7d2cb646 RW |
6384 | (source |
6385 | (origin | |
6386 | (method url-fetch) | |
6387 | (uri (bioconductor-uri "gdsfmt" version)) | |
6388 | (sha256 | |
6389 | (base32 | |
f5ef7dd6 | 6390 | "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9")) |
7d2cb646 RW |
6391 | (modules '((guix build utils))) |
6392 | ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build | |
6393 | ;; them and link with system libraries instead. | |
6394 | (snippet | |
6395 | '(begin | |
6396 | (for-each delete-file-recursively | |
6397 | '("src/LZ4" | |
6398 | "src/XZ" | |
6399 | "src/ZLIB")) | |
6400 | (substitute* "src/Makevars" | |
6401 | (("all: \\$\\(SHLIB\\)") "all:") | |
6402 | (("\\$\\(SHLIB\\): liblzma.a") "") | |
6403 | (("(ZLIB|LZ4)/.*") "") | |
6404 | (("CoreArray/dVLIntGDS.cpp.*") | |
6405 | "CoreArray/dVLIntGDS.cpp") | |
6406 | (("CoreArray/dVLIntGDS.o.*") | |
6407 | "CoreArray/dVLIntGDS.o") | |
6408 | (("PKG_LIBS = ./liblzma.a") | |
6409 | "PKG_LIBS = -llz4")) | |
6410 | (substitute* "src/CoreArray/dStream.h" | |
6411 | (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) | |
6412 | (string-append "include <" header ">"))) | |
6413 | #t)))) | |
6414 | (properties `((upstream-name . "gdsfmt"))) | |
6415 | (build-system r-build-system) | |
6416 | (inputs | |
6417 | `(("lz4" ,lz4) | |
6418 | ("xz" ,xz) | |
6419 | ("zlib" ,zlib))) | |
6420 | (home-page "http://corearray.sourceforge.net/") | |
6421 | (synopsis | |
6422 | "R Interface to CoreArray Genomic Data Structure (GDS) Files") | |
6423 | (description | |
6424 | "This package provides a high-level R interface to CoreArray @dfn{Genomic | |
6425 | Data Structure} (GDS) data files, which are portable across platforms with | |
6426 | hierarchical structure to store multiple scalable array-oriented data sets | |
6427 | with metadata information. It is suited for large-scale datasets, especially | |
6428 | for data which are much larger than the available random-access memory. The | |
6429 | @code{gdsfmt} package offers efficient operations specifically designed for | |
6430 | integers of less than 8 bits, since a diploid genotype, like | |
6431 | @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a | |
6432 | byte. Data compression and decompression are available with relatively | |
6433 | efficient random access. It is also allowed to read a GDS file in parallel | |
6434 | with multiple R processes supported by the package @code{parallel}.") | |
6435 | (license license:lgpl3))) | |
6b5f59c7 RW |
6436 | |
6437 | (define-public r-bigmelon | |
6438 | (package | |
6439 | (name "r-bigmelon") | |
8b941a50 | 6440 | (version "1.12.0") |
6b5f59c7 RW |
6441 | (source |
6442 | (origin | |
6443 | (method url-fetch) | |
6444 | (uri (bioconductor-uri "bigmelon" version)) | |
6445 | (sha256 | |
6446 | (base32 | |
8b941a50 | 6447 | "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls")))) |
6b5f59c7 RW |
6448 | (properties `((upstream-name . "bigmelon"))) |
6449 | (build-system r-build-system) | |
6450 | (propagated-inputs | |
6451 | `(("r-biobase" ,r-biobase) | |
6452 | ("r-biocgenerics" ,r-biocgenerics) | |
6453 | ("r-gdsfmt" ,r-gdsfmt) | |
6454 | ("r-geoquery" ,r-geoquery) | |
6455 | ("r-methylumi" ,r-methylumi) | |
6456 | ("r-minfi" ,r-minfi) | |
6457 | ("r-watermelon" ,r-watermelon))) | |
6458 | (home-page "https://bioconductor.org/packages/bigmelon/") | |
6459 | (synopsis "Illumina methylation array analysis for large experiments") | |
6460 | (description | |
6461 | "This package provides methods for working with Illumina arrays using the | |
6462 | @code{gdsfmt} package.") | |
6463 | (license license:gpl3))) | |
739b2d10 | 6464 | |
e5dfcd8e RW |
6465 | (define-public r-seqbias |
6466 | (package | |
6467 | (name "r-seqbias") | |
2223bbc7 | 6468 | (version "1.34.0") |
e5dfcd8e RW |
6469 | (source |
6470 | (origin | |
6471 | (method url-fetch) | |
6472 | (uri (bioconductor-uri "seqbias" version)) | |
6473 | (sha256 | |
6474 | (base32 | |
2223bbc7 | 6475 | "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq")))) |
e5dfcd8e RW |
6476 | (properties `((upstream-name . "seqbias"))) |
6477 | (build-system r-build-system) | |
6478 | (propagated-inputs | |
6479 | `(("r-biostrings" ,r-biostrings) | |
6480 | ("r-genomicranges" ,r-genomicranges) | |
6481 | ("r-rhtslib" ,r-rhtslib))) | |
6482 | (inputs | |
6483 | `(("zlib" ,zlib))) ; This comes from rhtslib. | |
6484 | (home-page "https://bioconductor.org/packages/seqbias/") | |
6485 | (synopsis "Estimation of per-position bias in high-throughput sequencing data") | |
6486 | (description | |
6487 | "This package implements a model of per-position sequencing bias in | |
6488 | high-throughput sequencing data using a simple Bayesian network, the structure | |
6489 | and parameters of which are trained on a set of aligned reads and a reference | |
6490 | genome sequence.") | |
6491 | (license license:lgpl3))) | |
6492 | ||
63daca1e RJ |
6493 | (define-public r-snplocs-hsapiens-dbsnp144-grch37 |
6494 | (package | |
6495 | (name "r-snplocs-hsapiens-dbsnp144-grch37") | |
6496 | (version "0.99.20") | |
6497 | (source (origin | |
6498 | (method url-fetch) | |
6499 | (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" | |
6500 | version 'annotation)) | |
6501 | (sha256 | |
6502 | (base32 | |
6503 | "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) | |
6504 | (build-system r-build-system) | |
6505 | ;; As this package provides little more than a very large data file it | |
6506 | ;; doesn't make sense to build substitutes. | |
6507 | (arguments `(#:substitutable? #f)) | |
6508 | (propagated-inputs | |
6509 | `(("r-biocgenerics" ,r-biocgenerics) | |
6510 | ("r-s4vectors" ,r-s4vectors) | |
6511 | ("r-iranges" ,r-iranges) | |
6512 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6513 | ("r-genomicranges" ,r-genomicranges) | |
6514 | ("r-bsgenome" ,r-bsgenome) | |
6515 | ("r-biostrings" ,r-biostrings))) | |
6516 | (home-page | |
6517 | "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") | |
6518 | (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") | |
6519 | (description "This package provides SNP locations and alleles for Homo | |
6520 | sapiens extracted from NCBI dbSNP Build 144. The source data files used for | |
6521 | this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped | |
6522 | to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a | |
6523 | patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, | |
1408e2ab | 6524 | X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for |
63daca1e RJ |
6525 | the mitochondrion chromosome. Therefore, the SNPs in this package can be |
6526 | injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the | |
6527 | correct position but this injection will exclude chrM (i.e. nothing will be | |
6528 | injected in that sequence).") | |
6529 | (license license:artistic2.0))) | |
6530 | ||
bb0024dc RW |
6531 | (define-public r-reqon |
6532 | (package | |
6533 | (name "r-reqon") | |
02c18abe | 6534 | (version "1.32.0") |
bb0024dc RW |
6535 | (source |
6536 | (origin | |
6537 | (method url-fetch) | |
6538 | (uri (bioconductor-uri "ReQON" version)) | |
6539 | (sha256 | |
6540 | (base32 | |
02c18abe | 6541 | "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx")))) |
bb0024dc RW |
6542 | (properties `((upstream-name . "ReQON"))) |
6543 | (build-system r-build-system) | |
6544 | (propagated-inputs | |
6545 | `(("r-rjava" ,r-rjava) | |
6546 | ("r-rsamtools" ,r-rsamtools) | |
6547 | ("r-seqbias" ,r-seqbias))) | |
6548 | (home-page "https://bioconductor.org/packages/ReQON/") | |
6549 | (synopsis "Recalibrating quality of nucleotides") | |
6550 | (description | |
6551 | "This package provides an implementation of an algorithm for | |
6552 | recalibrating the base quality scores for aligned sequencing data in BAM | |
6553 | format.") | |
6554 | (license license:gpl2))) | |
6555 | ||
739b2d10 RW |
6556 | (define-public r-wavcluster |
6557 | (package | |
6558 | (name "r-wavcluster") | |
c0cba4b5 | 6559 | (version "2.20.0") |
739b2d10 RW |
6560 | (source |
6561 | (origin | |
6562 | (method url-fetch) | |
6563 | (uri (bioconductor-uri "wavClusteR" version)) | |
6564 | (sha256 | |
6565 | (base32 | |
c0cba4b5 | 6566 | "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y")))) |
739b2d10 RW |
6567 | (properties `((upstream-name . "wavClusteR"))) |
6568 | (build-system r-build-system) | |
6569 | (propagated-inputs | |
6570 | `(("r-biocgenerics" ,r-biocgenerics) | |
6571 | ("r-biostrings" ,r-biostrings) | |
6572 | ("r-foreach" ,r-foreach) | |
6573 | ("r-genomicfeatures" ,r-genomicfeatures) | |
6574 | ("r-genomicranges" ,r-genomicranges) | |
6575 | ("r-ggplot2" ,r-ggplot2) | |
6576 | ("r-hmisc" ,r-hmisc) | |
6577 | ("r-iranges" ,r-iranges) | |
6578 | ("r-mclust" ,r-mclust) | |
6579 | ("r-rsamtools" ,r-rsamtools) | |
6580 | ("r-rtracklayer" ,r-rtracklayer) | |
6581 | ("r-s4vectors" ,r-s4vectors) | |
6582 | ("r-seqinr" ,r-seqinr) | |
6583 | ("r-stringr" ,r-stringr) | |
6584 | ("r-wmtsa" ,r-wmtsa))) | |
6585 | (home-page "https://bioconductor.org/packages/wavClusteR/") | |
6586 | (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") | |
6587 | (description | |
6588 | "This package provides an integrated pipeline for the analysis of | |
6589 | PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from | |
6590 | sequencing errors, SNPs and additional non-experimental sources by a non- | |
6591 | parametric mixture model. The protein binding sites (clusters) are then | |
6592 | resolved at high resolution and cluster statistics are estimated using a | |
6593 | rigorous Bayesian framework. Post-processing of the results, data export for | |
6594 | UCSC genome browser visualization and motif search analysis are provided. In | |
e40ecf8a | 6595 | addition, the package integrates RNA-Seq data to estimate the False |
739b2d10 RW |
6596 | Discovery Rate of cluster detection. Key functions support parallel multicore |
6597 | computing. While wavClusteR was designed for PAR-CLIP data analysis, it can | |
6598 | be applied to the analysis of other NGS data obtained from experimental | |
6599 | procedures that induce nucleotide substitutions (e.g. BisSeq).") | |
6600 | (license license:gpl2))) | |
853211a5 RW |
6601 | |
6602 | (define-public r-timeseriesexperiment | |
6603 | (package | |
6604 | (name "r-timeseriesexperiment") | |
cb734c60 | 6605 | (version "1.4.0") |
853211a5 RW |
6606 | (source |
6607 | (origin | |
6608 | (method url-fetch) | |
6609 | (uri (bioconductor-uri "TimeSeriesExperiment" version)) | |
6610 | (sha256 | |
6611 | (base32 | |
cb734c60 | 6612 | "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm")))) |
853211a5 RW |
6613 | (properties |
6614 | `((upstream-name . "TimeSeriesExperiment"))) | |
6615 | (build-system r-build-system) | |
6616 | (propagated-inputs | |
6617 | `(("r-deseq2" ,r-deseq2) | |
6618 | ("r-dplyr" ,r-dplyr) | |
6619 | ("r-dynamictreecut" ,r-dynamictreecut) | |
6620 | ("r-edger" ,r-edger) | |
6621 | ("r-ggplot2" ,r-ggplot2) | |
6622 | ("r-hmisc" ,r-hmisc) | |
6623 | ("r-limma" ,r-limma) | |
6624 | ("r-magrittr" ,r-magrittr) | |
6625 | ("r-proxy" ,r-proxy) | |
6626 | ("r-s4vectors" ,r-s4vectors) | |
6627 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6628 | ("r-tibble" ,r-tibble) | |
6629 | ("r-tidyr" ,r-tidyr) | |
6630 | ("r-vegan" ,r-vegan) | |
6631 | ("r-viridis" ,r-viridis))) | |
6632 | (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") | |
6633 | (synopsis "Analysis for short time-series data") | |
6634 | (description | |
6635 | "This package is a visualization and analysis toolbox for short time | |
6636 | course data which includes dimensionality reduction, clustering, two-sample | |
6637 | differential expression testing and gene ranking techniques. The package also | |
6638 | provides methods for retrieving enriched pathways.") | |
6639 | (license license:lgpl3+))) | |
df8576e5 RW |
6640 | |
6641 | (define-public r-variantfiltering | |
6642 | (package | |
6643 | (name "r-variantfiltering") | |
6f5415d5 | 6644 | (version "1.22.0") |
df8576e5 RW |
6645 | (source |
6646 | (origin | |
6647 | (method url-fetch) | |
6648 | (uri (bioconductor-uri "VariantFiltering" version)) | |
6649 | (sha256 | |
6650 | (base32 | |
6f5415d5 | 6651 | "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8")))) |
df8576e5 RW |
6652 | (properties |
6653 | `((upstream-name . "VariantFiltering"))) | |
6654 | (build-system r-build-system) | |
6655 | (propagated-inputs | |
6656 | `(("r-annotationdbi" ,r-annotationdbi) | |
6657 | ("r-biobase" ,r-biobase) | |
6658 | ("r-biocgenerics" ,r-biocgenerics) | |
6659 | ("r-biocparallel" ,r-biocparallel) | |
6660 | ("r-biostrings" ,r-biostrings) | |
6661 | ("r-bsgenome" ,r-bsgenome) | |
6662 | ("r-dt" ,r-dt) | |
6663 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6664 | ("r-genomicfeatures" ,r-genomicfeatures) | |
6665 | ("r-genomicranges" ,r-genomicranges) | |
6666 | ("r-genomicscores" ,r-genomicscores) | |
6667 | ("r-graph" ,r-graph) | |
6668 | ("r-gviz" ,r-gviz) | |
6669 | ("r-iranges" ,r-iranges) | |
6670 | ("r-rbgl" ,r-rbgl) | |
6671 | ("r-rsamtools" ,r-rsamtools) | |
6672 | ("r-s4vectors" ,r-s4vectors) | |
6673 | ("r-shiny" ,r-shiny) | |
6674 | ("r-shinyjs" ,r-shinyjs) | |
6675 | ("r-shinythemes" ,r-shinythemes) | |
6676 | ("r-shinytree" ,r-shinytree) | |
6677 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6678 | ("r-variantannotation" ,r-variantannotation) | |
6679 | ("r-xvector" ,r-xvector))) | |
6680 | (home-page "https://github.com/rcastelo/VariantFiltering") | |
6681 | (synopsis "Filtering of coding and non-coding genetic variants") | |
6682 | (description | |
6683 | "Filter genetic variants using different criteria such as inheritance | |
6684 | model, amino acid change consequence, minor allele frequencies across human | |
6685 | populations, splice site strength, conservation, etc.") | |
6686 | (license license:artistic2.0))) | |
f5349b4d RW |
6687 | |
6688 | (define-public r-genomegraphs | |
6689 | (package | |
6690 | (name "r-genomegraphs") | |
053a2127 | 6691 | (version "1.46.0") |
f5349b4d RW |
6692 | (source |
6693 | (origin | |
6694 | (method url-fetch) | |
6695 | (uri (bioconductor-uri "GenomeGraphs" version)) | |
6696 | (sha256 | |
6697 | (base32 | |
053a2127 | 6698 | "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) |
f5349b4d RW |
6699 | (properties `((upstream-name . "GenomeGraphs"))) |
6700 | (build-system r-build-system) | |
6701 | (propagated-inputs | |
6702 | `(("r-biomart" ,r-biomart))) | |
6703 | (home-page "https://bioconductor.org/packages/GenomeGraphs/") | |
6704 | (synopsis "Plotting genomic information from Ensembl") | |
6705 | (description | |
6706 | "Genomic data analyses requires integrated visualization of known genomic | |
6707 | information and new experimental data. GenomeGraphs uses the biomaRt package | |
6708 | to perform live annotation queries to Ensembl and translates this to e.g. | |
6709 | gene/transcript structures in viewports of the grid graphics package. This | |
6710 | results in genomic information plotted together with your data. Another | |
6711 | strength of GenomeGraphs is to plot different data types such as array CGH, | |
6712 | gene expression, sequencing and other data, together in one plot using the | |
6713 | same genome coordinate system.") | |
6714 | (license license:artistic2.0))) | |
2a360cf6 RW |
6715 | |
6716 | (define-public r-wavetiling | |
6717 | (package | |
6718 | (name "r-wavetiling") | |
e13f9773 | 6719 | (version "1.28.0") |
2a360cf6 RW |
6720 | (source |
6721 | (origin | |
6722 | (method url-fetch) | |
6723 | (uri (bioconductor-uri "waveTiling" version)) | |
6724 | (sha256 | |
6725 | (base32 | |
e13f9773 | 6726 | "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) |
2a360cf6 RW |
6727 | (properties `((upstream-name . "waveTiling"))) |
6728 | (build-system r-build-system) | |
6729 | (propagated-inputs | |
6730 | `(("r-affy" ,r-affy) | |
6731 | ("r-biobase" ,r-biobase) | |
6732 | ("r-biostrings" ,r-biostrings) | |
6733 | ("r-genomegraphs" ,r-genomegraphs) | |
6734 | ("r-genomicranges" ,r-genomicranges) | |
6735 | ("r-iranges" ,r-iranges) | |
6736 | ("r-oligo" ,r-oligo) | |
6737 | ("r-oligoclasses" ,r-oligoclasses) | |
6738 | ("r-preprocesscore" ,r-preprocesscore) | |
6739 | ("r-waveslim" ,r-waveslim))) | |
6740 | (home-page "https://r-forge.r-project.org/projects/wavetiling/") | |
6741 | (synopsis "Wavelet-based models for tiling array transcriptome analysis") | |
6742 | (description | |
6743 | "This package is designed to conduct transcriptome analysis for tiling | |
6744 | arrays based on fast wavelet-based functional models.") | |
6745 | (license license:gpl2+))) | |
d80a1569 RW |
6746 | |
6747 | (define-public r-variancepartition | |
6748 | (package | |
6749 | (name "r-variancepartition") | |
d1ac6430 | 6750 | (version "1.16.1") |
d80a1569 RW |
6751 | (source |
6752 | (origin | |
6753 | (method url-fetch) | |
6754 | (uri (bioconductor-uri "variancePartition" version)) | |
6755 | (sha256 | |
6756 | (base32 | |
d1ac6430 | 6757 | "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g")))) |
d80a1569 RW |
6758 | (properties |
6759 | `((upstream-name . "variancePartition"))) | |
6760 | (build-system r-build-system) | |
6761 | (propagated-inputs | |
6762 | `(("r-biobase" ,r-biobase) | |
326746e1 | 6763 | ("r-biocparallel" ,r-biocparallel) |
d80a1569 RW |
6764 | ("r-colorramps" ,r-colorramps) |
6765 | ("r-doparallel" ,r-doparallel) | |
6766 | ("r-foreach" ,r-foreach) | |
6767 | ("r-ggplot2" ,r-ggplot2) | |
6768 | ("r-gplots" ,r-gplots) | |
6769 | ("r-iterators" ,r-iterators) | |
6770 | ("r-limma" ,r-limma) | |
6771 | ("r-lme4" ,r-lme4) | |
6772 | ("r-lmertest" ,r-lmertest) | |
6773 | ("r-mass" ,r-mass) | |
6774 | ("r-pbkrtest" ,r-pbkrtest) | |
6775 | ("r-progress" ,r-progress) | |
6776 | ("r-reshape2" ,r-reshape2) | |
6777 | ("r-scales" ,r-scales))) | |
6778 | (home-page "https://bioconductor.org/packages/variancePartition/") | |
6779 | (synopsis "Analyze variation in gene expression experiments") | |
6780 | (description | |
6781 | "This is a package providing tools to quantify and interpret multiple | |
6782 | sources of biological and technical variation in gene expression experiments. | |
6783 | It uses a linear mixed model to quantify variation in gene expression | |
6784 | attributable to individual, tissue, time point, or technical variables. The | |
6785 | package includes dream differential expression analysis for repeated | |
6786 | measures.") | |
6787 | (license license:gpl2+))) | |
16e2e4f2 | 6788 | |
6789 | (define-public r-htqpcr | |
6790 | (package | |
6791 | (name "r-htqpcr") | |
0b0906c8 | 6792 | (version "1.40.0") |
16e2e4f2 | 6793 | (source |
6794 | (origin | |
6795 | (method url-fetch) | |
6796 | (uri (bioconductor-uri "HTqPCR" version)) | |
6797 | (sha256 | |
6798 | (base32 | |
0b0906c8 | 6799 | "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx")))) |
16e2e4f2 | 6800 | (properties `((upstream-name . "HTqPCR"))) |
6801 | (build-system r-build-system) | |
6802 | (propagated-inputs | |
6803 | `(("r-affy" ,r-affy) | |
6804 | ("r-biobase" ,r-biobase) | |
6805 | ("r-gplots" ,r-gplots) | |
6806 | ("r-limma" ,r-limma) | |
6807 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
486a0800 TGR |
6808 | (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" |
6809 | "groups/bertone/software/HTqPCR.pdf")) | |
16e2e4f2 | 6810 | (synopsis "Automated analysis of high-throughput qPCR data") |
6811 | (description | |
6812 | "Analysis of Ct values from high throughput quantitative real-time | |
6813 | PCR (qPCR) assays across multiple conditions or replicates. The input data | |
6814 | can be from spatially-defined formats such ABI TaqMan Low Density Arrays or | |
6815 | OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad | |
6816 | Laboratories; conventional 96- or 384-well plates; or microfluidic devices | |
6817 | such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data | |
6818 | loading, quality assessment, normalization, visualization and parametric or | |
6819 | non-parametric testing for statistical significance in Ct values between | |
6820 | features (e.g. genes, microRNAs).") | |
6821 | (license license:artistic2.0))) | |
86fb2c63 | 6822 | |
6823 | (define-public r-unifiedwmwqpcr | |
6824 | (package | |
6825 | (name "r-unifiedwmwqpcr") | |
989be6df | 6826 | (version "1.22.0") |
86fb2c63 | 6827 | (source |
6828 | (origin | |
6829 | (method url-fetch) | |
6830 | (uri (bioconductor-uri "unifiedWMWqPCR" version)) | |
6831 | (sha256 | |
6832 | (base32 | |
989be6df | 6833 | "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj")))) |
86fb2c63 | 6834 | (properties |
6835 | `((upstream-name . "unifiedWMWqPCR"))) | |
6836 | (build-system r-build-system) | |
6837 | (propagated-inputs | |
6838 | `(("r-biocgenerics" ,r-biocgenerics) | |
6839 | ("r-htqpcr" ,r-htqpcr))) | |
6840 | (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") | |
6841 | (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") | |
6842 | (description | |
b5b0ee3b | 6843 | "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR |
86fb2c63 | 6844 | data. This modified test allows for testing differential expression in qPCR |
6845 | data.") | |
6846 | (license license:gpl2+))) | |
72b67e0b RW |
6847 | |
6848 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put | |
6849 | ;; it here. | |
6850 | (define-public r-activedriverwgs | |
6851 | (package | |
6852 | (name "r-activedriverwgs") | |
6853 | (version "1.0.1") | |
6854 | (source | |
6855 | (origin | |
6856 | (method url-fetch) | |
6857 | (uri (cran-uri "ActiveDriverWGS" version)) | |
6858 | (sha256 | |
6859 | (base32 | |
6860 | "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1")))) | |
6861 | (properties | |
6862 | `((upstream-name . "ActiveDriverWGS"))) | |
6863 | (build-system r-build-system) | |
6864 | (propagated-inputs | |
6865 | `(("r-biostrings" ,r-biostrings) | |
6866 | ("r-bsgenome" ,r-bsgenome) | |
6867 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
6868 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6869 | ("r-genomicranges" ,r-genomicranges) | |
6870 | ("r-iranges" ,r-iranges) | |
6871 | ("r-plyr" ,r-plyr) | |
6872 | ("r-s4vectors" ,r-s4vectors))) | |
6873 | (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") | |
6874 | (synopsis "Driver discovery tool for cancer whole genomes") | |
6875 | (description | |
6876 | "This package provides a method for finding an enrichment of cancer | |
6877 | simple somatic mutations (SNVs and Indels) in functional elements across the | |
6878 | human genome. ActiveDriverWGS detects coding and noncoding driver elements | |
6879 | using whole genome sequencing data.") | |
6880 | (license license:gpl3))) | |
8e6f63dd RW |
6881 | |
6882 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put | |
6883 | ;; it here. | |
6884 | (define-public r-activepathways | |
6885 | (package | |
6886 | (name "r-activepathways") | |
6887 | (version "1.0.1") | |
6888 | (source | |
6889 | (origin | |
6890 | (method url-fetch) | |
6891 | (uri (cran-uri "ActivePathways" version)) | |
6892 | (sha256 | |
6893 | (base32 | |
6894 | "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20")))) | |
6895 | (properties | |
6896 | `((upstream-name . "ActivePathways"))) | |
6897 | (build-system r-build-system) | |
6898 | (propagated-inputs | |
6899 | `(("r-data-table" ,r-data-table) | |
6900 | ("r-ggplot2" ,r-ggplot2) | |
6901 | ("r-metap" ,r-metap))) | |
229736aa RW |
6902 | (native-inputs |
6903 | `(("r-knitr" ,r-knitr))) | |
8e6f63dd RW |
6904 | (home-page "https://cran.r-project.org/web/packages/ActivePathways/") |
6905 | (synopsis "Multivariate pathway enrichment analysis") | |
6906 | (description | |
6907 | "This package represents an integrative method of analyzing multi omics | |
6908 | data that conducts enrichment analysis of annotated gene sets. ActivePathways | |
6909 | uses a statistical data fusion approach, rationalizes contributing evidence | |
6910 | and highlights associated genes, improving systems-level understanding of | |
6911 | cellular organization in health and disease.") | |
6912 | (license license:gpl3))) | |
d11d6fea RW |
6913 | |
6914 | (define-public r-bgmix | |
6915 | (package | |
6916 | (name "r-bgmix") | |
6917 | (version "1.46.0") | |
6918 | (source | |
6919 | (origin | |
6920 | (method url-fetch) | |
6921 | (uri (bioconductor-uri "BGmix" version)) | |
6922 | (sha256 | |
6923 | (base32 | |
6924 | "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683")))) | |
6925 | (properties `((upstream-name . "BGmix"))) | |
6926 | (build-system r-build-system) | |
6927 | (propagated-inputs | |
6928 | `(("r-kernsmooth" ,r-kernsmooth))) | |
6929 | (home-page "https://bioconductor.org/packages/BGmix/") | |
6930 | (synopsis "Bayesian models for differential gene expression") | |
6931 | (description | |
6932 | "This package provides fully Bayesian mixture models for differential | |
6933 | gene expression.") | |
6934 | (license license:gpl2))) | |
75eb1149 RW |
6935 | |
6936 | (define-public r-bgx | |
6937 | (package | |
6938 | (name "r-bgx") | |
6939 | (version "1.52.0") | |
6940 | (source | |
6941 | (origin | |
6942 | (method url-fetch) | |
6943 | (uri (bioconductor-uri "bgx" version)) | |
6944 | (sha256 | |
6945 | (base32 | |
6946 | "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm")))) | |
6947 | (properties `((upstream-name . "bgx"))) | |
6948 | (build-system r-build-system) | |
6949 | (propagated-inputs | |
6950 | `(("r-affy" ,r-affy) | |
6951 | ("r-biobase" ,r-biobase) | |
6952 | ("r-gcrma" ,r-gcrma) | |
6953 | ("r-rcpp" ,r-rcpp))) | |
6954 | (home-page "https://bioconductor.org/packages/bgx/") | |
6955 | (synopsis "Bayesian gene expression") | |
6956 | (description | |
6957 | "This package provides tools for Bayesian integrated analysis of | |
6958 | Affymetrix GeneChips.") | |
6959 | (license license:gpl2))) | |
6bd50acf RW |
6960 | |
6961 | (define-public r-bhc | |
6962 | (package | |
6963 | (name "r-bhc") | |
6964 | (version "1.38.0") | |
6965 | (source | |
6966 | (origin | |
6967 | (method url-fetch) | |
6968 | (uri (bioconductor-uri "BHC" version)) | |
6969 | (sha256 | |
6970 | (base32 | |
6971 | "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh")))) | |
6972 | (properties `((upstream-name . "BHC"))) | |
6973 | (build-system r-build-system) | |
6974 | (home-page "https://bioconductor.org/packages/BHC/") | |
6975 | (synopsis "Bayesian hierarchical clustering") | |
6976 | (description | |
6977 | "The method implemented in this package performs bottom-up hierarchical | |
6978 | clustering, using a Dirichlet Process (infinite mixture) to model uncertainty | |
6979 | in the data and Bayesian model selection to decide at each step which clusters | |
6980 | to merge. This avoids several limitations of traditional methods, for example | |
6981 | how many clusters there should be and how to choose a principled distance | |
6982 | metric. This implementation accepts multinomial (i.e. discrete, with 2+ | |
6983 | categories) or time-series data. This version also includes a randomised | |
6984 | algorithm which is more efficient for larger data sets.") | |
6985 | (license license:gpl3))) | |
de9374b7 RW |
6986 | |
6987 | (define-public r-bicare | |
6988 | (package | |
6989 | (name "r-bicare") | |
6990 | (version "1.44.0") | |
6991 | (source | |
6992 | (origin | |
6993 | (method url-fetch) | |
6994 | (uri (bioconductor-uri "BicARE" version)) | |
6995 | (sha256 | |
6996 | (base32 | |
6997 | "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs")))) | |
6998 | (properties `((upstream-name . "BicARE"))) | |
6999 | (build-system r-build-system) | |
7000 | (propagated-inputs | |
7001 | `(("r-biobase" ,r-biobase) | |
7002 | ("r-gseabase" ,r-gseabase) | |
7003 | ("r-multtest" ,r-multtest))) | |
7004 | (home-page "http://bioinfo.curie.fr") | |
7005 | (synopsis "Biclustering analysis and results exploration") | |
7006 | (description | |
7007 | "This is a package for biclustering analysis and exploration of | |
7008 | results.") | |
7009 | (license license:gpl2))) | |
40fe63ad RW |
7010 | |
7011 | (define-public r-bifet | |
7012 | (package | |
7013 | (name "r-bifet") | |
7014 | (version "1.6.0") | |
7015 | (source | |
7016 | (origin | |
7017 | (method url-fetch) | |
7018 | (uri (bioconductor-uri "BiFET" version)) | |
7019 | (sha256 | |
7020 | (base32 | |
7021 | "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k")))) | |
7022 | (properties `((upstream-name . "BiFET"))) | |
7023 | (build-system r-build-system) | |
7024 | (propagated-inputs | |
7025 | `(("r-genomicranges" ,r-genomicranges) | |
7026 | ("r-poibin" ,r-poibin))) | |
7027 | (home-page "https://bioconductor.org/packages/BiFET") | |
7028 | (synopsis "Bias-free footprint enrichment test") | |
7029 | (description | |
7030 | "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are | |
7031 | over-represented in target regions compared to background regions after | |
7032 | correcting for the bias arising from the imbalance in read counts and GC | |
7033 | contents between the target and background regions. For a given TF k, BiFET | |
7034 | tests the null hypothesis that the target regions have the same probability of | |
7035 | having footprints for the TF k as the background regions while correcting for | |
7036 | the read count and GC content bias.") | |
7037 | (license license:gpl3))) | |
e823337c RW |
7038 | |
7039 | (define-public r-rsbml | |
7040 | (package | |
7041 | (name "r-rsbml") | |
7042 | (version "2.44.0") | |
7043 | (source | |
7044 | (origin | |
7045 | (method url-fetch) | |
7046 | (uri (bioconductor-uri "rsbml" version)) | |
7047 | (sha256 | |
7048 | (base32 | |
7049 | "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa")))) | |
7050 | (properties `((upstream-name . "rsbml"))) | |
7051 | (build-system r-build-system) | |
7052 | (inputs | |
7053 | `(("libsbml" ,libsbml) | |
7054 | ("zlib" ,zlib))) | |
7055 | (propagated-inputs | |
7056 | `(("r-biocgenerics" ,r-biocgenerics) | |
7057 | ("r-graph" ,r-graph))) | |
7058 | (native-inputs | |
7059 | `(("pkg-config" ,pkg-config))) | |
7060 | (home-page "http://www.sbml.org") | |
7061 | (synopsis "R support for SBML") | |
7062 | (description | |
7063 | "This package provides an R interface to libsbml for SBML parsing, | |
7064 | validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") | |
7065 | (license license:artistic2.0))) | |
75a8bb31 RW |
7066 | |
7067 | (define-public r-hypergraph | |
7068 | (package | |
7069 | (name "r-hypergraph") | |
7070 | (version "1.58.0") | |
7071 | (source | |
7072 | (origin | |
7073 | (method url-fetch) | |
7074 | (uri (bioconductor-uri "hypergraph" version)) | |
7075 | (sha256 | |
7076 | (base32 | |
7077 | "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m")))) | |
7078 | (properties `((upstream-name . "hypergraph"))) | |
7079 | (build-system r-build-system) | |
7080 | (propagated-inputs | |
7081 | `(("r-graph" ,r-graph))) | |
7082 | (home-page "https://bioconductor.org/packages/hypergraph") | |
7083 | (synopsis "Hypergraph data structures") | |
7084 | (description | |
7085 | "This package implements some simple capabilities for representing and | |
7086 | manipulating hypergraphs.") | |
7087 | (license license:artistic2.0))) | |
5aef09bd RW |
7088 | |
7089 | (define-public r-hyperdraw | |
7090 | (package | |
7091 | (name "r-hyperdraw") | |
7092 | (version "1.38.0") | |
7093 | (source | |
7094 | (origin | |
7095 | (method url-fetch) | |
7096 | (uri (bioconductor-uri "hyperdraw" version)) | |
7097 | (sha256 | |
7098 | (base32 | |
7099 | "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj")))) | |
7100 | (properties `((upstream-name . "hyperdraw"))) | |
7101 | (build-system r-build-system) | |
7102 | (inputs `(("graphviz" ,graphviz))) | |
7103 | (propagated-inputs | |
7104 | `(("r-graph" ,r-graph) | |
7105 | ("r-hypergraph" ,r-hypergraph) | |
7106 | ("r-rgraphviz" ,r-rgraphviz))) | |
7107 | (home-page "https://bioconductor.org/packages/hyperdraw") | |
7108 | (synopsis "Visualizing hypergraphs") | |
7109 | (description | |
7110 | "This package provides functions for visualizing hypergraphs.") | |
7111 | (license license:gpl2+))) | |
6ca6f866 RW |
7112 | |
7113 | (define-public r-biggr | |
7114 | (package | |
7115 | (name "r-biggr") | |
7116 | (version "1.22.0") | |
7117 | (source | |
7118 | (origin | |
7119 | (method url-fetch) | |
7120 | (uri (bioconductor-uri "BiGGR" version)) | |
7121 | (sha256 | |
7122 | (base32 | |
7123 | "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif")))) | |
7124 | (properties `((upstream-name . "BiGGR"))) | |
7125 | (build-system r-build-system) | |
7126 | (propagated-inputs | |
7127 | `(("r-hyperdraw" ,r-hyperdraw) | |
7128 | ("r-hypergraph" ,r-hypergraph) | |
7129 | ("r-lim" ,r-lim) | |
7130 | ("r-limsolve" ,r-limsolve) | |
7131 | ("r-rsbml" ,r-rsbml) | |
7132 | ("r-stringr" ,r-stringr))) | |
7133 | (home-page "https://bioconductor.org/packages/BiGGR/") | |
7134 | (synopsis "Constraint based modeling using metabolic reconstruction databases") | |
7135 | (description | |
7136 | "This package provides an interface to simulate metabolic reconstruction | |
7137 | from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic | |
7138 | reconstruction databases. The package facilitates @dfn{flux balance | |
7139 | analysis} (FBA) and the sampling of feasible flux distributions. Metabolic | |
7140 | networks and estimated fluxes can be visualized with hypergraphs.") | |
7141 | (license license:gpl3+))) | |
820373db RW |
7142 | |
7143 | (define-public r-bigmemoryextras | |
7144 | (package | |
7145 | (name "r-bigmemoryextras") | |
7146 | (version "1.34.0") | |
7147 | (source | |
7148 | (origin | |
7149 | (method url-fetch) | |
7150 | (uri (bioconductor-uri "bigmemoryExtras" version)) | |
7151 | (sha256 | |
7152 | (base32 | |
7153 | "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq")))) | |
7154 | (properties | |
7155 | `((upstream-name . "bigmemoryExtras"))) | |
7156 | (build-system r-build-system) | |
7157 | (propagated-inputs | |
7158 | `(("r-bigmemory" ,r-bigmemory))) | |
7159 | (home-page "https://github.com/phaverty/bigmemoryExtras") | |
7160 | (synopsis "Extension of the bigmemory package") | |
7161 | (description | |
7162 | "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds | |
7163 | safety and convenience features to the @code{filebacked.big.matrix} class from | |
7164 | the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by | |
7165 | monitoring and gracefully restoring the connection to on-disk data and it also | |
7166 | protects against accidental data modification with a filesystem-based | |
7167 | permissions system. Utilities are provided for using @code{BigMatrix}-derived | |
7168 | classes as @code{assayData} matrices within the @code{Biobase} package's | |
7169 | @code{eSet} family of classes. @code{BigMatrix} provides some optimizations | |
7170 | related to attaching to, and indexing into, file-backed matrices with | |
7171 | dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, | |
7172 | a file-backed matrix with factor properties.") | |
7173 | (license license:artistic2.0))) | |
d38775b1 RW |
7174 | |
7175 | (define-public r-bigpint | |
7176 | (package | |
7177 | (name "r-bigpint") | |
1f2f01ae | 7178 | (version "1.2.2") |
d38775b1 RW |
7179 | (source |
7180 | (origin | |
7181 | (method url-fetch) | |
7182 | (uri (bioconductor-uri "bigPint" version)) | |
7183 | (sha256 | |
7184 | (base32 | |
1f2f01ae | 7185 | "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs")))) |
d38775b1 RW |
7186 | (properties `((upstream-name . "bigPint"))) |
7187 | (build-system r-build-system) | |
7188 | (propagated-inputs | |
7189 | `(("r-dplyr" ,r-dplyr) | |
7190 | ("r-ggally" ,r-ggally) | |
7191 | ("r-ggplot2" ,r-ggplot2) | |
7192 | ("r-gridextra" ,r-gridextra) | |
7193 | ("r-hexbin" ,r-hexbin) | |
7194 | ("r-hmisc" ,r-hmisc) | |
7195 | ("r-htmlwidgets" ,r-htmlwidgets) | |
7196 | ("r-plotly" ,r-plotly) | |
7197 | ("r-plyr" ,r-plyr) | |
7198 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
7199 | ("r-reshape" ,r-reshape) | |
7200 | ("r-shiny" ,r-shiny) | |
7201 | ("r-shinycssloaders" ,r-shinycssloaders) | |
7202 | ("r-shinydashboard" ,r-shinydashboard) | |
7203 | ("r-stringr" ,r-stringr) | |
7204 | ("r-tidyr" ,r-tidyr))) | |
1f2f01ae RW |
7205 | (native-inputs |
7206 | `(("r-knitr" ,r-knitr))) | |
d38775b1 RW |
7207 | (home-page "https://github.com/lindsayrutter/bigPint") |
7208 | (synopsis "Big multivariate data plotted interactively") | |
7209 | (description | |
7210 | "This package provides methods for visualizing large multivariate | |
7211 | datasets using static and interactive scatterplot matrices, parallel | |
7212 | coordinate plots, volcano plots, and litre plots. It includes examples for | |
7213 | visualizing RNA-sequencing datasets and differentially expressed genes.") | |
7214 | (license license:gpl3))) | |
991554fc RW |
7215 | |
7216 | (define-public r-chemminer | |
7217 | (package | |
7218 | (name "r-chemminer") | |
7219 | (version "3.38.0") | |
7220 | (source | |
7221 | (origin | |
7222 | (method url-fetch) | |
7223 | (uri (bioconductor-uri "ChemmineR" version)) | |
7224 | (sha256 | |
7225 | (base32 | |
7226 | "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga")))) | |
7227 | (properties `((upstream-name . "ChemmineR"))) | |
7228 | (build-system r-build-system) | |
7229 | (propagated-inputs | |
7230 | `(("r-base64enc" ,r-base64enc) | |
7231 | ("r-bh" ,r-bh) | |
7232 | ("r-biocgenerics" ,r-biocgenerics) | |
7233 | ("r-dbi" ,r-dbi) | |
7234 | ("r-digest" ,r-digest) | |
7235 | ("r-dt" ,r-dt) | |
7236 | ("r-ggplot2" ,r-ggplot2) | |
7237 | ("r-gridextra" ,r-gridextra) | |
7238 | ("r-png" ,r-png) | |
7239 | ("r-rcpp" ,r-rcpp) | |
7240 | ("r-rcurl" ,r-rcurl) | |
7241 | ("r-rjson" ,r-rjson) | |
7242 | ("r-rsvg" ,r-rsvg))) | |
7243 | (home-page "https://github.com/girke-lab/ChemmineR") | |
7244 | (synopsis "Cheminformatics toolkit for R") | |
7245 | (description | |
7246 | "ChemmineR is a cheminformatics package for analyzing drug-like small | |
7247 | molecule data in R. It contains functions for efficient processing of large | |
7248 | numbers of molecules, physicochemical/structural property predictions, | |
7249 | structural similarity searching, classification and clustering of compound | |
7250 | libraries with a wide spectrum of algorithms. In addition, it offers | |
7251 | visualization functions for compound clustering results and chemical | |
7252 | structures.") | |
7253 | (license license:artistic2.0))) | |
48bcbef0 RW |
7254 | |
7255 | (define-public r-bioassayr | |
7256 | (package | |
7257 | (name "r-bioassayr") | |
7258 | (version "1.24.0") | |
7259 | (source | |
7260 | (origin | |
7261 | (method url-fetch) | |
7262 | (uri (bioconductor-uri "bioassayR" version)) | |
7263 | (sha256 | |
7264 | (base32 | |
7265 | "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw")))) | |
7266 | (properties `((upstream-name . "bioassayR"))) | |
7267 | (build-system r-build-system) | |
7268 | (propagated-inputs | |
7269 | `(("r-biocgenerics" ,r-biocgenerics) | |
7270 | ("r-chemminer" ,r-chemminer) | |
7271 | ("r-dbi" ,r-dbi) | |
7272 | ("r-matrix" ,r-matrix) | |
7273 | ("r-rjson" ,r-rjson) | |
7274 | ("r-rsqlite" ,r-rsqlite) | |
7275 | ("r-xml" ,r-xml))) | |
faaf2b35 RW |
7276 | (native-inputs |
7277 | `(("r-knitr" ,r-knitr))) | |
48bcbef0 RW |
7278 | (home-page "https://github.com/TylerBackman/bioassayR") |
7279 | (synopsis "Cross-target analysis of small molecule bioactivity") | |
7280 | (description | |
7281 | "bioassayR is a computational tool that enables simultaneous analysis of | |
7282 | thousands of bioassay experiments performed over a diverse set of compounds | |
7283 | and biological targets. Unique features include support for large-scale | |
7284 | cross-target analyses of both public and custom bioassays, generation of | |
7285 | @dfn{high throughput screening fingerprints} (HTSFPs), and an optional | |
7286 | preloaded database that provides access to a substantial portion of publicly | |
7287 | available bioactivity data.") | |
7288 | (license license:artistic2.0))) | |
29fd736a RW |
7289 | |
7290 | (define-public r-biobroom | |
7291 | (package | |
7292 | (name "r-biobroom") | |
7293 | (version "1.18.0") | |
7294 | (source | |
7295 | (origin | |
7296 | (method url-fetch) | |
7297 | (uri (bioconductor-uri "biobroom" version)) | |
7298 | (sha256 | |
7299 | (base32 | |
7300 | "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb")))) | |
7301 | (properties `((upstream-name . "biobroom"))) | |
7302 | (build-system r-build-system) | |
7303 | (propagated-inputs | |
7304 | `(("r-biobase" ,r-biobase) | |
7305 | ("r-broom" ,r-broom) | |
7306 | ("r-dplyr" ,r-dplyr) | |
7307 | ("r-tidyr" ,r-tidyr))) | |
7308 | (home-page "https://github.com/StoreyLab/biobroom") | |
7309 | (synopsis "Turn Bioconductor objects into tidy data frames") | |
7310 | (description | |
7311 | "This package contains methods for converting standard objects | |
7312 | constructed by bioinformatics packages, especially those in Bioconductor, and | |
7313 | converting them to @code{tidy} data. It thus serves as a complement to the | |
7314 | @code{broom} package, and follows the same tidy, augment, glance division of | |
7315 | tidying methods. Tidying data makes it easy to recombine, reshape and | |
7316 | visualize bioinformatics analyses.") | |
7317 | ;; Any version of the LGPL. | |
7318 | (license license:lgpl3+))) | |
c373223e RW |
7319 | |
7320 | (define-public r-graphite | |
7321 | (package | |
7322 | (name "r-graphite") | |
7323 | (version "1.32.0") | |
7324 | (source | |
7325 | (origin | |
7326 | (method url-fetch) | |
7327 | (uri (bioconductor-uri "graphite" version)) | |
7328 | (sha256 | |
7329 | (base32 | |
7330 | "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd")))) | |
7331 | (properties `((upstream-name . "graphite"))) | |
7332 | (build-system r-build-system) | |
7333 | (propagated-inputs | |
7334 | `(("r-annotationdbi" ,r-annotationdbi) | |
7335 | ("r-checkmate" ,r-checkmate) | |
7336 | ("r-graph" ,r-graph) | |
7337 | ("r-httr" ,r-httr) | |
7338 | ("r-rappdirs" ,r-rappdirs))) | |
7339 | (home-page "https://bioconductor.org/packages/graphite/") | |
7340 | (synopsis "Networks from pathway databases") | |
7341 | (description | |
7342 | "Graphite provides networks derived from eight public pathway databases, | |
7343 | and automates the conversion of node identifiers (e.g. from Entrez IDs to gene | |
7344 | symbols).") | |
7345 | (license license:agpl3+))) | |
f388834e RW |
7346 | |
7347 | (define-public r-reactomepa | |
7348 | (package | |
7349 | (name "r-reactomepa") | |
7350 | (version "1.30.0") | |
7351 | (source | |
7352 | (origin | |
7353 | (method url-fetch) | |
7354 | (uri (bioconductor-uri "ReactomePA" version)) | |
7355 | (sha256 | |
7356 | (base32 | |
7357 | "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1")))) | |
7358 | (properties `((upstream-name . "ReactomePA"))) | |
7359 | (build-system r-build-system) | |
7360 | (propagated-inputs | |
7361 | `(("r-annotationdbi" ,r-annotationdbi) | |
7362 | ("r-dose" ,r-dose) | |
7363 | ("r-enrichplot" ,r-enrichplot) | |
7364 | ("r-ggplot2" ,r-ggplot2) | |
7365 | ("r-ggraph" ,r-ggraph) | |
7366 | ("r-graphite" ,r-graphite) | |
7367 | ("r-igraph" ,r-igraph) | |
7368 | ("r-reactome-db" ,r-reactome-db))) | |
7369 | (home-page "https://guangchuangyu.github.io/software/ReactomePA") | |
7370 | (synopsis "Reactome pathway analysis") | |
7371 | (description | |
7372 | "This package provides functions for pathway analysis based on the | |
7373 | REACTOME pathway database. It implements enrichment analysis, gene set | |
7374 | enrichment analysis and several functions for visualization.") | |
7375 | (license license:gpl2))) | |
21afe920 RW |
7376 | |
7377 | (define-public r-ebarrays | |
7378 | (package | |
7379 | (name "r-ebarrays") | |
7380 | (version "2.50.0") | |
7381 | (source | |
7382 | (origin | |
7383 | (method url-fetch) | |
7384 | (uri (bioconductor-uri "EBarrays" version)) | |
7385 | (sha256 | |
7386 | (base32 | |
7387 | "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13")))) | |
7388 | (properties `((upstream-name . "EBarrays"))) | |
7389 | (build-system r-build-system) | |
7390 | (propagated-inputs | |
7391 | `(("r-biobase" ,r-biobase) | |
7392 | ("r-cluster" ,r-cluster) | |
7393 | ("r-lattice" ,r-lattice))) | |
7394 | (home-page "https://bioconductor.org/packages/EBarrays/") | |
7395 | (synopsis "Gene clustering and differential expression identification") | |
7396 | (description | |
7397 | "EBarrays provides tools for the analysis of replicated/unreplicated | |
7398 | microarray data.") | |
7399 | (license license:gpl2+))) | |
f180be29 RW |
7400 | |
7401 | (define-public r-bioccasestudies | |
7402 | (package | |
7403 | (name "r-bioccasestudies") | |
7404 | (version "1.48.0") | |
7405 | (source | |
7406 | (origin | |
7407 | (method url-fetch) | |
7408 | (uri (bioconductor-uri "BiocCaseStudies" version)) | |
7409 | (sha256 | |
7410 | (base32 | |
7411 | "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd")))) | |
7412 | (properties | |
7413 | `((upstream-name . "BiocCaseStudies"))) | |
7414 | (build-system r-build-system) | |
7415 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
7416 | (home-page "https://bioconductor.org/packages/BiocCaseStudies") | |
7417 | (synopsis "Support for the case studies monograph") | |
7418 | (description | |
7419 | "This package provides software and data to support the case studies | |
7420 | monograph.") | |
7421 | (license license:artistic2.0))) | |
49f0860b RW |
7422 | |
7423 | (define-public r-biocgraph | |
7424 | (package | |
7425 | (name "r-biocgraph") | |
7426 | (version "1.48.0") | |
7427 | (source | |
7428 | (origin | |
7429 | (method url-fetch) | |
7430 | (uri (bioconductor-uri "biocGraph" version)) | |
7431 | (sha256 | |
7432 | (base32 | |
7433 | "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw")))) | |
7434 | (properties `((upstream-name . "biocGraph"))) | |
7435 | (build-system r-build-system) | |
7436 | (propagated-inputs | |
7437 | `(("r-biocgenerics" ,r-biocgenerics) | |
7438 | ("r-geneplotter" ,r-geneplotter) | |
7439 | ("r-graph" ,r-graph) | |
7440 | ("r-rgraphviz" ,r-rgraphviz))) | |
7441 | (home-page "https://bioconductor.org/packages/biocGraph/") | |
7442 | (synopsis "Graph examples and use cases in Bioinformatics") | |
7443 | (description | |
7444 | "This package provides examples and code that make use of the | |
7445 | different graph related packages produced by Bioconductor.") | |
7446 | (license license:artistic2.0))) | |
244270e6 RW |
7447 | |
7448 | (define-public r-experimenthub | |
7449 | (package | |
7450 | (name "r-experimenthub") | |
7451 | (version "1.12.0") | |
7452 | (source | |
7453 | (origin | |
7454 | (method url-fetch) | |
7455 | (uri (bioconductor-uri "ExperimentHub" version)) | |
7456 | (sha256 | |
7457 | (base32 | |
7458 | "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24")))) | |
7459 | (properties `((upstream-name . "ExperimentHub"))) | |
7460 | (build-system r-build-system) | |
7461 | (propagated-inputs | |
7462 | `(("r-annotationhub" ,r-annotationhub) | |
7463 | ("r-biocfilecache" ,r-biocfilecache) | |
7464 | ("r-biocgenerics" ,r-biocgenerics) | |
7465 | ("r-biocmanager" ,r-biocmanager) | |
7466 | ("r-curl" ,r-curl) | |
7467 | ("r-rappdirs" ,r-rappdirs) | |
7468 | ("r-s4vectors" ,r-s4vectors))) | |
7469 | (home-page "https://bioconductor.org/packages/ExperimentHub/") | |
7470 | (synopsis "Client to access ExperimentHub resources") | |
7471 | (description | |
7472 | "This package provides a client for the Bioconductor ExperimentHub web | |
7473 | resource. ExperimentHub provides a central location where curated data from | |
7474 | experiments, publications or training courses can be accessed. Each resource | |
7475 | has associated metadata, tags and date of modification. The client creates | |
7476 | and manages a local cache of files retrieved enabling quick and reproducible | |
7477 | access.") | |
7478 | (license license:artistic2.0))) | |
06784793 RW |
7479 | |
7480 | (define-public r-multiassayexperiment | |
7481 | (package | |
7482 | (name "r-multiassayexperiment") | |
2ba52530 | 7483 | (version "1.12.6") |
06784793 RW |
7484 | (source |
7485 | (origin | |
7486 | (method url-fetch) | |
7487 | (uri (bioconductor-uri "MultiAssayExperiment" version)) | |
7488 | (sha256 | |
7489 | (base32 | |
2ba52530 | 7490 | "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi")))) |
06784793 RW |
7491 | (properties |
7492 | `((upstream-name . "MultiAssayExperiment"))) | |
7493 | (build-system r-build-system) | |
7494 | (propagated-inputs | |
7495 | `(("r-biobase" ,r-biobase) | |
7496 | ("r-biocgenerics" ,r-biocgenerics) | |
7497 | ("r-genomicranges" ,r-genomicranges) | |
7498 | ("r-iranges" ,r-iranges) | |
7499 | ("r-s4vectors" ,r-s4vectors) | |
7500 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
7501 | ("r-tidyr" ,r-tidyr))) | |
5d45d711 RW |
7502 | (native-inputs |
7503 | `(("r-knitr" ,r-knitr))) | |
798ca8d0 | 7504 | (home-page "https://waldronlab.io/MultiAssayExperiment/") |
06784793 RW |
7505 | (synopsis "Integration of multi-omics experiments in Bioconductor") |
7506 | (description | |
7507 | "MultiAssayExperiment harmonizes data management of multiple assays | |
7508 | performed on an overlapping set of specimens. It provides a familiar | |
7509 | Bioconductor user experience by extending concepts from | |
7510 | @code{SummarizedExperiment}, supporting an open-ended mix of standard data | |
7511 | classes for individual assays, and allowing subsetting by genomic ranges or | |
7512 | rownames.") | |
7513 | (license license:artistic2.0))) | |
c2b36a04 RW |
7514 | |
7515 | (define-public r-bioconcotk | |
7516 | (package | |
7517 | (name "r-bioconcotk") | |
7518 | (version "1.6.0") | |
7519 | (source | |
7520 | (origin | |
7521 | (method url-fetch) | |
7522 | (uri (bioconductor-uri "BiocOncoTK" version)) | |
7523 | (sha256 | |
7524 | (base32 | |
7525 | "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj")))) | |
7526 | (properties `((upstream-name . "BiocOncoTK"))) | |
7527 | (build-system r-build-system) | |
7528 | (propagated-inputs | |
7529 | `(("r-bigrquery" ,r-bigrquery) | |
7530 | ("r-car" ,r-car) | |
7531 | ("r-complexheatmap" ,r-complexheatmap) | |
7532 | ("r-curatedtcgadata" ,r-curatedtcgadata) | |
7533 | ("r-dbi" ,r-dbi) | |
7534 | ("r-dplyr" ,r-dplyr) | |
7535 | ("r-dt" ,r-dt) | |
7536 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7537 | ("r-genomicranges" ,r-genomicranges) | |
7538 | ("r-ggplot2" ,r-ggplot2) | |
7539 | ("r-ggpubr" ,r-ggpubr) | |
7540 | ("r-graph" ,r-graph) | |
7541 | ("r-httr" ,r-httr) | |
7542 | ("r-iranges" ,r-iranges) | |
7543 | ("r-magrittr" ,r-magrittr) | |
7544 | ("r-plyr" ,r-plyr) | |
7545 | ("r-rgraphviz" ,r-rgraphviz) | |
7546 | ("r-rjson" ,r-rjson) | |
7547 | ("r-s4vectors" ,r-s4vectors) | |
7548 | ("r-scales" ,r-scales) | |
7549 | ("r-shiny" ,r-shiny) | |
7550 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
7551 | (home-page "https://bioconductor.org/packages/BiocOncoTK") | |
7552 | (synopsis "Bioconductor components for general cancer genomics") | |
7553 | (description | |
7554 | "The purpose of this package is to provide a central interface to various | |
7555 | tools for genome-scale analysis of cancer studies.") | |
7556 | (license license:artistic2.0))) | |
4d12c1e3 RW |
7557 | |
7558 | (define-public r-biocor | |
7559 | (package | |
7560 | (name "r-biocor") | |
7561 | (version "1.10.0") | |
7562 | (source | |
7563 | (origin | |
7564 | (method url-fetch) | |
7565 | (uri (bioconductor-uri "BioCor" version)) | |
7566 | (sha256 | |
7567 | (base32 | |
7568 | "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl")))) | |
7569 | (properties `((upstream-name . "BioCor"))) | |
7570 | (build-system r-build-system) | |
7571 | (propagated-inputs | |
7572 | `(("r-biocparallel" ,r-biocparallel) | |
7573 | ("r-gseabase" ,r-gseabase) | |
7574 | ("r-matrix" ,r-matrix))) | |
7575 | (home-page "https://llrs.github.io/BioCor/") | |
7576 | (synopsis "Functional similarities") | |
7577 | (description | |
7578 | "This package provides tools to calculate functional similarities based | |
7579 | on the pathways described on KEGG and REACTOME or in gene sets. These | |
7580 | similarities can be calculated for pathways or gene sets, genes, or clusters | |
7581 | and combined with other similarities. They can be used to improve networks, | |
7582 | gene selection, testing relationships, and so on.") | |
7583 | (license license:expat))) | |
4a18112d RW |
7584 | |
7585 | (define-public r-biocpkgtools | |
7586 | (package | |
7587 | (name "r-biocpkgtools") | |
2d6a7bca | 7588 | (version "1.4.6") |
4a18112d RW |
7589 | (source |
7590 | (origin | |
7591 | (method url-fetch) | |
7592 | (uri (bioconductor-uri "BiocPkgTools" version)) | |
7593 | (sha256 | |
7594 | (base32 | |
2d6a7bca | 7595 | "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a")))) |
4a18112d RW |
7596 | (properties `((upstream-name . "BiocPkgTools"))) |
7597 | (build-system r-build-system) | |
7598 | (propagated-inputs | |
2d6a7bca RW |
7599 | `(("r-biocfilecache" ,r-biocfilecache) |
7600 | ("r-biocmanager" ,r-biocmanager) | |
4a18112d RW |
7601 | ("r-biocviews" ,r-biocviews) |
7602 | ("r-dplyr" ,r-dplyr) | |
7603 | ("r-dt" ,r-dt) | |
7604 | ("r-gh" ,r-gh) | |
7605 | ("r-graph" ,r-graph) | |
7606 | ("r-htmltools" ,r-htmltools) | |
7607 | ("r-htmlwidgets" ,r-htmlwidgets) | |
7608 | ("r-httr" ,r-httr) | |
7609 | ("r-igraph" ,r-igraph) | |
7610 | ("r-jsonlite" ,r-jsonlite) | |
7611 | ("r-magrittr" ,r-magrittr) | |
2d6a7bca | 7612 | ("r-rappdirs" ,r-rappdirs) |
4a18112d RW |
7613 | ("r-rbgl" ,r-rbgl) |
7614 | ("r-readr" ,r-readr) | |
7615 | ("r-rex" ,r-rex) | |
2d6a7bca | 7616 | ("r-rlang" ,r-rlang) |
4a18112d RW |
7617 | ("r-rvest" ,r-rvest) |
7618 | ("r-stringr" ,r-stringr) | |
7619 | ("r-tibble" ,r-tibble) | |
7620 | ("r-tidyr" ,r-tidyr) | |
2d6a7bca | 7621 | ("r-tidyselect" ,r-tidyselect) |
4a18112d | 7622 | ("r-xml2" ,r-xml2))) |
2d6a7bca RW |
7623 | (native-inputs |
7624 | `(("r-knitr" ,r-knitr))) | |
4a18112d RW |
7625 | (home-page "https://github.com/seandavi/BiocPkgTools") |
7626 | (synopsis "Collection of tools for learning about Bioconductor packages") | |
7627 | (description | |
7628 | "Bioconductor has a rich ecosystem of metadata around packages, usage, | |
7629 | and build status. This package is a simple collection of functions to access | |
7630 | that metadata from R. The goal is to expose metadata for data mining and | |
7631 | value-added functionality such as package searching, text mining, and | |
7632 | analytics on packages.") | |
7633 | (license license:expat))) | |
43b66e3f RW |
7634 | |
7635 | (define-public r-biocset | |
7636 | (package | |
7637 | (name "r-biocset") | |
7638 | (version "1.0.1") | |
7639 | (source | |
7640 | (origin | |
7641 | (method url-fetch) | |
7642 | (uri (bioconductor-uri "BiocSet" version)) | |
7643 | (sha256 | |
7644 | (base32 | |
7645 | "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9")))) | |
7646 | (properties `((upstream-name . "BiocSet"))) | |
7647 | (build-system r-build-system) | |
7648 | (propagated-inputs | |
7649 | `(("r-annotationdbi" ,r-annotationdbi) | |
7650 | ("r-dplyr" ,r-dplyr) | |
7651 | ("r-keggrest" ,r-keggrest) | |
7652 | ("r-plyr" ,r-plyr) | |
7653 | ("r-rlang" ,r-rlang) | |
7654 | ("r-rtracklayer" ,r-rtracklayer) | |
7655 | ("r-tibble" ,r-tibble))) | |
7656 | (home-page | |
7657 | "https://bioconductor.org/packages/BiocSet") | |
7658 | (synopsis | |
7659 | "Representing Different Biological Sets") | |
7660 | (description | |
7661 | "BiocSet displays different biological sets in a triple tibble format. | |
7662 | These three tibbles are @code{element}, @code{set}, and @code{elementset}. | |
5b98473a | 7663 | The user has the ability to activate one of these three tibbles to perform |
43b66e3f RW |
7664 | common functions from the @code{dplyr} package. Mapping functionality and |
7665 | accessing web references for elements/sets are also available in BiocSet.") | |
7666 | (license license:artistic2.0))) | |
0156297f RW |
7667 | |
7668 | (define-public r-biocworkflowtools | |
7669 | (package | |
7670 | (name "r-biocworkflowtools") | |
4ecba230 | 7671 | (version "1.12.1") |
0156297f RW |
7672 | (source |
7673 | (origin | |
7674 | (method url-fetch) | |
7675 | (uri (bioconductor-uri "BiocWorkflowTools" version)) | |
7676 | (sha256 | |
7677 | (base32 | |
4ecba230 | 7678 | "0z28s572wg9qxv52dmixxz1xf1z3fyp2j7kzk0k32fp628918wr6")))) |
0156297f RW |
7679 | (properties |
7680 | `((upstream-name . "BiocWorkflowTools"))) | |
7681 | (build-system r-build-system) | |
7682 | (propagated-inputs | |
7683 | `(("r-biocstyle" ,r-biocstyle) | |
7684 | ("r-bookdown" ,r-bookdown) | |
7685 | ("r-git2r" ,r-git2r) | |
7686 | ("r-httr" ,r-httr) | |
7687 | ("r-knitr" ,r-knitr) | |
7688 | ("r-rmarkdown" ,r-rmarkdown) | |
7689 | ("r-rstudioapi" ,r-rstudioapi) | |
7690 | ("r-stringr" ,r-stringr) | |
7691 | ("r-usethis" ,r-usethis))) | |
4ecba230 RW |
7692 | (native-inputs |
7693 | `(("r-knitr" ,r-knitr))) | |
0156297f RW |
7694 | (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") |
7695 | (synopsis "Tools to aid the development of Bioconductor Workflow packages") | |
7696 | (description | |
7697 | "This package provides functions to ease the transition between | |
7698 | Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") | |
7699 | (license license:expat))) | |
77e2de36 RW |
7700 | |
7701 | (define-public r-biodist | |
7702 | (package | |
7703 | (name "r-biodist") | |
7704 | (version "1.58.0") | |
7705 | (source | |
7706 | (origin | |
7707 | (method url-fetch) | |
7708 | (uri (bioconductor-uri "bioDist" version)) | |
7709 | (sha256 | |
7710 | (base32 | |
7711 | "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q")))) | |
7712 | (properties `((upstream-name . "bioDist"))) | |
7713 | (build-system r-build-system) | |
7714 | (propagated-inputs | |
7715 | `(("r-biobase" ,r-biobase) | |
7716 | ("r-kernsmooth" ,r-kernsmooth))) | |
7717 | (home-page "https://bioconductor.org/packages/bioDist/") | |
7718 | (synopsis "Different distance measures") | |
7719 | (description | |
7720 | "This package provides a collection of software tools for calculating | |
7721 | distance measures.") | |
7722 | (license license:artistic2.0))) |