Commit | Line | Data |
---|---|---|
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> |
25f4e652 | 5 | ;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com> |
488001eb | 6 | ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> |
f4d920b9 | 7 | ;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> |
c61268c1 | 8 | ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> |
fa596599 RW |
9 | ;;; |
10 | ;;; This file is part of GNU Guix. | |
11 | ;;; | |
12 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
13 | ;;; under the terms of the GNU General Public License as published by | |
14 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
15 | ;;; your option) any later version. | |
16 | ;;; | |
17 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
18 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
19 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
20 | ;;; GNU General Public License for more details. | |
21 | ;;; | |
22 | ;;; You should have received a copy of the GNU General Public License | |
23 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
24 | ||
25 | (define-module (gnu packages bioconductor) | |
26 | #:use-module ((guix licenses) #:prefix license:) | |
27 | #:use-module (guix packages) | |
28 | #:use-module (guix download) | |
b2dce6b5 | 29 | #:use-module (guix git-download) |
fa596599 | 30 | #:use-module (guix build-system r) |
183ce988 | 31 | #:use-module (gnu packages) |
58656064 | 32 | #:use-module (gnu packages base) |
cf9a29b2 | 33 | #:use-module (gnu packages bioinformatics) |
a5b56a53 RJ |
34 | #:use-module (gnu packages cran) |
35 | #:use-module (gnu packages compression) | |
c18dccff | 36 | #:use-module (gnu packages gcc) |
cf9a29b2 | 37 | #:use-module (gnu packages graph) |
5aef09bd | 38 | #:use-module (gnu packages graphviz) |
dddbc90c | 39 | #:use-module (gnu packages haskell-xyz) |
5cfa4bff | 40 | #:use-module (gnu packages image) |
b64ce4b7 | 41 | #:use-module (gnu packages maths) |
6b12f213 RW |
42 | #:use-module (gnu packages netpbm) |
43 | #:use-module (gnu packages perl) | |
2cb71d81 | 44 | #:use-module (gnu packages pkg-config) |
f4235c0e | 45 | #:use-module (gnu packages statistics) |
14bb1c48 | 46 | #:use-module (gnu packages web) |
7a62d5e0 | 47 | #:use-module (gnu packages xml) |
14bb1c48 | 48 | #:use-module (srfi srfi-1)) |
fa596599 | 49 | |
557a1089 RW |
50 | \f |
51 | ;;; Annotations | |
52 | ||
6f15ea24 RW |
53 | (define-public r-reactome-db |
54 | (package | |
55 | (name "r-reactome-db") | |
56 | (version "1.70.0") | |
57 | (source | |
58 | (origin | |
59 | (method url-fetch) | |
60 | (uri (bioconductor-uri "reactome.db" version 'annotation)) | |
61 | (sha256 | |
62 | (base32 | |
63 | "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg")))) | |
64 | (properties `((upstream-name . "reactome.db"))) | |
65 | (build-system r-build-system) | |
66 | (propagated-inputs | |
67 | `(("r-annotationdbi" ,r-annotationdbi))) | |
68 | (home-page "https://bioconductor.org/packages/reactome.db/") | |
69 | (synopsis "Annotation maps for reactome") | |
70 | (description | |
71 | "This package provides a set of annotation maps for the REACTOME | |
72 | database, assembled using data from REACTOME.") | |
73 | (license license:cc-by4.0))) | |
74 | ||
a23310ff RJ |
75 | (define-public r-bluster |
76 | (package | |
77 | (name "r-bluster") | |
78 | (version "1.0.0") | |
79 | (source (origin | |
80 | (method url-fetch) | |
81 | (uri (bioconductor-uri "bluster" version)) | |
82 | (sha256 | |
83 | (base32 | |
84 | "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61")))) | |
85 | (properties `((upstream-name . "bluster"))) | |
86 | (build-system r-build-system) | |
87 | (propagated-inputs | |
88 | `(("r-biocneighbors" ,r-biocneighbors) | |
89 | ("r-biocparallel" ,r-biocparallel) | |
90 | ("r-igraph" ,r-igraph) | |
91 | ("r-matrix" ,r-matrix) | |
92 | ("r-rcpp" ,r-rcpp) | |
93 | ("r-s4vectors" ,r-s4vectors))) | |
94 | (native-inputs | |
95 | `(("r-knitr" ,r-knitr))) | |
96 | (home-page "https://bioconductor.org/packages/bluster") | |
97 | (synopsis "Clustering algorithms for Bioconductor") | |
98 | (description"This package wraps common clustering algorithms in an easily | |
99 | extended S4 framework. Backends are implemented for hierarchical, k-means | |
100 | and graph-based clustering. Several utilities are also provided to compare | |
101 | and evaluate clustering results.") | |
102 | (license license:gpl3))) | |
103 | ||
b7d93cf5 RW |
104 | (define-public r-bsgenome-celegans-ucsc-ce6 |
105 | (package | |
106 | (name "r-bsgenome-celegans-ucsc-ce6") | |
107 | (version "1.4.0") | |
108 | (source (origin | |
109 | (method url-fetch) | |
86ced7b2 RW |
110 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6" |
111 | version 'annotation)) | |
b7d93cf5 RW |
112 | (sha256 |
113 | (base32 | |
114 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
115 | (properties | |
116 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
117 | (build-system r-build-system) | |
b7d93cf5 RW |
118 | (propagated-inputs |
119 | `(("r-bsgenome" ,r-bsgenome))) | |
120 | (home-page | |
121 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
122 | (synopsis "Full genome sequences for Worm") | |
123 | (description | |
124 | "This package provides full genome sequences for Caenorhabditis | |
125 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
0c792ffb RW |
126 | objects.") |
127 | (license license:artistic2.0))) | |
128 | ||
129 | (define-public r-bsgenome-celegans-ucsc-ce10 | |
130 | (package | |
131 | (name "r-bsgenome-celegans-ucsc-ce10") | |
132 | (version "1.4.0") | |
133 | (source (origin | |
134 | (method url-fetch) | |
6998ecba RW |
135 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10" |
136 | version 'annotation)) | |
0c792ffb RW |
137 | (sha256 |
138 | (base32 | |
139 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
140 | (properties | |
141 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
142 | (build-system r-build-system) | |
0c792ffb RW |
143 | (propagated-inputs |
144 | `(("r-bsgenome" ,r-bsgenome))) | |
145 | (home-page | |
146 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
147 | (synopsis "Full genome sequences for Worm") | |
148 | (description | |
149 | "This package provides full genome sequences for Caenorhabditis | |
150 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
b7d93cf5 RW |
151 | objects.") |
152 | (license license:artistic2.0))) | |
153 | ||
183db725 RW |
154 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
155 | (package | |
156 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
157 | (version "1.4.1") | |
158 | (source (origin | |
159 | (method url-fetch) | |
149f351f RW |
160 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6" |
161 | version 'annotation)) | |
183db725 RW |
162 | (sha256 |
163 | (base32 | |
164 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
165 | (properties | |
166 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
167 | (build-system r-build-system) | |
183db725 RW |
168 | (propagated-inputs |
169 | `(("r-bsgenome" ,r-bsgenome))) | |
170 | (home-page | |
171 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
172 | (synopsis "Full genome sequences for Fly") | |
173 | (description | |
174 | "This package provides full genome sequences for Drosophila | |
175 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
176 | objects.") | |
177 | (license license:artistic2.0))) | |
178 | ||
13dabd69 RW |
179 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
180 | (package | |
181 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
182 | (version "1.4.0") | |
183 | (source (origin | |
184 | (method url-fetch) | |
87073b7e RW |
185 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3" |
186 | version 'annotation)) | |
13dabd69 RW |
187 | (sha256 |
188 | (base32 | |
189 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
190 | (properties | |
191 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
192 | (build-system r-build-system) | |
13dabd69 RW |
193 | (propagated-inputs |
194 | `(("r-bsgenome" ,r-bsgenome))) | |
195 | (home-page | |
196 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
197 | (synopsis "Full genome sequences for Fly") | |
198 | (description | |
199 | "This package provides full genome sequences for Drosophila | |
200 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
201 | Biostrings objects.") | |
202 | (license license:artistic2.0))) | |
203 | ||
dfac7eb9 RW |
204 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
205 | (package | |
206 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
207 | (version "1.3.99") | |
208 | (source (origin | |
209 | (method url-fetch) | |
bf05ece1 RW |
210 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked" |
211 | version 'annotation)) | |
dfac7eb9 RW |
212 | (sha256 |
213 | (base32 | |
214 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
215 | (properties | |
216 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
217 | (build-system r-build-system) | |
218 | (propagated-inputs | |
219 | `(("r-bsgenome" ,r-bsgenome) | |
220 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
221 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
222 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
223 | (synopsis "Full masked genome sequences for Fly") | |
224 | (description | |
225 | "This package provides full masked genome sequences for Drosophila | |
226 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
227 | Biostrings objects. The sequences are the same as in | |
228 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
229 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
230 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
231 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
232 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
233 | (license license:artistic2.0))) | |
234 | ||
40a65057 RW |
235 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
236 | (package | |
237 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
238 | (version "0.99.1") | |
239 | (source (origin | |
240 | (method url-fetch) | |
88e7c7db RW |
241 | (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5" |
242 | version 'annotation)) | |
40a65057 RW |
243 | (sha256 |
244 | (base32 | |
245 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
246 | (properties | |
247 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
248 | (build-system r-build-system) | |
40a65057 RW |
249 | (propagated-inputs |
250 | `(("r-bsgenome" ,r-bsgenome))) | |
251 | (home-page | |
252 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
253 | (synopsis "Full genome sequences for Homo sapiens") | |
254 | (description | |
255 | "This package provides full genome sequences for Homo sapiens from | |
256 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
257 | (license license:artistic2.0))) | |
258 | ||
c51c0033 MIP |
259 | (define-public r-bsgenome-hsapiens-ncbi-grch38 |
260 | (package | |
261 | (name "r-bsgenome-hsapiens-ncbi-grch38") | |
262 | (version "1.3.1000") | |
263 | (source | |
264 | (origin | |
265 | (method url-fetch) | |
266 | (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38" | |
267 | version 'annotation)) | |
268 | (sha256 | |
269 | (base32 | |
270 | "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) | |
271 | (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) | |
272 | (build-system r-build-system) | |
273 | (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) | |
274 | (home-page | |
275 | "https://bioconductor.org/packages/release/data/annotation/html/\ | |
276 | BSgenome.Hsapiens.NCBI.GRCh38.html") | |
277 | (synopsis "Full genome sequences for Homo sapiens (GRCh38)") | |
278 | (description | |
279 | "This package provides full genome sequences for Homo sapiens (Human) as | |
280 | provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") | |
281 | (license license:artistic2.0))) | |
282 | ||
6fbd759b RW |
283 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
284 | (package | |
285 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
286 | (version "1.3.99") | |
287 | (source (origin | |
288 | (method url-fetch) | |
a47646bd RW |
289 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" |
290 | version 'annotation)) | |
6fbd759b RW |
291 | (sha256 |
292 | (base32 | |
293 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
294 | (properties | |
295 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
296 | (build-system r-build-system) | |
297 | (propagated-inputs | |
298 | `(("r-bsgenome" ,r-bsgenome) | |
299 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
300 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
301 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
302 | (synopsis "Full masked genome sequences for Homo sapiens") | |
303 | (description | |
304 | "This package provides full genome sequences for Homo sapiens (Human) as | |
305 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
306 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
307 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
308 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
309 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
310 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
311 | default.") | |
312 | (license license:artistic2.0))) | |
313 | ||
5acb9052 RW |
314 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
315 | (package | |
316 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
317 | (version "1.4.0") | |
318 | (source (origin | |
319 | (method url-fetch) | |
21f6dae7 RW |
320 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9" |
321 | version 'annotation)) | |
5acb9052 RW |
322 | (sha256 |
323 | (base32 | |
324 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
325 | (properties | |
326 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
327 | (build-system r-build-system) | |
5acb9052 RW |
328 | (propagated-inputs |
329 | `(("r-bsgenome" ,r-bsgenome))) | |
330 | (home-page | |
331 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
332 | (synopsis "Full genome sequences for Mouse") | |
333 | (description | |
334 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
335 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
336 | (license license:artistic2.0))) | |
337 | ||
2bece692 RW |
338 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
339 | (package | |
340 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
341 | (version "1.3.99") | |
342 | (source (origin | |
343 | (method url-fetch) | |
51dc4a2d RW |
344 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked" |
345 | version 'annotation)) | |
2bece692 RW |
346 | (sha256 |
347 | (base32 | |
348 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
349 | (properties | |
350 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
351 | (build-system r-build-system) | |
352 | (propagated-inputs | |
353 | `(("r-bsgenome" ,r-bsgenome) | |
354 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
355 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
99db6db7 | 356 | (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") |
2bece692 RW |
357 | (synopsis "Full masked genome sequences for Mouse") |
358 | (description | |
359 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
360 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
361 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
362 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
363 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
364 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
365 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
366 | default." ) | |
367 | (license license:artistic2.0))) | |
368 | ||
c3adc830 RW |
369 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
370 | (package | |
371 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
372 | (version "1.4.0") | |
373 | (source (origin | |
374 | (method url-fetch) | |
f83404bc RW |
375 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10" |
376 | version 'annotation)) | |
c3adc830 RW |
377 | (sha256 |
378 | (base32 | |
379 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
380 | (properties | |
381 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
382 | (build-system r-build-system) | |
c3adc830 RW |
383 | (propagated-inputs |
384 | `(("r-bsgenome" ,r-bsgenome))) | |
385 | (home-page | |
386 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
387 | (synopsis "Full genome sequences for Mouse") | |
388 | (description | |
389 | "This package provides full genome sequences for Mus | |
390 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
391 | in Biostrings objects.") | |
392 | (license license:artistic2.0))) | |
393 | ||
3a08940e RW |
394 | (define-public r-org-ce-eg-db |
395 | (package | |
396 | (name "r-org-ce-eg-db") | |
397 | (version "3.7.0") | |
398 | (source (origin | |
399 | (method url-fetch) | |
1c05e637 | 400 | (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation)) |
3a08940e RW |
401 | (sha256 |
402 | (base32 | |
403 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) | |
404 | (properties | |
405 | `((upstream-name . "org.Ce.eg.db"))) | |
406 | (build-system r-build-system) | |
407 | (propagated-inputs | |
408 | `(("r-annotationdbi" ,r-annotationdbi))) | |
409 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") | |
410 | (synopsis "Genome wide annotation for Worm") | |
411 | (description | |
412 | "This package provides mappings from Entrez gene identifiers to various | |
413 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
414 | (license license:artistic2.0))) | |
415 | ||
f8780e96 RW |
416 | (define-public r-org-dm-eg-db |
417 | (package | |
418 | (name "r-org-dm-eg-db") | |
419 | (version "3.7.0") | |
420 | (source (origin | |
421 | (method url-fetch) | |
b0dfc79b | 422 | (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation)) |
f8780e96 RW |
423 | (sha256 |
424 | (base32 | |
425 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) | |
426 | (properties | |
427 | `((upstream-name . "org.Dm.eg.db"))) | |
428 | (build-system r-build-system) | |
429 | (propagated-inputs | |
430 | `(("r-annotationdbi" ,r-annotationdbi))) | |
431 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") | |
432 | (synopsis "Genome wide annotation for Fly") | |
433 | (description | |
434 | "This package provides mappings from Entrez gene identifiers to various | |
435 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
436 | (license license:artistic2.0))) | |
437 | ||
3dad6087 RW |
438 | (define-public r-org-dr-eg-db |
439 | (package | |
440 | (name "r-org-dr-eg-db") | |
441 | (version "3.7.0") | |
442 | (source (origin | |
443 | (method url-fetch) | |
7bb65a22 | 444 | (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation)) |
3dad6087 RW |
445 | (sha256 |
446 | (base32 | |
447 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) | |
448 | (properties | |
449 | `((upstream-name . "org.Dr.eg.db"))) | |
450 | (build-system r-build-system) | |
451 | (propagated-inputs | |
452 | `(("r-annotationdbi" ,r-annotationdbi))) | |
453 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") | |
454 | (synopsis "Annotation for Zebrafish") | |
455 | (description | |
456 | "This package provides genome wide annotations for Zebrafish, primarily | |
457 | based on mapping using Entrez Gene identifiers.") | |
458 | (license license:artistic2.0))) | |
459 | ||
d56df35a RW |
460 | (define-public r-org-hs-eg-db |
461 | (package | |
462 | (name "r-org-hs-eg-db") | |
463 | (version "3.7.0") | |
464 | (source (origin | |
465 | (method url-fetch) | |
f53becc6 | 466 | (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) |
d56df35a RW |
467 | (sha256 |
468 | (base32 | |
469 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) | |
470 | (properties | |
471 | `((upstream-name . "org.Hs.eg.db"))) | |
472 | (build-system r-build-system) | |
473 | (propagated-inputs | |
474 | `(("r-annotationdbi" ,r-annotationdbi))) | |
475 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") | |
476 | (synopsis "Genome wide annotation for Human") | |
477 | (description | |
478 | "This package contains genome-wide annotations for Human, primarily based | |
479 | on mapping using Entrez Gene identifiers.") | |
480 | (license license:artistic2.0))) | |
481 | ||
8035819f RW |
482 | (define-public r-org-mm-eg-db |
483 | (package | |
484 | (name "r-org-mm-eg-db") | |
485 | (version "3.7.0") | |
486 | (source (origin | |
487 | (method url-fetch) | |
411be88b | 488 | (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation)) |
8035819f RW |
489 | (sha256 |
490 | (base32 | |
491 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) | |
492 | (properties | |
493 | `((upstream-name . "org.Mm.eg.db"))) | |
494 | (build-system r-build-system) | |
495 | (propagated-inputs | |
496 | `(("r-annotationdbi" ,r-annotationdbi))) | |
497 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") | |
498 | (synopsis "Genome wide annotation for Mouse") | |
499 | (description | |
500 | "This package provides mappings from Entrez gene identifiers to various | |
501 | annotations for the genome of the model mouse Mus musculus.") | |
502 | (license license:artistic2.0))) | |
503 | ||
fe0b76e2 RW |
504 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
505 | (package | |
506 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
507 | (version "1.4.0") | |
508 | (source (origin | |
509 | (method url-fetch) | |
e7a8cf2e RW |
510 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19" |
511 | version 'annotation)) | |
fe0b76e2 RW |
512 | (sha256 |
513 | (base32 | |
514 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) | |
515 | (properties | |
516 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
517 | (build-system r-build-system) | |
fe0b76e2 RW |
518 | (propagated-inputs |
519 | `(("r-bsgenome" ,r-bsgenome))) | |
520 | (home-page | |
521 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
522 | (synopsis "Full genome sequences for Homo sapiens") | |
523 | (description | |
524 | "This package provides full genome sequences for Homo sapiens as provided | |
525 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
526 | (license license:artistic2.0))) | |
527 | ||
8ce240fd RJ |
528 | (define-public r-bsgenome-hsapiens-ucsc-hg38 |
529 | (package | |
530 | (name "r-bsgenome-hsapiens-ucsc-hg38") | |
531 | (version "1.4.1") | |
532 | (source (origin | |
533 | (method url-fetch) | |
534 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38" | |
535 | version 'annotation)) | |
536 | (sha256 | |
537 | (base32 | |
538 | "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi")))) | |
539 | (properties | |
540 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) | |
541 | (build-system r-build-system) | |
542 | (propagated-inputs | |
543 | `(("r-bsgenome" ,r-bsgenome))) | |
544 | (home-page | |
545 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") | |
546 | (synopsis "Full genome sequences for Homo sapiens") | |
547 | (description | |
548 | "This package provides full genome sequences for Homo sapiens (Human) | |
549 | as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") | |
550 | (license license:artistic2.0))) | |
551 | ||
8324e64c RW |
552 | (define-public r-ensdb-hsapiens-v75 |
553 | (package | |
554 | (name "r-ensdb-hsapiens-v75") | |
555 | (version "2.99.0") | |
556 | (source | |
557 | (origin | |
558 | (method url-fetch) | |
559 | (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) | |
560 | (sha256 | |
561 | (base32 | |
562 | "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) | |
563 | (properties | |
564 | `((upstream-name . "EnsDb.Hsapiens.v75"))) | |
565 | (build-system r-build-system) | |
566 | (propagated-inputs | |
567 | `(("r-ensembldb" ,r-ensembldb))) | |
568 | (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") | |
569 | (synopsis "Ensembl based annotation package") | |
570 | (description | |
571 | "This package exposes an annotation database generated from Ensembl.") | |
572 | (license license:artistic2.0))) | |
573 | ||
2cc51108 RW |
574 | (define-public r-genelendatabase |
575 | (package | |
576 | (name "r-genelendatabase") | |
daeb3cd9 | 577 | (version "1.18.0") |
2cc51108 RW |
578 | (source |
579 | (origin | |
580 | (method url-fetch) | |
717d7cda | 581 | (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) |
2cc51108 RW |
582 | (sha256 |
583 | (base32 | |
daeb3cd9 | 584 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
2cc51108 RW |
585 | (properties |
586 | `((upstream-name . "geneLenDataBase"))) | |
587 | (build-system r-build-system) | |
588 | (propagated-inputs | |
589 | `(("r-rtracklayer" ,r-rtracklayer) | |
590 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
591 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
592 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
593 | (description | |
594 | "This package provides the lengths of mRNA transcripts for a number of | |
595 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
596 | (license license:lgpl2.0+))) | |
597 | ||
66e35ce6 RW |
598 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
599 | (package | |
600 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
601 | (version "3.2.2") | |
602 | (source (origin | |
603 | (method url-fetch) | |
f2580a13 RW |
604 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene" |
605 | version 'annotation)) | |
66e35ce6 RW |
606 | (sha256 |
607 | (base32 | |
608 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
609 | (properties | |
610 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
611 | (build-system r-build-system) | |
66e35ce6 RW |
612 | (propagated-inputs |
613 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
614 | (home-page | |
615 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
616 | (synopsis "Annotation package for human genome in TxDb format") | |
617 | (description | |
618 | "This package provides an annotation database of Homo sapiens genome | |
619 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
798b80ce RW |
620 | track. The database is exposed as a @code{TxDb} object.") |
621 | (license license:artistic2.0))) | |
622 | ||
623 | (define-public r-txdb-hsapiens-ucsc-hg38-knowngene | |
624 | (package | |
625 | (name "r-txdb-hsapiens-ucsc-hg38-knowngene") | |
626 | (version "3.4.6") | |
627 | (source (origin | |
628 | (method url-fetch) | |
d78db088 RW |
629 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" |
630 | version 'annotation)) | |
798b80ce RW |
631 | (sha256 |
632 | (base32 | |
633 | "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) | |
634 | (properties | |
635 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) | |
636 | (build-system r-build-system) | |
637 | (propagated-inputs | |
638 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
639 | (home-page | |
640 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") | |
641 | (synopsis "Annotation package for human genome in TxDb format") | |
642 | (description | |
643 | "This package provides an annotation database of Homo sapiens genome | |
644 | data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" | |
66e35ce6 RW |
645 | track. The database is exposed as a @code{TxDb} object.") |
646 | (license license:artistic2.0))) | |
647 | ||
d220babf RW |
648 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
649 | (package | |
650 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
651 | (version "3.2.2") | |
652 | (source (origin | |
653 | (method url-fetch) | |
1afdf41b RW |
654 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene" |
655 | version 'annotation)) | |
d220babf RW |
656 | (sha256 |
657 | (base32 | |
658 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
659 | (properties | |
660 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
661 | (build-system r-build-system) | |
662 | (propagated-inputs | |
663 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
664 | ("r-annotationdbi" ,r-annotationdbi))) | |
665 | (home-page | |
666 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
667 | (synopsis "Annotation package for mouse genome in TxDb format") | |
668 | (description | |
669 | "This package provides an annotation database of Mouse genome data. It | |
670 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
671 | database is exposed as a @code{TxDb} object.") | |
672 | (license license:artistic2.0))) | |
673 | ||
7bc5d1b0 RW |
674 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
675 | (package | |
676 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
b69c7703 | 677 | (version "3.10.0") |
7bc5d1b0 RW |
678 | (source (origin |
679 | (method url-fetch) | |
c271d990 RW |
680 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene" |
681 | version 'annotation)) | |
7bc5d1b0 RW |
682 | (sha256 |
683 | (base32 | |
b69c7703 | 684 | "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9")))) |
7bc5d1b0 RW |
685 | (properties |
686 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
687 | (build-system r-build-system) | |
7bc5d1b0 RW |
688 | (propagated-inputs |
689 | `(("r-bsgenome" ,r-bsgenome) | |
690 | ("r-genomicfeatures" ,r-genomicfeatures) | |
691 | ("r-annotationdbi" ,r-annotationdbi))) | |
692 | (home-page | |
693 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
694 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
695 | (description | |
696 | "This package loads a TxDb object, which is an R interface to | |
697 | prefabricated databases contained in this package. This package provides | |
698 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
699 | based on the knownGene track.") | |
700 | (license license:artistic2.0))) | |
701 | ||
7cd446fd RW |
702 | (define-public r-txdb-celegans-ucsc-ce6-ensgene |
703 | (package | |
704 | (name "r-txdb-celegans-ucsc-ce6-ensgene") | |
705 | (version "3.2.2") | |
706 | (source | |
707 | (origin | |
708 | (method url-fetch) | |
709 | (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene" | |
710 | version 'annotation)) | |
711 | (sha256 | |
712 | (base32 | |
713 | "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90")))) | |
714 | (properties | |
715 | `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) | |
716 | (build-system r-build-system) | |
717 | (propagated-inputs | |
718 | `(("r-annotationdbi" ,r-annotationdbi) | |
719 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
720 | (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") | |
721 | (synopsis "Annotation package for C elegans TxDb objects") | |
722 | (description | |
723 | "This package exposes a C elegans annotation database generated from UCSC | |
724 | by exposing these as TxDb objects.") | |
725 | (license license:artistic2.0))) | |
726 | ||
0f5c9cec RW |
727 | (define-public r-fdb-infiniummethylation-hg19 |
728 | (package | |
729 | (name "r-fdb-infiniummethylation-hg19") | |
730 | (version "2.2.0") | |
731 | (source (origin | |
732 | (method url-fetch) | |
6aca4054 RW |
733 | (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19" |
734 | version 'annotation)) | |
0f5c9cec RW |
735 | (sha256 |
736 | (base32 | |
737 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) | |
738 | (properties | |
739 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) | |
740 | (build-system r-build-system) | |
741 | (propagated-inputs | |
742 | `(("r-biostrings" ,r-biostrings) | |
743 | ("r-genomicfeatures" ,r-genomicfeatures) | |
744 | ("r-annotationdbi" ,r-annotationdbi) | |
745 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
746 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) | |
747 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") | |
748 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") | |
749 | (description | |
750 | "This is an annotation package for Illumina Infinium DNA methylation | |
751 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 | |
752 | annotations.") | |
753 | (license license:artistic2.0))) | |
754 | ||
9475a248 RW |
755 | (define-public r-illuminahumanmethylationepicmanifest |
756 | (package | |
757 | (name "r-illuminahumanmethylationepicmanifest") | |
758 | (version "0.3.0") | |
759 | (source (origin | |
760 | (method url-fetch) | |
25f567a8 RW |
761 | (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest" |
762 | version 'annotation)) | |
9475a248 RW |
763 | (sha256 |
764 | (base32 | |
765 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) | |
766 | (properties | |
767 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) | |
768 | (build-system r-build-system) | |
769 | (propagated-inputs | |
770 | `(("r-minfi" ,r-minfi))) | |
771 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") | |
772 | (synopsis "Manifest for Illumina's EPIC methylation arrays") | |
773 | (description | |
774 | "This is a manifest package for Illumina's EPIC methylation arrays.") | |
775 | (license license:artistic2.0))) | |
e8d435f7 RJ |
776 | |
777 | (define-public r-ideoviz | |
778 | (package | |
779 | (name "r-ideoviz") | |
25f4e652 | 780 | (version "1.26.0") |
e8d435f7 RJ |
781 | (source (origin |
782 | (method url-fetch) | |
783 | (uri (bioconductor-uri "IdeoViz" version)) | |
784 | (sha256 | |
785 | (base32 | |
25f4e652 | 786 | "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq")))) |
e8d435f7 RJ |
787 | (build-system r-build-system) |
788 | (propagated-inputs | |
789 | `(("r-biobase" ,r-biobase) | |
790 | ("r-iranges" ,r-iranges) | |
791 | ("r-genomicranges" ,r-genomicranges) | |
792 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
793 | ("r-rtracklayer" ,r-rtracklayer) | |
794 | ("r-genomeinfodb" ,r-genomeinfodb))) | |
795 | (home-page "https://bioconductor.org/packages/IdeoViz/") | |
796 | (synopsis "Plots data along a chromosomal ideogram") | |
797 | (description "This package provides functions to plot data associated with | |
798 | arbitrary genomic intervals along chromosomal ideogram.") | |
799 | (license license:gpl2))) | |
9475a248 | 800 | |
a38bf7c8 RJ |
801 | ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 |
802 | ;; from Bioconductor. | |
803 | (define-public r-deconstructsigs | |
804 | (package | |
805 | (name "r-deconstructsigs") | |
806 | (version "1.8.0") | |
807 | (source (origin | |
808 | (method url-fetch) | |
809 | (uri (cran-uri "deconstructSigs" version)) | |
810 | (sha256 | |
811 | (base32 | |
812 | "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) | |
813 | (properties | |
814 | `((upstream-name . "deconstructSigs"))) | |
815 | (build-system r-build-system) | |
816 | (propagated-inputs | |
817 | `(("r-bsgenome" ,r-bsgenome) | |
818 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
819 | ("r-genomeinfodb" ,r-genomeinfodb) | |
820 | ("r-reshape2" ,r-reshape2))) | |
821 | (home-page "https://github.com/raerose01/deconstructSigs") | |
822 | (synopsis "Identifies signatures present in a tumor sample") | |
823 | (description "This package takes sample information in the form of the | |
824 | fraction of mutations in each of 96 trinucleotide contexts and identifies | |
825 | the weighted combination of published signatures that, when summed, most | |
826 | closely reconstructs the mutational profile.") | |
827 | (license license:gpl2+))) | |
828 | ||
7c9d8a5d RW |
829 | ;; This is a CRAN package, but it depends on Bioconductor packages. |
830 | (define-public r-nmf | |
831 | (package | |
832 | (name "r-nmf") | |
0a41d9be | 833 | (version "0.23.0") |
7c9d8a5d RW |
834 | (source |
835 | (origin | |
836 | (method url-fetch) | |
837 | (uri (cran-uri "NMF" version)) | |
838 | (sha256 | |
839 | (base32 | |
0a41d9be | 840 | "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g")))) |
7c9d8a5d RW |
841 | (properties `((upstream-name . "NMF"))) |
842 | (build-system r-build-system) | |
843 | (propagated-inputs | |
844 | `(("r-cluster" ,r-cluster) | |
be1042b3 RW |
845 | ("r-biobase" ,r-biobase) |
846 | ("r-biocmanager" ,r-biocmanager) | |
7c9d8a5d RW |
847 | ("r-bigmemory" ,r-bigmemory) ; suggested |
848 | ("r-synchronicity" ,r-synchronicity) ; suggested | |
849 | ("r-colorspace" ,r-colorspace) | |
850 | ("r-digest" ,r-digest) | |
851 | ("r-doparallel" ,r-doparallel) | |
852 | ("r-foreach" ,r-foreach) | |
853 | ("r-ggplot2" ,r-ggplot2) | |
854 | ("r-gridbase" ,r-gridbase) | |
855 | ("r-pkgmaker" ,r-pkgmaker) | |
856 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
857 | ("r-registry" ,r-registry) | |
858 | ("r-reshape2" ,r-reshape2) | |
859 | ("r-rngtools" ,r-rngtools) | |
860 | ("r-stringr" ,r-stringr))) | |
0a41d9be RW |
861 | (native-inputs |
862 | `(("r-knitr" ,r-knitr))) | |
7c9d8a5d RW |
863 | (home-page "http://renozao.github.io/NMF") |
864 | (synopsis "Algorithms and framework for nonnegative matrix factorization") | |
865 | (description | |
866 | "This package provides a framework to perform Non-negative Matrix | |
867 | Factorization (NMF). The package implements a set of already published | |
868 | algorithms and seeding methods, and provides a framework to test, develop and | |
869 | plug new or custom algorithms. Most of the built-in algorithms have been | |
870 | optimized in C++, and the main interface function provides an easy way of | |
871 | performing parallel computations on multicore machines.") | |
872 | (license license:gpl2+))) | |
873 | ||
f8a5af46 RW |
874 | (define-public r-do-db |
875 | (package | |
876 | (name "r-do-db") | |
877 | (version "2.9") | |
878 | (source (origin | |
879 | (method url-fetch) | |
eed2766a | 880 | (uri (bioconductor-uri "DO.db" version 'annotation)) |
f8a5af46 RW |
881 | (sha256 |
882 | (base32 | |
883 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) | |
884 | (properties | |
885 | `((upstream-name . "DO.db"))) | |
886 | (build-system r-build-system) | |
887 | (propagated-inputs | |
888 | `(("r-annotationdbi" ,r-annotationdbi))) | |
889 | (home-page "https://www.bioconductor.org/packages/DO.db/") | |
890 | (synopsis "Annotation maps describing the entire Disease Ontology") | |
891 | (description | |
892 | "This package provides a set of annotation maps describing the entire | |
893 | Disease Ontology.") | |
894 | (license license:artistic2.0))) | |
895 | ||
ec20858a RJ |
896 | (define-public r-pasilla |
897 | (package | |
898 | (name "r-pasilla") | |
899 | (version "1.14.0") | |
900 | (source (origin | |
901 | (method url-fetch) | |
902 | (uri (string-append | |
903 | "http://bioconductor.org/packages/release/data/experiment" | |
904 | "/src/contrib/pasilla_" version ".tar.gz")) | |
905 | (sha256 | |
906 | (base32 | |
907 | "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) | |
908 | (build-system r-build-system) | |
909 | (propagated-inputs | |
910 | `(("r-biocstyle" ,r-biocstyle) | |
911 | ("r-dexseq" ,r-dexseq) | |
912 | ("r-knitr" ,r-knitr) | |
913 | ("r-rmarkdown" ,r-rmarkdown))) | |
914 | (home-page "https://www.bioconductor.org/packages/pasilla/") | |
915 | (synopsis "Data package with per-exon and per-gene read counts") | |
916 | (description "This package provides per-exon and per-gene read counts | |
917 | computed for selected genes from RNA-seq data that were presented in the | |
918 | article 'Conservation of an RNA regulatory map between Drosophila and mammals' | |
919 | by Brooks et al., Genome Research 2011.") | |
920 | (license license:lgpl2.1+))) | |
921 | ||
83b42091 RW |
922 | (define-public r-pfam-db |
923 | (package | |
924 | (name "r-pfam-db") | |
925 | (version "3.8.2") | |
926 | (source | |
927 | (origin | |
928 | (method url-fetch) | |
929 | (uri (bioconductor-uri "PFAM.db" version 'annotation)) | |
930 | (sha256 | |
931 | (base32 | |
932 | "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) | |
933 | (properties `((upstream-name . "PFAM.db"))) | |
934 | (build-system r-build-system) | |
935 | (propagated-inputs | |
936 | `(("r-annotationdbi" ,r-annotationdbi))) | |
937 | (home-page "https://bioconductor.org/packages/PFAM.db") | |
938 | (synopsis "Set of protein ID mappings for PFAM") | |
939 | (description | |
940 | "This package provides a set of protein ID mappings for PFAM, assembled | |
941 | using data from public repositories.") | |
942 | (license license:artistic2.0))) | |
943 | ||
40be965e RW |
944 | (define-public r-phastcons100way-ucsc-hg19 |
945 | (package | |
946 | (name "r-phastcons100way-ucsc-hg19") | |
947 | (version "3.7.2") | |
948 | (source | |
949 | (origin | |
950 | (method url-fetch) | |
951 | (uri (bioconductor-uri "phastCons100way.UCSC.hg19" | |
952 | version 'annotation)) | |
953 | (sha256 | |
954 | (base32 | |
955 | "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa")))) | |
956 | (properties | |
957 | `((upstream-name . "phastCons100way.UCSC.hg19"))) | |
958 | (build-system r-build-system) | |
959 | (propagated-inputs | |
960 | `(("r-bsgenome" ,r-bsgenome) | |
961 | ("r-genomeinfodb" ,r-genomeinfodb) | |
962 | ("r-genomicranges" ,r-genomicranges) | |
963 | ("r-genomicscores" ,r-genomicscores) | |
964 | ("r-iranges" ,r-iranges) | |
965 | ("r-s4vectors" ,r-s4vectors))) | |
966 | (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") | |
967 | (synopsis "UCSC phastCons conservation scores for hg19") | |
968 | (description | |
969 | "This package provides UCSC phastCons conservation scores for the human | |
970 | genome (hg19) calculated from multiple alignments with other 99 vertebrate | |
971 | species.") | |
972 | (license license:artistic2.0))) | |
973 | ||
2cc51108 | 974 | \f |
557a1089 RW |
975 | ;;; Experiment data |
976 | ||
692bce15 RW |
977 | (define-public r-abadata |
978 | (package | |
979 | (name "r-abadata") | |
980 | (version "1.12.0") | |
981 | (source (origin | |
982 | (method url-fetch) | |
ced61edf | 983 | (uri (bioconductor-uri "ABAData" version 'experiment)) |
692bce15 RW |
984 | (sha256 |
985 | (base32 | |
986 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) | |
987 | (properties | |
988 | `((upstream-name . "ABAData"))) | |
989 | (build-system r-build-system) | |
990 | (propagated-inputs | |
991 | `(("r-annotationdbi" ,r-annotationdbi))) | |
992 | (home-page "https://www.bioconductor.org/packages/ABAData/") | |
993 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") | |
994 | (description | |
995 | "This package provides the data for the gene expression enrichment | |
996 | analysis conducted in the package ABAEnrichment. The package includes three | |
997 | datasets which are derived from the Allen Brain Atlas: | |
998 | ||
999 | @enumerate | |
1000 | @item Gene expression data from Human Brain (adults) averaged across donors, | |
1001 | @item Gene expression data from the Developing Human Brain pooled into five | |
1002 | age categories and averaged across donors, and | |
1003 | @item a developmental effect score based on the Developing Human Brain | |
1004 | expression data. | |
1005 | @end enumerate | |
1006 | ||
1007 | All datasets are restricted to protein coding genes.") | |
1008 | (license license:gpl2+))) | |
1009 | ||
b50c9660 RW |
1010 | (define-public r-arrmdata |
1011 | (package | |
1012 | (name "r-arrmdata") | |
1013 | (version "1.18.0") | |
1014 | (source (origin | |
1015 | (method url-fetch) | |
b86f7746 | 1016 | (uri (bioconductor-uri "ARRmData" version 'experiment)) |
b50c9660 RW |
1017 | (sha256 |
1018 | (base32 | |
1019 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) | |
1020 | (properties | |
1021 | `((upstream-name . "ARRmData"))) | |
1022 | (build-system r-build-system) | |
1023 | (home-page "https://www.bioconductor.org/packages/ARRmData/") | |
1024 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") | |
1025 | (description | |
1026 | "This package provides raw beta values from 36 samples across 3 groups | |
1027 | from Illumina 450k methylation arrays.") | |
1028 | (license license:artistic2.0))) | |
1029 | ||
557a1089 RW |
1030 | (define-public r-hsmmsinglecell |
1031 | (package | |
1032 | (name "r-hsmmsinglecell") | |
1033 | (version "1.2.0") | |
1034 | (source (origin | |
1035 | (method url-fetch) | |
545e67ac | 1036 | (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) |
557a1089 RW |
1037 | (sha256 |
1038 | (base32 | |
1039 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) | |
1040 | (properties | |
1041 | `((upstream-name . "HSMMSingleCell"))) | |
1042 | (build-system r-build-system) | |
1043 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") | |
1044 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") | |
1045 | (description | |
1046 | "Skeletal myoblasts undergo a well-characterized sequence of | |
1047 | morphological and transcriptional changes during differentiation. In this | |
1048 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded | |
1049 | under high mitogen conditions (GM) and then differentiated by switching to | |
1050 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several | |
1051 | hundred cells taken over a time-course of serum-induced differentiation. | |
1052 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, | |
1053 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. | |
1054 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, | |
1055 | which were then sequenced to a depth of ~4 million reads per library, | |
1056 | resulting in a complete gene expression profile for each cell.") | |
1057 | (license license:artistic2.0))) | |
ad8f46c6 | 1058 | |
1059 | (define-public r-all | |
1060 | (package | |
1061 | (name "r-all") | |
1062 | (version "1.26.0") | |
1063 | (source (origin | |
1064 | (method url-fetch) | |
41728d23 | 1065 | (uri (bioconductor-uri "ALL" version 'experiment)) |
ad8f46c6 | 1066 | (sha256 |
1067 | (base32 | |
1068 | "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) | |
1069 | (properties `((upstream-name . "ALL"))) | |
1070 | (build-system r-build-system) | |
1071 | (propagated-inputs | |
1072 | `(("r-biobase" ,r-biobase))) | |
1073 | (home-page "https://bioconductor.org/packages/ALL") | |
1074 | (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") | |
1075 | (description | |
1076 | "The data consist of microarrays from 128 different individuals with | |
1077 | @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates | |
1078 | are available. The data have been normalized (using rma) and it is the | |
1079 | jointly normalized data that are available here. The data are presented in | |
1080 | the form of an @code{exprSet} object.") | |
1081 | (license license:artistic2.0))) | |
557a1089 | 1082 | |
53b1e10f RW |
1083 | (define-public r-affydata |
1084 | (package | |
1085 | (name "r-affydata") | |
1086 | (version "1.32.0") | |
1087 | (source | |
1088 | (origin | |
1089 | (method url-fetch) | |
1090 | (uri (bioconductor-uri "affydata" version 'experiment)) | |
1091 | (sha256 | |
1092 | (base32 | |
1093 | "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) | |
1094 | (properties `((upstream-name . "affydata"))) | |
1095 | (build-system r-build-system) | |
1096 | (propagated-inputs | |
1097 | `(("r-affy" ,r-affy))) | |
1098 | (home-page "https://bioconductor.org/packages/affydata/") | |
1099 | (synopsis "Affymetrix data for demonstration purposes") | |
1100 | (description | |
1101 | "This package provides example datasets that represent 'real world | |
1102 | examples' of Affymetrix data, unlike the artificial examples included in the | |
1103 | package @code{affy}.") | |
1104 | (license license:gpl2+))) | |
1105 | ||
0c0ef9c5 RJ |
1106 | (define-public r-coverageview |
1107 | (package | |
1108 | (name "r-coverageview") | |
5ef637dd | 1109 | (version "1.28.0") |
0c0ef9c5 RJ |
1110 | (source (origin |
1111 | (method url-fetch) | |
1112 | (uri (bioconductor-uri "CoverageView" version)) | |
1113 | (sha256 | |
1114 | (base32 | |
5ef637dd | 1115 | "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj")))) |
0c0ef9c5 RJ |
1116 | (build-system r-build-system) |
1117 | (propagated-inputs | |
1118 | `(("r-s4vectors" ,r-s4vectors) | |
1119 | ("r-iranges" ,r-iranges) | |
1120 | ("r-genomicranges" ,r-genomicranges) | |
1121 | ("r-genomicalignments" ,r-genomicalignments) | |
1122 | ("r-rtracklayer" ,r-rtracklayer) | |
1123 | ("r-rsamtools" ,r-rsamtools))) | |
1124 | (home-page "https://bioconductor.org/packages/CoverageView/") | |
1125 | (synopsis "Coverage visualization package for R") | |
1126 | (description "This package provides a framework for the visualization of | |
1127 | genome coverage profiles. It can be used for ChIP-seq experiments, but it can | |
1128 | be also used for genome-wide nucleosome positioning experiments or other | |
1129 | experiment types where it is important to have a framework in order to inspect | |
1130 | how the coverage distributed across the genome.") | |
1131 | (license license:artistic2.0))) | |
06fc1a51 RJ |
1132 | |
1133 | (define-public r-cummerbund | |
1134 | (package | |
1135 | (name "r-cummerbund") | |
a3e2e538 | 1136 | (version "2.32.0") |
06fc1a51 RJ |
1137 | (source (origin |
1138 | (method url-fetch) | |
1139 | (uri (bioconductor-uri "cummeRbund" version)) | |
1140 | (sha256 | |
1141 | (base32 | |
a3e2e538 | 1142 | "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj")))) |
06fc1a51 RJ |
1143 | (build-system r-build-system) |
1144 | (propagated-inputs | |
1145 | `(("r-biobase" ,r-biobase) | |
1146 | ("r-biocgenerics" ,r-biocgenerics) | |
1628d57b | 1147 | ("r-fastcluster" ,r-fastcluster) |
06fc1a51 RJ |
1148 | ("r-ggplot2" ,r-ggplot2) |
1149 | ("r-gviz" ,r-gviz) | |
1150 | ("r-plyr" ,r-plyr) | |
1151 | ("r-reshape2" ,r-reshape2) | |
1152 | ("r-rsqlite" ,r-rsqlite) | |
1153 | ("r-rtracklayer" ,r-rtracklayer) | |
1154 | ("r-s4vectors" ,r-s4vectors))) | |
1155 | (home-page "https://bioconductor.org/packages/cummeRbund/") | |
1156 | (synopsis "Analyze Cufflinks high-throughput sequencing data") | |
1157 | (description "This package allows for persistent storage, access, | |
1158 | exploration, and manipulation of Cufflinks high-throughput sequencing | |
1159 | data. In addition, provides numerous plotting functions for commonly | |
1160 | used visualizations.") | |
1161 | (license license:artistic2.0))) | |
0c0ef9c5 | 1162 | |
ff1146b9 RW |
1163 | (define-public r-curatedtcgadata |
1164 | (package | |
1165 | (name "r-curatedtcgadata") | |
1166 | (version "1.8.0") | |
1167 | (source | |
1168 | (origin | |
1169 | (method url-fetch) | |
1170 | (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) | |
1171 | (sha256 | |
1172 | (base32 | |
1173 | "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) | |
1174 | (properties | |
1175 | `((upstream-name . "curatedTCGAData"))) | |
1176 | (build-system r-build-system) | |
1177 | (propagated-inputs | |
1178 | `(("r-annotationhub" ,r-annotationhub) | |
1179 | ("r-experimenthub" ,r-experimenthub) | |
1180 | ("r-hdf5array" ,r-hdf5array) | |
1181 | ("r-multiassayexperiment" ,r-multiassayexperiment) | |
1182 | ("r-s4vectors" ,r-s4vectors) | |
1183 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1184 | (home-page "https://bioconductor.org/packages/curatedTCGAData/") | |
1185 | (synopsis "Curated data from The Cancer Genome Atlas") | |
1186 | (description | |
1187 | "This package provides publicly available data from The Cancer Genome | |
1188 | Atlas (TCGA) as @code{MultiAssayExperiment} objects. | |
1189 | @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy | |
1190 | number, mutation, microRNA, protein, and others) with clinical / pathological | |
1191 | data. It also links assay barcodes with patient identifiers, enabling | |
1192 | harmonized subsetting of rows (features) and columns (patients / samples) | |
1193 | across the entire multi-'omics experiment.") | |
1194 | (license license:artistic2.0))) | |
1195 | ||
557a1089 RW |
1196 | \f |
1197 | ;;; Packages | |
1198 | ||
e5d722fb RW |
1199 | (define-public r-biocversion |
1200 | (package | |
1201 | (name "r-biocversion") | |
70ab9909 | 1202 | (version "3.12.0") |
e5d722fb RW |
1203 | (source |
1204 | (origin | |
1205 | (method url-fetch) | |
1206 | (uri (bioconductor-uri "BiocVersion" version)) | |
1207 | (sha256 | |
1208 | (base32 | |
70ab9909 | 1209 | "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk")))) |
e5d722fb RW |
1210 | (properties `((upstream-name . "BiocVersion"))) |
1211 | (build-system r-build-system) | |
1212 | (home-page "https://bioconductor.org/packages/BiocVersion/") | |
1213 | (synopsis "Set the appropriate version of Bioconductor packages") | |
1214 | (description | |
1215 | "This package provides repository information for the appropriate version | |
1216 | of Bioconductor.") | |
1217 | (license license:artistic2.0))) | |
1218 | ||
14bba460 RW |
1219 | (define-public r-biocgenerics |
1220 | (package | |
1221 | (name "r-biocgenerics") | |
aa311eaa | 1222 | (version "0.36.0") |
14bba460 RW |
1223 | (source (origin |
1224 | (method url-fetch) | |
1225 | (uri (bioconductor-uri "BiocGenerics" version)) | |
1226 | (sha256 | |
1227 | (base32 | |
aa311eaa | 1228 | "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q")))) |
14bba460 RW |
1229 | (properties |
1230 | `((upstream-name . "BiocGenerics"))) | |
1231 | (build-system r-build-system) | |
1232 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
1233 | (synopsis "S4 generic functions for Bioconductor") | |
1234 | (description | |
1235 | "This package provides S4 generic functions needed by many Bioconductor | |
1236 | packages.") | |
1237 | (license license:artistic2.0))) | |
1238 | ||
5cf940de RW |
1239 | (define-public r-affycomp |
1240 | (package | |
1241 | (name "r-affycomp") | |
c472549f | 1242 | (version "1.66.0") |
5cf940de RW |
1243 | (source |
1244 | (origin | |
1245 | (method url-fetch) | |
1246 | (uri (bioconductor-uri "affycomp" version)) | |
1247 | (sha256 | |
1248 | (base32 | |
c472549f | 1249 | "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk")))) |
5cf940de RW |
1250 | (properties `((upstream-name . "affycomp"))) |
1251 | (build-system r-build-system) | |
1252 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
1253 | (home-page "https://bioconductor.org/packages/affycomp/") | |
1254 | (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") | |
1255 | (description | |
1256 | "The package contains functions that can be used to compare expression | |
1257 | measures for Affymetrix Oligonucleotide Arrays.") | |
1258 | (license license:gpl2+))) | |
1259 | ||
5094aa94 RW |
1260 | (define-public r-affycompatible |
1261 | (package | |
1262 | (name "r-affycompatible") | |
fa2d16cc | 1263 | (version "1.50.0") |
5094aa94 RW |
1264 | (source |
1265 | (origin | |
1266 | (method url-fetch) | |
1267 | (uri (bioconductor-uri "AffyCompatible" version)) | |
1268 | (sha256 | |
1269 | (base32 | |
fa2d16cc | 1270 | "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x")))) |
5094aa94 RW |
1271 | (properties |
1272 | `((upstream-name . "AffyCompatible"))) | |
1273 | (build-system r-build-system) | |
1274 | (propagated-inputs | |
1275 | `(("r-biostrings" ,r-biostrings) | |
1276 | ("r-rcurl" ,r-rcurl) | |
1277 | ("r-xml" ,r-xml))) | |
1278 | (home-page "https://bioconductor.org/packages/AffyCompatible/") | |
1279 | (synopsis "Work with Affymetrix GeneChip files") | |
1280 | (description | |
1281 | "This package provides an interface to Affymetrix chip annotation and | |
1282 | sample attribute files. The package allows an easy way for users to download | |
1283 | and manage local data bases of Affynmetrix NetAffx annotation files. It also | |
1284 | provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip | |
1285 | Command Console} (AGCC)-compatible sample annotation files.") | |
1286 | (license license:artistic2.0))) | |
1287 | ||
4ca2d6c1 RW |
1288 | (define-public r-affycontam |
1289 | (package | |
1290 | (name "r-affycontam") | |
3e82f9cc | 1291 | (version "1.48.0") |
4ca2d6c1 RW |
1292 | (source |
1293 | (origin | |
1294 | (method url-fetch) | |
1295 | (uri (bioconductor-uri "affyContam" version)) | |
1296 | (sha256 | |
1297 | (base32 | |
3e82f9cc | 1298 | "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b")))) |
4ca2d6c1 RW |
1299 | (properties `((upstream-name . "affyContam"))) |
1300 | (build-system r-build-system) | |
1301 | (propagated-inputs | |
1302 | `(("r-affy" ,r-affy) | |
1303 | ("r-affydata" ,r-affydata) | |
1304 | ("r-biobase" ,r-biobase))) | |
1305 | (home-page "https://bioconductor.org/packages/affyContam/") | |
1306 | (synopsis "Structured corruption of Affymetrix CEL file data") | |
1307 | (description | |
1308 | "Microarray quality assessment is a major concern of microarray analysts. | |
1309 | This package provides some simple approaches to in silico creation of quality | |
1310 | problems in CEL-level data to help evaluate performance of quality metrics.") | |
1311 | (license license:artistic2.0))) | |
1312 | ||
12105c6c RW |
1313 | (define-public r-affycoretools |
1314 | (package | |
1315 | (name "r-affycoretools") | |
a92219b4 | 1316 | (version "1.62.0") |
12105c6c RW |
1317 | (source |
1318 | (origin | |
1319 | (method url-fetch) | |
1320 | (uri (bioconductor-uri "affycoretools" version)) | |
1321 | (sha256 | |
1322 | (base32 | |
a92219b4 | 1323 | "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0")))) |
12105c6c RW |
1324 | (properties `((upstream-name . "affycoretools"))) |
1325 | (build-system r-build-system) | |
1326 | (propagated-inputs | |
1327 | `(("r-affy" ,r-affy) | |
1328 | ("r-annotationdbi" ,r-annotationdbi) | |
1329 | ("r-biobase" ,r-biobase) | |
1330 | ("r-biocgenerics" ,r-biocgenerics) | |
1331 | ("r-dbi" ,r-dbi) | |
1332 | ("r-edger" ,r-edger) | |
1333 | ("r-gcrma" ,r-gcrma) | |
f8f181ae | 1334 | ("r-glimma" ,r-glimma) |
12105c6c RW |
1335 | ("r-ggplot2" ,r-ggplot2) |
1336 | ("r-gostats" ,r-gostats) | |
1337 | ("r-gplots" ,r-gplots) | |
1338 | ("r-hwriter" ,r-hwriter) | |
1339 | ("r-lattice" ,r-lattice) | |
1340 | ("r-limma" ,r-limma) | |
1341 | ("r-oligoclasses" ,r-oligoclasses) | |
1342 | ("r-reportingtools" ,r-reportingtools) | |
1343 | ("r-rsqlite" ,r-rsqlite) | |
1344 | ("r-s4vectors" ,r-s4vectors) | |
1345 | ("r-xtable" ,r-xtable))) | |
fa610697 RW |
1346 | (native-inputs |
1347 | `(("r-knitr" ,r-knitr))) | |
12105c6c RW |
1348 | (home-page "https://bioconductor.org/packages/affycoretools/") |
1349 | (synopsis "Functions for analyses with Affymetrix GeneChips") | |
1350 | (description | |
1351 | "This package provides various wrapper functions that have been written | |
1352 | to streamline the more common analyses that a Biostatistician might see.") | |
1353 | (license license:artistic2.0))) | |
1354 | ||
d6a5d9b2 RW |
1355 | (define-public r-affxparser |
1356 | (package | |
1357 | (name "r-affxparser") | |
8e6a2c32 | 1358 | (version "1.62.0") |
d6a5d9b2 RW |
1359 | (source |
1360 | (origin | |
1361 | (method url-fetch) | |
1362 | (uri (bioconductor-uri "affxparser" version)) | |
1363 | (sha256 | |
1364 | (base32 | |
8e6a2c32 | 1365 | "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p")))) |
d6a5d9b2 RW |
1366 | (properties `((upstream-name . "affxparser"))) |
1367 | (build-system r-build-system) | |
1368 | (home-page "https://github.com/HenrikBengtsson/affxparser") | |
1369 | (synopsis "Affymetrix File Parsing SDK") | |
1370 | (description | |
1371 | "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, | |
1372 | BAR). It provides methods for fast and memory efficient parsing of Affymetrix | |
1373 | files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files | |
1374 | are supported. Currently, there are methods for reading @dfn{chip definition | |
1375 | file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read | |
1376 | either in full or in part. For example, probe signals from a few probesets | |
1377 | can be extracted very quickly from a set of CEL files into a convenient list | |
1378 | structure.") | |
1379 | ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is | |
1380 | ;; under LGPLv2+. | |
1381 | (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2)))) | |
1382 | ||
7097c700 RW |
1383 | (define-public r-annotate |
1384 | (package | |
1385 | (name "r-annotate") | |
7d563023 | 1386 | (version "1.68.0") |
7097c700 RW |
1387 | (source |
1388 | (origin | |
1389 | (method url-fetch) | |
1390 | (uri (bioconductor-uri "annotate" version)) | |
1391 | (sha256 | |
1392 | (base32 | |
7d563023 | 1393 | "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l")))) |
7097c700 RW |
1394 | (build-system r-build-system) |
1395 | (propagated-inputs | |
1396 | `(("r-annotationdbi" ,r-annotationdbi) | |
1397 | ("r-biobase" ,r-biobase) | |
1398 | ("r-biocgenerics" ,r-biocgenerics) | |
1399 | ("r-dbi" ,r-dbi) | |
7d563023 | 1400 | ("r-httr" ,r-httr) |
7097c700 RW |
1401 | ("r-xml" ,r-xml) |
1402 | ("r-xtable" ,r-xtable))) | |
1403 | (home-page | |
1404 | "https://bioconductor.org/packages/annotate") | |
1405 | (synopsis "Annotation for microarrays") | |
1406 | (description "This package provides R environments for the annotation of | |
1407 | microarrays.") | |
1408 | (license license:artistic2.0))) | |
1409 | ||
fa596599 RW |
1410 | (define-public r-hpar |
1411 | (package | |
1412 | (name "r-hpar") | |
fa7578b3 | 1413 | (version "1.32.1") |
fa596599 RW |
1414 | (source |
1415 | (origin | |
1416 | (method url-fetch) | |
1417 | (uri (bioconductor-uri "hpar" version)) | |
1418 | (sha256 | |
1419 | (base32 | |
fa7578b3 | 1420 | "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr")))) |
fa596599 | 1421 | (build-system r-build-system) |
07bea010 RW |
1422 | (native-inputs |
1423 | `(("r-knitr" ,r-knitr))) | |
fa596599 RW |
1424 | (home-page "https://bioconductor.org/packages/hpar/") |
1425 | (synopsis "Human Protein Atlas in R") | |
1426 | (description "This package provides a simple interface to and data from | |
1427 | the Human Protein Atlas project.") | |
1428 | (license license:artistic2.0))) | |
183ce988 RJ |
1429 | |
1430 | (define-public r-regioner | |
1431 | (package | |
1432 | (name "r-regioner") | |
d1ff3604 | 1433 | (version "1.22.0") |
183ce988 RJ |
1434 | (source |
1435 | (origin | |
1436 | (method url-fetch) | |
1437 | (uri (bioconductor-uri "regioneR" version)) | |
1438 | (sha256 | |
1439 | (base32 | |
d1ff3604 | 1440 | "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi")))) |
183ce988 RJ |
1441 | (properties `((upstream-name . "regioneR"))) |
1442 | (build-system r-build-system) | |
1443 | (propagated-inputs | |
d639d888 | 1444 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 1445 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 1446 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 1447 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 1448 | ("r-iranges" ,r-iranges) |
d639d888 RW |
1449 | ("r-memoise" ,r-memoise) |
1450 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 1451 | ("r-s4vectors" ,r-s4vectors))) |
7f34dd58 RW |
1452 | (native-inputs |
1453 | `(("r-knitr" ,r-knitr))) | |
183ce988 RJ |
1454 | (home-page "https://bioconductor.org/packages/regioneR/") |
1455 | (synopsis "Association analysis of genomic regions") | |
1456 | (description "This package offers a statistical framework based on | |
1457 | customizable permutation tests to assess the association between genomic | |
1458 | region sets and other genomic features.") | |
1459 | (license license:artistic2.0))) | |
a5b56a53 | 1460 | |
15184fb3 RW |
1461 | (define-public r-reportingtools |
1462 | (package | |
1463 | (name "r-reportingtools") | |
c03c7634 | 1464 | (version "2.30.0") |
15184fb3 RW |
1465 | (source |
1466 | (origin | |
1467 | (method url-fetch) | |
1468 | (uri (bioconductor-uri "ReportingTools" version)) | |
1469 | (sha256 | |
1470 | (base32 | |
c03c7634 | 1471 | "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31")))) |
15184fb3 RW |
1472 | (properties |
1473 | `((upstream-name . "ReportingTools"))) | |
1474 | (build-system r-build-system) | |
1475 | (propagated-inputs | |
1476 | `(("r-annotate" ,r-annotate) | |
1477 | ("r-annotationdbi" ,r-annotationdbi) | |
1478 | ("r-biobase" ,r-biobase) | |
1479 | ("r-biocgenerics" ,r-biocgenerics) | |
1480 | ("r-category" ,r-category) | |
1481 | ("r-deseq2" ,r-deseq2) | |
1482 | ("r-edger" ,r-edger) | |
1483 | ("r-ggbio" ,r-ggbio) | |
1484 | ("r-ggplot2" ,r-ggplot2) | |
1485 | ("r-gostats" ,r-gostats) | |
1486 | ("r-gseabase" ,r-gseabase) | |
1487 | ("r-hwriter" ,r-hwriter) | |
1488 | ("r-iranges" ,r-iranges) | |
1489 | ("r-knitr" ,r-knitr) | |
1490 | ("r-lattice" ,r-lattice) | |
1491 | ("r-limma" ,r-limma) | |
1492 | ("r-pfam-db" ,r-pfam-db) | |
1493 | ("r-r-utils" ,r-r-utils) | |
1494 | ("r-xml" ,r-xml))) | |
7f94cf01 RW |
1495 | (native-inputs |
1496 | `(("r-knitr" ,r-knitr))) | |
15184fb3 RW |
1497 | (home-page "https://bioconductor.org/packages/ReportingTools/") |
1498 | (synopsis "Tools for making reports in various formats") | |
1499 | (description | |
1500 | "The ReportingTools package enables users to easily display reports of | |
1501 | analysis results generated from sources such as microarray and sequencing | |
1502 | data. The package allows users to create HTML pages that may be viewed on a | |
1503 | web browser, or in other formats. Users can generate tables with sortable and | |
1504 | filterable columns, make and display plots, and link table entries to other | |
1505 | data sources such as NCBI or larger plots within the HTML page. Using the | |
1506 | package, users can also produce a table of contents page to link various | |
1507 | reports together for a particular project that can be viewed in a web | |
1508 | browser.") | |
1509 | (license license:artistic2.0))) | |
1510 | ||
bfb93b48 RW |
1511 | (define-public r-geneplotter |
1512 | (package | |
1513 | (name "r-geneplotter") | |
d72c4c98 | 1514 | (version "1.68.0") |
bfb93b48 RW |
1515 | (source |
1516 | (origin | |
1517 | (method url-fetch) | |
1518 | (uri (bioconductor-uri "geneplotter" version)) | |
1519 | (sha256 | |
1520 | (base32 | |
d72c4c98 | 1521 | "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx")))) |
bfb93b48 RW |
1522 | (build-system r-build-system) |
1523 | (propagated-inputs | |
1524 | `(("r-annotate" ,r-annotate) | |
1525 | ("r-annotationdbi" ,r-annotationdbi) | |
1526 | ("r-biobase" ,r-biobase) | |
1527 | ("r-biocgenerics" ,r-biocgenerics) | |
1528 | ("r-lattice" ,r-lattice) | |
1529 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
1530 | (home-page "https://bioconductor.org/packages/geneplotter") | |
1531 | (synopsis "Graphics functions for genomic data") | |
1532 | (description | |
1533 | "This package provides functions for plotting genomic data.") | |
1534 | (license license:artistic2.0))) | |
1535 | ||
01c7ba99 RW |
1536 | (define-public r-oligoclasses |
1537 | (package | |
1538 | (name "r-oligoclasses") | |
464df5cc | 1539 | (version "1.52.0") |
01c7ba99 RW |
1540 | (source |
1541 | (origin | |
1542 | (method url-fetch) | |
1543 | (uri (bioconductor-uri "oligoClasses" version)) | |
1544 | (sha256 | |
1545 | (base32 | |
464df5cc | 1546 | "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy")))) |
01c7ba99 RW |
1547 | (properties `((upstream-name . "oligoClasses"))) |
1548 | (build-system r-build-system) | |
1549 | (propagated-inputs | |
1550 | `(("r-affyio" ,r-affyio) | |
1551 | ("r-biobase" ,r-biobase) | |
1552 | ("r-biocgenerics" ,r-biocgenerics) | |
1553 | ("r-biocmanager" ,r-biocmanager) | |
1554 | ("r-biostrings" ,r-biostrings) | |
1555 | ("r-dbi" ,r-dbi) | |
1556 | ("r-ff" ,r-ff) | |
1557 | ("r-foreach" ,r-foreach) | |
1558 | ("r-genomicranges" ,r-genomicranges) | |
1559 | ("r-iranges" ,r-iranges) | |
1560 | ("r-rsqlite" ,r-rsqlite) | |
1561 | ("r-s4vectors" ,r-s4vectors) | |
1562 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1563 | (home-page "https://bioconductor.org/packages/oligoClasses/") | |
1564 | (synopsis "Classes for high-throughput arrays") | |
1565 | (description | |
1566 | "This package contains class definitions, validity checks, and | |
1567 | initialization methods for classes used by the @code{oligo} and @code{crlmm} | |
1568 | packages.") | |
1569 | (license license:gpl2+))) | |
1570 | ||
4c63eeb8 RW |
1571 | (define-public r-oligo |
1572 | (package | |
1573 | (name "r-oligo") | |
9af6fdf8 | 1574 | (version "1.54.1") |
4c63eeb8 RW |
1575 | (source |
1576 | (origin | |
1577 | (method url-fetch) | |
1578 | (uri (bioconductor-uri "oligo" version)) | |
1579 | (sha256 | |
1580 | (base32 | |
9af6fdf8 | 1581 | "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3")))) |
4c63eeb8 RW |
1582 | (properties `((upstream-name . "oligo"))) |
1583 | (build-system r-build-system) | |
1584 | (inputs `(("zlib" ,zlib))) | |
1585 | (propagated-inputs | |
1586 | `(("r-affxparser" ,r-affxparser) | |
1587 | ("r-affyio" ,r-affyio) | |
1588 | ("r-biobase" ,r-biobase) | |
1589 | ("r-biocgenerics" ,r-biocgenerics) | |
1590 | ("r-biostrings" ,r-biostrings) | |
1591 | ("r-dbi" ,r-dbi) | |
1592 | ("r-ff" ,r-ff) | |
1593 | ("r-oligoclasses" ,r-oligoclasses) | |
1594 | ("r-preprocesscore" ,r-preprocesscore) | |
1595 | ("r-rsqlite" ,r-rsqlite) | |
1596 | ("r-zlibbioc" ,r-zlibbioc))) | |
ace82f80 RW |
1597 | (native-inputs |
1598 | `(("r-knitr" ,r-knitr))) | |
4c63eeb8 RW |
1599 | (home-page "https://bioconductor.org/packages/oligo/") |
1600 | (synopsis "Preprocessing tools for oligonucleotide arrays") | |
1601 | (description | |
1602 | "This package provides a package to analyze oligonucleotide | |
1603 | arrays (expression/SNP/tiling/exon) at probe-level. It currently supports | |
1604 | Affymetrix (CEL files) and NimbleGen arrays (XYS files).") | |
1605 | (license license:lgpl2.0+))) | |
1606 | ||
4dc2ecc2 RW |
1607 | (define-public r-qvalue |
1608 | (package | |
1609 | (name "r-qvalue") | |
e9b60a29 | 1610 | (version "2.22.0") |
4dc2ecc2 RW |
1611 | (source |
1612 | (origin | |
1613 | (method url-fetch) | |
1614 | (uri (bioconductor-uri "qvalue" version)) | |
1615 | (sha256 | |
1616 | (base32 | |
e9b60a29 | 1617 | "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5")))) |
4dc2ecc2 RW |
1618 | (build-system r-build-system) |
1619 | (propagated-inputs | |
1620 | `(("r-ggplot2" ,r-ggplot2) | |
1621 | ("r-reshape2" ,r-reshape2))) | |
f9a24759 RW |
1622 | (native-inputs |
1623 | `(("r-knitr" ,r-knitr))) | |
702a1012 | 1624 | (home-page "https://github.com/StoreyLab/qvalue") |
4dc2ecc2 RW |
1625 | (synopsis "Q-value estimation for false discovery rate control") |
1626 | (description | |
1627 | "This package takes a list of p-values resulting from the simultaneous | |
1628 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
1629 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
1630 | of false positives incurred when that particular test is called significant. | |
1631 | The local FDR measures the posterior probability the null hypothesis is true | |
1632 | given the test's p-value. Various plots are automatically generated, allowing | |
1633 | one to make sensible significance cut-offs. The software can be applied to | |
1634 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
1635 | ;; Any version of the LGPL. | |
1636 | (license license:lgpl3+))) | |
1637 | ||
a0df9b93 RJ |
1638 | (define r-rcppnumerical |
1639 | (package | |
1640 | (name "r-rcppnumerical") | |
1641 | (version "0.4-0") | |
1642 | (source (origin | |
1643 | (method url-fetch) | |
1644 | (uri (cran-uri "RcppNumerical" version)) | |
1645 | (sha256 | |
1646 | (base32 | |
1647 | "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) | |
1648 | (properties `((upstream-name . "RcppNumerical"))) | |
1649 | (build-system r-build-system) | |
1650 | (propagated-inputs | |
1651 | `(("r-rcpp" ,r-rcpp) | |
1652 | ("r-rcppeigen" ,r-rcppeigen))) | |
1653 | (native-inputs | |
1654 | `(("r-knitr" ,r-knitr))) | |
1655 | (home-page "https://github.com/yixuan/RcppNumerical") | |
1656 | (synopsis "Rcpp integration for numerical computing libraries") | |
1657 | (description "This package provides a collection of open source libraries | |
1658 | for numerical computing (numerical integration, optimization, etc.) and their | |
1659 | integration with @code{Rcpp}.") | |
1660 | (license license:gpl2+))) | |
1661 | ||
3b399e51 RJ |
1662 | (define-public r-apeglm |
1663 | (package | |
1664 | (name "r-apeglm") | |
1665 | (version "1.12.0") | |
1666 | (source (origin | |
1667 | (method url-fetch) | |
1668 | (uri (bioconductor-uri "apeglm" version)) | |
1669 | (sha256 | |
1670 | (base32 | |
1671 | "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2")))) | |
1672 | (properties `((upstream-name . "apeglm"))) | |
1673 | (build-system r-build-system) | |
1674 | (propagated-inputs | |
1675 | `(("r-emdbook" ,r-emdbook) | |
1676 | ("r-genomicranges" ,r-genomicranges) | |
1677 | ("r-rcpp" ,r-rcpp) | |
1678 | ("r-rcppeigen" ,r-rcppeigen) | |
1679 | ("r-rcppnumerical" ,r-rcppnumerical) | |
1680 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1681 | (native-inputs `(("r-knitr" ,r-knitr))) | |
1682 | (home-page "https://bioconductor.org/packages/apeglm") | |
1683 | (synopsis "Approximate posterior estimation for GLM coefficients") | |
1684 | (description "This package provides Bayesian shrinkage estimators for | |
1685 | effect sizes for a variety of GLM models, using approximation of the | |
1686 | posterior for individual coefficients.") | |
1687 | (license license:gpl2))) | |
1688 | ||
6e396c4b RJ |
1689 | (define-public r-greylistchip |
1690 | (package | |
1691 | (name "r-greylistchip") | |
1692 | (version "1.22.0") | |
1693 | (source (origin | |
1694 | (method url-fetch) | |
1695 | (uri (bioconductor-uri "GreyListChIP" version)) | |
1696 | (sha256 | |
1697 | (base32 | |
1698 | "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6")))) | |
1699 | (properties `((upstream-name . "GreyListChIP"))) | |
1700 | (build-system r-build-system) | |
1701 | (propagated-inputs | |
1702 | `(("r-bsgenome" ,r-bsgenome) | |
1703 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1704 | ("r-genomicalignments" ,r-genomicalignments) | |
1705 | ("r-genomicranges" ,r-genomicranges) | |
1706 | ("r-mass" ,r-mass) | |
1707 | ("r-rsamtools" ,r-rsamtools) | |
1708 | ("r-rtracklayer" ,r-rtracklayer) | |
1709 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1710 | (home-page "https://bioconductor.org/packages/GreyListChIP") | |
1711 | (synopsis "Greylist artefact regions based on ChIP inputs") | |
1712 | (description "This package identifies regions of ChIP experiments with high | |
1713 | signal in the input, that lead to spurious peaks during peak calling.") | |
1714 | (license license:artistic2.0))) | |
1715 | ||
a5b56a53 RJ |
1716 | (define-public r-diffbind |
1717 | (package | |
1718 | (name "r-diffbind") | |
341ebaaa | 1719 | (version "3.0.7") |
a5b56a53 RJ |
1720 | (source |
1721 | (origin | |
1722 | (method url-fetch) | |
1723 | (uri (bioconductor-uri "DiffBind" version)) | |
1724 | (sha256 | |
1725 | (base32 | |
341ebaaa | 1726 | "0irhqsi6rrkrkc7dhwmfpqfd0mnigs17027czcx8vgbrbra4lcvd")))) |
a5b56a53 RJ |
1727 | (properties `((upstream-name . "DiffBind"))) |
1728 | (build-system r-build-system) | |
1729 | (inputs | |
1730 | `(("zlib" ,zlib))) | |
1731 | (propagated-inputs | |
1732 | `(("r-amap" ,r-amap) | |
341ebaaa RJ |
1733 | ("r-apeglm" ,r-apeglm) |
1734 | ("r-ashr" ,r-ashr) | |
a5b56a53 RJ |
1735 | ("r-biocparallel" ,r-biocparallel) |
1736 | ("r-deseq2" ,r-deseq2) | |
1737 | ("r-dplyr" ,r-dplyr) | |
a5b56a53 | 1738 | ("r-genomicalignments" ,r-genomicalignments) |
45bbccf4 RW |
1739 | ("r-genomicranges" ,r-genomicranges) |
1740 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
1741 | ("r-ggrepel" ,r-ggrepel) |
1742 | ("r-gplots" ,r-gplots) | |
341ebaaa | 1743 | ("r-greylistchip" ,r-greylistchip) |
a5b56a53 RJ |
1744 | ("r-iranges" ,r-iranges) |
1745 | ("r-lattice" ,r-lattice) | |
1746 | ("r-limma" ,r-limma) | |
1747 | ("r-locfit" ,r-locfit) | |
1748 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
1749 | ("r-rcpp" ,r-rcpp) | |
4c221b3b | 1750 | ("r-rhtslib" ,r-rhtslib) |
a5b56a53 RJ |
1751 | ("r-rsamtools" ,r-rsamtools) |
1752 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 1753 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
4c221b3b | 1754 | ("r-systempiper" ,r-systempiper))) |
99db6db7 | 1755 | (home-page "https://bioconductor.org/packages/DiffBind") |
a5b56a53 RJ |
1756 | (synopsis "Differential binding analysis of ChIP-Seq peak data") |
1757 | (description | |
1758 | "This package computes differentially bound sites from multiple | |
1759 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
1760 | occupancy (overlap) analysis and plotting functions.") | |
1761 | (license license:artistic2.0))) | |
6d94bf6b RJ |
1762 | |
1763 | (define-public r-ripseeker | |
1764 | (package | |
1765 | (name "r-ripseeker") | |
ba74434f | 1766 | (version "1.26.0") |
6d94bf6b RJ |
1767 | (source |
1768 | (origin | |
1769 | (method url-fetch) | |
1770 | (uri (bioconductor-uri "RIPSeeker" version)) | |
1771 | (sha256 | |
1772 | (base32 | |
ba74434f | 1773 | "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) |
6d94bf6b RJ |
1774 | (properties `((upstream-name . "RIPSeeker"))) |
1775 | (build-system r-build-system) | |
1776 | (propagated-inputs | |
1777 | `(("r-s4vectors" ,r-s4vectors) | |
1778 | ("r-iranges" ,r-iranges) | |
1779 | ("r-genomicranges" ,r-genomicranges) | |
1780 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1781 | ("r-rsamtools" ,r-rsamtools) | |
1782 | ("r-genomicalignments" ,r-genomicalignments) | |
1783 | ("r-rtracklayer" ,r-rtracklayer))) | |
99db6db7 | 1784 | (home-page "https://bioconductor.org/packages/RIPSeeker") |
6d94bf6b RJ |
1785 | (synopsis |
1786 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
1787 | (description | |
1788 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
1789 | using two-state HMM with negative binomial emission probability. While | |
1790 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
1791 | a suite of bioinformatics tools integrated within this self-contained software | |
1792 | package comprehensively addressing issues ranging from post-alignments | |
1793 | processing to visualization and annotation.") | |
1794 | (license license:gpl2))) | |
a6ae9ffd RJ |
1795 | |
1796 | (define-public r-multtest | |
1797 | (package | |
1798 | (name "r-multtest") | |
1e6920c5 | 1799 | (version "2.46.0") |
a6ae9ffd RJ |
1800 | (source |
1801 | (origin | |
1802 | (method url-fetch) | |
1803 | (uri (bioconductor-uri "multtest" version)) | |
1804 | (sha256 | |
1805 | (base32 | |
1e6920c5 | 1806 | "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q")))) |
a6ae9ffd RJ |
1807 | (build-system r-build-system) |
1808 | (propagated-inputs | |
1809 | `(("r-survival" ,r-survival) | |
1810 | ("r-biocgenerics" ,r-biocgenerics) | |
1811 | ("r-biobase" ,r-biobase) | |
1812 | ("r-mass" ,r-mass))) | |
99db6db7 | 1813 | (home-page "https://bioconductor.org/packages/multtest") |
a6ae9ffd RJ |
1814 | (synopsis "Resampling-based multiple hypothesis testing") |
1815 | (description | |
1816 | "This package can do non-parametric bootstrap and permutation | |
1817 | resampling-based multiple testing procedures (including empirical Bayes | |
1818 | methods) for controlling the family-wise error rate (FWER), generalized | |
1819 | family-wise error rate (gFWER), tail probability of the proportion of | |
1820 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
1821 | of bootstrap-based null distribution are implemented (centered, centered | |
1822 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
1823 | available. Tests based on a variety of T- and F-statistics (including | |
1824 | T-statistics based on regression parameters from linear and survival models | |
1825 | as well as those based on correlation parameters) are included. When probing | |
1826 | hypotheses with T-statistics, users may also select a potentially faster null | |
1827 | distribution which is multivariate normal with mean zero and variance | |
1828 | covariance matrix derived from the vector influence function. Results are | |
1829 | reported in terms of adjusted P-values, confidence regions and test statistic | |
1830 | cutoffs. The procedures are directly applicable to identifying differentially | |
1831 | expressed genes in DNA microarray experiments.") | |
1832 | (license license:lgpl3))) | |
793f83ef | 1833 | |
5dfe4912 RW |
1834 | (define-public r-graph |
1835 | (package | |
1836 | (name "r-graph") | |
f519b4dc | 1837 | (version "1.68.0") |
5dfe4912 RW |
1838 | (source (origin |
1839 | (method url-fetch) | |
1840 | (uri (bioconductor-uri "graph" version)) | |
1841 | (sha256 | |
1842 | (base32 | |
f519b4dc | 1843 | "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4")))) |
5dfe4912 RW |
1844 | (build-system r-build-system) |
1845 | (propagated-inputs | |
1846 | `(("r-biocgenerics" ,r-biocgenerics))) | |
1847 | (home-page "https://bioconductor.org/packages/graph") | |
1848 | (synopsis "Handle graph data structures in R") | |
1849 | (description | |
1850 | "This package implements some simple graph handling capabilities for R.") | |
1851 | (license license:artistic2.0))) | |
1852 | ||
8017eb0a RW |
1853 | ;; This is a CRAN package, but it depends on a Bioconductor package. |
1854 | (define-public r-ggm | |
1855 | (package | |
1856 | (name "r-ggm") | |
1857 | (version "2.5") | |
1858 | (source | |
1859 | (origin | |
1860 | (method url-fetch) | |
1861 | (uri (cran-uri "ggm" version)) | |
1862 | (sha256 | |
1863 | (base32 | |
1864 | "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) | |
1865 | (properties `((upstream-name . "ggm"))) | |
1866 | (build-system r-build-system) | |
1867 | (propagated-inputs | |
1868 | `(("r-graph" ,r-graph) | |
1869 | ("r-igraph" ,r-igraph))) | |
1870 | (home-page "https://cran.r-project.org/package=ggm") | |
1871 | (synopsis "Functions for graphical Markov models") | |
1872 | (description | |
1873 | "This package provides functions and datasets for maximum likelihood | |
1874 | fitting of some classes of graphical Markov models.") | |
1875 | (license license:gpl2+))) | |
1876 | ||
a07717cc RW |
1877 | ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph. |
1878 | (define-public r-perfmeas | |
1879 | (package | |
1880 | (name "r-perfmeas") | |
1881 | (version "1.2.1") | |
1882 | (source | |
1883 | (origin | |
1884 | (method url-fetch) | |
1885 | (uri (cran-uri "PerfMeas" version)) | |
1886 | (sha256 | |
1887 | (base32 | |
1888 | "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93")))) | |
1889 | (properties `((upstream-name . "PerfMeas"))) | |
1890 | (build-system r-build-system) | |
1891 | (propagated-inputs | |
1892 | `(("r-graph" ,r-graph) | |
1893 | ("r-limma" ,r-limma) | |
1894 | ("r-rbgl" ,r-rbgl))) | |
1895 | (home-page "https://cran.r-project.org/web/packages/PerfMeas/") | |
1896 | (synopsis "Performance measures for ranking and classification tasks") | |
1897 | (description | |
1898 | "This package implements different performance measures for | |
1899 | classification and ranking tasks. @dfn{Area under curve} (AUC), precision at | |
1900 | a given recall, F-score for single and multiple classes are available.") | |
1901 | (license license:gpl2+))) | |
1902 | ||
b17ace24 | 1903 | ;; This is a CRAN package, but it depends on a Bioconductor package. |
a207bca2 RW |
1904 | (define-public r-codedepends |
1905 | (package | |
1906 | (name "r-codedepends") | |
1907 | (version "0.6.5") | |
1908 | (source | |
1909 | (origin | |
1910 | (method url-fetch) | |
1911 | (uri (cran-uri "CodeDepends" version)) | |
1912 | (sha256 | |
1913 | (base32 | |
1914 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
1915 | (properties `((upstream-name . "CodeDepends"))) | |
1916 | (build-system r-build-system) | |
1917 | (propagated-inputs | |
1918 | `(("r-codetools" ,r-codetools) | |
1919 | ("r-graph" ,r-graph) | |
1920 | ("r-xml" ,r-xml))) | |
5e1f2362 | 1921 | (home-page "https://cran.r-project.org/web/packages/CodeDepends") |
a207bca2 RW |
1922 | (synopsis "Analysis of R code for reproducible research and code comprehension") |
1923 | (description | |
1924 | "This package provides tools for analyzing R expressions or blocks of | |
1925 | code and determining the dependencies between them. It focuses on R scripts, | |
1926 | but can be used on the bodies of functions. There are many facilities | |
1927 | including the ability to summarize or get a high-level view of code, | |
1928 | determining dependencies between variables, code improvement suggestions.") | |
1929 | ;; Any version of the GPL | |
1930 | (license (list license:gpl2+ license:gpl3+)))) | |
1931 | ||
793f83ef RJ |
1932 | (define-public r-chippeakanno |
1933 | (package | |
1934 | (name "r-chippeakanno") | |
d068d967 | 1935 | (version "3.24.1") |
793f83ef RJ |
1936 | (source |
1937 | (origin | |
1938 | (method url-fetch) | |
1939 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
1940 | (sha256 | |
1941 | (base32 | |
d068d967 | 1942 | "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj")))) |
793f83ef RJ |
1943 | (properties `((upstream-name . "ChIPpeakAnno"))) |
1944 | (build-system r-build-system) | |
1945 | (propagated-inputs | |
85c1d20f | 1946 | `(("r-annotationdbi" ,r-annotationdbi) |
85c1d20f | 1947 | ("r-biocgenerics" ,r-biocgenerics) |
793f83ef | 1948 | ("r-biomart" ,r-biomart) |
85c1d20f | 1949 | ("r-biostrings" ,r-biostrings) |
85c1d20f | 1950 | ("r-dbi" ,r-dbi) |
85c1d20f RW |
1951 | ("r-ensembldb" ,r-ensembldb) |
1952 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1953 | ("r-genomicalignments" ,r-genomicalignments) | |
793f83ef | 1954 | ("r-genomicfeatures" ,r-genomicfeatures) |
f794e85d | 1955 | ("r-genomicranges" ,r-genomicranges) |
d068d967 | 1956 | ("r-ggplot2" ,r-ggplot2) |
85c1d20f | 1957 | ("r-graph" ,r-graph) |
f794e85d | 1958 | ("r-iranges" ,r-iranges) |
d068d967 | 1959 | ("r-keggrest" ,r-keggrest) |
85c1d20f | 1960 | ("r-matrixstats" ,r-matrixstats) |
793f83ef RJ |
1961 | ("r-multtest" ,r-multtest) |
1962 | ("r-rbgl" ,r-rbgl) | |
793f83ef | 1963 | ("r-regioner" ,r-regioner) |
85c1d20f RW |
1964 | ("r-rsamtools" ,r-rsamtools) |
1965 | ("r-rtracklayer" ,r-rtracklayer) | |
f794e85d | 1966 | ("r-s4vectors" ,r-s4vectors) |
793f83ef | 1967 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
793f83ef | 1968 | ("r-venndiagram" ,r-venndiagram))) |
dc24de46 RW |
1969 | (native-inputs |
1970 | `(("r-knitr" ,r-knitr))) | |
99db6db7 | 1971 | (home-page "https://bioconductor.org/packages/ChIPpeakAnno") |
793f83ef RJ |
1972 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") |
1973 | (description | |
1974 | "The package includes functions to retrieve the sequences around the peak, | |
1975 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
1976 | custom features such as most conserved elements and other transcription factor | |
1977 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
1978 | for finding the peaks with bi-directional promoters with summary statistics | |
1979 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
1980 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
1981 | enrichedGO (addGeneIDs).") | |
1982 | (license license:gpl2+))) | |
164502d8 | 1983 | |
c8da0137 RJ |
1984 | (define-public r-matrixgenerics |
1985 | (package | |
1986 | (name "r-matrixgenerics") | |
1987 | (version "1.2.0") | |
1988 | (source (origin | |
1989 | (method url-fetch) | |
1990 | (uri (bioconductor-uri "MatrixGenerics" version)) | |
1991 | (sha256 | |
1992 | (base32 | |
1993 | "1a3sw79185d6rld3wlrynkzcbp754a7jkracrmvn0ra964ia8zvc")))) | |
1994 | (properties | |
1995 | `((upstream-name . "MatrixGenerics"))) | |
1996 | (build-system r-build-system) | |
1997 | (propagated-inputs | |
1998 | `(("r-matrixstats" ,r-matrixstats))) | |
1999 | (home-page "https://bioconductor.org/packages/MatrixGenerics") | |
2000 | (synopsis "S4 generic summary statistic functions for matrix-like objects") | |
2001 | (description | |
2002 | "This package provides S4 generic functions modeled after the | |
2003 | @code{matrixStats} API for alternative matrix implementations. Packages with | |
2004 | alternative matrix implementation can depend on this package and implement the | |
2005 | generic functions that are defined here for a useful set of row and column | |
2006 | summary statistics. Other package developers can import this package and | |
2007 | handle a different matrix implementations without worrying about | |
2008 | incompatibilities.") | |
2009 | (license license:artistic2.0))) | |
2010 | ||
164502d8 RJ |
2011 | (define-public r-marray |
2012 | (package | |
2013 | (name "r-marray") | |
6e6c6272 | 2014 | (version "1.68.0") |
164502d8 RJ |
2015 | (source (origin |
2016 | (method url-fetch) | |
2017 | (uri (bioconductor-uri "marray" version)) | |
2018 | (sha256 | |
6e6c6272 | 2019 | (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray")))) |
164502d8 RJ |
2020 | (build-system r-build-system) |
2021 | (propagated-inputs | |
67487088 | 2022 | `(("r-limma" ,r-limma))) |
99db6db7 | 2023 | (home-page "https://bioconductor.org/packages/marray") |
164502d8 RJ |
2024 | (synopsis "Exploratory analysis for two-color spotted microarray data") |
2025 | (description "This package contains class definitions for two-color spotted | |
ab8979fc | 2026 | microarray data. It also includes functions for data input, diagnostic plots, |
164502d8 RJ |
2027 | normalization and quality checking.") |
2028 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
2029 | |
2030 | (define-public r-cghbase | |
2031 | (package | |
2032 | (name "r-cghbase") | |
ee052d05 | 2033 | (version "1.50.0") |
0416a0d4 RJ |
2034 | (source (origin |
2035 | (method url-fetch) | |
2036 | (uri (bioconductor-uri "CGHbase" version)) | |
2037 | (sha256 | |
ee052d05 | 2038 | (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4")))) |
0416a0d4 RJ |
2039 | (properties `((upstream-name . "CGHbase"))) |
2040 | (build-system r-build-system) | |
2041 | (propagated-inputs | |
2042 | `(("r-biobase" ,r-biobase) | |
2043 | ("r-marray" ,r-marray))) | |
99db6db7 | 2044 | (home-page "https://bioconductor.org/packages/CGHbase") |
0416a0d4 RJ |
2045 | (synopsis "Base functions and classes for arrayCGH data analysis") |
2046 | (description "This package contains functions and classes that are needed by | |
2047 | the @code{arrayCGH} packages.") | |
2048 | (license license:gpl2+))) | |
67ee83d6 RJ |
2049 | |
2050 | (define-public r-cghcall | |
2051 | (package | |
2052 | (name "r-cghcall") | |
72400035 | 2053 | (version "2.52.0") |
67ee83d6 RJ |
2054 | (source (origin |
2055 | (method url-fetch) | |
2056 | (uri (bioconductor-uri "CGHcall" version)) | |
2057 | (sha256 | |
72400035 | 2058 | (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba")))) |
67ee83d6 RJ |
2059 | (properties `((upstream-name . "CGHcall"))) |
2060 | (build-system r-build-system) | |
2061 | (propagated-inputs | |
2062 | `(("r-biobase" ,r-biobase) | |
2063 | ("r-cghbase" ,r-cghbase) | |
2064 | ("r-impute" ,r-impute) | |
2065 | ("r-dnacopy" ,r-dnacopy) | |
2066 | ("r-snowfall" ,r-snowfall))) | |
99db6db7 | 2067 | (home-page "https://bioconductor.org/packages/CGHcall") |
67ee83d6 RJ |
2068 | (synopsis "Base functions and classes for arrayCGH data analysis") |
2069 | (description "This package contains functions and classes that are needed by | |
2070 | @code{arrayCGH} packages.") | |
2071 | (license license:gpl2+))) | |
0ef8cc9c RJ |
2072 | |
2073 | (define-public r-qdnaseq | |
2074 | (package | |
2075 | (name "r-qdnaseq") | |
3b648409 | 2076 | (version "1.26.0") |
0ef8cc9c RJ |
2077 | (source (origin |
2078 | (method url-fetch) | |
2079 | (uri (bioconductor-uri "QDNAseq" version)) | |
2080 | (sha256 | |
3b648409 | 2081 | (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph")))) |
0ef8cc9c RJ |
2082 | (properties `((upstream-name . "QDNAseq"))) |
2083 | (build-system r-build-system) | |
2084 | (propagated-inputs | |
2085 | `(("r-biobase" ,r-biobase) | |
2086 | ("r-cghbase" ,r-cghbase) | |
2087 | ("r-cghcall" ,r-cghcall) | |
2088 | ("r-dnacopy" ,r-dnacopy) | |
23ce5ad1 RW |
2089 | ("r-future" ,r-future) |
2090 | ("r-future-apply" ,r-future-apply) | |
0ef8cc9c RJ |
2091 | ("r-genomicranges" ,r-genomicranges) |
2092 | ("r-iranges" ,r-iranges) | |
2093 | ("r-matrixstats" ,r-matrixstats) | |
2094 | ("r-r-utils" ,r-r-utils) | |
2095 | ("r-rsamtools" ,r-rsamtools))) | |
99db6db7 | 2096 | (home-page "https://bioconductor.org/packages/QDNAseq") |
0ef8cc9c RJ |
2097 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") |
2098 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
2099 | number of sequence reads in each counted, adjusted with a simultaneous | |
2100 | two-dimensional loess correction for sequence mappability and GC content, and | |
2101 | filtered to remove spurious regions in the genome. Downstream steps of | |
2102 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
2103 | respectively.") | |
2104 | (license license:gpl2+))) | |
bb15b581 RW |
2105 | |
2106 | (define-public r-bayseq | |
2107 | (package | |
2108 | (name "r-bayseq") | |
63572b0c | 2109 | (version "2.24.0") |
bb15b581 RW |
2110 | (source |
2111 | (origin | |
2112 | (method url-fetch) | |
2113 | (uri (bioconductor-uri "baySeq" version)) | |
2114 | (sha256 | |
2115 | (base32 | |
63572b0c | 2116 | "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215")))) |
bb15b581 RW |
2117 | (properties `((upstream-name . "baySeq"))) |
2118 | (build-system r-build-system) | |
2119 | (propagated-inputs | |
2120 | `(("r-abind" ,r-abind) | |
2121 | ("r-edger" ,r-edger) | |
2122 | ("r-genomicranges" ,r-genomicranges))) | |
2123 | (home-page "https://bioconductor.org/packages/baySeq/") | |
2124 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
2125 | (description | |
2126 | "This package identifies differential expression in high-throughput count | |
2127 | data, such as that derived from next-generation sequencing machines, | |
2128 | calculating estimated posterior likelihoods of differential expression (or | |
2129 | more complex hypotheses) via empirical Bayesian methods.") | |
2130 | (license license:gpl3))) | |
609f4ad1 RW |
2131 | |
2132 | (define-public r-chipcomp | |
2133 | (package | |
2134 | (name "r-chipcomp") | |
ef1d3231 | 2135 | (version "1.18.0") |
609f4ad1 RW |
2136 | (source |
2137 | (origin | |
2138 | (method url-fetch) | |
2139 | (uri (bioconductor-uri "ChIPComp" version)) | |
2140 | (sha256 | |
2141 | (base32 | |
ef1d3231 | 2142 | "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp")))) |
609f4ad1 RW |
2143 | (properties `((upstream-name . "ChIPComp"))) |
2144 | (build-system r-build-system) | |
2145 | (propagated-inputs | |
2146 | `(("r-biocgenerics" ,r-biocgenerics) | |
2147 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
2148 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
2149 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2150 | ("r-genomicranges" ,r-genomicranges) | |
2151 | ("r-iranges" ,r-iranges) | |
2152 | ("r-limma" ,r-limma) | |
2153 | ("r-rsamtools" ,r-rsamtools) | |
2154 | ("r-rtracklayer" ,r-rtracklayer) | |
2155 | ("r-s4vectors" ,r-s4vectors))) | |
2156 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
2157 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
2158 | (description | |
2159 | "ChIPComp implements a statistical method for quantitative comparison of | |
2160 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
2161 | sites across multiple conditions considering matching control in ChIP-seq | |
2162 | datasets.") | |
2163 | ;; Any version of the GPL. | |
2164 | (license license:gpl3+))) | |
0490f9de RW |
2165 | |
2166 | (define-public r-riboprofiling | |
2167 | (package | |
2168 | (name "r-riboprofiling") | |
03b655c5 | 2169 | (version "1.20.0") |
0490f9de RW |
2170 | (source |
2171 | (origin | |
2172 | (method url-fetch) | |
2173 | (uri (bioconductor-uri "RiboProfiling" version)) | |
2174 | (sha256 | |
2175 | (base32 | |
03b655c5 | 2176 | "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg")))) |
0490f9de RW |
2177 | (properties `((upstream-name . "RiboProfiling"))) |
2178 | (build-system r-build-system) | |
2179 | (propagated-inputs | |
2180 | `(("r-biocgenerics" ,r-biocgenerics) | |
2181 | ("r-biostrings" ,r-biostrings) | |
2182 | ("r-data-table" ,r-data-table) | |
2183 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2184 | ("r-genomicalignments" ,r-genomicalignments) | |
2185 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2186 | ("r-genomicranges" ,r-genomicranges) | |
2187 | ("r-ggbio" ,r-ggbio) | |
2188 | ("r-ggplot2" ,r-ggplot2) | |
2189 | ("r-iranges" ,r-iranges) | |
2190 | ("r-plyr" ,r-plyr) | |
2191 | ("r-reshape2" ,r-reshape2) | |
2192 | ("r-rsamtools" ,r-rsamtools) | |
2193 | ("r-rtracklayer" ,r-rtracklayer) | |
2194 | ("r-s4vectors" ,r-s4vectors) | |
2195 | ("r-sqldf" ,r-sqldf))) | |
7aae05a9 RW |
2196 | (native-inputs |
2197 | `(("r-knitr" ,r-knitr))) | |
0490f9de RW |
2198 | (home-page "https://bioconductor.org/packages/RiboProfiling/") |
2199 | (synopsis "Ribosome profiling data analysis") | |
2200 | (description "Starting with a BAM file, this package provides the | |
2201 | necessary functions for quality assessment, read start position recalibration, | |
2202 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
2203 | of count data: pairs, log fold-change, codon frequency and coverage | |
2204 | assessment, principal component analysis on codon coverage.") | |
2205 | (license license:gpl3))) | |
6ffdfe6a RW |
2206 | |
2207 | (define-public r-riboseqr | |
2208 | (package | |
2209 | (name "r-riboseqr") | |
3813c9fe | 2210 | (version "1.24.0") |
6ffdfe6a RW |
2211 | (source |
2212 | (origin | |
2213 | (method url-fetch) | |
2214 | (uri (bioconductor-uri "riboSeqR" version)) | |
2215 | (sha256 | |
2216 | (base32 | |
3813c9fe | 2217 | "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr")))) |
6ffdfe6a RW |
2218 | (properties `((upstream-name . "riboSeqR"))) |
2219 | (build-system r-build-system) | |
2220 | (propagated-inputs | |
2221 | `(("r-abind" ,r-abind) | |
2222 | ("r-bayseq" ,r-bayseq) | |
2223 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2224 | ("r-genomicranges" ,r-genomicranges) | |
2225 | ("r-iranges" ,r-iranges) | |
2226 | ("r-rsamtools" ,r-rsamtools) | |
2227 | ("r-seqlogo" ,r-seqlogo))) | |
2228 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
2229 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
2230 | (description | |
2231 | "This package provides plotting functions, frameshift detection and | |
2232 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
2233 | (license license:gpl3))) | |
a32279ff RW |
2234 | |
2235 | (define-public r-interactionset | |
35dae951 | 2236 | (package ;BROKEN |
a32279ff | 2237 | (name "r-interactionset") |
35dae951 | 2238 | (version "1.18.0") |
a32279ff RW |
2239 | (source |
2240 | (origin | |
2241 | (method url-fetch) | |
2242 | (uri (bioconductor-uri "InteractionSet" version)) | |
2243 | (sha256 | |
2244 | (base32 | |
35dae951 | 2245 | "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31")))) |
a32279ff RW |
2246 | (properties |
2247 | `((upstream-name . "InteractionSet"))) | |
2248 | (build-system r-build-system) | |
2249 | (propagated-inputs | |
2250 | `(("r-biocgenerics" ,r-biocgenerics) | |
2251 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2252 | ("r-genomicranges" ,r-genomicranges) | |
2253 | ("r-iranges" ,r-iranges) | |
2254 | ("r-matrix" ,r-matrix) | |
2255 | ("r-rcpp" ,r-rcpp) | |
2256 | ("r-s4vectors" ,r-s4vectors) | |
2257 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
861a903f RW |
2258 | (native-inputs |
2259 | `(("r-knitr" ,r-knitr))) | |
a32279ff RW |
2260 | (home-page "https://bioconductor.org/packages/InteractionSet") |
2261 | (synopsis "Base classes for storing genomic interaction data") | |
2262 | (description | |
02fe0976 | 2263 | "This package provides the @code{GInteractions}, |
a32279ff RW |
2264 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
2265 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
2266 | experiments.") | |
2267 | (license license:gpl3))) | |
cf9a29b2 RW |
2268 | |
2269 | (define-public r-genomicinteractions | |
2270 | (package | |
2271 | (name "r-genomicinteractions") | |
dd9341ff | 2272 | (version "1.24.0") |
cf9a29b2 RW |
2273 | (source |
2274 | (origin | |
2275 | (method url-fetch) | |
2276 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
2277 | (sha256 | |
2278 | (base32 | |
dd9341ff | 2279 | "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd")))) |
cf9a29b2 RW |
2280 | (properties |
2281 | `((upstream-name . "GenomicInteractions"))) | |
2282 | (build-system r-build-system) | |
2283 | (propagated-inputs | |
2284 | `(("r-biobase" ,r-biobase) | |
2285 | ("r-biocgenerics" ,r-biocgenerics) | |
2286 | ("r-data-table" ,r-data-table) | |
2287 | ("r-dplyr" ,r-dplyr) | |
2288 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2289 | ("r-genomicranges" ,r-genomicranges) | |
2290 | ("r-ggplot2" ,r-ggplot2) | |
2291 | ("r-gridextra" ,r-gridextra) | |
2292 | ("r-gviz" ,r-gviz) | |
2293 | ("r-igraph" ,r-igraph) | |
2294 | ("r-interactionset" ,r-interactionset) | |
2295 | ("r-iranges" ,r-iranges) | |
2296 | ("r-rsamtools" ,r-rsamtools) | |
2297 | ("r-rtracklayer" ,r-rtracklayer) | |
2298 | ("r-s4vectors" ,r-s4vectors) | |
2299 | ("r-stringr" ,r-stringr))) | |
81a37891 RW |
2300 | (native-inputs |
2301 | `(("r-knitr" ,r-knitr))) | |
cf9a29b2 RW |
2302 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") |
2303 | (synopsis "R package for handling genomic interaction data") | |
2304 | (description | |
2305 | "This R package provides tools for handling genomic interaction data, | |
2306 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
2307 | information and producing various plots and statistics.") | |
2308 | (license license:gpl3))) | |
27c51606 RW |
2309 | |
2310 | (define-public r-ctc | |
2311 | (package | |
2312 | (name "r-ctc") | |
d27dfbf7 | 2313 | (version "1.64.0") |
27c51606 RW |
2314 | (source |
2315 | (origin | |
2316 | (method url-fetch) | |
2317 | (uri (bioconductor-uri "ctc" version)) | |
2318 | (sha256 | |
2319 | (base32 | |
d27dfbf7 | 2320 | "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp")))) |
27c51606 RW |
2321 | (build-system r-build-system) |
2322 | (propagated-inputs `(("r-amap" ,r-amap))) | |
2323 | (home-page "https://bioconductor.org/packages/ctc/") | |
2324 | (synopsis "Cluster and tree conversion") | |
2325 | (description | |
2326 | "This package provides tools for exporting and importing classification | |
2327 | trees and clusters to other programs.") | |
2328 | (license license:gpl2))) | |
5da0e142 RW |
2329 | |
2330 | (define-public r-goseq | |
2331 | (package | |
2332 | (name "r-goseq") | |
c97bcfbd | 2333 | (version "1.42.0") |
5da0e142 RW |
2334 | (source |
2335 | (origin | |
2336 | (method url-fetch) | |
2337 | (uri (bioconductor-uri "goseq" version)) | |
2338 | (sha256 | |
2339 | (base32 | |
c97bcfbd | 2340 | "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509")))) |
5da0e142 RW |
2341 | (build-system r-build-system) |
2342 | (propagated-inputs | |
2343 | `(("r-annotationdbi" ,r-annotationdbi) | |
2344 | ("r-biasedurn" ,r-biasedurn) | |
2345 | ("r-biocgenerics" ,r-biocgenerics) | |
2346 | ("r-genelendatabase" ,r-genelendatabase) | |
2347 | ("r-go-db" ,r-go-db) | |
2348 | ("r-mgcv" ,r-mgcv))) | |
2349 | (home-page "https://bioconductor.org/packages/goseq/") | |
2350 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
2351 | (description | |
2352 | "This package provides tools to detect Gene Ontology and/or other user | |
2353 | defined categories which are over/under represented in RNA-seq data.") | |
2354 | (license license:lgpl2.0+))) | |
f4235c0e RW |
2355 | |
2356 | (define-public r-glimma | |
2357 | (package | |
2358 | (name "r-glimma") | |
3dab4570 | 2359 | (version "2.0.0") |
f4235c0e RW |
2360 | (source |
2361 | (origin | |
2362 | (method url-fetch) | |
2363 | (uri (bioconductor-uri "Glimma" version)) | |
2364 | (sha256 | |
2365 | (base32 | |
3dab4570 | 2366 | "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv")))) |
f4235c0e RW |
2367 | (properties `((upstream-name . "Glimma"))) |
2368 | (build-system r-build-system) | |
2369 | (propagated-inputs | |
3dab4570 | 2370 | `(("r-deseq2" ,r-deseq2) |
2371 | ("r-edger" ,r-edger) | |
2372 | ("r-htmlwidgets" ,r-htmlwidgets) | |
f4235c0e | 2373 | ("r-jsonlite" ,r-jsonlite) |
3dab4570 | 2374 | ("r-limma" ,r-limma) |
2375 | ("r-s4vectors" ,r-s4vectors) | |
2376 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
a6251d6e RW |
2377 | (native-inputs |
2378 | `(("r-knitr" ,r-knitr))) | |
f4235c0e RW |
2379 | (home-page "https://github.com/Shians/Glimma") |
2380 | (synopsis "Interactive HTML graphics") | |
2381 | (description | |
2382 | "This package generates interactive visualisations for analysis of | |
2383 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
2384 | HTML page. The interactions are built on top of the popular static | |
2385 | representations of analysis results in order to provide additional | |
2386 | information.") | |
2387 | (license license:lgpl3))) | |
aa388dc7 RW |
2388 | |
2389 | (define-public r-rots | |
2390 | (package | |
2391 | (name "r-rots") | |
0ef40b23 | 2392 | (version "1.18.0") |
aa388dc7 RW |
2393 | (source |
2394 | (origin | |
2395 | (method url-fetch) | |
2396 | (uri (bioconductor-uri "ROTS" version)) | |
2397 | (sha256 | |
2398 | (base32 | |
0ef40b23 | 2399 | "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n")))) |
aa388dc7 RW |
2400 | (properties `((upstream-name . "ROTS"))) |
2401 | (build-system r-build-system) | |
2402 | (propagated-inputs | |
2403 | `(("r-biobase" ,r-biobase) | |
2404 | ("r-rcpp" ,r-rcpp))) | |
2405 | (home-page "https://bioconductor.org/packages/ROTS/") | |
2406 | (synopsis "Reproducibility-Optimized Test Statistic") | |
2407 | (description | |
2408 | "This package provides tools for calculating the | |
2409 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
2410 | in omics data.") | |
2411 | (license license:gpl2+))) | |
b64ce4b7 | 2412 | |
cad6fb2d RW |
2413 | (define-public r-plgem |
2414 | (package | |
2415 | (name "r-plgem") | |
1c9bdfcf | 2416 | (version "1.62.0") |
cad6fb2d RW |
2417 | (source |
2418 | (origin | |
2419 | (method url-fetch) | |
2420 | (uri (bioconductor-uri "plgem" version)) | |
2421 | (sha256 | |
2422 | (base32 | |
1c9bdfcf | 2423 | "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a")))) |
cad6fb2d RW |
2424 | (build-system r-build-system) |
2425 | (propagated-inputs | |
2426 | `(("r-biobase" ,r-biobase) | |
2427 | ("r-mass" ,r-mass))) | |
2428 | (home-page "http://www.genopolis.it") | |
2429 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
2430 | (description | |
2431 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
2432 | model the variance-versus-mean dependence that exists in a variety of | |
2433 | genome-wide datasets, including microarray and proteomics data. The use of | |
2434 | PLGEM has been shown to improve the detection of differentially expressed | |
2435 | genes or proteins in these datasets.") | |
2436 | (license license:gpl2))) | |
2437 | ||
b64ce4b7 RW |
2438 | (define-public r-inspect |
2439 | (package | |
2440 | (name "r-inspect") | |
41d6b41f | 2441 | (version "1.20.0") |
b64ce4b7 RW |
2442 | (source |
2443 | (origin | |
2444 | (method url-fetch) | |
2445 | (uri (bioconductor-uri "INSPEcT" version)) | |
2446 | (sha256 | |
2447 | (base32 | |
41d6b41f | 2448 | "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483")))) |
b64ce4b7 RW |
2449 | (properties `((upstream-name . "INSPEcT"))) |
2450 | (build-system r-build-system) | |
2451 | (propagated-inputs | |
2452 | `(("r-biobase" ,r-biobase) | |
2453 | ("r-biocgenerics" ,r-biocgenerics) | |
2454 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 2455 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 | 2456 | ("r-desolve" ,r-desolve) |
bd824de3 | 2457 | ("r-gdata" ,r-gdata) |
74bb4cdf | 2458 | ("r-genomeinfodb" ,r-genomeinfodb) |
b64ce4b7 RW |
2459 | ("r-genomicalignments" ,r-genomicalignments) |
2460 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2461 | ("r-genomicranges" ,r-genomicranges) | |
2462 | ("r-iranges" ,r-iranges) | |
74bb4cdf | 2463 | ("r-kernsmooth" ,r-kernsmooth) |
c86fc969 | 2464 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
2465 | ("r-proc" ,r-proc) |
2466 | ("r-rootsolve" ,r-rootsolve) | |
2467 | ("r-rsamtools" ,r-rsamtools) | |
437bc4dd | 2468 | ("r-rtracklayer" ,r-rtracklayer) |
c86fc969 RW |
2469 | ("r-s4vectors" ,r-s4vectors) |
2470 | ("r-shiny" ,r-shiny) | |
2471 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
2472 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
2473 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
437bc4dd RW |
2474 | (native-inputs |
2475 | `(("r-knitr" ,r-knitr))) | |
b64ce4b7 RW |
2476 | (home-page "https://bioconductor.org/packages/INSPEcT") |
2477 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
2478 | (description | |
2479 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
2480 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
2481 | order to evaluate synthesis, processing and degradation rates and assess via | |
2482 | modeling the rates that determines changes in mature mRNA levels.") | |
2483 | (license license:gpl2))) | |
f6e99763 RW |
2484 | |
2485 | (define-public r-dnabarcodes | |
2486 | (package | |
2487 | (name "r-dnabarcodes") | |
874a774f | 2488 | (version "1.20.0") |
f6e99763 RW |
2489 | (source |
2490 | (origin | |
2491 | (method url-fetch) | |
2492 | (uri (bioconductor-uri "DNABarcodes" version)) | |
2493 | (sha256 | |
2494 | (base32 | |
874a774f | 2495 | "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg")))) |
f6e99763 RW |
2496 | (properties `((upstream-name . "DNABarcodes"))) |
2497 | (build-system r-build-system) | |
2498 | (propagated-inputs | |
2499 | `(("r-bh" ,r-bh) | |
2500 | ("r-matrix" ,r-matrix) | |
2501 | ("r-rcpp" ,r-rcpp))) | |
14f40ae8 RW |
2502 | (native-inputs |
2503 | `(("r-knitr" ,r-knitr))) | |
f6e99763 RW |
2504 | (home-page "https://bioconductor.org/packages/DNABarcodes") |
2505 | (synopsis "Create and analyze DNA barcodes") | |
2506 | (description | |
2507 | "This package offers tools to create DNA barcode sets capable of | |
2508 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
2509 | can be analyzed regarding their minimal, maximal and average distances between | |
2510 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
2511 | demultiplexed, i.e. assigned to their original reference barcode.") | |
2512 | (license license:gpl2))) | |
09aa3d06 RW |
2513 | |
2514 | (define-public r-ruvseq | |
2515 | (package | |
2516 | (name "r-ruvseq") | |
a55b1622 | 2517 | (version "1.24.0") |
09aa3d06 RW |
2518 | (source |
2519 | (origin | |
2520 | (method url-fetch) | |
2521 | (uri (bioconductor-uri "RUVSeq" version)) | |
2522 | (sha256 | |
2523 | (base32 | |
a55b1622 | 2524 | "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh")))) |
09aa3d06 RW |
2525 | (properties `((upstream-name . "RUVSeq"))) |
2526 | (build-system r-build-system) | |
2527 | (propagated-inputs | |
2528 | `(("r-biobase" ,r-biobase) | |
2529 | ("r-edaseq" ,r-edaseq) | |
2530 | ("r-edger" ,r-edger) | |
2531 | ("r-mass" ,r-mass))) | |
ae0fcaa6 RW |
2532 | (native-inputs |
2533 | `(("r-knitr" ,r-knitr))) | |
09aa3d06 RW |
2534 | (home-page "https://github.com/drisso/RUVSeq") |
2535 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
2536 | (description | |
2537 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
2538 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
2539 | samples.") | |
2540 | (license license:artistic2.0))) | |
286157dc RW |
2541 | |
2542 | (define-public r-biocneighbors | |
2543 | (package | |
2544 | (name "r-biocneighbors") | |
bbae34aa | 2545 | (version "1.8.1") |
286157dc RW |
2546 | (source |
2547 | (origin | |
2548 | (method url-fetch) | |
2549 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
2550 | (sha256 | |
2551 | (base32 | |
bbae34aa | 2552 | "0hip1sgi3zkrf8g9bw12alaszivja3difalnybr5s7gvh8qd5sf4")))) |
286157dc RW |
2553 | (properties `((upstream-name . "BiocNeighbors"))) |
2554 | (build-system r-build-system) | |
2555 | (propagated-inputs | |
12e2aa96 RW |
2556 | `(("r-biocparallel" ,r-biocparallel) |
2557 | ("r-matrix" ,r-matrix) | |
286157dc RW |
2558 | ("r-rcpp" ,r-rcpp) |
2559 | ("r-rcppannoy" ,r-rcppannoy) | |
6fc161fc | 2560 | ("r-rcpphnsw" ,r-rcpphnsw) |
286157dc | 2561 | ("r-s4vectors" ,r-s4vectors))) |
f5864c11 RW |
2562 | (native-inputs |
2563 | `(("r-knitr" ,r-knitr))) | |
286157dc RW |
2564 | (home-page "https://bioconductor.org/packages/BiocNeighbors") |
2565 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
2566 | (description | |
2567 | "This package implements exact and approximate methods for nearest | |
2568 | neighbor detection, in a framework that allows them to be easily switched | |
2569 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
2570 | using pre-clustering with the k-means algorithm. Functions are also provided | |
2571 | to search for all neighbors within a given distance. Parallelization is | |
2572 | achieved for all methods using the BiocParallel framework.") | |
2573 | (license license:gpl3))) | |
8a587c89 | 2574 | |
99391290 RW |
2575 | (define-public r-biocsingular |
2576 | (package | |
2577 | (name "r-biocsingular") | |
798ec289 | 2578 | (version "1.6.0") |
99391290 RW |
2579 | (source |
2580 | (origin | |
2581 | (method url-fetch) | |
2582 | (uri (bioconductor-uri "BiocSingular" version)) | |
2583 | (sha256 | |
2584 | (base32 | |
798ec289 | 2585 | "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni")))) |
99391290 RW |
2586 | (properties `((upstream-name . "BiocSingular"))) |
2587 | (build-system r-build-system) | |
2588 | (propagated-inputs | |
2589 | `(("r-beachmat" ,r-beachmat) | |
2590 | ("r-biocgenerics" ,r-biocgenerics) | |
2591 | ("r-biocparallel" ,r-biocparallel) | |
2592 | ("r-delayedarray" ,r-delayedarray) | |
2593 | ("r-irlba" ,r-irlba) | |
2594 | ("r-matrix" ,r-matrix) | |
2595 | ("r-rcpp" ,r-rcpp) | |
2596 | ("r-rsvd" ,r-rsvd) | |
2597 | ("r-s4vectors" ,r-s4vectors))) | |
a8351d46 RW |
2598 | (native-inputs |
2599 | `(("r-knitr" ,r-knitr))) | |
99391290 RW |
2600 | (home-page "https://github.com/LTLA/BiocSingular") |
2601 | (synopsis "Singular value decomposition for Bioconductor packages") | |
2602 | (description | |
2603 | "This package implements exact and approximate methods for singular value | |
2604 | decomposition and principal components analysis, in a framework that allows | |
2605 | them to be easily switched within Bioconductor packages or workflows. Where | |
2606 | possible, parallelization is achieved using the BiocParallel framework.") | |
2607 | (license license:gpl3))) | |
2608 | ||
a961ae46 RW |
2609 | (define-public r-destiny |
2610 | (package | |
2611 | (name "r-destiny") | |
4217307f | 2612 | (version "3.4.0") |
a961ae46 RW |
2613 | (source |
2614 | (origin | |
2615 | (method url-fetch) | |
2616 | (uri (bioconductor-uri "destiny" version)) | |
2617 | (sha256 | |
2618 | (base32 | |
4217307f | 2619 | "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) |
a961ae46 RW |
2620 | (build-system r-build-system) |
2621 | (propagated-inputs | |
2622 | `(("r-biobase" ,r-biobase) | |
2623 | ("r-biocgenerics" ,r-biocgenerics) | |
6e10ac07 | 2624 | ("r-ggplot-multistats" ,r-ggplot-multistats) |
0aa72f2d | 2625 | ("r-ggplot2" ,r-ggplot2) |
a961ae46 | 2626 | ("r-ggthemes" ,r-ggthemes) |
6e10ac07 RW |
2627 | ("r-irlba" ,r-irlba) |
2628 | ("r-knn-covertree" ,r-knn-covertree) | |
a961ae46 | 2629 | ("r-matrix" ,r-matrix) |
6e10ac07 | 2630 | ("r-pcamethods" ,r-pcamethods) |
a961ae46 RW |
2631 | ("r-proxy" ,r-proxy) |
2632 | ("r-rcpp" ,r-rcpp) | |
2633 | ("r-rcppeigen" ,r-rcppeigen) | |
6e10ac07 RW |
2634 | ("r-rcpphnsw" ,r-rcpphnsw) |
2635 | ("r-rspectra" ,r-rspectra) | |
a961ae46 RW |
2636 | ("r-scales" ,r-scales) |
2637 | ("r-scatterplot3d" ,r-scatterplot3d) | |
6e10ac07 | 2638 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
a961ae46 RW |
2639 | ("r-smoother" ,r-smoother) |
2640 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6e10ac07 RW |
2641 | ("r-tidyr" ,r-tidyr) |
2642 | ("r-tidyselect" ,r-tidyselect) | |
a961ae46 | 2643 | ("r-vim" ,r-vim))) |
3f782a6d RW |
2644 | (native-inputs |
2645 | `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes | |
a961ae46 RW |
2646 | (home-page "https://bioconductor.org/packages/destiny/") |
2647 | (synopsis "Create and plot diffusion maps") | |
2648 | (description "This package provides tools to create and plot diffusion | |
2649 | maps.") | |
2650 | ;; Any version of the GPL | |
2651 | (license license:gpl3+))) | |
2652 | ||
8a587c89 RW |
2653 | (define-public r-savr |
2654 | (package | |
2655 | (name "r-savr") | |
967fc583 | 2656 | (version "1.28.0") |
8a587c89 RW |
2657 | (source |
2658 | (origin | |
2659 | (method url-fetch) | |
2660 | (uri (bioconductor-uri "savR" version)) | |
2661 | (sha256 | |
2662 | (base32 | |
967fc583 | 2663 | "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic")))) |
8a587c89 RW |
2664 | (properties `((upstream-name . "savR"))) |
2665 | (build-system r-build-system) | |
2666 | (propagated-inputs | |
2667 | `(("r-ggplot2" ,r-ggplot2) | |
2668 | ("r-gridextra" ,r-gridextra) | |
2669 | ("r-reshape2" ,r-reshape2) | |
2670 | ("r-scales" ,r-scales) | |
2671 | ("r-xml" ,r-xml))) | |
2672 | (home-page "https://github.com/bcalder/savR") | |
2673 | (synopsis "Parse and analyze Illumina SAV files") | |
2674 | (description | |
2675 | "This package provides tools to parse Illumina Sequence Analysis | |
2676 | Viewer (SAV) files, access data, and generate QC plots.") | |
2677 | (license license:agpl3+))) | |
41ffc214 RW |
2678 | |
2679 | (define-public r-chipexoqual | |
2680 | (package | |
2681 | (name "r-chipexoqual") | |
ff4d0804 | 2682 | (version "1.14.0") |
41ffc214 RW |
2683 | (source |
2684 | (origin | |
2685 | (method url-fetch) | |
2686 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
2687 | (sha256 | |
2688 | (base32 | |
ff4d0804 | 2689 | "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag")))) |
41ffc214 RW |
2690 | (properties `((upstream-name . "ChIPexoQual"))) |
2691 | (build-system r-build-system) | |
2692 | (propagated-inputs | |
2693 | `(("r-biocparallel" ,r-biocparallel) | |
2694 | ("r-biovizbase" ,r-biovizbase) | |
2695 | ("r-broom" ,r-broom) | |
2696 | ("r-data-table" ,r-data-table) | |
2697 | ("r-dplyr" ,r-dplyr) | |
2698 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2699 | ("r-genomicalignments" ,r-genomicalignments) | |
2700 | ("r-genomicranges" ,r-genomicranges) | |
2701 | ("r-ggplot2" ,r-ggplot2) | |
2702 | ("r-hexbin" ,r-hexbin) | |
2703 | ("r-iranges" ,r-iranges) | |
2704 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2705 | ("r-rmarkdown" ,r-rmarkdown) | |
2706 | ("r-rsamtools" ,r-rsamtools) | |
2707 | ("r-s4vectors" ,r-s4vectors) | |
2708 | ("r-scales" ,r-scales) | |
2709 | ("r-viridis" ,r-viridis))) | |
9697afb1 RW |
2710 | (native-inputs |
2711 | `(("r-knitr" ,r-knitr))) | |
41ffc214 RW |
2712 | (home-page "https://github.com/keleslab/ChIPexoQual") |
2713 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
2714 | (description | |
2715 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
2716 | sequencing data.") | |
2717 | (license license:gpl2+))) | |
c18dccff | 2718 | |
3d13b448 RW |
2719 | (define-public r-copynumber |
2720 | (package | |
2721 | (name "r-copynumber") | |
43d8db04 | 2722 | (version "1.30.0") |
3d13b448 RW |
2723 | (source (origin |
2724 | (method url-fetch) | |
2725 | (uri (bioconductor-uri "copynumber" version)) | |
2726 | (sha256 | |
2727 | (base32 | |
43d8db04 | 2728 | "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm")))) |
3d13b448 RW |
2729 | (build-system r-build-system) |
2730 | (propagated-inputs | |
2731 | `(("r-s4vectors" ,r-s4vectors) | |
2732 | ("r-iranges" ,r-iranges) | |
2733 | ("r-genomicranges" ,r-genomicranges) | |
2734 | ("r-biocgenerics" ,r-biocgenerics))) | |
2735 | (home-page "https://bioconductor.org/packages/copynumber") | |
2736 | (synopsis "Segmentation of single- and multi-track copy number data") | |
2737 | (description | |
2738 | "This package segments single- and multi-track copy number data by a | |
2739 | penalized least squares regression method.") | |
2740 | (license license:artistic2.0))) | |
2741 | ||
c18dccff RW |
2742 | (define-public r-dnacopy |
2743 | (package | |
2744 | (name "r-dnacopy") | |
850f4c2a | 2745 | (version "1.64.0") |
c18dccff RW |
2746 | (source |
2747 | (origin | |
2748 | (method url-fetch) | |
2749 | (uri (bioconductor-uri "DNAcopy" version)) | |
2750 | (sha256 | |
2751 | (base32 | |
850f4c2a | 2752 | "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc")))) |
c18dccff RW |
2753 | (properties `((upstream-name . "DNAcopy"))) |
2754 | (build-system r-build-system) | |
2755 | (native-inputs `(("gfortran" ,gfortran))) | |
2756 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
2757 | (synopsis "DNA copy number data analysis") | |
2758 | (description | |
2759 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
2760 | algorithm to segment DNA copy number data and identify genomic regions with | |
2761 | abnormal copy number.") | |
2762 | (license license:gpl2+))) | |
3a0babac RW |
2763 | |
2764 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
2765 | ;; Bioconductor package. | |
2766 | (define-public r-htscluster | |
2767 | (package | |
2768 | (name "r-htscluster") | |
2769 | (version "2.0.8") | |
2770 | (source | |
2771 | (origin | |
2772 | (method url-fetch) | |
2773 | (uri (cran-uri "HTSCluster" version)) | |
2774 | (sha256 | |
2775 | (base32 | |
2776 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
2777 | (properties `((upstream-name . "HTSCluster"))) | |
2778 | (build-system r-build-system) | |
2779 | (propagated-inputs | |
2780 | `(("r-capushe" ,r-capushe) | |
2781 | ("r-edger" ,r-edger) | |
2782 | ("r-plotrix" ,r-plotrix))) | |
2783 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
2784 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
2785 | (description | |
2786 | "This package provides a Poisson mixture model is implemented to cluster | |
2787 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
2788 | estimation is performed using either the EM or CEM algorithm, and the slope | |
2789 | heuristics are used for model selection (i.e., to choose the number of | |
2790 | clusters).") | |
2791 | (license license:gpl3+))) | |
173c9960 RW |
2792 | |
2793 | (define-public r-deds | |
2794 | (package | |
2795 | (name "r-deds") | |
96030bf7 | 2796 | (version "1.60.0") |
173c9960 RW |
2797 | (source |
2798 | (origin | |
2799 | (method url-fetch) | |
2800 | (uri (bioconductor-uri "DEDS" version)) | |
2801 | (sha256 | |
2802 | (base32 | |
96030bf7 | 2803 | "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8")))) |
173c9960 RW |
2804 | (properties `((upstream-name . "DEDS"))) |
2805 | (build-system r-build-system) | |
2806 | (home-page "https://bioconductor.org/packages/DEDS/") | |
2807 | (synopsis "Differential expression via distance summary for microarray data") | |
2808 | (description | |
2809 | "This library contains functions that calculate various statistics of | |
2810 | differential expression for microarray data, including t statistics, fold | |
2811 | change, F statistics, SAM, moderated t and F statistics and B statistics. It | |
2812 | also implements a new methodology called DEDS (Differential Expression via | |
2813 | Distance Summary), which selects differentially expressed genes by integrating | |
2814 | and summarizing a set of statistics using a weighted distance approach.") | |
2815 | ;; Any version of the LGPL. | |
2816 | (license license:lgpl3+))) | |
7ed869f7 RW |
2817 | |
2818 | ;; This is a CRAN package, but since it depends on a Bioconductor package we | |
2819 | ;; put it here. | |
2820 | (define-public r-nbpseq | |
2821 | (package | |
2822 | (name "r-nbpseq") | |
2823 | (version "0.3.0") | |
2824 | (source | |
2825 | (origin | |
2826 | (method url-fetch) | |
2827 | (uri (cran-uri "NBPSeq" version)) | |
2828 | (sha256 | |
2829 | (base32 | |
2830 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) | |
2831 | (properties `((upstream-name . "NBPSeq"))) | |
2832 | (build-system r-build-system) | |
2833 | (propagated-inputs | |
2834 | `(("r-qvalue" ,r-qvalue))) | |
2835 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") | |
2836 | (synopsis "Negative binomial models for RNA-Seq data") | |
2837 | (description | |
2838 | "This package provides negative binomial models for two-group comparisons | |
2839 | and regression inferences from RNA-sequencing data.") | |
2840 | (license license:gpl2))) | |
3087a2f3 RW |
2841 | |
2842 | (define-public r-ebseq | |
2843 | (package | |
2844 | (name "r-ebseq") | |
939c888d | 2845 | (version "1.30.0") |
3087a2f3 RW |
2846 | (source |
2847 | (origin | |
2848 | (method url-fetch) | |
2849 | (uri (bioconductor-uri "EBSeq" version)) | |
2850 | (sha256 | |
2851 | (base32 | |
939c888d | 2852 | "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny")))) |
3087a2f3 RW |
2853 | (properties `((upstream-name . "EBSeq"))) |
2854 | (build-system r-build-system) | |
2855 | (propagated-inputs | |
2856 | `(("r-blockmodeling" ,r-blockmodeling) | |
2857 | ("r-gplots" ,r-gplots) | |
2858 | ("r-testthat" ,r-testthat))) | |
2859 | (home-page "https://bioconductor.org/packages/EBSeq") | |
2860 | (synopsis "Differential expression analysis of RNA-seq data") | |
2861 | (description | |
2862 | "This package provides tools for differential expression analysis at both | |
2863 | gene and isoform level using RNA-seq data") | |
2864 | (license license:artistic2.0))) | |
cb1ab035 RJ |
2865 | |
2866 | (define-public r-karyoploter | |
2867 | (package | |
2868 | (name "r-karyoploter") | |
37da4513 | 2869 | (version "1.16.0") |
cb1ab035 RJ |
2870 | (source (origin |
2871 | (method url-fetch) | |
2872 | (uri (bioconductor-uri "karyoploteR" version)) | |
2873 | (sha256 | |
2874 | (base32 | |
37da4513 | 2875 | "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2")))) |
cb1ab035 RJ |
2876 | (build-system r-build-system) |
2877 | (propagated-inputs | |
6e2dc9e3 RW |
2878 | `(("r-annotationdbi" ,r-annotationdbi) |
2879 | ("r-bamsignals" ,r-bamsignals) | |
2880 | ("r-bezier" ,r-bezier) | |
2881 | ("r-biovizbase" ,r-biovizbase) | |
2882 | ("r-digest" ,r-digest) | |
2883 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2884 | ("r-genomicfeatures" ,r-genomicfeatures) | |
cb1ab035 RJ |
2885 | ("r-genomicranges" ,r-genomicranges) |
2886 | ("r-iranges" ,r-iranges) | |
cb1ab035 | 2887 | ("r-memoise" ,r-memoise) |
6e2dc9e3 RW |
2888 | ("r-regioner" ,r-regioner) |
2889 | ("r-rsamtools" ,r-rsamtools) | |
cb1ab035 | 2890 | ("r-rtracklayer" ,r-rtracklayer) |
cb1ab035 | 2891 | ("r-s4vectors" ,r-s4vectors) |
cb1ab035 | 2892 | ("r-variantannotation" ,r-variantannotation))) |
6e2dc9e3 RW |
2893 | (native-inputs |
2894 | `(("r-knitr" ,r-knitr))) | |
cb1ab035 RJ |
2895 | (home-page "https://bioconductor.org/packages/karyoploteR/") |
2896 | (synopsis "Plot customizable linear genomes displaying arbitrary data") | |
2897 | (description "This package creates karyotype plots of arbitrary genomes and | |
7230f6d5 | 2898 | offers a complete set of functions to plot arbitrary data on them. It mimics |
cb1ab035 RJ |
2899 | many R base graphics functions coupling them with a coordinate change function |
2900 | automatically mapping the chromosome and data coordinates into the plot | |
2901 | coordinates.") | |
2902 | (license license:artistic2.0))) | |
2cb71d81 RW |
2903 | |
2904 | (define-public r-lpsymphony | |
2905 | (package | |
2906 | (name "r-lpsymphony") | |
378d67c9 | 2907 | (version "1.18.0") |
2cb71d81 RW |
2908 | (source |
2909 | (origin | |
2910 | (method url-fetch) | |
2911 | (uri (bioconductor-uri "lpsymphony" version)) | |
2912 | (sha256 | |
2913 | (base32 | |
378d67c9 | 2914 | "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9")))) |
2cb71d81 RW |
2915 | (build-system r-build-system) |
2916 | (inputs | |
0653b8b0 | 2917 | `(("zlib" ,zlib))) |
2cb71d81 | 2918 | (native-inputs |
0653b8b0 RW |
2919 | `(("pkg-config" ,pkg-config) |
2920 | ("r-knitr" ,r-knitr))) | |
c756328e | 2921 | (home-page "https://r-forge.r-project.org/projects/rsymphony") |
2cb71d81 RW |
2922 | (synopsis "Symphony integer linear programming solver in R") |
2923 | (description | |
2924 | "This package was derived from Rsymphony. The package provides an R | |
2925 | interface to SYMPHONY, a linear programming solver written in C++. The main | |
2926 | difference between this package and Rsymphony is that it includes the solver | |
2927 | source code, while Rsymphony expects to find header and library files on the | |
2928 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy | |
2929 | to install interface to SYMPHONY.") | |
2930 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. | |
2931 | ;; lpsimphony is released under the same terms. | |
2932 | (license license:epl1.0))) | |
704de8f5 RW |
2933 | |
2934 | (define-public r-ihw | |
2935 | (package | |
2936 | (name "r-ihw") | |
95b1f350 | 2937 | (version "1.18.0") |
704de8f5 RW |
2938 | (source |
2939 | (origin | |
2940 | (method url-fetch) | |
2941 | (uri (bioconductor-uri "IHW" version)) | |
2942 | (sha256 | |
2943 | (base32 | |
95b1f350 | 2944 | "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0")))) |
704de8f5 RW |
2945 | (properties `((upstream-name . "IHW"))) |
2946 | (build-system r-build-system) | |
2947 | (propagated-inputs | |
2948 | `(("r-biocgenerics" ,r-biocgenerics) | |
2949 | ("r-fdrtool" ,r-fdrtool) | |
2950 | ("r-lpsymphony" ,r-lpsymphony) | |
2951 | ("r-slam" ,r-slam))) | |
359a084a RW |
2952 | (native-inputs |
2953 | `(("r-knitr" ,r-knitr))) | |
704de8f5 RW |
2954 | (home-page "https://bioconductor.org/packages/IHW") |
2955 | (synopsis "Independent hypothesis weighting") | |
2956 | (description | |
2957 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing | |
2958 | procedure that increases power compared to the method of Benjamini and | |
2959 | Hochberg by assigning data-driven weights to each hypothesis. The input to | |
2960 | IHW is a two-column table of p-values and covariates. The covariate can be | |
2961 | any continuous-valued or categorical variable that is thought to be | |
2962 | informative on the statistical properties of each hypothesis test, while it is | |
2963 | independent of the p-value under the null hypothesis.") | |
2964 | (license license:artistic2.0))) | |
251e0830 RW |
2965 | |
2966 | (define-public r-icobra | |
2967 | (package | |
2968 | (name "r-icobra") | |
e26b5eef | 2969 | (version "1.18.0") |
251e0830 RW |
2970 | (source |
2971 | (origin | |
2972 | (method url-fetch) | |
2973 | (uri (bioconductor-uri "iCOBRA" version)) | |
2974 | (sha256 | |
2975 | (base32 | |
e26b5eef | 2976 | "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s")))) |
251e0830 RW |
2977 | (properties `((upstream-name . "iCOBRA"))) |
2978 | (build-system r-build-system) | |
2979 | (propagated-inputs | |
2980 | `(("r-dplyr" ,r-dplyr) | |
2981 | ("r-dt" ,r-dt) | |
2982 | ("r-ggplot2" ,r-ggplot2) | |
2983 | ("r-limma" ,r-limma) | |
2984 | ("r-reshape2" ,r-reshape2) | |
2985 | ("r-rocr" ,r-rocr) | |
2986 | ("r-scales" ,r-scales) | |
2987 | ("r-shiny" ,r-shiny) | |
2988 | ("r-shinybs" ,r-shinybs) | |
2989 | ("r-shinydashboard" ,r-shinydashboard) | |
2990 | ("r-upsetr" ,r-upsetr))) | |
ee1e8fee RW |
2991 | (native-inputs |
2992 | `(("r-knitr" ,r-knitr))) | |
251e0830 RW |
2993 | (home-page "https://bioconductor.org/packages/iCOBRA") |
2994 | (synopsis "Comparison and visualization of ranking and assignment methods") | |
2995 | (description | |
2996 | "This package provides functions for calculation and visualization of | |
2997 | performance metrics for evaluation of ranking and binary | |
2998 | classification (assignment) methods. It also contains a Shiny application for | |
2999 | interactive exploration of results.") | |
3000 | (license license:gpl2+))) | |
925fcdbb RW |
3001 | |
3002 | (define-public r-mast | |
3003 | (package | |
3004 | (name "r-mast") | |
532b1068 | 3005 | (version "1.16.0") |
925fcdbb RW |
3006 | (source |
3007 | (origin | |
3008 | (method url-fetch) | |
3009 | (uri (bioconductor-uri "MAST" version)) | |
3010 | (sha256 | |
3011 | (base32 | |
532b1068 | 3012 | "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn")))) |
925fcdbb RW |
3013 | (properties `((upstream-name . "MAST"))) |
3014 | (build-system r-build-system) | |
3015 | (propagated-inputs | |
3016 | `(("r-abind" ,r-abind) | |
3017 | ("r-biobase" ,r-biobase) | |
3018 | ("r-biocgenerics" ,r-biocgenerics) | |
3019 | ("r-data-table" ,r-data-table) | |
3020 | ("r-ggplot2" ,r-ggplot2) | |
3021 | ("r-plyr" ,r-plyr) | |
3022 | ("r-progress" ,r-progress) | |
3023 | ("r-reshape2" ,r-reshape2) | |
3024 | ("r-s4vectors" ,r-s4vectors) | |
3025 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
3026 | ("r-stringr" ,r-stringr) | |
3027 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
51d1a7a2 RW |
3028 | (native-inputs |
3029 | `(("r-knitr" ,r-knitr))) | |
925fcdbb RW |
3030 | (home-page "https://github.com/RGLab/MAST/") |
3031 | (synopsis "Model-based analysis of single cell transcriptomics") | |
3032 | (description | |
3033 | "This package provides methods and models for handling zero-inflated | |
3034 | single cell assay data.") | |
3035 | (license license:gpl2+))) | |
2d7627cf RW |
3036 | |
3037 | (define-public r-monocle | |
3038 | (package | |
3039 | (name "r-monocle") | |
38bc0bf8 | 3040 | (version "2.18.0") |
2d7627cf RW |
3041 | (source |
3042 | (origin | |
3043 | (method url-fetch) | |
3044 | (uri (bioconductor-uri "monocle" version)) | |
3045 | (sha256 | |
3046 | (base32 | |
38bc0bf8 | 3047 | "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx")))) |
2d7627cf RW |
3048 | (build-system r-build-system) |
3049 | (propagated-inputs | |
3050 | `(("r-biobase" ,r-biobase) | |
3051 | ("r-biocgenerics" ,r-biocgenerics) | |
3052 | ("r-biocviews" ,r-biocviews) | |
3053 | ("r-cluster" ,r-cluster) | |
3054 | ("r-combinat" ,r-combinat) | |
3055 | ("r-ddrtree" ,r-ddrtree) | |
3056 | ("r-densityclust" ,r-densityclust) | |
3057 | ("r-dplyr" ,r-dplyr) | |
3058 | ("r-fastica" ,r-fastica) | |
3059 | ("r-ggplot2" ,r-ggplot2) | |
3060 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) | |
3061 | ("r-igraph" ,r-igraph) | |
3062 | ("r-irlba" ,r-irlba) | |
3063 | ("r-limma" ,r-limma) | |
3064 | ("r-mass" ,r-mass) | |
3065 | ("r-matrix" ,r-matrix) | |
3066 | ("r-matrixstats" ,r-matrixstats) | |
3067 | ("r-pheatmap" ,r-pheatmap) | |
3068 | ("r-plyr" ,r-plyr) | |
3069 | ("r-proxy" ,r-proxy) | |
3070 | ("r-qlcmatrix" ,r-qlcmatrix) | |
3071 | ("r-rann" ,r-rann) | |
3072 | ("r-rcpp" ,r-rcpp) | |
3073 | ("r-reshape2" ,r-reshape2) | |
3074 | ("r-rtsne" ,r-rtsne) | |
3075 | ("r-slam" ,r-slam) | |
3076 | ("r-stringr" ,r-stringr) | |
3077 | ("r-tibble" ,r-tibble) | |
3078 | ("r-vgam" ,r-vgam) | |
3079 | ("r-viridis" ,r-viridis))) | |
d1f3c371 RW |
3080 | (native-inputs |
3081 | `(("r-knitr" ,r-knitr))) | |
2d7627cf RW |
3082 | (home-page "https://bioconductor.org/packages/monocle") |
3083 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") | |
3084 | (description | |
3085 | "Monocle performs differential expression and time-series analysis for | |
3086 | single-cell expression experiments. It orders individual cells according to | |
3087 | progress through a biological process, without knowing ahead of time which | |
3088 | genes define progress through that process. Monocle also performs | |
3089 | differential expression analysis, clustering, visualization, and other useful | |
3090 | tasks on single cell expression data. It is designed to work with RNA-Seq and | |
3091 | qPCR data, but could be used with other types as well.") | |
3092 | (license license:artistic2.0))) | |
6213e441 | 3093 | |
b2dce6b5 RW |
3094 | (define-public r-monocle3 |
3095 | (package | |
3096 | (name "r-monocle3") | |
3097 | (version "0.1.2") | |
3098 | (source | |
3099 | (origin | |
3100 | (method git-fetch) | |
3101 | (uri (git-reference | |
b0e7b699 | 3102 | (url "https://github.com/cole-trapnell-lab/monocle3") |
b2dce6b5 RW |
3103 | (commit version))) |
3104 | (file-name (git-file-name name version)) | |
3105 | (sha256 | |
3106 | (base32 | |
3107 | "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) | |
3108 | (build-system r-build-system) | |
3109 | (propagated-inputs | |
3110 | `(("r-biobase" ,r-biobase) | |
3111 | ("r-biocgenerics" ,r-biocgenerics) | |
3112 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
3113 | ("r-dplyr" ,r-dplyr) | |
3114 | ("r-ggplot2" ,r-ggplot2) | |
3115 | ("r-ggrepel" ,r-ggrepel) | |
3116 | ("r-grr" ,r-grr) | |
3117 | ("r-htmlwidgets" ,r-htmlwidgets) | |
3118 | ("r-igraph" ,r-igraph) | |
3119 | ("r-irlba" ,r-irlba) | |
3120 | ("r-limma" ,r-limma) | |
3121 | ("r-lmtest" ,r-lmtest) | |
3122 | ("r-mass" ,r-mass) | |
3123 | ("r-matrix" ,r-matrix) | |
3124 | ("r-matrix-utils" ,r-matrix-utils) | |
3125 | ("r-pbapply" ,r-pbapply) | |
3126 | ("r-pbmcapply" ,r-pbmcapply) | |
3127 | ("r-pheatmap" ,r-pheatmap) | |
3128 | ("r-plotly" ,r-plotly) | |
3129 | ("r-pryr" ,r-pryr) | |
3130 | ("r-proxy" ,r-proxy) | |
3131 | ("r-pscl" ,r-pscl) | |
3132 | ("r-purrr" ,r-purrr) | |
3133 | ("r-rann" ,r-rann) | |
3134 | ("r-rcpp" ,r-rcpp) | |
3135 | ("r-rcppparallel" ,r-rcppparallel) | |
3136 | ("r-reshape2" ,r-reshape2) | |
3137 | ("r-reticulate" ,r-reticulate) | |
3138 | ("r-rhpcblasctl" ,r-rhpcblasctl) | |
3139 | ("r-rtsne" ,r-rtsne) | |
3140 | ("r-shiny" ,r-shiny) | |
3141 | ("r-slam" ,r-slam) | |
3142 | ("r-spdep" ,r-spdep) | |
3143 | ("r-speedglm" ,r-speedglm) | |
3144 | ("r-stringr" ,r-stringr) | |
3145 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
3146 | ("r-tibble" ,r-tibble) | |
3147 | ("r-tidyr" ,r-tidyr) | |
3148 | ("r-uwot" ,r-uwot) | |
3149 | ("r-viridis" ,r-viridis))) | |
3150 | (home-page "https://github.com/cole-trapnell-lab/monocle3") | |
3151 | (synopsis "Analysis toolkit for single-cell RNA-Seq data") | |
3152 | (description | |
3153 | "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") | |
3154 | (license license:expat))) | |
3155 | ||
6213e441 RW |
3156 | (define-public r-noiseq |
3157 | (package | |
3158 | (name "r-noiseq") | |
8396c45e | 3159 | (version "2.34.0") |
6213e441 RW |
3160 | (source |
3161 | (origin | |
3162 | (method url-fetch) | |
3163 | (uri (bioconductor-uri "NOISeq" version)) | |
3164 | (sha256 | |
3165 | (base32 | |
8396c45e | 3166 | "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f")))) |
6213e441 RW |
3167 | (properties `((upstream-name . "NOISeq"))) |
3168 | (build-system r-build-system) | |
3169 | (propagated-inputs | |
3170 | `(("r-biobase" ,r-biobase) | |
3171 | ("r-matrix" ,r-matrix))) | |
3172 | (home-page "https://bioconductor.org/packages/NOISeq") | |
3173 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") | |
3174 | (description | |
3175 | "This package provides tools to support the analysis of RNA-seq | |
3176 | expression data or other similar kind of data. It provides exploratory plots | |
3177 | to evaluate saturation, count distribution, expression per chromosome, type of | |
3178 | detected features, features length, etc. It also supports the analysis of | |
3179 | differential expression between two experimental conditions with no parametric | |
3180 | assumptions.") | |
3181 | (license license:artistic2.0))) | |
b409c357 RW |
3182 | |
3183 | (define-public r-scdd | |
3184 | (package | |
3185 | (name "r-scdd") | |
ce9e19bc | 3186 | (version "1.12.0") |
b409c357 RW |
3187 | (source |
3188 | (origin | |
3189 | (method url-fetch) | |
3190 | (uri (bioconductor-uri "scDD" version)) | |
3191 | (sha256 | |
3192 | (base32 | |
ce9e19bc | 3193 | "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx")))) |
b409c357 RW |
3194 | (properties `((upstream-name . "scDD"))) |
3195 | (build-system r-build-system) | |
3196 | (propagated-inputs | |
3197 | `(("r-arm" ,r-arm) | |
3198 | ("r-biocparallel" ,r-biocparallel) | |
3199 | ("r-ebseq" ,r-ebseq) | |
3200 | ("r-fields" ,r-fields) | |
3201 | ("r-ggplot2" ,r-ggplot2) | |
3202 | ("r-mclust" ,r-mclust) | |
3203 | ("r-outliers" ,r-outliers) | |
3204 | ("r-s4vectors" ,r-s4vectors) | |
3205 | ("r-scran" ,r-scran) | |
3206 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
3207 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
ce9e19bc RW |
3208 | (native-inputs |
3209 | `(("r-knitr" ,r-knitr))) | |
b409c357 RW |
3210 | (home-page "https://github.com/kdkorthauer/scDD") |
3211 | (synopsis "Mixture modeling of single-cell RNA-seq data") | |
3212 | (description | |
3213 | "This package implements a method to analyze single-cell RNA-seq data | |
3214 | utilizing flexible Dirichlet Process mixture models. Genes with differential | |
3215 | distributions of expression are classified into several interesting patterns | |
3216 | of differences between two conditions. The package also includes functions | |
3217 | for simulating data with these patterns from negative binomial | |
3218 | distributions.") | |
3219 | (license license:gpl2))) | |
f0887757 RW |
3220 | |
3221 | (define-public r-scone | |
3222 | (package | |
3223 | (name "r-scone") | |
bde9dc5b | 3224 | (version "1.14.0") |
f0887757 RW |
3225 | (source |
3226 | (origin | |
3227 | (method url-fetch) | |
3228 | (uri (bioconductor-uri "scone" version)) | |
3229 | (sha256 | |
3230 | (base32 | |
bde9dc5b | 3231 | "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73")))) |
f0887757 RW |
3232 | (build-system r-build-system) |
3233 | (propagated-inputs | |
3234 | `(("r-aroma-light" ,r-aroma-light) | |
3235 | ("r-biocparallel" ,r-biocparallel) | |
3236 | ("r-boot" ,r-boot) | |
3237 | ("r-class" ,r-class) | |
3238 | ("r-cluster" ,r-cluster) | |
3239 | ("r-compositions" ,r-compositions) | |
3240 | ("r-diptest" ,r-diptest) | |
3241 | ("r-edger" ,r-edger) | |
3242 | ("r-fpc" ,r-fpc) | |
3243 | ("r-gplots" ,r-gplots) | |
3244 | ("r-hexbin" ,r-hexbin) | |
3245 | ("r-limma" ,r-limma) | |
3246 | ("r-matrixstats" ,r-matrixstats) | |
3247 | ("r-mixtools" ,r-mixtools) | |
3248 | ("r-rarpack" ,r-rarpack) | |
3249 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3250 | ("r-rhdf5" ,r-rhdf5) | |
3251 | ("r-ruvseq" ,r-ruvseq) | |
3252 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
3fc1e039 RW |
3253 | (native-inputs |
3254 | `(("r-knitr" ,r-knitr))) | |
f0887757 RW |
3255 | (home-page "https://bioconductor.org/packages/scone") |
3256 | (synopsis "Single cell overview of normalized expression data") | |
3257 | (description | |
3258 | "SCONE is an R package for comparing and ranking the performance of | |
3259 | different normalization schemes for single-cell RNA-seq and other | |
3260 | high-throughput analyses.") | |
3261 | (license license:artistic2.0))) | |
f9201d67 RW |
3262 | |
3263 | (define-public r-geoquery | |
3264 | (package | |
3265 | (name "r-geoquery") | |
5c4edeef | 3266 | (version "2.58.0") |
f9201d67 RW |
3267 | (source |
3268 | (origin | |
3269 | (method url-fetch) | |
3270 | (uri (bioconductor-uri "GEOquery" version)) | |
3271 | (sha256 | |
3272 | (base32 | |
5c4edeef | 3273 | "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4")))) |
f9201d67 RW |
3274 | (properties `((upstream-name . "GEOquery"))) |
3275 | (build-system r-build-system) | |
3276 | (propagated-inputs | |
3277 | `(("r-biobase" ,r-biobase) | |
3278 | ("r-dplyr" ,r-dplyr) | |
3279 | ("r-httr" ,r-httr) | |
3280 | ("r-limma" ,r-limma) | |
3281 | ("r-magrittr" ,r-magrittr) | |
3282 | ("r-readr" ,r-readr) | |
3283 | ("r-tidyr" ,r-tidyr) | |
3284 | ("r-xml2" ,r-xml2))) | |
159e427c RW |
3285 | (native-inputs |
3286 | `(("r-knitr" ,r-knitr))) | |
f9201d67 RW |
3287 | (home-page "https://github.com/seandavi/GEOquery/") |
3288 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") | |
3289 | (description | |
3290 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of | |
3291 | microarray data. Given the rich and varied nature of this resource, it is | |
3292 | only natural to want to apply BioConductor tools to these data. GEOquery is | |
3293 | the bridge between GEO and BioConductor.") | |
3294 | (license license:gpl2))) | |
eed6ff03 RW |
3295 | |
3296 | (define-public r-illuminaio | |
3297 | (package | |
3298 | (name "r-illuminaio") | |
e89966e9 | 3299 | (version "0.32.0") |
eed6ff03 RW |
3300 | (source |
3301 | (origin | |
3302 | (method url-fetch) | |
3303 | (uri (bioconductor-uri "illuminaio" version)) | |
3304 | (sha256 | |
3305 | (base32 | |
e89966e9 | 3306 | "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay")))) |
eed6ff03 RW |
3307 | (build-system r-build-system) |
3308 | (propagated-inputs | |
3309 | `(("r-base64" ,r-base64))) | |
3310 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") | |
3311 | (synopsis "Parse Illumina microarray output files") | |
3312 | (description | |
3313 | "This package provides tools for parsing Illumina's microarray output | |
3314 | files, including IDAT.") | |
3315 | (license license:gpl2))) | |
f4eac096 RW |
3316 | |
3317 | (define-public r-siggenes | |
3318 | (package | |
3319 | (name "r-siggenes") | |
0fd830fe | 3320 | (version "1.64.0") |
f4eac096 RW |
3321 | (source |
3322 | (origin | |
3323 | (method url-fetch) | |
3324 | (uri (bioconductor-uri "siggenes" version)) | |
3325 | (sha256 | |
3326 | (base32 | |
0fd830fe | 3327 | "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w")))) |
f4eac096 RW |
3328 | (build-system r-build-system) |
3329 | (propagated-inputs | |
3330 | `(("r-biobase" ,r-biobase) | |
409f4dd6 RW |
3331 | ("r-multtest" ,r-multtest) |
3332 | ("r-scrime" ,r-scrime))) | |
f4eac096 RW |
3333 | (home-page "https://bioconductor.org/packages/siggenes/") |
3334 | (synopsis | |
3335 | "Multiple testing using SAM and Efron's empirical Bayes approaches") | |
3336 | (description | |
3337 | "This package provides tools for the identification of differentially | |
3338 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using | |
3339 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical | |
3340 | Bayes Analyses of Microarrays} (EBAM).") | |
3341 | (license license:lgpl2.0+))) | |
34a24f95 RW |
3342 | |
3343 | (define-public r-bumphunter | |
3344 | (package | |
3345 | (name "r-bumphunter") | |
50c5fee6 | 3346 | (version "1.32.0") |
34a24f95 RW |
3347 | (source |
3348 | (origin | |
3349 | (method url-fetch) | |
3350 | (uri (bioconductor-uri "bumphunter" version)) | |
3351 | (sha256 | |
3352 | (base32 | |
50c5fee6 | 3353 | "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk")))) |
34a24f95 RW |
3354 | (build-system r-build-system) |
3355 | (propagated-inputs | |
3356 | `(("r-annotationdbi" ,r-annotationdbi) | |
3357 | ("r-biocgenerics" ,r-biocgenerics) | |
3358 | ("r-dorng" ,r-dorng) | |
3359 | ("r-foreach" ,r-foreach) | |
3360 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3361 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3362 | ("r-genomicranges" ,r-genomicranges) | |
3363 | ("r-iranges" ,r-iranges) | |
3364 | ("r-iterators" ,r-iterators) | |
3365 | ("r-limma" ,r-limma) | |
3366 | ("r-locfit" ,r-locfit) | |
3367 | ("r-matrixstats" ,r-matrixstats) | |
3368 | ("r-s4vectors" ,r-s4vectors))) | |
3369 | (home-page "https://github.com/ririzarr/bumphunter") | |
3370 | (synopsis "Find bumps in genomic data") | |
3371 | (description | |
3372 | "This package provides tools for finding bumps in genomic data in order | |
3373 | to identify differentially methylated regions in epigenetic epidemiology | |
3374 | studies.") | |
3375 | (license license:artistic2.0))) | |
0fbaf195 RW |
3376 | |
3377 | (define-public r-minfi | |
3378 | (package | |
3379 | (name "r-minfi") | |
83e6ffda | 3380 | (version "1.34.0") |
0fbaf195 RW |
3381 | (source |
3382 | (origin | |
3383 | (method url-fetch) | |
3384 | (uri (bioconductor-uri "minfi" version)) | |
3385 | (sha256 | |
3386 | (base32 | |
83e6ffda | 3387 | "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w")))) |
0fbaf195 RW |
3388 | (build-system r-build-system) |
3389 | (propagated-inputs | |
3390 | `(("r-beanplot" ,r-beanplot) | |
3391 | ("r-biobase" ,r-biobase) | |
3392 | ("r-biocgenerics" ,r-biocgenerics) | |
3393 | ("r-biocparallel" ,r-biocparallel) | |
3394 | ("r-biostrings" ,r-biostrings) | |
3395 | ("r-bumphunter" ,r-bumphunter) | |
3396 | ("r-data-table" ,r-data-table) | |
3397 | ("r-delayedarray" ,r-delayedarray) | |
3398 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
3399 | ("r-genefilter" ,r-genefilter) | |
3400 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3401 | ("r-genomicranges" ,r-genomicranges) | |
3402 | ("r-geoquery" ,r-geoquery) | |
3403 | ("r-hdf5array" ,r-hdf5array) | |
3404 | ("r-illuminaio" ,r-illuminaio) | |
3405 | ("r-iranges" ,r-iranges) | |
3406 | ("r-lattice" ,r-lattice) | |
3407 | ("r-limma" ,r-limma) | |
3408 | ("r-mass" ,r-mass) | |
3409 | ("r-mclust" ,r-mclust) | |
3410 | ("r-nlme" ,r-nlme) | |
3411 | ("r-nor1mix" ,r-nor1mix) | |
3412 | ("r-preprocesscore" ,r-preprocesscore) | |
3413 | ("r-quadprog" ,r-quadprog) | |
3414 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3415 | ("r-reshape" ,r-reshape) | |
3416 | ("r-s4vectors" ,r-s4vectors) | |
3417 | ("r-siggenes" ,r-siggenes) | |
3418 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
83e6ffda RW |
3419 | (native-inputs |
3420 | `(("r-knitr" ,r-knitr))) | |
0fbaf195 RW |
3421 | (home-page "https://github.com/hansenlab/minfi") |
3422 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") | |
3423 | (description | |
3424 | "This package provides tools to analyze and visualize Illumina Infinium | |
3425 | methylation arrays.") | |
3426 | (license license:artistic2.0))) | |
5ec5ba02 RW |
3427 | |
3428 | (define-public r-methylumi | |
3429 | (package | |
3430 | (name "r-methylumi") | |
5f25d5f8 | 3431 | (version "2.34.0") |
5ec5ba02 RW |
3432 | (source |
3433 | (origin | |
3434 | (method url-fetch) | |
3435 | (uri (bioconductor-uri "methylumi" version)) | |
3436 | (sha256 | |
3437 | (base32 | |
5f25d5f8 | 3438 | "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr")))) |
5ec5ba02 RW |
3439 | (build-system r-build-system) |
3440 | (propagated-inputs | |
3441 | `(("r-annotate" ,r-annotate) | |
3442 | ("r-annotationdbi" ,r-annotationdbi) | |
3443 | ("r-biobase" ,r-biobase) | |
3444 | ("r-biocgenerics" ,r-biocgenerics) | |
3445 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) | |
3446 | ("r-genefilter" ,r-genefilter) | |
3447 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3448 | ("r-genomicranges" ,r-genomicranges) | |
3449 | ("r-ggplot2" ,r-ggplot2) | |
3450 | ("r-illuminaio" ,r-illuminaio) | |
3451 | ("r-iranges" ,r-iranges) | |
3452 | ("r-lattice" ,r-lattice) | |
3453 | ("r-matrixstats" ,r-matrixstats) | |
3454 | ("r-minfi" ,r-minfi) | |
3455 | ("r-reshape2" ,r-reshape2) | |
3456 | ("r-s4vectors" ,r-s4vectors) | |
3457 | ("r-scales" ,r-scales) | |
3458 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5f25d5f8 RW |
3459 | (native-inputs |
3460 | `(("r-knitr" ,r-knitr))) | |
5ec5ba02 RW |
3461 | (home-page "https://bioconductor.org/packages/methylumi") |
3462 | (synopsis "Handle Illumina methylation data") | |
3463 | (description | |
3464 | "This package provides classes for holding and manipulating Illumina | |
3465 | methylation data. Based on eSet, it can contain MIAME information, sample | |
3466 | information, feature information, and multiple matrices of data. An | |
3467 | \"intelligent\" import function, methylumiR can read the Illumina text files | |
3468 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from | |
3469 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, | |
3470 | background correction, and quality control features for GoldenGate, Infinium, | |
3471 | and Infinium HD arrays are also included.") | |
3472 | (license license:gpl2))) | |
09605cb2 RW |
3473 | |
3474 | (define-public r-lumi | |
3475 | (package | |
3476 | (name "r-lumi") | |
ae1c51a1 | 3477 | (version "2.40.0") |
09605cb2 RW |
3478 | (source |
3479 | (origin | |
3480 | (method url-fetch) | |
3481 | (uri (bioconductor-uri "lumi" version)) | |
3482 | (sha256 | |
3483 | (base32 | |
ae1c51a1 | 3484 | "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9")))) |
09605cb2 RW |
3485 | (build-system r-build-system) |
3486 | (propagated-inputs | |
3487 | `(("r-affy" ,r-affy) | |
3488 | ("r-annotate" ,r-annotate) | |
3489 | ("r-annotationdbi" ,r-annotationdbi) | |
3490 | ("r-biobase" ,r-biobase) | |
3491 | ("r-dbi" ,r-dbi) | |
3492 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3493 | ("r-genomicranges" ,r-genomicranges) | |
3494 | ("r-kernsmooth" ,r-kernsmooth) | |
3495 | ("r-lattice" ,r-lattice) | |
3496 | ("r-mass" ,r-mass) | |
3497 | ("r-methylumi" ,r-methylumi) | |
3498 | ("r-mgcv" ,r-mgcv) | |
3499 | ("r-nleqslv" ,r-nleqslv) | |
3500 | ("r-preprocesscore" ,r-preprocesscore) | |
3501 | ("r-rsqlite" ,r-rsqlite))) | |
3502 | (home-page "https://bioconductor.org/packages/lumi") | |
3503 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") | |
3504 | (description | |
3505 | "The lumi package provides an integrated solution for the Illumina | |
3506 | microarray data analysis. It includes functions of Illumina | |
3507 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific | |
3508 | variance stabilization, normalization and gene annotation at the probe level. | |
3509 | It also includes the functions of processing Illumina methylation microarrays, | |
3510 | especially Illumina Infinium methylation microarrays.") | |
3511 | (license license:lgpl2.0+))) | |
4291f36a RW |
3512 | |
3513 | (define-public r-linnorm | |
3514 | (package | |
3515 | (name "r-linnorm") | |
37e09611 | 3516 | (version "2.14.0") |
4291f36a RW |
3517 | (source |
3518 | (origin | |
3519 | (method url-fetch) | |
3520 | (uri (bioconductor-uri "Linnorm" version)) | |
3521 | (sha256 | |
3522 | (base32 | |
37e09611 | 3523 | "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3")))) |
4291f36a RW |
3524 | (properties `((upstream-name . "Linnorm"))) |
3525 | (build-system r-build-system) | |
3526 | (propagated-inputs | |
3527 | `(("r-amap" ,r-amap) | |
3528 | ("r-apcluster" ,r-apcluster) | |
3529 | ("r-ellipse" ,r-ellipse) | |
3530 | ("r-fastcluster" ,r-fastcluster) | |
3531 | ("r-fpc" ,r-fpc) | |
3532 | ("r-ggdendro" ,r-ggdendro) | |
3533 | ("r-ggplot2" ,r-ggplot2) | |
3534 | ("r-gmodels" ,r-gmodels) | |
3535 | ("r-igraph" ,r-igraph) | |
3536 | ("r-limma" ,r-limma) | |
3537 | ("r-mass" ,r-mass) | |
3538 | ("r-mclust" ,r-mclust) | |
3539 | ("r-rcpp" ,r-rcpp) | |
3540 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
3541 | ("r-rtsne" ,r-rtsne) | |
3542 | ("r-statmod" ,r-statmod) | |
3543 | ("r-vegan" ,r-vegan) | |
3544 | ("r-zoo" ,r-zoo))) | |
1465873c RW |
3545 | (native-inputs |
3546 | `(("r-knitr" ,r-knitr))) | |
4291f36a RW |
3547 | (home-page "http://www.jjwanglab.org/Linnorm/") |
3548 | (synopsis "Linear model and normality based transformation method") | |
3549 | (description | |
3550 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq | |
3551 | count data or any large scale count data. It transforms such datasets for | |
3552 | parametric tests. In addition to the transformtion function (@code{Linnorm}), | |
3553 | the following pipelines are implemented: | |
3554 | ||
3555 | @enumerate | |
3556 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) | |
3557 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means | |
3558 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, | |
3559 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) | |
3560 | @item Differential expression analysis or differential peak detection using | |
3561 | limma (@code{Linnorm.limma}) | |
3562 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) | |
3563 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) | |
3564 | @item Stable gene selection for scRNA-seq data; for users without or who do | |
3565 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) | |
3566 | @item Data imputation (@code{Linnorm.DataImput}). | |
3567 | @end enumerate | |
3568 | ||
3569 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the | |
3570 | @code{RnaXSim} function is included for simulating RNA-seq data for the | |
3571 | evaluation of DEG analysis methods.") | |
3572 | (license license:expat))) | |
e4a17532 RW |
3573 | |
3574 | (define-public r-ioniser | |
3575 | (package | |
3576 | (name "r-ioniser") | |
2a1a6d74 | 3577 | (version "2.14.0") |
e4a17532 RW |
3578 | (source |
3579 | (origin | |
3580 | (method url-fetch) | |
3581 | (uri (bioconductor-uri "IONiseR" version)) | |
3582 | (sha256 | |
3583 | (base32 | |
2a1a6d74 | 3584 | "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx")))) |
e4a17532 RW |
3585 | (properties `((upstream-name . "IONiseR"))) |
3586 | (build-system r-build-system) | |
3587 | (propagated-inputs | |
3588 | `(("r-biocgenerics" ,r-biocgenerics) | |
3589 | ("r-biocparallel" ,r-biocparallel) | |
3590 | ("r-biostrings" ,r-biostrings) | |
3591 | ("r-bit64" ,r-bit64) | |
3592 | ("r-dplyr" ,r-dplyr) | |
3593 | ("r-ggplot2" ,r-ggplot2) | |
3594 | ("r-magrittr" ,r-magrittr) | |
3595 | ("r-rhdf5" ,r-rhdf5) | |
3596 | ("r-shortread" ,r-shortread) | |
3597 | ("r-stringr" ,r-stringr) | |
3598 | ("r-tibble" ,r-tibble) | |
3599 | ("r-tidyr" ,r-tidyr) | |
3600 | ("r-xvector" ,r-xvector))) | |
293fb8a1 RW |
3601 | (native-inputs |
3602 | `(("r-knitr" ,r-knitr))) | |
e4a17532 RW |
3603 | (home-page "https://bioconductor.org/packages/IONiseR/") |
3604 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") | |
3605 | (description | |
3606 | "IONiseR provides tools for the quality assessment of Oxford Nanopore | |
3607 | MinION data. It extracts summary statistics from a set of fast5 files and can | |
3608 | be used either before or after base calling. In addition to standard | |
3609 | summaries of the read-types produced, it provides a number of plots for | |
3610 | visualising metrics relative to experiment run time or spatially over the | |
3611 | surface of a flowcell.") | |
3612 | (license license:expat))) | |
80eb01c7 RW |
3613 | |
3614 | ;; This is a CRAN package, but it depends on packages from Bioconductor. | |
3615 | (define-public r-gkmsvm | |
3616 | (package | |
3617 | (name "r-gkmsvm") | |
e1636671 | 3618 | (version "0.81.0") |
80eb01c7 RW |
3619 | (source |
3620 | (origin | |
3621 | (method url-fetch) | |
3622 | (uri (cran-uri "gkmSVM" version)) | |
3623 | (sha256 | |
3624 | (base32 | |
e1636671 | 3625 | "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) |
80eb01c7 RW |
3626 | (properties `((upstream-name . "gkmSVM"))) |
3627 | (build-system r-build-system) | |
3628 | (propagated-inputs | |
975cfe26 | 3629 | `(("r-kernlab" ,r-kernlab) |
80eb01c7 RW |
3630 | ("r-rcpp" ,r-rcpp) |
3631 | ("r-rocr" ,r-rocr) | |
80eb01c7 RW |
3632 | ("r-seqinr" ,r-seqinr))) |
3633 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") | |
3634 | (synopsis "Gapped-kmer support vector machine") | |
3635 | (description | |
3636 | "This R package provides tools for training gapped-kmer SVM classifiers | |
3637 | for DNA and protein sequences. This package supports several sequence | |
3638 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
3639 | (license license:gpl2+))) | |
8a5460b4 | 3640 | |
f2114762 RW |
3641 | ;; This is a CRAN package, but it depends on multtest from Bioconductor. |
3642 | (define-public r-mutoss | |
3643 | (package | |
3644 | (name "r-mutoss") | |
3645 | (version "0.1-12") | |
3646 | (source | |
3647 | (origin | |
3648 | (method url-fetch) | |
3649 | (uri (cran-uri "mutoss" version)) | |
3650 | (sha256 | |
3651 | (base32 | |
3652 | "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298")))) | |
3653 | (properties `((upstream-name . "mutoss"))) | |
3654 | (build-system r-build-system) | |
3655 | (propagated-inputs | |
3656 | `(("r-multcomp" ,r-multcomp) | |
3657 | ("r-multtest" ,r-multtest) | |
3658 | ("r-mvtnorm" ,r-mvtnorm) | |
3659 | ("r-plotrix" ,r-plotrix))) | |
3660 | (home-page "https://github.com/kornl/mutoss/") | |
3661 | (synopsis "Unified multiple testing procedures") | |
3662 | (description | |
3663 | "This package is designed to ease the application and comparison of | |
3664 | multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods | |
3665 | are standardized and usable by the accompanying mutossGUI package.") | |
3666 | ;; Any version of the GPL. | |
3667 | (license (list license:gpl2+ license:gpl3+)))) | |
3668 | ||
bf770d92 RW |
3669 | ;; This is a CRAN package, but it depends on mutoss, which depends on multtest |
3670 | ;; from Bioconductor, so we put it here. | |
3671 | (define-public r-metap | |
3672 | (package | |
3673 | (name "r-metap") | |
fd6412cd | 3674 | (version "1.3") |
bf770d92 RW |
3675 | (source |
3676 | (origin | |
3677 | (method url-fetch) | |
3678 | (uri (cran-uri "metap" version)) | |
3679 | (sha256 | |
3680 | (base32 | |
fd6412cd | 3681 | "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) |
bf770d92 RW |
3682 | (build-system r-build-system) |
3683 | (propagated-inputs | |
3684 | `(("r-lattice" ,r-lattice) | |
3685 | ("r-mutoss" ,r-mutoss) | |
3686 | ("r-rdpack" ,r-rdpack) | |
3687 | ("r-tfisher" ,r-tfisher))) | |
3688 | (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") | |
3689 | (synopsis "Meta-analysis of significance values") | |
3690 | (description | |
3691 | "The canonical way to perform meta-analysis involves using effect sizes. | |
3692 | When they are not available this package provides a number of methods for | |
3693 | meta-analysis of significance values including the methods of Edgington, | |
3694 | Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate | |
3695 | published results; and a routine for graphical display.") | |
3696 | (license license:gpl2))) | |
3697 | ||
8a5460b4 RW |
3698 | (define-public r-triform |
3699 | (package | |
3700 | (name "r-triform") | |
ecb4e165 | 3701 | (version "1.29.0") |
8a5460b4 RW |
3702 | (source |
3703 | (origin | |
3704 | (method url-fetch) | |
3705 | (uri (bioconductor-uri "triform" version)) | |
3706 | (sha256 | |
3707 | (base32 | |
ecb4e165 | 3708 | "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) |
8a5460b4 RW |
3709 | (build-system r-build-system) |
3710 | (propagated-inputs | |
3711 | `(("r-biocgenerics" ,r-biocgenerics) | |
3712 | ("r-iranges" ,r-iranges) | |
3713 | ("r-yaml" ,r-yaml))) | |
3714 | (home-page "https://bioconductor.org/packages/triform/") | |
3715 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") | |
3716 | (description | |
3717 | "The Triform algorithm uses model-free statistics to identify peak-like | |
3718 | distributions of TF ChIP sequencing reads, taking advantage of an improved | |
3719 | peak definition in combination with known profile characteristics.") | |
3720 | (license license:gpl2))) | |
c538bcdd RW |
3721 | |
3722 | (define-public r-varianttools | |
3723 | (package | |
3724 | (name "r-varianttools") | |
67837d4a | 3725 | (version "1.32.0") |
c538bcdd RW |
3726 | (source |
3727 | (origin | |
3728 | (method url-fetch) | |
3729 | (uri (bioconductor-uri "VariantTools" version)) | |
3730 | (sha256 | |
3731 | (base32 | |
67837d4a | 3732 | "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89")))) |
c538bcdd RW |
3733 | (properties `((upstream-name . "VariantTools"))) |
3734 | (build-system r-build-system) | |
3735 | (propagated-inputs | |
3736 | `(("r-biobase" ,r-biobase) | |
3737 | ("r-biocgenerics" ,r-biocgenerics) | |
3738 | ("r-biocparallel" ,r-biocparallel) | |
3739 | ("r-biostrings" ,r-biostrings) | |
3740 | ("r-bsgenome" ,r-bsgenome) | |
3741 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3742 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3743 | ("r-genomicranges" ,r-genomicranges) | |
3744 | ("r-iranges" ,r-iranges) | |
3745 | ("r-matrix" ,r-matrix) | |
3746 | ("r-rsamtools" ,r-rsamtools) | |
3747 | ("r-rtracklayer" ,r-rtracklayer) | |
3748 | ("r-s4vectors" ,r-s4vectors) | |
3749 | ("r-variantannotation" ,r-variantannotation))) | |
3750 | (home-page "https://bioconductor.org/packages/VariantTools/") | |
3751 | (synopsis "Tools for exploratory analysis of variant calls") | |
3752 | (description | |
3753 | "Explore, diagnose, and compare variant calls using filters. The | |
3754 | VariantTools package supports a workflow for loading data, calling single | |
3755 | sample variants and tumor-specific somatic mutations or other sample-specific | |
3756 | variant types (e.g., RNA editing). Most of the functions operate on | |
3757 | alignments (BAM files) or datasets of called variants. The user is expected | |
3758 | to have already aligned the reads with a separate tool, e.g., GSNAP via | |
3759 | gmapR.") | |
3760 | (license license:artistic2.0))) | |
3e41919d RW |
3761 | |
3762 | (define-public r-heatplus | |
3763 | (package | |
3764 | (name "r-heatplus") | |
9813d24d | 3765 | (version "2.36.0") |
3e41919d RW |
3766 | (source |
3767 | (origin | |
3768 | (method url-fetch) | |
3769 | (uri (bioconductor-uri "Heatplus" version)) | |
3770 | (sha256 | |
3771 | (base32 | |
9813d24d | 3772 | "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n")))) |
3e41919d RW |
3773 | (properties `((upstream-name . "Heatplus"))) |
3774 | (build-system r-build-system) | |
3775 | (propagated-inputs | |
3776 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) | |
3777 | (home-page "https://github.com/alexploner/Heatplus") | |
3778 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") | |
3779 | (description | |
3780 | "This package provides tools to display a rectangular heatmap (intensity | |
3781 | plot) of a data matrix. By default, both samples (columns) and features (row) | |
3782 | of the matrix are sorted according to a hierarchical clustering, and the | |
3783 | corresponding dendrogram is plotted. Optionally, panels with additional | |
3784 | information about samples and features can be added to the plot.") | |
3785 | (license license:gpl2+))) | |
c04f230e RW |
3786 | |
3787 | (define-public r-gosemsim | |
3788 | (package | |
3789 | (name "r-gosemsim") | |
b2084e4d | 3790 | (version "2.16.1") |
c04f230e RW |
3791 | (source |
3792 | (origin | |
3793 | (method url-fetch) | |
3794 | (uri (bioconductor-uri "GOSemSim" version)) | |
3795 | (sha256 | |
3796 | (base32 | |
b2084e4d | 3797 | "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs")))) |
c04f230e RW |
3798 | (properties `((upstream-name . "GOSemSim"))) |
3799 | (build-system r-build-system) | |
3800 | (propagated-inputs | |
3801 | `(("r-annotationdbi" ,r-annotationdbi) | |
3802 | ("r-go-db" ,r-go-db) | |
3803 | ("r-rcpp" ,r-rcpp))) | |
d5951dc4 RW |
3804 | (native-inputs |
3805 | `(("r-knitr" ,r-knitr))) | |
c04f230e RW |
3806 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") |
3807 | (synopsis "GO-terms semantic similarity measures") | |
3808 | (description | |
3809 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide | |
3810 | quantitative ways to compute similarities between genes and gene groups, and | |
3811 | have became important basis for many bioinformatics analysis approaches. | |
3812 | GOSemSim is an R package for semantic similarity computation among GO terms, | |
3813 | sets of GO terms, gene products and gene clusters.") | |
3814 | (license license:artistic2.0))) | |
9d0f7942 RW |
3815 | |
3816 | (define-public r-anota | |
3817 | (package | |
3818 | (name "r-anota") | |
33c905b9 | 3819 | (version "1.38.0") |
9d0f7942 RW |
3820 | (source |
3821 | (origin | |
3822 | (method url-fetch) | |
3823 | (uri (bioconductor-uri "anota" version)) | |
3824 | (sha256 | |
3825 | (base32 | |
33c905b9 | 3826 | "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x")))) |
9d0f7942 RW |
3827 | (build-system r-build-system) |
3828 | (propagated-inputs | |
3829 | `(("r-multtest" ,r-multtest) | |
3830 | ("r-qvalue" ,r-qvalue))) | |
3831 | (home-page "https://bioconductor.org/packages/anota/") | |
3832 | (synopsis "Analysis of translational activity") | |
3833 | (description | |
3834 | "Genome wide studies of translational control is emerging as a tool to | |
0cea26bd | 3835 | study various biological conditions. The output from such analysis is both |
7230f6d5 | 3836 | the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively |
9d0f7942 RW |
3837 | involved in translation (the actively translating mRNA level) for each mRNA. |
3838 | The standard analysis of such data strives towards identifying differential | |
3839 | translational between two or more sample classes - i.e. differences in | |
3840 | actively translated mRNA levels that are independent of underlying differences | |
3841 | in cytosolic mRNA levels. This package allows for such analysis using partial | |
3842 | variances and the random variance model. As 10s of thousands of mRNAs are | |
4f664004 | 3843 | analyzed in parallel the library performs a number of tests to assure that |
9d0f7942 RW |
3844 | the data set is suitable for such analysis.") |
3845 | (license license:gpl3))) | |
a6d867fe RW |
3846 | |
3847 | (define-public r-sigpathway | |
3848 | (package | |
3849 | (name "r-sigpathway") | |
7dabc629 | 3850 | (version "1.58.0") |
a6d867fe RW |
3851 | (source |
3852 | (origin | |
3853 | (method url-fetch) | |
3854 | (uri (bioconductor-uri "sigPathway" version)) | |
3855 | (sha256 | |
3856 | (base32 | |
7dabc629 | 3857 | "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l")))) |
a6d867fe RW |
3858 | (properties `((upstream-name . "sigPathway"))) |
3859 | (build-system r-build-system) | |
3860 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") | |
3861 | (synopsis "Pathway analysis") | |
3862 | (description | |
3863 | "This package is used to conduct pathway analysis by calculating the NT_k | |
3864 | and NE_k statistics in a statistical framework for determining whether a | |
3865 | specified group of genes for a pathway has a coordinated association with a | |
3866 | phenotype of interest.") | |
3867 | (license license:gpl2))) | |
af26c7ae RW |
3868 | |
3869 | (define-public r-fgsea | |
3870 | (package | |
3871 | (name "r-fgsea") | |
d68a9ffa | 3872 | (version "1.16.0") |
af26c7ae RW |
3873 | (source |
3874 | (origin | |
3875 | (method url-fetch) | |
3876 | (uri (bioconductor-uri "fgsea" version)) | |
3877 | (sha256 | |
3878 | (base32 | |
d68a9ffa | 3879 | "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n")))) |
af26c7ae RW |
3880 | (build-system r-build-system) |
3881 | (propagated-inputs | |
ebffd24c RW |
3882 | `(("r-bh" ,r-bh) |
3883 | ("r-biocparallel" ,r-biocparallel) | |
af26c7ae RW |
3884 | ("r-data-table" ,r-data-table) |
3885 | ("r-fastmatch" ,r-fastmatch) | |
3886 | ("r-ggplot2" ,r-ggplot2) | |
3887 | ("r-gridextra" ,r-gridextra) | |
3888 | ("r-matrix" ,r-matrix) | |
3889 | ("r-rcpp" ,r-rcpp))) | |
1dec455c RW |
3890 | (native-inputs |
3891 | `(("r-knitr" ,r-knitr))) | |
af26c7ae RW |
3892 | (home-page "https://github.com/ctlab/fgsea/") |
3893 | (synopsis "Fast gene set enrichment analysis") | |
3894 | (description | |
3895 | "The package implements an algorithm for fast gene set enrichment | |
23c8ef71 VC |
3896 | analysis. Using the fast algorithm makes more permutations and gets |
3897 | more fine grained p-values, which allows using accurate standard approaches | |
af26c7ae RW |
3898 | to multiple hypothesis correction.") |
3899 | (license license:expat))) | |
305050b5 RW |
3900 | |
3901 | (define-public r-dose | |
3902 | (package | |
3903 | (name "r-dose") | |
aeb1d56f | 3904 | (version "3.16.0") |
305050b5 RW |
3905 | (source |
3906 | (origin | |
3907 | (method url-fetch) | |
3908 | (uri (bioconductor-uri "DOSE" version)) | |
3909 | (sha256 | |
3910 | (base32 | |
aeb1d56f | 3911 | "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4")))) |
305050b5 RW |
3912 | (properties `((upstream-name . "DOSE"))) |
3913 | (build-system r-build-system) | |
3914 | (propagated-inputs | |
3915 | `(("r-annotationdbi" ,r-annotationdbi) | |
3916 | ("r-biocparallel" ,r-biocparallel) | |
3917 | ("r-do-db" ,r-do-db) | |
3918 | ("r-fgsea" ,r-fgsea) | |
3919 | ("r-ggplot2" ,r-ggplot2) | |
3920 | ("r-gosemsim" ,r-gosemsim) | |
3921 | ("r-qvalue" ,r-qvalue) | |
3a80f1cf | 3922 | ("r-reshape2" ,r-reshape2))) |
5ef2b749 RW |
3923 | (native-inputs |
3924 | `(("r-knitr" ,r-knitr))) | |
305050b5 RW |
3925 | (home-page "https://guangchuangyu.github.io/software/DOSE/") |
3926 | (synopsis "Disease ontology semantic and enrichment analysis") | |
3927 | (description | |
3928 | "This package implements five methods proposed by Resnik, Schlicker, | |
3929 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among | |
3930 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses | |
3931 | including hypergeometric model and gene set enrichment analysis are also | |
3932 | implemented for discovering disease associations of high-throughput biological | |
3933 | data.") | |
3934 | (license license:artistic2.0))) | |
9c30cf65 RW |
3935 | |
3936 | (define-public r-enrichplot | |
3937 | (package | |
3938 | (name "r-enrichplot") | |
eb3d17eb | 3939 | (version "1.10.1") |
9c30cf65 RW |
3940 | (source |
3941 | (origin | |
3942 | (method url-fetch) | |
3943 | (uri (bioconductor-uri "enrichplot" version)) | |
3944 | (sha256 | |
3945 | (base32 | |
eb3d17eb | 3946 | "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd")))) |
9c30cf65 RW |
3947 | (build-system r-build-system) |
3948 | (propagated-inputs | |
eb3d17eb | 3949 | `(("r-cowplot" ,r-cowplot) |
9c30cf65 | 3950 | ("r-dose" ,r-dose) |
9c30cf65 | 3951 | ("r-ggplot2" ,r-ggplot2) |
9c30cf65 | 3952 | ("r-ggraph" ,r-ggraph) |
9c30cf65 | 3953 | ("r-gosemsim" ,r-gosemsim) |
9c30cf65 | 3954 | ("r-igraph" ,r-igraph) |
eb3d17eb | 3955 | ("r-magrittr" ,r-magrittr) |
43fb14ce | 3956 | ("r-plyr" ,r-plyr) |
9c30cf65 RW |
3957 | ("r-purrr" ,r-purrr) |
3958 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
43fb14ce | 3959 | ("r-reshape2" ,r-reshape2) |
eb3d17eb RJ |
3960 | ("r-scatterpie" ,r-scatterpie) |
3961 | ("r-shadowtext" ,r-shadowtext))) | |
43fb14ce RW |
3962 | (native-inputs |
3963 | `(("r-knitr" ,r-knitr))) | |
9c30cf65 RW |
3964 | (home-page "https://github.com/GuangchuangYu/enrichplot") |
3965 | (synopsis "Visualization of functional enrichment result") | |
3966 | (description | |
3967 | "The enrichplot package implements several visualization methods for | |
3968 | interpreting functional enrichment results obtained from ORA or GSEA analyses. | |
3969 | All the visualization methods are developed based on ggplot2 graphics.") | |
3970 | (license license:artistic2.0))) | |
f8295ee6 RW |
3971 | |
3972 | (define-public r-clusterprofiler | |
3973 | (package | |
3974 | (name "r-clusterprofiler") | |
3fd84a46 | 3975 | (version "3.18.0") |
f8295ee6 RW |
3976 | (source |
3977 | (origin | |
3978 | (method url-fetch) | |
3979 | (uri (bioconductor-uri "clusterProfiler" version)) | |
3980 | (sha256 | |
3981 | (base32 | |
3fd84a46 | 3982 | "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9")))) |
f8295ee6 RW |
3983 | (properties |
3984 | `((upstream-name . "clusterProfiler"))) | |
3985 | (build-system r-build-system) | |
3986 | (propagated-inputs | |
3987 | `(("r-annotationdbi" ,r-annotationdbi) | |
3988 | ("r-dose" ,r-dose) | |
63c8323a RW |
3989 | ("r-downloader" ,r-downloader) |
3990 | ("r-dplyr" ,r-dplyr) | |
f8295ee6 | 3991 | ("r-enrichplot" ,r-enrichplot) |
f8295ee6 RW |
3992 | ("r-go-db" ,r-go-db) |
3993 | ("r-gosemsim" ,r-gosemsim) | |
3994 | ("r-magrittr" ,r-magrittr) | |
3995 | ("r-plyr" ,r-plyr) | |
3996 | ("r-qvalue" ,r-qvalue) | |
69f3b278 | 3997 | ("r-rlang" ,r-rlang) |
f8295ee6 RW |
3998 | ("r-rvcheck" ,r-rvcheck) |
3999 | ("r-tidyr" ,r-tidyr))) | |
63c8323a RW |
4000 | (native-inputs |
4001 | `(("r-knitr" ,r-knitr))) | |
f8295ee6 RW |
4002 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") |
4003 | (synopsis "Analysis and visualization of functional profiles for gene clusters") | |
4004 | (description | |
4005 | "This package implements methods to analyze and visualize functional | |
4006 | profiles (GO and KEGG) of gene and gene clusters.") | |
4007 | (license license:artistic2.0))) | |
ce77562a RW |
4008 | |
4009 | (define-public r-mlinterfaces | |
4010 | (package | |
4011 | (name "r-mlinterfaces") | |
4f82931d | 4012 | (version "1.70.0") |
ce77562a RW |
4013 | (source |
4014 | (origin | |
4015 | (method url-fetch) | |
4016 | (uri (bioconductor-uri "MLInterfaces" version)) | |
4017 | (sha256 | |
4018 | (base32 | |
4f82931d | 4019 | "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r")))) |
ce77562a RW |
4020 | (properties `((upstream-name . "MLInterfaces"))) |
4021 | (build-system r-build-system) | |
4022 | (propagated-inputs | |
4023 | `(("r-annotate" ,r-annotate) | |
4024 | ("r-biobase" ,r-biobase) | |
4025 | ("r-biocgenerics" ,r-biocgenerics) | |
4026 | ("r-cluster" ,r-cluster) | |
4027 | ("r-fpc" ,r-fpc) | |
4028 | ("r-gbm" ,r-gbm) | |
4029 | ("r-gdata" ,r-gdata) | |
4030 | ("r-genefilter" ,r-genefilter) | |
4031 | ("r-ggvis" ,r-ggvis) | |
4032 | ("r-hwriter" ,r-hwriter) | |
4033 | ("r-mass" ,r-mass) | |
4034 | ("r-mlbench" ,r-mlbench) | |
4035 | ("r-pls" ,r-pls) | |
4036 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
500f7df8 | 4037 | ("r-rcpp" ,r-rcpp) |
ce77562a RW |
4038 | ("r-rpart" ,r-rpart) |
4039 | ("r-sfsmisc" ,r-sfsmisc) | |
4040 | ("r-shiny" ,r-shiny) | |
4041 | ("r-threejs" ,r-threejs))) | |
4042 | (home-page "https://bioconductor.org/packages/MLInterfaces/") | |
4043 | (synopsis "Interfaces to R machine learning procedures") | |
4044 | (description | |
4045 | "This package provides uniform interfaces to machine learning code for | |
4046 | data in R and Bioconductor containers.") | |
4047 | ;; Any version of the LGPL. | |
4048 | (license license:lgpl2.1+))) | |
a793e88c RW |
4049 | |
4050 | (define-public r-annaffy | |
4051 | (package | |
4052 | (name "r-annaffy") | |
aca4ebe4 | 4053 | (version "1.62.0") |
a793e88c RW |
4054 | (source |
4055 | (origin | |
4056 | (method url-fetch) | |
4057 | (uri (bioconductor-uri "annaffy" version)) | |
4058 | (sha256 | |
4059 | (base32 | |
aca4ebe4 | 4060 | "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i")))) |
a793e88c RW |
4061 | (build-system r-build-system) |
4062 | (arguments | |
4063 | `(#:phases | |
4064 | (modify-phases %standard-phases | |
4065 | (add-after 'unpack 'remove-reference-to-non-free-data | |
4066 | (lambda _ | |
4067 | (substitute* "DESCRIPTION" | |
4068 | ((", KEGG.db") "")) | |
4069 | #t))))) | |
4070 | (propagated-inputs | |
4071 | `(("r-annotationdbi" ,r-annotationdbi) | |
4072 | ("r-biobase" ,r-biobase) | |
4073 | ("r-dbi" ,r-dbi) | |
4074 | ("r-go-db" ,r-go-db))) | |
4075 | (home-page "https://bioconductor.org/packages/annaffy/") | |
4076 | (synopsis "Annotation tools for Affymetrix biological metadata") | |
4077 | (description | |
4078 | "This package provides functions for handling data from Bioconductor | |
4079 | Affymetrix annotation data packages. It produces compact HTML and text | |
4080 | reports including experimental data and URL links to many online databases. | |
4081 | It allows searching of biological metadata using various criteria.") | |
4082 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of | |
4083 | ;; the LGPL 2.1 is included. | |
4084 | (license license:lgpl2.1+))) | |
0ec0a5ec RW |
4085 | |
4086 | (define-public r-a4core | |
4087 | (package | |
4088 | (name "r-a4core") | |
c47a8cd9 | 4089 | (version "1.38.0") |
0ec0a5ec RW |
4090 | (source |
4091 | (origin | |
4092 | (method url-fetch) | |
4093 | (uri (bioconductor-uri "a4Core" version)) | |
4094 | (sha256 | |
4095 | (base32 | |
c47a8cd9 | 4096 | "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2")))) |
0ec0a5ec RW |
4097 | (properties `((upstream-name . "a4Core"))) |
4098 | (build-system r-build-system) | |
4099 | (propagated-inputs | |
4100 | `(("r-biobase" ,r-biobase) | |
4101 | ("r-glmnet" ,r-glmnet))) | |
c47a8cd9 | 4102 | (native-inputs |
4103 | `(("r-knitr" ,r-knitr))) | |
0ec0a5ec RW |
4104 | (home-page "https://bioconductor.org/packages/a4Core") |
4105 | (synopsis "Automated Affymetrix array analysis core package") | |
4106 | (description | |
4107 | "This is the core package for the automated analysis of Affymetrix | |
4108 | arrays.") | |
4109 | (license license:gpl3))) | |
9ae37581 RW |
4110 | |
4111 | (define-public r-a4classif | |
4112 | (package | |
4113 | (name "r-a4classif") | |
fa51705f | 4114 | (version "1.38.0") |
9ae37581 RW |
4115 | (source |
4116 | (origin | |
4117 | (method url-fetch) | |
4118 | (uri (bioconductor-uri "a4Classif" version)) | |
4119 | (sha256 | |
4120 | (base32 | |
fa51705f | 4121 | "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz")))) |
9ae37581 RW |
4122 | (properties `((upstream-name . "a4Classif"))) |
4123 | (build-system r-build-system) | |
4124 | (propagated-inputs | |
4125 | `(("r-a4core" ,r-a4core) | |
4126 | ("r-a4preproc" ,r-a4preproc) | |
fa51705f | 4127 | ("r-biobase" ,r-biobase) |
9ae37581 | 4128 | ("r-glmnet" ,r-glmnet) |
9ae37581 RW |
4129 | ("r-pamr" ,r-pamr) |
4130 | ("r-rocr" ,r-rocr) | |
4131 | ("r-varselrf" ,r-varselrf))) | |
fa51705f | 4132 | (native-inputs |
4133 | `(("r-knitr" ,r-knitr))) | |
9ae37581 RW |
4134 | (home-page "https://bioconductor.org/packages/a4Classif/") |
4135 | (synopsis "Automated Affymetrix array analysis classification package") | |
4136 | (description | |
4137 | "This is the classification package for the automated analysis of | |
4138 | Affymetrix arrays.") | |
4139 | (license license:gpl3))) | |
b8d13e2c RW |
4140 | |
4141 | (define-public r-a4preproc | |
4142 | (package | |
4143 | (name "r-a4preproc") | |
85155e2e | 4144 | (version "1.38.0") |
b8d13e2c RW |
4145 | (source |
4146 | (origin | |
4147 | (method url-fetch) | |
4148 | (uri (bioconductor-uri "a4Preproc" version)) | |
4149 | (sha256 | |
4150 | (base32 | |
85155e2e | 4151 | "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i")))) |
b8d13e2c RW |
4152 | (properties `((upstream-name . "a4Preproc"))) |
4153 | (build-system r-build-system) | |
4154 | (propagated-inputs | |
85155e2e | 4155 | `(("r-biobase" ,r-biobase) |
4156 | ("r-biocgenerics" ,r-biocgenerics))) | |
4157 | (native-inputs | |
4158 | `(("r-knitr" ,r-knitr))) | |
b8d13e2c RW |
4159 | (home-page "https://bioconductor.org/packages/a4Preproc/") |
4160 | (synopsis "Automated Affymetrix array analysis preprocessing package") | |
4161 | (description | |
4162 | "This is a package for the automated analysis of Affymetrix arrays. It | |
4163 | is used for preprocessing the arrays.") | |
4164 | (license license:gpl3))) | |
8e15f861 RW |
4165 | |
4166 | (define-public r-a4reporting | |
4167 | (package | |
4168 | (name "r-a4reporting") | |
2fb8298c | 4169 | (version "1.38.0") |
8e15f861 RW |
4170 | (source |
4171 | (origin | |
4172 | (method url-fetch) | |
4173 | (uri (bioconductor-uri "a4Reporting" version)) | |
4174 | (sha256 | |
4175 | (base32 | |
2fb8298c | 4176 | "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy")))) |
8e15f861 RW |
4177 | (properties `((upstream-name . "a4Reporting"))) |
4178 | (build-system r-build-system) | |
4179 | (propagated-inputs | |
2fb8298c | 4180 | `(("r-xtable" ,r-xtable))) |
4181 | (native-inputs | |
4182 | `(("r-knitr" ,r-knitr))) | |
8e15f861 RW |
4183 | (home-page "https://bioconductor.org/packages/a4Reporting/") |
4184 | (synopsis "Automated Affymetrix array analysis reporting package") | |
4185 | (description | |
4186 | "This is a package for the automated analysis of Affymetrix arrays. It | |
4187 | provides reporting features.") | |
4188 | (license license:gpl3))) | |
dbfe3375 RW |
4189 | |
4190 | (define-public r-a4base | |
4191 | (package | |
4192 | (name "r-a4base") | |
564d4279 | 4193 | (version "1.38.0") |
dbfe3375 RW |
4194 | (source |
4195 | (origin | |
4196 | (method url-fetch) | |
4197 | (uri (bioconductor-uri "a4Base" version)) | |
4198 | (sha256 | |
4199 | (base32 | |
564d4279 | 4200 | "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp")))) |
dbfe3375 RW |
4201 | (properties `((upstream-name . "a4Base"))) |
4202 | (build-system r-build-system) | |
4203 | (propagated-inputs | |
4204 | `(("r-a4core" ,r-a4core) | |
4205 | ("r-a4preproc" ,r-a4preproc) | |
4206 | ("r-annaffy" ,r-annaffy) | |
dbfe3375 RW |
4207 | ("r-biobase" ,r-biobase) |
4208 | ("r-genefilter" ,r-genefilter) | |
4209 | ("r-glmnet" ,r-glmnet) | |
4210 | ("r-gplots" ,r-gplots) | |
4211 | ("r-limma" ,r-limma) | |
4212 | ("r-mpm" ,r-mpm) | |
4213 | ("r-multtest" ,r-multtest))) | |
4214 | (home-page "https://bioconductor.org/packages/a4Base/") | |
4215 | (synopsis "Automated Affymetrix array analysis base package") | |
4216 | (description | |
4217 | "This package provides basic features for the automated analysis of | |
4218 | Affymetrix arrays.") | |
4219 | (license license:gpl3))) | |
84ad024e RW |
4220 | |
4221 | (define-public r-a4 | |
4222 | (package | |
4223 | (name "r-a4") | |
68efaafe | 4224 | (version "1.38.0") |
84ad024e RW |
4225 | (source |
4226 | (origin | |
4227 | (method url-fetch) | |
4228 | (uri (bioconductor-uri "a4" version)) | |
4229 | (sha256 | |
4230 | (base32 | |
68efaafe | 4231 | "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79")))) |
84ad024e RW |
4232 | (build-system r-build-system) |
4233 | (propagated-inputs | |
4234 | `(("r-a4base" ,r-a4base) | |
4235 | ("r-a4classif" ,r-a4classif) | |
4236 | ("r-a4core" ,r-a4core) | |
4237 | ("r-a4preproc" ,r-a4preproc) | |
4238 | ("r-a4reporting" ,r-a4reporting))) | |
4239 | (home-page "https://bioconductor.org/packages/a4/") | |
4240 | (synopsis "Automated Affymetrix array analysis umbrella package") | |
4241 | (description | |
4242 | "This package provides a software suite for the automated analysis of | |
4243 | Affymetrix arrays.") | |
4244 | (license license:gpl3))) | |
59d331f1 RW |
4245 | |
4246 | (define-public r-abseqr | |
4247 | (package | |
4248 | (name "r-abseqr") | |
8816139e | 4249 | (version "1.8.0") |
59d331f1 RW |
4250 | (source |
4251 | (origin | |
4252 | (method url-fetch) | |
4253 | (uri (bioconductor-uri "abseqR" version)) | |
4254 | (sha256 | |
4255 | (base32 | |
8816139e | 4256 | "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f")))) |
59d331f1 RW |
4257 | (properties `((upstream-name . "abseqR"))) |
4258 | (build-system r-build-system) | |
4259 | (inputs | |
8816139e | 4260 | `(("pandoc" ,pandoc))) |
59d331f1 RW |
4261 | (propagated-inputs |
4262 | `(("r-biocparallel" ,r-biocparallel) | |
4263 | ("r-biocstyle" ,r-biocstyle) | |
4264 | ("r-circlize" ,r-circlize) | |
4265 | ("r-flexdashboard" ,r-flexdashboard) | |
4266 | ("r-ggcorrplot" ,r-ggcorrplot) | |
4267 | ("r-ggdendro" ,r-ggdendro) | |
4268 | ("r-ggplot2" ,r-ggplot2) | |
4269 | ("r-gridextra" ,r-gridextra) | |
4270 | ("r-knitr" ,r-knitr) | |
4271 | ("r-plotly" ,r-plotly) | |
4272 | ("r-plyr" ,r-plyr) | |
4273 | ("r-png" ,r-png) | |
4274 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4275 | ("r-reshape2" ,r-reshape2) | |
4276 | ("r-rmarkdown" ,r-rmarkdown) | |
4277 | ("r-stringr" ,r-stringr) | |
4278 | ("r-vegan" ,r-vegan) | |
4279 | ("r-venndiagram" ,r-venndiagram))) | |
35bcfaef RW |
4280 | (native-inputs |
4281 | `(("r-knitr" ,r-knitr))) | |
59d331f1 RW |
4282 | (home-page "https://github.com/malhamdoosh/abseqR") |
4283 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") | |
4284 | (description | |
4285 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of | |
4286 | sequencing datasets generated from antibody libraries and abseqR is one of its | |
4287 | packages. AbseqR empowers the users of abseqPy with plotting and reporting | |
4288 | capabilities and allows them to generate interactive HTML reports for the | |
4289 | convenience of viewing and sharing with other researchers. Additionally, | |
4290 | abseqR extends abseqPy to compare multiple repertoire analyses and perform | |
4291 | further downstream analysis on its output.") | |
4292 | (license license:gpl3))) | |
41aab7d1 RW |
4293 | |
4294 | (define-public r-bacon | |
4295 | (package | |
4296 | (name "r-bacon") | |
d5dcf1bb | 4297 | (version "1.18.0") |
41aab7d1 RW |
4298 | (source |
4299 | (origin | |
4300 | (method url-fetch) | |
4301 | (uri (bioconductor-uri "bacon" version)) | |
4302 | (sha256 | |
4303 | (base32 | |
d5dcf1bb | 4304 | "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47")))) |
41aab7d1 RW |
4305 | (build-system r-build-system) |
4306 | (propagated-inputs | |
4307 | `(("r-biocparallel" ,r-biocparallel) | |
4308 | ("r-ellipse" ,r-ellipse) | |
4309 | ("r-ggplot2" ,r-ggplot2))) | |
506cbeab RW |
4310 | (native-inputs |
4311 | `(("r-knitr" ,r-knitr))) | |
41aab7d1 RW |
4312 | (home-page "https://bioconductor.org/packages/bacon/") |
4313 | (synopsis "Controlling bias and inflation in association studies") | |
4314 | (description | |
4315 | "Bacon can be used to remove inflation and bias often observed in | |
4316 | epigenome- and transcriptome-wide association studies. To this end bacon | |
4317 | constructs an empirical null distribution using a Gibbs Sampling algorithm by | |
4318 | fitting a three-component normal mixture on z-scores.") | |
4319 | (license license:gpl2+))) | |
051e8e1a RW |
4320 | |
4321 | (define-public r-rgadem | |
4322 | (package | |
4323 | (name "r-rgadem") | |
41071edc | 4324 | (version "2.38.0") |
051e8e1a RW |
4325 | (source |
4326 | (origin | |
4327 | (method url-fetch) | |
4328 | (uri (bioconductor-uri "rGADEM" version)) | |
4329 | (sha256 | |
4330 | (base32 | |
41071edc | 4331 | "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw")))) |
051e8e1a RW |
4332 | (properties `((upstream-name . "rGADEM"))) |
4333 | (build-system r-build-system) | |
4334 | (propagated-inputs | |
4335 | `(("r-biostrings" ,r-biostrings) | |
4336 | ("r-bsgenome" ,r-bsgenome) | |
07189489 | 4337 | ("r-genomicranges" ,r-genomicranges) |
051e8e1a RW |
4338 | ("r-iranges" ,r-iranges) |
4339 | ("r-seqlogo" ,r-seqlogo))) | |
4340 | (home-page "https://bioconductor.org/packages/rGADEM/") | |
4341 | (synopsis "De novo sequence motif discovery") | |
4342 | (description | |
4343 | "rGADEM is an efficient de novo motif discovery tool for large-scale | |
4344 | genomic sequence data.") | |
4345 | (license license:artistic2.0))) | |
229f97c3 RW |
4346 | |
4347 | (define-public r-motiv | |
4348 | (package | |
4349 | (name "r-motiv") | |
352cfa34 | 4350 | (version "1.43.0") |
229f97c3 RW |
4351 | (source |
4352 | (origin | |
4353 | (method url-fetch) | |
4354 | (uri (bioconductor-uri "MotIV" version)) | |
4355 | (sha256 | |
4356 | (base32 | |
352cfa34 | 4357 | "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6")))) |
229f97c3 RW |
4358 | (properties `((upstream-name . "MotIV"))) |
4359 | (build-system r-build-system) | |
4360 | (inputs | |
4361 | `(("gsl" ,gsl))) | |
4362 | (propagated-inputs | |
4363 | `(("r-biocgenerics" ,r-biocgenerics) | |
4364 | ("r-biostrings" ,r-biostrings) | |
35a1b3ec | 4365 | ("r-genomicranges" ,r-genomicranges) |
229f97c3 RW |
4366 | ("r-iranges" ,r-iranges) |
4367 | ("r-lattice" ,r-lattice) | |
4368 | ("r-rgadem" ,r-rgadem) | |
4369 | ("r-s4vectors" ,r-s4vectors))) | |
4370 | (home-page "https://bioconductor.org/packages/MotIV/") | |
4371 | (synopsis "Motif identification and validation") | |
4372 | (description | |
4373 | "This package is used for the identification and validation of sequence | |
4374 | motifs. It makes use of STAMP for comparing a set of motifs to a given | |
4375 | database (e.g. JASPAR). It can also be used to visualize motifs, motif | |
4376 | distributions, modules and filter motifs.") | |
4377 | (license license:gpl2))) | |
2a72ef56 | 4378 | |
3699bcf5 RJ |
4379 | (define-public r-motifdb |
4380 | (package | |
4381 | (name "r-motifdb") | |
a2bae167 | 4382 | (version "1.32.0") |
3699bcf5 RJ |
4383 | (source (origin |
4384 | (method url-fetch) | |
4385 | (uri (bioconductor-uri "MotifDb" version)) | |
4386 | (sha256 | |
a2bae167 | 4387 | (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5")))) |
3699bcf5 RJ |
4388 | (properties `((upstream-name . "MotifDb"))) |
4389 | (build-system r-build-system) | |
4390 | (propagated-inputs | |
4391 | `(("r-biocgenerics" ,r-biocgenerics) | |
4392 | ("r-biostrings" ,r-biostrings) | |
da6a75fe | 4393 | ("r-genomicranges" ,r-genomicranges) |
3699bcf5 RJ |
4394 | ("r-iranges" ,r-iranges) |
4395 | ("r-rtracklayer" ,r-rtracklayer) | |
4396 | ("r-s4vectors" ,r-s4vectors) | |
4397 | ("r-splitstackshape" ,r-splitstackshape))) | |
da6a75fe RW |
4398 | (native-inputs |
4399 | `(("r-knitr" ,r-knitr))) | |
3699bcf5 RJ |
4400 | (home-page "https://www.bioconductor.org/packages/MotifDb/") |
4401 | (synopsis "Annotated collection of protein-DNA binding sequence motifs") | |
4402 | (description "This package provides more than 2000 annotated position | |
4403 | frequency matrices from nine public sources, for multiple organisms.") | |
4404 | (license license:artistic2.0))) | |
4405 | ||
886125d7 RJ |
4406 | (define-public r-motifbreakr |
4407 | (package | |
4408 | (name "r-motifbreakr") | |
301e549c | 4409 | (version "2.4.0") |
886125d7 RJ |
4410 | (source (origin |
4411 | (method url-fetch) | |
4412 | (uri (bioconductor-uri "motifbreakR" version)) | |
4413 | (sha256 | |
301e549c | 4414 | (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7")))) |
886125d7 RJ |
4415 | (properties `((upstream-name . "motifbreakR"))) |
4416 | (build-system r-build-system) | |
4417 | (propagated-inputs | |
e65783e0 RW |
4418 | `(("r-biocgenerics" ,r-biocgenerics) |
4419 | ("r-biocparallel" ,r-biocparallel) | |
886125d7 RJ |
4420 | ("r-biostrings" ,r-biostrings) |
4421 | ("r-bsgenome" ,r-bsgenome) | |
e65783e0 RW |
4422 | ("r-genomeinfodb" ,r-genomeinfodb) |
4423 | ("r-genomicranges" ,r-genomicranges) | |
4424 | ("r-grimport" ,r-grimport) | |
886125d7 | 4425 | ("r-gviz" ,r-gviz) |
e65783e0 | 4426 | ("r-iranges" ,r-iranges) |
886125d7 | 4427 | ("r-matrixstats" ,r-matrixstats) |
e65783e0 RW |
4428 | ("r-motifdb" ,r-motifdb) |
4429 | ("r-motifstack" ,r-motifstack) | |
4430 | ("r-rtracklayer" ,r-rtracklayer) | |
4431 | ("r-s4vectors" ,r-s4vectors) | |
4432 | ("r-stringr" ,r-stringr) | |
4433 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
886125d7 | 4434 | ("r-tfmpvalue" ,r-tfmpvalue) |
e65783e0 RW |
4435 | ("r-variantannotation" ,r-variantannotation))) |
4436 | (native-inputs | |
4437 | `(("r-knitr" ,r-knitr))) | |
886125d7 RJ |
4438 | (home-page "https://www.bioconductor.org/packages/motifbreakR/") |
4439 | (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") | |
4440 | (description "This package allows biologists to judge in the first place | |
4441 | whether the sequence surrounding the polymorphism is a good match, and in | |
4442 | the second place how much information is gained or lost in one allele of | |
4443 | the polymorphism relative to another. This package gives a choice of | |
4444 | algorithms for interrogation of genomes with motifs from public sources: | |
4445 | @enumerate | |
4446 | @item a weighted-sum probability matrix; | |
4447 | @item log-probabilities; | |
4448 | @item weighted by relative entropy. | |
4449 | @end enumerate | |
4450 | ||
4451 | This package can predict effects for novel or previously described variants in | |
4452 | public databases, making it suitable for tasks beyond the scope of its original | |
4453 | design. Lastly, it can be used to interrogate any genome curated within | |
4454 | Bioconductor.") | |
4455 | (license license:gpl2+))) | |
4456 | ||
2a72ef56 RW |
4457 | (define-public r-motifstack |
4458 | (package | |
4459 | (name "r-motifstack") | |
4b4cd2b8 | 4460 | (version "1.34.0") |
2a72ef56 RW |
4461 | (source |
4462 | (origin | |
4463 | (method url-fetch) | |
4464 | (uri (bioconductor-uri "motifStack" version)) | |
4465 | (sha256 | |
4466 | (base32 | |
4b4cd2b8 | 4467 | "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb")))) |
2a72ef56 RW |
4468 | (properties `((upstream-name . "motifStack"))) |
4469 | (build-system r-build-system) | |
4470 | (propagated-inputs | |
4471 | `(("r-ade4" ,r-ade4) | |
4472 | ("r-biostrings" ,r-biostrings) | |
dda936ca | 4473 | ("r-ggplot2" ,r-ggplot2) |
2a72ef56 | 4474 | ("r-htmlwidgets" ,r-htmlwidgets) |
2a72ef56 | 4475 | ("r-xml" ,r-xml))) |
e6fbaf0c RW |
4476 | (native-inputs |
4477 | `(("r-knitr" ,r-knitr))) | |
2a72ef56 RW |
4478 | (home-page "https://bioconductor.org/packages/motifStack/") |
4479 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") | |
4480 | (description | |
4481 | "The motifStack package is designed for graphic representation of | |
4482 | multiple motifs with different similarity scores. It works with both DNA/RNA | |
4483 | sequence motifs and amino acid sequence motifs. In addition, it provides the | |
4484 | flexibility for users to customize the graphic parameters such as the font | |
4485 | type and symbol colors.") | |
4486 | (license license:gpl2+))) | |
e5bff307 RW |
4487 | |
4488 | (define-public r-genomicscores | |
4489 | (package | |
4490 | (name "r-genomicscores") | |
39280618 | 4491 | (version "2.2.0") |
e5bff307 RW |
4492 | (source |
4493 | (origin | |
4494 | (method url-fetch) | |
4495 | (uri (bioconductor-uri "GenomicScores" version)) | |
4496 | (sha256 | |
4497 | (base32 | |
39280618 | 4498 | "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr")))) |
e5bff307 RW |
4499 | (properties `((upstream-name . "GenomicScores"))) |
4500 | (build-system r-build-system) | |
4501 | (propagated-inputs | |
4502 | `(("r-annotationhub" ,r-annotationhub) | |
4503 | ("r-biobase" ,r-biobase) | |
39280618 | 4504 | ("r-biocfilecache" ,r-biocfilecache) |
e5bff307 | 4505 | ("r-biocgenerics" ,r-biocgenerics) |
39280618 | 4506 | ("r-biocmanager" ,r-biocmanager) |
e5bff307 | 4507 | ("r-biostrings" ,r-biostrings) |
785c7596 | 4508 | ("r-delayedarray" ,r-delayedarray) |
e5bff307 RW |
4509 | ("r-genomeinfodb" ,r-genomeinfodb) |
4510 | ("r-genomicranges" ,r-genomicranges) | |
785c7596 | 4511 | ("r-hdf5array" ,r-hdf5array) |
e5bff307 | 4512 | ("r-iranges" ,r-iranges) |
785c7596 | 4513 | ("r-rhdf5" ,r-rhdf5) |
e5bff307 RW |
4514 | ("r-s4vectors" ,r-s4vectors) |
4515 | ("r-xml" ,r-xml))) | |
785c7596 RW |
4516 | (native-inputs |
4517 | `(("r-knitr" ,r-knitr))) | |
e5bff307 RW |
4518 | (home-page "https://github.com/rcastelo/GenomicScores/") |
4519 | (synopsis "Work with genome-wide position-specific scores") | |
4520 | (description | |
4521 | "This package provides infrastructure to store and access genome-wide | |
4522 | position-specific scores within R and Bioconductor.") | |
4523 | (license license:artistic2.0))) | |
32e0f906 RW |
4524 | |
4525 | (define-public r-atacseqqc | |
4526 | (package | |
4527 | (name "r-atacseqqc") | |
2ba61c67 | 4528 | (version "1.14.4") |
32e0f906 RW |
4529 | (source |
4530 | (origin | |
4531 | (method url-fetch) | |
4532 | (uri (bioconductor-uri "ATACseqQC" version)) | |
4533 | (sha256 | |
4534 | (base32 | |
2ba61c67 | 4535 | "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9")))) |
32e0f906 RW |
4536 | (properties `((upstream-name . "ATACseqQC"))) |
4537 | (build-system r-build-system) | |
4538 | (propagated-inputs | |
4539 | `(("r-biocgenerics" ,r-biocgenerics) | |
4540 | ("r-biostrings" ,r-biostrings) | |
4541 | ("r-bsgenome" ,r-bsgenome) | |
4542 | ("r-chippeakanno" ,r-chippeakanno) | |
bcc233c1 | 4543 | ("r-edger" ,r-edger) |
32e0f906 RW |
4544 | ("r-genomeinfodb" ,r-genomeinfodb) |
4545 | ("r-genomicalignments" ,r-genomicalignments) | |
4546 | ("r-genomicranges" ,r-genomicranges) | |
4547 | ("r-genomicscores" ,r-genomicscores) | |
4548 | ("r-iranges" ,r-iranges) | |
4549 | ("r-kernsmooth" ,r-kernsmooth) | |
4550 | ("r-limma" ,r-limma) | |
4551 | ("r-motifstack" ,r-motifstack) | |
4552 | ("r-preseqr" ,r-preseqr) | |
4553 | ("r-randomforest" ,r-randomforest) | |
4554 | ("r-rsamtools" ,r-rsamtools) | |
4555 | ("r-rtracklayer" ,r-rtracklayer) | |
4556 | ("r-s4vectors" ,r-s4vectors))) | |
dc30cc03 RW |
4557 | (native-inputs |
4558 | `(("r-knitr" ,r-knitr))) | |
32e0f906 RW |
4559 | (home-page "https://bioconductor.org/packages/ATACseqQC/") |
4560 | (synopsis "ATAC-seq quality control") | |
4561 | (description | |
4562 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using | |
4563 | sequencing, is a rapid and sensitive method for chromatin accessibility | |
4564 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq | |
4565 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly | |
4566 | assess whether their ATAC-seq experiment is successful. It includes | |
4567 | diagnostic plots of fragment size distribution, proportion of mitochondria | |
4568 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor | |
4569 | footprints.") | |
4570 | (license license:gpl2+))) | |
3972cfce RW |
4571 | |
4572 | (define-public r-gofuncr | |
4573 | (package | |
4574 | (name "r-gofuncr") | |
c3b69d63 | 4575 | (version "1.10.0") |
3972cfce RW |
4576 | (source |
4577 | (origin | |
4578 | (method url-fetch) | |
4579 | (uri (bioconductor-uri "GOfuncR" version)) | |
4580 | (sha256 | |
4581 | (base32 | |
c3b69d63 | 4582 | "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq")))) |
3972cfce RW |
4583 | (properties `((upstream-name . "GOfuncR"))) |
4584 | (build-system r-build-system) | |
4585 | (propagated-inputs | |
4586 | `(("r-annotationdbi" ,r-annotationdbi) | |
4587 | ("r-genomicranges" ,r-genomicranges) | |
4588 | ("r-gtools" ,r-gtools) | |
4589 | ("r-iranges" ,r-iranges) | |
4590 | ("r-mapplots" ,r-mapplots) | |
4591 | ("r-rcpp" ,r-rcpp) | |
4592 | ("r-vioplot" ,r-vioplot))) | |
028fd6f7 RW |
4593 | (native-inputs |
4594 | `(("r-knitr" ,r-knitr))) | |
3972cfce RW |
4595 | (home-page "https://bioconductor.org/packages/GOfuncR/") |
4596 | (synopsis "Gene ontology enrichment using FUNC") | |
4597 | (description | |
4598 | "GOfuncR performs a gene ontology enrichment analysis based on the | |
4599 | ontology enrichment software FUNC. GO-annotations are obtained from | |
4600 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is | |
4601 | included in the package and updated regularly. GOfuncR provides the standard | |
4602 | candidate vs background enrichment analysis using the hypergeometric test, as | |
4603 | well as three additional tests: | |
4604 | ||
4605 | @enumerate | |
4606 | @item the Wilcoxon rank-sum test that is used when genes are ranked, | |
4607 | @item a binomial test that is used when genes are associated with two counts, | |
4608 | and | |
4609 | @item a Chi-square or Fisher's exact test that is used in cases when genes are | |
4610 | associated with four counts. | |
4611 | @end enumerate | |
4612 | ||
4613 | To correct for multiple testing and interdependency of the tests, family-wise | |
4614 | error rates are computed based on random permutations of the gene-associated | |
4615 | variables. GOfuncR also provides tools for exploring the ontology graph and | |
4616 | the annotations, and options to take gene-length or spatial clustering of | |
4617 | genes into account. It is also possible to provide custom gene coordinates, | |
4618 | annotations and ontologies.") | |
4619 | (license license:gpl2+))) | |
9bf4bb19 RW |
4620 | |
4621 | (define-public r-abaenrichment | |
4622 | (package | |
4623 | (name "r-abaenrichment") | |
8a7f7112 | 4624 | (version "1.20.0") |
9bf4bb19 RW |
4625 | (source |
4626 | (origin | |
4627 | (method url-fetch) | |
4628 | (uri (bioconductor-uri "ABAEnrichment" version)) | |
4629 | (sha256 | |
4630 | (base32 | |
8a7f7112 | 4631 | "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c")))) |
9bf4bb19 RW |
4632 | (properties `((upstream-name . "ABAEnrichment"))) |
4633 | (build-system r-build-system) | |
4634 | (propagated-inputs | |
4635 | `(("r-abadata" ,r-abadata) | |
4636 | ("r-data-table" ,r-data-table) | |
4637 | ("r-gofuncr" ,r-gofuncr) | |
4638 | ("r-gplots" ,r-gplots) | |
4639 | ("r-gtools" ,r-gtools) | |
4640 | ("r-rcpp" ,r-rcpp))) | |
6a65ac15 RW |
4641 | (native-inputs |
4642 | `(("r-knitr" ,r-knitr))) | |
9bf4bb19 RW |
4643 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") |
4644 | (synopsis "Gene expression enrichment in human brain regions") | |
4645 | (description | |
4646 | "The package ABAEnrichment is designed to test for enrichment of user | |
4647 | defined candidate genes in the set of expressed genes in different human brain | |
4648 | regions. The core function @code{aba_enrich} integrates the expression of the | |
4649 | candidate gene set (averaged across donors) and the structural information of | |
4650 | the brain using an ontology, both provided by the Allen Brain Atlas project.") | |
4651 | (license license:gpl2+))) | |
0b91b7b9 RW |
4652 | |
4653 | (define-public r-annotationfuncs | |
4654 | (package | |
4655 | (name "r-annotationfuncs") | |
bc12a4b6 | 4656 | (version "1.40.0") |
0b91b7b9 RW |
4657 | (source |
4658 | (origin | |
4659 | (method url-fetch) | |
4660 | (uri (bioconductor-uri "AnnotationFuncs" version)) | |
4661 | (sha256 | |
4662 | (base32 | |
bc12a4b6 | 4663 | "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr")))) |
0b91b7b9 RW |
4664 | (properties |
4665 | `((upstream-name . "AnnotationFuncs"))) | |
4666 | (build-system r-build-system) | |
4667 | (propagated-inputs | |
4668 | `(("r-annotationdbi" ,r-annotationdbi) | |
4669 | ("r-dbi" ,r-dbi))) | |
4670 | (home-page "https://www.iysik.com/r/annotationfuncs") | |
4671 | (synopsis "Annotation translation functions") | |
4672 | (description | |
4673 | "This package provides functions for handling translating between | |
4674 | different identifieres using the Biocore Data Team data-packages (e.g. | |
4675 | @code{org.Bt.eg.db}).") | |
4676 | (license license:gpl2))) | |
adf7d813 RW |
4677 | |
4678 | (define-public r-annotationtools | |
4679 | (package | |
4680 | (name "r-annotationtools") | |
57791542 | 4681 | (version "1.64.0") |
adf7d813 RW |
4682 | (source |
4683 | (origin | |
4684 | (method url-fetch) | |
4685 | (uri (bioconductor-uri "annotationTools" version)) | |
4686 | (sha256 | |
4687 | (base32 | |
57791542 | 4688 | "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224")))) |
adf7d813 RW |
4689 | (properties |
4690 | `((upstream-name . "annotationTools"))) | |
4691 | (build-system r-build-system) | |
4692 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4693 | (home-page "https://bioconductor.org/packages/annotationTools/") | |
4694 | (synopsis "Annotate microarrays and perform gene expression analyses") | |
4695 | (description | |
4696 | "This package provides functions to annotate microarrays, find orthologs, | |
4697 | and integrate heterogeneous gene expression profiles using annotation and | |
4698 | other molecular biology information available as flat file database (plain | |
4699 | text files).") | |
4700 | ;; Any version of the GPL. | |
4701 | (license (list license:gpl2+)))) | |
f31e10f8 RW |
4702 | |
4703 | (define-public r-allelicimbalance | |
4704 | (package | |
4705 | (name "r-allelicimbalance") | |
85c6636b | 4706 | (version "1.28.0") |
f31e10f8 RW |
4707 | (source |
4708 | (origin | |
4709 | (method url-fetch) | |
4710 | (uri (bioconductor-uri "AllelicImbalance" version)) | |
4711 | (sha256 | |
4712 | (base32 | |
85c6636b | 4713 | "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl")))) |
f31e10f8 RW |
4714 | (properties |
4715 | `((upstream-name . "AllelicImbalance"))) | |
4716 | (build-system r-build-system) | |
4717 | (propagated-inputs | |
4718 | `(("r-annotationdbi" ,r-annotationdbi) | |
4719 | ("r-biocgenerics" ,r-biocgenerics) | |
4720 | ("r-biostrings" ,r-biostrings) | |
4721 | ("r-bsgenome" ,r-bsgenome) | |
4722 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4723 | ("r-genomicalignments" ,r-genomicalignments) | |
4724 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4725 | ("r-genomicranges" ,r-genomicranges) | |
4726 | ("r-gridextra" ,r-gridextra) | |
4727 | ("r-gviz" ,r-gviz) | |
4728 | ("r-iranges" ,r-iranges) | |
4729 | ("r-lattice" ,r-lattice) | |
4730 | ("r-latticeextra" ,r-latticeextra) | |
4731 | ("r-nlme" ,r-nlme) | |
4732 | ("r-rsamtools" ,r-rsamtools) | |
4733 | ("r-s4vectors" ,r-s4vectors) | |
4734 | ("r-seqinr" ,r-seqinr) | |
4735 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
4736 | ("r-variantannotation" ,r-variantannotation))) | |
63149388 RW |
4737 | (native-inputs |
4738 | `(("r-knitr" ,r-knitr))) | |
f31e10f8 RW |
4739 | (home-page "https://github.com/pappewaio/AllelicImbalance") |
4740 | (synopsis "Investigate allele-specific expression") | |
4741 | (description | |
4742 | "This package provides a framework for allele-specific expression | |
4743 | investigation using RNA-seq data.") | |
4744 | (license license:gpl3))) | |
ffe7029b RW |
4745 | |
4746 | (define-public r-aucell | |
4747 | (package | |
4748 | (name "r-aucell") | |
ff8b9153 | 4749 | (version "1.12.0") |
ffe7029b RW |
4750 | (source |
4751 | (origin | |
4752 | (method url-fetch) | |
4753 | (uri (bioconductor-uri "AUCell" version)) | |
4754 | (sha256 | |
4755 | (base32 | |
ff8b9153 | 4756 | "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx")))) |
ffe7029b RW |
4757 | (properties `((upstream-name . "AUCell"))) |
4758 | (build-system r-build-system) | |
4759 | (propagated-inputs | |
3a35d274 RW |
4760 | `(("r-biocgenerics" ,r-biocgenerics) |
4761 | ("r-data-table" ,r-data-table) | |
ffe7029b RW |
4762 | ("r-gseabase" ,r-gseabase) |
4763 | ("r-mixtools" ,r-mixtools) | |
4764 | ("r-r-utils" ,r-r-utils) | |
3a35d274 | 4765 | ("r-s4vectors" ,r-s4vectors) |
ffe7029b RW |
4766 | ("r-shiny" ,r-shiny) |
4767 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
e059ab25 RW |
4768 | (native-inputs |
4769 | `(("r-knitr" ,r-knitr))) | |
ffe7029b RW |
4770 | (home-page "https://bioconductor.org/packages/AUCell/") |
4771 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") | |
4772 | (description | |
8c4bf6c2 | 4773 | "AUCell identifies cells with active gene sets (e.g. signatures, |
ffe7029b RW |
4774 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area |
4775 | Under the Curve} (AUC) to calculate whether a critical subset of the input | |
4776 | gene set is enriched within the expressed genes for each cell. The | |
4777 | distribution of AUC scores across all the cells allows exploring the relative | |
4778 | expression of the signature. Since the scoring method is ranking-based, | |
4779 | AUCell is independent of the gene expression units and the normalization | |
4780 | procedure. In addition, since the cells are evaluated individually, it can | |
4781 | easily be applied to bigger datasets, subsetting the expression matrix if | |
4782 | needed.") | |
4783 | (license license:gpl3))) | |
5cfa4bff RW |
4784 | |
4785 | (define-public r-ebimage | |
4786 | (package | |
4787 | (name "r-ebimage") | |
ba0bf98d | 4788 | (version "4.32.0") |
5cfa4bff RW |
4789 | (source |
4790 | (origin | |
4791 | (method url-fetch) | |
4792 | (uri (bioconductor-uri "EBImage" version)) | |
4793 | (sha256 | |
4794 | (base32 | |
ba0bf98d | 4795 | "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww")))) |
5cfa4bff RW |
4796 | (properties `((upstream-name . "EBImage"))) |
4797 | (build-system r-build-system) | |
4798 | (propagated-inputs | |
4799 | `(("r-abind" ,r-abind) | |
4800 | ("r-biocgenerics" ,r-biocgenerics) | |
4801 | ("r-fftwtools" ,r-fftwtools) | |
4802 | ("r-htmltools" ,r-htmltools) | |
4803 | ("r-htmlwidgets" ,r-htmlwidgets) | |
4804 | ("r-jpeg" ,r-jpeg) | |
4805 | ("r-locfit" ,r-locfit) | |
4806 | ("r-png" ,r-png) | |
4807 | ("r-rcurl" ,r-rcurl) | |
4808 | ("r-tiff" ,r-tiff))) | |
4809 | (native-inputs | |
4810 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
4811 | (home-page "https://github.com/aoles/EBImage") | |
4812 | (synopsis "Image processing and analysis toolbox for R") | |
4813 | (description | |
4814 | "EBImage provides general purpose functionality for image processing and | |
4815 | analysis. In the context of (high-throughput) microscopy-based cellular | |
4816 | assays, EBImage offers tools to segment cells and extract quantitative | |
4817 | cellular descriptors. This allows the automation of such tasks using the R | |
4818 | programming language and facilitates the use of other tools in the R | |
4819 | environment for signal processing, statistical modeling, machine learning and | |
4820 | visualization with image data.") | |
4821 | ;; Any version of the LGPL. | |
4822 | (license license:lgpl2.1+))) | |
51e98f7e RW |
4823 | |
4824 | (define-public r-yamss | |
4825 | (package | |
4826 | (name "r-yamss") | |
65ba4ba5 | 4827 | (version "1.16.0") |
51e98f7e RW |
4828 | (source |
4829 | (origin | |
4830 | (method url-fetch) | |
4831 | (uri (bioconductor-uri "yamss" version)) | |
4832 | (sha256 | |
4833 | (base32 | |
65ba4ba5 | 4834 | "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w")))) |
51e98f7e RW |
4835 | (build-system r-build-system) |
4836 | (propagated-inputs | |
4837 | `(("r-biocgenerics" ,r-biocgenerics) | |
4838 | ("r-data-table" ,r-data-table) | |
4839 | ("r-ebimage" ,r-ebimage) | |
4840 | ("r-iranges" ,r-iranges) | |
4841 | ("r-limma" ,r-limma) | |
4842 | ("r-matrix" ,r-matrix) | |
4843 | ("r-mzr" ,r-mzr) | |
4844 | ("r-s4vectors" ,r-s4vectors) | |
4845 | ("r-summarizedexperiment" | |
4846 | ,r-summarizedexperiment))) | |
6e397aad RW |
4847 | (native-inputs |
4848 | `(("r-knitr" ,r-knitr))) | |
51e98f7e RW |
4849 | (home-page "https://github.com/hansenlab/yamss") |
4850 | (synopsis "Tools for high-throughput metabolomics") | |
4851 | (description | |
4852 | "This package provides tools to analyze and visualize high-throughput | |
9b19734c | 4853 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
51e98f7e RW |
4854 | preprocess data in a way that enables reliable and powerful differential |
4855 | analysis.") | |
4856 | (license license:artistic2.0))) | |
398c4a93 RW |
4857 | |
4858 | (define-public r-gtrellis | |
4859 | (package | |
4860 | (name "r-gtrellis") | |
0836ef6b | 4861 | (version "1.22.0") |
398c4a93 RW |
4862 | (source |
4863 | (origin | |
4864 | (method url-fetch) | |
4865 | (uri (bioconductor-uri "gtrellis" version)) | |
4866 | (sha256 | |
4867 | (base32 | |
0836ef6b | 4868 | "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw")))) |
398c4a93 RW |
4869 | (build-system r-build-system) |
4870 | (propagated-inputs | |
4871 | `(("r-circlize" ,r-circlize) | |
4872 | ("r-genomicranges" ,r-genomicranges) | |
4873 | ("r-getoptlong" ,r-getoptlong) | |
4874 | ("r-iranges" ,r-iranges))) | |
a471def0 RW |
4875 | (native-inputs |
4876 | `(("r-knitr" ,r-knitr))) | |
398c4a93 RW |
4877 | (home-page "https://github.com/jokergoo/gtrellis") |
4878 | (synopsis "Genome level Trellis layout") | |
4879 | (description | |
4880 | "Genome level Trellis graph visualizes genomic data conditioned by | |
4881 | genomic categories (e.g. chromosomes). For each genomic category, multiple | |
4882 | dimensional data which are represented as tracks describe different features | |
4883 | from different aspects. This package provides high flexibility to arrange | |
4884 | genomic categories and to add self-defined graphics in the plot.") | |
4885 | (license license:expat))) | |
28098414 RW |
4886 | |
4887 | (define-public r-somaticsignatures | |
4888 | (package | |
4889 | (name "r-somaticsignatures") | |
36f3a19a | 4890 | (version "2.26.0") |
28098414 RW |
4891 | (source |
4892 | (origin | |
4893 | (method url-fetch) | |
4894 | (uri (bioconductor-uri "SomaticSignatures" version)) | |
4895 | (sha256 | |
4896 | (base32 | |
36f3a19a | 4897 | "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801")))) |
28098414 RW |
4898 | (properties |
4899 | `((upstream-name . "SomaticSignatures"))) | |
4900 | (build-system r-build-system) | |
4901 | (propagated-inputs | |
4902 | `(("r-biobase" ,r-biobase) | |
4903 | ("r-biostrings" ,r-biostrings) | |
4904 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4905 | ("r-genomicranges" ,r-genomicranges) | |
4906 | ("r-ggbio" ,r-ggbio) | |
4907 | ("r-ggplot2" ,r-ggplot2) | |
4908 | ("r-iranges" ,r-iranges) | |
4909 | ("r-nmf" ,r-nmf) | |
4910 | ("r-pcamethods" ,r-pcamethods) | |
4911 | ("r-proxy" ,r-proxy) | |
4912 | ("r-reshape2" ,r-reshape2) | |
4913 | ("r-s4vectors" ,r-s4vectors) | |
4914 | ("r-variantannotation" ,r-variantannotation))) | |
63c14717 RW |
4915 | (native-inputs |
4916 | `(("r-knitr" ,r-knitr))) | |
28098414 RW |
4917 | (home-page "https://github.com/juliangehring/SomaticSignatures") |
4918 | (synopsis "Somatic signatures") | |
4919 | (description | |
4920 | "This package identifies mutational signatures of @dfn{single nucleotide | |
4921 | variants} (SNVs). It provides a infrastructure related to the methodology | |
4922 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix | |
4923 | decomposition algorithms.") | |
4924 | (license license:expat))) | |
303f2ed1 RW |
4925 | |
4926 | (define-public r-yapsa | |
4927 | (package | |
4928 | (name "r-yapsa") | |
d0db04fc | 4929 | (version "1.16.0") |
303f2ed1 RW |
4930 | (source |
4931 | (origin | |
4932 | (method url-fetch) | |
4933 | (uri (bioconductor-uri "YAPSA" version)) | |
4934 | (sha256 | |
4935 | (base32 | |
d0db04fc | 4936 | "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb")))) |
303f2ed1 RW |
4937 | (properties `((upstream-name . "YAPSA"))) |
4938 | (build-system r-build-system) | |
4939 | (propagated-inputs | |
8a5abc62 RW |
4940 | `(("r-biostrings" ,r-biostrings) |
4941 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
4942 | ("r-circlize" ,r-circlize) | |
303f2ed1 RW |
4943 | ("r-complexheatmap" ,r-complexheatmap) |
4944 | ("r-corrplot" ,r-corrplot) | |
4945 | ("r-dendextend" ,r-dendextend) | |
8a5abc62 RW |
4946 | ("r-doparallel" ,r-doparallel) |
4947 | ("r-dplyr" ,r-dplyr) | |
303f2ed1 RW |
4948 | ("r-genomeinfodb" ,r-genomeinfodb) |
4949 | ("r-genomicranges" ,r-genomicranges) | |
4950 | ("r-getoptlong" ,r-getoptlong) | |
8a5abc62 | 4951 | ("r-ggbeeswarm" ,r-ggbeeswarm) |
303f2ed1 RW |
4952 | ("r-ggplot2" ,r-ggplot2) |
4953 | ("r-gridextra" ,r-gridextra) | |
4954 | ("r-gtrellis" ,r-gtrellis) | |
4955 | ("r-keggrest" ,r-keggrest) | |
d0db04fc | 4956 | ("r-limsolve" ,r-limsolve) |
8a5abc62 | 4957 | ("r-magrittr" ,r-magrittr) |
303f2ed1 | 4958 | ("r-pmcmr" ,r-pmcmr) |
8a5abc62 | 4959 | ("r-pracma" ,r-pracma) |
303f2ed1 RW |
4960 | ("r-reshape2" ,r-reshape2) |
4961 | ("r-somaticsignatures" ,r-somaticsignatures) | |
4962 | ("r-variantannotation" ,r-variantannotation))) | |
8a5abc62 RW |
4963 | (native-inputs |
4964 | `(("r-knitr" ,r-knitr))) | |
303f2ed1 RW |
4965 | (home-page "https://bioconductor.org/packages/YAPSA/") |
4966 | (synopsis "Yet another package for signature analysis") | |
4967 | (description | |
4968 | "This package provides functions and routines useful in the analysis of | |
4969 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, | |
4970 | functions to perform a signature analysis with known signatures and a | |
4971 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are | |
4972 | provided.") | |
4973 | (license license:gpl3))) | |
e99380d6 RW |
4974 | |
4975 | (define-public r-gcrma | |
4976 | (package | |
4977 | (name "r-gcrma") | |
3d41f0c2 | 4978 | (version "2.62.0") |
e99380d6 RW |
4979 | (source |
4980 | (origin | |
4981 | (method url-fetch) | |
4982 | (uri (bioconductor-uri "gcrma" version)) | |
4983 | (sha256 | |
4984 | (base32 | |
3d41f0c2 | 4985 | "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00")))) |
e99380d6 RW |
4986 | (build-system r-build-system) |
4987 | (propagated-inputs | |
4988 | `(("r-affy" ,r-affy) | |
4989 | ("r-affyio" ,r-affyio) | |
4990 | ("r-biobase" ,r-biobase) | |
4991 | ("r-biocmanager" ,r-biocmanager) | |
4992 | ("r-biostrings" ,r-biostrings) | |
4993 | ("r-xvector" ,r-xvector))) | |
4994 | (home-page "https://bioconductor.org/packages/gcrma/") | |
4995 | (synopsis "Background adjustment using sequence information") | |
4996 | (description | |
4997 | "Gcrma adjusts for background intensities in Affymetrix array data which | |
4998 | include optical noise and @dfn{non-specific binding} (NSB). The main function | |
4999 | @code{gcrma} converts background adjusted probe intensities to expression | |
5000 | measures using the same normalization and summarization methods as a | |
5001 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information | |
5002 | to estimate probe affinity to NSB. The sequence information is summarized in | |
5003 | a more complex way than the simple GC content. Instead, the base types (A, T, | |
5004 | G or C) at each position along the probe determine the affinity of each probe. | |
5005 | The parameters of the position-specific base contributions to the probe | |
5006 | affinity is estimated in an NSB experiment in which only NSB but no | |
7230f6d5 | 5007 | gene-specific binding is expected.") |
e99380d6 RW |
5008 | ;; Any version of the LGPL |
5009 | (license license:lgpl2.1+))) | |
4675b3cf RW |
5010 | |
5011 | (define-public r-simpleaffy | |
5012 | (package | |
5013 | (name "r-simpleaffy") | |
48aaef23 | 5014 | (version "2.66.0") |
4675b3cf RW |
5015 | (source |
5016 | (origin | |
5017 | (method url-fetch) | |
5018 | (uri (bioconductor-uri "simpleaffy" version)) | |
5019 | (sha256 | |
5020 | (base32 | |
48aaef23 | 5021 | "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb")))) |
4675b3cf RW |
5022 | (build-system r-build-system) |
5023 | (propagated-inputs | |
5024 | `(("r-affy" ,r-affy) | |
5025 | ("r-biobase" ,r-biobase) | |
5026 | ("r-biocgenerics" ,r-biocgenerics) | |
5027 | ("r-gcrma" ,r-gcrma) | |
5028 | ("r-genefilter" ,r-genefilter))) | |
5029 | (home-page "https://bioconductor.org/packages/simpleaffy/") | |
5030 | (synopsis "Very simple high level analysis of Affymetrix data") | |
5031 | (description | |
5032 | "This package provides high level functions for reading Affy @file{.CEL} | |
5033 | files, phenotypic data, and then computing simple things with it, such as | |
5034 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} | |
5035 | library. It also has some basic scatter plot functions and mechanisms for | |
5036 | generating high resolution journal figures.") | |
5037 | (license license:gpl2+))) | |
f562c90a RW |
5038 | |
5039 | (define-public r-yaqcaffy | |
5040 | (package | |
5041 | (name "r-yaqcaffy") | |
94dee0af | 5042 | (version "1.50.0") |
f562c90a RW |
5043 | (source |
5044 | (origin | |
5045 | (method url-fetch) | |
5046 | (uri (bioconductor-uri "yaqcaffy" version)) | |
5047 | (sha256 | |
5048 | (base32 | |
94dee0af | 5049 | "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96")))) |
f562c90a RW |
5050 | (build-system r-build-system) |
5051 | (propagated-inputs | |
5052 | `(("r-simpleaffy" ,r-simpleaffy))) | |
5053 | (home-page "https://bioconductor.org/packages/yaqcaffy/") | |
5054 | (synopsis "Affymetrix quality control and reproducibility analysis") | |
5055 | (description | |
5056 | "This is a package that can be used for quality control of Affymetrix | |
5057 | GeneChip expression data and reproducibility analysis of human whole genome | |
5058 | chips with the MAQC reference datasets.") | |
5059 | (license license:artistic2.0))) | |
59cf2629 RW |
5060 | |
5061 | (define-public r-quantro | |
5062 | (package | |
5063 | (name "r-quantro") | |
70d90ae7 | 5064 | (version "1.22.0") |
59cf2629 RW |
5065 | (source |
5066 | (origin | |
5067 | (method url-fetch) | |
5068 | (uri (bioconductor-uri "quantro" version)) | |
5069 | (sha256 | |
5070 | (base32 | |
70d90ae7 | 5071 | "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz")))) |
59cf2629 RW |
5072 | (build-system r-build-system) |
5073 | (propagated-inputs | |
5074 | `(("r-biobase" ,r-biobase) | |
5075 | ("r-doparallel" ,r-doparallel) | |
5076 | ("r-foreach" ,r-foreach) | |
5077 | ("r-ggplot2" ,r-ggplot2) | |
5078 | ("r-iterators" ,r-iterators) | |
5079 | ("r-minfi" ,r-minfi) | |
5080 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
70d90ae7 RW |
5081 | (native-inputs |
5082 | `(("r-knitr" ,r-knitr))) | |
59cf2629 RW |
5083 | (home-page "https://bioconductor.org/packages/quantro/") |
5084 | (synopsis "Test for when to use quantile normalization") | |
5085 | (description | |
5086 | "This package provides a data-driven test for the assumptions of quantile | |
5087 | normalization using raw data such as objects that inherit eSets (e.g. | |
5088 | ExpressionSet, MethylSet). Group level information about each sample (such as | |
5089 | Tumor / Normal status) must also be provided because the test assesses if | |
5090 | there are global differences in the distributions between the user-defined | |
5091 | groups.") | |
5092 | (license license:gpl3+))) | |
98a2af31 RW |
5093 | |
5094 | (define-public r-yarn | |
5095 | (package | |
5096 | (name "r-yarn") | |
a37a6ffb | 5097 | (version "1.14.0") |
98a2af31 RW |
5098 | (source |
5099 | (origin | |
5100 | (method url-fetch) | |
5101 | (uri (bioconductor-uri "yarn" version)) | |
5102 | (sha256 | |
5103 | (base32 | |
a37a6ffb | 5104 | "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx")))) |
98a2af31 RW |
5105 | (build-system r-build-system) |
5106 | (propagated-inputs | |
5107 | `(("r-biobase" ,r-biobase) | |
5108 | ("r-biomart" ,r-biomart) | |
5109 | ("r-downloader" ,r-downloader) | |
5110 | ("r-edger" ,r-edger) | |
5111 | ("r-gplots" ,r-gplots) | |
5112 | ("r-limma" ,r-limma) | |
5113 | ("r-matrixstats" ,r-matrixstats) | |
5114 | ("r-preprocesscore" ,r-preprocesscore) | |
5115 | ("r-quantro" ,r-quantro) | |
5116 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5117 | ("r-readr" ,r-readr))) | |
a37a6ffb RW |
5118 | (native-inputs |
5119 | `(("r-knitr" ,r-knitr))) | |
98a2af31 RW |
5120 | (home-page "https://bioconductor.org/packages/yarn/") |
5121 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") | |
5122 | (description | |
5123 | "Expedite large RNA-Seq analyses using a combination of previously | |
5124 | developed tools. YARN is meant to make it easier for the user in performing | |
5125 | basic mis-annotation quality control, filtering, and condition-aware | |
5126 | normalization. YARN leverages many Bioconductor tools and statistical | |
5127 | techniques to account for the large heterogeneity and sparsity found in very | |
5128 | large RNA-seq experiments.") | |
5129 | (license license:artistic2.0))) | |
a6e1eb1a RW |
5130 | |
5131 | (define-public r-roar | |
5132 | (package | |
5133 | (name "r-roar") | |
72476ade | 5134 | (version "1.26.0") |
a6e1eb1a RW |
5135 | (source |
5136 | (origin | |
5137 | (method url-fetch) | |
5138 | (uri (bioconductor-uri "roar" version)) | |
5139 | (sha256 | |
5140 | (base32 | |
72476ade | 5141 | "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw")))) |
a6e1eb1a RW |
5142 | (build-system r-build-system) |
5143 | (propagated-inputs | |
5144 | `(("r-biocgenerics" ,r-biocgenerics) | |
5145 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5146 | ("r-genomicalignments" ,r-genomicalignments) | |
5147 | ("r-genomicranges" ,r-genomicranges) | |
5148 | ("r-iranges" ,r-iranges) | |
5149 | ("r-rtracklayer" ,r-rtracklayer) | |
5150 | ("r-s4vectors" ,r-s4vectors) | |
5151 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5152 | (home-page "https://github.com/vodkatad/roar/") | |
5153 | (synopsis "Identify differential APA usage from RNA-seq alignments") | |
5154 | (description | |
5155 | "This package provides tools for identifying preferential usage of APA | |
5156 | sites, comparing two biological conditions, starting from known alternative | |
5157 | sites and alignments obtained from standard RNA-seq experiments.") | |
5158 | (license license:gpl3))) | |
50d91770 RW |
5159 | |
5160 | (define-public r-xbseq | |
5161 | (package | |
5162 | (name "r-xbseq") | |
7f71341e | 5163 | (version "1.22.0") |
50d91770 RW |
5164 | (source |
5165 | (origin | |
5166 | (method url-fetch) | |
5167 | (uri (bioconductor-uri "XBSeq" version)) | |
5168 | (sha256 | |
5169 | (base32 | |
7f71341e | 5170 | "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz")))) |
50d91770 RW |
5171 | (properties `((upstream-name . "XBSeq"))) |
5172 | (build-system r-build-system) | |
5173 | (propagated-inputs | |
5174 | `(("r-biobase" ,r-biobase) | |
5175 | ("r-deseq2" ,r-deseq2) | |
5176 | ("r-dplyr" ,r-dplyr) | |
5177 | ("r-ggplot2" ,r-ggplot2) | |
5178 | ("r-locfit" ,r-locfit) | |
5179 | ("r-magrittr" ,r-magrittr) | |
5180 | ("r-matrixstats" ,r-matrixstats) | |
5181 | ("r-pracma" ,r-pracma) | |
5182 | ("r-roar" ,r-roar))) | |
bcd06bdb RW |
5183 | (native-inputs |
5184 | `(("r-knitr" ,r-knitr))) | |
50d91770 RW |
5185 | (home-page "https://github.com/Liuy12/XBSeq") |
5186 | (synopsis "Test for differential expression for RNA-seq data") | |
5187 | (description | |
5188 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential | |
5189 | expression} (DE), where a statistical model was established based on the | |
5190 | assumption that observed signals are the convolution of true expression | |
5191 | signals and sequencing noises. The mapped reads in non-exonic regions are | |
5192 | considered as sequencing noises, which follows a Poisson distribution. Given | |
5193 | measurable observed signal and background noise from RNA-seq data, true | |
5194 | expression signals, assuming governed by the negative binomial distribution, | |
5195 | can be delineated and thus the accurate detection of differential expressed | |
5196 | genes.") | |
5197 | (license license:gpl3+))) | |
c8310056 RW |
5198 | |
5199 | (define-public r-massspecwavelet | |
5200 | (package | |
5201 | (name "r-massspecwavelet") | |
f4e19e62 | 5202 | (version "1.56.0") |
c8310056 RW |
5203 | (source |
5204 | (origin | |
5205 | (method url-fetch) | |
5206 | (uri (bioconductor-uri "MassSpecWavelet" version)) | |
5207 | (sha256 | |
5208 | (base32 | |
f4e19e62 | 5209 | "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3")))) |
c8310056 RW |
5210 | (properties |
5211 | `((upstream-name . "MassSpecWavelet"))) | |
5212 | (build-system r-build-system) | |
5213 | (propagated-inputs | |
5214 | `(("r-waveslim" ,r-waveslim))) | |
5215 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") | |
5216 | (synopsis "Mass spectrum processing by wavelet-based algorithms") | |
5217 | (description | |
5218 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) | |
5219 | data mainly through the use of wavelet transforms. It supports peak detection | |
5220 | based on @dfn{Continuous Wavelet Transform} (CWT).") | |
5221 | (license license:lgpl2.0+))) | |
ec12e537 RW |
5222 | |
5223 | (define-public r-xcms | |
5224 | (package | |
5225 | (name "r-xcms") | |
a3af40ea | 5226 | (version "3.12.0") |
ec12e537 RW |
5227 | (source |
5228 | (origin | |
5229 | (method url-fetch) | |
5230 | (uri (bioconductor-uri "xcms" version)) | |
5231 | (sha256 | |
5232 | (base32 | |
a3af40ea | 5233 | "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv")))) |
ec12e537 RW |
5234 | (build-system r-build-system) |
5235 | (propagated-inputs | |
5236 | `(("r-biobase" ,r-biobase) | |
5237 | ("r-biocgenerics" ,r-biocgenerics) | |
5238 | ("r-biocparallel" ,r-biocparallel) | |
4fb52345 | 5239 | ("r-iranges" ,r-iranges) |
ec12e537 RW |
5240 | ("r-lattice" ,r-lattice) |
5241 | ("r-massspecwavelet" ,r-massspecwavelet) | |
a3af40ea | 5242 | ("r-mscoreutils" ,r-mscoreutils) |
ec12e537 | 5243 | ("r-msnbase" ,r-msnbase) |
ec12e537 RW |
5244 | ("r-mzr" ,r-mzr) |
5245 | ("r-plyr" ,r-plyr) | |
5246 | ("r-protgenerics" ,r-protgenerics) | |
5247 | ("r-rann" ,r-rann) | |
5248 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5249 | ("r-robustbase" ,r-robustbase) | |
ff9f179a RW |
5250 | ("r-s4vectors" ,r-s4vectors) |
5251 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5252 | (native-inputs | |
5253 | `(("r-knitr" ,r-knitr))) | |
ec12e537 RW |
5254 | (home-page "https://bioconductor.org/packages/xcms/") |
5255 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") | |
5256 | (description | |
5257 | "This package provides a framework for processing and visualization of | |
5258 | chromatographically separated and single-spectra mass spectral data. It | |
5259 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses | |
5260 | data for high-throughput, untargeted analyte profiling.") | |
5261 | (license license:gpl2+))) | |
8830664d RW |
5262 | |
5263 | (define-public r-wrench | |
5264 | (package | |
5265 | (name "r-wrench") | |
dc7c6368 | 5266 | (version "1.8.0") |
8830664d RW |
5267 | (source |
5268 | (origin | |
5269 | (method url-fetch) | |
5270 | (uri (bioconductor-uri "Wrench" version)) | |
5271 | (sha256 | |
5272 | (base32 | |
dc7c6368 | 5273 | "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx")))) |
8830664d RW |
5274 | (properties `((upstream-name . "Wrench"))) |
5275 | (build-system r-build-system) | |
5276 | (propagated-inputs | |
5277 | `(("r-limma" ,r-limma) | |
5278 | ("r-locfit" ,r-locfit) | |
5279 | ("r-matrixstats" ,r-matrixstats))) | |
996f07b5 RW |
5280 | (native-inputs |
5281 | `(("r-knitr" ,r-knitr))) | |
8830664d RW |
5282 | (home-page "https://github.com/HCBravoLab/Wrench") |
5283 | (synopsis "Wrench normalization for sparse count data") | |
5284 | (description | |
5285 | "Wrench is a package for normalization sparse genomic count data, like | |
5286 | that arising from 16s metagenomic surveys.") | |
5287 | (license license:artistic2.0))) | |
b9b8b447 RW |
5288 | |
5289 | (define-public r-wiggleplotr | |
5290 | (package | |
5291 | (name "r-wiggleplotr") | |
397bcd2c | 5292 | (version "1.14.0") |
b9b8b447 RW |
5293 | (source |
5294 | (origin | |
5295 | (method url-fetch) | |
5296 | (uri (bioconductor-uri "wiggleplotr" version)) | |
5297 | (sha256 | |
5298 | (base32 | |
397bcd2c | 5299 | "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad")))) |
b9b8b447 RW |
5300 | (build-system r-build-system) |
5301 | (propagated-inputs | |
5302 | `(("r-assertthat" ,r-assertthat) | |
5303 | ("r-cowplot" ,r-cowplot) | |
5304 | ("r-dplyr" ,r-dplyr) | |
5305 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5306 | ("r-genomicranges" ,r-genomicranges) | |
5307 | ("r-ggplot2" ,r-ggplot2) | |
5308 | ("r-iranges" ,r-iranges) | |
5309 | ("r-purrr" ,r-purrr) | |
5310 | ("r-rtracklayer" ,r-rtracklayer) | |
5311 | ("r-s4vectors" ,r-s4vectors))) | |
ee0f7460 RW |
5312 | (native-inputs |
5313 | `(("r-knitr" ,r-knitr))) | |
b9b8b447 RW |
5314 | (home-page "https://bioconductor.org/packages/wiggleplotr/") |
5315 | (synopsis "Make read coverage plots from BigWig files") | |
5316 | (description | |
5317 | "This package provides tools to visualize read coverage from sequencing | |
5318 | experiments together with genomic annotations (genes, transcripts, peaks). | |
5319 | Introns of long transcripts can be rescaled to a fixed length for better | |
5320 | visualization of exonic read coverage.") | |
5321 | (license license:asl2.0))) | |
7b5101c5 RW |
5322 | |
5323 | (define-public r-widgettools | |
5324 | (package | |
5325 | (name "r-widgettools") | |
ba53681a | 5326 | (version "1.68.0") |
7b5101c5 RW |
5327 | (source |
5328 | (origin | |
5329 | (method url-fetch) | |
5330 | (uri (bioconductor-uri "widgetTools" version)) | |
5331 | (sha256 | |
5332 | (base32 | |
ba53681a | 5333 | "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w")))) |
7b5101c5 RW |
5334 | (properties `((upstream-name . "widgetTools"))) |
5335 | (build-system r-build-system) | |
5336 | (home-page "https://bioconductor.org/packages/widgetTools/") | |
5337 | (synopsis "Tools for creating interactive tcltk widgets") | |
5338 | (description | |
337bdc17 | 5339 | "This package contains tools to support the construction of tcltk |
7b5101c5 RW |
5340 | widgets in R.") |
5341 | ;; Any version of the LGPL. | |
5342 | (license license:lgpl3+))) | |
6b12f213 RW |
5343 | |
5344 | (define-public r-webbioc | |
5345 | (package | |
5346 | (name "r-webbioc") | |
d176ad34 | 5347 | (version "1.62.0") |
6b12f213 RW |
5348 | (source |
5349 | (origin | |
5350 | (method url-fetch) | |
5351 | (uri (bioconductor-uri "webbioc" version)) | |
5352 | (sha256 | |
5353 | (base32 | |
d176ad34 | 5354 | "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj")))) |
6b12f213 RW |
5355 | (build-system r-build-system) |
5356 | (inputs | |
5357 | `(("netpbm" ,netpbm) | |
5358 | ("perl" ,perl))) | |
5359 | (propagated-inputs | |
5360 | `(("r-affy" ,r-affy) | |
5361 | ("r-annaffy" ,r-annaffy) | |
5362 | ("r-biobase" ,r-biobase) | |
5363 | ("r-biocmanager" ,r-biocmanager) | |
5364 | ("r-gcrma" ,r-gcrma) | |
5365 | ("r-multtest" ,r-multtest) | |
5366 | ("r-qvalue" ,r-qvalue) | |
5367 | ("r-vsn" ,r-vsn))) | |
5368 | (home-page "https://www.bioconductor.org/") | |
5369 | (synopsis "Bioconductor web interface") | |
5370 | (description | |
5371 | "This package provides an integrated web interface for doing microarray | |
5372 | analysis using several of the Bioconductor packages. It is intended to be | |
5373 | deployed as a centralized bioinformatics resource for use by many users. | |
5374 | Currently only Affymetrix oligonucleotide analysis is supported.") | |
5375 | (license license:gpl2+))) | |
9800d859 RW |
5376 | |
5377 | (define-public r-zfpkm | |
5378 | (package | |
5379 | (name "r-zfpkm") | |
59fafa19 | 5380 | (version "1.12.0") |
9800d859 RW |
5381 | (source |
5382 | (origin | |
5383 | (method url-fetch) | |
5384 | (uri (bioconductor-uri "zFPKM" version)) | |
5385 | (sha256 | |
5386 | (base32 | |
59fafa19 | 5387 | "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm")))) |
9800d859 RW |
5388 | (properties `((upstream-name . "zFPKM"))) |
5389 | (build-system r-build-system) | |
5390 | (propagated-inputs | |
5391 | `(("r-checkmate" ,r-checkmate) | |
5392 | ("r-dplyr" ,r-dplyr) | |
5393 | ("r-ggplot2" ,r-ggplot2) | |
5394 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
5395 | ("r-tidyr" ,r-tidyr))) | |
8fdca89b RW |
5396 | (native-inputs |
5397 | `(("r-knitr" ,r-knitr))) | |
9800d859 RW |
5398 | (home-page "https://github.com/ronammar/zFPKM/") |
5399 | (synopsis "Functions to facilitate zFPKM transformations") | |
5400 | (description | |
5401 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. | |
5402 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID | |
5403 | 24215113).") | |
5404 | (license license:gpl3))) | |
2bdc88fc RW |
5405 | |
5406 | (define-public r-rbowtie2 | |
5407 | (package | |
5408 | (name "r-rbowtie2") | |
9834d1ab | 5409 | (version "1.12.0") |
2bdc88fc RW |
5410 | (source |
5411 | (origin | |
5412 | (method url-fetch) | |
5413 | (uri (bioconductor-uri "Rbowtie2" version)) | |
5414 | (sha256 | |
5415 | (base32 | |
9834d1ab | 5416 | "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5")))) |
2bdc88fc RW |
5417 | (properties `((upstream-name . "Rbowtie2"))) |
5418 | (build-system r-build-system) | |
5419 | (inputs | |
5420 | `(("zlib" ,zlib))) | |
297854e6 RW |
5421 | (native-inputs |
5422 | `(("r-knitr" ,r-knitr))) | |
2bdc88fc RW |
5423 | (home-page "https://bioconductor.org/packages/Rbowtie2/") |
5424 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") | |
5425 | (description | |
5426 | "This package provides an R wrapper of the popular @code{bowtie2} | |
5427 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for | |
5428 | rapid adapter trimming, identification, and read merging.") | |
5429 | (license license:gpl3+))) | |
5622628f RW |
5430 | |
5431 | (define-public r-progeny | |
5432 | (package | |
5433 | (name "r-progeny") | |
d115db7f | 5434 | (version "1.12.0") |
5622628f RW |
5435 | (source |
5436 | (origin | |
5437 | (method url-fetch) | |
5438 | (uri (bioconductor-uri "progeny" version)) | |
5439 | (sha256 | |
5440 | (base32 | |
d115db7f | 5441 | "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7")))) |
5622628f | 5442 | (build-system r-build-system) |
8e5933a8 RW |
5443 | (propagated-inputs |
5444 | `(("r-biobase" ,r-biobase) | |
5445 | ("r-dplyr" ,r-dplyr) | |
5446 | ("r-ggplot2" ,r-ggplot2) | |
5447 | ("r-ggrepel" ,r-ggrepel) | |
5448 | ("r-gridextra" ,r-gridextra) | |
5449 | ("r-tidyr" ,r-tidyr))) | |
5450 | (native-inputs | |
5451 | `(("r-knitr" ,r-knitr))) | |
5622628f RW |
5452 | (home-page "https://github.com/saezlab/progeny") |
5453 | (synopsis "Pathway responsive gene activity inference") | |
5454 | (description | |
5455 | "This package provides a function to infer pathway activity from gene | |
5456 | expression. It contains the linear model inferred in the publication | |
5457 | \"Perturbation-response genes reveal signaling footprints in cancer gene | |
5458 | expression\".") | |
5459 | (license license:asl2.0))) | |
307586c1 RW |
5460 | |
5461 | (define-public r-arrmnormalization | |
5462 | (package | |
5463 | (name "r-arrmnormalization") | |
0067589a | 5464 | (version "1.30.0") |
307586c1 RW |
5465 | (source |
5466 | (origin | |
5467 | (method url-fetch) | |
5468 | (uri (bioconductor-uri "ARRmNormalization" version)) | |
5469 | (sha256 | |
5470 | (base32 | |
0067589a | 5471 | "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95")))) |
307586c1 RW |
5472 | (properties |
5473 | `((upstream-name . "ARRmNormalization"))) | |
5474 | (build-system r-build-system) | |
5475 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) | |
5476 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") | |
5477 | (synopsis "Adaptive robust regression normalization for methylation data") | |
5478 | (description | |
5479 | "This is a package to perform the @dfn{Adaptive Robust Regression | |
5480 | method} (ARRm) for the normalization of methylation data from the Illumina | |
5481 | Infinium HumanMethylation 450k assay.") | |
5482 | (license license:artistic2.0))) | |
fbf34949 RW |
5483 | |
5484 | (define-public r-biocfilecache | |
5485 | (package | |
5486 | (name "r-biocfilecache") | |
e65e81d2 | 5487 | (version "1.14.0") |
fbf34949 RW |
5488 | (source |
5489 | (origin | |
5490 | (method url-fetch) | |
5491 | (uri (bioconductor-uri "BiocFileCache" version)) | |
5492 | (sha256 | |
5493 | (base32 | |
e65e81d2 | 5494 | "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1")))) |
fbf34949 RW |
5495 | (properties `((upstream-name . "BiocFileCache"))) |
5496 | (build-system r-build-system) | |
5497 | (propagated-inputs | |
5498 | `(("r-curl" ,r-curl) | |
5499 | ("r-dbi" ,r-dbi) | |
5500 | ("r-dbplyr" ,r-dbplyr) | |
5501 | ("r-dplyr" ,r-dplyr) | |
5502 | ("r-httr" ,r-httr) | |
5503 | ("r-rappdirs" ,r-rappdirs) | |
5504 | ("r-rsqlite" ,r-rsqlite))) | |
173844fc RW |
5505 | (native-inputs |
5506 | `(("r-knitr" ,r-knitr))) | |
fbf34949 RW |
5507 | (home-page "https://bioconductor.org/packages/BiocFileCache/") |
5508 | (synopsis "Manage files across sessions") | |
5509 | (description | |
5510 | "This package creates a persistent on-disk cache of files that the user | |
5511 | can add, update, and retrieve. It is useful for managing resources (such as | |
5512 | custom Txdb objects) that are costly or difficult to create, web resources, | |
5513 | and data files used across sessions.") | |
5514 | (license license:artistic2.0))) | |
8c42f8f6 RW |
5515 | |
5516 | (define-public r-iclusterplus | |
5517 | (package | |
5518 | (name "r-iclusterplus") | |
4bc0675d | 5519 | (version "1.26.0") |
8c42f8f6 RW |
5520 | (source |
5521 | (origin | |
5522 | (method url-fetch) | |
5523 | (uri (bioconductor-uri "iClusterPlus" version)) | |
5524 | (sha256 | |
5525 | (base32 | |
4bc0675d | 5526 | "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q")))) |
8c42f8f6 RW |
5527 | (properties `((upstream-name . "iClusterPlus"))) |
5528 | (build-system r-build-system) | |
5529 | (native-inputs `(("gfortran" ,gfortran))) | |
5530 | (home-page "https://bioconductor.org/packages/iClusterPlus/") | |
5531 | (synopsis "Integrative clustering of multi-type genomic data") | |
5532 | (description | |
5533 | "iClusterPlus is developed for integrative clustering analysis of | |
5534 | multi-type genomic data and is an enhanced version of iCluster proposed and | |
5535 | developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise | |
5536 | from the experiments where biological samples (e.g. tumor samples) are | |
5537 | analyzed by multiple techniques, for instance, @dfn{array comparative genomic | |
5538 | hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so | |
5539 | on. In the iClusterPlus model, binary observations such as somatic mutation | |
5540 | are modeled as Binomial processes; categorical observations such as copy | |
5541 | number states are realizations of Multinomial random variables; counts are | |
5542 | modeled as Poisson random processes; and continuous measures are modeled by | |
5543 | Gaussian distributions.") | |
5544 | (license license:gpl2+))) | |
4d06ef4b RW |
5545 | |
5546 | (define-public r-rbowtie | |
5547 | (package | |
5548 | (name "r-rbowtie") | |
ea86d93e | 5549 | (version "1.30.0") |
4d06ef4b RW |
5550 | (source |
5551 | (origin | |
5552 | (method url-fetch) | |
5553 | (uri (bioconductor-uri "Rbowtie" version)) | |
5554 | (sha256 | |
5555 | (base32 | |
ea86d93e | 5556 | "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507")))) |
4d06ef4b RW |
5557 | (properties `((upstream-name . "Rbowtie"))) |
5558 | (build-system r-build-system) | |
5559 | (inputs | |
5560 | `(("zlib" ,zlib))) | |
568c3929 RW |
5561 | (native-inputs |
5562 | `(("r-knitr" ,r-knitr))) | |
4d06ef4b RW |
5563 | (home-page "https://bioconductor.org/packages/Rbowtie/") |
5564 | (synopsis "R bowtie wrapper") | |
5565 | (description | |
5566 | "This package provides an R wrapper around the popular bowtie short read | |
5567 | aligner and around SpliceMap, a de novo splice junction discovery and | |
5568 | alignment tool.") | |
5569 | (license license:artistic2.0))) | |
14441539 RW |
5570 | |
5571 | (define-public r-sgseq | |
5572 | (package | |
5573 | (name "r-sgseq") | |
ca0271c5 | 5574 | (version "1.24.0") |
14441539 RW |
5575 | (source |
5576 | (origin | |
5577 | (method url-fetch) | |
5578 | (uri (bioconductor-uri "SGSeq" version)) | |
5579 | (sha256 | |
5580 | (base32 | |
ca0271c5 | 5581 | "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx")))) |
14441539 RW |
5582 | (properties `((upstream-name . "SGSeq"))) |
5583 | (build-system r-build-system) | |
5584 | (propagated-inputs | |
5585 | `(("r-annotationdbi" ,r-annotationdbi) | |
5586 | ("r-biocgenerics" ,r-biocgenerics) | |
5587 | ("r-biostrings" ,r-biostrings) | |
5588 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5589 | ("r-genomicalignments" ,r-genomicalignments) | |
5590 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5591 | ("r-genomicranges" ,r-genomicranges) | |
5592 | ("r-igraph" ,r-igraph) | |
5593 | ("r-iranges" ,r-iranges) | |
5594 | ("r-rsamtools" ,r-rsamtools) | |
5595 | ("r-rtracklayer" ,r-rtracklayer) | |
5596 | ("r-runit" ,r-runit) | |
5597 | ("r-s4vectors" ,r-s4vectors) | |
5598 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
201902bc RW |
5599 | (native-inputs |
5600 | `(("r-knitr" ,r-knitr))) | |
14441539 RW |
5601 | (home-page "https://bioconductor.org/packages/SGSeq/") |
5602 | (synopsis "Splice event prediction and quantification from RNA-seq data") | |
5603 | (description | |
5604 | "SGSeq is a package for analyzing splice events from RNA-seq data. Input | |
5605 | data are RNA-seq reads mapped to a reference genome in BAM format. Genes are | |
5606 | represented as a splice graph, which can be obtained from existing annotation | |
5607 | or predicted from the mapped sequence reads. Splice events are identified | |
5608 | from the graph and are quantified locally using structurally compatible reads | |
5609 | at the start or end of each splice variant. The software includes functions | |
5610 | for splice event prediction, quantification, visualization and | |
5611 | interpretation.") | |
5612 | (license license:artistic2.0))) | |
58656064 RW |
5613 | |
5614 | (define-public r-rhisat2 | |
5615 | (package | |
5616 | (name "r-rhisat2") | |
c36d888f | 5617 | (version "1.6.0") |
58656064 RW |
5618 | (source |
5619 | (origin | |
5620 | (method url-fetch) | |
5621 | (uri (bioconductor-uri "Rhisat2" version)) | |
5622 | (sha256 | |
5623 | (base32 | |
c36d888f | 5624 | "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb")))) |
58656064 RW |
5625 | (properties `((upstream-name . "Rhisat2"))) |
5626 | (build-system r-build-system) | |
3dd2450e RW |
5627 | (arguments |
5628 | `(#:phases | |
5629 | (modify-phases %standard-phases | |
5630 | (add-after 'unpack 'make-reproducible | |
5631 | (lambda _ | |
5632 | (substitute* "src/Makefile" | |
5633 | (("`hostname`") "guix") | |
5634 | (("`date`") "0") | |
5635 | ;; Avoid shelling out to "which". | |
5636 | (("^CC =.*") (which "gcc")) | |
5637 | (("^CPP =.*") (which "g++"))) | |
5638 | #t))))) | |
58656064 RW |
5639 | (propagated-inputs |
5640 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
5641 | ("r-genomicranges" ,r-genomicranges) | |
5642 | ("r-sgseq" ,r-sgseq))) | |
2aff2724 RW |
5643 | (native-inputs |
5644 | `(("r-knitr" ,r-knitr))) | |
58656064 RW |
5645 | (home-page "https://github.com/fmicompbio/Rhisat2") |
5646 | (synopsis "R Wrapper for HISAT2 sequence aligner") | |
5647 | (description | |
5648 | "This package provides an R interface to the HISAT2 spliced short-read | |
5649 | aligner by Kim et al. (2015). The package contains wrapper functions to | |
5650 | create a genome index and to perform the read alignment to the generated | |
5651 | index.") | |
5652 | (license license:gpl3))) | |
5e0241db RW |
5653 | |
5654 | (define-public r-quasr | |
5655 | (package | |
5656 | (name "r-quasr") | |
1b4c2719 | 5657 | (version "1.30.0") |
5e0241db RW |
5658 | (source |
5659 | (origin | |
5660 | (method url-fetch) | |
5661 | (uri (bioconductor-uri "QuasR" version)) | |
5662 | (sha256 | |
5663 | (base32 | |
1b4c2719 | 5664 | "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8")))) |
5e0241db RW |
5665 | (properties `((upstream-name . "QuasR"))) |
5666 | (build-system r-build-system) | |
5667 | (inputs | |
5668 | `(("zlib" ,zlib))) | |
5669 | (propagated-inputs | |
5670 | `(("r-annotationdbi" ,r-annotationdbi) | |
5671 | ("r-biobase" ,r-biobase) | |
5672 | ("r-biocgenerics" ,r-biocgenerics) | |
5673 | ("r-biocmanager" ,r-biocmanager) | |
5674 | ("r-biocparallel" ,r-biocparallel) | |
5675 | ("r-biostrings" ,r-biostrings) | |
5676 | ("r-bsgenome" ,r-bsgenome) | |
5677 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5678 | ("r-genomicalignments" ,r-genomicalignments) | |
5679 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5680 | ("r-genomicfiles" ,r-genomicfiles) | |
5681 | ("r-genomicranges" ,r-genomicranges) | |
5682 | ("r-iranges" ,r-iranges) | |
5683 | ("r-rbowtie" ,r-rbowtie) | |
5684 | ("r-rhisat2" ,r-rhisat2) | |
5685 | ("r-rhtslib" ,r-rhtslib) | |
5686 | ("r-rsamtools" ,r-rsamtools) | |
5687 | ("r-rtracklayer" ,r-rtracklayer) | |
5688 | ("r-s4vectors" ,r-s4vectors) | |
5689 | ("r-shortread" ,r-shortread))) | |
a84abf43 RW |
5690 | (native-inputs |
5691 | `(("r-knitr" ,r-knitr))) | |
5e0241db RW |
5692 | (home-page "https://bioconductor.org/packages/QuasR/") |
5693 | (synopsis "Quantify and annotate short reads in R") | |
5694 | (description | |
5695 | "This package provides a framework for the quantification and analysis of | |
5696 | short genomic reads. It covers a complete workflow starting from raw sequence | |
5697 | reads, over creation of alignments and quality control plots, to the | |
5698 | quantification of genomic regions of interest.") | |
5699 | (license license:gpl2))) | |
496b024f RW |
5700 | |
5701 | (define-public r-rqc | |
5702 | (package | |
5703 | (name "r-rqc") | |
d8a7bf76 | 5704 | (version "1.24.0") |
496b024f RW |
5705 | (source |
5706 | (origin | |
5707 | (method url-fetch) | |
5708 | (uri (bioconductor-uri "Rqc" version)) | |
5709 | (sha256 | |
5710 | (base32 | |
d8a7bf76 | 5711 | "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9")))) |
496b024f RW |
5712 | (properties `((upstream-name . "Rqc"))) |
5713 | (build-system r-build-system) | |
5714 | (propagated-inputs | |
5715 | `(("r-biocgenerics" ,r-biocgenerics) | |
5716 | ("r-biocparallel" ,r-biocparallel) | |
5717 | ("r-biocstyle" ,r-biocstyle) | |
5718 | ("r-biostrings" ,r-biostrings) | |
5719 | ("r-biovizbase" ,r-biovizbase) | |
5720 | ("r-genomicalignments" ,r-genomicalignments) | |
5721 | ("r-genomicfiles" ,r-genomicfiles) | |
5722 | ("r-ggplot2" ,r-ggplot2) | |
5723 | ("r-iranges" ,r-iranges) | |
5724 | ("r-knitr" ,r-knitr) | |
5725 | ("r-markdown" ,r-markdown) | |
5726 | ("r-plyr" ,r-plyr) | |
5727 | ("r-rcpp" ,r-rcpp) | |
5728 | ("r-reshape2" ,r-reshape2) | |
5729 | ("r-rsamtools" ,r-rsamtools) | |
5730 | ("r-s4vectors" ,r-s4vectors) | |
5731 | ("r-shiny" ,r-shiny) | |
5732 | ("r-shortread" ,r-shortread))) | |
1c5360ac RW |
5733 | (native-inputs |
5734 | `(("r-knitr" ,r-knitr))) | |
496b024f RW |
5735 | (home-page "https://github.com/labbcb/Rqc") |
5736 | (synopsis "Quality control tool for high-throughput sequencing data") | |
5737 | (description | |
5738 | "Rqc is an optimized tool designed for quality control and assessment of | |
5739 | high-throughput sequencing data. It performs parallel processing of entire | |
5740 | files and produces a report which contains a set of high-resolution | |
5741 | graphics.") | |
5742 | (license license:gpl2+))) | |
81e3de01 RW |
5743 | |
5744 | (define-public r-birewire | |
5745 | (package | |
5746 | (name "r-birewire") | |
979b1edc | 5747 | (version "3.22.0") |
81e3de01 RW |
5748 | (source |
5749 | (origin | |
5750 | (method url-fetch) | |
5751 | (uri (bioconductor-uri "BiRewire" version)) | |
5752 | (sha256 | |
5753 | (base32 | |
979b1edc | 5754 | "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw")))) |
81e3de01 RW |
5755 | (properties `((upstream-name . "BiRewire"))) |
5756 | (build-system r-build-system) | |
5757 | (propagated-inputs | |
5758 | `(("r-igraph" ,r-igraph) | |
5759 | ("r-matrix" ,r-matrix) | |
5760 | ("r-slam" ,r-slam) | |
5761 | ("r-tsne" ,r-tsne))) | |
5762 | (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") | |
5763 | (synopsis "Tools for randomization of bipartite graphs") | |
5764 | (description | |
5765 | "This package provides functions for bipartite network rewiring through N | |
5766 | consecutive switching steps and for the computation of the minimal number of | |
5767 | switching steps to be performed in order to maximise the dissimilarity with | |
5768 | respect to the original network. It includes functions for the analysis of | |
5769 | the introduced randomness across the switching steps and several other | |
5770 | routines to analyse the resulting networks and their natural projections.") | |
5771 | (license license:gpl3))) | |
1a24f855 RW |
5772 | |
5773 | (define-public r-birta | |
5774 | (package | |
5775 | (name "r-birta") | |
cb941ca0 | 5776 | (version "1.31.0") |
1a24f855 RW |
5777 | (source |
5778 | (origin | |
5779 | (method url-fetch) | |
5780 | (uri (bioconductor-uri "birta" version)) | |
5781 | (sha256 | |
5782 | (base32 | |
cb941ca0 | 5783 | "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) |
1a24f855 RW |
5784 | (build-system r-build-system) |
5785 | (propagated-inputs | |
5786 | `(("r-biobase" ,r-biobase) | |
5787 | ("r-limma" ,r-limma) | |
5788 | ("r-mass" ,r-mass))) | |
5789 | (home-page "https://bioconductor.org/packages/birta") | |
5790 | (synopsis "Bayesian inference of regulation of transcriptional activity") | |
5791 | (description | |
5792 | "Expression levels of mRNA molecules are regulated by different | |
5793 | processes, comprising inhibition or activation by transcription factors and | |
5794 | post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian | |
5795 | Inference of Regulation of Transcriptional Activity) uses the regulatory | |
5796 | networks of transcription factors and miRNAs together with mRNA and miRNA | |
5797 | expression data to predict switches in regulatory activity between two | |
5798 | conditions. A Bayesian network is used to model the regulatory structure and | |
5799 | Markov-Chain-Monte-Carlo is applied to sample the activity states.") | |
5800 | (license license:gpl2+))) | |
a9fac3f4 | 5801 | |
b4a22cca RW |
5802 | (define-public r-multidataset |
5803 | (package | |
5804 | (name "r-multidataset") | |
e78e04d2 | 5805 | (version "1.18.0") |
b4a22cca RW |
5806 | (source |
5807 | (origin | |
5808 | (method url-fetch) | |
5809 | (uri (bioconductor-uri "MultiDataSet" version)) | |
5810 | (sha256 | |
5811 | (base32 | |
e78e04d2 | 5812 | "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w")))) |
b4a22cca RW |
5813 | (properties `((upstream-name . "MultiDataSet"))) |
5814 | (build-system r-build-system) | |
5815 | (propagated-inputs | |
5816 | `(("r-biobase" ,r-biobase) | |
5817 | ("r-biocgenerics" ,r-biocgenerics) | |
5818 | ("r-genomicranges" ,r-genomicranges) | |
5819 | ("r-ggplot2" ,r-ggplot2) | |
5820 | ("r-ggrepel" ,r-ggrepel) | |
5821 | ("r-iranges" ,r-iranges) | |
5822 | ("r-limma" ,r-limma) | |
5823 | ("r-qqman" ,r-qqman) | |
5824 | ("r-s4vectors" ,r-s4vectors) | |
5825 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
905bbb13 RW |
5826 | (native-inputs |
5827 | `(("r-knitr" ,r-knitr))) | |
b4a22cca RW |
5828 | (home-page "https://bioconductor.org/packages/MultiDataSet/") |
5829 | (synopsis "Implementation of MultiDataSet and ResultSet") | |
5830 | (description | |
5831 | "This package provides an implementation of the BRGE's (Bioinformatic | |
5832 | Research Group in Epidemiology from Center for Research in Environmental | |
5833 | Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for | |
5834 | integrating multi omics data sets and ResultSet is a container for omics | |
5835 | results. This package contains base classes for MEAL and rexposome | |
5836 | packages.") | |
5837 | (license license:expat))) | |
5838 | ||
a9fac3f4 RW |
5839 | (define-public r-ropls |
5840 | (package | |
5841 | (name "r-ropls") | |
59daf6ed | 5842 | (version "1.22.0") |
a9fac3f4 RW |
5843 | (source |
5844 | (origin | |
5845 | (method url-fetch) | |
5846 | (uri (bioconductor-uri "ropls" version)) | |
5847 | (sha256 | |
5848 | (base32 | |
59daf6ed | 5849 | "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5")))) |
a9fac3f4 | 5850 | (build-system r-build-system) |
643aaf7e RW |
5851 | (propagated-inputs |
5852 | `(("r-biobase" ,r-biobase) | |
5853 | ("r-multidataset" ,r-multidataset))) | |
a9fac3f4 RW |
5854 | (native-inputs |
5855 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
5856 | (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") | |
5857 | (synopsis "Multivariate analysis and feature selection of omics data") | |
5858 | (description | |
5859 | "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) | |
5860 | and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, | |
5861 | regression, classification, and feature selection of omics data where the | |
5862 | number of variables exceeds the number of samples and with multicollinearity | |
5863 | among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to | |
5864 | separately model the variation correlated (predictive) to the factor of | |
5865 | interest and the uncorrelated (orthogonal) variation. While performing | |
5866 | similarly to PLS, OPLS facilitates interpretation. | |
5867 | ||
5868 | This package provides imlementations of PCA, PLS, and OPLS for multivariate | |
5869 | analysis and feature selection of omics data. In addition to scores, loadings | |
5870 | and weights plots, the package provides metrics and graphics to determine the | |
5871 | optimal number of components (e.g. with the R2 and Q2 coefficients), check the | |
5872 | validity of the model by permutation testing, detect outliers, and perform | |
5873 | feature selection (e.g. with Variable Importance in Projection or regression | |
5874 | coefficients).") | |
5875 | (license license:cecill))) | |
075a9094 RW |
5876 | |
5877 | (define-public r-biosigner | |
5878 | (package | |
5879 | (name "r-biosigner") | |
26e41706 | 5880 | (version "1.18.0") |
075a9094 RW |
5881 | (source |
5882 | (origin | |
5883 | (method url-fetch) | |
5884 | (uri (bioconductor-uri "biosigner" version)) | |
5885 | (sha256 | |
5886 | (base32 | |
26e41706 | 5887 | "1rqfmn9lpaajij9p302dfwv57pm4hw7xn2p7lx7hvpb3psa719xm")))) |
075a9094 RW |
5888 | (build-system r-build-system) |
5889 | (propagated-inputs | |
5890 | `(("r-biobase" ,r-biobase) | |
5891 | ("r-e1071" ,r-e1071) | |
7d29dc9c | 5892 | ("r-multidataset" ,r-multidataset) |
075a9094 RW |
5893 | ("r-randomforest" ,r-randomforest) |
5894 | ("r-ropls" ,r-ropls))) | |
5895 | (native-inputs | |
f7100eda | 5896 | `(("r-knitr" ,r-knitr))) |
075a9094 RW |
5897 | (home-page "https://bioconductor.org/packages/biosigner/") |
5898 | (synopsis "Signature discovery from omics data") | |
5899 | (description | |
5900 | "Feature selection is critical in omics data analysis to extract | |
5901 | restricted and meaningful molecular signatures from complex and high-dimension | |
5902 | data, and to build robust classifiers. This package implements a method to | |
5903 | assess the relevance of the variables for the prediction performances of the | |
5904 | classifier. The approach can be run in parallel with the PLS-DA, Random | |
5905 | Forest, and SVM binary classifiers. The signatures and the corresponding | |
5906 | 'restricted' models are returned, enabling future predictions on new | |
5907 | datasets.") | |
5908 | (license license:cecill))) | |
ae6fa185 RW |
5909 | |
5910 | (define-public r-annotatr | |
5911 | (package | |
5912 | (name "r-annotatr") | |
458aa446 | 5913 | (version "1.16.0") |
ae6fa185 RW |
5914 | (source |
5915 | (origin | |
5916 | (method url-fetch) | |
5917 | (uri (bioconductor-uri "annotatr" version)) | |
5918 | (sha256 | |
5919 | (base32 | |
458aa446 | 5920 | "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9")))) |
ae6fa185 RW |
5921 | (build-system r-build-system) |
5922 | (propagated-inputs | |
5923 | `(("r-annotationdbi" ,r-annotationdbi) | |
5924 | ("r-annotationhub" ,r-annotationhub) | |
5925 | ("r-dplyr" ,r-dplyr) | |
5926 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5927 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5928 | ("r-genomicranges" ,r-genomicranges) | |
5929 | ("r-ggplot2" ,r-ggplot2) | |
5930 | ("r-iranges" ,r-iranges) | |
5931 | ("r-readr" ,r-readr) | |
5932 | ("r-regioner" ,r-regioner) | |
5933 | ("r-reshape2" ,r-reshape2) | |
5934 | ("r-rtracklayer" ,r-rtracklayer) | |
5935 | ("r-s4vectors" ,r-s4vectors))) | |
5ca991bf RW |
5936 | (native-inputs |
5937 | `(("r-knitr" ,r-knitr))) | |
ae6fa185 RW |
5938 | (home-page "https://bioconductor.org/packages/annotatr/") |
5939 | (synopsis "Annotation of genomic regions to genomic annotations") | |
5940 | (description | |
5941 | "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, | |
5942 | differentially methylated CpGs or regions, SNPs, etc.) it is often of interest | |
5943 | to investigate the intersecting genomic annotations. Such annotations include | |
5944 | those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), | |
5945 | CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as | |
5946 | enhancers. The annotatr package provides an easy way to summarize and | |
5947 | visualize the intersection of genomic sites/regions with genomic | |
5948 | annotations.") | |
5949 | (license license:gpl3))) | |
2cb738a6 RW |
5950 | |
5951 | (define-public r-rsubread | |
5952 | (package | |
5953 | (name "r-rsubread") | |
d764f1e7 | 5954 | (version "2.4.2") |
2cb738a6 RW |
5955 | (source |
5956 | (origin | |
5957 | (method url-fetch) | |
5958 | (uri (bioconductor-uri "Rsubread" version)) | |
5959 | (sha256 | |
5960 | (base32 | |
d764f1e7 | 5961 | "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra")))) |
2cb738a6 RW |
5962 | (properties `((upstream-name . "Rsubread"))) |
5963 | (build-system r-build-system) | |
5964 | (inputs `(("zlib" ,zlib))) | |
5d63f69b RW |
5965 | (propagated-inputs |
5966 | `(("r-matrix" ,r-matrix))) | |
2cb738a6 RW |
5967 | (home-page "https://bioconductor.org/packages/Rsubread/") |
5968 | (synopsis "Subread sequence alignment and counting for R") | |
5969 | (description | |
5970 | "This package provides tools for alignment, quantification and analysis | |
5971 | of second and third generation sequencing data. It includes functionality for | |
5972 | read mapping, read counting, SNP calling, structural variant detection and | |
5973 | gene fusion discovery. It can be applied to all major sequencing techologies | |
5974 | and to both short and long sequence reads.") | |
5975 | (license license:gpl3))) | |
a6fedf1f | 5976 | |
a0422d18 | 5977 | (define-public r-flowutils |
5978 | (package | |
5979 | (name "r-flowutils") | |
d361222d | 5980 | (version "1.54.0") |
a0422d18 | 5981 | (source |
5982 | (origin | |
5983 | (method url-fetch) | |
5984 | (uri (bioconductor-uri "flowUtils" version)) | |
5985 | (sha256 | |
5986 | (base32 | |
d361222d | 5987 | "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09")))) |
a0422d18 | 5988 | (properties `((upstream-name . "flowUtils"))) |
5989 | (build-system r-build-system) | |
5990 | (propagated-inputs | |
5991 | `(("r-biobase" ,r-biobase) | |
5992 | ("r-corpcor" ,r-corpcor) | |
5993 | ("r-flowcore" ,r-flowcore) | |
5994 | ("r-graph" ,r-graph) | |
5995 | ("r-runit" ,r-runit) | |
5996 | ("r-xml" ,r-xml))) | |
5997 | (home-page "https://github.com/jspidlen/flowUtils") | |
5998 | (synopsis "Utilities for flow cytometry") | |
5999 | (description | |
6000 | "This package provides utilities for flow cytometry data.") | |
6001 | (license license:artistic2.0))) | |
6002 | ||
ed6f49fc | 6003 | (define-public r-consensusclusterplus |
6004 | (package | |
6005 | (name "r-consensusclusterplus") | |
a49024e6 | 6006 | (version "1.54.0") |
ed6f49fc | 6007 | (source |
6008 | (origin | |
6009 | (method url-fetch) | |
6010 | (uri (bioconductor-uri "ConsensusClusterPlus" version)) | |
6011 | (sha256 | |
6012 | (base32 | |
a49024e6 | 6013 | "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp")))) |
ed6f49fc | 6014 | (properties |
6015 | `((upstream-name . "ConsensusClusterPlus"))) | |
6016 | (build-system r-build-system) | |
6017 | (propagated-inputs | |
6018 | `(("r-all" ,r-all) | |
6019 | ("r-biobase" ,r-biobase) | |
6020 | ("r-cluster" ,r-cluster))) | |
6021 | (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") | |
6022 | (synopsis "Clustering algorithm") | |
6023 | (description | |
6024 | "This package provides an implementation of an algorithm for determining | |
6025 | cluster count and membership by stability evidence in unsupervised analysis.") | |
6026 | (license license:gpl2))) | |
6027 | ||
b4aee31d RW |
6028 | (define-public r-cytolib |
6029 | (package | |
6030 | (name "r-cytolib") | |
c6ccd4fc | 6031 | (version "2.2.0") |
b4aee31d RW |
6032 | (source |
6033 | (origin | |
6034 | (method url-fetch) | |
6035 | (uri (bioconductor-uri "cytolib" version)) | |
6036 | (sha256 | |
6037 | (base32 | |
c6ccd4fc | 6038 | "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw")))) |
b4aee31d RW |
6039 | (properties `((upstream-name . "cytolib"))) |
6040 | (build-system r-build-system) | |
b58c4e76 | 6041 | (arguments |
6042 | `(#:phases | |
6043 | (modify-phases %standard-phases | |
6044 | (add-after 'unpack 'fix-linking | |
6045 | (lambda _ | |
6046 | (substitute* "src/Makevars.in" | |
6047 | ;; This is to avoid having a plain directory on the list of | |
6048 | ;; libraries to link. | |
6049 | (("\\(RHDF5_LIBS\\)" match) | |
6050 | (string-append match "/libhdf5.a"))) | |
6051 | #t))))) | |
3c73d7c5 RW |
6052 | (inputs |
6053 | `(("zlib" ,zlib))) | |
6054 | (native-inputs | |
c6ccd4fc | 6055 | `(("r-knitr" ,r-knitr) |
6056 | ("pkg-config" ,pkg-config))) | |
3c73d7c5 RW |
6057 | (propagated-inputs |
6058 | `(("r-bh" ,r-bh) | |
6059 | ("r-rcpp" ,r-rcpp) | |
6060 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
6061 | ("r-rcppparallel" ,r-rcppparallel) | |
6062 | ("r-rhdf5lib" ,r-rhdf5lib) | |
6063 | ("r-rprotobuflib" ,r-rprotobuflib))) | |
b4aee31d RW |
6064 | (home-page "https://bioconductor.org/packages/cytolib/") |
6065 | (synopsis "C++ infrastructure for working with gated cytometry") | |
6066 | (description | |
6067 | "This package provides the core data structure and API to represent and | |
6068 | interact with gated cytometry data.") | |
6069 | (license license:artistic2.0))) | |
6070 | ||
a6fedf1f | 6071 | (define-public r-flowcore |
6072 | (package | |
6073 | (name "r-flowcore") | |
3f0e93b4 | 6074 | (version "2.2.0") |
a6fedf1f | 6075 | (source |
6076 | (origin | |
6077 | (method url-fetch) | |
6078 | (uri (bioconductor-uri "flowCore" version)) | |
6079 | (sha256 | |
6080 | (base32 | |
3f0e93b4 | 6081 | "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8")))) |
a6fedf1f | 6082 | (properties `((upstream-name . "flowCore"))) |
6083 | (build-system r-build-system) | |
6084 | (propagated-inputs | |
6085 | `(("r-bh" ,r-bh) | |
6086 | ("r-biobase" ,r-biobase) | |
6087 | ("r-biocgenerics" ,r-biocgenerics) | |
b2a2f321 | 6088 | ("r-cytolib" ,r-cytolib) |
a6fedf1f | 6089 | ("r-matrixstats" ,r-matrixstats) |
faff2de0 RW |
6090 | ("r-rcpp" ,r-rcpp) |
6091 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
3f0e93b4 | 6092 | ("r-rprotobuflib" ,r-rprotobuflib) |
6093 | ("r-s4vectors" ,r-s4vectors))) | |
faff2de0 RW |
6094 | (native-inputs |
6095 | `(("r-knitr" ,r-knitr))) | |
a6fedf1f | 6096 | (home-page "https://bioconductor.org/packages/flowCore") |
6097 | (synopsis "Basic structures for flow cytometry data") | |
6098 | (description | |
6099 | "This package provides S4 data structures and basic functions to deal | |
6100 | with flow cytometry data.") | |
6101 | (license license:artistic2.0))) | |
e0cb053e | 6102 | |
6103 | (define-public r-flowmeans | |
6104 | (package | |
6105 | (name "r-flowmeans") | |
2cd78131 | 6106 | (version "1.50.0") |
e0cb053e | 6107 | (source |
6108 | (origin | |
6109 | (method url-fetch) | |
6110 | (uri (bioconductor-uri "flowMeans" version)) | |
6111 | (sha256 | |
6112 | (base32 | |
2cd78131 | 6113 | "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734")))) |
e0cb053e | 6114 | (properties `((upstream-name . "flowMeans"))) |
6115 | (build-system r-build-system) | |
6116 | (propagated-inputs | |
6117 | `(("r-biobase" ,r-biobase) | |
6118 | ("r-feature" ,r-feature) | |
6119 | ("r-flowcore" ,r-flowcore) | |
6120 | ("r-rrcov" ,r-rrcov))) | |
6121 | (home-page "https://bioconductor.org/packages/flowMeans") | |
6122 | (synopsis "Non-parametric flow cytometry data gating") | |
6123 | (description | |
6124 | "This package provides tools to identify cell populations in Flow | |
6125 | Cytometry data using non-parametric clustering and segmented-regression-based | |
6126 | change point detection.") | |
6127 | (license license:artistic2.0))) | |
1502751b | 6128 | |
15ac0c19 RW |
6129 | (define-public r-ncdfflow |
6130 | (package | |
6131 | (name "r-ncdfflow") | |
eac1eaaa | 6132 | (version "2.36.0") |
15ac0c19 RW |
6133 | (source |
6134 | (origin | |
6135 | (method url-fetch) | |
6136 | (uri (bioconductor-uri "ncdfFlow" version)) | |
6137 | (sha256 | |
6138 | (base32 | |
eac1eaaa | 6139 | "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac")))) |
15ac0c19 RW |
6140 | (properties `((upstream-name . "ncdfFlow"))) |
6141 | (build-system r-build-system) | |
0022e9f4 | 6142 | (arguments |
6143 | `(#:phases | |
6144 | (modify-phases %standard-phases | |
6145 | (add-after 'unpack 'fix-linking | |
6146 | (lambda _ | |
6147 | (substitute* "src/Makevars" | |
6148 | ;; This is to avoid having a plain directory on the list of | |
6149 | ;; libraries to link. | |
6150 | (("\\(RHDF5_LIBS\\)" match) | |
6151 | (string-append match "/libhdf5.a"))) | |
6152 | #t))))) | |
15ac0c19 RW |
6153 | (inputs |
6154 | `(("zlib" ,zlib))) | |
6155 | (propagated-inputs | |
6156 | `(("r-bh" ,r-bh) | |
6157 | ("r-biobase" ,r-biobase) | |
6158 | ("r-biocgenerics" ,r-biocgenerics) | |
6159 | ("r-flowcore" ,r-flowcore) | |
6160 | ("r-rcpp" ,r-rcpp) | |
6161 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
6162 | ("r-rhdf5lib" ,r-rhdf5lib) | |
6163 | ("r-zlibbioc" ,r-zlibbioc))) | |
631b12ca RW |
6164 | (native-inputs |
6165 | `(("r-knitr" ,r-knitr))) | |
15ac0c19 RW |
6166 | (home-page "https://bioconductor.org/packages/ncdfFlow/") |
6167 | (synopsis "HDF5 based storage for flow cytometry data") | |
6168 | (description | |
6169 | "This package provides HDF5 storage based methods and functions for | |
6170 | manipulation of flow cytometry data.") | |
6171 | (license license:artistic2.0))) | |
6172 | ||
f5f44031 RW |
6173 | (define-public r-ggcyto |
6174 | (package | |
6175 | (name "r-ggcyto") | |
3407dfa6 | 6176 | (version "1.16.0") |
f5f44031 RW |
6177 | (source |
6178 | (origin | |
6179 | (method url-fetch) | |
6180 | (uri (bioconductor-uri "ggcyto" version)) | |
6181 | (sha256 | |
6182 | (base32 | |
3407dfa6 | 6183 | "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0")))) |
f5f44031 RW |
6184 | (properties `((upstream-name . "ggcyto"))) |
6185 | (build-system r-build-system) | |
6186 | (propagated-inputs | |
6187 | `(("r-data-table" ,r-data-table) | |
6188 | ("r-flowcore" ,r-flowcore) | |
6189 | ("r-flowworkspace" ,r-flowworkspace) | |
6190 | ("r-ggplot2" ,r-ggplot2) | |
6191 | ("r-gridextra" ,r-gridextra) | |
3407dfa6 | 6192 | ("r-hexbin" ,r-hexbin) |
f5f44031 RW |
6193 | ("r-ncdfflow" ,r-ncdfflow) |
6194 | ("r-plyr" ,r-plyr) | |
6195 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6196 | ("r-rlang" ,r-rlang) | |
6197 | ("r-scales" ,r-scales))) | |
0754fefb RW |
6198 | (native-inputs |
6199 | `(("r-knitr" ,r-knitr))) | |
f5f44031 RW |
6200 | (home-page "https://github.com/RGLab/ggcyto/issues") |
6201 | (synopsis "Visualize Cytometry data with ggplot") | |
6202 | (description | |
6203 | "With the dedicated fortify method implemented for @code{flowSet}, | |
6204 | @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow | |
6205 | cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper | |
6206 | and some custom layers also make it easy to add gates and population | |
6207 | statistics to the plot.") | |
6208 | (license license:artistic2.0))) | |
6209 | ||
0dd4b7d7 RW |
6210 | (define-public r-flowviz |
6211 | (package | |
6212 | (name "r-flowviz") | |
d5a53ab7 | 6213 | (version "1.54.0") |
0dd4b7d7 RW |
6214 | (source |
6215 | (origin | |
6216 | (method url-fetch) | |
6217 | (uri (bioconductor-uri "flowViz" version)) | |
6218 | (sha256 | |
6219 | (base32 | |
d5a53ab7 | 6220 | "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k")))) |
0dd4b7d7 RW |
6221 | (properties `((upstream-name . "flowViz"))) |
6222 | (build-system r-build-system) | |
6223 | (propagated-inputs | |
6224 | `(("r-biobase" ,r-biobase) | |
6225 | ("r-flowcore" ,r-flowcore) | |
6226 | ("r-hexbin" ,r-hexbin) | |
6227 | ("r-idpmisc" ,r-idpmisc) | |
6228 | ("r-kernsmooth" ,r-kernsmooth) | |
6229 | ("r-lattice" ,r-lattice) | |
6230 | ("r-latticeextra" ,r-latticeextra) | |
6231 | ("r-mass" ,r-mass) | |
6232 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
062789b8 RW |
6233 | (native-inputs |
6234 | `(("r-knitr" ,r-knitr))) | |
0dd4b7d7 RW |
6235 | (home-page "https://bioconductor.org/packages/flowViz/") |
6236 | (synopsis "Visualization for flow cytometry") | |
6237 | (description | |
6238 | "This package provides visualization tools for flow cytometry data.") | |
6239 | (license license:artistic2.0))) | |
6240 | ||
c8ab9eb1 RW |
6241 | (define-public r-flowclust |
6242 | (package | |
6243 | (name "r-flowclust") | |
33c5b6d7 | 6244 | (version "3.28.0") |
c8ab9eb1 RW |
6245 | (source |
6246 | (origin | |
6247 | (method url-fetch) | |
6248 | (uri (bioconductor-uri "flowClust" version)) | |
6249 | (sha256 | |
6250 | (base32 | |
33c5b6d7 | 6251 | "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq")))) |
c8ab9eb1 RW |
6252 | (properties `((upstream-name . "flowClust"))) |
6253 | (build-system r-build-system) | |
6254 | (arguments | |
6255 | `(#:configure-flags | |
6256 | (list "--configure-args=--enable-bundled-gsl=no"))) | |
6257 | (propagated-inputs | |
6258 | `(("r-biobase" ,r-biobase) | |
6259 | ("r-biocgenerics" ,r-biocgenerics) | |
6260 | ("r-clue" ,r-clue) | |
6261 | ("r-corpcor" ,r-corpcor) | |
6262 | ("r-ellipse" ,r-ellipse) | |
6263 | ("r-flowcore" ,r-flowcore) | |
6264 | ("r-flowviz" ,r-flowviz) | |
6265 | ("r-graph" ,r-graph) | |
6266 | ("r-mnormt" ,r-mnormt))) | |
6267 | (inputs | |
6268 | `(("gsl" ,gsl))) | |
6269 | (native-inputs | |
b347d6c3 RW |
6270 | `(("pkg-config" ,pkg-config) |
6271 | ("r-knitr" ,r-knitr))) | |
c8ab9eb1 RW |
6272 | (home-page "https://bioconductor.org/packages/flowClust") |
6273 | (synopsis "Clustering for flow cytometry") | |
6274 | (description | |
6275 | "This package provides robust model-based clustering using a t-mixture | |
6276 | model with Box-Cox transformation.") | |
6277 | (license license:artistic2.0))) | |
6278 | ||
f1964519 RW |
6279 | ;; TODO: this package bundles an old version of protobuf. It's not easy to |
6280 | ;; make it use our protobuf package instead. | |
6281 | (define-public r-rprotobuflib | |
6282 | (package | |
6283 | (name "r-rprotobuflib") | |
5bab0b7e | 6284 | (version "2.2.0") |
f1964519 RW |
6285 | (source |
6286 | (origin | |
6287 | (method url-fetch) | |
6288 | (uri (bioconductor-uri "RProtoBufLib" version)) | |
6289 | (sha256 | |
6290 | (base32 | |
5bab0b7e | 6291 | "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz")))) |
f1964519 RW |
6292 | (properties `((upstream-name . "RProtoBufLib"))) |
6293 | (build-system r-build-system) | |
6294 | (arguments | |
6295 | `(#:phases | |
6296 | (modify-phases %standard-phases | |
6297 | (add-after 'unpack 'unpack-bundled-sources | |
6298 | (lambda _ | |
6299 | (with-directory-excursion "src" | |
bafade83 | 6300 | (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) |
f1964519 | 6301 | #t))))) |
bafade83 RW |
6302 | (native-inputs |
6303 | `(("r-knitr" ,r-knitr))) | |
f1964519 RW |
6304 | (home-page "https://bioconductor.org/packages/RProtoBufLib/") |
6305 | (synopsis "C++ headers and static libraries of Protocol buffers") | |
6306 | (description | |
6307 | "This package provides the headers and static library of Protocol buffers | |
6308 | for other R packages to compile and link against.") | |
6309 | (license license:bsd-3))) | |
6310 | ||
82c11117 RW |
6311 | (define-public r-flowworkspace |
6312 | (package | |
6313 | (name "r-flowworkspace") | |
1b347814 | 6314 | (version "4.2.0") |
82c11117 RW |
6315 | (source |
6316 | (origin | |
6317 | (method url-fetch) | |
6318 | (uri (bioconductor-uri "flowWorkspace" version)) | |
6319 | (sha256 | |
6320 | (base32 | |
1b347814 | 6321 | "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag")))) |
82c11117 RW |
6322 | (properties `((upstream-name . "flowWorkspace"))) |
6323 | (build-system r-build-system) | |
ece564f0 | 6324 | (arguments |
6325 | `(#:phases | |
6326 | (modify-phases %standard-phases | |
6327 | (add-after 'unpack 'fix-linking | |
6328 | (lambda _ | |
6329 | (substitute* "src/Makevars" | |
6330 | ;; This is to avoid having a plain directory on the list of | |
6331 | ;; libraries to link. | |
6332 | (("\\{h5lib\\}" match) | |
6333 | (string-append match "/libhdf5.a"))) | |
6334 | #t))))) | |
1b347814 | 6335 | (inputs |
6336 | `(("zlib" ,zlib))) | |
82c11117 | 6337 | (propagated-inputs |
1b347814 | 6338 | `(("r-aws-s3" ,r-aws-s3) |
6339 | ("r-aws-signature" ,r-aws-signature) | |
6340 | ("r-bh" ,r-bh) | |
82c11117 RW |
6341 | ("r-biobase" ,r-biobase) |
6342 | ("r-biocgenerics" ,r-biocgenerics) | |
6343 | ("r-cytolib" ,r-cytolib) | |
6344 | ("r-data-table" ,r-data-table) | |
6345 | ("r-digest" ,r-digest) | |
6346 | ("r-dplyr" ,r-dplyr) | |
6347 | ("r-flowcore" ,r-flowcore) | |
a9af09df | 6348 | ("r-ggplot2" ,r-ggplot2) |
82c11117 | 6349 | ("r-graph" ,r-graph) |
82c11117 RW |
6350 | ("r-lattice" ,r-lattice) |
6351 | ("r-latticeextra" ,r-latticeextra) | |
6352 | ("r-matrixstats" ,r-matrixstats) | |
6353 | ("r-ncdfflow" ,r-ncdfflow) | |
6354 | ("r-rbgl" ,r-rbgl) | |
82c11117 | 6355 | ("r-rcpp" ,r-rcpp) |
a9af09df | 6356 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
82c11117 RW |
6357 | ("r-rcppparallel" ,r-rcppparallel) |
6358 | ("r-rgraphviz" ,r-rgraphviz) | |
a9af09df | 6359 | ("r-rhdf5lib" ,r-rhdf5lib) |
82c11117 RW |
6360 | ("r-rprotobuflib" ,r-rprotobuflib) |
6361 | ("r-scales" ,r-scales) | |
a9af09df RW |
6362 | ("r-xml" ,r-xml))) |
6363 | (native-inputs | |
6364 | `(("r-knitr" ,r-knitr))) | |
82c11117 RW |
6365 | (home-page "https://bioconductor.org/packages/flowWorkspace/") |
6366 | (synopsis "Infrastructure for working with cytometry data") | |
6367 | (description | |
6368 | "This package is designed to facilitate comparison of automated gating | |
6369 | methods against manual gating done in flowJo. This package allows you to | |
6370 | import basic flowJo workspaces into BioConductor and replicate the gating from | |
6371 | flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of | |
6372 | samples, compensation, and transformation are performed so that the output | |
6373 | matches the flowJo analysis.") | |
6374 | (license license:artistic2.0))) | |
6375 | ||
b700b9ec RW |
6376 | (define-public r-flowstats |
6377 | (package | |
6378 | (name "r-flowstats") | |
fd11c7b8 | 6379 | (version "4.2.0") |
b700b9ec RW |
6380 | (source |
6381 | (origin | |
6382 | (method url-fetch) | |
6383 | (uri (bioconductor-uri "flowStats" version)) | |
6384 | (sha256 | |
6385 | (base32 | |
fd11c7b8 | 6386 | "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x")))) |
b700b9ec RW |
6387 | (properties `((upstream-name . "flowStats"))) |
6388 | (build-system r-build-system) | |
6389 | (propagated-inputs | |
6390 | `(("r-biobase" ,r-biobase) | |
6391 | ("r-biocgenerics" ,r-biocgenerics) | |
6392 | ("r-cluster" ,r-cluster) | |
6393 | ("r-fda" ,r-fda) | |
6394 | ("r-flowcore" ,r-flowcore) | |
6395 | ("r-flowviz" ,r-flowviz) | |
6396 | ("r-flowworkspace" ,r-flowworkspace) | |
6397 | ("r-kernsmooth" ,r-kernsmooth) | |
6398 | ("r-ks" ,r-ks) | |
6399 | ("r-lattice" ,r-lattice) | |
6400 | ("r-mass" ,r-mass) | |
6401 | ("r-ncdfflow" ,r-ncdfflow) | |
6402 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6403 | ("r-rrcov" ,r-rrcov))) | |
6404 | (home-page "http://www.github.com/RGLab/flowStats") | |
6405 | (synopsis "Statistical methods for the analysis of flow cytometry data") | |
6406 | (description | |
6407 | "This package provides methods and functionality to analyze flow data | |
6408 | that is beyond the basic infrastructure provided by the @code{flowCore} | |
6409 | package.") | |
6410 | (license license:artistic2.0))) | |
6411 | ||
6aedc805 RW |
6412 | (define-public r-opencyto |
6413 | (package | |
6414 | (name "r-opencyto") | |
5abf0a0d | 6415 | (version "2.2.0") |
6aedc805 RW |
6416 | (source |
6417 | (origin | |
6418 | (method url-fetch) | |
6419 | (uri (bioconductor-uri "openCyto" version)) | |
6420 | (sha256 | |
6421 | (base32 | |
5abf0a0d | 6422 | "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v")))) |
6aedc805 RW |
6423 | (properties `((upstream-name . "openCyto"))) |
6424 | (build-system r-build-system) | |
6425 | (propagated-inputs | |
6426 | `(("r-biobase" ,r-biobase) | |
6427 | ("r-biocgenerics" ,r-biocgenerics) | |
6428 | ("r-clue" ,r-clue) | |
6429 | ("r-data-table" ,r-data-table) | |
6430 | ("r-flowclust" ,r-flowclust) | |
6431 | ("r-flowcore" ,r-flowcore) | |
6432 | ("r-flowstats" ,r-flowstats) | |
6433 | ("r-flowviz" ,r-flowviz) | |
6434 | ("r-flowworkspace" ,r-flowworkspace) | |
6435 | ("r-graph" ,r-graph) | |
6436 | ("r-gtools" ,r-gtools) | |
6437 | ("r-ks" ,r-ks) | |
6438 | ("r-lattice" ,r-lattice) | |
6439 | ("r-mass" ,r-mass) | |
6440 | ("r-ncdfflow" ,r-ncdfflow) | |
6441 | ("r-plyr" ,r-plyr) | |
6442 | ("r-r-utils" ,r-r-utils) | |
6443 | ("r-rbgl" ,r-rbgl) | |
6444 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6445 | ("r-rcpp" ,r-rcpp) | |
6446 | ("r-rrcov" ,r-rrcov))) | |
8f5e1674 RW |
6447 | (native-inputs |
6448 | `(("r-knitr" ,r-knitr))) | |
6aedc805 RW |
6449 | (home-page "https://bioconductor.org/packages/openCyto") |
6450 | (synopsis "Hierarchical gating pipeline for flow cytometry data") | |
6451 | (description | |
6452 | "This package is designed to facilitate the automated gating methods in a | |
6453 | sequential way to mimic the manual gating strategy.") | |
6454 | (license license:artistic2.0))) | |
6455 | ||
7a62d5e0 RW |
6456 | (define-public r-cytoml |
6457 | (package | |
6458 | (name "r-cytoml") | |
63033b15 | 6459 | (version "2.2.1") |
7a62d5e0 RW |
6460 | (source |
6461 | (origin | |
6462 | (method url-fetch) | |
6463 | (uri (bioconductor-uri "CytoML" version)) | |
6464 | (sha256 | |
6465 | (base32 | |
63033b15 | 6466 | "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq")))) |
7a62d5e0 RW |
6467 | (properties `((upstream-name . "CytoML"))) |
6468 | (build-system r-build-system) | |
2b224f90 | 6469 | (arguments |
6470 | `(#:phases | |
6471 | (modify-phases %standard-phases | |
6472 | (add-after 'unpack 'fix-linking | |
6473 | (lambda _ | |
6474 | (substitute* "src/Makevars.in" | |
6475 | ;; This is to avoid having a plain directory on the list of | |
6476 | ;; libraries to link. | |
6477 | (("\\{h5lib\\}" match) | |
6478 | (string-append match "/libhdf5.a"))) | |
6479 | #t))))) | |
7a62d5e0 RW |
6480 | (inputs |
6481 | `(("libxml2" ,libxml2))) | |
6482 | (propagated-inputs | |
6483 | `(("r-base64enc" ,r-base64enc) | |
6484 | ("r-bh" ,r-bh) | |
6485 | ("r-biobase" ,r-biobase) | |
6486 | ("r-corpcor" ,r-corpcor) | |
6487 | ("r-cytolib" ,r-cytolib) | |
6488 | ("r-data-table" ,r-data-table) | |
6489 | ("r-dplyr" ,r-dplyr) | |
6490 | ("r-flowcore" ,r-flowcore) | |
6491 | ("r-flowworkspace" ,r-flowworkspace) | |
6492 | ("r-ggcyto" ,r-ggcyto) | |
6493 | ("r-graph" ,r-graph) | |
6494 | ("r-jsonlite" ,r-jsonlite) | |
6495 | ("r-lattice" ,r-lattice) | |
7a62d5e0 RW |
6496 | ("r-opencyto" ,r-opencyto) |
6497 | ("r-plyr" ,r-plyr) | |
6498 | ("r-rbgl" ,r-rbgl) | |
6499 | ("r-rcpp" ,r-rcpp) | |
8d5a83b7 | 6500 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
7a62d5e0 RW |
6501 | ("r-rcppparallel" ,r-rcppparallel) |
6502 | ("r-rgraphviz" ,r-rgraphviz) | |
8d5a83b7 | 6503 | ("r-rhdf5lib" ,r-rhdf5lib) |
7a62d5e0 RW |
6504 | ("r-rprotobuflib" ,r-rprotobuflib) |
6505 | ("r-runit" ,r-runit) | |
8d5a83b7 | 6506 | ("r-tibble" ,r-tibble) |
7a62d5e0 | 6507 | ("r-xml" ,r-xml) |
ef588757 | 6508 | ("r-xml2" ,r-xml2) |
7a62d5e0 | 6509 | ("r-yaml" ,r-yaml))) |
d49e3f01 RW |
6510 | (native-inputs |
6511 | `(("r-knitr" ,r-knitr))) | |
7a62d5e0 RW |
6512 | (home-page "https://github.com/RGLab/CytoML") |
6513 | (synopsis "GatingML interface for cross platform cytometry data sharing") | |
6514 | (description | |
6515 | "This package provides an interface to implementations of the GatingML2.0 | |
6516 | standard to exchange gated cytometry data with other software platforms.") | |
6517 | (license license:artistic2.0))) | |
6518 | ||
1502751b | 6519 | (define-public r-flowsom |
6520 | (package | |
6521 | (name "r-flowsom") | |
1f7ddaf0 | 6522 | (version "1.22.0") |
1502751b | 6523 | (source |
6524 | (origin | |
6525 | (method url-fetch) | |
6526 | (uri (bioconductor-uri "FlowSOM" version)) | |
6527 | (sha256 | |
6528 | (base32 | |
1f7ddaf0 | 6529 | "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf")))) |
1502751b | 6530 | (properties `((upstream-name . "FlowSOM"))) |
6531 | (build-system r-build-system) | |
6532 | (propagated-inputs | |
6533 | `(("r-biocgenerics" ,r-biocgenerics) | |
6534 | ("r-consensusclusterplus" ,r-consensusclusterplus) | |
ba71567a | 6535 | ("r-cytoml" ,r-cytoml) |
1502751b | 6536 | ("r-flowcore" ,r-flowcore) |
ba71567a | 6537 | ("r-flowworkspace" ,r-flowworkspace) |
1502751b | 6538 | ("r-igraph" ,r-igraph) |
ba71567a | 6539 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
1502751b | 6540 | ("r-tsne" ,r-tsne) |
6541 | ("r-xml" ,r-xml))) | |
6542 | (home-page "https://bioconductor.org/packages/FlowSOM/") | |
6543 | (synopsis "Visualize and interpret cytometry data") | |
6544 | (description | |
6545 | "FlowSOM offers visualization options for cytometry data, by using | |
6546 | self-organizing map clustering and minimal spanning trees.") | |
6547 | (license license:gpl2+))) | |
1adb9cbc | 6548 | |
6549 | (define-public r-mixomics | |
6550 | (package | |
6551 | (name "r-mixomics") | |
0e78ce36 | 6552 | (version "6.14.0") |
1adb9cbc | 6553 | (source |
6554 | (origin | |
6555 | (method url-fetch) | |
6556 | (uri (bioconductor-uri "mixOmics" version)) | |
6557 | (sha256 | |
6558 | (base32 | |
0e78ce36 | 6559 | "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q")))) |
1adb9cbc | 6560 | (properties `((upstream-name . "mixOmics"))) |
6561 | (build-system r-build-system) | |
6562 | (propagated-inputs | |
6563 | `(("r-corpcor" ,r-corpcor) | |
6564 | ("r-dplyr" ,r-dplyr) | |
6565 | ("r-ellipse" ,r-ellipse) | |
0e78ce36 | 6566 | ("r-ggrepel" ,r-ggrepel) |
1adb9cbc | 6567 | ("r-ggplot2" ,r-ggplot2) |
6568 | ("r-gridextra" ,r-gridextra) | |
6569 | ("r-igraph" ,r-igraph) | |
6570 | ("r-lattice" ,r-lattice) | |
6571 | ("r-mass" ,r-mass) | |
6572 | ("r-matrixstats" ,r-matrixstats) | |
6573 | ("r-rarpack" ,r-rarpack) | |
6574 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6575 | ("r-reshape2" ,r-reshape2) | |
6576 | ("r-tidyr" ,r-tidyr))) | |
9669bc17 RW |
6577 | (native-inputs |
6578 | `(("r-knitr" ,r-knitr))) | |
1adb9cbc | 6579 | (home-page "http://www.mixOmics.org") |
6580 | (synopsis "Multivariate methods for exploration of biological datasets") | |
6581 | (description | |
6582 | "mixOmics offers a wide range of multivariate methods for the exploration | |
6583 | and integration of biological datasets with a particular focus on variable | |
6584 | selection. The package proposes several sparse multivariate models we have | |
6585 | developed to identify the key variables that are highly correlated, and/or | |
6586 | explain the biological outcome of interest. The data that can be analysed | |
6587 | with mixOmics may come from high throughput sequencing technologies, such as | |
6588 | omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but | |
6589 | also beyond the realm of omics (e.g. spectral imaging). The methods | |
6590 | implemented in mixOmics can also handle missing values without having to | |
6591 | delete entire rows with missing data.") | |
6592 | (license license:gpl2+))) | |
a0efa069 | 6593 | |
6594 | (define-public r-depecher | |
fafaeab4 | 6595 | (package ;Source/Weave error |
a0efa069 | 6596 | (name "r-depecher") |
fafaeab4 | 6597 | (version "1.6.0") |
a0efa069 | 6598 | (source |
6599 | (origin | |
6600 | (method url-fetch) | |
6601 | (uri (bioconductor-uri "DepecheR" version)) | |
6602 | (sha256 | |
6603 | (base32 | |
fafaeab4 | 6604 | "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469")))) |
a0efa069 | 6605 | (properties `((upstream-name . "DepecheR"))) |
6606 | (build-system r-build-system) | |
a0efa069 | 6607 | (propagated-inputs |
6608 | `(("r-beanplot" ,r-beanplot) | |
a0efa069 | 6609 | ("r-dosnow" ,r-dosnow) |
6610 | ("r-dplyr" ,r-dplyr) | |
2c8433ca | 6611 | ("r-fnn" ,r-fnn) |
a0efa069 | 6612 | ("r-foreach" ,r-foreach) |
6613 | ("r-ggplot2" ,r-ggplot2) | |
fafaeab4 | 6614 | ("r-gmodels" ,r-gmodels) |
a0efa069 | 6615 | ("r-gplots" ,r-gplots) |
6616 | ("r-mass" ,r-mass) | |
6617 | ("r-matrixstats" ,r-matrixstats) | |
6618 | ("r-mixomics" ,r-mixomics) | |
6619 | ("r-moments" ,r-moments) | |
6620 | ("r-rcpp" ,r-rcpp) | |
6621 | ("r-rcppeigen" ,r-rcppeigen) | |
6622 | ("r-reshape2" ,r-reshape2) | |
2c8433ca | 6623 | ("r-robustbase" ,r-robustbase) |
a0efa069 | 6624 | ("r-viridis" ,r-viridis))) |
bf3722f9 RW |
6625 | (native-inputs |
6626 | `(("r-knitr" ,r-knitr))) | |
a0efa069 | 6627 | (home-page "https://bioconductor.org/packages/DepecheR/") |
6628 | (synopsis "Identify traits of clusters in high-dimensional entities") | |
6629 | (description | |
6630 | "The purpose of this package is to identify traits in a dataset that can | |
6631 | separate groups. This is done on two levels. First, clustering is performed, | |
6632 | using an implementation of sparse K-means. Secondly, the generated clusters | |
6633 | are used to predict outcomes of groups of individuals based on their | |
6634 | distribution of observations in the different clusters. As certain clusters | |
6635 | with separating information will be identified, and these clusters are defined | |
6636 | by a sparse number of variables, this method can reduce the complexity of | |
6637 | data, to only emphasize the data that actually matters.") | |
6638 | (license license:expat))) | |
b46a0ee7 | 6639 | |
bb88417f RW |
6640 | (define-public r-rcistarget |
6641 | (package | |
6642 | (name "r-rcistarget") | |
64813573 | 6643 | (version "1.10.0") |
bb88417f RW |
6644 | (source |
6645 | (origin | |
6646 | (method url-fetch) | |
6647 | (uri (bioconductor-uri "RcisTarget" version)) | |
6648 | (sha256 | |
6649 | (base32 | |
64813573 | 6650 | "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf")))) |
bb88417f RW |
6651 | (properties `((upstream-name . "RcisTarget"))) |
6652 | (build-system r-build-system) | |
6653 | (propagated-inputs | |
6654 | `(("r-aucell" ,r-aucell) | |
6655 | ("r-biocgenerics" ,r-biocgenerics) | |
6656 | ("r-data-table" ,r-data-table) | |
6657 | ("r-feather" ,r-feather) | |
6658 | ("r-gseabase" ,r-gseabase) | |
6659 | ("r-r-utils" ,r-r-utils) | |
6660 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
93235b1e RW |
6661 | (native-inputs |
6662 | `(("r-knitr" ,r-knitr))) | |
bb88417f RW |
6663 | (home-page "https://aertslab.org/#scenic") |
6664 | (synopsis "Identify transcription factor binding motifs enriched on a gene list") | |
6665 | (description | |
6666 | "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) | |
6667 | over-represented on a gene list. In a first step, RcisTarget selects DNA | |
6668 | motifs that are significantly over-represented in the surroundings of the | |
6669 | @dfn{transcription start site} (TSS) of the genes in the gene-set. This is | |
6670 | achieved by using a database that contains genome-wide cross-species rankings | |
6671 | for each motif. The motifs that are then annotated to TFs and those that have | |
6672 | a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for | |
6673 | each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. | |
6674 | genes in the gene-set that are ranked above the leading edge).") | |
6675 | (license license:gpl3))) | |
6676 | ||
b46a0ee7 RW |
6677 | (define-public r-cicero |
6678 | (package | |
6679 | (name "r-cicero") | |
7954fe16 | 6680 | (version "1.8.0") |
b46a0ee7 RW |
6681 | (source |
6682 | (origin | |
6683 | (method url-fetch) | |
6684 | (uri (bioconductor-uri "cicero" version)) | |
6685 | (sha256 | |
6686 | (base32 | |
7954fe16 | 6687 | "0hrra9ngpzmd57dwm0058zy0g7ymsil4pmvi3sgppfzimgviqiwf")))) |
b46a0ee7 RW |
6688 | (build-system r-build-system) |
6689 | (propagated-inputs | |
6690 | `(("r-assertthat" ,r-assertthat) | |
6691 | ("r-biobase" ,r-biobase) | |
6692 | ("r-biocgenerics" ,r-biocgenerics) | |
6693 | ("r-data-table" ,r-data-table) | |
6694 | ("r-dplyr" ,r-dplyr) | |
6695 | ("r-fnn" ,r-fnn) | |
6696 | ("r-genomicranges" ,r-genomicranges) | |
6697 | ("r-ggplot2" ,r-ggplot2) | |
6698 | ("r-glasso" ,r-glasso) | |
6699 | ("r-gviz" ,r-gviz) | |
6700 | ("r-igraph" ,r-igraph) | |
6701 | ("r-iranges" ,r-iranges) | |
6702 | ("r-matrix" ,r-matrix) | |
6703 | ("r-monocle" ,r-monocle) | |
6704 | ("r-plyr" ,r-plyr) | |
6705 | ("r-reshape2" ,r-reshape2) | |
6706 | ("r-s4vectors" ,r-s4vectors) | |
1893092d | 6707 | ("r-stringi" ,r-stringi) |
b46a0ee7 RW |
6708 | ("r-stringr" ,r-stringr) |
6709 | ("r-tibble" ,r-tibble) | |
5ea4f604 | 6710 | ("r-tidyr" ,r-tidyr) |
b46a0ee7 | 6711 | ("r-vgam" ,r-vgam))) |
6bd6097e RW |
6712 | (native-inputs |
6713 | `(("r-knitr" ,r-knitr))) | |
b46a0ee7 RW |
6714 | (home-page "https://bioconductor.org/packages/cicero/") |
6715 | (synopsis "Predict cis-co-accessibility from single-cell data") | |
6716 | (description | |
6717 | "Cicero computes putative cis-regulatory maps from single-cell chromatin | |
6718 | accessibility data. It also extends the monocle package for use in chromatin | |
6719 | accessibility data.") | |
6720 | (license license:expat))) | |
14bb1c48 RW |
6721 | |
6722 | ;; This is the latest commit on the "monocle3" branch. | |
6723 | (define-public r-cicero-monocle3 | |
6724 | (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") | |
6725 | (revision "1")) | |
6726 | (package (inherit r-cicero) | |
6727 | (name "r-cicero-monocle3") | |
6728 | (version (git-version "1.3.2" revision commit)) | |
6729 | (source | |
6730 | (origin | |
6731 | (method git-fetch) | |
6732 | (uri (git-reference | |
b0e7b699 | 6733 | (url "https://github.com/cole-trapnell-lab/cicero-release") |
14bb1c48 RW |
6734 | (commit commit))) |
6735 | (file-name (git-file-name name version)) | |
6736 | (sha256 | |
6737 | (base32 | |
6738 | "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) | |
6739 | (propagated-inputs | |
6740 | `(("r-monocle3" ,r-monocle3) | |
6741 | ,@(alist-delete "r-monocle" | |
6742 | (package-propagated-inputs r-cicero))))))) | |
a9815a6c RW |
6743 | |
6744 | (define-public r-cistopic | |
6745 | (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") | |
6746 | (revision "0")) | |
6747 | (package | |
6748 | (name "r-cistopic") | |
6749 | (version (git-version "0.2.1" revision commit)) | |
6750 | (source | |
6751 | (origin | |
6752 | (method git-fetch) | |
6753 | (uri (git-reference | |
b0e7b699 | 6754 | (url "https://github.com/aertslab/cisTopic") |
a9815a6c RW |
6755 | (commit commit))) |
6756 | (file-name (git-file-name name version)) | |
6757 | (sha256 | |
6758 | (base32 | |
6759 | "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) | |
6760 | (build-system r-build-system) | |
6761 | (propagated-inputs | |
6762 | `(("r-aucell" ,r-aucell) | |
6763 | ("r-data-table" ,r-data-table) | |
6764 | ("r-dplyr" ,r-dplyr) | |
6765 | ("r-dosnow" ,r-dosnow) | |
6766 | ("r-dt" ,r-dt) | |
6767 | ("r-feather" ,r-feather) | |
6768 | ("r-fitdistrplus" ,r-fitdistrplus) | |
6769 | ("r-genomicranges" ,r-genomicranges) | |
6770 | ("r-ggplot2" ,r-ggplot2) | |
6771 | ("r-lda" ,r-lda) | |
6772 | ("r-matrix" ,r-matrix) | |
6773 | ("r-plyr" ,r-plyr) | |
6774 | ("r-rcistarget" ,r-rcistarget) | |
6775 | ("r-rtracklayer" ,r-rtracklayer) | |
6776 | ("r-s4vectors" ,r-s4vectors))) | |
6777 | (home-page "https://github.com/aertslab/cisTopic") | |
6778 | (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") | |
6779 | (description | |
6780 | "The sparse nature of single cell epigenomics data can be overruled using | |
6781 | probabilistic modelling methods such as @dfn{Latent Dirichlet | |
6782 | Allocation} (LDA). This package allows the probabilistic modelling of | |
6783 | cis-regulatory topics (cisTopics) from single cell epigenomics data, and | |
6784 | includes functionalities to identify cell states based on the contribution of | |
6785 | cisTopics and explore the nature and regulatory proteins driving them.") | |
6786 | (license license:gpl3)))) | |
d85c0f98 RW |
6787 | |
6788 | (define-public r-genie3 | |
6789 | (package | |
6790 | (name "r-genie3") | |
5d1bd611 | 6791 | (version "1.12.0") |
d85c0f98 RW |
6792 | (source |
6793 | (origin | |
6794 | (method url-fetch) | |
6795 | (uri (bioconductor-uri "GENIE3" version)) | |
6796 | (sha256 | |
6797 | (base32 | |
5d1bd611 | 6798 | "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5")))) |
d85c0f98 RW |
6799 | (properties `((upstream-name . "GENIE3"))) |
6800 | (build-system r-build-system) | |
6801 | (propagated-inputs `(("r-reshape2" ,r-reshape2))) | |
b3280883 RW |
6802 | (native-inputs |
6803 | `(("r-knitr" ,r-knitr))) | |
d85c0f98 RW |
6804 | (home-page "https://bioconductor.org/packages/GENIE3") |
6805 | (synopsis "Gene network inference with ensemble of trees") | |
6806 | (description | |
6807 | "This package implements the GENIE3 algorithm for inferring gene | |
6808 | regulatory networks from expression data.") | |
6809 | (license license:gpl2+))) | |
db316d73 RW |
6810 | |
6811 | (define-public r-roc | |
6812 | (package | |
6813 | (name "r-roc") | |
e7b61ba7 | 6814 | (version "1.66.0") |
db316d73 RW |
6815 | (source |
6816 | (origin | |
6817 | (method url-fetch) | |
6818 | (uri (bioconductor-uri "ROC" version)) | |
6819 | (sha256 | |
6820 | (base32 | |
e7b61ba7 | 6821 | "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9")))) |
db316d73 RW |
6822 | (properties `((upstream-name . "ROC"))) |
6823 | (build-system r-build-system) | |
3672b74f RW |
6824 | (propagated-inputs |
6825 | `(("r-knitr" ,r-knitr))) | |
db316d73 RW |
6826 | (home-page "https://www.bioconductor.org/packages/ROC/") |
6827 | (synopsis "Utilities for ROC curves") | |
6828 | (description | |
6829 | "This package provides utilities for @dfn{Receiver Operating | |
6830 | Characteristic} (ROC) curves, with a focus on micro arrays.") | |
6831 | (license license:artistic2.0))) | |
46721dea RW |
6832 | |
6833 | (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 | |
6834 | (package | |
6835 | (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") | |
6836 | (version "0.6.0") | |
6837 | (source | |
6838 | (origin | |
6839 | (method url-fetch) | |
6840 | (uri (bioconductor-uri | |
6841 | "IlluminaHumanMethylation450kanno.ilmn12.hg19" | |
6842 | version 'annotation)) | |
6843 | (sha256 | |
6844 | (base32 | |
6845 | "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) | |
6846 | (properties | |
6847 | `((upstream-name | |
6848 | . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) | |
6849 | (build-system r-build-system) | |
6850 | (propagated-inputs `(("r-minfi" ,r-minfi))) | |
6851 | (home-page | |
6852 | "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") | |
6853 | (synopsis "Annotation for Illumina's 450k methylation arrays") | |
6854 | (description | |
6855 | "This package provides manifests and annotation for Illumina's 450k array | |
6856 | data.") | |
6857 | (license license:artistic2.0))) | |
38babeaa RW |
6858 | |
6859 | (define-public r-watermelon | |
6860 | (package | |
6861 | (name "r-watermelon") | |
939ace96 | 6862 | (version "1.32.0") |
38babeaa RW |
6863 | (source |
6864 | (origin | |
6865 | (method url-fetch) | |
6866 | (uri (bioconductor-uri "wateRmelon" version)) | |
6867 | (sha256 | |
6868 | (base32 | |
939ace96 | 6869 | "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn")))) |
38babeaa RW |
6870 | (properties `((upstream-name . "wateRmelon"))) |
6871 | (build-system r-build-system) | |
6872 | (propagated-inputs | |
6873 | `(("r-biobase" ,r-biobase) | |
6874 | ("r-illuminahumanmethylation450kanno-ilmn12-hg19" | |
6875 | ,r-illuminahumanmethylation450kanno-ilmn12-hg19) | |
6876 | ("r-illuminaio" ,r-illuminaio) | |
6877 | ("r-limma" ,r-limma) | |
6878 | ("r-lumi" ,r-lumi) | |
6879 | ("r-matrixstats" ,r-matrixstats) | |
6880 | ("r-methylumi" ,r-methylumi) | |
6881 | ("r-roc" ,r-roc))) | |
6882 | (home-page "https://bioconductor.org/packages/wateRmelon/") | |
6883 | (synopsis "Illumina 450 methylation array normalization and metrics") | |
6884 | (description | |
6885 | "The standard index of DNA methylation (beta) is computed from methylated | |
6886 | and unmethylated signal intensities. Betas calculated from raw signal | |
6887 | intensities perform well, but using 11 methylomic datasets we demonstrate that | |
6888 | quantile normalization methods produce marked improvement. The commonly used | |
6889 | procedure of normalizing betas is inferior to the separate normalization of M | |
6890 | and U, and it is also advantageous to normalize Type I and Type II assays | |
6891 | separately. This package provides 15 flavours of betas and three performance | |
6892 | metrics, with methods for objects produced by the @code{methylumi} and | |
6893 | @code{minfi} packages.") | |
6894 | (license license:gpl3))) | |
7d2cb646 RW |
6895 | |
6896 | (define-public r-gdsfmt | |
6897 | (package | |
6898 | (name "r-gdsfmt") | |
a50779b8 | 6899 | (version "1.26.0") |
7d2cb646 RW |
6900 | (source |
6901 | (origin | |
6902 | (method url-fetch) | |
6903 | (uri (bioconductor-uri "gdsfmt" version)) | |
6904 | (sha256 | |
6905 | (base32 | |
a50779b8 | 6906 | "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a")) |
7d2cb646 RW |
6907 | (modules '((guix build utils))) |
6908 | ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build | |
6909 | ;; them and link with system libraries instead. | |
6910 | (snippet | |
6911 | '(begin | |
6912 | (for-each delete-file-recursively | |
6913 | '("src/LZ4" | |
6914 | "src/XZ" | |
6915 | "src/ZLIB")) | |
6916 | (substitute* "src/Makevars" | |
6917 | (("all: \\$\\(SHLIB\\)") "all:") | |
6918 | (("\\$\\(SHLIB\\): liblzma.a") "") | |
6919 | (("(ZLIB|LZ4)/.*") "") | |
6920 | (("CoreArray/dVLIntGDS.cpp.*") | |
6921 | "CoreArray/dVLIntGDS.cpp") | |
6922 | (("CoreArray/dVLIntGDS.o.*") | |
6923 | "CoreArray/dVLIntGDS.o") | |
6924 | (("PKG_LIBS = ./liblzma.a") | |
6925 | "PKG_LIBS = -llz4")) | |
6926 | (substitute* "src/CoreArray/dStream.h" | |
6927 | (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) | |
6928 | (string-append "include <" header ">"))) | |
6929 | #t)))) | |
6930 | (properties `((upstream-name . "gdsfmt"))) | |
6931 | (build-system r-build-system) | |
6932 | (inputs | |
6933 | `(("lz4" ,lz4) | |
6934 | ("xz" ,xz) | |
6935 | ("zlib" ,zlib))) | |
f4954b0b RW |
6936 | (native-inputs |
6937 | `(("r-knitr" ,r-knitr))) | |
7d2cb646 RW |
6938 | (home-page "http://corearray.sourceforge.net/") |
6939 | (synopsis | |
6940 | "R Interface to CoreArray Genomic Data Structure (GDS) Files") | |
6941 | (description | |
6942 | "This package provides a high-level R interface to CoreArray @dfn{Genomic | |
6943 | Data Structure} (GDS) data files, which are portable across platforms with | |
6944 | hierarchical structure to store multiple scalable array-oriented data sets | |
6945 | with metadata information. It is suited for large-scale datasets, especially | |
6946 | for data which are much larger than the available random-access memory. The | |
6947 | @code{gdsfmt} package offers efficient operations specifically designed for | |
6948 | integers of less than 8 bits, since a diploid genotype, like | |
6949 | @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a | |
6950 | byte. Data compression and decompression are available with relatively | |
6951 | efficient random access. It is also allowed to read a GDS file in parallel | |
6952 | with multiple R processes supported by the package @code{parallel}.") | |
6953 | (license license:lgpl3))) | |
6b5f59c7 RW |
6954 | |
6955 | (define-public r-bigmelon | |
6956 | (package | |
6957 | (name "r-bigmelon") | |
8112796d | 6958 | (version "1.14.0") |
6b5f59c7 RW |
6959 | (source |
6960 | (origin | |
6961 | (method url-fetch) | |
6962 | (uri (bioconductor-uri "bigmelon" version)) | |
6963 | (sha256 | |
6964 | (base32 | |
8112796d | 6965 | "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y")))) |
6b5f59c7 RW |
6966 | (properties `((upstream-name . "bigmelon"))) |
6967 | (build-system r-build-system) | |
6968 | (propagated-inputs | |
6969 | `(("r-biobase" ,r-biobase) | |
6970 | ("r-biocgenerics" ,r-biocgenerics) | |
6971 | ("r-gdsfmt" ,r-gdsfmt) | |
6972 | ("r-geoquery" ,r-geoquery) | |
6973 | ("r-methylumi" ,r-methylumi) | |
6974 | ("r-minfi" ,r-minfi) | |
6975 | ("r-watermelon" ,r-watermelon))) | |
6976 | (home-page "https://bioconductor.org/packages/bigmelon/") | |
6977 | (synopsis "Illumina methylation array analysis for large experiments") | |
6978 | (description | |
6979 | "This package provides methods for working with Illumina arrays using the | |
6980 | @code{gdsfmt} package.") | |
6981 | (license license:gpl3))) | |
739b2d10 | 6982 | |
e5dfcd8e RW |
6983 | (define-public r-seqbias |
6984 | (package | |
6985 | (name "r-seqbias") | |
42e00c09 | 6986 | (version "1.38.0") |
e5dfcd8e RW |
6987 | (source |
6988 | (origin | |
6989 | (method url-fetch) | |
6990 | (uri (bioconductor-uri "seqbias" version)) | |
6991 | (sha256 | |
6992 | (base32 | |
42e00c09 | 6993 | "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2")))) |
e5dfcd8e RW |
6994 | (properties `((upstream-name . "seqbias"))) |
6995 | (build-system r-build-system) | |
6996 | (propagated-inputs | |
6997 | `(("r-biostrings" ,r-biostrings) | |
6998 | ("r-genomicranges" ,r-genomicranges) | |
6999 | ("r-rhtslib" ,r-rhtslib))) | |
7000 | (inputs | |
7001 | `(("zlib" ,zlib))) ; This comes from rhtslib. | |
7002 | (home-page "https://bioconductor.org/packages/seqbias/") | |
7003 | (synopsis "Estimation of per-position bias in high-throughput sequencing data") | |
7004 | (description | |
7005 | "This package implements a model of per-position sequencing bias in | |
7006 | high-throughput sequencing data using a simple Bayesian network, the structure | |
7007 | and parameters of which are trained on a set of aligned reads and a reference | |
7008 | genome sequence.") | |
7009 | (license license:lgpl3))) | |
7010 | ||
63daca1e RJ |
7011 | (define-public r-snplocs-hsapiens-dbsnp144-grch37 |
7012 | (package | |
7013 | (name "r-snplocs-hsapiens-dbsnp144-grch37") | |
7014 | (version "0.99.20") | |
7015 | (source (origin | |
7016 | (method url-fetch) | |
7017 | (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" | |
7018 | version 'annotation)) | |
7019 | (sha256 | |
7020 | (base32 | |
7021 | "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) | |
7022 | (build-system r-build-system) | |
7023 | ;; As this package provides little more than a very large data file it | |
7024 | ;; doesn't make sense to build substitutes. | |
7025 | (arguments `(#:substitutable? #f)) | |
7026 | (propagated-inputs | |
7027 | `(("r-biocgenerics" ,r-biocgenerics) | |
7028 | ("r-s4vectors" ,r-s4vectors) | |
7029 | ("r-iranges" ,r-iranges) | |
7030 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7031 | ("r-genomicranges" ,r-genomicranges) | |
7032 | ("r-bsgenome" ,r-bsgenome) | |
7033 | ("r-biostrings" ,r-biostrings))) | |
7034 | (home-page | |
7035 | "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") | |
7036 | (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") | |
7037 | (description "This package provides SNP locations and alleles for Homo | |
7038 | sapiens extracted from NCBI dbSNP Build 144. The source data files used for | |
7039 | this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped | |
7040 | to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a | |
7041 | patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, | |
1408e2ab | 7042 | X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for |
63daca1e RJ |
7043 | the mitochondrion chromosome. Therefore, the SNPs in this package can be |
7044 | injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the | |
7045 | correct position but this injection will exclude chrM (i.e. nothing will be | |
7046 | injected in that sequence).") | |
7047 | (license license:artistic2.0))) | |
7048 | ||
bb0024dc RW |
7049 | (define-public r-reqon |
7050 | (package | |
7051 | (name "r-reqon") | |
0c53f27d | 7052 | (version "1.36.0") |
bb0024dc RW |
7053 | (source |
7054 | (origin | |
7055 | (method url-fetch) | |
7056 | (uri (bioconductor-uri "ReQON" version)) | |
7057 | (sha256 | |
7058 | (base32 | |
0c53f27d | 7059 | "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq")))) |
bb0024dc RW |
7060 | (properties `((upstream-name . "ReQON"))) |
7061 | (build-system r-build-system) | |
7062 | (propagated-inputs | |
7063 | `(("r-rjava" ,r-rjava) | |
7064 | ("r-rsamtools" ,r-rsamtools) | |
7065 | ("r-seqbias" ,r-seqbias))) | |
7066 | (home-page "https://bioconductor.org/packages/ReQON/") | |
7067 | (synopsis "Recalibrating quality of nucleotides") | |
7068 | (description | |
7069 | "This package provides an implementation of an algorithm for | |
7070 | recalibrating the base quality scores for aligned sequencing data in BAM | |
7071 | format.") | |
7072 | (license license:gpl2))) | |
7073 | ||
739b2d10 RW |
7074 | (define-public r-wavcluster |
7075 | (package | |
7076 | (name "r-wavcluster") | |
fd7e23b5 | 7077 | (version "2.24.0") |
739b2d10 RW |
7078 | (source |
7079 | (origin | |
7080 | (method url-fetch) | |
7081 | (uri (bioconductor-uri "wavClusteR" version)) | |
7082 | (sha256 | |
7083 | (base32 | |
fd7e23b5 | 7084 | "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi")))) |
739b2d10 RW |
7085 | (properties `((upstream-name . "wavClusteR"))) |
7086 | (build-system r-build-system) | |
7087 | (propagated-inputs | |
7088 | `(("r-biocgenerics" ,r-biocgenerics) | |
7089 | ("r-biostrings" ,r-biostrings) | |
7090 | ("r-foreach" ,r-foreach) | |
7091 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7092 | ("r-genomicranges" ,r-genomicranges) | |
7093 | ("r-ggplot2" ,r-ggplot2) | |
7094 | ("r-hmisc" ,r-hmisc) | |
7095 | ("r-iranges" ,r-iranges) | |
7096 | ("r-mclust" ,r-mclust) | |
7097 | ("r-rsamtools" ,r-rsamtools) | |
7098 | ("r-rtracklayer" ,r-rtracklayer) | |
7099 | ("r-s4vectors" ,r-s4vectors) | |
7100 | ("r-seqinr" ,r-seqinr) | |
fd7e23b5 | 7101 | ("r-stringr" ,r-stringr))) |
12b255f2 RW |
7102 | (native-inputs |
7103 | `(("r-knitr" ,r-knitr))) | |
739b2d10 RW |
7104 | (home-page "https://bioconductor.org/packages/wavClusteR/") |
7105 | (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") | |
7106 | (description | |
7107 | "This package provides an integrated pipeline for the analysis of | |
7108 | PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from | |
7109 | sequencing errors, SNPs and additional non-experimental sources by a non- | |
7110 | parametric mixture model. The protein binding sites (clusters) are then | |
7111 | resolved at high resolution and cluster statistics are estimated using a | |
7112 | rigorous Bayesian framework. Post-processing of the results, data export for | |
7113 | UCSC genome browser visualization and motif search analysis are provided. In | |
e40ecf8a | 7114 | addition, the package integrates RNA-Seq data to estimate the False |
739b2d10 RW |
7115 | Discovery Rate of cluster detection. Key functions support parallel multicore |
7116 | computing. While wavClusteR was designed for PAR-CLIP data analysis, it can | |
7117 | be applied to the analysis of other NGS data obtained from experimental | |
7118 | procedures that induce nucleotide substitutions (e.g. BisSeq).") | |
7119 | (license license:gpl2))) | |
853211a5 RW |
7120 | |
7121 | (define-public r-timeseriesexperiment | |
7122 | (package | |
7123 | (name "r-timeseriesexperiment") | |
87f704b4 | 7124 | (version "1.8.0") |
853211a5 RW |
7125 | (source |
7126 | (origin | |
7127 | (method url-fetch) | |
7128 | (uri (bioconductor-uri "TimeSeriesExperiment" version)) | |
7129 | (sha256 | |
7130 | (base32 | |
87f704b4 | 7131 | "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn")))) |
853211a5 RW |
7132 | (properties |
7133 | `((upstream-name . "TimeSeriesExperiment"))) | |
7134 | (build-system r-build-system) | |
7135 | (propagated-inputs | |
7136 | `(("r-deseq2" ,r-deseq2) | |
7137 | ("r-dplyr" ,r-dplyr) | |
7138 | ("r-dynamictreecut" ,r-dynamictreecut) | |
7139 | ("r-edger" ,r-edger) | |
7140 | ("r-ggplot2" ,r-ggplot2) | |
7141 | ("r-hmisc" ,r-hmisc) | |
7142 | ("r-limma" ,r-limma) | |
7143 | ("r-magrittr" ,r-magrittr) | |
7144 | ("r-proxy" ,r-proxy) | |
7145 | ("r-s4vectors" ,r-s4vectors) | |
7146 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
7147 | ("r-tibble" ,r-tibble) | |
7148 | ("r-tidyr" ,r-tidyr) | |
7149 | ("r-vegan" ,r-vegan) | |
7150 | ("r-viridis" ,r-viridis))) | |
49dd5041 RW |
7151 | (native-inputs |
7152 | `(("r-knitr" ,r-knitr))) | |
853211a5 RW |
7153 | (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") |
7154 | (synopsis "Analysis for short time-series data") | |
7155 | (description | |
7156 | "This package is a visualization and analysis toolbox for short time | |
7157 | course data which includes dimensionality reduction, clustering, two-sample | |
7158 | differential expression testing and gene ranking techniques. The package also | |
7159 | provides methods for retrieving enriched pathways.") | |
7160 | (license license:lgpl3+))) | |
df8576e5 RW |
7161 | |
7162 | (define-public r-variantfiltering | |
7163 | (package | |
7164 | (name "r-variantfiltering") | |
45ea773f | 7165 | (version "1.26.0") |
df8576e5 RW |
7166 | (source |
7167 | (origin | |
7168 | (method url-fetch) | |
7169 | (uri (bioconductor-uri "VariantFiltering" version)) | |
7170 | (sha256 | |
7171 | (base32 | |
45ea773f | 7172 | "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5")))) |
df8576e5 RW |
7173 | (properties |
7174 | `((upstream-name . "VariantFiltering"))) | |
7175 | (build-system r-build-system) | |
7176 | (propagated-inputs | |
7177 | `(("r-annotationdbi" ,r-annotationdbi) | |
7178 | ("r-biobase" ,r-biobase) | |
7179 | ("r-biocgenerics" ,r-biocgenerics) | |
7180 | ("r-biocparallel" ,r-biocparallel) | |
7181 | ("r-biostrings" ,r-biostrings) | |
7182 | ("r-bsgenome" ,r-bsgenome) | |
7183 | ("r-dt" ,r-dt) | |
7184 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7185 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7186 | ("r-genomicranges" ,r-genomicranges) | |
7187 | ("r-genomicscores" ,r-genomicscores) | |
7188 | ("r-graph" ,r-graph) | |
7189 | ("r-gviz" ,r-gviz) | |
7190 | ("r-iranges" ,r-iranges) | |
7191 | ("r-rbgl" ,r-rbgl) | |
7192 | ("r-rsamtools" ,r-rsamtools) | |
7193 | ("r-s4vectors" ,r-s4vectors) | |
7194 | ("r-shiny" ,r-shiny) | |
7195 | ("r-shinyjs" ,r-shinyjs) | |
7196 | ("r-shinythemes" ,r-shinythemes) | |
7197 | ("r-shinytree" ,r-shinytree) | |
7198 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
7199 | ("r-variantannotation" ,r-variantannotation) | |
7200 | ("r-xvector" ,r-xvector))) | |
7201 | (home-page "https://github.com/rcastelo/VariantFiltering") | |
7202 | (synopsis "Filtering of coding and non-coding genetic variants") | |
7203 | (description | |
7204 | "Filter genetic variants using different criteria such as inheritance | |
7205 | model, amino acid change consequence, minor allele frequencies across human | |
7206 | populations, splice site strength, conservation, etc.") | |
7207 | (license license:artistic2.0))) | |
f5349b4d RW |
7208 | |
7209 | (define-public r-genomegraphs | |
7210 | (package | |
7211 | (name "r-genomegraphs") | |
053a2127 | 7212 | (version "1.46.0") |
f5349b4d RW |
7213 | (source |
7214 | (origin | |
7215 | (method url-fetch) | |
7216 | (uri (bioconductor-uri "GenomeGraphs" version)) | |
7217 | (sha256 | |
7218 | (base32 | |
053a2127 | 7219 | "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) |
f5349b4d RW |
7220 | (properties `((upstream-name . "GenomeGraphs"))) |
7221 | (build-system r-build-system) | |
7222 | (propagated-inputs | |
7223 | `(("r-biomart" ,r-biomart))) | |
7224 | (home-page "https://bioconductor.org/packages/GenomeGraphs/") | |
7225 | (synopsis "Plotting genomic information from Ensembl") | |
7226 | (description | |
7227 | "Genomic data analyses requires integrated visualization of known genomic | |
7228 | information and new experimental data. GenomeGraphs uses the biomaRt package | |
7229 | to perform live annotation queries to Ensembl and translates this to e.g. | |
7230 | gene/transcript structures in viewports of the grid graphics package. This | |
7231 | results in genomic information plotted together with your data. Another | |
7232 | strength of GenomeGraphs is to plot different data types such as array CGH, | |
7233 | gene expression, sequencing and other data, together in one plot using the | |
7234 | same genome coordinate system.") | |
7235 | (license license:artistic2.0))) | |
2a360cf6 RW |
7236 | |
7237 | (define-public r-wavetiling | |
7238 | (package | |
7239 | (name "r-wavetiling") | |
e13f9773 | 7240 | (version "1.28.0") |
2a360cf6 RW |
7241 | (source |
7242 | (origin | |
7243 | (method url-fetch) | |
7244 | (uri (bioconductor-uri "waveTiling" version)) | |
7245 | (sha256 | |
7246 | (base32 | |
e13f9773 | 7247 | "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) |
2a360cf6 RW |
7248 | (properties `((upstream-name . "waveTiling"))) |
7249 | (build-system r-build-system) | |
7250 | (propagated-inputs | |
7251 | `(("r-affy" ,r-affy) | |
7252 | ("r-biobase" ,r-biobase) | |
7253 | ("r-biostrings" ,r-biostrings) | |
7254 | ("r-genomegraphs" ,r-genomegraphs) | |
7255 | ("r-genomicranges" ,r-genomicranges) | |
7256 | ("r-iranges" ,r-iranges) | |
7257 | ("r-oligo" ,r-oligo) | |
7258 | ("r-oligoclasses" ,r-oligoclasses) | |
7259 | ("r-preprocesscore" ,r-preprocesscore) | |
7260 | ("r-waveslim" ,r-waveslim))) | |
7261 | (home-page "https://r-forge.r-project.org/projects/wavetiling/") | |
7262 | (synopsis "Wavelet-based models for tiling array transcriptome analysis") | |
7263 | (description | |
7264 | "This package is designed to conduct transcriptome analysis for tiling | |
7265 | arrays based on fast wavelet-based functional models.") | |
7266 | (license license:gpl2+))) | |
d80a1569 RW |
7267 | |
7268 | (define-public r-variancepartition | |
7269 | (package | |
7270 | (name "r-variancepartition") | |
44ecd5f7 | 7271 | (version "1.20.0") |
d80a1569 RW |
7272 | (source |
7273 | (origin | |
7274 | (method url-fetch) | |
7275 | (uri (bioconductor-uri "variancePartition" version)) | |
7276 | (sha256 | |
7277 | (base32 | |
44ecd5f7 | 7278 | "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah")))) |
d80a1569 RW |
7279 | (properties |
7280 | `((upstream-name . "variancePartition"))) | |
7281 | (build-system r-build-system) | |
7282 | (propagated-inputs | |
7283 | `(("r-biobase" ,r-biobase) | |
326746e1 | 7284 | ("r-biocparallel" ,r-biocparallel) |
d80a1569 RW |
7285 | ("r-colorramps" ,r-colorramps) |
7286 | ("r-doparallel" ,r-doparallel) | |
7287 | ("r-foreach" ,r-foreach) | |
7288 | ("r-ggplot2" ,r-ggplot2) | |
7289 | ("r-gplots" ,r-gplots) | |
7290 | ("r-iterators" ,r-iterators) | |
7291 | ("r-limma" ,r-limma) | |
7292 | ("r-lme4" ,r-lme4) | |
7293 | ("r-lmertest" ,r-lmertest) | |
7294 | ("r-mass" ,r-mass) | |
7295 | ("r-pbkrtest" ,r-pbkrtest) | |
7296 | ("r-progress" ,r-progress) | |
7297 | ("r-reshape2" ,r-reshape2) | |
7298 | ("r-scales" ,r-scales))) | |
fbbaf5ae RW |
7299 | (native-inputs |
7300 | `(("r-knitr" ,r-knitr))) | |
d80a1569 RW |
7301 | (home-page "https://bioconductor.org/packages/variancePartition/") |
7302 | (synopsis "Analyze variation in gene expression experiments") | |
7303 | (description | |
7304 | "This is a package providing tools to quantify and interpret multiple | |
7305 | sources of biological and technical variation in gene expression experiments. | |
7306 | It uses a linear mixed model to quantify variation in gene expression | |
7307 | attributable to individual, tissue, time point, or technical variables. The | |
7308 | package includes dream differential expression analysis for repeated | |
7309 | measures.") | |
7310 | (license license:gpl2+))) | |
16e2e4f2 | 7311 | |
7312 | (define-public r-htqpcr | |
7313 | (package | |
7314 | (name "r-htqpcr") | |
949626f2 | 7315 | (version "1.44.0") |
16e2e4f2 | 7316 | (source |
7317 | (origin | |
7318 | (method url-fetch) | |
7319 | (uri (bioconductor-uri "HTqPCR" version)) | |
7320 | (sha256 | |
7321 | (base32 | |
949626f2 | 7322 | "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji")))) |
16e2e4f2 | 7323 | (properties `((upstream-name . "HTqPCR"))) |
7324 | (build-system r-build-system) | |
7325 | (propagated-inputs | |
7326 | `(("r-affy" ,r-affy) | |
7327 | ("r-biobase" ,r-biobase) | |
7328 | ("r-gplots" ,r-gplots) | |
7329 | ("r-limma" ,r-limma) | |
7330 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
486a0800 TGR |
7331 | (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" |
7332 | "groups/bertone/software/HTqPCR.pdf")) | |
16e2e4f2 | 7333 | (synopsis "Automated analysis of high-throughput qPCR data") |
7334 | (description | |
7335 | "Analysis of Ct values from high throughput quantitative real-time | |
7336 | PCR (qPCR) assays across multiple conditions or replicates. The input data | |
7337 | can be from spatially-defined formats such ABI TaqMan Low Density Arrays or | |
7338 | OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad | |
7339 | Laboratories; conventional 96- or 384-well plates; or microfluidic devices | |
7340 | such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data | |
7341 | loading, quality assessment, normalization, visualization and parametric or | |
7342 | non-parametric testing for statistical significance in Ct values between | |
7343 | features (e.g. genes, microRNAs).") | |
7344 | (license license:artistic2.0))) | |
86fb2c63 | 7345 | |
7346 | (define-public r-unifiedwmwqpcr | |
7347 | (package | |
7348 | (name "r-unifiedwmwqpcr") | |
fa7e2429 | 7349 | (version "1.26.0") |
86fb2c63 | 7350 | (source |
7351 | (origin | |
7352 | (method url-fetch) | |
7353 | (uri (bioconductor-uri "unifiedWMWqPCR" version)) | |
7354 | (sha256 | |
7355 | (base32 | |
fa7e2429 | 7356 | "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv")))) |
86fb2c63 | 7357 | (properties |
7358 | `((upstream-name . "unifiedWMWqPCR"))) | |
7359 | (build-system r-build-system) | |
7360 | (propagated-inputs | |
7361 | `(("r-biocgenerics" ,r-biocgenerics) | |
7362 | ("r-htqpcr" ,r-htqpcr))) | |
7363 | (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") | |
7364 | (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") | |
7365 | (description | |
b5b0ee3b | 7366 | "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR |
86fb2c63 | 7367 | data. This modified test allows for testing differential expression in qPCR |
7368 | data.") | |
7369 | (license license:gpl2+))) | |
72b67e0b RW |
7370 | |
7371 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put | |
7372 | ;; it here. | |
7373 | (define-public r-activedriverwgs | |
7374 | (package | |
7375 | (name "r-activedriverwgs") | |
5412da84 | 7376 | (version "1.1.1") |
72b67e0b RW |
7377 | (source |
7378 | (origin | |
7379 | (method url-fetch) | |
7380 | (uri (cran-uri "ActiveDriverWGS" version)) | |
7381 | (sha256 | |
7382 | (base32 | |
5412da84 | 7383 | "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say")))) |
72b67e0b RW |
7384 | (properties |
7385 | `((upstream-name . "ActiveDriverWGS"))) | |
7386 | (build-system r-build-system) | |
7387 | (propagated-inputs | |
7388 | `(("r-biostrings" ,r-biostrings) | |
7389 | ("r-bsgenome" ,r-bsgenome) | |
7390 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
7391 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7392 | ("r-genomicranges" ,r-genomicranges) | |
7393 | ("r-iranges" ,r-iranges) | |
72b67e0b | 7394 | ("r-s4vectors" ,r-s4vectors))) |
e1ce10e3 RW |
7395 | (native-inputs |
7396 | `(("r-knitr" ,r-knitr))) | |
72b67e0b RW |
7397 | (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") |
7398 | (synopsis "Driver discovery tool for cancer whole genomes") | |
7399 | (description | |
7400 | "This package provides a method for finding an enrichment of cancer | |
7401 | simple somatic mutations (SNVs and Indels) in functional elements across the | |
7402 | human genome. ActiveDriverWGS detects coding and noncoding driver elements | |
7403 | using whole genome sequencing data.") | |
7404 | (license license:gpl3))) | |
8e6f63dd RW |
7405 | |
7406 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put | |
7407 | ;; it here. | |
7408 | (define-public r-activepathways | |
7409 | (package | |
7410 | (name "r-activepathways") | |
a9a91280 | 7411 | (version "1.0.2") |
8e6f63dd RW |
7412 | (source |
7413 | (origin | |
7414 | (method url-fetch) | |
7415 | (uri (cran-uri "ActivePathways" version)) | |
7416 | (sha256 | |
7417 | (base32 | |
a9a91280 | 7418 | "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l")))) |
8e6f63dd RW |
7419 | (properties |
7420 | `((upstream-name . "ActivePathways"))) | |
7421 | (build-system r-build-system) | |
7422 | (propagated-inputs | |
7423 | `(("r-data-table" ,r-data-table) | |
a9a91280 | 7424 | ("r-ggplot2" ,r-ggplot2))) |
229736aa RW |
7425 | (native-inputs |
7426 | `(("r-knitr" ,r-knitr))) | |
8e6f63dd RW |
7427 | (home-page "https://cran.r-project.org/web/packages/ActivePathways/") |
7428 | (synopsis "Multivariate pathway enrichment analysis") | |
7429 | (description | |
7430 | "This package represents an integrative method of analyzing multi omics | |
7431 | data that conducts enrichment analysis of annotated gene sets. ActivePathways | |
7432 | uses a statistical data fusion approach, rationalizes contributing evidence | |
7433 | and highlights associated genes, improving systems-level understanding of | |
7434 | cellular organization in health and disease.") | |
7435 | (license license:gpl3))) | |
d11d6fea RW |
7436 | |
7437 | (define-public r-bgmix | |
7438 | (package | |
7439 | (name "r-bgmix") | |
fad5da32 | 7440 | (version "1.50.0") |
d11d6fea RW |
7441 | (source |
7442 | (origin | |
7443 | (method url-fetch) | |
7444 | (uri (bioconductor-uri "BGmix" version)) | |
7445 | (sha256 | |
7446 | (base32 | |
fad5da32 | 7447 | "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50")))) |
d11d6fea RW |
7448 | (properties `((upstream-name . "BGmix"))) |
7449 | (build-system r-build-system) | |
7450 | (propagated-inputs | |
7451 | `(("r-kernsmooth" ,r-kernsmooth))) | |
7452 | (home-page "https://bioconductor.org/packages/BGmix/") | |
7453 | (synopsis "Bayesian models for differential gene expression") | |
7454 | (description | |
7455 | "This package provides fully Bayesian mixture models for differential | |
7456 | gene expression.") | |
7457 | (license license:gpl2))) | |
75eb1149 RW |
7458 | |
7459 | (define-public r-bgx | |
7460 | (package | |
7461 | (name "r-bgx") | |
3cebe274 | 7462 | (version "1.56.0") |
75eb1149 RW |
7463 | (source |
7464 | (origin | |
7465 | (method url-fetch) | |
7466 | (uri (bioconductor-uri "bgx" version)) | |
7467 | (sha256 | |
7468 | (base32 | |
3cebe274 | 7469 | "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im")))) |
75eb1149 RW |
7470 | (properties `((upstream-name . "bgx"))) |
7471 | (build-system r-build-system) | |
7472 | (propagated-inputs | |
7473 | `(("r-affy" ,r-affy) | |
7474 | ("r-biobase" ,r-biobase) | |
7475 | ("r-gcrma" ,r-gcrma) | |
7476 | ("r-rcpp" ,r-rcpp))) | |
7477 | (home-page "https://bioconductor.org/packages/bgx/") | |
7478 | (synopsis "Bayesian gene expression") | |
7479 | (description | |
7480 | "This package provides tools for Bayesian integrated analysis of | |
7481 | Affymetrix GeneChips.") | |
7482 | (license license:gpl2))) | |
6bd50acf RW |
7483 | |
7484 | (define-public r-bhc | |
7485 | (package | |
7486 | (name "r-bhc") | |
2219bef1 | 7487 | (version "1.42.0") |
6bd50acf RW |
7488 | (source |
7489 | (origin | |
7490 | (method url-fetch) | |
7491 | (uri (bioconductor-uri "BHC" version)) | |
7492 | (sha256 | |
7493 | (base32 | |
2219bef1 | 7494 | "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn")))) |
6bd50acf RW |
7495 | (properties `((upstream-name . "BHC"))) |
7496 | (build-system r-build-system) | |
7497 | (home-page "https://bioconductor.org/packages/BHC/") | |
7498 | (synopsis "Bayesian hierarchical clustering") | |
7499 | (description | |
7500 | "The method implemented in this package performs bottom-up hierarchical | |
7501 | clustering, using a Dirichlet Process (infinite mixture) to model uncertainty | |
7502 | in the data and Bayesian model selection to decide at each step which clusters | |
7503 | to merge. This avoids several limitations of traditional methods, for example | |
7504 | how many clusters there should be and how to choose a principled distance | |
7505 | metric. This implementation accepts multinomial (i.e. discrete, with 2+ | |
7506 | categories) or time-series data. This version also includes a randomised | |
7507 | algorithm which is more efficient for larger data sets.") | |
7508 | (license license:gpl3))) | |
de9374b7 RW |
7509 | |
7510 | (define-public r-bicare | |
7511 | (package | |
7512 | (name "r-bicare") | |
4ec66569 | 7513 | (version "1.48.0") |
de9374b7 RW |
7514 | (source |
7515 | (origin | |
7516 | (method url-fetch) | |
7517 | (uri (bioconductor-uri "BicARE" version)) | |
7518 | (sha256 | |
7519 | (base32 | |
4ec66569 | 7520 | "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k")))) |
de9374b7 RW |
7521 | (properties `((upstream-name . "BicARE"))) |
7522 | (build-system r-build-system) | |
7523 | (propagated-inputs | |
7524 | `(("r-biobase" ,r-biobase) | |
7525 | ("r-gseabase" ,r-gseabase) | |
7526 | ("r-multtest" ,r-multtest))) | |
7527 | (home-page "http://bioinfo.curie.fr") | |
7528 | (synopsis "Biclustering analysis and results exploration") | |
7529 | (description | |
7530 | "This is a package for biclustering analysis and exploration of | |
7531 | results.") | |
7532 | (license license:gpl2))) | |
40fe63ad RW |
7533 | |
7534 | (define-public r-bifet | |
7535 | (package | |
7536 | (name "r-bifet") | |
d57be633 | 7537 | (version "1.10.0") |
40fe63ad RW |
7538 | (source |
7539 | (origin | |
7540 | (method url-fetch) | |
7541 | (uri (bioconductor-uri "BiFET" version)) | |
7542 | (sha256 | |
7543 | (base32 | |
d57be633 | 7544 | "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a")))) |
40fe63ad RW |
7545 | (properties `((upstream-name . "BiFET"))) |
7546 | (build-system r-build-system) | |
7547 | (propagated-inputs | |
7548 | `(("r-genomicranges" ,r-genomicranges) | |
7549 | ("r-poibin" ,r-poibin))) | |
a54fd409 RW |
7550 | (native-inputs |
7551 | `(("r-knitr" ,r-knitr))) | |
40fe63ad RW |
7552 | (home-page "https://bioconductor.org/packages/BiFET") |
7553 | (synopsis "Bias-free footprint enrichment test") | |
7554 | (description | |
7555 | "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are | |
7556 | over-represented in target regions compared to background regions after | |
7557 | correcting for the bias arising from the imbalance in read counts and GC | |
7558 | contents between the target and background regions. For a given TF k, BiFET | |
7559 | tests the null hypothesis that the target regions have the same probability of | |
7560 | having footprints for the TF k as the background regions while correcting for | |
7561 | the read count and GC content bias.") | |
7562 | (license license:gpl3))) | |
e823337c RW |
7563 | |
7564 | (define-public r-rsbml | |
7565 | (package | |
7566 | (name "r-rsbml") | |
3320f044 | 7567 | (version "2.48.0") |
e823337c RW |
7568 | (source |
7569 | (origin | |
7570 | (method url-fetch) | |
7571 | (uri (bioconductor-uri "rsbml" version)) | |
7572 | (sha256 | |
7573 | (base32 | |
3320f044 | 7574 | "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61")))) |
e823337c RW |
7575 | (properties `((upstream-name . "rsbml"))) |
7576 | (build-system r-build-system) | |
7577 | (inputs | |
7578 | `(("libsbml" ,libsbml) | |
7579 | ("zlib" ,zlib))) | |
7580 | (propagated-inputs | |
7581 | `(("r-biocgenerics" ,r-biocgenerics) | |
7582 | ("r-graph" ,r-graph))) | |
7583 | (native-inputs | |
7584 | `(("pkg-config" ,pkg-config))) | |
7585 | (home-page "http://www.sbml.org") | |
7586 | (synopsis "R support for SBML") | |
7587 | (description | |
7588 | "This package provides an R interface to libsbml for SBML parsing, | |
7589 | validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") | |
7590 | (license license:artistic2.0))) | |
75a8bb31 RW |
7591 | |
7592 | (define-public r-hypergraph | |
7593 | (package | |
7594 | (name "r-hypergraph") | |
294fd58a | 7595 | (version "1.62.0") |
75a8bb31 RW |
7596 | (source |
7597 | (origin | |
7598 | (method url-fetch) | |
7599 | (uri (bioconductor-uri "hypergraph" version)) | |
7600 | (sha256 | |
7601 | (base32 | |
294fd58a | 7602 | "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97")))) |
75a8bb31 RW |
7603 | (properties `((upstream-name . "hypergraph"))) |
7604 | (build-system r-build-system) | |
7605 | (propagated-inputs | |
7606 | `(("r-graph" ,r-graph))) | |
7607 | (home-page "https://bioconductor.org/packages/hypergraph") | |
7608 | (synopsis "Hypergraph data structures") | |
7609 | (description | |
7610 | "This package implements some simple capabilities for representing and | |
7611 | manipulating hypergraphs.") | |
7612 | (license license:artistic2.0))) | |
5aef09bd RW |
7613 | |
7614 | (define-public r-hyperdraw | |
7615 | (package | |
7616 | (name "r-hyperdraw") | |
249b7030 | 7617 | (version "1.42.0") |
5aef09bd RW |
7618 | (source |
7619 | (origin | |
7620 | (method url-fetch) | |
7621 | (uri (bioconductor-uri "hyperdraw" version)) | |
7622 | (sha256 | |
7623 | (base32 | |
249b7030 | 7624 | "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz")))) |
5aef09bd RW |
7625 | (properties `((upstream-name . "hyperdraw"))) |
7626 | (build-system r-build-system) | |
7627 | (inputs `(("graphviz" ,graphviz))) | |
7628 | (propagated-inputs | |
7629 | `(("r-graph" ,r-graph) | |
7630 | ("r-hypergraph" ,r-hypergraph) | |
7631 | ("r-rgraphviz" ,r-rgraphviz))) | |
7632 | (home-page "https://bioconductor.org/packages/hyperdraw") | |
7633 | (synopsis "Visualizing hypergraphs") | |
7634 | (description | |
7635 | "This package provides functions for visualizing hypergraphs.") | |
7636 | (license license:gpl2+))) | |
6ca6f866 RW |
7637 | |
7638 | (define-public r-biggr | |
7639 | (package | |
7640 | (name "r-biggr") | |
0f94a9ed | 7641 | (version "1.26.0") |
6ca6f866 RW |
7642 | (source |
7643 | (origin | |
7644 | (method url-fetch) | |
7645 | (uri (bioconductor-uri "BiGGR" version)) | |
7646 | (sha256 | |
7647 | (base32 | |
0f94a9ed | 7648 | "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y")))) |
6ca6f866 RW |
7649 | (properties `((upstream-name . "BiGGR"))) |
7650 | (build-system r-build-system) | |
7651 | (propagated-inputs | |
7652 | `(("r-hyperdraw" ,r-hyperdraw) | |
7653 | ("r-hypergraph" ,r-hypergraph) | |
7654 | ("r-lim" ,r-lim) | |
7655 | ("r-limsolve" ,r-limsolve) | |
7656 | ("r-rsbml" ,r-rsbml) | |
7657 | ("r-stringr" ,r-stringr))) | |
7658 | (home-page "https://bioconductor.org/packages/BiGGR/") | |
7659 | (synopsis "Constraint based modeling using metabolic reconstruction databases") | |
7660 | (description | |
7661 | "This package provides an interface to simulate metabolic reconstruction | |
7662 | from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic | |
7663 | reconstruction databases. The package facilitates @dfn{flux balance | |
7664 | analysis} (FBA) and the sampling of feasible flux distributions. Metabolic | |
7665 | networks and estimated fluxes can be visualized with hypergraphs.") | |
7666 | (license license:gpl3+))) | |
820373db RW |
7667 | |
7668 | (define-public r-bigmemoryextras | |
7669 | (package | |
7670 | (name "r-bigmemoryextras") | |
e80f8262 | 7671 | (version "1.38.0") |
820373db RW |
7672 | (source |
7673 | (origin | |
7674 | (method url-fetch) | |
7675 | (uri (bioconductor-uri "bigmemoryExtras" version)) | |
7676 | (sha256 | |
7677 | (base32 | |
e80f8262 | 7678 | "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj")))) |
820373db RW |
7679 | (properties |
7680 | `((upstream-name . "bigmemoryExtras"))) | |
7681 | (build-system r-build-system) | |
7682 | (propagated-inputs | |
7683 | `(("r-bigmemory" ,r-bigmemory))) | |
eef9c99c RW |
7684 | (native-inputs |
7685 | `(("r-knitr" ,r-knitr))) | |
820373db RW |
7686 | (home-page "https://github.com/phaverty/bigmemoryExtras") |
7687 | (synopsis "Extension of the bigmemory package") | |
7688 | (description | |
7689 | "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds | |
7690 | safety and convenience features to the @code{filebacked.big.matrix} class from | |
7691 | the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by | |
7692 | monitoring and gracefully restoring the connection to on-disk data and it also | |
7230f6d5 | 7693 | protects against accidental data modification with a file-system-based |
820373db RW |
7694 | permissions system. Utilities are provided for using @code{BigMatrix}-derived |
7695 | classes as @code{assayData} matrices within the @code{Biobase} package's | |
7696 | @code{eSet} family of classes. @code{BigMatrix} provides some optimizations | |
7697 | related to attaching to, and indexing into, file-backed matrices with | |
7698 | dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, | |
7699 | a file-backed matrix with factor properties.") | |
7700 | (license license:artistic2.0))) | |
d38775b1 RW |
7701 | |
7702 | (define-public r-bigpint | |
7703 | (package | |
7704 | (name "r-bigpint") | |
1e288678 | 7705 | (version "1.6.0") |
d38775b1 RW |
7706 | (source |
7707 | (origin | |
7708 | (method url-fetch) | |
7709 | (uri (bioconductor-uri "bigPint" version)) | |
7710 | (sha256 | |
7711 | (base32 | |
1e288678 | 7712 | "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis")))) |
d38775b1 RW |
7713 | (properties `((upstream-name . "bigPint"))) |
7714 | (build-system r-build-system) | |
7715 | (propagated-inputs | |
d0badcc1 RW |
7716 | `(("r-delayedarray" ,r-delayedarray) |
7717 | ("r-dplyr" ,r-dplyr) | |
d38775b1 RW |
7718 | ("r-ggally" ,r-ggally) |
7719 | ("r-ggplot2" ,r-ggplot2) | |
7720 | ("r-gridextra" ,r-gridextra) | |
7721 | ("r-hexbin" ,r-hexbin) | |
7722 | ("r-hmisc" ,r-hmisc) | |
7723 | ("r-htmlwidgets" ,r-htmlwidgets) | |
7724 | ("r-plotly" ,r-plotly) | |
7725 | ("r-plyr" ,r-plyr) | |
7726 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
7727 | ("r-reshape" ,r-reshape) | |
7728 | ("r-shiny" ,r-shiny) | |
7729 | ("r-shinycssloaders" ,r-shinycssloaders) | |
7730 | ("r-shinydashboard" ,r-shinydashboard) | |
7731 | ("r-stringr" ,r-stringr) | |
d0badcc1 | 7732 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
d38775b1 | 7733 | ("r-tidyr" ,r-tidyr))) |
1f2f01ae RW |
7734 | (native-inputs |
7735 | `(("r-knitr" ,r-knitr))) | |
d38775b1 RW |
7736 | (home-page "https://github.com/lindsayrutter/bigPint") |
7737 | (synopsis "Big multivariate data plotted interactively") | |
7738 | (description | |
7739 | "This package provides methods for visualizing large multivariate | |
7740 | datasets using static and interactive scatterplot matrices, parallel | |
7741 | coordinate plots, volcano plots, and litre plots. It includes examples for | |
7742 | visualizing RNA-sequencing datasets and differentially expressed genes.") | |
7743 | (license license:gpl3))) | |
991554fc RW |
7744 | |
7745 | (define-public r-chemminer | |
7746 | (package | |
7747 | (name "r-chemminer") | |
95ef2681 | 7748 | (version "3.42.0") |
991554fc RW |
7749 | (source |
7750 | (origin | |
7751 | (method url-fetch) | |
7752 | (uri (bioconductor-uri "ChemmineR" version)) | |
7753 | (sha256 | |
7754 | (base32 | |
95ef2681 | 7755 | "14q9zhhxgkx5skj424i2rbjdbp5j8jfkxspkhnkwv5i45cvkgh19")))) |
991554fc RW |
7756 | (properties `((upstream-name . "ChemmineR"))) |
7757 | (build-system r-build-system) | |
7758 | (propagated-inputs | |
7759 | `(("r-base64enc" ,r-base64enc) | |
7760 | ("r-bh" ,r-bh) | |
7761 | ("r-biocgenerics" ,r-biocgenerics) | |
7762 | ("r-dbi" ,r-dbi) | |
7763 | ("r-digest" ,r-digest) | |
7764 | ("r-dt" ,r-dt) | |
7765 | ("r-ggplot2" ,r-ggplot2) | |
7766 | ("r-gridextra" ,r-gridextra) | |
7767 | ("r-png" ,r-png) | |
7768 | ("r-rcpp" ,r-rcpp) | |
7769 | ("r-rcurl" ,r-rcurl) | |
7770 | ("r-rjson" ,r-rjson) | |
7771 | ("r-rsvg" ,r-rsvg))) | |
06908a73 RW |
7772 | (native-inputs |
7773 | `(("r-knitr" ,r-knitr))) | |
991554fc RW |
7774 | (home-page "https://github.com/girke-lab/ChemmineR") |
7775 | (synopsis "Cheminformatics toolkit for R") | |
7776 | (description | |
7777 | "ChemmineR is a cheminformatics package for analyzing drug-like small | |
7778 | molecule data in R. It contains functions for efficient processing of large | |
7779 | numbers of molecules, physicochemical/structural property predictions, | |
7780 | structural similarity searching, classification and clustering of compound | |
7781 | libraries with a wide spectrum of algorithms. In addition, it offers | |
7782 | visualization functions for compound clustering results and chemical | |
7783 | structures.") | |
7784 | (license license:artistic2.0))) | |
48bcbef0 RW |
7785 | |
7786 | (define-public r-bioassayr | |
7787 | (package | |
7788 | (name "r-bioassayr") | |
2f36b040 | 7789 | (version "1.28.0") |
48bcbef0 RW |
7790 | (source |
7791 | (origin | |
7792 | (method url-fetch) | |
7793 | (uri (bioconductor-uri "bioassayR" version)) | |
7794 | (sha256 | |
7795 | (base32 | |
2f36b040 | 7796 | "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f")))) |
48bcbef0 RW |
7797 | (properties `((upstream-name . "bioassayR"))) |
7798 | (build-system r-build-system) | |
7799 | (propagated-inputs | |
7800 | `(("r-biocgenerics" ,r-biocgenerics) | |
7801 | ("r-chemminer" ,r-chemminer) | |
7802 | ("r-dbi" ,r-dbi) | |
7803 | ("r-matrix" ,r-matrix) | |
7804 | ("r-rjson" ,r-rjson) | |
7805 | ("r-rsqlite" ,r-rsqlite) | |
7806 | ("r-xml" ,r-xml))) | |
faaf2b35 RW |
7807 | (native-inputs |
7808 | `(("r-knitr" ,r-knitr))) | |
48bcbef0 RW |
7809 | (home-page "https://github.com/TylerBackman/bioassayR") |
7810 | (synopsis "Cross-target analysis of small molecule bioactivity") | |
7811 | (description | |
7812 | "bioassayR is a computational tool that enables simultaneous analysis of | |
7813 | thousands of bioassay experiments performed over a diverse set of compounds | |
7814 | and biological targets. Unique features include support for large-scale | |
7815 | cross-target analyses of both public and custom bioassays, generation of | |
7816 | @dfn{high throughput screening fingerprints} (HTSFPs), and an optional | |
7817 | preloaded database that provides access to a substantial portion of publicly | |
7818 | available bioactivity data.") | |
7819 | (license license:artistic2.0))) | |
29fd736a RW |
7820 | |
7821 | (define-public r-biobroom | |
7822 | (package | |
7823 | (name "r-biobroom") | |
95e30d8f | 7824 | (version "1.22.0") |
29fd736a RW |
7825 | (source |
7826 | (origin | |
7827 | (method url-fetch) | |
7828 | (uri (bioconductor-uri "biobroom" version)) | |
7829 | (sha256 | |
7830 | (base32 | |
95e30d8f | 7831 | "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv")))) |
29fd736a RW |
7832 | (properties `((upstream-name . "biobroom"))) |
7833 | (build-system r-build-system) | |
7834 | (propagated-inputs | |
7835 | `(("r-biobase" ,r-biobase) | |
7836 | ("r-broom" ,r-broom) | |
7837 | ("r-dplyr" ,r-dplyr) | |
7838 | ("r-tidyr" ,r-tidyr))) | |
e09ca033 RW |
7839 | (native-inputs |
7840 | `(("r-knitr" ,r-knitr))) | |
29fd736a RW |
7841 | (home-page "https://github.com/StoreyLab/biobroom") |
7842 | (synopsis "Turn Bioconductor objects into tidy data frames") | |
7843 | (description | |
7844 | "This package contains methods for converting standard objects | |
7845 | constructed by bioinformatics packages, especially those in Bioconductor, and | |
7846 | converting them to @code{tidy} data. It thus serves as a complement to the | |
7847 | @code{broom} package, and follows the same tidy, augment, glance division of | |
7848 | tidying methods. Tidying data makes it easy to recombine, reshape and | |
7849 | visualize bioinformatics analyses.") | |
7850 | ;; Any version of the LGPL. | |
7851 | (license license:lgpl3+))) | |
c373223e RW |
7852 | |
7853 | (define-public r-graphite | |
7854 | (package | |
7855 | (name "r-graphite") | |
26224e09 | 7856 | (version "1.36.0") |
c373223e RW |
7857 | (source |
7858 | (origin | |
7859 | (method url-fetch) | |
7860 | (uri (bioconductor-uri "graphite" version)) | |
7861 | (sha256 | |
7862 | (base32 | |
26224e09 | 7863 | "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk")))) |
c373223e RW |
7864 | (properties `((upstream-name . "graphite"))) |
7865 | (build-system r-build-system) | |
7866 | (propagated-inputs | |
7867 | `(("r-annotationdbi" ,r-annotationdbi) | |
7868 | ("r-checkmate" ,r-checkmate) | |
7869 | ("r-graph" ,r-graph) | |
7870 | ("r-httr" ,r-httr) | |
7871 | ("r-rappdirs" ,r-rappdirs))) | |
7872 | (home-page "https://bioconductor.org/packages/graphite/") | |
7873 | (synopsis "Networks from pathway databases") | |
7874 | (description | |
7875 | "Graphite provides networks derived from eight public pathway databases, | |
7876 | and automates the conversion of node identifiers (e.g. from Entrez IDs to gene | |
7877 | symbols).") | |
7878 | (license license:agpl3+))) | |
f388834e RW |
7879 | |
7880 | (define-public r-reactomepa | |
7881 | (package | |
7882 | (name "r-reactomepa") | |
a4f4a552 | 7883 | (version "1.34.0") |
f388834e RW |
7884 | (source |
7885 | (origin | |
7886 | (method url-fetch) | |
7887 | (uri (bioconductor-uri "ReactomePA" version)) | |
7888 | (sha256 | |
7889 | (base32 | |
a4f4a552 | 7890 | "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m")))) |
f388834e RW |
7891 | (properties `((upstream-name . "ReactomePA"))) |
7892 | (build-system r-build-system) | |
7893 | (propagated-inputs | |
7894 | `(("r-annotationdbi" ,r-annotationdbi) | |
7895 | ("r-dose" ,r-dose) | |
7896 | ("r-enrichplot" ,r-enrichplot) | |
7897 | ("r-ggplot2" ,r-ggplot2) | |
7898 | ("r-ggraph" ,r-ggraph) | |
7899 | ("r-graphite" ,r-graphite) | |
7900 | ("r-igraph" ,r-igraph) | |
7901 | ("r-reactome-db" ,r-reactome-db))) | |
affb4ab3 RW |
7902 | (native-inputs |
7903 | `(("r-knitr" ,r-knitr))) | |
f388834e RW |
7904 | (home-page "https://guangchuangyu.github.io/software/ReactomePA") |
7905 | (synopsis "Reactome pathway analysis") | |
7906 | (description | |
7907 | "This package provides functions for pathway analysis based on the | |
7908 | REACTOME pathway database. It implements enrichment analysis, gene set | |
7909 | enrichment analysis and several functions for visualization.") | |
7910 | (license license:gpl2))) | |
21afe920 RW |
7911 | |
7912 | (define-public r-ebarrays | |
7913 | (package | |
7914 | (name "r-ebarrays") | |
b0f3bfe4 | 7915 | (version "2.54.0") |
21afe920 RW |
7916 | (source |
7917 | (origin | |
7918 | (method url-fetch) | |
7919 | (uri (bioconductor-uri "EBarrays" version)) | |
7920 | (sha256 | |
7921 | (base32 | |
b0f3bfe4 | 7922 | "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd")))) |
21afe920 RW |
7923 | (properties `((upstream-name . "EBarrays"))) |
7924 | (build-system r-build-system) | |
7925 | (propagated-inputs | |
7926 | `(("r-biobase" ,r-biobase) | |
7927 | ("r-cluster" ,r-cluster) | |
7928 | ("r-lattice" ,r-lattice))) | |
7929 | (home-page "https://bioconductor.org/packages/EBarrays/") | |
7930 | (synopsis "Gene clustering and differential expression identification") | |
7931 | (description | |
7932 | "EBarrays provides tools for the analysis of replicated/unreplicated | |
7933 | microarray data.") | |
7934 | (license license:gpl2+))) | |
f180be29 RW |
7935 | |
7936 | (define-public r-bioccasestudies | |
7937 | (package | |
7938 | (name "r-bioccasestudies") | |
7dced9ad | 7939 | (version "1.52.0") |
f180be29 RW |
7940 | (source |
7941 | (origin | |
7942 | (method url-fetch) | |
7943 | (uri (bioconductor-uri "BiocCaseStudies" version)) | |
7944 | (sha256 | |
7945 | (base32 | |
7dced9ad | 7946 | "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1")))) |
f180be29 RW |
7947 | (properties |
7948 | `((upstream-name . "BiocCaseStudies"))) | |
7949 | (build-system r-build-system) | |
7950 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
7951 | (home-page "https://bioconductor.org/packages/BiocCaseStudies") | |
7952 | (synopsis "Support for the case studies monograph") | |
7953 | (description | |
7954 | "This package provides software and data to support the case studies | |
7955 | monograph.") | |
7956 | (license license:artistic2.0))) | |
49f0860b RW |
7957 | |
7958 | (define-public r-biocgraph | |
7959 | (package | |
7960 | (name "r-biocgraph") | |
abc18fc5 | 7961 | (version "1.52.0") |
49f0860b RW |
7962 | (source |
7963 | (origin | |
7964 | (method url-fetch) | |
7965 | (uri (bioconductor-uri "biocGraph" version)) | |
7966 | (sha256 | |
7967 | (base32 | |
abc18fc5 | 7968 | "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75")))) |
49f0860b RW |
7969 | (properties `((upstream-name . "biocGraph"))) |
7970 | (build-system r-build-system) | |
7971 | (propagated-inputs | |
7972 | `(("r-biocgenerics" ,r-biocgenerics) | |
7973 | ("r-geneplotter" ,r-geneplotter) | |
7974 | ("r-graph" ,r-graph) | |
7975 | ("r-rgraphviz" ,r-rgraphviz))) | |
7976 | (home-page "https://bioconductor.org/packages/biocGraph/") | |
7977 | (synopsis "Graph examples and use cases in Bioinformatics") | |
7978 | (description | |
7979 | "This package provides examples and code that make use of the | |
7980 | different graph related packages produced by Bioconductor.") | |
7981 | (license license:artistic2.0))) | |
244270e6 RW |
7982 | |
7983 | (define-public r-experimenthub | |
7984 | (package | |
7985 | (name "r-experimenthub") | |
49a72858 | 7986 | (version "1.16.0") |
244270e6 RW |
7987 | (source |
7988 | (origin | |
7989 | (method url-fetch) | |
7990 | (uri (bioconductor-uri "ExperimentHub" version)) | |
7991 | (sha256 | |
7992 | (base32 | |
49a72858 | 7993 | "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg")))) |
244270e6 RW |
7994 | (properties `((upstream-name . "ExperimentHub"))) |
7995 | (build-system r-build-system) | |
7996 | (propagated-inputs | |
7997 | `(("r-annotationhub" ,r-annotationhub) | |
7998 | ("r-biocfilecache" ,r-biocfilecache) | |
7999 | ("r-biocgenerics" ,r-biocgenerics) | |
8000 | ("r-biocmanager" ,r-biocmanager) | |
8001 | ("r-curl" ,r-curl) | |
8002 | ("r-rappdirs" ,r-rappdirs) | |
8003 | ("r-s4vectors" ,r-s4vectors))) | |
b56a3462 RW |
8004 | (native-inputs |
8005 | `(("r-knitr" ,r-knitr))) | |
244270e6 RW |
8006 | (home-page "https://bioconductor.org/packages/ExperimentHub/") |
8007 | (synopsis "Client to access ExperimentHub resources") | |
8008 | (description | |
8009 | "This package provides a client for the Bioconductor ExperimentHub web | |
8010 | resource. ExperimentHub provides a central location where curated data from | |
8011 | experiments, publications or training courses can be accessed. Each resource | |
8012 | has associated metadata, tags and date of modification. The client creates | |
8013 | and manages a local cache of files retrieved enabling quick and reproducible | |
8014 | access.") | |
8015 | (license license:artistic2.0))) | |
06784793 RW |
8016 | |
8017 | (define-public r-multiassayexperiment | |
8018 | (package | |
8019 | (name "r-multiassayexperiment") | |
13d0b780 | 8020 | (version "1.16.0") |
06784793 RW |
8021 | (source |
8022 | (origin | |
8023 | (method url-fetch) | |
8024 | (uri (bioconductor-uri "MultiAssayExperiment" version)) | |
8025 | (sha256 | |
8026 | (base32 | |
13d0b780 | 8027 | "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs")))) |
06784793 RW |
8028 | (properties |
8029 | `((upstream-name . "MultiAssayExperiment"))) | |
8030 | (build-system r-build-system) | |
8031 | (propagated-inputs | |
8032 | `(("r-biobase" ,r-biobase) | |
8033 | ("r-biocgenerics" ,r-biocgenerics) | |
8034 | ("r-genomicranges" ,r-genomicranges) | |
8035 | ("r-iranges" ,r-iranges) | |
8036 | ("r-s4vectors" ,r-s4vectors) | |
8037 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
8038 | ("r-tidyr" ,r-tidyr))) | |
5d45d711 RW |
8039 | (native-inputs |
8040 | `(("r-knitr" ,r-knitr))) | |
798ca8d0 | 8041 | (home-page "https://waldronlab.io/MultiAssayExperiment/") |
06784793 RW |
8042 | (synopsis "Integration of multi-omics experiments in Bioconductor") |
8043 | (description | |
8044 | "MultiAssayExperiment harmonizes data management of multiple assays | |
8045 | performed on an overlapping set of specimens. It provides a familiar | |
8046 | Bioconductor user experience by extending concepts from | |
8047 | @code{SummarizedExperiment}, supporting an open-ended mix of standard data | |
8048 | classes for individual assays, and allowing subsetting by genomic ranges or | |
8049 | rownames.") | |
8050 | (license license:artistic2.0))) | |
c2b36a04 RW |
8051 | |
8052 | (define-public r-bioconcotk | |
8053 | (package | |
8054 | (name "r-bioconcotk") | |
e29b15ee | 8055 | (version "1.10.0") |
c2b36a04 RW |
8056 | (source |
8057 | (origin | |
8058 | (method url-fetch) | |
8059 | (uri (bioconductor-uri "BiocOncoTK" version)) | |
8060 | (sha256 | |
8061 | (base32 | |
e29b15ee | 8062 | "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108")))) |
c2b36a04 RW |
8063 | (properties `((upstream-name . "BiocOncoTK"))) |
8064 | (build-system r-build-system) | |
8065 | (propagated-inputs | |
8066 | `(("r-bigrquery" ,r-bigrquery) | |
8067 | ("r-car" ,r-car) | |
8068 | ("r-complexheatmap" ,r-complexheatmap) | |
8069 | ("r-curatedtcgadata" ,r-curatedtcgadata) | |
8070 | ("r-dbi" ,r-dbi) | |
8071 | ("r-dplyr" ,r-dplyr) | |
8072 | ("r-dt" ,r-dt) | |
8073 | ("r-genomicfeatures" ,r-genomicfeatures) | |
8074 | ("r-genomicranges" ,r-genomicranges) | |
8075 | ("r-ggplot2" ,r-ggplot2) | |
8076 | ("r-ggpubr" ,r-ggpubr) | |
8077 | ("r-graph" ,r-graph) | |
8078 | ("r-httr" ,r-httr) | |
8079 | ("r-iranges" ,r-iranges) | |
8080 | ("r-magrittr" ,r-magrittr) | |
8081 | ("r-plyr" ,r-plyr) | |
8082 | ("r-rgraphviz" ,r-rgraphviz) | |
8083 | ("r-rjson" ,r-rjson) | |
8084 | ("r-s4vectors" ,r-s4vectors) | |
8085 | ("r-scales" ,r-scales) | |
8086 | ("r-shiny" ,r-shiny) | |
8087 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1c518215 RW |
8088 | (native-inputs |
8089 | `(("r-knitr" ,r-knitr))) | |
c2b36a04 RW |
8090 | (home-page "https://bioconductor.org/packages/BiocOncoTK") |
8091 | (synopsis "Bioconductor components for general cancer genomics") | |
8092 | (description | |
8093 | "The purpose of this package is to provide a central interface to various | |
8094 | tools for genome-scale analysis of cancer studies.") | |
8095 | (license license:artistic2.0))) | |
4d12c1e3 RW |
8096 | |
8097 | (define-public r-biocor | |
8098 | (package | |
8099 | (name "r-biocor") | |
072f722f | 8100 | (version "1.14.0") |
4d12c1e3 RW |
8101 | (source |
8102 | (origin | |
8103 | (method url-fetch) | |
8104 | (uri (bioconductor-uri "BioCor" version)) | |
8105 | (sha256 | |
8106 | (base32 | |
072f722f | 8107 | "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19")))) |
4d12c1e3 RW |
8108 | (properties `((upstream-name . "BioCor"))) |
8109 | (build-system r-build-system) | |
8110 | (propagated-inputs | |
8111 | `(("r-biocparallel" ,r-biocparallel) | |
8112 | ("r-gseabase" ,r-gseabase) | |
8113 | ("r-matrix" ,r-matrix))) | |
132abe5f RW |
8114 | (native-inputs |
8115 | `(("r-knitr" ,r-knitr))) | |
4d12c1e3 RW |
8116 | (home-page "https://llrs.github.io/BioCor/") |
8117 | (synopsis "Functional similarities") | |
8118 | (description | |
8119 | "This package provides tools to calculate functional similarities based | |
8120 | on the pathways described on KEGG and REACTOME or in gene sets. These | |
8121 | similarities can be calculated for pathways or gene sets, genes, or clusters | |
8122 | and combined with other similarities. They can be used to improve networks, | |
8123 | gene selection, testing relationships, and so on.") | |
8124 | (license license:expat))) | |
4a18112d RW |
8125 | |
8126 | (define-public r-biocpkgtools | |
8127 | (package | |
8128 | (name "r-biocpkgtools") | |
6a5d8cad | 8129 | (version "1.8.0") |
4a18112d RW |
8130 | (source |
8131 | (origin | |
8132 | (method url-fetch) | |
8133 | (uri (bioconductor-uri "BiocPkgTools" version)) | |
8134 | (sha256 | |
8135 | (base32 | |
6a5d8cad | 8136 | "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m")))) |
4a18112d RW |
8137 | (properties `((upstream-name . "BiocPkgTools"))) |
8138 | (build-system r-build-system) | |
8139 | (propagated-inputs | |
2d6a7bca RW |
8140 | `(("r-biocfilecache" ,r-biocfilecache) |
8141 | ("r-biocmanager" ,r-biocmanager) | |
4a18112d RW |
8142 | ("r-biocviews" ,r-biocviews) |
8143 | ("r-dplyr" ,r-dplyr) | |
8144 | ("r-dt" ,r-dt) | |
8145 | ("r-gh" ,r-gh) | |
8146 | ("r-graph" ,r-graph) | |
8147 | ("r-htmltools" ,r-htmltools) | |
8148 | ("r-htmlwidgets" ,r-htmlwidgets) | |
8149 | ("r-httr" ,r-httr) | |
8150 | ("r-igraph" ,r-igraph) | |
8151 | ("r-jsonlite" ,r-jsonlite) | |
8152 | ("r-magrittr" ,r-magrittr) | |
2d6a7bca | 8153 | ("r-rappdirs" ,r-rappdirs) |
4a18112d RW |
8154 | ("r-rbgl" ,r-rbgl) |
8155 | ("r-readr" ,r-readr) | |
8156 | ("r-rex" ,r-rex) | |
2d6a7bca | 8157 | ("r-rlang" ,r-rlang) |
4a18112d RW |
8158 | ("r-rvest" ,r-rvest) |
8159 | ("r-stringr" ,r-stringr) | |
8160 | ("r-tibble" ,r-tibble) | |
8161 | ("r-tidyr" ,r-tidyr) | |
2d6a7bca | 8162 | ("r-tidyselect" ,r-tidyselect) |
4a18112d | 8163 | ("r-xml2" ,r-xml2))) |
2d6a7bca RW |
8164 | (native-inputs |
8165 | `(("r-knitr" ,r-knitr))) | |
4a18112d RW |
8166 | (home-page "https://github.com/seandavi/BiocPkgTools") |
8167 | (synopsis "Collection of tools for learning about Bioconductor packages") | |
8168 | (description | |
8169 | "Bioconductor has a rich ecosystem of metadata around packages, usage, | |
8170 | and build status. This package is a simple collection of functions to access | |
8171 | that metadata from R. The goal is to expose metadata for data mining and | |
8172 | value-added functionality such as package searching, text mining, and | |
8173 | analytics on packages.") | |
8174 | (license license:expat))) | |
43b66e3f RW |
8175 | |
8176 | (define-public r-biocset | |
8177 | (package | |
8178 | (name "r-biocset") | |
feb0cbf4 | 8179 | (version "1.4.0") |
43b66e3f RW |
8180 | (source |
8181 | (origin | |
8182 | (method url-fetch) | |
8183 | (uri (bioconductor-uri "BiocSet" version)) | |
8184 | (sha256 | |
8185 | (base32 | |
feb0cbf4 | 8186 | "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg")))) |
43b66e3f RW |
8187 | (properties `((upstream-name . "BiocSet"))) |
8188 | (build-system r-build-system) | |
8189 | (propagated-inputs | |
8190 | `(("r-annotationdbi" ,r-annotationdbi) | |
feb0cbf4 | 8191 | ("r-biocio" ,r-biocio) |
43b66e3f RW |
8192 | ("r-dplyr" ,r-dplyr) |
8193 | ("r-keggrest" ,r-keggrest) | |
feb0cbf4 | 8194 | ("r-ontologyindex" ,r-ontologyindex) |
43b66e3f RW |
8195 | ("r-plyr" ,r-plyr) |
8196 | ("r-rlang" ,r-rlang) | |
feb0cbf4 | 8197 | ("r-s4vectors" ,r-s4vectors) |
8198 | ("r-tibble" ,r-tibble) | |
8199 | ("r-tidyr" ,r-tidyr))) | |
723fa00d RW |
8200 | (native-inputs |
8201 | `(("r-knitr" ,r-knitr))) | |
43b66e3f RW |
8202 | (home-page |
8203 | "https://bioconductor.org/packages/BiocSet") | |
8204 | (synopsis | |
8205 | "Representing Different Biological Sets") | |
8206 | (description | |
8207 | "BiocSet displays different biological sets in a triple tibble format. | |
8208 | These three tibbles are @code{element}, @code{set}, and @code{elementset}. | |
5b98473a | 8209 | The user has the ability to activate one of these three tibbles to perform |
43b66e3f RW |
8210 | common functions from the @code{dplyr} package. Mapping functionality and |
8211 | accessing web references for elements/sets are also available in BiocSet.") | |
8212 | (license license:artistic2.0))) | |
0156297f RW |
8213 | |
8214 | (define-public r-biocworkflowtools | |
8215 | (package | |
8216 | (name "r-biocworkflowtools") | |
7891c83c | 8217 | (version "1.16.0") |
0156297f RW |
8218 | (source |
8219 | (origin | |
8220 | (method url-fetch) | |
8221 | (uri (bioconductor-uri "BiocWorkflowTools" version)) | |
8222 | (sha256 | |
8223 | (base32 | |
7891c83c | 8224 | "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6")))) |
0156297f RW |
8225 | (properties |
8226 | `((upstream-name . "BiocWorkflowTools"))) | |
8227 | (build-system r-build-system) | |
8228 | (propagated-inputs | |
8229 | `(("r-biocstyle" ,r-biocstyle) | |
8230 | ("r-bookdown" ,r-bookdown) | |
8231 | ("r-git2r" ,r-git2r) | |
8232 | ("r-httr" ,r-httr) | |
8233 | ("r-knitr" ,r-knitr) | |
8234 | ("r-rmarkdown" ,r-rmarkdown) | |
8235 | ("r-rstudioapi" ,r-rstudioapi) | |
8236 | ("r-stringr" ,r-stringr) | |
8237 | ("r-usethis" ,r-usethis))) | |
4ecba230 RW |
8238 | (native-inputs |
8239 | `(("r-knitr" ,r-knitr))) | |
0156297f RW |
8240 | (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") |
8241 | (synopsis "Tools to aid the development of Bioconductor Workflow packages") | |
8242 | (description | |
8243 | "This package provides functions to ease the transition between | |
8244 | Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") | |
8245 | (license license:expat))) | |
77e2de36 RW |
8246 | |
8247 | (define-public r-biodist | |
8248 | (package | |
8249 | (name "r-biodist") | |
15be98c1 | 8250 | (version "1.62.0") |
77e2de36 RW |
8251 | (source |
8252 | (origin | |
8253 | (method url-fetch) | |
8254 | (uri (bioconductor-uri "bioDist" version)) | |
8255 | (sha256 | |
8256 | (base32 | |
15be98c1 | 8257 | "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap")))) |
77e2de36 RW |
8258 | (properties `((upstream-name . "bioDist"))) |
8259 | (build-system r-build-system) | |
8260 | (propagated-inputs | |
8261 | `(("r-biobase" ,r-biobase) | |
8262 | ("r-kernsmooth" ,r-kernsmooth))) | |
8263 | (home-page "https://bioconductor.org/packages/bioDist/") | |
8264 | (synopsis "Different distance measures") | |
8265 | (description | |
8266 | "This package provides a collection of software tools for calculating | |
8267 | distance measures.") | |
8268 | (license license:artistic2.0))) | |
9bc516ba RW |
8269 | |
8270 | (define-public r-pcatools | |
8271 | (package | |
8272 | (name "r-pcatools") | |
8273 | (version "2.0.0") | |
8274 | (source | |
8275 | (origin | |
8276 | (method url-fetch) | |
8277 | (uri (bioconductor-uri "PCAtools" version)) | |
8278 | (sha256 | |
8279 | (base32 | |
8280 | "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc")))) | |
8281 | (properties `((upstream-name . "PCAtools"))) | |
8282 | (build-system r-build-system) | |
8283 | (propagated-inputs | |
8284 | `(("r-beachmat" ,r-beachmat) | |
8285 | ("r-bh" ,r-bh) | |
8286 | ("r-biocparallel" ,r-biocparallel) | |
8287 | ("r-biocsingular" ,r-biocsingular) | |
8288 | ("r-cowplot" ,r-cowplot) | |
8289 | ("r-delayedarray" ,r-delayedarray) | |
8290 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
8291 | ("r-dqrng" ,r-dqrng) | |
8292 | ("r-ggplot2" ,r-ggplot2) | |
8293 | ("r-ggrepel" ,r-ggrepel) | |
8294 | ("r-lattice" ,r-lattice) | |
8295 | ("r-matrix" ,r-matrix) | |
8296 | ("r-rcpp" ,r-rcpp) | |
8297 | ("r-reshape2" ,r-reshape2))) | |
8298 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8299 | (home-page "https://github.com/kevinblighe/PCAtools") | |
8300 | (synopsis "PCAtools: everything Principal Components Analysis") | |
8301 | (description | |
8302 | "@dfn{Principal Component Analysis} (PCA) extracts the fundamental | |
8303 | structure of the data without the need to build any model to represent it. | |
8304 | This \"summary\" of the data is arrived at through a process of reduction that | |
8305 | can transform the large number of variables into a lesser number that are | |
8306 | uncorrelated (i.e. the 'principal components'), while at the same time being | |
8307 | capable of easy interpretation on the original data. PCAtools provides | |
8308 | functions for data exploration via PCA, and allows the user to generate | |
8309 | publication-ready figures. PCA is performed via @code{BiocSingular}; users | |
8310 | can also identify an optimal number of principal components via different | |
8311 | metrics, such as the elbow method and Horn's parallel analysis, which has | |
8312 | relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high | |
8313 | dimensional mass cytometry data.") | |
8314 | (license license:gpl3))) | |
c89afe75 RW |
8315 | |
8316 | (define-public r-rgreat | |
8317 | (package | |
8318 | (name "r-rgreat") | |
7a242042 | 8319 | (version "1.22.0") |
c89afe75 RW |
8320 | (source |
8321 | (origin | |
8322 | (method url-fetch) | |
8323 | (uri (bioconductor-uri "rGREAT" version)) | |
8324 | (sha256 | |
8325 | (base32 | |
7a242042 | 8326 | "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj")))) |
c89afe75 RW |
8327 | (properties `((upstream-name . "rGREAT"))) |
8328 | (build-system r-build-system) | |
8329 | (propagated-inputs | |
8330 | `(("r-genomicranges" ,r-genomicranges) | |
8331 | ("r-getoptlong" ,r-getoptlong) | |
8332 | ("r-iranges" ,r-iranges) | |
8333 | ("r-rcurl" ,r-rcurl) | |
8334 | ("r-rjson" ,r-rjson))) | |
8335 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8336 | (home-page "https://github.com/jokergoo/rGREAT") | |
8337 | (synopsis "Client for GREAT analysis") | |
8338 | (description | |
8339 | "This package makes GREAT (Genomic Regions Enrichment of Annotations | |
8340 | Tool) analysis automatic by constructing a HTTP POST request according to | |
8341 | user's input and automatically retrieving results from GREAT web server.") | |
8342 | (license license:expat))) | |
0b8c7e4b RW |
8343 | |
8344 | (define-public r-m3c | |
8345 | (package | |
8346 | (name "r-m3c") | |
126846a0 | 8347 | (version "1.12.0") |
0b8c7e4b RW |
8348 | (source |
8349 | (origin | |
8350 | (method url-fetch) | |
8351 | (uri (bioconductor-uri "M3C" version)) | |
8352 | (sha256 | |
8353 | (base32 | |
126846a0 | 8354 | "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5")))) |
0b8c7e4b RW |
8355 | (properties `((upstream-name . "M3C"))) |
8356 | (build-system r-build-system) | |
8357 | (propagated-inputs | |
8358 | `(("r-cluster" ,r-cluster) | |
8359 | ("r-corpcor" ,r-corpcor) | |
8360 | ("r-doparallel" ,r-doparallel) | |
8361 | ("r-dosnow" ,r-dosnow) | |
8362 | ("r-foreach" ,r-foreach) | |
8363 | ("r-ggplot2" ,r-ggplot2) | |
8364 | ("r-matrix" ,r-matrix) | |
8365 | ("r-matrixcalc" ,r-matrixcalc) | |
8366 | ("r-rtsne" ,r-rtsne) | |
8367 | ("r-umap" ,r-umap))) | |
8368 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8369 | (home-page "https://bioconductor.org/packages/M3C") | |
8370 | (synopsis "Monte Carlo reference-based consensus clustering") | |
8371 | (description | |
8372 | "M3C is a consensus clustering algorithm that uses a Monte Carlo | |
8373 | simulation to eliminate overestimation of @code{K} and can reject the null | |
8374 | hypothesis @code{K=1}.") | |
8375 | (license license:agpl3+))) | |
488001eb PL |
8376 | |
8377 | (define-public r-icens | |
8378 | (package | |
8379 | (name "r-icens") | |
3cacc3bd | 8380 | (version "1.62.0") |
488001eb PL |
8381 | (source |
8382 | (origin | |
8383 | (method url-fetch) | |
8384 | (uri (bioconductor-uri "Icens" version)) | |
8385 | (sha256 | |
8386 | (base32 | |
3cacc3bd | 8387 | "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr")))) |
488001eb PL |
8388 | (properties `((upstream-name . "Icens"))) |
8389 | (build-system r-build-system) | |
8390 | (propagated-inputs | |
8391 | `(("r-survival" ,r-survival))) | |
8392 | (home-page "https://bioconductor.org/packages/Icens") | |
8393 | (synopsis "NPMLE for censored and truncated data") | |
8394 | (description | |
8395 | "This package provides many functions for computing the | |
8396 | @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and | |
8397 | truncated data.") | |
8398 | (license license:artistic2.0))) | |
655c4bb2 PL |
8399 | |
8400 | ;; This is a CRAN package but it depends on r-icens, which is published on | |
8401 | ;; Bioconductor. | |
8402 | (define-public r-interval | |
8403 | (package | |
8404 | (name "r-interval") | |
65e361f9 | 8405 | (version "1.1-0.7") |
655c4bb2 PL |
8406 | (source |
8407 | (origin | |
8408 | (method url-fetch) | |
8409 | (uri (cran-uri "interval" version)) | |
8410 | (sha256 | |
8411 | (base32 | |
65e361f9 | 8412 | "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9")))) |
655c4bb2 PL |
8413 | (properties `((upstream-name . "interval"))) |
8414 | (build-system r-build-system) | |
8415 | (propagated-inputs | |
8416 | `(("r-icens" ,r-icens) | |
8417 | ("r-mlecens" ,r-mlecens) | |
8418 | ("r-perm" ,r-perm) | |
8419 | ("r-survival" ,r-survival))) | |
8420 | (home-page "https://cran.r-project.org/web/packages/interval/") | |
8421 | (synopsis "Weighted Logrank tests and NPMLE for interval censored data") | |
8422 | (description | |
8423 | "This package provides functions to fit nonparametric survival curves, | |
8424 | plot them, and perform logrank or Wilcoxon type tests.") | |
8425 | (license license:gpl2+))) | |
7e88ee9f PL |
8426 | |
8427 | ;; This is a CRAN package, but it depends on r-interval, which depends on a | |
8428 | ;; Bioconductor package. | |
8429 | (define-public r-fhtest | |
8430 | (package | |
8431 | (name "r-fhtest") | |
d7cfdc12 | 8432 | (version "1.5") |
7e88ee9f PL |
8433 | (source |
8434 | (origin | |
8435 | (method url-fetch) | |
8436 | (uri (cran-uri "FHtest" version)) | |
8437 | (sha256 | |
8438 | (base32 | |
d7cfdc12 | 8439 | "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q")))) |
7e88ee9f PL |
8440 | (properties `((upstream-name . "FHtest"))) |
8441 | (build-system r-build-system) | |
8442 | (propagated-inputs | |
8443 | `(("r-interval" ,r-interval) | |
8444 | ("r-kmsurv" ,r-kmsurv) | |
8445 | ("r-mass" ,r-mass) | |
8446 | ("r-perm" ,r-perm) | |
8447 | ("r-survival" ,r-survival))) | |
8448 | (home-page "https://cran.r-project.org/web/packages/FHtest/") | |
8449 | (synopsis "Tests for survival data based on the Fleming-Harrington class") | |
8450 | (description | |
8451 | "This package provides functions to compare two or more survival curves | |
8452 | with: | |
8453 | ||
8454 | @itemize | |
8455 | @item The Fleming-Harrington test for right-censored data based on | |
8456 | permutations and on counting processes. | |
8457 | @item An extension of the Fleming-Harrington test for interval-censored data | |
8458 | based on a permutation distribution and on a score vector distribution. | |
8459 | @end itemize | |
8460 | ") | |
8461 | (license license:gpl2+))) | |
f4d920b9 | 8462 | |
8463 | (define-public r-fourcseq | |
8464 | (package | |
8465 | (name "r-fourcseq") | |
e5b2c80d | 8466 | (version "1.24.0") |
f4d920b9 | 8467 | (source |
8468 | (origin | |
8469 | (method url-fetch) | |
8470 | (uri (bioconductor-uri "FourCSeq" version)) | |
8471 | (sha256 | |
e5b2c80d | 8472 | (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb")))) |
f4d920b9 | 8473 | (properties `((upstream-name . "FourCSeq"))) |
8474 | (build-system r-build-system) | |
8475 | (propagated-inputs | |
8476 | `(("r-biobase" ,r-biobase) | |
8477 | ("r-biostrings" ,r-biostrings) | |
8478 | ("r-deseq2" ,r-deseq2) | |
8479 | ("r-fda" ,r-fda) | |
8480 | ("r-genomicalignments" ,r-genomicalignments) | |
8481 | ("r-genomicranges" ,r-genomicranges) | |
8482 | ("r-ggbio" ,r-ggbio) | |
8483 | ("r-ggplot2" ,r-ggplot2) | |
8484 | ("r-gtools" ,r-gtools) | |
8485 | ("r-lsd" ,r-lsd) | |
8486 | ("r-matrix" ,r-matrix) | |
8487 | ("r-reshape2" ,r-reshape2) | |
8488 | ("r-rsamtools" ,r-rsamtools) | |
8489 | ("r-rtracklayer" ,r-rtracklayer) | |
8490 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
8491 | (native-inputs | |
8492 | `(("r-knitr" ,r-knitr))) | |
8493 | (home-page | |
8494 | "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") | |
8495 | (synopsis "Analysis of multiplexed 4C sequencing data") | |
8496 | (description | |
8497 | "This package is an R package dedicated to the analysis of (multiplexed) | |
8498 | 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific | |
8499 | interactions between DNA elements and identify differential interactions | |
8500 | between conditions. The statistical analysis in R starts with individual bam | |
8501 | files for each sample as inputs. To obtain these files, the package contains | |
8502 | a Python script to demultiplex libraries and trim off primer sequences. With | |
8503 | a standard alignment software the required bam files can be then be | |
8504 | generated.") | |
8505 | (license license:gpl3+))) | |
6e0ab26f | 8506 | |
8507 | (define-public r-preprocesscore | |
8508 | (package | |
8509 | (name "r-preprocesscore") | |
8fa30df0 | 8510 | (version "1.52.0") |
6e0ab26f | 8511 | (source |
8512 | (origin | |
8513 | (method url-fetch) | |
8514 | (uri (bioconductor-uri "preprocessCore" version)) | |
8515 | (sha256 | |
8516 | (base32 | |
8fa30df0 | 8517 | "1i5ky3bfbkrz4lgfs72fkckr8q3wq48p38mp05cjmnmh1chmdw38")))) |
6e0ab26f | 8518 | (properties |
8519 | `((upstream-name . "preprocessCore"))) | |
8520 | (build-system r-build-system) | |
8521 | (home-page "https://github.com/bmbolstad/preprocessCore") | |
8522 | (synopsis "Collection of pre-processing functions") | |
8523 | (description | |
8524 | "This package provides a library of core pre-processing and normalization | |
8525 | routines.") | |
8526 | (license license:lgpl2.0+))) | |
b3a99837 | 8527 | |
3159fcf1 RW |
8528 | ;; This is a CRAN package, but it depends on preprocessorcore, which is a |
8529 | ;; Bioconductor package. | |
8530 | (define-public r-wgcna | |
8531 | (package | |
8532 | (name "r-wgcna") | |
8533 | (version "1.69") | |
8534 | (source | |
8535 | (origin | |
8536 | (method url-fetch) | |
8537 | (uri (cran-uri "WGCNA" version)) | |
8538 | (sha256 | |
8539 | (base32 | |
8540 | "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f")))) | |
8541 | (properties `((upstream-name . "WGCNA"))) | |
8542 | (build-system r-build-system) | |
8543 | (propagated-inputs | |
8544 | `(("r-annotationdbi" ,r-annotationdbi) | |
8545 | ("r-doparallel" ,r-doparallel) | |
8546 | ("r-dynamictreecut" ,r-dynamictreecut) | |
8547 | ("r-fastcluster" ,r-fastcluster) | |
8548 | ("r-foreach" ,r-foreach) | |
8549 | ("r-go-db" ,r-go-db) | |
8550 | ("r-hmisc" ,r-hmisc) | |
8551 | ("r-impute" ,r-impute) | |
8552 | ("r-rcpp" ,r-rcpp) | |
8553 | ("r-survival" ,r-survival) | |
8554 | ("r-matrixstats" ,r-matrixstats) | |
8555 | ("r-preprocesscore" ,r-preprocesscore))) | |
8556 | (home-page | |
8557 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") | |
8558 | (synopsis "Weighted correlation network analysis") | |
8559 | (description | |
8560 | "This package provides functions necessary to perform Weighted | |
8561 | Correlation Network Analysis on high-dimensional data. It includes functions | |
8562 | for rudimentary data cleaning, construction and summarization of correlation | |
8563 | networks, module identification and functions for relating both variables and | |
8564 | modules to sample traits. It also includes a number of utility functions for | |
8565 | data manipulation and visualization.") | |
8566 | (license license:gpl2+))) | |
8567 | ||
b3a99837 | 8568 | (define-public r-rgraphviz |
8569 | (package | |
8570 | (name "r-rgraphviz") | |
b6348b0e | 8571 | (version "2.34.0") |
b3a99837 | 8572 | (source |
8573 | (origin | |
8574 | (method url-fetch) | |
8575 | (uri (bioconductor-uri "Rgraphviz" version)) | |
8576 | (sha256 | |
8577 | (base32 | |
b6348b0e | 8578 | "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77")))) |
b3a99837 | 8579 | (properties `((upstream-name . "Rgraphviz"))) |
8580 | (build-system r-build-system) | |
8581 | (arguments | |
8582 | `(#:phases | |
8583 | (modify-phases %standard-phases | |
8584 | (add-after 'unpack 'make-reproducible | |
8585 | (lambda _ | |
8586 | ;; The replacement value is taken from src/graphviz/builddate.h | |
8587 | (substitute* "src/graphviz/configure" | |
8588 | (("VERSION_DATE=.*") | |
8589 | "VERSION_DATE=20200427.2341\n")) | |
8590 | #t))))) | |
8591 | ;; FIXME: Rgraphviz bundles the sources of an older variant of | |
8592 | ;; graphviz. It does not build with the latest version of graphviz, so | |
8593 | ;; we do not add graphviz to the inputs. | |
8594 | (inputs `(("zlib" ,zlib))) | |
8595 | (propagated-inputs | |
8596 | `(("r-graph" ,r-graph))) | |
8597 | (native-inputs | |
8598 | `(("pkg-config" ,pkg-config))) | |
8599 | (home-page "https://bioconductor.org/packages/Rgraphviz") | |
8600 | (synopsis "Plotting capabilities for R graph objects") | |
8601 | (description | |
8602 | "This package interfaces R with the graphviz library for plotting R graph | |
8603 | objects from the @code{graph} package.") | |
8604 | (license license:epl1.0))) | |
8c7c6db4 | 8605 | |
3292f6ed | 8606 | (define-public r-fithic |
8607 | (package | |
8608 | (name "r-fithic") | |
7105658e | 8609 | (version "1.16.0") |
3292f6ed | 8610 | (source (origin |
8611 | (method url-fetch) | |
8612 | (uri (bioconductor-uri "FitHiC" version)) | |
8613 | (sha256 | |
8614 | (base32 | |
7105658e | 8615 | "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2")))) |
3292f6ed | 8616 | (properties `((upstream-name . "FitHiC"))) |
8617 | (build-system r-build-system) | |
8618 | (propagated-inputs | |
8619 | `(("r-data-table" ,r-data-table) | |
8620 | ("r-fdrtool" ,r-fdrtool) | |
8621 | ("r-rcpp" ,r-rcpp))) | |
8622 | (native-inputs | |
8623 | `(("r-knitr" ,r-knitr))) | |
8624 | (home-page "https://bioconductor.org/packages/FitHiC") | |
8625 | (synopsis "Confidence estimation for intra-chromosomal contact maps") | |
8626 | (description | |
8627 | "Fit-Hi-C is a tool for assigning statistical confidence estimates to | |
8628 | intra-chromosomal contact maps produced by genome-wide genome architecture | |
8629 | assays such as Hi-C.") | |
8630 | (license license:gpl2+))) | |
8631 | ||
7df42d37 | 8632 | (define-public r-hitc |
8633 | (package | |
8634 | (name "r-hitc") | |
ed44a72a | 8635 | (version "1.34.0") |
7df42d37 | 8636 | (source (origin |
8637 | (method url-fetch) | |
8638 | (uri (bioconductor-uri "HiTC" version)) | |
8639 | (sha256 | |
8640 | (base32 | |
ed44a72a | 8641 | "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy")))) |
7df42d37 | 8642 | (properties `((upstream-name . "HiTC"))) |
8643 | (build-system r-build-system) | |
8644 | (propagated-inputs | |
8645 | `(("r-biostrings" ,r-biostrings) | |
8646 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8647 | ("r-genomicranges" ,r-genomicranges) | |
8648 | ("r-iranges" ,r-iranges) | |
8649 | ("r-matrix" ,r-matrix) | |
8650 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
8651 | ("r-rtracklayer" ,r-rtracklayer))) | |
8652 | (home-page "https://bioconductor.org/packages/HiTC") | |
8653 | (synopsis "High throughput chromosome conformation capture analysis") | |
8654 | (description | |
8655 | "The HiTC package was developed to explore high-throughput \"C\" data | |
8656 | such as 5C or Hi-C. Dedicated R classes as well as standard methods for | |
8657 | quality controls, normalization, visualization, and further analysis are also | |
8658 | provided.") | |
8659 | (license license:artistic2.0))) | |
8660 | ||
63b75c01 | 8661 | (define-public r-hdf5array |
8662 | (package | |
8663 | (name "r-hdf5array") | |
5992c25e | 8664 | (version "1.18.0") |
63b75c01 | 8665 | (source |
8666 | (origin | |
8667 | (method url-fetch) | |
8668 | (uri (bioconductor-uri "HDF5Array" version)) | |
8669 | (sha256 | |
8670 | (base32 | |
5992c25e | 8671 | "1hr149q03p09y1cjnx8av854j53041wfyq66xpsjw4mypzjf6f28")))) |
63b75c01 | 8672 | (properties `((upstream-name . "HDF5Array"))) |
8673 | (build-system r-build-system) | |
26cf5eb5 | 8674 | (arguments |
8675 | `(#:phases | |
8676 | (modify-phases %standard-phases | |
8677 | (add-after 'unpack 'fix-linking | |
8678 | (lambda _ | |
8679 | (substitute* "src/Makevars" | |
8680 | ;; This is to avoid having a plain directory on the list of | |
8681 | ;; libraries to link. | |
8682 | (("\\(RHDF5LIB_LIBS\\)" match) | |
8683 | (string-append match "/libhdf5.a"))) | |
8684 | #t))))) | |
63b75c01 | 8685 | (inputs |
8686 | `(("zlib" ,zlib))) | |
8687 | (propagated-inputs | |
8688 | `(("r-biocgenerics" ,r-biocgenerics) | |
8689 | ("r-delayedarray" ,r-delayedarray) | |
8690 | ("r-iranges" ,r-iranges) | |
8691 | ("r-matrix" ,r-matrix) | |
8692 | ("r-rhdf5" ,r-rhdf5) | |
8693 | ("r-rhdf5lib" ,r-rhdf5lib) | |
8694 | ("r-s4vectors" ,r-s4vectors))) | |
8695 | (home-page "https://bioconductor.org/packages/HDF5Array") | |
8696 | (synopsis "HDF5 back end for DelayedArray objects") | |
8697 | (description "This package provides an array-like container for convenient | |
8698 | access and manipulation of HDF5 datasets. It supports delayed operations and | |
8699 | block processing.") | |
8700 | (license license:artistic2.0))) | |
8701 | ||
c61268c1 | 8702 | (define-public r-rhdf5lib |
8703 | (package | |
8704 | (name "r-rhdf5lib") | |
79cb6af3 | 8705 | (version "1.12.0") |
c61268c1 | 8706 | (source |
8707 | (origin | |
8708 | (method url-fetch) | |
8709 | (uri (bioconductor-uri "Rhdf5lib" version)) | |
8710 | (sha256 | |
8711 | (base32 | |
79cb6af3 | 8712 | "0wia85a6dkgibsjcmpqas5068msck3h3bqpgw2x07bk189z4vay2")) |
c61268c1 | 8713 | (modules '((guix build utils))) |
8714 | (snippet | |
8715 | '(begin | |
8716 | ;; Delete bundled binaries | |
8717 | (delete-file-recursively "src/wininclude/") | |
8718 | (delete-file-recursively "src/winlib-4.9.3/") | |
8719 | (delete-file-recursively "src/winlib-8.3.0/") | |
8720 | (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") | |
8721 | #t)))) | |
8722 | (properties `((upstream-name . "Rhdf5lib"))) | |
8723 | (build-system r-build-system) | |
8724 | (arguments | |
8725 | `(#:phases | |
8726 | (modify-phases %standard-phases | |
8727 | (add-after 'unpack 'do-not-use-bundled-hdf5 | |
8728 | (lambda* (#:key inputs #:allow-other-keys) | |
8729 | (for-each delete-file '("configure" "configure.ac")) | |
8730 | ;; Do not make other packages link with the proprietary libsz. | |
8731 | (substitute* "R/zzz.R" | |
8732 | ((" \"%s/libsz.a\"") "")) | |
8733 | (with-directory-excursion "src" | |
8734 | (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) | |
8735 | (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) | |
8736 | "hdf5") | |
8737 | ;; Remove timestamp and host system information to make | |
8738 | ;; the build reproducible. | |
8739 | (substitute* "hdf5/src/libhdf5.settings.in" | |
8740 | (("Configured on: @CONFIG_DATE@") | |
8741 | "Configured on: Guix") | |
8742 | (("Uname information:.*") | |
8743 | "Uname information: Linux\n") | |
8744 | ;; Remove unnecessary store reference. | |
8745 | (("C Compiler:.*") | |
8746 | "C Compiler: GCC\n")) | |
c5ae5c1c RJ |
8747 | (rename-file "hdf5/src/libhdf5.settings.in" |
8748 | "hdf5/src/libhdf5.settings") | |
c61268c1 | 8749 | (rename-file "Makevars.in" "Makevars") |
8750 | (substitute* "Makevars" | |
8751 | (("@ZLIB_LIB@") "-lz") | |
8752 | (("@ZLIB_INCLUDE@") "") | |
8753 | (("HDF5_CXX_LIB=.*") | |
8754 | (string-append "HDF5_CXX_LIB=" | |
8755 | (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) | |
8756 | (("HDF5_LIB=.*") | |
8757 | (string-append "HDF5_LIB=" | |
8758 | (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) | |
8759 | (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") | |
8760 | (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") | |
8761 | (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") | |
8762 | (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") | |
8763 | (("HDF5_HL_LIB=.*") | |
8764 | (string-append "HDF5_HL_LIB=" | |
8765 | (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) | |
8766 | (("HDF5_HL_CXX_LIB=.*") | |
8767 | (string-append "HDF5_HL_CXX_LIB=" | |
8768 | (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) | |
8769 | ;; szip is non-free software | |
8770 | (("cp \"\\$\\{SZIP_LIB\\}.*") "") | |
8771 | (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) | |
8772 | #t))))) | |
8773 | (inputs | |
8774 | `(("zlib" ,zlib))) | |
8775 | (propagated-inputs | |
8776 | `(("hdf5" ,hdf5-1.10))) | |
8777 | (native-inputs | |
8778 | `(("hdf5-source" ,(package-source hdf5-1.10)) | |
8779 | ("r-knitr" ,r-knitr))) | |
8780 | (home-page "https://bioconductor.org/packages/Rhdf5lib") | |
8781 | (synopsis "HDF5 library as an R package") | |
8782 | (description "This package provides C and C++ HDF5 libraries for use in R | |
8783 | packages.") | |
8784 | (license license:artistic2.0))) | |
8785 | ||
8863c14c | 8786 | (define-public r-beachmat |
8787 | (package | |
8788 | (name "r-beachmat") | |
fe4ce29a | 8789 | (version "2.6.1") |
8863c14c | 8790 | (source |
8791 | (origin | |
8792 | (method url-fetch) | |
8793 | (uri (bioconductor-uri "beachmat" version)) | |
8794 | (sha256 | |
8795 | (base32 | |
fe4ce29a | 8796 | "0dkh3igvwbvir4p0y6x4q07mcv51b35qhva63vrjd6bbkdjn9brr")))) |
8863c14c | 8797 | (build-system r-build-system) |
8798 | (propagated-inputs | |
8799 | `(("r-biocgenerics" ,r-biocgenerics) | |
8800 | ("r-delayedarray" ,r-delayedarray) | |
8801 | ("r-matrix" ,r-matrix))) | |
8802 | (native-inputs | |
8803 | `(("r-knitr" ,r-knitr))) | |
8804 | (home-page "https://bioconductor.org/packages/beachmat") | |
8805 | (synopsis "Compiling Bioconductor to handle each matrix type") | |
8806 | (description "This package provides a consistent C++ class interface for a | |
8807 | variety of commonly used matrix types, including sparse and HDF5-backed | |
8808 | matrices.") | |
8809 | (license license:gpl3))) | |
8810 | ||
916a3e59 | 8811 | (define-public r-singlecellexperiment |
8812 | (package | |
8813 | (name "r-singlecellexperiment") | |
4ef898d4 | 8814 | (version "1.12.0") |
916a3e59 | 8815 | (source |
8816 | (origin | |
8817 | (method url-fetch) | |
8818 | (uri (bioconductor-uri "SingleCellExperiment" version)) | |
8819 | (sha256 | |
8820 | (base32 | |
4ef898d4 | 8821 | "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2")))) |
916a3e59 | 8822 | (properties |
8823 | `((upstream-name . "SingleCellExperiment"))) | |
8824 | (build-system r-build-system) | |
8825 | (propagated-inputs | |
8826 | `(("r-biocgenerics" ,r-biocgenerics) | |
8827 | ("r-s4vectors" ,r-s4vectors) | |
8828 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
8829 | (native-inputs | |
8830 | `(("r-knitr" ,r-knitr))) | |
8831 | (home-page "https://bioconductor.org/packages/SingleCellExperiment") | |
8832 | (synopsis "S4 classes for single cell data") | |
8833 | (description "This package defines an S4 class for storing data from | |
8834 | single-cell experiments. This includes specialized methods to store and | |
8835 | retrieve spike-in information, dimensionality reduction coordinates and size | |
8836 | factors for each cell, along with the usual metadata for genes and | |
8837 | libraries.") | |
8838 | (license license:gpl3))) | |
8839 | ||
6b1946b3 | 8840 | (define-public r-scater |
8841 | (package | |
8842 | (name "r-scater") | |
8843 | (version "1.16.2") | |
8844 | (source (origin | |
8845 | (method url-fetch) | |
8846 | (uri (bioconductor-uri "scater" version)) | |
8847 | (sha256 | |
8848 | (base32 | |
8849 | "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33")))) | |
8850 | (build-system r-build-system) | |
8851 | (propagated-inputs | |
8852 | `(("r-beachmat" ,r-beachmat) | |
8853 | ("r-biocgenerics" ,r-biocgenerics) | |
8854 | ("r-biocneighbors" ,r-biocneighbors) | |
8855 | ("r-biocparallel" ,r-biocparallel) | |
8856 | ("r-biocsingular" ,r-biocsingular) | |
8857 | ("r-delayedarray" ,r-delayedarray) | |
8858 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
8859 | ("r-ggbeeswarm" ,r-ggbeeswarm) | |
8860 | ("r-ggplot2" ,r-ggplot2) | |
8861 | ("r-matrix" ,r-matrix) | |
8862 | ("r-rcpp" ,r-rcpp) | |
8863 | ("r-rlang" ,r-rlang) | |
8864 | ("r-s4vectors" ,r-s4vectors) | |
8865 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
8866 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
8867 | ("r-viridis" ,r-viridis))) | |
8868 | (native-inputs | |
8869 | `(("r-knitr" ,r-knitr))) | |
8870 | (home-page "https://github.com/davismcc/scater") | |
8871 | (synopsis "Single-cell analysis toolkit for gene expression data in R") | |
8872 | (description "This package provides a collection of tools for doing | |
8873 | various analyses of single-cell RNA-seq gene expression data, with a focus on | |
8874 | quality control.") | |
8875 | (license license:gpl2+))) | |
8876 | ||
1193b77e | 8877 | (define-public r-scran |
8878 | (package | |
8879 | (name "r-scran") | |
8880 | (version "1.16.0") | |
8881 | (source | |
8882 | (origin | |
8883 | (method url-fetch) | |
8884 | (uri (bioconductor-uri "scran" version)) | |
8885 | (sha256 | |
8886 | (base32 | |
8887 | "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) | |
8888 | (build-system r-build-system) | |
8889 | (propagated-inputs | |
8890 | `(("r-beachmat" ,r-beachmat) | |
8891 | ("r-bh" ,r-bh) | |
8892 | ("r-biocgenerics" ,r-biocgenerics) | |
8893 | ("r-biocneighbors" ,r-biocneighbors) | |
8894 | ("r-biocparallel" ,r-biocparallel) | |
8895 | ("r-biocsingular" ,r-biocsingular) | |
8896 | ("r-delayedarray" ,r-delayedarray) | |
8897 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
8898 | ("r-dqrng" ,r-dqrng) | |
8899 | ("r-edger" ,r-edger) | |
8900 | ("r-igraph" ,r-igraph) | |
8901 | ("r-iranges" ,r-iranges) | |
8902 | ("r-limma" ,r-limma) | |
8903 | ("r-matrix" ,r-matrix) | |
8904 | ("r-rcpp" ,r-rcpp) | |
8905 | ("r-s4vectors" ,r-s4vectors) | |
8906 | ("r-scater" ,r-scater) | |
8907 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
8908 | ("r-statmod" ,r-statmod) | |
8909 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
8910 | (native-inputs | |
8911 | `(("r-knitr" ,r-knitr))) | |
8912 | (home-page "https://bioconductor.org/packages/scran") | |
8913 | (synopsis "Methods for single-cell RNA-Seq data analysis") | |
8914 | (description "This package implements a variety of low-level analyses of | |
8915 | single-cell RNA-seq data. Methods are provided for normalization of | |
8916 | cell-specific biases, assignment of cell cycle phase, and detection of highly | |
8917 | variable and significantly correlated genes.") | |
8918 | (license license:gpl3))) | |
8919 | ||
5e719988 RW |
8920 | (define-public r-sparsematrixstats |
8921 | (package | |
8922 | (name "r-sparsematrixstats") | |
8923 | (version "1.2.0") | |
8924 | (source | |
8925 | (origin | |
8926 | (method url-fetch) | |
8927 | (uri (bioconductor-uri "sparseMatrixStats" version)) | |
8928 | (sha256 | |
8929 | (base32 | |
8930 | "0d1idbda1pzhdam9m0i5rn0c6pl7gwv0v3mcrv4wi5760v9qd5qh")))) | |
8931 | (properties | |
8932 | `((upstream-name . "sparseMatrixStats"))) | |
8933 | (build-system r-build-system) | |
8934 | (propagated-inputs | |
8935 | `(("r-matrix" ,r-matrix) | |
8936 | ("r-matrixgenerics" ,r-matrixgenerics) | |
8937 | ("r-matrixstats" ,r-matrixstats) | |
8938 | ("r-rcpp" ,r-rcpp))) | |
8939 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8940 | (home-page "https://bioconductor.org/packages/sparseMatrixStats/") | |
8941 | (synopsis "Summary statistics for rows and columns of sparse matrices") | |
8942 | (description | |
8943 | "This package provides high performance functions for row and column | |
8944 | operations on sparse matrices. Currently, the optimizations are limited to | |
8945 | data in the column sparse format.") | |
8946 | (license license:expat))) | |
8947 | ||
8c7c6db4 | 8948 | (define-public r-delayedmatrixstats |
8949 | (package | |
8950 | (name "r-delayedmatrixstats") | |
8951 | (version "1.10.1") | |
8952 | (source | |
8953 | (origin | |
8954 | (method url-fetch) | |
8955 | (uri (bioconductor-uri "DelayedMatrixStats" version)) | |
8956 | (sha256 | |
8957 | (base32 | |
8958 | "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx")))) | |
8959 | (properties | |
8960 | `((upstream-name . "DelayedMatrixStats"))) | |
8961 | (build-system r-build-system) | |
8962 | (propagated-inputs | |
8963 | `(("r-biocparallel" ,r-biocparallel) | |
8964 | ("r-delayedarray" ,r-delayedarray) | |
8965 | ("r-hdf5array" ,r-hdf5array) | |
8966 | ("r-iranges" ,r-iranges) | |
8967 | ("r-matrix" ,r-matrix) | |
8968 | ("r-matrixstats" ,r-matrixstats) | |
8969 | ("r-s4vectors" ,r-s4vectors))) | |
8970 | (native-inputs | |
8971 | `(("r-knitr" ,r-knitr))) | |
8972 | (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") | |
8973 | (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") | |
8974 | (description | |
8975 | "This package provides a port of the @code{matrixStats} API for use with | |
8976 | @code{DelayedMatrix} objects from the @code{DelayedArray} package. It | |
8977 | contains high-performing functions operating on rows and columns of | |
8978 | @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, | |
8979 | @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions | |
8980 | are optimized per data type and for subsetted calculations such that both | |
8981 | memory usage and processing time is minimized.") | |
8982 | (license license:expat))) | |
fa2201c1 | 8983 | |
8984 | (define-public r-mscoreutils | |
8985 | (package | |
8986 | (name "r-mscoreutils") | |
8987 | (version "1.2.0") | |
8988 | (source | |
8989 | (origin | |
8990 | (method url-fetch) | |
8991 | (uri (bioconductor-uri "MsCoreUtils" version)) | |
8992 | (sha256 | |
8993 | (base32 | |
8994 | "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630")))) | |
8995 | (properties `((upstream-name . "MsCoreUtils"))) | |
8996 | (build-system r-build-system) | |
8997 | (propagated-inputs | |
8998 | `(("r-mass" ,r-mass) | |
8999 | ("r-rcpp" ,r-rcpp) | |
9000 | ("r-s4vectors" ,r-s4vectors))) | |
9001 | (native-inputs | |
9002 | `(("r-knitr" ,r-knitr))) | |
9003 | (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils") | |
9004 | (synopsis "Core utils for mass spectrometry data") | |
9005 | (description | |
9006 | "This package defines low-level functions for mass spectrometry data and | |
9007 | is independent of any high-level data structures. These functions include | |
9008 | mass spectra processing functions (noise estimation, smoothing, binning), | |
9009 | quantitative aggregation functions (median polish, robust summarisation, | |
9010 | etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as | |
9011 | well as misc helper functions, that are used across high-level data structure | |
9012 | within the R for Mass Spectrometry packages.") | |
9013 | (license license:artistic2.0))) | |
ff4834c0 | 9014 | |
9015 | (define-public r-biocio | |
9016 | (package | |
9017 | (name "r-biocio") | |
9018 | (version "1.0.1") | |
9019 | (source | |
9020 | (origin | |
9021 | (method url-fetch) | |
9022 | (uri (bioconductor-uri "BiocIO" version)) | |
9023 | (sha256 | |
9024 | (base32 | |
9025 | "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18")))) | |
9026 | (properties `((upstream-name . "BiocIO"))) | |
9027 | (build-system r-build-system) | |
9028 | (propagated-inputs | |
9029 | `(("r-biocgenerics" ,r-biocgenerics) | |
9030 | ("r-genomicranges" ,r-genomicranges) | |
9031 | ("r-rcurl" ,r-rcurl) | |
9032 | ("r-s4vectors" ,r-s4vectors))) | |
9033 | (native-inputs | |
9034 | `(("r-knitr" ,r-knitr))) | |
9035 | (home-page "https://bioconductor.org/packages/BiocIO") | |
9036 | (synopsis "Standard input and output for Bioconductor packages") | |
9037 | (description | |
9038 | "This package implements `import()` and `export()` standard generics for | |
9039 | importing and exporting biological data formats. `import()` supports | |
9040 | whole-file as well as chunk-wise iterative import. The `import()` interface | |
9041 | optionally provides a standard mechanism for 'lazy' access via `filter()` (on | |
9042 | row or element-like components of the file resource), `select()` (on | |
9043 | column-like components of the file resource) and `collect()`. The `import()` | |
9044 | interface optionally provides transparent access to remote (e.g. via https) | |
9045 | as well as local access. Developers can register a file extension, e.g., | |
9046 | `.loom` for dispatch from character-based URIs to specific `import()` / | |
9047 | `export()` methods based on classes representing file types, e.g., | |
9048 | `LoomFile()`.") | |
9049 | (license license:artistic2.0))) | |
e520c68f | 9050 | |
9051 | (define-public r-msmseda | |
9052 | (package | |
9053 | (name "r-msmseda") | |
9054 | (version "1.28.0") | |
9055 | (source | |
9056 | (origin | |
9057 | (method url-fetch) | |
9058 | (uri (bioconductor-uri "msmsEDA" version)) | |
9059 | (sha256 | |
9060 | (base32 | |
9061 | "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx")))) | |
9062 | (properties `((upstream-name . "msmsEDA"))) | |
9063 | (build-system r-build-system) | |
9064 | (propagated-inputs | |
9065 | `(("r-gplots" ,r-gplots) | |
9066 | ("r-mass" ,r-mass) | |
9067 | ("r-msnbase" ,r-msnbase) | |
9068 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
9069 | (home-page | |
9070 | "https://bioconductor.org/packages/msmsEDA") | |
9071 | (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts") | |
9072 | (description | |
9073 | "Exploratory data analysis to assess the quality of a set of LC-MS/MS | |
9074 | experiments, and visualize de influence of the involved factors.") | |
9075 | (license license:gpl2))) | |
16f16b5e | 9076 | |
9077 | (define-public r-msmstests | |
9078 | (package | |
9079 | (name "r-msmstests") | |
9080 | (version "1.28.0") | |
9081 | (source | |
9082 | (origin | |
9083 | (method url-fetch) | |
9084 | (uri (bioconductor-uri "msmsTests" version)) | |
9085 | (sha256 | |
9086 | (base32 | |
9087 | "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j")))) | |
9088 | (properties `((upstream-name . "msmsTests"))) | |
9089 | (build-system r-build-system) | |
9090 | (propagated-inputs | |
9091 | `(("r-edger" ,r-edger) | |
9092 | ("r-msmseda" ,r-msmseda) | |
9093 | ("r-msnbase" ,r-msnbase) | |
9094 | ("r-qvalue" ,r-qvalue))) | |
9095 | (home-page | |
9096 | "https://bioconductor.org/packages/msmsTests") | |
9097 | (synopsis "Differential LC-MS/MS expression tests") | |
9098 | (description | |
9099 | "This packages provides statistical tests for label-free LC-MS/MS data | |
9100 | by spectral counts, to discover differentially expressed proteins between two | |
9101 | biological conditions. Three tests are available: Poisson GLM regression, | |
9102 | quasi-likelihood GLM regression, and the negative binomial of the edgeR | |
9103 | package.The three models admit blocking factors to control for nuissance | |
9104 | variables.To assure a good level of reproducibility a post-test filter is | |
9105 | available, where we may set the minimum effect size considered biologicaly | |
9106 | relevant, and the minimum expression of the most abundant condition.") | |
9107 | (license license:gpl2))) |