Commit | Line | Data |
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fa596599 | 1 | ;;; GNU Guix --- Functional package management for GNU |
f8f181ae | 2 | ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> |
e8d435f7 | 3 | ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> |
61242625 | 4 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
16e2e4f2 | 5 | ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com> |
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 | ||
b7d93cf5 RW |
75 | (define-public r-bsgenome-celegans-ucsc-ce6 |
76 | (package | |
77 | (name "r-bsgenome-celegans-ucsc-ce6") | |
78 | (version "1.4.0") | |
79 | (source (origin | |
80 | (method url-fetch) | |
86ced7b2 RW |
81 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6" |
82 | version 'annotation)) | |
b7d93cf5 RW |
83 | (sha256 |
84 | (base32 | |
85 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
86 | (properties | |
87 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
88 | (build-system r-build-system) | |
b7d93cf5 RW |
89 | (propagated-inputs |
90 | `(("r-bsgenome" ,r-bsgenome))) | |
91 | (home-page | |
92 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
93 | (synopsis "Full genome sequences for Worm") | |
94 | (description | |
95 | "This package provides full genome sequences for Caenorhabditis | |
96 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
0c792ffb RW |
97 | objects.") |
98 | (license license:artistic2.0))) | |
99 | ||
100 | (define-public r-bsgenome-celegans-ucsc-ce10 | |
101 | (package | |
102 | (name "r-bsgenome-celegans-ucsc-ce10") | |
103 | (version "1.4.0") | |
104 | (source (origin | |
105 | (method url-fetch) | |
6998ecba RW |
106 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10" |
107 | version 'annotation)) | |
0c792ffb RW |
108 | (sha256 |
109 | (base32 | |
110 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
111 | (properties | |
112 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
113 | (build-system r-build-system) | |
0c792ffb RW |
114 | (propagated-inputs |
115 | `(("r-bsgenome" ,r-bsgenome))) | |
116 | (home-page | |
117 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
118 | (synopsis "Full genome sequences for Worm") | |
119 | (description | |
120 | "This package provides full genome sequences for Caenorhabditis | |
121 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
b7d93cf5 RW |
122 | objects.") |
123 | (license license:artistic2.0))) | |
124 | ||
183db725 RW |
125 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
126 | (package | |
127 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
128 | (version "1.4.1") | |
129 | (source (origin | |
130 | (method url-fetch) | |
149f351f RW |
131 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6" |
132 | version 'annotation)) | |
183db725 RW |
133 | (sha256 |
134 | (base32 | |
135 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
136 | (properties | |
137 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
138 | (build-system r-build-system) | |
183db725 RW |
139 | (propagated-inputs |
140 | `(("r-bsgenome" ,r-bsgenome))) | |
141 | (home-page | |
142 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
143 | (synopsis "Full genome sequences for Fly") | |
144 | (description | |
145 | "This package provides full genome sequences for Drosophila | |
146 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
147 | objects.") | |
148 | (license license:artistic2.0))) | |
149 | ||
13dabd69 RW |
150 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
151 | (package | |
152 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
153 | (version "1.4.0") | |
154 | (source (origin | |
155 | (method url-fetch) | |
87073b7e RW |
156 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3" |
157 | version 'annotation)) | |
13dabd69 RW |
158 | (sha256 |
159 | (base32 | |
160 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
161 | (properties | |
162 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
163 | (build-system r-build-system) | |
13dabd69 RW |
164 | (propagated-inputs |
165 | `(("r-bsgenome" ,r-bsgenome))) | |
166 | (home-page | |
167 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
168 | (synopsis "Full genome sequences for Fly") | |
169 | (description | |
170 | "This package provides full genome sequences for Drosophila | |
171 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
172 | Biostrings objects.") | |
173 | (license license:artistic2.0))) | |
174 | ||
dfac7eb9 RW |
175 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
176 | (package | |
177 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
178 | (version "1.3.99") | |
179 | (source (origin | |
180 | (method url-fetch) | |
bf05ece1 RW |
181 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked" |
182 | version 'annotation)) | |
dfac7eb9 RW |
183 | (sha256 |
184 | (base32 | |
185 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
186 | (properties | |
187 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
188 | (build-system r-build-system) | |
189 | (propagated-inputs | |
190 | `(("r-bsgenome" ,r-bsgenome) | |
191 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
192 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
193 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
194 | (synopsis "Full masked genome sequences for Fly") | |
195 | (description | |
196 | "This package provides full masked genome sequences for Drosophila | |
197 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
198 | Biostrings objects. The sequences are the same as in | |
199 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
200 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
201 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
202 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
203 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
204 | (license license:artistic2.0))) | |
205 | ||
40a65057 RW |
206 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
207 | (package | |
208 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
209 | (version "0.99.1") | |
210 | (source (origin | |
211 | (method url-fetch) | |
88e7c7db RW |
212 | (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5" |
213 | version 'annotation)) | |
40a65057 RW |
214 | (sha256 |
215 | (base32 | |
216 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
217 | (properties | |
218 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
219 | (build-system r-build-system) | |
40a65057 RW |
220 | (propagated-inputs |
221 | `(("r-bsgenome" ,r-bsgenome))) | |
222 | (home-page | |
223 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
224 | (synopsis "Full genome sequences for Homo sapiens") | |
225 | (description | |
226 | "This package provides full genome sequences for Homo sapiens from | |
227 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
228 | (license license:artistic2.0))) | |
229 | ||
c51c0033 MIP |
230 | (define-public r-bsgenome-hsapiens-ncbi-grch38 |
231 | (package | |
232 | (name "r-bsgenome-hsapiens-ncbi-grch38") | |
233 | (version "1.3.1000") | |
234 | (source | |
235 | (origin | |
236 | (method url-fetch) | |
237 | (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38" | |
238 | version 'annotation)) | |
239 | (sha256 | |
240 | (base32 | |
241 | "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) | |
242 | (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) | |
243 | (build-system r-build-system) | |
244 | (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) | |
245 | (home-page | |
246 | "https://bioconductor.org/packages/release/data/annotation/html/\ | |
247 | BSgenome.Hsapiens.NCBI.GRCh38.html") | |
248 | (synopsis "Full genome sequences for Homo sapiens (GRCh38)") | |
249 | (description | |
250 | "This package provides full genome sequences for Homo sapiens (Human) as | |
251 | provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") | |
252 | (license license:artistic2.0))) | |
253 | ||
6fbd759b RW |
254 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
255 | (package | |
256 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
257 | (version "1.3.99") | |
258 | (source (origin | |
259 | (method url-fetch) | |
a47646bd RW |
260 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" |
261 | version 'annotation)) | |
6fbd759b RW |
262 | (sha256 |
263 | (base32 | |
264 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
265 | (properties | |
266 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
267 | (build-system r-build-system) | |
268 | (propagated-inputs | |
269 | `(("r-bsgenome" ,r-bsgenome) | |
270 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
271 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
272 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
273 | (synopsis "Full masked genome sequences for Homo sapiens") | |
274 | (description | |
275 | "This package provides full genome sequences for Homo sapiens (Human) as | |
276 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
277 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
278 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
279 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
280 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
281 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
282 | default.") | |
283 | (license license:artistic2.0))) | |
284 | ||
5acb9052 RW |
285 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
286 | (package | |
287 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
288 | (version "1.4.0") | |
289 | (source (origin | |
290 | (method url-fetch) | |
21f6dae7 RW |
291 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9" |
292 | version 'annotation)) | |
5acb9052 RW |
293 | (sha256 |
294 | (base32 | |
295 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
296 | (properties | |
297 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
298 | (build-system r-build-system) | |
5acb9052 RW |
299 | (propagated-inputs |
300 | `(("r-bsgenome" ,r-bsgenome))) | |
301 | (home-page | |
302 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
303 | (synopsis "Full genome sequences for Mouse") | |
304 | (description | |
305 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
306 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
307 | (license license:artistic2.0))) | |
308 | ||
2bece692 RW |
309 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
310 | (package | |
311 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
312 | (version "1.3.99") | |
313 | (source (origin | |
314 | (method url-fetch) | |
51dc4a2d RW |
315 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked" |
316 | version 'annotation)) | |
2bece692 RW |
317 | (sha256 |
318 | (base32 | |
319 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
320 | (properties | |
321 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
322 | (build-system r-build-system) | |
323 | (propagated-inputs | |
324 | `(("r-bsgenome" ,r-bsgenome) | |
325 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
326 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
99db6db7 | 327 | (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") |
2bece692 RW |
328 | (synopsis "Full masked genome sequences for Mouse") |
329 | (description | |
330 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
331 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
332 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
333 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
334 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
335 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
336 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
337 | default." ) | |
338 | (license license:artistic2.0))) | |
339 | ||
c3adc830 RW |
340 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
341 | (package | |
342 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
343 | (version "1.4.0") | |
344 | (source (origin | |
345 | (method url-fetch) | |
f83404bc RW |
346 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10" |
347 | version 'annotation)) | |
c3adc830 RW |
348 | (sha256 |
349 | (base32 | |
350 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
351 | (properties | |
352 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
353 | (build-system r-build-system) | |
c3adc830 RW |
354 | (propagated-inputs |
355 | `(("r-bsgenome" ,r-bsgenome))) | |
356 | (home-page | |
357 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
358 | (synopsis "Full genome sequences for Mouse") | |
359 | (description | |
360 | "This package provides full genome sequences for Mus | |
361 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
362 | in Biostrings objects.") | |
363 | (license license:artistic2.0))) | |
364 | ||
3a08940e RW |
365 | (define-public r-org-ce-eg-db |
366 | (package | |
367 | (name "r-org-ce-eg-db") | |
368 | (version "3.7.0") | |
369 | (source (origin | |
370 | (method url-fetch) | |
1c05e637 | 371 | (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation)) |
3a08940e RW |
372 | (sha256 |
373 | (base32 | |
374 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) | |
375 | (properties | |
376 | `((upstream-name . "org.Ce.eg.db"))) | |
377 | (build-system r-build-system) | |
378 | (propagated-inputs | |
379 | `(("r-annotationdbi" ,r-annotationdbi))) | |
380 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") | |
381 | (synopsis "Genome wide annotation for Worm") | |
382 | (description | |
383 | "This package provides mappings from Entrez gene identifiers to various | |
384 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
385 | (license license:artistic2.0))) | |
386 | ||
f8780e96 RW |
387 | (define-public r-org-dm-eg-db |
388 | (package | |
389 | (name "r-org-dm-eg-db") | |
390 | (version "3.7.0") | |
391 | (source (origin | |
392 | (method url-fetch) | |
b0dfc79b | 393 | (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation)) |
f8780e96 RW |
394 | (sha256 |
395 | (base32 | |
396 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) | |
397 | (properties | |
398 | `((upstream-name . "org.Dm.eg.db"))) | |
399 | (build-system r-build-system) | |
400 | (propagated-inputs | |
401 | `(("r-annotationdbi" ,r-annotationdbi))) | |
402 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") | |
403 | (synopsis "Genome wide annotation for Fly") | |
404 | (description | |
405 | "This package provides mappings from Entrez gene identifiers to various | |
406 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
407 | (license license:artistic2.0))) | |
408 | ||
3dad6087 RW |
409 | (define-public r-org-dr-eg-db |
410 | (package | |
411 | (name "r-org-dr-eg-db") | |
412 | (version "3.7.0") | |
413 | (source (origin | |
414 | (method url-fetch) | |
7bb65a22 | 415 | (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation)) |
3dad6087 RW |
416 | (sha256 |
417 | (base32 | |
418 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) | |
419 | (properties | |
420 | `((upstream-name . "org.Dr.eg.db"))) | |
421 | (build-system r-build-system) | |
422 | (propagated-inputs | |
423 | `(("r-annotationdbi" ,r-annotationdbi))) | |
424 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") | |
425 | (synopsis "Annotation for Zebrafish") | |
426 | (description | |
427 | "This package provides genome wide annotations for Zebrafish, primarily | |
428 | based on mapping using Entrez Gene identifiers.") | |
429 | (license license:artistic2.0))) | |
430 | ||
d56df35a RW |
431 | (define-public r-org-hs-eg-db |
432 | (package | |
433 | (name "r-org-hs-eg-db") | |
434 | (version "3.7.0") | |
435 | (source (origin | |
436 | (method url-fetch) | |
f53becc6 | 437 | (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) |
d56df35a RW |
438 | (sha256 |
439 | (base32 | |
440 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) | |
441 | (properties | |
442 | `((upstream-name . "org.Hs.eg.db"))) | |
443 | (build-system r-build-system) | |
444 | (propagated-inputs | |
445 | `(("r-annotationdbi" ,r-annotationdbi))) | |
446 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") | |
447 | (synopsis "Genome wide annotation for Human") | |
448 | (description | |
449 | "This package contains genome-wide annotations for Human, primarily based | |
450 | on mapping using Entrez Gene identifiers.") | |
451 | (license license:artistic2.0))) | |
452 | ||
8035819f RW |
453 | (define-public r-org-mm-eg-db |
454 | (package | |
455 | (name "r-org-mm-eg-db") | |
456 | (version "3.7.0") | |
457 | (source (origin | |
458 | (method url-fetch) | |
411be88b | 459 | (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation)) |
8035819f RW |
460 | (sha256 |
461 | (base32 | |
462 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) | |
463 | (properties | |
464 | `((upstream-name . "org.Mm.eg.db"))) | |
465 | (build-system r-build-system) | |
466 | (propagated-inputs | |
467 | `(("r-annotationdbi" ,r-annotationdbi))) | |
468 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") | |
469 | (synopsis "Genome wide annotation for Mouse") | |
470 | (description | |
471 | "This package provides mappings from Entrez gene identifiers to various | |
472 | annotations for the genome of the model mouse Mus musculus.") | |
473 | (license license:artistic2.0))) | |
474 | ||
fe0b76e2 RW |
475 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
476 | (package | |
477 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
478 | (version "1.4.0") | |
479 | (source (origin | |
480 | (method url-fetch) | |
e7a8cf2e RW |
481 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19" |
482 | version 'annotation)) | |
fe0b76e2 RW |
483 | (sha256 |
484 | (base32 | |
485 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) | |
486 | (properties | |
487 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
488 | (build-system r-build-system) | |
fe0b76e2 RW |
489 | (propagated-inputs |
490 | `(("r-bsgenome" ,r-bsgenome))) | |
491 | (home-page | |
492 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
493 | (synopsis "Full genome sequences for Homo sapiens") | |
494 | (description | |
495 | "This package provides full genome sequences for Homo sapiens as provided | |
496 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
497 | (license license:artistic2.0))) | |
498 | ||
8ce240fd RJ |
499 | (define-public r-bsgenome-hsapiens-ucsc-hg38 |
500 | (package | |
501 | (name "r-bsgenome-hsapiens-ucsc-hg38") | |
502 | (version "1.4.1") | |
503 | (source (origin | |
504 | (method url-fetch) | |
505 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38" | |
506 | version 'annotation)) | |
507 | (sha256 | |
508 | (base32 | |
509 | "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi")))) | |
510 | (properties | |
511 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) | |
512 | (build-system r-build-system) | |
513 | (propagated-inputs | |
514 | `(("r-bsgenome" ,r-bsgenome))) | |
515 | (home-page | |
516 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") | |
517 | (synopsis "Full genome sequences for Homo sapiens") | |
518 | (description | |
519 | "This package provides full genome sequences for Homo sapiens (Human) | |
520 | as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") | |
521 | (license license:artistic2.0))) | |
522 | ||
8324e64c RW |
523 | (define-public r-ensdb-hsapiens-v75 |
524 | (package | |
525 | (name "r-ensdb-hsapiens-v75") | |
526 | (version "2.99.0") | |
527 | (source | |
528 | (origin | |
529 | (method url-fetch) | |
530 | (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) | |
531 | (sha256 | |
532 | (base32 | |
533 | "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) | |
534 | (properties | |
535 | `((upstream-name . "EnsDb.Hsapiens.v75"))) | |
536 | (build-system r-build-system) | |
537 | (propagated-inputs | |
538 | `(("r-ensembldb" ,r-ensembldb))) | |
539 | (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") | |
540 | (synopsis "Ensembl based annotation package") | |
541 | (description | |
542 | "This package exposes an annotation database generated from Ensembl.") | |
543 | (license license:artistic2.0))) | |
544 | ||
2cc51108 RW |
545 | (define-public r-genelendatabase |
546 | (package | |
547 | (name "r-genelendatabase") | |
daeb3cd9 | 548 | (version "1.18.0") |
2cc51108 RW |
549 | (source |
550 | (origin | |
551 | (method url-fetch) | |
717d7cda | 552 | (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) |
2cc51108 RW |
553 | (sha256 |
554 | (base32 | |
daeb3cd9 | 555 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
2cc51108 RW |
556 | (properties |
557 | `((upstream-name . "geneLenDataBase"))) | |
558 | (build-system r-build-system) | |
559 | (propagated-inputs | |
560 | `(("r-rtracklayer" ,r-rtracklayer) | |
561 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
562 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
563 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
564 | (description | |
565 | "This package provides the lengths of mRNA transcripts for a number of | |
566 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
567 | (license license:lgpl2.0+))) | |
568 | ||
66e35ce6 RW |
569 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
570 | (package | |
571 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
572 | (version "3.2.2") | |
573 | (source (origin | |
574 | (method url-fetch) | |
f2580a13 RW |
575 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene" |
576 | version 'annotation)) | |
66e35ce6 RW |
577 | (sha256 |
578 | (base32 | |
579 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
580 | (properties | |
581 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
582 | (build-system r-build-system) | |
66e35ce6 RW |
583 | (propagated-inputs |
584 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
585 | (home-page | |
586 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
587 | (synopsis "Annotation package for human genome in TxDb format") | |
588 | (description | |
589 | "This package provides an annotation database of Homo sapiens genome | |
590 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
798b80ce RW |
591 | track. The database is exposed as a @code{TxDb} object.") |
592 | (license license:artistic2.0))) | |
593 | ||
594 | (define-public r-txdb-hsapiens-ucsc-hg38-knowngene | |
595 | (package | |
596 | (name "r-txdb-hsapiens-ucsc-hg38-knowngene") | |
597 | (version "3.4.6") | |
598 | (source (origin | |
599 | (method url-fetch) | |
d78db088 RW |
600 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" |
601 | version 'annotation)) | |
798b80ce RW |
602 | (sha256 |
603 | (base32 | |
604 | "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) | |
605 | (properties | |
606 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) | |
607 | (build-system r-build-system) | |
608 | (propagated-inputs | |
609 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
610 | (home-page | |
611 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") | |
612 | (synopsis "Annotation package for human genome in TxDb format") | |
613 | (description | |
614 | "This package provides an annotation database of Homo sapiens genome | |
615 | data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" | |
66e35ce6 RW |
616 | track. The database is exposed as a @code{TxDb} object.") |
617 | (license license:artistic2.0))) | |
618 | ||
d220babf RW |
619 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
620 | (package | |
621 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
622 | (version "3.2.2") | |
623 | (source (origin | |
624 | (method url-fetch) | |
1afdf41b RW |
625 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene" |
626 | version 'annotation)) | |
d220babf RW |
627 | (sha256 |
628 | (base32 | |
629 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
630 | (properties | |
631 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
632 | (build-system r-build-system) | |
633 | (propagated-inputs | |
634 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
635 | ("r-annotationdbi" ,r-annotationdbi))) | |
636 | (home-page | |
637 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
638 | (synopsis "Annotation package for mouse genome in TxDb format") | |
639 | (description | |
640 | "This package provides an annotation database of Mouse genome data. It | |
641 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
642 | database is exposed as a @code{TxDb} object.") | |
643 | (license license:artistic2.0))) | |
644 | ||
7bc5d1b0 RW |
645 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
646 | (package | |
647 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
b69c7703 | 648 | (version "3.10.0") |
7bc5d1b0 RW |
649 | (source (origin |
650 | (method url-fetch) | |
c271d990 RW |
651 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene" |
652 | version 'annotation)) | |
7bc5d1b0 RW |
653 | (sha256 |
654 | (base32 | |
b69c7703 | 655 | "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9")))) |
7bc5d1b0 RW |
656 | (properties |
657 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
658 | (build-system r-build-system) | |
7bc5d1b0 RW |
659 | (propagated-inputs |
660 | `(("r-bsgenome" ,r-bsgenome) | |
661 | ("r-genomicfeatures" ,r-genomicfeatures) | |
662 | ("r-annotationdbi" ,r-annotationdbi))) | |
663 | (home-page | |
664 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
665 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
666 | (description | |
667 | "This package loads a TxDb object, which is an R interface to | |
668 | prefabricated databases contained in this package. This package provides | |
669 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
670 | based on the knownGene track.") | |
671 | (license license:artistic2.0))) | |
672 | ||
7cd446fd RW |
673 | (define-public r-txdb-celegans-ucsc-ce6-ensgene |
674 | (package | |
675 | (name "r-txdb-celegans-ucsc-ce6-ensgene") | |
676 | (version "3.2.2") | |
677 | (source | |
678 | (origin | |
679 | (method url-fetch) | |
680 | (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene" | |
681 | version 'annotation)) | |
682 | (sha256 | |
683 | (base32 | |
684 | "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90")))) | |
685 | (properties | |
686 | `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) | |
687 | (build-system r-build-system) | |
688 | (propagated-inputs | |
689 | `(("r-annotationdbi" ,r-annotationdbi) | |
690 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
691 | (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") | |
692 | (synopsis "Annotation package for C elegans TxDb objects") | |
693 | (description | |
694 | "This package exposes a C elegans annotation database generated from UCSC | |
695 | by exposing these as TxDb objects.") | |
696 | (license license:artistic2.0))) | |
697 | ||
0f5c9cec RW |
698 | (define-public r-fdb-infiniummethylation-hg19 |
699 | (package | |
700 | (name "r-fdb-infiniummethylation-hg19") | |
701 | (version "2.2.0") | |
702 | (source (origin | |
703 | (method url-fetch) | |
6aca4054 RW |
704 | (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19" |
705 | version 'annotation)) | |
0f5c9cec RW |
706 | (sha256 |
707 | (base32 | |
708 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) | |
709 | (properties | |
710 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) | |
711 | (build-system r-build-system) | |
712 | (propagated-inputs | |
713 | `(("r-biostrings" ,r-biostrings) | |
714 | ("r-genomicfeatures" ,r-genomicfeatures) | |
715 | ("r-annotationdbi" ,r-annotationdbi) | |
716 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
717 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) | |
718 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") | |
719 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") | |
720 | (description | |
721 | "This is an annotation package for Illumina Infinium DNA methylation | |
722 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 | |
723 | annotations.") | |
724 | (license license:artistic2.0))) | |
725 | ||
9475a248 RW |
726 | (define-public r-illuminahumanmethylationepicmanifest |
727 | (package | |
728 | (name "r-illuminahumanmethylationepicmanifest") | |
729 | (version "0.3.0") | |
730 | (source (origin | |
731 | (method url-fetch) | |
25f567a8 RW |
732 | (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest" |
733 | version 'annotation)) | |
9475a248 RW |
734 | (sha256 |
735 | (base32 | |
736 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) | |
737 | (properties | |
738 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) | |
739 | (build-system r-build-system) | |
740 | (propagated-inputs | |
741 | `(("r-minfi" ,r-minfi))) | |
742 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") | |
743 | (synopsis "Manifest for Illumina's EPIC methylation arrays") | |
744 | (description | |
745 | "This is a manifest package for Illumina's EPIC methylation arrays.") | |
746 | (license license:artistic2.0))) | |
e8d435f7 RJ |
747 | |
748 | (define-public r-ideoviz | |
749 | (package | |
750 | (name "r-ideoviz") | |
725eea00 | 751 | (version "1.24.0") |
e8d435f7 RJ |
752 | (source (origin |
753 | (method url-fetch) | |
754 | (uri (bioconductor-uri "IdeoViz" version)) | |
755 | (sha256 | |
756 | (base32 | |
725eea00 | 757 | "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50")))) |
e8d435f7 RJ |
758 | (build-system r-build-system) |
759 | (propagated-inputs | |
760 | `(("r-biobase" ,r-biobase) | |
761 | ("r-iranges" ,r-iranges) | |
762 | ("r-genomicranges" ,r-genomicranges) | |
763 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
764 | ("r-rtracklayer" ,r-rtracklayer) | |
765 | ("r-genomeinfodb" ,r-genomeinfodb))) | |
766 | (home-page "https://bioconductor.org/packages/IdeoViz/") | |
767 | (synopsis "Plots data along a chromosomal ideogram") | |
768 | (description "This package provides functions to plot data associated with | |
769 | arbitrary genomic intervals along chromosomal ideogram.") | |
770 | (license license:gpl2))) | |
9475a248 | 771 | |
a38bf7c8 RJ |
772 | ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 |
773 | ;; from Bioconductor. | |
774 | (define-public r-deconstructsigs | |
775 | (package | |
776 | (name "r-deconstructsigs") | |
777 | (version "1.8.0") | |
778 | (source (origin | |
779 | (method url-fetch) | |
780 | (uri (cran-uri "deconstructSigs" version)) | |
781 | (sha256 | |
782 | (base32 | |
783 | "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) | |
784 | (properties | |
785 | `((upstream-name . "deconstructSigs"))) | |
786 | (build-system r-build-system) | |
787 | (propagated-inputs | |
788 | `(("r-bsgenome" ,r-bsgenome) | |
789 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
790 | ("r-genomeinfodb" ,r-genomeinfodb) | |
791 | ("r-reshape2" ,r-reshape2))) | |
792 | (home-page "https://github.com/raerose01/deconstructSigs") | |
793 | (synopsis "Identifies signatures present in a tumor sample") | |
794 | (description "This package takes sample information in the form of the | |
795 | fraction of mutations in each of 96 trinucleotide contexts and identifies | |
796 | the weighted combination of published signatures that, when summed, most | |
797 | closely reconstructs the mutational profile.") | |
798 | (license license:gpl2+))) | |
799 | ||
7c9d8a5d RW |
800 | ;; This is a CRAN package, but it depends on Bioconductor packages. |
801 | (define-public r-nmf | |
802 | (package | |
803 | (name "r-nmf") | |
0a41d9be | 804 | (version "0.23.0") |
7c9d8a5d RW |
805 | (source |
806 | (origin | |
807 | (method url-fetch) | |
808 | (uri (cran-uri "NMF" version)) | |
809 | (sha256 | |
810 | (base32 | |
0a41d9be | 811 | "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g")))) |
7c9d8a5d RW |
812 | (properties `((upstream-name . "NMF"))) |
813 | (build-system r-build-system) | |
814 | (propagated-inputs | |
815 | `(("r-cluster" ,r-cluster) | |
be1042b3 RW |
816 | ("r-biobase" ,r-biobase) |
817 | ("r-biocmanager" ,r-biocmanager) | |
7c9d8a5d RW |
818 | ("r-bigmemory" ,r-bigmemory) ; suggested |
819 | ("r-synchronicity" ,r-synchronicity) ; suggested | |
820 | ("r-colorspace" ,r-colorspace) | |
821 | ("r-digest" ,r-digest) | |
822 | ("r-doparallel" ,r-doparallel) | |
823 | ("r-foreach" ,r-foreach) | |
824 | ("r-ggplot2" ,r-ggplot2) | |
825 | ("r-gridbase" ,r-gridbase) | |
826 | ("r-pkgmaker" ,r-pkgmaker) | |
827 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
828 | ("r-registry" ,r-registry) | |
829 | ("r-reshape2" ,r-reshape2) | |
830 | ("r-rngtools" ,r-rngtools) | |
831 | ("r-stringr" ,r-stringr))) | |
0a41d9be RW |
832 | (native-inputs |
833 | `(("r-knitr" ,r-knitr))) | |
7c9d8a5d RW |
834 | (home-page "http://renozao.github.io/NMF") |
835 | (synopsis "Algorithms and framework for nonnegative matrix factorization") | |
836 | (description | |
837 | "This package provides a framework to perform Non-negative Matrix | |
838 | Factorization (NMF). The package implements a set of already published | |
839 | algorithms and seeding methods, and provides a framework to test, develop and | |
840 | plug new or custom algorithms. Most of the built-in algorithms have been | |
841 | optimized in C++, and the main interface function provides an easy way of | |
842 | performing parallel computations on multicore machines.") | |
843 | (license license:gpl2+))) | |
844 | ||
f8a5af46 RW |
845 | (define-public r-do-db |
846 | (package | |
847 | (name "r-do-db") | |
848 | (version "2.9") | |
849 | (source (origin | |
850 | (method url-fetch) | |
eed2766a | 851 | (uri (bioconductor-uri "DO.db" version 'annotation)) |
f8a5af46 RW |
852 | (sha256 |
853 | (base32 | |
854 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) | |
855 | (properties | |
856 | `((upstream-name . "DO.db"))) | |
857 | (build-system r-build-system) | |
858 | (propagated-inputs | |
859 | `(("r-annotationdbi" ,r-annotationdbi))) | |
860 | (home-page "https://www.bioconductor.org/packages/DO.db/") | |
861 | (synopsis "Annotation maps describing the entire Disease Ontology") | |
862 | (description | |
863 | "This package provides a set of annotation maps describing the entire | |
864 | Disease Ontology.") | |
865 | (license license:artistic2.0))) | |
866 | ||
ec20858a RJ |
867 | (define-public r-pasilla |
868 | (package | |
869 | (name "r-pasilla") | |
870 | (version "1.14.0") | |
871 | (source (origin | |
872 | (method url-fetch) | |
873 | (uri (string-append | |
874 | "http://bioconductor.org/packages/release/data/experiment" | |
875 | "/src/contrib/pasilla_" version ".tar.gz")) | |
876 | (sha256 | |
877 | (base32 | |
878 | "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) | |
879 | (build-system r-build-system) | |
880 | (propagated-inputs | |
881 | `(("r-biocstyle" ,r-biocstyle) | |
882 | ("r-dexseq" ,r-dexseq) | |
883 | ("r-knitr" ,r-knitr) | |
884 | ("r-rmarkdown" ,r-rmarkdown))) | |
885 | (home-page "https://www.bioconductor.org/packages/pasilla/") | |
886 | (synopsis "Data package with per-exon and per-gene read counts") | |
887 | (description "This package provides per-exon and per-gene read counts | |
888 | computed for selected genes from RNA-seq data that were presented in the | |
889 | article 'Conservation of an RNA regulatory map between Drosophila and mammals' | |
890 | by Brooks et al., Genome Research 2011.") | |
891 | (license license:lgpl2.1+))) | |
892 | ||
83b42091 RW |
893 | (define-public r-pfam-db |
894 | (package | |
895 | (name "r-pfam-db") | |
896 | (version "3.8.2") | |
897 | (source | |
898 | (origin | |
899 | (method url-fetch) | |
900 | (uri (bioconductor-uri "PFAM.db" version 'annotation)) | |
901 | (sha256 | |
902 | (base32 | |
903 | "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) | |
904 | (properties `((upstream-name . "PFAM.db"))) | |
905 | (build-system r-build-system) | |
906 | (propagated-inputs | |
907 | `(("r-annotationdbi" ,r-annotationdbi))) | |
908 | (home-page "https://bioconductor.org/packages/PFAM.db") | |
909 | (synopsis "Set of protein ID mappings for PFAM") | |
910 | (description | |
911 | "This package provides a set of protein ID mappings for PFAM, assembled | |
912 | using data from public repositories.") | |
913 | (license license:artistic2.0))) | |
914 | ||
40be965e RW |
915 | (define-public r-phastcons100way-ucsc-hg19 |
916 | (package | |
917 | (name "r-phastcons100way-ucsc-hg19") | |
918 | (version "3.7.2") | |
919 | (source | |
920 | (origin | |
921 | (method url-fetch) | |
922 | (uri (bioconductor-uri "phastCons100way.UCSC.hg19" | |
923 | version 'annotation)) | |
924 | (sha256 | |
925 | (base32 | |
926 | "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa")))) | |
927 | (properties | |
928 | `((upstream-name . "phastCons100way.UCSC.hg19"))) | |
929 | (build-system r-build-system) | |
930 | (propagated-inputs | |
931 | `(("r-bsgenome" ,r-bsgenome) | |
932 | ("r-genomeinfodb" ,r-genomeinfodb) | |
933 | ("r-genomicranges" ,r-genomicranges) | |
934 | ("r-genomicscores" ,r-genomicscores) | |
935 | ("r-iranges" ,r-iranges) | |
936 | ("r-s4vectors" ,r-s4vectors))) | |
937 | (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") | |
938 | (synopsis "UCSC phastCons conservation scores for hg19") | |
939 | (description | |
940 | "This package provides UCSC phastCons conservation scores for the human | |
941 | genome (hg19) calculated from multiple alignments with other 99 vertebrate | |
942 | species.") | |
943 | (license license:artistic2.0))) | |
944 | ||
2cc51108 | 945 | \f |
557a1089 RW |
946 | ;;; Experiment data |
947 | ||
692bce15 RW |
948 | (define-public r-abadata |
949 | (package | |
950 | (name "r-abadata") | |
951 | (version "1.12.0") | |
952 | (source (origin | |
953 | (method url-fetch) | |
ced61edf | 954 | (uri (bioconductor-uri "ABAData" version 'experiment)) |
692bce15 RW |
955 | (sha256 |
956 | (base32 | |
957 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) | |
958 | (properties | |
959 | `((upstream-name . "ABAData"))) | |
960 | (build-system r-build-system) | |
961 | (propagated-inputs | |
962 | `(("r-annotationdbi" ,r-annotationdbi))) | |
963 | (home-page "https://www.bioconductor.org/packages/ABAData/") | |
964 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") | |
965 | (description | |
966 | "This package provides the data for the gene expression enrichment | |
967 | analysis conducted in the package ABAEnrichment. The package includes three | |
968 | datasets which are derived from the Allen Brain Atlas: | |
969 | ||
970 | @enumerate | |
971 | @item Gene expression data from Human Brain (adults) averaged across donors, | |
972 | @item Gene expression data from the Developing Human Brain pooled into five | |
973 | age categories and averaged across donors, and | |
974 | @item a developmental effect score based on the Developing Human Brain | |
975 | expression data. | |
976 | @end enumerate | |
977 | ||
978 | All datasets are restricted to protein coding genes.") | |
979 | (license license:gpl2+))) | |
980 | ||
b50c9660 RW |
981 | (define-public r-arrmdata |
982 | (package | |
983 | (name "r-arrmdata") | |
984 | (version "1.18.0") | |
985 | (source (origin | |
986 | (method url-fetch) | |
b86f7746 | 987 | (uri (bioconductor-uri "ARRmData" version 'experiment)) |
b50c9660 RW |
988 | (sha256 |
989 | (base32 | |
990 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) | |
991 | (properties | |
992 | `((upstream-name . "ARRmData"))) | |
993 | (build-system r-build-system) | |
994 | (home-page "https://www.bioconductor.org/packages/ARRmData/") | |
995 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") | |
996 | (description | |
997 | "This package provides raw beta values from 36 samples across 3 groups | |
998 | from Illumina 450k methylation arrays.") | |
999 | (license license:artistic2.0))) | |
1000 | ||
557a1089 RW |
1001 | (define-public r-hsmmsinglecell |
1002 | (package | |
1003 | (name "r-hsmmsinglecell") | |
1004 | (version "1.2.0") | |
1005 | (source (origin | |
1006 | (method url-fetch) | |
545e67ac | 1007 | (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) |
557a1089 RW |
1008 | (sha256 |
1009 | (base32 | |
1010 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) | |
1011 | (properties | |
1012 | `((upstream-name . "HSMMSingleCell"))) | |
1013 | (build-system r-build-system) | |
1014 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") | |
1015 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") | |
1016 | (description | |
1017 | "Skeletal myoblasts undergo a well-characterized sequence of | |
1018 | morphological and transcriptional changes during differentiation. In this | |
1019 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded | |
1020 | under high mitogen conditions (GM) and then differentiated by switching to | |
1021 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several | |
1022 | hundred cells taken over a time-course of serum-induced differentiation. | |
1023 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, | |
1024 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. | |
1025 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, | |
1026 | which were then sequenced to a depth of ~4 million reads per library, | |
1027 | resulting in a complete gene expression profile for each cell.") | |
1028 | (license license:artistic2.0))) | |
ad8f46c6 | 1029 | |
1030 | (define-public r-all | |
1031 | (package | |
1032 | (name "r-all") | |
1033 | (version "1.26.0") | |
1034 | (source (origin | |
1035 | (method url-fetch) | |
41728d23 | 1036 | (uri (bioconductor-uri "ALL" version 'experiment)) |
ad8f46c6 | 1037 | (sha256 |
1038 | (base32 | |
1039 | "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) | |
1040 | (properties `((upstream-name . "ALL"))) | |
1041 | (build-system r-build-system) | |
1042 | (propagated-inputs | |
1043 | `(("r-biobase" ,r-biobase))) | |
1044 | (home-page "https://bioconductor.org/packages/ALL") | |
1045 | (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") | |
1046 | (description | |
1047 | "The data consist of microarrays from 128 different individuals with | |
1048 | @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates | |
1049 | are available. The data have been normalized (using rma) and it is the | |
1050 | jointly normalized data that are available here. The data are presented in | |
1051 | the form of an @code{exprSet} object.") | |
1052 | (license license:artistic2.0))) | |
557a1089 | 1053 | |
53b1e10f RW |
1054 | (define-public r-affydata |
1055 | (package | |
1056 | (name "r-affydata") | |
1057 | (version "1.32.0") | |
1058 | (source | |
1059 | (origin | |
1060 | (method url-fetch) | |
1061 | (uri (bioconductor-uri "affydata" version 'experiment)) | |
1062 | (sha256 | |
1063 | (base32 | |
1064 | "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) | |
1065 | (properties `((upstream-name . "affydata"))) | |
1066 | (build-system r-build-system) | |
1067 | (propagated-inputs | |
1068 | `(("r-affy" ,r-affy))) | |
1069 | (home-page "https://bioconductor.org/packages/affydata/") | |
1070 | (synopsis "Affymetrix data for demonstration purposes") | |
1071 | (description | |
1072 | "This package provides example datasets that represent 'real world | |
1073 | examples' of Affymetrix data, unlike the artificial examples included in the | |
1074 | package @code{affy}.") | |
1075 | (license license:gpl2+))) | |
1076 | ||
0c0ef9c5 RJ |
1077 | (define-public r-coverageview |
1078 | (package | |
1079 | (name "r-coverageview") | |
751fa8ff | 1080 | (version "1.26.0") |
0c0ef9c5 RJ |
1081 | (source (origin |
1082 | (method url-fetch) | |
1083 | (uri (bioconductor-uri "CoverageView" version)) | |
1084 | (sha256 | |
1085 | (base32 | |
751fa8ff | 1086 | "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj")))) |
0c0ef9c5 RJ |
1087 | (build-system r-build-system) |
1088 | (propagated-inputs | |
1089 | `(("r-s4vectors" ,r-s4vectors) | |
1090 | ("r-iranges" ,r-iranges) | |
1091 | ("r-genomicranges" ,r-genomicranges) | |
1092 | ("r-genomicalignments" ,r-genomicalignments) | |
1093 | ("r-rtracklayer" ,r-rtracklayer) | |
1094 | ("r-rsamtools" ,r-rsamtools))) | |
1095 | (home-page "https://bioconductor.org/packages/CoverageView/") | |
1096 | (synopsis "Coverage visualization package for R") | |
1097 | (description "This package provides a framework for the visualization of | |
1098 | genome coverage profiles. It can be used for ChIP-seq experiments, but it can | |
1099 | be also used for genome-wide nucleosome positioning experiments or other | |
1100 | experiment types where it is important to have a framework in order to inspect | |
1101 | how the coverage distributed across the genome.") | |
1102 | (license license:artistic2.0))) | |
06fc1a51 RJ |
1103 | |
1104 | (define-public r-cummerbund | |
1105 | (package | |
1106 | (name "r-cummerbund") | |
1ab0380d | 1107 | (version "2.30.0") |
06fc1a51 RJ |
1108 | (source (origin |
1109 | (method url-fetch) | |
1110 | (uri (bioconductor-uri "cummeRbund" version)) | |
1111 | (sha256 | |
1112 | (base32 | |
1ab0380d | 1113 | "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc")))) |
06fc1a51 RJ |
1114 | (build-system r-build-system) |
1115 | (propagated-inputs | |
1116 | `(("r-biobase" ,r-biobase) | |
1117 | ("r-biocgenerics" ,r-biocgenerics) | |
1118 | ("r-fastcluster", r-fastcluster) | |
1119 | ("r-ggplot2" ,r-ggplot2) | |
1120 | ("r-gviz" ,r-gviz) | |
1121 | ("r-plyr" ,r-plyr) | |
1122 | ("r-reshape2" ,r-reshape2) | |
1123 | ("r-rsqlite" ,r-rsqlite) | |
1124 | ("r-rtracklayer" ,r-rtracklayer) | |
1125 | ("r-s4vectors" ,r-s4vectors))) | |
1126 | (home-page "https://bioconductor.org/packages/cummeRbund/") | |
1127 | (synopsis "Analyze Cufflinks high-throughput sequencing data") | |
1128 | (description "This package allows for persistent storage, access, | |
1129 | exploration, and manipulation of Cufflinks high-throughput sequencing | |
1130 | data. In addition, provides numerous plotting functions for commonly | |
1131 | used visualizations.") | |
1132 | (license license:artistic2.0))) | |
0c0ef9c5 | 1133 | |
ff1146b9 RW |
1134 | (define-public r-curatedtcgadata |
1135 | (package | |
1136 | (name "r-curatedtcgadata") | |
1137 | (version "1.8.0") | |
1138 | (source | |
1139 | (origin | |
1140 | (method url-fetch) | |
1141 | (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) | |
1142 | (sha256 | |
1143 | (base32 | |
1144 | "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) | |
1145 | (properties | |
1146 | `((upstream-name . "curatedTCGAData"))) | |
1147 | (build-system r-build-system) | |
1148 | (propagated-inputs | |
1149 | `(("r-annotationhub" ,r-annotationhub) | |
1150 | ("r-experimenthub" ,r-experimenthub) | |
1151 | ("r-hdf5array" ,r-hdf5array) | |
1152 | ("r-multiassayexperiment" ,r-multiassayexperiment) | |
1153 | ("r-s4vectors" ,r-s4vectors) | |
1154 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1155 | (home-page "https://bioconductor.org/packages/curatedTCGAData/") | |
1156 | (synopsis "Curated data from The Cancer Genome Atlas") | |
1157 | (description | |
1158 | "This package provides publicly available data from The Cancer Genome | |
1159 | Atlas (TCGA) as @code{MultiAssayExperiment} objects. | |
1160 | @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy | |
1161 | number, mutation, microRNA, protein, and others) with clinical / pathological | |
1162 | data. It also links assay barcodes with patient identifiers, enabling | |
1163 | harmonized subsetting of rows (features) and columns (patients / samples) | |
1164 | across the entire multi-'omics experiment.") | |
1165 | (license license:artistic2.0))) | |
1166 | ||
557a1089 RW |
1167 | \f |
1168 | ;;; Packages | |
1169 | ||
e5d722fb RW |
1170 | (define-public r-biocversion |
1171 | (package | |
1172 | (name "r-biocversion") | |
bc217e4c | 1173 | (version "3.11.1") |
e5d722fb RW |
1174 | (source |
1175 | (origin | |
1176 | (method url-fetch) | |
1177 | (uri (bioconductor-uri "BiocVersion" version)) | |
1178 | (sha256 | |
1179 | (base32 | |
bc217e4c | 1180 | "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz")))) |
e5d722fb RW |
1181 | (properties `((upstream-name . "BiocVersion"))) |
1182 | (build-system r-build-system) | |
1183 | (home-page "https://bioconductor.org/packages/BiocVersion/") | |
1184 | (synopsis "Set the appropriate version of Bioconductor packages") | |
1185 | (description | |
1186 | "This package provides repository information for the appropriate version | |
1187 | of Bioconductor.") | |
1188 | (license license:artistic2.0))) | |
1189 | ||
14bba460 RW |
1190 | (define-public r-biocgenerics |
1191 | (package | |
1192 | (name "r-biocgenerics") | |
2e15c16f | 1193 | (version "0.34.0") |
14bba460 RW |
1194 | (source (origin |
1195 | (method url-fetch) | |
1196 | (uri (bioconductor-uri "BiocGenerics" version)) | |
1197 | (sha256 | |
1198 | (base32 | |
2e15c16f | 1199 | "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk")))) |
14bba460 RW |
1200 | (properties |
1201 | `((upstream-name . "BiocGenerics"))) | |
1202 | (build-system r-build-system) | |
1203 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
1204 | (synopsis "S4 generic functions for Bioconductor") | |
1205 | (description | |
1206 | "This package provides S4 generic functions needed by many Bioconductor | |
1207 | packages.") | |
1208 | (license license:artistic2.0))) | |
1209 | ||
5cf940de RW |
1210 | (define-public r-affycomp |
1211 | (package | |
1212 | (name "r-affycomp") | |
66aeb1b4 | 1213 | (version "1.64.0") |
5cf940de RW |
1214 | (source |
1215 | (origin | |
1216 | (method url-fetch) | |
1217 | (uri (bioconductor-uri "affycomp" version)) | |
1218 | (sha256 | |
1219 | (base32 | |
66aeb1b4 | 1220 | "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0")))) |
5cf940de RW |
1221 | (properties `((upstream-name . "affycomp"))) |
1222 | (build-system r-build-system) | |
1223 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
1224 | (home-page "https://bioconductor.org/packages/affycomp/") | |
1225 | (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") | |
1226 | (description | |
1227 | "The package contains functions that can be used to compare expression | |
1228 | measures for Affymetrix Oligonucleotide Arrays.") | |
1229 | (license license:gpl2+))) | |
1230 | ||
5094aa94 RW |
1231 | (define-public r-affycompatible |
1232 | (package | |
1233 | (name "r-affycompatible") | |
251c18f1 | 1234 | (version "1.48.0") |
5094aa94 RW |
1235 | (source |
1236 | (origin | |
1237 | (method url-fetch) | |
1238 | (uri (bioconductor-uri "AffyCompatible" version)) | |
1239 | (sha256 | |
1240 | (base32 | |
251c18f1 | 1241 | "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd")))) |
5094aa94 RW |
1242 | (properties |
1243 | `((upstream-name . "AffyCompatible"))) | |
1244 | (build-system r-build-system) | |
1245 | (propagated-inputs | |
1246 | `(("r-biostrings" ,r-biostrings) | |
1247 | ("r-rcurl" ,r-rcurl) | |
1248 | ("r-xml" ,r-xml))) | |
1249 | (home-page "https://bioconductor.org/packages/AffyCompatible/") | |
1250 | (synopsis "Work with Affymetrix GeneChip files") | |
1251 | (description | |
1252 | "This package provides an interface to Affymetrix chip annotation and | |
1253 | sample attribute files. The package allows an easy way for users to download | |
1254 | and manage local data bases of Affynmetrix NetAffx annotation files. It also | |
1255 | provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip | |
1256 | Command Console} (AGCC)-compatible sample annotation files.") | |
1257 | (license license:artistic2.0))) | |
1258 | ||
4ca2d6c1 RW |
1259 | (define-public r-affycontam |
1260 | (package | |
1261 | (name "r-affycontam") | |
36d4ca41 | 1262 | (version "1.46.0") |
4ca2d6c1 RW |
1263 | (source |
1264 | (origin | |
1265 | (method url-fetch) | |
1266 | (uri (bioconductor-uri "affyContam" version)) | |
1267 | (sha256 | |
1268 | (base32 | |
36d4ca41 | 1269 | "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i")))) |
4ca2d6c1 RW |
1270 | (properties `((upstream-name . "affyContam"))) |
1271 | (build-system r-build-system) | |
1272 | (propagated-inputs | |
1273 | `(("r-affy" ,r-affy) | |
1274 | ("r-affydata" ,r-affydata) | |
1275 | ("r-biobase" ,r-biobase))) | |
1276 | (home-page "https://bioconductor.org/packages/affyContam/") | |
1277 | (synopsis "Structured corruption of Affymetrix CEL file data") | |
1278 | (description | |
1279 | "Microarray quality assessment is a major concern of microarray analysts. | |
1280 | This package provides some simple approaches to in silico creation of quality | |
1281 | problems in CEL-level data to help evaluate performance of quality metrics.") | |
1282 | (license license:artistic2.0))) | |
1283 | ||
12105c6c RW |
1284 | (define-public r-affycoretools |
1285 | (package | |
1286 | (name "r-affycoretools") | |
fa610697 | 1287 | (version "1.60.1") |
12105c6c RW |
1288 | (source |
1289 | (origin | |
1290 | (method url-fetch) | |
1291 | (uri (bioconductor-uri "affycoretools" version)) | |
1292 | (sha256 | |
1293 | (base32 | |
fa610697 | 1294 | "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s")))) |
12105c6c RW |
1295 | (properties `((upstream-name . "affycoretools"))) |
1296 | (build-system r-build-system) | |
1297 | (propagated-inputs | |
1298 | `(("r-affy" ,r-affy) | |
1299 | ("r-annotationdbi" ,r-annotationdbi) | |
1300 | ("r-biobase" ,r-biobase) | |
1301 | ("r-biocgenerics" ,r-biocgenerics) | |
1302 | ("r-dbi" ,r-dbi) | |
1303 | ("r-edger" ,r-edger) | |
1304 | ("r-gcrma" ,r-gcrma) | |
f8f181ae | 1305 | ("r-glimma" ,r-glimma) |
12105c6c RW |
1306 | ("r-ggplot2" ,r-ggplot2) |
1307 | ("r-gostats" ,r-gostats) | |
1308 | ("r-gplots" ,r-gplots) | |
1309 | ("r-hwriter" ,r-hwriter) | |
1310 | ("r-lattice" ,r-lattice) | |
1311 | ("r-limma" ,r-limma) | |
1312 | ("r-oligoclasses" ,r-oligoclasses) | |
1313 | ("r-reportingtools" ,r-reportingtools) | |
1314 | ("r-rsqlite" ,r-rsqlite) | |
1315 | ("r-s4vectors" ,r-s4vectors) | |
1316 | ("r-xtable" ,r-xtable))) | |
fa610697 RW |
1317 | (native-inputs |
1318 | `(("r-knitr" ,r-knitr))) | |
12105c6c RW |
1319 | (home-page "https://bioconductor.org/packages/affycoretools/") |
1320 | (synopsis "Functions for analyses with Affymetrix GeneChips") | |
1321 | (description | |
1322 | "This package provides various wrapper functions that have been written | |
1323 | to streamline the more common analyses that a Biostatistician might see.") | |
1324 | (license license:artistic2.0))) | |
1325 | ||
d6a5d9b2 RW |
1326 | (define-public r-affxparser |
1327 | (package | |
1328 | (name "r-affxparser") | |
acaf8a23 | 1329 | (version "1.60.0") |
d6a5d9b2 RW |
1330 | (source |
1331 | (origin | |
1332 | (method url-fetch) | |
1333 | (uri (bioconductor-uri "affxparser" version)) | |
1334 | (sha256 | |
1335 | (base32 | |
acaf8a23 | 1336 | "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq")))) |
d6a5d9b2 RW |
1337 | (properties `((upstream-name . "affxparser"))) |
1338 | (build-system r-build-system) | |
1339 | (home-page "https://github.com/HenrikBengtsson/affxparser") | |
1340 | (synopsis "Affymetrix File Parsing SDK") | |
1341 | (description | |
1342 | "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, | |
1343 | BAR). It provides methods for fast and memory efficient parsing of Affymetrix | |
1344 | files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files | |
1345 | are supported. Currently, there are methods for reading @dfn{chip definition | |
1346 | file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read | |
1347 | either in full or in part. For example, probe signals from a few probesets | |
1348 | can be extracted very quickly from a set of CEL files into a convenient list | |
1349 | structure.") | |
1350 | ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is | |
1351 | ;; under LGPLv2+. | |
1352 | (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2)))) | |
1353 | ||
7097c700 RW |
1354 | (define-public r-annotate |
1355 | (package | |
1356 | (name "r-annotate") | |
c2f4ad96 | 1357 | (version "1.66.0") |
7097c700 RW |
1358 | (source |
1359 | (origin | |
1360 | (method url-fetch) | |
1361 | (uri (bioconductor-uri "annotate" version)) | |
1362 | (sha256 | |
1363 | (base32 | |
c2f4ad96 | 1364 | "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w")))) |
7097c700 RW |
1365 | (build-system r-build-system) |
1366 | (propagated-inputs | |
1367 | `(("r-annotationdbi" ,r-annotationdbi) | |
1368 | ("r-biobase" ,r-biobase) | |
1369 | ("r-biocgenerics" ,r-biocgenerics) | |
1370 | ("r-dbi" ,r-dbi) | |
1371 | ("r-rcurl" ,r-rcurl) | |
1372 | ("r-xml" ,r-xml) | |
1373 | ("r-xtable" ,r-xtable))) | |
1374 | (home-page | |
1375 | "https://bioconductor.org/packages/annotate") | |
1376 | (synopsis "Annotation for microarrays") | |
1377 | (description "This package provides R environments for the annotation of | |
1378 | microarrays.") | |
1379 | (license license:artistic2.0))) | |
1380 | ||
fa596599 RW |
1381 | (define-public r-hpar |
1382 | (package | |
1383 | (name "r-hpar") | |
07bea010 | 1384 | (version "1.30.0") |
fa596599 RW |
1385 | (source |
1386 | (origin | |
1387 | (method url-fetch) | |
1388 | (uri (bioconductor-uri "hpar" version)) | |
1389 | (sha256 | |
1390 | (base32 | |
07bea010 | 1391 | "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9")))) |
fa596599 | 1392 | (build-system r-build-system) |
07bea010 RW |
1393 | (native-inputs |
1394 | `(("r-knitr" ,r-knitr))) | |
fa596599 RW |
1395 | (home-page "https://bioconductor.org/packages/hpar/") |
1396 | (synopsis "Human Protein Atlas in R") | |
1397 | (description "This package provides a simple interface to and data from | |
1398 | the Human Protein Atlas project.") | |
1399 | (license license:artistic2.0))) | |
183ce988 RJ |
1400 | |
1401 | (define-public r-regioner | |
1402 | (package | |
1403 | (name "r-regioner") | |
8c06ce3c | 1404 | (version "1.20.1") |
183ce988 RJ |
1405 | (source |
1406 | (origin | |
1407 | (method url-fetch) | |
1408 | (uri (bioconductor-uri "regioneR" version)) | |
1409 | (sha256 | |
1410 | (base32 | |
8c06ce3c | 1411 | "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c")))) |
183ce988 RJ |
1412 | (properties `((upstream-name . "regioneR"))) |
1413 | (build-system r-build-system) | |
1414 | (propagated-inputs | |
d639d888 | 1415 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 1416 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 1417 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 1418 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 1419 | ("r-iranges" ,r-iranges) |
d639d888 RW |
1420 | ("r-memoise" ,r-memoise) |
1421 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 1422 | ("r-s4vectors" ,r-s4vectors))) |
7f34dd58 RW |
1423 | (native-inputs |
1424 | `(("r-knitr" ,r-knitr))) | |
183ce988 RJ |
1425 | (home-page "https://bioconductor.org/packages/regioneR/") |
1426 | (synopsis "Association analysis of genomic regions") | |
1427 | (description "This package offers a statistical framework based on | |
1428 | customizable permutation tests to assess the association between genomic | |
1429 | region sets and other genomic features.") | |
1430 | (license license:artistic2.0))) | |
a5b56a53 | 1431 | |
15184fb3 RW |
1432 | (define-public r-reportingtools |
1433 | (package | |
1434 | (name "r-reportingtools") | |
7f94cf01 | 1435 | (version "2.28.0") |
15184fb3 RW |
1436 | (source |
1437 | (origin | |
1438 | (method url-fetch) | |
1439 | (uri (bioconductor-uri "ReportingTools" version)) | |
1440 | (sha256 | |
1441 | (base32 | |
7f94cf01 | 1442 | "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx")))) |
15184fb3 RW |
1443 | (properties |
1444 | `((upstream-name . "ReportingTools"))) | |
1445 | (build-system r-build-system) | |
1446 | (propagated-inputs | |
1447 | `(("r-annotate" ,r-annotate) | |
1448 | ("r-annotationdbi" ,r-annotationdbi) | |
1449 | ("r-biobase" ,r-biobase) | |
1450 | ("r-biocgenerics" ,r-biocgenerics) | |
1451 | ("r-category" ,r-category) | |
1452 | ("r-deseq2" ,r-deseq2) | |
1453 | ("r-edger" ,r-edger) | |
1454 | ("r-ggbio" ,r-ggbio) | |
1455 | ("r-ggplot2" ,r-ggplot2) | |
1456 | ("r-gostats" ,r-gostats) | |
1457 | ("r-gseabase" ,r-gseabase) | |
1458 | ("r-hwriter" ,r-hwriter) | |
1459 | ("r-iranges" ,r-iranges) | |
1460 | ("r-knitr" ,r-knitr) | |
1461 | ("r-lattice" ,r-lattice) | |
1462 | ("r-limma" ,r-limma) | |
1463 | ("r-pfam-db" ,r-pfam-db) | |
1464 | ("r-r-utils" ,r-r-utils) | |
1465 | ("r-xml" ,r-xml))) | |
7f94cf01 RW |
1466 | (native-inputs |
1467 | `(("r-knitr" ,r-knitr))) | |
15184fb3 RW |
1468 | (home-page "https://bioconductor.org/packages/ReportingTools/") |
1469 | (synopsis "Tools for making reports in various formats") | |
1470 | (description | |
1471 | "The ReportingTools package enables users to easily display reports of | |
1472 | analysis results generated from sources such as microarray and sequencing | |
1473 | data. The package allows users to create HTML pages that may be viewed on a | |
1474 | web browser, or in other formats. Users can generate tables with sortable and | |
1475 | filterable columns, make and display plots, and link table entries to other | |
1476 | data sources such as NCBI or larger plots within the HTML page. Using the | |
1477 | package, users can also produce a table of contents page to link various | |
1478 | reports together for a particular project that can be viewed in a web | |
1479 | browser.") | |
1480 | (license license:artistic2.0))) | |
1481 | ||
bfb93b48 RW |
1482 | (define-public r-geneplotter |
1483 | (package | |
1484 | (name "r-geneplotter") | |
53e42019 | 1485 | (version "1.66.0") |
bfb93b48 RW |
1486 | (source |
1487 | (origin | |
1488 | (method url-fetch) | |
1489 | (uri (bioconductor-uri "geneplotter" version)) | |
1490 | (sha256 | |
1491 | (base32 | |
53e42019 | 1492 | "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5")))) |
bfb93b48 RW |
1493 | (build-system r-build-system) |
1494 | (propagated-inputs | |
1495 | `(("r-annotate" ,r-annotate) | |
1496 | ("r-annotationdbi" ,r-annotationdbi) | |
1497 | ("r-biobase" ,r-biobase) | |
1498 | ("r-biocgenerics" ,r-biocgenerics) | |
1499 | ("r-lattice" ,r-lattice) | |
1500 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
1501 | (home-page "https://bioconductor.org/packages/geneplotter") | |
1502 | (synopsis "Graphics functions for genomic data") | |
1503 | (description | |
1504 | "This package provides functions for plotting genomic data.") | |
1505 | (license license:artistic2.0))) | |
1506 | ||
01c7ba99 RW |
1507 | (define-public r-oligoclasses |
1508 | (package | |
1509 | (name "r-oligoclasses") | |
1c43c6fa | 1510 | (version "1.50.4") |
01c7ba99 RW |
1511 | (source |
1512 | (origin | |
1513 | (method url-fetch) | |
1514 | (uri (bioconductor-uri "oligoClasses" version)) | |
1515 | (sha256 | |
1516 | (base32 | |
1c43c6fa | 1517 | "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67")))) |
01c7ba99 RW |
1518 | (properties `((upstream-name . "oligoClasses"))) |
1519 | (build-system r-build-system) | |
1520 | (propagated-inputs | |
1521 | `(("r-affyio" ,r-affyio) | |
1522 | ("r-biobase" ,r-biobase) | |
1523 | ("r-biocgenerics" ,r-biocgenerics) | |
1524 | ("r-biocmanager" ,r-biocmanager) | |
1525 | ("r-biostrings" ,r-biostrings) | |
1526 | ("r-dbi" ,r-dbi) | |
1527 | ("r-ff" ,r-ff) | |
1528 | ("r-foreach" ,r-foreach) | |
1529 | ("r-genomicranges" ,r-genomicranges) | |
1530 | ("r-iranges" ,r-iranges) | |
1531 | ("r-rsqlite" ,r-rsqlite) | |
1532 | ("r-s4vectors" ,r-s4vectors) | |
1533 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1534 | (home-page "https://bioconductor.org/packages/oligoClasses/") | |
1535 | (synopsis "Classes for high-throughput arrays") | |
1536 | (description | |
1537 | "This package contains class definitions, validity checks, and | |
1538 | initialization methods for classes used by the @code{oligo} and @code{crlmm} | |
1539 | packages.") | |
1540 | (license license:gpl2+))) | |
1541 | ||
4c63eeb8 RW |
1542 | (define-public r-oligo |
1543 | (package | |
1544 | (name "r-oligo") | |
0827e0be | 1545 | (version "1.52.1") |
4c63eeb8 RW |
1546 | (source |
1547 | (origin | |
1548 | (method url-fetch) | |
1549 | (uri (bioconductor-uri "oligo" version)) | |
1550 | (sha256 | |
1551 | (base32 | |
0827e0be | 1552 | "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd")))) |
4c63eeb8 RW |
1553 | (properties `((upstream-name . "oligo"))) |
1554 | (build-system r-build-system) | |
1555 | (inputs `(("zlib" ,zlib))) | |
1556 | (propagated-inputs | |
1557 | `(("r-affxparser" ,r-affxparser) | |
1558 | ("r-affyio" ,r-affyio) | |
1559 | ("r-biobase" ,r-biobase) | |
1560 | ("r-biocgenerics" ,r-biocgenerics) | |
1561 | ("r-biostrings" ,r-biostrings) | |
1562 | ("r-dbi" ,r-dbi) | |
1563 | ("r-ff" ,r-ff) | |
1564 | ("r-oligoclasses" ,r-oligoclasses) | |
1565 | ("r-preprocesscore" ,r-preprocesscore) | |
1566 | ("r-rsqlite" ,r-rsqlite) | |
1567 | ("r-zlibbioc" ,r-zlibbioc))) | |
ace82f80 RW |
1568 | (native-inputs |
1569 | `(("r-knitr" ,r-knitr))) | |
4c63eeb8 RW |
1570 | (home-page "https://bioconductor.org/packages/oligo/") |
1571 | (synopsis "Preprocessing tools for oligonucleotide arrays") | |
1572 | (description | |
1573 | "This package provides a package to analyze oligonucleotide | |
1574 | arrays (expression/SNP/tiling/exon) at probe-level. It currently supports | |
1575 | Affymetrix (CEL files) and NimbleGen arrays (XYS files).") | |
1576 | (license license:lgpl2.0+))) | |
1577 | ||
4dc2ecc2 RW |
1578 | (define-public r-qvalue |
1579 | (package | |
1580 | (name "r-qvalue") | |
f9a24759 | 1581 | (version "2.20.0") |
4dc2ecc2 RW |
1582 | (source |
1583 | (origin | |
1584 | (method url-fetch) | |
1585 | (uri (bioconductor-uri "qvalue" version)) | |
1586 | (sha256 | |
1587 | (base32 | |
f9a24759 | 1588 | "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f")))) |
4dc2ecc2 RW |
1589 | (build-system r-build-system) |
1590 | (propagated-inputs | |
1591 | `(("r-ggplot2" ,r-ggplot2) | |
1592 | ("r-reshape2" ,r-reshape2))) | |
f9a24759 RW |
1593 | (native-inputs |
1594 | `(("r-knitr" ,r-knitr))) | |
702a1012 | 1595 | (home-page "https://github.com/StoreyLab/qvalue") |
4dc2ecc2 RW |
1596 | (synopsis "Q-value estimation for false discovery rate control") |
1597 | (description | |
1598 | "This package takes a list of p-values resulting from the simultaneous | |
1599 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
1600 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
1601 | of false positives incurred when that particular test is called significant. | |
1602 | The local FDR measures the posterior probability the null hypothesis is true | |
1603 | given the test's p-value. Various plots are automatically generated, allowing | |
1604 | one to make sensible significance cut-offs. The software can be applied to | |
1605 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
1606 | ;; Any version of the LGPL. | |
1607 | (license license:lgpl3+))) | |
1608 | ||
a5b56a53 RJ |
1609 | (define-public r-diffbind |
1610 | (package | |
1611 | (name "r-diffbind") | |
b47b649a | 1612 | (version "2.16.0") |
a5b56a53 RJ |
1613 | (source |
1614 | (origin | |
1615 | (method url-fetch) | |
1616 | (uri (bioconductor-uri "DiffBind" version)) | |
1617 | (sha256 | |
1618 | (base32 | |
b47b649a | 1619 | "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5")))) |
a5b56a53 RJ |
1620 | (properties `((upstream-name . "DiffBind"))) |
1621 | (build-system r-build-system) | |
1622 | (inputs | |
1623 | `(("zlib" ,zlib))) | |
1624 | (propagated-inputs | |
1625 | `(("r-amap" ,r-amap) | |
1626 | ("r-biocparallel" ,r-biocparallel) | |
1627 | ("r-deseq2" ,r-deseq2) | |
1628 | ("r-dplyr" ,r-dplyr) | |
1629 | ("r-edger" ,r-edger) | |
1630 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
1631 | ("r-genomicranges" ,r-genomicranges) |
1632 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
1633 | ("r-ggrepel" ,r-ggrepel) |
1634 | ("r-gplots" ,r-gplots) | |
1635 | ("r-iranges" ,r-iranges) | |
1636 | ("r-lattice" ,r-lattice) | |
1637 | ("r-limma" ,r-limma) | |
1638 | ("r-locfit" ,r-locfit) | |
1639 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
1640 | ("r-rcpp" ,r-rcpp) | |
4c221b3b | 1641 | ("r-rhtslib" ,r-rhtslib) |
a5b56a53 RJ |
1642 | ("r-rsamtools" ,r-rsamtools) |
1643 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 1644 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
4c221b3b | 1645 | ("r-systempiper" ,r-systempiper))) |
99db6db7 | 1646 | (home-page "https://bioconductor.org/packages/DiffBind") |
a5b56a53 RJ |
1647 | (synopsis "Differential binding analysis of ChIP-Seq peak data") |
1648 | (description | |
1649 | "This package computes differentially bound sites from multiple | |
1650 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
1651 | occupancy (overlap) analysis and plotting functions.") | |
1652 | (license license:artistic2.0))) | |
6d94bf6b RJ |
1653 | |
1654 | (define-public r-ripseeker | |
1655 | (package | |
1656 | (name "r-ripseeker") | |
ba74434f | 1657 | (version "1.26.0") |
6d94bf6b RJ |
1658 | (source |
1659 | (origin | |
1660 | (method url-fetch) | |
1661 | (uri (bioconductor-uri "RIPSeeker" version)) | |
1662 | (sha256 | |
1663 | (base32 | |
ba74434f | 1664 | "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) |
6d94bf6b RJ |
1665 | (properties `((upstream-name . "RIPSeeker"))) |
1666 | (build-system r-build-system) | |
1667 | (propagated-inputs | |
1668 | `(("r-s4vectors" ,r-s4vectors) | |
1669 | ("r-iranges" ,r-iranges) | |
1670 | ("r-genomicranges" ,r-genomicranges) | |
1671 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1672 | ("r-rsamtools" ,r-rsamtools) | |
1673 | ("r-genomicalignments" ,r-genomicalignments) | |
1674 | ("r-rtracklayer" ,r-rtracklayer))) | |
99db6db7 | 1675 | (home-page "https://bioconductor.org/packages/RIPSeeker") |
6d94bf6b RJ |
1676 | (synopsis |
1677 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
1678 | (description | |
1679 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
1680 | using two-state HMM with negative binomial emission probability. While | |
1681 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
1682 | a suite of bioinformatics tools integrated within this self-contained software | |
1683 | package comprehensively addressing issues ranging from post-alignments | |
1684 | processing to visualization and annotation.") | |
1685 | (license license:gpl2))) | |
a6ae9ffd RJ |
1686 | |
1687 | (define-public r-multtest | |
1688 | (package | |
1689 | (name "r-multtest") | |
8cadf253 | 1690 | (version "2.44.0") |
a6ae9ffd RJ |
1691 | (source |
1692 | (origin | |
1693 | (method url-fetch) | |
1694 | (uri (bioconductor-uri "multtest" version)) | |
1695 | (sha256 | |
1696 | (base32 | |
8cadf253 | 1697 | "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2")))) |
a6ae9ffd RJ |
1698 | (build-system r-build-system) |
1699 | (propagated-inputs | |
1700 | `(("r-survival" ,r-survival) | |
1701 | ("r-biocgenerics" ,r-biocgenerics) | |
1702 | ("r-biobase" ,r-biobase) | |
1703 | ("r-mass" ,r-mass))) | |
99db6db7 | 1704 | (home-page "https://bioconductor.org/packages/multtest") |
a6ae9ffd RJ |
1705 | (synopsis "Resampling-based multiple hypothesis testing") |
1706 | (description | |
1707 | "This package can do non-parametric bootstrap and permutation | |
1708 | resampling-based multiple testing procedures (including empirical Bayes | |
1709 | methods) for controlling the family-wise error rate (FWER), generalized | |
1710 | family-wise error rate (gFWER), tail probability of the proportion of | |
1711 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
1712 | of bootstrap-based null distribution are implemented (centered, centered | |
1713 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
1714 | available. Tests based on a variety of T- and F-statistics (including | |
1715 | T-statistics based on regression parameters from linear and survival models | |
1716 | as well as those based on correlation parameters) are included. When probing | |
1717 | hypotheses with T-statistics, users may also select a potentially faster null | |
1718 | distribution which is multivariate normal with mean zero and variance | |
1719 | covariance matrix derived from the vector influence function. Results are | |
1720 | reported in terms of adjusted P-values, confidence regions and test statistic | |
1721 | cutoffs. The procedures are directly applicable to identifying differentially | |
1722 | expressed genes in DNA microarray experiments.") | |
1723 | (license license:lgpl3))) | |
793f83ef | 1724 | |
5dfe4912 RW |
1725 | (define-public r-graph |
1726 | (package | |
1727 | (name "r-graph") | |
7d37c6d9 | 1728 | (version "1.66.0") |
5dfe4912 RW |
1729 | (source (origin |
1730 | (method url-fetch) | |
1731 | (uri (bioconductor-uri "graph" version)) | |
1732 | (sha256 | |
1733 | (base32 | |
7d37c6d9 | 1734 | "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g")))) |
5dfe4912 RW |
1735 | (build-system r-build-system) |
1736 | (propagated-inputs | |
1737 | `(("r-biocgenerics" ,r-biocgenerics))) | |
1738 | (home-page "https://bioconductor.org/packages/graph") | |
1739 | (synopsis "Handle graph data structures in R") | |
1740 | (description | |
1741 | "This package implements some simple graph handling capabilities for R.") | |
1742 | (license license:artistic2.0))) | |
1743 | ||
8017eb0a RW |
1744 | ;; This is a CRAN package, but it depends on a Bioconductor package. |
1745 | (define-public r-ggm | |
1746 | (package | |
1747 | (name "r-ggm") | |
1748 | (version "2.5") | |
1749 | (source | |
1750 | (origin | |
1751 | (method url-fetch) | |
1752 | (uri (cran-uri "ggm" version)) | |
1753 | (sha256 | |
1754 | (base32 | |
1755 | "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) | |
1756 | (properties `((upstream-name . "ggm"))) | |
1757 | (build-system r-build-system) | |
1758 | (propagated-inputs | |
1759 | `(("r-graph" ,r-graph) | |
1760 | ("r-igraph" ,r-igraph))) | |
1761 | (home-page "https://cran.r-project.org/package=ggm") | |
1762 | (synopsis "Functions for graphical Markov models") | |
1763 | (description | |
1764 | "This package provides functions and datasets for maximum likelihood | |
1765 | fitting of some classes of graphical Markov models.") | |
1766 | (license license:gpl2+))) | |
1767 | ||
b17ace24 | 1768 | ;; This is a CRAN package, but it depends on a Bioconductor package. |
a207bca2 RW |
1769 | (define-public r-codedepends |
1770 | (package | |
1771 | (name "r-codedepends") | |
1772 | (version "0.6.5") | |
1773 | (source | |
1774 | (origin | |
1775 | (method url-fetch) | |
1776 | (uri (cran-uri "CodeDepends" version)) | |
1777 | (sha256 | |
1778 | (base32 | |
1779 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
1780 | (properties `((upstream-name . "CodeDepends"))) | |
1781 | (build-system r-build-system) | |
1782 | (propagated-inputs | |
1783 | `(("r-codetools" ,r-codetools) | |
1784 | ("r-graph" ,r-graph) | |
1785 | ("r-xml" ,r-xml))) | |
5e1f2362 | 1786 | (home-page "https://cran.r-project.org/web/packages/CodeDepends") |
a207bca2 RW |
1787 | (synopsis "Analysis of R code for reproducible research and code comprehension") |
1788 | (description | |
1789 | "This package provides tools for analyzing R expressions or blocks of | |
1790 | code and determining the dependencies between them. It focuses on R scripts, | |
1791 | but can be used on the bodies of functions. There are many facilities | |
1792 | including the ability to summarize or get a high-level view of code, | |
1793 | determining dependencies between variables, code improvement suggestions.") | |
1794 | ;; Any version of the GPL | |
1795 | (license (list license:gpl2+ license:gpl3+)))) | |
1796 | ||
793f83ef RJ |
1797 | (define-public r-chippeakanno |
1798 | (package | |
1799 | (name "r-chippeakanno") | |
0d2369be | 1800 | (version "3.22.3") |
793f83ef RJ |
1801 | (source |
1802 | (origin | |
1803 | (method url-fetch) | |
1804 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
1805 | (sha256 | |
1806 | (base32 | |
0d2369be | 1807 | "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y")))) |
793f83ef RJ |
1808 | (properties `((upstream-name . "ChIPpeakAnno"))) |
1809 | (build-system r-build-system) | |
1810 | (propagated-inputs | |
85c1d20f RW |
1811 | `(("r-annotationdbi" ,r-annotationdbi) |
1812 | ("r-biobase" ,r-biobase) | |
1813 | ("r-biocgenerics" ,r-biocgenerics) | |
57d2fcd9 | 1814 | ("r-biocmanager" ,r-biocmanager) |
793f83ef | 1815 | ("r-biomart" ,r-biomart) |
85c1d20f | 1816 | ("r-biostrings" ,r-biostrings) |
793f83ef | 1817 | ("r-bsgenome" ,r-bsgenome) |
85c1d20f RW |
1818 | ("r-dbi" ,r-dbi) |
1819 | ("r-delayedarray" ,r-delayedarray) | |
1820 | ("r-ensembldb" ,r-ensembldb) | |
1821 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1822 | ("r-genomicalignments" ,r-genomicalignments) | |
793f83ef | 1823 | ("r-genomicfeatures" ,r-genomicfeatures) |
f794e85d | 1824 | ("r-genomicranges" ,r-genomicranges) |
85c1d20f RW |
1825 | ("r-go-db" ,r-go-db) |
1826 | ("r-graph" ,r-graph) | |
1827 | ("r-idr" ,r-idr) | |
f794e85d | 1828 | ("r-iranges" ,r-iranges) |
793f83ef | 1829 | ("r-limma" ,r-limma) |
85c1d20f | 1830 | ("r-matrixstats" ,r-matrixstats) |
793f83ef RJ |
1831 | ("r-multtest" ,r-multtest) |
1832 | ("r-rbgl" ,r-rbgl) | |
793f83ef | 1833 | ("r-regioner" ,r-regioner) |
85c1d20f RW |
1834 | ("r-rsamtools" ,r-rsamtools) |
1835 | ("r-rtracklayer" ,r-rtracklayer) | |
f794e85d | 1836 | ("r-s4vectors" ,r-s4vectors) |
793f83ef | 1837 | ("r-seqinr" ,r-seqinr) |
793f83ef | 1838 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
793f83ef | 1839 | ("r-venndiagram" ,r-venndiagram))) |
dc24de46 RW |
1840 | (native-inputs |
1841 | `(("r-knitr" ,r-knitr))) | |
99db6db7 | 1842 | (home-page "https://bioconductor.org/packages/ChIPpeakAnno") |
793f83ef RJ |
1843 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") |
1844 | (description | |
1845 | "The package includes functions to retrieve the sequences around the peak, | |
1846 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
1847 | custom features such as most conserved elements and other transcription factor | |
1848 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
1849 | for finding the peaks with bi-directional promoters with summary statistics | |
1850 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
1851 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
1852 | enrichedGO (addGeneIDs).") | |
1853 | (license license:gpl2+))) | |
164502d8 RJ |
1854 | |
1855 | (define-public r-marray | |
1856 | (package | |
1857 | (name "r-marray") | |
49d589e5 | 1858 | (version "1.66.0") |
164502d8 RJ |
1859 | (source (origin |
1860 | (method url-fetch) | |
1861 | (uri (bioconductor-uri "marray" version)) | |
1862 | (sha256 | |
49d589e5 | 1863 | (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd")))) |
164502d8 RJ |
1864 | (build-system r-build-system) |
1865 | (propagated-inputs | |
67487088 | 1866 | `(("r-limma" ,r-limma))) |
99db6db7 | 1867 | (home-page "https://bioconductor.org/packages/marray") |
164502d8 RJ |
1868 | (synopsis "Exploratory analysis for two-color spotted microarray data") |
1869 | (description "This package contains class definitions for two-color spotted | |
ab8979fc | 1870 | microarray data. It also includes functions for data input, diagnostic plots, |
164502d8 RJ |
1871 | normalization and quality checking.") |
1872 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
1873 | |
1874 | (define-public r-cghbase | |
1875 | (package | |
1876 | (name "r-cghbase") | |
bd93ec4c | 1877 | (version "1.48.0") |
0416a0d4 RJ |
1878 | (source (origin |
1879 | (method url-fetch) | |
1880 | (uri (bioconductor-uri "CGHbase" version)) | |
1881 | (sha256 | |
bd93ec4c | 1882 | (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf")))) |
0416a0d4 RJ |
1883 | (properties `((upstream-name . "CGHbase"))) |
1884 | (build-system r-build-system) | |
1885 | (propagated-inputs | |
1886 | `(("r-biobase" ,r-biobase) | |
1887 | ("r-marray" ,r-marray))) | |
99db6db7 | 1888 | (home-page "https://bioconductor.org/packages/CGHbase") |
0416a0d4 RJ |
1889 | (synopsis "Base functions and classes for arrayCGH data analysis") |
1890 | (description "This package contains functions and classes that are needed by | |
1891 | the @code{arrayCGH} packages.") | |
1892 | (license license:gpl2+))) | |
67ee83d6 RJ |
1893 | |
1894 | (define-public r-cghcall | |
1895 | (package | |
1896 | (name "r-cghcall") | |
de4a352e | 1897 | (version "2.50.0") |
67ee83d6 RJ |
1898 | (source (origin |
1899 | (method url-fetch) | |
1900 | (uri (bioconductor-uri "CGHcall" version)) | |
1901 | (sha256 | |
de4a352e | 1902 | (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg")))) |
67ee83d6 RJ |
1903 | (properties `((upstream-name . "CGHcall"))) |
1904 | (build-system r-build-system) | |
1905 | (propagated-inputs | |
1906 | `(("r-biobase" ,r-biobase) | |
1907 | ("r-cghbase" ,r-cghbase) | |
1908 | ("r-impute" ,r-impute) | |
1909 | ("r-dnacopy" ,r-dnacopy) | |
1910 | ("r-snowfall" ,r-snowfall))) | |
99db6db7 | 1911 | (home-page "https://bioconductor.org/packages/CGHcall") |
67ee83d6 RJ |
1912 | (synopsis "Base functions and classes for arrayCGH data analysis") |
1913 | (description "This package contains functions and classes that are needed by | |
1914 | @code{arrayCGH} packages.") | |
1915 | (license license:gpl2+))) | |
0ef8cc9c RJ |
1916 | |
1917 | (define-public r-qdnaseq | |
1918 | (package | |
1919 | (name "r-qdnaseq") | |
f4ef5645 | 1920 | (version "1.24.0") |
0ef8cc9c RJ |
1921 | (source (origin |
1922 | (method url-fetch) | |
1923 | (uri (bioconductor-uri "QDNAseq" version)) | |
1924 | (sha256 | |
f4ef5645 | 1925 | (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86")))) |
0ef8cc9c RJ |
1926 | (properties `((upstream-name . "QDNAseq"))) |
1927 | (build-system r-build-system) | |
1928 | (propagated-inputs | |
1929 | `(("r-biobase" ,r-biobase) | |
1930 | ("r-cghbase" ,r-cghbase) | |
1931 | ("r-cghcall" ,r-cghcall) | |
1932 | ("r-dnacopy" ,r-dnacopy) | |
23ce5ad1 RW |
1933 | ("r-future" ,r-future) |
1934 | ("r-future-apply" ,r-future-apply) | |
0ef8cc9c RJ |
1935 | ("r-genomicranges" ,r-genomicranges) |
1936 | ("r-iranges" ,r-iranges) | |
1937 | ("r-matrixstats" ,r-matrixstats) | |
1938 | ("r-r-utils" ,r-r-utils) | |
1939 | ("r-rsamtools" ,r-rsamtools))) | |
99db6db7 | 1940 | (home-page "https://bioconductor.org/packages/QDNAseq") |
0ef8cc9c RJ |
1941 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") |
1942 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
1943 | number of sequence reads in each counted, adjusted with a simultaneous | |
1944 | two-dimensional loess correction for sequence mappability and GC content, and | |
1945 | filtered to remove spurious regions in the genome. Downstream steps of | |
1946 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
1947 | respectively.") | |
1948 | (license license:gpl2+))) | |
bb15b581 RW |
1949 | |
1950 | (define-public r-bayseq | |
1951 | (package | |
1952 | (name "r-bayseq") | |
9834c367 | 1953 | (version "2.22.0") |
bb15b581 RW |
1954 | (source |
1955 | (origin | |
1956 | (method url-fetch) | |
1957 | (uri (bioconductor-uri "baySeq" version)) | |
1958 | (sha256 | |
1959 | (base32 | |
9834c367 | 1960 | "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj")))) |
bb15b581 RW |
1961 | (properties `((upstream-name . "baySeq"))) |
1962 | (build-system r-build-system) | |
1963 | (propagated-inputs | |
1964 | `(("r-abind" ,r-abind) | |
1965 | ("r-edger" ,r-edger) | |
1966 | ("r-genomicranges" ,r-genomicranges))) | |
1967 | (home-page "https://bioconductor.org/packages/baySeq/") | |
1968 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
1969 | (description | |
1970 | "This package identifies differential expression in high-throughput count | |
1971 | data, such as that derived from next-generation sequencing machines, | |
1972 | calculating estimated posterior likelihoods of differential expression (or | |
1973 | more complex hypotheses) via empirical Bayesian methods.") | |
1974 | (license license:gpl3))) | |
609f4ad1 RW |
1975 | |
1976 | (define-public r-chipcomp | |
1977 | (package | |
1978 | (name "r-chipcomp") | |
ef1d3231 | 1979 | (version "1.18.0") |
609f4ad1 RW |
1980 | (source |
1981 | (origin | |
1982 | (method url-fetch) | |
1983 | (uri (bioconductor-uri "ChIPComp" version)) | |
1984 | (sha256 | |
1985 | (base32 | |
ef1d3231 | 1986 | "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp")))) |
609f4ad1 RW |
1987 | (properties `((upstream-name . "ChIPComp"))) |
1988 | (build-system r-build-system) | |
1989 | (propagated-inputs | |
1990 | `(("r-biocgenerics" ,r-biocgenerics) | |
1991 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
1992 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
1993 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1994 | ("r-genomicranges" ,r-genomicranges) | |
1995 | ("r-iranges" ,r-iranges) | |
1996 | ("r-limma" ,r-limma) | |
1997 | ("r-rsamtools" ,r-rsamtools) | |
1998 | ("r-rtracklayer" ,r-rtracklayer) | |
1999 | ("r-s4vectors" ,r-s4vectors))) | |
2000 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
2001 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
2002 | (description | |
2003 | "ChIPComp implements a statistical method for quantitative comparison of | |
2004 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
2005 | sites across multiple conditions considering matching control in ChIP-seq | |
2006 | datasets.") | |
2007 | ;; Any version of the GPL. | |
2008 | (license license:gpl3+))) | |
0490f9de RW |
2009 | |
2010 | (define-public r-riboprofiling | |
2011 | (package | |
2012 | (name "r-riboprofiling") | |
7aae05a9 | 2013 | (version "1.18.0") |
0490f9de RW |
2014 | (source |
2015 | (origin | |
2016 | (method url-fetch) | |
2017 | (uri (bioconductor-uri "RiboProfiling" version)) | |
2018 | (sha256 | |
2019 | (base32 | |
7aae05a9 | 2020 | "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha")))) |
0490f9de RW |
2021 | (properties `((upstream-name . "RiboProfiling"))) |
2022 | (build-system r-build-system) | |
2023 | (propagated-inputs | |
2024 | `(("r-biocgenerics" ,r-biocgenerics) | |
2025 | ("r-biostrings" ,r-biostrings) | |
2026 | ("r-data-table" ,r-data-table) | |
2027 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2028 | ("r-genomicalignments" ,r-genomicalignments) | |
2029 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2030 | ("r-genomicranges" ,r-genomicranges) | |
2031 | ("r-ggbio" ,r-ggbio) | |
2032 | ("r-ggplot2" ,r-ggplot2) | |
2033 | ("r-iranges" ,r-iranges) | |
2034 | ("r-plyr" ,r-plyr) | |
2035 | ("r-reshape2" ,r-reshape2) | |
2036 | ("r-rsamtools" ,r-rsamtools) | |
2037 | ("r-rtracklayer" ,r-rtracklayer) | |
2038 | ("r-s4vectors" ,r-s4vectors) | |
2039 | ("r-sqldf" ,r-sqldf))) | |
7aae05a9 RW |
2040 | (native-inputs |
2041 | `(("r-knitr" ,r-knitr))) | |
0490f9de RW |
2042 | (home-page "https://bioconductor.org/packages/RiboProfiling/") |
2043 | (synopsis "Ribosome profiling data analysis") | |
2044 | (description "Starting with a BAM file, this package provides the | |
2045 | necessary functions for quality assessment, read start position recalibration, | |
2046 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
2047 | of count data: pairs, log fold-change, codon frequency and coverage | |
2048 | assessment, principal component analysis on codon coverage.") | |
2049 | (license license:gpl3))) | |
6ffdfe6a RW |
2050 | |
2051 | (define-public r-riboseqr | |
2052 | (package | |
2053 | (name "r-riboseqr") | |
6b78a91b | 2054 | (version "1.22.0") |
6ffdfe6a RW |
2055 | (source |
2056 | (origin | |
2057 | (method url-fetch) | |
2058 | (uri (bioconductor-uri "riboSeqR" version)) | |
2059 | (sha256 | |
2060 | (base32 | |
6b78a91b | 2061 | "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk")))) |
6ffdfe6a RW |
2062 | (properties `((upstream-name . "riboSeqR"))) |
2063 | (build-system r-build-system) | |
2064 | (propagated-inputs | |
2065 | `(("r-abind" ,r-abind) | |
2066 | ("r-bayseq" ,r-bayseq) | |
2067 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2068 | ("r-genomicranges" ,r-genomicranges) | |
2069 | ("r-iranges" ,r-iranges) | |
2070 | ("r-rsamtools" ,r-rsamtools) | |
2071 | ("r-seqlogo" ,r-seqlogo))) | |
2072 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
2073 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
2074 | (description | |
2075 | "This package provides plotting functions, frameshift detection and | |
2076 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
2077 | (license license:gpl3))) | |
a32279ff RW |
2078 | |
2079 | (define-public r-interactionset | |
2080 | (package | |
2081 | (name "r-interactionset") | |
861a903f | 2082 | (version "1.16.0") |
a32279ff RW |
2083 | (source |
2084 | (origin | |
2085 | (method url-fetch) | |
2086 | (uri (bioconductor-uri "InteractionSet" version)) | |
2087 | (sha256 | |
2088 | (base32 | |
861a903f | 2089 | "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v")))) |
a32279ff RW |
2090 | (properties |
2091 | `((upstream-name . "InteractionSet"))) | |
2092 | (build-system r-build-system) | |
2093 | (propagated-inputs | |
2094 | `(("r-biocgenerics" ,r-biocgenerics) | |
2095 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2096 | ("r-genomicranges" ,r-genomicranges) | |
2097 | ("r-iranges" ,r-iranges) | |
2098 | ("r-matrix" ,r-matrix) | |
2099 | ("r-rcpp" ,r-rcpp) | |
2100 | ("r-s4vectors" ,r-s4vectors) | |
2101 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
861a903f RW |
2102 | (native-inputs |
2103 | `(("r-knitr" ,r-knitr))) | |
a32279ff RW |
2104 | (home-page "https://bioconductor.org/packages/InteractionSet") |
2105 | (synopsis "Base classes for storing genomic interaction data") | |
2106 | (description | |
02fe0976 | 2107 | "This package provides the @code{GInteractions}, |
a32279ff RW |
2108 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
2109 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
2110 | experiments.") | |
2111 | (license license:gpl3))) | |
cf9a29b2 RW |
2112 | |
2113 | (define-public r-genomicinteractions | |
2114 | (package | |
2115 | (name "r-genomicinteractions") | |
76dd036e | 2116 | (version "1.22.0") |
cf9a29b2 RW |
2117 | (source |
2118 | (origin | |
2119 | (method url-fetch) | |
2120 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
2121 | (sha256 | |
2122 | (base32 | |
76dd036e | 2123 | "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy")))) |
cf9a29b2 RW |
2124 | (properties |
2125 | `((upstream-name . "GenomicInteractions"))) | |
2126 | (build-system r-build-system) | |
2127 | (propagated-inputs | |
2128 | `(("r-biobase" ,r-biobase) | |
2129 | ("r-biocgenerics" ,r-biocgenerics) | |
2130 | ("r-data-table" ,r-data-table) | |
2131 | ("r-dplyr" ,r-dplyr) | |
2132 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2133 | ("r-genomicranges" ,r-genomicranges) | |
2134 | ("r-ggplot2" ,r-ggplot2) | |
2135 | ("r-gridextra" ,r-gridextra) | |
2136 | ("r-gviz" ,r-gviz) | |
2137 | ("r-igraph" ,r-igraph) | |
2138 | ("r-interactionset" ,r-interactionset) | |
2139 | ("r-iranges" ,r-iranges) | |
2140 | ("r-rsamtools" ,r-rsamtools) | |
2141 | ("r-rtracklayer" ,r-rtracklayer) | |
2142 | ("r-s4vectors" ,r-s4vectors) | |
2143 | ("r-stringr" ,r-stringr))) | |
81a37891 RW |
2144 | (native-inputs |
2145 | `(("r-knitr" ,r-knitr))) | |
cf9a29b2 RW |
2146 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") |
2147 | (synopsis "R package for handling genomic interaction data") | |
2148 | (description | |
2149 | "This R package provides tools for handling genomic interaction data, | |
2150 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
2151 | information and producing various plots and statistics.") | |
2152 | (license license:gpl3))) | |
27c51606 RW |
2153 | |
2154 | (define-public r-ctc | |
2155 | (package | |
2156 | (name "r-ctc") | |
c7be592f | 2157 | (version "1.62.0") |
27c51606 RW |
2158 | (source |
2159 | (origin | |
2160 | (method url-fetch) | |
2161 | (uri (bioconductor-uri "ctc" version)) | |
2162 | (sha256 | |
2163 | (base32 | |
c7be592f | 2164 | "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6")))) |
27c51606 RW |
2165 | (build-system r-build-system) |
2166 | (propagated-inputs `(("r-amap" ,r-amap))) | |
2167 | (home-page "https://bioconductor.org/packages/ctc/") | |
2168 | (synopsis "Cluster and tree conversion") | |
2169 | (description | |
2170 | "This package provides tools for exporting and importing classification | |
2171 | trees and clusters to other programs.") | |
2172 | (license license:gpl2))) | |
5da0e142 RW |
2173 | |
2174 | (define-public r-goseq | |
2175 | (package | |
2176 | (name "r-goseq") | |
7fbd9774 | 2177 | (version "1.40.0") |
5da0e142 RW |
2178 | (source |
2179 | (origin | |
2180 | (method url-fetch) | |
2181 | (uri (bioconductor-uri "goseq" version)) | |
2182 | (sha256 | |
2183 | (base32 | |
7fbd9774 | 2184 | "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym")))) |
5da0e142 RW |
2185 | (build-system r-build-system) |
2186 | (propagated-inputs | |
2187 | `(("r-annotationdbi" ,r-annotationdbi) | |
2188 | ("r-biasedurn" ,r-biasedurn) | |
2189 | ("r-biocgenerics" ,r-biocgenerics) | |
2190 | ("r-genelendatabase" ,r-genelendatabase) | |
2191 | ("r-go-db" ,r-go-db) | |
2192 | ("r-mgcv" ,r-mgcv))) | |
2193 | (home-page "https://bioconductor.org/packages/goseq/") | |
2194 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
2195 | (description | |
2196 | "This package provides tools to detect Gene Ontology and/or other user | |
2197 | defined categories which are over/under represented in RNA-seq data.") | |
2198 | (license license:lgpl2.0+))) | |
f4235c0e RW |
2199 | |
2200 | (define-public r-glimma | |
2201 | (package | |
2202 | (name "r-glimma") | |
a6251d6e | 2203 | (version "1.16.0") |
f4235c0e RW |
2204 | (source |
2205 | (origin | |
2206 | (method url-fetch) | |
2207 | (uri (bioconductor-uri "Glimma" version)) | |
2208 | (sha256 | |
2209 | (base32 | |
a6251d6e | 2210 | "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y")))) |
f4235c0e RW |
2211 | (properties `((upstream-name . "Glimma"))) |
2212 | (build-system r-build-system) | |
2213 | (propagated-inputs | |
2214 | `(("r-edger" ,r-edger) | |
2215 | ("r-jsonlite" ,r-jsonlite) | |
2216 | ("r-s4vectors" ,r-s4vectors))) | |
a6251d6e RW |
2217 | (native-inputs |
2218 | `(("r-knitr" ,r-knitr))) | |
f4235c0e RW |
2219 | (home-page "https://github.com/Shians/Glimma") |
2220 | (synopsis "Interactive HTML graphics") | |
2221 | (description | |
2222 | "This package generates interactive visualisations for analysis of | |
2223 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
2224 | HTML page. The interactions are built on top of the popular static | |
2225 | representations of analysis results in order to provide additional | |
2226 | information.") | |
2227 | (license license:lgpl3))) | |
aa388dc7 RW |
2228 | |
2229 | (define-public r-rots | |
2230 | (package | |
2231 | (name "r-rots") | |
ee73dea6 | 2232 | (version "1.16.0") |
aa388dc7 RW |
2233 | (source |
2234 | (origin | |
2235 | (method url-fetch) | |
2236 | (uri (bioconductor-uri "ROTS" version)) | |
2237 | (sha256 | |
2238 | (base32 | |
ee73dea6 | 2239 | "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm")))) |
aa388dc7 RW |
2240 | (properties `((upstream-name . "ROTS"))) |
2241 | (build-system r-build-system) | |
2242 | (propagated-inputs | |
2243 | `(("r-biobase" ,r-biobase) | |
2244 | ("r-rcpp" ,r-rcpp))) | |
2245 | (home-page "https://bioconductor.org/packages/ROTS/") | |
2246 | (synopsis "Reproducibility-Optimized Test Statistic") | |
2247 | (description | |
2248 | "This package provides tools for calculating the | |
2249 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
2250 | in omics data.") | |
2251 | (license license:gpl2+))) | |
b64ce4b7 | 2252 | |
cad6fb2d RW |
2253 | (define-public r-plgem |
2254 | (package | |
2255 | (name "r-plgem") | |
46a973bc | 2256 | (version "1.60.0") |
cad6fb2d RW |
2257 | (source |
2258 | (origin | |
2259 | (method url-fetch) | |
2260 | (uri (bioconductor-uri "plgem" version)) | |
2261 | (sha256 | |
2262 | (base32 | |
46a973bc | 2263 | "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a")))) |
cad6fb2d RW |
2264 | (build-system r-build-system) |
2265 | (propagated-inputs | |
2266 | `(("r-biobase" ,r-biobase) | |
2267 | ("r-mass" ,r-mass))) | |
2268 | (home-page "http://www.genopolis.it") | |
2269 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
2270 | (description | |
2271 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
2272 | model the variance-versus-mean dependence that exists in a variety of | |
2273 | genome-wide datasets, including microarray and proteomics data. The use of | |
2274 | PLGEM has been shown to improve the detection of differentially expressed | |
2275 | genes or proteins in these datasets.") | |
2276 | (license license:gpl2))) | |
2277 | ||
b64ce4b7 RW |
2278 | (define-public r-inspect |
2279 | (package | |
2280 | (name "r-inspect") | |
437bc4dd | 2281 | (version "1.18.0") |
b64ce4b7 RW |
2282 | (source |
2283 | (origin | |
2284 | (method url-fetch) | |
2285 | (uri (bioconductor-uri "INSPEcT" version)) | |
2286 | (sha256 | |
2287 | (base32 | |
437bc4dd | 2288 | "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z")))) |
b64ce4b7 RW |
2289 | (properties `((upstream-name . "INSPEcT"))) |
2290 | (build-system r-build-system) | |
2291 | (propagated-inputs | |
2292 | `(("r-biobase" ,r-biobase) | |
2293 | ("r-biocgenerics" ,r-biocgenerics) | |
2294 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 2295 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 | 2296 | ("r-desolve" ,r-desolve) |
bd824de3 | 2297 | ("r-gdata" ,r-gdata) |
74bb4cdf | 2298 | ("r-genomeinfodb" ,r-genomeinfodb) |
b64ce4b7 RW |
2299 | ("r-genomicalignments" ,r-genomicalignments) |
2300 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2301 | ("r-genomicranges" ,r-genomicranges) | |
2302 | ("r-iranges" ,r-iranges) | |
74bb4cdf | 2303 | ("r-kernsmooth" ,r-kernsmooth) |
c86fc969 | 2304 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
2305 | ("r-proc" ,r-proc) |
2306 | ("r-rootsolve" ,r-rootsolve) | |
2307 | ("r-rsamtools" ,r-rsamtools) | |
437bc4dd | 2308 | ("r-rtracklayer" ,r-rtracklayer) |
c86fc969 RW |
2309 | ("r-s4vectors" ,r-s4vectors) |
2310 | ("r-shiny" ,r-shiny) | |
2311 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
2312 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
2313 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
437bc4dd RW |
2314 | (native-inputs |
2315 | `(("r-knitr" ,r-knitr))) | |
b64ce4b7 RW |
2316 | (home-page "https://bioconductor.org/packages/INSPEcT") |
2317 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
2318 | (description | |
2319 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
2320 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
2321 | order to evaluate synthesis, processing and degradation rates and assess via | |
2322 | modeling the rates that determines changes in mature mRNA levels.") | |
2323 | (license license:gpl2))) | |
f6e99763 RW |
2324 | |
2325 | (define-public r-dnabarcodes | |
2326 | (package | |
2327 | (name "r-dnabarcodes") | |
14f40ae8 | 2328 | (version "1.18.0") |
f6e99763 RW |
2329 | (source |
2330 | (origin | |
2331 | (method url-fetch) | |
2332 | (uri (bioconductor-uri "DNABarcodes" version)) | |
2333 | (sha256 | |
2334 | (base32 | |
14f40ae8 | 2335 | "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7")))) |
f6e99763 RW |
2336 | (properties `((upstream-name . "DNABarcodes"))) |
2337 | (build-system r-build-system) | |
2338 | (propagated-inputs | |
2339 | `(("r-bh" ,r-bh) | |
2340 | ("r-matrix" ,r-matrix) | |
2341 | ("r-rcpp" ,r-rcpp))) | |
14f40ae8 RW |
2342 | (native-inputs |
2343 | `(("r-knitr" ,r-knitr))) | |
f6e99763 RW |
2344 | (home-page "https://bioconductor.org/packages/DNABarcodes") |
2345 | (synopsis "Create and analyze DNA barcodes") | |
2346 | (description | |
2347 | "This package offers tools to create DNA barcode sets capable of | |
2348 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
2349 | can be analyzed regarding their minimal, maximal and average distances between | |
2350 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
2351 | demultiplexed, i.e. assigned to their original reference barcode.") | |
2352 | (license license:gpl2))) | |
09aa3d06 RW |
2353 | |
2354 | (define-public r-ruvseq | |
2355 | (package | |
2356 | (name "r-ruvseq") | |
ae0fcaa6 | 2357 | (version "1.22.0") |
09aa3d06 RW |
2358 | (source |
2359 | (origin | |
2360 | (method url-fetch) | |
2361 | (uri (bioconductor-uri "RUVSeq" version)) | |
2362 | (sha256 | |
2363 | (base32 | |
ae0fcaa6 | 2364 | "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x")))) |
09aa3d06 RW |
2365 | (properties `((upstream-name . "RUVSeq"))) |
2366 | (build-system r-build-system) | |
2367 | (propagated-inputs | |
2368 | `(("r-biobase" ,r-biobase) | |
2369 | ("r-edaseq" ,r-edaseq) | |
2370 | ("r-edger" ,r-edger) | |
2371 | ("r-mass" ,r-mass))) | |
ae0fcaa6 RW |
2372 | (native-inputs |
2373 | `(("r-knitr" ,r-knitr))) | |
09aa3d06 RW |
2374 | (home-page "https://github.com/drisso/RUVSeq") |
2375 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
2376 | (description | |
2377 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
2378 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
2379 | samples.") | |
2380 | (license license:artistic2.0))) | |
286157dc RW |
2381 | |
2382 | (define-public r-biocneighbors | |
2383 | (package | |
2384 | (name "r-biocneighbors") | |
f5864c11 | 2385 | (version "1.6.0") |
286157dc RW |
2386 | (source |
2387 | (origin | |
2388 | (method url-fetch) | |
2389 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
2390 | (sha256 | |
2391 | (base32 | |
f5864c11 | 2392 | "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy")))) |
286157dc RW |
2393 | (properties `((upstream-name . "BiocNeighbors"))) |
2394 | (build-system r-build-system) | |
2395 | (propagated-inputs | |
12e2aa96 RW |
2396 | `(("r-biocparallel" ,r-biocparallel) |
2397 | ("r-matrix" ,r-matrix) | |
286157dc RW |
2398 | ("r-rcpp" ,r-rcpp) |
2399 | ("r-rcppannoy" ,r-rcppannoy) | |
6fc161fc | 2400 | ("r-rcpphnsw" ,r-rcpphnsw) |
286157dc | 2401 | ("r-s4vectors" ,r-s4vectors))) |
f5864c11 RW |
2402 | (native-inputs |
2403 | `(("r-knitr" ,r-knitr))) | |
286157dc RW |
2404 | (home-page "https://bioconductor.org/packages/BiocNeighbors") |
2405 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
2406 | (description | |
2407 | "This package implements exact and approximate methods for nearest | |
2408 | neighbor detection, in a framework that allows them to be easily switched | |
2409 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
2410 | using pre-clustering with the k-means algorithm. Functions are also provided | |
2411 | to search for all neighbors within a given distance. Parallelization is | |
2412 | achieved for all methods using the BiocParallel framework.") | |
2413 | (license license:gpl3))) | |
8a587c89 | 2414 | |
99391290 RW |
2415 | (define-public r-biocsingular |
2416 | (package | |
2417 | (name "r-biocsingular") | |
a8351d46 | 2418 | (version "1.4.0") |
99391290 RW |
2419 | (source |
2420 | (origin | |
2421 | (method url-fetch) | |
2422 | (uri (bioconductor-uri "BiocSingular" version)) | |
2423 | (sha256 | |
2424 | (base32 | |
a8351d46 | 2425 | "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih")))) |
99391290 RW |
2426 | (properties `((upstream-name . "BiocSingular"))) |
2427 | (build-system r-build-system) | |
2428 | (propagated-inputs | |
2429 | `(("r-beachmat" ,r-beachmat) | |
2430 | ("r-biocgenerics" ,r-biocgenerics) | |
2431 | ("r-biocparallel" ,r-biocparallel) | |
2432 | ("r-delayedarray" ,r-delayedarray) | |
2433 | ("r-irlba" ,r-irlba) | |
2434 | ("r-matrix" ,r-matrix) | |
2435 | ("r-rcpp" ,r-rcpp) | |
2436 | ("r-rsvd" ,r-rsvd) | |
2437 | ("r-s4vectors" ,r-s4vectors))) | |
a8351d46 RW |
2438 | (native-inputs |
2439 | `(("r-knitr" ,r-knitr))) | |
99391290 RW |
2440 | (home-page "https://github.com/LTLA/BiocSingular") |
2441 | (synopsis "Singular value decomposition for Bioconductor packages") | |
2442 | (description | |
2443 | "This package implements exact and approximate methods for singular value | |
2444 | decomposition and principal components analysis, in a framework that allows | |
2445 | them to be easily switched within Bioconductor packages or workflows. Where | |
2446 | possible, parallelization is achieved using the BiocParallel framework.") | |
2447 | (license license:gpl3))) | |
2448 | ||
a961ae46 RW |
2449 | (define-public r-destiny |
2450 | (package | |
2451 | (name "r-destiny") | |
265b6450 | 2452 | (version "3.2.0") |
a961ae46 RW |
2453 | (source |
2454 | (origin | |
2455 | (method url-fetch) | |
2456 | (uri (bioconductor-uri "destiny" version)) | |
2457 | (sha256 | |
2458 | (base32 | |
265b6450 | 2459 | "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n")))) |
a961ae46 RW |
2460 | (build-system r-build-system) |
2461 | (propagated-inputs | |
2462 | `(("r-biobase" ,r-biobase) | |
2463 | ("r-biocgenerics" ,r-biocgenerics) | |
6e10ac07 | 2464 | ("r-ggplot-multistats" ,r-ggplot-multistats) |
0aa72f2d | 2465 | ("r-ggplot2" ,r-ggplot2) |
a961ae46 | 2466 | ("r-ggthemes" ,r-ggthemes) |
6e10ac07 RW |
2467 | ("r-irlba" ,r-irlba) |
2468 | ("r-knn-covertree" ,r-knn-covertree) | |
a961ae46 | 2469 | ("r-matrix" ,r-matrix) |
265b6450 | 2470 | ("r-nbconvertr" ,r-nbconvertr) |
6e10ac07 | 2471 | ("r-pcamethods" ,r-pcamethods) |
a961ae46 RW |
2472 | ("r-proxy" ,r-proxy) |
2473 | ("r-rcpp" ,r-rcpp) | |
2474 | ("r-rcppeigen" ,r-rcppeigen) | |
6e10ac07 RW |
2475 | ("r-rcpphnsw" ,r-rcpphnsw) |
2476 | ("r-rspectra" ,r-rspectra) | |
a961ae46 RW |
2477 | ("r-scales" ,r-scales) |
2478 | ("r-scatterplot3d" ,r-scatterplot3d) | |
6e10ac07 | 2479 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
a961ae46 RW |
2480 | ("r-smoother" ,r-smoother) |
2481 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6e10ac07 RW |
2482 | ("r-tidyr" ,r-tidyr) |
2483 | ("r-tidyselect" ,r-tidyselect) | |
a961ae46 | 2484 | ("r-vim" ,r-vim))) |
3f782a6d RW |
2485 | (native-inputs |
2486 | `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes | |
a961ae46 RW |
2487 | (home-page "https://bioconductor.org/packages/destiny/") |
2488 | (synopsis "Create and plot diffusion maps") | |
2489 | (description "This package provides tools to create and plot diffusion | |
2490 | maps.") | |
2491 | ;; Any version of the GPL | |
2492 | (license license:gpl3+))) | |
2493 | ||
8a587c89 RW |
2494 | (define-public r-savr |
2495 | (package | |
2496 | (name "r-savr") | |
784d1670 | 2497 | (version "1.26.0") |
8a587c89 RW |
2498 | (source |
2499 | (origin | |
2500 | (method url-fetch) | |
2501 | (uri (bioconductor-uri "savR" version)) | |
2502 | (sha256 | |
2503 | (base32 | |
784d1670 | 2504 | "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a")))) |
8a587c89 RW |
2505 | (properties `((upstream-name . "savR"))) |
2506 | (build-system r-build-system) | |
2507 | (propagated-inputs | |
2508 | `(("r-ggplot2" ,r-ggplot2) | |
2509 | ("r-gridextra" ,r-gridextra) | |
2510 | ("r-reshape2" ,r-reshape2) | |
2511 | ("r-scales" ,r-scales) | |
2512 | ("r-xml" ,r-xml))) | |
2513 | (home-page "https://github.com/bcalder/savR") | |
2514 | (synopsis "Parse and analyze Illumina SAV files") | |
2515 | (description | |
2516 | "This package provides tools to parse Illumina Sequence Analysis | |
2517 | Viewer (SAV) files, access data, and generate QC plots.") | |
2518 | (license license:agpl3+))) | |
41ffc214 RW |
2519 | |
2520 | (define-public r-chipexoqual | |
2521 | (package | |
2522 | (name "r-chipexoqual") | |
9697afb1 | 2523 | (version "1.12.0") |
41ffc214 RW |
2524 | (source |
2525 | (origin | |
2526 | (method url-fetch) | |
2527 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
2528 | (sha256 | |
2529 | (base32 | |
9697afb1 | 2530 | "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp")))) |
41ffc214 RW |
2531 | (properties `((upstream-name . "ChIPexoQual"))) |
2532 | (build-system r-build-system) | |
2533 | (propagated-inputs | |
2534 | `(("r-biocparallel" ,r-biocparallel) | |
2535 | ("r-biovizbase" ,r-biovizbase) | |
2536 | ("r-broom" ,r-broom) | |
2537 | ("r-data-table" ,r-data-table) | |
2538 | ("r-dplyr" ,r-dplyr) | |
2539 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2540 | ("r-genomicalignments" ,r-genomicalignments) | |
2541 | ("r-genomicranges" ,r-genomicranges) | |
2542 | ("r-ggplot2" ,r-ggplot2) | |
2543 | ("r-hexbin" ,r-hexbin) | |
2544 | ("r-iranges" ,r-iranges) | |
2545 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2546 | ("r-rmarkdown" ,r-rmarkdown) | |
2547 | ("r-rsamtools" ,r-rsamtools) | |
2548 | ("r-s4vectors" ,r-s4vectors) | |
2549 | ("r-scales" ,r-scales) | |
2550 | ("r-viridis" ,r-viridis))) | |
9697afb1 RW |
2551 | (native-inputs |
2552 | `(("r-knitr" ,r-knitr))) | |
41ffc214 RW |
2553 | (home-page "https://github.com/keleslab/ChIPexoQual") |
2554 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
2555 | (description | |
2556 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
2557 | sequencing data.") | |
2558 | (license license:gpl2+))) | |
c18dccff | 2559 | |
3d13b448 RW |
2560 | (define-public r-copynumber |
2561 | (package | |
2562 | (name "r-copynumber") | |
866939b7 | 2563 | (version "1.28.0") |
3d13b448 RW |
2564 | (source (origin |
2565 | (method url-fetch) | |
2566 | (uri (bioconductor-uri "copynumber" version)) | |
2567 | (sha256 | |
2568 | (base32 | |
866939b7 | 2569 | "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my")))) |
3d13b448 RW |
2570 | (build-system r-build-system) |
2571 | (propagated-inputs | |
2572 | `(("r-s4vectors" ,r-s4vectors) | |
2573 | ("r-iranges" ,r-iranges) | |
2574 | ("r-genomicranges" ,r-genomicranges) | |
2575 | ("r-biocgenerics" ,r-biocgenerics))) | |
2576 | (home-page "https://bioconductor.org/packages/copynumber") | |
2577 | (synopsis "Segmentation of single- and multi-track copy number data") | |
2578 | (description | |
2579 | "This package segments single- and multi-track copy number data by a | |
2580 | penalized least squares regression method.") | |
2581 | (license license:artistic2.0))) | |
2582 | ||
c18dccff RW |
2583 | (define-public r-dnacopy |
2584 | (package | |
2585 | (name "r-dnacopy") | |
6a7cfd5f | 2586 | (version "1.62.0") |
c18dccff RW |
2587 | (source |
2588 | (origin | |
2589 | (method url-fetch) | |
2590 | (uri (bioconductor-uri "DNAcopy" version)) | |
2591 | (sha256 | |
2592 | (base32 | |
6a7cfd5f | 2593 | "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza")))) |
c18dccff RW |
2594 | (properties `((upstream-name . "DNAcopy"))) |
2595 | (build-system r-build-system) | |
2596 | (native-inputs `(("gfortran" ,gfortran))) | |
2597 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
2598 | (synopsis "DNA copy number data analysis") | |
2599 | (description | |
2600 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
2601 | algorithm to segment DNA copy number data and identify genomic regions with | |
2602 | abnormal copy number.") | |
2603 | (license license:gpl2+))) | |
3a0babac RW |
2604 | |
2605 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
2606 | ;; Bioconductor package. | |
2607 | (define-public r-htscluster | |
2608 | (package | |
2609 | (name "r-htscluster") | |
2610 | (version "2.0.8") | |
2611 | (source | |
2612 | (origin | |
2613 | (method url-fetch) | |
2614 | (uri (cran-uri "HTSCluster" version)) | |
2615 | (sha256 | |
2616 | (base32 | |
2617 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
2618 | (properties `((upstream-name . "HTSCluster"))) | |
2619 | (build-system r-build-system) | |
2620 | (propagated-inputs | |
2621 | `(("r-capushe" ,r-capushe) | |
2622 | ("r-edger" ,r-edger) | |
2623 | ("r-plotrix" ,r-plotrix))) | |
2624 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
2625 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
2626 | (description | |
2627 | "This package provides a Poisson mixture model is implemented to cluster | |
2628 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
2629 | estimation is performed using either the EM or CEM algorithm, and the slope | |
2630 | heuristics are used for model selection (i.e., to choose the number of | |
2631 | clusters).") | |
2632 | (license license:gpl3+))) | |
173c9960 RW |
2633 | |
2634 | (define-public r-deds | |
2635 | (package | |
2636 | (name "r-deds") | |
96030bf7 | 2637 | (version "1.60.0") |
173c9960 RW |
2638 | (source |
2639 | (origin | |
2640 | (method url-fetch) | |
2641 | (uri (bioconductor-uri "DEDS" version)) | |
2642 | (sha256 | |
2643 | (base32 | |
96030bf7 | 2644 | "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8")))) |
173c9960 RW |
2645 | (properties `((upstream-name . "DEDS"))) |
2646 | (build-system r-build-system) | |
2647 | (home-page "https://bioconductor.org/packages/DEDS/") | |
2648 | (synopsis "Differential expression via distance summary for microarray data") | |
2649 | (description | |
2650 | "This library contains functions that calculate various statistics of | |
2651 | differential expression for microarray data, including t statistics, fold | |
2652 | change, F statistics, SAM, moderated t and F statistics and B statistics. It | |
2653 | also implements a new methodology called DEDS (Differential Expression via | |
2654 | Distance Summary), which selects differentially expressed genes by integrating | |
2655 | and summarizing a set of statistics using a weighted distance approach.") | |
2656 | ;; Any version of the LGPL. | |
2657 | (license license:lgpl3+))) | |
7ed869f7 RW |
2658 | |
2659 | ;; This is a CRAN package, but since it depends on a Bioconductor package we | |
2660 | ;; put it here. | |
2661 | (define-public r-nbpseq | |
2662 | (package | |
2663 | (name "r-nbpseq") | |
2664 | (version "0.3.0") | |
2665 | (source | |
2666 | (origin | |
2667 | (method url-fetch) | |
2668 | (uri (cran-uri "NBPSeq" version)) | |
2669 | (sha256 | |
2670 | (base32 | |
2671 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) | |
2672 | (properties `((upstream-name . "NBPSeq"))) | |
2673 | (build-system r-build-system) | |
2674 | (propagated-inputs | |
2675 | `(("r-qvalue" ,r-qvalue))) | |
2676 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") | |
2677 | (synopsis "Negative binomial models for RNA-Seq data") | |
2678 | (description | |
2679 | "This package provides negative binomial models for two-group comparisons | |
2680 | and regression inferences from RNA-sequencing data.") | |
2681 | (license license:gpl2))) | |
3087a2f3 RW |
2682 | |
2683 | (define-public r-ebseq | |
2684 | (package | |
2685 | (name "r-ebseq") | |
1e37caca | 2686 | (version "1.28.0") |
3087a2f3 RW |
2687 | (source |
2688 | (origin | |
2689 | (method url-fetch) | |
2690 | (uri (bioconductor-uri "EBSeq" version)) | |
2691 | (sha256 | |
2692 | (base32 | |
1e37caca | 2693 | "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f")))) |
3087a2f3 RW |
2694 | (properties `((upstream-name . "EBSeq"))) |
2695 | (build-system r-build-system) | |
2696 | (propagated-inputs | |
2697 | `(("r-blockmodeling" ,r-blockmodeling) | |
2698 | ("r-gplots" ,r-gplots) | |
2699 | ("r-testthat" ,r-testthat))) | |
2700 | (home-page "https://bioconductor.org/packages/EBSeq") | |
2701 | (synopsis "Differential expression analysis of RNA-seq data") | |
2702 | (description | |
2703 | "This package provides tools for differential expression analysis at both | |
2704 | gene and isoform level using RNA-seq data") | |
2705 | (license license:artistic2.0))) | |
cb1ab035 RJ |
2706 | |
2707 | (define-public r-karyoploter | |
2708 | (package | |
2709 | (name "r-karyoploter") | |
6e2dc9e3 | 2710 | (version "1.14.0") |
cb1ab035 RJ |
2711 | (source (origin |
2712 | (method url-fetch) | |
2713 | (uri (bioconductor-uri "karyoploteR" version)) | |
2714 | (sha256 | |
2715 | (base32 | |
6e2dc9e3 | 2716 | "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs")))) |
cb1ab035 RJ |
2717 | (build-system r-build-system) |
2718 | (propagated-inputs | |
6e2dc9e3 RW |
2719 | `(("r-annotationdbi" ,r-annotationdbi) |
2720 | ("r-bamsignals" ,r-bamsignals) | |
2721 | ("r-bezier" ,r-bezier) | |
2722 | ("r-biovizbase" ,r-biovizbase) | |
2723 | ("r-digest" ,r-digest) | |
2724 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2725 | ("r-genomicfeatures" ,r-genomicfeatures) | |
cb1ab035 RJ |
2726 | ("r-genomicranges" ,r-genomicranges) |
2727 | ("r-iranges" ,r-iranges) | |
cb1ab035 | 2728 | ("r-memoise" ,r-memoise) |
6e2dc9e3 RW |
2729 | ("r-regioner" ,r-regioner) |
2730 | ("r-rsamtools" ,r-rsamtools) | |
cb1ab035 | 2731 | ("r-rtracklayer" ,r-rtracklayer) |
cb1ab035 | 2732 | ("r-s4vectors" ,r-s4vectors) |
cb1ab035 | 2733 | ("r-variantannotation" ,r-variantannotation))) |
6e2dc9e3 RW |
2734 | (native-inputs |
2735 | `(("r-knitr" ,r-knitr))) | |
cb1ab035 RJ |
2736 | (home-page "https://bioconductor.org/packages/karyoploteR/") |
2737 | (synopsis "Plot customizable linear genomes displaying arbitrary data") | |
2738 | (description "This package creates karyotype plots of arbitrary genomes and | |
2739 | offers a complete set of functions to plot arbitrary data on them. It mimicks | |
2740 | many R base graphics functions coupling them with a coordinate change function | |
2741 | automatically mapping the chromosome and data coordinates into the plot | |
2742 | coordinates.") | |
2743 | (license license:artistic2.0))) | |
2cb71d81 RW |
2744 | |
2745 | (define-public r-lpsymphony | |
2746 | (package | |
2747 | (name "r-lpsymphony") | |
0653b8b0 | 2748 | (version "1.16.0") |
2cb71d81 RW |
2749 | (source |
2750 | (origin | |
2751 | (method url-fetch) | |
2752 | (uri (bioconductor-uri "lpsymphony" version)) | |
2753 | (sha256 | |
2754 | (base32 | |
0653b8b0 | 2755 | "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4")))) |
2cb71d81 RW |
2756 | (build-system r-build-system) |
2757 | (inputs | |
0653b8b0 | 2758 | `(("zlib" ,zlib))) |
2cb71d81 | 2759 | (native-inputs |
0653b8b0 RW |
2760 | `(("pkg-config" ,pkg-config) |
2761 | ("r-knitr" ,r-knitr))) | |
c756328e | 2762 | (home-page "https://r-forge.r-project.org/projects/rsymphony") |
2cb71d81 RW |
2763 | (synopsis "Symphony integer linear programming solver in R") |
2764 | (description | |
2765 | "This package was derived from Rsymphony. The package provides an R | |
2766 | interface to SYMPHONY, a linear programming solver written in C++. The main | |
2767 | difference between this package and Rsymphony is that it includes the solver | |
2768 | source code, while Rsymphony expects to find header and library files on the | |
2769 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy | |
2770 | to install interface to SYMPHONY.") | |
2771 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. | |
2772 | ;; lpsimphony is released under the same terms. | |
2773 | (license license:epl1.0))) | |
704de8f5 RW |
2774 | |
2775 | (define-public r-ihw | |
2776 | (package | |
2777 | (name "r-ihw") | |
359a084a | 2778 | (version "1.16.0") |
704de8f5 RW |
2779 | (source |
2780 | (origin | |
2781 | (method url-fetch) | |
2782 | (uri (bioconductor-uri "IHW" version)) | |
2783 | (sha256 | |
2784 | (base32 | |
359a084a | 2785 | "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j")))) |
704de8f5 RW |
2786 | (properties `((upstream-name . "IHW"))) |
2787 | (build-system r-build-system) | |
2788 | (propagated-inputs | |
2789 | `(("r-biocgenerics" ,r-biocgenerics) | |
2790 | ("r-fdrtool" ,r-fdrtool) | |
2791 | ("r-lpsymphony" ,r-lpsymphony) | |
2792 | ("r-slam" ,r-slam))) | |
359a084a RW |
2793 | (native-inputs |
2794 | `(("r-knitr" ,r-knitr))) | |
704de8f5 RW |
2795 | (home-page "https://bioconductor.org/packages/IHW") |
2796 | (synopsis "Independent hypothesis weighting") | |
2797 | (description | |
2798 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing | |
2799 | procedure that increases power compared to the method of Benjamini and | |
2800 | Hochberg by assigning data-driven weights to each hypothesis. The input to | |
2801 | IHW is a two-column table of p-values and covariates. The covariate can be | |
2802 | any continuous-valued or categorical variable that is thought to be | |
2803 | informative on the statistical properties of each hypothesis test, while it is | |
2804 | independent of the p-value under the null hypothesis.") | |
2805 | (license license:artistic2.0))) | |
251e0830 RW |
2806 | |
2807 | (define-public r-icobra | |
2808 | (package | |
2809 | (name "r-icobra") | |
ee1e8fee | 2810 | (version "1.16.0") |
251e0830 RW |
2811 | (source |
2812 | (origin | |
2813 | (method url-fetch) | |
2814 | (uri (bioconductor-uri "iCOBRA" version)) | |
2815 | (sha256 | |
2816 | (base32 | |
ee1e8fee | 2817 | "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1")))) |
251e0830 RW |
2818 | (properties `((upstream-name . "iCOBRA"))) |
2819 | (build-system r-build-system) | |
2820 | (propagated-inputs | |
2821 | `(("r-dplyr" ,r-dplyr) | |
2822 | ("r-dt" ,r-dt) | |
2823 | ("r-ggplot2" ,r-ggplot2) | |
2824 | ("r-limma" ,r-limma) | |
2825 | ("r-reshape2" ,r-reshape2) | |
2826 | ("r-rocr" ,r-rocr) | |
2827 | ("r-scales" ,r-scales) | |
2828 | ("r-shiny" ,r-shiny) | |
2829 | ("r-shinybs" ,r-shinybs) | |
2830 | ("r-shinydashboard" ,r-shinydashboard) | |
2831 | ("r-upsetr" ,r-upsetr))) | |
ee1e8fee RW |
2832 | (native-inputs |
2833 | `(("r-knitr" ,r-knitr))) | |
251e0830 RW |
2834 | (home-page "https://bioconductor.org/packages/iCOBRA") |
2835 | (synopsis "Comparison and visualization of ranking and assignment methods") | |
2836 | (description | |
2837 | "This package provides functions for calculation and visualization of | |
2838 | performance metrics for evaluation of ranking and binary | |
2839 | classification (assignment) methods. It also contains a Shiny application for | |
2840 | interactive exploration of results.") | |
2841 | (license license:gpl2+))) | |
925fcdbb RW |
2842 | |
2843 | (define-public r-mast | |
2844 | (package | |
2845 | (name "r-mast") | |
97cba97a | 2846 | (version "1.14.0") |
925fcdbb RW |
2847 | (source |
2848 | (origin | |
2849 | (method url-fetch) | |
2850 | (uri (bioconductor-uri "MAST" version)) | |
2851 | (sha256 | |
2852 | (base32 | |
97cba97a | 2853 | "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr")))) |
925fcdbb RW |
2854 | (properties `((upstream-name . "MAST"))) |
2855 | (build-system r-build-system) | |
2856 | (propagated-inputs | |
2857 | `(("r-abind" ,r-abind) | |
2858 | ("r-biobase" ,r-biobase) | |
2859 | ("r-biocgenerics" ,r-biocgenerics) | |
2860 | ("r-data-table" ,r-data-table) | |
2861 | ("r-ggplot2" ,r-ggplot2) | |
2862 | ("r-plyr" ,r-plyr) | |
2863 | ("r-progress" ,r-progress) | |
2864 | ("r-reshape2" ,r-reshape2) | |
2865 | ("r-s4vectors" ,r-s4vectors) | |
2866 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2867 | ("r-stringr" ,r-stringr) | |
2868 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
51d1a7a2 RW |
2869 | (native-inputs |
2870 | `(("r-knitr" ,r-knitr))) | |
925fcdbb RW |
2871 | (home-page "https://github.com/RGLab/MAST/") |
2872 | (synopsis "Model-based analysis of single cell transcriptomics") | |
2873 | (description | |
2874 | "This package provides methods and models for handling zero-inflated | |
2875 | single cell assay data.") | |
2876 | (license license:gpl2+))) | |
2d7627cf RW |
2877 | |
2878 | (define-public r-monocle | |
2879 | (package | |
2880 | (name "r-monocle") | |
d1f3c371 | 2881 | (version "2.16.0") |
2d7627cf RW |
2882 | (source |
2883 | (origin | |
2884 | (method url-fetch) | |
2885 | (uri (bioconductor-uri "monocle" version)) | |
2886 | (sha256 | |
2887 | (base32 | |
d1f3c371 | 2888 | "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd")))) |
2d7627cf RW |
2889 | (build-system r-build-system) |
2890 | (propagated-inputs | |
2891 | `(("r-biobase" ,r-biobase) | |
2892 | ("r-biocgenerics" ,r-biocgenerics) | |
2893 | ("r-biocviews" ,r-biocviews) | |
2894 | ("r-cluster" ,r-cluster) | |
2895 | ("r-combinat" ,r-combinat) | |
2896 | ("r-ddrtree" ,r-ddrtree) | |
2897 | ("r-densityclust" ,r-densityclust) | |
2898 | ("r-dplyr" ,r-dplyr) | |
2899 | ("r-fastica" ,r-fastica) | |
2900 | ("r-ggplot2" ,r-ggplot2) | |
2901 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) | |
2902 | ("r-igraph" ,r-igraph) | |
2903 | ("r-irlba" ,r-irlba) | |
2904 | ("r-limma" ,r-limma) | |
2905 | ("r-mass" ,r-mass) | |
2906 | ("r-matrix" ,r-matrix) | |
2907 | ("r-matrixstats" ,r-matrixstats) | |
2908 | ("r-pheatmap" ,r-pheatmap) | |
2909 | ("r-plyr" ,r-plyr) | |
2910 | ("r-proxy" ,r-proxy) | |
2911 | ("r-qlcmatrix" ,r-qlcmatrix) | |
2912 | ("r-rann" ,r-rann) | |
2913 | ("r-rcpp" ,r-rcpp) | |
2914 | ("r-reshape2" ,r-reshape2) | |
2915 | ("r-rtsne" ,r-rtsne) | |
2916 | ("r-slam" ,r-slam) | |
2917 | ("r-stringr" ,r-stringr) | |
2918 | ("r-tibble" ,r-tibble) | |
2919 | ("r-vgam" ,r-vgam) | |
2920 | ("r-viridis" ,r-viridis))) | |
d1f3c371 RW |
2921 | (native-inputs |
2922 | `(("r-knitr" ,r-knitr))) | |
2d7627cf RW |
2923 | (home-page "https://bioconductor.org/packages/monocle") |
2924 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") | |
2925 | (description | |
2926 | "Monocle performs differential expression and time-series analysis for | |
2927 | single-cell expression experiments. It orders individual cells according to | |
2928 | progress through a biological process, without knowing ahead of time which | |
2929 | genes define progress through that process. Monocle also performs | |
2930 | differential expression analysis, clustering, visualization, and other useful | |
2931 | tasks on single cell expression data. It is designed to work with RNA-Seq and | |
2932 | qPCR data, but could be used with other types as well.") | |
2933 | (license license:artistic2.0))) | |
6213e441 | 2934 | |
b2dce6b5 RW |
2935 | (define-public r-monocle3 |
2936 | (package | |
2937 | (name "r-monocle3") | |
2938 | (version "0.1.2") | |
2939 | (source | |
2940 | (origin | |
2941 | (method git-fetch) | |
2942 | (uri (git-reference | |
b0e7b699 | 2943 | (url "https://github.com/cole-trapnell-lab/monocle3") |
b2dce6b5 RW |
2944 | (commit version))) |
2945 | (file-name (git-file-name name version)) | |
2946 | (sha256 | |
2947 | (base32 | |
2948 | "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) | |
2949 | (build-system r-build-system) | |
2950 | (propagated-inputs | |
2951 | `(("r-biobase" ,r-biobase) | |
2952 | ("r-biocgenerics" ,r-biocgenerics) | |
2953 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
2954 | ("r-dplyr" ,r-dplyr) | |
2955 | ("r-ggplot2" ,r-ggplot2) | |
2956 | ("r-ggrepel" ,r-ggrepel) | |
2957 | ("r-grr" ,r-grr) | |
2958 | ("r-htmlwidgets" ,r-htmlwidgets) | |
2959 | ("r-igraph" ,r-igraph) | |
2960 | ("r-irlba" ,r-irlba) | |
2961 | ("r-limma" ,r-limma) | |
2962 | ("r-lmtest" ,r-lmtest) | |
2963 | ("r-mass" ,r-mass) | |
2964 | ("r-matrix" ,r-matrix) | |
2965 | ("r-matrix-utils" ,r-matrix-utils) | |
2966 | ("r-pbapply" ,r-pbapply) | |
2967 | ("r-pbmcapply" ,r-pbmcapply) | |
2968 | ("r-pheatmap" ,r-pheatmap) | |
2969 | ("r-plotly" ,r-plotly) | |
2970 | ("r-pryr" ,r-pryr) | |
2971 | ("r-proxy" ,r-proxy) | |
2972 | ("r-pscl" ,r-pscl) | |
2973 | ("r-purrr" ,r-purrr) | |
2974 | ("r-rann" ,r-rann) | |
2975 | ("r-rcpp" ,r-rcpp) | |
2976 | ("r-rcppparallel" ,r-rcppparallel) | |
2977 | ("r-reshape2" ,r-reshape2) | |
2978 | ("r-reticulate" ,r-reticulate) | |
2979 | ("r-rhpcblasctl" ,r-rhpcblasctl) | |
2980 | ("r-rtsne" ,r-rtsne) | |
2981 | ("r-shiny" ,r-shiny) | |
2982 | ("r-slam" ,r-slam) | |
2983 | ("r-spdep" ,r-spdep) | |
2984 | ("r-speedglm" ,r-speedglm) | |
2985 | ("r-stringr" ,r-stringr) | |
2986 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
2987 | ("r-tibble" ,r-tibble) | |
2988 | ("r-tidyr" ,r-tidyr) | |
2989 | ("r-uwot" ,r-uwot) | |
2990 | ("r-viridis" ,r-viridis))) | |
2991 | (home-page "https://github.com/cole-trapnell-lab/monocle3") | |
2992 | (synopsis "Analysis toolkit for single-cell RNA-Seq data") | |
2993 | (description | |
2994 | "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") | |
2995 | (license license:expat))) | |
2996 | ||
6213e441 RW |
2997 | (define-public r-noiseq |
2998 | (package | |
2999 | (name "r-noiseq") | |
22c084ba | 3000 | (version "2.31.0") |
6213e441 RW |
3001 | (source |
3002 | (origin | |
3003 | (method url-fetch) | |
3004 | (uri (bioconductor-uri "NOISeq" version)) | |
3005 | (sha256 | |
3006 | (base32 | |
22c084ba | 3007 | "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33")))) |
6213e441 RW |
3008 | (properties `((upstream-name . "NOISeq"))) |
3009 | (build-system r-build-system) | |
3010 | (propagated-inputs | |
3011 | `(("r-biobase" ,r-biobase) | |
3012 | ("r-matrix" ,r-matrix))) | |
3013 | (home-page "https://bioconductor.org/packages/NOISeq") | |
3014 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") | |
3015 | (description | |
3016 | "This package provides tools to support the analysis of RNA-seq | |
3017 | expression data or other similar kind of data. It provides exploratory plots | |
3018 | to evaluate saturation, count distribution, expression per chromosome, type of | |
3019 | detected features, features length, etc. It also supports the analysis of | |
3020 | differential expression between two experimental conditions with no parametric | |
3021 | assumptions.") | |
3022 | (license license:artistic2.0))) | |
b409c357 RW |
3023 | |
3024 | (define-public r-scdd | |
3025 | (package | |
3026 | (name "r-scdd") | |
ce9e19bc | 3027 | (version "1.12.0") |
b409c357 RW |
3028 | (source |
3029 | (origin | |
3030 | (method url-fetch) | |
3031 | (uri (bioconductor-uri "scDD" version)) | |
3032 | (sha256 | |
3033 | (base32 | |
ce9e19bc | 3034 | "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx")))) |
b409c357 RW |
3035 | (properties `((upstream-name . "scDD"))) |
3036 | (build-system r-build-system) | |
3037 | (propagated-inputs | |
3038 | `(("r-arm" ,r-arm) | |
3039 | ("r-biocparallel" ,r-biocparallel) | |
3040 | ("r-ebseq" ,r-ebseq) | |
3041 | ("r-fields" ,r-fields) | |
3042 | ("r-ggplot2" ,r-ggplot2) | |
3043 | ("r-mclust" ,r-mclust) | |
3044 | ("r-outliers" ,r-outliers) | |
3045 | ("r-s4vectors" ,r-s4vectors) | |
3046 | ("r-scran" ,r-scran) | |
3047 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
3048 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
ce9e19bc RW |
3049 | (native-inputs |
3050 | `(("r-knitr" ,r-knitr))) | |
b409c357 RW |
3051 | (home-page "https://github.com/kdkorthauer/scDD") |
3052 | (synopsis "Mixture modeling of single-cell RNA-seq data") | |
3053 | (description | |
3054 | "This package implements a method to analyze single-cell RNA-seq data | |
3055 | utilizing flexible Dirichlet Process mixture models. Genes with differential | |
3056 | distributions of expression are classified into several interesting patterns | |
3057 | of differences between two conditions. The package also includes functions | |
3058 | for simulating data with these patterns from negative binomial | |
3059 | distributions.") | |
3060 | (license license:gpl2))) | |
f0887757 RW |
3061 | |
3062 | (define-public r-scone | |
3063 | (package | |
3064 | (name "r-scone") | |
3fc1e039 | 3065 | (version "1.12.0") |
f0887757 RW |
3066 | (source |
3067 | (origin | |
3068 | (method url-fetch) | |
3069 | (uri (bioconductor-uri "scone" version)) | |
3070 | (sha256 | |
3071 | (base32 | |
3fc1e039 | 3072 | "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g")))) |
f0887757 RW |
3073 | (build-system r-build-system) |
3074 | (propagated-inputs | |
3075 | `(("r-aroma-light" ,r-aroma-light) | |
3076 | ("r-biocparallel" ,r-biocparallel) | |
3077 | ("r-boot" ,r-boot) | |
3078 | ("r-class" ,r-class) | |
3079 | ("r-cluster" ,r-cluster) | |
3080 | ("r-compositions" ,r-compositions) | |
3081 | ("r-diptest" ,r-diptest) | |
3082 | ("r-edger" ,r-edger) | |
3083 | ("r-fpc" ,r-fpc) | |
3084 | ("r-gplots" ,r-gplots) | |
3085 | ("r-hexbin" ,r-hexbin) | |
3086 | ("r-limma" ,r-limma) | |
3087 | ("r-matrixstats" ,r-matrixstats) | |
3088 | ("r-mixtools" ,r-mixtools) | |
3089 | ("r-rarpack" ,r-rarpack) | |
3090 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3091 | ("r-rhdf5" ,r-rhdf5) | |
3092 | ("r-ruvseq" ,r-ruvseq) | |
3093 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
3fc1e039 RW |
3094 | (native-inputs |
3095 | `(("r-knitr" ,r-knitr))) | |
f0887757 RW |
3096 | (home-page "https://bioconductor.org/packages/scone") |
3097 | (synopsis "Single cell overview of normalized expression data") | |
3098 | (description | |
3099 | "SCONE is an R package for comparing and ranking the performance of | |
3100 | different normalization schemes for single-cell RNA-seq and other | |
3101 | high-throughput analyses.") | |
3102 | (license license:artistic2.0))) | |
f9201d67 RW |
3103 | |
3104 | (define-public r-geoquery | |
3105 | (package | |
3106 | (name "r-geoquery") | |
159e427c | 3107 | (version "2.56.0") |
f9201d67 RW |
3108 | (source |
3109 | (origin | |
3110 | (method url-fetch) | |
3111 | (uri (bioconductor-uri "GEOquery" version)) | |
3112 | (sha256 | |
3113 | (base32 | |
159e427c | 3114 | "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m")))) |
f9201d67 RW |
3115 | (properties `((upstream-name . "GEOquery"))) |
3116 | (build-system r-build-system) | |
3117 | (propagated-inputs | |
3118 | `(("r-biobase" ,r-biobase) | |
3119 | ("r-dplyr" ,r-dplyr) | |
3120 | ("r-httr" ,r-httr) | |
3121 | ("r-limma" ,r-limma) | |
3122 | ("r-magrittr" ,r-magrittr) | |
3123 | ("r-readr" ,r-readr) | |
3124 | ("r-tidyr" ,r-tidyr) | |
3125 | ("r-xml2" ,r-xml2))) | |
159e427c RW |
3126 | (native-inputs |
3127 | `(("r-knitr" ,r-knitr))) | |
f9201d67 RW |
3128 | (home-page "https://github.com/seandavi/GEOquery/") |
3129 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") | |
3130 | (description | |
3131 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of | |
3132 | microarray data. Given the rich and varied nature of this resource, it is | |
3133 | only natural to want to apply BioConductor tools to these data. GEOquery is | |
3134 | the bridge between GEO and BioConductor.") | |
3135 | (license license:gpl2))) | |
eed6ff03 RW |
3136 | |
3137 | (define-public r-illuminaio | |
3138 | (package | |
3139 | (name "r-illuminaio") | |
d784a478 | 3140 | (version "0.30.0") |
eed6ff03 RW |
3141 | (source |
3142 | (origin | |
3143 | (method url-fetch) | |
3144 | (uri (bioconductor-uri "illuminaio" version)) | |
3145 | (sha256 | |
3146 | (base32 | |
d784a478 | 3147 | "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c")))) |
eed6ff03 RW |
3148 | (build-system r-build-system) |
3149 | (propagated-inputs | |
3150 | `(("r-base64" ,r-base64))) | |
3151 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") | |
3152 | (synopsis "Parse Illumina microarray output files") | |
3153 | (description | |
3154 | "This package provides tools for parsing Illumina's microarray output | |
3155 | files, including IDAT.") | |
3156 | (license license:gpl2))) | |
f4eac096 RW |
3157 | |
3158 | (define-public r-siggenes | |
3159 | (package | |
3160 | (name "r-siggenes") | |
debaa0f3 | 3161 | (version "1.62.0") |
f4eac096 RW |
3162 | (source |
3163 | (origin | |
3164 | (method url-fetch) | |
3165 | (uri (bioconductor-uri "siggenes" version)) | |
3166 | (sha256 | |
3167 | (base32 | |
debaa0f3 | 3168 | "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy")))) |
f4eac096 RW |
3169 | (build-system r-build-system) |
3170 | (propagated-inputs | |
3171 | `(("r-biobase" ,r-biobase) | |
409f4dd6 RW |
3172 | ("r-multtest" ,r-multtest) |
3173 | ("r-scrime" ,r-scrime))) | |
f4eac096 RW |
3174 | (home-page "https://bioconductor.org/packages/siggenes/") |
3175 | (synopsis | |
3176 | "Multiple testing using SAM and Efron's empirical Bayes approaches") | |
3177 | (description | |
3178 | "This package provides tools for the identification of differentially | |
3179 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using | |
3180 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical | |
3181 | Bayes Analyses of Microarrays} (EBAM).") | |
3182 | (license license:lgpl2.0+))) | |
34a24f95 RW |
3183 | |
3184 | (define-public r-bumphunter | |
3185 | (package | |
3186 | (name "r-bumphunter") | |
e3fbcb28 | 3187 | (version "1.30.0") |
34a24f95 RW |
3188 | (source |
3189 | (origin | |
3190 | (method url-fetch) | |
3191 | (uri (bioconductor-uri "bumphunter" version)) | |
3192 | (sha256 | |
3193 | (base32 | |
e3fbcb28 | 3194 | "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq")))) |
34a24f95 RW |
3195 | (build-system r-build-system) |
3196 | (propagated-inputs | |
3197 | `(("r-annotationdbi" ,r-annotationdbi) | |
3198 | ("r-biocgenerics" ,r-biocgenerics) | |
3199 | ("r-dorng" ,r-dorng) | |
3200 | ("r-foreach" ,r-foreach) | |
3201 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3202 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3203 | ("r-genomicranges" ,r-genomicranges) | |
3204 | ("r-iranges" ,r-iranges) | |
3205 | ("r-iterators" ,r-iterators) | |
3206 | ("r-limma" ,r-limma) | |
3207 | ("r-locfit" ,r-locfit) | |
3208 | ("r-matrixstats" ,r-matrixstats) | |
3209 | ("r-s4vectors" ,r-s4vectors))) | |
3210 | (home-page "https://github.com/ririzarr/bumphunter") | |
3211 | (synopsis "Find bumps in genomic data") | |
3212 | (description | |
3213 | "This package provides tools for finding bumps in genomic data in order | |
3214 | to identify differentially methylated regions in epigenetic epidemiology | |
3215 | studies.") | |
3216 | (license license:artistic2.0))) | |
0fbaf195 RW |
3217 | |
3218 | (define-public r-minfi | |
3219 | (package | |
3220 | (name "r-minfi") | |
83e6ffda | 3221 | (version "1.34.0") |
0fbaf195 RW |
3222 | (source |
3223 | (origin | |
3224 | (method url-fetch) | |
3225 | (uri (bioconductor-uri "minfi" version)) | |
3226 | (sha256 | |
3227 | (base32 | |
83e6ffda | 3228 | "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w")))) |
0fbaf195 RW |
3229 | (build-system r-build-system) |
3230 | (propagated-inputs | |
3231 | `(("r-beanplot" ,r-beanplot) | |
3232 | ("r-biobase" ,r-biobase) | |
3233 | ("r-biocgenerics" ,r-biocgenerics) | |
3234 | ("r-biocparallel" ,r-biocparallel) | |
3235 | ("r-biostrings" ,r-biostrings) | |
3236 | ("r-bumphunter" ,r-bumphunter) | |
3237 | ("r-data-table" ,r-data-table) | |
3238 | ("r-delayedarray" ,r-delayedarray) | |
3239 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
3240 | ("r-genefilter" ,r-genefilter) | |
3241 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3242 | ("r-genomicranges" ,r-genomicranges) | |
3243 | ("r-geoquery" ,r-geoquery) | |
3244 | ("r-hdf5array" ,r-hdf5array) | |
3245 | ("r-illuminaio" ,r-illuminaio) | |
3246 | ("r-iranges" ,r-iranges) | |
3247 | ("r-lattice" ,r-lattice) | |
3248 | ("r-limma" ,r-limma) | |
3249 | ("r-mass" ,r-mass) | |
3250 | ("r-mclust" ,r-mclust) | |
3251 | ("r-nlme" ,r-nlme) | |
3252 | ("r-nor1mix" ,r-nor1mix) | |
3253 | ("r-preprocesscore" ,r-preprocesscore) | |
3254 | ("r-quadprog" ,r-quadprog) | |
3255 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3256 | ("r-reshape" ,r-reshape) | |
3257 | ("r-s4vectors" ,r-s4vectors) | |
3258 | ("r-siggenes" ,r-siggenes) | |
3259 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
83e6ffda RW |
3260 | (native-inputs |
3261 | `(("r-knitr" ,r-knitr))) | |
0fbaf195 RW |
3262 | (home-page "https://github.com/hansenlab/minfi") |
3263 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") | |
3264 | (description | |
3265 | "This package provides tools to analyze and visualize Illumina Infinium | |
3266 | methylation arrays.") | |
3267 | (license license:artistic2.0))) | |
5ec5ba02 RW |
3268 | |
3269 | (define-public r-methylumi | |
3270 | (package | |
3271 | (name "r-methylumi") | |
5f25d5f8 | 3272 | (version "2.34.0") |
5ec5ba02 RW |
3273 | (source |
3274 | (origin | |
3275 | (method url-fetch) | |
3276 | (uri (bioconductor-uri "methylumi" version)) | |
3277 | (sha256 | |
3278 | (base32 | |
5f25d5f8 | 3279 | "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr")))) |
5ec5ba02 RW |
3280 | (build-system r-build-system) |
3281 | (propagated-inputs | |
3282 | `(("r-annotate" ,r-annotate) | |
3283 | ("r-annotationdbi" ,r-annotationdbi) | |
3284 | ("r-biobase" ,r-biobase) | |
3285 | ("r-biocgenerics" ,r-biocgenerics) | |
3286 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) | |
3287 | ("r-genefilter" ,r-genefilter) | |
3288 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3289 | ("r-genomicranges" ,r-genomicranges) | |
3290 | ("r-ggplot2" ,r-ggplot2) | |
3291 | ("r-illuminaio" ,r-illuminaio) | |
3292 | ("r-iranges" ,r-iranges) | |
3293 | ("r-lattice" ,r-lattice) | |
3294 | ("r-matrixstats" ,r-matrixstats) | |
3295 | ("r-minfi" ,r-minfi) | |
3296 | ("r-reshape2" ,r-reshape2) | |
3297 | ("r-s4vectors" ,r-s4vectors) | |
3298 | ("r-scales" ,r-scales) | |
3299 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5f25d5f8 RW |
3300 | (native-inputs |
3301 | `(("r-knitr" ,r-knitr))) | |
5ec5ba02 RW |
3302 | (home-page "https://bioconductor.org/packages/methylumi") |
3303 | (synopsis "Handle Illumina methylation data") | |
3304 | (description | |
3305 | "This package provides classes for holding and manipulating Illumina | |
3306 | methylation data. Based on eSet, it can contain MIAME information, sample | |
3307 | information, feature information, and multiple matrices of data. An | |
3308 | \"intelligent\" import function, methylumiR can read the Illumina text files | |
3309 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from | |
3310 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, | |
3311 | background correction, and quality control features for GoldenGate, Infinium, | |
3312 | and Infinium HD arrays are also included.") | |
3313 | (license license:gpl2))) | |
09605cb2 RW |
3314 | |
3315 | (define-public r-lumi | |
3316 | (package | |
3317 | (name "r-lumi") | |
ae1c51a1 | 3318 | (version "2.40.0") |
09605cb2 RW |
3319 | (source |
3320 | (origin | |
3321 | (method url-fetch) | |
3322 | (uri (bioconductor-uri "lumi" version)) | |
3323 | (sha256 | |
3324 | (base32 | |
ae1c51a1 | 3325 | "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9")))) |
09605cb2 RW |
3326 | (build-system r-build-system) |
3327 | (propagated-inputs | |
3328 | `(("r-affy" ,r-affy) | |
3329 | ("r-annotate" ,r-annotate) | |
3330 | ("r-annotationdbi" ,r-annotationdbi) | |
3331 | ("r-biobase" ,r-biobase) | |
3332 | ("r-dbi" ,r-dbi) | |
3333 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3334 | ("r-genomicranges" ,r-genomicranges) | |
3335 | ("r-kernsmooth" ,r-kernsmooth) | |
3336 | ("r-lattice" ,r-lattice) | |
3337 | ("r-mass" ,r-mass) | |
3338 | ("r-methylumi" ,r-methylumi) | |
3339 | ("r-mgcv" ,r-mgcv) | |
3340 | ("r-nleqslv" ,r-nleqslv) | |
3341 | ("r-preprocesscore" ,r-preprocesscore) | |
3342 | ("r-rsqlite" ,r-rsqlite))) | |
3343 | (home-page "https://bioconductor.org/packages/lumi") | |
3344 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") | |
3345 | (description | |
3346 | "The lumi package provides an integrated solution for the Illumina | |
3347 | microarray data analysis. It includes functions of Illumina | |
3348 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific | |
3349 | variance stabilization, normalization and gene annotation at the probe level. | |
3350 | It also includes the functions of processing Illumina methylation microarrays, | |
3351 | especially Illumina Infinium methylation microarrays.") | |
3352 | (license license:lgpl2.0+))) | |
4291f36a RW |
3353 | |
3354 | (define-public r-linnorm | |
3355 | (package | |
3356 | (name "r-linnorm") | |
1465873c | 3357 | (version "2.12.0") |
4291f36a RW |
3358 | (source |
3359 | (origin | |
3360 | (method url-fetch) | |
3361 | (uri (bioconductor-uri "Linnorm" version)) | |
3362 | (sha256 | |
3363 | (base32 | |
1465873c | 3364 | "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp")))) |
4291f36a RW |
3365 | (properties `((upstream-name . "Linnorm"))) |
3366 | (build-system r-build-system) | |
3367 | (propagated-inputs | |
3368 | `(("r-amap" ,r-amap) | |
3369 | ("r-apcluster" ,r-apcluster) | |
3370 | ("r-ellipse" ,r-ellipse) | |
3371 | ("r-fastcluster" ,r-fastcluster) | |
3372 | ("r-fpc" ,r-fpc) | |
3373 | ("r-ggdendro" ,r-ggdendro) | |
3374 | ("r-ggplot2" ,r-ggplot2) | |
3375 | ("r-gmodels" ,r-gmodels) | |
3376 | ("r-igraph" ,r-igraph) | |
3377 | ("r-limma" ,r-limma) | |
3378 | ("r-mass" ,r-mass) | |
3379 | ("r-mclust" ,r-mclust) | |
3380 | ("r-rcpp" ,r-rcpp) | |
3381 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
3382 | ("r-rtsne" ,r-rtsne) | |
3383 | ("r-statmod" ,r-statmod) | |
3384 | ("r-vegan" ,r-vegan) | |
3385 | ("r-zoo" ,r-zoo))) | |
1465873c RW |
3386 | (native-inputs |
3387 | `(("r-knitr" ,r-knitr))) | |
4291f36a RW |
3388 | (home-page "http://www.jjwanglab.org/Linnorm/") |
3389 | (synopsis "Linear model and normality based transformation method") | |
3390 | (description | |
3391 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq | |
3392 | count data or any large scale count data. It transforms such datasets for | |
3393 | parametric tests. In addition to the transformtion function (@code{Linnorm}), | |
3394 | the following pipelines are implemented: | |
3395 | ||
3396 | @enumerate | |
3397 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) | |
3398 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means | |
3399 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, | |
3400 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) | |
3401 | @item Differential expression analysis or differential peak detection using | |
3402 | limma (@code{Linnorm.limma}) | |
3403 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) | |
3404 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) | |
3405 | @item Stable gene selection for scRNA-seq data; for users without or who do | |
3406 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) | |
3407 | @item Data imputation (@code{Linnorm.DataImput}). | |
3408 | @end enumerate | |
3409 | ||
3410 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the | |
3411 | @code{RnaXSim} function is included for simulating RNA-seq data for the | |
3412 | evaluation of DEG analysis methods.") | |
3413 | (license license:expat))) | |
e4a17532 RW |
3414 | |
3415 | (define-public r-ioniser | |
3416 | (package | |
3417 | (name "r-ioniser") | |
293fb8a1 | 3418 | (version "2.12.0") |
e4a17532 RW |
3419 | (source |
3420 | (origin | |
3421 | (method url-fetch) | |
3422 | (uri (bioconductor-uri "IONiseR" version)) | |
3423 | (sha256 | |
3424 | (base32 | |
293fb8a1 | 3425 | "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w")))) |
e4a17532 RW |
3426 | (properties `((upstream-name . "IONiseR"))) |
3427 | (build-system r-build-system) | |
3428 | (propagated-inputs | |
3429 | `(("r-biocgenerics" ,r-biocgenerics) | |
3430 | ("r-biocparallel" ,r-biocparallel) | |
3431 | ("r-biostrings" ,r-biostrings) | |
3432 | ("r-bit64" ,r-bit64) | |
3433 | ("r-dplyr" ,r-dplyr) | |
3434 | ("r-ggplot2" ,r-ggplot2) | |
3435 | ("r-magrittr" ,r-magrittr) | |
3436 | ("r-rhdf5" ,r-rhdf5) | |
3437 | ("r-shortread" ,r-shortread) | |
3438 | ("r-stringr" ,r-stringr) | |
3439 | ("r-tibble" ,r-tibble) | |
3440 | ("r-tidyr" ,r-tidyr) | |
3441 | ("r-xvector" ,r-xvector))) | |
293fb8a1 RW |
3442 | (native-inputs |
3443 | `(("r-knitr" ,r-knitr))) | |
e4a17532 RW |
3444 | (home-page "https://bioconductor.org/packages/IONiseR/") |
3445 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") | |
3446 | (description | |
3447 | "IONiseR provides tools for the quality assessment of Oxford Nanopore | |
3448 | MinION data. It extracts summary statistics from a set of fast5 files and can | |
3449 | be used either before or after base calling. In addition to standard | |
3450 | summaries of the read-types produced, it provides a number of plots for | |
3451 | visualising metrics relative to experiment run time or spatially over the | |
3452 | surface of a flowcell.") | |
3453 | (license license:expat))) | |
80eb01c7 RW |
3454 | |
3455 | ;; This is a CRAN package, but it depends on packages from Bioconductor. | |
3456 | (define-public r-gkmsvm | |
3457 | (package | |
3458 | (name "r-gkmsvm") | |
e1636671 | 3459 | (version "0.81.0") |
80eb01c7 RW |
3460 | (source |
3461 | (origin | |
3462 | (method url-fetch) | |
3463 | (uri (cran-uri "gkmSVM" version)) | |
3464 | (sha256 | |
3465 | (base32 | |
e1636671 | 3466 | "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) |
80eb01c7 RW |
3467 | (properties `((upstream-name . "gkmSVM"))) |
3468 | (build-system r-build-system) | |
3469 | (propagated-inputs | |
975cfe26 | 3470 | `(("r-kernlab" ,r-kernlab) |
80eb01c7 RW |
3471 | ("r-rcpp" ,r-rcpp) |
3472 | ("r-rocr" ,r-rocr) | |
80eb01c7 RW |
3473 | ("r-seqinr" ,r-seqinr))) |
3474 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") | |
3475 | (synopsis "Gapped-kmer support vector machine") | |
3476 | (description | |
3477 | "This R package provides tools for training gapped-kmer SVM classifiers | |
3478 | for DNA and protein sequences. This package supports several sequence | |
3479 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
3480 | (license license:gpl2+))) | |
8a5460b4 | 3481 | |
f2114762 RW |
3482 | ;; This is a CRAN package, but it depends on multtest from Bioconductor. |
3483 | (define-public r-mutoss | |
3484 | (package | |
3485 | (name "r-mutoss") | |
3486 | (version "0.1-12") | |
3487 | (source | |
3488 | (origin | |
3489 | (method url-fetch) | |
3490 | (uri (cran-uri "mutoss" version)) | |
3491 | (sha256 | |
3492 | (base32 | |
3493 | "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298")))) | |
3494 | (properties `((upstream-name . "mutoss"))) | |
3495 | (build-system r-build-system) | |
3496 | (propagated-inputs | |
3497 | `(("r-multcomp" ,r-multcomp) | |
3498 | ("r-multtest" ,r-multtest) | |
3499 | ("r-mvtnorm" ,r-mvtnorm) | |
3500 | ("r-plotrix" ,r-plotrix))) | |
3501 | (home-page "https://github.com/kornl/mutoss/") | |
3502 | (synopsis "Unified multiple testing procedures") | |
3503 | (description | |
3504 | "This package is designed to ease the application and comparison of | |
3505 | multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods | |
3506 | are standardized and usable by the accompanying mutossGUI package.") | |
3507 | ;; Any version of the GPL. | |
3508 | (license (list license:gpl2+ license:gpl3+)))) | |
3509 | ||
bf770d92 RW |
3510 | ;; This is a CRAN package, but it depends on mutoss, which depends on multtest |
3511 | ;; from Bioconductor, so we put it here. | |
3512 | (define-public r-metap | |
3513 | (package | |
3514 | (name "r-metap") | |
fd6412cd | 3515 | (version "1.3") |
bf770d92 RW |
3516 | (source |
3517 | (origin | |
3518 | (method url-fetch) | |
3519 | (uri (cran-uri "metap" version)) | |
3520 | (sha256 | |
3521 | (base32 | |
fd6412cd | 3522 | "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) |
bf770d92 RW |
3523 | (build-system r-build-system) |
3524 | (propagated-inputs | |
3525 | `(("r-lattice" ,r-lattice) | |
3526 | ("r-mutoss" ,r-mutoss) | |
3527 | ("r-rdpack" ,r-rdpack) | |
3528 | ("r-tfisher" ,r-tfisher))) | |
3529 | (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") | |
3530 | (synopsis "Meta-analysis of significance values") | |
3531 | (description | |
3532 | "The canonical way to perform meta-analysis involves using effect sizes. | |
3533 | When they are not available this package provides a number of methods for | |
3534 | meta-analysis of significance values including the methods of Edgington, | |
3535 | Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate | |
3536 | published results; and a routine for graphical display.") | |
3537 | (license license:gpl2))) | |
3538 | ||
8a5460b4 RW |
3539 | (define-public r-triform |
3540 | (package | |
3541 | (name "r-triform") | |
ecb4e165 | 3542 | (version "1.29.0") |
8a5460b4 RW |
3543 | (source |
3544 | (origin | |
3545 | (method url-fetch) | |
3546 | (uri (bioconductor-uri "triform" version)) | |
3547 | (sha256 | |
3548 | (base32 | |
ecb4e165 | 3549 | "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) |
8a5460b4 RW |
3550 | (build-system r-build-system) |
3551 | (propagated-inputs | |
3552 | `(("r-biocgenerics" ,r-biocgenerics) | |
3553 | ("r-iranges" ,r-iranges) | |
3554 | ("r-yaml" ,r-yaml))) | |
3555 | (home-page "https://bioconductor.org/packages/triform/") | |
3556 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") | |
3557 | (description | |
3558 | "The Triform algorithm uses model-free statistics to identify peak-like | |
3559 | distributions of TF ChIP sequencing reads, taking advantage of an improved | |
3560 | peak definition in combination with known profile characteristics.") | |
3561 | (license license:gpl2))) | |
c538bcdd RW |
3562 | |
3563 | (define-public r-varianttools | |
3564 | (package | |
3565 | (name "r-varianttools") | |
f2b686f6 | 3566 | (version "1.30.0") |
c538bcdd RW |
3567 | (source |
3568 | (origin | |
3569 | (method url-fetch) | |
3570 | (uri (bioconductor-uri "VariantTools" version)) | |
3571 | (sha256 | |
3572 | (base32 | |
f2b686f6 | 3573 | "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx")))) |
c538bcdd RW |
3574 | (properties `((upstream-name . "VariantTools"))) |
3575 | (build-system r-build-system) | |
3576 | (propagated-inputs | |
3577 | `(("r-biobase" ,r-biobase) | |
3578 | ("r-biocgenerics" ,r-biocgenerics) | |
3579 | ("r-biocparallel" ,r-biocparallel) | |
3580 | ("r-biostrings" ,r-biostrings) | |
3581 | ("r-bsgenome" ,r-bsgenome) | |
3582 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3583 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3584 | ("r-genomicranges" ,r-genomicranges) | |
3585 | ("r-iranges" ,r-iranges) | |
3586 | ("r-matrix" ,r-matrix) | |
3587 | ("r-rsamtools" ,r-rsamtools) | |
3588 | ("r-rtracklayer" ,r-rtracklayer) | |
3589 | ("r-s4vectors" ,r-s4vectors) | |
3590 | ("r-variantannotation" ,r-variantannotation))) | |
3591 | (home-page "https://bioconductor.org/packages/VariantTools/") | |
3592 | (synopsis "Tools for exploratory analysis of variant calls") | |
3593 | (description | |
3594 | "Explore, diagnose, and compare variant calls using filters. The | |
3595 | VariantTools package supports a workflow for loading data, calling single | |
3596 | sample variants and tumor-specific somatic mutations or other sample-specific | |
3597 | variant types (e.g., RNA editing). Most of the functions operate on | |
3598 | alignments (BAM files) or datasets of called variants. The user is expected | |
3599 | to have already aligned the reads with a separate tool, e.g., GSNAP via | |
3600 | gmapR.") | |
3601 | (license license:artistic2.0))) | |
3e41919d RW |
3602 | |
3603 | (define-public r-heatplus | |
3604 | (package | |
3605 | (name "r-heatplus") | |
65e0a7b1 | 3606 | (version "2.34.0") |
3e41919d RW |
3607 | (source |
3608 | (origin | |
3609 | (method url-fetch) | |
3610 | (uri (bioconductor-uri "Heatplus" version)) | |
3611 | (sha256 | |
3612 | (base32 | |
65e0a7b1 | 3613 | "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw")))) |
3e41919d RW |
3614 | (properties `((upstream-name . "Heatplus"))) |
3615 | (build-system r-build-system) | |
3616 | (propagated-inputs | |
3617 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) | |
3618 | (home-page "https://github.com/alexploner/Heatplus") | |
3619 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") | |
3620 | (description | |
3621 | "This package provides tools to display a rectangular heatmap (intensity | |
3622 | plot) of a data matrix. By default, both samples (columns) and features (row) | |
3623 | of the matrix are sorted according to a hierarchical clustering, and the | |
3624 | corresponding dendrogram is plotted. Optionally, panels with additional | |
3625 | information about samples and features can be added to the plot.") | |
3626 | (license license:gpl2+))) | |
c04f230e RW |
3627 | |
3628 | (define-public r-gosemsim | |
3629 | (package | |
3630 | (name "r-gosemsim") | |
fc1c3c6f | 3631 | (version "2.14.1") |
c04f230e RW |
3632 | (source |
3633 | (origin | |
3634 | (method url-fetch) | |
3635 | (uri (bioconductor-uri "GOSemSim" version)) | |
3636 | (sha256 | |
3637 | (base32 | |
fc1c3c6f | 3638 | "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln")))) |
c04f230e RW |
3639 | (properties `((upstream-name . "GOSemSim"))) |
3640 | (build-system r-build-system) | |
3641 | (propagated-inputs | |
3642 | `(("r-annotationdbi" ,r-annotationdbi) | |
3643 | ("r-go-db" ,r-go-db) | |
3644 | ("r-rcpp" ,r-rcpp))) | |
d5951dc4 RW |
3645 | (native-inputs |
3646 | `(("r-knitr" ,r-knitr))) | |
c04f230e RW |
3647 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") |
3648 | (synopsis "GO-terms semantic similarity measures") | |
3649 | (description | |
3650 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide | |
3651 | quantitative ways to compute similarities between genes and gene groups, and | |
3652 | have became important basis for many bioinformatics analysis approaches. | |
3653 | GOSemSim is an R package for semantic similarity computation among GO terms, | |
3654 | sets of GO terms, gene products and gene clusters.") | |
3655 | (license license:artistic2.0))) | |
9d0f7942 RW |
3656 | |
3657 | (define-public r-anota | |
3658 | (package | |
3659 | (name "r-anota") | |
8d30d59a | 3660 | (version "1.36.0") |
9d0f7942 RW |
3661 | (source |
3662 | (origin | |
3663 | (method url-fetch) | |
3664 | (uri (bioconductor-uri "anota" version)) | |
3665 | (sha256 | |
3666 | (base32 | |
8d30d59a | 3667 | "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm")))) |
9d0f7942 RW |
3668 | (build-system r-build-system) |
3669 | (propagated-inputs | |
3670 | `(("r-multtest" ,r-multtest) | |
3671 | ("r-qvalue" ,r-qvalue))) | |
3672 | (home-page "https://bioconductor.org/packages/anota/") | |
3673 | (synopsis "Analysis of translational activity") | |
3674 | (description | |
3675 | "Genome wide studies of translational control is emerging as a tool to | |
0cea26bd | 3676 | study various biological conditions. The output from such analysis is both |
9d0f7942 RW |
3677 | the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively |
3678 | involved in translation (the actively translating mRNA level) for each mRNA. | |
3679 | The standard analysis of such data strives towards identifying differential | |
3680 | translational between two or more sample classes - i.e. differences in | |
3681 | actively translated mRNA levels that are independent of underlying differences | |
3682 | in cytosolic mRNA levels. This package allows for such analysis using partial | |
3683 | variances and the random variance model. As 10s of thousands of mRNAs are | |
4f664004 | 3684 | analyzed in parallel the library performs a number of tests to assure that |
9d0f7942 RW |
3685 | the data set is suitable for such analysis.") |
3686 | (license license:gpl3))) | |
a6d867fe RW |
3687 | |
3688 | (define-public r-sigpathway | |
3689 | (package | |
3690 | (name "r-sigpathway") | |
b1d76ad0 | 3691 | (version "1.56.0") |
a6d867fe RW |
3692 | (source |
3693 | (origin | |
3694 | (method url-fetch) | |
3695 | (uri (bioconductor-uri "sigPathway" version)) | |
3696 | (sha256 | |
3697 | (base32 | |
b1d76ad0 | 3698 | "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5")))) |
a6d867fe RW |
3699 | (properties `((upstream-name . "sigPathway"))) |
3700 | (build-system r-build-system) | |
3701 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") | |
3702 | (synopsis "Pathway analysis") | |
3703 | (description | |
3704 | "This package is used to conduct pathway analysis by calculating the NT_k | |
3705 | and NE_k statistics in a statistical framework for determining whether a | |
3706 | specified group of genes for a pathway has a coordinated association with a | |
3707 | phenotype of interest.") | |
3708 | (license license:gpl2))) | |
af26c7ae RW |
3709 | |
3710 | (define-public r-fgsea | |
3711 | (package | |
3712 | (name "r-fgsea") | |
1dec455c | 3713 | (version "1.14.0") |
af26c7ae RW |
3714 | (source |
3715 | (origin | |
3716 | (method url-fetch) | |
3717 | (uri (bioconductor-uri "fgsea" version)) | |
3718 | (sha256 | |
3719 | (base32 | |
1dec455c | 3720 | "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc")))) |
af26c7ae RW |
3721 | (build-system r-build-system) |
3722 | (propagated-inputs | |
ebffd24c RW |
3723 | `(("r-bh" ,r-bh) |
3724 | ("r-biocparallel" ,r-biocparallel) | |
af26c7ae RW |
3725 | ("r-data-table" ,r-data-table) |
3726 | ("r-fastmatch" ,r-fastmatch) | |
3727 | ("r-ggplot2" ,r-ggplot2) | |
3728 | ("r-gridextra" ,r-gridextra) | |
3729 | ("r-matrix" ,r-matrix) | |
3730 | ("r-rcpp" ,r-rcpp))) | |
1dec455c RW |
3731 | (native-inputs |
3732 | `(("r-knitr" ,r-knitr))) | |
af26c7ae RW |
3733 | (home-page "https://github.com/ctlab/fgsea/") |
3734 | (synopsis "Fast gene set enrichment analysis") | |
3735 | (description | |
3736 | "The package implements an algorithm for fast gene set enrichment | |
23c8ef71 VC |
3737 | analysis. Using the fast algorithm makes more permutations and gets |
3738 | more fine grained p-values, which allows using accurate standard approaches | |
af26c7ae RW |
3739 | to multiple hypothesis correction.") |
3740 | (license license:expat))) | |
305050b5 RW |
3741 | |
3742 | (define-public r-dose | |
3743 | (package | |
3744 | (name "r-dose") | |
3a80f1cf | 3745 | (version "3.14.0") |
305050b5 RW |
3746 | (source |
3747 | (origin | |
3748 | (method url-fetch) | |
3749 | (uri (bioconductor-uri "DOSE" version)) | |
3750 | (sha256 | |
3751 | (base32 | |
3a80f1cf | 3752 | "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8")))) |
305050b5 RW |
3753 | (properties `((upstream-name . "DOSE"))) |
3754 | (build-system r-build-system) | |
3755 | (propagated-inputs | |
3756 | `(("r-annotationdbi" ,r-annotationdbi) | |
3757 | ("r-biocparallel" ,r-biocparallel) | |
3758 | ("r-do-db" ,r-do-db) | |
3759 | ("r-fgsea" ,r-fgsea) | |
3760 | ("r-ggplot2" ,r-ggplot2) | |
3761 | ("r-gosemsim" ,r-gosemsim) | |
3762 | ("r-qvalue" ,r-qvalue) | |
3a80f1cf | 3763 | ("r-reshape2" ,r-reshape2))) |
5ef2b749 RW |
3764 | (native-inputs |
3765 | `(("r-knitr" ,r-knitr))) | |
305050b5 RW |
3766 | (home-page "https://guangchuangyu.github.io/software/DOSE/") |
3767 | (synopsis "Disease ontology semantic and enrichment analysis") | |
3768 | (description | |
3769 | "This package implements five methods proposed by Resnik, Schlicker, | |
3770 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among | |
3771 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses | |
3772 | including hypergeometric model and gene set enrichment analysis are also | |
3773 | implemented for discovering disease associations of high-throughput biological | |
3774 | data.") | |
3775 | (license license:artistic2.0))) | |
9c30cf65 RW |
3776 | |
3777 | (define-public r-enrichplot | |
3778 | (package | |
3779 | (name "r-enrichplot") | |
43fb14ce | 3780 | (version "1.8.1") |
9c30cf65 RW |
3781 | (source |
3782 | (origin | |
3783 | (method url-fetch) | |
3784 | (uri (bioconductor-uri "enrichplot" version)) | |
3785 | (sha256 | |
3786 | (base32 | |
43fb14ce | 3787 | "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7")))) |
9c30cf65 RW |
3788 | (build-system r-build-system) |
3789 | (propagated-inputs | |
3790 | `(("r-annotationdbi" ,r-annotationdbi) | |
3791 | ("r-cowplot" ,r-cowplot) | |
3792 | ("r-dose" ,r-dose) | |
3793 | ("r-europepmc" ,r-europepmc) | |
3794 | ("r-ggplot2" ,r-ggplot2) | |
3795 | ("r-ggplotify" ,r-ggplotify) | |
3796 | ("r-ggraph" ,r-ggraph) | |
3797 | ("r-ggridges" ,r-ggridges) | |
3798 | ("r-gosemsim" ,r-gosemsim) | |
3799 | ("r-gridextra" ,r-gridextra) | |
3800 | ("r-igraph" ,r-igraph) | |
43fb14ce | 3801 | ("r-plyr" ,r-plyr) |
9c30cf65 RW |
3802 | ("r-purrr" ,r-purrr) |
3803 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
43fb14ce RW |
3804 | ("r-reshape2" ,r-reshape2) |
3805 | ("r-scatterpie" ,r-scatterpie))) | |
3806 | (native-inputs | |
3807 | `(("r-knitr" ,r-knitr))) | |
9c30cf65 RW |
3808 | (home-page "https://github.com/GuangchuangYu/enrichplot") |
3809 | (synopsis "Visualization of functional enrichment result") | |
3810 | (description | |
3811 | "The enrichplot package implements several visualization methods for | |
3812 | interpreting functional enrichment results obtained from ORA or GSEA analyses. | |
3813 | All the visualization methods are developed based on ggplot2 graphics.") | |
3814 | (license license:artistic2.0))) | |
f8295ee6 RW |
3815 | |
3816 | (define-public r-clusterprofiler | |
3817 | (package | |
3818 | (name "r-clusterprofiler") | |
69f3b278 | 3819 | (version "3.16.1") |
f8295ee6 RW |
3820 | (source |
3821 | (origin | |
3822 | (method url-fetch) | |
3823 | (uri (bioconductor-uri "clusterProfiler" version)) | |
3824 | (sha256 | |
3825 | (base32 | |
69f3b278 | 3826 | "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb")))) |
f8295ee6 RW |
3827 | (properties |
3828 | `((upstream-name . "clusterProfiler"))) | |
3829 | (build-system r-build-system) | |
3830 | (propagated-inputs | |
3831 | `(("r-annotationdbi" ,r-annotationdbi) | |
3832 | ("r-dose" ,r-dose) | |
63c8323a RW |
3833 | ("r-downloader" ,r-downloader) |
3834 | ("r-dplyr" ,r-dplyr) | |
f8295ee6 | 3835 | ("r-enrichplot" ,r-enrichplot) |
f8295ee6 RW |
3836 | ("r-go-db" ,r-go-db) |
3837 | ("r-gosemsim" ,r-gosemsim) | |
3838 | ("r-magrittr" ,r-magrittr) | |
3839 | ("r-plyr" ,r-plyr) | |
3840 | ("r-qvalue" ,r-qvalue) | |
69f3b278 | 3841 | ("r-rlang" ,r-rlang) |
f8295ee6 RW |
3842 | ("r-rvcheck" ,r-rvcheck) |
3843 | ("r-tidyr" ,r-tidyr))) | |
63c8323a RW |
3844 | (native-inputs |
3845 | `(("r-knitr" ,r-knitr))) | |
f8295ee6 RW |
3846 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") |
3847 | (synopsis "Analysis and visualization of functional profiles for gene clusters") | |
3848 | (description | |
3849 | "This package implements methods to analyze and visualize functional | |
3850 | profiles (GO and KEGG) of gene and gene clusters.") | |
3851 | (license license:artistic2.0))) | |
ce77562a RW |
3852 | |
3853 | (define-public r-mlinterfaces | |
3854 | (package | |
3855 | (name "r-mlinterfaces") | |
500f7df8 | 3856 | (version "1.68.0") |
ce77562a RW |
3857 | (source |
3858 | (origin | |
3859 | (method url-fetch) | |
3860 | (uri (bioconductor-uri "MLInterfaces" version)) | |
3861 | (sha256 | |
3862 | (base32 | |
500f7df8 | 3863 | "0x3mnvb5a6kri4q5w0wfmx02v79my08zhmkaik9pqlprd7y5wynq")))) |
ce77562a RW |
3864 | (properties `((upstream-name . "MLInterfaces"))) |
3865 | (build-system r-build-system) | |
3866 | (propagated-inputs | |
3867 | `(("r-annotate" ,r-annotate) | |
3868 | ("r-biobase" ,r-biobase) | |
3869 | ("r-biocgenerics" ,r-biocgenerics) | |
3870 | ("r-cluster" ,r-cluster) | |
3871 | ("r-fpc" ,r-fpc) | |
3872 | ("r-gbm" ,r-gbm) | |
3873 | ("r-gdata" ,r-gdata) | |
3874 | ("r-genefilter" ,r-genefilter) | |
3875 | ("r-ggvis" ,r-ggvis) | |
3876 | ("r-hwriter" ,r-hwriter) | |
3877 | ("r-mass" ,r-mass) | |
3878 | ("r-mlbench" ,r-mlbench) | |
3879 | ("r-pls" ,r-pls) | |
3880 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
500f7df8 | 3881 | ("r-rcpp" ,r-rcpp) |
ce77562a RW |
3882 | ("r-rpart" ,r-rpart) |
3883 | ("r-sfsmisc" ,r-sfsmisc) | |
3884 | ("r-shiny" ,r-shiny) | |
3885 | ("r-threejs" ,r-threejs))) | |
3886 | (home-page "https://bioconductor.org/packages/MLInterfaces/") | |
3887 | (synopsis "Interfaces to R machine learning procedures") | |
3888 | (description | |
3889 | "This package provides uniform interfaces to machine learning code for | |
3890 | data in R and Bioconductor containers.") | |
3891 | ;; Any version of the LGPL. | |
3892 | (license license:lgpl2.1+))) | |
a793e88c RW |
3893 | |
3894 | (define-public r-annaffy | |
3895 | (package | |
3896 | (name "r-annaffy") | |
d200b4dc | 3897 | (version "1.60.0") |
a793e88c RW |
3898 | (source |
3899 | (origin | |
3900 | (method url-fetch) | |
3901 | (uri (bioconductor-uri "annaffy" version)) | |
3902 | (sha256 | |
3903 | (base32 | |
d200b4dc | 3904 | "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4")))) |
a793e88c RW |
3905 | (build-system r-build-system) |
3906 | (arguments | |
3907 | `(#:phases | |
3908 | (modify-phases %standard-phases | |
3909 | (add-after 'unpack 'remove-reference-to-non-free-data | |
3910 | (lambda _ | |
3911 | (substitute* "DESCRIPTION" | |
3912 | ((", KEGG.db") "")) | |
3913 | #t))))) | |
3914 | (propagated-inputs | |
3915 | `(("r-annotationdbi" ,r-annotationdbi) | |
3916 | ("r-biobase" ,r-biobase) | |
3917 | ("r-dbi" ,r-dbi) | |
3918 | ("r-go-db" ,r-go-db))) | |
3919 | (home-page "https://bioconductor.org/packages/annaffy/") | |
3920 | (synopsis "Annotation tools for Affymetrix biological metadata") | |
3921 | (description | |
3922 | "This package provides functions for handling data from Bioconductor | |
3923 | Affymetrix annotation data packages. It produces compact HTML and text | |
3924 | reports including experimental data and URL links to many online databases. | |
3925 | It allows searching of biological metadata using various criteria.") | |
3926 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of | |
3927 | ;; the LGPL 2.1 is included. | |
3928 | (license license:lgpl2.1+))) | |
0ec0a5ec RW |
3929 | |
3930 | (define-public r-a4core | |
3931 | (package | |
3932 | (name "r-a4core") | |
4f2112ad | 3933 | (version "1.36.0") |
0ec0a5ec RW |
3934 | (source |
3935 | (origin | |
3936 | (method url-fetch) | |
3937 | (uri (bioconductor-uri "a4Core" version)) | |
3938 | (sha256 | |
3939 | (base32 | |
4f2112ad | 3940 | "1hn9lkaib1bx5n52as882f8zwsln8w40sx8hxbrnimjvgfxrbvnp")))) |
0ec0a5ec RW |
3941 | (properties `((upstream-name . "a4Core"))) |
3942 | (build-system r-build-system) | |
3943 | (propagated-inputs | |
3944 | `(("r-biobase" ,r-biobase) | |
3945 | ("r-glmnet" ,r-glmnet))) | |
3946 | (home-page "https://bioconductor.org/packages/a4Core") | |
3947 | (synopsis "Automated Affymetrix array analysis core package") | |
3948 | (description | |
3949 | "This is the core package for the automated analysis of Affymetrix | |
3950 | arrays.") | |
3951 | (license license:gpl3))) | |
9ae37581 RW |
3952 | |
3953 | (define-public r-a4classif | |
3954 | (package | |
3955 | (name "r-a4classif") | |
33c9c856 | 3956 | (version "1.36.0") |
9ae37581 RW |
3957 | (source |
3958 | (origin | |
3959 | (method url-fetch) | |
3960 | (uri (bioconductor-uri "a4Classif" version)) | |
3961 | (sha256 | |
3962 | (base32 | |
33c9c856 | 3963 | "0bj8m4nprw3maahd1qx9jjdxfip9ihbbpydbzwjxn6dlgw2i8mcr")))) |
9ae37581 RW |
3964 | (properties `((upstream-name . "a4Classif"))) |
3965 | (build-system r-build-system) | |
3966 | (propagated-inputs | |
3967 | `(("r-a4core" ,r-a4core) | |
3968 | ("r-a4preproc" ,r-a4preproc) | |
3969 | ("r-glmnet" ,r-glmnet) | |
3970 | ("r-mlinterfaces" ,r-mlinterfaces) | |
3971 | ("r-pamr" ,r-pamr) | |
3972 | ("r-rocr" ,r-rocr) | |
3973 | ("r-varselrf" ,r-varselrf))) | |
3974 | (home-page "https://bioconductor.org/packages/a4Classif/") | |
3975 | (synopsis "Automated Affymetrix array analysis classification package") | |
3976 | (description | |
3977 | "This is the classification package for the automated analysis of | |
3978 | Affymetrix arrays.") | |
3979 | (license license:gpl3))) | |
b8d13e2c RW |
3980 | |
3981 | (define-public r-a4preproc | |
3982 | (package | |
3983 | (name "r-a4preproc") | |
6afea4ea | 3984 | (version "1.36.0") |
b8d13e2c RW |
3985 | (source |
3986 | (origin | |
3987 | (method url-fetch) | |
3988 | (uri (bioconductor-uri "a4Preproc" version)) | |
3989 | (sha256 | |
3990 | (base32 | |
6afea4ea | 3991 | "1hy3jvhdjyjzzmw5wkil3cs26hvqnb056r09x0p2bjg5sc9hh8b8")))) |
b8d13e2c RW |
3992 | (properties `((upstream-name . "a4Preproc"))) |
3993 | (build-system r-build-system) | |
3994 | (propagated-inputs | |
3995 | `(("r-annotationdbi" ,r-annotationdbi))) | |
3996 | (home-page "https://bioconductor.org/packages/a4Preproc/") | |
3997 | (synopsis "Automated Affymetrix array analysis preprocessing package") | |
3998 | (description | |
3999 | "This is a package for the automated analysis of Affymetrix arrays. It | |
4000 | is used for preprocessing the arrays.") | |
4001 | (license license:gpl3))) | |
8e15f861 RW |
4002 | |
4003 | (define-public r-a4reporting | |
4004 | (package | |
4005 | (name "r-a4reporting") | |
e47f9f48 | 4006 | (version "1.36.0") |
8e15f861 RW |
4007 | (source |
4008 | (origin | |
4009 | (method url-fetch) | |
4010 | (uri (bioconductor-uri "a4Reporting" version)) | |
4011 | (sha256 | |
4012 | (base32 | |
e47f9f48 | 4013 | "1jhlxqwfbgflcyzy9gyxznzcadj9zxchl3lfdlc4ffm0hwz5jl2f")))) |
8e15f861 RW |
4014 | (properties `((upstream-name . "a4Reporting"))) |
4015 | (build-system r-build-system) | |
4016 | (propagated-inputs | |
4017 | `(("r-annaffy" ,r-annaffy) | |
4018 | ("r-xtable" ,r-xtable))) | |
4019 | (home-page "https://bioconductor.org/packages/a4Reporting/") | |
4020 | (synopsis "Automated Affymetrix array analysis reporting package") | |
4021 | (description | |
4022 | "This is a package for the automated analysis of Affymetrix arrays. It | |
4023 | provides reporting features.") | |
4024 | (license license:gpl3))) | |
dbfe3375 RW |
4025 | |
4026 | (define-public r-a4base | |
4027 | (package | |
4028 | (name "r-a4base") | |
2a91c987 | 4029 | (version "1.36.0") |
dbfe3375 RW |
4030 | (source |
4031 | (origin | |
4032 | (method url-fetch) | |
4033 | (uri (bioconductor-uri "a4Base" version)) | |
4034 | (sha256 | |
4035 | (base32 | |
2a91c987 | 4036 | "0b7fy1wcydb9z43wb1663skswvhivn7ji15g00gqcshwkkiq4x02")))) |
dbfe3375 RW |
4037 | (properties `((upstream-name . "a4Base"))) |
4038 | (build-system r-build-system) | |
4039 | (propagated-inputs | |
4040 | `(("r-a4core" ,r-a4core) | |
4041 | ("r-a4preproc" ,r-a4preproc) | |
4042 | ("r-annaffy" ,r-annaffy) | |
4043 | ("r-annotationdbi" ,r-annotationdbi) | |
4044 | ("r-biobase" ,r-biobase) | |
4045 | ("r-genefilter" ,r-genefilter) | |
4046 | ("r-glmnet" ,r-glmnet) | |
4047 | ("r-gplots" ,r-gplots) | |
4048 | ("r-limma" ,r-limma) | |
4049 | ("r-mpm" ,r-mpm) | |
4050 | ("r-multtest" ,r-multtest))) | |
4051 | (home-page "https://bioconductor.org/packages/a4Base/") | |
4052 | (synopsis "Automated Affymetrix array analysis base package") | |
4053 | (description | |
4054 | "This package provides basic features for the automated analysis of | |
4055 | Affymetrix arrays.") | |
4056 | (license license:gpl3))) | |
84ad024e RW |
4057 | |
4058 | (define-public r-a4 | |
4059 | (package | |
4060 | (name "r-a4") | |
b391b1e4 | 4061 | (version "1.36.0") |
84ad024e RW |
4062 | (source |
4063 | (origin | |
4064 | (method url-fetch) | |
4065 | (uri (bioconductor-uri "a4" version)) | |
4066 | (sha256 | |
4067 | (base32 | |
b391b1e4 | 4068 | "1rzxg1h48jnlwqfjyyqzz6i3zlkfzc0i714rfplry7dyni6asgr7")))) |
84ad024e RW |
4069 | (build-system r-build-system) |
4070 | (propagated-inputs | |
4071 | `(("r-a4base" ,r-a4base) | |
4072 | ("r-a4classif" ,r-a4classif) | |
4073 | ("r-a4core" ,r-a4core) | |
4074 | ("r-a4preproc" ,r-a4preproc) | |
4075 | ("r-a4reporting" ,r-a4reporting))) | |
4076 | (home-page "https://bioconductor.org/packages/a4/") | |
4077 | (synopsis "Automated Affymetrix array analysis umbrella package") | |
4078 | (description | |
4079 | "This package provides a software suite for the automated analysis of | |
4080 | Affymetrix arrays.") | |
4081 | (license license:gpl3))) | |
59d331f1 RW |
4082 | |
4083 | (define-public r-abseqr | |
4084 | (package | |
4085 | (name "r-abseqr") | |
35bcfaef | 4086 | (version "1.6.0") |
59d331f1 RW |
4087 | (source |
4088 | (origin | |
4089 | (method url-fetch) | |
4090 | (uri (bioconductor-uri "abseqR" version)) | |
4091 | (sha256 | |
4092 | (base32 | |
35bcfaef | 4093 | "0pzyfn0jv41rja6l4jbgwgsqy0q1d3kz23m9m6pc67p2a231i9c5")))) |
59d331f1 RW |
4094 | (properties `((upstream-name . "abseqR"))) |
4095 | (build-system r-build-system) | |
4096 | (inputs | |
8fe3ef5d RW |
4097 | `(("pandoc" ,pandoc) |
4098 | ("pandoc-citeproc" ,pandoc-citeproc))) | |
59d331f1 RW |
4099 | (propagated-inputs |
4100 | `(("r-biocparallel" ,r-biocparallel) | |
4101 | ("r-biocstyle" ,r-biocstyle) | |
4102 | ("r-circlize" ,r-circlize) | |
4103 | ("r-flexdashboard" ,r-flexdashboard) | |
4104 | ("r-ggcorrplot" ,r-ggcorrplot) | |
4105 | ("r-ggdendro" ,r-ggdendro) | |
4106 | ("r-ggplot2" ,r-ggplot2) | |
4107 | ("r-gridextra" ,r-gridextra) | |
4108 | ("r-knitr" ,r-knitr) | |
4109 | ("r-plotly" ,r-plotly) | |
4110 | ("r-plyr" ,r-plyr) | |
4111 | ("r-png" ,r-png) | |
4112 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4113 | ("r-reshape2" ,r-reshape2) | |
4114 | ("r-rmarkdown" ,r-rmarkdown) | |
4115 | ("r-stringr" ,r-stringr) | |
4116 | ("r-vegan" ,r-vegan) | |
4117 | ("r-venndiagram" ,r-venndiagram))) | |
35bcfaef RW |
4118 | (native-inputs |
4119 | `(("r-knitr" ,r-knitr))) | |
59d331f1 RW |
4120 | (home-page "https://github.com/malhamdoosh/abseqR") |
4121 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") | |
4122 | (description | |
4123 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of | |
4124 | sequencing datasets generated from antibody libraries and abseqR is one of its | |
4125 | packages. AbseqR empowers the users of abseqPy with plotting and reporting | |
4126 | capabilities and allows them to generate interactive HTML reports for the | |
4127 | convenience of viewing and sharing with other researchers. Additionally, | |
4128 | abseqR extends abseqPy to compare multiple repertoire analyses and perform | |
4129 | further downstream analysis on its output.") | |
4130 | (license license:gpl3))) | |
41aab7d1 RW |
4131 | |
4132 | (define-public r-bacon | |
4133 | (package | |
4134 | (name "r-bacon") | |
7450edca | 4135 | (version "1.16.0") |
41aab7d1 RW |
4136 | (source |
4137 | (origin | |
4138 | (method url-fetch) | |
4139 | (uri (bioconductor-uri "bacon" version)) | |
4140 | (sha256 | |
4141 | (base32 | |
7450edca | 4142 | "066b9vyp8ivnzm9741mb5z763a7z40ar9m8w31yw84fjiv01v3dl")))) |
41aab7d1 RW |
4143 | (build-system r-build-system) |
4144 | (propagated-inputs | |
4145 | `(("r-biocparallel" ,r-biocparallel) | |
4146 | ("r-ellipse" ,r-ellipse) | |
4147 | ("r-ggplot2" ,r-ggplot2))) | |
506cbeab RW |
4148 | (native-inputs |
4149 | `(("r-knitr" ,r-knitr))) | |
41aab7d1 RW |
4150 | (home-page "https://bioconductor.org/packages/bacon/") |
4151 | (synopsis "Controlling bias and inflation in association studies") | |
4152 | (description | |
4153 | "Bacon can be used to remove inflation and bias often observed in | |
4154 | epigenome- and transcriptome-wide association studies. To this end bacon | |
4155 | constructs an empirical null distribution using a Gibbs Sampling algorithm by | |
4156 | fitting a three-component normal mixture on z-scores.") | |
4157 | (license license:gpl2+))) | |
051e8e1a RW |
4158 | |
4159 | (define-public r-rgadem | |
4160 | (package | |
4161 | (name "r-rgadem") | |
6d02e171 | 4162 | (version "2.36.0") |
051e8e1a RW |
4163 | (source |
4164 | (origin | |
4165 | (method url-fetch) | |
4166 | (uri (bioconductor-uri "rGADEM" version)) | |
4167 | (sha256 | |
4168 | (base32 | |
6d02e171 | 4169 | "14mflbwhhj9f3b05zdlsdjwxmpb120r23fy306qkvxjprdqn4sz8")))) |
051e8e1a RW |
4170 | (properties `((upstream-name . "rGADEM"))) |
4171 | (build-system r-build-system) | |
4172 | (propagated-inputs | |
4173 | `(("r-biostrings" ,r-biostrings) | |
4174 | ("r-bsgenome" ,r-bsgenome) | |
07189489 | 4175 | ("r-genomicranges" ,r-genomicranges) |
051e8e1a RW |
4176 | ("r-iranges" ,r-iranges) |
4177 | ("r-seqlogo" ,r-seqlogo))) | |
4178 | (home-page "https://bioconductor.org/packages/rGADEM/") | |
4179 | (synopsis "De novo sequence motif discovery") | |
4180 | (description | |
4181 | "rGADEM is an efficient de novo motif discovery tool for large-scale | |
4182 | genomic sequence data.") | |
4183 | (license license:artistic2.0))) | |
229f97c3 RW |
4184 | |
4185 | (define-public r-motiv | |
4186 | (package | |
4187 | (name "r-motiv") | |
352cfa34 | 4188 | (version "1.43.0") |
229f97c3 RW |
4189 | (source |
4190 | (origin | |
4191 | (method url-fetch) | |
4192 | (uri (bioconductor-uri "MotIV" version)) | |
4193 | (sha256 | |
4194 | (base32 | |
352cfa34 | 4195 | "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6")))) |
229f97c3 RW |
4196 | (properties `((upstream-name . "MotIV"))) |
4197 | (build-system r-build-system) | |
4198 | (inputs | |
4199 | `(("gsl" ,gsl))) | |
4200 | (propagated-inputs | |
4201 | `(("r-biocgenerics" ,r-biocgenerics) | |
4202 | ("r-biostrings" ,r-biostrings) | |
35a1b3ec | 4203 | ("r-genomicranges" ,r-genomicranges) |
229f97c3 RW |
4204 | ("r-iranges" ,r-iranges) |
4205 | ("r-lattice" ,r-lattice) | |
4206 | ("r-rgadem" ,r-rgadem) | |
4207 | ("r-s4vectors" ,r-s4vectors))) | |
4208 | (home-page "https://bioconductor.org/packages/MotIV/") | |
4209 | (synopsis "Motif identification and validation") | |
4210 | (description | |
4211 | "This package is used for the identification and validation of sequence | |
4212 | motifs. It makes use of STAMP for comparing a set of motifs to a given | |
4213 | database (e.g. JASPAR). It can also be used to visualize motifs, motif | |
4214 | distributions, modules and filter motifs.") | |
4215 | (license license:gpl2))) | |
2a72ef56 | 4216 | |
3699bcf5 RJ |
4217 | (define-public r-motifdb |
4218 | (package | |
4219 | (name "r-motifdb") | |
da6a75fe | 4220 | (version "1.30.0") |
3699bcf5 RJ |
4221 | (source (origin |
4222 | (method url-fetch) | |
4223 | (uri (bioconductor-uri "MotifDb" version)) | |
4224 | (sha256 | |
da6a75fe | 4225 | (base32 "0ixmdqp0s0xv9ar85n2wirbbssrzlk8a892wam55jdsf9y8aabkm")))) |
3699bcf5 RJ |
4226 | (properties `((upstream-name . "MotifDb"))) |
4227 | (build-system r-build-system) | |
4228 | (propagated-inputs | |
4229 | `(("r-biocgenerics" ,r-biocgenerics) | |
4230 | ("r-biostrings" ,r-biostrings) | |
da6a75fe | 4231 | ("r-genomicranges" ,r-genomicranges) |
3699bcf5 RJ |
4232 | ("r-iranges" ,r-iranges) |
4233 | ("r-rtracklayer" ,r-rtracklayer) | |
4234 | ("r-s4vectors" ,r-s4vectors) | |
4235 | ("r-splitstackshape" ,r-splitstackshape))) | |
da6a75fe RW |
4236 | (native-inputs |
4237 | `(("r-knitr" ,r-knitr))) | |
3699bcf5 RJ |
4238 | (home-page "https://www.bioconductor.org/packages/MotifDb/") |
4239 | (synopsis "Annotated collection of protein-DNA binding sequence motifs") | |
4240 | (description "This package provides more than 2000 annotated position | |
4241 | frequency matrices from nine public sources, for multiple organisms.") | |
4242 | (license license:artistic2.0))) | |
4243 | ||
886125d7 RJ |
4244 | (define-public r-motifbreakr |
4245 | (package | |
4246 | (name "r-motifbreakr") | |
e65783e0 | 4247 | (version "2.2.0") |
886125d7 RJ |
4248 | (source (origin |
4249 | (method url-fetch) | |
4250 | (uri (bioconductor-uri "motifbreakR" version)) | |
4251 | (sha256 | |
e65783e0 | 4252 | (base32 "09czgmyjcycsvyvadpjddwwvqvxzd0ba3zhczh4mqc09gwa6vhlm")))) |
886125d7 RJ |
4253 | (properties `((upstream-name . "motifbreakR"))) |
4254 | (build-system r-build-system) | |
4255 | (propagated-inputs | |
e65783e0 RW |
4256 | `(("r-biocgenerics" ,r-biocgenerics) |
4257 | ("r-biocparallel" ,r-biocparallel) | |
886125d7 RJ |
4258 | ("r-biostrings" ,r-biostrings) |
4259 | ("r-bsgenome" ,r-bsgenome) | |
e65783e0 RW |
4260 | ("r-genomeinfodb" ,r-genomeinfodb) |
4261 | ("r-genomicranges" ,r-genomicranges) | |
4262 | ("r-grimport" ,r-grimport) | |
886125d7 | 4263 | ("r-gviz" ,r-gviz) |
e65783e0 | 4264 | ("r-iranges" ,r-iranges) |
886125d7 | 4265 | ("r-matrixstats" ,r-matrixstats) |
e65783e0 RW |
4266 | ("r-motifdb" ,r-motifdb) |
4267 | ("r-motifstack" ,r-motifstack) | |
4268 | ("r-rtracklayer" ,r-rtracklayer) | |
4269 | ("r-s4vectors" ,r-s4vectors) | |
4270 | ("r-stringr" ,r-stringr) | |
4271 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
886125d7 | 4272 | ("r-tfmpvalue" ,r-tfmpvalue) |
e65783e0 RW |
4273 | ("r-variantannotation" ,r-variantannotation))) |
4274 | (native-inputs | |
4275 | `(("r-knitr" ,r-knitr))) | |
886125d7 RJ |
4276 | (home-page "https://www.bioconductor.org/packages/motifbreakR/") |
4277 | (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") | |
4278 | (description "This package allows biologists to judge in the first place | |
4279 | whether the sequence surrounding the polymorphism is a good match, and in | |
4280 | the second place how much information is gained or lost in one allele of | |
4281 | the polymorphism relative to another. This package gives a choice of | |
4282 | algorithms for interrogation of genomes with motifs from public sources: | |
4283 | @enumerate | |
4284 | @item a weighted-sum probability matrix; | |
4285 | @item log-probabilities; | |
4286 | @item weighted by relative entropy. | |
4287 | @end enumerate | |
4288 | ||
4289 | This package can predict effects for novel or previously described variants in | |
4290 | public databases, making it suitable for tasks beyond the scope of its original | |
4291 | design. Lastly, it can be used to interrogate any genome curated within | |
4292 | Bioconductor.") | |
4293 | (license license:gpl2+))) | |
4294 | ||
2a72ef56 RW |
4295 | (define-public r-motifstack |
4296 | (package | |
4297 | (name "r-motifstack") | |
a8840a04 | 4298 | (version "1.32.1") |
2a72ef56 RW |
4299 | (source |
4300 | (origin | |
4301 | (method url-fetch) | |
4302 | (uri (bioconductor-uri "motifStack" version)) | |
4303 | (sha256 | |
4304 | (base32 | |
a8840a04 | 4305 | "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd")))) |
2a72ef56 RW |
4306 | (properties `((upstream-name . "motifStack"))) |
4307 | (build-system r-build-system) | |
4308 | (propagated-inputs | |
4309 | `(("r-ade4" ,r-ade4) | |
4310 | ("r-biostrings" ,r-biostrings) | |
dda936ca | 4311 | ("r-ggplot2" ,r-ggplot2) |
aa0ebfd2 | 4312 | ("r-grimport2" ,r-grimport2) |
2a72ef56 RW |
4313 | ("r-htmlwidgets" ,r-htmlwidgets) |
4314 | ("r-motiv" ,r-motiv) | |
4315 | ("r-scales" ,r-scales) | |
4316 | ("r-xml" ,r-xml))) | |
e6fbaf0c RW |
4317 | (native-inputs |
4318 | `(("r-knitr" ,r-knitr))) | |
2a72ef56 RW |
4319 | (home-page "https://bioconductor.org/packages/motifStack/") |
4320 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") | |
4321 | (description | |
4322 | "The motifStack package is designed for graphic representation of | |
4323 | multiple motifs with different similarity scores. It works with both DNA/RNA | |
4324 | sequence motifs and amino acid sequence motifs. In addition, it provides the | |
4325 | flexibility for users to customize the graphic parameters such as the font | |
4326 | type and symbol colors.") | |
4327 | (license license:gpl2+))) | |
e5bff307 RW |
4328 | |
4329 | (define-public r-genomicscores | |
4330 | (package | |
4331 | (name "r-genomicscores") | |
785c7596 | 4332 | (version "2.0.0") |
e5bff307 RW |
4333 | (source |
4334 | (origin | |
4335 | (method url-fetch) | |
4336 | (uri (bioconductor-uri "GenomicScores" version)) | |
4337 | (sha256 | |
4338 | (base32 | |
785c7596 | 4339 | "0si2lgc37mkah4w990q1q2bf8xmshxj7cbx92bcrp0zaipjr96bb")))) |
e5bff307 RW |
4340 | (properties `((upstream-name . "GenomicScores"))) |
4341 | (build-system r-build-system) | |
4342 | (propagated-inputs | |
4343 | `(("r-annotationhub" ,r-annotationhub) | |
4344 | ("r-biobase" ,r-biobase) | |
4345 | ("r-biocgenerics" ,r-biocgenerics) | |
4346 | ("r-biostrings" ,r-biostrings) | |
785c7596 | 4347 | ("r-delayedarray" ,r-delayedarray) |
e5bff307 RW |
4348 | ("r-genomeinfodb" ,r-genomeinfodb) |
4349 | ("r-genomicranges" ,r-genomicranges) | |
785c7596 | 4350 | ("r-hdf5array" ,r-hdf5array) |
e5bff307 | 4351 | ("r-iranges" ,r-iranges) |
785c7596 | 4352 | ("r-rhdf5" ,r-rhdf5) |
e5bff307 RW |
4353 | ("r-s4vectors" ,r-s4vectors) |
4354 | ("r-xml" ,r-xml))) | |
785c7596 RW |
4355 | (native-inputs |
4356 | `(("r-knitr" ,r-knitr))) | |
e5bff307 RW |
4357 | (home-page "https://github.com/rcastelo/GenomicScores/") |
4358 | (synopsis "Work with genome-wide position-specific scores") | |
4359 | (description | |
4360 | "This package provides infrastructure to store and access genome-wide | |
4361 | position-specific scores within R and Bioconductor.") | |
4362 | (license license:artistic2.0))) | |
32e0f906 RW |
4363 | |
4364 | (define-public r-atacseqqc | |
4365 | (package | |
4366 | (name "r-atacseqqc") | |
60cc8384 | 4367 | (version "1.12.4") |
32e0f906 RW |
4368 | (source |
4369 | (origin | |
4370 | (method url-fetch) | |
4371 | (uri (bioconductor-uri "ATACseqQC" version)) | |
4372 | (sha256 | |
4373 | (base32 | |
60cc8384 | 4374 | "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh")))) |
32e0f906 RW |
4375 | (properties `((upstream-name . "ATACseqQC"))) |
4376 | (build-system r-build-system) | |
4377 | (propagated-inputs | |
4378 | `(("r-biocgenerics" ,r-biocgenerics) | |
4379 | ("r-biostrings" ,r-biostrings) | |
4380 | ("r-bsgenome" ,r-bsgenome) | |
4381 | ("r-chippeakanno" ,r-chippeakanno) | |
bcc233c1 | 4382 | ("r-edger" ,r-edger) |
32e0f906 RW |
4383 | ("r-genomeinfodb" ,r-genomeinfodb) |
4384 | ("r-genomicalignments" ,r-genomicalignments) | |
4385 | ("r-genomicranges" ,r-genomicranges) | |
4386 | ("r-genomicscores" ,r-genomicscores) | |
4387 | ("r-iranges" ,r-iranges) | |
4388 | ("r-kernsmooth" ,r-kernsmooth) | |
4389 | ("r-limma" ,r-limma) | |
4390 | ("r-motifstack" ,r-motifstack) | |
4391 | ("r-preseqr" ,r-preseqr) | |
4392 | ("r-randomforest" ,r-randomforest) | |
4393 | ("r-rsamtools" ,r-rsamtools) | |
4394 | ("r-rtracklayer" ,r-rtracklayer) | |
4395 | ("r-s4vectors" ,r-s4vectors))) | |
dc30cc03 RW |
4396 | (native-inputs |
4397 | `(("r-knitr" ,r-knitr))) | |
32e0f906 RW |
4398 | (home-page "https://bioconductor.org/packages/ATACseqQC/") |
4399 | (synopsis "ATAC-seq quality control") | |
4400 | (description | |
4401 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using | |
4402 | sequencing, is a rapid and sensitive method for chromatin accessibility | |
4403 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq | |
4404 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly | |
4405 | assess whether their ATAC-seq experiment is successful. It includes | |
4406 | diagnostic plots of fragment size distribution, proportion of mitochondria | |
4407 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor | |
4408 | footprints.") | |
4409 | (license license:gpl2+))) | |
3972cfce RW |
4410 | |
4411 | (define-public r-gofuncr | |
4412 | (package | |
4413 | (name "r-gofuncr") | |
19b39ac5 | 4414 | (version "1.8.0") |
3972cfce RW |
4415 | (source |
4416 | (origin | |
4417 | (method url-fetch) | |
4418 | (uri (bioconductor-uri "GOfuncR" version)) | |
4419 | (sha256 | |
4420 | (base32 | |
19b39ac5 | 4421 | "1ixjkqb9wpwqfzxsg0h96c6fa63wrk72sfh6x4pq0kpyrcc0ind1")))) |
3972cfce RW |
4422 | (properties `((upstream-name . "GOfuncR"))) |
4423 | (build-system r-build-system) | |
4424 | (propagated-inputs | |
4425 | `(("r-annotationdbi" ,r-annotationdbi) | |
4426 | ("r-genomicranges" ,r-genomicranges) | |
4427 | ("r-gtools" ,r-gtools) | |
4428 | ("r-iranges" ,r-iranges) | |
4429 | ("r-mapplots" ,r-mapplots) | |
4430 | ("r-rcpp" ,r-rcpp) | |
4431 | ("r-vioplot" ,r-vioplot))) | |
028fd6f7 RW |
4432 | (native-inputs |
4433 | `(("r-knitr" ,r-knitr))) | |
3972cfce RW |
4434 | (home-page "https://bioconductor.org/packages/GOfuncR/") |
4435 | (synopsis "Gene ontology enrichment using FUNC") | |
4436 | (description | |
4437 | "GOfuncR performs a gene ontology enrichment analysis based on the | |
4438 | ontology enrichment software FUNC. GO-annotations are obtained from | |
4439 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is | |
4440 | included in the package and updated regularly. GOfuncR provides the standard | |
4441 | candidate vs background enrichment analysis using the hypergeometric test, as | |
4442 | well as three additional tests: | |
4443 | ||
4444 | @enumerate | |
4445 | @item the Wilcoxon rank-sum test that is used when genes are ranked, | |
4446 | @item a binomial test that is used when genes are associated with two counts, | |
4447 | and | |
4448 | @item a Chi-square or Fisher's exact test that is used in cases when genes are | |
4449 | associated with four counts. | |
4450 | @end enumerate | |
4451 | ||
4452 | To correct for multiple testing and interdependency of the tests, family-wise | |
4453 | error rates are computed based on random permutations of the gene-associated | |
4454 | variables. GOfuncR also provides tools for exploring the ontology graph and | |
4455 | the annotations, and options to take gene-length or spatial clustering of | |
4456 | genes into account. It is also possible to provide custom gene coordinates, | |
4457 | annotations and ontologies.") | |
4458 | (license license:gpl2+))) | |
9bf4bb19 RW |
4459 | |
4460 | (define-public r-abaenrichment | |
4461 | (package | |
4462 | (name "r-abaenrichment") | |
6a65ac15 | 4463 | (version "1.18.0") |
9bf4bb19 RW |
4464 | (source |
4465 | (origin | |
4466 | (method url-fetch) | |
4467 | (uri (bioconductor-uri "ABAEnrichment" version)) | |
4468 | (sha256 | |
4469 | (base32 | |
6a65ac15 | 4470 | "09ihbgxrhpcz2q7svldhm710a0yrhiqk9p0q0myv11c2w50ymwkw")))) |
9bf4bb19 RW |
4471 | (properties `((upstream-name . "ABAEnrichment"))) |
4472 | (build-system r-build-system) | |
4473 | (propagated-inputs | |
4474 | `(("r-abadata" ,r-abadata) | |
4475 | ("r-data-table" ,r-data-table) | |
4476 | ("r-gofuncr" ,r-gofuncr) | |
4477 | ("r-gplots" ,r-gplots) | |
4478 | ("r-gtools" ,r-gtools) | |
4479 | ("r-rcpp" ,r-rcpp))) | |
6a65ac15 RW |
4480 | (native-inputs |
4481 | `(("r-knitr" ,r-knitr))) | |
9bf4bb19 RW |
4482 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") |
4483 | (synopsis "Gene expression enrichment in human brain regions") | |
4484 | (description | |
4485 | "The package ABAEnrichment is designed to test for enrichment of user | |
4486 | defined candidate genes in the set of expressed genes in different human brain | |
4487 | regions. The core function @code{aba_enrich} integrates the expression of the | |
4488 | candidate gene set (averaged across donors) and the structural information of | |
4489 | the brain using an ontology, both provided by the Allen Brain Atlas project.") | |
4490 | (license license:gpl2+))) | |
0b91b7b9 RW |
4491 | |
4492 | (define-public r-annotationfuncs | |
4493 | (package | |
4494 | (name "r-annotationfuncs") | |
7866994c | 4495 | (version "1.38.0") |
0b91b7b9 RW |
4496 | (source |
4497 | (origin | |
4498 | (method url-fetch) | |
4499 | (uri (bioconductor-uri "AnnotationFuncs" version)) | |
4500 | (sha256 | |
4501 | (base32 | |
7866994c | 4502 | "1yfsxzn7s1nlc3xz2yj39j6hmdfapc9qj9h0cd71gkaxj53ial7d")))) |
0b91b7b9 RW |
4503 | (properties |
4504 | `((upstream-name . "AnnotationFuncs"))) | |
4505 | (build-system r-build-system) | |
4506 | (propagated-inputs | |
4507 | `(("r-annotationdbi" ,r-annotationdbi) | |
4508 | ("r-dbi" ,r-dbi))) | |
4509 | (home-page "https://www.iysik.com/r/annotationfuncs") | |
4510 | (synopsis "Annotation translation functions") | |
4511 | (description | |
4512 | "This package provides functions for handling translating between | |
4513 | different identifieres using the Biocore Data Team data-packages (e.g. | |
4514 | @code{org.Bt.eg.db}).") | |
4515 | (license license:gpl2))) | |
adf7d813 RW |
4516 | |
4517 | (define-public r-annotationtools | |
4518 | (package | |
4519 | (name "r-annotationtools") | |
231898d5 | 4520 | (version "1.62.0") |
adf7d813 RW |
4521 | (source |
4522 | (origin | |
4523 | (method url-fetch) | |
4524 | (uri (bioconductor-uri "annotationTools" version)) | |
4525 | (sha256 | |
4526 | (base32 | |
231898d5 | 4527 | "1b1yfnknr9vbn4y2mxdfyx57i5jbabhp9pwx8axlg2a7lawkfmdk")))) |
adf7d813 RW |
4528 | (properties |
4529 | `((upstream-name . "annotationTools"))) | |
4530 | (build-system r-build-system) | |
4531 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4532 | (home-page "https://bioconductor.org/packages/annotationTools/") | |
4533 | (synopsis "Annotate microarrays and perform gene expression analyses") | |
4534 | (description | |
4535 | "This package provides functions to annotate microarrays, find orthologs, | |
4536 | and integrate heterogeneous gene expression profiles using annotation and | |
4537 | other molecular biology information available as flat file database (plain | |
4538 | text files).") | |
4539 | ;; Any version of the GPL. | |
4540 | (license (list license:gpl2+)))) | |
f31e10f8 RW |
4541 | |
4542 | (define-public r-allelicimbalance | |
4543 | (package | |
4544 | (name "r-allelicimbalance") | |
63149388 | 4545 | (version "1.26.0") |
f31e10f8 RW |
4546 | (source |
4547 | (origin | |
4548 | (method url-fetch) | |
4549 | (uri (bioconductor-uri "AllelicImbalance" version)) | |
4550 | (sha256 | |
4551 | (base32 | |
63149388 | 4552 | "0irn4xdlvazdkv0055f45693y6zvqaz7j3vml5xscnh45ls6vmqr")))) |
f31e10f8 RW |
4553 | (properties |
4554 | `((upstream-name . "AllelicImbalance"))) | |
4555 | (build-system r-build-system) | |
4556 | (propagated-inputs | |
4557 | `(("r-annotationdbi" ,r-annotationdbi) | |
4558 | ("r-biocgenerics" ,r-biocgenerics) | |
4559 | ("r-biostrings" ,r-biostrings) | |
4560 | ("r-bsgenome" ,r-bsgenome) | |
4561 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4562 | ("r-genomicalignments" ,r-genomicalignments) | |
4563 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4564 | ("r-genomicranges" ,r-genomicranges) | |
4565 | ("r-gridextra" ,r-gridextra) | |
4566 | ("r-gviz" ,r-gviz) | |
4567 | ("r-iranges" ,r-iranges) | |
4568 | ("r-lattice" ,r-lattice) | |
4569 | ("r-latticeextra" ,r-latticeextra) | |
4570 | ("r-nlme" ,r-nlme) | |
4571 | ("r-rsamtools" ,r-rsamtools) | |
4572 | ("r-s4vectors" ,r-s4vectors) | |
4573 | ("r-seqinr" ,r-seqinr) | |
4574 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
4575 | ("r-variantannotation" ,r-variantannotation))) | |
63149388 RW |
4576 | (native-inputs |
4577 | `(("r-knitr" ,r-knitr))) | |
f31e10f8 RW |
4578 | (home-page "https://github.com/pappewaio/AllelicImbalance") |
4579 | (synopsis "Investigate allele-specific expression") | |
4580 | (description | |
4581 | "This package provides a framework for allele-specific expression | |
4582 | investigation using RNA-seq data.") | |
4583 | (license license:gpl3))) | |
ffe7029b RW |
4584 | |
4585 | (define-public r-aucell | |
4586 | (package | |
4587 | (name "r-aucell") | |
e059ab25 | 4588 | (version "1.10.0") |
ffe7029b RW |
4589 | (source |
4590 | (origin | |
4591 | (method url-fetch) | |
4592 | (uri (bioconductor-uri "AUCell" version)) | |
4593 | (sha256 | |
4594 | (base32 | |
e059ab25 | 4595 | "0fgqkgjhf92vkljkwn44lm8cjvzq1lvk80nk6xhsp5q6s5isbmns")))) |
ffe7029b RW |
4596 | (properties `((upstream-name . "AUCell"))) |
4597 | (build-system r-build-system) | |
4598 | (propagated-inputs | |
3a35d274 RW |
4599 | `(("r-biocgenerics" ,r-biocgenerics) |
4600 | ("r-data-table" ,r-data-table) | |
ffe7029b RW |
4601 | ("r-gseabase" ,r-gseabase) |
4602 | ("r-mixtools" ,r-mixtools) | |
4603 | ("r-r-utils" ,r-r-utils) | |
3a35d274 | 4604 | ("r-s4vectors" ,r-s4vectors) |
ffe7029b RW |
4605 | ("r-shiny" ,r-shiny) |
4606 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
e059ab25 RW |
4607 | (native-inputs |
4608 | `(("r-knitr" ,r-knitr))) | |
ffe7029b RW |
4609 | (home-page "https://bioconductor.org/packages/AUCell/") |
4610 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") | |
4611 | (description | |
8c4bf6c2 | 4612 | "AUCell identifies cells with active gene sets (e.g. signatures, |
ffe7029b RW |
4613 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area |
4614 | Under the Curve} (AUC) to calculate whether a critical subset of the input | |
4615 | gene set is enriched within the expressed genes for each cell. The | |
4616 | distribution of AUC scores across all the cells allows exploring the relative | |
4617 | expression of the signature. Since the scoring method is ranking-based, | |
4618 | AUCell is independent of the gene expression units and the normalization | |
4619 | procedure. In addition, since the cells are evaluated individually, it can | |
4620 | easily be applied to bigger datasets, subsetting the expression matrix if | |
4621 | needed.") | |
4622 | (license license:gpl3))) | |
5cfa4bff RW |
4623 | |
4624 | (define-public r-ebimage | |
4625 | (package | |
4626 | (name "r-ebimage") | |
4eccf8e5 | 4627 | (version "4.30.0") |
5cfa4bff RW |
4628 | (source |
4629 | (origin | |
4630 | (method url-fetch) | |
4631 | (uri (bioconductor-uri "EBImage" version)) | |
4632 | (sha256 | |
4633 | (base32 | |
4eccf8e5 | 4634 | "13amrbh545hwk7sygndzyv7wpa0m2y0lzlwj89jm1xm62x577w9v")))) |
5cfa4bff RW |
4635 | (properties `((upstream-name . "EBImage"))) |
4636 | (build-system r-build-system) | |
4637 | (propagated-inputs | |
4638 | `(("r-abind" ,r-abind) | |
4639 | ("r-biocgenerics" ,r-biocgenerics) | |
4640 | ("r-fftwtools" ,r-fftwtools) | |
4641 | ("r-htmltools" ,r-htmltools) | |
4642 | ("r-htmlwidgets" ,r-htmlwidgets) | |
4643 | ("r-jpeg" ,r-jpeg) | |
4644 | ("r-locfit" ,r-locfit) | |
4645 | ("r-png" ,r-png) | |
4646 | ("r-rcurl" ,r-rcurl) | |
4647 | ("r-tiff" ,r-tiff))) | |
4648 | (native-inputs | |
4649 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
4650 | (home-page "https://github.com/aoles/EBImage") | |
4651 | (synopsis "Image processing and analysis toolbox for R") | |
4652 | (description | |
4653 | "EBImage provides general purpose functionality for image processing and | |
4654 | analysis. In the context of (high-throughput) microscopy-based cellular | |
4655 | assays, EBImage offers tools to segment cells and extract quantitative | |
4656 | cellular descriptors. This allows the automation of such tasks using the R | |
4657 | programming language and facilitates the use of other tools in the R | |
4658 | environment for signal processing, statistical modeling, machine learning and | |
4659 | visualization with image data.") | |
4660 | ;; Any version of the LGPL. | |
4661 | (license license:lgpl2.1+))) | |
51e98f7e RW |
4662 | |
4663 | (define-public r-yamss | |
4664 | (package | |
4665 | (name "r-yamss") | |
6e397aad | 4666 | (version "1.14.0") |
51e98f7e RW |
4667 | (source |
4668 | (origin | |
4669 | (method url-fetch) | |
4670 | (uri (bioconductor-uri "yamss" version)) | |
4671 | (sha256 | |
4672 | (base32 | |
6e397aad | 4673 | "00x2lnssgzbmhy5bb2m0f8rq2nsz3lb5xlp2vhkcagza39h3xb0c")))) |
51e98f7e RW |
4674 | (build-system r-build-system) |
4675 | (propagated-inputs | |
4676 | `(("r-biocgenerics" ,r-biocgenerics) | |
4677 | ("r-data-table" ,r-data-table) | |
4678 | ("r-ebimage" ,r-ebimage) | |
4679 | ("r-iranges" ,r-iranges) | |
4680 | ("r-limma" ,r-limma) | |
4681 | ("r-matrix" ,r-matrix) | |
4682 | ("r-mzr" ,r-mzr) | |
4683 | ("r-s4vectors" ,r-s4vectors) | |
4684 | ("r-summarizedexperiment" | |
4685 | ,r-summarizedexperiment))) | |
6e397aad RW |
4686 | (native-inputs |
4687 | `(("r-knitr" ,r-knitr))) | |
51e98f7e RW |
4688 | (home-page "https://github.com/hansenlab/yamss") |
4689 | (synopsis "Tools for high-throughput metabolomics") | |
4690 | (description | |
4691 | "This package provides tools to analyze and visualize high-throughput | |
9b19734c | 4692 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
51e98f7e RW |
4693 | preprocess data in a way that enables reliable and powerful differential |
4694 | analysis.") | |
4695 | (license license:artistic2.0))) | |
398c4a93 RW |
4696 | |
4697 | (define-public r-gtrellis | |
4698 | (package | |
4699 | (name "r-gtrellis") | |
a471def0 | 4700 | (version "1.20.1") |
398c4a93 RW |
4701 | (source |
4702 | (origin | |
4703 | (method url-fetch) | |
4704 | (uri (bioconductor-uri "gtrellis" version)) | |
4705 | (sha256 | |
4706 | (base32 | |
a471def0 | 4707 | "1v2l7r945xx4cf9s8m19csj7716n2ayxy05adkl8zqgxk0gxzqm1")))) |
398c4a93 RW |
4708 | (build-system r-build-system) |
4709 | (propagated-inputs | |
4710 | `(("r-circlize" ,r-circlize) | |
4711 | ("r-genomicranges" ,r-genomicranges) | |
4712 | ("r-getoptlong" ,r-getoptlong) | |
4713 | ("r-iranges" ,r-iranges))) | |
a471def0 RW |
4714 | (native-inputs |
4715 | `(("r-knitr" ,r-knitr))) | |
398c4a93 RW |
4716 | (home-page "https://github.com/jokergoo/gtrellis") |
4717 | (synopsis "Genome level Trellis layout") | |
4718 | (description | |
4719 | "Genome level Trellis graph visualizes genomic data conditioned by | |
4720 | genomic categories (e.g. chromosomes). For each genomic category, multiple | |
4721 | dimensional data which are represented as tracks describe different features | |
4722 | from different aspects. This package provides high flexibility to arrange | |
4723 | genomic categories and to add self-defined graphics in the plot.") | |
4724 | (license license:expat))) | |
28098414 RW |
4725 | |
4726 | (define-public r-somaticsignatures | |
4727 | (package | |
4728 | (name "r-somaticsignatures") | |
63c14717 | 4729 | (version "2.24.0") |
28098414 RW |
4730 | (source |
4731 | (origin | |
4732 | (method url-fetch) | |
4733 | (uri (bioconductor-uri "SomaticSignatures" version)) | |
4734 | (sha256 | |
4735 | (base32 | |
63c14717 | 4736 | "0d34mss73w1jdnmilk060a1fywlfmqbnlir089q9m3q1p3x0j4c1")))) |
28098414 RW |
4737 | (properties |
4738 | `((upstream-name . "SomaticSignatures"))) | |
4739 | (build-system r-build-system) | |
4740 | (propagated-inputs | |
4741 | `(("r-biobase" ,r-biobase) | |
4742 | ("r-biostrings" ,r-biostrings) | |
4743 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4744 | ("r-genomicranges" ,r-genomicranges) | |
4745 | ("r-ggbio" ,r-ggbio) | |
4746 | ("r-ggplot2" ,r-ggplot2) | |
4747 | ("r-iranges" ,r-iranges) | |
4748 | ("r-nmf" ,r-nmf) | |
4749 | ("r-pcamethods" ,r-pcamethods) | |
4750 | ("r-proxy" ,r-proxy) | |
4751 | ("r-reshape2" ,r-reshape2) | |
4752 | ("r-s4vectors" ,r-s4vectors) | |
4753 | ("r-variantannotation" ,r-variantannotation))) | |
63c14717 RW |
4754 | (native-inputs |
4755 | `(("r-knitr" ,r-knitr))) | |
28098414 RW |
4756 | (home-page "https://github.com/juliangehring/SomaticSignatures") |
4757 | (synopsis "Somatic signatures") | |
4758 | (description | |
4759 | "This package identifies mutational signatures of @dfn{single nucleotide | |
4760 | variants} (SNVs). It provides a infrastructure related to the methodology | |
4761 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix | |
4762 | decomposition algorithms.") | |
4763 | (license license:expat))) | |
303f2ed1 RW |
4764 | |
4765 | (define-public r-yapsa | |
4766 | (package | |
4767 | (name "r-yapsa") | |
8a5abc62 | 4768 | (version "1.14.0") |
303f2ed1 RW |
4769 | (source |
4770 | (origin | |
4771 | (method url-fetch) | |
4772 | (uri (bioconductor-uri "YAPSA" version)) | |
4773 | (sha256 | |
4774 | (base32 | |
8a5abc62 | 4775 | "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k")))) |
303f2ed1 RW |
4776 | (properties `((upstream-name . "YAPSA"))) |
4777 | (build-system r-build-system) | |
4778 | (propagated-inputs | |
8a5abc62 RW |
4779 | `(("r-biostrings" ,r-biostrings) |
4780 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
4781 | ("r-circlize" ,r-circlize) | |
303f2ed1 RW |
4782 | ("r-complexheatmap" ,r-complexheatmap) |
4783 | ("r-corrplot" ,r-corrplot) | |
4784 | ("r-dendextend" ,r-dendextend) | |
8a5abc62 RW |
4785 | ("r-doparallel" ,r-doparallel) |
4786 | ("r-dplyr" ,r-dplyr) | |
303f2ed1 RW |
4787 | ("r-genomeinfodb" ,r-genomeinfodb) |
4788 | ("r-genomicranges" ,r-genomicranges) | |
4789 | ("r-getoptlong" ,r-getoptlong) | |
8a5abc62 | 4790 | ("r-ggbeeswarm" ,r-ggbeeswarm) |
303f2ed1 RW |
4791 | ("r-ggplot2" ,r-ggplot2) |
4792 | ("r-gridextra" ,r-gridextra) | |
4793 | ("r-gtrellis" ,r-gtrellis) | |
4794 | ("r-keggrest" ,r-keggrest) | |
4795 | ("r-lsei" ,r-lsei) | |
8a5abc62 | 4796 | ("r-magrittr" ,r-magrittr) |
303f2ed1 | 4797 | ("r-pmcmr" ,r-pmcmr) |
8a5abc62 | 4798 | ("r-pracma" ,r-pracma) |
303f2ed1 RW |
4799 | ("r-reshape2" ,r-reshape2) |
4800 | ("r-somaticsignatures" ,r-somaticsignatures) | |
4801 | ("r-variantannotation" ,r-variantannotation))) | |
8a5abc62 RW |
4802 | (native-inputs |
4803 | `(("r-knitr" ,r-knitr))) | |
303f2ed1 RW |
4804 | (home-page "https://bioconductor.org/packages/YAPSA/") |
4805 | (synopsis "Yet another package for signature analysis") | |
4806 | (description | |
4807 | "This package provides functions and routines useful in the analysis of | |
4808 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, | |
4809 | functions to perform a signature analysis with known signatures and a | |
4810 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are | |
4811 | provided.") | |
4812 | (license license:gpl3))) | |
e99380d6 RW |
4813 | |
4814 | (define-public r-gcrma | |
4815 | (package | |
4816 | (name "r-gcrma") | |
f0439a17 | 4817 | (version "2.60.0") |
e99380d6 RW |
4818 | (source |
4819 | (origin | |
4820 | (method url-fetch) | |
4821 | (uri (bioconductor-uri "gcrma" version)) | |
4822 | (sha256 | |
4823 | (base32 | |
f0439a17 | 4824 | "1klbnygc1i5ac1x00bsk0rjw5h5dn6pn65fa3y9r09q47gpy1c5g")))) |
e99380d6 RW |
4825 | (build-system r-build-system) |
4826 | (propagated-inputs | |
4827 | `(("r-affy" ,r-affy) | |
4828 | ("r-affyio" ,r-affyio) | |
4829 | ("r-biobase" ,r-biobase) | |
4830 | ("r-biocmanager" ,r-biocmanager) | |
4831 | ("r-biostrings" ,r-biostrings) | |
4832 | ("r-xvector" ,r-xvector))) | |
4833 | (home-page "https://bioconductor.org/packages/gcrma/") | |
4834 | (synopsis "Background adjustment using sequence information") | |
4835 | (description | |
4836 | "Gcrma adjusts for background intensities in Affymetrix array data which | |
4837 | include optical noise and @dfn{non-specific binding} (NSB). The main function | |
4838 | @code{gcrma} converts background adjusted probe intensities to expression | |
4839 | measures using the same normalization and summarization methods as a | |
4840 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information | |
4841 | to estimate probe affinity to NSB. The sequence information is summarized in | |
4842 | a more complex way than the simple GC content. Instead, the base types (A, T, | |
4843 | G or C) at each position along the probe determine the affinity of each probe. | |
4844 | The parameters of the position-specific base contributions to the probe | |
4845 | affinity is estimated in an NSB experiment in which only NSB but no | |
4846 | gene-specific bidning is expected.") | |
4847 | ;; Any version of the LGPL | |
4848 | (license license:lgpl2.1+))) | |
4675b3cf RW |
4849 | |
4850 | (define-public r-simpleaffy | |
4851 | (package | |
4852 | (name "r-simpleaffy") | |
9ce80f93 | 4853 | (version "2.64.0") |
4675b3cf RW |
4854 | (source |
4855 | (origin | |
4856 | (method url-fetch) | |
4857 | (uri (bioconductor-uri "simpleaffy" version)) | |
4858 | (sha256 | |
4859 | (base32 | |
9ce80f93 | 4860 | "040043spblr8v67lkn3nnxhgfmfh2iwaizph4fnms1ik6qz662x7")))) |
4675b3cf RW |
4861 | (build-system r-build-system) |
4862 | (propagated-inputs | |
4863 | `(("r-affy" ,r-affy) | |
4864 | ("r-biobase" ,r-biobase) | |
4865 | ("r-biocgenerics" ,r-biocgenerics) | |
4866 | ("r-gcrma" ,r-gcrma) | |
4867 | ("r-genefilter" ,r-genefilter))) | |
4868 | (home-page "https://bioconductor.org/packages/simpleaffy/") | |
4869 | (synopsis "Very simple high level analysis of Affymetrix data") | |
4870 | (description | |
4871 | "This package provides high level functions for reading Affy @file{.CEL} | |
4872 | files, phenotypic data, and then computing simple things with it, such as | |
4873 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} | |
4874 | library. It also has some basic scatter plot functions and mechanisms for | |
4875 | generating high resolution journal figures.") | |
4876 | (license license:gpl2+))) | |
f562c90a RW |
4877 | |
4878 | (define-public r-yaqcaffy | |
4879 | (package | |
4880 | (name "r-yaqcaffy") | |
761c9427 | 4881 | (version "1.48.0") |
f562c90a RW |
4882 | (source |
4883 | (origin | |
4884 | (method url-fetch) | |
4885 | (uri (bioconductor-uri "yaqcaffy" version)) | |
4886 | (sha256 | |
4887 | (base32 | |
761c9427 | 4888 | "1l0cblh9sfrsil15bjya7d8kkas8bj6klj2w3c4384njdsjsjcf0")))) |
f562c90a RW |
4889 | (build-system r-build-system) |
4890 | (propagated-inputs | |
4891 | `(("r-simpleaffy" ,r-simpleaffy))) | |
4892 | (home-page "https://bioconductor.org/packages/yaqcaffy/") | |
4893 | (synopsis "Affymetrix quality control and reproducibility analysis") | |
4894 | (description | |
4895 | "This is a package that can be used for quality control of Affymetrix | |
4896 | GeneChip expression data and reproducibility analysis of human whole genome | |
4897 | chips with the MAQC reference datasets.") | |
4898 | (license license:artistic2.0))) | |
59cf2629 RW |
4899 | |
4900 | (define-public r-quantro | |
4901 | (package | |
4902 | (name "r-quantro") | |
70d90ae7 | 4903 | (version "1.22.0") |
59cf2629 RW |
4904 | (source |
4905 | (origin | |
4906 | (method url-fetch) | |
4907 | (uri (bioconductor-uri "quantro" version)) | |
4908 | (sha256 | |
4909 | (base32 | |
70d90ae7 | 4910 | "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz")))) |
59cf2629 RW |
4911 | (build-system r-build-system) |
4912 | (propagated-inputs | |
4913 | `(("r-biobase" ,r-biobase) | |
4914 | ("r-doparallel" ,r-doparallel) | |
4915 | ("r-foreach" ,r-foreach) | |
4916 | ("r-ggplot2" ,r-ggplot2) | |
4917 | ("r-iterators" ,r-iterators) | |
4918 | ("r-minfi" ,r-minfi) | |
4919 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
70d90ae7 RW |
4920 | (native-inputs |
4921 | `(("r-knitr" ,r-knitr))) | |
59cf2629 RW |
4922 | (home-page "https://bioconductor.org/packages/quantro/") |
4923 | (synopsis "Test for when to use quantile normalization") | |
4924 | (description | |
4925 | "This package provides a data-driven test for the assumptions of quantile | |
4926 | normalization using raw data such as objects that inherit eSets (e.g. | |
4927 | ExpressionSet, MethylSet). Group level information about each sample (such as | |
4928 | Tumor / Normal status) must also be provided because the test assesses if | |
4929 | there are global differences in the distributions between the user-defined | |
4930 | groups.") | |
4931 | (license license:gpl3+))) | |
98a2af31 RW |
4932 | |
4933 | (define-public r-yarn | |
4934 | (package | |
4935 | (name "r-yarn") | |
a37a6ffb | 4936 | (version "1.14.0") |
98a2af31 RW |
4937 | (source |
4938 | (origin | |
4939 | (method url-fetch) | |
4940 | (uri (bioconductor-uri "yarn" version)) | |
4941 | (sha256 | |
4942 | (base32 | |
a37a6ffb | 4943 | "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx")))) |
98a2af31 RW |
4944 | (build-system r-build-system) |
4945 | (propagated-inputs | |
4946 | `(("r-biobase" ,r-biobase) | |
4947 | ("r-biomart" ,r-biomart) | |
4948 | ("r-downloader" ,r-downloader) | |
4949 | ("r-edger" ,r-edger) | |
4950 | ("r-gplots" ,r-gplots) | |
4951 | ("r-limma" ,r-limma) | |
4952 | ("r-matrixstats" ,r-matrixstats) | |
4953 | ("r-preprocesscore" ,r-preprocesscore) | |
4954 | ("r-quantro" ,r-quantro) | |
4955 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4956 | ("r-readr" ,r-readr))) | |
a37a6ffb RW |
4957 | (native-inputs |
4958 | `(("r-knitr" ,r-knitr))) | |
98a2af31 RW |
4959 | (home-page "https://bioconductor.org/packages/yarn/") |
4960 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") | |
4961 | (description | |
4962 | "Expedite large RNA-Seq analyses using a combination of previously | |
4963 | developed tools. YARN is meant to make it easier for the user in performing | |
4964 | basic mis-annotation quality control, filtering, and condition-aware | |
4965 | normalization. YARN leverages many Bioconductor tools and statistical | |
4966 | techniques to account for the large heterogeneity and sparsity found in very | |
4967 | large RNA-seq experiments.") | |
4968 | (license license:artistic2.0))) | |
a6e1eb1a RW |
4969 | |
4970 | (define-public r-roar | |
4971 | (package | |
4972 | (name "r-roar") | |
1ec10e19 | 4973 | (version "1.24.0") |
a6e1eb1a RW |
4974 | (source |
4975 | (origin | |
4976 | (method url-fetch) | |
4977 | (uri (bioconductor-uri "roar" version)) | |
4978 | (sha256 | |
4979 | (base32 | |
1ec10e19 | 4980 | "069g887migvk70n0377dqr0fk7wjbz3w0asgk42bwhp8xpjfym6f")))) |
a6e1eb1a RW |
4981 | (build-system r-build-system) |
4982 | (propagated-inputs | |
4983 | `(("r-biocgenerics" ,r-biocgenerics) | |
4984 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4985 | ("r-genomicalignments" ,r-genomicalignments) | |
4986 | ("r-genomicranges" ,r-genomicranges) | |
4987 | ("r-iranges" ,r-iranges) | |
4988 | ("r-rtracklayer" ,r-rtracklayer) | |
4989 | ("r-s4vectors" ,r-s4vectors) | |
4990 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
4991 | (home-page "https://github.com/vodkatad/roar/") | |
4992 | (synopsis "Identify differential APA usage from RNA-seq alignments") | |
4993 | (description | |
4994 | "This package provides tools for identifying preferential usage of APA | |
4995 | sites, comparing two biological conditions, starting from known alternative | |
4996 | sites and alignments obtained from standard RNA-seq experiments.") | |
4997 | (license license:gpl3))) | |
50d91770 RW |
4998 | |
4999 | (define-public r-xbseq | |
5000 | (package | |
5001 | (name "r-xbseq") | |
bcd06bdb | 5002 | (version "1.20.0") |
50d91770 RW |
5003 | (source |
5004 | (origin | |
5005 | (method url-fetch) | |
5006 | (uri (bioconductor-uri "XBSeq" version)) | |
5007 | (sha256 | |
5008 | (base32 | |
bcd06bdb | 5009 | "13br7x1q6dg8daxahskwq24f09wbxr8kyszl1z7dhc26bid2pvy0")))) |
50d91770 RW |
5010 | (properties `((upstream-name . "XBSeq"))) |
5011 | (build-system r-build-system) | |
5012 | (propagated-inputs | |
5013 | `(("r-biobase" ,r-biobase) | |
5014 | ("r-deseq2" ,r-deseq2) | |
5015 | ("r-dplyr" ,r-dplyr) | |
5016 | ("r-ggplot2" ,r-ggplot2) | |
5017 | ("r-locfit" ,r-locfit) | |
5018 | ("r-magrittr" ,r-magrittr) | |
5019 | ("r-matrixstats" ,r-matrixstats) | |
5020 | ("r-pracma" ,r-pracma) | |
5021 | ("r-roar" ,r-roar))) | |
bcd06bdb RW |
5022 | (native-inputs |
5023 | `(("r-knitr" ,r-knitr))) | |
50d91770 RW |
5024 | (home-page "https://github.com/Liuy12/XBSeq") |
5025 | (synopsis "Test for differential expression for RNA-seq data") | |
5026 | (description | |
5027 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential | |
5028 | expression} (DE), where a statistical model was established based on the | |
5029 | assumption that observed signals are the convolution of true expression | |
5030 | signals and sequencing noises. The mapped reads in non-exonic regions are | |
5031 | considered as sequencing noises, which follows a Poisson distribution. Given | |
5032 | measurable observed signal and background noise from RNA-seq data, true | |
5033 | expression signals, assuming governed by the negative binomial distribution, | |
5034 | can be delineated and thus the accurate detection of differential expressed | |
5035 | genes.") | |
5036 | (license license:gpl3+))) | |
c8310056 RW |
5037 | |
5038 | (define-public r-massspecwavelet | |
5039 | (package | |
5040 | (name "r-massspecwavelet") | |
11cf2d7b | 5041 | (version "1.54.0") |
c8310056 RW |
5042 | (source |
5043 | (origin | |
5044 | (method url-fetch) | |
5045 | (uri (bioconductor-uri "MassSpecWavelet" version)) | |
5046 | (sha256 | |
5047 | (base32 | |
11cf2d7b | 5048 | "0nv1r68g7f1rps6sqaccd4n4x0i19wklvyabhp4b03cdk22gl3nq")))) |
c8310056 RW |
5049 | (properties |
5050 | `((upstream-name . "MassSpecWavelet"))) | |
5051 | (build-system r-build-system) | |
5052 | (propagated-inputs | |
5053 | `(("r-waveslim" ,r-waveslim))) | |
5054 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") | |
5055 | (synopsis "Mass spectrum processing by wavelet-based algorithms") | |
5056 | (description | |
5057 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) | |
5058 | data mainly through the use of wavelet transforms. It supports peak detection | |
5059 | based on @dfn{Continuous Wavelet Transform} (CWT).") | |
5060 | (license license:lgpl2.0+))) | |
ec12e537 RW |
5061 | |
5062 | (define-public r-xcms | |
5063 | (package | |
5064 | (name "r-xcms") | |
ff9f179a | 5065 | (version "3.10.1") |
ec12e537 RW |
5066 | (source |
5067 | (origin | |
5068 | (method url-fetch) | |
5069 | (uri (bioconductor-uri "xcms" version)) | |
5070 | (sha256 | |
5071 | (base32 | |
ff9f179a | 5072 | "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn")))) |
ec12e537 RW |
5073 | (build-system r-build-system) |
5074 | (propagated-inputs | |
5075 | `(("r-biobase" ,r-biobase) | |
5076 | ("r-biocgenerics" ,r-biocgenerics) | |
5077 | ("r-biocparallel" ,r-biocparallel) | |
4fb52345 | 5078 | ("r-iranges" ,r-iranges) |
ec12e537 RW |
5079 | ("r-lattice" ,r-lattice) |
5080 | ("r-massspecwavelet" ,r-massspecwavelet) | |
5081 | ("r-msnbase" ,r-msnbase) | |
ec12e537 RW |
5082 | ("r-mzr" ,r-mzr) |
5083 | ("r-plyr" ,r-plyr) | |
5084 | ("r-protgenerics" ,r-protgenerics) | |
5085 | ("r-rann" ,r-rann) | |
5086 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5087 | ("r-robustbase" ,r-robustbase) | |
ff9f179a RW |
5088 | ("r-s4vectors" ,r-s4vectors) |
5089 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5090 | (native-inputs | |
5091 | `(("r-knitr" ,r-knitr))) | |
ec12e537 RW |
5092 | (home-page "https://bioconductor.org/packages/xcms/") |
5093 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") | |
5094 | (description | |
5095 | "This package provides a framework for processing and visualization of | |
5096 | chromatographically separated and single-spectra mass spectral data. It | |
5097 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses | |
5098 | data for high-throughput, untargeted analyte profiling.") | |
5099 | (license license:gpl2+))) | |
8830664d RW |
5100 | |
5101 | (define-public r-wrench | |
5102 | (package | |
5103 | (name "r-wrench") | |
996f07b5 | 5104 | (version "1.6.0") |
8830664d RW |
5105 | (source |
5106 | (origin | |
5107 | (method url-fetch) | |
5108 | (uri (bioconductor-uri "Wrench" version)) | |
5109 | (sha256 | |
5110 | (base32 | |
996f07b5 | 5111 | "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6")))) |
8830664d RW |
5112 | (properties `((upstream-name . "Wrench"))) |
5113 | (build-system r-build-system) | |
5114 | (propagated-inputs | |
5115 | `(("r-limma" ,r-limma) | |
5116 | ("r-locfit" ,r-locfit) | |
5117 | ("r-matrixstats" ,r-matrixstats))) | |
996f07b5 RW |
5118 | (native-inputs |
5119 | `(("r-knitr" ,r-knitr))) | |
8830664d RW |
5120 | (home-page "https://github.com/HCBravoLab/Wrench") |
5121 | (synopsis "Wrench normalization for sparse count data") | |
5122 | (description | |
5123 | "Wrench is a package for normalization sparse genomic count data, like | |
5124 | that arising from 16s metagenomic surveys.") | |
5125 | (license license:artistic2.0))) | |
b9b8b447 RW |
5126 | |
5127 | (define-public r-wiggleplotr | |
5128 | (package | |
5129 | (name "r-wiggleplotr") | |
015ff0bf | 5130 | (version "1.12.1") |
b9b8b447 RW |
5131 | (source |
5132 | (origin | |
5133 | (method url-fetch) | |
5134 | (uri (bioconductor-uri "wiggleplotr" version)) | |
5135 | (sha256 | |
5136 | (base32 | |
015ff0bf | 5137 | "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp")))) |
b9b8b447 RW |
5138 | (build-system r-build-system) |
5139 | (propagated-inputs | |
5140 | `(("r-assertthat" ,r-assertthat) | |
5141 | ("r-cowplot" ,r-cowplot) | |
5142 | ("r-dplyr" ,r-dplyr) | |
5143 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5144 | ("r-genomicranges" ,r-genomicranges) | |
5145 | ("r-ggplot2" ,r-ggplot2) | |
5146 | ("r-iranges" ,r-iranges) | |
5147 | ("r-purrr" ,r-purrr) | |
5148 | ("r-rtracklayer" ,r-rtracklayer) | |
5149 | ("r-s4vectors" ,r-s4vectors))) | |
ee0f7460 RW |
5150 | (native-inputs |
5151 | `(("r-knitr" ,r-knitr))) | |
b9b8b447 RW |
5152 | (home-page "https://bioconductor.org/packages/wiggleplotr/") |
5153 | (synopsis "Make read coverage plots from BigWig files") | |
5154 | (description | |
5155 | "This package provides tools to visualize read coverage from sequencing | |
5156 | experiments together with genomic annotations (genes, transcripts, peaks). | |
5157 | Introns of long transcripts can be rescaled to a fixed length for better | |
5158 | visualization of exonic read coverage.") | |
5159 | (license license:asl2.0))) | |
7b5101c5 RW |
5160 | |
5161 | (define-public r-widgettools | |
5162 | (package | |
5163 | (name "r-widgettools") | |
08c4d314 | 5164 | (version "1.66.0") |
7b5101c5 RW |
5165 | (source |
5166 | (origin | |
5167 | (method url-fetch) | |
5168 | (uri (bioconductor-uri "widgetTools" version)) | |
5169 | (sha256 | |
5170 | (base32 | |
08c4d314 | 5171 | "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx")))) |
7b5101c5 RW |
5172 | (properties `((upstream-name . "widgetTools"))) |
5173 | (build-system r-build-system) | |
5174 | (home-page "https://bioconductor.org/packages/widgetTools/") | |
5175 | (synopsis "Tools for creating interactive tcltk widgets") | |
5176 | (description | |
337bdc17 | 5177 | "This package contains tools to support the construction of tcltk |
7b5101c5 RW |
5178 | widgets in R.") |
5179 | ;; Any version of the LGPL. | |
5180 | (license license:lgpl3+))) | |
6b12f213 RW |
5181 | |
5182 | (define-public r-webbioc | |
5183 | (package | |
5184 | (name "r-webbioc") | |
620cc4d9 | 5185 | (version "1.60.0") |
6b12f213 RW |
5186 | (source |
5187 | (origin | |
5188 | (method url-fetch) | |
5189 | (uri (bioconductor-uri "webbioc" version)) | |
5190 | (sha256 | |
5191 | (base32 | |
620cc4d9 | 5192 | "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f")))) |
6b12f213 RW |
5193 | (build-system r-build-system) |
5194 | (inputs | |
5195 | `(("netpbm" ,netpbm) | |
5196 | ("perl" ,perl))) | |
5197 | (propagated-inputs | |
5198 | `(("r-affy" ,r-affy) | |
5199 | ("r-annaffy" ,r-annaffy) | |
5200 | ("r-biobase" ,r-biobase) | |
5201 | ("r-biocmanager" ,r-biocmanager) | |
5202 | ("r-gcrma" ,r-gcrma) | |
5203 | ("r-multtest" ,r-multtest) | |
5204 | ("r-qvalue" ,r-qvalue) | |
5205 | ("r-vsn" ,r-vsn))) | |
5206 | (home-page "https://www.bioconductor.org/") | |
5207 | (synopsis "Bioconductor web interface") | |
5208 | (description | |
5209 | "This package provides an integrated web interface for doing microarray | |
5210 | analysis using several of the Bioconductor packages. It is intended to be | |
5211 | deployed as a centralized bioinformatics resource for use by many users. | |
5212 | Currently only Affymetrix oligonucleotide analysis is supported.") | |
5213 | (license license:gpl2+))) | |
9800d859 RW |
5214 | |
5215 | (define-public r-zfpkm | |
5216 | (package | |
5217 | (name "r-zfpkm") | |
8fdca89b | 5218 | (version "1.10.0") |
9800d859 RW |
5219 | (source |
5220 | (origin | |
5221 | (method url-fetch) | |
5222 | (uri (bioconductor-uri "zFPKM" version)) | |
5223 | (sha256 | |
5224 | (base32 | |
8fdca89b | 5225 | "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys")))) |
9800d859 RW |
5226 | (properties `((upstream-name . "zFPKM"))) |
5227 | (build-system r-build-system) | |
5228 | (propagated-inputs | |
5229 | `(("r-checkmate" ,r-checkmate) | |
5230 | ("r-dplyr" ,r-dplyr) | |
5231 | ("r-ggplot2" ,r-ggplot2) | |
5232 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
5233 | ("r-tidyr" ,r-tidyr))) | |
8fdca89b RW |
5234 | (native-inputs |
5235 | `(("r-knitr" ,r-knitr))) | |
9800d859 RW |
5236 | (home-page "https://github.com/ronammar/zFPKM/") |
5237 | (synopsis "Functions to facilitate zFPKM transformations") | |
5238 | (description | |
5239 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. | |
5240 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID | |
5241 | 24215113).") | |
5242 | (license license:gpl3))) | |
2bdc88fc RW |
5243 | |
5244 | (define-public r-rbowtie2 | |
5245 | (package | |
5246 | (name "r-rbowtie2") | |
82cb9a99 | 5247 | (version "1.10.1") |
2bdc88fc RW |
5248 | (source |
5249 | (origin | |
5250 | (method url-fetch) | |
5251 | (uri (bioconductor-uri "Rbowtie2" version)) | |
5252 | (sha256 | |
5253 | (base32 | |
82cb9a99 | 5254 | "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7")))) |
2bdc88fc RW |
5255 | (properties `((upstream-name . "Rbowtie2"))) |
5256 | (build-system r-build-system) | |
5257 | (inputs | |
5258 | `(("zlib" ,zlib))) | |
297854e6 RW |
5259 | (native-inputs |
5260 | `(("r-knitr" ,r-knitr))) | |
2bdc88fc RW |
5261 | (home-page "https://bioconductor.org/packages/Rbowtie2/") |
5262 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") | |
5263 | (description | |
5264 | "This package provides an R wrapper of the popular @code{bowtie2} | |
5265 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for | |
5266 | rapid adapter trimming, identification, and read merging.") | |
5267 | (license license:gpl3+))) | |
5622628f RW |
5268 | |
5269 | (define-public r-progeny | |
5270 | (package | |
5271 | (name "r-progeny") | |
8e5933a8 | 5272 | (version "1.10.0") |
5622628f RW |
5273 | (source |
5274 | (origin | |
5275 | (method url-fetch) | |
5276 | (uri (bioconductor-uri "progeny" version)) | |
5277 | (sha256 | |
5278 | (base32 | |
8e5933a8 | 5279 | "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh")))) |
5622628f | 5280 | (build-system r-build-system) |
8e5933a8 RW |
5281 | (propagated-inputs |
5282 | `(("r-biobase" ,r-biobase) | |
5283 | ("r-dplyr" ,r-dplyr) | |
5284 | ("r-ggplot2" ,r-ggplot2) | |
5285 | ("r-ggrepel" ,r-ggrepel) | |
5286 | ("r-gridextra" ,r-gridextra) | |
5287 | ("r-tidyr" ,r-tidyr))) | |
5288 | (native-inputs | |
5289 | `(("r-knitr" ,r-knitr))) | |
5622628f RW |
5290 | (home-page "https://github.com/saezlab/progeny") |
5291 | (synopsis "Pathway responsive gene activity inference") | |
5292 | (description | |
5293 | "This package provides a function to infer pathway activity from gene | |
5294 | expression. It contains the linear model inferred in the publication | |
5295 | \"Perturbation-response genes reveal signaling footprints in cancer gene | |
5296 | expression\".") | |
5297 | (license license:asl2.0))) | |
307586c1 RW |
5298 | |
5299 | (define-public r-arrmnormalization | |
5300 | (package | |
5301 | (name "r-arrmnormalization") | |
989b7bb6 | 5302 | (version "1.28.0") |
307586c1 RW |
5303 | (source |
5304 | (origin | |
5305 | (method url-fetch) | |
5306 | (uri (bioconductor-uri "ARRmNormalization" version)) | |
5307 | (sha256 | |
5308 | (base32 | |
989b7bb6 | 5309 | "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv")))) |
307586c1 RW |
5310 | (properties |
5311 | `((upstream-name . "ARRmNormalization"))) | |
5312 | (build-system r-build-system) | |
5313 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) | |
5314 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") | |
5315 | (synopsis "Adaptive robust regression normalization for methylation data") | |
5316 | (description | |
5317 | "This is a package to perform the @dfn{Adaptive Robust Regression | |
5318 | method} (ARRm) for the normalization of methylation data from the Illumina | |
5319 | Infinium HumanMethylation 450k assay.") | |
5320 | (license license:artistic2.0))) | |
fbf34949 RW |
5321 | |
5322 | (define-public r-biocfilecache | |
5323 | (package | |
5324 | (name "r-biocfilecache") | |
4a504b80 | 5325 | (version "1.12.1") |
fbf34949 RW |
5326 | (source |
5327 | (origin | |
5328 | (method url-fetch) | |
5329 | (uri (bioconductor-uri "BiocFileCache" version)) | |
5330 | (sha256 | |
5331 | (base32 | |
4a504b80 | 5332 | "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf")))) |
fbf34949 RW |
5333 | (properties `((upstream-name . "BiocFileCache"))) |
5334 | (build-system r-build-system) | |
5335 | (propagated-inputs | |
5336 | `(("r-curl" ,r-curl) | |
5337 | ("r-dbi" ,r-dbi) | |
5338 | ("r-dbplyr" ,r-dbplyr) | |
5339 | ("r-dplyr" ,r-dplyr) | |
5340 | ("r-httr" ,r-httr) | |
5341 | ("r-rappdirs" ,r-rappdirs) | |
5342 | ("r-rsqlite" ,r-rsqlite))) | |
173844fc RW |
5343 | (native-inputs |
5344 | `(("r-knitr" ,r-knitr))) | |
fbf34949 RW |
5345 | (home-page "https://bioconductor.org/packages/BiocFileCache/") |
5346 | (synopsis "Manage files across sessions") | |
5347 | (description | |
5348 | "This package creates a persistent on-disk cache of files that the user | |
5349 | can add, update, and retrieve. It is useful for managing resources (such as | |
5350 | custom Txdb objects) that are costly or difficult to create, web resources, | |
5351 | and data files used across sessions.") | |
5352 | (license license:artistic2.0))) | |
8c42f8f6 RW |
5353 | |
5354 | (define-public r-iclusterplus | |
5355 | (package | |
5356 | (name "r-iclusterplus") | |
ca8d80c9 | 5357 | (version "1.24.0") |
8c42f8f6 RW |
5358 | (source |
5359 | (origin | |
5360 | (method url-fetch) | |
5361 | (uri (bioconductor-uri "iClusterPlus" version)) | |
5362 | (sha256 | |
5363 | (base32 | |
ca8d80c9 | 5364 | "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w")))) |
8c42f8f6 RW |
5365 | (properties `((upstream-name . "iClusterPlus"))) |
5366 | (build-system r-build-system) | |
5367 | (native-inputs `(("gfortran" ,gfortran))) | |
5368 | (home-page "https://bioconductor.org/packages/iClusterPlus/") | |
5369 | (synopsis "Integrative clustering of multi-type genomic data") | |
5370 | (description | |
5371 | "iClusterPlus is developed for integrative clustering analysis of | |
5372 | multi-type genomic data and is an enhanced version of iCluster proposed and | |
5373 | developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise | |
5374 | from the experiments where biological samples (e.g. tumor samples) are | |
5375 | analyzed by multiple techniques, for instance, @dfn{array comparative genomic | |
5376 | hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so | |
5377 | on. In the iClusterPlus model, binary observations such as somatic mutation | |
5378 | are modeled as Binomial processes; categorical observations such as copy | |
5379 | number states are realizations of Multinomial random variables; counts are | |
5380 | modeled as Poisson random processes; and continuous measures are modeled by | |
5381 | Gaussian distributions.") | |
5382 | (license license:gpl2+))) | |
4d06ef4b RW |
5383 | |
5384 | (define-public r-rbowtie | |
5385 | (package | |
5386 | (name "r-rbowtie") | |
a20538ab | 5387 | (version "1.28.1") |
4d06ef4b RW |
5388 | (source |
5389 | (origin | |
5390 | (method url-fetch) | |
5391 | (uri (bioconductor-uri "Rbowtie" version)) | |
5392 | (sha256 | |
5393 | (base32 | |
a20538ab | 5394 | "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3")))) |
4d06ef4b RW |
5395 | (properties `((upstream-name . "Rbowtie"))) |
5396 | (build-system r-build-system) | |
5397 | (inputs | |
5398 | `(("zlib" ,zlib))) | |
568c3929 RW |
5399 | (native-inputs |
5400 | `(("r-knitr" ,r-knitr))) | |
4d06ef4b RW |
5401 | (home-page "https://bioconductor.org/packages/Rbowtie/") |
5402 | (synopsis "R bowtie wrapper") | |
5403 | (description | |
5404 | "This package provides an R wrapper around the popular bowtie short read | |
5405 | aligner and around SpliceMap, a de novo splice junction discovery and | |
5406 | alignment tool.") | |
5407 | (license license:artistic2.0))) | |
14441539 RW |
5408 | |
5409 | (define-public r-sgseq | |
5410 | (package | |
5411 | (name "r-sgseq") | |
201902bc | 5412 | (version "1.22.0") |
14441539 RW |
5413 | (source |
5414 | (origin | |
5415 | (method url-fetch) | |
5416 | (uri (bioconductor-uri "SGSeq" version)) | |
5417 | (sha256 | |
5418 | (base32 | |
201902bc | 5419 | "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c")))) |
14441539 RW |
5420 | (properties `((upstream-name . "SGSeq"))) |
5421 | (build-system r-build-system) | |
5422 | (propagated-inputs | |
5423 | `(("r-annotationdbi" ,r-annotationdbi) | |
5424 | ("r-biocgenerics" ,r-biocgenerics) | |
5425 | ("r-biostrings" ,r-biostrings) | |
5426 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5427 | ("r-genomicalignments" ,r-genomicalignments) | |
5428 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5429 | ("r-genomicranges" ,r-genomicranges) | |
5430 | ("r-igraph" ,r-igraph) | |
5431 | ("r-iranges" ,r-iranges) | |
5432 | ("r-rsamtools" ,r-rsamtools) | |
5433 | ("r-rtracklayer" ,r-rtracklayer) | |
5434 | ("r-runit" ,r-runit) | |
5435 | ("r-s4vectors" ,r-s4vectors) | |
5436 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
201902bc RW |
5437 | (native-inputs |
5438 | `(("r-knitr" ,r-knitr))) | |
14441539 RW |
5439 | (home-page "https://bioconductor.org/packages/SGSeq/") |
5440 | (synopsis "Splice event prediction and quantification from RNA-seq data") | |
5441 | (description | |
5442 | "SGSeq is a package for analyzing splice events from RNA-seq data. Input | |
5443 | data are RNA-seq reads mapped to a reference genome in BAM format. Genes are | |
5444 | represented as a splice graph, which can be obtained from existing annotation | |
5445 | or predicted from the mapped sequence reads. Splice events are identified | |
5446 | from the graph and are quantified locally using structurally compatible reads | |
5447 | at the start or end of each splice variant. The software includes functions | |
5448 | for splice event prediction, quantification, visualization and | |
5449 | interpretation.") | |
5450 | (license license:artistic2.0))) | |
58656064 RW |
5451 | |
5452 | (define-public r-rhisat2 | |
5453 | (package | |
5454 | (name "r-rhisat2") | |
2aff2724 | 5455 | (version "1.4.0") |
58656064 RW |
5456 | (source |
5457 | (origin | |
5458 | (method url-fetch) | |
5459 | (uri (bioconductor-uri "Rhisat2" version)) | |
5460 | (sha256 | |
5461 | (base32 | |
2aff2724 | 5462 | "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a")))) |
58656064 RW |
5463 | (properties `((upstream-name . "Rhisat2"))) |
5464 | (build-system r-build-system) | |
3dd2450e RW |
5465 | (arguments |
5466 | `(#:phases | |
5467 | (modify-phases %standard-phases | |
5468 | (add-after 'unpack 'make-reproducible | |
5469 | (lambda _ | |
5470 | (substitute* "src/Makefile" | |
5471 | (("`hostname`") "guix") | |
5472 | (("`date`") "0") | |
5473 | ;; Avoid shelling out to "which". | |
5474 | (("^CC =.*") (which "gcc")) | |
5475 | (("^CPP =.*") (which "g++"))) | |
5476 | #t))))) | |
58656064 RW |
5477 | (propagated-inputs |
5478 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
5479 | ("r-genomicranges" ,r-genomicranges) | |
5480 | ("r-sgseq" ,r-sgseq))) | |
2aff2724 RW |
5481 | (native-inputs |
5482 | `(("r-knitr" ,r-knitr))) | |
58656064 RW |
5483 | (home-page "https://github.com/fmicompbio/Rhisat2") |
5484 | (synopsis "R Wrapper for HISAT2 sequence aligner") | |
5485 | (description | |
5486 | "This package provides an R interface to the HISAT2 spliced short-read | |
5487 | aligner by Kim et al. (2015). The package contains wrapper functions to | |
5488 | create a genome index and to perform the read alignment to the generated | |
5489 | index.") | |
5490 | (license license:gpl3))) | |
5e0241db RW |
5491 | |
5492 | (define-public r-quasr | |
5493 | (package | |
5494 | (name "r-quasr") | |
a84abf43 | 5495 | (version "1.28.0") |
5e0241db RW |
5496 | (source |
5497 | (origin | |
5498 | (method url-fetch) | |
5499 | (uri (bioconductor-uri "QuasR" version)) | |
5500 | (sha256 | |
5501 | (base32 | |
a84abf43 | 5502 | "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8")))) |
5e0241db RW |
5503 | (properties `((upstream-name . "QuasR"))) |
5504 | (build-system r-build-system) | |
5505 | (inputs | |
5506 | `(("zlib" ,zlib))) | |
5507 | (propagated-inputs | |
5508 | `(("r-annotationdbi" ,r-annotationdbi) | |
5509 | ("r-biobase" ,r-biobase) | |
5510 | ("r-biocgenerics" ,r-biocgenerics) | |
5511 | ("r-biocmanager" ,r-biocmanager) | |
5512 | ("r-biocparallel" ,r-biocparallel) | |
5513 | ("r-biostrings" ,r-biostrings) | |
5514 | ("r-bsgenome" ,r-bsgenome) | |
5515 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5516 | ("r-genomicalignments" ,r-genomicalignments) | |
5517 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5518 | ("r-genomicfiles" ,r-genomicfiles) | |
5519 | ("r-genomicranges" ,r-genomicranges) | |
5520 | ("r-iranges" ,r-iranges) | |
5521 | ("r-rbowtie" ,r-rbowtie) | |
5522 | ("r-rhisat2" ,r-rhisat2) | |
5523 | ("r-rhtslib" ,r-rhtslib) | |
5524 | ("r-rsamtools" ,r-rsamtools) | |
5525 | ("r-rtracklayer" ,r-rtracklayer) | |
5526 | ("r-s4vectors" ,r-s4vectors) | |
5527 | ("r-shortread" ,r-shortread))) | |
a84abf43 RW |
5528 | (native-inputs |
5529 | `(("r-knitr" ,r-knitr))) | |
5e0241db RW |
5530 | (home-page "https://bioconductor.org/packages/QuasR/") |
5531 | (synopsis "Quantify and annotate short reads in R") | |
5532 | (description | |
5533 | "This package provides a framework for the quantification and analysis of | |
5534 | short genomic reads. It covers a complete workflow starting from raw sequence | |
5535 | reads, over creation of alignments and quality control plots, to the | |
5536 | quantification of genomic regions of interest.") | |
5537 | (license license:gpl2))) | |
496b024f RW |
5538 | |
5539 | (define-public r-rqc | |
5540 | (package | |
5541 | (name "r-rqc") | |
1c5360ac | 5542 | (version "1.22.0") |
496b024f RW |
5543 | (source |
5544 | (origin | |
5545 | (method url-fetch) | |
5546 | (uri (bioconductor-uri "Rqc" version)) | |
5547 | (sha256 | |
5548 | (base32 | |
1c5360ac | 5549 | "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3")))) |
496b024f RW |
5550 | (properties `((upstream-name . "Rqc"))) |
5551 | (build-system r-build-system) | |
5552 | (propagated-inputs | |
5553 | `(("r-biocgenerics" ,r-biocgenerics) | |
5554 | ("r-biocparallel" ,r-biocparallel) | |
5555 | ("r-biocstyle" ,r-biocstyle) | |
5556 | ("r-biostrings" ,r-biostrings) | |
5557 | ("r-biovizbase" ,r-biovizbase) | |
5558 | ("r-genomicalignments" ,r-genomicalignments) | |
5559 | ("r-genomicfiles" ,r-genomicfiles) | |
5560 | ("r-ggplot2" ,r-ggplot2) | |
5561 | ("r-iranges" ,r-iranges) | |
5562 | ("r-knitr" ,r-knitr) | |
5563 | ("r-markdown" ,r-markdown) | |
5564 | ("r-plyr" ,r-plyr) | |
5565 | ("r-rcpp" ,r-rcpp) | |
5566 | ("r-reshape2" ,r-reshape2) | |
5567 | ("r-rsamtools" ,r-rsamtools) | |
5568 | ("r-s4vectors" ,r-s4vectors) | |
5569 | ("r-shiny" ,r-shiny) | |
5570 | ("r-shortread" ,r-shortread))) | |
1c5360ac RW |
5571 | (native-inputs |
5572 | `(("r-knitr" ,r-knitr))) | |
496b024f RW |
5573 | (home-page "https://github.com/labbcb/Rqc") |
5574 | (synopsis "Quality control tool for high-throughput sequencing data") | |
5575 | (description | |
5576 | "Rqc is an optimized tool designed for quality control and assessment of | |
5577 | high-throughput sequencing data. It performs parallel processing of entire | |
5578 | files and produces a report which contains a set of high-resolution | |
5579 | graphics.") | |
5580 | (license license:gpl2+))) | |
81e3de01 RW |
5581 | |
5582 | (define-public r-birewire | |
5583 | (package | |
5584 | (name "r-birewire") | |
f50609ab | 5585 | (version "3.20.0") |
81e3de01 RW |
5586 | (source |
5587 | (origin | |
5588 | (method url-fetch) | |
5589 | (uri (bioconductor-uri "BiRewire" version)) | |
5590 | (sha256 | |
5591 | (base32 | |
f50609ab | 5592 | "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g")))) |
81e3de01 RW |
5593 | (properties `((upstream-name . "BiRewire"))) |
5594 | (build-system r-build-system) | |
5595 | (propagated-inputs | |
5596 | `(("r-igraph" ,r-igraph) | |
5597 | ("r-matrix" ,r-matrix) | |
5598 | ("r-slam" ,r-slam) | |
5599 | ("r-tsne" ,r-tsne))) | |
5600 | (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") | |
5601 | (synopsis "Tools for randomization of bipartite graphs") | |
5602 | (description | |
5603 | "This package provides functions for bipartite network rewiring through N | |
5604 | consecutive switching steps and for the computation of the minimal number of | |
5605 | switching steps to be performed in order to maximise the dissimilarity with | |
5606 | respect to the original network. It includes functions for the analysis of | |
5607 | the introduced randomness across the switching steps and several other | |
5608 | routines to analyse the resulting networks and their natural projections.") | |
5609 | (license license:gpl3))) | |
1a24f855 RW |
5610 | |
5611 | (define-public r-birta | |
5612 | (package | |
5613 | (name "r-birta") | |
cb941ca0 | 5614 | (version "1.31.0") |
1a24f855 RW |
5615 | (source |
5616 | (origin | |
5617 | (method url-fetch) | |
5618 | (uri (bioconductor-uri "birta" version)) | |
5619 | (sha256 | |
5620 | (base32 | |
cb941ca0 | 5621 | "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) |
1a24f855 RW |
5622 | (build-system r-build-system) |
5623 | (propagated-inputs | |
5624 | `(("r-biobase" ,r-biobase) | |
5625 | ("r-limma" ,r-limma) | |
5626 | ("r-mass" ,r-mass))) | |
5627 | (home-page "https://bioconductor.org/packages/birta") | |
5628 | (synopsis "Bayesian inference of regulation of transcriptional activity") | |
5629 | (description | |
5630 | "Expression levels of mRNA molecules are regulated by different | |
5631 | processes, comprising inhibition or activation by transcription factors and | |
5632 | post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian | |
5633 | Inference of Regulation of Transcriptional Activity) uses the regulatory | |
5634 | networks of transcription factors and miRNAs together with mRNA and miRNA | |
5635 | expression data to predict switches in regulatory activity between two | |
5636 | conditions. A Bayesian network is used to model the regulatory structure and | |
5637 | Markov-Chain-Monte-Carlo is applied to sample the activity states.") | |
5638 | (license license:gpl2+))) | |
a9fac3f4 | 5639 | |
b4a22cca RW |
5640 | (define-public r-multidataset |
5641 | (package | |
5642 | (name "r-multidataset") | |
905bbb13 | 5643 | (version "1.16.0") |
b4a22cca RW |
5644 | (source |
5645 | (origin | |
5646 | (method url-fetch) | |
5647 | (uri (bioconductor-uri "MultiDataSet" version)) | |
5648 | (sha256 | |
5649 | (base32 | |
905bbb13 | 5650 | "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39")))) |
b4a22cca RW |
5651 | (properties `((upstream-name . "MultiDataSet"))) |
5652 | (build-system r-build-system) | |
5653 | (propagated-inputs | |
5654 | `(("r-biobase" ,r-biobase) | |
5655 | ("r-biocgenerics" ,r-biocgenerics) | |
5656 | ("r-genomicranges" ,r-genomicranges) | |
5657 | ("r-ggplot2" ,r-ggplot2) | |
5658 | ("r-ggrepel" ,r-ggrepel) | |
5659 | ("r-iranges" ,r-iranges) | |
5660 | ("r-limma" ,r-limma) | |
5661 | ("r-qqman" ,r-qqman) | |
5662 | ("r-s4vectors" ,r-s4vectors) | |
5663 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
905bbb13 RW |
5664 | (native-inputs |
5665 | `(("r-knitr" ,r-knitr))) | |
b4a22cca RW |
5666 | (home-page "https://bioconductor.org/packages/MultiDataSet/") |
5667 | (synopsis "Implementation of MultiDataSet and ResultSet") | |
5668 | (description | |
5669 | "This package provides an implementation of the BRGE's (Bioinformatic | |
5670 | Research Group in Epidemiology from Center for Research in Environmental | |
5671 | Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for | |
5672 | integrating multi omics data sets and ResultSet is a container for omics | |
5673 | results. This package contains base classes for MEAL and rexposome | |
5674 | packages.") | |
5675 | (license license:expat))) | |
5676 | ||
a9fac3f4 RW |
5677 | (define-public r-ropls |
5678 | (package | |
5679 | (name "r-ropls") | |
77334168 | 5680 | (version "1.20.0") |
a9fac3f4 RW |
5681 | (source |
5682 | (origin | |
5683 | (method url-fetch) | |
5684 | (uri (bioconductor-uri "ropls" version)) | |
5685 | (sha256 | |
5686 | (base32 | |
77334168 | 5687 | "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx")))) |
a9fac3f4 | 5688 | (build-system r-build-system) |
643aaf7e RW |
5689 | (propagated-inputs |
5690 | `(("r-biobase" ,r-biobase) | |
5691 | ("r-multidataset" ,r-multidataset))) | |
a9fac3f4 RW |
5692 | (native-inputs |
5693 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
5694 | (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") | |
5695 | (synopsis "Multivariate analysis and feature selection of omics data") | |
5696 | (description | |
5697 | "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) | |
5698 | and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, | |
5699 | regression, classification, and feature selection of omics data where the | |
5700 | number of variables exceeds the number of samples and with multicollinearity | |
5701 | among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to | |
5702 | separately model the variation correlated (predictive) to the factor of | |
5703 | interest and the uncorrelated (orthogonal) variation. While performing | |
5704 | similarly to PLS, OPLS facilitates interpretation. | |
5705 | ||
5706 | This package provides imlementations of PCA, PLS, and OPLS for multivariate | |
5707 | analysis and feature selection of omics data. In addition to scores, loadings | |
5708 | and weights plots, the package provides metrics and graphics to determine the | |
5709 | optimal number of components (e.g. with the R2 and Q2 coefficients), check the | |
5710 | validity of the model by permutation testing, detect outliers, and perform | |
5711 | feature selection (e.g. with Variable Importance in Projection or regression | |
5712 | coefficients).") | |
5713 | (license license:cecill))) | |
075a9094 RW |
5714 | |
5715 | (define-public r-biosigner | |
5716 | (package | |
5717 | (name "r-biosigner") | |
8b6f26e6 | 5718 | (version "1.16.0") |
075a9094 RW |
5719 | (source |
5720 | (origin | |
5721 | (method url-fetch) | |
5722 | (uri (bioconductor-uri "biosigner" version)) | |
5723 | (sha256 | |
5724 | (base32 | |
8b6f26e6 | 5725 | "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06")))) |
075a9094 RW |
5726 | (build-system r-build-system) |
5727 | (propagated-inputs | |
5728 | `(("r-biobase" ,r-biobase) | |
5729 | ("r-e1071" ,r-e1071) | |
7d29dc9c | 5730 | ("r-multidataset" ,r-multidataset) |
075a9094 RW |
5731 | ("r-randomforest" ,r-randomforest) |
5732 | ("r-ropls" ,r-ropls))) | |
5733 | (native-inputs | |
f7100eda | 5734 | `(("r-knitr" ,r-knitr))) |
075a9094 RW |
5735 | (home-page "https://bioconductor.org/packages/biosigner/") |
5736 | (synopsis "Signature discovery from omics data") | |
5737 | (description | |
5738 | "Feature selection is critical in omics data analysis to extract | |
5739 | restricted and meaningful molecular signatures from complex and high-dimension | |
5740 | data, and to build robust classifiers. This package implements a method to | |
5741 | assess the relevance of the variables for the prediction performances of the | |
5742 | classifier. The approach can be run in parallel with the PLS-DA, Random | |
5743 | Forest, and SVM binary classifiers. The signatures and the corresponding | |
5744 | 'restricted' models are returned, enabling future predictions on new | |
5745 | datasets.") | |
5746 | (license license:cecill))) | |
ae6fa185 RW |
5747 | |
5748 | (define-public r-annotatr | |
5749 | (package | |
5750 | (name "r-annotatr") | |
5ca991bf | 5751 | (version "1.14.0") |
ae6fa185 RW |
5752 | (source |
5753 | (origin | |
5754 | (method url-fetch) | |
5755 | (uri (bioconductor-uri "annotatr" version)) | |
5756 | (sha256 | |
5757 | (base32 | |
5ca991bf | 5758 | "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl")))) |
ae6fa185 RW |
5759 | (build-system r-build-system) |
5760 | (propagated-inputs | |
5761 | `(("r-annotationdbi" ,r-annotationdbi) | |
5762 | ("r-annotationhub" ,r-annotationhub) | |
5763 | ("r-dplyr" ,r-dplyr) | |
5764 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5765 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5766 | ("r-genomicranges" ,r-genomicranges) | |
5767 | ("r-ggplot2" ,r-ggplot2) | |
5768 | ("r-iranges" ,r-iranges) | |
5769 | ("r-readr" ,r-readr) | |
5770 | ("r-regioner" ,r-regioner) | |
5771 | ("r-reshape2" ,r-reshape2) | |
5772 | ("r-rtracklayer" ,r-rtracklayer) | |
5773 | ("r-s4vectors" ,r-s4vectors))) | |
5ca991bf RW |
5774 | (native-inputs |
5775 | `(("r-knitr" ,r-knitr))) | |
ae6fa185 RW |
5776 | (home-page "https://bioconductor.org/packages/annotatr/") |
5777 | (synopsis "Annotation of genomic regions to genomic annotations") | |
5778 | (description | |
5779 | "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, | |
5780 | differentially methylated CpGs or regions, SNPs, etc.) it is often of interest | |
5781 | to investigate the intersecting genomic annotations. Such annotations include | |
5782 | those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), | |
5783 | CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as | |
5784 | enhancers. The annotatr package provides an easy way to summarize and | |
5785 | visualize the intersection of genomic sites/regions with genomic | |
5786 | annotations.") | |
5787 | (license license:gpl3))) | |
2cb738a6 RW |
5788 | |
5789 | (define-public r-rsubread | |
5790 | (package | |
5791 | (name "r-rsubread") | |
1bf63066 | 5792 | (version "2.2.6") |
2cb738a6 RW |
5793 | (source |
5794 | (origin | |
5795 | (method url-fetch) | |
5796 | (uri (bioconductor-uri "Rsubread" version)) | |
5797 | (sha256 | |
5798 | (base32 | |
1bf63066 | 5799 | "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm")))) |
2cb738a6 RW |
5800 | (properties `((upstream-name . "Rsubread"))) |
5801 | (build-system r-build-system) | |
5802 | (inputs `(("zlib" ,zlib))) | |
5d63f69b RW |
5803 | (propagated-inputs |
5804 | `(("r-matrix" ,r-matrix))) | |
2cb738a6 RW |
5805 | (home-page "https://bioconductor.org/packages/Rsubread/") |
5806 | (synopsis "Subread sequence alignment and counting for R") | |
5807 | (description | |
5808 | "This package provides tools for alignment, quantification and analysis | |
5809 | of second and third generation sequencing data. It includes functionality for | |
5810 | read mapping, read counting, SNP calling, structural variant detection and | |
5811 | gene fusion discovery. It can be applied to all major sequencing techologies | |
5812 | and to both short and long sequence reads.") | |
5813 | (license license:gpl3))) | |
a6fedf1f | 5814 | |
a0422d18 | 5815 | (define-public r-flowutils |
5816 | (package | |
5817 | (name "r-flowutils") | |
6954950f | 5818 | (version "1.52.0") |
a0422d18 | 5819 | (source |
5820 | (origin | |
5821 | (method url-fetch) | |
5822 | (uri (bioconductor-uri "flowUtils" version)) | |
5823 | (sha256 | |
5824 | (base32 | |
6954950f | 5825 | "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4")))) |
a0422d18 | 5826 | (properties `((upstream-name . "flowUtils"))) |
5827 | (build-system r-build-system) | |
5828 | (propagated-inputs | |
5829 | `(("r-biobase" ,r-biobase) | |
5830 | ("r-corpcor" ,r-corpcor) | |
5831 | ("r-flowcore" ,r-flowcore) | |
5832 | ("r-graph" ,r-graph) | |
5833 | ("r-runit" ,r-runit) | |
5834 | ("r-xml" ,r-xml))) | |
5835 | (home-page "https://github.com/jspidlen/flowUtils") | |
5836 | (synopsis "Utilities for flow cytometry") | |
5837 | (description | |
5838 | "This package provides utilities for flow cytometry data.") | |
5839 | (license license:artistic2.0))) | |
5840 | ||
ed6f49fc | 5841 | (define-public r-consensusclusterplus |
5842 | (package | |
5843 | (name "r-consensusclusterplus") | |
0c2573e7 | 5844 | (version "1.52.0") |
ed6f49fc | 5845 | (source |
5846 | (origin | |
5847 | (method url-fetch) | |
5848 | (uri (bioconductor-uri "ConsensusClusterPlus" version)) | |
5849 | (sha256 | |
5850 | (base32 | |
0c2573e7 | 5851 | "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq")))) |
ed6f49fc | 5852 | (properties |
5853 | `((upstream-name . "ConsensusClusterPlus"))) | |
5854 | (build-system r-build-system) | |
5855 | (propagated-inputs | |
5856 | `(("r-all" ,r-all) | |
5857 | ("r-biobase" ,r-biobase) | |
5858 | ("r-cluster" ,r-cluster))) | |
5859 | (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") | |
5860 | (synopsis "Clustering algorithm") | |
5861 | (description | |
5862 | "This package provides an implementation of an algorithm for determining | |
5863 | cluster count and membership by stability evidence in unsupervised analysis.") | |
5864 | (license license:gpl2))) | |
5865 | ||
b4aee31d RW |
5866 | (define-public r-cytolib |
5867 | (package | |
5868 | (name "r-cytolib") | |
3c73d7c5 | 5869 | (version "2.0.3") |
b4aee31d RW |
5870 | (source |
5871 | (origin | |
5872 | (method url-fetch) | |
5873 | (uri (bioconductor-uri "cytolib" version)) | |
5874 | (sha256 | |
5875 | (base32 | |
3c73d7c5 | 5876 | "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj")))) |
b4aee31d RW |
5877 | (properties `((upstream-name . "cytolib"))) |
5878 | (build-system r-build-system) | |
3c73d7c5 RW |
5879 | (inputs |
5880 | `(("zlib" ,zlib))) | |
5881 | (native-inputs | |
5882 | `(("r-knitr" ,r-knitr))) | |
5883 | (propagated-inputs | |
5884 | `(("r-bh" ,r-bh) | |
5885 | ("r-rcpp" ,r-rcpp) | |
5886 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
5887 | ("r-rcppparallel" ,r-rcppparallel) | |
5888 | ("r-rhdf5lib" ,r-rhdf5lib) | |
5889 | ("r-rprotobuflib" ,r-rprotobuflib))) | |
b4aee31d RW |
5890 | (home-page "https://bioconductor.org/packages/cytolib/") |
5891 | (synopsis "C++ infrastructure for working with gated cytometry") | |
5892 | (description | |
5893 | "This package provides the core data structure and API to represent and | |
5894 | interact with gated cytometry data.") | |
5895 | (license license:artistic2.0))) | |
5896 | ||
a6fedf1f | 5897 | (define-public r-flowcore |
5898 | (package | |
5899 | (name "r-flowcore") | |
faff2de0 | 5900 | (version "2.0.1") |
a6fedf1f | 5901 | (source |
5902 | (origin | |
5903 | (method url-fetch) | |
5904 | (uri (bioconductor-uri "flowCore" version)) | |
5905 | (sha256 | |
5906 | (base32 | |
faff2de0 | 5907 | "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p")))) |
a6fedf1f | 5908 | (properties `((upstream-name . "flowCore"))) |
5909 | (build-system r-build-system) | |
5910 | (propagated-inputs | |
5911 | `(("r-bh" ,r-bh) | |
5912 | ("r-biobase" ,r-biobase) | |
5913 | ("r-biocgenerics" ,r-biocgenerics) | |
b2a2f321 | 5914 | ("r-cytolib" ,r-cytolib) |
a6fedf1f | 5915 | ("r-matrixstats" ,r-matrixstats) |
faff2de0 RW |
5916 | ("r-rcpp" ,r-rcpp) |
5917 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
5918 | ("r-rprotobuflib" ,r-rprotobuflib))) | |
5919 | (native-inputs | |
5920 | `(("r-knitr" ,r-knitr))) | |
a6fedf1f | 5921 | (home-page "https://bioconductor.org/packages/flowCore") |
5922 | (synopsis "Basic structures for flow cytometry data") | |
5923 | (description | |
5924 | "This package provides S4 data structures and basic functions to deal | |
5925 | with flow cytometry data.") | |
5926 | (license license:artistic2.0))) | |
e0cb053e | 5927 | |
5928 | (define-public r-flowmeans | |
5929 | (package | |
5930 | (name "r-flowmeans") | |
76b163d6 | 5931 | (version "1.48.0") |
e0cb053e | 5932 | (source |
5933 | (origin | |
5934 | (method url-fetch) | |
5935 | (uri (bioconductor-uri "flowMeans" version)) | |
5936 | (sha256 | |
5937 | (base32 | |
76b163d6 | 5938 | "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7")))) |
e0cb053e | 5939 | (properties `((upstream-name . "flowMeans"))) |
5940 | (build-system r-build-system) | |
5941 | (propagated-inputs | |
5942 | `(("r-biobase" ,r-biobase) | |
5943 | ("r-feature" ,r-feature) | |
5944 | ("r-flowcore" ,r-flowcore) | |
5945 | ("r-rrcov" ,r-rrcov))) | |
5946 | (home-page "https://bioconductor.org/packages/flowMeans") | |
5947 | (synopsis "Non-parametric flow cytometry data gating") | |
5948 | (description | |
5949 | "This package provides tools to identify cell populations in Flow | |
5950 | Cytometry data using non-parametric clustering and segmented-regression-based | |
5951 | change point detection.") | |
5952 | (license license:artistic2.0))) | |
1502751b | 5953 | |
15ac0c19 RW |
5954 | (define-public r-ncdfflow |
5955 | (package | |
5956 | (name "r-ncdfflow") | |
631b12ca | 5957 | (version "2.34.0") |
15ac0c19 RW |
5958 | (source |
5959 | (origin | |
5960 | (method url-fetch) | |
5961 | (uri (bioconductor-uri "ncdfFlow" version)) | |
5962 | (sha256 | |
5963 | (base32 | |
631b12ca | 5964 | "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f")))) |
15ac0c19 RW |
5965 | (properties `((upstream-name . "ncdfFlow"))) |
5966 | (build-system r-build-system) | |
5967 | (inputs | |
5968 | `(("zlib" ,zlib))) | |
5969 | (propagated-inputs | |
5970 | `(("r-bh" ,r-bh) | |
5971 | ("r-biobase" ,r-biobase) | |
5972 | ("r-biocgenerics" ,r-biocgenerics) | |
5973 | ("r-flowcore" ,r-flowcore) | |
5974 | ("r-rcpp" ,r-rcpp) | |
5975 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
5976 | ("r-rhdf5lib" ,r-rhdf5lib) | |
5977 | ("r-zlibbioc" ,r-zlibbioc))) | |
631b12ca RW |
5978 | (native-inputs |
5979 | `(("r-knitr" ,r-knitr))) | |
15ac0c19 RW |
5980 | (home-page "https://bioconductor.org/packages/ncdfFlow/") |
5981 | (synopsis "HDF5 based storage for flow cytometry data") | |
5982 | (description | |
5983 | "This package provides HDF5 storage based methods and functions for | |
5984 | manipulation of flow cytometry data.") | |
5985 | (license license:artistic2.0))) | |
5986 | ||
f5f44031 RW |
5987 | (define-public r-ggcyto |
5988 | (package | |
5989 | (name "r-ggcyto") | |
3407dfa6 | 5990 | (version "1.16.0") |
f5f44031 RW |
5991 | (source |
5992 | (origin | |
5993 | (method url-fetch) | |
5994 | (uri (bioconductor-uri "ggcyto" version)) | |
5995 | (sha256 | |
5996 | (base32 | |
3407dfa6 | 5997 | "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0")))) |
f5f44031 RW |
5998 | (properties `((upstream-name . "ggcyto"))) |
5999 | (build-system r-build-system) | |
6000 | (propagated-inputs | |
6001 | `(("r-data-table" ,r-data-table) | |
6002 | ("r-flowcore" ,r-flowcore) | |
6003 | ("r-flowworkspace" ,r-flowworkspace) | |
6004 | ("r-ggplot2" ,r-ggplot2) | |
6005 | ("r-gridextra" ,r-gridextra) | |
3407dfa6 | 6006 | ("r-hexbin" ,r-hexbin) |
f5f44031 RW |
6007 | ("r-ncdfflow" ,r-ncdfflow) |
6008 | ("r-plyr" ,r-plyr) | |
6009 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6010 | ("r-rlang" ,r-rlang) | |
6011 | ("r-scales" ,r-scales))) | |
0754fefb RW |
6012 | (native-inputs |
6013 | `(("r-knitr" ,r-knitr))) | |
f5f44031 RW |
6014 | (home-page "https://github.com/RGLab/ggcyto/issues") |
6015 | (synopsis "Visualize Cytometry data with ggplot") | |
6016 | (description | |
6017 | "With the dedicated fortify method implemented for @code{flowSet}, | |
6018 | @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow | |
6019 | cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper | |
6020 | and some custom layers also make it easy to add gates and population | |
6021 | statistics to the plot.") | |
6022 | (license license:artistic2.0))) | |
6023 | ||
0dd4b7d7 RW |
6024 | (define-public r-flowviz |
6025 | (package | |
6026 | (name "r-flowviz") | |
062789b8 | 6027 | (version "1.52.0") |
0dd4b7d7 RW |
6028 | (source |
6029 | (origin | |
6030 | (method url-fetch) | |
6031 | (uri (bioconductor-uri "flowViz" version)) | |
6032 | (sha256 | |
6033 | (base32 | |
062789b8 | 6034 | "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq")))) |
0dd4b7d7 RW |
6035 | (properties `((upstream-name . "flowViz"))) |
6036 | (build-system r-build-system) | |
6037 | (propagated-inputs | |
6038 | `(("r-biobase" ,r-biobase) | |
6039 | ("r-flowcore" ,r-flowcore) | |
6040 | ("r-hexbin" ,r-hexbin) | |
6041 | ("r-idpmisc" ,r-idpmisc) | |
6042 | ("r-kernsmooth" ,r-kernsmooth) | |
6043 | ("r-lattice" ,r-lattice) | |
6044 | ("r-latticeextra" ,r-latticeextra) | |
6045 | ("r-mass" ,r-mass) | |
6046 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
062789b8 RW |
6047 | (native-inputs |
6048 | `(("r-knitr" ,r-knitr))) | |
0dd4b7d7 RW |
6049 | (home-page "https://bioconductor.org/packages/flowViz/") |
6050 | (synopsis "Visualization for flow cytometry") | |
6051 | (description | |
6052 | "This package provides visualization tools for flow cytometry data.") | |
6053 | (license license:artistic2.0))) | |
6054 | ||
c8ab9eb1 RW |
6055 | (define-public r-flowclust |
6056 | (package | |
6057 | (name "r-flowclust") | |
b347d6c3 | 6058 | (version "3.26.0") |
c8ab9eb1 RW |
6059 | (source |
6060 | (origin | |
6061 | (method url-fetch) | |
6062 | (uri (bioconductor-uri "flowClust" version)) | |
6063 | (sha256 | |
6064 | (base32 | |
b347d6c3 | 6065 | "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b")))) |
c8ab9eb1 RW |
6066 | (properties `((upstream-name . "flowClust"))) |
6067 | (build-system r-build-system) | |
6068 | (arguments | |
6069 | `(#:configure-flags | |
6070 | (list "--configure-args=--enable-bundled-gsl=no"))) | |
6071 | (propagated-inputs | |
6072 | `(("r-biobase" ,r-biobase) | |
6073 | ("r-biocgenerics" ,r-biocgenerics) | |
6074 | ("r-clue" ,r-clue) | |
6075 | ("r-corpcor" ,r-corpcor) | |
6076 | ("r-ellipse" ,r-ellipse) | |
6077 | ("r-flowcore" ,r-flowcore) | |
6078 | ("r-flowviz" ,r-flowviz) | |
6079 | ("r-graph" ,r-graph) | |
6080 | ("r-mnormt" ,r-mnormt))) | |
6081 | (inputs | |
6082 | `(("gsl" ,gsl))) | |
6083 | (native-inputs | |
b347d6c3 RW |
6084 | `(("pkg-config" ,pkg-config) |
6085 | ("r-knitr" ,r-knitr))) | |
c8ab9eb1 RW |
6086 | (home-page "https://bioconductor.org/packages/flowClust") |
6087 | (synopsis "Clustering for flow cytometry") | |
6088 | (description | |
6089 | "This package provides robust model-based clustering using a t-mixture | |
6090 | model with Box-Cox transformation.") | |
6091 | (license license:artistic2.0))) | |
6092 | ||
f1964519 RW |
6093 | ;; TODO: this package bundles an old version of protobuf. It's not easy to |
6094 | ;; make it use our protobuf package instead. | |
6095 | (define-public r-rprotobuflib | |
6096 | (package | |
6097 | (name "r-rprotobuflib") | |
bafade83 | 6098 | (version "2.0.0") |
f1964519 RW |
6099 | (source |
6100 | (origin | |
6101 | (method url-fetch) | |
6102 | (uri (bioconductor-uri "RProtoBufLib" version)) | |
6103 | (sha256 | |
6104 | (base32 | |
bafade83 | 6105 | "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps")))) |
f1964519 RW |
6106 | (properties `((upstream-name . "RProtoBufLib"))) |
6107 | (build-system r-build-system) | |
6108 | (arguments | |
6109 | `(#:phases | |
6110 | (modify-phases %standard-phases | |
6111 | (add-after 'unpack 'unpack-bundled-sources | |
6112 | (lambda _ | |
6113 | (with-directory-excursion "src" | |
bafade83 | 6114 | (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) |
f1964519 | 6115 | #t))))) |
bafade83 RW |
6116 | (native-inputs |
6117 | `(("r-knitr" ,r-knitr))) | |
f1964519 RW |
6118 | (home-page "https://bioconductor.org/packages/RProtoBufLib/") |
6119 | (synopsis "C++ headers and static libraries of Protocol buffers") | |
6120 | (description | |
6121 | "This package provides the headers and static library of Protocol buffers | |
6122 | for other R packages to compile and link against.") | |
6123 | (license license:bsd-3))) | |
6124 | ||
82c11117 RW |
6125 | (define-public r-flowworkspace |
6126 | (package | |
6127 | (name "r-flowworkspace") | |
214ee827 | 6128 | (version "4.0.6") |
82c11117 RW |
6129 | (source |
6130 | (origin | |
6131 | (method url-fetch) | |
6132 | (uri (bioconductor-uri "flowWorkspace" version)) | |
6133 | (sha256 | |
6134 | (base32 | |
214ee827 | 6135 | "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v")))) |
82c11117 RW |
6136 | (properties `((upstream-name . "flowWorkspace"))) |
6137 | (build-system r-build-system) | |
6138 | (propagated-inputs | |
6139 | `(("r-bh" ,r-bh) | |
6140 | ("r-biobase" ,r-biobase) | |
6141 | ("r-biocgenerics" ,r-biocgenerics) | |
6142 | ("r-cytolib" ,r-cytolib) | |
6143 | ("r-data-table" ,r-data-table) | |
6144 | ("r-digest" ,r-digest) | |
6145 | ("r-dplyr" ,r-dplyr) | |
6146 | ("r-flowcore" ,r-flowcore) | |
a9af09df | 6147 | ("r-ggplot2" ,r-ggplot2) |
82c11117 | 6148 | ("r-graph" ,r-graph) |
82c11117 RW |
6149 | ("r-lattice" ,r-lattice) |
6150 | ("r-latticeextra" ,r-latticeextra) | |
6151 | ("r-matrixstats" ,r-matrixstats) | |
6152 | ("r-ncdfflow" ,r-ncdfflow) | |
6153 | ("r-rbgl" ,r-rbgl) | |
82c11117 | 6154 | ("r-rcpp" ,r-rcpp) |
a9af09df | 6155 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
82c11117 RW |
6156 | ("r-rcppparallel" ,r-rcppparallel) |
6157 | ("r-rgraphviz" ,r-rgraphviz) | |
a9af09df | 6158 | ("r-rhdf5lib" ,r-rhdf5lib) |
82c11117 RW |
6159 | ("r-rprotobuflib" ,r-rprotobuflib) |
6160 | ("r-scales" ,r-scales) | |
a9af09df RW |
6161 | ("r-stringr" ,r-stringr) |
6162 | ("r-xml" ,r-xml))) | |
6163 | (native-inputs | |
6164 | `(("r-knitr" ,r-knitr))) | |
82c11117 RW |
6165 | (home-page "https://bioconductor.org/packages/flowWorkspace/") |
6166 | (synopsis "Infrastructure for working with cytometry data") | |
6167 | (description | |
6168 | "This package is designed to facilitate comparison of automated gating | |
6169 | methods against manual gating done in flowJo. This package allows you to | |
6170 | import basic flowJo workspaces into BioConductor and replicate the gating from | |
6171 | flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of | |
6172 | samples, compensation, and transformation are performed so that the output | |
6173 | matches the flowJo analysis.") | |
6174 | (license license:artistic2.0))) | |
6175 | ||
b700b9ec RW |
6176 | (define-public r-flowstats |
6177 | (package | |
6178 | (name "r-flowstats") | |
372caae6 | 6179 | (version "4.0.0") |
b700b9ec RW |
6180 | (source |
6181 | (origin | |
6182 | (method url-fetch) | |
6183 | (uri (bioconductor-uri "flowStats" version)) | |
6184 | (sha256 | |
6185 | (base32 | |
372caae6 | 6186 | "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir")))) |
b700b9ec RW |
6187 | (properties `((upstream-name . "flowStats"))) |
6188 | (build-system r-build-system) | |
6189 | (propagated-inputs | |
6190 | `(("r-biobase" ,r-biobase) | |
6191 | ("r-biocgenerics" ,r-biocgenerics) | |
6192 | ("r-cluster" ,r-cluster) | |
6193 | ("r-fda" ,r-fda) | |
6194 | ("r-flowcore" ,r-flowcore) | |
6195 | ("r-flowviz" ,r-flowviz) | |
6196 | ("r-flowworkspace" ,r-flowworkspace) | |
6197 | ("r-kernsmooth" ,r-kernsmooth) | |
6198 | ("r-ks" ,r-ks) | |
6199 | ("r-lattice" ,r-lattice) | |
6200 | ("r-mass" ,r-mass) | |
6201 | ("r-ncdfflow" ,r-ncdfflow) | |
6202 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6203 | ("r-rrcov" ,r-rrcov))) | |
6204 | (home-page "http://www.github.com/RGLab/flowStats") | |
6205 | (synopsis "Statistical methods for the analysis of flow cytometry data") | |
6206 | (description | |
6207 | "This package provides methods and functionality to analyze flow data | |
6208 | that is beyond the basic infrastructure provided by the @code{flowCore} | |
6209 | package.") | |
6210 | (license license:artistic2.0))) | |
6211 | ||
6aedc805 RW |
6212 | (define-public r-opencyto |
6213 | (package | |
6214 | (name "r-opencyto") | |
8f5e1674 | 6215 | (version "2.0.0") |
6aedc805 RW |
6216 | (source |
6217 | (origin | |
6218 | (method url-fetch) | |
6219 | (uri (bioconductor-uri "openCyto" version)) | |
6220 | (sha256 | |
6221 | (base32 | |
8f5e1674 | 6222 | "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m")))) |
6aedc805 RW |
6223 | (properties `((upstream-name . "openCyto"))) |
6224 | (build-system r-build-system) | |
6225 | (propagated-inputs | |
6226 | `(("r-biobase" ,r-biobase) | |
6227 | ("r-biocgenerics" ,r-biocgenerics) | |
6228 | ("r-clue" ,r-clue) | |
6229 | ("r-data-table" ,r-data-table) | |
6230 | ("r-flowclust" ,r-flowclust) | |
6231 | ("r-flowcore" ,r-flowcore) | |
6232 | ("r-flowstats" ,r-flowstats) | |
6233 | ("r-flowviz" ,r-flowviz) | |
6234 | ("r-flowworkspace" ,r-flowworkspace) | |
6235 | ("r-graph" ,r-graph) | |
6236 | ("r-gtools" ,r-gtools) | |
6237 | ("r-ks" ,r-ks) | |
6238 | ("r-lattice" ,r-lattice) | |
6239 | ("r-mass" ,r-mass) | |
6240 | ("r-ncdfflow" ,r-ncdfflow) | |
6241 | ("r-plyr" ,r-plyr) | |
6242 | ("r-r-utils" ,r-r-utils) | |
6243 | ("r-rbgl" ,r-rbgl) | |
6244 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6245 | ("r-rcpp" ,r-rcpp) | |
6246 | ("r-rrcov" ,r-rrcov))) | |
8f5e1674 RW |
6247 | (native-inputs |
6248 | `(("r-knitr" ,r-knitr))) | |
6aedc805 RW |
6249 | (home-page "https://bioconductor.org/packages/openCyto") |
6250 | (synopsis "Hierarchical gating pipeline for flow cytometry data") | |
6251 | (description | |
6252 | "This package is designed to facilitate the automated gating methods in a | |
6253 | sequential way to mimic the manual gating strategy.") | |
6254 | (license license:artistic2.0))) | |
6255 | ||
7a62d5e0 RW |
6256 | (define-public r-cytoml |
6257 | (package | |
6258 | (name "r-cytoml") | |
ef588757 | 6259 | (version "2.0.5") |
7a62d5e0 RW |
6260 | (source |
6261 | (origin | |
6262 | (method url-fetch) | |
6263 | (uri (bioconductor-uri "CytoML" version)) | |
6264 | (sha256 | |
6265 | (base32 | |
ef588757 | 6266 | "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n")))) |
7a62d5e0 RW |
6267 | (properties `((upstream-name . "CytoML"))) |
6268 | (build-system r-build-system) | |
6269 | (inputs | |
6270 | `(("libxml2" ,libxml2))) | |
6271 | (propagated-inputs | |
6272 | `(("r-base64enc" ,r-base64enc) | |
6273 | ("r-bh" ,r-bh) | |
6274 | ("r-biobase" ,r-biobase) | |
6275 | ("r-corpcor" ,r-corpcor) | |
6276 | ("r-cytolib" ,r-cytolib) | |
6277 | ("r-data-table" ,r-data-table) | |
6278 | ("r-dplyr" ,r-dplyr) | |
6279 | ("r-flowcore" ,r-flowcore) | |
6280 | ("r-flowworkspace" ,r-flowworkspace) | |
6281 | ("r-ggcyto" ,r-ggcyto) | |
6282 | ("r-graph" ,r-graph) | |
6283 | ("r-jsonlite" ,r-jsonlite) | |
6284 | ("r-lattice" ,r-lattice) | |
7a62d5e0 RW |
6285 | ("r-opencyto" ,r-opencyto) |
6286 | ("r-plyr" ,r-plyr) | |
6287 | ("r-rbgl" ,r-rbgl) | |
6288 | ("r-rcpp" ,r-rcpp) | |
8d5a83b7 | 6289 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
7a62d5e0 RW |
6290 | ("r-rcppparallel" ,r-rcppparallel) |
6291 | ("r-rgraphviz" ,r-rgraphviz) | |
8d5a83b7 | 6292 | ("r-rhdf5lib" ,r-rhdf5lib) |
7a62d5e0 RW |
6293 | ("r-rprotobuflib" ,r-rprotobuflib) |
6294 | ("r-runit" ,r-runit) | |
8d5a83b7 | 6295 | ("r-tibble" ,r-tibble) |
7a62d5e0 | 6296 | ("r-xml" ,r-xml) |
ef588757 | 6297 | ("r-xml2" ,r-xml2) |
7a62d5e0 | 6298 | ("r-yaml" ,r-yaml))) |
d49e3f01 RW |
6299 | (native-inputs |
6300 | `(("r-knitr" ,r-knitr))) | |
7a62d5e0 RW |
6301 | (home-page "https://github.com/RGLab/CytoML") |
6302 | (synopsis "GatingML interface for cross platform cytometry data sharing") | |
6303 | (description | |
6304 | "This package provides an interface to implementations of the GatingML2.0 | |
6305 | standard to exchange gated cytometry data with other software platforms.") | |
6306 | (license license:artistic2.0))) | |
6307 | ||
1502751b | 6308 | (define-public r-flowsom |
6309 | (package | |
6310 | (name "r-flowsom") | |
32bd0295 | 6311 | (version "1.20.0") |
1502751b | 6312 | (source |
6313 | (origin | |
6314 | (method url-fetch) | |
6315 | (uri (bioconductor-uri "FlowSOM" version)) | |
6316 | (sha256 | |
6317 | (base32 | |
32bd0295 | 6318 | "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78")))) |
1502751b | 6319 | (properties `((upstream-name . "FlowSOM"))) |
6320 | (build-system r-build-system) | |
6321 | (propagated-inputs | |
6322 | `(("r-biocgenerics" ,r-biocgenerics) | |
6323 | ("r-consensusclusterplus" ,r-consensusclusterplus) | |
ba71567a | 6324 | ("r-cytoml" ,r-cytoml) |
1502751b | 6325 | ("r-flowcore" ,r-flowcore) |
ba71567a | 6326 | ("r-flowworkspace" ,r-flowworkspace) |
1502751b | 6327 | ("r-igraph" ,r-igraph) |
ba71567a | 6328 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
1502751b | 6329 | ("r-tsne" ,r-tsne) |
6330 | ("r-xml" ,r-xml))) | |
6331 | (home-page "https://bioconductor.org/packages/FlowSOM/") | |
6332 | (synopsis "Visualize and interpret cytometry data") | |
6333 | (description | |
6334 | "FlowSOM offers visualization options for cytometry data, by using | |
6335 | self-organizing map clustering and minimal spanning trees.") | |
6336 | (license license:gpl2+))) | |
1adb9cbc | 6337 | |
6338 | (define-public r-mixomics | |
6339 | (package | |
6340 | (name "r-mixomics") | |
6bc6a711 | 6341 | (version "6.12.2") |
1adb9cbc | 6342 | (source |
6343 | (origin | |
6344 | (method url-fetch) | |
6345 | (uri (bioconductor-uri "mixOmics" version)) | |
6346 | (sha256 | |
6347 | (base32 | |
6bc6a711 | 6348 | "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc")))) |
1adb9cbc | 6349 | (properties `((upstream-name . "mixOmics"))) |
6350 | (build-system r-build-system) | |
6351 | (propagated-inputs | |
6352 | `(("r-corpcor" ,r-corpcor) | |
6353 | ("r-dplyr" ,r-dplyr) | |
6354 | ("r-ellipse" ,r-ellipse) | |
6355 | ("r-ggplot2" ,r-ggplot2) | |
6356 | ("r-gridextra" ,r-gridextra) | |
6357 | ("r-igraph" ,r-igraph) | |
6358 | ("r-lattice" ,r-lattice) | |
6359 | ("r-mass" ,r-mass) | |
6360 | ("r-matrixstats" ,r-matrixstats) | |
6361 | ("r-rarpack" ,r-rarpack) | |
6362 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6363 | ("r-reshape2" ,r-reshape2) | |
6364 | ("r-tidyr" ,r-tidyr))) | |
9669bc17 RW |
6365 | (native-inputs |
6366 | `(("r-knitr" ,r-knitr))) | |
1adb9cbc | 6367 | (home-page "http://www.mixOmics.org") |
6368 | (synopsis "Multivariate methods for exploration of biological datasets") | |
6369 | (description | |
6370 | "mixOmics offers a wide range of multivariate methods for the exploration | |
6371 | and integration of biological datasets with a particular focus on variable | |
6372 | selection. The package proposes several sparse multivariate models we have | |
6373 | developed to identify the key variables that are highly correlated, and/or | |
6374 | explain the biological outcome of interest. The data that can be analysed | |
6375 | with mixOmics may come from high throughput sequencing technologies, such as | |
6376 | omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but | |
6377 | also beyond the realm of omics (e.g. spectral imaging). The methods | |
6378 | implemented in mixOmics can also handle missing values without having to | |
6379 | delete entire rows with missing data.") | |
6380 | (license license:gpl2+))) | |
a0efa069 | 6381 | |
6382 | (define-public r-depecher | |
6383 | (package | |
6384 | (name "r-depecher") | |
54e04fed | 6385 | (version "1.4.1") |
a0efa069 | 6386 | (source |
6387 | (origin | |
6388 | (method url-fetch) | |
6389 | (uri (bioconductor-uri "DepecheR" version)) | |
6390 | (sha256 | |
6391 | (base32 | |
54e04fed | 6392 | "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v")))) |
a0efa069 | 6393 | (properties `((upstream-name . "DepecheR"))) |
6394 | (build-system r-build-system) | |
a0efa069 | 6395 | (propagated-inputs |
6396 | `(("r-beanplot" ,r-beanplot) | |
a0efa069 | 6397 | ("r-dosnow" ,r-dosnow) |
6398 | ("r-dplyr" ,r-dplyr) | |
2c8433ca | 6399 | ("r-fnn" ,r-fnn) |
a0efa069 | 6400 | ("r-foreach" ,r-foreach) |
6401 | ("r-ggplot2" ,r-ggplot2) | |
6402 | ("r-gplots" ,r-gplots) | |
6403 | ("r-mass" ,r-mass) | |
6404 | ("r-matrixstats" ,r-matrixstats) | |
6405 | ("r-mixomics" ,r-mixomics) | |
6406 | ("r-moments" ,r-moments) | |
6407 | ("r-rcpp" ,r-rcpp) | |
6408 | ("r-rcppeigen" ,r-rcppeigen) | |
6409 | ("r-reshape2" ,r-reshape2) | |
2c8433ca | 6410 | ("r-robustbase" ,r-robustbase) |
a0efa069 | 6411 | ("r-viridis" ,r-viridis))) |
bf3722f9 RW |
6412 | (native-inputs |
6413 | `(("r-knitr" ,r-knitr))) | |
a0efa069 | 6414 | (home-page "https://bioconductor.org/packages/DepecheR/") |
6415 | (synopsis "Identify traits of clusters in high-dimensional entities") | |
6416 | (description | |
6417 | "The purpose of this package is to identify traits in a dataset that can | |
6418 | separate groups. This is done on two levels. First, clustering is performed, | |
6419 | using an implementation of sparse K-means. Secondly, the generated clusters | |
6420 | are used to predict outcomes of groups of individuals based on their | |
6421 | distribution of observations in the different clusters. As certain clusters | |
6422 | with separating information will be identified, and these clusters are defined | |
6423 | by a sparse number of variables, this method can reduce the complexity of | |
6424 | data, to only emphasize the data that actually matters.") | |
6425 | (license license:expat))) | |
b46a0ee7 | 6426 | |
bb88417f RW |
6427 | (define-public r-rcistarget |
6428 | (package | |
6429 | (name "r-rcistarget") | |
93235b1e | 6430 | (version "1.8.0") |
bb88417f RW |
6431 | (source |
6432 | (origin | |
6433 | (method url-fetch) | |
6434 | (uri (bioconductor-uri "RcisTarget" version)) | |
6435 | (sha256 | |
6436 | (base32 | |
93235b1e | 6437 | "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i")))) |
bb88417f RW |
6438 | (properties `((upstream-name . "RcisTarget"))) |
6439 | (build-system r-build-system) | |
6440 | (propagated-inputs | |
6441 | `(("r-aucell" ,r-aucell) | |
6442 | ("r-biocgenerics" ,r-biocgenerics) | |
6443 | ("r-data-table" ,r-data-table) | |
6444 | ("r-feather" ,r-feather) | |
6445 | ("r-gseabase" ,r-gseabase) | |
6446 | ("r-r-utils" ,r-r-utils) | |
6447 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
93235b1e RW |
6448 | (native-inputs |
6449 | `(("r-knitr" ,r-knitr))) | |
bb88417f RW |
6450 | (home-page "https://aertslab.org/#scenic") |
6451 | (synopsis "Identify transcription factor binding motifs enriched on a gene list") | |
6452 | (description | |
6453 | "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) | |
6454 | over-represented on a gene list. In a first step, RcisTarget selects DNA | |
6455 | motifs that are significantly over-represented in the surroundings of the | |
6456 | @dfn{transcription start site} (TSS) of the genes in the gene-set. This is | |
6457 | achieved by using a database that contains genome-wide cross-species rankings | |
6458 | for each motif. The motifs that are then annotated to TFs and those that have | |
6459 | a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for | |
6460 | each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. | |
6461 | genes in the gene-set that are ranked above the leading edge).") | |
6462 | (license license:gpl3))) | |
6463 | ||
b46a0ee7 RW |
6464 | (define-public r-cicero |
6465 | (package | |
6466 | (name "r-cicero") | |
40f378e1 | 6467 | (version "1.6.2") |
b46a0ee7 RW |
6468 | (source |
6469 | (origin | |
6470 | (method url-fetch) | |
6471 | (uri (bioconductor-uri "cicero" version)) | |
6472 | (sha256 | |
6473 | (base32 | |
40f378e1 | 6474 | "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh")))) |
b46a0ee7 RW |
6475 | (build-system r-build-system) |
6476 | (propagated-inputs | |
6477 | `(("r-assertthat" ,r-assertthat) | |
6478 | ("r-biobase" ,r-biobase) | |
6479 | ("r-biocgenerics" ,r-biocgenerics) | |
6480 | ("r-data-table" ,r-data-table) | |
6481 | ("r-dplyr" ,r-dplyr) | |
6482 | ("r-fnn" ,r-fnn) | |
6483 | ("r-genomicranges" ,r-genomicranges) | |
6484 | ("r-ggplot2" ,r-ggplot2) | |
6485 | ("r-glasso" ,r-glasso) | |
6486 | ("r-gviz" ,r-gviz) | |
6487 | ("r-igraph" ,r-igraph) | |
6488 | ("r-iranges" ,r-iranges) | |
6489 | ("r-matrix" ,r-matrix) | |
6490 | ("r-monocle" ,r-monocle) | |
6491 | ("r-plyr" ,r-plyr) | |
6492 | ("r-reshape2" ,r-reshape2) | |
6493 | ("r-s4vectors" ,r-s4vectors) | |
1893092d | 6494 | ("r-stringi" ,r-stringi) |
b46a0ee7 RW |
6495 | ("r-stringr" ,r-stringr) |
6496 | ("r-tibble" ,r-tibble) | |
5ea4f604 | 6497 | ("r-tidyr" ,r-tidyr) |
b46a0ee7 | 6498 | ("r-vgam" ,r-vgam))) |
6bd6097e RW |
6499 | (native-inputs |
6500 | `(("r-knitr" ,r-knitr))) | |
b46a0ee7 RW |
6501 | (home-page "https://bioconductor.org/packages/cicero/") |
6502 | (synopsis "Predict cis-co-accessibility from single-cell data") | |
6503 | (description | |
6504 | "Cicero computes putative cis-regulatory maps from single-cell chromatin | |
6505 | accessibility data. It also extends the monocle package for use in chromatin | |
6506 | accessibility data.") | |
6507 | (license license:expat))) | |
14bb1c48 RW |
6508 | |
6509 | ;; This is the latest commit on the "monocle3" branch. | |
6510 | (define-public r-cicero-monocle3 | |
6511 | (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") | |
6512 | (revision "1")) | |
6513 | (package (inherit r-cicero) | |
6514 | (name "r-cicero-monocle3") | |
6515 | (version (git-version "1.3.2" revision commit)) | |
6516 | (source | |
6517 | (origin | |
6518 | (method git-fetch) | |
6519 | (uri (git-reference | |
b0e7b699 | 6520 | (url "https://github.com/cole-trapnell-lab/cicero-release") |
14bb1c48 RW |
6521 | (commit commit))) |
6522 | (file-name (git-file-name name version)) | |
6523 | (sha256 | |
6524 | (base32 | |
6525 | "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) | |
6526 | (propagated-inputs | |
6527 | `(("r-monocle3" ,r-monocle3) | |
6528 | ,@(alist-delete "r-monocle" | |
6529 | (package-propagated-inputs r-cicero))))))) | |
a9815a6c RW |
6530 | |
6531 | (define-public r-cistopic | |
6532 | (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") | |
6533 | (revision "0")) | |
6534 | (package | |
6535 | (name "r-cistopic") | |
6536 | (version (git-version "0.2.1" revision commit)) | |
6537 | (source | |
6538 | (origin | |
6539 | (method git-fetch) | |
6540 | (uri (git-reference | |
b0e7b699 | 6541 | (url "https://github.com/aertslab/cisTopic") |
a9815a6c RW |
6542 | (commit commit))) |
6543 | (file-name (git-file-name name version)) | |
6544 | (sha256 | |
6545 | (base32 | |
6546 | "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) | |
6547 | (build-system r-build-system) | |
6548 | (propagated-inputs | |
6549 | `(("r-aucell" ,r-aucell) | |
6550 | ("r-data-table" ,r-data-table) | |
6551 | ("r-dplyr" ,r-dplyr) | |
6552 | ("r-dosnow" ,r-dosnow) | |
6553 | ("r-dt" ,r-dt) | |
6554 | ("r-feather" ,r-feather) | |
6555 | ("r-fitdistrplus" ,r-fitdistrplus) | |
6556 | ("r-genomicranges" ,r-genomicranges) | |
6557 | ("r-ggplot2" ,r-ggplot2) | |
6558 | ("r-lda" ,r-lda) | |
6559 | ("r-matrix" ,r-matrix) | |
6560 | ("r-plyr" ,r-plyr) | |
6561 | ("r-rcistarget" ,r-rcistarget) | |
6562 | ("r-rtracklayer" ,r-rtracklayer) | |
6563 | ("r-s4vectors" ,r-s4vectors))) | |
6564 | (home-page "https://github.com/aertslab/cisTopic") | |
6565 | (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") | |
6566 | (description | |
6567 | "The sparse nature of single cell epigenomics data can be overruled using | |
6568 | probabilistic modelling methods such as @dfn{Latent Dirichlet | |
6569 | Allocation} (LDA). This package allows the probabilistic modelling of | |
6570 | cis-regulatory topics (cisTopics) from single cell epigenomics data, and | |
6571 | includes functionalities to identify cell states based on the contribution of | |
6572 | cisTopics and explore the nature and regulatory proteins driving them.") | |
6573 | (license license:gpl3)))) | |
d85c0f98 RW |
6574 | |
6575 | (define-public r-genie3 | |
6576 | (package | |
6577 | (name "r-genie3") | |
b3280883 | 6578 | (version "1.10.0") |
d85c0f98 RW |
6579 | (source |
6580 | (origin | |
6581 | (method url-fetch) | |
6582 | (uri (bioconductor-uri "GENIE3" version)) | |
6583 | (sha256 | |
6584 | (base32 | |
b3280883 | 6585 | "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7")))) |
d85c0f98 RW |
6586 | (properties `((upstream-name . "GENIE3"))) |
6587 | (build-system r-build-system) | |
6588 | (propagated-inputs `(("r-reshape2" ,r-reshape2))) | |
b3280883 RW |
6589 | (native-inputs |
6590 | `(("r-knitr" ,r-knitr))) | |
d85c0f98 RW |
6591 | (home-page "https://bioconductor.org/packages/GENIE3") |
6592 | (synopsis "Gene network inference with ensemble of trees") | |
6593 | (description | |
6594 | "This package implements the GENIE3 algorithm for inferring gene | |
6595 | regulatory networks from expression data.") | |
6596 | (license license:gpl2+))) | |
db316d73 RW |
6597 | |
6598 | (define-public r-roc | |
6599 | (package | |
6600 | (name "r-roc") | |
cad8a509 | 6601 | (version "1.64.0") |
db316d73 RW |
6602 | (source |
6603 | (origin | |
6604 | (method url-fetch) | |
6605 | (uri (bioconductor-uri "ROC" version)) | |
6606 | (sha256 | |
6607 | (base32 | |
cad8a509 | 6608 | "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89")))) |
db316d73 RW |
6609 | (properties `((upstream-name . "ROC"))) |
6610 | (build-system r-build-system) | |
3672b74f RW |
6611 | (propagated-inputs |
6612 | `(("r-knitr" ,r-knitr))) | |
db316d73 RW |
6613 | (home-page "https://www.bioconductor.org/packages/ROC/") |
6614 | (synopsis "Utilities for ROC curves") | |
6615 | (description | |
6616 | "This package provides utilities for @dfn{Receiver Operating | |
6617 | Characteristic} (ROC) curves, with a focus on micro arrays.") | |
6618 | (license license:artistic2.0))) | |
46721dea RW |
6619 | |
6620 | (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 | |
6621 | (package | |
6622 | (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") | |
6623 | (version "0.6.0") | |
6624 | (source | |
6625 | (origin | |
6626 | (method url-fetch) | |
6627 | (uri (bioconductor-uri | |
6628 | "IlluminaHumanMethylation450kanno.ilmn12.hg19" | |
6629 | version 'annotation)) | |
6630 | (sha256 | |
6631 | (base32 | |
6632 | "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) | |
6633 | (properties | |
6634 | `((upstream-name | |
6635 | . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) | |
6636 | (build-system r-build-system) | |
6637 | (propagated-inputs `(("r-minfi" ,r-minfi))) | |
6638 | (home-page | |
6639 | "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") | |
6640 | (synopsis "Annotation for Illumina's 450k methylation arrays") | |
6641 | (description | |
6642 | "This package provides manifests and annotation for Illumina's 450k array | |
6643 | data.") | |
6644 | (license license:artistic2.0))) | |
38babeaa RW |
6645 | |
6646 | (define-public r-watermelon | |
6647 | (package | |
6648 | (name "r-watermelon") | |
939ace96 | 6649 | (version "1.32.0") |
38babeaa RW |
6650 | (source |
6651 | (origin | |
6652 | (method url-fetch) | |
6653 | (uri (bioconductor-uri "wateRmelon" version)) | |
6654 | (sha256 | |
6655 | (base32 | |
939ace96 | 6656 | "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn")))) |
38babeaa RW |
6657 | (properties `((upstream-name . "wateRmelon"))) |
6658 | (build-system r-build-system) | |
6659 | (propagated-inputs | |
6660 | `(("r-biobase" ,r-biobase) | |
6661 | ("r-illuminahumanmethylation450kanno-ilmn12-hg19" | |
6662 | ,r-illuminahumanmethylation450kanno-ilmn12-hg19) | |
6663 | ("r-illuminaio" ,r-illuminaio) | |
6664 | ("r-limma" ,r-limma) | |
6665 | ("r-lumi" ,r-lumi) | |
6666 | ("r-matrixstats" ,r-matrixstats) | |
6667 | ("r-methylumi" ,r-methylumi) | |
6668 | ("r-roc" ,r-roc))) | |
6669 | (home-page "https://bioconductor.org/packages/wateRmelon/") | |
6670 | (synopsis "Illumina 450 methylation array normalization and metrics") | |
6671 | (description | |
6672 | "The standard index of DNA methylation (beta) is computed from methylated | |
6673 | and unmethylated signal intensities. Betas calculated from raw signal | |
6674 | intensities perform well, but using 11 methylomic datasets we demonstrate that | |
6675 | quantile normalization methods produce marked improvement. The commonly used | |
6676 | procedure of normalizing betas is inferior to the separate normalization of M | |
6677 | and U, and it is also advantageous to normalize Type I and Type II assays | |
6678 | separately. This package provides 15 flavours of betas and three performance | |
6679 | metrics, with methods for objects produced by the @code{methylumi} and | |
6680 | @code{minfi} packages.") | |
6681 | (license license:gpl3))) | |
7d2cb646 RW |
6682 | |
6683 | (define-public r-gdsfmt | |
6684 | (package | |
6685 | (name "r-gdsfmt") | |
f7d5721b | 6686 | (version "1.24.1") |
7d2cb646 RW |
6687 | (source |
6688 | (origin | |
6689 | (method url-fetch) | |
6690 | (uri (bioconductor-uri "gdsfmt" version)) | |
6691 | (sha256 | |
6692 | (base32 | |
f7d5721b | 6693 | "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67")) |
7d2cb646 RW |
6694 | (modules '((guix build utils))) |
6695 | ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build | |
6696 | ;; them and link with system libraries instead. | |
6697 | (snippet | |
6698 | '(begin | |
6699 | (for-each delete-file-recursively | |
6700 | '("src/LZ4" | |
6701 | "src/XZ" | |
6702 | "src/ZLIB")) | |
6703 | (substitute* "src/Makevars" | |
6704 | (("all: \\$\\(SHLIB\\)") "all:") | |
6705 | (("\\$\\(SHLIB\\): liblzma.a") "") | |
6706 | (("(ZLIB|LZ4)/.*") "") | |
6707 | (("CoreArray/dVLIntGDS.cpp.*") | |
6708 | "CoreArray/dVLIntGDS.cpp") | |
6709 | (("CoreArray/dVLIntGDS.o.*") | |
6710 | "CoreArray/dVLIntGDS.o") | |
6711 | (("PKG_LIBS = ./liblzma.a") | |
6712 | "PKG_LIBS = -llz4")) | |
6713 | (substitute* "src/CoreArray/dStream.h" | |
6714 | (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) | |
6715 | (string-append "include <" header ">"))) | |
6716 | #t)))) | |
6717 | (properties `((upstream-name . "gdsfmt"))) | |
6718 | (build-system r-build-system) | |
6719 | (inputs | |
6720 | `(("lz4" ,lz4) | |
6721 | ("xz" ,xz) | |
6722 | ("zlib" ,zlib))) | |
f4954b0b RW |
6723 | (native-inputs |
6724 | `(("r-knitr" ,r-knitr))) | |
7d2cb646 RW |
6725 | (home-page "http://corearray.sourceforge.net/") |
6726 | (synopsis | |
6727 | "R Interface to CoreArray Genomic Data Structure (GDS) Files") | |
6728 | (description | |
6729 | "This package provides a high-level R interface to CoreArray @dfn{Genomic | |
6730 | Data Structure} (GDS) data files, which are portable across platforms with | |
6731 | hierarchical structure to store multiple scalable array-oriented data sets | |
6732 | with metadata information. It is suited for large-scale datasets, especially | |
6733 | for data which are much larger than the available random-access memory. The | |
6734 | @code{gdsfmt} package offers efficient operations specifically designed for | |
6735 | integers of less than 8 bits, since a diploid genotype, like | |
6736 | @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a | |
6737 | byte. Data compression and decompression are available with relatively | |
6738 | efficient random access. It is also allowed to read a GDS file in parallel | |
6739 | with multiple R processes supported by the package @code{parallel}.") | |
6740 | (license license:lgpl3))) | |
6b5f59c7 RW |
6741 | |
6742 | (define-public r-bigmelon | |
6743 | (package | |
6744 | (name "r-bigmelon") | |
8112796d | 6745 | (version "1.14.0") |
6b5f59c7 RW |
6746 | (source |
6747 | (origin | |
6748 | (method url-fetch) | |
6749 | (uri (bioconductor-uri "bigmelon" version)) | |
6750 | (sha256 | |
6751 | (base32 | |
8112796d | 6752 | "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y")))) |
6b5f59c7 RW |
6753 | (properties `((upstream-name . "bigmelon"))) |
6754 | (build-system r-build-system) | |
6755 | (propagated-inputs | |
6756 | `(("r-biobase" ,r-biobase) | |
6757 | ("r-biocgenerics" ,r-biocgenerics) | |
6758 | ("r-gdsfmt" ,r-gdsfmt) | |
6759 | ("r-geoquery" ,r-geoquery) | |
6760 | ("r-methylumi" ,r-methylumi) | |
6761 | ("r-minfi" ,r-minfi) | |
6762 | ("r-watermelon" ,r-watermelon))) | |
6763 | (home-page "https://bioconductor.org/packages/bigmelon/") | |
6764 | (synopsis "Illumina methylation array analysis for large experiments") | |
6765 | (description | |
6766 | "This package provides methods for working with Illumina arrays using the | |
6767 | @code{gdsfmt} package.") | |
6768 | (license license:gpl3))) | |
739b2d10 | 6769 | |
e5dfcd8e RW |
6770 | (define-public r-seqbias |
6771 | (package | |
6772 | (name "r-seqbias") | |
83b7625c | 6773 | (version "1.36.0") |
e5dfcd8e RW |
6774 | (source |
6775 | (origin | |
6776 | (method url-fetch) | |
6777 | (uri (bioconductor-uri "seqbias" version)) | |
6778 | (sha256 | |
6779 | (base32 | |
83b7625c | 6780 | "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai")))) |
e5dfcd8e RW |
6781 | (properties `((upstream-name . "seqbias"))) |
6782 | (build-system r-build-system) | |
6783 | (propagated-inputs | |
6784 | `(("r-biostrings" ,r-biostrings) | |
6785 | ("r-genomicranges" ,r-genomicranges) | |
6786 | ("r-rhtslib" ,r-rhtslib))) | |
6787 | (inputs | |
6788 | `(("zlib" ,zlib))) ; This comes from rhtslib. | |
6789 | (home-page "https://bioconductor.org/packages/seqbias/") | |
6790 | (synopsis "Estimation of per-position bias in high-throughput sequencing data") | |
6791 | (description | |
6792 | "This package implements a model of per-position sequencing bias in | |
6793 | high-throughput sequencing data using a simple Bayesian network, the structure | |
6794 | and parameters of which are trained on a set of aligned reads and a reference | |
6795 | genome sequence.") | |
6796 | (license license:lgpl3))) | |
6797 | ||
63daca1e RJ |
6798 | (define-public r-snplocs-hsapiens-dbsnp144-grch37 |
6799 | (package | |
6800 | (name "r-snplocs-hsapiens-dbsnp144-grch37") | |
6801 | (version "0.99.20") | |
6802 | (source (origin | |
6803 | (method url-fetch) | |
6804 | (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" | |
6805 | version 'annotation)) | |
6806 | (sha256 | |
6807 | (base32 | |
6808 | "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) | |
6809 | (build-system r-build-system) | |
6810 | ;; As this package provides little more than a very large data file it | |
6811 | ;; doesn't make sense to build substitutes. | |
6812 | (arguments `(#:substitutable? #f)) | |
6813 | (propagated-inputs | |
6814 | `(("r-biocgenerics" ,r-biocgenerics) | |
6815 | ("r-s4vectors" ,r-s4vectors) | |
6816 | ("r-iranges" ,r-iranges) | |
6817 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6818 | ("r-genomicranges" ,r-genomicranges) | |
6819 | ("r-bsgenome" ,r-bsgenome) | |
6820 | ("r-biostrings" ,r-biostrings))) | |
6821 | (home-page | |
6822 | "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") | |
6823 | (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") | |
6824 | (description "This package provides SNP locations and alleles for Homo | |
6825 | sapiens extracted from NCBI dbSNP Build 144. The source data files used for | |
6826 | this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped | |
6827 | to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a | |
6828 | patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, | |
1408e2ab | 6829 | X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for |
63daca1e RJ |
6830 | the mitochondrion chromosome. Therefore, the SNPs in this package can be |
6831 | injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the | |
6832 | correct position but this injection will exclude chrM (i.e. nothing will be | |
6833 | injected in that sequence).") | |
6834 | (license license:artistic2.0))) | |
6835 | ||
bb0024dc RW |
6836 | (define-public r-reqon |
6837 | (package | |
6838 | (name "r-reqon") | |
efb44ebc | 6839 | (version "1.34.0") |
bb0024dc RW |
6840 | (source |
6841 | (origin | |
6842 | (method url-fetch) | |
6843 | (uri (bioconductor-uri "ReQON" version)) | |
6844 | (sha256 | |
6845 | (base32 | |
efb44ebc | 6846 | "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz")))) |
bb0024dc RW |
6847 | (properties `((upstream-name . "ReQON"))) |
6848 | (build-system r-build-system) | |
6849 | (propagated-inputs | |
6850 | `(("r-rjava" ,r-rjava) | |
6851 | ("r-rsamtools" ,r-rsamtools) | |
6852 | ("r-seqbias" ,r-seqbias))) | |
6853 | (home-page "https://bioconductor.org/packages/ReQON/") | |
6854 | (synopsis "Recalibrating quality of nucleotides") | |
6855 | (description | |
6856 | "This package provides an implementation of an algorithm for | |
6857 | recalibrating the base quality scores for aligned sequencing data in BAM | |
6858 | format.") | |
6859 | (license license:gpl2))) | |
6860 | ||
739b2d10 RW |
6861 | (define-public r-wavcluster |
6862 | (package | |
6863 | (name "r-wavcluster") | |
12b255f2 | 6864 | (version "2.22.0") |
739b2d10 RW |
6865 | (source |
6866 | (origin | |
6867 | (method url-fetch) | |
6868 | (uri (bioconductor-uri "wavClusteR" version)) | |
6869 | (sha256 | |
6870 | (base32 | |
12b255f2 | 6871 | "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk")))) |
739b2d10 RW |
6872 | (properties `((upstream-name . "wavClusteR"))) |
6873 | (build-system r-build-system) | |
6874 | (propagated-inputs | |
6875 | `(("r-biocgenerics" ,r-biocgenerics) | |
6876 | ("r-biostrings" ,r-biostrings) | |
6877 | ("r-foreach" ,r-foreach) | |
6878 | ("r-genomicfeatures" ,r-genomicfeatures) | |
6879 | ("r-genomicranges" ,r-genomicranges) | |
6880 | ("r-ggplot2" ,r-ggplot2) | |
6881 | ("r-hmisc" ,r-hmisc) | |
6882 | ("r-iranges" ,r-iranges) | |
6883 | ("r-mclust" ,r-mclust) | |
6884 | ("r-rsamtools" ,r-rsamtools) | |
6885 | ("r-rtracklayer" ,r-rtracklayer) | |
6886 | ("r-s4vectors" ,r-s4vectors) | |
6887 | ("r-seqinr" ,r-seqinr) | |
6888 | ("r-stringr" ,r-stringr) | |
6889 | ("r-wmtsa" ,r-wmtsa))) | |
12b255f2 RW |
6890 | (native-inputs |
6891 | `(("r-knitr" ,r-knitr))) | |
739b2d10 RW |
6892 | (home-page "https://bioconductor.org/packages/wavClusteR/") |
6893 | (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") | |
6894 | (description | |
6895 | "This package provides an integrated pipeline for the analysis of | |
6896 | PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from | |
6897 | sequencing errors, SNPs and additional non-experimental sources by a non- | |
6898 | parametric mixture model. The protein binding sites (clusters) are then | |
6899 | resolved at high resolution and cluster statistics are estimated using a | |
6900 | rigorous Bayesian framework. Post-processing of the results, data export for | |
6901 | UCSC genome browser visualization and motif search analysis are provided. In | |
e40ecf8a | 6902 | addition, the package integrates RNA-Seq data to estimate the False |
739b2d10 RW |
6903 | Discovery Rate of cluster detection. Key functions support parallel multicore |
6904 | computing. While wavClusteR was designed for PAR-CLIP data analysis, it can | |
6905 | be applied to the analysis of other NGS data obtained from experimental | |
6906 | procedures that induce nucleotide substitutions (e.g. BisSeq).") | |
6907 | (license license:gpl2))) | |
853211a5 RW |
6908 | |
6909 | (define-public r-timeseriesexperiment | |
6910 | (package | |
6911 | (name "r-timeseriesexperiment") | |
49dd5041 | 6912 | (version "1.6.0") |
853211a5 RW |
6913 | (source |
6914 | (origin | |
6915 | (method url-fetch) | |
6916 | (uri (bioconductor-uri "TimeSeriesExperiment" version)) | |
6917 | (sha256 | |
6918 | (base32 | |
49dd5041 | 6919 | "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3")))) |
853211a5 RW |
6920 | (properties |
6921 | `((upstream-name . "TimeSeriesExperiment"))) | |
6922 | (build-system r-build-system) | |
6923 | (propagated-inputs | |
6924 | `(("r-deseq2" ,r-deseq2) | |
6925 | ("r-dplyr" ,r-dplyr) | |
6926 | ("r-dynamictreecut" ,r-dynamictreecut) | |
6927 | ("r-edger" ,r-edger) | |
6928 | ("r-ggplot2" ,r-ggplot2) | |
6929 | ("r-hmisc" ,r-hmisc) | |
6930 | ("r-limma" ,r-limma) | |
6931 | ("r-magrittr" ,r-magrittr) | |
6932 | ("r-proxy" ,r-proxy) | |
6933 | ("r-s4vectors" ,r-s4vectors) | |
6934 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6935 | ("r-tibble" ,r-tibble) | |
6936 | ("r-tidyr" ,r-tidyr) | |
6937 | ("r-vegan" ,r-vegan) | |
6938 | ("r-viridis" ,r-viridis))) | |
49dd5041 RW |
6939 | (native-inputs |
6940 | `(("r-knitr" ,r-knitr))) | |
853211a5 RW |
6941 | (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") |
6942 | (synopsis "Analysis for short time-series data") | |
6943 | (description | |
6944 | "This package is a visualization and analysis toolbox for short time | |
6945 | course data which includes dimensionality reduction, clustering, two-sample | |
6946 | differential expression testing and gene ranking techniques. The package also | |
6947 | provides methods for retrieving enriched pathways.") | |
6948 | (license license:lgpl3+))) | |
df8576e5 RW |
6949 | |
6950 | (define-public r-variantfiltering | |
6951 | (package | |
6952 | (name "r-variantfiltering") | |
41f7fe4a | 6953 | (version "1.24.0") |
df8576e5 RW |
6954 | (source |
6955 | (origin | |
6956 | (method url-fetch) | |
6957 | (uri (bioconductor-uri "VariantFiltering" version)) | |
6958 | (sha256 | |
6959 | (base32 | |
41f7fe4a | 6960 | "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4")))) |
df8576e5 RW |
6961 | (properties |
6962 | `((upstream-name . "VariantFiltering"))) | |
6963 | (build-system r-build-system) | |
6964 | (propagated-inputs | |
6965 | `(("r-annotationdbi" ,r-annotationdbi) | |
6966 | ("r-biobase" ,r-biobase) | |
6967 | ("r-biocgenerics" ,r-biocgenerics) | |
6968 | ("r-biocparallel" ,r-biocparallel) | |
6969 | ("r-biostrings" ,r-biostrings) | |
6970 | ("r-bsgenome" ,r-bsgenome) | |
6971 | ("r-dt" ,r-dt) | |
6972 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6973 | ("r-genomicfeatures" ,r-genomicfeatures) | |
6974 | ("r-genomicranges" ,r-genomicranges) | |
6975 | ("r-genomicscores" ,r-genomicscores) | |
6976 | ("r-graph" ,r-graph) | |
6977 | ("r-gviz" ,r-gviz) | |
6978 | ("r-iranges" ,r-iranges) | |
6979 | ("r-rbgl" ,r-rbgl) | |
6980 | ("r-rsamtools" ,r-rsamtools) | |
6981 | ("r-s4vectors" ,r-s4vectors) | |
6982 | ("r-shiny" ,r-shiny) | |
6983 | ("r-shinyjs" ,r-shinyjs) | |
6984 | ("r-shinythemes" ,r-shinythemes) | |
6985 | ("r-shinytree" ,r-shinytree) | |
6986 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6987 | ("r-variantannotation" ,r-variantannotation) | |
6988 | ("r-xvector" ,r-xvector))) | |
6989 | (home-page "https://github.com/rcastelo/VariantFiltering") | |
6990 | (synopsis "Filtering of coding and non-coding genetic variants") | |
6991 | (description | |
6992 | "Filter genetic variants using different criteria such as inheritance | |
6993 | model, amino acid change consequence, minor allele frequencies across human | |
6994 | populations, splice site strength, conservation, etc.") | |
6995 | (license license:artistic2.0))) | |
f5349b4d RW |
6996 | |
6997 | (define-public r-genomegraphs | |
6998 | (package | |
6999 | (name "r-genomegraphs") | |
053a2127 | 7000 | (version "1.46.0") |
f5349b4d RW |
7001 | (source |
7002 | (origin | |
7003 | (method url-fetch) | |
7004 | (uri (bioconductor-uri "GenomeGraphs" version)) | |
7005 | (sha256 | |
7006 | (base32 | |
053a2127 | 7007 | "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) |
f5349b4d RW |
7008 | (properties `((upstream-name . "GenomeGraphs"))) |
7009 | (build-system r-build-system) | |
7010 | (propagated-inputs | |
7011 | `(("r-biomart" ,r-biomart))) | |
7012 | (home-page "https://bioconductor.org/packages/GenomeGraphs/") | |
7013 | (synopsis "Plotting genomic information from Ensembl") | |
7014 | (description | |
7015 | "Genomic data analyses requires integrated visualization of known genomic | |
7016 | information and new experimental data. GenomeGraphs uses the biomaRt package | |
7017 | to perform live annotation queries to Ensembl and translates this to e.g. | |
7018 | gene/transcript structures in viewports of the grid graphics package. This | |
7019 | results in genomic information plotted together with your data. Another | |
7020 | strength of GenomeGraphs is to plot different data types such as array CGH, | |
7021 | gene expression, sequencing and other data, together in one plot using the | |
7022 | same genome coordinate system.") | |
7023 | (license license:artistic2.0))) | |
2a360cf6 RW |
7024 | |
7025 | (define-public r-wavetiling | |
7026 | (package | |
7027 | (name "r-wavetiling") | |
e13f9773 | 7028 | (version "1.28.0") |
2a360cf6 RW |
7029 | (source |
7030 | (origin | |
7031 | (method url-fetch) | |
7032 | (uri (bioconductor-uri "waveTiling" version)) | |
7033 | (sha256 | |
7034 | (base32 | |
e13f9773 | 7035 | "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) |
2a360cf6 RW |
7036 | (properties `((upstream-name . "waveTiling"))) |
7037 | (build-system r-build-system) | |
7038 | (propagated-inputs | |
7039 | `(("r-affy" ,r-affy) | |
7040 | ("r-biobase" ,r-biobase) | |
7041 | ("r-biostrings" ,r-biostrings) | |
7042 | ("r-genomegraphs" ,r-genomegraphs) | |
7043 | ("r-genomicranges" ,r-genomicranges) | |
7044 | ("r-iranges" ,r-iranges) | |
7045 | ("r-oligo" ,r-oligo) | |
7046 | ("r-oligoclasses" ,r-oligoclasses) | |
7047 | ("r-preprocesscore" ,r-preprocesscore) | |
7048 | ("r-waveslim" ,r-waveslim))) | |
7049 | (home-page "https://r-forge.r-project.org/projects/wavetiling/") | |
7050 | (synopsis "Wavelet-based models for tiling array transcriptome analysis") | |
7051 | (description | |
7052 | "This package is designed to conduct transcriptome analysis for tiling | |
7053 | arrays based on fast wavelet-based functional models.") | |
7054 | (license license:gpl2+))) | |
d80a1569 RW |
7055 | |
7056 | (define-public r-variancepartition | |
7057 | (package | |
7058 | (name "r-variancepartition") | |
1bdc770d | 7059 | (version "1.18.3") |
d80a1569 RW |
7060 | (source |
7061 | (origin | |
7062 | (method url-fetch) | |
7063 | (uri (bioconductor-uri "variancePartition" version)) | |
7064 | (sha256 | |
7065 | (base32 | |
1bdc770d | 7066 | "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0")))) |
d80a1569 RW |
7067 | (properties |
7068 | `((upstream-name . "variancePartition"))) | |
7069 | (build-system r-build-system) | |
7070 | (propagated-inputs | |
7071 | `(("r-biobase" ,r-biobase) | |
326746e1 | 7072 | ("r-biocparallel" ,r-biocparallel) |
d80a1569 RW |
7073 | ("r-colorramps" ,r-colorramps) |
7074 | ("r-doparallel" ,r-doparallel) | |
7075 | ("r-foreach" ,r-foreach) | |
7076 | ("r-ggplot2" ,r-ggplot2) | |
7077 | ("r-gplots" ,r-gplots) | |
7078 | ("r-iterators" ,r-iterators) | |
7079 | ("r-limma" ,r-limma) | |
7080 | ("r-lme4" ,r-lme4) | |
7081 | ("r-lmertest" ,r-lmertest) | |
7082 | ("r-mass" ,r-mass) | |
7083 | ("r-pbkrtest" ,r-pbkrtest) | |
7084 | ("r-progress" ,r-progress) | |
7085 | ("r-reshape2" ,r-reshape2) | |
7086 | ("r-scales" ,r-scales))) | |
fbbaf5ae RW |
7087 | (native-inputs |
7088 | `(("r-knitr" ,r-knitr))) | |
d80a1569 RW |
7089 | (home-page "https://bioconductor.org/packages/variancePartition/") |
7090 | (synopsis "Analyze variation in gene expression experiments") | |
7091 | (description | |
7092 | "This is a package providing tools to quantify and interpret multiple | |
7093 | sources of biological and technical variation in gene expression experiments. | |
7094 | It uses a linear mixed model to quantify variation in gene expression | |
7095 | attributable to individual, tissue, time point, or technical variables. The | |
7096 | package includes dream differential expression analysis for repeated | |
7097 | measures.") | |
7098 | (license license:gpl2+))) | |
16e2e4f2 | 7099 | |
7100 | (define-public r-htqpcr | |
7101 | (package | |
7102 | (name "r-htqpcr") | |
518050a7 | 7103 | (version "1.42.0") |
16e2e4f2 | 7104 | (source |
7105 | (origin | |
7106 | (method url-fetch) | |
7107 | (uri (bioconductor-uri "HTqPCR" version)) | |
7108 | (sha256 | |
7109 | (base32 | |
518050a7 | 7110 | "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j")))) |
16e2e4f2 | 7111 | (properties `((upstream-name . "HTqPCR"))) |
7112 | (build-system r-build-system) | |
7113 | (propagated-inputs | |
7114 | `(("r-affy" ,r-affy) | |
7115 | ("r-biobase" ,r-biobase) | |
7116 | ("r-gplots" ,r-gplots) | |
7117 | ("r-limma" ,r-limma) | |
7118 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
486a0800 TGR |
7119 | (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" |
7120 | "groups/bertone/software/HTqPCR.pdf")) | |
16e2e4f2 | 7121 | (synopsis "Automated analysis of high-throughput qPCR data") |
7122 | (description | |
7123 | "Analysis of Ct values from high throughput quantitative real-time | |
7124 | PCR (qPCR) assays across multiple conditions or replicates. The input data | |
7125 | can be from spatially-defined formats such ABI TaqMan Low Density Arrays or | |
7126 | OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad | |
7127 | Laboratories; conventional 96- or 384-well plates; or microfluidic devices | |
7128 | such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data | |
7129 | loading, quality assessment, normalization, visualization and parametric or | |
7130 | non-parametric testing for statistical significance in Ct values between | |
7131 | features (e.g. genes, microRNAs).") | |
7132 | (license license:artistic2.0))) | |
86fb2c63 | 7133 | |
7134 | (define-public r-unifiedwmwqpcr | |
7135 | (package | |
7136 | (name "r-unifiedwmwqpcr") | |
a9148d06 | 7137 | (version "1.24.0") |
86fb2c63 | 7138 | (source |
7139 | (origin | |
7140 | (method url-fetch) | |
7141 | (uri (bioconductor-uri "unifiedWMWqPCR" version)) | |
7142 | (sha256 | |
7143 | (base32 | |
a9148d06 | 7144 | "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81")))) |
86fb2c63 | 7145 | (properties |
7146 | `((upstream-name . "unifiedWMWqPCR"))) | |
7147 | (build-system r-build-system) | |
7148 | (propagated-inputs | |
7149 | `(("r-biocgenerics" ,r-biocgenerics) | |
7150 | ("r-htqpcr" ,r-htqpcr))) | |
7151 | (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") | |
7152 | (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") | |
7153 | (description | |
b5b0ee3b | 7154 | "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR |
86fb2c63 | 7155 | data. This modified test allows for testing differential expression in qPCR |
7156 | data.") | |
7157 | (license license:gpl2+))) | |
72b67e0b RW |
7158 | |
7159 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put | |
7160 | ;; it here. | |
7161 | (define-public r-activedriverwgs | |
7162 | (package | |
7163 | (name "r-activedriverwgs") | |
e1ce10e3 | 7164 | (version "1.1.0") |
72b67e0b RW |
7165 | (source |
7166 | (origin | |
7167 | (method url-fetch) | |
7168 | (uri (cran-uri "ActiveDriverWGS" version)) | |
7169 | (sha256 | |
7170 | (base32 | |
e1ce10e3 | 7171 | "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag")))) |
72b67e0b RW |
7172 | (properties |
7173 | `((upstream-name . "ActiveDriverWGS"))) | |
7174 | (build-system r-build-system) | |
7175 | (propagated-inputs | |
7176 | `(("r-biostrings" ,r-biostrings) | |
7177 | ("r-bsgenome" ,r-bsgenome) | |
7178 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
7179 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7180 | ("r-genomicranges" ,r-genomicranges) | |
7181 | ("r-iranges" ,r-iranges) | |
72b67e0b | 7182 | ("r-s4vectors" ,r-s4vectors))) |
e1ce10e3 RW |
7183 | (native-inputs |
7184 | `(("r-knitr" ,r-knitr))) | |
72b67e0b RW |
7185 | (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") |
7186 | (synopsis "Driver discovery tool for cancer whole genomes") | |
7187 | (description | |
7188 | "This package provides a method for finding an enrichment of cancer | |
7189 | simple somatic mutations (SNVs and Indels) in functional elements across the | |
7190 | human genome. ActiveDriverWGS detects coding and noncoding driver elements | |
7191 | using whole genome sequencing data.") | |
7192 | (license license:gpl3))) | |
8e6f63dd RW |
7193 | |
7194 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put | |
7195 | ;; it here. | |
7196 | (define-public r-activepathways | |
7197 | (package | |
7198 | (name "r-activepathways") | |
a9a91280 | 7199 | (version "1.0.2") |
8e6f63dd RW |
7200 | (source |
7201 | (origin | |
7202 | (method url-fetch) | |
7203 | (uri (cran-uri "ActivePathways" version)) | |
7204 | (sha256 | |
7205 | (base32 | |
a9a91280 | 7206 | "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l")))) |
8e6f63dd RW |
7207 | (properties |
7208 | `((upstream-name . "ActivePathways"))) | |
7209 | (build-system r-build-system) | |
7210 | (propagated-inputs | |
7211 | `(("r-data-table" ,r-data-table) | |
a9a91280 | 7212 | ("r-ggplot2" ,r-ggplot2))) |
229736aa RW |
7213 | (native-inputs |
7214 | `(("r-knitr" ,r-knitr))) | |
8e6f63dd RW |
7215 | (home-page "https://cran.r-project.org/web/packages/ActivePathways/") |
7216 | (synopsis "Multivariate pathway enrichment analysis") | |
7217 | (description | |
7218 | "This package represents an integrative method of analyzing multi omics | |
7219 | data that conducts enrichment analysis of annotated gene sets. ActivePathways | |
7220 | uses a statistical data fusion approach, rationalizes contributing evidence | |
7221 | and highlights associated genes, improving systems-level understanding of | |
7222 | cellular organization in health and disease.") | |
7223 | (license license:gpl3))) | |
d11d6fea RW |
7224 | |
7225 | (define-public r-bgmix | |
7226 | (package | |
7227 | (name "r-bgmix") | |
296992be | 7228 | (version "1.48.0") |
d11d6fea RW |
7229 | (source |
7230 | (origin | |
7231 | (method url-fetch) | |
7232 | (uri (bioconductor-uri "BGmix" version)) | |
7233 | (sha256 | |
7234 | (base32 | |
296992be | 7235 | "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n")))) |
d11d6fea RW |
7236 | (properties `((upstream-name . "BGmix"))) |
7237 | (build-system r-build-system) | |
7238 | (propagated-inputs | |
7239 | `(("r-kernsmooth" ,r-kernsmooth))) | |
7240 | (home-page "https://bioconductor.org/packages/BGmix/") | |
7241 | (synopsis "Bayesian models for differential gene expression") | |
7242 | (description | |
7243 | "This package provides fully Bayesian mixture models for differential | |
7244 | gene expression.") | |
7245 | (license license:gpl2))) | |
75eb1149 RW |
7246 | |
7247 | (define-public r-bgx | |
7248 | (package | |
7249 | (name "r-bgx") | |
de91f15a | 7250 | (version "1.54.0") |
75eb1149 RW |
7251 | (source |
7252 | (origin | |
7253 | (method url-fetch) | |
7254 | (uri (bioconductor-uri "bgx" version)) | |
7255 | (sha256 | |
7256 | (base32 | |
de91f15a | 7257 | "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx")))) |
75eb1149 RW |
7258 | (properties `((upstream-name . "bgx"))) |
7259 | (build-system r-build-system) | |
7260 | (propagated-inputs | |
7261 | `(("r-affy" ,r-affy) | |
7262 | ("r-biobase" ,r-biobase) | |
7263 | ("r-gcrma" ,r-gcrma) | |
7264 | ("r-rcpp" ,r-rcpp))) | |
7265 | (home-page "https://bioconductor.org/packages/bgx/") | |
7266 | (synopsis "Bayesian gene expression") | |
7267 | (description | |
7268 | "This package provides tools for Bayesian integrated analysis of | |
7269 | Affymetrix GeneChips.") | |
7270 | (license license:gpl2))) | |
6bd50acf RW |
7271 | |
7272 | (define-public r-bhc | |
7273 | (package | |
7274 | (name "r-bhc") | |
2415576e | 7275 | (version "1.40.0") |
6bd50acf RW |
7276 | (source |
7277 | (origin | |
7278 | (method url-fetch) | |
7279 | (uri (bioconductor-uri "BHC" version)) | |
7280 | (sha256 | |
7281 | (base32 | |
2415576e | 7282 | "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr")))) |
6bd50acf RW |
7283 | (properties `((upstream-name . "BHC"))) |
7284 | (build-system r-build-system) | |
7285 | (home-page "https://bioconductor.org/packages/BHC/") | |
7286 | (synopsis "Bayesian hierarchical clustering") | |
7287 | (description | |
7288 | "The method implemented in this package performs bottom-up hierarchical | |
7289 | clustering, using a Dirichlet Process (infinite mixture) to model uncertainty | |
7290 | in the data and Bayesian model selection to decide at each step which clusters | |
7291 | to merge. This avoids several limitations of traditional methods, for example | |
7292 | how many clusters there should be and how to choose a principled distance | |
7293 | metric. This implementation accepts multinomial (i.e. discrete, with 2+ | |
7294 | categories) or time-series data. This version also includes a randomised | |
7295 | algorithm which is more efficient for larger data sets.") | |
7296 | (license license:gpl3))) | |
de9374b7 RW |
7297 | |
7298 | (define-public r-bicare | |
7299 | (package | |
7300 | (name "r-bicare") | |
76425173 | 7301 | (version "1.46.0") |
de9374b7 RW |
7302 | (source |
7303 | (origin | |
7304 | (method url-fetch) | |
7305 | (uri (bioconductor-uri "BicARE" version)) | |
7306 | (sha256 | |
7307 | (base32 | |
76425173 | 7308 | "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y")))) |
de9374b7 RW |
7309 | (properties `((upstream-name . "BicARE"))) |
7310 | (build-system r-build-system) | |
7311 | (propagated-inputs | |
7312 | `(("r-biobase" ,r-biobase) | |
7313 | ("r-gseabase" ,r-gseabase) | |
7314 | ("r-multtest" ,r-multtest))) | |
7315 | (home-page "http://bioinfo.curie.fr") | |
7316 | (synopsis "Biclustering analysis and results exploration") | |
7317 | (description | |
7318 | "This is a package for biclustering analysis and exploration of | |
7319 | results.") | |
7320 | (license license:gpl2))) | |
40fe63ad RW |
7321 | |
7322 | (define-public r-bifet | |
7323 | (package | |
7324 | (name "r-bifet") | |
a54fd409 | 7325 | (version "1.8.0") |
40fe63ad RW |
7326 | (source |
7327 | (origin | |
7328 | (method url-fetch) | |
7329 | (uri (bioconductor-uri "BiFET" version)) | |
7330 | (sha256 | |
7331 | (base32 | |
a54fd409 | 7332 | "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5")))) |
40fe63ad RW |
7333 | (properties `((upstream-name . "BiFET"))) |
7334 | (build-system r-build-system) | |
7335 | (propagated-inputs | |
7336 | `(("r-genomicranges" ,r-genomicranges) | |
7337 | ("r-poibin" ,r-poibin))) | |
a54fd409 RW |
7338 | (native-inputs |
7339 | `(("r-knitr" ,r-knitr))) | |
40fe63ad RW |
7340 | (home-page "https://bioconductor.org/packages/BiFET") |
7341 | (synopsis "Bias-free footprint enrichment test") | |
7342 | (description | |
7343 | "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are | |
7344 | over-represented in target regions compared to background regions after | |
7345 | correcting for the bias arising from the imbalance in read counts and GC | |
7346 | contents between the target and background regions. For a given TF k, BiFET | |
7347 | tests the null hypothesis that the target regions have the same probability of | |
7348 | having footprints for the TF k as the background regions while correcting for | |
7349 | the read count and GC content bias.") | |
7350 | (license license:gpl3))) | |
e823337c RW |
7351 | |
7352 | (define-public r-rsbml | |
7353 | (package | |
7354 | (name "r-rsbml") | |
d65bdbb2 | 7355 | (version "2.46.0") |
e823337c RW |
7356 | (source |
7357 | (origin | |
7358 | (method url-fetch) | |
7359 | (uri (bioconductor-uri "rsbml" version)) | |
7360 | (sha256 | |
7361 | (base32 | |
d65bdbb2 | 7362 | "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx")))) |
e823337c RW |
7363 | (properties `((upstream-name . "rsbml"))) |
7364 | (build-system r-build-system) | |
7365 | (inputs | |
7366 | `(("libsbml" ,libsbml) | |
7367 | ("zlib" ,zlib))) | |
7368 | (propagated-inputs | |
7369 | `(("r-biocgenerics" ,r-biocgenerics) | |
7370 | ("r-graph" ,r-graph))) | |
7371 | (native-inputs | |
7372 | `(("pkg-config" ,pkg-config))) | |
7373 | (home-page "http://www.sbml.org") | |
7374 | (synopsis "R support for SBML") | |
7375 | (description | |
7376 | "This package provides an R interface to libsbml for SBML parsing, | |
7377 | validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") | |
7378 | (license license:artistic2.0))) | |
75a8bb31 RW |
7379 | |
7380 | (define-public r-hypergraph | |
7381 | (package | |
7382 | (name "r-hypergraph") | |
0ff72461 | 7383 | (version "1.60.0") |
75a8bb31 RW |
7384 | (source |
7385 | (origin | |
7386 | (method url-fetch) | |
7387 | (uri (bioconductor-uri "hypergraph" version)) | |
7388 | (sha256 | |
7389 | (base32 | |
0ff72461 | 7390 | "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7")))) |
75a8bb31 RW |
7391 | (properties `((upstream-name . "hypergraph"))) |
7392 | (build-system r-build-system) | |
7393 | (propagated-inputs | |
7394 | `(("r-graph" ,r-graph))) | |
7395 | (home-page "https://bioconductor.org/packages/hypergraph") | |
7396 | (synopsis "Hypergraph data structures") | |
7397 | (description | |
7398 | "This package implements some simple capabilities for representing and | |
7399 | manipulating hypergraphs.") | |
7400 | (license license:artistic2.0))) | |
5aef09bd RW |
7401 | |
7402 | (define-public r-hyperdraw | |
7403 | (package | |
7404 | (name "r-hyperdraw") | |
31169986 | 7405 | (version "1.40.0") |
5aef09bd RW |
7406 | (source |
7407 | (origin | |
7408 | (method url-fetch) | |
7409 | (uri (bioconductor-uri "hyperdraw" version)) | |
7410 | (sha256 | |
7411 | (base32 | |
31169986 | 7412 | "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf")))) |
5aef09bd RW |
7413 | (properties `((upstream-name . "hyperdraw"))) |
7414 | (build-system r-build-system) | |
7415 | (inputs `(("graphviz" ,graphviz))) | |
7416 | (propagated-inputs | |
7417 | `(("r-graph" ,r-graph) | |
7418 | ("r-hypergraph" ,r-hypergraph) | |
7419 | ("r-rgraphviz" ,r-rgraphviz))) | |
7420 | (home-page "https://bioconductor.org/packages/hyperdraw") | |
7421 | (synopsis "Visualizing hypergraphs") | |
7422 | (description | |
7423 | "This package provides functions for visualizing hypergraphs.") | |
7424 | (license license:gpl2+))) | |
6ca6f866 RW |
7425 | |
7426 | (define-public r-biggr | |
7427 | (package | |
7428 | (name "r-biggr") | |
f31edb01 | 7429 | (version "1.24.0") |
6ca6f866 RW |
7430 | (source |
7431 | (origin | |
7432 | (method url-fetch) | |
7433 | (uri (bioconductor-uri "BiGGR" version)) | |
7434 | (sha256 | |
7435 | (base32 | |
f31edb01 | 7436 | "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk")))) |
6ca6f866 RW |
7437 | (properties `((upstream-name . "BiGGR"))) |
7438 | (build-system r-build-system) | |
7439 | (propagated-inputs | |
7440 | `(("r-hyperdraw" ,r-hyperdraw) | |
7441 | ("r-hypergraph" ,r-hypergraph) | |
7442 | ("r-lim" ,r-lim) | |
7443 | ("r-limsolve" ,r-limsolve) | |
7444 | ("r-rsbml" ,r-rsbml) | |
7445 | ("r-stringr" ,r-stringr))) | |
7446 | (home-page "https://bioconductor.org/packages/BiGGR/") | |
7447 | (synopsis "Constraint based modeling using metabolic reconstruction databases") | |
7448 | (description | |
7449 | "This package provides an interface to simulate metabolic reconstruction | |
7450 | from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic | |
7451 | reconstruction databases. The package facilitates @dfn{flux balance | |
7452 | analysis} (FBA) and the sampling of feasible flux distributions. Metabolic | |
7453 | networks and estimated fluxes can be visualized with hypergraphs.") | |
7454 | (license license:gpl3+))) | |
820373db RW |
7455 | |
7456 | (define-public r-bigmemoryextras | |
7457 | (package | |
7458 | (name "r-bigmemoryextras") | |
eef9c99c | 7459 | (version "1.36.0") |
820373db RW |
7460 | (source |
7461 | (origin | |
7462 | (method url-fetch) | |
7463 | (uri (bioconductor-uri "bigmemoryExtras" version)) | |
7464 | (sha256 | |
7465 | (base32 | |
eef9c99c | 7466 | "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g")))) |
820373db RW |
7467 | (properties |
7468 | `((upstream-name . "bigmemoryExtras"))) | |
7469 | (build-system r-build-system) | |
7470 | (propagated-inputs | |
7471 | `(("r-bigmemory" ,r-bigmemory))) | |
eef9c99c RW |
7472 | (native-inputs |
7473 | `(("r-knitr" ,r-knitr))) | |
820373db RW |
7474 | (home-page "https://github.com/phaverty/bigmemoryExtras") |
7475 | (synopsis "Extension of the bigmemory package") | |
7476 | (description | |
7477 | "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds | |
7478 | safety and convenience features to the @code{filebacked.big.matrix} class from | |
7479 | the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by | |
7480 | monitoring and gracefully restoring the connection to on-disk data and it also | |
7481 | protects against accidental data modification with a filesystem-based | |
7482 | permissions system. Utilities are provided for using @code{BigMatrix}-derived | |
7483 | classes as @code{assayData} matrices within the @code{Biobase} package's | |
7484 | @code{eSet} family of classes. @code{BigMatrix} provides some optimizations | |
7485 | related to attaching to, and indexing into, file-backed matrices with | |
7486 | dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, | |
7487 | a file-backed matrix with factor properties.") | |
7488 | (license license:artistic2.0))) | |
d38775b1 RW |
7489 | |
7490 | (define-public r-bigpint | |
7491 | (package | |
7492 | (name "r-bigpint") | |
d0badcc1 | 7493 | (version "1.4.0") |
d38775b1 RW |
7494 | (source |
7495 | (origin | |
7496 | (method url-fetch) | |
7497 | (uri (bioconductor-uri "bigPint" version)) | |
7498 | (sha256 | |
7499 | (base32 | |
d0badcc1 | 7500 | "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8")))) |
d38775b1 RW |
7501 | (properties `((upstream-name . "bigPint"))) |
7502 | (build-system r-build-system) | |
7503 | (propagated-inputs | |
d0badcc1 RW |
7504 | `(("r-delayedarray" ,r-delayedarray) |
7505 | ("r-dplyr" ,r-dplyr) | |
d38775b1 RW |
7506 | ("r-ggally" ,r-ggally) |
7507 | ("r-ggplot2" ,r-ggplot2) | |
7508 | ("r-gridextra" ,r-gridextra) | |
7509 | ("r-hexbin" ,r-hexbin) | |
7510 | ("r-hmisc" ,r-hmisc) | |
7511 | ("r-htmlwidgets" ,r-htmlwidgets) | |
7512 | ("r-plotly" ,r-plotly) | |
7513 | ("r-plyr" ,r-plyr) | |
7514 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
7515 | ("r-reshape" ,r-reshape) | |
7516 | ("r-shiny" ,r-shiny) | |
7517 | ("r-shinycssloaders" ,r-shinycssloaders) | |
7518 | ("r-shinydashboard" ,r-shinydashboard) | |
7519 | ("r-stringr" ,r-stringr) | |
d0badcc1 | 7520 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
d38775b1 | 7521 | ("r-tidyr" ,r-tidyr))) |
1f2f01ae RW |
7522 | (native-inputs |
7523 | `(("r-knitr" ,r-knitr))) | |
d38775b1 RW |
7524 | (home-page "https://github.com/lindsayrutter/bigPint") |
7525 | (synopsis "Big multivariate data plotted interactively") | |
7526 | (description | |
7527 | "This package provides methods for visualizing large multivariate | |
7528 | datasets using static and interactive scatterplot matrices, parallel | |
7529 | coordinate plots, volcano plots, and litre plots. It includes examples for | |
7530 | visualizing RNA-sequencing datasets and differentially expressed genes.") | |
7531 | (license license:gpl3))) | |
991554fc RW |
7532 | |
7533 | (define-public r-chemminer | |
7534 | (package | |
7535 | (name "r-chemminer") | |
06908a73 | 7536 | (version "3.40.0") |
991554fc RW |
7537 | (source |
7538 | (origin | |
7539 | (method url-fetch) | |
7540 | (uri (bioconductor-uri "ChemmineR" version)) | |
7541 | (sha256 | |
7542 | (base32 | |
06908a73 | 7543 | "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf")))) |
991554fc RW |
7544 | (properties `((upstream-name . "ChemmineR"))) |
7545 | (build-system r-build-system) | |
7546 | (propagated-inputs | |
7547 | `(("r-base64enc" ,r-base64enc) | |
7548 | ("r-bh" ,r-bh) | |
7549 | ("r-biocgenerics" ,r-biocgenerics) | |
7550 | ("r-dbi" ,r-dbi) | |
7551 | ("r-digest" ,r-digest) | |
7552 | ("r-dt" ,r-dt) | |
7553 | ("r-ggplot2" ,r-ggplot2) | |
7554 | ("r-gridextra" ,r-gridextra) | |
7555 | ("r-png" ,r-png) | |
7556 | ("r-rcpp" ,r-rcpp) | |
7557 | ("r-rcurl" ,r-rcurl) | |
7558 | ("r-rjson" ,r-rjson) | |
7559 | ("r-rsvg" ,r-rsvg))) | |
06908a73 RW |
7560 | (native-inputs |
7561 | `(("r-knitr" ,r-knitr))) | |
991554fc RW |
7562 | (home-page "https://github.com/girke-lab/ChemmineR") |
7563 | (synopsis "Cheminformatics toolkit for R") | |
7564 | (description | |
7565 | "ChemmineR is a cheminformatics package for analyzing drug-like small | |
7566 | molecule data in R. It contains functions for efficient processing of large | |
7567 | numbers of molecules, physicochemical/structural property predictions, | |
7568 | structural similarity searching, classification and clustering of compound | |
7569 | libraries with a wide spectrum of algorithms. In addition, it offers | |
7570 | visualization functions for compound clustering results and chemical | |
7571 | structures.") | |
7572 | (license license:artistic2.0))) | |
48bcbef0 RW |
7573 | |
7574 | (define-public r-bioassayr | |
7575 | (package | |
7576 | (name "r-bioassayr") | |
c8cbde9f | 7577 | (version "1.26.0") |
48bcbef0 RW |
7578 | (source |
7579 | (origin | |
7580 | (method url-fetch) | |
7581 | (uri (bioconductor-uri "bioassayR" version)) | |
7582 | (sha256 | |
7583 | (base32 | |
c8cbde9f | 7584 | "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy")))) |
48bcbef0 RW |
7585 | (properties `((upstream-name . "bioassayR"))) |
7586 | (build-system r-build-system) | |
7587 | (propagated-inputs | |
7588 | `(("r-biocgenerics" ,r-biocgenerics) | |
7589 | ("r-chemminer" ,r-chemminer) | |
7590 | ("r-dbi" ,r-dbi) | |
7591 | ("r-matrix" ,r-matrix) | |
7592 | ("r-rjson" ,r-rjson) | |
7593 | ("r-rsqlite" ,r-rsqlite) | |
7594 | ("r-xml" ,r-xml))) | |
faaf2b35 RW |
7595 | (native-inputs |
7596 | `(("r-knitr" ,r-knitr))) | |
48bcbef0 RW |
7597 | (home-page "https://github.com/TylerBackman/bioassayR") |
7598 | (synopsis "Cross-target analysis of small molecule bioactivity") | |
7599 | (description | |
7600 | "bioassayR is a computational tool that enables simultaneous analysis of | |
7601 | thousands of bioassay experiments performed over a diverse set of compounds | |
7602 | and biological targets. Unique features include support for large-scale | |
7603 | cross-target analyses of both public and custom bioassays, generation of | |
7604 | @dfn{high throughput screening fingerprints} (HTSFPs), and an optional | |
7605 | preloaded database that provides access to a substantial portion of publicly | |
7606 | available bioactivity data.") | |
7607 | (license license:artistic2.0))) | |
29fd736a RW |
7608 | |
7609 | (define-public r-biobroom | |
7610 | (package | |
7611 | (name "r-biobroom") | |
e09ca033 | 7612 | (version "1.20.0") |
29fd736a RW |
7613 | (source |
7614 | (origin | |
7615 | (method url-fetch) | |
7616 | (uri (bioconductor-uri "biobroom" version)) | |
7617 | (sha256 | |
7618 | (base32 | |
e09ca033 | 7619 | "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf")))) |
29fd736a RW |
7620 | (properties `((upstream-name . "biobroom"))) |
7621 | (build-system r-build-system) | |
7622 | (propagated-inputs | |
7623 | `(("r-biobase" ,r-biobase) | |
7624 | ("r-broom" ,r-broom) | |
7625 | ("r-dplyr" ,r-dplyr) | |
7626 | ("r-tidyr" ,r-tidyr))) | |
e09ca033 RW |
7627 | (native-inputs |
7628 | `(("r-knitr" ,r-knitr))) | |
29fd736a RW |
7629 | (home-page "https://github.com/StoreyLab/biobroom") |
7630 | (synopsis "Turn Bioconductor objects into tidy data frames") | |
7631 | (description | |
7632 | "This package contains methods for converting standard objects | |
7633 | constructed by bioinformatics packages, especially those in Bioconductor, and | |
7634 | converting them to @code{tidy} data. It thus serves as a complement to the | |
7635 | @code{broom} package, and follows the same tidy, augment, glance division of | |
7636 | tidying methods. Tidying data makes it easy to recombine, reshape and | |
7637 | visualize bioinformatics analyses.") | |
7638 | ;; Any version of the LGPL. | |
7639 | (license license:lgpl3+))) | |
c373223e RW |
7640 | |
7641 | (define-public r-graphite | |
7642 | (package | |
7643 | (name "r-graphite") | |
29b17027 | 7644 | (version "1.34.0") |
c373223e RW |
7645 | (source |
7646 | (origin | |
7647 | (method url-fetch) | |
7648 | (uri (bioconductor-uri "graphite" version)) | |
7649 | (sha256 | |
7650 | (base32 | |
29b17027 | 7651 | "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p")))) |
c373223e RW |
7652 | (properties `((upstream-name . "graphite"))) |
7653 | (build-system r-build-system) | |
7654 | (propagated-inputs | |
7655 | `(("r-annotationdbi" ,r-annotationdbi) | |
7656 | ("r-checkmate" ,r-checkmate) | |
7657 | ("r-graph" ,r-graph) | |
7658 | ("r-httr" ,r-httr) | |
7659 | ("r-rappdirs" ,r-rappdirs))) | |
7660 | (home-page "https://bioconductor.org/packages/graphite/") | |
7661 | (synopsis "Networks from pathway databases") | |
7662 | (description | |
7663 | "Graphite provides networks derived from eight public pathway databases, | |
7664 | and automates the conversion of node identifiers (e.g. from Entrez IDs to gene | |
7665 | symbols).") | |
7666 | (license license:agpl3+))) | |
f388834e RW |
7667 | |
7668 | (define-public r-reactomepa | |
7669 | (package | |
7670 | (name "r-reactomepa") | |
affb4ab3 | 7671 | (version "1.32.0") |
f388834e RW |
7672 | (source |
7673 | (origin | |
7674 | (method url-fetch) | |
7675 | (uri (bioconductor-uri "ReactomePA" version)) | |
7676 | (sha256 | |
7677 | (base32 | |
affb4ab3 | 7678 | "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x")))) |
f388834e RW |
7679 | (properties `((upstream-name . "ReactomePA"))) |
7680 | (build-system r-build-system) | |
7681 | (propagated-inputs | |
7682 | `(("r-annotationdbi" ,r-annotationdbi) | |
7683 | ("r-dose" ,r-dose) | |
7684 | ("r-enrichplot" ,r-enrichplot) | |
7685 | ("r-ggplot2" ,r-ggplot2) | |
7686 | ("r-ggraph" ,r-ggraph) | |
7687 | ("r-graphite" ,r-graphite) | |
7688 | ("r-igraph" ,r-igraph) | |
7689 | ("r-reactome-db" ,r-reactome-db))) | |
affb4ab3 RW |
7690 | (native-inputs |
7691 | `(("r-knitr" ,r-knitr))) | |
f388834e RW |
7692 | (home-page "https://guangchuangyu.github.io/software/ReactomePA") |
7693 | (synopsis "Reactome pathway analysis") | |
7694 | (description | |
7695 | "This package provides functions for pathway analysis based on the | |
7696 | REACTOME pathway database. It implements enrichment analysis, gene set | |
7697 | enrichment analysis and several functions for visualization.") | |
7698 | (license license:gpl2))) | |
21afe920 RW |
7699 | |
7700 | (define-public r-ebarrays | |
7701 | (package | |
7702 | (name "r-ebarrays") | |
a74a427b | 7703 | (version "2.52.0") |
21afe920 RW |
7704 | (source |
7705 | (origin | |
7706 | (method url-fetch) | |
7707 | (uri (bioconductor-uri "EBarrays" version)) | |
7708 | (sha256 | |
7709 | (base32 | |
a74a427b | 7710 | "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf")))) |
21afe920 RW |
7711 | (properties `((upstream-name . "EBarrays"))) |
7712 | (build-system r-build-system) | |
7713 | (propagated-inputs | |
7714 | `(("r-biobase" ,r-biobase) | |
7715 | ("r-cluster" ,r-cluster) | |
7716 | ("r-lattice" ,r-lattice))) | |
7717 | (home-page "https://bioconductor.org/packages/EBarrays/") | |
7718 | (synopsis "Gene clustering and differential expression identification") | |
7719 | (description | |
7720 | "EBarrays provides tools for the analysis of replicated/unreplicated | |
7721 | microarray data.") | |
7722 | (license license:gpl2+))) | |
f180be29 RW |
7723 | |
7724 | (define-public r-bioccasestudies | |
7725 | (package | |
7726 | (name "r-bioccasestudies") | |
8b71b141 | 7727 | (version "1.50.0") |
f180be29 RW |
7728 | (source |
7729 | (origin | |
7730 | (method url-fetch) | |
7731 | (uri (bioconductor-uri "BiocCaseStudies" version)) | |
7732 | (sha256 | |
7733 | (base32 | |
8b71b141 | 7734 | "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix")))) |
f180be29 RW |
7735 | (properties |
7736 | `((upstream-name . "BiocCaseStudies"))) | |
7737 | (build-system r-build-system) | |
7738 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
7739 | (home-page "https://bioconductor.org/packages/BiocCaseStudies") | |
7740 | (synopsis "Support for the case studies monograph") | |
7741 | (description | |
7742 | "This package provides software and data to support the case studies | |
7743 | monograph.") | |
7744 | (license license:artistic2.0))) | |
49f0860b RW |
7745 | |
7746 | (define-public r-biocgraph | |
7747 | (package | |
7748 | (name "r-biocgraph") | |
543c63f2 | 7749 | (version "1.50.0") |
49f0860b RW |
7750 | (source |
7751 | (origin | |
7752 | (method url-fetch) | |
7753 | (uri (bioconductor-uri "biocGraph" version)) | |
7754 | (sha256 | |
7755 | (base32 | |
543c63f2 | 7756 | "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj")))) |
49f0860b RW |
7757 | (properties `((upstream-name . "biocGraph"))) |
7758 | (build-system r-build-system) | |
7759 | (propagated-inputs | |
7760 | `(("r-biocgenerics" ,r-biocgenerics) | |
7761 | ("r-geneplotter" ,r-geneplotter) | |
7762 | ("r-graph" ,r-graph) | |
7763 | ("r-rgraphviz" ,r-rgraphviz))) | |
7764 | (home-page "https://bioconductor.org/packages/biocGraph/") | |
7765 | (synopsis "Graph examples and use cases in Bioinformatics") | |
7766 | (description | |
7767 | "This package provides examples and code that make use of the | |
7768 | different graph related packages produced by Bioconductor.") | |
7769 | (license license:artistic2.0))) | |
244270e6 RW |
7770 | |
7771 | (define-public r-experimenthub | |
7772 | (package | |
7773 | (name "r-experimenthub") | |
a27a402e | 7774 | (version "1.14.2") |
244270e6 RW |
7775 | (source |
7776 | (origin | |
7777 | (method url-fetch) | |
7778 | (uri (bioconductor-uri "ExperimentHub" version)) | |
7779 | (sha256 | |
7780 | (base32 | |
a27a402e | 7781 | "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x")))) |
244270e6 RW |
7782 | (properties `((upstream-name . "ExperimentHub"))) |
7783 | (build-system r-build-system) | |
7784 | (propagated-inputs | |
7785 | `(("r-annotationhub" ,r-annotationhub) | |
7786 | ("r-biocfilecache" ,r-biocfilecache) | |
7787 | ("r-biocgenerics" ,r-biocgenerics) | |
7788 | ("r-biocmanager" ,r-biocmanager) | |
7789 | ("r-curl" ,r-curl) | |
7790 | ("r-rappdirs" ,r-rappdirs) | |
7791 | ("r-s4vectors" ,r-s4vectors))) | |
b56a3462 RW |
7792 | (native-inputs |
7793 | `(("r-knitr" ,r-knitr))) | |
244270e6 RW |
7794 | (home-page "https://bioconductor.org/packages/ExperimentHub/") |
7795 | (synopsis "Client to access ExperimentHub resources") | |
7796 | (description | |
7797 | "This package provides a client for the Bioconductor ExperimentHub web | |
7798 | resource. ExperimentHub provides a central location where curated data from | |
7799 | experiments, publications or training courses can be accessed. Each resource | |
7800 | has associated metadata, tags and date of modification. The client creates | |
7801 | and manages a local cache of files retrieved enabling quick and reproducible | |
7802 | access.") | |
7803 | (license license:artistic2.0))) | |
06784793 RW |
7804 | |
7805 | (define-public r-multiassayexperiment | |
7806 | (package | |
7807 | (name "r-multiassayexperiment") | |
4091eae2 | 7808 | (version "1.14.0") |
06784793 RW |
7809 | (source |
7810 | (origin | |
7811 | (method url-fetch) | |
7812 | (uri (bioconductor-uri "MultiAssayExperiment" version)) | |
7813 | (sha256 | |
7814 | (base32 | |
4091eae2 | 7815 | "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh")))) |
06784793 RW |
7816 | (properties |
7817 | `((upstream-name . "MultiAssayExperiment"))) | |
7818 | (build-system r-build-system) | |
7819 | (propagated-inputs | |
7820 | `(("r-biobase" ,r-biobase) | |
7821 | ("r-biocgenerics" ,r-biocgenerics) | |
7822 | ("r-genomicranges" ,r-genomicranges) | |
7823 | ("r-iranges" ,r-iranges) | |
7824 | ("r-s4vectors" ,r-s4vectors) | |
7825 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
7826 | ("r-tidyr" ,r-tidyr))) | |
5d45d711 RW |
7827 | (native-inputs |
7828 | `(("r-knitr" ,r-knitr))) | |
798ca8d0 | 7829 | (home-page "https://waldronlab.io/MultiAssayExperiment/") |
06784793 RW |
7830 | (synopsis "Integration of multi-omics experiments in Bioconductor") |
7831 | (description | |
7832 | "MultiAssayExperiment harmonizes data management of multiple assays | |
7833 | performed on an overlapping set of specimens. It provides a familiar | |
7834 | Bioconductor user experience by extending concepts from | |
7835 | @code{SummarizedExperiment}, supporting an open-ended mix of standard data | |
7836 | classes for individual assays, and allowing subsetting by genomic ranges or | |
7837 | rownames.") | |
7838 | (license license:artistic2.0))) | |
c2b36a04 RW |
7839 | |
7840 | (define-public r-bioconcotk | |
7841 | (package | |
7842 | (name "r-bioconcotk") | |
1c518215 | 7843 | (version "1.8.0") |
c2b36a04 RW |
7844 | (source |
7845 | (origin | |
7846 | (method url-fetch) | |
7847 | (uri (bioconductor-uri "BiocOncoTK" version)) | |
7848 | (sha256 | |
7849 | (base32 | |
1c518215 | 7850 | "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk")))) |
c2b36a04 RW |
7851 | (properties `((upstream-name . "BiocOncoTK"))) |
7852 | (build-system r-build-system) | |
7853 | (propagated-inputs | |
7854 | `(("r-bigrquery" ,r-bigrquery) | |
7855 | ("r-car" ,r-car) | |
7856 | ("r-complexheatmap" ,r-complexheatmap) | |
7857 | ("r-curatedtcgadata" ,r-curatedtcgadata) | |
7858 | ("r-dbi" ,r-dbi) | |
7859 | ("r-dplyr" ,r-dplyr) | |
7860 | ("r-dt" ,r-dt) | |
7861 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7862 | ("r-genomicranges" ,r-genomicranges) | |
7863 | ("r-ggplot2" ,r-ggplot2) | |
7864 | ("r-ggpubr" ,r-ggpubr) | |
7865 | ("r-graph" ,r-graph) | |
7866 | ("r-httr" ,r-httr) | |
7867 | ("r-iranges" ,r-iranges) | |
7868 | ("r-magrittr" ,r-magrittr) | |
7869 | ("r-plyr" ,r-plyr) | |
7870 | ("r-rgraphviz" ,r-rgraphviz) | |
7871 | ("r-rjson" ,r-rjson) | |
7872 | ("r-s4vectors" ,r-s4vectors) | |
7873 | ("r-scales" ,r-scales) | |
7874 | ("r-shiny" ,r-shiny) | |
7875 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1c518215 RW |
7876 | (native-inputs |
7877 | `(("r-knitr" ,r-knitr))) | |
c2b36a04 RW |
7878 | (home-page "https://bioconductor.org/packages/BiocOncoTK") |
7879 | (synopsis "Bioconductor components for general cancer genomics") | |
7880 | (description | |
7881 | "The purpose of this package is to provide a central interface to various | |
7882 | tools for genome-scale analysis of cancer studies.") | |
7883 | (license license:artistic2.0))) | |
4d12c1e3 RW |
7884 | |
7885 | (define-public r-biocor | |
7886 | (package | |
7887 | (name "r-biocor") | |
132abe5f | 7888 | (version "1.12.0") |
4d12c1e3 RW |
7889 | (source |
7890 | (origin | |
7891 | (method url-fetch) | |
7892 | (uri (bioconductor-uri "BioCor" version)) | |
7893 | (sha256 | |
7894 | (base32 | |
132abe5f | 7895 | "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy")))) |
4d12c1e3 RW |
7896 | (properties `((upstream-name . "BioCor"))) |
7897 | (build-system r-build-system) | |
7898 | (propagated-inputs | |
7899 | `(("r-biocparallel" ,r-biocparallel) | |
7900 | ("r-gseabase" ,r-gseabase) | |
7901 | ("r-matrix" ,r-matrix))) | |
132abe5f RW |
7902 | (native-inputs |
7903 | `(("r-knitr" ,r-knitr))) | |
4d12c1e3 RW |
7904 | (home-page "https://llrs.github.io/BioCor/") |
7905 | (synopsis "Functional similarities") | |
7906 | (description | |
7907 | "This package provides tools to calculate functional similarities based | |
7908 | on the pathways described on KEGG and REACTOME or in gene sets. These | |
7909 | similarities can be calculated for pathways or gene sets, genes, or clusters | |
7910 | and combined with other similarities. They can be used to improve networks, | |
7911 | gene selection, testing relationships, and so on.") | |
7912 | (license license:expat))) | |
4a18112d RW |
7913 | |
7914 | (define-public r-biocpkgtools | |
7915 | (package | |
7916 | (name "r-biocpkgtools") | |
1759a13d | 7917 | (version "1.6.0") |
4a18112d RW |
7918 | (source |
7919 | (origin | |
7920 | (method url-fetch) | |
7921 | (uri (bioconductor-uri "BiocPkgTools" version)) | |
7922 | (sha256 | |
7923 | (base32 | |
1759a13d | 7924 | "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr")))) |
4a18112d RW |
7925 | (properties `((upstream-name . "BiocPkgTools"))) |
7926 | (build-system r-build-system) | |
7927 | (propagated-inputs | |
2d6a7bca RW |
7928 | `(("r-biocfilecache" ,r-biocfilecache) |
7929 | ("r-biocmanager" ,r-biocmanager) | |
4a18112d RW |
7930 | ("r-biocviews" ,r-biocviews) |
7931 | ("r-dplyr" ,r-dplyr) | |
7932 | ("r-dt" ,r-dt) | |
7933 | ("r-gh" ,r-gh) | |
7934 | ("r-graph" ,r-graph) | |
7935 | ("r-htmltools" ,r-htmltools) | |
7936 | ("r-htmlwidgets" ,r-htmlwidgets) | |
7937 | ("r-httr" ,r-httr) | |
7938 | ("r-igraph" ,r-igraph) | |
7939 | ("r-jsonlite" ,r-jsonlite) | |
7940 | ("r-magrittr" ,r-magrittr) | |
2d6a7bca | 7941 | ("r-rappdirs" ,r-rappdirs) |
4a18112d RW |
7942 | ("r-rbgl" ,r-rbgl) |
7943 | ("r-readr" ,r-readr) | |
7944 | ("r-rex" ,r-rex) | |
2d6a7bca | 7945 | ("r-rlang" ,r-rlang) |
4a18112d RW |
7946 | ("r-rvest" ,r-rvest) |
7947 | ("r-stringr" ,r-stringr) | |
7948 | ("r-tibble" ,r-tibble) | |
7949 | ("r-tidyr" ,r-tidyr) | |
2d6a7bca | 7950 | ("r-tidyselect" ,r-tidyselect) |
4a18112d | 7951 | ("r-xml2" ,r-xml2))) |
2d6a7bca RW |
7952 | (native-inputs |
7953 | `(("r-knitr" ,r-knitr))) | |
4a18112d RW |
7954 | (home-page "https://github.com/seandavi/BiocPkgTools") |
7955 | (synopsis "Collection of tools for learning about Bioconductor packages") | |
7956 | (description | |
7957 | "Bioconductor has a rich ecosystem of metadata around packages, usage, | |
7958 | and build status. This package is a simple collection of functions to access | |
7959 | that metadata from R. The goal is to expose metadata for data mining and | |
7960 | value-added functionality such as package searching, text mining, and | |
7961 | analytics on packages.") | |
7962 | (license license:expat))) | |
43b66e3f RW |
7963 | |
7964 | (define-public r-biocset | |
7965 | (package | |
7966 | (name "r-biocset") | |
b828c3ea | 7967 | (version "1.2.2") |
43b66e3f RW |
7968 | (source |
7969 | (origin | |
7970 | (method url-fetch) | |
7971 | (uri (bioconductor-uri "BiocSet" version)) | |
7972 | (sha256 | |
7973 | (base32 | |
b828c3ea | 7974 | "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj")))) |
43b66e3f RW |
7975 | (properties `((upstream-name . "BiocSet"))) |
7976 | (build-system r-build-system) | |
7977 | (propagated-inputs | |
7978 | `(("r-annotationdbi" ,r-annotationdbi) | |
7979 | ("r-dplyr" ,r-dplyr) | |
7980 | ("r-keggrest" ,r-keggrest) | |
7981 | ("r-plyr" ,r-plyr) | |
7982 | ("r-rlang" ,r-rlang) | |
7983 | ("r-rtracklayer" ,r-rtracklayer) | |
7984 | ("r-tibble" ,r-tibble))) | |
723fa00d RW |
7985 | (native-inputs |
7986 | `(("r-knitr" ,r-knitr))) | |
43b66e3f RW |
7987 | (home-page |
7988 | "https://bioconductor.org/packages/BiocSet") | |
7989 | (synopsis | |
7990 | "Representing Different Biological Sets") | |
7991 | (description | |
7992 | "BiocSet displays different biological sets in a triple tibble format. | |
7993 | These three tibbles are @code{element}, @code{set}, and @code{elementset}. | |
5b98473a | 7994 | The user has the ability to activate one of these three tibbles to perform |
43b66e3f RW |
7995 | common functions from the @code{dplyr} package. Mapping functionality and |
7996 | accessing web references for elements/sets are also available in BiocSet.") | |
7997 | (license license:artistic2.0))) | |
0156297f RW |
7998 | |
7999 | (define-public r-biocworkflowtools | |
8000 | (package | |
8001 | (name "r-biocworkflowtools") | |
6a88291d | 8002 | (version "1.14.0") |
0156297f RW |
8003 | (source |
8004 | (origin | |
8005 | (method url-fetch) | |
8006 | (uri (bioconductor-uri "BiocWorkflowTools" version)) | |
8007 | (sha256 | |
8008 | (base32 | |
6a88291d | 8009 | "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy")))) |
0156297f RW |
8010 | (properties |
8011 | `((upstream-name . "BiocWorkflowTools"))) | |
8012 | (build-system r-build-system) | |
8013 | (propagated-inputs | |
8014 | `(("r-biocstyle" ,r-biocstyle) | |
8015 | ("r-bookdown" ,r-bookdown) | |
8016 | ("r-git2r" ,r-git2r) | |
8017 | ("r-httr" ,r-httr) | |
8018 | ("r-knitr" ,r-knitr) | |
8019 | ("r-rmarkdown" ,r-rmarkdown) | |
8020 | ("r-rstudioapi" ,r-rstudioapi) | |
8021 | ("r-stringr" ,r-stringr) | |
8022 | ("r-usethis" ,r-usethis))) | |
4ecba230 RW |
8023 | (native-inputs |
8024 | `(("r-knitr" ,r-knitr))) | |
0156297f RW |
8025 | (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") |
8026 | (synopsis "Tools to aid the development of Bioconductor Workflow packages") | |
8027 | (description | |
8028 | "This package provides functions to ease the transition between | |
8029 | Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") | |
8030 | (license license:expat))) | |
77e2de36 RW |
8031 | |
8032 | (define-public r-biodist | |
8033 | (package | |
8034 | (name "r-biodist") | |
6b9e3b92 | 8035 | (version "1.60.0") |
77e2de36 RW |
8036 | (source |
8037 | (origin | |
8038 | (method url-fetch) | |
8039 | (uri (bioconductor-uri "bioDist" version)) | |
8040 | (sha256 | |
8041 | (base32 | |
6b9e3b92 | 8042 | "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp")))) |
77e2de36 RW |
8043 | (properties `((upstream-name . "bioDist"))) |
8044 | (build-system r-build-system) | |
8045 | (propagated-inputs | |
8046 | `(("r-biobase" ,r-biobase) | |
8047 | ("r-kernsmooth" ,r-kernsmooth))) | |
8048 | (home-page "https://bioconductor.org/packages/bioDist/") | |
8049 | (synopsis "Different distance measures") | |
8050 | (description | |
8051 | "This package provides a collection of software tools for calculating | |
8052 | distance measures.") | |
8053 | (license license:artistic2.0))) | |
9bc516ba RW |
8054 | |
8055 | (define-public r-pcatools | |
8056 | (package | |
8057 | (name "r-pcatools") | |
8058 | (version "2.0.0") | |
8059 | (source | |
8060 | (origin | |
8061 | (method url-fetch) | |
8062 | (uri (bioconductor-uri "PCAtools" version)) | |
8063 | (sha256 | |
8064 | (base32 | |
8065 | "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc")))) | |
8066 | (properties `((upstream-name . "PCAtools"))) | |
8067 | (build-system r-build-system) | |
8068 | (propagated-inputs | |
8069 | `(("r-beachmat" ,r-beachmat) | |
8070 | ("r-bh" ,r-bh) | |
8071 | ("r-biocparallel" ,r-biocparallel) | |
8072 | ("r-biocsingular" ,r-biocsingular) | |
8073 | ("r-cowplot" ,r-cowplot) | |
8074 | ("r-delayedarray" ,r-delayedarray) | |
8075 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
8076 | ("r-dqrng" ,r-dqrng) | |
8077 | ("r-ggplot2" ,r-ggplot2) | |
8078 | ("r-ggrepel" ,r-ggrepel) | |
8079 | ("r-lattice" ,r-lattice) | |
8080 | ("r-matrix" ,r-matrix) | |
8081 | ("r-rcpp" ,r-rcpp) | |
8082 | ("r-reshape2" ,r-reshape2))) | |
8083 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8084 | (home-page "https://github.com/kevinblighe/PCAtools") | |
8085 | (synopsis "PCAtools: everything Principal Components Analysis") | |
8086 | (description | |
8087 | "@dfn{Principal Component Analysis} (PCA) extracts the fundamental | |
8088 | structure of the data without the need to build any model to represent it. | |
8089 | This \"summary\" of the data is arrived at through a process of reduction that | |
8090 | can transform the large number of variables into a lesser number that are | |
8091 | uncorrelated (i.e. the 'principal components'), while at the same time being | |
8092 | capable of easy interpretation on the original data. PCAtools provides | |
8093 | functions for data exploration via PCA, and allows the user to generate | |
8094 | publication-ready figures. PCA is performed via @code{BiocSingular}; users | |
8095 | can also identify an optimal number of principal components via different | |
8096 | metrics, such as the elbow method and Horn's parallel analysis, which has | |
8097 | relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high | |
8098 | dimensional mass cytometry data.") | |
8099 | (license license:gpl3))) | |
c89afe75 RW |
8100 | |
8101 | (define-public r-rgreat | |
8102 | (package | |
8103 | (name "r-rgreat") | |
8104 | (version "1.20.0") | |
8105 | (source | |
8106 | (origin | |
8107 | (method url-fetch) | |
8108 | (uri (bioconductor-uri "rGREAT" version)) | |
8109 | (sha256 | |
8110 | (base32 | |
8111 | "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v")))) | |
8112 | (properties `((upstream-name . "rGREAT"))) | |
8113 | (build-system r-build-system) | |
8114 | (propagated-inputs | |
8115 | `(("r-genomicranges" ,r-genomicranges) | |
8116 | ("r-getoptlong" ,r-getoptlong) | |
8117 | ("r-iranges" ,r-iranges) | |
8118 | ("r-rcurl" ,r-rcurl) | |
8119 | ("r-rjson" ,r-rjson))) | |
8120 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8121 | (home-page "https://github.com/jokergoo/rGREAT") | |
8122 | (synopsis "Client for GREAT analysis") | |
8123 | (description | |
8124 | "This package makes GREAT (Genomic Regions Enrichment of Annotations | |
8125 | Tool) analysis automatic by constructing a HTTP POST request according to | |
8126 | user's input and automatically retrieving results from GREAT web server.") | |
8127 | (license license:expat))) | |
0b8c7e4b RW |
8128 | |
8129 | (define-public r-m3c | |
8130 | (package | |
8131 | (name "r-m3c") | |
8132 | (version "1.10.0") | |
8133 | (source | |
8134 | (origin | |
8135 | (method url-fetch) | |
8136 | (uri (bioconductor-uri "M3C" version)) | |
8137 | (sha256 | |
8138 | (base32 | |
8139 | "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y")))) | |
8140 | (properties `((upstream-name . "M3C"))) | |
8141 | (build-system r-build-system) | |
8142 | (propagated-inputs | |
8143 | `(("r-cluster" ,r-cluster) | |
8144 | ("r-corpcor" ,r-corpcor) | |
8145 | ("r-doparallel" ,r-doparallel) | |
8146 | ("r-dosnow" ,r-dosnow) | |
8147 | ("r-foreach" ,r-foreach) | |
8148 | ("r-ggplot2" ,r-ggplot2) | |
8149 | ("r-matrix" ,r-matrix) | |
8150 | ("r-matrixcalc" ,r-matrixcalc) | |
8151 | ("r-rtsne" ,r-rtsne) | |
8152 | ("r-umap" ,r-umap))) | |
8153 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8154 | (home-page "https://bioconductor.org/packages/M3C") | |
8155 | (synopsis "Monte Carlo reference-based consensus clustering") | |
8156 | (description | |
8157 | "M3C is a consensus clustering algorithm that uses a Monte Carlo | |
8158 | simulation to eliminate overestimation of @code{K} and can reject the null | |
8159 | hypothesis @code{K=1}.") | |
8160 | (license license:agpl3+))) | |
488001eb PL |
8161 | |
8162 | (define-public r-icens | |
8163 | (package | |
8164 | (name "r-icens") | |
8165 | (version "1.60.0") | |
8166 | (source | |
8167 | (origin | |
8168 | (method url-fetch) | |
8169 | (uri (bioconductor-uri "Icens" version)) | |
8170 | (sha256 | |
8171 | (base32 | |
8172 | "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp")))) | |
8173 | (properties `((upstream-name . "Icens"))) | |
8174 | (build-system r-build-system) | |
8175 | (propagated-inputs | |
8176 | `(("r-survival" ,r-survival))) | |
8177 | (home-page "https://bioconductor.org/packages/Icens") | |
8178 | (synopsis "NPMLE for censored and truncated data") | |
8179 | (description | |
8180 | "This package provides many functions for computing the | |
8181 | @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and | |
8182 | truncated data.") | |
8183 | (license license:artistic2.0))) | |
655c4bb2 PL |
8184 | |
8185 | ;; This is a CRAN package but it depends on r-icens, which is published on | |
8186 | ;; Bioconductor. | |
8187 | (define-public r-interval | |
8188 | (package | |
8189 | (name "r-interval") | |
8190 | (version "1.1-0.1") | |
8191 | (source | |
8192 | (origin | |
8193 | (method url-fetch) | |
8194 | (uri (cran-uri "interval" version)) | |
8195 | (sha256 | |
8196 | (base32 | |
8197 | "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8")))) | |
8198 | (properties `((upstream-name . "interval"))) | |
8199 | (build-system r-build-system) | |
8200 | (propagated-inputs | |
8201 | `(("r-icens" ,r-icens) | |
8202 | ("r-mlecens" ,r-mlecens) | |
8203 | ("r-perm" ,r-perm) | |
8204 | ("r-survival" ,r-survival))) | |
8205 | (home-page "https://cran.r-project.org/web/packages/interval/") | |
8206 | (synopsis "Weighted Logrank tests and NPMLE for interval censored data") | |
8207 | (description | |
8208 | "This package provides functions to fit nonparametric survival curves, | |
8209 | plot them, and perform logrank or Wilcoxon type tests.") | |
8210 | (license license:gpl2+))) | |
7e88ee9f PL |
8211 | |
8212 | ;; This is a CRAN package, but it depends on r-interval, which depends on a | |
8213 | ;; Bioconductor package. | |
8214 | (define-public r-fhtest | |
8215 | (package | |
8216 | (name "r-fhtest") | |
8217 | (version "1.4") | |
8218 | (source | |
8219 | (origin | |
8220 | (method url-fetch) | |
8221 | (uri (cran-uri "FHtest" version)) | |
8222 | (sha256 | |
8223 | (base32 | |
8224 | "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2")))) | |
8225 | (properties `((upstream-name . "FHtest"))) | |
8226 | (build-system r-build-system) | |
8227 | (propagated-inputs | |
8228 | `(("r-interval" ,r-interval) | |
8229 | ("r-kmsurv" ,r-kmsurv) | |
8230 | ("r-mass" ,r-mass) | |
8231 | ("r-perm" ,r-perm) | |
8232 | ("r-survival" ,r-survival))) | |
8233 | (home-page "https://cran.r-project.org/web/packages/FHtest/") | |
8234 | (synopsis "Tests for survival data based on the Fleming-Harrington class") | |
8235 | (description | |
8236 | "This package provides functions to compare two or more survival curves | |
8237 | with: | |
8238 | ||
8239 | @itemize | |
8240 | @item The Fleming-Harrington test for right-censored data based on | |
8241 | permutations and on counting processes. | |
8242 | @item An extension of the Fleming-Harrington test for interval-censored data | |
8243 | based on a permutation distribution and on a score vector distribution. | |
8244 | @end itemize | |
8245 | ") | |
8246 | (license license:gpl2+))) | |
f4d920b9 | 8247 | |
8248 | (define-public r-fourcseq | |
8249 | (package | |
8250 | (name "r-fourcseq") | |
8251 | (version "1.22.1") | |
8252 | (source | |
8253 | (origin | |
8254 | (method url-fetch) | |
8255 | (uri (bioconductor-uri "FourCSeq" version)) | |
8256 | (sha256 | |
8257 | (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b")))) | |
8258 | (properties `((upstream-name . "FourCSeq"))) | |
8259 | (build-system r-build-system) | |
8260 | (propagated-inputs | |
8261 | `(("r-biobase" ,r-biobase) | |
8262 | ("r-biostrings" ,r-biostrings) | |
8263 | ("r-deseq2" ,r-deseq2) | |
8264 | ("r-fda" ,r-fda) | |
8265 | ("r-genomicalignments" ,r-genomicalignments) | |
8266 | ("r-genomicranges" ,r-genomicranges) | |
8267 | ("r-ggbio" ,r-ggbio) | |
8268 | ("r-ggplot2" ,r-ggplot2) | |
8269 | ("r-gtools" ,r-gtools) | |
8270 | ("r-lsd" ,r-lsd) | |
8271 | ("r-matrix" ,r-matrix) | |
8272 | ("r-reshape2" ,r-reshape2) | |
8273 | ("r-rsamtools" ,r-rsamtools) | |
8274 | ("r-rtracklayer" ,r-rtracklayer) | |
8275 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
8276 | (native-inputs | |
8277 | `(("r-knitr" ,r-knitr))) | |
8278 | (home-page | |
8279 | "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") | |
8280 | (synopsis "Analysis of multiplexed 4C sequencing data") | |
8281 | (description | |
8282 | "This package is an R package dedicated to the analysis of (multiplexed) | |
8283 | 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific | |
8284 | interactions between DNA elements and identify differential interactions | |
8285 | between conditions. The statistical analysis in R starts with individual bam | |
8286 | files for each sample as inputs. To obtain these files, the package contains | |
8287 | a Python script to demultiplex libraries and trim off primer sequences. With | |
8288 | a standard alignment software the required bam files can be then be | |
8289 | generated.") | |
8290 | (license license:gpl3+))) | |
6e0ab26f | 8291 | |
8292 | (define-public r-preprocesscore | |
8293 | (package | |
8294 | (name "r-preprocesscore") | |
8295 | (version "1.50.0") | |
8296 | (source | |
8297 | (origin | |
8298 | (method url-fetch) | |
8299 | (uri (bioconductor-uri "preprocessCore" version)) | |
8300 | (sha256 | |
8301 | (base32 | |
8302 | "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl")))) | |
8303 | (properties | |
8304 | `((upstream-name . "preprocessCore"))) | |
8305 | (build-system r-build-system) | |
8306 | (home-page "https://github.com/bmbolstad/preprocessCore") | |
8307 | (synopsis "Collection of pre-processing functions") | |
8308 | (description | |
8309 | "This package provides a library of core pre-processing and normalization | |
8310 | routines.") | |
8311 | (license license:lgpl2.0+))) | |
b3a99837 | 8312 | |
3159fcf1 RW |
8313 | ;; This is a CRAN package, but it depends on preprocessorcore, which is a |
8314 | ;; Bioconductor package. | |
8315 | (define-public r-wgcna | |
8316 | (package | |
8317 | (name "r-wgcna") | |
8318 | (version "1.69") | |
8319 | (source | |
8320 | (origin | |
8321 | (method url-fetch) | |
8322 | (uri (cran-uri "WGCNA" version)) | |
8323 | (sha256 | |
8324 | (base32 | |
8325 | "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f")))) | |
8326 | (properties `((upstream-name . "WGCNA"))) | |
8327 | (build-system r-build-system) | |
8328 | (propagated-inputs | |
8329 | `(("r-annotationdbi" ,r-annotationdbi) | |
8330 | ("r-doparallel" ,r-doparallel) | |
8331 | ("r-dynamictreecut" ,r-dynamictreecut) | |
8332 | ("r-fastcluster" ,r-fastcluster) | |
8333 | ("r-foreach" ,r-foreach) | |
8334 | ("r-go-db" ,r-go-db) | |
8335 | ("r-hmisc" ,r-hmisc) | |
8336 | ("r-impute" ,r-impute) | |
8337 | ("r-rcpp" ,r-rcpp) | |
8338 | ("r-survival" ,r-survival) | |
8339 | ("r-matrixstats" ,r-matrixstats) | |
8340 | ("r-preprocesscore" ,r-preprocesscore))) | |
8341 | (home-page | |
8342 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") | |
8343 | (synopsis "Weighted correlation network analysis") | |
8344 | (description | |
8345 | "This package provides functions necessary to perform Weighted | |
8346 | Correlation Network Analysis on high-dimensional data. It includes functions | |
8347 | for rudimentary data cleaning, construction and summarization of correlation | |
8348 | networks, module identification and functions for relating both variables and | |
8349 | modules to sample traits. It also includes a number of utility functions for | |
8350 | data manipulation and visualization.") | |
8351 | (license license:gpl2+))) | |
8352 | ||
b3a99837 | 8353 | (define-public r-rgraphviz |
8354 | (package | |
8355 | (name "r-rgraphviz") | |
8356 | (version "2.32.0") | |
8357 | (source | |
8358 | (origin | |
8359 | (method url-fetch) | |
8360 | (uri (bioconductor-uri "Rgraphviz" version)) | |
8361 | (sha256 | |
8362 | (base32 | |
8363 | "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y")))) | |
8364 | (properties `((upstream-name . "Rgraphviz"))) | |
8365 | (build-system r-build-system) | |
8366 | (arguments | |
8367 | `(#:phases | |
8368 | (modify-phases %standard-phases | |
8369 | (add-after 'unpack 'make-reproducible | |
8370 | (lambda _ | |
8371 | ;; The replacement value is taken from src/graphviz/builddate.h | |
8372 | (substitute* "src/graphviz/configure" | |
8373 | (("VERSION_DATE=.*") | |
8374 | "VERSION_DATE=20200427.2341\n")) | |
8375 | #t))))) | |
8376 | ;; FIXME: Rgraphviz bundles the sources of an older variant of | |
8377 | ;; graphviz. It does not build with the latest version of graphviz, so | |
8378 | ;; we do not add graphviz to the inputs. | |
8379 | (inputs `(("zlib" ,zlib))) | |
8380 | (propagated-inputs | |
8381 | `(("r-graph" ,r-graph))) | |
8382 | (native-inputs | |
8383 | `(("pkg-config" ,pkg-config))) | |
8384 | (home-page "https://bioconductor.org/packages/Rgraphviz") | |
8385 | (synopsis "Plotting capabilities for R graph objects") | |
8386 | (description | |
8387 | "This package interfaces R with the graphviz library for plotting R graph | |
8388 | objects from the @code{graph} package.") | |
8389 | (license license:epl1.0))) | |
8c7c6db4 | 8390 | |
3292f6ed | 8391 | (define-public r-fithic |
8392 | (package | |
8393 | (name "r-fithic") | |
8394 | (version "1.14.0") | |
8395 | (source (origin | |
8396 | (method url-fetch) | |
8397 | (uri (bioconductor-uri "FitHiC" version)) | |
8398 | (sha256 | |
8399 | (base32 | |
8400 | "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp")))) | |
8401 | (properties `((upstream-name . "FitHiC"))) | |
8402 | (build-system r-build-system) | |
8403 | (propagated-inputs | |
8404 | `(("r-data-table" ,r-data-table) | |
8405 | ("r-fdrtool" ,r-fdrtool) | |
8406 | ("r-rcpp" ,r-rcpp))) | |
8407 | (native-inputs | |
8408 | `(("r-knitr" ,r-knitr))) | |
8409 | (home-page "https://bioconductor.org/packages/FitHiC") | |
8410 | (synopsis "Confidence estimation for intra-chromosomal contact maps") | |
8411 | (description | |
8412 | "Fit-Hi-C is a tool for assigning statistical confidence estimates to | |
8413 | intra-chromosomal contact maps produced by genome-wide genome architecture | |
8414 | assays such as Hi-C.") | |
8415 | (license license:gpl2+))) | |
8416 | ||
7df42d37 | 8417 | (define-public r-hitc |
8418 | (package | |
8419 | (name "r-hitc") | |
8420 | (version "1.32.0") | |
8421 | (source (origin | |
8422 | (method url-fetch) | |
8423 | (uri (bioconductor-uri "HiTC" version)) | |
8424 | (sha256 | |
8425 | (base32 | |
8426 | "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) | |
8427 | (properties `((upstream-name . "HiTC"))) | |
8428 | (build-system r-build-system) | |
8429 | (propagated-inputs | |
8430 | `(("r-biostrings" ,r-biostrings) | |
8431 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8432 | ("r-genomicranges" ,r-genomicranges) | |
8433 | ("r-iranges" ,r-iranges) | |
8434 | ("r-matrix" ,r-matrix) | |
8435 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
8436 | ("r-rtracklayer" ,r-rtracklayer))) | |
8437 | (home-page "https://bioconductor.org/packages/HiTC") | |
8438 | (synopsis "High throughput chromosome conformation capture analysis") | |
8439 | (description | |
8440 | "The HiTC package was developed to explore high-throughput \"C\" data | |
8441 | such as 5C or Hi-C. Dedicated R classes as well as standard methods for | |
8442 | quality controls, normalization, visualization, and further analysis are also | |
8443 | provided.") | |
8444 | (license license:artistic2.0))) | |
8445 | ||
63b75c01 | 8446 | (define-public r-hdf5array |
8447 | (package | |
8448 | (name "r-hdf5array") | |
8449 | (version "1.16.1") | |
8450 | (source | |
8451 | (origin | |
8452 | (method url-fetch) | |
8453 | (uri (bioconductor-uri "HDF5Array" version)) | |
8454 | (sha256 | |
8455 | (base32 | |
8456 | "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn")))) | |
8457 | (properties `((upstream-name . "HDF5Array"))) | |
8458 | (build-system r-build-system) | |
8459 | (inputs | |
8460 | `(("zlib" ,zlib))) | |
8461 | (propagated-inputs | |
8462 | `(("r-biocgenerics" ,r-biocgenerics) | |
8463 | ("r-delayedarray" ,r-delayedarray) | |
8464 | ("r-iranges" ,r-iranges) | |
8465 | ("r-matrix" ,r-matrix) | |
8466 | ("r-rhdf5" ,r-rhdf5) | |
8467 | ("r-rhdf5lib" ,r-rhdf5lib) | |
8468 | ("r-s4vectors" ,r-s4vectors))) | |
8469 | (home-page "https://bioconductor.org/packages/HDF5Array") | |
8470 | (synopsis "HDF5 back end for DelayedArray objects") | |
8471 | (description "This package provides an array-like container for convenient | |
8472 | access and manipulation of HDF5 datasets. It supports delayed operations and | |
8473 | block processing.") | |
8474 | (license license:artistic2.0))) | |
8475 | ||
c61268c1 | 8476 | (define-public r-rhdf5lib |
8477 | (package | |
8478 | (name "r-rhdf5lib") | |
8479 | (version "1.10.1") | |
8480 | (source | |
8481 | (origin | |
8482 | (method url-fetch) | |
8483 | (uri (bioconductor-uri "Rhdf5lib" version)) | |
8484 | (sha256 | |
8485 | (base32 | |
8486 | "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) | |
8487 | (modules '((guix build utils))) | |
8488 | (snippet | |
8489 | '(begin | |
8490 | ;; Delete bundled binaries | |
8491 | (delete-file-recursively "src/wininclude/") | |
8492 | (delete-file-recursively "src/winlib-4.9.3/") | |
8493 | (delete-file-recursively "src/winlib-8.3.0/") | |
8494 | (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") | |
8495 | #t)))) | |
8496 | (properties `((upstream-name . "Rhdf5lib"))) | |
8497 | (build-system r-build-system) | |
8498 | (arguments | |
8499 | `(#:phases | |
8500 | (modify-phases %standard-phases | |
8501 | (add-after 'unpack 'do-not-use-bundled-hdf5 | |
8502 | (lambda* (#:key inputs #:allow-other-keys) | |
8503 | (for-each delete-file '("configure" "configure.ac")) | |
8504 | ;; Do not make other packages link with the proprietary libsz. | |
8505 | (substitute* "R/zzz.R" | |
8506 | ((" \"%s/libsz.a\"") "")) | |
8507 | (with-directory-excursion "src" | |
8508 | (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) | |
8509 | (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) | |
8510 | "hdf5") | |
8511 | ;; Remove timestamp and host system information to make | |
8512 | ;; the build reproducible. | |
8513 | (substitute* "hdf5/src/libhdf5.settings.in" | |
8514 | (("Configured on: @CONFIG_DATE@") | |
8515 | "Configured on: Guix") | |
8516 | (("Uname information:.*") | |
8517 | "Uname information: Linux\n") | |
8518 | ;; Remove unnecessary store reference. | |
8519 | (("C Compiler:.*") | |
8520 | "C Compiler: GCC\n")) | |
8521 | (rename-file "Makevars.in" "Makevars") | |
8522 | (substitute* "Makevars" | |
8523 | (("@ZLIB_LIB@") "-lz") | |
8524 | (("@ZLIB_INCLUDE@") "") | |
8525 | (("HDF5_CXX_LIB=.*") | |
8526 | (string-append "HDF5_CXX_LIB=" | |
8527 | (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) | |
8528 | (("HDF5_LIB=.*") | |
8529 | (string-append "HDF5_LIB=" | |
8530 | (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) | |
8531 | (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") | |
8532 | (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") | |
8533 | (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") | |
8534 | (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") | |
8535 | (("HDF5_HL_LIB=.*") | |
8536 | (string-append "HDF5_HL_LIB=" | |
8537 | (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) | |
8538 | (("HDF5_HL_CXX_LIB=.*") | |
8539 | (string-append "HDF5_HL_CXX_LIB=" | |
8540 | (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) | |
8541 | ;; szip is non-free software | |
8542 | (("cp \"\\$\\{SZIP_LIB\\}.*") "") | |
8543 | (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) | |
8544 | #t))))) | |
8545 | (inputs | |
8546 | `(("zlib" ,zlib))) | |
8547 | (propagated-inputs | |
8548 | `(("hdf5" ,hdf5-1.10))) | |
8549 | (native-inputs | |
8550 | `(("hdf5-source" ,(package-source hdf5-1.10)) | |
8551 | ("r-knitr" ,r-knitr))) | |
8552 | (home-page "https://bioconductor.org/packages/Rhdf5lib") | |
8553 | (synopsis "HDF5 library as an R package") | |
8554 | (description "This package provides C and C++ HDF5 libraries for use in R | |
8555 | packages.") | |
8556 | (license license:artistic2.0))) | |
8557 | ||
8863c14c | 8558 | (define-public r-beachmat |
8559 | (package | |
8560 | (name "r-beachmat") | |
8561 | (version "2.4.0") | |
8562 | (source | |
8563 | (origin | |
8564 | (method url-fetch) | |
8565 | (uri (bioconductor-uri "beachmat" version)) | |
8566 | (sha256 | |
8567 | (base32 | |
8568 | "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi")))) | |
8569 | (build-system r-build-system) | |
8570 | (propagated-inputs | |
8571 | `(("r-biocgenerics" ,r-biocgenerics) | |
8572 | ("r-delayedarray" ,r-delayedarray) | |
8573 | ("r-matrix" ,r-matrix))) | |
8574 | (native-inputs | |
8575 | `(("r-knitr" ,r-knitr))) | |
8576 | (home-page "https://bioconductor.org/packages/beachmat") | |
8577 | (synopsis "Compiling Bioconductor to handle each matrix type") | |
8578 | (description "This package provides a consistent C++ class interface for a | |
8579 | variety of commonly used matrix types, including sparse and HDF5-backed | |
8580 | matrices.") | |
8581 | (license license:gpl3))) | |
8582 | ||
916a3e59 | 8583 | (define-public r-singlecellexperiment |
8584 | (package | |
8585 | (name "r-singlecellexperiment") | |
8586 | (version "1.10.1") | |
8587 | (source | |
8588 | (origin | |
8589 | (method url-fetch) | |
8590 | (uri (bioconductor-uri "SingleCellExperiment" version)) | |
8591 | (sha256 | |
8592 | (base32 | |
8593 | "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp")))) | |
8594 | (properties | |
8595 | `((upstream-name . "SingleCellExperiment"))) | |
8596 | (build-system r-build-system) | |
8597 | (propagated-inputs | |
8598 | `(("r-biocgenerics" ,r-biocgenerics) | |
8599 | ("r-s4vectors" ,r-s4vectors) | |
8600 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
8601 | (native-inputs | |
8602 | `(("r-knitr" ,r-knitr))) | |
8603 | (home-page "https://bioconductor.org/packages/SingleCellExperiment") | |
8604 | (synopsis "S4 classes for single cell data") | |
8605 | (description "This package defines an S4 class for storing data from | |
8606 | single-cell experiments. This includes specialized methods to store and | |
8607 | retrieve spike-in information, dimensionality reduction coordinates and size | |
8608 | factors for each cell, along with the usual metadata for genes and | |
8609 | libraries.") | |
8610 | (license license:gpl3))) | |
8611 | ||
6b1946b3 | 8612 | (define-public r-scater |
8613 | (package | |
8614 | (name "r-scater") | |
8615 | (version "1.16.2") | |
8616 | (source (origin | |
8617 | (method url-fetch) | |
8618 | (uri (bioconductor-uri "scater" version)) | |
8619 | (sha256 | |
8620 | (base32 | |
8621 | "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33")))) | |
8622 | (build-system r-build-system) | |
8623 | (propagated-inputs | |
8624 | `(("r-beachmat" ,r-beachmat) | |
8625 | ("r-biocgenerics" ,r-biocgenerics) | |
8626 | ("r-biocneighbors" ,r-biocneighbors) | |
8627 | ("r-biocparallel" ,r-biocparallel) | |
8628 | ("r-biocsingular" ,r-biocsingular) | |
8629 | ("r-delayedarray" ,r-delayedarray) | |
8630 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
8631 | ("r-ggbeeswarm" ,r-ggbeeswarm) | |
8632 | ("r-ggplot2" ,r-ggplot2) | |
8633 | ("r-matrix" ,r-matrix) | |
8634 | ("r-rcpp" ,r-rcpp) | |
8635 | ("r-rlang" ,r-rlang) | |
8636 | ("r-s4vectors" ,r-s4vectors) | |
8637 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
8638 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
8639 | ("r-viridis" ,r-viridis))) | |
8640 | (native-inputs | |
8641 | `(("r-knitr" ,r-knitr))) | |
8642 | (home-page "https://github.com/davismcc/scater") | |
8643 | (synopsis "Single-cell analysis toolkit for gene expression data in R") | |
8644 | (description "This package provides a collection of tools for doing | |
8645 | various analyses of single-cell RNA-seq gene expression data, with a focus on | |
8646 | quality control.") | |
8647 | (license license:gpl2+))) | |
8648 | ||
1193b77e | 8649 | (define-public r-scran |
8650 | (package | |
8651 | (name "r-scran") | |
8652 | (version "1.16.0") | |
8653 | (source | |
8654 | (origin | |
8655 | (method url-fetch) | |
8656 | (uri (bioconductor-uri "scran" version)) | |
8657 | (sha256 | |
8658 | (base32 | |
8659 | "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) | |
8660 | (build-system r-build-system) | |
8661 | (propagated-inputs | |
8662 | `(("r-beachmat" ,r-beachmat) | |
8663 | ("r-bh" ,r-bh) | |
8664 | ("r-biocgenerics" ,r-biocgenerics) | |
8665 | ("r-biocneighbors" ,r-biocneighbors) | |
8666 | ("r-biocparallel" ,r-biocparallel) | |
8667 | ("r-biocsingular" ,r-biocsingular) | |
8668 | ("r-delayedarray" ,r-delayedarray) | |
8669 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
8670 | ("r-dqrng" ,r-dqrng) | |
8671 | ("r-edger" ,r-edger) | |
8672 | ("r-igraph" ,r-igraph) | |
8673 | ("r-iranges" ,r-iranges) | |
8674 | ("r-limma" ,r-limma) | |
8675 | ("r-matrix" ,r-matrix) | |
8676 | ("r-rcpp" ,r-rcpp) | |
8677 | ("r-s4vectors" ,r-s4vectors) | |
8678 | ("r-scater" ,r-scater) | |
8679 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
8680 | ("r-statmod" ,r-statmod) | |
8681 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
8682 | (native-inputs | |
8683 | `(("r-knitr" ,r-knitr))) | |
8684 | (home-page "https://bioconductor.org/packages/scran") | |
8685 | (synopsis "Methods for single-cell RNA-Seq data analysis") | |
8686 | (description "This package implements a variety of low-level analyses of | |
8687 | single-cell RNA-seq data. Methods are provided for normalization of | |
8688 | cell-specific biases, assignment of cell cycle phase, and detection of highly | |
8689 | variable and significantly correlated genes.") | |
8690 | (license license:gpl3))) | |
8691 | ||
8c7c6db4 | 8692 | (define-public r-delayedmatrixstats |
8693 | (package | |
8694 | (name "r-delayedmatrixstats") | |
8695 | (version "1.10.1") | |
8696 | (source | |
8697 | (origin | |
8698 | (method url-fetch) | |
8699 | (uri (bioconductor-uri "DelayedMatrixStats" version)) | |
8700 | (sha256 | |
8701 | (base32 | |
8702 | "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx")))) | |
8703 | (properties | |
8704 | `((upstream-name . "DelayedMatrixStats"))) | |
8705 | (build-system r-build-system) | |
8706 | (propagated-inputs | |
8707 | `(("r-biocparallel" ,r-biocparallel) | |
8708 | ("r-delayedarray" ,r-delayedarray) | |
8709 | ("r-hdf5array" ,r-hdf5array) | |
8710 | ("r-iranges" ,r-iranges) | |
8711 | ("r-matrix" ,r-matrix) | |
8712 | ("r-matrixstats" ,r-matrixstats) | |
8713 | ("r-s4vectors" ,r-s4vectors))) | |
8714 | (native-inputs | |
8715 | `(("r-knitr" ,r-knitr))) | |
8716 | (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") | |
8717 | (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") | |
8718 | (description | |
8719 | "This package provides a port of the @code{matrixStats} API for use with | |
8720 | @code{DelayedMatrix} objects from the @code{DelayedArray} package. It | |
8721 | contains high-performing functions operating on rows and columns of | |
8722 | @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, | |
8723 | @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions | |
8724 | are optimized per data type and for subsetted calculations such that both | |
8725 | memory usage and processing time is minimized.") | |
8726 | (license license:expat))) |