Commit | Line | Data |
---|---|---|
fa596599 | 1 | ;;; GNU Guix --- Functional package management for GNU |
f8f181ae | 2 | ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> |
e8d435f7 | 3 | ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> |
61242625 | 4 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
25f4e652 | 5 | ;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com> |
488001eb | 6 | ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> |
f4d920b9 | 7 | ;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> |
c61268c1 | 8 | ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> |
fa596599 RW |
9 | ;;; |
10 | ;;; This file is part of GNU Guix. | |
11 | ;;; | |
12 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
13 | ;;; under the terms of the GNU General Public License as published by | |
14 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
15 | ;;; your option) any later version. | |
16 | ;;; | |
17 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
18 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
19 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
20 | ;;; GNU General Public License for more details. | |
21 | ;;; | |
22 | ;;; You should have received a copy of the GNU General Public License | |
23 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
24 | ||
25 | (define-module (gnu packages bioconductor) | |
26 | #:use-module ((guix licenses) #:prefix license:) | |
27 | #:use-module (guix packages) | |
28 | #:use-module (guix download) | |
b2dce6b5 | 29 | #:use-module (guix git-download) |
fa596599 | 30 | #:use-module (guix build-system r) |
183ce988 | 31 | #:use-module (gnu packages) |
58656064 | 32 | #:use-module (gnu packages base) |
cf9a29b2 | 33 | #:use-module (gnu packages bioinformatics) |
a5b56a53 RJ |
34 | #:use-module (gnu packages cran) |
35 | #:use-module (gnu packages compression) | |
c18dccff | 36 | #:use-module (gnu packages gcc) |
cf9a29b2 | 37 | #:use-module (gnu packages graph) |
5aef09bd | 38 | #:use-module (gnu packages graphviz) |
dddbc90c | 39 | #:use-module (gnu packages haskell-xyz) |
5cfa4bff | 40 | #:use-module (gnu packages image) |
b64ce4b7 | 41 | #:use-module (gnu packages maths) |
6b12f213 RW |
42 | #:use-module (gnu packages netpbm) |
43 | #:use-module (gnu packages perl) | |
2cb71d81 | 44 | #:use-module (gnu packages pkg-config) |
f4235c0e | 45 | #:use-module (gnu packages statistics) |
14bb1c48 | 46 | #:use-module (gnu packages web) |
7a62d5e0 | 47 | #:use-module (gnu packages xml) |
14bb1c48 | 48 | #:use-module (srfi srfi-1)) |
fa596599 | 49 | |
557a1089 RW |
50 | \f |
51 | ;;; Annotations | |
52 | ||
04a05946 MIP |
53 | (define-public r-org-eck12-eg-db |
54 | (package | |
55 | (name "r-org-eck12-eg-db") | |
56 | (version "3.12.0") | |
57 | (source | |
58 | (origin | |
59 | (method url-fetch) | |
60 | (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation)) | |
61 | (sha256 | |
62 | (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs")))) | |
63 | (properties | |
64 | `((upstream-name . "org.EcK12.eg.db"))) | |
65 | (build-system r-build-system) | |
66 | (propagated-inputs | |
67 | `(("r-annotationdbi" ,r-annotationdbi))) | |
68 | (home-page "https://bioconductor.org/packages/org.EcK12.eg.db") | |
69 | (synopsis "Genome wide annotation for E coli strain K12") | |
70 | (description | |
71 | "This package provides genome wide annotation for E coli strain K12, | |
72 | primarily based on mapping using Entrez Gene identifiers. Entrez Gene is | |
73 | National Center for Biotechnology Information (NCBI)’s database for | |
74 | gene-specific information. Entrez Gene maintains records from genomes which | |
75 | have been completely sequenced, which have an active research community to | |
76 | submit gene-specific information, or which are scheduled for intense sequence | |
77 | analysis.") | |
78 | (license license:artistic2.0))) | |
79 | ||
6f15ea24 RW |
80 | (define-public r-reactome-db |
81 | (package | |
82 | (name "r-reactome-db") | |
83 | (version "1.70.0") | |
84 | (source | |
85 | (origin | |
86 | (method url-fetch) | |
87 | (uri (bioconductor-uri "reactome.db" version 'annotation)) | |
88 | (sha256 | |
89 | (base32 | |
90 | "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg")))) | |
91 | (properties `((upstream-name . "reactome.db"))) | |
92 | (build-system r-build-system) | |
93 | (propagated-inputs | |
94 | `(("r-annotationdbi" ,r-annotationdbi))) | |
95 | (home-page "https://bioconductor.org/packages/reactome.db/") | |
96 | (synopsis "Annotation maps for reactome") | |
97 | (description | |
98 | "This package provides a set of annotation maps for the REACTOME | |
99 | database, assembled using data from REACTOME.") | |
100 | (license license:cc-by4.0))) | |
101 | ||
b7d93cf5 RW |
102 | (define-public r-bsgenome-celegans-ucsc-ce6 |
103 | (package | |
104 | (name "r-bsgenome-celegans-ucsc-ce6") | |
105 | (version "1.4.0") | |
106 | (source (origin | |
107 | (method url-fetch) | |
86ced7b2 RW |
108 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6" |
109 | version 'annotation)) | |
b7d93cf5 RW |
110 | (sha256 |
111 | (base32 | |
112 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
113 | (properties | |
114 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
115 | (build-system r-build-system) | |
b7d93cf5 RW |
116 | (propagated-inputs |
117 | `(("r-bsgenome" ,r-bsgenome))) | |
118 | (home-page | |
119 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
120 | (synopsis "Full genome sequences for Worm") | |
121 | (description | |
122 | "This package provides full genome sequences for Caenorhabditis | |
123 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
0c792ffb RW |
124 | objects.") |
125 | (license license:artistic2.0))) | |
126 | ||
127 | (define-public r-bsgenome-celegans-ucsc-ce10 | |
128 | (package | |
129 | (name "r-bsgenome-celegans-ucsc-ce10") | |
130 | (version "1.4.0") | |
131 | (source (origin | |
132 | (method url-fetch) | |
6998ecba RW |
133 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10" |
134 | version 'annotation)) | |
0c792ffb RW |
135 | (sha256 |
136 | (base32 | |
137 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
138 | (properties | |
139 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
140 | (build-system r-build-system) | |
0c792ffb RW |
141 | (propagated-inputs |
142 | `(("r-bsgenome" ,r-bsgenome))) | |
143 | (home-page | |
144 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
145 | (synopsis "Full genome sequences for Worm") | |
146 | (description | |
147 | "This package provides full genome sequences for Caenorhabditis | |
148 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
b7d93cf5 RW |
149 | objects.") |
150 | (license license:artistic2.0))) | |
151 | ||
183db725 RW |
152 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
153 | (package | |
154 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
155 | (version "1.4.1") | |
156 | (source (origin | |
157 | (method url-fetch) | |
149f351f RW |
158 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6" |
159 | version 'annotation)) | |
183db725 RW |
160 | (sha256 |
161 | (base32 | |
162 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
163 | (properties | |
164 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
165 | (build-system r-build-system) | |
183db725 RW |
166 | (propagated-inputs |
167 | `(("r-bsgenome" ,r-bsgenome))) | |
168 | (home-page | |
169 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
170 | (synopsis "Full genome sequences for Fly") | |
171 | (description | |
172 | "This package provides full genome sequences for Drosophila | |
173 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
174 | objects.") | |
175 | (license license:artistic2.0))) | |
176 | ||
13dabd69 RW |
177 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
178 | (package | |
179 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
180 | (version "1.4.0") | |
181 | (source (origin | |
182 | (method url-fetch) | |
87073b7e RW |
183 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3" |
184 | version 'annotation)) | |
13dabd69 RW |
185 | (sha256 |
186 | (base32 | |
187 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
188 | (properties | |
189 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
190 | (build-system r-build-system) | |
13dabd69 RW |
191 | (propagated-inputs |
192 | `(("r-bsgenome" ,r-bsgenome))) | |
193 | (home-page | |
194 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
195 | (synopsis "Full genome sequences for Fly") | |
196 | (description | |
197 | "This package provides full genome sequences for Drosophila | |
198 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
199 | Biostrings objects.") | |
200 | (license license:artistic2.0))) | |
201 | ||
dfac7eb9 RW |
202 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
203 | (package | |
204 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
205 | (version "1.3.99") | |
206 | (source (origin | |
207 | (method url-fetch) | |
bf05ece1 RW |
208 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked" |
209 | version 'annotation)) | |
dfac7eb9 RW |
210 | (sha256 |
211 | (base32 | |
212 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
213 | (properties | |
214 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
215 | (build-system r-build-system) | |
216 | (propagated-inputs | |
217 | `(("r-bsgenome" ,r-bsgenome) | |
218 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
219 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
220 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
221 | (synopsis "Full masked genome sequences for Fly") | |
222 | (description | |
223 | "This package provides full masked genome sequences for Drosophila | |
224 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
225 | Biostrings objects. The sequences are the same as in | |
226 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
227 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
228 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
229 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
230 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
231 | (license license:artistic2.0))) | |
232 | ||
40a65057 RW |
233 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
234 | (package | |
235 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
236 | (version "0.99.1") | |
237 | (source (origin | |
238 | (method url-fetch) | |
88e7c7db RW |
239 | (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5" |
240 | version 'annotation)) | |
40a65057 RW |
241 | (sha256 |
242 | (base32 | |
243 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
244 | (properties | |
245 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
246 | (build-system r-build-system) | |
40a65057 RW |
247 | (propagated-inputs |
248 | `(("r-bsgenome" ,r-bsgenome))) | |
249 | (home-page | |
250 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
251 | (synopsis "Full genome sequences for Homo sapiens") | |
252 | (description | |
253 | "This package provides full genome sequences for Homo sapiens from | |
254 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
255 | (license license:artistic2.0))) | |
256 | ||
c51c0033 MIP |
257 | (define-public r-bsgenome-hsapiens-ncbi-grch38 |
258 | (package | |
259 | (name "r-bsgenome-hsapiens-ncbi-grch38") | |
260 | (version "1.3.1000") | |
261 | (source | |
262 | (origin | |
263 | (method url-fetch) | |
264 | (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38" | |
265 | version 'annotation)) | |
266 | (sha256 | |
267 | (base32 | |
268 | "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) | |
269 | (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) | |
270 | (build-system r-build-system) | |
271 | (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) | |
272 | (home-page | |
273 | "https://bioconductor.org/packages/release/data/annotation/html/\ | |
274 | BSgenome.Hsapiens.NCBI.GRCh38.html") | |
275 | (synopsis "Full genome sequences for Homo sapiens (GRCh38)") | |
276 | (description | |
277 | "This package provides full genome sequences for Homo sapiens (Human) as | |
278 | provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") | |
279 | (license license:artistic2.0))) | |
280 | ||
6fbd759b RW |
281 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
282 | (package | |
283 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
284 | (version "1.3.99") | |
285 | (source (origin | |
286 | (method url-fetch) | |
a47646bd RW |
287 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" |
288 | version 'annotation)) | |
6fbd759b RW |
289 | (sha256 |
290 | (base32 | |
291 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
292 | (properties | |
293 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
294 | (build-system r-build-system) | |
295 | (propagated-inputs | |
296 | `(("r-bsgenome" ,r-bsgenome) | |
297 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
298 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
299 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
300 | (synopsis "Full masked genome sequences for Homo sapiens") | |
301 | (description | |
302 | "This package provides full genome sequences for Homo sapiens (Human) as | |
303 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
304 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
305 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
306 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
307 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
308 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
309 | default.") | |
310 | (license license:artistic2.0))) | |
311 | ||
5acb9052 RW |
312 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
313 | (package | |
314 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
315 | (version "1.4.0") | |
316 | (source (origin | |
317 | (method url-fetch) | |
21f6dae7 RW |
318 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9" |
319 | version 'annotation)) | |
5acb9052 RW |
320 | (sha256 |
321 | (base32 | |
322 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
323 | (properties | |
324 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
325 | (build-system r-build-system) | |
5acb9052 RW |
326 | (propagated-inputs |
327 | `(("r-bsgenome" ,r-bsgenome))) | |
328 | (home-page | |
329 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
330 | (synopsis "Full genome sequences for Mouse") | |
331 | (description | |
332 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
333 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
334 | (license license:artistic2.0))) | |
335 | ||
2bece692 RW |
336 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
337 | (package | |
338 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
339 | (version "1.3.99") | |
340 | (source (origin | |
341 | (method url-fetch) | |
51dc4a2d RW |
342 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked" |
343 | version 'annotation)) | |
2bece692 RW |
344 | (sha256 |
345 | (base32 | |
346 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
347 | (properties | |
348 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
349 | (build-system r-build-system) | |
350 | (propagated-inputs | |
351 | `(("r-bsgenome" ,r-bsgenome) | |
352 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
353 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
99db6db7 | 354 | (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") |
2bece692 RW |
355 | (synopsis "Full masked genome sequences for Mouse") |
356 | (description | |
357 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
358 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
359 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
360 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
361 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
362 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
363 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
364 | default." ) | |
365 | (license license:artistic2.0))) | |
366 | ||
c3adc830 RW |
367 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
368 | (package | |
369 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
370 | (version "1.4.0") | |
371 | (source (origin | |
372 | (method url-fetch) | |
f83404bc RW |
373 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10" |
374 | version 'annotation)) | |
c3adc830 RW |
375 | (sha256 |
376 | (base32 | |
377 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
378 | (properties | |
379 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
380 | (build-system r-build-system) | |
c3adc830 RW |
381 | (propagated-inputs |
382 | `(("r-bsgenome" ,r-bsgenome))) | |
383 | (home-page | |
384 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
385 | (synopsis "Full genome sequences for Mouse") | |
386 | (description | |
387 | "This package provides full genome sequences for Mus | |
388 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
389 | in Biostrings objects.") | |
390 | (license license:artistic2.0))) | |
391 | ||
3a08940e RW |
392 | (define-public r-org-ce-eg-db |
393 | (package | |
394 | (name "r-org-ce-eg-db") | |
395 | (version "3.7.0") | |
396 | (source (origin | |
397 | (method url-fetch) | |
1c05e637 | 398 | (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation)) |
3a08940e RW |
399 | (sha256 |
400 | (base32 | |
401 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) | |
402 | (properties | |
403 | `((upstream-name . "org.Ce.eg.db"))) | |
404 | (build-system r-build-system) | |
405 | (propagated-inputs | |
406 | `(("r-annotationdbi" ,r-annotationdbi))) | |
407 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") | |
408 | (synopsis "Genome wide annotation for Worm") | |
409 | (description | |
410 | "This package provides mappings from Entrez gene identifiers to various | |
411 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
412 | (license license:artistic2.0))) | |
413 | ||
f8780e96 RW |
414 | (define-public r-org-dm-eg-db |
415 | (package | |
416 | (name "r-org-dm-eg-db") | |
417 | (version "3.7.0") | |
418 | (source (origin | |
419 | (method url-fetch) | |
b0dfc79b | 420 | (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation)) |
f8780e96 RW |
421 | (sha256 |
422 | (base32 | |
423 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) | |
424 | (properties | |
425 | `((upstream-name . "org.Dm.eg.db"))) | |
426 | (build-system r-build-system) | |
427 | (propagated-inputs | |
428 | `(("r-annotationdbi" ,r-annotationdbi))) | |
429 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") | |
430 | (synopsis "Genome wide annotation for Fly") | |
431 | (description | |
432 | "This package provides mappings from Entrez gene identifiers to various | |
433 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
434 | (license license:artistic2.0))) | |
435 | ||
3dad6087 RW |
436 | (define-public r-org-dr-eg-db |
437 | (package | |
438 | (name "r-org-dr-eg-db") | |
439 | (version "3.7.0") | |
440 | (source (origin | |
441 | (method url-fetch) | |
7bb65a22 | 442 | (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation)) |
3dad6087 RW |
443 | (sha256 |
444 | (base32 | |
445 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) | |
446 | (properties | |
447 | `((upstream-name . "org.Dr.eg.db"))) | |
448 | (build-system r-build-system) | |
449 | (propagated-inputs | |
450 | `(("r-annotationdbi" ,r-annotationdbi))) | |
451 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") | |
452 | (synopsis "Annotation for Zebrafish") | |
453 | (description | |
454 | "This package provides genome wide annotations for Zebrafish, primarily | |
455 | based on mapping using Entrez Gene identifiers.") | |
456 | (license license:artistic2.0))) | |
457 | ||
d56df35a RW |
458 | (define-public r-org-hs-eg-db |
459 | (package | |
460 | (name "r-org-hs-eg-db") | |
461 | (version "3.7.0") | |
462 | (source (origin | |
463 | (method url-fetch) | |
f53becc6 | 464 | (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) |
d56df35a RW |
465 | (sha256 |
466 | (base32 | |
467 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) | |
468 | (properties | |
469 | `((upstream-name . "org.Hs.eg.db"))) | |
470 | (build-system r-build-system) | |
471 | (propagated-inputs | |
472 | `(("r-annotationdbi" ,r-annotationdbi))) | |
473 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") | |
474 | (synopsis "Genome wide annotation for Human") | |
475 | (description | |
476 | "This package contains genome-wide annotations for Human, primarily based | |
477 | on mapping using Entrez Gene identifiers.") | |
478 | (license license:artistic2.0))) | |
479 | ||
8035819f RW |
480 | (define-public r-org-mm-eg-db |
481 | (package | |
482 | (name "r-org-mm-eg-db") | |
483 | (version "3.7.0") | |
484 | (source (origin | |
485 | (method url-fetch) | |
411be88b | 486 | (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation)) |
8035819f RW |
487 | (sha256 |
488 | (base32 | |
489 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) | |
490 | (properties | |
491 | `((upstream-name . "org.Mm.eg.db"))) | |
492 | (build-system r-build-system) | |
493 | (propagated-inputs | |
494 | `(("r-annotationdbi" ,r-annotationdbi))) | |
495 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") | |
496 | (synopsis "Genome wide annotation for Mouse") | |
497 | (description | |
498 | "This package provides mappings from Entrez gene identifiers to various | |
499 | annotations for the genome of the model mouse Mus musculus.") | |
500 | (license license:artistic2.0))) | |
501 | ||
fe0b76e2 RW |
502 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
503 | (package | |
504 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
505 | (version "1.4.0") | |
506 | (source (origin | |
507 | (method url-fetch) | |
e7a8cf2e RW |
508 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19" |
509 | version 'annotation)) | |
fe0b76e2 RW |
510 | (sha256 |
511 | (base32 | |
512 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) | |
513 | (properties | |
514 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
515 | (build-system r-build-system) | |
fe0b76e2 RW |
516 | (propagated-inputs |
517 | `(("r-bsgenome" ,r-bsgenome))) | |
518 | (home-page | |
519 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
520 | (synopsis "Full genome sequences for Homo sapiens") | |
521 | (description | |
522 | "This package provides full genome sequences for Homo sapiens as provided | |
523 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
524 | (license license:artistic2.0))) | |
525 | ||
8ce240fd RJ |
526 | (define-public r-bsgenome-hsapiens-ucsc-hg38 |
527 | (package | |
528 | (name "r-bsgenome-hsapiens-ucsc-hg38") | |
529 | (version "1.4.1") | |
530 | (source (origin | |
531 | (method url-fetch) | |
532 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38" | |
533 | version 'annotation)) | |
534 | (sha256 | |
535 | (base32 | |
536 | "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi")))) | |
537 | (properties | |
538 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) | |
539 | (build-system r-build-system) | |
540 | (propagated-inputs | |
541 | `(("r-bsgenome" ,r-bsgenome))) | |
542 | (home-page | |
543 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") | |
544 | (synopsis "Full genome sequences for Homo sapiens") | |
545 | (description | |
546 | "This package provides full genome sequences for Homo sapiens (Human) | |
547 | as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") | |
548 | (license license:artistic2.0))) | |
549 | ||
8324e64c RW |
550 | (define-public r-ensdb-hsapiens-v75 |
551 | (package | |
552 | (name "r-ensdb-hsapiens-v75") | |
553 | (version "2.99.0") | |
554 | (source | |
555 | (origin | |
556 | (method url-fetch) | |
557 | (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) | |
558 | (sha256 | |
559 | (base32 | |
560 | "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) | |
561 | (properties | |
562 | `((upstream-name . "EnsDb.Hsapiens.v75"))) | |
563 | (build-system r-build-system) | |
564 | (propagated-inputs | |
565 | `(("r-ensembldb" ,r-ensembldb))) | |
566 | (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") | |
567 | (synopsis "Ensembl based annotation package") | |
568 | (description | |
569 | "This package exposes an annotation database generated from Ensembl.") | |
570 | (license license:artistic2.0))) | |
571 | ||
2cc51108 RW |
572 | (define-public r-genelendatabase |
573 | (package | |
574 | (name "r-genelendatabase") | |
daeb3cd9 | 575 | (version "1.18.0") |
2cc51108 RW |
576 | (source |
577 | (origin | |
578 | (method url-fetch) | |
717d7cda | 579 | (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) |
2cc51108 RW |
580 | (sha256 |
581 | (base32 | |
daeb3cd9 | 582 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
2cc51108 RW |
583 | (properties |
584 | `((upstream-name . "geneLenDataBase"))) | |
585 | (build-system r-build-system) | |
586 | (propagated-inputs | |
587 | `(("r-rtracklayer" ,r-rtracklayer) | |
588 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
589 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
590 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
591 | (description | |
592 | "This package provides the lengths of mRNA transcripts for a number of | |
593 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
594 | (license license:lgpl2.0+))) | |
595 | ||
66e35ce6 RW |
596 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
597 | (package | |
598 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
599 | (version "3.2.2") | |
600 | (source (origin | |
601 | (method url-fetch) | |
f2580a13 RW |
602 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene" |
603 | version 'annotation)) | |
66e35ce6 RW |
604 | (sha256 |
605 | (base32 | |
606 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
607 | (properties | |
608 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
609 | (build-system r-build-system) | |
66e35ce6 RW |
610 | (propagated-inputs |
611 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
612 | (home-page | |
613 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
614 | (synopsis "Annotation package for human genome in TxDb format") | |
615 | (description | |
616 | "This package provides an annotation database of Homo sapiens genome | |
617 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
798b80ce RW |
618 | track. The database is exposed as a @code{TxDb} object.") |
619 | (license license:artistic2.0))) | |
620 | ||
621 | (define-public r-txdb-hsapiens-ucsc-hg38-knowngene | |
622 | (package | |
623 | (name "r-txdb-hsapiens-ucsc-hg38-knowngene") | |
624 | (version "3.4.6") | |
625 | (source (origin | |
626 | (method url-fetch) | |
d78db088 RW |
627 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" |
628 | version 'annotation)) | |
798b80ce RW |
629 | (sha256 |
630 | (base32 | |
631 | "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) | |
632 | (properties | |
633 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) | |
634 | (build-system r-build-system) | |
635 | (propagated-inputs | |
636 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
637 | (home-page | |
638 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") | |
639 | (synopsis "Annotation package for human genome in TxDb format") | |
640 | (description | |
641 | "This package provides an annotation database of Homo sapiens genome | |
642 | data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" | |
66e35ce6 RW |
643 | track. The database is exposed as a @code{TxDb} object.") |
644 | (license license:artistic2.0))) | |
645 | ||
d220babf RW |
646 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
647 | (package | |
648 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
649 | (version "3.2.2") | |
650 | (source (origin | |
651 | (method url-fetch) | |
1afdf41b RW |
652 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene" |
653 | version 'annotation)) | |
d220babf RW |
654 | (sha256 |
655 | (base32 | |
656 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
657 | (properties | |
658 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
659 | (build-system r-build-system) | |
660 | (propagated-inputs | |
661 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
662 | ("r-annotationdbi" ,r-annotationdbi))) | |
663 | (home-page | |
664 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
665 | (synopsis "Annotation package for mouse genome in TxDb format") | |
666 | (description | |
667 | "This package provides an annotation database of Mouse genome data. It | |
668 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
669 | database is exposed as a @code{TxDb} object.") | |
670 | (license license:artistic2.0))) | |
671 | ||
7bc5d1b0 RW |
672 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
673 | (package | |
674 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
b69c7703 | 675 | (version "3.10.0") |
7bc5d1b0 RW |
676 | (source (origin |
677 | (method url-fetch) | |
c271d990 RW |
678 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene" |
679 | version 'annotation)) | |
7bc5d1b0 RW |
680 | (sha256 |
681 | (base32 | |
b69c7703 | 682 | "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9")))) |
7bc5d1b0 RW |
683 | (properties |
684 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
685 | (build-system r-build-system) | |
7bc5d1b0 RW |
686 | (propagated-inputs |
687 | `(("r-bsgenome" ,r-bsgenome) | |
688 | ("r-genomicfeatures" ,r-genomicfeatures) | |
689 | ("r-annotationdbi" ,r-annotationdbi))) | |
690 | (home-page | |
691 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
692 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
693 | (description | |
694 | "This package loads a TxDb object, which is an R interface to | |
695 | prefabricated databases contained in this package. This package provides | |
696 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
697 | based on the knownGene track.") | |
698 | (license license:artistic2.0))) | |
699 | ||
7cd446fd RW |
700 | (define-public r-txdb-celegans-ucsc-ce6-ensgene |
701 | (package | |
702 | (name "r-txdb-celegans-ucsc-ce6-ensgene") | |
703 | (version "3.2.2") | |
704 | (source | |
705 | (origin | |
706 | (method url-fetch) | |
707 | (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene" | |
708 | version 'annotation)) | |
709 | (sha256 | |
710 | (base32 | |
711 | "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90")))) | |
712 | (properties | |
713 | `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) | |
714 | (build-system r-build-system) | |
715 | (propagated-inputs | |
716 | `(("r-annotationdbi" ,r-annotationdbi) | |
717 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
718 | (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") | |
719 | (synopsis "Annotation package for C elegans TxDb objects") | |
720 | (description | |
721 | "This package exposes a C elegans annotation database generated from UCSC | |
722 | by exposing these as TxDb objects.") | |
723 | (license license:artistic2.0))) | |
724 | ||
0f5c9cec RW |
725 | (define-public r-fdb-infiniummethylation-hg19 |
726 | (package | |
727 | (name "r-fdb-infiniummethylation-hg19") | |
728 | (version "2.2.0") | |
729 | (source (origin | |
730 | (method url-fetch) | |
6aca4054 RW |
731 | (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19" |
732 | version 'annotation)) | |
0f5c9cec RW |
733 | (sha256 |
734 | (base32 | |
735 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) | |
736 | (properties | |
737 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) | |
738 | (build-system r-build-system) | |
739 | (propagated-inputs | |
740 | `(("r-biostrings" ,r-biostrings) | |
741 | ("r-genomicfeatures" ,r-genomicfeatures) | |
742 | ("r-annotationdbi" ,r-annotationdbi) | |
743 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
744 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) | |
745 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") | |
746 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") | |
747 | (description | |
748 | "This is an annotation package for Illumina Infinium DNA methylation | |
749 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 | |
750 | annotations.") | |
751 | (license license:artistic2.0))) | |
752 | ||
9475a248 RW |
753 | (define-public r-illuminahumanmethylationepicmanifest |
754 | (package | |
755 | (name "r-illuminahumanmethylationepicmanifest") | |
756 | (version "0.3.0") | |
757 | (source (origin | |
758 | (method url-fetch) | |
25f567a8 RW |
759 | (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest" |
760 | version 'annotation)) | |
9475a248 RW |
761 | (sha256 |
762 | (base32 | |
763 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) | |
764 | (properties | |
765 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) | |
766 | (build-system r-build-system) | |
767 | (propagated-inputs | |
768 | `(("r-minfi" ,r-minfi))) | |
769 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") | |
770 | (synopsis "Manifest for Illumina's EPIC methylation arrays") | |
771 | (description | |
772 | "This is a manifest package for Illumina's EPIC methylation arrays.") | |
773 | (license license:artistic2.0))) | |
e8d435f7 RJ |
774 | |
775 | (define-public r-ideoviz | |
776 | (package | |
777 | (name "r-ideoviz") | |
25f4e652 | 778 | (version "1.26.0") |
e8d435f7 RJ |
779 | (source (origin |
780 | (method url-fetch) | |
781 | (uri (bioconductor-uri "IdeoViz" version)) | |
782 | (sha256 | |
783 | (base32 | |
25f4e652 | 784 | "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq")))) |
e8d435f7 RJ |
785 | (build-system r-build-system) |
786 | (propagated-inputs | |
787 | `(("r-biobase" ,r-biobase) | |
788 | ("r-iranges" ,r-iranges) | |
789 | ("r-genomicranges" ,r-genomicranges) | |
790 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
791 | ("r-rtracklayer" ,r-rtracklayer) | |
792 | ("r-genomeinfodb" ,r-genomeinfodb))) | |
793 | (home-page "https://bioconductor.org/packages/IdeoViz/") | |
794 | (synopsis "Plots data along a chromosomal ideogram") | |
795 | (description "This package provides functions to plot data associated with | |
796 | arbitrary genomic intervals along chromosomal ideogram.") | |
797 | (license license:gpl2))) | |
9475a248 | 798 | |
a38bf7c8 RJ |
799 | ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 |
800 | ;; from Bioconductor. | |
801 | (define-public r-deconstructsigs | |
802 | (package | |
803 | (name "r-deconstructsigs") | |
804 | (version "1.8.0") | |
805 | (source (origin | |
806 | (method url-fetch) | |
807 | (uri (cran-uri "deconstructSigs" version)) | |
808 | (sha256 | |
809 | (base32 | |
810 | "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) | |
811 | (properties | |
812 | `((upstream-name . "deconstructSigs"))) | |
813 | (build-system r-build-system) | |
814 | (propagated-inputs | |
815 | `(("r-bsgenome" ,r-bsgenome) | |
816 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
817 | ("r-genomeinfodb" ,r-genomeinfodb) | |
818 | ("r-reshape2" ,r-reshape2))) | |
819 | (home-page "https://github.com/raerose01/deconstructSigs") | |
820 | (synopsis "Identifies signatures present in a tumor sample") | |
821 | (description "This package takes sample information in the form of the | |
822 | fraction of mutations in each of 96 trinucleotide contexts and identifies | |
823 | the weighted combination of published signatures that, when summed, most | |
824 | closely reconstructs the mutational profile.") | |
825 | (license license:gpl2+))) | |
826 | ||
7c9d8a5d RW |
827 | ;; This is a CRAN package, but it depends on Bioconductor packages. |
828 | (define-public r-nmf | |
829 | (package | |
830 | (name "r-nmf") | |
0a41d9be | 831 | (version "0.23.0") |
7c9d8a5d RW |
832 | (source |
833 | (origin | |
834 | (method url-fetch) | |
835 | (uri (cran-uri "NMF" version)) | |
836 | (sha256 | |
837 | (base32 | |
0a41d9be | 838 | "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g")))) |
7c9d8a5d RW |
839 | (properties `((upstream-name . "NMF"))) |
840 | (build-system r-build-system) | |
841 | (propagated-inputs | |
842 | `(("r-cluster" ,r-cluster) | |
be1042b3 RW |
843 | ("r-biobase" ,r-biobase) |
844 | ("r-biocmanager" ,r-biocmanager) | |
7c9d8a5d RW |
845 | ("r-bigmemory" ,r-bigmemory) ; suggested |
846 | ("r-synchronicity" ,r-synchronicity) ; suggested | |
847 | ("r-colorspace" ,r-colorspace) | |
848 | ("r-digest" ,r-digest) | |
849 | ("r-doparallel" ,r-doparallel) | |
850 | ("r-foreach" ,r-foreach) | |
851 | ("r-ggplot2" ,r-ggplot2) | |
852 | ("r-gridbase" ,r-gridbase) | |
853 | ("r-pkgmaker" ,r-pkgmaker) | |
854 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
855 | ("r-registry" ,r-registry) | |
856 | ("r-reshape2" ,r-reshape2) | |
857 | ("r-rngtools" ,r-rngtools) | |
858 | ("r-stringr" ,r-stringr))) | |
0a41d9be RW |
859 | (native-inputs |
860 | `(("r-knitr" ,r-knitr))) | |
7c9d8a5d RW |
861 | (home-page "http://renozao.github.io/NMF") |
862 | (synopsis "Algorithms and framework for nonnegative matrix factorization") | |
863 | (description | |
864 | "This package provides a framework to perform Non-negative Matrix | |
865 | Factorization (NMF). The package implements a set of already published | |
866 | algorithms and seeding methods, and provides a framework to test, develop and | |
867 | plug new or custom algorithms. Most of the built-in algorithms have been | |
868 | optimized in C++, and the main interface function provides an easy way of | |
869 | performing parallel computations on multicore machines.") | |
870 | (license license:gpl2+))) | |
871 | ||
f8a5af46 RW |
872 | (define-public r-do-db |
873 | (package | |
874 | (name "r-do-db") | |
875 | (version "2.9") | |
876 | (source (origin | |
877 | (method url-fetch) | |
eed2766a | 878 | (uri (bioconductor-uri "DO.db" version 'annotation)) |
f8a5af46 RW |
879 | (sha256 |
880 | (base32 | |
881 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) | |
882 | (properties | |
883 | `((upstream-name . "DO.db"))) | |
884 | (build-system r-build-system) | |
885 | (propagated-inputs | |
886 | `(("r-annotationdbi" ,r-annotationdbi))) | |
887 | (home-page "https://www.bioconductor.org/packages/DO.db/") | |
888 | (synopsis "Annotation maps describing the entire Disease Ontology") | |
889 | (description | |
890 | "This package provides a set of annotation maps describing the entire | |
891 | Disease Ontology.") | |
892 | (license license:artistic2.0))) | |
893 | ||
ec20858a RJ |
894 | (define-public r-pasilla |
895 | (package | |
896 | (name "r-pasilla") | |
897 | (version "1.14.0") | |
898 | (source (origin | |
899 | (method url-fetch) | |
900 | (uri (string-append | |
901 | "http://bioconductor.org/packages/release/data/experiment" | |
902 | "/src/contrib/pasilla_" version ".tar.gz")) | |
903 | (sha256 | |
904 | (base32 | |
905 | "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) | |
906 | (build-system r-build-system) | |
907 | (propagated-inputs | |
908 | `(("r-biocstyle" ,r-biocstyle) | |
909 | ("r-dexseq" ,r-dexseq) | |
910 | ("r-knitr" ,r-knitr) | |
911 | ("r-rmarkdown" ,r-rmarkdown))) | |
912 | (home-page "https://www.bioconductor.org/packages/pasilla/") | |
913 | (synopsis "Data package with per-exon and per-gene read counts") | |
914 | (description "This package provides per-exon and per-gene read counts | |
915 | computed for selected genes from RNA-seq data that were presented in the | |
916 | article 'Conservation of an RNA regulatory map between Drosophila and mammals' | |
917 | by Brooks et al., Genome Research 2011.") | |
918 | (license license:lgpl2.1+))) | |
919 | ||
83b42091 RW |
920 | (define-public r-pfam-db |
921 | (package | |
922 | (name "r-pfam-db") | |
923 | (version "3.8.2") | |
924 | (source | |
925 | (origin | |
926 | (method url-fetch) | |
927 | (uri (bioconductor-uri "PFAM.db" version 'annotation)) | |
928 | (sha256 | |
929 | (base32 | |
930 | "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) | |
931 | (properties `((upstream-name . "PFAM.db"))) | |
932 | (build-system r-build-system) | |
933 | (propagated-inputs | |
934 | `(("r-annotationdbi" ,r-annotationdbi))) | |
935 | (home-page "https://bioconductor.org/packages/PFAM.db") | |
936 | (synopsis "Set of protein ID mappings for PFAM") | |
937 | (description | |
938 | "This package provides a set of protein ID mappings for PFAM, assembled | |
939 | using data from public repositories.") | |
940 | (license license:artistic2.0))) | |
941 | ||
40be965e RW |
942 | (define-public r-phastcons100way-ucsc-hg19 |
943 | (package | |
944 | (name "r-phastcons100way-ucsc-hg19") | |
945 | (version "3.7.2") | |
946 | (source | |
947 | (origin | |
948 | (method url-fetch) | |
949 | (uri (bioconductor-uri "phastCons100way.UCSC.hg19" | |
950 | version 'annotation)) | |
951 | (sha256 | |
952 | (base32 | |
953 | "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa")))) | |
954 | (properties | |
955 | `((upstream-name . "phastCons100way.UCSC.hg19"))) | |
956 | (build-system r-build-system) | |
957 | (propagated-inputs | |
958 | `(("r-bsgenome" ,r-bsgenome) | |
959 | ("r-genomeinfodb" ,r-genomeinfodb) | |
960 | ("r-genomicranges" ,r-genomicranges) | |
961 | ("r-genomicscores" ,r-genomicscores) | |
962 | ("r-iranges" ,r-iranges) | |
963 | ("r-s4vectors" ,r-s4vectors))) | |
964 | (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") | |
965 | (synopsis "UCSC phastCons conservation scores for hg19") | |
966 | (description | |
967 | "This package provides UCSC phastCons conservation scores for the human | |
968 | genome (hg19) calculated from multiple alignments with other 99 vertebrate | |
969 | species.") | |
970 | (license license:artistic2.0))) | |
971 | ||
2cc51108 | 972 | \f |
557a1089 RW |
973 | ;;; Experiment data |
974 | ||
692bce15 RW |
975 | (define-public r-abadata |
976 | (package | |
977 | (name "r-abadata") | |
978 | (version "1.12.0") | |
979 | (source (origin | |
980 | (method url-fetch) | |
ced61edf | 981 | (uri (bioconductor-uri "ABAData" version 'experiment)) |
692bce15 RW |
982 | (sha256 |
983 | (base32 | |
984 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) | |
985 | (properties | |
986 | `((upstream-name . "ABAData"))) | |
987 | (build-system r-build-system) | |
988 | (propagated-inputs | |
989 | `(("r-annotationdbi" ,r-annotationdbi))) | |
990 | (home-page "https://www.bioconductor.org/packages/ABAData/") | |
991 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") | |
992 | (description | |
993 | "This package provides the data for the gene expression enrichment | |
994 | analysis conducted in the package ABAEnrichment. The package includes three | |
995 | datasets which are derived from the Allen Brain Atlas: | |
996 | ||
997 | @enumerate | |
998 | @item Gene expression data from Human Brain (adults) averaged across donors, | |
999 | @item Gene expression data from the Developing Human Brain pooled into five | |
1000 | age categories and averaged across donors, and | |
1001 | @item a developmental effect score based on the Developing Human Brain | |
1002 | expression data. | |
1003 | @end enumerate | |
1004 | ||
1005 | All datasets are restricted to protein coding genes.") | |
1006 | (license license:gpl2+))) | |
1007 | ||
b50c9660 RW |
1008 | (define-public r-arrmdata |
1009 | (package | |
1010 | (name "r-arrmdata") | |
1011 | (version "1.18.0") | |
1012 | (source (origin | |
1013 | (method url-fetch) | |
b86f7746 | 1014 | (uri (bioconductor-uri "ARRmData" version 'experiment)) |
b50c9660 RW |
1015 | (sha256 |
1016 | (base32 | |
1017 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) | |
1018 | (properties | |
1019 | `((upstream-name . "ARRmData"))) | |
1020 | (build-system r-build-system) | |
1021 | (home-page "https://www.bioconductor.org/packages/ARRmData/") | |
1022 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") | |
1023 | (description | |
1024 | "This package provides raw beta values from 36 samples across 3 groups | |
1025 | from Illumina 450k methylation arrays.") | |
1026 | (license license:artistic2.0))) | |
1027 | ||
557a1089 RW |
1028 | (define-public r-hsmmsinglecell |
1029 | (package | |
1030 | (name "r-hsmmsinglecell") | |
1031 | (version "1.2.0") | |
1032 | (source (origin | |
1033 | (method url-fetch) | |
545e67ac | 1034 | (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) |
557a1089 RW |
1035 | (sha256 |
1036 | (base32 | |
1037 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) | |
1038 | (properties | |
1039 | `((upstream-name . "HSMMSingleCell"))) | |
1040 | (build-system r-build-system) | |
1041 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") | |
1042 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") | |
1043 | (description | |
1044 | "Skeletal myoblasts undergo a well-characterized sequence of | |
1045 | morphological and transcriptional changes during differentiation. In this | |
1046 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded | |
1047 | under high mitogen conditions (GM) and then differentiated by switching to | |
1048 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several | |
1049 | hundred cells taken over a time-course of serum-induced differentiation. | |
1050 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, | |
1051 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. | |
1052 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, | |
1053 | which were then sequenced to a depth of ~4 million reads per library, | |
1054 | resulting in a complete gene expression profile for each cell.") | |
1055 | (license license:artistic2.0))) | |
ad8f46c6 | 1056 | |
1057 | (define-public r-all | |
1058 | (package | |
1059 | (name "r-all") | |
1060 | (version "1.26.0") | |
1061 | (source (origin | |
1062 | (method url-fetch) | |
41728d23 | 1063 | (uri (bioconductor-uri "ALL" version 'experiment)) |
ad8f46c6 | 1064 | (sha256 |
1065 | (base32 | |
1066 | "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) | |
1067 | (properties `((upstream-name . "ALL"))) | |
1068 | (build-system r-build-system) | |
1069 | (propagated-inputs | |
1070 | `(("r-biobase" ,r-biobase))) | |
1071 | (home-page "https://bioconductor.org/packages/ALL") | |
1072 | (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") | |
1073 | (description | |
1074 | "The data consist of microarrays from 128 different individuals with | |
1075 | @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates | |
1076 | are available. The data have been normalized (using rma) and it is the | |
1077 | jointly normalized data that are available here. The data are presented in | |
1078 | the form of an @code{exprSet} object.") | |
1079 | (license license:artistic2.0))) | |
557a1089 | 1080 | |
53b1e10f RW |
1081 | (define-public r-affydata |
1082 | (package | |
1083 | (name "r-affydata") | |
1084 | (version "1.32.0") | |
1085 | (source | |
1086 | (origin | |
1087 | (method url-fetch) | |
1088 | (uri (bioconductor-uri "affydata" version 'experiment)) | |
1089 | (sha256 | |
1090 | (base32 | |
1091 | "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) | |
1092 | (properties `((upstream-name . "affydata"))) | |
1093 | (build-system r-build-system) | |
1094 | (propagated-inputs | |
1095 | `(("r-affy" ,r-affy))) | |
1096 | (home-page "https://bioconductor.org/packages/affydata/") | |
1097 | (synopsis "Affymetrix data for demonstration purposes") | |
1098 | (description | |
1099 | "This package provides example datasets that represent 'real world | |
1100 | examples' of Affymetrix data, unlike the artificial examples included in the | |
1101 | package @code{affy}.") | |
1102 | (license license:gpl2+))) | |
1103 | ||
eb2f1a7d MIP |
1104 | (define-public r-gagedata |
1105 | (package | |
1106 | (name "r-gagedata") | |
1107 | (version "2.28.0") | |
1108 | (source | |
1109 | (origin | |
1110 | (method url-fetch) | |
1111 | (uri (bioconductor-uri "gageData" version 'experiment)) | |
1112 | (sha256 | |
1113 | (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn")))) | |
1114 | (properties `((upstream-name . "gageData"))) | |
1115 | (build-system r-build-system) | |
1116 | (home-page "https://bioconductor.org/packages/gageData") | |
1117 | (synopsis "Auxillary data for gage package") | |
1118 | (description | |
1119 | "This is a supportive data package for the software package @code{gage}. | |
1120 | However, the data supplied here are also useful for gene set or pathway | |
1121 | analysis or microarray data analysis in general. In this package, we provide | |
1122 | two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and | |
1123 | BMP6 (originally published as an demo dataset for GAGE, also registered as | |
1124 | GSE13604 in GEO). This package also includes commonly used gene set data based | |
1125 | on KEGG pathways and GO terms for major research species, including human, | |
1126 | mouse, rat and budding yeast. Mapping data between common gene IDs for budding | |
1127 | yeast are also included.") | |
1128 | (license license:gpl2+))) | |
1129 | ||
ff1146b9 RW |
1130 | (define-public r-curatedtcgadata |
1131 | (package | |
1132 | (name "r-curatedtcgadata") | |
1133 | (version "1.8.0") | |
1134 | (source | |
1135 | (origin | |
1136 | (method url-fetch) | |
1137 | (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) | |
1138 | (sha256 | |
1139 | (base32 | |
1140 | "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) | |
1141 | (properties | |
1142 | `((upstream-name . "curatedTCGAData"))) | |
1143 | (build-system r-build-system) | |
1144 | (propagated-inputs | |
1145 | `(("r-annotationhub" ,r-annotationhub) | |
1146 | ("r-experimenthub" ,r-experimenthub) | |
1147 | ("r-hdf5array" ,r-hdf5array) | |
1148 | ("r-multiassayexperiment" ,r-multiassayexperiment) | |
1149 | ("r-s4vectors" ,r-s4vectors) | |
1150 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1151 | (home-page "https://bioconductor.org/packages/curatedTCGAData/") | |
1152 | (synopsis "Curated data from The Cancer Genome Atlas") | |
1153 | (description | |
1154 | "This package provides publicly available data from The Cancer Genome | |
1155 | Atlas (TCGA) as @code{MultiAssayExperiment} objects. | |
1156 | @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy | |
1157 | number, mutation, microRNA, protein, and others) with clinical / pathological | |
1158 | data. It also links assay barcodes with patient identifiers, enabling | |
1159 | harmonized subsetting of rows (features) and columns (patients / samples) | |
1160 | across the entire multi-'omics experiment.") | |
1161 | (license license:artistic2.0))) | |
1162 | ||
557a1089 RW |
1163 | \f |
1164 | ;;; Packages | |
1165 | ||
e5d722fb RW |
1166 | (define-public r-biocversion |
1167 | (package | |
1168 | (name "r-biocversion") | |
70ab9909 | 1169 | (version "3.12.0") |
e5d722fb RW |
1170 | (source |
1171 | (origin | |
1172 | (method url-fetch) | |
1173 | (uri (bioconductor-uri "BiocVersion" version)) | |
1174 | (sha256 | |
1175 | (base32 | |
70ab9909 | 1176 | "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk")))) |
e5d722fb RW |
1177 | (properties `((upstream-name . "BiocVersion"))) |
1178 | (build-system r-build-system) | |
1179 | (home-page "https://bioconductor.org/packages/BiocVersion/") | |
1180 | (synopsis "Set the appropriate version of Bioconductor packages") | |
1181 | (description | |
1182 | "This package provides repository information for the appropriate version | |
1183 | of Bioconductor.") | |
1184 | (license license:artistic2.0))) | |
1185 | ||
14bba460 RW |
1186 | (define-public r-biocgenerics |
1187 | (package | |
1188 | (name "r-biocgenerics") | |
aa311eaa | 1189 | (version "0.36.0") |
14bba460 RW |
1190 | (source (origin |
1191 | (method url-fetch) | |
1192 | (uri (bioconductor-uri "BiocGenerics" version)) | |
1193 | (sha256 | |
1194 | (base32 | |
aa311eaa | 1195 | "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q")))) |
14bba460 RW |
1196 | (properties |
1197 | `((upstream-name . "BiocGenerics"))) | |
1198 | (build-system r-build-system) | |
1199 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
1200 | (synopsis "S4 generic functions for Bioconductor") | |
1201 | (description | |
1202 | "This package provides S4 generic functions needed by many Bioconductor | |
1203 | packages.") | |
1204 | (license license:artistic2.0))) | |
1205 | ||
17d95689 RW |
1206 | (define-public r-coverageview |
1207 | (package | |
1208 | (name "r-coverageview") | |
1209 | (version "1.28.0") | |
1210 | (source (origin | |
1211 | (method url-fetch) | |
1212 | (uri (bioconductor-uri "CoverageView" version)) | |
1213 | (sha256 | |
1214 | (base32 | |
1215 | "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj")))) | |
1216 | (build-system r-build-system) | |
1217 | (propagated-inputs | |
1218 | `(("r-s4vectors" ,r-s4vectors) | |
1219 | ("r-iranges" ,r-iranges) | |
1220 | ("r-genomicranges" ,r-genomicranges) | |
1221 | ("r-genomicalignments" ,r-genomicalignments) | |
1222 | ("r-rtracklayer" ,r-rtracklayer) | |
1223 | ("r-rsamtools" ,r-rsamtools))) | |
1224 | (home-page "https://bioconductor.org/packages/CoverageView/") | |
1225 | (synopsis "Coverage visualization package for R") | |
1226 | (description "This package provides a framework for the visualization of | |
1227 | genome coverage profiles. It can be used for ChIP-seq experiments, but it can | |
1228 | be also used for genome-wide nucleosome positioning experiments or other | |
1229 | experiment types where it is important to have a framework in order to inspect | |
1230 | how the coverage distributed across the genome.") | |
1231 | (license license:artistic2.0))) | |
1232 | ||
1abb6a2a RW |
1233 | (define-public r-cummerbund |
1234 | (package | |
1235 | (name "r-cummerbund") | |
1236 | (version "2.32.0") | |
1237 | (source (origin | |
1238 | (method url-fetch) | |
1239 | (uri (bioconductor-uri "cummeRbund" version)) | |
1240 | (sha256 | |
1241 | (base32 | |
1242 | "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj")))) | |
1243 | (build-system r-build-system) | |
1244 | (propagated-inputs | |
1245 | `(("r-biobase" ,r-biobase) | |
1246 | ("r-biocgenerics" ,r-biocgenerics) | |
1247 | ("r-fastcluster" ,r-fastcluster) | |
1248 | ("r-ggplot2" ,r-ggplot2) | |
1249 | ("r-gviz" ,r-gviz) | |
1250 | ("r-plyr" ,r-plyr) | |
1251 | ("r-reshape2" ,r-reshape2) | |
1252 | ("r-rsqlite" ,r-rsqlite) | |
1253 | ("r-rtracklayer" ,r-rtracklayer) | |
1254 | ("r-s4vectors" ,r-s4vectors))) | |
1255 | (home-page "https://bioconductor.org/packages/cummeRbund/") | |
1256 | (synopsis "Analyze Cufflinks high-throughput sequencing data") | |
1257 | (description "This package allows for persistent storage, access, | |
1258 | exploration, and manipulation of Cufflinks high-throughput sequencing | |
1259 | data. In addition, provides numerous plotting functions for commonly | |
1260 | used visualizations.") | |
1261 | (license license:artistic2.0))) | |
1262 | ||
30a4bd3b RW |
1263 | (define-public r-bluster |
1264 | (package | |
1265 | (name "r-bluster") | |
1266 | (version "1.0.0") | |
1267 | (source (origin | |
1268 | (method url-fetch) | |
1269 | (uri (bioconductor-uri "bluster" version)) | |
1270 | (sha256 | |
1271 | (base32 | |
1272 | "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61")))) | |
1273 | (properties `((upstream-name . "bluster"))) | |
1274 | (build-system r-build-system) | |
1275 | (propagated-inputs | |
1276 | `(("r-biocneighbors" ,r-biocneighbors) | |
1277 | ("r-biocparallel" ,r-biocparallel) | |
1278 | ("r-igraph" ,r-igraph) | |
1279 | ("r-matrix" ,r-matrix) | |
1280 | ("r-rcpp" ,r-rcpp) | |
1281 | ("r-s4vectors" ,r-s4vectors))) | |
1282 | (native-inputs | |
1283 | `(("r-knitr" ,r-knitr))) | |
1284 | (home-page "https://bioconductor.org/packages/bluster") | |
1285 | (synopsis "Clustering algorithms for Bioconductor") | |
1286 | (description"This package wraps common clustering algorithms in an easily | |
1287 | extended S4 framework. Backends are implemented for hierarchical, k-means | |
1288 | and graph-based clustering. Several utilities are also provided to compare | |
1289 | and evaluate clustering results.") | |
1290 | (license license:gpl3))) | |
1291 | ||
5cf940de RW |
1292 | (define-public r-affycomp |
1293 | (package | |
1294 | (name "r-affycomp") | |
c472549f | 1295 | (version "1.66.0") |
5cf940de RW |
1296 | (source |
1297 | (origin | |
1298 | (method url-fetch) | |
1299 | (uri (bioconductor-uri "affycomp" version)) | |
1300 | (sha256 | |
1301 | (base32 | |
c472549f | 1302 | "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk")))) |
5cf940de RW |
1303 | (properties `((upstream-name . "affycomp"))) |
1304 | (build-system r-build-system) | |
1305 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
1306 | (home-page "https://bioconductor.org/packages/affycomp/") | |
1307 | (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") | |
1308 | (description | |
1309 | "The package contains functions that can be used to compare expression | |
1310 | measures for Affymetrix Oligonucleotide Arrays.") | |
1311 | (license license:gpl2+))) | |
1312 | ||
5094aa94 RW |
1313 | (define-public r-affycompatible |
1314 | (package | |
1315 | (name "r-affycompatible") | |
fa2d16cc | 1316 | (version "1.50.0") |
5094aa94 RW |
1317 | (source |
1318 | (origin | |
1319 | (method url-fetch) | |
1320 | (uri (bioconductor-uri "AffyCompatible" version)) | |
1321 | (sha256 | |
1322 | (base32 | |
fa2d16cc | 1323 | "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x")))) |
5094aa94 RW |
1324 | (properties |
1325 | `((upstream-name . "AffyCompatible"))) | |
1326 | (build-system r-build-system) | |
1327 | (propagated-inputs | |
1328 | `(("r-biostrings" ,r-biostrings) | |
1329 | ("r-rcurl" ,r-rcurl) | |
1330 | ("r-xml" ,r-xml))) | |
1331 | (home-page "https://bioconductor.org/packages/AffyCompatible/") | |
1332 | (synopsis "Work with Affymetrix GeneChip files") | |
1333 | (description | |
1334 | "This package provides an interface to Affymetrix chip annotation and | |
1335 | sample attribute files. The package allows an easy way for users to download | |
1336 | and manage local data bases of Affynmetrix NetAffx annotation files. It also | |
1337 | provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip | |
1338 | Command Console} (AGCC)-compatible sample annotation files.") | |
1339 | (license license:artistic2.0))) | |
1340 | ||
4ca2d6c1 RW |
1341 | (define-public r-affycontam |
1342 | (package | |
1343 | (name "r-affycontam") | |
3e82f9cc | 1344 | (version "1.48.0") |
4ca2d6c1 RW |
1345 | (source |
1346 | (origin | |
1347 | (method url-fetch) | |
1348 | (uri (bioconductor-uri "affyContam" version)) | |
1349 | (sha256 | |
1350 | (base32 | |
3e82f9cc | 1351 | "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b")))) |
4ca2d6c1 RW |
1352 | (properties `((upstream-name . "affyContam"))) |
1353 | (build-system r-build-system) | |
1354 | (propagated-inputs | |
1355 | `(("r-affy" ,r-affy) | |
1356 | ("r-affydata" ,r-affydata) | |
1357 | ("r-biobase" ,r-biobase))) | |
1358 | (home-page "https://bioconductor.org/packages/affyContam/") | |
1359 | (synopsis "Structured corruption of Affymetrix CEL file data") | |
1360 | (description | |
1361 | "Microarray quality assessment is a major concern of microarray analysts. | |
1362 | This package provides some simple approaches to in silico creation of quality | |
1363 | problems in CEL-level data to help evaluate performance of quality metrics.") | |
1364 | (license license:artistic2.0))) | |
1365 | ||
12105c6c RW |
1366 | (define-public r-affycoretools |
1367 | (package | |
1368 | (name "r-affycoretools") | |
a92219b4 | 1369 | (version "1.62.0") |
12105c6c RW |
1370 | (source |
1371 | (origin | |
1372 | (method url-fetch) | |
1373 | (uri (bioconductor-uri "affycoretools" version)) | |
1374 | (sha256 | |
1375 | (base32 | |
a92219b4 | 1376 | "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0")))) |
12105c6c RW |
1377 | (properties `((upstream-name . "affycoretools"))) |
1378 | (build-system r-build-system) | |
1379 | (propagated-inputs | |
1380 | `(("r-affy" ,r-affy) | |
1381 | ("r-annotationdbi" ,r-annotationdbi) | |
1382 | ("r-biobase" ,r-biobase) | |
1383 | ("r-biocgenerics" ,r-biocgenerics) | |
1384 | ("r-dbi" ,r-dbi) | |
1385 | ("r-edger" ,r-edger) | |
1386 | ("r-gcrma" ,r-gcrma) | |
f8f181ae | 1387 | ("r-glimma" ,r-glimma) |
12105c6c RW |
1388 | ("r-ggplot2" ,r-ggplot2) |
1389 | ("r-gostats" ,r-gostats) | |
1390 | ("r-gplots" ,r-gplots) | |
1391 | ("r-hwriter" ,r-hwriter) | |
1392 | ("r-lattice" ,r-lattice) | |
1393 | ("r-limma" ,r-limma) | |
1394 | ("r-oligoclasses" ,r-oligoclasses) | |
1395 | ("r-reportingtools" ,r-reportingtools) | |
1396 | ("r-rsqlite" ,r-rsqlite) | |
1397 | ("r-s4vectors" ,r-s4vectors) | |
1398 | ("r-xtable" ,r-xtable))) | |
fa610697 RW |
1399 | (native-inputs |
1400 | `(("r-knitr" ,r-knitr))) | |
12105c6c RW |
1401 | (home-page "https://bioconductor.org/packages/affycoretools/") |
1402 | (synopsis "Functions for analyses with Affymetrix GeneChips") | |
1403 | (description | |
1404 | "This package provides various wrapper functions that have been written | |
1405 | to streamline the more common analyses that a Biostatistician might see.") | |
1406 | (license license:artistic2.0))) | |
1407 | ||
d6a5d9b2 RW |
1408 | (define-public r-affxparser |
1409 | (package | |
1410 | (name "r-affxparser") | |
8e6a2c32 | 1411 | (version "1.62.0") |
d6a5d9b2 RW |
1412 | (source |
1413 | (origin | |
1414 | (method url-fetch) | |
1415 | (uri (bioconductor-uri "affxparser" version)) | |
1416 | (sha256 | |
1417 | (base32 | |
8e6a2c32 | 1418 | "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p")))) |
d6a5d9b2 RW |
1419 | (properties `((upstream-name . "affxparser"))) |
1420 | (build-system r-build-system) | |
1421 | (home-page "https://github.com/HenrikBengtsson/affxparser") | |
1422 | (synopsis "Affymetrix File Parsing SDK") | |
1423 | (description | |
1424 | "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, | |
1425 | BAR). It provides methods for fast and memory efficient parsing of Affymetrix | |
1426 | files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files | |
1427 | are supported. Currently, there are methods for reading @dfn{chip definition | |
1428 | file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read | |
1429 | either in full or in part. For example, probe signals from a few probesets | |
1430 | can be extracted very quickly from a set of CEL files into a convenient list | |
1431 | structure.") | |
1432 | ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is | |
1433 | ;; under LGPLv2+. | |
1434 | (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2)))) | |
1435 | ||
7097c700 RW |
1436 | (define-public r-annotate |
1437 | (package | |
1438 | (name "r-annotate") | |
7d563023 | 1439 | (version "1.68.0") |
7097c700 RW |
1440 | (source |
1441 | (origin | |
1442 | (method url-fetch) | |
1443 | (uri (bioconductor-uri "annotate" version)) | |
1444 | (sha256 | |
1445 | (base32 | |
7d563023 | 1446 | "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l")))) |
7097c700 RW |
1447 | (build-system r-build-system) |
1448 | (propagated-inputs | |
1449 | `(("r-annotationdbi" ,r-annotationdbi) | |
1450 | ("r-biobase" ,r-biobase) | |
1451 | ("r-biocgenerics" ,r-biocgenerics) | |
1452 | ("r-dbi" ,r-dbi) | |
7d563023 | 1453 | ("r-httr" ,r-httr) |
7097c700 RW |
1454 | ("r-xml" ,r-xml) |
1455 | ("r-xtable" ,r-xtable))) | |
1456 | (home-page | |
1457 | "https://bioconductor.org/packages/annotate") | |
1458 | (synopsis "Annotation for microarrays") | |
1459 | (description "This package provides R environments for the annotation of | |
1460 | microarrays.") | |
1461 | (license license:artistic2.0))) | |
1462 | ||
fa596599 RW |
1463 | (define-public r-hpar |
1464 | (package | |
1465 | (name "r-hpar") | |
fa7578b3 | 1466 | (version "1.32.1") |
fa596599 RW |
1467 | (source |
1468 | (origin | |
1469 | (method url-fetch) | |
1470 | (uri (bioconductor-uri "hpar" version)) | |
1471 | (sha256 | |
1472 | (base32 | |
fa7578b3 | 1473 | "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr")))) |
fa596599 | 1474 | (build-system r-build-system) |
07bea010 RW |
1475 | (native-inputs |
1476 | `(("r-knitr" ,r-knitr))) | |
fa596599 RW |
1477 | (home-page "https://bioconductor.org/packages/hpar/") |
1478 | (synopsis "Human Protein Atlas in R") | |
1479 | (description "This package provides a simple interface to and data from | |
1480 | the Human Protein Atlas project.") | |
1481 | (license license:artistic2.0))) | |
183ce988 RJ |
1482 | |
1483 | (define-public r-regioner | |
1484 | (package | |
1485 | (name "r-regioner") | |
d1ff3604 | 1486 | (version "1.22.0") |
183ce988 RJ |
1487 | (source |
1488 | (origin | |
1489 | (method url-fetch) | |
1490 | (uri (bioconductor-uri "regioneR" version)) | |
1491 | (sha256 | |
1492 | (base32 | |
d1ff3604 | 1493 | "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi")))) |
183ce988 RJ |
1494 | (properties `((upstream-name . "regioneR"))) |
1495 | (build-system r-build-system) | |
1496 | (propagated-inputs | |
d639d888 | 1497 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 1498 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 1499 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 1500 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 1501 | ("r-iranges" ,r-iranges) |
d639d888 RW |
1502 | ("r-memoise" ,r-memoise) |
1503 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 1504 | ("r-s4vectors" ,r-s4vectors))) |
7f34dd58 RW |
1505 | (native-inputs |
1506 | `(("r-knitr" ,r-knitr))) | |
183ce988 RJ |
1507 | (home-page "https://bioconductor.org/packages/regioneR/") |
1508 | (synopsis "Association analysis of genomic regions") | |
1509 | (description "This package offers a statistical framework based on | |
1510 | customizable permutation tests to assess the association between genomic | |
1511 | region sets and other genomic features.") | |
1512 | (license license:artistic2.0))) | |
a5b56a53 | 1513 | |
15184fb3 RW |
1514 | (define-public r-reportingtools |
1515 | (package | |
1516 | (name "r-reportingtools") | |
c03c7634 | 1517 | (version "2.30.0") |
15184fb3 RW |
1518 | (source |
1519 | (origin | |
1520 | (method url-fetch) | |
1521 | (uri (bioconductor-uri "ReportingTools" version)) | |
1522 | (sha256 | |
1523 | (base32 | |
c03c7634 | 1524 | "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31")))) |
15184fb3 RW |
1525 | (properties |
1526 | `((upstream-name . "ReportingTools"))) | |
1527 | (build-system r-build-system) | |
1528 | (propagated-inputs | |
1529 | `(("r-annotate" ,r-annotate) | |
1530 | ("r-annotationdbi" ,r-annotationdbi) | |
1531 | ("r-biobase" ,r-biobase) | |
1532 | ("r-biocgenerics" ,r-biocgenerics) | |
1533 | ("r-category" ,r-category) | |
1534 | ("r-deseq2" ,r-deseq2) | |
1535 | ("r-edger" ,r-edger) | |
1536 | ("r-ggbio" ,r-ggbio) | |
1537 | ("r-ggplot2" ,r-ggplot2) | |
1538 | ("r-gostats" ,r-gostats) | |
1539 | ("r-gseabase" ,r-gseabase) | |
1540 | ("r-hwriter" ,r-hwriter) | |
1541 | ("r-iranges" ,r-iranges) | |
1542 | ("r-knitr" ,r-knitr) | |
1543 | ("r-lattice" ,r-lattice) | |
1544 | ("r-limma" ,r-limma) | |
1545 | ("r-pfam-db" ,r-pfam-db) | |
1546 | ("r-r-utils" ,r-r-utils) | |
1547 | ("r-xml" ,r-xml))) | |
7f94cf01 RW |
1548 | (native-inputs |
1549 | `(("r-knitr" ,r-knitr))) | |
15184fb3 RW |
1550 | (home-page "https://bioconductor.org/packages/ReportingTools/") |
1551 | (synopsis "Tools for making reports in various formats") | |
1552 | (description | |
1553 | "The ReportingTools package enables users to easily display reports of | |
1554 | analysis results generated from sources such as microarray and sequencing | |
1555 | data. The package allows users to create HTML pages that may be viewed on a | |
1556 | web browser, or in other formats. Users can generate tables with sortable and | |
1557 | filterable columns, make and display plots, and link table entries to other | |
1558 | data sources such as NCBI or larger plots within the HTML page. Using the | |
1559 | package, users can also produce a table of contents page to link various | |
1560 | reports together for a particular project that can be viewed in a web | |
1561 | browser.") | |
1562 | (license license:artistic2.0))) | |
1563 | ||
bfb93b48 RW |
1564 | (define-public r-geneplotter |
1565 | (package | |
1566 | (name "r-geneplotter") | |
d72c4c98 | 1567 | (version "1.68.0") |
bfb93b48 RW |
1568 | (source |
1569 | (origin | |
1570 | (method url-fetch) | |
1571 | (uri (bioconductor-uri "geneplotter" version)) | |
1572 | (sha256 | |
1573 | (base32 | |
d72c4c98 | 1574 | "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx")))) |
bfb93b48 RW |
1575 | (build-system r-build-system) |
1576 | (propagated-inputs | |
1577 | `(("r-annotate" ,r-annotate) | |
1578 | ("r-annotationdbi" ,r-annotationdbi) | |
1579 | ("r-biobase" ,r-biobase) | |
1580 | ("r-biocgenerics" ,r-biocgenerics) | |
1581 | ("r-lattice" ,r-lattice) | |
1582 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
1583 | (home-page "https://bioconductor.org/packages/geneplotter") | |
1584 | (synopsis "Graphics functions for genomic data") | |
1585 | (description | |
1586 | "This package provides functions for plotting genomic data.") | |
1587 | (license license:artistic2.0))) | |
1588 | ||
01c7ba99 RW |
1589 | (define-public r-oligoclasses |
1590 | (package | |
1591 | (name "r-oligoclasses") | |
464df5cc | 1592 | (version "1.52.0") |
01c7ba99 RW |
1593 | (source |
1594 | (origin | |
1595 | (method url-fetch) | |
1596 | (uri (bioconductor-uri "oligoClasses" version)) | |
1597 | (sha256 | |
1598 | (base32 | |
464df5cc | 1599 | "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy")))) |
01c7ba99 RW |
1600 | (properties `((upstream-name . "oligoClasses"))) |
1601 | (build-system r-build-system) | |
1602 | (propagated-inputs | |
1603 | `(("r-affyio" ,r-affyio) | |
1604 | ("r-biobase" ,r-biobase) | |
1605 | ("r-biocgenerics" ,r-biocgenerics) | |
1606 | ("r-biocmanager" ,r-biocmanager) | |
1607 | ("r-biostrings" ,r-biostrings) | |
1608 | ("r-dbi" ,r-dbi) | |
1609 | ("r-ff" ,r-ff) | |
1610 | ("r-foreach" ,r-foreach) | |
1611 | ("r-genomicranges" ,r-genomicranges) | |
1612 | ("r-iranges" ,r-iranges) | |
1613 | ("r-rsqlite" ,r-rsqlite) | |
1614 | ("r-s4vectors" ,r-s4vectors) | |
1615 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1616 | (home-page "https://bioconductor.org/packages/oligoClasses/") | |
1617 | (synopsis "Classes for high-throughput arrays") | |
1618 | (description | |
1619 | "This package contains class definitions, validity checks, and | |
1620 | initialization methods for classes used by the @code{oligo} and @code{crlmm} | |
1621 | packages.") | |
1622 | (license license:gpl2+))) | |
1623 | ||
4c63eeb8 RW |
1624 | (define-public r-oligo |
1625 | (package | |
1626 | (name "r-oligo") | |
9af6fdf8 | 1627 | (version "1.54.1") |
4c63eeb8 RW |
1628 | (source |
1629 | (origin | |
1630 | (method url-fetch) | |
1631 | (uri (bioconductor-uri "oligo" version)) | |
1632 | (sha256 | |
1633 | (base32 | |
9af6fdf8 | 1634 | "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3")))) |
4c63eeb8 RW |
1635 | (properties `((upstream-name . "oligo"))) |
1636 | (build-system r-build-system) | |
1637 | (inputs `(("zlib" ,zlib))) | |
1638 | (propagated-inputs | |
1639 | `(("r-affxparser" ,r-affxparser) | |
1640 | ("r-affyio" ,r-affyio) | |
1641 | ("r-biobase" ,r-biobase) | |
1642 | ("r-biocgenerics" ,r-biocgenerics) | |
1643 | ("r-biostrings" ,r-biostrings) | |
1644 | ("r-dbi" ,r-dbi) | |
1645 | ("r-ff" ,r-ff) | |
1646 | ("r-oligoclasses" ,r-oligoclasses) | |
1647 | ("r-preprocesscore" ,r-preprocesscore) | |
1648 | ("r-rsqlite" ,r-rsqlite) | |
1649 | ("r-zlibbioc" ,r-zlibbioc))) | |
ace82f80 RW |
1650 | (native-inputs |
1651 | `(("r-knitr" ,r-knitr))) | |
4c63eeb8 RW |
1652 | (home-page "https://bioconductor.org/packages/oligo/") |
1653 | (synopsis "Preprocessing tools for oligonucleotide arrays") | |
1654 | (description | |
1655 | "This package provides a package to analyze oligonucleotide | |
1656 | arrays (expression/SNP/tiling/exon) at probe-level. It currently supports | |
1657 | Affymetrix (CEL files) and NimbleGen arrays (XYS files).") | |
1658 | (license license:lgpl2.0+))) | |
1659 | ||
4dc2ecc2 RW |
1660 | (define-public r-qvalue |
1661 | (package | |
1662 | (name "r-qvalue") | |
e9b60a29 | 1663 | (version "2.22.0") |
4dc2ecc2 RW |
1664 | (source |
1665 | (origin | |
1666 | (method url-fetch) | |
1667 | (uri (bioconductor-uri "qvalue" version)) | |
1668 | (sha256 | |
1669 | (base32 | |
e9b60a29 | 1670 | "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5")))) |
4dc2ecc2 RW |
1671 | (build-system r-build-system) |
1672 | (propagated-inputs | |
1673 | `(("r-ggplot2" ,r-ggplot2) | |
1674 | ("r-reshape2" ,r-reshape2))) | |
f9a24759 RW |
1675 | (native-inputs |
1676 | `(("r-knitr" ,r-knitr))) | |
702a1012 | 1677 | (home-page "https://github.com/StoreyLab/qvalue") |
4dc2ecc2 RW |
1678 | (synopsis "Q-value estimation for false discovery rate control") |
1679 | (description | |
1680 | "This package takes a list of p-values resulting from the simultaneous | |
1681 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
1682 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
1683 | of false positives incurred when that particular test is called significant. | |
1684 | The local FDR measures the posterior probability the null hypothesis is true | |
1685 | given the test's p-value. Various plots are automatically generated, allowing | |
1686 | one to make sensible significance cut-offs. The software can be applied to | |
1687 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
1688 | ;; Any version of the LGPL. | |
1689 | (license license:lgpl3+))) | |
1690 | ||
a0df9b93 RJ |
1691 | (define r-rcppnumerical |
1692 | (package | |
1693 | (name "r-rcppnumerical") | |
1694 | (version "0.4-0") | |
1695 | (source (origin | |
1696 | (method url-fetch) | |
1697 | (uri (cran-uri "RcppNumerical" version)) | |
1698 | (sha256 | |
1699 | (base32 | |
1700 | "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) | |
1701 | (properties `((upstream-name . "RcppNumerical"))) | |
1702 | (build-system r-build-system) | |
1703 | (propagated-inputs | |
1704 | `(("r-rcpp" ,r-rcpp) | |
1705 | ("r-rcppeigen" ,r-rcppeigen))) | |
1706 | (native-inputs | |
1707 | `(("r-knitr" ,r-knitr))) | |
1708 | (home-page "https://github.com/yixuan/RcppNumerical") | |
1709 | (synopsis "Rcpp integration for numerical computing libraries") | |
1710 | (description "This package provides a collection of open source libraries | |
1711 | for numerical computing (numerical integration, optimization, etc.) and their | |
1712 | integration with @code{Rcpp}.") | |
1713 | (license license:gpl2+))) | |
1714 | ||
3b399e51 RJ |
1715 | (define-public r-apeglm |
1716 | (package | |
1717 | (name "r-apeglm") | |
1718 | (version "1.12.0") | |
1719 | (source (origin | |
1720 | (method url-fetch) | |
1721 | (uri (bioconductor-uri "apeglm" version)) | |
1722 | (sha256 | |
1723 | (base32 | |
1724 | "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2")))) | |
1725 | (properties `((upstream-name . "apeglm"))) | |
1726 | (build-system r-build-system) | |
1727 | (propagated-inputs | |
1728 | `(("r-emdbook" ,r-emdbook) | |
1729 | ("r-genomicranges" ,r-genomicranges) | |
1730 | ("r-rcpp" ,r-rcpp) | |
1731 | ("r-rcppeigen" ,r-rcppeigen) | |
1732 | ("r-rcppnumerical" ,r-rcppnumerical) | |
1733 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1734 | (native-inputs `(("r-knitr" ,r-knitr))) | |
1735 | (home-page "https://bioconductor.org/packages/apeglm") | |
1736 | (synopsis "Approximate posterior estimation for GLM coefficients") | |
1737 | (description "This package provides Bayesian shrinkage estimators for | |
1738 | effect sizes for a variety of GLM models, using approximation of the | |
1739 | posterior for individual coefficients.") | |
1740 | (license license:gpl2))) | |
1741 | ||
6e396c4b RJ |
1742 | (define-public r-greylistchip |
1743 | (package | |
1744 | (name "r-greylistchip") | |
1745 | (version "1.22.0") | |
1746 | (source (origin | |
1747 | (method url-fetch) | |
1748 | (uri (bioconductor-uri "GreyListChIP" version)) | |
1749 | (sha256 | |
1750 | (base32 | |
1751 | "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6")))) | |
1752 | (properties `((upstream-name . "GreyListChIP"))) | |
1753 | (build-system r-build-system) | |
1754 | (propagated-inputs | |
1755 | `(("r-bsgenome" ,r-bsgenome) | |
1756 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1757 | ("r-genomicalignments" ,r-genomicalignments) | |
1758 | ("r-genomicranges" ,r-genomicranges) | |
1759 | ("r-mass" ,r-mass) | |
1760 | ("r-rsamtools" ,r-rsamtools) | |
1761 | ("r-rtracklayer" ,r-rtracklayer) | |
1762 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1763 | (home-page "https://bioconductor.org/packages/GreyListChIP") | |
1764 | (synopsis "Greylist artefact regions based on ChIP inputs") | |
1765 | (description "This package identifies regions of ChIP experiments with high | |
1766 | signal in the input, that lead to spurious peaks during peak calling.") | |
1767 | (license license:artistic2.0))) | |
1768 | ||
a5b56a53 RJ |
1769 | (define-public r-diffbind |
1770 | (package | |
1771 | (name "r-diffbind") | |
ebf11de4 | 1772 | (version "3.0.8") |
a5b56a53 RJ |
1773 | (source |
1774 | (origin | |
1775 | (method url-fetch) | |
1776 | (uri (bioconductor-uri "DiffBind" version)) | |
1777 | (sha256 | |
1778 | (base32 | |
ebf11de4 | 1779 | "11svdfjp4faswrmzwkryzhd0ji2pl9vwsd35lvbfjgakbpxnyn8a")))) |
a5b56a53 RJ |
1780 | (properties `((upstream-name . "DiffBind"))) |
1781 | (build-system r-build-system) | |
a5b56a53 RJ |
1782 | (propagated-inputs |
1783 | `(("r-amap" ,r-amap) | |
341ebaaa RJ |
1784 | ("r-apeglm" ,r-apeglm) |
1785 | ("r-ashr" ,r-ashr) | |
a5b56a53 RJ |
1786 | ("r-biocparallel" ,r-biocparallel) |
1787 | ("r-deseq2" ,r-deseq2) | |
1788 | ("r-dplyr" ,r-dplyr) | |
a5b56a53 | 1789 | ("r-genomicalignments" ,r-genomicalignments) |
45bbccf4 RW |
1790 | ("r-genomicranges" ,r-genomicranges) |
1791 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
1792 | ("r-ggrepel" ,r-ggrepel) |
1793 | ("r-gplots" ,r-gplots) | |
341ebaaa | 1794 | ("r-greylistchip" ,r-greylistchip) |
a5b56a53 RJ |
1795 | ("r-iranges" ,r-iranges) |
1796 | ("r-lattice" ,r-lattice) | |
1797 | ("r-limma" ,r-limma) | |
1798 | ("r-locfit" ,r-locfit) | |
1799 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
1800 | ("r-rcpp" ,r-rcpp) | |
4c221b3b | 1801 | ("r-rhtslib" ,r-rhtslib) |
a5b56a53 RJ |
1802 | ("r-rsamtools" ,r-rsamtools) |
1803 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 1804 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
4c221b3b | 1805 | ("r-systempiper" ,r-systempiper))) |
99db6db7 | 1806 | (home-page "https://bioconductor.org/packages/DiffBind") |
a5b56a53 RJ |
1807 | (synopsis "Differential binding analysis of ChIP-Seq peak data") |
1808 | (description | |
1809 | "This package computes differentially bound sites from multiple | |
1810 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
1811 | occupancy (overlap) analysis and plotting functions.") | |
1812 | (license license:artistic2.0))) | |
6d94bf6b RJ |
1813 | |
1814 | (define-public r-ripseeker | |
1815 | (package | |
1816 | (name "r-ripseeker") | |
ba74434f | 1817 | (version "1.26.0") |
6d94bf6b RJ |
1818 | (source |
1819 | (origin | |
1820 | (method url-fetch) | |
1821 | (uri (bioconductor-uri "RIPSeeker" version)) | |
1822 | (sha256 | |
1823 | (base32 | |
ba74434f | 1824 | "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) |
6d94bf6b RJ |
1825 | (properties `((upstream-name . "RIPSeeker"))) |
1826 | (build-system r-build-system) | |
1827 | (propagated-inputs | |
1828 | `(("r-s4vectors" ,r-s4vectors) | |
1829 | ("r-iranges" ,r-iranges) | |
1830 | ("r-genomicranges" ,r-genomicranges) | |
1831 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1832 | ("r-rsamtools" ,r-rsamtools) | |
1833 | ("r-genomicalignments" ,r-genomicalignments) | |
1834 | ("r-rtracklayer" ,r-rtracklayer))) | |
99db6db7 | 1835 | (home-page "https://bioconductor.org/packages/RIPSeeker") |
6d94bf6b RJ |
1836 | (synopsis |
1837 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
1838 | (description | |
1839 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
1840 | using two-state HMM with negative binomial emission probability. While | |
1841 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
1842 | a suite of bioinformatics tools integrated within this self-contained software | |
1843 | package comprehensively addressing issues ranging from post-alignments | |
1844 | processing to visualization and annotation.") | |
1845 | (license license:gpl2))) | |
a6ae9ffd RJ |
1846 | |
1847 | (define-public r-multtest | |
1848 | (package | |
1849 | (name "r-multtest") | |
1e6920c5 | 1850 | (version "2.46.0") |
a6ae9ffd RJ |
1851 | (source |
1852 | (origin | |
1853 | (method url-fetch) | |
1854 | (uri (bioconductor-uri "multtest" version)) | |
1855 | (sha256 | |
1856 | (base32 | |
1e6920c5 | 1857 | "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q")))) |
a6ae9ffd RJ |
1858 | (build-system r-build-system) |
1859 | (propagated-inputs | |
1860 | `(("r-survival" ,r-survival) | |
1861 | ("r-biocgenerics" ,r-biocgenerics) | |
1862 | ("r-biobase" ,r-biobase) | |
1863 | ("r-mass" ,r-mass))) | |
99db6db7 | 1864 | (home-page "https://bioconductor.org/packages/multtest") |
a6ae9ffd RJ |
1865 | (synopsis "Resampling-based multiple hypothesis testing") |
1866 | (description | |
1867 | "This package can do non-parametric bootstrap and permutation | |
1868 | resampling-based multiple testing procedures (including empirical Bayes | |
1869 | methods) for controlling the family-wise error rate (FWER), generalized | |
1870 | family-wise error rate (gFWER), tail probability of the proportion of | |
1871 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
1872 | of bootstrap-based null distribution are implemented (centered, centered | |
1873 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
1874 | available. Tests based on a variety of T- and F-statistics (including | |
1875 | T-statistics based on regression parameters from linear and survival models | |
1876 | as well as those based on correlation parameters) are included. When probing | |
1877 | hypotheses with T-statistics, users may also select a potentially faster null | |
1878 | distribution which is multivariate normal with mean zero and variance | |
1879 | covariance matrix derived from the vector influence function. Results are | |
1880 | reported in terms of adjusted P-values, confidence regions and test statistic | |
1881 | cutoffs. The procedures are directly applicable to identifying differentially | |
1882 | expressed genes in DNA microarray experiments.") | |
1883 | (license license:lgpl3))) | |
793f83ef | 1884 | |
5dfe4912 RW |
1885 | (define-public r-graph |
1886 | (package | |
1887 | (name "r-graph") | |
f519b4dc | 1888 | (version "1.68.0") |
5dfe4912 RW |
1889 | (source (origin |
1890 | (method url-fetch) | |
1891 | (uri (bioconductor-uri "graph" version)) | |
1892 | (sha256 | |
1893 | (base32 | |
f519b4dc | 1894 | "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4")))) |
5dfe4912 RW |
1895 | (build-system r-build-system) |
1896 | (propagated-inputs | |
1897 | `(("r-biocgenerics" ,r-biocgenerics))) | |
1898 | (home-page "https://bioconductor.org/packages/graph") | |
1899 | (synopsis "Handle graph data structures in R") | |
1900 | (description | |
1901 | "This package implements some simple graph handling capabilities for R.") | |
1902 | (license license:artistic2.0))) | |
1903 | ||
8017eb0a RW |
1904 | ;; This is a CRAN package, but it depends on a Bioconductor package. |
1905 | (define-public r-ggm | |
1906 | (package | |
1907 | (name "r-ggm") | |
1908 | (version "2.5") | |
1909 | (source | |
1910 | (origin | |
1911 | (method url-fetch) | |
1912 | (uri (cran-uri "ggm" version)) | |
1913 | (sha256 | |
1914 | (base32 | |
1915 | "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) | |
1916 | (properties `((upstream-name . "ggm"))) | |
1917 | (build-system r-build-system) | |
1918 | (propagated-inputs | |
1919 | `(("r-graph" ,r-graph) | |
1920 | ("r-igraph" ,r-igraph))) | |
1921 | (home-page "https://cran.r-project.org/package=ggm") | |
1922 | (synopsis "Functions for graphical Markov models") | |
1923 | (description | |
1924 | "This package provides functions and datasets for maximum likelihood | |
1925 | fitting of some classes of graphical Markov models.") | |
1926 | (license license:gpl2+))) | |
1927 | ||
a07717cc RW |
1928 | ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph. |
1929 | (define-public r-perfmeas | |
1930 | (package | |
1931 | (name "r-perfmeas") | |
1932 | (version "1.2.1") | |
1933 | (source | |
1934 | (origin | |
1935 | (method url-fetch) | |
1936 | (uri (cran-uri "PerfMeas" version)) | |
1937 | (sha256 | |
1938 | (base32 | |
1939 | "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93")))) | |
1940 | (properties `((upstream-name . "PerfMeas"))) | |
1941 | (build-system r-build-system) | |
1942 | (propagated-inputs | |
1943 | `(("r-graph" ,r-graph) | |
1944 | ("r-limma" ,r-limma) | |
1945 | ("r-rbgl" ,r-rbgl))) | |
1946 | (home-page "https://cran.r-project.org/web/packages/PerfMeas/") | |
1947 | (synopsis "Performance measures for ranking and classification tasks") | |
1948 | (description | |
1949 | "This package implements different performance measures for | |
1950 | classification and ranking tasks. @dfn{Area under curve} (AUC), precision at | |
1951 | a given recall, F-score for single and multiple classes are available.") | |
1952 | (license license:gpl2+))) | |
1953 | ||
b17ace24 | 1954 | ;; This is a CRAN package, but it depends on a Bioconductor package. |
a207bca2 RW |
1955 | (define-public r-codedepends |
1956 | (package | |
1957 | (name "r-codedepends") | |
1958 | (version "0.6.5") | |
1959 | (source | |
1960 | (origin | |
1961 | (method url-fetch) | |
1962 | (uri (cran-uri "CodeDepends" version)) | |
1963 | (sha256 | |
1964 | (base32 | |
1965 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
1966 | (properties `((upstream-name . "CodeDepends"))) | |
1967 | (build-system r-build-system) | |
1968 | (propagated-inputs | |
1969 | `(("r-codetools" ,r-codetools) | |
1970 | ("r-graph" ,r-graph) | |
1971 | ("r-xml" ,r-xml))) | |
5e1f2362 | 1972 | (home-page "https://cran.r-project.org/web/packages/CodeDepends") |
a207bca2 RW |
1973 | (synopsis "Analysis of R code for reproducible research and code comprehension") |
1974 | (description | |
1975 | "This package provides tools for analyzing R expressions or blocks of | |
1976 | code and determining the dependencies between them. It focuses on R scripts, | |
1977 | but can be used on the bodies of functions. There are many facilities | |
1978 | including the ability to summarize or get a high-level view of code, | |
1979 | determining dependencies between variables, code improvement suggestions.") | |
1980 | ;; Any version of the GPL | |
1981 | (license (list license:gpl2+ license:gpl3+)))) | |
1982 | ||
793f83ef RJ |
1983 | (define-public r-chippeakanno |
1984 | (package | |
1985 | (name "r-chippeakanno") | |
d068d967 | 1986 | (version "3.24.1") |
793f83ef RJ |
1987 | (source |
1988 | (origin | |
1989 | (method url-fetch) | |
1990 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
1991 | (sha256 | |
1992 | (base32 | |
d068d967 | 1993 | "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj")))) |
793f83ef RJ |
1994 | (properties `((upstream-name . "ChIPpeakAnno"))) |
1995 | (build-system r-build-system) | |
1996 | (propagated-inputs | |
85c1d20f | 1997 | `(("r-annotationdbi" ,r-annotationdbi) |
85c1d20f | 1998 | ("r-biocgenerics" ,r-biocgenerics) |
793f83ef | 1999 | ("r-biomart" ,r-biomart) |
85c1d20f | 2000 | ("r-biostrings" ,r-biostrings) |
85c1d20f | 2001 | ("r-dbi" ,r-dbi) |
85c1d20f RW |
2002 | ("r-ensembldb" ,r-ensembldb) |
2003 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2004 | ("r-genomicalignments" ,r-genomicalignments) | |
793f83ef | 2005 | ("r-genomicfeatures" ,r-genomicfeatures) |
f794e85d | 2006 | ("r-genomicranges" ,r-genomicranges) |
d068d967 | 2007 | ("r-ggplot2" ,r-ggplot2) |
85c1d20f | 2008 | ("r-graph" ,r-graph) |
f794e85d | 2009 | ("r-iranges" ,r-iranges) |
d068d967 | 2010 | ("r-keggrest" ,r-keggrest) |
85c1d20f | 2011 | ("r-matrixstats" ,r-matrixstats) |
793f83ef RJ |
2012 | ("r-multtest" ,r-multtest) |
2013 | ("r-rbgl" ,r-rbgl) | |
793f83ef | 2014 | ("r-regioner" ,r-regioner) |
85c1d20f RW |
2015 | ("r-rsamtools" ,r-rsamtools) |
2016 | ("r-rtracklayer" ,r-rtracklayer) | |
f794e85d | 2017 | ("r-s4vectors" ,r-s4vectors) |
793f83ef | 2018 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
793f83ef | 2019 | ("r-venndiagram" ,r-venndiagram))) |
dc24de46 RW |
2020 | (native-inputs |
2021 | `(("r-knitr" ,r-knitr))) | |
99db6db7 | 2022 | (home-page "https://bioconductor.org/packages/ChIPpeakAnno") |
793f83ef RJ |
2023 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") |
2024 | (description | |
2025 | "The package includes functions to retrieve the sequences around the peak, | |
2026 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
2027 | custom features such as most conserved elements and other transcription factor | |
2028 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
2029 | for finding the peaks with bi-directional promoters with summary statistics | |
2030 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
2031 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
2032 | enrichedGO (addGeneIDs).") | |
2033 | (license license:gpl2+))) | |
164502d8 | 2034 | |
c8da0137 RJ |
2035 | (define-public r-matrixgenerics |
2036 | (package | |
2037 | (name "r-matrixgenerics") | |
2038 | (version "1.2.0") | |
2039 | (source (origin | |
2040 | (method url-fetch) | |
2041 | (uri (bioconductor-uri "MatrixGenerics" version)) | |
2042 | (sha256 | |
2043 | (base32 | |
2044 | "1a3sw79185d6rld3wlrynkzcbp754a7jkracrmvn0ra964ia8zvc")))) | |
2045 | (properties | |
2046 | `((upstream-name . "MatrixGenerics"))) | |
2047 | (build-system r-build-system) | |
2048 | (propagated-inputs | |
2049 | `(("r-matrixstats" ,r-matrixstats))) | |
2050 | (home-page "https://bioconductor.org/packages/MatrixGenerics") | |
2051 | (synopsis "S4 generic summary statistic functions for matrix-like objects") | |
2052 | (description | |
2053 | "This package provides S4 generic functions modeled after the | |
2054 | @code{matrixStats} API for alternative matrix implementations. Packages with | |
2055 | alternative matrix implementation can depend on this package and implement the | |
2056 | generic functions that are defined here for a useful set of row and column | |
2057 | summary statistics. Other package developers can import this package and | |
2058 | handle a different matrix implementations without worrying about | |
2059 | incompatibilities.") | |
2060 | (license license:artistic2.0))) | |
2061 | ||
164502d8 RJ |
2062 | (define-public r-marray |
2063 | (package | |
2064 | (name "r-marray") | |
6e6c6272 | 2065 | (version "1.68.0") |
164502d8 RJ |
2066 | (source (origin |
2067 | (method url-fetch) | |
2068 | (uri (bioconductor-uri "marray" version)) | |
2069 | (sha256 | |
6e6c6272 | 2070 | (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray")))) |
164502d8 RJ |
2071 | (build-system r-build-system) |
2072 | (propagated-inputs | |
67487088 | 2073 | `(("r-limma" ,r-limma))) |
99db6db7 | 2074 | (home-page "https://bioconductor.org/packages/marray") |
164502d8 RJ |
2075 | (synopsis "Exploratory analysis for two-color spotted microarray data") |
2076 | (description "This package contains class definitions for two-color spotted | |
ab8979fc | 2077 | microarray data. It also includes functions for data input, diagnostic plots, |
164502d8 RJ |
2078 | normalization and quality checking.") |
2079 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
2080 | |
2081 | (define-public r-cghbase | |
2082 | (package | |
2083 | (name "r-cghbase") | |
ee052d05 | 2084 | (version "1.50.0") |
0416a0d4 RJ |
2085 | (source (origin |
2086 | (method url-fetch) | |
2087 | (uri (bioconductor-uri "CGHbase" version)) | |
2088 | (sha256 | |
ee052d05 | 2089 | (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4")))) |
0416a0d4 RJ |
2090 | (properties `((upstream-name . "CGHbase"))) |
2091 | (build-system r-build-system) | |
2092 | (propagated-inputs | |
2093 | `(("r-biobase" ,r-biobase) | |
2094 | ("r-marray" ,r-marray))) | |
99db6db7 | 2095 | (home-page "https://bioconductor.org/packages/CGHbase") |
0416a0d4 RJ |
2096 | (synopsis "Base functions and classes for arrayCGH data analysis") |
2097 | (description "This package contains functions and classes that are needed by | |
2098 | the @code{arrayCGH} packages.") | |
2099 | (license license:gpl2+))) | |
67ee83d6 RJ |
2100 | |
2101 | (define-public r-cghcall | |
2102 | (package | |
2103 | (name "r-cghcall") | |
72400035 | 2104 | (version "2.52.0") |
67ee83d6 RJ |
2105 | (source (origin |
2106 | (method url-fetch) | |
2107 | (uri (bioconductor-uri "CGHcall" version)) | |
2108 | (sha256 | |
72400035 | 2109 | (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba")))) |
67ee83d6 RJ |
2110 | (properties `((upstream-name . "CGHcall"))) |
2111 | (build-system r-build-system) | |
2112 | (propagated-inputs | |
2113 | `(("r-biobase" ,r-biobase) | |
2114 | ("r-cghbase" ,r-cghbase) | |
2115 | ("r-impute" ,r-impute) | |
2116 | ("r-dnacopy" ,r-dnacopy) | |
2117 | ("r-snowfall" ,r-snowfall))) | |
99db6db7 | 2118 | (home-page "https://bioconductor.org/packages/CGHcall") |
67ee83d6 RJ |
2119 | (synopsis "Base functions and classes for arrayCGH data analysis") |
2120 | (description "This package contains functions and classes that are needed by | |
2121 | @code{arrayCGH} packages.") | |
2122 | (license license:gpl2+))) | |
0ef8cc9c RJ |
2123 | |
2124 | (define-public r-qdnaseq | |
2125 | (package | |
2126 | (name "r-qdnaseq") | |
3b648409 | 2127 | (version "1.26.0") |
0ef8cc9c RJ |
2128 | (source (origin |
2129 | (method url-fetch) | |
2130 | (uri (bioconductor-uri "QDNAseq" version)) | |
2131 | (sha256 | |
3b648409 | 2132 | (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph")))) |
0ef8cc9c RJ |
2133 | (properties `((upstream-name . "QDNAseq"))) |
2134 | (build-system r-build-system) | |
2135 | (propagated-inputs | |
2136 | `(("r-biobase" ,r-biobase) | |
2137 | ("r-cghbase" ,r-cghbase) | |
2138 | ("r-cghcall" ,r-cghcall) | |
2139 | ("r-dnacopy" ,r-dnacopy) | |
23ce5ad1 RW |
2140 | ("r-future" ,r-future) |
2141 | ("r-future-apply" ,r-future-apply) | |
0ef8cc9c RJ |
2142 | ("r-genomicranges" ,r-genomicranges) |
2143 | ("r-iranges" ,r-iranges) | |
2144 | ("r-matrixstats" ,r-matrixstats) | |
2145 | ("r-r-utils" ,r-r-utils) | |
2146 | ("r-rsamtools" ,r-rsamtools))) | |
99db6db7 | 2147 | (home-page "https://bioconductor.org/packages/QDNAseq") |
0ef8cc9c RJ |
2148 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") |
2149 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
2150 | number of sequence reads in each counted, adjusted with a simultaneous | |
2151 | two-dimensional loess correction for sequence mappability and GC content, and | |
2152 | filtered to remove spurious regions in the genome. Downstream steps of | |
2153 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
2154 | respectively.") | |
2155 | (license license:gpl2+))) | |
bb15b581 RW |
2156 | |
2157 | (define-public r-bayseq | |
2158 | (package | |
2159 | (name "r-bayseq") | |
63572b0c | 2160 | (version "2.24.0") |
bb15b581 RW |
2161 | (source |
2162 | (origin | |
2163 | (method url-fetch) | |
2164 | (uri (bioconductor-uri "baySeq" version)) | |
2165 | (sha256 | |
2166 | (base32 | |
63572b0c | 2167 | "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215")))) |
bb15b581 RW |
2168 | (properties `((upstream-name . "baySeq"))) |
2169 | (build-system r-build-system) | |
2170 | (propagated-inputs | |
2171 | `(("r-abind" ,r-abind) | |
2172 | ("r-edger" ,r-edger) | |
2173 | ("r-genomicranges" ,r-genomicranges))) | |
2174 | (home-page "https://bioconductor.org/packages/baySeq/") | |
2175 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
2176 | (description | |
2177 | "This package identifies differential expression in high-throughput count | |
2178 | data, such as that derived from next-generation sequencing machines, | |
2179 | calculating estimated posterior likelihoods of differential expression (or | |
2180 | more complex hypotheses) via empirical Bayesian methods.") | |
2181 | (license license:gpl3))) | |
609f4ad1 RW |
2182 | |
2183 | (define-public r-chipcomp | |
2184 | (package | |
2185 | (name "r-chipcomp") | |
3f04b816 | 2186 | (version "1.20.0") |
609f4ad1 RW |
2187 | (source |
2188 | (origin | |
2189 | (method url-fetch) | |
2190 | (uri (bioconductor-uri "ChIPComp" version)) | |
2191 | (sha256 | |
2192 | (base32 | |
3f04b816 | 2193 | "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7")))) |
609f4ad1 RW |
2194 | (properties `((upstream-name . "ChIPComp"))) |
2195 | (build-system r-build-system) | |
2196 | (propagated-inputs | |
2197 | `(("r-biocgenerics" ,r-biocgenerics) | |
2198 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
2199 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
2200 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2201 | ("r-genomicranges" ,r-genomicranges) | |
2202 | ("r-iranges" ,r-iranges) | |
2203 | ("r-limma" ,r-limma) | |
2204 | ("r-rsamtools" ,r-rsamtools) | |
2205 | ("r-rtracklayer" ,r-rtracklayer) | |
2206 | ("r-s4vectors" ,r-s4vectors))) | |
2207 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
2208 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
2209 | (description | |
2210 | "ChIPComp implements a statistical method for quantitative comparison of | |
2211 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
2212 | sites across multiple conditions considering matching control in ChIP-seq | |
2213 | datasets.") | |
2214 | ;; Any version of the GPL. | |
2215 | (license license:gpl3+))) | |
0490f9de RW |
2216 | |
2217 | (define-public r-riboprofiling | |
2218 | (package | |
2219 | (name "r-riboprofiling") | |
03b655c5 | 2220 | (version "1.20.0") |
0490f9de RW |
2221 | (source |
2222 | (origin | |
2223 | (method url-fetch) | |
2224 | (uri (bioconductor-uri "RiboProfiling" version)) | |
2225 | (sha256 | |
2226 | (base32 | |
03b655c5 | 2227 | "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg")))) |
0490f9de RW |
2228 | (properties `((upstream-name . "RiboProfiling"))) |
2229 | (build-system r-build-system) | |
2230 | (propagated-inputs | |
2231 | `(("r-biocgenerics" ,r-biocgenerics) | |
2232 | ("r-biostrings" ,r-biostrings) | |
2233 | ("r-data-table" ,r-data-table) | |
2234 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2235 | ("r-genomicalignments" ,r-genomicalignments) | |
2236 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2237 | ("r-genomicranges" ,r-genomicranges) | |
2238 | ("r-ggbio" ,r-ggbio) | |
2239 | ("r-ggplot2" ,r-ggplot2) | |
2240 | ("r-iranges" ,r-iranges) | |
2241 | ("r-plyr" ,r-plyr) | |
2242 | ("r-reshape2" ,r-reshape2) | |
2243 | ("r-rsamtools" ,r-rsamtools) | |
2244 | ("r-rtracklayer" ,r-rtracklayer) | |
2245 | ("r-s4vectors" ,r-s4vectors) | |
2246 | ("r-sqldf" ,r-sqldf))) | |
7aae05a9 RW |
2247 | (native-inputs |
2248 | `(("r-knitr" ,r-knitr))) | |
0490f9de RW |
2249 | (home-page "https://bioconductor.org/packages/RiboProfiling/") |
2250 | (synopsis "Ribosome profiling data analysis") | |
2251 | (description "Starting with a BAM file, this package provides the | |
2252 | necessary functions for quality assessment, read start position recalibration, | |
2253 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
2254 | of count data: pairs, log fold-change, codon frequency and coverage | |
2255 | assessment, principal component analysis on codon coverage.") | |
2256 | (license license:gpl3))) | |
6ffdfe6a RW |
2257 | |
2258 | (define-public r-riboseqr | |
2259 | (package | |
2260 | (name "r-riboseqr") | |
3813c9fe | 2261 | (version "1.24.0") |
6ffdfe6a RW |
2262 | (source |
2263 | (origin | |
2264 | (method url-fetch) | |
2265 | (uri (bioconductor-uri "riboSeqR" version)) | |
2266 | (sha256 | |
2267 | (base32 | |
3813c9fe | 2268 | "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr")))) |
6ffdfe6a RW |
2269 | (properties `((upstream-name . "riboSeqR"))) |
2270 | (build-system r-build-system) | |
2271 | (propagated-inputs | |
2272 | `(("r-abind" ,r-abind) | |
2273 | ("r-bayseq" ,r-bayseq) | |
2274 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2275 | ("r-genomicranges" ,r-genomicranges) | |
2276 | ("r-iranges" ,r-iranges) | |
2277 | ("r-rsamtools" ,r-rsamtools) | |
2278 | ("r-seqlogo" ,r-seqlogo))) | |
2279 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
2280 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
2281 | (description | |
2282 | "This package provides plotting functions, frameshift detection and | |
2283 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
2284 | (license license:gpl3))) | |
a32279ff RW |
2285 | |
2286 | (define-public r-interactionset | |
35dae951 | 2287 | (package ;BROKEN |
a32279ff | 2288 | (name "r-interactionset") |
35dae951 | 2289 | (version "1.18.0") |
a32279ff RW |
2290 | (source |
2291 | (origin | |
2292 | (method url-fetch) | |
2293 | (uri (bioconductor-uri "InteractionSet" version)) | |
2294 | (sha256 | |
2295 | (base32 | |
35dae951 | 2296 | "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31")))) |
a32279ff RW |
2297 | (properties |
2298 | `((upstream-name . "InteractionSet"))) | |
2299 | (build-system r-build-system) | |
2300 | (propagated-inputs | |
2301 | `(("r-biocgenerics" ,r-biocgenerics) | |
2302 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2303 | ("r-genomicranges" ,r-genomicranges) | |
2304 | ("r-iranges" ,r-iranges) | |
2305 | ("r-matrix" ,r-matrix) | |
2306 | ("r-rcpp" ,r-rcpp) | |
2307 | ("r-s4vectors" ,r-s4vectors) | |
2308 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
861a903f RW |
2309 | (native-inputs |
2310 | `(("r-knitr" ,r-knitr))) | |
a32279ff RW |
2311 | (home-page "https://bioconductor.org/packages/InteractionSet") |
2312 | (synopsis "Base classes for storing genomic interaction data") | |
2313 | (description | |
02fe0976 | 2314 | "This package provides the @code{GInteractions}, |
a32279ff RW |
2315 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
2316 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
2317 | experiments.") | |
2318 | (license license:gpl3))) | |
cf9a29b2 RW |
2319 | |
2320 | (define-public r-genomicinteractions | |
2321 | (package | |
2322 | (name "r-genomicinteractions") | |
dd9341ff | 2323 | (version "1.24.0") |
cf9a29b2 RW |
2324 | (source |
2325 | (origin | |
2326 | (method url-fetch) | |
2327 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
2328 | (sha256 | |
2329 | (base32 | |
dd9341ff | 2330 | "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd")))) |
cf9a29b2 RW |
2331 | (properties |
2332 | `((upstream-name . "GenomicInteractions"))) | |
2333 | (build-system r-build-system) | |
2334 | (propagated-inputs | |
2335 | `(("r-biobase" ,r-biobase) | |
2336 | ("r-biocgenerics" ,r-biocgenerics) | |
2337 | ("r-data-table" ,r-data-table) | |
2338 | ("r-dplyr" ,r-dplyr) | |
2339 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2340 | ("r-genomicranges" ,r-genomicranges) | |
2341 | ("r-ggplot2" ,r-ggplot2) | |
2342 | ("r-gridextra" ,r-gridextra) | |
2343 | ("r-gviz" ,r-gviz) | |
2344 | ("r-igraph" ,r-igraph) | |
2345 | ("r-interactionset" ,r-interactionset) | |
2346 | ("r-iranges" ,r-iranges) | |
2347 | ("r-rsamtools" ,r-rsamtools) | |
2348 | ("r-rtracklayer" ,r-rtracklayer) | |
2349 | ("r-s4vectors" ,r-s4vectors) | |
2350 | ("r-stringr" ,r-stringr))) | |
81a37891 RW |
2351 | (native-inputs |
2352 | `(("r-knitr" ,r-knitr))) | |
cf9a29b2 RW |
2353 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") |
2354 | (synopsis "R package for handling genomic interaction data") | |
2355 | (description | |
2356 | "This R package provides tools for handling genomic interaction data, | |
2357 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
2358 | information and producing various plots and statistics.") | |
2359 | (license license:gpl3))) | |
27c51606 RW |
2360 | |
2361 | (define-public r-ctc | |
2362 | (package | |
2363 | (name "r-ctc") | |
d27dfbf7 | 2364 | (version "1.64.0") |
27c51606 RW |
2365 | (source |
2366 | (origin | |
2367 | (method url-fetch) | |
2368 | (uri (bioconductor-uri "ctc" version)) | |
2369 | (sha256 | |
2370 | (base32 | |
d27dfbf7 | 2371 | "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp")))) |
27c51606 RW |
2372 | (build-system r-build-system) |
2373 | (propagated-inputs `(("r-amap" ,r-amap))) | |
2374 | (home-page "https://bioconductor.org/packages/ctc/") | |
2375 | (synopsis "Cluster and tree conversion") | |
2376 | (description | |
2377 | "This package provides tools for exporting and importing classification | |
2378 | trees and clusters to other programs.") | |
2379 | (license license:gpl2))) | |
5da0e142 RW |
2380 | |
2381 | (define-public r-goseq | |
2382 | (package | |
2383 | (name "r-goseq") | |
c97bcfbd | 2384 | (version "1.42.0") |
5da0e142 RW |
2385 | (source |
2386 | (origin | |
2387 | (method url-fetch) | |
2388 | (uri (bioconductor-uri "goseq" version)) | |
2389 | (sha256 | |
2390 | (base32 | |
c97bcfbd | 2391 | "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509")))) |
5da0e142 RW |
2392 | (build-system r-build-system) |
2393 | (propagated-inputs | |
2394 | `(("r-annotationdbi" ,r-annotationdbi) | |
2395 | ("r-biasedurn" ,r-biasedurn) | |
2396 | ("r-biocgenerics" ,r-biocgenerics) | |
2397 | ("r-genelendatabase" ,r-genelendatabase) | |
2398 | ("r-go-db" ,r-go-db) | |
2399 | ("r-mgcv" ,r-mgcv))) | |
2400 | (home-page "https://bioconductor.org/packages/goseq/") | |
2401 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
2402 | (description | |
2403 | "This package provides tools to detect Gene Ontology and/or other user | |
2404 | defined categories which are over/under represented in RNA-seq data.") | |
2405 | (license license:lgpl2.0+))) | |
f4235c0e RW |
2406 | |
2407 | (define-public r-glimma | |
2408 | (package | |
2409 | (name "r-glimma") | |
3dab4570 | 2410 | (version "2.0.0") |
f4235c0e RW |
2411 | (source |
2412 | (origin | |
2413 | (method url-fetch) | |
2414 | (uri (bioconductor-uri "Glimma" version)) | |
2415 | (sha256 | |
2416 | (base32 | |
3dab4570 | 2417 | "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv")))) |
f4235c0e RW |
2418 | (properties `((upstream-name . "Glimma"))) |
2419 | (build-system r-build-system) | |
2420 | (propagated-inputs | |
3dab4570 | 2421 | `(("r-deseq2" ,r-deseq2) |
2422 | ("r-edger" ,r-edger) | |
2423 | ("r-htmlwidgets" ,r-htmlwidgets) | |
f4235c0e | 2424 | ("r-jsonlite" ,r-jsonlite) |
3dab4570 | 2425 | ("r-limma" ,r-limma) |
2426 | ("r-s4vectors" ,r-s4vectors) | |
2427 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
a6251d6e RW |
2428 | (native-inputs |
2429 | `(("r-knitr" ,r-knitr))) | |
f4235c0e RW |
2430 | (home-page "https://github.com/Shians/Glimma") |
2431 | (synopsis "Interactive HTML graphics") | |
2432 | (description | |
2433 | "This package generates interactive visualisations for analysis of | |
2434 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
2435 | HTML page. The interactions are built on top of the popular static | |
2436 | representations of analysis results in order to provide additional | |
2437 | information.") | |
2438 | (license license:lgpl3))) | |
aa388dc7 RW |
2439 | |
2440 | (define-public r-rots | |
2441 | (package | |
2442 | (name "r-rots") | |
0ef40b23 | 2443 | (version "1.18.0") |
aa388dc7 RW |
2444 | (source |
2445 | (origin | |
2446 | (method url-fetch) | |
2447 | (uri (bioconductor-uri "ROTS" version)) | |
2448 | (sha256 | |
2449 | (base32 | |
0ef40b23 | 2450 | "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n")))) |
aa388dc7 RW |
2451 | (properties `((upstream-name . "ROTS"))) |
2452 | (build-system r-build-system) | |
2453 | (propagated-inputs | |
2454 | `(("r-biobase" ,r-biobase) | |
2455 | ("r-rcpp" ,r-rcpp))) | |
2456 | (home-page "https://bioconductor.org/packages/ROTS/") | |
2457 | (synopsis "Reproducibility-Optimized Test Statistic") | |
2458 | (description | |
2459 | "This package provides tools for calculating the | |
2460 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
2461 | in omics data.") | |
2462 | (license license:gpl2+))) | |
b64ce4b7 | 2463 | |
cad6fb2d RW |
2464 | (define-public r-plgem |
2465 | (package | |
2466 | (name "r-plgem") | |
1c9bdfcf | 2467 | (version "1.62.0") |
cad6fb2d RW |
2468 | (source |
2469 | (origin | |
2470 | (method url-fetch) | |
2471 | (uri (bioconductor-uri "plgem" version)) | |
2472 | (sha256 | |
2473 | (base32 | |
1c9bdfcf | 2474 | "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a")))) |
cad6fb2d RW |
2475 | (build-system r-build-system) |
2476 | (propagated-inputs | |
2477 | `(("r-biobase" ,r-biobase) | |
2478 | ("r-mass" ,r-mass))) | |
2479 | (home-page "http://www.genopolis.it") | |
2480 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
2481 | (description | |
2482 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
2483 | model the variance-versus-mean dependence that exists in a variety of | |
2484 | genome-wide datasets, including microarray and proteomics data. The use of | |
2485 | PLGEM has been shown to improve the detection of differentially expressed | |
2486 | genes or proteins in these datasets.") | |
2487 | (license license:gpl2))) | |
2488 | ||
b64ce4b7 RW |
2489 | (define-public r-inspect |
2490 | (package | |
2491 | (name "r-inspect") | |
41d6b41f | 2492 | (version "1.20.0") |
b64ce4b7 RW |
2493 | (source |
2494 | (origin | |
2495 | (method url-fetch) | |
2496 | (uri (bioconductor-uri "INSPEcT" version)) | |
2497 | (sha256 | |
2498 | (base32 | |
41d6b41f | 2499 | "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483")))) |
b64ce4b7 RW |
2500 | (properties `((upstream-name . "INSPEcT"))) |
2501 | (build-system r-build-system) | |
2502 | (propagated-inputs | |
2503 | `(("r-biobase" ,r-biobase) | |
2504 | ("r-biocgenerics" ,r-biocgenerics) | |
2505 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 2506 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 | 2507 | ("r-desolve" ,r-desolve) |
bd824de3 | 2508 | ("r-gdata" ,r-gdata) |
74bb4cdf | 2509 | ("r-genomeinfodb" ,r-genomeinfodb) |
b64ce4b7 RW |
2510 | ("r-genomicalignments" ,r-genomicalignments) |
2511 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2512 | ("r-genomicranges" ,r-genomicranges) | |
2513 | ("r-iranges" ,r-iranges) | |
74bb4cdf | 2514 | ("r-kernsmooth" ,r-kernsmooth) |
c86fc969 | 2515 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
2516 | ("r-proc" ,r-proc) |
2517 | ("r-rootsolve" ,r-rootsolve) | |
2518 | ("r-rsamtools" ,r-rsamtools) | |
437bc4dd | 2519 | ("r-rtracklayer" ,r-rtracklayer) |
c86fc969 RW |
2520 | ("r-s4vectors" ,r-s4vectors) |
2521 | ("r-shiny" ,r-shiny) | |
2522 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
2523 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
2524 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
437bc4dd RW |
2525 | (native-inputs |
2526 | `(("r-knitr" ,r-knitr))) | |
b64ce4b7 RW |
2527 | (home-page "https://bioconductor.org/packages/INSPEcT") |
2528 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
2529 | (description | |
2530 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
2531 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
2532 | order to evaluate synthesis, processing and degradation rates and assess via | |
2533 | modeling the rates that determines changes in mature mRNA levels.") | |
2534 | (license license:gpl2))) | |
f6e99763 RW |
2535 | |
2536 | (define-public r-dnabarcodes | |
2537 | (package | |
2538 | (name "r-dnabarcodes") | |
874a774f | 2539 | (version "1.20.0") |
f6e99763 RW |
2540 | (source |
2541 | (origin | |
2542 | (method url-fetch) | |
2543 | (uri (bioconductor-uri "DNABarcodes" version)) | |
2544 | (sha256 | |
2545 | (base32 | |
874a774f | 2546 | "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg")))) |
f6e99763 RW |
2547 | (properties `((upstream-name . "DNABarcodes"))) |
2548 | (build-system r-build-system) | |
2549 | (propagated-inputs | |
2550 | `(("r-bh" ,r-bh) | |
2551 | ("r-matrix" ,r-matrix) | |
2552 | ("r-rcpp" ,r-rcpp))) | |
14f40ae8 RW |
2553 | (native-inputs |
2554 | `(("r-knitr" ,r-knitr))) | |
f6e99763 RW |
2555 | (home-page "https://bioconductor.org/packages/DNABarcodes") |
2556 | (synopsis "Create and analyze DNA barcodes") | |
2557 | (description | |
2558 | "This package offers tools to create DNA barcode sets capable of | |
2559 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
2560 | can be analyzed regarding their minimal, maximal and average distances between | |
2561 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
2562 | demultiplexed, i.e. assigned to their original reference barcode.") | |
2563 | (license license:gpl2))) | |
09aa3d06 RW |
2564 | |
2565 | (define-public r-ruvseq | |
2566 | (package | |
2567 | (name "r-ruvseq") | |
a55b1622 | 2568 | (version "1.24.0") |
09aa3d06 RW |
2569 | (source |
2570 | (origin | |
2571 | (method url-fetch) | |
2572 | (uri (bioconductor-uri "RUVSeq" version)) | |
2573 | (sha256 | |
2574 | (base32 | |
a55b1622 | 2575 | "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh")))) |
09aa3d06 RW |
2576 | (properties `((upstream-name . "RUVSeq"))) |
2577 | (build-system r-build-system) | |
2578 | (propagated-inputs | |
2579 | `(("r-biobase" ,r-biobase) | |
2580 | ("r-edaseq" ,r-edaseq) | |
2581 | ("r-edger" ,r-edger) | |
2582 | ("r-mass" ,r-mass))) | |
ae0fcaa6 RW |
2583 | (native-inputs |
2584 | `(("r-knitr" ,r-knitr))) | |
09aa3d06 RW |
2585 | (home-page "https://github.com/drisso/RUVSeq") |
2586 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
2587 | (description | |
2588 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
2589 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
2590 | samples.") | |
2591 | (license license:artistic2.0))) | |
286157dc RW |
2592 | |
2593 | (define-public r-biocneighbors | |
2594 | (package | |
2595 | (name "r-biocneighbors") | |
47147877 | 2596 | (version "1.8.2") |
286157dc RW |
2597 | (source |
2598 | (origin | |
2599 | (method url-fetch) | |
2600 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
2601 | (sha256 | |
2602 | (base32 | |
47147877 | 2603 | "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7")))) |
286157dc RW |
2604 | (properties `((upstream-name . "BiocNeighbors"))) |
2605 | (build-system r-build-system) | |
2606 | (propagated-inputs | |
12e2aa96 RW |
2607 | `(("r-biocparallel" ,r-biocparallel) |
2608 | ("r-matrix" ,r-matrix) | |
286157dc | 2609 | ("r-rcpp" ,r-rcpp) |
6fc161fc | 2610 | ("r-rcpphnsw" ,r-rcpphnsw) |
286157dc | 2611 | ("r-s4vectors" ,r-s4vectors))) |
f5864c11 RW |
2612 | (native-inputs |
2613 | `(("r-knitr" ,r-knitr))) | |
286157dc RW |
2614 | (home-page "https://bioconductor.org/packages/BiocNeighbors") |
2615 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
2616 | (description | |
2617 | "This package implements exact and approximate methods for nearest | |
2618 | neighbor detection, in a framework that allows them to be easily switched | |
2619 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
2620 | using pre-clustering with the k-means algorithm. Functions are also provided | |
2621 | to search for all neighbors within a given distance. Parallelization is | |
2622 | achieved for all methods using the BiocParallel framework.") | |
2623 | (license license:gpl3))) | |
8a587c89 | 2624 | |
99391290 RW |
2625 | (define-public r-biocsingular |
2626 | (package | |
2627 | (name "r-biocsingular") | |
798ec289 | 2628 | (version "1.6.0") |
99391290 RW |
2629 | (source |
2630 | (origin | |
2631 | (method url-fetch) | |
2632 | (uri (bioconductor-uri "BiocSingular" version)) | |
2633 | (sha256 | |
2634 | (base32 | |
798ec289 | 2635 | "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni")))) |
99391290 RW |
2636 | (properties `((upstream-name . "BiocSingular"))) |
2637 | (build-system r-build-system) | |
2638 | (propagated-inputs | |
2639 | `(("r-beachmat" ,r-beachmat) | |
2640 | ("r-biocgenerics" ,r-biocgenerics) | |
2641 | ("r-biocparallel" ,r-biocparallel) | |
2642 | ("r-delayedarray" ,r-delayedarray) | |
2643 | ("r-irlba" ,r-irlba) | |
2644 | ("r-matrix" ,r-matrix) | |
2645 | ("r-rcpp" ,r-rcpp) | |
2646 | ("r-rsvd" ,r-rsvd) | |
2647 | ("r-s4vectors" ,r-s4vectors))) | |
a8351d46 RW |
2648 | (native-inputs |
2649 | `(("r-knitr" ,r-knitr))) | |
99391290 RW |
2650 | (home-page "https://github.com/LTLA/BiocSingular") |
2651 | (synopsis "Singular value decomposition for Bioconductor packages") | |
2652 | (description | |
2653 | "This package implements exact and approximate methods for singular value | |
2654 | decomposition and principal components analysis, in a framework that allows | |
2655 | them to be easily switched within Bioconductor packages or workflows. Where | |
2656 | possible, parallelization is achieved using the BiocParallel framework.") | |
2657 | (license license:gpl3))) | |
2658 | ||
a961ae46 RW |
2659 | (define-public r-destiny |
2660 | (package | |
2661 | (name "r-destiny") | |
4217307f | 2662 | (version "3.4.0") |
a961ae46 RW |
2663 | (source |
2664 | (origin | |
2665 | (method url-fetch) | |
2666 | (uri (bioconductor-uri "destiny" version)) | |
2667 | (sha256 | |
2668 | (base32 | |
4217307f | 2669 | "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) |
a961ae46 RW |
2670 | (build-system r-build-system) |
2671 | (propagated-inputs | |
2672 | `(("r-biobase" ,r-biobase) | |
2673 | ("r-biocgenerics" ,r-biocgenerics) | |
6e10ac07 | 2674 | ("r-ggplot-multistats" ,r-ggplot-multistats) |
0aa72f2d | 2675 | ("r-ggplot2" ,r-ggplot2) |
a961ae46 | 2676 | ("r-ggthemes" ,r-ggthemes) |
6e10ac07 RW |
2677 | ("r-irlba" ,r-irlba) |
2678 | ("r-knn-covertree" ,r-knn-covertree) | |
a961ae46 | 2679 | ("r-matrix" ,r-matrix) |
6e10ac07 | 2680 | ("r-pcamethods" ,r-pcamethods) |
a961ae46 RW |
2681 | ("r-proxy" ,r-proxy) |
2682 | ("r-rcpp" ,r-rcpp) | |
2683 | ("r-rcppeigen" ,r-rcppeigen) | |
6e10ac07 RW |
2684 | ("r-rcpphnsw" ,r-rcpphnsw) |
2685 | ("r-rspectra" ,r-rspectra) | |
a961ae46 RW |
2686 | ("r-scales" ,r-scales) |
2687 | ("r-scatterplot3d" ,r-scatterplot3d) | |
6e10ac07 | 2688 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
a961ae46 RW |
2689 | ("r-smoother" ,r-smoother) |
2690 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6e10ac07 RW |
2691 | ("r-tidyr" ,r-tidyr) |
2692 | ("r-tidyselect" ,r-tidyselect) | |
a961ae46 | 2693 | ("r-vim" ,r-vim))) |
3f782a6d RW |
2694 | (native-inputs |
2695 | `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes | |
a961ae46 RW |
2696 | (home-page "https://bioconductor.org/packages/destiny/") |
2697 | (synopsis "Create and plot diffusion maps") | |
2698 | (description "This package provides tools to create and plot diffusion | |
2699 | maps.") | |
2700 | ;; Any version of the GPL | |
2701 | (license license:gpl3+))) | |
2702 | ||
8a587c89 RW |
2703 | (define-public r-savr |
2704 | (package | |
2705 | (name "r-savr") | |
967fc583 | 2706 | (version "1.28.0") |
8a587c89 RW |
2707 | (source |
2708 | (origin | |
2709 | (method url-fetch) | |
2710 | (uri (bioconductor-uri "savR" version)) | |
2711 | (sha256 | |
2712 | (base32 | |
967fc583 | 2713 | "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic")))) |
8a587c89 RW |
2714 | (properties `((upstream-name . "savR"))) |
2715 | (build-system r-build-system) | |
2716 | (propagated-inputs | |
2717 | `(("r-ggplot2" ,r-ggplot2) | |
2718 | ("r-gridextra" ,r-gridextra) | |
2719 | ("r-reshape2" ,r-reshape2) | |
2720 | ("r-scales" ,r-scales) | |
2721 | ("r-xml" ,r-xml))) | |
2722 | (home-page "https://github.com/bcalder/savR") | |
2723 | (synopsis "Parse and analyze Illumina SAV files") | |
2724 | (description | |
2725 | "This package provides tools to parse Illumina Sequence Analysis | |
2726 | Viewer (SAV) files, access data, and generate QC plots.") | |
2727 | (license license:agpl3+))) | |
41ffc214 RW |
2728 | |
2729 | (define-public r-chipexoqual | |
2730 | (package | |
2731 | (name "r-chipexoqual") | |
ff4d0804 | 2732 | (version "1.14.0") |
41ffc214 RW |
2733 | (source |
2734 | (origin | |
2735 | (method url-fetch) | |
2736 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
2737 | (sha256 | |
2738 | (base32 | |
ff4d0804 | 2739 | "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag")))) |
41ffc214 RW |
2740 | (properties `((upstream-name . "ChIPexoQual"))) |
2741 | (build-system r-build-system) | |
2742 | (propagated-inputs | |
2743 | `(("r-biocparallel" ,r-biocparallel) | |
2744 | ("r-biovizbase" ,r-biovizbase) | |
2745 | ("r-broom" ,r-broom) | |
2746 | ("r-data-table" ,r-data-table) | |
2747 | ("r-dplyr" ,r-dplyr) | |
2748 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2749 | ("r-genomicalignments" ,r-genomicalignments) | |
2750 | ("r-genomicranges" ,r-genomicranges) | |
2751 | ("r-ggplot2" ,r-ggplot2) | |
2752 | ("r-hexbin" ,r-hexbin) | |
2753 | ("r-iranges" ,r-iranges) | |
2754 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2755 | ("r-rmarkdown" ,r-rmarkdown) | |
2756 | ("r-rsamtools" ,r-rsamtools) | |
2757 | ("r-s4vectors" ,r-s4vectors) | |
2758 | ("r-scales" ,r-scales) | |
2759 | ("r-viridis" ,r-viridis))) | |
9697afb1 RW |
2760 | (native-inputs |
2761 | `(("r-knitr" ,r-knitr))) | |
41ffc214 RW |
2762 | (home-page "https://github.com/keleslab/ChIPexoQual") |
2763 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
2764 | (description | |
2765 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
2766 | sequencing data.") | |
2767 | (license license:gpl2+))) | |
c18dccff | 2768 | |
3d13b448 RW |
2769 | (define-public r-copynumber |
2770 | (package | |
2771 | (name "r-copynumber") | |
43d8db04 | 2772 | (version "1.30.0") |
3d13b448 RW |
2773 | (source (origin |
2774 | (method url-fetch) | |
2775 | (uri (bioconductor-uri "copynumber" version)) | |
2776 | (sha256 | |
2777 | (base32 | |
43d8db04 | 2778 | "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm")))) |
3d13b448 RW |
2779 | (build-system r-build-system) |
2780 | (propagated-inputs | |
2781 | `(("r-s4vectors" ,r-s4vectors) | |
2782 | ("r-iranges" ,r-iranges) | |
2783 | ("r-genomicranges" ,r-genomicranges) | |
2784 | ("r-biocgenerics" ,r-biocgenerics))) | |
2785 | (home-page "https://bioconductor.org/packages/copynumber") | |
2786 | (synopsis "Segmentation of single- and multi-track copy number data") | |
2787 | (description | |
2788 | "This package segments single- and multi-track copy number data by a | |
2789 | penalized least squares regression method.") | |
2790 | (license license:artistic2.0))) | |
2791 | ||
c18dccff RW |
2792 | (define-public r-dnacopy |
2793 | (package | |
2794 | (name "r-dnacopy") | |
850f4c2a | 2795 | (version "1.64.0") |
c18dccff RW |
2796 | (source |
2797 | (origin | |
2798 | (method url-fetch) | |
2799 | (uri (bioconductor-uri "DNAcopy" version)) | |
2800 | (sha256 | |
2801 | (base32 | |
850f4c2a | 2802 | "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc")))) |
c18dccff RW |
2803 | (properties `((upstream-name . "DNAcopy"))) |
2804 | (build-system r-build-system) | |
2805 | (native-inputs `(("gfortran" ,gfortran))) | |
2806 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
2807 | (synopsis "DNA copy number data analysis") | |
2808 | (description | |
2809 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
2810 | algorithm to segment DNA copy number data and identify genomic regions with | |
2811 | abnormal copy number.") | |
2812 | (license license:gpl2+))) | |
3a0babac RW |
2813 | |
2814 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
2815 | ;; Bioconductor package. | |
2816 | (define-public r-htscluster | |
2817 | (package | |
2818 | (name "r-htscluster") | |
2819 | (version "2.0.8") | |
2820 | (source | |
2821 | (origin | |
2822 | (method url-fetch) | |
2823 | (uri (cran-uri "HTSCluster" version)) | |
2824 | (sha256 | |
2825 | (base32 | |
2826 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
2827 | (properties `((upstream-name . "HTSCluster"))) | |
2828 | (build-system r-build-system) | |
2829 | (propagated-inputs | |
2830 | `(("r-capushe" ,r-capushe) | |
2831 | ("r-edger" ,r-edger) | |
2832 | ("r-plotrix" ,r-plotrix))) | |
2833 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
2834 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
2835 | (description | |
2836 | "This package provides a Poisson mixture model is implemented to cluster | |
2837 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
2838 | estimation is performed using either the EM or CEM algorithm, and the slope | |
2839 | heuristics are used for model selection (i.e., to choose the number of | |
2840 | clusters).") | |
2841 | (license license:gpl3+))) | |
173c9960 RW |
2842 | |
2843 | (define-public r-deds | |
2844 | (package | |
2845 | (name "r-deds") | |
96030bf7 | 2846 | (version "1.60.0") |
173c9960 RW |
2847 | (source |
2848 | (origin | |
2849 | (method url-fetch) | |
2850 | (uri (bioconductor-uri "DEDS" version)) | |
2851 | (sha256 | |
2852 | (base32 | |
96030bf7 | 2853 | "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8")))) |
173c9960 RW |
2854 | (properties `((upstream-name . "DEDS"))) |
2855 | (build-system r-build-system) | |
2856 | (home-page "https://bioconductor.org/packages/DEDS/") | |
2857 | (synopsis "Differential expression via distance summary for microarray data") | |
2858 | (description | |
2859 | "This library contains functions that calculate various statistics of | |
2860 | differential expression for microarray data, including t statistics, fold | |
2861 | change, F statistics, SAM, moderated t and F statistics and B statistics. It | |
2862 | also implements a new methodology called DEDS (Differential Expression via | |
2863 | Distance Summary), which selects differentially expressed genes by integrating | |
2864 | and summarizing a set of statistics using a weighted distance approach.") | |
2865 | ;; Any version of the LGPL. | |
2866 | (license license:lgpl3+))) | |
7ed869f7 RW |
2867 | |
2868 | ;; This is a CRAN package, but since it depends on a Bioconductor package we | |
2869 | ;; put it here. | |
2870 | (define-public r-nbpseq | |
2871 | (package | |
2872 | (name "r-nbpseq") | |
2873 | (version "0.3.0") | |
2874 | (source | |
2875 | (origin | |
2876 | (method url-fetch) | |
2877 | (uri (cran-uri "NBPSeq" version)) | |
2878 | (sha256 | |
2879 | (base32 | |
2880 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) | |
2881 | (properties `((upstream-name . "NBPSeq"))) | |
2882 | (build-system r-build-system) | |
2883 | (propagated-inputs | |
2884 | `(("r-qvalue" ,r-qvalue))) | |
2885 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") | |
2886 | (synopsis "Negative binomial models for RNA-Seq data") | |
2887 | (description | |
2888 | "This package provides negative binomial models for two-group comparisons | |
2889 | and regression inferences from RNA-sequencing data.") | |
2890 | (license license:gpl2))) | |
3087a2f3 RW |
2891 | |
2892 | (define-public r-ebseq | |
2893 | (package | |
2894 | (name "r-ebseq") | |
939c888d | 2895 | (version "1.30.0") |
3087a2f3 RW |
2896 | (source |
2897 | (origin | |
2898 | (method url-fetch) | |
2899 | (uri (bioconductor-uri "EBSeq" version)) | |
2900 | (sha256 | |
2901 | (base32 | |
939c888d | 2902 | "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny")))) |
3087a2f3 RW |
2903 | (properties `((upstream-name . "EBSeq"))) |
2904 | (build-system r-build-system) | |
2905 | (propagated-inputs | |
2906 | `(("r-blockmodeling" ,r-blockmodeling) | |
2907 | ("r-gplots" ,r-gplots) | |
2908 | ("r-testthat" ,r-testthat))) | |
2909 | (home-page "https://bioconductor.org/packages/EBSeq") | |
2910 | (synopsis "Differential expression analysis of RNA-seq data") | |
2911 | (description | |
2912 | "This package provides tools for differential expression analysis at both | |
2913 | gene and isoform level using RNA-seq data") | |
2914 | (license license:artistic2.0))) | |
cb1ab035 RJ |
2915 | |
2916 | (define-public r-karyoploter | |
2917 | (package | |
2918 | (name "r-karyoploter") | |
37da4513 | 2919 | (version "1.16.0") |
cb1ab035 RJ |
2920 | (source (origin |
2921 | (method url-fetch) | |
2922 | (uri (bioconductor-uri "karyoploteR" version)) | |
2923 | (sha256 | |
2924 | (base32 | |
37da4513 | 2925 | "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2")))) |
cb1ab035 RJ |
2926 | (build-system r-build-system) |
2927 | (propagated-inputs | |
6e2dc9e3 RW |
2928 | `(("r-annotationdbi" ,r-annotationdbi) |
2929 | ("r-bamsignals" ,r-bamsignals) | |
2930 | ("r-bezier" ,r-bezier) | |
2931 | ("r-biovizbase" ,r-biovizbase) | |
2932 | ("r-digest" ,r-digest) | |
2933 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2934 | ("r-genomicfeatures" ,r-genomicfeatures) | |
cb1ab035 RJ |
2935 | ("r-genomicranges" ,r-genomicranges) |
2936 | ("r-iranges" ,r-iranges) | |
cb1ab035 | 2937 | ("r-memoise" ,r-memoise) |
6e2dc9e3 RW |
2938 | ("r-regioner" ,r-regioner) |
2939 | ("r-rsamtools" ,r-rsamtools) | |
cb1ab035 | 2940 | ("r-rtracklayer" ,r-rtracklayer) |
cb1ab035 | 2941 | ("r-s4vectors" ,r-s4vectors) |
cb1ab035 | 2942 | ("r-variantannotation" ,r-variantannotation))) |
6e2dc9e3 RW |
2943 | (native-inputs |
2944 | `(("r-knitr" ,r-knitr))) | |
cb1ab035 RJ |
2945 | (home-page "https://bioconductor.org/packages/karyoploteR/") |
2946 | (synopsis "Plot customizable linear genomes displaying arbitrary data") | |
2947 | (description "This package creates karyotype plots of arbitrary genomes and | |
7230f6d5 | 2948 | offers a complete set of functions to plot arbitrary data on them. It mimics |
cb1ab035 RJ |
2949 | many R base graphics functions coupling them with a coordinate change function |
2950 | automatically mapping the chromosome and data coordinates into the plot | |
2951 | coordinates.") | |
2952 | (license license:artistic2.0))) | |
2cb71d81 RW |
2953 | |
2954 | (define-public r-lpsymphony | |
2955 | (package | |
2956 | (name "r-lpsymphony") | |
378d67c9 | 2957 | (version "1.18.0") |
2cb71d81 RW |
2958 | (source |
2959 | (origin | |
2960 | (method url-fetch) | |
2961 | (uri (bioconductor-uri "lpsymphony" version)) | |
2962 | (sha256 | |
2963 | (base32 | |
378d67c9 | 2964 | "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9")))) |
2cb71d81 RW |
2965 | (build-system r-build-system) |
2966 | (inputs | |
0653b8b0 | 2967 | `(("zlib" ,zlib))) |
2cb71d81 | 2968 | (native-inputs |
0653b8b0 RW |
2969 | `(("pkg-config" ,pkg-config) |
2970 | ("r-knitr" ,r-knitr))) | |
c756328e | 2971 | (home-page "https://r-forge.r-project.org/projects/rsymphony") |
2cb71d81 RW |
2972 | (synopsis "Symphony integer linear programming solver in R") |
2973 | (description | |
2974 | "This package was derived from Rsymphony. The package provides an R | |
2975 | interface to SYMPHONY, a linear programming solver written in C++. The main | |
2976 | difference between this package and Rsymphony is that it includes the solver | |
2977 | source code, while Rsymphony expects to find header and library files on the | |
2978 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy | |
2979 | to install interface to SYMPHONY.") | |
2980 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. | |
2981 | ;; lpsimphony is released under the same terms. | |
2982 | (license license:epl1.0))) | |
704de8f5 RW |
2983 | |
2984 | (define-public r-ihw | |
2985 | (package | |
2986 | (name "r-ihw") | |
95b1f350 | 2987 | (version "1.18.0") |
704de8f5 RW |
2988 | (source |
2989 | (origin | |
2990 | (method url-fetch) | |
2991 | (uri (bioconductor-uri "IHW" version)) | |
2992 | (sha256 | |
2993 | (base32 | |
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704de8f5 RW |
2995 | (properties `((upstream-name . "IHW"))) |
2996 | (build-system r-build-system) | |
2997 | (propagated-inputs | |
2998 | `(("r-biocgenerics" ,r-biocgenerics) | |
2999 | ("r-fdrtool" ,r-fdrtool) | |
3000 | ("r-lpsymphony" ,r-lpsymphony) | |
3001 | ("r-slam" ,r-slam))) | |
359a084a RW |
3002 | (native-inputs |
3003 | `(("r-knitr" ,r-knitr))) | |
704de8f5 RW |
3004 | (home-page "https://bioconductor.org/packages/IHW") |
3005 | (synopsis "Independent hypothesis weighting") | |
3006 | (description | |
3007 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing | |
3008 | procedure that increases power compared to the method of Benjamini and | |
3009 | Hochberg by assigning data-driven weights to each hypothesis. The input to | |
3010 | IHW is a two-column table of p-values and covariates. The covariate can be | |
3011 | any continuous-valued or categorical variable that is thought to be | |
3012 | informative on the statistical properties of each hypothesis test, while it is | |
3013 | independent of the p-value under the null hypothesis.") | |
3014 | (license license:artistic2.0))) | |
251e0830 RW |
3015 | |
3016 | (define-public r-icobra | |
3017 | (package | |
3018 | (name "r-icobra") | |
e26b5eef | 3019 | (version "1.18.0") |
251e0830 RW |
3020 | (source |
3021 | (origin | |
3022 | (method url-fetch) | |
3023 | (uri (bioconductor-uri "iCOBRA" version)) | |
3024 | (sha256 | |
3025 | (base32 | |
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251e0830 RW |
3027 | (properties `((upstream-name . "iCOBRA"))) |
3028 | (build-system r-build-system) | |
3029 | (propagated-inputs | |
3030 | `(("r-dplyr" ,r-dplyr) | |
3031 | ("r-dt" ,r-dt) | |
3032 | ("r-ggplot2" ,r-ggplot2) | |
3033 | ("r-limma" ,r-limma) | |
3034 | ("r-reshape2" ,r-reshape2) | |
3035 | ("r-rocr" ,r-rocr) | |
3036 | ("r-scales" ,r-scales) | |
3037 | ("r-shiny" ,r-shiny) | |
3038 | ("r-shinybs" ,r-shinybs) | |
3039 | ("r-shinydashboard" ,r-shinydashboard) | |
3040 | ("r-upsetr" ,r-upsetr))) | |
ee1e8fee RW |
3041 | (native-inputs |
3042 | `(("r-knitr" ,r-knitr))) | |
251e0830 RW |
3043 | (home-page "https://bioconductor.org/packages/iCOBRA") |
3044 | (synopsis "Comparison and visualization of ranking and assignment methods") | |
3045 | (description | |
3046 | "This package provides functions for calculation and visualization of | |
3047 | performance metrics for evaluation of ranking and binary | |
3048 | classification (assignment) methods. It also contains a Shiny application for | |
3049 | interactive exploration of results.") | |
3050 | (license license:gpl2+))) | |
925fcdbb RW |
3051 | |
3052 | (define-public r-mast | |
3053 | (package | |
3054 | (name "r-mast") | |
532b1068 | 3055 | (version "1.16.0") |
925fcdbb RW |
3056 | (source |
3057 | (origin | |
3058 | (method url-fetch) | |
3059 | (uri (bioconductor-uri "MAST" version)) | |
3060 | (sha256 | |
3061 | (base32 | |
532b1068 | 3062 | "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn")))) |
925fcdbb RW |
3063 | (properties `((upstream-name . "MAST"))) |
3064 | (build-system r-build-system) | |
3065 | (propagated-inputs | |
3066 | `(("r-abind" ,r-abind) | |
3067 | ("r-biobase" ,r-biobase) | |
3068 | ("r-biocgenerics" ,r-biocgenerics) | |
3069 | ("r-data-table" ,r-data-table) | |
3070 | ("r-ggplot2" ,r-ggplot2) | |
3071 | ("r-plyr" ,r-plyr) | |
3072 | ("r-progress" ,r-progress) | |
3073 | ("r-reshape2" ,r-reshape2) | |
3074 | ("r-s4vectors" ,r-s4vectors) | |
3075 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
3076 | ("r-stringr" ,r-stringr) | |
3077 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
51d1a7a2 RW |
3078 | (native-inputs |
3079 | `(("r-knitr" ,r-knitr))) | |
925fcdbb RW |
3080 | (home-page "https://github.com/RGLab/MAST/") |
3081 | (synopsis "Model-based analysis of single cell transcriptomics") | |
3082 | (description | |
3083 | "This package provides methods and models for handling zero-inflated | |
3084 | single cell assay data.") | |
3085 | (license license:gpl2+))) | |
2d7627cf RW |
3086 | |
3087 | (define-public r-monocle | |
3088 | (package | |
3089 | (name "r-monocle") | |
38bc0bf8 | 3090 | (version "2.18.0") |
2d7627cf RW |
3091 | (source |
3092 | (origin | |
3093 | (method url-fetch) | |
3094 | (uri (bioconductor-uri "monocle" version)) | |
3095 | (sha256 | |
3096 | (base32 | |
38bc0bf8 | 3097 | "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx")))) |
2d7627cf RW |
3098 | (build-system r-build-system) |
3099 | (propagated-inputs | |
3100 | `(("r-biobase" ,r-biobase) | |
3101 | ("r-biocgenerics" ,r-biocgenerics) | |
3102 | ("r-biocviews" ,r-biocviews) | |
3103 | ("r-cluster" ,r-cluster) | |
3104 | ("r-combinat" ,r-combinat) | |
3105 | ("r-ddrtree" ,r-ddrtree) | |
3106 | ("r-densityclust" ,r-densityclust) | |
3107 | ("r-dplyr" ,r-dplyr) | |
3108 | ("r-fastica" ,r-fastica) | |
3109 | ("r-ggplot2" ,r-ggplot2) | |
3110 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) | |
3111 | ("r-igraph" ,r-igraph) | |
3112 | ("r-irlba" ,r-irlba) | |
3113 | ("r-limma" ,r-limma) | |
3114 | ("r-mass" ,r-mass) | |
3115 | ("r-matrix" ,r-matrix) | |
3116 | ("r-matrixstats" ,r-matrixstats) | |
3117 | ("r-pheatmap" ,r-pheatmap) | |
3118 | ("r-plyr" ,r-plyr) | |
3119 | ("r-proxy" ,r-proxy) | |
3120 | ("r-qlcmatrix" ,r-qlcmatrix) | |
3121 | ("r-rann" ,r-rann) | |
3122 | ("r-rcpp" ,r-rcpp) | |
3123 | ("r-reshape2" ,r-reshape2) | |
3124 | ("r-rtsne" ,r-rtsne) | |
3125 | ("r-slam" ,r-slam) | |
3126 | ("r-stringr" ,r-stringr) | |
3127 | ("r-tibble" ,r-tibble) | |
3128 | ("r-vgam" ,r-vgam) | |
3129 | ("r-viridis" ,r-viridis))) | |
d1f3c371 RW |
3130 | (native-inputs |
3131 | `(("r-knitr" ,r-knitr))) | |
2d7627cf RW |
3132 | (home-page "https://bioconductor.org/packages/monocle") |
3133 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") | |
3134 | (description | |
3135 | "Monocle performs differential expression and time-series analysis for | |
3136 | single-cell expression experiments. It orders individual cells according to | |
3137 | progress through a biological process, without knowing ahead of time which | |
3138 | genes define progress through that process. Monocle also performs | |
3139 | differential expression analysis, clustering, visualization, and other useful | |
3140 | tasks on single cell expression data. It is designed to work with RNA-Seq and | |
3141 | qPCR data, but could be used with other types as well.") | |
3142 | (license license:artistic2.0))) | |
6213e441 | 3143 | |
b2dce6b5 RW |
3144 | (define-public r-monocle3 |
3145 | (package | |
3146 | (name "r-monocle3") | |
3147 | (version "0.1.2") | |
3148 | (source | |
3149 | (origin | |
3150 | (method git-fetch) | |
3151 | (uri (git-reference | |
b0e7b699 | 3152 | (url "https://github.com/cole-trapnell-lab/monocle3") |
b2dce6b5 RW |
3153 | (commit version))) |
3154 | (file-name (git-file-name name version)) | |
3155 | (sha256 | |
3156 | (base32 | |
3157 | "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) | |
3158 | (build-system r-build-system) | |
3159 | (propagated-inputs | |
3160 | `(("r-biobase" ,r-biobase) | |
3161 | ("r-biocgenerics" ,r-biocgenerics) | |
3162 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
3163 | ("r-dplyr" ,r-dplyr) | |
3164 | ("r-ggplot2" ,r-ggplot2) | |
3165 | ("r-ggrepel" ,r-ggrepel) | |
3166 | ("r-grr" ,r-grr) | |
3167 | ("r-htmlwidgets" ,r-htmlwidgets) | |
3168 | ("r-igraph" ,r-igraph) | |
3169 | ("r-irlba" ,r-irlba) | |
3170 | ("r-limma" ,r-limma) | |
3171 | ("r-lmtest" ,r-lmtest) | |
3172 | ("r-mass" ,r-mass) | |
3173 | ("r-matrix" ,r-matrix) | |
3174 | ("r-matrix-utils" ,r-matrix-utils) | |
3175 | ("r-pbapply" ,r-pbapply) | |
3176 | ("r-pbmcapply" ,r-pbmcapply) | |
3177 | ("r-pheatmap" ,r-pheatmap) | |
3178 | ("r-plotly" ,r-plotly) | |
3179 | ("r-pryr" ,r-pryr) | |
3180 | ("r-proxy" ,r-proxy) | |
3181 | ("r-pscl" ,r-pscl) | |
3182 | ("r-purrr" ,r-purrr) | |
3183 | ("r-rann" ,r-rann) | |
3184 | ("r-rcpp" ,r-rcpp) | |
3185 | ("r-rcppparallel" ,r-rcppparallel) | |
3186 | ("r-reshape2" ,r-reshape2) | |
3187 | ("r-reticulate" ,r-reticulate) | |
3188 | ("r-rhpcblasctl" ,r-rhpcblasctl) | |
3189 | ("r-rtsne" ,r-rtsne) | |
3190 | ("r-shiny" ,r-shiny) | |
3191 | ("r-slam" ,r-slam) | |
3192 | ("r-spdep" ,r-spdep) | |
3193 | ("r-speedglm" ,r-speedglm) | |
3194 | ("r-stringr" ,r-stringr) | |
3195 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
3196 | ("r-tibble" ,r-tibble) | |
3197 | ("r-tidyr" ,r-tidyr) | |
3198 | ("r-uwot" ,r-uwot) | |
3199 | ("r-viridis" ,r-viridis))) | |
3200 | (home-page "https://github.com/cole-trapnell-lab/monocle3") | |
3201 | (synopsis "Analysis toolkit for single-cell RNA-Seq data") | |
3202 | (description | |
3203 | "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") | |
3204 | (license license:expat))) | |
3205 | ||
6213e441 RW |
3206 | (define-public r-noiseq |
3207 | (package | |
3208 | (name "r-noiseq") | |
8396c45e | 3209 | (version "2.34.0") |
6213e441 RW |
3210 | (source |
3211 | (origin | |
3212 | (method url-fetch) | |
3213 | (uri (bioconductor-uri "NOISeq" version)) | |
3214 | (sha256 | |
3215 | (base32 | |
8396c45e | 3216 | "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f")))) |
6213e441 RW |
3217 | (properties `((upstream-name . "NOISeq"))) |
3218 | (build-system r-build-system) | |
3219 | (propagated-inputs | |
3220 | `(("r-biobase" ,r-biobase) | |
3221 | ("r-matrix" ,r-matrix))) | |
3222 | (home-page "https://bioconductor.org/packages/NOISeq") | |
3223 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") | |
3224 | (description | |
3225 | "This package provides tools to support the analysis of RNA-seq | |
3226 | expression data or other similar kind of data. It provides exploratory plots | |
3227 | to evaluate saturation, count distribution, expression per chromosome, type of | |
3228 | detected features, features length, etc. It also supports the analysis of | |
3229 | differential expression between two experimental conditions with no parametric | |
3230 | assumptions.") | |
3231 | (license license:artistic2.0))) | |
b409c357 RW |
3232 | |
3233 | (define-public r-scdd | |
3234 | (package | |
3235 | (name "r-scdd") | |
b856a487 | 3236 | (version "1.14.0") |
b409c357 RW |
3237 | (source |
3238 | (origin | |
3239 | (method url-fetch) | |
3240 | (uri (bioconductor-uri "scDD" version)) | |
3241 | (sha256 | |
3242 | (base32 | |
b856a487 | 3243 | "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g")))) |
b409c357 RW |
3244 | (properties `((upstream-name . "scDD"))) |
3245 | (build-system r-build-system) | |
3246 | (propagated-inputs | |
3247 | `(("r-arm" ,r-arm) | |
3248 | ("r-biocparallel" ,r-biocparallel) | |
3249 | ("r-ebseq" ,r-ebseq) | |
3250 | ("r-fields" ,r-fields) | |
3251 | ("r-ggplot2" ,r-ggplot2) | |
3252 | ("r-mclust" ,r-mclust) | |
3253 | ("r-outliers" ,r-outliers) | |
3254 | ("r-s4vectors" ,r-s4vectors) | |
3255 | ("r-scran" ,r-scran) | |
3256 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
3257 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
ce9e19bc RW |
3258 | (native-inputs |
3259 | `(("r-knitr" ,r-knitr))) | |
b409c357 RW |
3260 | (home-page "https://github.com/kdkorthauer/scDD") |
3261 | (synopsis "Mixture modeling of single-cell RNA-seq data") | |
3262 | (description | |
3263 | "This package implements a method to analyze single-cell RNA-seq data | |
3264 | utilizing flexible Dirichlet Process mixture models. Genes with differential | |
3265 | distributions of expression are classified into several interesting patterns | |
3266 | of differences between two conditions. The package also includes functions | |
3267 | for simulating data with these patterns from negative binomial | |
3268 | distributions.") | |
3269 | (license license:gpl2))) | |
f0887757 RW |
3270 | |
3271 | (define-public r-scone | |
3272 | (package | |
3273 | (name "r-scone") | |
bde9dc5b | 3274 | (version "1.14.0") |
f0887757 RW |
3275 | (source |
3276 | (origin | |
3277 | (method url-fetch) | |
3278 | (uri (bioconductor-uri "scone" version)) | |
3279 | (sha256 | |
3280 | (base32 | |
bde9dc5b | 3281 | "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73")))) |
f0887757 RW |
3282 | (build-system r-build-system) |
3283 | (propagated-inputs | |
3284 | `(("r-aroma-light" ,r-aroma-light) | |
3285 | ("r-biocparallel" ,r-biocparallel) | |
3286 | ("r-boot" ,r-boot) | |
3287 | ("r-class" ,r-class) | |
3288 | ("r-cluster" ,r-cluster) | |
3289 | ("r-compositions" ,r-compositions) | |
3290 | ("r-diptest" ,r-diptest) | |
3291 | ("r-edger" ,r-edger) | |
3292 | ("r-fpc" ,r-fpc) | |
3293 | ("r-gplots" ,r-gplots) | |
3294 | ("r-hexbin" ,r-hexbin) | |
3295 | ("r-limma" ,r-limma) | |
3296 | ("r-matrixstats" ,r-matrixstats) | |
3297 | ("r-mixtools" ,r-mixtools) | |
3298 | ("r-rarpack" ,r-rarpack) | |
3299 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3300 | ("r-rhdf5" ,r-rhdf5) | |
3301 | ("r-ruvseq" ,r-ruvseq) | |
3302 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
3fc1e039 RW |
3303 | (native-inputs |
3304 | `(("r-knitr" ,r-knitr))) | |
f0887757 RW |
3305 | (home-page "https://bioconductor.org/packages/scone") |
3306 | (synopsis "Single cell overview of normalized expression data") | |
3307 | (description | |
3308 | "SCONE is an R package for comparing and ranking the performance of | |
3309 | different normalization schemes for single-cell RNA-seq and other | |
3310 | high-throughput analyses.") | |
3311 | (license license:artistic2.0))) | |
f9201d67 RW |
3312 | |
3313 | (define-public r-geoquery | |
3314 | (package | |
3315 | (name "r-geoquery") | |
5c4edeef | 3316 | (version "2.58.0") |
f9201d67 RW |
3317 | (source |
3318 | (origin | |
3319 | (method url-fetch) | |
3320 | (uri (bioconductor-uri "GEOquery" version)) | |
3321 | (sha256 | |
3322 | (base32 | |
5c4edeef | 3323 | "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4")))) |
f9201d67 RW |
3324 | (properties `((upstream-name . "GEOquery"))) |
3325 | (build-system r-build-system) | |
3326 | (propagated-inputs | |
3327 | `(("r-biobase" ,r-biobase) | |
3328 | ("r-dplyr" ,r-dplyr) | |
3329 | ("r-httr" ,r-httr) | |
3330 | ("r-limma" ,r-limma) | |
3331 | ("r-magrittr" ,r-magrittr) | |
3332 | ("r-readr" ,r-readr) | |
3333 | ("r-tidyr" ,r-tidyr) | |
3334 | ("r-xml2" ,r-xml2))) | |
159e427c RW |
3335 | (native-inputs |
3336 | `(("r-knitr" ,r-knitr))) | |
f9201d67 RW |
3337 | (home-page "https://github.com/seandavi/GEOquery/") |
3338 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") | |
3339 | (description | |
3340 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of | |
3341 | microarray data. Given the rich and varied nature of this resource, it is | |
3342 | only natural to want to apply BioConductor tools to these data. GEOquery is | |
3343 | the bridge between GEO and BioConductor.") | |
3344 | (license license:gpl2))) | |
eed6ff03 RW |
3345 | |
3346 | (define-public r-illuminaio | |
3347 | (package | |
3348 | (name "r-illuminaio") | |
e89966e9 | 3349 | (version "0.32.0") |
eed6ff03 RW |
3350 | (source |
3351 | (origin | |
3352 | (method url-fetch) | |
3353 | (uri (bioconductor-uri "illuminaio" version)) | |
3354 | (sha256 | |
3355 | (base32 | |
e89966e9 | 3356 | "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay")))) |
eed6ff03 RW |
3357 | (build-system r-build-system) |
3358 | (propagated-inputs | |
3359 | `(("r-base64" ,r-base64))) | |
3360 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") | |
3361 | (synopsis "Parse Illumina microarray output files") | |
3362 | (description | |
3363 | "This package provides tools for parsing Illumina's microarray output | |
3364 | files, including IDAT.") | |
3365 | (license license:gpl2))) | |
f4eac096 RW |
3366 | |
3367 | (define-public r-siggenes | |
3368 | (package | |
3369 | (name "r-siggenes") | |
0fd830fe | 3370 | (version "1.64.0") |
f4eac096 RW |
3371 | (source |
3372 | (origin | |
3373 | (method url-fetch) | |
3374 | (uri (bioconductor-uri "siggenes" version)) | |
3375 | (sha256 | |
3376 | (base32 | |
0fd830fe | 3377 | "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w")))) |
f4eac096 RW |
3378 | (build-system r-build-system) |
3379 | (propagated-inputs | |
3380 | `(("r-biobase" ,r-biobase) | |
409f4dd6 RW |
3381 | ("r-multtest" ,r-multtest) |
3382 | ("r-scrime" ,r-scrime))) | |
f4eac096 RW |
3383 | (home-page "https://bioconductor.org/packages/siggenes/") |
3384 | (synopsis | |
3385 | "Multiple testing using SAM and Efron's empirical Bayes approaches") | |
3386 | (description | |
3387 | "This package provides tools for the identification of differentially | |
3388 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using | |
3389 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical | |
3390 | Bayes Analyses of Microarrays} (EBAM).") | |
3391 | (license license:lgpl2.0+))) | |
34a24f95 RW |
3392 | |
3393 | (define-public r-bumphunter | |
3394 | (package | |
3395 | (name "r-bumphunter") | |
50c5fee6 | 3396 | (version "1.32.0") |
34a24f95 RW |
3397 | (source |
3398 | (origin | |
3399 | (method url-fetch) | |
3400 | (uri (bioconductor-uri "bumphunter" version)) | |
3401 | (sha256 | |
3402 | (base32 | |
50c5fee6 | 3403 | "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk")))) |
34a24f95 RW |
3404 | (build-system r-build-system) |
3405 | (propagated-inputs | |
3406 | `(("r-annotationdbi" ,r-annotationdbi) | |
3407 | ("r-biocgenerics" ,r-biocgenerics) | |
3408 | ("r-dorng" ,r-dorng) | |
3409 | ("r-foreach" ,r-foreach) | |
3410 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3411 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3412 | ("r-genomicranges" ,r-genomicranges) | |
3413 | ("r-iranges" ,r-iranges) | |
3414 | ("r-iterators" ,r-iterators) | |
3415 | ("r-limma" ,r-limma) | |
3416 | ("r-locfit" ,r-locfit) | |
3417 | ("r-matrixstats" ,r-matrixstats) | |
3418 | ("r-s4vectors" ,r-s4vectors))) | |
3419 | (home-page "https://github.com/ririzarr/bumphunter") | |
3420 | (synopsis "Find bumps in genomic data") | |
3421 | (description | |
3422 | "This package provides tools for finding bumps in genomic data in order | |
3423 | to identify differentially methylated regions in epigenetic epidemiology | |
3424 | studies.") | |
3425 | (license license:artistic2.0))) | |
0fbaf195 RW |
3426 | |
3427 | (define-public r-minfi | |
3428 | (package | |
3429 | (name "r-minfi") | |
e5a4198b | 3430 | (version "1.36.0") |
0fbaf195 RW |
3431 | (source |
3432 | (origin | |
3433 | (method url-fetch) | |
3434 | (uri (bioconductor-uri "minfi" version)) | |
3435 | (sha256 | |
3436 | (base32 | |
e5a4198b | 3437 | "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi")))) |
0fbaf195 RW |
3438 | (build-system r-build-system) |
3439 | (propagated-inputs | |
3440 | `(("r-beanplot" ,r-beanplot) | |
3441 | ("r-biobase" ,r-biobase) | |
3442 | ("r-biocgenerics" ,r-biocgenerics) | |
3443 | ("r-biocparallel" ,r-biocparallel) | |
3444 | ("r-biostrings" ,r-biostrings) | |
3445 | ("r-bumphunter" ,r-bumphunter) | |
3446 | ("r-data-table" ,r-data-table) | |
3447 | ("r-delayedarray" ,r-delayedarray) | |
3448 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
3449 | ("r-genefilter" ,r-genefilter) | |
3450 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3451 | ("r-genomicranges" ,r-genomicranges) | |
3452 | ("r-geoquery" ,r-geoquery) | |
3453 | ("r-hdf5array" ,r-hdf5array) | |
3454 | ("r-illuminaio" ,r-illuminaio) | |
3455 | ("r-iranges" ,r-iranges) | |
3456 | ("r-lattice" ,r-lattice) | |
3457 | ("r-limma" ,r-limma) | |
3458 | ("r-mass" ,r-mass) | |
3459 | ("r-mclust" ,r-mclust) | |
3460 | ("r-nlme" ,r-nlme) | |
3461 | ("r-nor1mix" ,r-nor1mix) | |
3462 | ("r-preprocesscore" ,r-preprocesscore) | |
3463 | ("r-quadprog" ,r-quadprog) | |
3464 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3465 | ("r-reshape" ,r-reshape) | |
3466 | ("r-s4vectors" ,r-s4vectors) | |
3467 | ("r-siggenes" ,r-siggenes) | |
3468 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
83e6ffda RW |
3469 | (native-inputs |
3470 | `(("r-knitr" ,r-knitr))) | |
0fbaf195 RW |
3471 | (home-page "https://github.com/hansenlab/minfi") |
3472 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") | |
3473 | (description | |
3474 | "This package provides tools to analyze and visualize Illumina Infinium | |
3475 | methylation arrays.") | |
3476 | (license license:artistic2.0))) | |
5ec5ba02 RW |
3477 | |
3478 | (define-public r-methylumi | |
3479 | (package | |
3480 | (name "r-methylumi") | |
0b7dd447 | 3481 | (version "2.36.0") |
5ec5ba02 RW |
3482 | (source |
3483 | (origin | |
3484 | (method url-fetch) | |
3485 | (uri (bioconductor-uri "methylumi" version)) | |
3486 | (sha256 | |
3487 | (base32 | |
0b7dd447 | 3488 | "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh")))) |
5ec5ba02 RW |
3489 | (build-system r-build-system) |
3490 | (propagated-inputs | |
3491 | `(("r-annotate" ,r-annotate) | |
3492 | ("r-annotationdbi" ,r-annotationdbi) | |
3493 | ("r-biobase" ,r-biobase) | |
3494 | ("r-biocgenerics" ,r-biocgenerics) | |
3495 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) | |
3496 | ("r-genefilter" ,r-genefilter) | |
3497 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3498 | ("r-genomicranges" ,r-genomicranges) | |
3499 | ("r-ggplot2" ,r-ggplot2) | |
3500 | ("r-illuminaio" ,r-illuminaio) | |
3501 | ("r-iranges" ,r-iranges) | |
3502 | ("r-lattice" ,r-lattice) | |
3503 | ("r-matrixstats" ,r-matrixstats) | |
3504 | ("r-minfi" ,r-minfi) | |
3505 | ("r-reshape2" ,r-reshape2) | |
3506 | ("r-s4vectors" ,r-s4vectors) | |
3507 | ("r-scales" ,r-scales) | |
3508 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5f25d5f8 RW |
3509 | (native-inputs |
3510 | `(("r-knitr" ,r-knitr))) | |
5ec5ba02 RW |
3511 | (home-page "https://bioconductor.org/packages/methylumi") |
3512 | (synopsis "Handle Illumina methylation data") | |
3513 | (description | |
3514 | "This package provides classes for holding and manipulating Illumina | |
3515 | methylation data. Based on eSet, it can contain MIAME information, sample | |
3516 | information, feature information, and multiple matrices of data. An | |
3517 | \"intelligent\" import function, methylumiR can read the Illumina text files | |
3518 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from | |
3519 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, | |
3520 | background correction, and quality control features for GoldenGate, Infinium, | |
3521 | and Infinium HD arrays are also included.") | |
3522 | (license license:gpl2))) | |
09605cb2 RW |
3523 | |
3524 | (define-public r-lumi | |
3525 | (package | |
3526 | (name "r-lumi") | |
4eeaa159 | 3527 | (version "2.42.0") |
09605cb2 RW |
3528 | (source |
3529 | (origin | |
3530 | (method url-fetch) | |
3531 | (uri (bioconductor-uri "lumi" version)) | |
3532 | (sha256 | |
3533 | (base32 | |
4eeaa159 | 3534 | "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3")))) |
09605cb2 RW |
3535 | (build-system r-build-system) |
3536 | (propagated-inputs | |
3537 | `(("r-affy" ,r-affy) | |
3538 | ("r-annotate" ,r-annotate) | |
3539 | ("r-annotationdbi" ,r-annotationdbi) | |
3540 | ("r-biobase" ,r-biobase) | |
3541 | ("r-dbi" ,r-dbi) | |
3542 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3543 | ("r-genomicranges" ,r-genomicranges) | |
3544 | ("r-kernsmooth" ,r-kernsmooth) | |
3545 | ("r-lattice" ,r-lattice) | |
3546 | ("r-mass" ,r-mass) | |
3547 | ("r-methylumi" ,r-methylumi) | |
3548 | ("r-mgcv" ,r-mgcv) | |
3549 | ("r-nleqslv" ,r-nleqslv) | |
3550 | ("r-preprocesscore" ,r-preprocesscore) | |
3551 | ("r-rsqlite" ,r-rsqlite))) | |
3552 | (home-page "https://bioconductor.org/packages/lumi") | |
3553 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") | |
3554 | (description | |
3555 | "The lumi package provides an integrated solution for the Illumina | |
3556 | microarray data analysis. It includes functions of Illumina | |
3557 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific | |
3558 | variance stabilization, normalization and gene annotation at the probe level. | |
3559 | It also includes the functions of processing Illumina methylation microarrays, | |
3560 | especially Illumina Infinium methylation microarrays.") | |
3561 | (license license:lgpl2.0+))) | |
4291f36a RW |
3562 | |
3563 | (define-public r-linnorm | |
3564 | (package | |
3565 | (name "r-linnorm") | |
37e09611 | 3566 | (version "2.14.0") |
4291f36a RW |
3567 | (source |
3568 | (origin | |
3569 | (method url-fetch) | |
3570 | (uri (bioconductor-uri "Linnorm" version)) | |
3571 | (sha256 | |
3572 | (base32 | |
37e09611 | 3573 | "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3")))) |
4291f36a RW |
3574 | (properties `((upstream-name . "Linnorm"))) |
3575 | (build-system r-build-system) | |
3576 | (propagated-inputs | |
3577 | `(("r-amap" ,r-amap) | |
3578 | ("r-apcluster" ,r-apcluster) | |
3579 | ("r-ellipse" ,r-ellipse) | |
3580 | ("r-fastcluster" ,r-fastcluster) | |
3581 | ("r-fpc" ,r-fpc) | |
3582 | ("r-ggdendro" ,r-ggdendro) | |
3583 | ("r-ggplot2" ,r-ggplot2) | |
3584 | ("r-gmodels" ,r-gmodels) | |
3585 | ("r-igraph" ,r-igraph) | |
3586 | ("r-limma" ,r-limma) | |
3587 | ("r-mass" ,r-mass) | |
3588 | ("r-mclust" ,r-mclust) | |
3589 | ("r-rcpp" ,r-rcpp) | |
3590 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
3591 | ("r-rtsne" ,r-rtsne) | |
3592 | ("r-statmod" ,r-statmod) | |
3593 | ("r-vegan" ,r-vegan) | |
3594 | ("r-zoo" ,r-zoo))) | |
1465873c RW |
3595 | (native-inputs |
3596 | `(("r-knitr" ,r-knitr))) | |
4291f36a RW |
3597 | (home-page "http://www.jjwanglab.org/Linnorm/") |
3598 | (synopsis "Linear model and normality based transformation method") | |
3599 | (description | |
3600 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq | |
3601 | count data or any large scale count data. It transforms such datasets for | |
3602 | parametric tests. In addition to the transformtion function (@code{Linnorm}), | |
3603 | the following pipelines are implemented: | |
3604 | ||
3605 | @enumerate | |
3606 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) | |
3607 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means | |
3608 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, | |
3609 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) | |
3610 | @item Differential expression analysis or differential peak detection using | |
3611 | limma (@code{Linnorm.limma}) | |
3612 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) | |
3613 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) | |
3614 | @item Stable gene selection for scRNA-seq data; for users without or who do | |
3615 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) | |
3616 | @item Data imputation (@code{Linnorm.DataImput}). | |
3617 | @end enumerate | |
3618 | ||
3619 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the | |
3620 | @code{RnaXSim} function is included for simulating RNA-seq data for the | |
3621 | evaluation of DEG analysis methods.") | |
3622 | (license license:expat))) | |
e4a17532 RW |
3623 | |
3624 | (define-public r-ioniser | |
3625 | (package | |
3626 | (name "r-ioniser") | |
2a1a6d74 | 3627 | (version "2.14.0") |
e4a17532 RW |
3628 | (source |
3629 | (origin | |
3630 | (method url-fetch) | |
3631 | (uri (bioconductor-uri "IONiseR" version)) | |
3632 | (sha256 | |
3633 | (base32 | |
2a1a6d74 | 3634 | "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx")))) |
e4a17532 RW |
3635 | (properties `((upstream-name . "IONiseR"))) |
3636 | (build-system r-build-system) | |
3637 | (propagated-inputs | |
3638 | `(("r-biocgenerics" ,r-biocgenerics) | |
3639 | ("r-biocparallel" ,r-biocparallel) | |
3640 | ("r-biostrings" ,r-biostrings) | |
3641 | ("r-bit64" ,r-bit64) | |
3642 | ("r-dplyr" ,r-dplyr) | |
3643 | ("r-ggplot2" ,r-ggplot2) | |
3644 | ("r-magrittr" ,r-magrittr) | |
3645 | ("r-rhdf5" ,r-rhdf5) | |
3646 | ("r-shortread" ,r-shortread) | |
3647 | ("r-stringr" ,r-stringr) | |
3648 | ("r-tibble" ,r-tibble) | |
3649 | ("r-tidyr" ,r-tidyr) | |
3650 | ("r-xvector" ,r-xvector))) | |
293fb8a1 RW |
3651 | (native-inputs |
3652 | `(("r-knitr" ,r-knitr))) | |
e4a17532 RW |
3653 | (home-page "https://bioconductor.org/packages/IONiseR/") |
3654 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") | |
3655 | (description | |
3656 | "IONiseR provides tools for the quality assessment of Oxford Nanopore | |
3657 | MinION data. It extracts summary statistics from a set of fast5 files and can | |
3658 | be used either before or after base calling. In addition to standard | |
3659 | summaries of the read-types produced, it provides a number of plots for | |
3660 | visualising metrics relative to experiment run time or spatially over the | |
3661 | surface of a flowcell.") | |
3662 | (license license:expat))) | |
80eb01c7 RW |
3663 | |
3664 | ;; This is a CRAN package, but it depends on packages from Bioconductor. | |
3665 | (define-public r-gkmsvm | |
3666 | (package | |
3667 | (name "r-gkmsvm") | |
e1636671 | 3668 | (version "0.81.0") |
80eb01c7 RW |
3669 | (source |
3670 | (origin | |
3671 | (method url-fetch) | |
3672 | (uri (cran-uri "gkmSVM" version)) | |
3673 | (sha256 | |
3674 | (base32 | |
e1636671 | 3675 | "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) |
80eb01c7 RW |
3676 | (properties `((upstream-name . "gkmSVM"))) |
3677 | (build-system r-build-system) | |
3678 | (propagated-inputs | |
975cfe26 | 3679 | `(("r-kernlab" ,r-kernlab) |
80eb01c7 RW |
3680 | ("r-rcpp" ,r-rcpp) |
3681 | ("r-rocr" ,r-rocr) | |
80eb01c7 RW |
3682 | ("r-seqinr" ,r-seqinr))) |
3683 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") | |
3684 | (synopsis "Gapped-kmer support vector machine") | |
3685 | (description | |
3686 | "This R package provides tools for training gapped-kmer SVM classifiers | |
3687 | for DNA and protein sequences. This package supports several sequence | |
3688 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
3689 | (license license:gpl2+))) | |
8a5460b4 | 3690 | |
f2114762 RW |
3691 | ;; This is a CRAN package, but it depends on multtest from Bioconductor. |
3692 | (define-public r-mutoss | |
3693 | (package | |
3694 | (name "r-mutoss") | |
3695 | (version "0.1-12") | |
3696 | (source | |
3697 | (origin | |
3698 | (method url-fetch) | |
3699 | (uri (cran-uri "mutoss" version)) | |
3700 | (sha256 | |
3701 | (base32 | |
3702 | "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298")))) | |
3703 | (properties `((upstream-name . "mutoss"))) | |
3704 | (build-system r-build-system) | |
3705 | (propagated-inputs | |
3706 | `(("r-multcomp" ,r-multcomp) | |
3707 | ("r-multtest" ,r-multtest) | |
3708 | ("r-mvtnorm" ,r-mvtnorm) | |
3709 | ("r-plotrix" ,r-plotrix))) | |
3710 | (home-page "https://github.com/kornl/mutoss/") | |
3711 | (synopsis "Unified multiple testing procedures") | |
3712 | (description | |
3713 | "This package is designed to ease the application and comparison of | |
3714 | multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods | |
3715 | are standardized and usable by the accompanying mutossGUI package.") | |
3716 | ;; Any version of the GPL. | |
3717 | (license (list license:gpl2+ license:gpl3+)))) | |
3718 | ||
bf770d92 RW |
3719 | ;; This is a CRAN package, but it depends on mutoss, which depends on multtest |
3720 | ;; from Bioconductor, so we put it here. | |
3721 | (define-public r-metap | |
3722 | (package | |
3723 | (name "r-metap") | |
fd6412cd | 3724 | (version "1.3") |
bf770d92 RW |
3725 | (source |
3726 | (origin | |
3727 | (method url-fetch) | |
3728 | (uri (cran-uri "metap" version)) | |
3729 | (sha256 | |
3730 | (base32 | |
fd6412cd | 3731 | "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) |
bf770d92 RW |
3732 | (build-system r-build-system) |
3733 | (propagated-inputs | |
3734 | `(("r-lattice" ,r-lattice) | |
3735 | ("r-mutoss" ,r-mutoss) | |
3736 | ("r-rdpack" ,r-rdpack) | |
3737 | ("r-tfisher" ,r-tfisher))) | |
3738 | (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") | |
3739 | (synopsis "Meta-analysis of significance values") | |
3740 | (description | |
3741 | "The canonical way to perform meta-analysis involves using effect sizes. | |
3742 | When they are not available this package provides a number of methods for | |
3743 | meta-analysis of significance values including the methods of Edgington, | |
3744 | Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate | |
3745 | published results; and a routine for graphical display.") | |
3746 | (license license:gpl2))) | |
3747 | ||
8a5460b4 RW |
3748 | (define-public r-triform |
3749 | (package | |
3750 | (name "r-triform") | |
ecb4e165 | 3751 | (version "1.29.0") |
8a5460b4 RW |
3752 | (source |
3753 | (origin | |
3754 | (method url-fetch) | |
3755 | (uri (bioconductor-uri "triform" version)) | |
3756 | (sha256 | |
3757 | (base32 | |
ecb4e165 | 3758 | "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) |
8a5460b4 RW |
3759 | (build-system r-build-system) |
3760 | (propagated-inputs | |
3761 | `(("r-biocgenerics" ,r-biocgenerics) | |
3762 | ("r-iranges" ,r-iranges) | |
3763 | ("r-yaml" ,r-yaml))) | |
3764 | (home-page "https://bioconductor.org/packages/triform/") | |
3765 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") | |
3766 | (description | |
3767 | "The Triform algorithm uses model-free statistics to identify peak-like | |
3768 | distributions of TF ChIP sequencing reads, taking advantage of an improved | |
3769 | peak definition in combination with known profile characteristics.") | |
3770 | (license license:gpl2))) | |
c538bcdd RW |
3771 | |
3772 | (define-public r-varianttools | |
3773 | (package | |
3774 | (name "r-varianttools") | |
67837d4a | 3775 | (version "1.32.0") |
c538bcdd RW |
3776 | (source |
3777 | (origin | |
3778 | (method url-fetch) | |
3779 | (uri (bioconductor-uri "VariantTools" version)) | |
3780 | (sha256 | |
3781 | (base32 | |
67837d4a | 3782 | "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89")))) |
c538bcdd RW |
3783 | (properties `((upstream-name . "VariantTools"))) |
3784 | (build-system r-build-system) | |
3785 | (propagated-inputs | |
3786 | `(("r-biobase" ,r-biobase) | |
3787 | ("r-biocgenerics" ,r-biocgenerics) | |
3788 | ("r-biocparallel" ,r-biocparallel) | |
3789 | ("r-biostrings" ,r-biostrings) | |
3790 | ("r-bsgenome" ,r-bsgenome) | |
3791 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3792 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3793 | ("r-genomicranges" ,r-genomicranges) | |
3794 | ("r-iranges" ,r-iranges) | |
3795 | ("r-matrix" ,r-matrix) | |
3796 | ("r-rsamtools" ,r-rsamtools) | |
3797 | ("r-rtracklayer" ,r-rtracklayer) | |
3798 | ("r-s4vectors" ,r-s4vectors) | |
3799 | ("r-variantannotation" ,r-variantannotation))) | |
3800 | (home-page "https://bioconductor.org/packages/VariantTools/") | |
3801 | (synopsis "Tools for exploratory analysis of variant calls") | |
3802 | (description | |
3803 | "Explore, diagnose, and compare variant calls using filters. The | |
3804 | VariantTools package supports a workflow for loading data, calling single | |
3805 | sample variants and tumor-specific somatic mutations or other sample-specific | |
3806 | variant types (e.g., RNA editing). Most of the functions operate on | |
3807 | alignments (BAM files) or datasets of called variants. The user is expected | |
3808 | to have already aligned the reads with a separate tool, e.g., GSNAP via | |
3809 | gmapR.") | |
3810 | (license license:artistic2.0))) | |
3e41919d RW |
3811 | |
3812 | (define-public r-heatplus | |
3813 | (package | |
3814 | (name "r-heatplus") | |
9813d24d | 3815 | (version "2.36.0") |
3e41919d RW |
3816 | (source |
3817 | (origin | |
3818 | (method url-fetch) | |
3819 | (uri (bioconductor-uri "Heatplus" version)) | |
3820 | (sha256 | |
3821 | (base32 | |
9813d24d | 3822 | "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n")))) |
3e41919d RW |
3823 | (properties `((upstream-name . "Heatplus"))) |
3824 | (build-system r-build-system) | |
3825 | (propagated-inputs | |
3826 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) | |
3827 | (home-page "https://github.com/alexploner/Heatplus") | |
3828 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") | |
3829 | (description | |
3830 | "This package provides tools to display a rectangular heatmap (intensity | |
3831 | plot) of a data matrix. By default, both samples (columns) and features (row) | |
3832 | of the matrix are sorted according to a hierarchical clustering, and the | |
3833 | corresponding dendrogram is plotted. Optionally, panels with additional | |
3834 | information about samples and features can be added to the plot.") | |
3835 | (license license:gpl2+))) | |
c04f230e RW |
3836 | |
3837 | (define-public r-gosemsim | |
3838 | (package | |
3839 | (name "r-gosemsim") | |
b2084e4d | 3840 | (version "2.16.1") |
c04f230e RW |
3841 | (source |
3842 | (origin | |
3843 | (method url-fetch) | |
3844 | (uri (bioconductor-uri "GOSemSim" version)) | |
3845 | (sha256 | |
3846 | (base32 | |
b2084e4d | 3847 | "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs")))) |
c04f230e RW |
3848 | (properties `((upstream-name . "GOSemSim"))) |
3849 | (build-system r-build-system) | |
3850 | (propagated-inputs | |
3851 | `(("r-annotationdbi" ,r-annotationdbi) | |
3852 | ("r-go-db" ,r-go-db) | |
3853 | ("r-rcpp" ,r-rcpp))) | |
d5951dc4 RW |
3854 | (native-inputs |
3855 | `(("r-knitr" ,r-knitr))) | |
c04f230e RW |
3856 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") |
3857 | (synopsis "GO-terms semantic similarity measures") | |
3858 | (description | |
3859 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide | |
3860 | quantitative ways to compute similarities between genes and gene groups, and | |
3861 | have became important basis for many bioinformatics analysis approaches. | |
3862 | GOSemSim is an R package for semantic similarity computation among GO terms, | |
3863 | sets of GO terms, gene products and gene clusters.") | |
3864 | (license license:artistic2.0))) | |
9d0f7942 RW |
3865 | |
3866 | (define-public r-anota | |
3867 | (package | |
3868 | (name "r-anota") | |
33c905b9 | 3869 | (version "1.38.0") |
9d0f7942 RW |
3870 | (source |
3871 | (origin | |
3872 | (method url-fetch) | |
3873 | (uri (bioconductor-uri "anota" version)) | |
3874 | (sha256 | |
3875 | (base32 | |
33c905b9 | 3876 | "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x")))) |
9d0f7942 RW |
3877 | (build-system r-build-system) |
3878 | (propagated-inputs | |
3879 | `(("r-multtest" ,r-multtest) | |
3880 | ("r-qvalue" ,r-qvalue))) | |
3881 | (home-page "https://bioconductor.org/packages/anota/") | |
3882 | (synopsis "Analysis of translational activity") | |
3883 | (description | |
3884 | "Genome wide studies of translational control is emerging as a tool to | |
0cea26bd | 3885 | study various biological conditions. The output from such analysis is both |
7230f6d5 | 3886 | the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively |
9d0f7942 RW |
3887 | involved in translation (the actively translating mRNA level) for each mRNA. |
3888 | The standard analysis of such data strives towards identifying differential | |
3889 | translational between two or more sample classes - i.e. differences in | |
3890 | actively translated mRNA levels that are independent of underlying differences | |
3891 | in cytosolic mRNA levels. This package allows for such analysis using partial | |
3892 | variances and the random variance model. As 10s of thousands of mRNAs are | |
4f664004 | 3893 | analyzed in parallel the library performs a number of tests to assure that |
9d0f7942 RW |
3894 | the data set is suitable for such analysis.") |
3895 | (license license:gpl3))) | |
a6d867fe RW |
3896 | |
3897 | (define-public r-sigpathway | |
3898 | (package | |
3899 | (name "r-sigpathway") | |
7dabc629 | 3900 | (version "1.58.0") |
a6d867fe RW |
3901 | (source |
3902 | (origin | |
3903 | (method url-fetch) | |
3904 | (uri (bioconductor-uri "sigPathway" version)) | |
3905 | (sha256 | |
3906 | (base32 | |
7dabc629 | 3907 | "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l")))) |
a6d867fe RW |
3908 | (properties `((upstream-name . "sigPathway"))) |
3909 | (build-system r-build-system) | |
3910 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") | |
3911 | (synopsis "Pathway analysis") | |
3912 | (description | |
3913 | "This package is used to conduct pathway analysis by calculating the NT_k | |
3914 | and NE_k statistics in a statistical framework for determining whether a | |
3915 | specified group of genes for a pathway has a coordinated association with a | |
3916 | phenotype of interest.") | |
3917 | (license license:gpl2))) | |
af26c7ae RW |
3918 | |
3919 | (define-public r-fgsea | |
3920 | (package | |
3921 | (name "r-fgsea") | |
d68a9ffa | 3922 | (version "1.16.0") |
af26c7ae RW |
3923 | (source |
3924 | (origin | |
3925 | (method url-fetch) | |
3926 | (uri (bioconductor-uri "fgsea" version)) | |
3927 | (sha256 | |
3928 | (base32 | |
d68a9ffa | 3929 | "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n")))) |
af26c7ae RW |
3930 | (build-system r-build-system) |
3931 | (propagated-inputs | |
ebffd24c RW |
3932 | `(("r-bh" ,r-bh) |
3933 | ("r-biocparallel" ,r-biocparallel) | |
af26c7ae RW |
3934 | ("r-data-table" ,r-data-table) |
3935 | ("r-fastmatch" ,r-fastmatch) | |
3936 | ("r-ggplot2" ,r-ggplot2) | |
3937 | ("r-gridextra" ,r-gridextra) | |
3938 | ("r-matrix" ,r-matrix) | |
3939 | ("r-rcpp" ,r-rcpp))) | |
1dec455c RW |
3940 | (native-inputs |
3941 | `(("r-knitr" ,r-knitr))) | |
af26c7ae RW |
3942 | (home-page "https://github.com/ctlab/fgsea/") |
3943 | (synopsis "Fast gene set enrichment analysis") | |
3944 | (description | |
3945 | "The package implements an algorithm for fast gene set enrichment | |
23c8ef71 VC |
3946 | analysis. Using the fast algorithm makes more permutations and gets |
3947 | more fine grained p-values, which allows using accurate standard approaches | |
af26c7ae RW |
3948 | to multiple hypothesis correction.") |
3949 | (license license:expat))) | |
305050b5 RW |
3950 | |
3951 | (define-public r-dose | |
3952 | (package | |
3953 | (name "r-dose") | |
aeb1d56f | 3954 | (version "3.16.0") |
305050b5 RW |
3955 | (source |
3956 | (origin | |
3957 | (method url-fetch) | |
3958 | (uri (bioconductor-uri "DOSE" version)) | |
3959 | (sha256 | |
3960 | (base32 | |
aeb1d56f | 3961 | "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4")))) |
305050b5 RW |
3962 | (properties `((upstream-name . "DOSE"))) |
3963 | (build-system r-build-system) | |
3964 | (propagated-inputs | |
3965 | `(("r-annotationdbi" ,r-annotationdbi) | |
3966 | ("r-biocparallel" ,r-biocparallel) | |
3967 | ("r-do-db" ,r-do-db) | |
3968 | ("r-fgsea" ,r-fgsea) | |
3969 | ("r-ggplot2" ,r-ggplot2) | |
3970 | ("r-gosemsim" ,r-gosemsim) | |
3971 | ("r-qvalue" ,r-qvalue) | |
3a80f1cf | 3972 | ("r-reshape2" ,r-reshape2))) |
5ef2b749 RW |
3973 | (native-inputs |
3974 | `(("r-knitr" ,r-knitr))) | |
305050b5 RW |
3975 | (home-page "https://guangchuangyu.github.io/software/DOSE/") |
3976 | (synopsis "Disease ontology semantic and enrichment analysis") | |
3977 | (description | |
3978 | "This package implements five methods proposed by Resnik, Schlicker, | |
3979 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among | |
3980 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses | |
3981 | including hypergeometric model and gene set enrichment analysis are also | |
3982 | implemented for discovering disease associations of high-throughput biological | |
3983 | data.") | |
3984 | (license license:artistic2.0))) | |
9c30cf65 RW |
3985 | |
3986 | (define-public r-enrichplot | |
3987 | (package | |
3988 | (name "r-enrichplot") | |
eb3d17eb | 3989 | (version "1.10.1") |
9c30cf65 RW |
3990 | (source |
3991 | (origin | |
3992 | (method url-fetch) | |
3993 | (uri (bioconductor-uri "enrichplot" version)) | |
3994 | (sha256 | |
3995 | (base32 | |
eb3d17eb | 3996 | "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd")))) |
9c30cf65 RW |
3997 | (build-system r-build-system) |
3998 | (propagated-inputs | |
eb3d17eb | 3999 | `(("r-cowplot" ,r-cowplot) |
9c30cf65 | 4000 | ("r-dose" ,r-dose) |
9c30cf65 | 4001 | ("r-ggplot2" ,r-ggplot2) |
9c30cf65 | 4002 | ("r-ggraph" ,r-ggraph) |
9c30cf65 | 4003 | ("r-gosemsim" ,r-gosemsim) |
9c30cf65 | 4004 | ("r-igraph" ,r-igraph) |
eb3d17eb | 4005 | ("r-magrittr" ,r-magrittr) |
43fb14ce | 4006 | ("r-plyr" ,r-plyr) |
9c30cf65 RW |
4007 | ("r-purrr" ,r-purrr) |
4008 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
43fb14ce | 4009 | ("r-reshape2" ,r-reshape2) |
eb3d17eb RJ |
4010 | ("r-scatterpie" ,r-scatterpie) |
4011 | ("r-shadowtext" ,r-shadowtext))) | |
43fb14ce RW |
4012 | (native-inputs |
4013 | `(("r-knitr" ,r-knitr))) | |
9c30cf65 RW |
4014 | (home-page "https://github.com/GuangchuangYu/enrichplot") |
4015 | (synopsis "Visualization of functional enrichment result") | |
4016 | (description | |
4017 | "The enrichplot package implements several visualization methods for | |
4018 | interpreting functional enrichment results obtained from ORA or GSEA analyses. | |
4019 | All the visualization methods are developed based on ggplot2 graphics.") | |
4020 | (license license:artistic2.0))) | |
f8295ee6 RW |
4021 | |
4022 | (define-public r-clusterprofiler | |
4023 | (package | |
4024 | (name "r-clusterprofiler") | |
3fd84a46 | 4025 | (version "3.18.0") |
f8295ee6 RW |
4026 | (source |
4027 | (origin | |
4028 | (method url-fetch) | |
4029 | (uri (bioconductor-uri "clusterProfiler" version)) | |
4030 | (sha256 | |
4031 | (base32 | |
3fd84a46 | 4032 | "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9")))) |
f8295ee6 RW |
4033 | (properties |
4034 | `((upstream-name . "clusterProfiler"))) | |
4035 | (build-system r-build-system) | |
4036 | (propagated-inputs | |
4037 | `(("r-annotationdbi" ,r-annotationdbi) | |
4038 | ("r-dose" ,r-dose) | |
63c8323a RW |
4039 | ("r-downloader" ,r-downloader) |
4040 | ("r-dplyr" ,r-dplyr) | |
f8295ee6 | 4041 | ("r-enrichplot" ,r-enrichplot) |
f8295ee6 RW |
4042 | ("r-go-db" ,r-go-db) |
4043 | ("r-gosemsim" ,r-gosemsim) | |
4044 | ("r-magrittr" ,r-magrittr) | |
4045 | ("r-plyr" ,r-plyr) | |
4046 | ("r-qvalue" ,r-qvalue) | |
69f3b278 | 4047 | ("r-rlang" ,r-rlang) |
f8295ee6 RW |
4048 | ("r-rvcheck" ,r-rvcheck) |
4049 | ("r-tidyr" ,r-tidyr))) | |
63c8323a RW |
4050 | (native-inputs |
4051 | `(("r-knitr" ,r-knitr))) | |
f8295ee6 RW |
4052 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") |
4053 | (synopsis "Analysis and visualization of functional profiles for gene clusters") | |
4054 | (description | |
4055 | "This package implements methods to analyze and visualize functional | |
4056 | profiles (GO and KEGG) of gene and gene clusters.") | |
4057 | (license license:artistic2.0))) | |
ce77562a RW |
4058 | |
4059 | (define-public r-mlinterfaces | |
4060 | (package | |
4061 | (name "r-mlinterfaces") | |
4f82931d | 4062 | (version "1.70.0") |
ce77562a RW |
4063 | (source |
4064 | (origin | |
4065 | (method url-fetch) | |
4066 | (uri (bioconductor-uri "MLInterfaces" version)) | |
4067 | (sha256 | |
4068 | (base32 | |
4f82931d | 4069 | "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r")))) |
ce77562a RW |
4070 | (properties `((upstream-name . "MLInterfaces"))) |
4071 | (build-system r-build-system) | |
4072 | (propagated-inputs | |
4073 | `(("r-annotate" ,r-annotate) | |
4074 | ("r-biobase" ,r-biobase) | |
4075 | ("r-biocgenerics" ,r-biocgenerics) | |
4076 | ("r-cluster" ,r-cluster) | |
4077 | ("r-fpc" ,r-fpc) | |
4078 | ("r-gbm" ,r-gbm) | |
4079 | ("r-gdata" ,r-gdata) | |
4080 | ("r-genefilter" ,r-genefilter) | |
4081 | ("r-ggvis" ,r-ggvis) | |
4082 | ("r-hwriter" ,r-hwriter) | |
4083 | ("r-mass" ,r-mass) | |
4084 | ("r-mlbench" ,r-mlbench) | |
4085 | ("r-pls" ,r-pls) | |
4086 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
500f7df8 | 4087 | ("r-rcpp" ,r-rcpp) |
ce77562a RW |
4088 | ("r-rpart" ,r-rpart) |
4089 | ("r-sfsmisc" ,r-sfsmisc) | |
4090 | ("r-shiny" ,r-shiny) | |
4091 | ("r-threejs" ,r-threejs))) | |
4092 | (home-page "https://bioconductor.org/packages/MLInterfaces/") | |
4093 | (synopsis "Interfaces to R machine learning procedures") | |
4094 | (description | |
4095 | "This package provides uniform interfaces to machine learning code for | |
4096 | data in R and Bioconductor containers.") | |
4097 | ;; Any version of the LGPL. | |
4098 | (license license:lgpl2.1+))) | |
a793e88c RW |
4099 | |
4100 | (define-public r-annaffy | |
4101 | (package | |
4102 | (name "r-annaffy") | |
aca4ebe4 | 4103 | (version "1.62.0") |
a793e88c RW |
4104 | (source |
4105 | (origin | |
4106 | (method url-fetch) | |
4107 | (uri (bioconductor-uri "annaffy" version)) | |
4108 | (sha256 | |
4109 | (base32 | |
aca4ebe4 | 4110 | "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i")))) |
a793e88c RW |
4111 | (build-system r-build-system) |
4112 | (arguments | |
4113 | `(#:phases | |
4114 | (modify-phases %standard-phases | |
4115 | (add-after 'unpack 'remove-reference-to-non-free-data | |
4116 | (lambda _ | |
4117 | (substitute* "DESCRIPTION" | |
4118 | ((", KEGG.db") "")) | |
4119 | #t))))) | |
4120 | (propagated-inputs | |
4121 | `(("r-annotationdbi" ,r-annotationdbi) | |
4122 | ("r-biobase" ,r-biobase) | |
4123 | ("r-dbi" ,r-dbi) | |
4124 | ("r-go-db" ,r-go-db))) | |
4125 | (home-page "https://bioconductor.org/packages/annaffy/") | |
4126 | (synopsis "Annotation tools for Affymetrix biological metadata") | |
4127 | (description | |
4128 | "This package provides functions for handling data from Bioconductor | |
4129 | Affymetrix annotation data packages. It produces compact HTML and text | |
4130 | reports including experimental data and URL links to many online databases. | |
4131 | It allows searching of biological metadata using various criteria.") | |
4132 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of | |
4133 | ;; the LGPL 2.1 is included. | |
4134 | (license license:lgpl2.1+))) | |
0ec0a5ec RW |
4135 | |
4136 | (define-public r-a4core | |
4137 | (package | |
4138 | (name "r-a4core") | |
c47a8cd9 | 4139 | (version "1.38.0") |
0ec0a5ec RW |
4140 | (source |
4141 | (origin | |
4142 | (method url-fetch) | |
4143 | (uri (bioconductor-uri "a4Core" version)) | |
4144 | (sha256 | |
4145 | (base32 | |
c47a8cd9 | 4146 | "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2")))) |
0ec0a5ec RW |
4147 | (properties `((upstream-name . "a4Core"))) |
4148 | (build-system r-build-system) | |
4149 | (propagated-inputs | |
4150 | `(("r-biobase" ,r-biobase) | |
4151 | ("r-glmnet" ,r-glmnet))) | |
c47a8cd9 | 4152 | (native-inputs |
4153 | `(("r-knitr" ,r-knitr))) | |
0ec0a5ec RW |
4154 | (home-page "https://bioconductor.org/packages/a4Core") |
4155 | (synopsis "Automated Affymetrix array analysis core package") | |
4156 | (description | |
4157 | "This is the core package for the automated analysis of Affymetrix | |
4158 | arrays.") | |
4159 | (license license:gpl3))) | |
9ae37581 RW |
4160 | |
4161 | (define-public r-a4classif | |
4162 | (package | |
4163 | (name "r-a4classif") | |
fa51705f | 4164 | (version "1.38.0") |
9ae37581 RW |
4165 | (source |
4166 | (origin | |
4167 | (method url-fetch) | |
4168 | (uri (bioconductor-uri "a4Classif" version)) | |
4169 | (sha256 | |
4170 | (base32 | |
fa51705f | 4171 | "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz")))) |
9ae37581 RW |
4172 | (properties `((upstream-name . "a4Classif"))) |
4173 | (build-system r-build-system) | |
4174 | (propagated-inputs | |
4175 | `(("r-a4core" ,r-a4core) | |
4176 | ("r-a4preproc" ,r-a4preproc) | |
fa51705f | 4177 | ("r-biobase" ,r-biobase) |
9ae37581 | 4178 | ("r-glmnet" ,r-glmnet) |
9ae37581 RW |
4179 | ("r-pamr" ,r-pamr) |
4180 | ("r-rocr" ,r-rocr) | |
4181 | ("r-varselrf" ,r-varselrf))) | |
fa51705f | 4182 | (native-inputs |
4183 | `(("r-knitr" ,r-knitr))) | |
9ae37581 RW |
4184 | (home-page "https://bioconductor.org/packages/a4Classif/") |
4185 | (synopsis "Automated Affymetrix array analysis classification package") | |
4186 | (description | |
4187 | "This is the classification package for the automated analysis of | |
4188 | Affymetrix arrays.") | |
4189 | (license license:gpl3))) | |
b8d13e2c RW |
4190 | |
4191 | (define-public r-a4preproc | |
4192 | (package | |
4193 | (name "r-a4preproc") | |
85155e2e | 4194 | (version "1.38.0") |
b8d13e2c RW |
4195 | (source |
4196 | (origin | |
4197 | (method url-fetch) | |
4198 | (uri (bioconductor-uri "a4Preproc" version)) | |
4199 | (sha256 | |
4200 | (base32 | |
85155e2e | 4201 | "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i")))) |
b8d13e2c RW |
4202 | (properties `((upstream-name . "a4Preproc"))) |
4203 | (build-system r-build-system) | |
4204 | (propagated-inputs | |
85155e2e | 4205 | `(("r-biobase" ,r-biobase) |
4206 | ("r-biocgenerics" ,r-biocgenerics))) | |
4207 | (native-inputs | |
4208 | `(("r-knitr" ,r-knitr))) | |
b8d13e2c RW |
4209 | (home-page "https://bioconductor.org/packages/a4Preproc/") |
4210 | (synopsis "Automated Affymetrix array analysis preprocessing package") | |
4211 | (description | |
4212 | "This is a package for the automated analysis of Affymetrix arrays. It | |
4213 | is used for preprocessing the arrays.") | |
4214 | (license license:gpl3))) | |
8e15f861 RW |
4215 | |
4216 | (define-public r-a4reporting | |
4217 | (package | |
4218 | (name "r-a4reporting") | |
2fb8298c | 4219 | (version "1.38.0") |
8e15f861 RW |
4220 | (source |
4221 | (origin | |
4222 | (method url-fetch) | |
4223 | (uri (bioconductor-uri "a4Reporting" version)) | |
4224 | (sha256 | |
4225 | (base32 | |
2fb8298c | 4226 | "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy")))) |
8e15f861 RW |
4227 | (properties `((upstream-name . "a4Reporting"))) |
4228 | (build-system r-build-system) | |
4229 | (propagated-inputs | |
2fb8298c | 4230 | `(("r-xtable" ,r-xtable))) |
4231 | (native-inputs | |
4232 | `(("r-knitr" ,r-knitr))) | |
8e15f861 RW |
4233 | (home-page "https://bioconductor.org/packages/a4Reporting/") |
4234 | (synopsis "Automated Affymetrix array analysis reporting package") | |
4235 | (description | |
4236 | "This is a package for the automated analysis of Affymetrix arrays. It | |
4237 | provides reporting features.") | |
4238 | (license license:gpl3))) | |
dbfe3375 RW |
4239 | |
4240 | (define-public r-a4base | |
4241 | (package | |
4242 | (name "r-a4base") | |
564d4279 | 4243 | (version "1.38.0") |
dbfe3375 RW |
4244 | (source |
4245 | (origin | |
4246 | (method url-fetch) | |
4247 | (uri (bioconductor-uri "a4Base" version)) | |
4248 | (sha256 | |
4249 | (base32 | |
564d4279 | 4250 | "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp")))) |
dbfe3375 RW |
4251 | (properties `((upstream-name . "a4Base"))) |
4252 | (build-system r-build-system) | |
4253 | (propagated-inputs | |
4254 | `(("r-a4core" ,r-a4core) | |
4255 | ("r-a4preproc" ,r-a4preproc) | |
4256 | ("r-annaffy" ,r-annaffy) | |
dbfe3375 RW |
4257 | ("r-biobase" ,r-biobase) |
4258 | ("r-genefilter" ,r-genefilter) | |
4259 | ("r-glmnet" ,r-glmnet) | |
4260 | ("r-gplots" ,r-gplots) | |
4261 | ("r-limma" ,r-limma) | |
4262 | ("r-mpm" ,r-mpm) | |
4263 | ("r-multtest" ,r-multtest))) | |
4264 | (home-page "https://bioconductor.org/packages/a4Base/") | |
4265 | (synopsis "Automated Affymetrix array analysis base package") | |
4266 | (description | |
4267 | "This package provides basic features for the automated analysis of | |
4268 | Affymetrix arrays.") | |
4269 | (license license:gpl3))) | |
84ad024e RW |
4270 | |
4271 | (define-public r-a4 | |
4272 | (package | |
4273 | (name "r-a4") | |
68efaafe | 4274 | (version "1.38.0") |
84ad024e RW |
4275 | (source |
4276 | (origin | |
4277 | (method url-fetch) | |
4278 | (uri (bioconductor-uri "a4" version)) | |
4279 | (sha256 | |
4280 | (base32 | |
68efaafe | 4281 | "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79")))) |
84ad024e RW |
4282 | (build-system r-build-system) |
4283 | (propagated-inputs | |
4284 | `(("r-a4base" ,r-a4base) | |
4285 | ("r-a4classif" ,r-a4classif) | |
4286 | ("r-a4core" ,r-a4core) | |
4287 | ("r-a4preproc" ,r-a4preproc) | |
4288 | ("r-a4reporting" ,r-a4reporting))) | |
4289 | (home-page "https://bioconductor.org/packages/a4/") | |
4290 | (synopsis "Automated Affymetrix array analysis umbrella package") | |
4291 | (description | |
4292 | "This package provides a software suite for the automated analysis of | |
4293 | Affymetrix arrays.") | |
4294 | (license license:gpl3))) | |
59d331f1 RW |
4295 | |
4296 | (define-public r-abseqr | |
4297 | (package | |
4298 | (name "r-abseqr") | |
8816139e | 4299 | (version "1.8.0") |
59d331f1 RW |
4300 | (source |
4301 | (origin | |
4302 | (method url-fetch) | |
4303 | (uri (bioconductor-uri "abseqR" version)) | |
4304 | (sha256 | |
4305 | (base32 | |
8816139e | 4306 | "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f")))) |
59d331f1 RW |
4307 | (properties `((upstream-name . "abseqR"))) |
4308 | (build-system r-build-system) | |
4309 | (inputs | |
8816139e | 4310 | `(("pandoc" ,pandoc))) |
59d331f1 RW |
4311 | (propagated-inputs |
4312 | `(("r-biocparallel" ,r-biocparallel) | |
4313 | ("r-biocstyle" ,r-biocstyle) | |
4314 | ("r-circlize" ,r-circlize) | |
4315 | ("r-flexdashboard" ,r-flexdashboard) | |
4316 | ("r-ggcorrplot" ,r-ggcorrplot) | |
4317 | ("r-ggdendro" ,r-ggdendro) | |
4318 | ("r-ggplot2" ,r-ggplot2) | |
4319 | ("r-gridextra" ,r-gridextra) | |
4320 | ("r-knitr" ,r-knitr) | |
4321 | ("r-plotly" ,r-plotly) | |
4322 | ("r-plyr" ,r-plyr) | |
4323 | ("r-png" ,r-png) | |
4324 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4325 | ("r-reshape2" ,r-reshape2) | |
4326 | ("r-rmarkdown" ,r-rmarkdown) | |
4327 | ("r-stringr" ,r-stringr) | |
4328 | ("r-vegan" ,r-vegan) | |
4329 | ("r-venndiagram" ,r-venndiagram))) | |
35bcfaef RW |
4330 | (native-inputs |
4331 | `(("r-knitr" ,r-knitr))) | |
59d331f1 RW |
4332 | (home-page "https://github.com/malhamdoosh/abseqR") |
4333 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") | |
4334 | (description | |
4335 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of | |
4336 | sequencing datasets generated from antibody libraries and abseqR is one of its | |
4337 | packages. AbseqR empowers the users of abseqPy with plotting and reporting | |
4338 | capabilities and allows them to generate interactive HTML reports for the | |
4339 | convenience of viewing and sharing with other researchers. Additionally, | |
4340 | abseqR extends abseqPy to compare multiple repertoire analyses and perform | |
4341 | further downstream analysis on its output.") | |
4342 | (license license:gpl3))) | |
41aab7d1 RW |
4343 | |
4344 | (define-public r-bacon | |
4345 | (package | |
4346 | (name "r-bacon") | |
d5dcf1bb | 4347 | (version "1.18.0") |
41aab7d1 RW |
4348 | (source |
4349 | (origin | |
4350 | (method url-fetch) | |
4351 | (uri (bioconductor-uri "bacon" version)) | |
4352 | (sha256 | |
4353 | (base32 | |
d5dcf1bb | 4354 | "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47")))) |
41aab7d1 RW |
4355 | (build-system r-build-system) |
4356 | (propagated-inputs | |
4357 | `(("r-biocparallel" ,r-biocparallel) | |
4358 | ("r-ellipse" ,r-ellipse) | |
4359 | ("r-ggplot2" ,r-ggplot2))) | |
506cbeab RW |
4360 | (native-inputs |
4361 | `(("r-knitr" ,r-knitr))) | |
41aab7d1 RW |
4362 | (home-page "https://bioconductor.org/packages/bacon/") |
4363 | (synopsis "Controlling bias and inflation in association studies") | |
4364 | (description | |
4365 | "Bacon can be used to remove inflation and bias often observed in | |
4366 | epigenome- and transcriptome-wide association studies. To this end bacon | |
4367 | constructs an empirical null distribution using a Gibbs Sampling algorithm by | |
4368 | fitting a three-component normal mixture on z-scores.") | |
4369 | (license license:gpl2+))) | |
051e8e1a RW |
4370 | |
4371 | (define-public r-rgadem | |
4372 | (package | |
4373 | (name "r-rgadem") | |
41071edc | 4374 | (version "2.38.0") |
051e8e1a RW |
4375 | (source |
4376 | (origin | |
4377 | (method url-fetch) | |
4378 | (uri (bioconductor-uri "rGADEM" version)) | |
4379 | (sha256 | |
4380 | (base32 | |
41071edc | 4381 | "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw")))) |
051e8e1a RW |
4382 | (properties `((upstream-name . "rGADEM"))) |
4383 | (build-system r-build-system) | |
4384 | (propagated-inputs | |
4385 | `(("r-biostrings" ,r-biostrings) | |
4386 | ("r-bsgenome" ,r-bsgenome) | |
07189489 | 4387 | ("r-genomicranges" ,r-genomicranges) |
051e8e1a RW |
4388 | ("r-iranges" ,r-iranges) |
4389 | ("r-seqlogo" ,r-seqlogo))) | |
4390 | (home-page "https://bioconductor.org/packages/rGADEM/") | |
4391 | (synopsis "De novo sequence motif discovery") | |
4392 | (description | |
4393 | "rGADEM is an efficient de novo motif discovery tool for large-scale | |
4394 | genomic sequence data.") | |
4395 | (license license:artistic2.0))) | |
229f97c3 RW |
4396 | |
4397 | (define-public r-motiv | |
4398 | (package | |
4399 | (name "r-motiv") | |
352cfa34 | 4400 | (version "1.43.0") |
229f97c3 RW |
4401 | (source |
4402 | (origin | |
4403 | (method url-fetch) | |
4404 | (uri (bioconductor-uri "MotIV" version)) | |
4405 | (sha256 | |
4406 | (base32 | |
352cfa34 | 4407 | "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6")))) |
229f97c3 RW |
4408 | (properties `((upstream-name . "MotIV"))) |
4409 | (build-system r-build-system) | |
4410 | (inputs | |
4411 | `(("gsl" ,gsl))) | |
4412 | (propagated-inputs | |
4413 | `(("r-biocgenerics" ,r-biocgenerics) | |
4414 | ("r-biostrings" ,r-biostrings) | |
35a1b3ec | 4415 | ("r-genomicranges" ,r-genomicranges) |
229f97c3 RW |
4416 | ("r-iranges" ,r-iranges) |
4417 | ("r-lattice" ,r-lattice) | |
4418 | ("r-rgadem" ,r-rgadem) | |
4419 | ("r-s4vectors" ,r-s4vectors))) | |
4420 | (home-page "https://bioconductor.org/packages/MotIV/") | |
4421 | (synopsis "Motif identification and validation") | |
4422 | (description | |
4423 | "This package is used for the identification and validation of sequence | |
4424 | motifs. It makes use of STAMP for comparing a set of motifs to a given | |
4425 | database (e.g. JASPAR). It can also be used to visualize motifs, motif | |
4426 | distributions, modules and filter motifs.") | |
4427 | (license license:gpl2))) | |
2a72ef56 | 4428 | |
3699bcf5 RJ |
4429 | (define-public r-motifdb |
4430 | (package | |
4431 | (name "r-motifdb") | |
a2bae167 | 4432 | (version "1.32.0") |
3699bcf5 RJ |
4433 | (source (origin |
4434 | (method url-fetch) | |
4435 | (uri (bioconductor-uri "MotifDb" version)) | |
4436 | (sha256 | |
a2bae167 | 4437 | (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5")))) |
3699bcf5 RJ |
4438 | (properties `((upstream-name . "MotifDb"))) |
4439 | (build-system r-build-system) | |
4440 | (propagated-inputs | |
4441 | `(("r-biocgenerics" ,r-biocgenerics) | |
4442 | ("r-biostrings" ,r-biostrings) | |
da6a75fe | 4443 | ("r-genomicranges" ,r-genomicranges) |
3699bcf5 RJ |
4444 | ("r-iranges" ,r-iranges) |
4445 | ("r-rtracklayer" ,r-rtracklayer) | |
4446 | ("r-s4vectors" ,r-s4vectors) | |
4447 | ("r-splitstackshape" ,r-splitstackshape))) | |
da6a75fe RW |
4448 | (native-inputs |
4449 | `(("r-knitr" ,r-knitr))) | |
3699bcf5 RJ |
4450 | (home-page "https://www.bioconductor.org/packages/MotifDb/") |
4451 | (synopsis "Annotated collection of protein-DNA binding sequence motifs") | |
4452 | (description "This package provides more than 2000 annotated position | |
4453 | frequency matrices from nine public sources, for multiple organisms.") | |
4454 | (license license:artistic2.0))) | |
4455 | ||
886125d7 RJ |
4456 | (define-public r-motifbreakr |
4457 | (package | |
4458 | (name "r-motifbreakr") | |
301e549c | 4459 | (version "2.4.0") |
886125d7 RJ |
4460 | (source (origin |
4461 | (method url-fetch) | |
4462 | (uri (bioconductor-uri "motifbreakR" version)) | |
4463 | (sha256 | |
301e549c | 4464 | (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7")))) |
886125d7 RJ |
4465 | (properties `((upstream-name . "motifbreakR"))) |
4466 | (build-system r-build-system) | |
4467 | (propagated-inputs | |
e65783e0 RW |
4468 | `(("r-biocgenerics" ,r-biocgenerics) |
4469 | ("r-biocparallel" ,r-biocparallel) | |
886125d7 RJ |
4470 | ("r-biostrings" ,r-biostrings) |
4471 | ("r-bsgenome" ,r-bsgenome) | |
e65783e0 RW |
4472 | ("r-genomeinfodb" ,r-genomeinfodb) |
4473 | ("r-genomicranges" ,r-genomicranges) | |
4474 | ("r-grimport" ,r-grimport) | |
886125d7 | 4475 | ("r-gviz" ,r-gviz) |
e65783e0 | 4476 | ("r-iranges" ,r-iranges) |
886125d7 | 4477 | ("r-matrixstats" ,r-matrixstats) |
e65783e0 RW |
4478 | ("r-motifdb" ,r-motifdb) |
4479 | ("r-motifstack" ,r-motifstack) | |
4480 | ("r-rtracklayer" ,r-rtracklayer) | |
4481 | ("r-s4vectors" ,r-s4vectors) | |
4482 | ("r-stringr" ,r-stringr) | |
4483 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
886125d7 | 4484 | ("r-tfmpvalue" ,r-tfmpvalue) |
e65783e0 RW |
4485 | ("r-variantannotation" ,r-variantannotation))) |
4486 | (native-inputs | |
4487 | `(("r-knitr" ,r-knitr))) | |
886125d7 RJ |
4488 | (home-page "https://www.bioconductor.org/packages/motifbreakR/") |
4489 | (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") | |
4490 | (description "This package allows biologists to judge in the first place | |
4491 | whether the sequence surrounding the polymorphism is a good match, and in | |
4492 | the second place how much information is gained or lost in one allele of | |
4493 | the polymorphism relative to another. This package gives a choice of | |
4494 | algorithms for interrogation of genomes with motifs from public sources: | |
4495 | @enumerate | |
4496 | @item a weighted-sum probability matrix; | |
4497 | @item log-probabilities; | |
4498 | @item weighted by relative entropy. | |
4499 | @end enumerate | |
4500 | ||
4501 | This package can predict effects for novel or previously described variants in | |
4502 | public databases, making it suitable for tasks beyond the scope of its original | |
4503 | design. Lastly, it can be used to interrogate any genome curated within | |
4504 | Bioconductor.") | |
4505 | (license license:gpl2+))) | |
4506 | ||
2a72ef56 RW |
4507 | (define-public r-motifstack |
4508 | (package | |
4509 | (name "r-motifstack") | |
4b4cd2b8 | 4510 | (version "1.34.0") |
2a72ef56 RW |
4511 | (source |
4512 | (origin | |
4513 | (method url-fetch) | |
4514 | (uri (bioconductor-uri "motifStack" version)) | |
4515 | (sha256 | |
4516 | (base32 | |
4b4cd2b8 | 4517 | "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb")))) |
2a72ef56 RW |
4518 | (properties `((upstream-name . "motifStack"))) |
4519 | (build-system r-build-system) | |
4520 | (propagated-inputs | |
4521 | `(("r-ade4" ,r-ade4) | |
4522 | ("r-biostrings" ,r-biostrings) | |
dda936ca | 4523 | ("r-ggplot2" ,r-ggplot2) |
2a72ef56 | 4524 | ("r-htmlwidgets" ,r-htmlwidgets) |
2a72ef56 | 4525 | ("r-xml" ,r-xml))) |
e6fbaf0c RW |
4526 | (native-inputs |
4527 | `(("r-knitr" ,r-knitr))) | |
2a72ef56 RW |
4528 | (home-page "https://bioconductor.org/packages/motifStack/") |
4529 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") | |
4530 | (description | |
4531 | "The motifStack package is designed for graphic representation of | |
4532 | multiple motifs with different similarity scores. It works with both DNA/RNA | |
4533 | sequence motifs and amino acid sequence motifs. In addition, it provides the | |
4534 | flexibility for users to customize the graphic parameters such as the font | |
4535 | type and symbol colors.") | |
4536 | (license license:gpl2+))) | |
e5bff307 RW |
4537 | |
4538 | (define-public r-genomicscores | |
4539 | (package | |
4540 | (name "r-genomicscores") | |
39280618 | 4541 | (version "2.2.0") |
e5bff307 RW |
4542 | (source |
4543 | (origin | |
4544 | (method url-fetch) | |
4545 | (uri (bioconductor-uri "GenomicScores" version)) | |
4546 | (sha256 | |
4547 | (base32 | |
39280618 | 4548 | "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr")))) |
e5bff307 RW |
4549 | (properties `((upstream-name . "GenomicScores"))) |
4550 | (build-system r-build-system) | |
4551 | (propagated-inputs | |
4552 | `(("r-annotationhub" ,r-annotationhub) | |
4553 | ("r-biobase" ,r-biobase) | |
39280618 | 4554 | ("r-biocfilecache" ,r-biocfilecache) |
e5bff307 | 4555 | ("r-biocgenerics" ,r-biocgenerics) |
39280618 | 4556 | ("r-biocmanager" ,r-biocmanager) |
e5bff307 | 4557 | ("r-biostrings" ,r-biostrings) |
785c7596 | 4558 | ("r-delayedarray" ,r-delayedarray) |
e5bff307 RW |
4559 | ("r-genomeinfodb" ,r-genomeinfodb) |
4560 | ("r-genomicranges" ,r-genomicranges) | |
785c7596 | 4561 | ("r-hdf5array" ,r-hdf5array) |
e5bff307 | 4562 | ("r-iranges" ,r-iranges) |
785c7596 | 4563 | ("r-rhdf5" ,r-rhdf5) |
e5bff307 RW |
4564 | ("r-s4vectors" ,r-s4vectors) |
4565 | ("r-xml" ,r-xml))) | |
785c7596 RW |
4566 | (native-inputs |
4567 | `(("r-knitr" ,r-knitr))) | |
e5bff307 RW |
4568 | (home-page "https://github.com/rcastelo/GenomicScores/") |
4569 | (synopsis "Work with genome-wide position-specific scores") | |
4570 | (description | |
4571 | "This package provides infrastructure to store and access genome-wide | |
4572 | position-specific scores within R and Bioconductor.") | |
4573 | (license license:artistic2.0))) | |
32e0f906 RW |
4574 | |
4575 | (define-public r-atacseqqc | |
4576 | (package | |
4577 | (name "r-atacseqqc") | |
2ba61c67 | 4578 | (version "1.14.4") |
32e0f906 RW |
4579 | (source |
4580 | (origin | |
4581 | (method url-fetch) | |
4582 | (uri (bioconductor-uri "ATACseqQC" version)) | |
4583 | (sha256 | |
4584 | (base32 | |
2ba61c67 | 4585 | "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9")))) |
32e0f906 RW |
4586 | (properties `((upstream-name . "ATACseqQC"))) |
4587 | (build-system r-build-system) | |
4588 | (propagated-inputs | |
4589 | `(("r-biocgenerics" ,r-biocgenerics) | |
4590 | ("r-biostrings" ,r-biostrings) | |
4591 | ("r-bsgenome" ,r-bsgenome) | |
4592 | ("r-chippeakanno" ,r-chippeakanno) | |
bcc233c1 | 4593 | ("r-edger" ,r-edger) |
32e0f906 RW |
4594 | ("r-genomeinfodb" ,r-genomeinfodb) |
4595 | ("r-genomicalignments" ,r-genomicalignments) | |
4596 | ("r-genomicranges" ,r-genomicranges) | |
4597 | ("r-genomicscores" ,r-genomicscores) | |
4598 | ("r-iranges" ,r-iranges) | |
4599 | ("r-kernsmooth" ,r-kernsmooth) | |
4600 | ("r-limma" ,r-limma) | |
4601 | ("r-motifstack" ,r-motifstack) | |
4602 | ("r-preseqr" ,r-preseqr) | |
4603 | ("r-randomforest" ,r-randomforest) | |
4604 | ("r-rsamtools" ,r-rsamtools) | |
4605 | ("r-rtracklayer" ,r-rtracklayer) | |
4606 | ("r-s4vectors" ,r-s4vectors))) | |
dc30cc03 RW |
4607 | (native-inputs |
4608 | `(("r-knitr" ,r-knitr))) | |
32e0f906 RW |
4609 | (home-page "https://bioconductor.org/packages/ATACseqQC/") |
4610 | (synopsis "ATAC-seq quality control") | |
4611 | (description | |
4612 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using | |
4613 | sequencing, is a rapid and sensitive method for chromatin accessibility | |
4614 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq | |
4615 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly | |
4616 | assess whether their ATAC-seq experiment is successful. It includes | |
4617 | diagnostic plots of fragment size distribution, proportion of mitochondria | |
4618 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor | |
4619 | footprints.") | |
4620 | (license license:gpl2+))) | |
3972cfce RW |
4621 | |
4622 | (define-public r-gofuncr | |
4623 | (package | |
4624 | (name "r-gofuncr") | |
c3b69d63 | 4625 | (version "1.10.0") |
3972cfce RW |
4626 | (source |
4627 | (origin | |
4628 | (method url-fetch) | |
4629 | (uri (bioconductor-uri "GOfuncR" version)) | |
4630 | (sha256 | |
4631 | (base32 | |
c3b69d63 | 4632 | "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq")))) |
3972cfce RW |
4633 | (properties `((upstream-name . "GOfuncR"))) |
4634 | (build-system r-build-system) | |
4635 | (propagated-inputs | |
4636 | `(("r-annotationdbi" ,r-annotationdbi) | |
4637 | ("r-genomicranges" ,r-genomicranges) | |
4638 | ("r-gtools" ,r-gtools) | |
4639 | ("r-iranges" ,r-iranges) | |
4640 | ("r-mapplots" ,r-mapplots) | |
4641 | ("r-rcpp" ,r-rcpp) | |
4642 | ("r-vioplot" ,r-vioplot))) | |
028fd6f7 RW |
4643 | (native-inputs |
4644 | `(("r-knitr" ,r-knitr))) | |
3972cfce RW |
4645 | (home-page "https://bioconductor.org/packages/GOfuncR/") |
4646 | (synopsis "Gene ontology enrichment using FUNC") | |
4647 | (description | |
4648 | "GOfuncR performs a gene ontology enrichment analysis based on the | |
4649 | ontology enrichment software FUNC. GO-annotations are obtained from | |
4650 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is | |
4651 | included in the package and updated regularly. GOfuncR provides the standard | |
4652 | candidate vs background enrichment analysis using the hypergeometric test, as | |
4653 | well as three additional tests: | |
4654 | ||
4655 | @enumerate | |
4656 | @item the Wilcoxon rank-sum test that is used when genes are ranked, | |
4657 | @item a binomial test that is used when genes are associated with two counts, | |
4658 | and | |
4659 | @item a Chi-square or Fisher's exact test that is used in cases when genes are | |
4660 | associated with four counts. | |
4661 | @end enumerate | |
4662 | ||
4663 | To correct for multiple testing and interdependency of the tests, family-wise | |
4664 | error rates are computed based on random permutations of the gene-associated | |
4665 | variables. GOfuncR also provides tools for exploring the ontology graph and | |
4666 | the annotations, and options to take gene-length or spatial clustering of | |
4667 | genes into account. It is also possible to provide custom gene coordinates, | |
4668 | annotations and ontologies.") | |
4669 | (license license:gpl2+))) | |
9bf4bb19 RW |
4670 | |
4671 | (define-public r-abaenrichment | |
4672 | (package | |
4673 | (name "r-abaenrichment") | |
8a7f7112 | 4674 | (version "1.20.0") |
9bf4bb19 RW |
4675 | (source |
4676 | (origin | |
4677 | (method url-fetch) | |
4678 | (uri (bioconductor-uri "ABAEnrichment" version)) | |
4679 | (sha256 | |
4680 | (base32 | |
8a7f7112 | 4681 | "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c")))) |
9bf4bb19 RW |
4682 | (properties `((upstream-name . "ABAEnrichment"))) |
4683 | (build-system r-build-system) | |
4684 | (propagated-inputs | |
4685 | `(("r-abadata" ,r-abadata) | |
4686 | ("r-data-table" ,r-data-table) | |
4687 | ("r-gofuncr" ,r-gofuncr) | |
4688 | ("r-gplots" ,r-gplots) | |
4689 | ("r-gtools" ,r-gtools) | |
4690 | ("r-rcpp" ,r-rcpp))) | |
6a65ac15 RW |
4691 | (native-inputs |
4692 | `(("r-knitr" ,r-knitr))) | |
9bf4bb19 RW |
4693 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") |
4694 | (synopsis "Gene expression enrichment in human brain regions") | |
4695 | (description | |
4696 | "The package ABAEnrichment is designed to test for enrichment of user | |
4697 | defined candidate genes in the set of expressed genes in different human brain | |
4698 | regions. The core function @code{aba_enrich} integrates the expression of the | |
4699 | candidate gene set (averaged across donors) and the structural information of | |
4700 | the brain using an ontology, both provided by the Allen Brain Atlas project.") | |
4701 | (license license:gpl2+))) | |
0b91b7b9 RW |
4702 | |
4703 | (define-public r-annotationfuncs | |
4704 | (package | |
4705 | (name "r-annotationfuncs") | |
bc12a4b6 | 4706 | (version "1.40.0") |
0b91b7b9 RW |
4707 | (source |
4708 | (origin | |
4709 | (method url-fetch) | |
4710 | (uri (bioconductor-uri "AnnotationFuncs" version)) | |
4711 | (sha256 | |
4712 | (base32 | |
bc12a4b6 | 4713 | "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr")))) |
0b91b7b9 RW |
4714 | (properties |
4715 | `((upstream-name . "AnnotationFuncs"))) | |
4716 | (build-system r-build-system) | |
4717 | (propagated-inputs | |
4718 | `(("r-annotationdbi" ,r-annotationdbi) | |
4719 | ("r-dbi" ,r-dbi))) | |
4720 | (home-page "https://www.iysik.com/r/annotationfuncs") | |
4721 | (synopsis "Annotation translation functions") | |
4722 | (description | |
4723 | "This package provides functions for handling translating between | |
4724 | different identifieres using the Biocore Data Team data-packages (e.g. | |
4725 | @code{org.Bt.eg.db}).") | |
4726 | (license license:gpl2))) | |
adf7d813 RW |
4727 | |
4728 | (define-public r-annotationtools | |
4729 | (package | |
4730 | (name "r-annotationtools") | |
57791542 | 4731 | (version "1.64.0") |
adf7d813 RW |
4732 | (source |
4733 | (origin | |
4734 | (method url-fetch) | |
4735 | (uri (bioconductor-uri "annotationTools" version)) | |
4736 | (sha256 | |
4737 | (base32 | |
57791542 | 4738 | "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224")))) |
adf7d813 RW |
4739 | (properties |
4740 | `((upstream-name . "annotationTools"))) | |
4741 | (build-system r-build-system) | |
4742 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
4743 | (home-page "https://bioconductor.org/packages/annotationTools/") | |
4744 | (synopsis "Annotate microarrays and perform gene expression analyses") | |
4745 | (description | |
4746 | "This package provides functions to annotate microarrays, find orthologs, | |
4747 | and integrate heterogeneous gene expression profiles using annotation and | |
4748 | other molecular biology information available as flat file database (plain | |
4749 | text files).") | |
4750 | ;; Any version of the GPL. | |
4751 | (license (list license:gpl2+)))) | |
f31e10f8 RW |
4752 | |
4753 | (define-public r-allelicimbalance | |
4754 | (package | |
4755 | (name "r-allelicimbalance") | |
85c6636b | 4756 | (version "1.28.0") |
f31e10f8 RW |
4757 | (source |
4758 | (origin | |
4759 | (method url-fetch) | |
4760 | (uri (bioconductor-uri "AllelicImbalance" version)) | |
4761 | (sha256 | |
4762 | (base32 | |
85c6636b | 4763 | "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl")))) |
f31e10f8 RW |
4764 | (properties |
4765 | `((upstream-name . "AllelicImbalance"))) | |
4766 | (build-system r-build-system) | |
4767 | (propagated-inputs | |
4768 | `(("r-annotationdbi" ,r-annotationdbi) | |
4769 | ("r-biocgenerics" ,r-biocgenerics) | |
4770 | ("r-biostrings" ,r-biostrings) | |
4771 | ("r-bsgenome" ,r-bsgenome) | |
4772 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4773 | ("r-genomicalignments" ,r-genomicalignments) | |
4774 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4775 | ("r-genomicranges" ,r-genomicranges) | |
4776 | ("r-gridextra" ,r-gridextra) | |
4777 | ("r-gviz" ,r-gviz) | |
4778 | ("r-iranges" ,r-iranges) | |
4779 | ("r-lattice" ,r-lattice) | |
4780 | ("r-latticeextra" ,r-latticeextra) | |
4781 | ("r-nlme" ,r-nlme) | |
4782 | ("r-rsamtools" ,r-rsamtools) | |
4783 | ("r-s4vectors" ,r-s4vectors) | |
4784 | ("r-seqinr" ,r-seqinr) | |
4785 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
4786 | ("r-variantannotation" ,r-variantannotation))) | |
63149388 RW |
4787 | (native-inputs |
4788 | `(("r-knitr" ,r-knitr))) | |
f31e10f8 RW |
4789 | (home-page "https://github.com/pappewaio/AllelicImbalance") |
4790 | (synopsis "Investigate allele-specific expression") | |
4791 | (description | |
4792 | "This package provides a framework for allele-specific expression | |
4793 | investigation using RNA-seq data.") | |
4794 | (license license:gpl3))) | |
ffe7029b RW |
4795 | |
4796 | (define-public r-aucell | |
4797 | (package | |
4798 | (name "r-aucell") | |
ff8b9153 | 4799 | (version "1.12.0") |
ffe7029b RW |
4800 | (source |
4801 | (origin | |
4802 | (method url-fetch) | |
4803 | (uri (bioconductor-uri "AUCell" version)) | |
4804 | (sha256 | |
4805 | (base32 | |
ff8b9153 | 4806 | "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx")))) |
ffe7029b RW |
4807 | (properties `((upstream-name . "AUCell"))) |
4808 | (build-system r-build-system) | |
4809 | (propagated-inputs | |
3a35d274 RW |
4810 | `(("r-biocgenerics" ,r-biocgenerics) |
4811 | ("r-data-table" ,r-data-table) | |
ffe7029b RW |
4812 | ("r-gseabase" ,r-gseabase) |
4813 | ("r-mixtools" ,r-mixtools) | |
4814 | ("r-r-utils" ,r-r-utils) | |
3a35d274 | 4815 | ("r-s4vectors" ,r-s4vectors) |
ffe7029b RW |
4816 | ("r-shiny" ,r-shiny) |
4817 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
e059ab25 RW |
4818 | (native-inputs |
4819 | `(("r-knitr" ,r-knitr))) | |
ffe7029b RW |
4820 | (home-page "https://bioconductor.org/packages/AUCell/") |
4821 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") | |
4822 | (description | |
8c4bf6c2 | 4823 | "AUCell identifies cells with active gene sets (e.g. signatures, |
ffe7029b RW |
4824 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area |
4825 | Under the Curve} (AUC) to calculate whether a critical subset of the input | |
4826 | gene set is enriched within the expressed genes for each cell. The | |
4827 | distribution of AUC scores across all the cells allows exploring the relative | |
4828 | expression of the signature. Since the scoring method is ranking-based, | |
4829 | AUCell is independent of the gene expression units and the normalization | |
4830 | procedure. In addition, since the cells are evaluated individually, it can | |
4831 | easily be applied to bigger datasets, subsetting the expression matrix if | |
4832 | needed.") | |
4833 | (license license:gpl3))) | |
5cfa4bff RW |
4834 | |
4835 | (define-public r-ebimage | |
4836 | (package | |
4837 | (name "r-ebimage") | |
ba0bf98d | 4838 | (version "4.32.0") |
5cfa4bff RW |
4839 | (source |
4840 | (origin | |
4841 | (method url-fetch) | |
4842 | (uri (bioconductor-uri "EBImage" version)) | |
4843 | (sha256 | |
4844 | (base32 | |
ba0bf98d | 4845 | "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww")))) |
5cfa4bff RW |
4846 | (properties `((upstream-name . "EBImage"))) |
4847 | (build-system r-build-system) | |
4848 | (propagated-inputs | |
4849 | `(("r-abind" ,r-abind) | |
4850 | ("r-biocgenerics" ,r-biocgenerics) | |
4851 | ("r-fftwtools" ,r-fftwtools) | |
4852 | ("r-htmltools" ,r-htmltools) | |
4853 | ("r-htmlwidgets" ,r-htmlwidgets) | |
4854 | ("r-jpeg" ,r-jpeg) | |
4855 | ("r-locfit" ,r-locfit) | |
4856 | ("r-png" ,r-png) | |
4857 | ("r-rcurl" ,r-rcurl) | |
4858 | ("r-tiff" ,r-tiff))) | |
4859 | (native-inputs | |
4860 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
4861 | (home-page "https://github.com/aoles/EBImage") | |
4862 | (synopsis "Image processing and analysis toolbox for R") | |
4863 | (description | |
4864 | "EBImage provides general purpose functionality for image processing and | |
4865 | analysis. In the context of (high-throughput) microscopy-based cellular | |
4866 | assays, EBImage offers tools to segment cells and extract quantitative | |
4867 | cellular descriptors. This allows the automation of such tasks using the R | |
4868 | programming language and facilitates the use of other tools in the R | |
4869 | environment for signal processing, statistical modeling, machine learning and | |
4870 | visualization with image data.") | |
4871 | ;; Any version of the LGPL. | |
4872 | (license license:lgpl2.1+))) | |
51e98f7e RW |
4873 | |
4874 | (define-public r-yamss | |
4875 | (package | |
4876 | (name "r-yamss") | |
65ba4ba5 | 4877 | (version "1.16.0") |
51e98f7e RW |
4878 | (source |
4879 | (origin | |
4880 | (method url-fetch) | |
4881 | (uri (bioconductor-uri "yamss" version)) | |
4882 | (sha256 | |
4883 | (base32 | |
65ba4ba5 | 4884 | "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w")))) |
51e98f7e RW |
4885 | (build-system r-build-system) |
4886 | (propagated-inputs | |
4887 | `(("r-biocgenerics" ,r-biocgenerics) | |
4888 | ("r-data-table" ,r-data-table) | |
4889 | ("r-ebimage" ,r-ebimage) | |
4890 | ("r-iranges" ,r-iranges) | |
4891 | ("r-limma" ,r-limma) | |
4892 | ("r-matrix" ,r-matrix) | |
4893 | ("r-mzr" ,r-mzr) | |
4894 | ("r-s4vectors" ,r-s4vectors) | |
4895 | ("r-summarizedexperiment" | |
4896 | ,r-summarizedexperiment))) | |
6e397aad RW |
4897 | (native-inputs |
4898 | `(("r-knitr" ,r-knitr))) | |
51e98f7e RW |
4899 | (home-page "https://github.com/hansenlab/yamss") |
4900 | (synopsis "Tools for high-throughput metabolomics") | |
4901 | (description | |
4902 | "This package provides tools to analyze and visualize high-throughput | |
9b19734c | 4903 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
51e98f7e RW |
4904 | preprocess data in a way that enables reliable and powerful differential |
4905 | analysis.") | |
4906 | (license license:artistic2.0))) | |
398c4a93 RW |
4907 | |
4908 | (define-public r-gtrellis | |
4909 | (package | |
4910 | (name "r-gtrellis") | |
0836ef6b | 4911 | (version "1.22.0") |
398c4a93 RW |
4912 | (source |
4913 | (origin | |
4914 | (method url-fetch) | |
4915 | (uri (bioconductor-uri "gtrellis" version)) | |
4916 | (sha256 | |
4917 | (base32 | |
0836ef6b | 4918 | "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw")))) |
398c4a93 RW |
4919 | (build-system r-build-system) |
4920 | (propagated-inputs | |
4921 | `(("r-circlize" ,r-circlize) | |
4922 | ("r-genomicranges" ,r-genomicranges) | |
4923 | ("r-getoptlong" ,r-getoptlong) | |
4924 | ("r-iranges" ,r-iranges))) | |
a471def0 RW |
4925 | (native-inputs |
4926 | `(("r-knitr" ,r-knitr))) | |
398c4a93 RW |
4927 | (home-page "https://github.com/jokergoo/gtrellis") |
4928 | (synopsis "Genome level Trellis layout") | |
4929 | (description | |
4930 | "Genome level Trellis graph visualizes genomic data conditioned by | |
4931 | genomic categories (e.g. chromosomes). For each genomic category, multiple | |
4932 | dimensional data which are represented as tracks describe different features | |
4933 | from different aspects. This package provides high flexibility to arrange | |
4934 | genomic categories and to add self-defined graphics in the plot.") | |
4935 | (license license:expat))) | |
28098414 RW |
4936 | |
4937 | (define-public r-somaticsignatures | |
4938 | (package | |
4939 | (name "r-somaticsignatures") | |
36f3a19a | 4940 | (version "2.26.0") |
28098414 RW |
4941 | (source |
4942 | (origin | |
4943 | (method url-fetch) | |
4944 | (uri (bioconductor-uri "SomaticSignatures" version)) | |
4945 | (sha256 | |
4946 | (base32 | |
36f3a19a | 4947 | "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801")))) |
28098414 RW |
4948 | (properties |
4949 | `((upstream-name . "SomaticSignatures"))) | |
4950 | (build-system r-build-system) | |
4951 | (propagated-inputs | |
4952 | `(("r-biobase" ,r-biobase) | |
4953 | ("r-biostrings" ,r-biostrings) | |
4954 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4955 | ("r-genomicranges" ,r-genomicranges) | |
4956 | ("r-ggbio" ,r-ggbio) | |
4957 | ("r-ggplot2" ,r-ggplot2) | |
4958 | ("r-iranges" ,r-iranges) | |
4959 | ("r-nmf" ,r-nmf) | |
4960 | ("r-pcamethods" ,r-pcamethods) | |
4961 | ("r-proxy" ,r-proxy) | |
4962 | ("r-reshape2" ,r-reshape2) | |
4963 | ("r-s4vectors" ,r-s4vectors) | |
4964 | ("r-variantannotation" ,r-variantannotation))) | |
63c14717 RW |
4965 | (native-inputs |
4966 | `(("r-knitr" ,r-knitr))) | |
28098414 RW |
4967 | (home-page "https://github.com/juliangehring/SomaticSignatures") |
4968 | (synopsis "Somatic signatures") | |
4969 | (description | |
4970 | "This package identifies mutational signatures of @dfn{single nucleotide | |
4971 | variants} (SNVs). It provides a infrastructure related to the methodology | |
4972 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix | |
4973 | decomposition algorithms.") | |
4974 | (license license:expat))) | |
303f2ed1 RW |
4975 | |
4976 | (define-public r-yapsa | |
4977 | (package | |
4978 | (name "r-yapsa") | |
d0db04fc | 4979 | (version "1.16.0") |
303f2ed1 RW |
4980 | (source |
4981 | (origin | |
4982 | (method url-fetch) | |
4983 | (uri (bioconductor-uri "YAPSA" version)) | |
4984 | (sha256 | |
4985 | (base32 | |
d0db04fc | 4986 | "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb")))) |
303f2ed1 RW |
4987 | (properties `((upstream-name . "YAPSA"))) |
4988 | (build-system r-build-system) | |
4989 | (propagated-inputs | |
8a5abc62 RW |
4990 | `(("r-biostrings" ,r-biostrings) |
4991 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
4992 | ("r-circlize" ,r-circlize) | |
303f2ed1 RW |
4993 | ("r-complexheatmap" ,r-complexheatmap) |
4994 | ("r-corrplot" ,r-corrplot) | |
4995 | ("r-dendextend" ,r-dendextend) | |
8a5abc62 RW |
4996 | ("r-doparallel" ,r-doparallel) |
4997 | ("r-dplyr" ,r-dplyr) | |
303f2ed1 RW |
4998 | ("r-genomeinfodb" ,r-genomeinfodb) |
4999 | ("r-genomicranges" ,r-genomicranges) | |
5000 | ("r-getoptlong" ,r-getoptlong) | |
8a5abc62 | 5001 | ("r-ggbeeswarm" ,r-ggbeeswarm) |
303f2ed1 RW |
5002 | ("r-ggplot2" ,r-ggplot2) |
5003 | ("r-gridextra" ,r-gridextra) | |
5004 | ("r-gtrellis" ,r-gtrellis) | |
5005 | ("r-keggrest" ,r-keggrest) | |
d0db04fc | 5006 | ("r-limsolve" ,r-limsolve) |
8a5abc62 | 5007 | ("r-magrittr" ,r-magrittr) |
303f2ed1 | 5008 | ("r-pmcmr" ,r-pmcmr) |
8a5abc62 | 5009 | ("r-pracma" ,r-pracma) |
303f2ed1 RW |
5010 | ("r-reshape2" ,r-reshape2) |
5011 | ("r-somaticsignatures" ,r-somaticsignatures) | |
5012 | ("r-variantannotation" ,r-variantannotation))) | |
8a5abc62 RW |
5013 | (native-inputs |
5014 | `(("r-knitr" ,r-knitr))) | |
303f2ed1 RW |
5015 | (home-page "https://bioconductor.org/packages/YAPSA/") |
5016 | (synopsis "Yet another package for signature analysis") | |
5017 | (description | |
5018 | "This package provides functions and routines useful in the analysis of | |
5019 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, | |
5020 | functions to perform a signature analysis with known signatures and a | |
5021 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are | |
5022 | provided.") | |
5023 | (license license:gpl3))) | |
e99380d6 RW |
5024 | |
5025 | (define-public r-gcrma | |
5026 | (package | |
5027 | (name "r-gcrma") | |
3d41f0c2 | 5028 | (version "2.62.0") |
e99380d6 RW |
5029 | (source |
5030 | (origin | |
5031 | (method url-fetch) | |
5032 | (uri (bioconductor-uri "gcrma" version)) | |
5033 | (sha256 | |
5034 | (base32 | |
3d41f0c2 | 5035 | "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00")))) |
e99380d6 RW |
5036 | (build-system r-build-system) |
5037 | (propagated-inputs | |
5038 | `(("r-affy" ,r-affy) | |
5039 | ("r-affyio" ,r-affyio) | |
5040 | ("r-biobase" ,r-biobase) | |
5041 | ("r-biocmanager" ,r-biocmanager) | |
5042 | ("r-biostrings" ,r-biostrings) | |
5043 | ("r-xvector" ,r-xvector))) | |
5044 | (home-page "https://bioconductor.org/packages/gcrma/") | |
5045 | (synopsis "Background adjustment using sequence information") | |
5046 | (description | |
5047 | "Gcrma adjusts for background intensities in Affymetrix array data which | |
5048 | include optical noise and @dfn{non-specific binding} (NSB). The main function | |
5049 | @code{gcrma} converts background adjusted probe intensities to expression | |
5050 | measures using the same normalization and summarization methods as a | |
5051 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information | |
5052 | to estimate probe affinity to NSB. The sequence information is summarized in | |
5053 | a more complex way than the simple GC content. Instead, the base types (A, T, | |
5054 | G or C) at each position along the probe determine the affinity of each probe. | |
5055 | The parameters of the position-specific base contributions to the probe | |
5056 | affinity is estimated in an NSB experiment in which only NSB but no | |
7230f6d5 | 5057 | gene-specific binding is expected.") |
e99380d6 RW |
5058 | ;; Any version of the LGPL |
5059 | (license license:lgpl2.1+))) | |
4675b3cf RW |
5060 | |
5061 | (define-public r-simpleaffy | |
5062 | (package | |
5063 | (name "r-simpleaffy") | |
48aaef23 | 5064 | (version "2.66.0") |
4675b3cf RW |
5065 | (source |
5066 | (origin | |
5067 | (method url-fetch) | |
5068 | (uri (bioconductor-uri "simpleaffy" version)) | |
5069 | (sha256 | |
5070 | (base32 | |
48aaef23 | 5071 | "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb")))) |
4675b3cf RW |
5072 | (build-system r-build-system) |
5073 | (propagated-inputs | |
5074 | `(("r-affy" ,r-affy) | |
5075 | ("r-biobase" ,r-biobase) | |
5076 | ("r-biocgenerics" ,r-biocgenerics) | |
5077 | ("r-gcrma" ,r-gcrma) | |
5078 | ("r-genefilter" ,r-genefilter))) | |
5079 | (home-page "https://bioconductor.org/packages/simpleaffy/") | |
5080 | (synopsis "Very simple high level analysis of Affymetrix data") | |
5081 | (description | |
5082 | "This package provides high level functions for reading Affy @file{.CEL} | |
5083 | files, phenotypic data, and then computing simple things with it, such as | |
5084 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} | |
5085 | library. It also has some basic scatter plot functions and mechanisms for | |
5086 | generating high resolution journal figures.") | |
5087 | (license license:gpl2+))) | |
f562c90a RW |
5088 | |
5089 | (define-public r-yaqcaffy | |
5090 | (package | |
5091 | (name "r-yaqcaffy") | |
94dee0af | 5092 | (version "1.50.0") |
f562c90a RW |
5093 | (source |
5094 | (origin | |
5095 | (method url-fetch) | |
5096 | (uri (bioconductor-uri "yaqcaffy" version)) | |
5097 | (sha256 | |
5098 | (base32 | |
94dee0af | 5099 | "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96")))) |
f562c90a RW |
5100 | (build-system r-build-system) |
5101 | (propagated-inputs | |
5102 | `(("r-simpleaffy" ,r-simpleaffy))) | |
5103 | (home-page "https://bioconductor.org/packages/yaqcaffy/") | |
5104 | (synopsis "Affymetrix quality control and reproducibility analysis") | |
5105 | (description | |
5106 | "This is a package that can be used for quality control of Affymetrix | |
5107 | GeneChip expression data and reproducibility analysis of human whole genome | |
5108 | chips with the MAQC reference datasets.") | |
5109 | (license license:artistic2.0))) | |
59cf2629 RW |
5110 | |
5111 | (define-public r-quantro | |
5112 | (package | |
5113 | (name "r-quantro") | |
adf6edc7 | 5114 | (version "1.24.0") |
59cf2629 RW |
5115 | (source |
5116 | (origin | |
5117 | (method url-fetch) | |
5118 | (uri (bioconductor-uri "quantro" version)) | |
5119 | (sha256 | |
5120 | (base32 | |
adf6edc7 | 5121 | "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2")))) |
59cf2629 RW |
5122 | (build-system r-build-system) |
5123 | (propagated-inputs | |
5124 | `(("r-biobase" ,r-biobase) | |
5125 | ("r-doparallel" ,r-doparallel) | |
5126 | ("r-foreach" ,r-foreach) | |
5127 | ("r-ggplot2" ,r-ggplot2) | |
5128 | ("r-iterators" ,r-iterators) | |
5129 | ("r-minfi" ,r-minfi) | |
5130 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
70d90ae7 RW |
5131 | (native-inputs |
5132 | `(("r-knitr" ,r-knitr))) | |
59cf2629 RW |
5133 | (home-page "https://bioconductor.org/packages/quantro/") |
5134 | (synopsis "Test for when to use quantile normalization") | |
5135 | (description | |
5136 | "This package provides a data-driven test for the assumptions of quantile | |
5137 | normalization using raw data such as objects that inherit eSets (e.g. | |
5138 | ExpressionSet, MethylSet). Group level information about each sample (such as | |
5139 | Tumor / Normal status) must also be provided because the test assesses if | |
5140 | there are global differences in the distributions between the user-defined | |
5141 | groups.") | |
5142 | (license license:gpl3+))) | |
98a2af31 RW |
5143 | |
5144 | (define-public r-yarn | |
5145 | (package | |
5146 | (name "r-yarn") | |
8db36c1f | 5147 | (version "1.16.0") |
98a2af31 RW |
5148 | (source |
5149 | (origin | |
5150 | (method url-fetch) | |
5151 | (uri (bioconductor-uri "yarn" version)) | |
5152 | (sha256 | |
5153 | (base32 | |
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98a2af31 RW |
5155 | (build-system r-build-system) |
5156 | (propagated-inputs | |
5157 | `(("r-biobase" ,r-biobase) | |
5158 | ("r-biomart" ,r-biomart) | |
5159 | ("r-downloader" ,r-downloader) | |
5160 | ("r-edger" ,r-edger) | |
5161 | ("r-gplots" ,r-gplots) | |
5162 | ("r-limma" ,r-limma) | |
5163 | ("r-matrixstats" ,r-matrixstats) | |
5164 | ("r-preprocesscore" ,r-preprocesscore) | |
5165 | ("r-quantro" ,r-quantro) | |
5166 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5167 | ("r-readr" ,r-readr))) | |
a37a6ffb RW |
5168 | (native-inputs |
5169 | `(("r-knitr" ,r-knitr))) | |
98a2af31 RW |
5170 | (home-page "https://bioconductor.org/packages/yarn/") |
5171 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") | |
5172 | (description | |
5173 | "Expedite large RNA-Seq analyses using a combination of previously | |
5174 | developed tools. YARN is meant to make it easier for the user in performing | |
5175 | basic mis-annotation quality control, filtering, and condition-aware | |
5176 | normalization. YARN leverages many Bioconductor tools and statistical | |
5177 | techniques to account for the large heterogeneity and sparsity found in very | |
5178 | large RNA-seq experiments.") | |
5179 | (license license:artistic2.0))) | |
a6e1eb1a RW |
5180 | |
5181 | (define-public r-roar | |
5182 | (package | |
5183 | (name "r-roar") | |
72476ade | 5184 | (version "1.26.0") |
a6e1eb1a RW |
5185 | (source |
5186 | (origin | |
5187 | (method url-fetch) | |
5188 | (uri (bioconductor-uri "roar" version)) | |
5189 | (sha256 | |
5190 | (base32 | |
72476ade | 5191 | "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw")))) |
a6e1eb1a RW |
5192 | (build-system r-build-system) |
5193 | (propagated-inputs | |
5194 | `(("r-biocgenerics" ,r-biocgenerics) | |
5195 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5196 | ("r-genomicalignments" ,r-genomicalignments) | |
5197 | ("r-genomicranges" ,r-genomicranges) | |
5198 | ("r-iranges" ,r-iranges) | |
5199 | ("r-rtracklayer" ,r-rtracklayer) | |
5200 | ("r-s4vectors" ,r-s4vectors) | |
5201 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5202 | (home-page "https://github.com/vodkatad/roar/") | |
5203 | (synopsis "Identify differential APA usage from RNA-seq alignments") | |
5204 | (description | |
5205 | "This package provides tools for identifying preferential usage of APA | |
5206 | sites, comparing two biological conditions, starting from known alternative | |
5207 | sites and alignments obtained from standard RNA-seq experiments.") | |
5208 | (license license:gpl3))) | |
50d91770 RW |
5209 | |
5210 | (define-public r-xbseq | |
5211 | (package | |
5212 | (name "r-xbseq") | |
7f71341e | 5213 | (version "1.22.0") |
50d91770 RW |
5214 | (source |
5215 | (origin | |
5216 | (method url-fetch) | |
5217 | (uri (bioconductor-uri "XBSeq" version)) | |
5218 | (sha256 | |
5219 | (base32 | |
7f71341e | 5220 | "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz")))) |
50d91770 RW |
5221 | (properties `((upstream-name . "XBSeq"))) |
5222 | (build-system r-build-system) | |
5223 | (propagated-inputs | |
5224 | `(("r-biobase" ,r-biobase) | |
5225 | ("r-deseq2" ,r-deseq2) | |
5226 | ("r-dplyr" ,r-dplyr) | |
5227 | ("r-ggplot2" ,r-ggplot2) | |
5228 | ("r-locfit" ,r-locfit) | |
5229 | ("r-magrittr" ,r-magrittr) | |
5230 | ("r-matrixstats" ,r-matrixstats) | |
5231 | ("r-pracma" ,r-pracma) | |
5232 | ("r-roar" ,r-roar))) | |
bcd06bdb RW |
5233 | (native-inputs |
5234 | `(("r-knitr" ,r-knitr))) | |
50d91770 RW |
5235 | (home-page "https://github.com/Liuy12/XBSeq") |
5236 | (synopsis "Test for differential expression for RNA-seq data") | |
5237 | (description | |
5238 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential | |
5239 | expression} (DE), where a statistical model was established based on the | |
5240 | assumption that observed signals are the convolution of true expression | |
5241 | signals and sequencing noises. The mapped reads in non-exonic regions are | |
5242 | considered as sequencing noises, which follows a Poisson distribution. Given | |
5243 | measurable observed signal and background noise from RNA-seq data, true | |
5244 | expression signals, assuming governed by the negative binomial distribution, | |
5245 | can be delineated and thus the accurate detection of differential expressed | |
5246 | genes.") | |
5247 | (license license:gpl3+))) | |
c8310056 RW |
5248 | |
5249 | (define-public r-massspecwavelet | |
5250 | (package | |
5251 | (name "r-massspecwavelet") | |
f4e19e62 | 5252 | (version "1.56.0") |
c8310056 RW |
5253 | (source |
5254 | (origin | |
5255 | (method url-fetch) | |
5256 | (uri (bioconductor-uri "MassSpecWavelet" version)) | |
5257 | (sha256 | |
5258 | (base32 | |
f4e19e62 | 5259 | "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3")))) |
c8310056 RW |
5260 | (properties |
5261 | `((upstream-name . "MassSpecWavelet"))) | |
5262 | (build-system r-build-system) | |
5263 | (propagated-inputs | |
5264 | `(("r-waveslim" ,r-waveslim))) | |
5265 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") | |
5266 | (synopsis "Mass spectrum processing by wavelet-based algorithms") | |
5267 | (description | |
5268 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) | |
5269 | data mainly through the use of wavelet transforms. It supports peak detection | |
5270 | based on @dfn{Continuous Wavelet Transform} (CWT).") | |
5271 | (license license:lgpl2.0+))) | |
ec12e537 RW |
5272 | |
5273 | (define-public r-xcms | |
5274 | (package | |
5275 | (name "r-xcms") | |
a3af40ea | 5276 | (version "3.12.0") |
ec12e537 RW |
5277 | (source |
5278 | (origin | |
5279 | (method url-fetch) | |
5280 | (uri (bioconductor-uri "xcms" version)) | |
5281 | (sha256 | |
5282 | (base32 | |
a3af40ea | 5283 | "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv")))) |
ec12e537 RW |
5284 | (build-system r-build-system) |
5285 | (propagated-inputs | |
5286 | `(("r-biobase" ,r-biobase) | |
5287 | ("r-biocgenerics" ,r-biocgenerics) | |
5288 | ("r-biocparallel" ,r-biocparallel) | |
4fb52345 | 5289 | ("r-iranges" ,r-iranges) |
ec12e537 RW |
5290 | ("r-lattice" ,r-lattice) |
5291 | ("r-massspecwavelet" ,r-massspecwavelet) | |
a3af40ea | 5292 | ("r-mscoreutils" ,r-mscoreutils) |
ec12e537 | 5293 | ("r-msnbase" ,r-msnbase) |
ec12e537 RW |
5294 | ("r-mzr" ,r-mzr) |
5295 | ("r-plyr" ,r-plyr) | |
5296 | ("r-protgenerics" ,r-protgenerics) | |
5297 | ("r-rann" ,r-rann) | |
5298 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5299 | ("r-robustbase" ,r-robustbase) | |
ff9f179a RW |
5300 | ("r-s4vectors" ,r-s4vectors) |
5301 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5302 | (native-inputs | |
5303 | `(("r-knitr" ,r-knitr))) | |
ec12e537 RW |
5304 | (home-page "https://bioconductor.org/packages/xcms/") |
5305 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") | |
5306 | (description | |
5307 | "This package provides a framework for processing and visualization of | |
5308 | chromatographically separated and single-spectra mass spectral data. It | |
5309 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses | |
5310 | data for high-throughput, untargeted analyte profiling.") | |
5311 | (license license:gpl2+))) | |
8830664d RW |
5312 | |
5313 | (define-public r-wrench | |
5314 | (package | |
5315 | (name "r-wrench") | |
dc7c6368 | 5316 | (version "1.8.0") |
8830664d RW |
5317 | (source |
5318 | (origin | |
5319 | (method url-fetch) | |
5320 | (uri (bioconductor-uri "Wrench" version)) | |
5321 | (sha256 | |
5322 | (base32 | |
dc7c6368 | 5323 | "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx")))) |
8830664d RW |
5324 | (properties `((upstream-name . "Wrench"))) |
5325 | (build-system r-build-system) | |
5326 | (propagated-inputs | |
5327 | `(("r-limma" ,r-limma) | |
5328 | ("r-locfit" ,r-locfit) | |
5329 | ("r-matrixstats" ,r-matrixstats))) | |
996f07b5 RW |
5330 | (native-inputs |
5331 | `(("r-knitr" ,r-knitr))) | |
8830664d RW |
5332 | (home-page "https://github.com/HCBravoLab/Wrench") |
5333 | (synopsis "Wrench normalization for sparse count data") | |
5334 | (description | |
5335 | "Wrench is a package for normalization sparse genomic count data, like | |
5336 | that arising from 16s metagenomic surveys.") | |
5337 | (license license:artistic2.0))) | |
b9b8b447 RW |
5338 | |
5339 | (define-public r-wiggleplotr | |
5340 | (package | |
5341 | (name "r-wiggleplotr") | |
397bcd2c | 5342 | (version "1.14.0") |
b9b8b447 RW |
5343 | (source |
5344 | (origin | |
5345 | (method url-fetch) | |
5346 | (uri (bioconductor-uri "wiggleplotr" version)) | |
5347 | (sha256 | |
5348 | (base32 | |
397bcd2c | 5349 | "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad")))) |
b9b8b447 RW |
5350 | (build-system r-build-system) |
5351 | (propagated-inputs | |
5352 | `(("r-assertthat" ,r-assertthat) | |
5353 | ("r-cowplot" ,r-cowplot) | |
5354 | ("r-dplyr" ,r-dplyr) | |
5355 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5356 | ("r-genomicranges" ,r-genomicranges) | |
5357 | ("r-ggplot2" ,r-ggplot2) | |
5358 | ("r-iranges" ,r-iranges) | |
5359 | ("r-purrr" ,r-purrr) | |
5360 | ("r-rtracklayer" ,r-rtracklayer) | |
5361 | ("r-s4vectors" ,r-s4vectors))) | |
ee0f7460 RW |
5362 | (native-inputs |
5363 | `(("r-knitr" ,r-knitr))) | |
b9b8b447 RW |
5364 | (home-page "https://bioconductor.org/packages/wiggleplotr/") |
5365 | (synopsis "Make read coverage plots from BigWig files") | |
5366 | (description | |
5367 | "This package provides tools to visualize read coverage from sequencing | |
5368 | experiments together with genomic annotations (genes, transcripts, peaks). | |
5369 | Introns of long transcripts can be rescaled to a fixed length for better | |
5370 | visualization of exonic read coverage.") | |
5371 | (license license:asl2.0))) | |
7b5101c5 RW |
5372 | |
5373 | (define-public r-widgettools | |
5374 | (package | |
5375 | (name "r-widgettools") | |
ba53681a | 5376 | (version "1.68.0") |
7b5101c5 RW |
5377 | (source |
5378 | (origin | |
5379 | (method url-fetch) | |
5380 | (uri (bioconductor-uri "widgetTools" version)) | |
5381 | (sha256 | |
5382 | (base32 | |
ba53681a | 5383 | "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w")))) |
7b5101c5 RW |
5384 | (properties `((upstream-name . "widgetTools"))) |
5385 | (build-system r-build-system) | |
5386 | (home-page "https://bioconductor.org/packages/widgetTools/") | |
5387 | (synopsis "Tools for creating interactive tcltk widgets") | |
5388 | (description | |
337bdc17 | 5389 | "This package contains tools to support the construction of tcltk |
7b5101c5 RW |
5390 | widgets in R.") |
5391 | ;; Any version of the LGPL. | |
5392 | (license license:lgpl3+))) | |
6b12f213 RW |
5393 | |
5394 | (define-public r-webbioc | |
5395 | (package | |
5396 | (name "r-webbioc") | |
d176ad34 | 5397 | (version "1.62.0") |
6b12f213 RW |
5398 | (source |
5399 | (origin | |
5400 | (method url-fetch) | |
5401 | (uri (bioconductor-uri "webbioc" version)) | |
5402 | (sha256 | |
5403 | (base32 | |
d176ad34 | 5404 | "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj")))) |
6b12f213 RW |
5405 | (build-system r-build-system) |
5406 | (inputs | |
5407 | `(("netpbm" ,netpbm) | |
5408 | ("perl" ,perl))) | |
5409 | (propagated-inputs | |
5410 | `(("r-affy" ,r-affy) | |
5411 | ("r-annaffy" ,r-annaffy) | |
5412 | ("r-biobase" ,r-biobase) | |
5413 | ("r-biocmanager" ,r-biocmanager) | |
5414 | ("r-gcrma" ,r-gcrma) | |
5415 | ("r-multtest" ,r-multtest) | |
5416 | ("r-qvalue" ,r-qvalue) | |
5417 | ("r-vsn" ,r-vsn))) | |
5418 | (home-page "https://www.bioconductor.org/") | |
5419 | (synopsis "Bioconductor web interface") | |
5420 | (description | |
5421 | "This package provides an integrated web interface for doing microarray | |
5422 | analysis using several of the Bioconductor packages. It is intended to be | |
5423 | deployed as a centralized bioinformatics resource for use by many users. | |
5424 | Currently only Affymetrix oligonucleotide analysis is supported.") | |
5425 | (license license:gpl2+))) | |
9800d859 RW |
5426 | |
5427 | (define-public r-zfpkm | |
5428 | (package | |
5429 | (name "r-zfpkm") | |
59fafa19 | 5430 | (version "1.12.0") |
9800d859 RW |
5431 | (source |
5432 | (origin | |
5433 | (method url-fetch) | |
5434 | (uri (bioconductor-uri "zFPKM" version)) | |
5435 | (sha256 | |
5436 | (base32 | |
59fafa19 | 5437 | "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm")))) |
9800d859 RW |
5438 | (properties `((upstream-name . "zFPKM"))) |
5439 | (build-system r-build-system) | |
5440 | (propagated-inputs | |
5441 | `(("r-checkmate" ,r-checkmate) | |
5442 | ("r-dplyr" ,r-dplyr) | |
5443 | ("r-ggplot2" ,r-ggplot2) | |
5444 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
5445 | ("r-tidyr" ,r-tidyr))) | |
8fdca89b RW |
5446 | (native-inputs |
5447 | `(("r-knitr" ,r-knitr))) | |
9800d859 RW |
5448 | (home-page "https://github.com/ronammar/zFPKM/") |
5449 | (synopsis "Functions to facilitate zFPKM transformations") | |
5450 | (description | |
5451 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. | |
5452 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID | |
5453 | 24215113).") | |
5454 | (license license:gpl3))) | |
2bdc88fc RW |
5455 | |
5456 | (define-public r-rbowtie2 | |
5457 | (package | |
5458 | (name "r-rbowtie2") | |
9834d1ab | 5459 | (version "1.12.0") |
2bdc88fc RW |
5460 | (source |
5461 | (origin | |
5462 | (method url-fetch) | |
5463 | (uri (bioconductor-uri "Rbowtie2" version)) | |
5464 | (sha256 | |
5465 | (base32 | |
9834d1ab | 5466 | "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5")))) |
2bdc88fc RW |
5467 | (properties `((upstream-name . "Rbowtie2"))) |
5468 | (build-system r-build-system) | |
5469 | (inputs | |
5470 | `(("zlib" ,zlib))) | |
297854e6 RW |
5471 | (native-inputs |
5472 | `(("r-knitr" ,r-knitr))) | |
2bdc88fc RW |
5473 | (home-page "https://bioconductor.org/packages/Rbowtie2/") |
5474 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") | |
5475 | (description | |
5476 | "This package provides an R wrapper of the popular @code{bowtie2} | |
5477 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for | |
5478 | rapid adapter trimming, identification, and read merging.") | |
5479 | (license license:gpl3+))) | |
5622628f RW |
5480 | |
5481 | (define-public r-progeny | |
5482 | (package | |
5483 | (name "r-progeny") | |
d115db7f | 5484 | (version "1.12.0") |
5622628f RW |
5485 | (source |
5486 | (origin | |
5487 | (method url-fetch) | |
5488 | (uri (bioconductor-uri "progeny" version)) | |
5489 | (sha256 | |
5490 | (base32 | |
d115db7f | 5491 | "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7")))) |
5622628f | 5492 | (build-system r-build-system) |
8e5933a8 RW |
5493 | (propagated-inputs |
5494 | `(("r-biobase" ,r-biobase) | |
5495 | ("r-dplyr" ,r-dplyr) | |
5496 | ("r-ggplot2" ,r-ggplot2) | |
5497 | ("r-ggrepel" ,r-ggrepel) | |
5498 | ("r-gridextra" ,r-gridextra) | |
5499 | ("r-tidyr" ,r-tidyr))) | |
5500 | (native-inputs | |
5501 | `(("r-knitr" ,r-knitr))) | |
5622628f RW |
5502 | (home-page "https://github.com/saezlab/progeny") |
5503 | (synopsis "Pathway responsive gene activity inference") | |
5504 | (description | |
5505 | "This package provides a function to infer pathway activity from gene | |
5506 | expression. It contains the linear model inferred in the publication | |
5507 | \"Perturbation-response genes reveal signaling footprints in cancer gene | |
5508 | expression\".") | |
5509 | (license license:asl2.0))) | |
307586c1 RW |
5510 | |
5511 | (define-public r-arrmnormalization | |
5512 | (package | |
5513 | (name "r-arrmnormalization") | |
0067589a | 5514 | (version "1.30.0") |
307586c1 RW |
5515 | (source |
5516 | (origin | |
5517 | (method url-fetch) | |
5518 | (uri (bioconductor-uri "ARRmNormalization" version)) | |
5519 | (sha256 | |
5520 | (base32 | |
0067589a | 5521 | "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95")))) |
307586c1 RW |
5522 | (properties |
5523 | `((upstream-name . "ARRmNormalization"))) | |
5524 | (build-system r-build-system) | |
5525 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) | |
5526 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") | |
5527 | (synopsis "Adaptive robust regression normalization for methylation data") | |
5528 | (description | |
5529 | "This is a package to perform the @dfn{Adaptive Robust Regression | |
5530 | method} (ARRm) for the normalization of methylation data from the Illumina | |
5531 | Infinium HumanMethylation 450k assay.") | |
5532 | (license license:artistic2.0))) | |
fbf34949 RW |
5533 | |
5534 | (define-public r-biocfilecache | |
5535 | (package | |
5536 | (name "r-biocfilecache") | |
e65e81d2 | 5537 | (version "1.14.0") |
fbf34949 RW |
5538 | (source |
5539 | (origin | |
5540 | (method url-fetch) | |
5541 | (uri (bioconductor-uri "BiocFileCache" version)) | |
5542 | (sha256 | |
5543 | (base32 | |
e65e81d2 | 5544 | "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1")))) |
fbf34949 RW |
5545 | (properties `((upstream-name . "BiocFileCache"))) |
5546 | (build-system r-build-system) | |
5547 | (propagated-inputs | |
5548 | `(("r-curl" ,r-curl) | |
5549 | ("r-dbi" ,r-dbi) | |
5550 | ("r-dbplyr" ,r-dbplyr) | |
5551 | ("r-dplyr" ,r-dplyr) | |
5552 | ("r-httr" ,r-httr) | |
5553 | ("r-rappdirs" ,r-rappdirs) | |
5554 | ("r-rsqlite" ,r-rsqlite))) | |
173844fc RW |
5555 | (native-inputs |
5556 | `(("r-knitr" ,r-knitr))) | |
fbf34949 RW |
5557 | (home-page "https://bioconductor.org/packages/BiocFileCache/") |
5558 | (synopsis "Manage files across sessions") | |
5559 | (description | |
5560 | "This package creates a persistent on-disk cache of files that the user | |
5561 | can add, update, and retrieve. It is useful for managing resources (such as | |
5562 | custom Txdb objects) that are costly or difficult to create, web resources, | |
5563 | and data files used across sessions.") | |
5564 | (license license:artistic2.0))) | |
8c42f8f6 RW |
5565 | |
5566 | (define-public r-iclusterplus | |
5567 | (package | |
5568 | (name "r-iclusterplus") | |
4bc0675d | 5569 | (version "1.26.0") |
8c42f8f6 RW |
5570 | (source |
5571 | (origin | |
5572 | (method url-fetch) | |
5573 | (uri (bioconductor-uri "iClusterPlus" version)) | |
5574 | (sha256 | |
5575 | (base32 | |
4bc0675d | 5576 | "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q")))) |
8c42f8f6 RW |
5577 | (properties `((upstream-name . "iClusterPlus"))) |
5578 | (build-system r-build-system) | |
5579 | (native-inputs `(("gfortran" ,gfortran))) | |
5580 | (home-page "https://bioconductor.org/packages/iClusterPlus/") | |
5581 | (synopsis "Integrative clustering of multi-type genomic data") | |
5582 | (description | |
5583 | "iClusterPlus is developed for integrative clustering analysis of | |
5584 | multi-type genomic data and is an enhanced version of iCluster proposed and | |
5585 | developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise | |
5586 | from the experiments where biological samples (e.g. tumor samples) are | |
5587 | analyzed by multiple techniques, for instance, @dfn{array comparative genomic | |
5588 | hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so | |
5589 | on. In the iClusterPlus model, binary observations such as somatic mutation | |
5590 | are modeled as Binomial processes; categorical observations such as copy | |
5591 | number states are realizations of Multinomial random variables; counts are | |
5592 | modeled as Poisson random processes; and continuous measures are modeled by | |
5593 | Gaussian distributions.") | |
5594 | (license license:gpl2+))) | |
4d06ef4b RW |
5595 | |
5596 | (define-public r-rbowtie | |
5597 | (package | |
5598 | (name "r-rbowtie") | |
ea86d93e | 5599 | (version "1.30.0") |
4d06ef4b RW |
5600 | (source |
5601 | (origin | |
5602 | (method url-fetch) | |
5603 | (uri (bioconductor-uri "Rbowtie" version)) | |
5604 | (sha256 | |
5605 | (base32 | |
ea86d93e | 5606 | "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507")))) |
4d06ef4b RW |
5607 | (properties `((upstream-name . "Rbowtie"))) |
5608 | (build-system r-build-system) | |
5609 | (inputs | |
5610 | `(("zlib" ,zlib))) | |
568c3929 RW |
5611 | (native-inputs |
5612 | `(("r-knitr" ,r-knitr))) | |
4d06ef4b RW |
5613 | (home-page "https://bioconductor.org/packages/Rbowtie/") |
5614 | (synopsis "R bowtie wrapper") | |
5615 | (description | |
5616 | "This package provides an R wrapper around the popular bowtie short read | |
5617 | aligner and around SpliceMap, a de novo splice junction discovery and | |
5618 | alignment tool.") | |
5619 | (license license:artistic2.0))) | |
14441539 RW |
5620 | |
5621 | (define-public r-sgseq | |
5622 | (package | |
5623 | (name "r-sgseq") | |
ca0271c5 | 5624 | (version "1.24.0") |
14441539 RW |
5625 | (source |
5626 | (origin | |
5627 | (method url-fetch) | |
5628 | (uri (bioconductor-uri "SGSeq" version)) | |
5629 | (sha256 | |
5630 | (base32 | |
ca0271c5 | 5631 | "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx")))) |
14441539 RW |
5632 | (properties `((upstream-name . "SGSeq"))) |
5633 | (build-system r-build-system) | |
5634 | (propagated-inputs | |
5635 | `(("r-annotationdbi" ,r-annotationdbi) | |
5636 | ("r-biocgenerics" ,r-biocgenerics) | |
5637 | ("r-biostrings" ,r-biostrings) | |
5638 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5639 | ("r-genomicalignments" ,r-genomicalignments) | |
5640 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5641 | ("r-genomicranges" ,r-genomicranges) | |
5642 | ("r-igraph" ,r-igraph) | |
5643 | ("r-iranges" ,r-iranges) | |
5644 | ("r-rsamtools" ,r-rsamtools) | |
5645 | ("r-rtracklayer" ,r-rtracklayer) | |
5646 | ("r-runit" ,r-runit) | |
5647 | ("r-s4vectors" ,r-s4vectors) | |
5648 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
201902bc RW |
5649 | (native-inputs |
5650 | `(("r-knitr" ,r-knitr))) | |
14441539 RW |
5651 | (home-page "https://bioconductor.org/packages/SGSeq/") |
5652 | (synopsis "Splice event prediction and quantification from RNA-seq data") | |
5653 | (description | |
5654 | "SGSeq is a package for analyzing splice events from RNA-seq data. Input | |
5655 | data are RNA-seq reads mapped to a reference genome in BAM format. Genes are | |
5656 | represented as a splice graph, which can be obtained from existing annotation | |
5657 | or predicted from the mapped sequence reads. Splice events are identified | |
5658 | from the graph and are quantified locally using structurally compatible reads | |
5659 | at the start or end of each splice variant. The software includes functions | |
5660 | for splice event prediction, quantification, visualization and | |
5661 | interpretation.") | |
5662 | (license license:artistic2.0))) | |
58656064 RW |
5663 | |
5664 | (define-public r-rhisat2 | |
5665 | (package | |
5666 | (name "r-rhisat2") | |
c36d888f | 5667 | (version "1.6.0") |
58656064 RW |
5668 | (source |
5669 | (origin | |
5670 | (method url-fetch) | |
5671 | (uri (bioconductor-uri "Rhisat2" version)) | |
5672 | (sha256 | |
5673 | (base32 | |
c36d888f | 5674 | "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb")))) |
58656064 RW |
5675 | (properties `((upstream-name . "Rhisat2"))) |
5676 | (build-system r-build-system) | |
3dd2450e RW |
5677 | (arguments |
5678 | `(#:phases | |
5679 | (modify-phases %standard-phases | |
5680 | (add-after 'unpack 'make-reproducible | |
5681 | (lambda _ | |
5682 | (substitute* "src/Makefile" | |
5683 | (("`hostname`") "guix") | |
5684 | (("`date`") "0") | |
5685 | ;; Avoid shelling out to "which". | |
5686 | (("^CC =.*") (which "gcc")) | |
5687 | (("^CPP =.*") (which "g++"))) | |
5688 | #t))))) | |
58656064 RW |
5689 | (propagated-inputs |
5690 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
5691 | ("r-genomicranges" ,r-genomicranges) | |
5692 | ("r-sgseq" ,r-sgseq))) | |
2aff2724 RW |
5693 | (native-inputs |
5694 | `(("r-knitr" ,r-knitr))) | |
58656064 RW |
5695 | (home-page "https://github.com/fmicompbio/Rhisat2") |
5696 | (synopsis "R Wrapper for HISAT2 sequence aligner") | |
5697 | (description | |
5698 | "This package provides an R interface to the HISAT2 spliced short-read | |
5699 | aligner by Kim et al. (2015). The package contains wrapper functions to | |
5700 | create a genome index and to perform the read alignment to the generated | |
5701 | index.") | |
5702 | (license license:gpl3))) | |
5e0241db RW |
5703 | |
5704 | (define-public r-quasr | |
5705 | (package | |
5706 | (name "r-quasr") | |
1b4c2719 | 5707 | (version "1.30.0") |
5e0241db RW |
5708 | (source |
5709 | (origin | |
5710 | (method url-fetch) | |
5711 | (uri (bioconductor-uri "QuasR" version)) | |
5712 | (sha256 | |
5713 | (base32 | |
1b4c2719 | 5714 | "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8")))) |
5e0241db RW |
5715 | (properties `((upstream-name . "QuasR"))) |
5716 | (build-system r-build-system) | |
5e0241db RW |
5717 | (propagated-inputs |
5718 | `(("r-annotationdbi" ,r-annotationdbi) | |
5719 | ("r-biobase" ,r-biobase) | |
5720 | ("r-biocgenerics" ,r-biocgenerics) | |
5721 | ("r-biocmanager" ,r-biocmanager) | |
5722 | ("r-biocparallel" ,r-biocparallel) | |
5723 | ("r-biostrings" ,r-biostrings) | |
5724 | ("r-bsgenome" ,r-bsgenome) | |
5725 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5726 | ("r-genomicalignments" ,r-genomicalignments) | |
5727 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5728 | ("r-genomicfiles" ,r-genomicfiles) | |
5729 | ("r-genomicranges" ,r-genomicranges) | |
5730 | ("r-iranges" ,r-iranges) | |
5731 | ("r-rbowtie" ,r-rbowtie) | |
5732 | ("r-rhisat2" ,r-rhisat2) | |
5733 | ("r-rhtslib" ,r-rhtslib) | |
5734 | ("r-rsamtools" ,r-rsamtools) | |
5735 | ("r-rtracklayer" ,r-rtracklayer) | |
5736 | ("r-s4vectors" ,r-s4vectors) | |
5737 | ("r-shortread" ,r-shortread))) | |
a84abf43 RW |
5738 | (native-inputs |
5739 | `(("r-knitr" ,r-knitr))) | |
5e0241db RW |
5740 | (home-page "https://bioconductor.org/packages/QuasR/") |
5741 | (synopsis "Quantify and annotate short reads in R") | |
5742 | (description | |
5743 | "This package provides a framework for the quantification and analysis of | |
5744 | short genomic reads. It covers a complete workflow starting from raw sequence | |
5745 | reads, over creation of alignments and quality control plots, to the | |
5746 | quantification of genomic regions of interest.") | |
5747 | (license license:gpl2))) | |
496b024f RW |
5748 | |
5749 | (define-public r-rqc | |
5750 | (package | |
5751 | (name "r-rqc") | |
d8a7bf76 | 5752 | (version "1.24.0") |
496b024f RW |
5753 | (source |
5754 | (origin | |
5755 | (method url-fetch) | |
5756 | (uri (bioconductor-uri "Rqc" version)) | |
5757 | (sha256 | |
5758 | (base32 | |
d8a7bf76 | 5759 | "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9")))) |
496b024f RW |
5760 | (properties `((upstream-name . "Rqc"))) |
5761 | (build-system r-build-system) | |
5762 | (propagated-inputs | |
5763 | `(("r-biocgenerics" ,r-biocgenerics) | |
5764 | ("r-biocparallel" ,r-biocparallel) | |
5765 | ("r-biocstyle" ,r-biocstyle) | |
5766 | ("r-biostrings" ,r-biostrings) | |
5767 | ("r-biovizbase" ,r-biovizbase) | |
5768 | ("r-genomicalignments" ,r-genomicalignments) | |
5769 | ("r-genomicfiles" ,r-genomicfiles) | |
5770 | ("r-ggplot2" ,r-ggplot2) | |
5771 | ("r-iranges" ,r-iranges) | |
5772 | ("r-knitr" ,r-knitr) | |
5773 | ("r-markdown" ,r-markdown) | |
5774 | ("r-plyr" ,r-plyr) | |
5775 | ("r-rcpp" ,r-rcpp) | |
5776 | ("r-reshape2" ,r-reshape2) | |
5777 | ("r-rsamtools" ,r-rsamtools) | |
5778 | ("r-s4vectors" ,r-s4vectors) | |
5779 | ("r-shiny" ,r-shiny) | |
5780 | ("r-shortread" ,r-shortread))) | |
1c5360ac RW |
5781 | (native-inputs |
5782 | `(("r-knitr" ,r-knitr))) | |
496b024f RW |
5783 | (home-page "https://github.com/labbcb/Rqc") |
5784 | (synopsis "Quality control tool for high-throughput sequencing data") | |
5785 | (description | |
5786 | "Rqc is an optimized tool designed for quality control and assessment of | |
5787 | high-throughput sequencing data. It performs parallel processing of entire | |
5788 | files and produces a report which contains a set of high-resolution | |
5789 | graphics.") | |
5790 | (license license:gpl2+))) | |
81e3de01 RW |
5791 | |
5792 | (define-public r-birewire | |
5793 | (package | |
5794 | (name "r-birewire") | |
979b1edc | 5795 | (version "3.22.0") |
81e3de01 RW |
5796 | (source |
5797 | (origin | |
5798 | (method url-fetch) | |
5799 | (uri (bioconductor-uri "BiRewire" version)) | |
5800 | (sha256 | |
5801 | (base32 | |
979b1edc | 5802 | "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw")))) |
81e3de01 RW |
5803 | (properties `((upstream-name . "BiRewire"))) |
5804 | (build-system r-build-system) | |
5805 | (propagated-inputs | |
5806 | `(("r-igraph" ,r-igraph) | |
5807 | ("r-matrix" ,r-matrix) | |
5808 | ("r-slam" ,r-slam) | |
5809 | ("r-tsne" ,r-tsne))) | |
5810 | (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") | |
5811 | (synopsis "Tools for randomization of bipartite graphs") | |
5812 | (description | |
5813 | "This package provides functions for bipartite network rewiring through N | |
5814 | consecutive switching steps and for the computation of the minimal number of | |
5815 | switching steps to be performed in order to maximise the dissimilarity with | |
5816 | respect to the original network. It includes functions for the analysis of | |
5817 | the introduced randomness across the switching steps and several other | |
5818 | routines to analyse the resulting networks and their natural projections.") | |
5819 | (license license:gpl3))) | |
1a24f855 RW |
5820 | |
5821 | (define-public r-birta | |
5822 | (package | |
5823 | (name "r-birta") | |
cb941ca0 | 5824 | (version "1.31.0") |
1a24f855 RW |
5825 | (source |
5826 | (origin | |
5827 | (method url-fetch) | |
5828 | (uri (bioconductor-uri "birta" version)) | |
5829 | (sha256 | |
5830 | (base32 | |
cb941ca0 | 5831 | "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) |
1a24f855 RW |
5832 | (build-system r-build-system) |
5833 | (propagated-inputs | |
5834 | `(("r-biobase" ,r-biobase) | |
5835 | ("r-limma" ,r-limma) | |
5836 | ("r-mass" ,r-mass))) | |
5837 | (home-page "https://bioconductor.org/packages/birta") | |
5838 | (synopsis "Bayesian inference of regulation of transcriptional activity") | |
5839 | (description | |
5840 | "Expression levels of mRNA molecules are regulated by different | |
5841 | processes, comprising inhibition or activation by transcription factors and | |
5842 | post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian | |
5843 | Inference of Regulation of Transcriptional Activity) uses the regulatory | |
5844 | networks of transcription factors and miRNAs together with mRNA and miRNA | |
5845 | expression data to predict switches in regulatory activity between two | |
5846 | conditions. A Bayesian network is used to model the regulatory structure and | |
5847 | Markov-Chain-Monte-Carlo is applied to sample the activity states.") | |
5848 | (license license:gpl2+))) | |
a9fac3f4 | 5849 | |
b4a22cca RW |
5850 | (define-public r-multidataset |
5851 | (package | |
5852 | (name "r-multidataset") | |
e78e04d2 | 5853 | (version "1.18.0") |
b4a22cca RW |
5854 | (source |
5855 | (origin | |
5856 | (method url-fetch) | |
5857 | (uri (bioconductor-uri "MultiDataSet" version)) | |
5858 | (sha256 | |
5859 | (base32 | |
e78e04d2 | 5860 | "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w")))) |
b4a22cca RW |
5861 | (properties `((upstream-name . "MultiDataSet"))) |
5862 | (build-system r-build-system) | |
5863 | (propagated-inputs | |
5864 | `(("r-biobase" ,r-biobase) | |
5865 | ("r-biocgenerics" ,r-biocgenerics) | |
5866 | ("r-genomicranges" ,r-genomicranges) | |
5867 | ("r-ggplot2" ,r-ggplot2) | |
5868 | ("r-ggrepel" ,r-ggrepel) | |
5869 | ("r-iranges" ,r-iranges) | |
5870 | ("r-limma" ,r-limma) | |
5871 | ("r-qqman" ,r-qqman) | |
5872 | ("r-s4vectors" ,r-s4vectors) | |
5873 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
905bbb13 RW |
5874 | (native-inputs |
5875 | `(("r-knitr" ,r-knitr))) | |
b4a22cca RW |
5876 | (home-page "https://bioconductor.org/packages/MultiDataSet/") |
5877 | (synopsis "Implementation of MultiDataSet and ResultSet") | |
5878 | (description | |
5879 | "This package provides an implementation of the BRGE's (Bioinformatic | |
5880 | Research Group in Epidemiology from Center for Research in Environmental | |
5881 | Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for | |
5882 | integrating multi omics data sets and ResultSet is a container for omics | |
5883 | results. This package contains base classes for MEAL and rexposome | |
5884 | packages.") | |
5885 | (license license:expat))) | |
5886 | ||
a9fac3f4 RW |
5887 | (define-public r-ropls |
5888 | (package | |
5889 | (name "r-ropls") | |
59daf6ed | 5890 | (version "1.22.0") |
a9fac3f4 RW |
5891 | (source |
5892 | (origin | |
5893 | (method url-fetch) | |
5894 | (uri (bioconductor-uri "ropls" version)) | |
5895 | (sha256 | |
5896 | (base32 | |
59daf6ed | 5897 | "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5")))) |
a9fac3f4 | 5898 | (build-system r-build-system) |
643aaf7e RW |
5899 | (propagated-inputs |
5900 | `(("r-biobase" ,r-biobase) | |
5901 | ("r-multidataset" ,r-multidataset))) | |
a9fac3f4 RW |
5902 | (native-inputs |
5903 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
5904 | (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") | |
5905 | (synopsis "Multivariate analysis and feature selection of omics data") | |
5906 | (description | |
5907 | "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) | |
5908 | and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, | |
5909 | regression, classification, and feature selection of omics data where the | |
5910 | number of variables exceeds the number of samples and with multicollinearity | |
5911 | among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to | |
5912 | separately model the variation correlated (predictive) to the factor of | |
5913 | interest and the uncorrelated (orthogonal) variation. While performing | |
5914 | similarly to PLS, OPLS facilitates interpretation. | |
5915 | ||
5916 | This package provides imlementations of PCA, PLS, and OPLS for multivariate | |
5917 | analysis and feature selection of omics data. In addition to scores, loadings | |
5918 | and weights plots, the package provides metrics and graphics to determine the | |
5919 | optimal number of components (e.g. with the R2 and Q2 coefficients), check the | |
5920 | validity of the model by permutation testing, detect outliers, and perform | |
5921 | feature selection (e.g. with Variable Importance in Projection or regression | |
5922 | coefficients).") | |
5923 | (license license:cecill))) | |
075a9094 RW |
5924 | |
5925 | (define-public r-biosigner | |
5926 | (package | |
5927 | (name "r-biosigner") | |
7cda2d41 | 5928 | (version "1.18.2") |
075a9094 RW |
5929 | (source |
5930 | (origin | |
5931 | (method url-fetch) | |
5932 | (uri (bioconductor-uri "biosigner" version)) | |
5933 | (sha256 | |
5934 | (base32 | |
7cda2d41 | 5935 | "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn")))) |
075a9094 RW |
5936 | (build-system r-build-system) |
5937 | (propagated-inputs | |
5938 | `(("r-biobase" ,r-biobase) | |
5939 | ("r-e1071" ,r-e1071) | |
7d29dc9c | 5940 | ("r-multidataset" ,r-multidataset) |
075a9094 RW |
5941 | ("r-randomforest" ,r-randomforest) |
5942 | ("r-ropls" ,r-ropls))) | |
5943 | (native-inputs | |
f7100eda | 5944 | `(("r-knitr" ,r-knitr))) |
075a9094 RW |
5945 | (home-page "https://bioconductor.org/packages/biosigner/") |
5946 | (synopsis "Signature discovery from omics data") | |
5947 | (description | |
5948 | "Feature selection is critical in omics data analysis to extract | |
5949 | restricted and meaningful molecular signatures from complex and high-dimension | |
5950 | data, and to build robust classifiers. This package implements a method to | |
5951 | assess the relevance of the variables for the prediction performances of the | |
5952 | classifier. The approach can be run in parallel with the PLS-DA, Random | |
5953 | Forest, and SVM binary classifiers. The signatures and the corresponding | |
5954 | 'restricted' models are returned, enabling future predictions on new | |
5955 | datasets.") | |
5956 | (license license:cecill))) | |
ae6fa185 RW |
5957 | |
5958 | (define-public r-annotatr | |
5959 | (package | |
5960 | (name "r-annotatr") | |
458aa446 | 5961 | (version "1.16.0") |
ae6fa185 RW |
5962 | (source |
5963 | (origin | |
5964 | (method url-fetch) | |
5965 | (uri (bioconductor-uri "annotatr" version)) | |
5966 | (sha256 | |
5967 | (base32 | |
458aa446 | 5968 | "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9")))) |
ae6fa185 RW |
5969 | (build-system r-build-system) |
5970 | (propagated-inputs | |
5971 | `(("r-annotationdbi" ,r-annotationdbi) | |
5972 | ("r-annotationhub" ,r-annotationhub) | |
5973 | ("r-dplyr" ,r-dplyr) | |
5974 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5975 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5976 | ("r-genomicranges" ,r-genomicranges) | |
5977 | ("r-ggplot2" ,r-ggplot2) | |
5978 | ("r-iranges" ,r-iranges) | |
5979 | ("r-readr" ,r-readr) | |
5980 | ("r-regioner" ,r-regioner) | |
5981 | ("r-reshape2" ,r-reshape2) | |
5982 | ("r-rtracklayer" ,r-rtracklayer) | |
5983 | ("r-s4vectors" ,r-s4vectors))) | |
5ca991bf RW |
5984 | (native-inputs |
5985 | `(("r-knitr" ,r-knitr))) | |
ae6fa185 RW |
5986 | (home-page "https://bioconductor.org/packages/annotatr/") |
5987 | (synopsis "Annotation of genomic regions to genomic annotations") | |
5988 | (description | |
5989 | "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, | |
5990 | differentially methylated CpGs or regions, SNPs, etc.) it is often of interest | |
5991 | to investigate the intersecting genomic annotations. Such annotations include | |
5992 | those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), | |
5993 | CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as | |
5994 | enhancers. The annotatr package provides an easy way to summarize and | |
5995 | visualize the intersection of genomic sites/regions with genomic | |
5996 | annotations.") | |
5997 | (license license:gpl3))) | |
2cb738a6 RW |
5998 | |
5999 | (define-public r-rsubread | |
6000 | (package | |
6001 | (name "r-rsubread") | |
d764f1e7 | 6002 | (version "2.4.2") |
2cb738a6 RW |
6003 | (source |
6004 | (origin | |
6005 | (method url-fetch) | |
6006 | (uri (bioconductor-uri "Rsubread" version)) | |
6007 | (sha256 | |
6008 | (base32 | |
d764f1e7 | 6009 | "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra")))) |
2cb738a6 RW |
6010 | (properties `((upstream-name . "Rsubread"))) |
6011 | (build-system r-build-system) | |
6012 | (inputs `(("zlib" ,zlib))) | |
5d63f69b RW |
6013 | (propagated-inputs |
6014 | `(("r-matrix" ,r-matrix))) | |
2cb738a6 RW |
6015 | (home-page "https://bioconductor.org/packages/Rsubread/") |
6016 | (synopsis "Subread sequence alignment and counting for R") | |
6017 | (description | |
6018 | "This package provides tools for alignment, quantification and analysis | |
6019 | of second and third generation sequencing data. It includes functionality for | |
6020 | read mapping, read counting, SNP calling, structural variant detection and | |
6021 | gene fusion discovery. It can be applied to all major sequencing techologies | |
6022 | and to both short and long sequence reads.") | |
6023 | (license license:gpl3))) | |
a6fedf1f | 6024 | |
a0422d18 | 6025 | (define-public r-flowutils |
6026 | (package | |
6027 | (name "r-flowutils") | |
d361222d | 6028 | (version "1.54.0") |
a0422d18 | 6029 | (source |
6030 | (origin | |
6031 | (method url-fetch) | |
6032 | (uri (bioconductor-uri "flowUtils" version)) | |
6033 | (sha256 | |
6034 | (base32 | |
d361222d | 6035 | "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09")))) |
a0422d18 | 6036 | (properties `((upstream-name . "flowUtils"))) |
6037 | (build-system r-build-system) | |
6038 | (propagated-inputs | |
6039 | `(("r-biobase" ,r-biobase) | |
6040 | ("r-corpcor" ,r-corpcor) | |
6041 | ("r-flowcore" ,r-flowcore) | |
6042 | ("r-graph" ,r-graph) | |
6043 | ("r-runit" ,r-runit) | |
6044 | ("r-xml" ,r-xml))) | |
6045 | (home-page "https://github.com/jspidlen/flowUtils") | |
6046 | (synopsis "Utilities for flow cytometry") | |
6047 | (description | |
6048 | "This package provides utilities for flow cytometry data.") | |
6049 | (license license:artistic2.0))) | |
6050 | ||
ed6f49fc | 6051 | (define-public r-consensusclusterplus |
6052 | (package | |
6053 | (name "r-consensusclusterplus") | |
a49024e6 | 6054 | (version "1.54.0") |
ed6f49fc | 6055 | (source |
6056 | (origin | |
6057 | (method url-fetch) | |
6058 | (uri (bioconductor-uri "ConsensusClusterPlus" version)) | |
6059 | (sha256 | |
6060 | (base32 | |
a49024e6 | 6061 | "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp")))) |
ed6f49fc | 6062 | (properties |
6063 | `((upstream-name . "ConsensusClusterPlus"))) | |
6064 | (build-system r-build-system) | |
6065 | (propagated-inputs | |
6066 | `(("r-all" ,r-all) | |
6067 | ("r-biobase" ,r-biobase) | |
6068 | ("r-cluster" ,r-cluster))) | |
6069 | (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") | |
6070 | (synopsis "Clustering algorithm") | |
6071 | (description | |
6072 | "This package provides an implementation of an algorithm for determining | |
6073 | cluster count and membership by stability evidence in unsupervised analysis.") | |
6074 | (license license:gpl2))) | |
6075 | ||
b4aee31d RW |
6076 | (define-public r-cytolib |
6077 | (package | |
6078 | (name "r-cytolib") | |
c6ccd4fc | 6079 | (version "2.2.0") |
b4aee31d RW |
6080 | (source |
6081 | (origin | |
6082 | (method url-fetch) | |
6083 | (uri (bioconductor-uri "cytolib" version)) | |
6084 | (sha256 | |
6085 | (base32 | |
c6ccd4fc | 6086 | "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw")))) |
b4aee31d RW |
6087 | (properties `((upstream-name . "cytolib"))) |
6088 | (build-system r-build-system) | |
b58c4e76 | 6089 | (arguments |
6090 | `(#:phases | |
6091 | (modify-phases %standard-phases | |
6092 | (add-after 'unpack 'fix-linking | |
6093 | (lambda _ | |
6094 | (substitute* "src/Makevars.in" | |
6095 | ;; This is to avoid having a plain directory on the list of | |
6096 | ;; libraries to link. | |
6097 | (("\\(RHDF5_LIBS\\)" match) | |
6098 | (string-append match "/libhdf5.a"))) | |
6099 | #t))))) | |
3c73d7c5 | 6100 | (native-inputs |
c6ccd4fc | 6101 | `(("r-knitr" ,r-knitr) |
6102 | ("pkg-config" ,pkg-config))) | |
3c73d7c5 RW |
6103 | (propagated-inputs |
6104 | `(("r-bh" ,r-bh) | |
6105 | ("r-rcpp" ,r-rcpp) | |
6106 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
6107 | ("r-rcppparallel" ,r-rcppparallel) | |
6108 | ("r-rhdf5lib" ,r-rhdf5lib) | |
6109 | ("r-rprotobuflib" ,r-rprotobuflib))) | |
b4aee31d RW |
6110 | (home-page "https://bioconductor.org/packages/cytolib/") |
6111 | (synopsis "C++ infrastructure for working with gated cytometry") | |
6112 | (description | |
6113 | "This package provides the core data structure and API to represent and | |
6114 | interact with gated cytometry data.") | |
6115 | (license license:artistic2.0))) | |
6116 | ||
a6fedf1f | 6117 | (define-public r-flowcore |
6118 | (package | |
6119 | (name "r-flowcore") | |
3f0e93b4 | 6120 | (version "2.2.0") |
a6fedf1f | 6121 | (source |
6122 | (origin | |
6123 | (method url-fetch) | |
6124 | (uri (bioconductor-uri "flowCore" version)) | |
6125 | (sha256 | |
6126 | (base32 | |
3f0e93b4 | 6127 | "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8")))) |
a6fedf1f | 6128 | (properties `((upstream-name . "flowCore"))) |
6129 | (build-system r-build-system) | |
6130 | (propagated-inputs | |
6131 | `(("r-bh" ,r-bh) | |
6132 | ("r-biobase" ,r-biobase) | |
6133 | ("r-biocgenerics" ,r-biocgenerics) | |
b2a2f321 | 6134 | ("r-cytolib" ,r-cytolib) |
a6fedf1f | 6135 | ("r-matrixstats" ,r-matrixstats) |
faff2de0 RW |
6136 | ("r-rcpp" ,r-rcpp) |
6137 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
3f0e93b4 | 6138 | ("r-rprotobuflib" ,r-rprotobuflib) |
6139 | ("r-s4vectors" ,r-s4vectors))) | |
faff2de0 RW |
6140 | (native-inputs |
6141 | `(("r-knitr" ,r-knitr))) | |
a6fedf1f | 6142 | (home-page "https://bioconductor.org/packages/flowCore") |
6143 | (synopsis "Basic structures for flow cytometry data") | |
6144 | (description | |
6145 | "This package provides S4 data structures and basic functions to deal | |
6146 | with flow cytometry data.") | |
6147 | (license license:artistic2.0))) | |
e0cb053e | 6148 | |
6149 | (define-public r-flowmeans | |
6150 | (package | |
6151 | (name "r-flowmeans") | |
2cd78131 | 6152 | (version "1.50.0") |
e0cb053e | 6153 | (source |
6154 | (origin | |
6155 | (method url-fetch) | |
6156 | (uri (bioconductor-uri "flowMeans" version)) | |
6157 | (sha256 | |
6158 | (base32 | |
2cd78131 | 6159 | "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734")))) |
e0cb053e | 6160 | (properties `((upstream-name . "flowMeans"))) |
6161 | (build-system r-build-system) | |
6162 | (propagated-inputs | |
6163 | `(("r-biobase" ,r-biobase) | |
6164 | ("r-feature" ,r-feature) | |
6165 | ("r-flowcore" ,r-flowcore) | |
6166 | ("r-rrcov" ,r-rrcov))) | |
6167 | (home-page "https://bioconductor.org/packages/flowMeans") | |
6168 | (synopsis "Non-parametric flow cytometry data gating") | |
6169 | (description | |
6170 | "This package provides tools to identify cell populations in Flow | |
6171 | Cytometry data using non-parametric clustering and segmented-regression-based | |
6172 | change point detection.") | |
6173 | (license license:artistic2.0))) | |
1502751b | 6174 | |
15ac0c19 RW |
6175 | (define-public r-ncdfflow |
6176 | (package | |
6177 | (name "r-ncdfflow") | |
eac1eaaa | 6178 | (version "2.36.0") |
15ac0c19 RW |
6179 | (source |
6180 | (origin | |
6181 | (method url-fetch) | |
6182 | (uri (bioconductor-uri "ncdfFlow" version)) | |
6183 | (sha256 | |
6184 | (base32 | |
eac1eaaa | 6185 | "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac")))) |
15ac0c19 RW |
6186 | (properties `((upstream-name . "ncdfFlow"))) |
6187 | (build-system r-build-system) | |
0022e9f4 | 6188 | (arguments |
6189 | `(#:phases | |
6190 | (modify-phases %standard-phases | |
6191 | (add-after 'unpack 'fix-linking | |
6192 | (lambda _ | |
6193 | (substitute* "src/Makevars" | |
6194 | ;; This is to avoid having a plain directory on the list of | |
6195 | ;; libraries to link. | |
6196 | (("\\(RHDF5_LIBS\\)" match) | |
6197 | (string-append match "/libhdf5.a"))) | |
6198 | #t))))) | |
15ac0c19 RW |
6199 | (propagated-inputs |
6200 | `(("r-bh" ,r-bh) | |
6201 | ("r-biobase" ,r-biobase) | |
6202 | ("r-biocgenerics" ,r-biocgenerics) | |
6203 | ("r-flowcore" ,r-flowcore) | |
6204 | ("r-rcpp" ,r-rcpp) | |
6205 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
6206 | ("r-rhdf5lib" ,r-rhdf5lib) | |
6207 | ("r-zlibbioc" ,r-zlibbioc))) | |
631b12ca RW |
6208 | (native-inputs |
6209 | `(("r-knitr" ,r-knitr))) | |
15ac0c19 RW |
6210 | (home-page "https://bioconductor.org/packages/ncdfFlow/") |
6211 | (synopsis "HDF5 based storage for flow cytometry data") | |
6212 | (description | |
6213 | "This package provides HDF5 storage based methods and functions for | |
6214 | manipulation of flow cytometry data.") | |
6215 | (license license:artistic2.0))) | |
6216 | ||
f5f44031 RW |
6217 | (define-public r-ggcyto |
6218 | (package | |
6219 | (name "r-ggcyto") | |
43bf50ec | 6220 | (version "1.18.0") |
f5f44031 RW |
6221 | (source |
6222 | (origin | |
6223 | (method url-fetch) | |
6224 | (uri (bioconductor-uri "ggcyto" version)) | |
6225 | (sha256 | |
6226 | (base32 | |
43bf50ec | 6227 | "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m")))) |
f5f44031 RW |
6228 | (properties `((upstream-name . "ggcyto"))) |
6229 | (build-system r-build-system) | |
6230 | (propagated-inputs | |
6231 | `(("r-data-table" ,r-data-table) | |
6232 | ("r-flowcore" ,r-flowcore) | |
6233 | ("r-flowworkspace" ,r-flowworkspace) | |
6234 | ("r-ggplot2" ,r-ggplot2) | |
6235 | ("r-gridextra" ,r-gridextra) | |
3407dfa6 | 6236 | ("r-hexbin" ,r-hexbin) |
f5f44031 RW |
6237 | ("r-ncdfflow" ,r-ncdfflow) |
6238 | ("r-plyr" ,r-plyr) | |
6239 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6240 | ("r-rlang" ,r-rlang) | |
6241 | ("r-scales" ,r-scales))) | |
0754fefb RW |
6242 | (native-inputs |
6243 | `(("r-knitr" ,r-knitr))) | |
f5f44031 RW |
6244 | (home-page "https://github.com/RGLab/ggcyto/issues") |
6245 | (synopsis "Visualize Cytometry data with ggplot") | |
6246 | (description | |
6247 | "With the dedicated fortify method implemented for @code{flowSet}, | |
6248 | @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow | |
6249 | cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper | |
6250 | and some custom layers also make it easy to add gates and population | |
6251 | statistics to the plot.") | |
6252 | (license license:artistic2.0))) | |
6253 | ||
0dd4b7d7 RW |
6254 | (define-public r-flowviz |
6255 | (package | |
6256 | (name "r-flowviz") | |
d5a53ab7 | 6257 | (version "1.54.0") |
0dd4b7d7 RW |
6258 | (source |
6259 | (origin | |
6260 | (method url-fetch) | |
6261 | (uri (bioconductor-uri "flowViz" version)) | |
6262 | (sha256 | |
6263 | (base32 | |
d5a53ab7 | 6264 | "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k")))) |
0dd4b7d7 RW |
6265 | (properties `((upstream-name . "flowViz"))) |
6266 | (build-system r-build-system) | |
6267 | (propagated-inputs | |
6268 | `(("r-biobase" ,r-biobase) | |
6269 | ("r-flowcore" ,r-flowcore) | |
6270 | ("r-hexbin" ,r-hexbin) | |
6271 | ("r-idpmisc" ,r-idpmisc) | |
6272 | ("r-kernsmooth" ,r-kernsmooth) | |
6273 | ("r-lattice" ,r-lattice) | |
6274 | ("r-latticeextra" ,r-latticeextra) | |
6275 | ("r-mass" ,r-mass) | |
6276 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
062789b8 RW |
6277 | (native-inputs |
6278 | `(("r-knitr" ,r-knitr))) | |
0dd4b7d7 RW |
6279 | (home-page "https://bioconductor.org/packages/flowViz/") |
6280 | (synopsis "Visualization for flow cytometry") | |
6281 | (description | |
6282 | "This package provides visualization tools for flow cytometry data.") | |
6283 | (license license:artistic2.0))) | |
6284 | ||
c8ab9eb1 RW |
6285 | (define-public r-flowclust |
6286 | (package | |
6287 | (name "r-flowclust") | |
33c5b6d7 | 6288 | (version "3.28.0") |
c8ab9eb1 RW |
6289 | (source |
6290 | (origin | |
6291 | (method url-fetch) | |
6292 | (uri (bioconductor-uri "flowClust" version)) | |
6293 | (sha256 | |
6294 | (base32 | |
33c5b6d7 | 6295 | "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq")))) |
c8ab9eb1 RW |
6296 | (properties `((upstream-name . "flowClust"))) |
6297 | (build-system r-build-system) | |
6298 | (arguments | |
6299 | `(#:configure-flags | |
6300 | (list "--configure-args=--enable-bundled-gsl=no"))) | |
6301 | (propagated-inputs | |
6302 | `(("r-biobase" ,r-biobase) | |
6303 | ("r-biocgenerics" ,r-biocgenerics) | |
6304 | ("r-clue" ,r-clue) | |
6305 | ("r-corpcor" ,r-corpcor) | |
6306 | ("r-ellipse" ,r-ellipse) | |
6307 | ("r-flowcore" ,r-flowcore) | |
6308 | ("r-flowviz" ,r-flowviz) | |
6309 | ("r-graph" ,r-graph) | |
6310 | ("r-mnormt" ,r-mnormt))) | |
6311 | (inputs | |
6312 | `(("gsl" ,gsl))) | |
6313 | (native-inputs | |
b347d6c3 RW |
6314 | `(("pkg-config" ,pkg-config) |
6315 | ("r-knitr" ,r-knitr))) | |
c8ab9eb1 RW |
6316 | (home-page "https://bioconductor.org/packages/flowClust") |
6317 | (synopsis "Clustering for flow cytometry") | |
6318 | (description | |
6319 | "This package provides robust model-based clustering using a t-mixture | |
6320 | model with Box-Cox transformation.") | |
6321 | (license license:artistic2.0))) | |
6322 | ||
f1964519 RW |
6323 | ;; TODO: this package bundles an old version of protobuf. It's not easy to |
6324 | ;; make it use our protobuf package instead. | |
6325 | (define-public r-rprotobuflib | |
6326 | (package | |
6327 | (name "r-rprotobuflib") | |
5bab0b7e | 6328 | (version "2.2.0") |
f1964519 RW |
6329 | (source |
6330 | (origin | |
6331 | (method url-fetch) | |
6332 | (uri (bioconductor-uri "RProtoBufLib" version)) | |
6333 | (sha256 | |
6334 | (base32 | |
5bab0b7e | 6335 | "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz")))) |
f1964519 RW |
6336 | (properties `((upstream-name . "RProtoBufLib"))) |
6337 | (build-system r-build-system) | |
6338 | (arguments | |
6339 | `(#:phases | |
6340 | (modify-phases %standard-phases | |
6341 | (add-after 'unpack 'unpack-bundled-sources | |
6342 | (lambda _ | |
6343 | (with-directory-excursion "src" | |
bafade83 | 6344 | (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) |
f1964519 | 6345 | #t))))) |
bafade83 RW |
6346 | (native-inputs |
6347 | `(("r-knitr" ,r-knitr))) | |
f1964519 RW |
6348 | (home-page "https://bioconductor.org/packages/RProtoBufLib/") |
6349 | (synopsis "C++ headers and static libraries of Protocol buffers") | |
6350 | (description | |
6351 | "This package provides the headers and static library of Protocol buffers | |
6352 | for other R packages to compile and link against.") | |
6353 | (license license:bsd-3))) | |
6354 | ||
82c11117 RW |
6355 | (define-public r-flowworkspace |
6356 | (package | |
6357 | (name "r-flowworkspace") | |
1b347814 | 6358 | (version "4.2.0") |
82c11117 RW |
6359 | (source |
6360 | (origin | |
6361 | (method url-fetch) | |
6362 | (uri (bioconductor-uri "flowWorkspace" version)) | |
6363 | (sha256 | |
6364 | (base32 | |
1b347814 | 6365 | "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag")))) |
82c11117 RW |
6366 | (properties `((upstream-name . "flowWorkspace"))) |
6367 | (build-system r-build-system) | |
ece564f0 | 6368 | (arguments |
6369 | `(#:phases | |
6370 | (modify-phases %standard-phases | |
6371 | (add-after 'unpack 'fix-linking | |
6372 | (lambda _ | |
6373 | (substitute* "src/Makevars" | |
6374 | ;; This is to avoid having a plain directory on the list of | |
6375 | ;; libraries to link. | |
6376 | (("\\{h5lib\\}" match) | |
6377 | (string-append match "/libhdf5.a"))) | |
6378 | #t))))) | |
82c11117 | 6379 | (propagated-inputs |
1b347814 | 6380 | `(("r-aws-s3" ,r-aws-s3) |
6381 | ("r-aws-signature" ,r-aws-signature) | |
6382 | ("r-bh" ,r-bh) | |
82c11117 RW |
6383 | ("r-biobase" ,r-biobase) |
6384 | ("r-biocgenerics" ,r-biocgenerics) | |
6385 | ("r-cytolib" ,r-cytolib) | |
6386 | ("r-data-table" ,r-data-table) | |
6387 | ("r-digest" ,r-digest) | |
6388 | ("r-dplyr" ,r-dplyr) | |
6389 | ("r-flowcore" ,r-flowcore) | |
a9af09df | 6390 | ("r-ggplot2" ,r-ggplot2) |
82c11117 | 6391 | ("r-graph" ,r-graph) |
82c11117 RW |
6392 | ("r-lattice" ,r-lattice) |
6393 | ("r-latticeextra" ,r-latticeextra) | |
6394 | ("r-matrixstats" ,r-matrixstats) | |
6395 | ("r-ncdfflow" ,r-ncdfflow) | |
6396 | ("r-rbgl" ,r-rbgl) | |
82c11117 | 6397 | ("r-rcpp" ,r-rcpp) |
a9af09df | 6398 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
82c11117 RW |
6399 | ("r-rcppparallel" ,r-rcppparallel) |
6400 | ("r-rgraphviz" ,r-rgraphviz) | |
a9af09df | 6401 | ("r-rhdf5lib" ,r-rhdf5lib) |
82c11117 RW |
6402 | ("r-rprotobuflib" ,r-rprotobuflib) |
6403 | ("r-scales" ,r-scales) | |
a9af09df RW |
6404 | ("r-xml" ,r-xml))) |
6405 | (native-inputs | |
6406 | `(("r-knitr" ,r-knitr))) | |
82c11117 RW |
6407 | (home-page "https://bioconductor.org/packages/flowWorkspace/") |
6408 | (synopsis "Infrastructure for working with cytometry data") | |
6409 | (description | |
6410 | "This package is designed to facilitate comparison of automated gating | |
6411 | methods against manual gating done in flowJo. This package allows you to | |
6412 | import basic flowJo workspaces into BioConductor and replicate the gating from | |
6413 | flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of | |
6414 | samples, compensation, and transformation are performed so that the output | |
6415 | matches the flowJo analysis.") | |
6416 | (license license:artistic2.0))) | |
6417 | ||
b700b9ec RW |
6418 | (define-public r-flowstats |
6419 | (package | |
6420 | (name "r-flowstats") | |
fd11c7b8 | 6421 | (version "4.2.0") |
b700b9ec RW |
6422 | (source |
6423 | (origin | |
6424 | (method url-fetch) | |
6425 | (uri (bioconductor-uri "flowStats" version)) | |
6426 | (sha256 | |
6427 | (base32 | |
fd11c7b8 | 6428 | "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x")))) |
b700b9ec RW |
6429 | (properties `((upstream-name . "flowStats"))) |
6430 | (build-system r-build-system) | |
6431 | (propagated-inputs | |
6432 | `(("r-biobase" ,r-biobase) | |
6433 | ("r-biocgenerics" ,r-biocgenerics) | |
6434 | ("r-cluster" ,r-cluster) | |
6435 | ("r-fda" ,r-fda) | |
6436 | ("r-flowcore" ,r-flowcore) | |
6437 | ("r-flowviz" ,r-flowviz) | |
6438 | ("r-flowworkspace" ,r-flowworkspace) | |
6439 | ("r-kernsmooth" ,r-kernsmooth) | |
6440 | ("r-ks" ,r-ks) | |
6441 | ("r-lattice" ,r-lattice) | |
6442 | ("r-mass" ,r-mass) | |
6443 | ("r-ncdfflow" ,r-ncdfflow) | |
6444 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6445 | ("r-rrcov" ,r-rrcov))) | |
6446 | (home-page "http://www.github.com/RGLab/flowStats") | |
6447 | (synopsis "Statistical methods for the analysis of flow cytometry data") | |
6448 | (description | |
6449 | "This package provides methods and functionality to analyze flow data | |
6450 | that is beyond the basic infrastructure provided by the @code{flowCore} | |
6451 | package.") | |
6452 | (license license:artistic2.0))) | |
6453 | ||
6aedc805 RW |
6454 | (define-public r-opencyto |
6455 | (package | |
6456 | (name "r-opencyto") | |
5abf0a0d | 6457 | (version "2.2.0") |
6aedc805 RW |
6458 | (source |
6459 | (origin | |
6460 | (method url-fetch) | |
6461 | (uri (bioconductor-uri "openCyto" version)) | |
6462 | (sha256 | |
6463 | (base32 | |
5abf0a0d | 6464 | "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v")))) |
6aedc805 RW |
6465 | (properties `((upstream-name . "openCyto"))) |
6466 | (build-system r-build-system) | |
6467 | (propagated-inputs | |
6468 | `(("r-biobase" ,r-biobase) | |
6469 | ("r-biocgenerics" ,r-biocgenerics) | |
6470 | ("r-clue" ,r-clue) | |
6471 | ("r-data-table" ,r-data-table) | |
6472 | ("r-flowclust" ,r-flowclust) | |
6473 | ("r-flowcore" ,r-flowcore) | |
6474 | ("r-flowstats" ,r-flowstats) | |
6475 | ("r-flowviz" ,r-flowviz) | |
6476 | ("r-flowworkspace" ,r-flowworkspace) | |
6477 | ("r-graph" ,r-graph) | |
6478 | ("r-gtools" ,r-gtools) | |
6479 | ("r-ks" ,r-ks) | |
6480 | ("r-lattice" ,r-lattice) | |
6481 | ("r-mass" ,r-mass) | |
6482 | ("r-ncdfflow" ,r-ncdfflow) | |
6483 | ("r-plyr" ,r-plyr) | |
6484 | ("r-r-utils" ,r-r-utils) | |
6485 | ("r-rbgl" ,r-rbgl) | |
6486 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6487 | ("r-rcpp" ,r-rcpp) | |
6488 | ("r-rrcov" ,r-rrcov))) | |
8f5e1674 RW |
6489 | (native-inputs |
6490 | `(("r-knitr" ,r-knitr))) | |
6aedc805 RW |
6491 | (home-page "https://bioconductor.org/packages/openCyto") |
6492 | (synopsis "Hierarchical gating pipeline for flow cytometry data") | |
6493 | (description | |
6494 | "This package is designed to facilitate the automated gating methods in a | |
6495 | sequential way to mimic the manual gating strategy.") | |
6496 | (license license:artistic2.0))) | |
6497 | ||
7a62d5e0 RW |
6498 | (define-public r-cytoml |
6499 | (package | |
6500 | (name "r-cytoml") | |
63033b15 | 6501 | (version "2.2.1") |
7a62d5e0 RW |
6502 | (source |
6503 | (origin | |
6504 | (method url-fetch) | |
6505 | (uri (bioconductor-uri "CytoML" version)) | |
6506 | (sha256 | |
6507 | (base32 | |
63033b15 | 6508 | "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq")))) |
7a62d5e0 RW |
6509 | (properties `((upstream-name . "CytoML"))) |
6510 | (build-system r-build-system) | |
2b224f90 | 6511 | (arguments |
6512 | `(#:phases | |
6513 | (modify-phases %standard-phases | |
6514 | (add-after 'unpack 'fix-linking | |
6515 | (lambda _ | |
6516 | (substitute* "src/Makevars.in" | |
6517 | ;; This is to avoid having a plain directory on the list of | |
6518 | ;; libraries to link. | |
6519 | (("\\{h5lib\\}" match) | |
6520 | (string-append match "/libhdf5.a"))) | |
6521 | #t))))) | |
7a62d5e0 RW |
6522 | (inputs |
6523 | `(("libxml2" ,libxml2))) | |
6524 | (propagated-inputs | |
6525 | `(("r-base64enc" ,r-base64enc) | |
6526 | ("r-bh" ,r-bh) | |
6527 | ("r-biobase" ,r-biobase) | |
6528 | ("r-corpcor" ,r-corpcor) | |
6529 | ("r-cytolib" ,r-cytolib) | |
6530 | ("r-data-table" ,r-data-table) | |
6531 | ("r-dplyr" ,r-dplyr) | |
6532 | ("r-flowcore" ,r-flowcore) | |
6533 | ("r-flowworkspace" ,r-flowworkspace) | |
6534 | ("r-ggcyto" ,r-ggcyto) | |
6535 | ("r-graph" ,r-graph) | |
6536 | ("r-jsonlite" ,r-jsonlite) | |
6537 | ("r-lattice" ,r-lattice) | |
7a62d5e0 RW |
6538 | ("r-opencyto" ,r-opencyto) |
6539 | ("r-plyr" ,r-plyr) | |
6540 | ("r-rbgl" ,r-rbgl) | |
6541 | ("r-rcpp" ,r-rcpp) | |
8d5a83b7 | 6542 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
7a62d5e0 RW |
6543 | ("r-rcppparallel" ,r-rcppparallel) |
6544 | ("r-rgraphviz" ,r-rgraphviz) | |
8d5a83b7 | 6545 | ("r-rhdf5lib" ,r-rhdf5lib) |
7a62d5e0 RW |
6546 | ("r-rprotobuflib" ,r-rprotobuflib) |
6547 | ("r-runit" ,r-runit) | |
8d5a83b7 | 6548 | ("r-tibble" ,r-tibble) |
7a62d5e0 | 6549 | ("r-xml" ,r-xml) |
ef588757 | 6550 | ("r-xml2" ,r-xml2) |
7a62d5e0 | 6551 | ("r-yaml" ,r-yaml))) |
d49e3f01 RW |
6552 | (native-inputs |
6553 | `(("r-knitr" ,r-knitr))) | |
7a62d5e0 RW |
6554 | (home-page "https://github.com/RGLab/CytoML") |
6555 | (synopsis "GatingML interface for cross platform cytometry data sharing") | |
6556 | (description | |
6557 | "This package provides an interface to implementations of the GatingML2.0 | |
6558 | standard to exchange gated cytometry data with other software platforms.") | |
6559 | (license license:artistic2.0))) | |
6560 | ||
1502751b | 6561 | (define-public r-flowsom |
6562 | (package | |
6563 | (name "r-flowsom") | |
1f7ddaf0 | 6564 | (version "1.22.0") |
1502751b | 6565 | (source |
6566 | (origin | |
6567 | (method url-fetch) | |
6568 | (uri (bioconductor-uri "FlowSOM" version)) | |
6569 | (sha256 | |
6570 | (base32 | |
1f7ddaf0 | 6571 | "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf")))) |
1502751b | 6572 | (properties `((upstream-name . "FlowSOM"))) |
6573 | (build-system r-build-system) | |
6574 | (propagated-inputs | |
6575 | `(("r-biocgenerics" ,r-biocgenerics) | |
6576 | ("r-consensusclusterplus" ,r-consensusclusterplus) | |
ba71567a | 6577 | ("r-cytoml" ,r-cytoml) |
1502751b | 6578 | ("r-flowcore" ,r-flowcore) |
ba71567a | 6579 | ("r-flowworkspace" ,r-flowworkspace) |
1502751b | 6580 | ("r-igraph" ,r-igraph) |
ba71567a | 6581 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
1502751b | 6582 | ("r-tsne" ,r-tsne) |
6583 | ("r-xml" ,r-xml))) | |
6584 | (home-page "https://bioconductor.org/packages/FlowSOM/") | |
6585 | (synopsis "Visualize and interpret cytometry data") | |
6586 | (description | |
6587 | "FlowSOM offers visualization options for cytometry data, by using | |
6588 | self-organizing map clustering and minimal spanning trees.") | |
6589 | (license license:gpl2+))) | |
1adb9cbc | 6590 | |
6591 | (define-public r-mixomics | |
6592 | (package | |
6593 | (name "r-mixomics") | |
0e78ce36 | 6594 | (version "6.14.0") |
1adb9cbc | 6595 | (source |
6596 | (origin | |
6597 | (method url-fetch) | |
6598 | (uri (bioconductor-uri "mixOmics" version)) | |
6599 | (sha256 | |
6600 | (base32 | |
0e78ce36 | 6601 | "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q")))) |
1adb9cbc | 6602 | (properties `((upstream-name . "mixOmics"))) |
6603 | (build-system r-build-system) | |
6604 | (propagated-inputs | |
6605 | `(("r-corpcor" ,r-corpcor) | |
6606 | ("r-dplyr" ,r-dplyr) | |
6607 | ("r-ellipse" ,r-ellipse) | |
0e78ce36 | 6608 | ("r-ggrepel" ,r-ggrepel) |
1adb9cbc | 6609 | ("r-ggplot2" ,r-ggplot2) |
6610 | ("r-gridextra" ,r-gridextra) | |
6611 | ("r-igraph" ,r-igraph) | |
6612 | ("r-lattice" ,r-lattice) | |
6613 | ("r-mass" ,r-mass) | |
6614 | ("r-matrixstats" ,r-matrixstats) | |
6615 | ("r-rarpack" ,r-rarpack) | |
6616 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6617 | ("r-reshape2" ,r-reshape2) | |
6618 | ("r-tidyr" ,r-tidyr))) | |
9669bc17 RW |
6619 | (native-inputs |
6620 | `(("r-knitr" ,r-knitr))) | |
1adb9cbc | 6621 | (home-page "http://www.mixOmics.org") |
6622 | (synopsis "Multivariate methods for exploration of biological datasets") | |
6623 | (description | |
6624 | "mixOmics offers a wide range of multivariate methods for the exploration | |
6625 | and integration of biological datasets with a particular focus on variable | |
6626 | selection. The package proposes several sparse multivariate models we have | |
6627 | developed to identify the key variables that are highly correlated, and/or | |
6628 | explain the biological outcome of interest. The data that can be analysed | |
6629 | with mixOmics may come from high throughput sequencing technologies, such as | |
6630 | omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but | |
6631 | also beyond the realm of omics (e.g. spectral imaging). The methods | |
6632 | implemented in mixOmics can also handle missing values without having to | |
6633 | delete entire rows with missing data.") | |
6634 | (license license:gpl2+))) | |
a0efa069 | 6635 | |
6636 | (define-public r-depecher | |
fafaeab4 | 6637 | (package ;Source/Weave error |
a0efa069 | 6638 | (name "r-depecher") |
fafaeab4 | 6639 | (version "1.6.0") |
a0efa069 | 6640 | (source |
6641 | (origin | |
6642 | (method url-fetch) | |
6643 | (uri (bioconductor-uri "DepecheR" version)) | |
6644 | (sha256 | |
6645 | (base32 | |
fafaeab4 | 6646 | "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469")))) |
a0efa069 | 6647 | (properties `((upstream-name . "DepecheR"))) |
6648 | (build-system r-build-system) | |
a0efa069 | 6649 | (propagated-inputs |
6650 | `(("r-beanplot" ,r-beanplot) | |
a0efa069 | 6651 | ("r-dosnow" ,r-dosnow) |
6652 | ("r-dplyr" ,r-dplyr) | |
2c8433ca | 6653 | ("r-fnn" ,r-fnn) |
a0efa069 | 6654 | ("r-foreach" ,r-foreach) |
6655 | ("r-ggplot2" ,r-ggplot2) | |
fafaeab4 | 6656 | ("r-gmodels" ,r-gmodels) |
a0efa069 | 6657 | ("r-gplots" ,r-gplots) |
6658 | ("r-mass" ,r-mass) | |
6659 | ("r-matrixstats" ,r-matrixstats) | |
6660 | ("r-mixomics" ,r-mixomics) | |
6661 | ("r-moments" ,r-moments) | |
6662 | ("r-rcpp" ,r-rcpp) | |
6663 | ("r-rcppeigen" ,r-rcppeigen) | |
6664 | ("r-reshape2" ,r-reshape2) | |
2c8433ca | 6665 | ("r-robustbase" ,r-robustbase) |
a0efa069 | 6666 | ("r-viridis" ,r-viridis))) |
bf3722f9 RW |
6667 | (native-inputs |
6668 | `(("r-knitr" ,r-knitr))) | |
a0efa069 | 6669 | (home-page "https://bioconductor.org/packages/DepecheR/") |
6670 | (synopsis "Identify traits of clusters in high-dimensional entities") | |
6671 | (description | |
6672 | "The purpose of this package is to identify traits in a dataset that can | |
6673 | separate groups. This is done on two levels. First, clustering is performed, | |
6674 | using an implementation of sparse K-means. Secondly, the generated clusters | |
6675 | are used to predict outcomes of groups of individuals based on their | |
6676 | distribution of observations in the different clusters. As certain clusters | |
6677 | with separating information will be identified, and these clusters are defined | |
6678 | by a sparse number of variables, this method can reduce the complexity of | |
6679 | data, to only emphasize the data that actually matters.") | |
6680 | (license license:expat))) | |
b46a0ee7 | 6681 | |
bb88417f RW |
6682 | (define-public r-rcistarget |
6683 | (package | |
6684 | (name "r-rcistarget") | |
64813573 | 6685 | (version "1.10.0") |
bb88417f RW |
6686 | (source |
6687 | (origin | |
6688 | (method url-fetch) | |
6689 | (uri (bioconductor-uri "RcisTarget" version)) | |
6690 | (sha256 | |
6691 | (base32 | |
64813573 | 6692 | "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf")))) |
bb88417f RW |
6693 | (properties `((upstream-name . "RcisTarget"))) |
6694 | (build-system r-build-system) | |
6695 | (propagated-inputs | |
6696 | `(("r-aucell" ,r-aucell) | |
6697 | ("r-biocgenerics" ,r-biocgenerics) | |
6698 | ("r-data-table" ,r-data-table) | |
6699 | ("r-feather" ,r-feather) | |
6700 | ("r-gseabase" ,r-gseabase) | |
6701 | ("r-r-utils" ,r-r-utils) | |
6702 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
93235b1e RW |
6703 | (native-inputs |
6704 | `(("r-knitr" ,r-knitr))) | |
bb88417f RW |
6705 | (home-page "https://aertslab.org/#scenic") |
6706 | (synopsis "Identify transcription factor binding motifs enriched on a gene list") | |
6707 | (description | |
6708 | "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) | |
6709 | over-represented on a gene list. In a first step, RcisTarget selects DNA | |
6710 | motifs that are significantly over-represented in the surroundings of the | |
6711 | @dfn{transcription start site} (TSS) of the genes in the gene-set. This is | |
6712 | achieved by using a database that contains genome-wide cross-species rankings | |
6713 | for each motif. The motifs that are then annotated to TFs and those that have | |
6714 | a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for | |
6715 | each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. | |
6716 | genes in the gene-set that are ranked above the leading edge).") | |
6717 | (license license:gpl3))) | |
6718 | ||
b46a0ee7 RW |
6719 | (define-public r-cicero |
6720 | (package | |
6721 | (name "r-cicero") | |
589ac422 | 6722 | (version "1.8.1") |
b46a0ee7 RW |
6723 | (source |
6724 | (origin | |
6725 | (method url-fetch) | |
6726 | (uri (bioconductor-uri "cicero" version)) | |
6727 | (sha256 | |
6728 | (base32 | |
589ac422 | 6729 | "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr")))) |
b46a0ee7 RW |
6730 | (build-system r-build-system) |
6731 | (propagated-inputs | |
6732 | `(("r-assertthat" ,r-assertthat) | |
6733 | ("r-biobase" ,r-biobase) | |
6734 | ("r-biocgenerics" ,r-biocgenerics) | |
6735 | ("r-data-table" ,r-data-table) | |
6736 | ("r-dplyr" ,r-dplyr) | |
6737 | ("r-fnn" ,r-fnn) | |
6738 | ("r-genomicranges" ,r-genomicranges) | |
6739 | ("r-ggplot2" ,r-ggplot2) | |
6740 | ("r-glasso" ,r-glasso) | |
6741 | ("r-gviz" ,r-gviz) | |
6742 | ("r-igraph" ,r-igraph) | |
6743 | ("r-iranges" ,r-iranges) | |
6744 | ("r-matrix" ,r-matrix) | |
6745 | ("r-monocle" ,r-monocle) | |
6746 | ("r-plyr" ,r-plyr) | |
6747 | ("r-reshape2" ,r-reshape2) | |
6748 | ("r-s4vectors" ,r-s4vectors) | |
1893092d | 6749 | ("r-stringi" ,r-stringi) |
b46a0ee7 RW |
6750 | ("r-stringr" ,r-stringr) |
6751 | ("r-tibble" ,r-tibble) | |
5ea4f604 | 6752 | ("r-tidyr" ,r-tidyr) |
b46a0ee7 | 6753 | ("r-vgam" ,r-vgam))) |
6bd6097e RW |
6754 | (native-inputs |
6755 | `(("r-knitr" ,r-knitr))) | |
b46a0ee7 RW |
6756 | (home-page "https://bioconductor.org/packages/cicero/") |
6757 | (synopsis "Predict cis-co-accessibility from single-cell data") | |
6758 | (description | |
6759 | "Cicero computes putative cis-regulatory maps from single-cell chromatin | |
6760 | accessibility data. It also extends the monocle package for use in chromatin | |
6761 | accessibility data.") | |
6762 | (license license:expat))) | |
14bb1c48 RW |
6763 | |
6764 | ;; This is the latest commit on the "monocle3" branch. | |
6765 | (define-public r-cicero-monocle3 | |
6766 | (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") | |
6767 | (revision "1")) | |
6768 | (package (inherit r-cicero) | |
6769 | (name "r-cicero-monocle3") | |
6770 | (version (git-version "1.3.2" revision commit)) | |
6771 | (source | |
6772 | (origin | |
6773 | (method git-fetch) | |
6774 | (uri (git-reference | |
b0e7b699 | 6775 | (url "https://github.com/cole-trapnell-lab/cicero-release") |
14bb1c48 RW |
6776 | (commit commit))) |
6777 | (file-name (git-file-name name version)) | |
6778 | (sha256 | |
6779 | (base32 | |
6780 | "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) | |
6781 | (propagated-inputs | |
6782 | `(("r-monocle3" ,r-monocle3) | |
6783 | ,@(alist-delete "r-monocle" | |
6784 | (package-propagated-inputs r-cicero))))))) | |
a9815a6c RW |
6785 | |
6786 | (define-public r-cistopic | |
6787 | (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") | |
6788 | (revision "0")) | |
6789 | (package | |
6790 | (name "r-cistopic") | |
6791 | (version (git-version "0.2.1" revision commit)) | |
6792 | (source | |
6793 | (origin | |
6794 | (method git-fetch) | |
6795 | (uri (git-reference | |
b0e7b699 | 6796 | (url "https://github.com/aertslab/cisTopic") |
a9815a6c RW |
6797 | (commit commit))) |
6798 | (file-name (git-file-name name version)) | |
6799 | (sha256 | |
6800 | (base32 | |
6801 | "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) | |
6802 | (build-system r-build-system) | |
6803 | (propagated-inputs | |
6804 | `(("r-aucell" ,r-aucell) | |
6805 | ("r-data-table" ,r-data-table) | |
6806 | ("r-dplyr" ,r-dplyr) | |
6807 | ("r-dosnow" ,r-dosnow) | |
6808 | ("r-dt" ,r-dt) | |
6809 | ("r-feather" ,r-feather) | |
6810 | ("r-fitdistrplus" ,r-fitdistrplus) | |
6811 | ("r-genomicranges" ,r-genomicranges) | |
6812 | ("r-ggplot2" ,r-ggplot2) | |
6813 | ("r-lda" ,r-lda) | |
6814 | ("r-matrix" ,r-matrix) | |
6815 | ("r-plyr" ,r-plyr) | |
6816 | ("r-rcistarget" ,r-rcistarget) | |
6817 | ("r-rtracklayer" ,r-rtracklayer) | |
6818 | ("r-s4vectors" ,r-s4vectors))) | |
6819 | (home-page "https://github.com/aertslab/cisTopic") | |
6820 | (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") | |
6821 | (description | |
6822 | "The sparse nature of single cell epigenomics data can be overruled using | |
6823 | probabilistic modelling methods such as @dfn{Latent Dirichlet | |
6824 | Allocation} (LDA). This package allows the probabilistic modelling of | |
6825 | cis-regulatory topics (cisTopics) from single cell epigenomics data, and | |
6826 | includes functionalities to identify cell states based on the contribution of | |
6827 | cisTopics and explore the nature and regulatory proteins driving them.") | |
6828 | (license license:gpl3)))) | |
d85c0f98 RW |
6829 | |
6830 | (define-public r-genie3 | |
6831 | (package | |
6832 | (name "r-genie3") | |
5d1bd611 | 6833 | (version "1.12.0") |
d85c0f98 RW |
6834 | (source |
6835 | (origin | |
6836 | (method url-fetch) | |
6837 | (uri (bioconductor-uri "GENIE3" version)) | |
6838 | (sha256 | |
6839 | (base32 | |
5d1bd611 | 6840 | "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5")))) |
d85c0f98 RW |
6841 | (properties `((upstream-name . "GENIE3"))) |
6842 | (build-system r-build-system) | |
6843 | (propagated-inputs `(("r-reshape2" ,r-reshape2))) | |
b3280883 RW |
6844 | (native-inputs |
6845 | `(("r-knitr" ,r-knitr))) | |
d85c0f98 RW |
6846 | (home-page "https://bioconductor.org/packages/GENIE3") |
6847 | (synopsis "Gene network inference with ensemble of trees") | |
6848 | (description | |
6849 | "This package implements the GENIE3 algorithm for inferring gene | |
6850 | regulatory networks from expression data.") | |
6851 | (license license:gpl2+))) | |
db316d73 RW |
6852 | |
6853 | (define-public r-roc | |
6854 | (package | |
6855 | (name "r-roc") | |
e7b61ba7 | 6856 | (version "1.66.0") |
db316d73 RW |
6857 | (source |
6858 | (origin | |
6859 | (method url-fetch) | |
6860 | (uri (bioconductor-uri "ROC" version)) | |
6861 | (sha256 | |
6862 | (base32 | |
e7b61ba7 | 6863 | "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9")))) |
db316d73 RW |
6864 | (properties `((upstream-name . "ROC"))) |
6865 | (build-system r-build-system) | |
3672b74f RW |
6866 | (propagated-inputs |
6867 | `(("r-knitr" ,r-knitr))) | |
db316d73 RW |
6868 | (home-page "https://www.bioconductor.org/packages/ROC/") |
6869 | (synopsis "Utilities for ROC curves") | |
6870 | (description | |
6871 | "This package provides utilities for @dfn{Receiver Operating | |
6872 | Characteristic} (ROC) curves, with a focus on micro arrays.") | |
6873 | (license license:artistic2.0))) | |
46721dea RW |
6874 | |
6875 | (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 | |
6876 | (package | |
6877 | (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") | |
6878 | (version "0.6.0") | |
6879 | (source | |
6880 | (origin | |
6881 | (method url-fetch) | |
6882 | (uri (bioconductor-uri | |
6883 | "IlluminaHumanMethylation450kanno.ilmn12.hg19" | |
6884 | version 'annotation)) | |
6885 | (sha256 | |
6886 | (base32 | |
6887 | "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) | |
6888 | (properties | |
6889 | `((upstream-name | |
6890 | . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) | |
6891 | (build-system r-build-system) | |
6892 | (propagated-inputs `(("r-minfi" ,r-minfi))) | |
6893 | (home-page | |
6894 | "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") | |
6895 | (synopsis "Annotation for Illumina's 450k methylation arrays") | |
6896 | (description | |
6897 | "This package provides manifests and annotation for Illumina's 450k array | |
6898 | data.") | |
6899 | (license license:artistic2.0))) | |
38babeaa RW |
6900 | |
6901 | (define-public r-watermelon | |
6902 | (package | |
6903 | (name "r-watermelon") | |
9f6e2bfe | 6904 | (version "1.34.0") |
38babeaa RW |
6905 | (source |
6906 | (origin | |
6907 | (method url-fetch) | |
6908 | (uri (bioconductor-uri "wateRmelon" version)) | |
6909 | (sha256 | |
6910 | (base32 | |
9f6e2bfe | 6911 | "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f")))) |
38babeaa RW |
6912 | (properties `((upstream-name . "wateRmelon"))) |
6913 | (build-system r-build-system) | |
6914 | (propagated-inputs | |
6915 | `(("r-biobase" ,r-biobase) | |
6916 | ("r-illuminahumanmethylation450kanno-ilmn12-hg19" | |
6917 | ,r-illuminahumanmethylation450kanno-ilmn12-hg19) | |
6918 | ("r-illuminaio" ,r-illuminaio) | |
6919 | ("r-limma" ,r-limma) | |
6920 | ("r-lumi" ,r-lumi) | |
6921 | ("r-matrixstats" ,r-matrixstats) | |
6922 | ("r-methylumi" ,r-methylumi) | |
6923 | ("r-roc" ,r-roc))) | |
6924 | (home-page "https://bioconductor.org/packages/wateRmelon/") | |
6925 | (synopsis "Illumina 450 methylation array normalization and metrics") | |
6926 | (description | |
6927 | "The standard index of DNA methylation (beta) is computed from methylated | |
6928 | and unmethylated signal intensities. Betas calculated from raw signal | |
6929 | intensities perform well, but using 11 methylomic datasets we demonstrate that | |
6930 | quantile normalization methods produce marked improvement. The commonly used | |
6931 | procedure of normalizing betas is inferior to the separate normalization of M | |
6932 | and U, and it is also advantageous to normalize Type I and Type II assays | |
6933 | separately. This package provides 15 flavours of betas and three performance | |
6934 | metrics, with methods for objects produced by the @code{methylumi} and | |
6935 | @code{minfi} packages.") | |
6936 | (license license:gpl3))) | |
7d2cb646 RW |
6937 | |
6938 | (define-public r-gdsfmt | |
6939 | (package | |
6940 | (name "r-gdsfmt") | |
a50779b8 | 6941 | (version "1.26.0") |
7d2cb646 RW |
6942 | (source |
6943 | (origin | |
6944 | (method url-fetch) | |
6945 | (uri (bioconductor-uri "gdsfmt" version)) | |
6946 | (sha256 | |
6947 | (base32 | |
a50779b8 | 6948 | "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a")) |
7d2cb646 RW |
6949 | (modules '((guix build utils))) |
6950 | ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build | |
6951 | ;; them and link with system libraries instead. | |
6952 | (snippet | |
6953 | '(begin | |
6954 | (for-each delete-file-recursively | |
6955 | '("src/LZ4" | |
6956 | "src/XZ" | |
6957 | "src/ZLIB")) | |
6958 | (substitute* "src/Makevars" | |
6959 | (("all: \\$\\(SHLIB\\)") "all:") | |
6960 | (("\\$\\(SHLIB\\): liblzma.a") "") | |
6961 | (("(ZLIB|LZ4)/.*") "") | |
6962 | (("CoreArray/dVLIntGDS.cpp.*") | |
6963 | "CoreArray/dVLIntGDS.cpp") | |
6964 | (("CoreArray/dVLIntGDS.o.*") | |
6965 | "CoreArray/dVLIntGDS.o") | |
6966 | (("PKG_LIBS = ./liblzma.a") | |
6967 | "PKG_LIBS = -llz4")) | |
6968 | (substitute* "src/CoreArray/dStream.h" | |
6969 | (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) | |
6970 | (string-append "include <" header ">"))) | |
6971 | #t)))) | |
6972 | (properties `((upstream-name . "gdsfmt"))) | |
6973 | (build-system r-build-system) | |
6974 | (inputs | |
6975 | `(("lz4" ,lz4) | |
6976 | ("xz" ,xz) | |
6977 | ("zlib" ,zlib))) | |
f4954b0b RW |
6978 | (native-inputs |
6979 | `(("r-knitr" ,r-knitr))) | |
7d2cb646 RW |
6980 | (home-page "http://corearray.sourceforge.net/") |
6981 | (synopsis | |
6982 | "R Interface to CoreArray Genomic Data Structure (GDS) Files") | |
6983 | (description | |
6984 | "This package provides a high-level R interface to CoreArray @dfn{Genomic | |
6985 | Data Structure} (GDS) data files, which are portable across platforms with | |
6986 | hierarchical structure to store multiple scalable array-oriented data sets | |
6987 | with metadata information. It is suited for large-scale datasets, especially | |
6988 | for data which are much larger than the available random-access memory. The | |
6989 | @code{gdsfmt} package offers efficient operations specifically designed for | |
6990 | integers of less than 8 bits, since a diploid genotype, like | |
6991 | @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a | |
6992 | byte. Data compression and decompression are available with relatively | |
6993 | efficient random access. It is also allowed to read a GDS file in parallel | |
6994 | with multiple R processes supported by the package @code{parallel}.") | |
6995 | (license license:lgpl3))) | |
6b5f59c7 RW |
6996 | |
6997 | (define-public r-bigmelon | |
6998 | (package | |
6999 | (name "r-bigmelon") | |
64f9fb30 | 7000 | (version "1.16.0") |
6b5f59c7 RW |
7001 | (source |
7002 | (origin | |
7003 | (method url-fetch) | |
7004 | (uri (bioconductor-uri "bigmelon" version)) | |
7005 | (sha256 | |
7006 | (base32 | |
64f9fb30 | 7007 | "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7")))) |
6b5f59c7 RW |
7008 | (properties `((upstream-name . "bigmelon"))) |
7009 | (build-system r-build-system) | |
7010 | (propagated-inputs | |
7011 | `(("r-biobase" ,r-biobase) | |
7012 | ("r-biocgenerics" ,r-biocgenerics) | |
7013 | ("r-gdsfmt" ,r-gdsfmt) | |
7014 | ("r-geoquery" ,r-geoquery) | |
7015 | ("r-methylumi" ,r-methylumi) | |
7016 | ("r-minfi" ,r-minfi) | |
7017 | ("r-watermelon" ,r-watermelon))) | |
7018 | (home-page "https://bioconductor.org/packages/bigmelon/") | |
7019 | (synopsis "Illumina methylation array analysis for large experiments") | |
7020 | (description | |
7021 | "This package provides methods for working with Illumina arrays using the | |
7022 | @code{gdsfmt} package.") | |
7023 | (license license:gpl3))) | |
739b2d10 | 7024 | |
e5dfcd8e RW |
7025 | (define-public r-seqbias |
7026 | (package | |
7027 | (name "r-seqbias") | |
42e00c09 | 7028 | (version "1.38.0") |
e5dfcd8e RW |
7029 | (source |
7030 | (origin | |
7031 | (method url-fetch) | |
7032 | (uri (bioconductor-uri "seqbias" version)) | |
7033 | (sha256 | |
7034 | (base32 | |
42e00c09 | 7035 | "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2")))) |
e5dfcd8e RW |
7036 | (properties `((upstream-name . "seqbias"))) |
7037 | (build-system r-build-system) | |
7038 | (propagated-inputs | |
7039 | `(("r-biostrings" ,r-biostrings) | |
7040 | ("r-genomicranges" ,r-genomicranges) | |
7041 | ("r-rhtslib" ,r-rhtslib))) | |
e5dfcd8e RW |
7042 | (home-page "https://bioconductor.org/packages/seqbias/") |
7043 | (synopsis "Estimation of per-position bias in high-throughput sequencing data") | |
7044 | (description | |
7045 | "This package implements a model of per-position sequencing bias in | |
7046 | high-throughput sequencing data using a simple Bayesian network, the structure | |
7047 | and parameters of which are trained on a set of aligned reads and a reference | |
7048 | genome sequence.") | |
7049 | (license license:lgpl3))) | |
7050 | ||
63daca1e RJ |
7051 | (define-public r-snplocs-hsapiens-dbsnp144-grch37 |
7052 | (package | |
7053 | (name "r-snplocs-hsapiens-dbsnp144-grch37") | |
7054 | (version "0.99.20") | |
7055 | (source (origin | |
7056 | (method url-fetch) | |
7057 | (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" | |
7058 | version 'annotation)) | |
7059 | (sha256 | |
7060 | (base32 | |
7061 | "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) | |
7062 | (build-system r-build-system) | |
7063 | ;; As this package provides little more than a very large data file it | |
7064 | ;; doesn't make sense to build substitutes. | |
7065 | (arguments `(#:substitutable? #f)) | |
7066 | (propagated-inputs | |
7067 | `(("r-biocgenerics" ,r-biocgenerics) | |
7068 | ("r-s4vectors" ,r-s4vectors) | |
7069 | ("r-iranges" ,r-iranges) | |
7070 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7071 | ("r-genomicranges" ,r-genomicranges) | |
7072 | ("r-bsgenome" ,r-bsgenome) | |
7073 | ("r-biostrings" ,r-biostrings))) | |
7074 | (home-page | |
7075 | "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") | |
7076 | (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") | |
7077 | (description "This package provides SNP locations and alleles for Homo | |
7078 | sapiens extracted from NCBI dbSNP Build 144. The source data files used for | |
7079 | this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped | |
7080 | to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a | |
7081 | patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, | |
1408e2ab | 7082 | X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for |
63daca1e RJ |
7083 | the mitochondrion chromosome. Therefore, the SNPs in this package can be |
7084 | injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the | |
7085 | correct position but this injection will exclude chrM (i.e. nothing will be | |
7086 | injected in that sequence).") | |
7087 | (license license:artistic2.0))) | |
7088 | ||
bb0024dc RW |
7089 | (define-public r-reqon |
7090 | (package | |
7091 | (name "r-reqon") | |
0c53f27d | 7092 | (version "1.36.0") |
bb0024dc RW |
7093 | (source |
7094 | (origin | |
7095 | (method url-fetch) | |
7096 | (uri (bioconductor-uri "ReQON" version)) | |
7097 | (sha256 | |
7098 | (base32 | |
0c53f27d | 7099 | "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq")))) |
bb0024dc RW |
7100 | (properties `((upstream-name . "ReQON"))) |
7101 | (build-system r-build-system) | |
7102 | (propagated-inputs | |
7103 | `(("r-rjava" ,r-rjava) | |
7104 | ("r-rsamtools" ,r-rsamtools) | |
7105 | ("r-seqbias" ,r-seqbias))) | |
7106 | (home-page "https://bioconductor.org/packages/ReQON/") | |
7107 | (synopsis "Recalibrating quality of nucleotides") | |
7108 | (description | |
7109 | "This package provides an implementation of an algorithm for | |
7110 | recalibrating the base quality scores for aligned sequencing data in BAM | |
7111 | format.") | |
7112 | (license license:gpl2))) | |
7113 | ||
739b2d10 RW |
7114 | (define-public r-wavcluster |
7115 | (package | |
7116 | (name "r-wavcluster") | |
fd7e23b5 | 7117 | (version "2.24.0") |
739b2d10 RW |
7118 | (source |
7119 | (origin | |
7120 | (method url-fetch) | |
7121 | (uri (bioconductor-uri "wavClusteR" version)) | |
7122 | (sha256 | |
7123 | (base32 | |
fd7e23b5 | 7124 | "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi")))) |
739b2d10 RW |
7125 | (properties `((upstream-name . "wavClusteR"))) |
7126 | (build-system r-build-system) | |
7127 | (propagated-inputs | |
7128 | `(("r-biocgenerics" ,r-biocgenerics) | |
7129 | ("r-biostrings" ,r-biostrings) | |
7130 | ("r-foreach" ,r-foreach) | |
7131 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7132 | ("r-genomicranges" ,r-genomicranges) | |
7133 | ("r-ggplot2" ,r-ggplot2) | |
7134 | ("r-hmisc" ,r-hmisc) | |
7135 | ("r-iranges" ,r-iranges) | |
7136 | ("r-mclust" ,r-mclust) | |
7137 | ("r-rsamtools" ,r-rsamtools) | |
7138 | ("r-rtracklayer" ,r-rtracklayer) | |
7139 | ("r-s4vectors" ,r-s4vectors) | |
7140 | ("r-seqinr" ,r-seqinr) | |
fd7e23b5 | 7141 | ("r-stringr" ,r-stringr))) |
12b255f2 RW |
7142 | (native-inputs |
7143 | `(("r-knitr" ,r-knitr))) | |
739b2d10 RW |
7144 | (home-page "https://bioconductor.org/packages/wavClusteR/") |
7145 | (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") | |
7146 | (description | |
7147 | "This package provides an integrated pipeline for the analysis of | |
7148 | PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from | |
7149 | sequencing errors, SNPs and additional non-experimental sources by a non- | |
7150 | parametric mixture model. The protein binding sites (clusters) are then | |
7151 | resolved at high resolution and cluster statistics are estimated using a | |
7152 | rigorous Bayesian framework. Post-processing of the results, data export for | |
7153 | UCSC genome browser visualization and motif search analysis are provided. In | |
e40ecf8a | 7154 | addition, the package integrates RNA-Seq data to estimate the False |
739b2d10 RW |
7155 | Discovery Rate of cluster detection. Key functions support parallel multicore |
7156 | computing. While wavClusteR was designed for PAR-CLIP data analysis, it can | |
7157 | be applied to the analysis of other NGS data obtained from experimental | |
7158 | procedures that induce nucleotide substitutions (e.g. BisSeq).") | |
7159 | (license license:gpl2))) | |
853211a5 RW |
7160 | |
7161 | (define-public r-timeseriesexperiment | |
7162 | (package | |
7163 | (name "r-timeseriesexperiment") | |
87f704b4 | 7164 | (version "1.8.0") |
853211a5 RW |
7165 | (source |
7166 | (origin | |
7167 | (method url-fetch) | |
7168 | (uri (bioconductor-uri "TimeSeriesExperiment" version)) | |
7169 | (sha256 | |
7170 | (base32 | |
87f704b4 | 7171 | "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn")))) |
853211a5 RW |
7172 | (properties |
7173 | `((upstream-name . "TimeSeriesExperiment"))) | |
7174 | (build-system r-build-system) | |
7175 | (propagated-inputs | |
7176 | `(("r-deseq2" ,r-deseq2) | |
7177 | ("r-dplyr" ,r-dplyr) | |
7178 | ("r-dynamictreecut" ,r-dynamictreecut) | |
7179 | ("r-edger" ,r-edger) | |
7180 | ("r-ggplot2" ,r-ggplot2) | |
7181 | ("r-hmisc" ,r-hmisc) | |
7182 | ("r-limma" ,r-limma) | |
7183 | ("r-magrittr" ,r-magrittr) | |
7184 | ("r-proxy" ,r-proxy) | |
7185 | ("r-s4vectors" ,r-s4vectors) | |
7186 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
7187 | ("r-tibble" ,r-tibble) | |
7188 | ("r-tidyr" ,r-tidyr) | |
7189 | ("r-vegan" ,r-vegan) | |
7190 | ("r-viridis" ,r-viridis))) | |
49dd5041 RW |
7191 | (native-inputs |
7192 | `(("r-knitr" ,r-knitr))) | |
853211a5 RW |
7193 | (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") |
7194 | (synopsis "Analysis for short time-series data") | |
7195 | (description | |
7196 | "This package is a visualization and analysis toolbox for short time | |
7197 | course data which includes dimensionality reduction, clustering, two-sample | |
7198 | differential expression testing and gene ranking techniques. The package also | |
7199 | provides methods for retrieving enriched pathways.") | |
7200 | (license license:lgpl3+))) | |
df8576e5 RW |
7201 | |
7202 | (define-public r-variantfiltering | |
7203 | (package | |
7204 | (name "r-variantfiltering") | |
45ea773f | 7205 | (version "1.26.0") |
df8576e5 RW |
7206 | (source |
7207 | (origin | |
7208 | (method url-fetch) | |
7209 | (uri (bioconductor-uri "VariantFiltering" version)) | |
7210 | (sha256 | |
7211 | (base32 | |
45ea773f | 7212 | "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5")))) |
df8576e5 RW |
7213 | (properties |
7214 | `((upstream-name . "VariantFiltering"))) | |
7215 | (build-system r-build-system) | |
7216 | (propagated-inputs | |
7217 | `(("r-annotationdbi" ,r-annotationdbi) | |
7218 | ("r-biobase" ,r-biobase) | |
7219 | ("r-biocgenerics" ,r-biocgenerics) | |
7220 | ("r-biocparallel" ,r-biocparallel) | |
7221 | ("r-biostrings" ,r-biostrings) | |
7222 | ("r-bsgenome" ,r-bsgenome) | |
7223 | ("r-dt" ,r-dt) | |
7224 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7225 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7226 | ("r-genomicranges" ,r-genomicranges) | |
7227 | ("r-genomicscores" ,r-genomicscores) | |
7228 | ("r-graph" ,r-graph) | |
7229 | ("r-gviz" ,r-gviz) | |
7230 | ("r-iranges" ,r-iranges) | |
7231 | ("r-rbgl" ,r-rbgl) | |
7232 | ("r-rsamtools" ,r-rsamtools) | |
7233 | ("r-s4vectors" ,r-s4vectors) | |
7234 | ("r-shiny" ,r-shiny) | |
7235 | ("r-shinyjs" ,r-shinyjs) | |
7236 | ("r-shinythemes" ,r-shinythemes) | |
7237 | ("r-shinytree" ,r-shinytree) | |
7238 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
7239 | ("r-variantannotation" ,r-variantannotation) | |
7240 | ("r-xvector" ,r-xvector))) | |
7241 | (home-page "https://github.com/rcastelo/VariantFiltering") | |
7242 | (synopsis "Filtering of coding and non-coding genetic variants") | |
7243 | (description | |
7244 | "Filter genetic variants using different criteria such as inheritance | |
7245 | model, amino acid change consequence, minor allele frequencies across human | |
7246 | populations, splice site strength, conservation, etc.") | |
7247 | (license license:artistic2.0))) | |
f5349b4d RW |
7248 | |
7249 | (define-public r-genomegraphs | |
7250 | (package | |
7251 | (name "r-genomegraphs") | |
053a2127 | 7252 | (version "1.46.0") |
f5349b4d RW |
7253 | (source |
7254 | (origin | |
7255 | (method url-fetch) | |
7256 | (uri (bioconductor-uri "GenomeGraphs" version)) | |
7257 | (sha256 | |
7258 | (base32 | |
053a2127 | 7259 | "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) |
f5349b4d RW |
7260 | (properties `((upstream-name . "GenomeGraphs"))) |
7261 | (build-system r-build-system) | |
7262 | (propagated-inputs | |
7263 | `(("r-biomart" ,r-biomart))) | |
7264 | (home-page "https://bioconductor.org/packages/GenomeGraphs/") | |
7265 | (synopsis "Plotting genomic information from Ensembl") | |
7266 | (description | |
7267 | "Genomic data analyses requires integrated visualization of known genomic | |
7268 | information and new experimental data. GenomeGraphs uses the biomaRt package | |
7269 | to perform live annotation queries to Ensembl and translates this to e.g. | |
7270 | gene/transcript structures in viewports of the grid graphics package. This | |
7271 | results in genomic information plotted together with your data. Another | |
7272 | strength of GenomeGraphs is to plot different data types such as array CGH, | |
7273 | gene expression, sequencing and other data, together in one plot using the | |
7274 | same genome coordinate system.") | |
7275 | (license license:artistic2.0))) | |
2a360cf6 RW |
7276 | |
7277 | (define-public r-wavetiling | |
7278 | (package | |
7279 | (name "r-wavetiling") | |
e13f9773 | 7280 | (version "1.28.0") |
2a360cf6 RW |
7281 | (source |
7282 | (origin | |
7283 | (method url-fetch) | |
7284 | (uri (bioconductor-uri "waveTiling" version)) | |
7285 | (sha256 | |
7286 | (base32 | |
e13f9773 | 7287 | "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) |
2a360cf6 RW |
7288 | (properties `((upstream-name . "waveTiling"))) |
7289 | (build-system r-build-system) | |
7290 | (propagated-inputs | |
7291 | `(("r-affy" ,r-affy) | |
7292 | ("r-biobase" ,r-biobase) | |
7293 | ("r-biostrings" ,r-biostrings) | |
7294 | ("r-genomegraphs" ,r-genomegraphs) | |
7295 | ("r-genomicranges" ,r-genomicranges) | |
7296 | ("r-iranges" ,r-iranges) | |
7297 | ("r-oligo" ,r-oligo) | |
7298 | ("r-oligoclasses" ,r-oligoclasses) | |
7299 | ("r-preprocesscore" ,r-preprocesscore) | |
7300 | ("r-waveslim" ,r-waveslim))) | |
7301 | (home-page "https://r-forge.r-project.org/projects/wavetiling/") | |
7302 | (synopsis "Wavelet-based models for tiling array transcriptome analysis") | |
7303 | (description | |
7304 | "This package is designed to conduct transcriptome analysis for tiling | |
7305 | arrays based on fast wavelet-based functional models.") | |
7306 | (license license:gpl2+))) | |
d80a1569 RW |
7307 | |
7308 | (define-public r-variancepartition | |
7309 | (package | |
7310 | (name "r-variancepartition") | |
44ecd5f7 | 7311 | (version "1.20.0") |
d80a1569 RW |
7312 | (source |
7313 | (origin | |
7314 | (method url-fetch) | |
7315 | (uri (bioconductor-uri "variancePartition" version)) | |
7316 | (sha256 | |
7317 | (base32 | |
44ecd5f7 | 7318 | "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah")))) |
d80a1569 RW |
7319 | (properties |
7320 | `((upstream-name . "variancePartition"))) | |
7321 | (build-system r-build-system) | |
7322 | (propagated-inputs | |
7323 | `(("r-biobase" ,r-biobase) | |
326746e1 | 7324 | ("r-biocparallel" ,r-biocparallel) |
d80a1569 RW |
7325 | ("r-colorramps" ,r-colorramps) |
7326 | ("r-doparallel" ,r-doparallel) | |
7327 | ("r-foreach" ,r-foreach) | |
7328 | ("r-ggplot2" ,r-ggplot2) | |
7329 | ("r-gplots" ,r-gplots) | |
7330 | ("r-iterators" ,r-iterators) | |
7331 | ("r-limma" ,r-limma) | |
7332 | ("r-lme4" ,r-lme4) | |
7333 | ("r-lmertest" ,r-lmertest) | |
7334 | ("r-mass" ,r-mass) | |
7335 | ("r-pbkrtest" ,r-pbkrtest) | |
7336 | ("r-progress" ,r-progress) | |
7337 | ("r-reshape2" ,r-reshape2) | |
7338 | ("r-scales" ,r-scales))) | |
fbbaf5ae RW |
7339 | (native-inputs |
7340 | `(("r-knitr" ,r-knitr))) | |
d80a1569 RW |
7341 | (home-page "https://bioconductor.org/packages/variancePartition/") |
7342 | (synopsis "Analyze variation in gene expression experiments") | |
7343 | (description | |
7344 | "This is a package providing tools to quantify and interpret multiple | |
7345 | sources of biological and technical variation in gene expression experiments. | |
7346 | It uses a linear mixed model to quantify variation in gene expression | |
7347 | attributable to individual, tissue, time point, or technical variables. The | |
7348 | package includes dream differential expression analysis for repeated | |
7349 | measures.") | |
7350 | (license license:gpl2+))) | |
16e2e4f2 | 7351 | |
7352 | (define-public r-htqpcr | |
7353 | (package | |
7354 | (name "r-htqpcr") | |
949626f2 | 7355 | (version "1.44.0") |
16e2e4f2 | 7356 | (source |
7357 | (origin | |
7358 | (method url-fetch) | |
7359 | (uri (bioconductor-uri "HTqPCR" version)) | |
7360 | (sha256 | |
7361 | (base32 | |
949626f2 | 7362 | "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji")))) |
16e2e4f2 | 7363 | (properties `((upstream-name . "HTqPCR"))) |
7364 | (build-system r-build-system) | |
7365 | (propagated-inputs | |
7366 | `(("r-affy" ,r-affy) | |
7367 | ("r-biobase" ,r-biobase) | |
7368 | ("r-gplots" ,r-gplots) | |
7369 | ("r-limma" ,r-limma) | |
7370 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
486a0800 TGR |
7371 | (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" |
7372 | "groups/bertone/software/HTqPCR.pdf")) | |
16e2e4f2 | 7373 | (synopsis "Automated analysis of high-throughput qPCR data") |
7374 | (description | |
7375 | "Analysis of Ct values from high throughput quantitative real-time | |
7376 | PCR (qPCR) assays across multiple conditions or replicates. The input data | |
7377 | can be from spatially-defined formats such ABI TaqMan Low Density Arrays or | |
7378 | OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad | |
7379 | Laboratories; conventional 96- or 384-well plates; or microfluidic devices | |
7380 | such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data | |
7381 | loading, quality assessment, normalization, visualization and parametric or | |
7382 | non-parametric testing for statistical significance in Ct values between | |
7383 | features (e.g. genes, microRNAs).") | |
7384 | (license license:artistic2.0))) | |
86fb2c63 | 7385 | |
7386 | (define-public r-unifiedwmwqpcr | |
7387 | (package | |
7388 | (name "r-unifiedwmwqpcr") | |
fa7e2429 | 7389 | (version "1.26.0") |
86fb2c63 | 7390 | (source |
7391 | (origin | |
7392 | (method url-fetch) | |
7393 | (uri (bioconductor-uri "unifiedWMWqPCR" version)) | |
7394 | (sha256 | |
7395 | (base32 | |
fa7e2429 | 7396 | "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv")))) |
86fb2c63 | 7397 | (properties |
7398 | `((upstream-name . "unifiedWMWqPCR"))) | |
7399 | (build-system r-build-system) | |
7400 | (propagated-inputs | |
7401 | `(("r-biocgenerics" ,r-biocgenerics) | |
7402 | ("r-htqpcr" ,r-htqpcr))) | |
7403 | (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") | |
7404 | (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") | |
7405 | (description | |
b5b0ee3b | 7406 | "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR |
86fb2c63 | 7407 | data. This modified test allows for testing differential expression in qPCR |
7408 | data.") | |
7409 | (license license:gpl2+))) | |
72b67e0b RW |
7410 | |
7411 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put | |
7412 | ;; it here. | |
7413 | (define-public r-activedriverwgs | |
7414 | (package | |
7415 | (name "r-activedriverwgs") | |
5412da84 | 7416 | (version "1.1.1") |
72b67e0b RW |
7417 | (source |
7418 | (origin | |
7419 | (method url-fetch) | |
7420 | (uri (cran-uri "ActiveDriverWGS" version)) | |
7421 | (sha256 | |
7422 | (base32 | |
5412da84 | 7423 | "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say")))) |
72b67e0b RW |
7424 | (properties |
7425 | `((upstream-name . "ActiveDriverWGS"))) | |
7426 | (build-system r-build-system) | |
7427 | (propagated-inputs | |
7428 | `(("r-biostrings" ,r-biostrings) | |
7429 | ("r-bsgenome" ,r-bsgenome) | |
7430 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
7431 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7432 | ("r-genomicranges" ,r-genomicranges) | |
7433 | ("r-iranges" ,r-iranges) | |
72b67e0b | 7434 | ("r-s4vectors" ,r-s4vectors))) |
e1ce10e3 RW |
7435 | (native-inputs |
7436 | `(("r-knitr" ,r-knitr))) | |
72b67e0b RW |
7437 | (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") |
7438 | (synopsis "Driver discovery tool for cancer whole genomes") | |
7439 | (description | |
7440 | "This package provides a method for finding an enrichment of cancer | |
7441 | simple somatic mutations (SNVs and Indels) in functional elements across the | |
7442 | human genome. ActiveDriverWGS detects coding and noncoding driver elements | |
7443 | using whole genome sequencing data.") | |
7444 | (license license:gpl3))) | |
8e6f63dd RW |
7445 | |
7446 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put | |
7447 | ;; it here. | |
7448 | (define-public r-activepathways | |
7449 | (package | |
7450 | (name "r-activepathways") | |
a9a91280 | 7451 | (version "1.0.2") |
8e6f63dd RW |
7452 | (source |
7453 | (origin | |
7454 | (method url-fetch) | |
7455 | (uri (cran-uri "ActivePathways" version)) | |
7456 | (sha256 | |
7457 | (base32 | |
a9a91280 | 7458 | "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l")))) |
8e6f63dd RW |
7459 | (properties |
7460 | `((upstream-name . "ActivePathways"))) | |
7461 | (build-system r-build-system) | |
7462 | (propagated-inputs | |
7463 | `(("r-data-table" ,r-data-table) | |
a9a91280 | 7464 | ("r-ggplot2" ,r-ggplot2))) |
229736aa RW |
7465 | (native-inputs |
7466 | `(("r-knitr" ,r-knitr))) | |
8e6f63dd RW |
7467 | (home-page "https://cran.r-project.org/web/packages/ActivePathways/") |
7468 | (synopsis "Multivariate pathway enrichment analysis") | |
7469 | (description | |
7470 | "This package represents an integrative method of analyzing multi omics | |
7471 | data that conducts enrichment analysis of annotated gene sets. ActivePathways | |
7472 | uses a statistical data fusion approach, rationalizes contributing evidence | |
7473 | and highlights associated genes, improving systems-level understanding of | |
7474 | cellular organization in health and disease.") | |
7475 | (license license:gpl3))) | |
d11d6fea RW |
7476 | |
7477 | (define-public r-bgmix | |
7478 | (package | |
7479 | (name "r-bgmix") | |
fad5da32 | 7480 | (version "1.50.0") |
d11d6fea RW |
7481 | (source |
7482 | (origin | |
7483 | (method url-fetch) | |
7484 | (uri (bioconductor-uri "BGmix" version)) | |
7485 | (sha256 | |
7486 | (base32 | |
fad5da32 | 7487 | "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50")))) |
d11d6fea RW |
7488 | (properties `((upstream-name . "BGmix"))) |
7489 | (build-system r-build-system) | |
7490 | (propagated-inputs | |
7491 | `(("r-kernsmooth" ,r-kernsmooth))) | |
7492 | (home-page "https://bioconductor.org/packages/BGmix/") | |
7493 | (synopsis "Bayesian models for differential gene expression") | |
7494 | (description | |
7495 | "This package provides fully Bayesian mixture models for differential | |
7496 | gene expression.") | |
7497 | (license license:gpl2))) | |
75eb1149 RW |
7498 | |
7499 | (define-public r-bgx | |
7500 | (package | |
7501 | (name "r-bgx") | |
3cebe274 | 7502 | (version "1.56.0") |
75eb1149 RW |
7503 | (source |
7504 | (origin | |
7505 | (method url-fetch) | |
7506 | (uri (bioconductor-uri "bgx" version)) | |
7507 | (sha256 | |
7508 | (base32 | |
3cebe274 | 7509 | "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im")))) |
75eb1149 RW |
7510 | (properties `((upstream-name . "bgx"))) |
7511 | (build-system r-build-system) | |
7512 | (propagated-inputs | |
7513 | `(("r-affy" ,r-affy) | |
7514 | ("r-biobase" ,r-biobase) | |
7515 | ("r-gcrma" ,r-gcrma) | |
7516 | ("r-rcpp" ,r-rcpp))) | |
7517 | (home-page "https://bioconductor.org/packages/bgx/") | |
7518 | (synopsis "Bayesian gene expression") | |
7519 | (description | |
7520 | "This package provides tools for Bayesian integrated analysis of | |
7521 | Affymetrix GeneChips.") | |
7522 | (license license:gpl2))) | |
6bd50acf RW |
7523 | |
7524 | (define-public r-bhc | |
7525 | (package | |
7526 | (name "r-bhc") | |
2219bef1 | 7527 | (version "1.42.0") |
6bd50acf RW |
7528 | (source |
7529 | (origin | |
7530 | (method url-fetch) | |
7531 | (uri (bioconductor-uri "BHC" version)) | |
7532 | (sha256 | |
7533 | (base32 | |
2219bef1 | 7534 | "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn")))) |
6bd50acf RW |
7535 | (properties `((upstream-name . "BHC"))) |
7536 | (build-system r-build-system) | |
7537 | (home-page "https://bioconductor.org/packages/BHC/") | |
7538 | (synopsis "Bayesian hierarchical clustering") | |
7539 | (description | |
7540 | "The method implemented in this package performs bottom-up hierarchical | |
7541 | clustering, using a Dirichlet Process (infinite mixture) to model uncertainty | |
7542 | in the data and Bayesian model selection to decide at each step which clusters | |
7543 | to merge. This avoids several limitations of traditional methods, for example | |
7544 | how many clusters there should be and how to choose a principled distance | |
7545 | metric. This implementation accepts multinomial (i.e. discrete, with 2+ | |
7546 | categories) or time-series data. This version also includes a randomised | |
7547 | algorithm which is more efficient for larger data sets.") | |
7548 | (license license:gpl3))) | |
de9374b7 RW |
7549 | |
7550 | (define-public r-bicare | |
7551 | (package | |
7552 | (name "r-bicare") | |
4ec66569 | 7553 | (version "1.48.0") |
de9374b7 RW |
7554 | (source |
7555 | (origin | |
7556 | (method url-fetch) | |
7557 | (uri (bioconductor-uri "BicARE" version)) | |
7558 | (sha256 | |
7559 | (base32 | |
4ec66569 | 7560 | "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k")))) |
de9374b7 RW |
7561 | (properties `((upstream-name . "BicARE"))) |
7562 | (build-system r-build-system) | |
7563 | (propagated-inputs | |
7564 | `(("r-biobase" ,r-biobase) | |
7565 | ("r-gseabase" ,r-gseabase) | |
7566 | ("r-multtest" ,r-multtest))) | |
7567 | (home-page "http://bioinfo.curie.fr") | |
7568 | (synopsis "Biclustering analysis and results exploration") | |
7569 | (description | |
7570 | "This is a package for biclustering analysis and exploration of | |
7571 | results.") | |
7572 | (license license:gpl2))) | |
40fe63ad RW |
7573 | |
7574 | (define-public r-bifet | |
7575 | (package | |
7576 | (name "r-bifet") | |
d57be633 | 7577 | (version "1.10.0") |
40fe63ad RW |
7578 | (source |
7579 | (origin | |
7580 | (method url-fetch) | |
7581 | (uri (bioconductor-uri "BiFET" version)) | |
7582 | (sha256 | |
7583 | (base32 | |
d57be633 | 7584 | "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a")))) |
40fe63ad RW |
7585 | (properties `((upstream-name . "BiFET"))) |
7586 | (build-system r-build-system) | |
7587 | (propagated-inputs | |
7588 | `(("r-genomicranges" ,r-genomicranges) | |
7589 | ("r-poibin" ,r-poibin))) | |
a54fd409 RW |
7590 | (native-inputs |
7591 | `(("r-knitr" ,r-knitr))) | |
40fe63ad RW |
7592 | (home-page "https://bioconductor.org/packages/BiFET") |
7593 | (synopsis "Bias-free footprint enrichment test") | |
7594 | (description | |
7595 | "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are | |
7596 | over-represented in target regions compared to background regions after | |
7597 | correcting for the bias arising from the imbalance in read counts and GC | |
7598 | contents between the target and background regions. For a given TF k, BiFET | |
7599 | tests the null hypothesis that the target regions have the same probability of | |
7600 | having footprints for the TF k as the background regions while correcting for | |
7601 | the read count and GC content bias.") | |
7602 | (license license:gpl3))) | |
e823337c RW |
7603 | |
7604 | (define-public r-rsbml | |
7605 | (package | |
7606 | (name "r-rsbml") | |
3320f044 | 7607 | (version "2.48.0") |
e823337c RW |
7608 | (source |
7609 | (origin | |
7610 | (method url-fetch) | |
7611 | (uri (bioconductor-uri "rsbml" version)) | |
7612 | (sha256 | |
7613 | (base32 | |
3320f044 | 7614 | "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61")))) |
e823337c RW |
7615 | (properties `((upstream-name . "rsbml"))) |
7616 | (build-system r-build-system) | |
7617 | (inputs | |
7618 | `(("libsbml" ,libsbml) | |
7619 | ("zlib" ,zlib))) | |
7620 | (propagated-inputs | |
7621 | `(("r-biocgenerics" ,r-biocgenerics) | |
7622 | ("r-graph" ,r-graph))) | |
7623 | (native-inputs | |
7624 | `(("pkg-config" ,pkg-config))) | |
7625 | (home-page "http://www.sbml.org") | |
7626 | (synopsis "R support for SBML") | |
7627 | (description | |
7628 | "This package provides an R interface to libsbml for SBML parsing, | |
7629 | validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") | |
7630 | (license license:artistic2.0))) | |
75a8bb31 RW |
7631 | |
7632 | (define-public r-hypergraph | |
7633 | (package | |
7634 | (name "r-hypergraph") | |
294fd58a | 7635 | (version "1.62.0") |
75a8bb31 RW |
7636 | (source |
7637 | (origin | |
7638 | (method url-fetch) | |
7639 | (uri (bioconductor-uri "hypergraph" version)) | |
7640 | (sha256 | |
7641 | (base32 | |
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75a8bb31 RW |
7643 | (properties `((upstream-name . "hypergraph"))) |
7644 | (build-system r-build-system) | |
7645 | (propagated-inputs | |
7646 | `(("r-graph" ,r-graph))) | |
7647 | (home-page "https://bioconductor.org/packages/hypergraph") | |
7648 | (synopsis "Hypergraph data structures") | |
7649 | (description | |
7650 | "This package implements some simple capabilities for representing and | |
7651 | manipulating hypergraphs.") | |
7652 | (license license:artistic2.0))) | |
5aef09bd RW |
7653 | |
7654 | (define-public r-hyperdraw | |
7655 | (package | |
7656 | (name "r-hyperdraw") | |
249b7030 | 7657 | (version "1.42.0") |
5aef09bd RW |
7658 | (source |
7659 | (origin | |
7660 | (method url-fetch) | |
7661 | (uri (bioconductor-uri "hyperdraw" version)) | |
7662 | (sha256 | |
7663 | (base32 | |
249b7030 | 7664 | "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz")))) |
5aef09bd RW |
7665 | (properties `((upstream-name . "hyperdraw"))) |
7666 | (build-system r-build-system) | |
7667 | (inputs `(("graphviz" ,graphviz))) | |
7668 | (propagated-inputs | |
7669 | `(("r-graph" ,r-graph) | |
7670 | ("r-hypergraph" ,r-hypergraph) | |
7671 | ("r-rgraphviz" ,r-rgraphviz))) | |
7672 | (home-page "https://bioconductor.org/packages/hyperdraw") | |
7673 | (synopsis "Visualizing hypergraphs") | |
7674 | (description | |
7675 | "This package provides functions for visualizing hypergraphs.") | |
7676 | (license license:gpl2+))) | |
6ca6f866 RW |
7677 | |
7678 | (define-public r-biggr | |
7679 | (package | |
7680 | (name "r-biggr") | |
0f94a9ed | 7681 | (version "1.26.0") |
6ca6f866 RW |
7682 | (source |
7683 | (origin | |
7684 | (method url-fetch) | |
7685 | (uri (bioconductor-uri "BiGGR" version)) | |
7686 | (sha256 | |
7687 | (base32 | |
0f94a9ed | 7688 | "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y")))) |
6ca6f866 RW |
7689 | (properties `((upstream-name . "BiGGR"))) |
7690 | (build-system r-build-system) | |
7691 | (propagated-inputs | |
7692 | `(("r-hyperdraw" ,r-hyperdraw) | |
7693 | ("r-hypergraph" ,r-hypergraph) | |
7694 | ("r-lim" ,r-lim) | |
7695 | ("r-limsolve" ,r-limsolve) | |
7696 | ("r-rsbml" ,r-rsbml) | |
7697 | ("r-stringr" ,r-stringr))) | |
7698 | (home-page "https://bioconductor.org/packages/BiGGR/") | |
7699 | (synopsis "Constraint based modeling using metabolic reconstruction databases") | |
7700 | (description | |
7701 | "This package provides an interface to simulate metabolic reconstruction | |
7702 | from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic | |
7703 | reconstruction databases. The package facilitates @dfn{flux balance | |
7704 | analysis} (FBA) and the sampling of feasible flux distributions. Metabolic | |
7705 | networks and estimated fluxes can be visualized with hypergraphs.") | |
7706 | (license license:gpl3+))) | |
820373db RW |
7707 | |
7708 | (define-public r-bigmemoryextras | |
7709 | (package | |
7710 | (name "r-bigmemoryextras") | |
e80f8262 | 7711 | (version "1.38.0") |
820373db RW |
7712 | (source |
7713 | (origin | |
7714 | (method url-fetch) | |
7715 | (uri (bioconductor-uri "bigmemoryExtras" version)) | |
7716 | (sha256 | |
7717 | (base32 | |
e80f8262 | 7718 | "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj")))) |
820373db RW |
7719 | (properties |
7720 | `((upstream-name . "bigmemoryExtras"))) | |
7721 | (build-system r-build-system) | |
7722 | (propagated-inputs | |
7723 | `(("r-bigmemory" ,r-bigmemory))) | |
eef9c99c RW |
7724 | (native-inputs |
7725 | `(("r-knitr" ,r-knitr))) | |
820373db RW |
7726 | (home-page "https://github.com/phaverty/bigmemoryExtras") |
7727 | (synopsis "Extension of the bigmemory package") | |
7728 | (description | |
7729 | "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds | |
7730 | safety and convenience features to the @code{filebacked.big.matrix} class from | |
7731 | the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by | |
7732 | monitoring and gracefully restoring the connection to on-disk data and it also | |
7230f6d5 | 7733 | protects against accidental data modification with a file-system-based |
820373db RW |
7734 | permissions system. Utilities are provided for using @code{BigMatrix}-derived |
7735 | classes as @code{assayData} matrices within the @code{Biobase} package's | |
7736 | @code{eSet} family of classes. @code{BigMatrix} provides some optimizations | |
7737 | related to attaching to, and indexing into, file-backed matrices with | |
7738 | dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, | |
7739 | a file-backed matrix with factor properties.") | |
7740 | (license license:artistic2.0))) | |
d38775b1 RW |
7741 | |
7742 | (define-public r-bigpint | |
7743 | (package | |
7744 | (name "r-bigpint") | |
1e288678 | 7745 | (version "1.6.0") |
d38775b1 RW |
7746 | (source |
7747 | (origin | |
7748 | (method url-fetch) | |
7749 | (uri (bioconductor-uri "bigPint" version)) | |
7750 | (sha256 | |
7751 | (base32 | |
1e288678 | 7752 | "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis")))) |
d38775b1 RW |
7753 | (properties `((upstream-name . "bigPint"))) |
7754 | (build-system r-build-system) | |
7755 | (propagated-inputs | |
d0badcc1 RW |
7756 | `(("r-delayedarray" ,r-delayedarray) |
7757 | ("r-dplyr" ,r-dplyr) | |
d38775b1 RW |
7758 | ("r-ggally" ,r-ggally) |
7759 | ("r-ggplot2" ,r-ggplot2) | |
7760 | ("r-gridextra" ,r-gridextra) | |
7761 | ("r-hexbin" ,r-hexbin) | |
7762 | ("r-hmisc" ,r-hmisc) | |
7763 | ("r-htmlwidgets" ,r-htmlwidgets) | |
7764 | ("r-plotly" ,r-plotly) | |
7765 | ("r-plyr" ,r-plyr) | |
7766 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
7767 | ("r-reshape" ,r-reshape) | |
7768 | ("r-shiny" ,r-shiny) | |
7769 | ("r-shinycssloaders" ,r-shinycssloaders) | |
7770 | ("r-shinydashboard" ,r-shinydashboard) | |
7771 | ("r-stringr" ,r-stringr) | |
d0badcc1 | 7772 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
d38775b1 | 7773 | ("r-tidyr" ,r-tidyr))) |
1f2f01ae RW |
7774 | (native-inputs |
7775 | `(("r-knitr" ,r-knitr))) | |
d38775b1 RW |
7776 | (home-page "https://github.com/lindsayrutter/bigPint") |
7777 | (synopsis "Big multivariate data plotted interactively") | |
7778 | (description | |
7779 | "This package provides methods for visualizing large multivariate | |
7780 | datasets using static and interactive scatterplot matrices, parallel | |
7781 | coordinate plots, volcano plots, and litre plots. It includes examples for | |
7782 | visualizing RNA-sequencing datasets and differentially expressed genes.") | |
7783 | (license license:gpl3))) | |
991554fc RW |
7784 | |
7785 | (define-public r-chemminer | |
7786 | (package | |
7787 | (name "r-chemminer") | |
95ef2681 | 7788 | (version "3.42.0") |
991554fc RW |
7789 | (source |
7790 | (origin | |
7791 | (method url-fetch) | |
7792 | (uri (bioconductor-uri "ChemmineR" version)) | |
7793 | (sha256 | |
7794 | (base32 | |
95ef2681 | 7795 | "14q9zhhxgkx5skj424i2rbjdbp5j8jfkxspkhnkwv5i45cvkgh19")))) |
991554fc RW |
7796 | (properties `((upstream-name . "ChemmineR"))) |
7797 | (build-system r-build-system) | |
7798 | (propagated-inputs | |
7799 | `(("r-base64enc" ,r-base64enc) | |
7800 | ("r-bh" ,r-bh) | |
7801 | ("r-biocgenerics" ,r-biocgenerics) | |
7802 | ("r-dbi" ,r-dbi) | |
7803 | ("r-digest" ,r-digest) | |
7804 | ("r-dt" ,r-dt) | |
7805 | ("r-ggplot2" ,r-ggplot2) | |
7806 | ("r-gridextra" ,r-gridextra) | |
7807 | ("r-png" ,r-png) | |
7808 | ("r-rcpp" ,r-rcpp) | |
7809 | ("r-rcurl" ,r-rcurl) | |
7810 | ("r-rjson" ,r-rjson) | |
7811 | ("r-rsvg" ,r-rsvg))) | |
06908a73 RW |
7812 | (native-inputs |
7813 | `(("r-knitr" ,r-knitr))) | |
991554fc RW |
7814 | (home-page "https://github.com/girke-lab/ChemmineR") |
7815 | (synopsis "Cheminformatics toolkit for R") | |
7816 | (description | |
7817 | "ChemmineR is a cheminformatics package for analyzing drug-like small | |
7818 | molecule data in R. It contains functions for efficient processing of large | |
7819 | numbers of molecules, physicochemical/structural property predictions, | |
7820 | structural similarity searching, classification and clustering of compound | |
7821 | libraries with a wide spectrum of algorithms. In addition, it offers | |
7822 | visualization functions for compound clustering results and chemical | |
7823 | structures.") | |
7824 | (license license:artistic2.0))) | |
48bcbef0 RW |
7825 | |
7826 | (define-public r-bioassayr | |
7827 | (package | |
7828 | (name "r-bioassayr") | |
2f36b040 | 7829 | (version "1.28.0") |
48bcbef0 RW |
7830 | (source |
7831 | (origin | |
7832 | (method url-fetch) | |
7833 | (uri (bioconductor-uri "bioassayR" version)) | |
7834 | (sha256 | |
7835 | (base32 | |
2f36b040 | 7836 | "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f")))) |
48bcbef0 RW |
7837 | (properties `((upstream-name . "bioassayR"))) |
7838 | (build-system r-build-system) | |
7839 | (propagated-inputs | |
7840 | `(("r-biocgenerics" ,r-biocgenerics) | |
7841 | ("r-chemminer" ,r-chemminer) | |
7842 | ("r-dbi" ,r-dbi) | |
7843 | ("r-matrix" ,r-matrix) | |
7844 | ("r-rjson" ,r-rjson) | |
7845 | ("r-rsqlite" ,r-rsqlite) | |
7846 | ("r-xml" ,r-xml))) | |
faaf2b35 RW |
7847 | (native-inputs |
7848 | `(("r-knitr" ,r-knitr))) | |
48bcbef0 RW |
7849 | (home-page "https://github.com/TylerBackman/bioassayR") |
7850 | (synopsis "Cross-target analysis of small molecule bioactivity") | |
7851 | (description | |
7852 | "bioassayR is a computational tool that enables simultaneous analysis of | |
7853 | thousands of bioassay experiments performed over a diverse set of compounds | |
7854 | and biological targets. Unique features include support for large-scale | |
7855 | cross-target analyses of both public and custom bioassays, generation of | |
7856 | @dfn{high throughput screening fingerprints} (HTSFPs), and an optional | |
7857 | preloaded database that provides access to a substantial portion of publicly | |
7858 | available bioactivity data.") | |
7859 | (license license:artistic2.0))) | |
29fd736a RW |
7860 | |
7861 | (define-public r-biobroom | |
7862 | (package | |
7863 | (name "r-biobroom") | |
95e30d8f | 7864 | (version "1.22.0") |
29fd736a RW |
7865 | (source |
7866 | (origin | |
7867 | (method url-fetch) | |
7868 | (uri (bioconductor-uri "biobroom" version)) | |
7869 | (sha256 | |
7870 | (base32 | |
95e30d8f | 7871 | "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv")))) |
29fd736a RW |
7872 | (properties `((upstream-name . "biobroom"))) |
7873 | (build-system r-build-system) | |
7874 | (propagated-inputs | |
7875 | `(("r-biobase" ,r-biobase) | |
7876 | ("r-broom" ,r-broom) | |
7877 | ("r-dplyr" ,r-dplyr) | |
7878 | ("r-tidyr" ,r-tidyr))) | |
e09ca033 RW |
7879 | (native-inputs |
7880 | `(("r-knitr" ,r-knitr))) | |
29fd736a RW |
7881 | (home-page "https://github.com/StoreyLab/biobroom") |
7882 | (synopsis "Turn Bioconductor objects into tidy data frames") | |
7883 | (description | |
7884 | "This package contains methods for converting standard objects | |
7885 | constructed by bioinformatics packages, especially those in Bioconductor, and | |
7886 | converting them to @code{tidy} data. It thus serves as a complement to the | |
7887 | @code{broom} package, and follows the same tidy, augment, glance division of | |
7888 | tidying methods. Tidying data makes it easy to recombine, reshape and | |
7889 | visualize bioinformatics analyses.") | |
7890 | ;; Any version of the LGPL. | |
7891 | (license license:lgpl3+))) | |
c373223e RW |
7892 | |
7893 | (define-public r-graphite | |
7894 | (package | |
7895 | (name "r-graphite") | |
26224e09 | 7896 | (version "1.36.0") |
c373223e RW |
7897 | (source |
7898 | (origin | |
7899 | (method url-fetch) | |
7900 | (uri (bioconductor-uri "graphite" version)) | |
7901 | (sha256 | |
7902 | (base32 | |
26224e09 | 7903 | "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk")))) |
c373223e RW |
7904 | (properties `((upstream-name . "graphite"))) |
7905 | (build-system r-build-system) | |
7906 | (propagated-inputs | |
7907 | `(("r-annotationdbi" ,r-annotationdbi) | |
7908 | ("r-checkmate" ,r-checkmate) | |
7909 | ("r-graph" ,r-graph) | |
7910 | ("r-httr" ,r-httr) | |
7911 | ("r-rappdirs" ,r-rappdirs))) | |
7912 | (home-page "https://bioconductor.org/packages/graphite/") | |
7913 | (synopsis "Networks from pathway databases") | |
7914 | (description | |
7915 | "Graphite provides networks derived from eight public pathway databases, | |
7916 | and automates the conversion of node identifiers (e.g. from Entrez IDs to gene | |
7917 | symbols).") | |
7918 | (license license:agpl3+))) | |
f388834e RW |
7919 | |
7920 | (define-public r-reactomepa | |
7921 | (package | |
7922 | (name "r-reactomepa") | |
a4f4a552 | 7923 | (version "1.34.0") |
f388834e RW |
7924 | (source |
7925 | (origin | |
7926 | (method url-fetch) | |
7927 | (uri (bioconductor-uri "ReactomePA" version)) | |
7928 | (sha256 | |
7929 | (base32 | |
a4f4a552 | 7930 | "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m")))) |
f388834e RW |
7931 | (properties `((upstream-name . "ReactomePA"))) |
7932 | (build-system r-build-system) | |
7933 | (propagated-inputs | |
7934 | `(("r-annotationdbi" ,r-annotationdbi) | |
7935 | ("r-dose" ,r-dose) | |
7936 | ("r-enrichplot" ,r-enrichplot) | |
7937 | ("r-ggplot2" ,r-ggplot2) | |
7938 | ("r-ggraph" ,r-ggraph) | |
7939 | ("r-graphite" ,r-graphite) | |
7940 | ("r-igraph" ,r-igraph) | |
7941 | ("r-reactome-db" ,r-reactome-db))) | |
affb4ab3 RW |
7942 | (native-inputs |
7943 | `(("r-knitr" ,r-knitr))) | |
f388834e RW |
7944 | (home-page "https://guangchuangyu.github.io/software/ReactomePA") |
7945 | (synopsis "Reactome pathway analysis") | |
7946 | (description | |
7947 | "This package provides functions for pathway analysis based on the | |
7948 | REACTOME pathway database. It implements enrichment analysis, gene set | |
7949 | enrichment analysis and several functions for visualization.") | |
7950 | (license license:gpl2))) | |
21afe920 RW |
7951 | |
7952 | (define-public r-ebarrays | |
7953 | (package | |
7954 | (name "r-ebarrays") | |
b0f3bfe4 | 7955 | (version "2.54.0") |
21afe920 RW |
7956 | (source |
7957 | (origin | |
7958 | (method url-fetch) | |
7959 | (uri (bioconductor-uri "EBarrays" version)) | |
7960 | (sha256 | |
7961 | (base32 | |
b0f3bfe4 | 7962 | "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd")))) |
21afe920 RW |
7963 | (properties `((upstream-name . "EBarrays"))) |
7964 | (build-system r-build-system) | |
7965 | (propagated-inputs | |
7966 | `(("r-biobase" ,r-biobase) | |
7967 | ("r-cluster" ,r-cluster) | |
7968 | ("r-lattice" ,r-lattice))) | |
7969 | (home-page "https://bioconductor.org/packages/EBarrays/") | |
7970 | (synopsis "Gene clustering and differential expression identification") | |
7971 | (description | |
7972 | "EBarrays provides tools for the analysis of replicated/unreplicated | |
7973 | microarray data.") | |
7974 | (license license:gpl2+))) | |
f180be29 RW |
7975 | |
7976 | (define-public r-bioccasestudies | |
7977 | (package | |
7978 | (name "r-bioccasestudies") | |
7dced9ad | 7979 | (version "1.52.0") |
f180be29 RW |
7980 | (source |
7981 | (origin | |
7982 | (method url-fetch) | |
7983 | (uri (bioconductor-uri "BiocCaseStudies" version)) | |
7984 | (sha256 | |
7985 | (base32 | |
7dced9ad | 7986 | "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1")))) |
f180be29 RW |
7987 | (properties |
7988 | `((upstream-name . "BiocCaseStudies"))) | |
7989 | (build-system r-build-system) | |
7990 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
7991 | (home-page "https://bioconductor.org/packages/BiocCaseStudies") | |
7992 | (synopsis "Support for the case studies monograph") | |
7993 | (description | |
7994 | "This package provides software and data to support the case studies | |
7995 | monograph.") | |
7996 | (license license:artistic2.0))) | |
49f0860b RW |
7997 | |
7998 | (define-public r-biocgraph | |
7999 | (package | |
8000 | (name "r-biocgraph") | |
abc18fc5 | 8001 | (version "1.52.0") |
49f0860b RW |
8002 | (source |
8003 | (origin | |
8004 | (method url-fetch) | |
8005 | (uri (bioconductor-uri "biocGraph" version)) | |
8006 | (sha256 | |
8007 | (base32 | |
abc18fc5 | 8008 | "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75")))) |
49f0860b RW |
8009 | (properties `((upstream-name . "biocGraph"))) |
8010 | (build-system r-build-system) | |
8011 | (propagated-inputs | |
8012 | `(("r-biocgenerics" ,r-biocgenerics) | |
8013 | ("r-geneplotter" ,r-geneplotter) | |
8014 | ("r-graph" ,r-graph) | |
8015 | ("r-rgraphviz" ,r-rgraphviz))) | |
8016 | (home-page "https://bioconductor.org/packages/biocGraph/") | |
8017 | (synopsis "Graph examples and use cases in Bioinformatics") | |
8018 | (description | |
8019 | "This package provides examples and code that make use of the | |
8020 | different graph related packages produced by Bioconductor.") | |
8021 | (license license:artistic2.0))) | |
244270e6 RW |
8022 | |
8023 | (define-public r-experimenthub | |
8024 | (package | |
8025 | (name "r-experimenthub") | |
49a72858 | 8026 | (version "1.16.0") |
244270e6 RW |
8027 | (source |
8028 | (origin | |
8029 | (method url-fetch) | |
8030 | (uri (bioconductor-uri "ExperimentHub" version)) | |
8031 | (sha256 | |
8032 | (base32 | |
49a72858 | 8033 | "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg")))) |
244270e6 RW |
8034 | (properties `((upstream-name . "ExperimentHub"))) |
8035 | (build-system r-build-system) | |
8036 | (propagated-inputs | |
8037 | `(("r-annotationhub" ,r-annotationhub) | |
8038 | ("r-biocfilecache" ,r-biocfilecache) | |
8039 | ("r-biocgenerics" ,r-biocgenerics) | |
8040 | ("r-biocmanager" ,r-biocmanager) | |
8041 | ("r-curl" ,r-curl) | |
8042 | ("r-rappdirs" ,r-rappdirs) | |
8043 | ("r-s4vectors" ,r-s4vectors))) | |
b56a3462 RW |
8044 | (native-inputs |
8045 | `(("r-knitr" ,r-knitr))) | |
244270e6 RW |
8046 | (home-page "https://bioconductor.org/packages/ExperimentHub/") |
8047 | (synopsis "Client to access ExperimentHub resources") | |
8048 | (description | |
8049 | "This package provides a client for the Bioconductor ExperimentHub web | |
8050 | resource. ExperimentHub provides a central location where curated data from | |
8051 | experiments, publications or training courses can be accessed. Each resource | |
8052 | has associated metadata, tags and date of modification. The client creates | |
8053 | and manages a local cache of files retrieved enabling quick and reproducible | |
8054 | access.") | |
8055 | (license license:artistic2.0))) | |
06784793 RW |
8056 | |
8057 | (define-public r-multiassayexperiment | |
8058 | (package | |
8059 | (name "r-multiassayexperiment") | |
13d0b780 | 8060 | (version "1.16.0") |
06784793 RW |
8061 | (source |
8062 | (origin | |
8063 | (method url-fetch) | |
8064 | (uri (bioconductor-uri "MultiAssayExperiment" version)) | |
8065 | (sha256 | |
8066 | (base32 | |
13d0b780 | 8067 | "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs")))) |
06784793 RW |
8068 | (properties |
8069 | `((upstream-name . "MultiAssayExperiment"))) | |
8070 | (build-system r-build-system) | |
8071 | (propagated-inputs | |
8072 | `(("r-biobase" ,r-biobase) | |
8073 | ("r-biocgenerics" ,r-biocgenerics) | |
8074 | ("r-genomicranges" ,r-genomicranges) | |
8075 | ("r-iranges" ,r-iranges) | |
8076 | ("r-s4vectors" ,r-s4vectors) | |
8077 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
8078 | ("r-tidyr" ,r-tidyr))) | |
5d45d711 RW |
8079 | (native-inputs |
8080 | `(("r-knitr" ,r-knitr))) | |
798ca8d0 | 8081 | (home-page "https://waldronlab.io/MultiAssayExperiment/") |
06784793 RW |
8082 | (synopsis "Integration of multi-omics experiments in Bioconductor") |
8083 | (description | |
8084 | "MultiAssayExperiment harmonizes data management of multiple assays | |
8085 | performed on an overlapping set of specimens. It provides a familiar | |
8086 | Bioconductor user experience by extending concepts from | |
8087 | @code{SummarizedExperiment}, supporting an open-ended mix of standard data | |
8088 | classes for individual assays, and allowing subsetting by genomic ranges or | |
8089 | rownames.") | |
8090 | (license license:artistic2.0))) | |
c2b36a04 RW |
8091 | |
8092 | (define-public r-bioconcotk | |
8093 | (package | |
8094 | (name "r-bioconcotk") | |
e29b15ee | 8095 | (version "1.10.0") |
c2b36a04 RW |
8096 | (source |
8097 | (origin | |
8098 | (method url-fetch) | |
8099 | (uri (bioconductor-uri "BiocOncoTK" version)) | |
8100 | (sha256 | |
8101 | (base32 | |
e29b15ee | 8102 | "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108")))) |
c2b36a04 RW |
8103 | (properties `((upstream-name . "BiocOncoTK"))) |
8104 | (build-system r-build-system) | |
8105 | (propagated-inputs | |
8106 | `(("r-bigrquery" ,r-bigrquery) | |
8107 | ("r-car" ,r-car) | |
8108 | ("r-complexheatmap" ,r-complexheatmap) | |
8109 | ("r-curatedtcgadata" ,r-curatedtcgadata) | |
8110 | ("r-dbi" ,r-dbi) | |
8111 | ("r-dplyr" ,r-dplyr) | |
8112 | ("r-dt" ,r-dt) | |
8113 | ("r-genomicfeatures" ,r-genomicfeatures) | |
8114 | ("r-genomicranges" ,r-genomicranges) | |
8115 | ("r-ggplot2" ,r-ggplot2) | |
8116 | ("r-ggpubr" ,r-ggpubr) | |
8117 | ("r-graph" ,r-graph) | |
8118 | ("r-httr" ,r-httr) | |
8119 | ("r-iranges" ,r-iranges) | |
8120 | ("r-magrittr" ,r-magrittr) | |
8121 | ("r-plyr" ,r-plyr) | |
8122 | ("r-rgraphviz" ,r-rgraphviz) | |
8123 | ("r-rjson" ,r-rjson) | |
8124 | ("r-s4vectors" ,r-s4vectors) | |
8125 | ("r-scales" ,r-scales) | |
8126 | ("r-shiny" ,r-shiny) | |
8127 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1c518215 RW |
8128 | (native-inputs |
8129 | `(("r-knitr" ,r-knitr))) | |
c2b36a04 RW |
8130 | (home-page "https://bioconductor.org/packages/BiocOncoTK") |
8131 | (synopsis "Bioconductor components for general cancer genomics") | |
8132 | (description | |
8133 | "The purpose of this package is to provide a central interface to various | |
8134 | tools for genome-scale analysis of cancer studies.") | |
8135 | (license license:artistic2.0))) | |
4d12c1e3 RW |
8136 | |
8137 | (define-public r-biocor | |
8138 | (package | |
8139 | (name "r-biocor") | |
072f722f | 8140 | (version "1.14.0") |
4d12c1e3 RW |
8141 | (source |
8142 | (origin | |
8143 | (method url-fetch) | |
8144 | (uri (bioconductor-uri "BioCor" version)) | |
8145 | (sha256 | |
8146 | (base32 | |
072f722f | 8147 | "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19")))) |
4d12c1e3 RW |
8148 | (properties `((upstream-name . "BioCor"))) |
8149 | (build-system r-build-system) | |
8150 | (propagated-inputs | |
8151 | `(("r-biocparallel" ,r-biocparallel) | |
8152 | ("r-gseabase" ,r-gseabase) | |
8153 | ("r-matrix" ,r-matrix))) | |
132abe5f RW |
8154 | (native-inputs |
8155 | `(("r-knitr" ,r-knitr))) | |
4d12c1e3 RW |
8156 | (home-page "https://llrs.github.io/BioCor/") |
8157 | (synopsis "Functional similarities") | |
8158 | (description | |
8159 | "This package provides tools to calculate functional similarities based | |
8160 | on the pathways described on KEGG and REACTOME or in gene sets. These | |
8161 | similarities can be calculated for pathways or gene sets, genes, or clusters | |
8162 | and combined with other similarities. They can be used to improve networks, | |
8163 | gene selection, testing relationships, and so on.") | |
8164 | (license license:expat))) | |
4a18112d RW |
8165 | |
8166 | (define-public r-biocpkgtools | |
8167 | (package | |
8168 | (name "r-biocpkgtools") | |
6a5d8cad | 8169 | (version "1.8.0") |
4a18112d RW |
8170 | (source |
8171 | (origin | |
8172 | (method url-fetch) | |
8173 | (uri (bioconductor-uri "BiocPkgTools" version)) | |
8174 | (sha256 | |
8175 | (base32 | |
6a5d8cad | 8176 | "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m")))) |
4a18112d RW |
8177 | (properties `((upstream-name . "BiocPkgTools"))) |
8178 | (build-system r-build-system) | |
8179 | (propagated-inputs | |
2d6a7bca RW |
8180 | `(("r-biocfilecache" ,r-biocfilecache) |
8181 | ("r-biocmanager" ,r-biocmanager) | |
4a18112d RW |
8182 | ("r-biocviews" ,r-biocviews) |
8183 | ("r-dplyr" ,r-dplyr) | |
8184 | ("r-dt" ,r-dt) | |
8185 | ("r-gh" ,r-gh) | |
8186 | ("r-graph" ,r-graph) | |
8187 | ("r-htmltools" ,r-htmltools) | |
8188 | ("r-htmlwidgets" ,r-htmlwidgets) | |
8189 | ("r-httr" ,r-httr) | |
8190 | ("r-igraph" ,r-igraph) | |
8191 | ("r-jsonlite" ,r-jsonlite) | |
8192 | ("r-magrittr" ,r-magrittr) | |
2d6a7bca | 8193 | ("r-rappdirs" ,r-rappdirs) |
4a18112d RW |
8194 | ("r-rbgl" ,r-rbgl) |
8195 | ("r-readr" ,r-readr) | |
8196 | ("r-rex" ,r-rex) | |
2d6a7bca | 8197 | ("r-rlang" ,r-rlang) |
4a18112d RW |
8198 | ("r-rvest" ,r-rvest) |
8199 | ("r-stringr" ,r-stringr) | |
8200 | ("r-tibble" ,r-tibble) | |
8201 | ("r-tidyr" ,r-tidyr) | |
2d6a7bca | 8202 | ("r-tidyselect" ,r-tidyselect) |
4a18112d | 8203 | ("r-xml2" ,r-xml2))) |
2d6a7bca RW |
8204 | (native-inputs |
8205 | `(("r-knitr" ,r-knitr))) | |
4a18112d RW |
8206 | (home-page "https://github.com/seandavi/BiocPkgTools") |
8207 | (synopsis "Collection of tools for learning about Bioconductor packages") | |
8208 | (description | |
8209 | "Bioconductor has a rich ecosystem of metadata around packages, usage, | |
8210 | and build status. This package is a simple collection of functions to access | |
8211 | that metadata from R. The goal is to expose metadata for data mining and | |
8212 | value-added functionality such as package searching, text mining, and | |
8213 | analytics on packages.") | |
8214 | (license license:expat))) | |
43b66e3f RW |
8215 | |
8216 | (define-public r-biocset | |
8217 | (package | |
8218 | (name "r-biocset") | |
feb0cbf4 | 8219 | (version "1.4.0") |
43b66e3f RW |
8220 | (source |
8221 | (origin | |
8222 | (method url-fetch) | |
8223 | (uri (bioconductor-uri "BiocSet" version)) | |
8224 | (sha256 | |
8225 | (base32 | |
feb0cbf4 | 8226 | "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg")))) |
43b66e3f RW |
8227 | (properties `((upstream-name . "BiocSet"))) |
8228 | (build-system r-build-system) | |
8229 | (propagated-inputs | |
8230 | `(("r-annotationdbi" ,r-annotationdbi) | |
feb0cbf4 | 8231 | ("r-biocio" ,r-biocio) |
43b66e3f RW |
8232 | ("r-dplyr" ,r-dplyr) |
8233 | ("r-keggrest" ,r-keggrest) | |
feb0cbf4 | 8234 | ("r-ontologyindex" ,r-ontologyindex) |
43b66e3f RW |
8235 | ("r-plyr" ,r-plyr) |
8236 | ("r-rlang" ,r-rlang) | |
feb0cbf4 | 8237 | ("r-s4vectors" ,r-s4vectors) |
8238 | ("r-tibble" ,r-tibble) | |
8239 | ("r-tidyr" ,r-tidyr))) | |
723fa00d RW |
8240 | (native-inputs |
8241 | `(("r-knitr" ,r-knitr))) | |
43b66e3f RW |
8242 | (home-page |
8243 | "https://bioconductor.org/packages/BiocSet") | |
8244 | (synopsis | |
8245 | "Representing Different Biological Sets") | |
8246 | (description | |
8247 | "BiocSet displays different biological sets in a triple tibble format. | |
8248 | These three tibbles are @code{element}, @code{set}, and @code{elementset}. | |
5b98473a | 8249 | The user has the ability to activate one of these three tibbles to perform |
43b66e3f RW |
8250 | common functions from the @code{dplyr} package. Mapping functionality and |
8251 | accessing web references for elements/sets are also available in BiocSet.") | |
8252 | (license license:artistic2.0))) | |
0156297f RW |
8253 | |
8254 | (define-public r-biocworkflowtools | |
8255 | (package | |
8256 | (name "r-biocworkflowtools") | |
7891c83c | 8257 | (version "1.16.0") |
0156297f RW |
8258 | (source |
8259 | (origin | |
8260 | (method url-fetch) | |
8261 | (uri (bioconductor-uri "BiocWorkflowTools" version)) | |
8262 | (sha256 | |
8263 | (base32 | |
7891c83c | 8264 | "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6")))) |
0156297f RW |
8265 | (properties |
8266 | `((upstream-name . "BiocWorkflowTools"))) | |
8267 | (build-system r-build-system) | |
8268 | (propagated-inputs | |
8269 | `(("r-biocstyle" ,r-biocstyle) | |
8270 | ("r-bookdown" ,r-bookdown) | |
8271 | ("r-git2r" ,r-git2r) | |
8272 | ("r-httr" ,r-httr) | |
8273 | ("r-knitr" ,r-knitr) | |
8274 | ("r-rmarkdown" ,r-rmarkdown) | |
8275 | ("r-rstudioapi" ,r-rstudioapi) | |
8276 | ("r-stringr" ,r-stringr) | |
8277 | ("r-usethis" ,r-usethis))) | |
4ecba230 RW |
8278 | (native-inputs |
8279 | `(("r-knitr" ,r-knitr))) | |
0156297f RW |
8280 | (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") |
8281 | (synopsis "Tools to aid the development of Bioconductor Workflow packages") | |
8282 | (description | |
8283 | "This package provides functions to ease the transition between | |
8284 | Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") | |
8285 | (license license:expat))) | |
77e2de36 RW |
8286 | |
8287 | (define-public r-biodist | |
8288 | (package | |
8289 | (name "r-biodist") | |
15be98c1 | 8290 | (version "1.62.0") |
77e2de36 RW |
8291 | (source |
8292 | (origin | |
8293 | (method url-fetch) | |
8294 | (uri (bioconductor-uri "bioDist" version)) | |
8295 | (sha256 | |
8296 | (base32 | |
15be98c1 | 8297 | "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap")))) |
77e2de36 RW |
8298 | (properties `((upstream-name . "bioDist"))) |
8299 | (build-system r-build-system) | |
8300 | (propagated-inputs | |
8301 | `(("r-biobase" ,r-biobase) | |
8302 | ("r-kernsmooth" ,r-kernsmooth))) | |
8303 | (home-page "https://bioconductor.org/packages/bioDist/") | |
8304 | (synopsis "Different distance measures") | |
8305 | (description | |
8306 | "This package provides a collection of software tools for calculating | |
8307 | distance measures.") | |
8308 | (license license:artistic2.0))) | |
9bc516ba RW |
8309 | |
8310 | (define-public r-pcatools | |
8311 | (package | |
8312 | (name "r-pcatools") | |
1174317e | 8313 | (version "2.2.0") |
9bc516ba RW |
8314 | (source |
8315 | (origin | |
8316 | (method url-fetch) | |
8317 | (uri (bioconductor-uri "PCAtools" version)) | |
8318 | (sha256 | |
8319 | (base32 | |
1174317e | 8320 | "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb")))) |
9bc516ba RW |
8321 | (properties `((upstream-name . "PCAtools"))) |
8322 | (build-system r-build-system) | |
8323 | (propagated-inputs | |
8324 | `(("r-beachmat" ,r-beachmat) | |
8325 | ("r-bh" ,r-bh) | |
8326 | ("r-biocparallel" ,r-biocparallel) | |
8327 | ("r-biocsingular" ,r-biocsingular) | |
8328 | ("r-cowplot" ,r-cowplot) | |
8329 | ("r-delayedarray" ,r-delayedarray) | |
8330 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
8331 | ("r-dqrng" ,r-dqrng) | |
8332 | ("r-ggplot2" ,r-ggplot2) | |
8333 | ("r-ggrepel" ,r-ggrepel) | |
8334 | ("r-lattice" ,r-lattice) | |
8335 | ("r-matrix" ,r-matrix) | |
8336 | ("r-rcpp" ,r-rcpp) | |
8337 | ("r-reshape2" ,r-reshape2))) | |
8338 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8339 | (home-page "https://github.com/kevinblighe/PCAtools") | |
8340 | (synopsis "PCAtools: everything Principal Components Analysis") | |
8341 | (description | |
8342 | "@dfn{Principal Component Analysis} (PCA) extracts the fundamental | |
8343 | structure of the data without the need to build any model to represent it. | |
8344 | This \"summary\" of the data is arrived at through a process of reduction that | |
8345 | can transform the large number of variables into a lesser number that are | |
8346 | uncorrelated (i.e. the 'principal components'), while at the same time being | |
8347 | capable of easy interpretation on the original data. PCAtools provides | |
8348 | functions for data exploration via PCA, and allows the user to generate | |
8349 | publication-ready figures. PCA is performed via @code{BiocSingular}; users | |
8350 | can also identify an optimal number of principal components via different | |
8351 | metrics, such as the elbow method and Horn's parallel analysis, which has | |
8352 | relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high | |
8353 | dimensional mass cytometry data.") | |
8354 | (license license:gpl3))) | |
c89afe75 RW |
8355 | |
8356 | (define-public r-rgreat | |
8357 | (package | |
8358 | (name "r-rgreat") | |
7a242042 | 8359 | (version "1.22.0") |
c89afe75 RW |
8360 | (source |
8361 | (origin | |
8362 | (method url-fetch) | |
8363 | (uri (bioconductor-uri "rGREAT" version)) | |
8364 | (sha256 | |
8365 | (base32 | |
7a242042 | 8366 | "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj")))) |
c89afe75 RW |
8367 | (properties `((upstream-name . "rGREAT"))) |
8368 | (build-system r-build-system) | |
8369 | (propagated-inputs | |
8370 | `(("r-genomicranges" ,r-genomicranges) | |
8371 | ("r-getoptlong" ,r-getoptlong) | |
8372 | ("r-iranges" ,r-iranges) | |
8373 | ("r-rcurl" ,r-rcurl) | |
8374 | ("r-rjson" ,r-rjson))) | |
8375 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8376 | (home-page "https://github.com/jokergoo/rGREAT") | |
8377 | (synopsis "Client for GREAT analysis") | |
8378 | (description | |
8379 | "This package makes GREAT (Genomic Regions Enrichment of Annotations | |
8380 | Tool) analysis automatic by constructing a HTTP POST request according to | |
8381 | user's input and automatically retrieving results from GREAT web server.") | |
8382 | (license license:expat))) | |
0b8c7e4b RW |
8383 | |
8384 | (define-public r-m3c | |
8385 | (package | |
8386 | (name "r-m3c") | |
126846a0 | 8387 | (version "1.12.0") |
0b8c7e4b RW |
8388 | (source |
8389 | (origin | |
8390 | (method url-fetch) | |
8391 | (uri (bioconductor-uri "M3C" version)) | |
8392 | (sha256 | |
8393 | (base32 | |
126846a0 | 8394 | "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5")))) |
0b8c7e4b RW |
8395 | (properties `((upstream-name . "M3C"))) |
8396 | (build-system r-build-system) | |
8397 | (propagated-inputs | |
8398 | `(("r-cluster" ,r-cluster) | |
8399 | ("r-corpcor" ,r-corpcor) | |
8400 | ("r-doparallel" ,r-doparallel) | |
8401 | ("r-dosnow" ,r-dosnow) | |
8402 | ("r-foreach" ,r-foreach) | |
8403 | ("r-ggplot2" ,r-ggplot2) | |
8404 | ("r-matrix" ,r-matrix) | |
8405 | ("r-matrixcalc" ,r-matrixcalc) | |
8406 | ("r-rtsne" ,r-rtsne) | |
8407 | ("r-umap" ,r-umap))) | |
8408 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8409 | (home-page "https://bioconductor.org/packages/M3C") | |
8410 | (synopsis "Monte Carlo reference-based consensus clustering") | |
8411 | (description | |
8412 | "M3C is a consensus clustering algorithm that uses a Monte Carlo | |
8413 | simulation to eliminate overestimation of @code{K} and can reject the null | |
8414 | hypothesis @code{K=1}.") | |
8415 | (license license:agpl3+))) | |
488001eb PL |
8416 | |
8417 | (define-public r-icens | |
8418 | (package | |
8419 | (name "r-icens") | |
3cacc3bd | 8420 | (version "1.62.0") |
488001eb PL |
8421 | (source |
8422 | (origin | |
8423 | (method url-fetch) | |
8424 | (uri (bioconductor-uri "Icens" version)) | |
8425 | (sha256 | |
8426 | (base32 | |
3cacc3bd | 8427 | "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr")))) |
488001eb PL |
8428 | (properties `((upstream-name . "Icens"))) |
8429 | (build-system r-build-system) | |
8430 | (propagated-inputs | |
8431 | `(("r-survival" ,r-survival))) | |
8432 | (home-page "https://bioconductor.org/packages/Icens") | |
8433 | (synopsis "NPMLE for censored and truncated data") | |
8434 | (description | |
8435 | "This package provides many functions for computing the | |
8436 | @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and | |
8437 | truncated data.") | |
8438 | (license license:artistic2.0))) | |
655c4bb2 PL |
8439 | |
8440 | ;; This is a CRAN package but it depends on r-icens, which is published on | |
8441 | ;; Bioconductor. | |
8442 | (define-public r-interval | |
8443 | (package | |
8444 | (name "r-interval") | |
65e361f9 | 8445 | (version "1.1-0.7") |
655c4bb2 PL |
8446 | (source |
8447 | (origin | |
8448 | (method url-fetch) | |
8449 | (uri (cran-uri "interval" version)) | |
8450 | (sha256 | |
8451 | (base32 | |
65e361f9 | 8452 | "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9")))) |
655c4bb2 PL |
8453 | (properties `((upstream-name . "interval"))) |
8454 | (build-system r-build-system) | |
8455 | (propagated-inputs | |
8456 | `(("r-icens" ,r-icens) | |
8457 | ("r-mlecens" ,r-mlecens) | |
8458 | ("r-perm" ,r-perm) | |
8459 | ("r-survival" ,r-survival))) | |
8460 | (home-page "https://cran.r-project.org/web/packages/interval/") | |
8461 | (synopsis "Weighted Logrank tests and NPMLE for interval censored data") | |
8462 | (description | |
8463 | "This package provides functions to fit nonparametric survival curves, | |
8464 | plot them, and perform logrank or Wilcoxon type tests.") | |
8465 | (license license:gpl2+))) | |
7e88ee9f PL |
8466 | |
8467 | ;; This is a CRAN package, but it depends on r-interval, which depends on a | |
8468 | ;; Bioconductor package. | |
8469 | (define-public r-fhtest | |
8470 | (package | |
8471 | (name "r-fhtest") | |
d7cfdc12 | 8472 | (version "1.5") |
7e88ee9f PL |
8473 | (source |
8474 | (origin | |
8475 | (method url-fetch) | |
8476 | (uri (cran-uri "FHtest" version)) | |
8477 | (sha256 | |
8478 | (base32 | |
d7cfdc12 | 8479 | "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q")))) |
7e88ee9f PL |
8480 | (properties `((upstream-name . "FHtest"))) |
8481 | (build-system r-build-system) | |
8482 | (propagated-inputs | |
8483 | `(("r-interval" ,r-interval) | |
8484 | ("r-kmsurv" ,r-kmsurv) | |
8485 | ("r-mass" ,r-mass) | |
8486 | ("r-perm" ,r-perm) | |
8487 | ("r-survival" ,r-survival))) | |
8488 | (home-page "https://cran.r-project.org/web/packages/FHtest/") | |
8489 | (synopsis "Tests for survival data based on the Fleming-Harrington class") | |
8490 | (description | |
8491 | "This package provides functions to compare two or more survival curves | |
8492 | with: | |
8493 | ||
8494 | @itemize | |
8495 | @item The Fleming-Harrington test for right-censored data based on | |
8496 | permutations and on counting processes. | |
8497 | @item An extension of the Fleming-Harrington test for interval-censored data | |
8498 | based on a permutation distribution and on a score vector distribution. | |
8499 | @end itemize | |
8500 | ") | |
8501 | (license license:gpl2+))) | |
f4d920b9 | 8502 | |
8503 | (define-public r-fourcseq | |
8504 | (package | |
8505 | (name "r-fourcseq") | |
e5b2c80d | 8506 | (version "1.24.0") |
f4d920b9 | 8507 | (source |
8508 | (origin | |
8509 | (method url-fetch) | |
8510 | (uri (bioconductor-uri "FourCSeq" version)) | |
8511 | (sha256 | |
e5b2c80d | 8512 | (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb")))) |
f4d920b9 | 8513 | (properties `((upstream-name . "FourCSeq"))) |
8514 | (build-system r-build-system) | |
8515 | (propagated-inputs | |
8516 | `(("r-biobase" ,r-biobase) | |
8517 | ("r-biostrings" ,r-biostrings) | |
8518 | ("r-deseq2" ,r-deseq2) | |
8519 | ("r-fda" ,r-fda) | |
8520 | ("r-genomicalignments" ,r-genomicalignments) | |
8521 | ("r-genomicranges" ,r-genomicranges) | |
8522 | ("r-ggbio" ,r-ggbio) | |
8523 | ("r-ggplot2" ,r-ggplot2) | |
8524 | ("r-gtools" ,r-gtools) | |
8525 | ("r-lsd" ,r-lsd) | |
8526 | ("r-matrix" ,r-matrix) | |
8527 | ("r-reshape2" ,r-reshape2) | |
8528 | ("r-rsamtools" ,r-rsamtools) | |
8529 | ("r-rtracklayer" ,r-rtracklayer) | |
8530 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
8531 | (native-inputs | |
8532 | `(("r-knitr" ,r-knitr))) | |
8533 | (home-page | |
8534 | "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") | |
8535 | (synopsis "Analysis of multiplexed 4C sequencing data") | |
8536 | (description | |
8537 | "This package is an R package dedicated to the analysis of (multiplexed) | |
8538 | 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific | |
8539 | interactions between DNA elements and identify differential interactions | |
8540 | between conditions. The statistical analysis in R starts with individual bam | |
8541 | files for each sample as inputs. To obtain these files, the package contains | |
8542 | a Python script to demultiplex libraries and trim off primer sequences. With | |
8543 | a standard alignment software the required bam files can be then be | |
8544 | generated.") | |
8545 | (license license:gpl3+))) | |
6e0ab26f | 8546 | |
8547 | (define-public r-preprocesscore | |
8548 | (package | |
8549 | (name "r-preprocesscore") | |
8fa30df0 | 8550 | (version "1.52.0") |
6e0ab26f | 8551 | (source |
8552 | (origin | |
8553 | (method url-fetch) | |
8554 | (uri (bioconductor-uri "preprocessCore" version)) | |
8555 | (sha256 | |
8556 | (base32 | |
8fa30df0 | 8557 | "1i5ky3bfbkrz4lgfs72fkckr8q3wq48p38mp05cjmnmh1chmdw38")))) |
6e0ab26f | 8558 | (properties |
8559 | `((upstream-name . "preprocessCore"))) | |
8560 | (build-system r-build-system) | |
8561 | (home-page "https://github.com/bmbolstad/preprocessCore") | |
8562 | (synopsis "Collection of pre-processing functions") | |
8563 | (description | |
8564 | "This package provides a library of core pre-processing and normalization | |
8565 | routines.") | |
8566 | (license license:lgpl2.0+))) | |
b3a99837 | 8567 | |
3159fcf1 RW |
8568 | ;; This is a CRAN package, but it depends on preprocessorcore, which is a |
8569 | ;; Bioconductor package. | |
8570 | (define-public r-wgcna | |
8571 | (package | |
8572 | (name "r-wgcna") | |
8573 | (version "1.69") | |
8574 | (source | |
8575 | (origin | |
8576 | (method url-fetch) | |
8577 | (uri (cran-uri "WGCNA" version)) | |
8578 | (sha256 | |
8579 | (base32 | |
8580 | "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f")))) | |
8581 | (properties `((upstream-name . "WGCNA"))) | |
8582 | (build-system r-build-system) | |
8583 | (propagated-inputs | |
8584 | `(("r-annotationdbi" ,r-annotationdbi) | |
8585 | ("r-doparallel" ,r-doparallel) | |
8586 | ("r-dynamictreecut" ,r-dynamictreecut) | |
8587 | ("r-fastcluster" ,r-fastcluster) | |
8588 | ("r-foreach" ,r-foreach) | |
8589 | ("r-go-db" ,r-go-db) | |
8590 | ("r-hmisc" ,r-hmisc) | |
8591 | ("r-impute" ,r-impute) | |
8592 | ("r-rcpp" ,r-rcpp) | |
8593 | ("r-survival" ,r-survival) | |
8594 | ("r-matrixstats" ,r-matrixstats) | |
8595 | ("r-preprocesscore" ,r-preprocesscore))) | |
8596 | (home-page | |
8597 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") | |
8598 | (synopsis "Weighted correlation network analysis") | |
8599 | (description | |
8600 | "This package provides functions necessary to perform Weighted | |
8601 | Correlation Network Analysis on high-dimensional data. It includes functions | |
8602 | for rudimentary data cleaning, construction and summarization of correlation | |
8603 | networks, module identification and functions for relating both variables and | |
8604 | modules to sample traits. It also includes a number of utility functions for | |
8605 | data manipulation and visualization.") | |
8606 | (license license:gpl2+))) | |
8607 | ||
b3a99837 | 8608 | (define-public r-rgraphviz |
8609 | (package | |
8610 | (name "r-rgraphviz") | |
b6348b0e | 8611 | (version "2.34.0") |
b3a99837 | 8612 | (source |
8613 | (origin | |
8614 | (method url-fetch) | |
8615 | (uri (bioconductor-uri "Rgraphviz" version)) | |
8616 | (sha256 | |
8617 | (base32 | |
b6348b0e | 8618 | "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77")))) |
b3a99837 | 8619 | (properties `((upstream-name . "Rgraphviz"))) |
8620 | (build-system r-build-system) | |
8621 | (arguments | |
8622 | `(#:phases | |
8623 | (modify-phases %standard-phases | |
8624 | (add-after 'unpack 'make-reproducible | |
8625 | (lambda _ | |
8626 | ;; The replacement value is taken from src/graphviz/builddate.h | |
8627 | (substitute* "src/graphviz/configure" | |
8628 | (("VERSION_DATE=.*") | |
8629 | "VERSION_DATE=20200427.2341\n")) | |
8630 | #t))))) | |
8631 | ;; FIXME: Rgraphviz bundles the sources of an older variant of | |
8632 | ;; graphviz. It does not build with the latest version of graphviz, so | |
8633 | ;; we do not add graphviz to the inputs. | |
8634 | (inputs `(("zlib" ,zlib))) | |
8635 | (propagated-inputs | |
8636 | `(("r-graph" ,r-graph))) | |
8637 | (native-inputs | |
8638 | `(("pkg-config" ,pkg-config))) | |
8639 | (home-page "https://bioconductor.org/packages/Rgraphviz") | |
8640 | (synopsis "Plotting capabilities for R graph objects") | |
8641 | (description | |
8642 | "This package interfaces R with the graphviz library for plotting R graph | |
8643 | objects from the @code{graph} package.") | |
8644 | (license license:epl1.0))) | |
8c7c6db4 | 8645 | |
3292f6ed | 8646 | (define-public r-fithic |
8647 | (package | |
8648 | (name "r-fithic") | |
7105658e | 8649 | (version "1.16.0") |
3292f6ed | 8650 | (source (origin |
8651 | (method url-fetch) | |
8652 | (uri (bioconductor-uri "FitHiC" version)) | |
8653 | (sha256 | |
8654 | (base32 | |
7105658e | 8655 | "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2")))) |
3292f6ed | 8656 | (properties `((upstream-name . "FitHiC"))) |
8657 | (build-system r-build-system) | |
8658 | (propagated-inputs | |
8659 | `(("r-data-table" ,r-data-table) | |
8660 | ("r-fdrtool" ,r-fdrtool) | |
8661 | ("r-rcpp" ,r-rcpp))) | |
8662 | (native-inputs | |
8663 | `(("r-knitr" ,r-knitr))) | |
8664 | (home-page "https://bioconductor.org/packages/FitHiC") | |
8665 | (synopsis "Confidence estimation for intra-chromosomal contact maps") | |
8666 | (description | |
8667 | "Fit-Hi-C is a tool for assigning statistical confidence estimates to | |
8668 | intra-chromosomal contact maps produced by genome-wide genome architecture | |
8669 | assays such as Hi-C.") | |
8670 | (license license:gpl2+))) | |
8671 | ||
7df42d37 | 8672 | (define-public r-hitc |
8673 | (package | |
8674 | (name "r-hitc") | |
ed44a72a | 8675 | (version "1.34.0") |
7df42d37 | 8676 | (source (origin |
8677 | (method url-fetch) | |
8678 | (uri (bioconductor-uri "HiTC" version)) | |
8679 | (sha256 | |
8680 | (base32 | |
ed44a72a | 8681 | "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy")))) |
7df42d37 | 8682 | (properties `((upstream-name . "HiTC"))) |
8683 | (build-system r-build-system) | |
8684 | (propagated-inputs | |
8685 | `(("r-biostrings" ,r-biostrings) | |
8686 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8687 | ("r-genomicranges" ,r-genomicranges) | |
8688 | ("r-iranges" ,r-iranges) | |
8689 | ("r-matrix" ,r-matrix) | |
8690 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
8691 | ("r-rtracklayer" ,r-rtracklayer))) | |
8692 | (home-page "https://bioconductor.org/packages/HiTC") | |
8693 | (synopsis "High throughput chromosome conformation capture analysis") | |
8694 | (description | |
8695 | "The HiTC package was developed to explore high-throughput \"C\" data | |
8696 | such as 5C or Hi-C. Dedicated R classes as well as standard methods for | |
8697 | quality controls, normalization, visualization, and further analysis are also | |
8698 | provided.") | |
8699 | (license license:artistic2.0))) | |
8700 | ||
63b75c01 | 8701 | (define-public r-hdf5array |
8702 | (package | |
8703 | (name "r-hdf5array") | |
5992c25e | 8704 | (version "1.18.0") |
63b75c01 | 8705 | (source |
8706 | (origin | |
8707 | (method url-fetch) | |
8708 | (uri (bioconductor-uri "HDF5Array" version)) | |
8709 | (sha256 | |
8710 | (base32 | |
5992c25e | 8711 | "1hr149q03p09y1cjnx8av854j53041wfyq66xpsjw4mypzjf6f28")))) |
63b75c01 | 8712 | (properties `((upstream-name . "HDF5Array"))) |
8713 | (build-system r-build-system) | |
26cf5eb5 | 8714 | (arguments |
8715 | `(#:phases | |
8716 | (modify-phases %standard-phases | |
8717 | (add-after 'unpack 'fix-linking | |
8718 | (lambda _ | |
8719 | (substitute* "src/Makevars" | |
8720 | ;; This is to avoid having a plain directory on the list of | |
8721 | ;; libraries to link. | |
8722 | (("\\(RHDF5LIB_LIBS\\)" match) | |
8723 | (string-append match "/libhdf5.a"))) | |
8724 | #t))))) | |
63b75c01 | 8725 | (inputs |
8726 | `(("zlib" ,zlib))) | |
8727 | (propagated-inputs | |
8728 | `(("r-biocgenerics" ,r-biocgenerics) | |
8729 | ("r-delayedarray" ,r-delayedarray) | |
8730 | ("r-iranges" ,r-iranges) | |
8731 | ("r-matrix" ,r-matrix) | |
8732 | ("r-rhdf5" ,r-rhdf5) | |
8733 | ("r-rhdf5lib" ,r-rhdf5lib) | |
8734 | ("r-s4vectors" ,r-s4vectors))) | |
8735 | (home-page "https://bioconductor.org/packages/HDF5Array") | |
8736 | (synopsis "HDF5 back end for DelayedArray objects") | |
8737 | (description "This package provides an array-like container for convenient | |
8738 | access and manipulation of HDF5 datasets. It supports delayed operations and | |
8739 | block processing.") | |
8740 | (license license:artistic2.0))) | |
8741 | ||
c61268c1 | 8742 | (define-public r-rhdf5lib |
8743 | (package | |
8744 | (name "r-rhdf5lib") | |
79cb6af3 | 8745 | (version "1.12.0") |
c61268c1 | 8746 | (source |
8747 | (origin | |
8748 | (method url-fetch) | |
8749 | (uri (bioconductor-uri "Rhdf5lib" version)) | |
8750 | (sha256 | |
8751 | (base32 | |
79cb6af3 | 8752 | "0wia85a6dkgibsjcmpqas5068msck3h3bqpgw2x07bk189z4vay2")) |
c61268c1 | 8753 | (modules '((guix build utils))) |
8754 | (snippet | |
8755 | '(begin | |
8756 | ;; Delete bundled binaries | |
8757 | (delete-file-recursively "src/wininclude/") | |
8758 | (delete-file-recursively "src/winlib-4.9.3/") | |
8759 | (delete-file-recursively "src/winlib-8.3.0/") | |
8760 | (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") | |
8761 | #t)))) | |
8762 | (properties `((upstream-name . "Rhdf5lib"))) | |
8763 | (build-system r-build-system) | |
8764 | (arguments | |
8765 | `(#:phases | |
8766 | (modify-phases %standard-phases | |
8767 | (add-after 'unpack 'do-not-use-bundled-hdf5 | |
8768 | (lambda* (#:key inputs #:allow-other-keys) | |
8769 | (for-each delete-file '("configure" "configure.ac")) | |
8770 | ;; Do not make other packages link with the proprietary libsz. | |
8771 | (substitute* "R/zzz.R" | |
8772 | ((" \"%s/libsz.a\"") "")) | |
8773 | (with-directory-excursion "src" | |
8774 | (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) | |
8775 | (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) | |
8776 | "hdf5") | |
8777 | ;; Remove timestamp and host system information to make | |
8778 | ;; the build reproducible. | |
8779 | (substitute* "hdf5/src/libhdf5.settings.in" | |
8780 | (("Configured on: @CONFIG_DATE@") | |
8781 | "Configured on: Guix") | |
8782 | (("Uname information:.*") | |
8783 | "Uname information: Linux\n") | |
8784 | ;; Remove unnecessary store reference. | |
8785 | (("C Compiler:.*") | |
8786 | "C Compiler: GCC\n")) | |
c5ae5c1c RJ |
8787 | (rename-file "hdf5/src/libhdf5.settings.in" |
8788 | "hdf5/src/libhdf5.settings") | |
c61268c1 | 8789 | (rename-file "Makevars.in" "Makevars") |
8790 | (substitute* "Makevars" | |
8791 | (("@ZLIB_LIB@") "-lz") | |
8792 | (("@ZLIB_INCLUDE@") "") | |
8793 | (("HDF5_CXX_LIB=.*") | |
8794 | (string-append "HDF5_CXX_LIB=" | |
8795 | (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) | |
8796 | (("HDF5_LIB=.*") | |
8797 | (string-append "HDF5_LIB=" | |
8798 | (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) | |
8799 | (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") | |
8800 | (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") | |
8801 | (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") | |
8802 | (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") | |
8803 | (("HDF5_HL_LIB=.*") | |
8804 | (string-append "HDF5_HL_LIB=" | |
8805 | (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) | |
8806 | (("HDF5_HL_CXX_LIB=.*") | |
8807 | (string-append "HDF5_HL_CXX_LIB=" | |
8808 | (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) | |
8809 | ;; szip is non-free software | |
8810 | (("cp \"\\$\\{SZIP_LIB\\}.*") "") | |
8811 | (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) | |
8812 | #t))))) | |
8813 | (inputs | |
8814 | `(("zlib" ,zlib))) | |
8815 | (propagated-inputs | |
8816 | `(("hdf5" ,hdf5-1.10))) | |
8817 | (native-inputs | |
8818 | `(("hdf5-source" ,(package-source hdf5-1.10)) | |
8819 | ("r-knitr" ,r-knitr))) | |
8820 | (home-page "https://bioconductor.org/packages/Rhdf5lib") | |
8821 | (synopsis "HDF5 library as an R package") | |
8822 | (description "This package provides C and C++ HDF5 libraries for use in R | |
8823 | packages.") | |
8824 | (license license:artistic2.0))) | |
8825 | ||
8863c14c | 8826 | (define-public r-beachmat |
8827 | (package | |
8828 | (name "r-beachmat") | |
eed72895 | 8829 | (version "2.6.2") |
8863c14c | 8830 | (source |
8831 | (origin | |
8832 | (method url-fetch) | |
8833 | (uri (bioconductor-uri "beachmat" version)) | |
8834 | (sha256 | |
8835 | (base32 | |
eed72895 | 8836 | "1yxm5andf4hsxxsmwrn5vl79707yfqkhzzajq6fvhsmaad3f97n7")))) |
8863c14c | 8837 | (build-system r-build-system) |
8838 | (propagated-inputs | |
8839 | `(("r-biocgenerics" ,r-biocgenerics) | |
8840 | ("r-delayedarray" ,r-delayedarray) | |
8841 | ("r-matrix" ,r-matrix))) | |
8842 | (native-inputs | |
8843 | `(("r-knitr" ,r-knitr))) | |
8844 | (home-page "https://bioconductor.org/packages/beachmat") | |
8845 | (synopsis "Compiling Bioconductor to handle each matrix type") | |
8846 | (description "This package provides a consistent C++ class interface for a | |
8847 | variety of commonly used matrix types, including sparse and HDF5-backed | |
8848 | matrices.") | |
8849 | (license license:gpl3))) | |
8850 | ||
916a3e59 | 8851 | (define-public r-singlecellexperiment |
8852 | (package | |
8853 | (name "r-singlecellexperiment") | |
4ef898d4 | 8854 | (version "1.12.0") |
916a3e59 | 8855 | (source |
8856 | (origin | |
8857 | (method url-fetch) | |
8858 | (uri (bioconductor-uri "SingleCellExperiment" version)) | |
8859 | (sha256 | |
8860 | (base32 | |
4ef898d4 | 8861 | "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2")))) |
916a3e59 | 8862 | (properties |
8863 | `((upstream-name . "SingleCellExperiment"))) | |
8864 | (build-system r-build-system) | |
8865 | (propagated-inputs | |
8866 | `(("r-biocgenerics" ,r-biocgenerics) | |
8867 | ("r-s4vectors" ,r-s4vectors) | |
8868 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
8869 | (native-inputs | |
8870 | `(("r-knitr" ,r-knitr))) | |
8871 | (home-page "https://bioconductor.org/packages/SingleCellExperiment") | |
8872 | (synopsis "S4 classes for single cell data") | |
8873 | (description "This package defines an S4 class for storing data from | |
8874 | single-cell experiments. This includes specialized methods to store and | |
8875 | retrieve spike-in information, dimensionality reduction coordinates and size | |
8876 | factors for each cell, along with the usual metadata for genes and | |
8877 | libraries.") | |
8878 | (license license:gpl3))) | |
8879 | ||
0e60dda0 RW |
8880 | (define-public r-scuttle |
8881 | (package | |
8882 | (name "r-scuttle") | |
3872153a | 8883 | (version "1.0.3") |
0e60dda0 RW |
8884 | (source |
8885 | (origin | |
8886 | (method url-fetch) | |
8887 | (uri (bioconductor-uri "scuttle" version)) | |
8888 | (sha256 | |
8889 | (base32 | |
3872153a | 8890 | "0l2r6fhyd33dllf2mc5a1pd5sawfvcin54pgh9l1nafqzg3sdv2m")))) |
0e60dda0 RW |
8891 | (properties `((upstream-name . "scuttle"))) |
8892 | (build-system r-build-system) | |
8893 | (propagated-inputs | |
8894 | `(("r-beachmat" ,r-beachmat) | |
8895 | ("r-biocgenerics" ,r-biocgenerics) | |
8896 | ("r-biocparallel" ,r-biocparallel) | |
8897 | ("r-delayedarray" ,r-delayedarray) | |
8898 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
3872153a | 8899 | ("r-genomicranges" ,r-genomicranges) |
0e60dda0 RW |
8900 | ("r-matrix" ,r-matrix) |
8901 | ("r-rcpp" ,r-rcpp) | |
8902 | ("r-s4vectors" ,r-s4vectors) | |
8903 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
8904 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
8905 | (native-inputs `(("r-knitr" ,r-knitr))) | |
8906 | (home-page "https://bioconductor.org/packages/scuttle") | |
8907 | (synopsis "Single-cell RNA-Seq analysis utilities") | |
8908 | (description | |
8909 | "This package provides basic utility functions for performing single-cell | |
8910 | analyses, focusing on simple normalization, quality control and data | |
8911 | transformations. It also provides some helper functions to assist development | |
8912 | of other packages.") | |
8913 | (license license:gpl3))) | |
8914 | ||
6b1946b3 | 8915 | (define-public r-scater |
8916 | (package | |
8917 | (name "r-scater") | |
d4b5d186 | 8918 | (version "1.18.3") |
6b1946b3 | 8919 | (source (origin |
8920 | (method url-fetch) | |
8921 | (uri (bioconductor-uri "scater" version)) | |
8922 | (sha256 | |
8923 | (base32 | |
d4b5d186 | 8924 | "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535")))) |
6b1946b3 | 8925 | (build-system r-build-system) |
8926 | (propagated-inputs | |
d4b5d186 | 8927 | `(("r-biocgenerics" ,r-biocgenerics) |
6b1946b3 | 8928 | ("r-biocneighbors" ,r-biocneighbors) |
8929 | ("r-biocparallel" ,r-biocparallel) | |
8930 | ("r-biocsingular" ,r-biocsingular) | |
8931 | ("r-delayedarray" ,r-delayedarray) | |
8932 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
8933 | ("r-ggbeeswarm" ,r-ggbeeswarm) | |
8934 | ("r-ggplot2" ,r-ggplot2) | |
d4b5d186 | 8935 | ("r-gridextra" ,r-gridextra) |
6b1946b3 | 8936 | ("r-matrix" ,r-matrix) |
6b1946b3 | 8937 | ("r-rlang" ,r-rlang) |
8938 | ("r-s4vectors" ,r-s4vectors) | |
d4b5d186 | 8939 | ("r-scuttle" ,r-scuttle) |
6b1946b3 | 8940 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
8941 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
8942 | ("r-viridis" ,r-viridis))) | |
8943 | (native-inputs | |
8944 | `(("r-knitr" ,r-knitr))) | |
8945 | (home-page "https://github.com/davismcc/scater") | |
8946 | (synopsis "Single-cell analysis toolkit for gene expression data in R") | |
8947 | (description "This package provides a collection of tools for doing | |
8948 | various analyses of single-cell RNA-seq gene expression data, with a focus on | |
8949 | quality control.") | |
8950 | (license license:gpl2+))) | |
8951 | ||
1193b77e | 8952 | (define-public r-scran |
8953 | (package | |
8954 | (name "r-scran") | |
b03c955c | 8955 | (version "1.18.1") |
1193b77e | 8956 | (source |
8957 | (origin | |
8958 | (method url-fetch) | |
8959 | (uri (bioconductor-uri "scran" version)) | |
8960 | (sha256 | |
8961 | (base32 | |
b03c955c | 8962 | "1zap12rm61z2hg6ykknbif478nr7g468v8mp50bj5hqgi69ywcww")))) |
1193b77e | 8963 | (build-system r-build-system) |
8964 | (propagated-inputs | |
8965 | `(("r-beachmat" ,r-beachmat) | |
8966 | ("r-bh" ,r-bh) | |
8967 | ("r-biocgenerics" ,r-biocgenerics) | |
8968 | ("r-biocneighbors" ,r-biocneighbors) | |
8969 | ("r-biocparallel" ,r-biocparallel) | |
8970 | ("r-biocsingular" ,r-biocsingular) | |
b03c955c | 8971 | ("r-bluster" ,r-bluster) |
1193b77e | 8972 | ("r-delayedarray" ,r-delayedarray) |
8973 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
8974 | ("r-dqrng" ,r-dqrng) | |
8975 | ("r-edger" ,r-edger) | |
8976 | ("r-igraph" ,r-igraph) | |
1193b77e | 8977 | ("r-limma" ,r-limma) |
8978 | ("r-matrix" ,r-matrix) | |
8979 | ("r-rcpp" ,r-rcpp) | |
8980 | ("r-s4vectors" ,r-s4vectors) | |
b03c955c | 8981 | ("r-scuttle" ,r-scuttle) |
1193b77e | 8982 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
8983 | ("r-statmod" ,r-statmod) | |
8984 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
8985 | (native-inputs | |
8986 | `(("r-knitr" ,r-knitr))) | |
8987 | (home-page "https://bioconductor.org/packages/scran") | |
8988 | (synopsis "Methods for single-cell RNA-Seq data analysis") | |
8989 | (description "This package implements a variety of low-level analyses of | |
8990 | single-cell RNA-seq data. Methods are provided for normalization of | |
8991 | cell-specific biases, assignment of cell cycle phase, and detection of highly | |
8992 | variable and significantly correlated genes.") | |
8993 | (license license:gpl3))) | |
8994 | ||
5e719988 RW |
8995 | (define-public r-sparsematrixstats |
8996 | (package | |
8997 | (name "r-sparsematrixstats") | |
8998 | (version "1.2.0") | |
8999 | (source | |
9000 | (origin | |
9001 | (method url-fetch) | |
9002 | (uri (bioconductor-uri "sparseMatrixStats" version)) | |
9003 | (sha256 | |
9004 | (base32 | |
9005 | "0d1idbda1pzhdam9m0i5rn0c6pl7gwv0v3mcrv4wi5760v9qd5qh")))) | |
9006 | (properties | |
9007 | `((upstream-name . "sparseMatrixStats"))) | |
9008 | (build-system r-build-system) | |
9009 | (propagated-inputs | |
9010 | `(("r-matrix" ,r-matrix) | |
9011 | ("r-matrixgenerics" ,r-matrixgenerics) | |
9012 | ("r-matrixstats" ,r-matrixstats) | |
9013 | ("r-rcpp" ,r-rcpp))) | |
9014 | (native-inputs `(("r-knitr" ,r-knitr))) | |
9015 | (home-page "https://bioconductor.org/packages/sparseMatrixStats/") | |
9016 | (synopsis "Summary statistics for rows and columns of sparse matrices") | |
9017 | (description | |
9018 | "This package provides high performance functions for row and column | |
9019 | operations on sparse matrices. Currently, the optimizations are limited to | |
9020 | data in the column sparse format.") | |
9021 | (license license:expat))) | |
9022 | ||
8c7c6db4 | 9023 | (define-public r-delayedmatrixstats |
9024 | (package | |
9025 | (name "r-delayedmatrixstats") | |
7601015f | 9026 | (version "1.12.1") |
8c7c6db4 | 9027 | (source |
9028 | (origin | |
9029 | (method url-fetch) | |
9030 | (uri (bioconductor-uri "DelayedMatrixStats" version)) | |
9031 | (sha256 | |
9032 | (base32 | |
7601015f | 9033 | "1cyvj6ffl10vaiip146dldc1w8if854kpz9nhi50ndhpkmdb8sa0")))) |
8c7c6db4 | 9034 | (properties |
9035 | `((upstream-name . "DelayedMatrixStats"))) | |
9036 | (build-system r-build-system) | |
9037 | (propagated-inputs | |
9038 | `(("r-biocparallel" ,r-biocparallel) | |
9039 | ("r-delayedarray" ,r-delayedarray) | |
9040 | ("r-hdf5array" ,r-hdf5array) | |
9041 | ("r-iranges" ,r-iranges) | |
9042 | ("r-matrix" ,r-matrix) | |
7601015f | 9043 | ("r-matrixgenerics" ,r-matrixgenerics) |
8c7c6db4 | 9044 | ("r-matrixstats" ,r-matrixstats) |
10c87ecf | 9045 | ("r-s4vectors" ,r-s4vectors) |
9046 | ("r-sparsematrixstats" ,r-sparsematrixstats))) | |
8c7c6db4 | 9047 | (native-inputs |
9048 | `(("r-knitr" ,r-knitr))) | |
9049 | (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") | |
9050 | (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") | |
9051 | (description | |
9052 | "This package provides a port of the @code{matrixStats} API for use with | |
9053 | @code{DelayedMatrix} objects from the @code{DelayedArray} package. It | |
9054 | contains high-performing functions operating on rows and columns of | |
9055 | @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, | |
9056 | @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions | |
9057 | are optimized per data type and for subsetted calculations such that both | |
9058 | memory usage and processing time is minimized.") | |
9059 | (license license:expat))) | |
fa2201c1 | 9060 | |
9061 | (define-public r-mscoreutils | |
9062 | (package | |
9063 | (name "r-mscoreutils") | |
9064 | (version "1.2.0") | |
9065 | (source | |
9066 | (origin | |
9067 | (method url-fetch) | |
9068 | (uri (bioconductor-uri "MsCoreUtils" version)) | |
9069 | (sha256 | |
9070 | (base32 | |
9071 | "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630")))) | |
9072 | (properties `((upstream-name . "MsCoreUtils"))) | |
9073 | (build-system r-build-system) | |
9074 | (propagated-inputs | |
9075 | `(("r-mass" ,r-mass) | |
9076 | ("r-rcpp" ,r-rcpp) | |
9077 | ("r-s4vectors" ,r-s4vectors))) | |
9078 | (native-inputs | |
9079 | `(("r-knitr" ,r-knitr))) | |
9080 | (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils") | |
9081 | (synopsis "Core utils for mass spectrometry data") | |
9082 | (description | |
9083 | "This package defines low-level functions for mass spectrometry data and | |
9084 | is independent of any high-level data structures. These functions include | |
9085 | mass spectra processing functions (noise estimation, smoothing, binning), | |
9086 | quantitative aggregation functions (median polish, robust summarisation, | |
9087 | etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as | |
9088 | well as misc helper functions, that are used across high-level data structure | |
9089 | within the R for Mass Spectrometry packages.") | |
9090 | (license license:artistic2.0))) | |
ff4834c0 | 9091 | |
9092 | (define-public r-biocio | |
9093 | (package | |
9094 | (name "r-biocio") | |
9095 | (version "1.0.1") | |
9096 | (source | |
9097 | (origin | |
9098 | (method url-fetch) | |
9099 | (uri (bioconductor-uri "BiocIO" version)) | |
9100 | (sha256 | |
9101 | (base32 | |
9102 | "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18")))) | |
9103 | (properties `((upstream-name . "BiocIO"))) | |
9104 | (build-system r-build-system) | |
9105 | (propagated-inputs | |
9106 | `(("r-biocgenerics" ,r-biocgenerics) | |
9107 | ("r-genomicranges" ,r-genomicranges) | |
9108 | ("r-rcurl" ,r-rcurl) | |
9109 | ("r-s4vectors" ,r-s4vectors))) | |
9110 | (native-inputs | |
9111 | `(("r-knitr" ,r-knitr))) | |
9112 | (home-page "https://bioconductor.org/packages/BiocIO") | |
9113 | (synopsis "Standard input and output for Bioconductor packages") | |
9114 | (description | |
9115 | "This package implements `import()` and `export()` standard generics for | |
9116 | importing and exporting biological data formats. `import()` supports | |
9117 | whole-file as well as chunk-wise iterative import. The `import()` interface | |
9118 | optionally provides a standard mechanism for 'lazy' access via `filter()` (on | |
9119 | row or element-like components of the file resource), `select()` (on | |
9120 | column-like components of the file resource) and `collect()`. The `import()` | |
9121 | interface optionally provides transparent access to remote (e.g. via https) | |
9122 | as well as local access. Developers can register a file extension, e.g., | |
9123 | `.loom` for dispatch from character-based URIs to specific `import()` / | |
9124 | `export()` methods based on classes representing file types, e.g., | |
9125 | `LoomFile()`.") | |
9126 | (license license:artistic2.0))) | |
e520c68f | 9127 | |
9128 | (define-public r-msmseda | |
9129 | (package | |
9130 | (name "r-msmseda") | |
9131 | (version "1.28.0") | |
9132 | (source | |
9133 | (origin | |
9134 | (method url-fetch) | |
9135 | (uri (bioconductor-uri "msmsEDA" version)) | |
9136 | (sha256 | |
9137 | (base32 | |
9138 | "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx")))) | |
9139 | (properties `((upstream-name . "msmsEDA"))) | |
9140 | (build-system r-build-system) | |
9141 | (propagated-inputs | |
9142 | `(("r-gplots" ,r-gplots) | |
9143 | ("r-mass" ,r-mass) | |
9144 | ("r-msnbase" ,r-msnbase) | |
9145 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
9146 | (home-page | |
9147 | "https://bioconductor.org/packages/msmsEDA") | |
9148 | (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts") | |
9149 | (description | |
9150 | "Exploratory data analysis to assess the quality of a set of LC-MS/MS | |
9151 | experiments, and visualize de influence of the involved factors.") | |
9152 | (license license:gpl2))) | |
16f16b5e | 9153 | |
9154 | (define-public r-msmstests | |
9155 | (package | |
9156 | (name "r-msmstests") | |
9157 | (version "1.28.0") | |
9158 | (source | |
9159 | (origin | |
9160 | (method url-fetch) | |
9161 | (uri (bioconductor-uri "msmsTests" version)) | |
9162 | (sha256 | |
9163 | (base32 | |
9164 | "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j")))) | |
9165 | (properties `((upstream-name . "msmsTests"))) | |
9166 | (build-system r-build-system) | |
9167 | (propagated-inputs | |
9168 | `(("r-edger" ,r-edger) | |
9169 | ("r-msmseda" ,r-msmseda) | |
9170 | ("r-msnbase" ,r-msnbase) | |
9171 | ("r-qvalue" ,r-qvalue))) | |
9172 | (home-page | |
9173 | "https://bioconductor.org/packages/msmsTests") | |
9174 | (synopsis "Differential LC-MS/MS expression tests") | |
9175 | (description | |
9176 | "This packages provides statistical tests for label-free LC-MS/MS data | |
9177 | by spectral counts, to discover differentially expressed proteins between two | |
9178 | biological conditions. Three tests are available: Poisson GLM regression, | |
9179 | quasi-likelihood GLM regression, and the negative binomial of the edgeR | |
9180 | package.The three models admit blocking factors to control for nuissance | |
9181 | variables.To assure a good level of reproducibility a post-test filter is | |
9182 | available, where we may set the minimum effect size considered biologicaly | |
9183 | relevant, and the minimum expression of the most abundant condition.") | |
9184 | (license license:gpl2))) | |
45dfb751 | 9185 | |
9186 | (define-public r-catalyst | |
9187 | (package | |
9188 | (name "r-catalyst") | |
9189 | (version "1.14.0") | |
9190 | (source | |
9191 | (origin | |
9192 | (method url-fetch) | |
9193 | (uri (bioconductor-uri "CATALYST" version)) | |
9194 | (sha256 | |
9195 | (base32 | |
9196 | "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh")))) | |
9197 | (properties `((upstream-name . "CATALYST"))) | |
9198 | (build-system r-build-system) | |
9199 | (propagated-inputs | |
9200 | `(("r-circlize" ,r-circlize) | |
9201 | ("r-complexheatmap" ,r-complexheatmap) | |
9202 | ("r-consensusclusterplus" ,r-consensusclusterplus) | |
9203 | ("r-cowplot" ,r-cowplot) | |
9204 | ("r-data-table" ,r-data-table) | |
9205 | ("r-dplyr" ,r-dplyr) | |
9206 | ("r-drc" ,r-drc) | |
9207 | ("r-flowcore" ,r-flowcore) | |
9208 | ("r-flowsom" ,r-flowsom) | |
9209 | ("r-ggplot2" ,r-ggplot2) | |
9210 | ("r-ggrepel" ,r-ggrepel) | |
9211 | ("r-ggridges" ,r-ggridges) | |
9212 | ("r-gridextra" ,r-gridextra) | |
9213 | ("r-magrittr" ,r-magrittr) | |
9214 | ("r-matrix" ,r-matrix) | |
9215 | ("r-matrixstats" ,r-matrixstats) | |
9216 | ("r-nnls" ,r-nnls) | |
9217 | ("r-purrr" ,r-purrr) | |
9218 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
9219 | ("r-reshape2" ,r-reshape2) | |
9220 | ("r-rtsne" ,r-rtsne) | |
9221 | ("r-s4vectors" ,r-s4vectors) | |
9222 | ("r-scales" ,r-scales) | |
9223 | ("r-scater" ,r-scater) | |
9224 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
9225 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
9226 | (native-inputs | |
9227 | `(("r-knitr" ,r-knitr))) | |
9228 | (home-page | |
9229 | "https://github.com/HelenaLC/CATALYST") | |
9230 | (synopsis "Cytometry data analysis tools") | |
9231 | (description | |
9232 | "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass | |
9233 | cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as | |
9234 | reporters to label antibodies, thereby substantially decreasing spectral | |
9235 | overlap and allowing for examination of over 50 parameters at the single cell | |
9236 | level. While spectral overlap is significantly less pronounced in CyTOF than | |
9237 | flow cytometry, spillover due to detection sensitivity, isotopic impurities, | |
9238 | and oxide formation can impede data interpretability. We designed | |
9239 | CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for | |
9240 | preprocessing of cytometry data, including i) normalization using bead | |
9241 | standards, ii) single-cell deconvolution, and iii) bead-based compensation.") | |
9242 | (license license:gpl2+))) | |
7395458d MIP |
9243 | |
9244 | (define-public r-kegggraph | |
9245 | (package | |
9246 | (name "r-kegggraph") | |
9247 | (version "1.50.0") | |
9248 | (source | |
9249 | (origin | |
9250 | (method url-fetch) | |
9251 | (uri (bioconductor-uri "KEGGgraph" version)) | |
9252 | (sha256 | |
9253 | (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v")))) | |
9254 | (properties `((upstream-name . "KEGGgraph"))) | |
9255 | (build-system r-build-system) | |
9256 | (propagated-inputs | |
9257 | `(("r-graph" ,r-graph) | |
9258 | ("r-rcurl" ,r-rcurl) | |
9259 | ("r-xml" ,r-xml))) | |
9260 | (home-page "https://bioconductor.org/packages/KEGGgraph") | |
9261 | (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") | |
9262 | (description | |
9263 | "@code{r-kegggraph} is an interface between Kegg Pathway database and graph | |
9264 | object as well as a collection of tools to analyze, dissect and visualize these | |
9265 | graphs. It parses the regularly updated kgml (Kegg XML) files into graph models | |
9266 | maintaining all essential pathway attributes. The package offers | |
9267 | functionalities including parsing, graph operation, visualization and etc.") | |
9268 | (license license:gpl2+))) | |
e4b0794e MIP |
9269 | |
9270 | (define-public r-pathview | |
9271 | (package | |
9272 | (name "r-pathview") | |
9273 | (version "1.30.1") | |
9274 | (source | |
9275 | (origin | |
9276 | (method url-fetch) | |
9277 | (uri (bioconductor-uri "pathview" version)) | |
9278 | (sha256 | |
9279 | (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4")))) | |
9280 | (properties `((upstream-name . "pathview"))) | |
9281 | (build-system r-build-system) | |
9282 | (propagated-inputs | |
9283 | `(("r-annotationdbi" ,r-annotationdbi) | |
9284 | ("r-graph" ,r-graph) | |
9285 | ("r-kegggraph" ,r-kegggraph) | |
9286 | ("r-keggrest" ,r-keggrest) | |
9287 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
9288 | ("r-png" ,r-png) | |
9289 | ("r-rgraphviz" ,r-rgraphviz) | |
9290 | ("r-xml" ,r-xml))) | |
9291 | (home-page "https://pathview.uncc.edu/") | |
9292 | (synopsis "Tool set for pathway based data integration and visualization") | |
9293 | (description | |
9294 | "@code{r-pathview} is a tool set for pathway based data integration and | |
9295 | visualization. It maps and renders a wide variety of biological data on | |
9296 | relevant pathway graphs. All users need is to supply their data and specify | |
9297 | the target pathway. This package automatically downloads the pathway graph | |
9298 | data, parses the data file, maps user data to the pathway, and render pathway | |
9299 | graph with the mapped data. In addition, @code{r-pathview} also seamlessly | |
9300 | integrates with pathway and gene set (enrichment) analysis tools for | |
9301 | large-scale and fully automated analysis.") | |
9302 | (license license:gpl3+))) |