Commit | Line | Data |
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fa596599 | 1 | ;;; GNU Guix --- Functional package management for GNU |
8bd3170b | 2 | ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net> |
18931166 | 3 | ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org> |
d64e3a48 | 4 | ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> |
9949f459 | 5 | ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> |
8d6d75ff | 6 | ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> |
61242625 | 7 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
4f617bfb | 8 | ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com> |
488001eb | 9 | ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> |
1353e536 | 10 | ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> |
c61268c1 | 11 | ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> |
1f958631 | 12 | ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> |
fa596599 RW |
13 | ;;; |
14 | ;;; This file is part of GNU Guix. | |
15 | ;;; | |
16 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
17 | ;;; under the terms of the GNU General Public License as published by | |
18 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
19 | ;;; your option) any later version. | |
20 | ;;; | |
21 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
22 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
23 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
24 | ;;; GNU General Public License for more details. | |
25 | ;;; | |
26 | ;;; You should have received a copy of the GNU General Public License | |
27 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
28 | ||
29 | (define-module (gnu packages bioconductor) | |
30 | #:use-module ((guix licenses) #:prefix license:) | |
31 | #:use-module (guix packages) | |
32 | #:use-module (guix download) | |
b2dce6b5 | 33 | #:use-module (guix git-download) |
fa596599 | 34 | #:use-module (guix build-system r) |
183ce988 | 35 | #:use-module (gnu packages) |
58656064 | 36 | #:use-module (gnu packages base) |
cf9a29b2 | 37 | #:use-module (gnu packages bioinformatics) |
a5b56a53 RJ |
38 | #:use-module (gnu packages cran) |
39 | #:use-module (gnu packages compression) | |
c18dccff | 40 | #:use-module (gnu packages gcc) |
cf9a29b2 | 41 | #:use-module (gnu packages graph) |
5aef09bd | 42 | #:use-module (gnu packages graphviz) |
dddbc90c | 43 | #:use-module (gnu packages haskell-xyz) |
5cfa4bff | 44 | #:use-module (gnu packages image) |
b64ce4b7 | 45 | #:use-module (gnu packages maths) |
6b12f213 RW |
46 | #:use-module (gnu packages netpbm) |
47 | #:use-module (gnu packages perl) | |
2cb71d81 | 48 | #:use-module (gnu packages pkg-config) |
f4235c0e | 49 | #:use-module (gnu packages statistics) |
14bb1c48 | 50 | #:use-module (gnu packages web) |
7a62d5e0 | 51 | #:use-module (gnu packages xml) |
14bb1c48 | 52 | #:use-module (srfi srfi-1)) |
fa596599 | 53 | |
557a1089 RW |
54 | \f |
55 | ;;; Annotations | |
56 | ||
04a05946 MIP |
57 | (define-public r-org-eck12-eg-db |
58 | (package | |
59 | (name "r-org-eck12-eg-db") | |
60 | (version "3.12.0") | |
61 | (source | |
62 | (origin | |
63 | (method url-fetch) | |
64 | (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation)) | |
65 | (sha256 | |
66 | (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs")))) | |
67 | (properties | |
68 | `((upstream-name . "org.EcK12.eg.db"))) | |
69 | (build-system r-build-system) | |
70 | (propagated-inputs | |
71 | `(("r-annotationdbi" ,r-annotationdbi))) | |
72 | (home-page "https://bioconductor.org/packages/org.EcK12.eg.db") | |
73 | (synopsis "Genome wide annotation for E coli strain K12") | |
74 | (description | |
75 | "This package provides genome wide annotation for E coli strain K12, | |
76 | primarily based on mapping using Entrez Gene identifiers. Entrez Gene is | |
77 | National Center for Biotechnology Information (NCBI)’s database for | |
78 | gene-specific information. Entrez Gene maintains records from genomes which | |
79 | have been completely sequenced, which have an active research community to | |
80 | submit gene-specific information, or which are scheduled for intense sequence | |
81 | analysis.") | |
82 | (license license:artistic2.0))) | |
83 | ||
6f15ea24 RW |
84 | (define-public r-reactome-db |
85 | (package | |
86 | (name "r-reactome-db") | |
87 | (version "1.70.0") | |
88 | (source | |
89 | (origin | |
90 | (method url-fetch) | |
91 | (uri (bioconductor-uri "reactome.db" version 'annotation)) | |
92 | (sha256 | |
93 | (base32 | |
94 | "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg")))) | |
95 | (properties `((upstream-name . "reactome.db"))) | |
96 | (build-system r-build-system) | |
97 | (propagated-inputs | |
98 | `(("r-annotationdbi" ,r-annotationdbi))) | |
99 | (home-page "https://bioconductor.org/packages/reactome.db/") | |
100 | (synopsis "Annotation maps for reactome") | |
101 | (description | |
102 | "This package provides a set of annotation maps for the REACTOME | |
103 | database, assembled using data from REACTOME.") | |
104 | (license license:cc-by4.0))) | |
105 | ||
9048e7f3 RJ |
106 | (define-public r-bsgenome-btaurus-ucsc-bostau8 |
107 | (package | |
108 | (name "r-bsgenome-btaurus-ucsc-bostau8") | |
109 | (version "1.4.2") | |
110 | (source (origin | |
111 | (method url-fetch) | |
112 | (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8" | |
113 | version 'annotation)) | |
114 | (sha256 | |
115 | (base32 | |
116 | "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6")))) | |
117 | (properties | |
118 | `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8"))) | |
119 | (build-system r-build-system) | |
120 | (propagated-inputs | |
121 | `(("r-bsgenome" ,r-bsgenome))) | |
122 | (home-page | |
123 | "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/") | |
124 | (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)") | |
125 | (description "This package provides the full genome sequences for Bos | |
126 | taurus (UCSC version bosTau8).") | |
127 | (license license:artistic2.0))) | |
128 | ||
b7d93cf5 RW |
129 | (define-public r-bsgenome-celegans-ucsc-ce6 |
130 | (package | |
131 | (name "r-bsgenome-celegans-ucsc-ce6") | |
132 | (version "1.4.0") | |
133 | (source (origin | |
134 | (method url-fetch) | |
86ced7b2 RW |
135 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6" |
136 | version 'annotation)) | |
b7d93cf5 RW |
137 | (sha256 |
138 | (base32 | |
139 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
140 | (properties | |
141 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
142 | (build-system r-build-system) | |
b7d93cf5 RW |
143 | (propagated-inputs |
144 | `(("r-bsgenome" ,r-bsgenome))) | |
145 | (home-page | |
146 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
147 | (synopsis "Full genome sequences for Worm") | |
148 | (description | |
149 | "This package provides full genome sequences for Caenorhabditis | |
150 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
0c792ffb RW |
151 | objects.") |
152 | (license license:artistic2.0))) | |
153 | ||
154 | (define-public r-bsgenome-celegans-ucsc-ce10 | |
155 | (package | |
156 | (name "r-bsgenome-celegans-ucsc-ce10") | |
157 | (version "1.4.0") | |
158 | (source (origin | |
159 | (method url-fetch) | |
6998ecba RW |
160 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10" |
161 | version 'annotation)) | |
0c792ffb RW |
162 | (sha256 |
163 | (base32 | |
164 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
165 | (properties | |
166 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
167 | (build-system r-build-system) | |
0c792ffb RW |
168 | (propagated-inputs |
169 | `(("r-bsgenome" ,r-bsgenome))) | |
170 | (home-page | |
171 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
172 | (synopsis "Full genome sequences for Worm") | |
173 | (description | |
174 | "This package provides full genome sequences for Caenorhabditis | |
175 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
b7d93cf5 RW |
176 | objects.") |
177 | (license license:artistic2.0))) | |
178 | ||
183db725 RW |
179 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
180 | (package | |
181 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
182 | (version "1.4.1") | |
183 | (source (origin | |
184 | (method url-fetch) | |
149f351f RW |
185 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6" |
186 | version 'annotation)) | |
183db725 RW |
187 | (sha256 |
188 | (base32 | |
189 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
190 | (properties | |
191 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
192 | (build-system r-build-system) | |
183db725 RW |
193 | (propagated-inputs |
194 | `(("r-bsgenome" ,r-bsgenome))) | |
195 | (home-page | |
196 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
197 | (synopsis "Full genome sequences for Fly") | |
198 | (description | |
199 | "This package provides full genome sequences for Drosophila | |
200 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
201 | objects.") | |
202 | (license license:artistic2.0))) | |
203 | ||
13dabd69 RW |
204 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
205 | (package | |
206 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
207 | (version "1.4.0") | |
208 | (source (origin | |
209 | (method url-fetch) | |
87073b7e RW |
210 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3" |
211 | version 'annotation)) | |
13dabd69 RW |
212 | (sha256 |
213 | (base32 | |
214 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
215 | (properties | |
216 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
217 | (build-system r-build-system) | |
13dabd69 RW |
218 | (propagated-inputs |
219 | `(("r-bsgenome" ,r-bsgenome))) | |
220 | (home-page | |
221 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
222 | (synopsis "Full genome sequences for Fly") | |
223 | (description | |
224 | "This package provides full genome sequences for Drosophila | |
225 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
226 | Biostrings objects.") | |
227 | (license license:artistic2.0))) | |
228 | ||
dfac7eb9 RW |
229 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
230 | (package | |
231 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
232 | (version "1.3.99") | |
233 | (source (origin | |
234 | (method url-fetch) | |
bf05ece1 RW |
235 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked" |
236 | version 'annotation)) | |
dfac7eb9 RW |
237 | (sha256 |
238 | (base32 | |
239 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
240 | (properties | |
241 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
242 | (build-system r-build-system) | |
243 | (propagated-inputs | |
244 | `(("r-bsgenome" ,r-bsgenome) | |
245 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
246 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
247 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
248 | (synopsis "Full masked genome sequences for Fly") | |
249 | (description | |
250 | "This package provides full masked genome sequences for Drosophila | |
251 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
252 | Biostrings objects. The sequences are the same as in | |
253 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
254 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
255 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
256 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
257 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
258 | (license license:artistic2.0))) | |
259 | ||
40a65057 RW |
260 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
261 | (package | |
262 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
263 | (version "0.99.1") | |
264 | (source (origin | |
265 | (method url-fetch) | |
88e7c7db RW |
266 | (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5" |
267 | version 'annotation)) | |
40a65057 RW |
268 | (sha256 |
269 | (base32 | |
270 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
271 | (properties | |
272 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
273 | (build-system r-build-system) | |
40a65057 RW |
274 | (propagated-inputs |
275 | `(("r-bsgenome" ,r-bsgenome))) | |
276 | (home-page | |
277 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
278 | (synopsis "Full genome sequences for Homo sapiens") | |
279 | (description | |
280 | "This package provides full genome sequences for Homo sapiens from | |
281 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
282 | (license license:artistic2.0))) | |
283 | ||
c51c0033 MIP |
284 | (define-public r-bsgenome-hsapiens-ncbi-grch38 |
285 | (package | |
286 | (name "r-bsgenome-hsapiens-ncbi-grch38") | |
287 | (version "1.3.1000") | |
288 | (source | |
289 | (origin | |
290 | (method url-fetch) | |
291 | (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38" | |
292 | version 'annotation)) | |
293 | (sha256 | |
294 | (base32 | |
295 | "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) | |
296 | (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) | |
297 | (build-system r-build-system) | |
298 | (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) | |
299 | (home-page | |
300 | "https://bioconductor.org/packages/release/data/annotation/html/\ | |
301 | BSgenome.Hsapiens.NCBI.GRCh38.html") | |
302 | (synopsis "Full genome sequences for Homo sapiens (GRCh38)") | |
303 | (description | |
304 | "This package provides full genome sequences for Homo sapiens (Human) as | |
305 | provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") | |
306 | (license license:artistic2.0))) | |
307 | ||
6fbd759b RW |
308 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
309 | (package | |
310 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
311 | (version "1.3.99") | |
312 | (source (origin | |
313 | (method url-fetch) | |
a47646bd RW |
314 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" |
315 | version 'annotation)) | |
6fbd759b RW |
316 | (sha256 |
317 | (base32 | |
318 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
319 | (properties | |
320 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
321 | (build-system r-build-system) | |
322 | (propagated-inputs | |
323 | `(("r-bsgenome" ,r-bsgenome) | |
324 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
325 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
326 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
327 | (synopsis "Full masked genome sequences for Homo sapiens") | |
328 | (description | |
329 | "This package provides full genome sequences for Homo sapiens (Human) as | |
330 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
331 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
332 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
333 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
334 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
335 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
336 | default.") | |
337 | (license license:artistic2.0))) | |
338 | ||
5acb9052 RW |
339 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
340 | (package | |
341 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
342 | (version "1.4.0") | |
343 | (source (origin | |
344 | (method url-fetch) | |
21f6dae7 RW |
345 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9" |
346 | version 'annotation)) | |
5acb9052 RW |
347 | (sha256 |
348 | (base32 | |
349 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
350 | (properties | |
351 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
352 | (build-system r-build-system) | |
5acb9052 RW |
353 | (propagated-inputs |
354 | `(("r-bsgenome" ,r-bsgenome))) | |
355 | (home-page | |
356 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
357 | (synopsis "Full genome sequences for Mouse") | |
358 | (description | |
359 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
360 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
361 | (license license:artistic2.0))) | |
362 | ||
2bece692 RW |
363 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
364 | (package | |
365 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
366 | (version "1.3.99") | |
367 | (source (origin | |
368 | (method url-fetch) | |
51dc4a2d RW |
369 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked" |
370 | version 'annotation)) | |
2bece692 RW |
371 | (sha256 |
372 | (base32 | |
373 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
374 | (properties | |
375 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
376 | (build-system r-build-system) | |
377 | (propagated-inputs | |
378 | `(("r-bsgenome" ,r-bsgenome) | |
379 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
380 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
99db6db7 | 381 | (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") |
2bece692 RW |
382 | (synopsis "Full masked genome sequences for Mouse") |
383 | (description | |
384 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
385 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
386 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
387 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
388 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
389 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
390 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
391 | default." ) | |
392 | (license license:artistic2.0))) | |
393 | ||
c3adc830 RW |
394 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
395 | (package | |
396 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
397 | (version "1.4.0") | |
398 | (source (origin | |
399 | (method url-fetch) | |
f83404bc RW |
400 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10" |
401 | version 'annotation)) | |
c3adc830 RW |
402 | (sha256 |
403 | (base32 | |
404 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
405 | (properties | |
406 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
407 | (build-system r-build-system) | |
c3adc830 RW |
408 | (propagated-inputs |
409 | `(("r-bsgenome" ,r-bsgenome))) | |
410 | (home-page | |
411 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
412 | (synopsis "Full genome sequences for Mouse") | |
413 | (description | |
414 | "This package provides full genome sequences for Mus | |
415 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
416 | in Biostrings objects.") | |
417 | (license license:artistic2.0))) | |
418 | ||
8d6d75ff | 419 | (define-public r-genomeinfodbdata |
420 | (package | |
421 | (name "r-genomeinfodbdata") | |
422 | (version "1.2.0") | |
423 | (source (origin | |
424 | (method url-fetch) | |
425 | (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation)) | |
426 | (sha256 | |
427 | (base32 | |
428 | "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c")))) | |
429 | (properties | |
430 | `((upstream-name . "GenomeInfoDbData"))) | |
431 | (build-system r-build-system) | |
432 | (home-page "https://bioconductor.org/packages/GenomeInfoDbData") | |
433 | (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb") | |
434 | (description "This package contains data for mapping between NCBI taxonomy | |
435 | ID and species. It is used by functions in the GenomeInfoDb package.") | |
436 | (license license:artistic2.0))) | |
437 | ||
a2c66d18 | 438 | (define-public r-homo-sapiens |
439 | (package | |
440 | (name "r-homo-sapiens") | |
441 | (version "1.3.1") | |
442 | (source (origin | |
443 | (method url-fetch) | |
444 | (uri (bioconductor-uri "Homo.sapiens" version 'annotation)) | |
445 | (sha256 | |
446 | (base32 | |
447 | "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) | |
448 | (properties | |
449 | `((upstream-name . "Homo.sapiens"))) | |
450 | (build-system r-build-system) | |
451 | (propagated-inputs | |
452 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
453 | ("r-go-db" ,r-go-db) | |
454 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
455 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) | |
456 | ("r-organismdbi" ,r-organismdbi) | |
457 | ("r-annotationdbi" ,r-annotationdbi))) | |
458 | (home-page "https://bioconductor.org/packages/Homo.sapiens/") | |
459 | (synopsis "Annotation package for the Homo.sapiens object") | |
460 | (description | |
461 | "This package contains the Homo.sapiens object to access data from | |
462 | several related annotation packages.") | |
463 | (license license:artistic2.0))) | |
464 | ||
3a08940e RW |
465 | (define-public r-org-ce-eg-db |
466 | (package | |
467 | (name "r-org-ce-eg-db") | |
468 | (version "3.7.0") | |
469 | (source (origin | |
470 | (method url-fetch) | |
1c05e637 | 471 | (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation)) |
3a08940e RW |
472 | (sha256 |
473 | (base32 | |
474 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) | |
475 | (properties | |
476 | `((upstream-name . "org.Ce.eg.db"))) | |
477 | (build-system r-build-system) | |
478 | (propagated-inputs | |
479 | `(("r-annotationdbi" ,r-annotationdbi))) | |
480 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") | |
481 | (synopsis "Genome wide annotation for Worm") | |
482 | (description | |
483 | "This package provides mappings from Entrez gene identifiers to various | |
484 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
485 | (license license:artistic2.0))) | |
486 | ||
f8780e96 RW |
487 | (define-public r-org-dm-eg-db |
488 | (package | |
489 | (name "r-org-dm-eg-db") | |
490 | (version "3.7.0") | |
491 | (source (origin | |
492 | (method url-fetch) | |
b0dfc79b | 493 | (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation)) |
f8780e96 RW |
494 | (sha256 |
495 | (base32 | |
496 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) | |
497 | (properties | |
498 | `((upstream-name . "org.Dm.eg.db"))) | |
499 | (build-system r-build-system) | |
500 | (propagated-inputs | |
501 | `(("r-annotationdbi" ,r-annotationdbi))) | |
502 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") | |
503 | (synopsis "Genome wide annotation for Fly") | |
504 | (description | |
505 | "This package provides mappings from Entrez gene identifiers to various | |
506 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
507 | (license license:artistic2.0))) | |
508 | ||
3dad6087 RW |
509 | (define-public r-org-dr-eg-db |
510 | (package | |
511 | (name "r-org-dr-eg-db") | |
512 | (version "3.7.0") | |
513 | (source (origin | |
514 | (method url-fetch) | |
7bb65a22 | 515 | (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation)) |
3dad6087 RW |
516 | (sha256 |
517 | (base32 | |
518 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) | |
519 | (properties | |
520 | `((upstream-name . "org.Dr.eg.db"))) | |
521 | (build-system r-build-system) | |
522 | (propagated-inputs | |
523 | `(("r-annotationdbi" ,r-annotationdbi))) | |
524 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") | |
525 | (synopsis "Annotation for Zebrafish") | |
526 | (description | |
527 | "This package provides genome wide annotations for Zebrafish, primarily | |
528 | based on mapping using Entrez Gene identifiers.") | |
529 | (license license:artistic2.0))) | |
530 | ||
d56df35a RW |
531 | (define-public r-org-hs-eg-db |
532 | (package | |
533 | (name "r-org-hs-eg-db") | |
534 | (version "3.7.0") | |
535 | (source (origin | |
536 | (method url-fetch) | |
f53becc6 | 537 | (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) |
d56df35a RW |
538 | (sha256 |
539 | (base32 | |
540 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) | |
541 | (properties | |
542 | `((upstream-name . "org.Hs.eg.db"))) | |
543 | (build-system r-build-system) | |
544 | (propagated-inputs | |
545 | `(("r-annotationdbi" ,r-annotationdbi))) | |
546 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") | |
547 | (synopsis "Genome wide annotation for Human") | |
548 | (description | |
549 | "This package contains genome-wide annotations for Human, primarily based | |
550 | on mapping using Entrez Gene identifiers.") | |
551 | (license license:artistic2.0))) | |
552 | ||
8035819f RW |
553 | (define-public r-org-mm-eg-db |
554 | (package | |
555 | (name "r-org-mm-eg-db") | |
556 | (version "3.7.0") | |
557 | (source (origin | |
558 | (method url-fetch) | |
411be88b | 559 | (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation)) |
8035819f RW |
560 | (sha256 |
561 | (base32 | |
562 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) | |
563 | (properties | |
564 | `((upstream-name . "org.Mm.eg.db"))) | |
565 | (build-system r-build-system) | |
566 | (propagated-inputs | |
567 | `(("r-annotationdbi" ,r-annotationdbi))) | |
568 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") | |
569 | (synopsis "Genome wide annotation for Mouse") | |
570 | (description | |
571 | "This package provides mappings from Entrez gene identifiers to various | |
572 | annotations for the genome of the model mouse Mus musculus.") | |
573 | (license license:artistic2.0))) | |
574 | ||
fe0b76e2 RW |
575 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
576 | (package | |
577 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
578 | (version "1.4.0") | |
579 | (source (origin | |
580 | (method url-fetch) | |
e7a8cf2e RW |
581 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19" |
582 | version 'annotation)) | |
fe0b76e2 RW |
583 | (sha256 |
584 | (base32 | |
585 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) | |
586 | (properties | |
587 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
588 | (build-system r-build-system) | |
fe0b76e2 RW |
589 | (propagated-inputs |
590 | `(("r-bsgenome" ,r-bsgenome))) | |
591 | (home-page | |
592 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
593 | (synopsis "Full genome sequences for Homo sapiens") | |
594 | (description | |
595 | "This package provides full genome sequences for Homo sapiens as provided | |
596 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
597 | (license license:artistic2.0))) | |
598 | ||
8ce240fd RJ |
599 | (define-public r-bsgenome-hsapiens-ucsc-hg38 |
600 | (package | |
601 | (name "r-bsgenome-hsapiens-ucsc-hg38") | |
602 | (version "1.4.1") | |
603 | (source (origin | |
604 | (method url-fetch) | |
605 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38" | |
606 | version 'annotation)) | |
607 | (sha256 | |
608 | (base32 | |
609 | "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi")))) | |
610 | (properties | |
611 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) | |
612 | (build-system r-build-system) | |
613 | (propagated-inputs | |
614 | `(("r-bsgenome" ,r-bsgenome))) | |
615 | (home-page | |
616 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") | |
617 | (synopsis "Full genome sequences for Homo sapiens") | |
618 | (description | |
619 | "This package provides full genome sequences for Homo sapiens (Human) | |
620 | as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") | |
621 | (license license:artistic2.0))) | |
622 | ||
8324e64c RW |
623 | (define-public r-ensdb-hsapiens-v75 |
624 | (package | |
625 | (name "r-ensdb-hsapiens-v75") | |
626 | (version "2.99.0") | |
627 | (source | |
628 | (origin | |
629 | (method url-fetch) | |
630 | (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) | |
631 | (sha256 | |
632 | (base32 | |
633 | "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) | |
634 | (properties | |
635 | `((upstream-name . "EnsDb.Hsapiens.v75"))) | |
636 | (build-system r-build-system) | |
637 | (propagated-inputs | |
638 | `(("r-ensembldb" ,r-ensembldb))) | |
639 | (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") | |
640 | (synopsis "Ensembl based annotation package") | |
641 | (description | |
642 | "This package exposes an annotation database generated from Ensembl.") | |
643 | (license license:artistic2.0))) | |
644 | ||
eb8da541 | 645 | (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene |
646 | (package | |
647 | (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene") | |
648 | (version "3.12.0") | |
649 | (source | |
650 | (origin | |
651 | (method url-fetch) | |
652 | (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene" | |
653 | version 'annotation)) | |
654 | (sha256 | |
655 | (base32 | |
656 | "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4")))) | |
657 | (properties | |
658 | `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene"))) | |
659 | (build-system r-build-system) | |
660 | (propagated-inputs | |
661 | `(("r-annotationdbi" ,r-annotationdbi) | |
662 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
663 | (home-page | |
664 | "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene") | |
665 | (synopsis "Annotation package for TxDb object(s)") | |
666 | (description | |
667 | "This package exposes an annotation databases generated from UCSC by | |
668 | exposing these as TxDb objects.") | |
669 | (license license:artistic2.0))) | |
670 | ||
66e35ce6 RW |
671 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
672 | (package | |
673 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
674 | (version "3.2.2") | |
675 | (source (origin | |
676 | (method url-fetch) | |
f2580a13 RW |
677 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene" |
678 | version 'annotation)) | |
66e35ce6 RW |
679 | (sha256 |
680 | (base32 | |
681 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
682 | (properties | |
683 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
684 | (build-system r-build-system) | |
66e35ce6 RW |
685 | (propagated-inputs |
686 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
687 | (home-page | |
688 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
689 | (synopsis "Annotation package for human genome in TxDb format") | |
690 | (description | |
691 | "This package provides an annotation database of Homo sapiens genome | |
692 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
798b80ce RW |
693 | track. The database is exposed as a @code{TxDb} object.") |
694 | (license license:artistic2.0))) | |
695 | ||
696 | (define-public r-txdb-hsapiens-ucsc-hg38-knowngene | |
697 | (package | |
698 | (name "r-txdb-hsapiens-ucsc-hg38-knowngene") | |
699 | (version "3.4.6") | |
700 | (source (origin | |
701 | (method url-fetch) | |
d78db088 RW |
702 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" |
703 | version 'annotation)) | |
798b80ce RW |
704 | (sha256 |
705 | (base32 | |
706 | "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) | |
707 | (properties | |
708 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) | |
709 | (build-system r-build-system) | |
710 | (propagated-inputs | |
711 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
712 | (home-page | |
713 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") | |
714 | (synopsis "Annotation package for human genome in TxDb format") | |
715 | (description | |
716 | "This package provides an annotation database of Homo sapiens genome | |
717 | data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" | |
66e35ce6 RW |
718 | track. The database is exposed as a @code{TxDb} object.") |
719 | (license license:artistic2.0))) | |
720 | ||
d220babf RW |
721 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
722 | (package | |
723 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
724 | (version "3.2.2") | |
725 | (source (origin | |
726 | (method url-fetch) | |
1afdf41b RW |
727 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene" |
728 | version 'annotation)) | |
d220babf RW |
729 | (sha256 |
730 | (base32 | |
731 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
732 | (properties | |
733 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
734 | (build-system r-build-system) | |
735 | (propagated-inputs | |
736 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
737 | ("r-annotationdbi" ,r-annotationdbi))) | |
738 | (home-page | |
739 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
740 | (synopsis "Annotation package for mouse genome in TxDb format") | |
741 | (description | |
742 | "This package provides an annotation database of Mouse genome data. It | |
743 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
744 | database is exposed as a @code{TxDb} object.") | |
745 | (license license:artistic2.0))) | |
746 | ||
7bc5d1b0 RW |
747 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
748 | (package | |
749 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
b69c7703 | 750 | (version "3.10.0") |
7bc5d1b0 RW |
751 | (source (origin |
752 | (method url-fetch) | |
c271d990 RW |
753 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene" |
754 | version 'annotation)) | |
7bc5d1b0 RW |
755 | (sha256 |
756 | (base32 | |
b69c7703 | 757 | "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9")))) |
7bc5d1b0 RW |
758 | (properties |
759 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
760 | (build-system r-build-system) | |
7bc5d1b0 RW |
761 | (propagated-inputs |
762 | `(("r-bsgenome" ,r-bsgenome) | |
763 | ("r-genomicfeatures" ,r-genomicfeatures) | |
764 | ("r-annotationdbi" ,r-annotationdbi))) | |
765 | (home-page | |
766 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
767 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
768 | (description | |
769 | "This package loads a TxDb object, which is an R interface to | |
770 | prefabricated databases contained in this package. This package provides | |
771 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
772 | based on the knownGene track.") | |
773 | (license license:artistic2.0))) | |
774 | ||
7cd446fd RW |
775 | (define-public r-txdb-celegans-ucsc-ce6-ensgene |
776 | (package | |
777 | (name "r-txdb-celegans-ucsc-ce6-ensgene") | |
778 | (version "3.2.2") | |
779 | (source | |
780 | (origin | |
781 | (method url-fetch) | |
782 | (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene" | |
783 | version 'annotation)) | |
784 | (sha256 | |
785 | (base32 | |
786 | "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90")))) | |
787 | (properties | |
788 | `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) | |
789 | (build-system r-build-system) | |
790 | (propagated-inputs | |
791 | `(("r-annotationdbi" ,r-annotationdbi) | |
792 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
793 | (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") | |
794 | (synopsis "Annotation package for C elegans TxDb objects") | |
795 | (description | |
796 | "This package exposes a C elegans annotation database generated from UCSC | |
797 | by exposing these as TxDb objects.") | |
798 | (license license:artistic2.0))) | |
799 | ||
0f5c9cec RW |
800 | (define-public r-fdb-infiniummethylation-hg19 |
801 | (package | |
802 | (name "r-fdb-infiniummethylation-hg19") | |
803 | (version "2.2.0") | |
804 | (source (origin | |
805 | (method url-fetch) | |
6aca4054 RW |
806 | (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19" |
807 | version 'annotation)) | |
0f5c9cec RW |
808 | (sha256 |
809 | (base32 | |
810 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) | |
811 | (properties | |
812 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) | |
813 | (build-system r-build-system) | |
814 | (propagated-inputs | |
815 | `(("r-biostrings" ,r-biostrings) | |
816 | ("r-genomicfeatures" ,r-genomicfeatures) | |
817 | ("r-annotationdbi" ,r-annotationdbi) | |
818 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
819 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) | |
820 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") | |
821 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") | |
822 | (description | |
823 | "This is an annotation package for Illumina Infinium DNA methylation | |
824 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 | |
825 | annotations.") | |
826 | (license license:artistic2.0))) | |
827 | ||
9475a248 RW |
828 | (define-public r-illuminahumanmethylationepicmanifest |
829 | (package | |
830 | (name "r-illuminahumanmethylationepicmanifest") | |
831 | (version "0.3.0") | |
832 | (source (origin | |
833 | (method url-fetch) | |
25f567a8 RW |
834 | (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest" |
835 | version 'annotation)) | |
9475a248 RW |
836 | (sha256 |
837 | (base32 | |
838 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) | |
839 | (properties | |
840 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) | |
841 | (build-system r-build-system) | |
842 | (propagated-inputs | |
843 | `(("r-minfi" ,r-minfi))) | |
844 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") | |
845 | (synopsis "Manifest for Illumina's EPIC methylation arrays") | |
846 | (description | |
847 | "This is a manifest package for Illumina's EPIC methylation arrays.") | |
848 | (license license:artistic2.0))) | |
e8d435f7 | 849 | |
f8a5af46 RW |
850 | (define-public r-do-db |
851 | (package | |
852 | (name "r-do-db") | |
853 | (version "2.9") | |
854 | (source (origin | |
855 | (method url-fetch) | |
eed2766a | 856 | (uri (bioconductor-uri "DO.db" version 'annotation)) |
f8a5af46 RW |
857 | (sha256 |
858 | (base32 | |
859 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) | |
860 | (properties | |
861 | `((upstream-name . "DO.db"))) | |
862 | (build-system r-build-system) | |
863 | (propagated-inputs | |
864 | `(("r-annotationdbi" ,r-annotationdbi))) | |
865 | (home-page "https://www.bioconductor.org/packages/DO.db/") | |
866 | (synopsis "Annotation maps describing the entire Disease Ontology") | |
867 | (description | |
868 | "This package provides a set of annotation maps describing the entire | |
869 | Disease Ontology.") | |
870 | (license license:artistic2.0))) | |
871 | ||
83b42091 RW |
872 | (define-public r-pfam-db |
873 | (package | |
874 | (name "r-pfam-db") | |
875 | (version "3.8.2") | |
876 | (source | |
877 | (origin | |
878 | (method url-fetch) | |
879 | (uri (bioconductor-uri "PFAM.db" version 'annotation)) | |
880 | (sha256 | |
881 | (base32 | |
882 | "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) | |
883 | (properties `((upstream-name . "PFAM.db"))) | |
884 | (build-system r-build-system) | |
885 | (propagated-inputs | |
886 | `(("r-annotationdbi" ,r-annotationdbi))) | |
887 | (home-page "https://bioconductor.org/packages/PFAM.db") | |
888 | (synopsis "Set of protein ID mappings for PFAM") | |
889 | (description | |
890 | "This package provides a set of protein ID mappings for PFAM, assembled | |
891 | using data from public repositories.") | |
892 | (license license:artistic2.0))) | |
893 | ||
40be965e RW |
894 | (define-public r-phastcons100way-ucsc-hg19 |
895 | (package | |
896 | (name "r-phastcons100way-ucsc-hg19") | |
897 | (version "3.7.2") | |
898 | (source | |
899 | (origin | |
900 | (method url-fetch) | |
901 | (uri (bioconductor-uri "phastCons100way.UCSC.hg19" | |
902 | version 'annotation)) | |
903 | (sha256 | |
904 | (base32 | |
905 | "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa")))) | |
906 | (properties | |
907 | `((upstream-name . "phastCons100way.UCSC.hg19"))) | |
908 | (build-system r-build-system) | |
909 | (propagated-inputs | |
910 | `(("r-bsgenome" ,r-bsgenome) | |
911 | ("r-genomeinfodb" ,r-genomeinfodb) | |
912 | ("r-genomicranges" ,r-genomicranges) | |
913 | ("r-genomicscores" ,r-genomicscores) | |
914 | ("r-iranges" ,r-iranges) | |
915 | ("r-s4vectors" ,r-s4vectors))) | |
916 | (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") | |
917 | (synopsis "UCSC phastCons conservation scores for hg19") | |
918 | (description | |
919 | "This package provides UCSC phastCons conservation scores for the human | |
920 | genome (hg19) calculated from multiple alignments with other 99 vertebrate | |
921 | species.") | |
922 | (license license:artistic2.0))) | |
923 | ||
2cc51108 | 924 | \f |
557a1089 RW |
925 | ;;; Experiment data |
926 | ||
692bce15 RW |
927 | (define-public r-abadata |
928 | (package | |
929 | (name "r-abadata") | |
930 | (version "1.12.0") | |
931 | (source (origin | |
932 | (method url-fetch) | |
ced61edf | 933 | (uri (bioconductor-uri "ABAData" version 'experiment)) |
692bce15 RW |
934 | (sha256 |
935 | (base32 | |
936 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) | |
937 | (properties | |
938 | `((upstream-name . "ABAData"))) | |
939 | (build-system r-build-system) | |
940 | (propagated-inputs | |
941 | `(("r-annotationdbi" ,r-annotationdbi))) | |
942 | (home-page "https://www.bioconductor.org/packages/ABAData/") | |
943 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") | |
944 | (description | |
945 | "This package provides the data for the gene expression enrichment | |
946 | analysis conducted in the package ABAEnrichment. The package includes three | |
947 | datasets which are derived from the Allen Brain Atlas: | |
948 | ||
949 | @enumerate | |
950 | @item Gene expression data from Human Brain (adults) averaged across donors, | |
951 | @item Gene expression data from the Developing Human Brain pooled into five | |
952 | age categories and averaged across donors, and | |
953 | @item a developmental effect score based on the Developing Human Brain | |
954 | expression data. | |
955 | @end enumerate | |
956 | ||
957 | All datasets are restricted to protein coding genes.") | |
958 | (license license:gpl2+))) | |
959 | ||
18931166 RJ |
960 | (define-public r-aneufinderdata |
961 | (package | |
962 | (name "r-aneufinderdata") | |
963 | (version "1.18.0") | |
964 | (source (origin | |
965 | (method url-fetch) | |
966 | (uri (bioconductor-uri "AneuFinderData" version 'experiment)) | |
967 | (sha256 | |
968 | (base32 | |
969 | "02vb3kmza5hv8bc424fdmfif608xvpdb759w8882kac8izpv29ks")))) | |
970 | (build-system r-build-system) | |
971 | (home-page "https://bioconductor.org/packages/AneuFinderData/") | |
972 | (synopsis "Data package for @code{AneuFinder}") | |
973 | (description "This package contains data used by @code{AneuFinder}.") | |
974 | (license license:artistic2.0))) | |
975 | ||
b84ead8c RJ |
976 | (define-public r-aneufinder |
977 | (package | |
978 | (name "r-aneufinder") | |
979 | (version "1.18.0") | |
980 | (source (origin | |
981 | (method url-fetch) | |
982 | (uri (bioconductor-uri "AneuFinder" version)) | |
983 | (sha256 | |
984 | (base32 | |
985 | "1j2n6i3ja63i98y1mbb8ndn6cn2a0pw97zz6al4myycnv55w49j3")))) | |
986 | (build-system r-build-system) | |
987 | (native-inputs | |
988 | `(("r-knitr" ,r-knitr))) | |
989 | (propagated-inputs | |
990 | `(("r-genomicranges" ,r-genomicranges) | |
991 | ("r-aneufinderdata" ,r-aneufinderdata) | |
992 | ("r-ecp" ,r-ecp) | |
993 | ("r-foreach" ,r-foreach) | |
994 | ("r-doparallel" ,r-doparallel) | |
995 | ("r-biocgenerics" ,r-biocgenerics) | |
996 | ("r-s4vectors" ,r-s4vectors) | |
997 | ("r-genomeinfodb" ,r-genomeinfodb) | |
998 | ("r-iranges" ,r-iranges) | |
999 | ("r-rsamtools" ,r-rsamtools) | |
1000 | ("r-bamsignals" ,r-bamsignals) | |
1001 | ("r-dnacopy" ,r-dnacopy) | |
1002 | ("r-biostrings" ,r-biostrings) | |
1003 | ("r-genomicalignments" ,r-genomicalignments) | |
1004 | ("r-ggplot2" ,r-ggplot2) | |
1005 | ("r-reshape2" ,r-reshape2) | |
1006 | ("r-ggdendro" ,r-ggdendro) | |
1007 | ("r-ggrepel" ,r-ggrepel) | |
1008 | ("r-reordercluster" ,r-reordercluster) | |
1009 | ("r-mclust" ,r-mclust) | |
1010 | ("r-cowplot" ,r-cowplot))) | |
1011 | (home-page "https://bioconductor.org/packages/AneuFinder/") | |
1012 | (synopsis "Copy number variation analysis in single-cell-sequencing data") | |
1013 | (description "This package implements functions for copy number variant | |
1014 | calling, plotting, export and analysis from whole-genome single cell | |
1015 | sequencing data.") | |
1016 | (license license:artistic2.0))) | |
1017 | ||
b50c9660 RW |
1018 | (define-public r-arrmdata |
1019 | (package | |
1020 | (name "r-arrmdata") | |
1021 | (version "1.18.0") | |
1022 | (source (origin | |
1023 | (method url-fetch) | |
b86f7746 | 1024 | (uri (bioconductor-uri "ARRmData" version 'experiment)) |
b50c9660 RW |
1025 | (sha256 |
1026 | (base32 | |
1027 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) | |
1028 | (properties | |
1029 | `((upstream-name . "ARRmData"))) | |
1030 | (build-system r-build-system) | |
1031 | (home-page "https://www.bioconductor.org/packages/ARRmData/") | |
1032 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") | |
1033 | (description | |
1034 | "This package provides raw beta values from 36 samples across 3 groups | |
1035 | from Illumina 450k methylation arrays.") | |
1036 | (license license:artistic2.0))) | |
1037 | ||
1f958631 HL |
1038 | (define-public r-chromstardata |
1039 | (package | |
1040 | (name "r-chromstardata") | |
1041 | (version "1.16.0") | |
1042 | (source | |
1043 | (origin | |
1044 | (method url-fetch) | |
1045 | (uri (bioconductor-uri "chromstaRData" version 'experiment)) | |
1046 | (sha256 | |
1047 | (base32 | |
1048 | "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab")))) | |
1049 | (properties `((upstream-name . "chromstaRData"))) | |
1050 | (build-system r-build-system) | |
1051 | (home-page "https://bioconductor.org/packages/chromstaRData/") | |
1052 | (synopsis "ChIP-seq data for demonstration purposes") | |
1053 | (description | |
1054 | "This package provides ChIP-seq data for demonstration purposes in the | |
1055 | chromstaR package.") | |
1056 | (license license:gpl3))) | |
1057 | ||
94b8ad44 RJ |
1058 | (define-public r-chipseeker |
1059 | (package | |
1060 | (name "r-chipseeker") | |
1061 | (version "1.26.2") | |
1062 | (source (origin | |
1063 | (method url-fetch) | |
1064 | (uri (bioconductor-uri "ChIPseeker" version)) | |
1065 | (sha256 | |
1066 | (base32 | |
1067 | "1r197qwsriap6s6nb2p9j3521pjs2f0lgyzvppvlxj1531sa6g6z")))) | |
1068 | (build-system r-build-system) | |
1069 | (inputs | |
1070 | `(("r-knitr" ,r-knitr))) | |
1071 | (propagated-inputs | |
1072 | `(("r-annotationdbi" ,r-annotationdbi) | |
1073 | ("r-biocgenerics" ,r-biocgenerics) | |
1074 | ("r-boot" ,r-boot) | |
1075 | ("r-enrichplot" ,r-enrichplot) | |
1076 | ("r-iranges" ,r-iranges) | |
1077 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1078 | ("r-genomicranges" ,r-genomicranges) | |
1079 | ("r-genomicfeatures" ,r-genomicfeatures) | |
1080 | ("r-ggplot2" ,r-ggplot2) | |
1081 | ("r-gplots" ,r-gplots) | |
1082 | ("r-gtools" ,r-gtools) | |
1083 | ("r-dplyr" ,r-dplyr) | |
1084 | ("r-plotrix" ,r-plotrix) | |
1085 | ("r-dplyr" ,r-dplyr) | |
1086 | ("r-magrittr" ,r-magrittr) | |
1087 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
1088 | ("r-rtracklayer" ,r-rtracklayer) | |
1089 | ("r-s4vectors" ,r-s4vectors) | |
1090 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" | |
1091 | ,r-txdb-hsapiens-ucsc-hg19-knowngene))) | |
1092 | (home-page "https://www.bioconductor.org/packages/ChIPseeker/") | |
1093 | (synopsis | |
1094 | "ChIPseeker for ChIP peak Annotation, Comparison, and Visualization") | |
1095 | (description "This package implements functions to retrieve the nearest | |
1096 | genes around the peak, annotate genomic region of the peak, statstical methods | |
1097 | for estimate the significance of overlap among ChIP peak data sets, and | |
1098 | incorporate GEO database for user to compare the own dataset with those | |
1099 | deposited in database. The comparison can be used to infer cooperative | |
1100 | regulation and thus can be used to generate hypotheses. Several visualization | |
1101 | functions are implemented to summarize the coverage of the peak experiment, | |
1102 | average profile and heatmap of peaks binding to TSS regions, genomic | |
1103 | annotation, distance to TSS, and overlap of peaks or genes.") | |
1104 | (license license:artistic2.0))) | |
1105 | ||
e5610fd9 RW |
1106 | (define-public r-genelendatabase |
1107 | (package | |
1108 | (name "r-genelendatabase") | |
1109 | (version "1.18.0") | |
1110 | (source | |
1111 | (origin | |
1112 | (method url-fetch) | |
1113 | (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) | |
1114 | (sha256 | |
1115 | (base32 | |
1116 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) | |
1117 | (properties | |
1118 | `((upstream-name . "geneLenDataBase"))) | |
1119 | (build-system r-build-system) | |
1120 | (propagated-inputs | |
1121 | `(("r-rtracklayer" ,r-rtracklayer) | |
1122 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
1123 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
1124 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
1125 | (description | |
1126 | "This package provides the lengths of mRNA transcripts for a number of | |
1127 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
1128 | (license license:lgpl2.0+))) | |
1129 | ||
834f6495 RJ |
1130 | (define-public r-geneoverlap |
1131 | (package | |
1132 | (name "r-geneoverlap") | |
1133 | (version "1.26.0") | |
1134 | (source (origin | |
1135 | (method url-fetch) | |
1136 | (uri (bioconductor-uri "GeneOverlap" version)) | |
1137 | (sha256 | |
1138 | (base32 | |
1139 | "0bvh00n4fx0h1m83bypib3jvln1ihcv77ywrrn9xm20y73gymhkh")))) | |
1140 | (build-system r-build-system) | |
1141 | (propagated-inputs | |
1142 | `(("r-rcolorbrewer" ,r-rcolorbrewer) | |
1143 | ("r-gplots" ,r-gplots))) | |
1144 | (home-page "https://www.bioconductor.org/packages/GeneOverlap/") | |
1145 | (synopsis "Test and visualize gene overlaps") | |
1146 | (description "This package can be used to test two sets of gene lists | |
1147 | and visualize the results.") | |
1148 | (license license:gpl3))) | |
1149 | ||
e7fa79fd RW |
1150 | (define-public r-pasilla |
1151 | (package | |
1152 | (name "r-pasilla") | |
1153 | (version "1.14.0") | |
1154 | (source (origin | |
1155 | (method url-fetch) | |
1156 | (uri (string-append | |
1157 | "http://bioconductor.org/packages/release/data/experiment" | |
1158 | "/src/contrib/pasilla_" version ".tar.gz")) | |
1159 | (sha256 | |
1160 | (base32 | |
1161 | "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) | |
1162 | (build-system r-build-system) | |
1163 | (propagated-inputs | |
1164 | `(("r-biocstyle" ,r-biocstyle) | |
1165 | ("r-dexseq" ,r-dexseq) | |
1166 | ("r-knitr" ,r-knitr) | |
1167 | ("r-rmarkdown" ,r-rmarkdown))) | |
1168 | (home-page "https://www.bioconductor.org/packages/pasilla/") | |
1169 | (synopsis "Data package with per-exon and per-gene read counts") | |
1170 | (description "This package provides per-exon and per-gene read counts | |
1171 | computed for selected genes from RNA-seq data that were presented in the | |
1172 | article 'Conservation of an RNA regulatory map between Drosophila and mammals' | |
1173 | by Brooks et al., Genome Research 2011.") | |
1174 | (license license:lgpl2.1+))) | |
1175 | ||
557a1089 RW |
1176 | (define-public r-hsmmsinglecell |
1177 | (package | |
1178 | (name "r-hsmmsinglecell") | |
1179 | (version "1.2.0") | |
1180 | (source (origin | |
1181 | (method url-fetch) | |
545e67ac | 1182 | (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) |
557a1089 RW |
1183 | (sha256 |
1184 | (base32 | |
1185 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) | |
1186 | (properties | |
1187 | `((upstream-name . "HSMMSingleCell"))) | |
1188 | (build-system r-build-system) | |
1189 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") | |
1190 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") | |
1191 | (description | |
1192 | "Skeletal myoblasts undergo a well-characterized sequence of | |
1193 | morphological and transcriptional changes during differentiation. In this | |
1194 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded | |
1195 | under high mitogen conditions (GM) and then differentiated by switching to | |
1196 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several | |
1197 | hundred cells taken over a time-course of serum-induced differentiation. | |
1198 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, | |
1199 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. | |
1200 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, | |
1201 | which were then sequenced to a depth of ~4 million reads per library, | |
1202 | resulting in a complete gene expression profile for each cell.") | |
1203 | (license license:artistic2.0))) | |
ad8f46c6 | 1204 | |
1205 | (define-public r-all | |
1206 | (package | |
1207 | (name "r-all") | |
1208 | (version "1.26.0") | |
1209 | (source (origin | |
1210 | (method url-fetch) | |
41728d23 | 1211 | (uri (bioconductor-uri "ALL" version 'experiment)) |
ad8f46c6 | 1212 | (sha256 |
1213 | (base32 | |
1214 | "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) | |
1215 | (properties `((upstream-name . "ALL"))) | |
1216 | (build-system r-build-system) | |
1217 | (propagated-inputs | |
1218 | `(("r-biobase" ,r-biobase))) | |
1219 | (home-page "https://bioconductor.org/packages/ALL") | |
1220 | (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") | |
1221 | (description | |
1222 | "The data consist of microarrays from 128 different individuals with | |
1223 | @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates | |
1224 | are available. The data have been normalized (using rma) and it is the | |
1225 | jointly normalized data that are available here. The data are presented in | |
1226 | the form of an @code{exprSet} object.") | |
1227 | (license license:artistic2.0))) | |
557a1089 | 1228 | |
53b1e10f RW |
1229 | (define-public r-affydata |
1230 | (package | |
1231 | (name "r-affydata") | |
1232 | (version "1.32.0") | |
1233 | (source | |
1234 | (origin | |
1235 | (method url-fetch) | |
1236 | (uri (bioconductor-uri "affydata" version 'experiment)) | |
1237 | (sha256 | |
1238 | (base32 | |
1239 | "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) | |
1240 | (properties `((upstream-name . "affydata"))) | |
1241 | (build-system r-build-system) | |
1242 | (propagated-inputs | |
1243 | `(("r-affy" ,r-affy))) | |
1244 | (home-page "https://bioconductor.org/packages/affydata/") | |
1245 | (synopsis "Affymetrix data for demonstration purposes") | |
1246 | (description | |
1247 | "This package provides example datasets that represent 'real world | |
1248 | examples' of Affymetrix data, unlike the artificial examples included in the | |
1249 | package @code{affy}.") | |
1250 | (license license:gpl2+))) | |
1251 | ||
eb2f1a7d MIP |
1252 | (define-public r-gagedata |
1253 | (package | |
1254 | (name "r-gagedata") | |
1255 | (version "2.28.0") | |
1256 | (source | |
1257 | (origin | |
1258 | (method url-fetch) | |
1259 | (uri (bioconductor-uri "gageData" version 'experiment)) | |
1260 | (sha256 | |
1261 | (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn")))) | |
1262 | (properties `((upstream-name . "gageData"))) | |
1263 | (build-system r-build-system) | |
1264 | (home-page "https://bioconductor.org/packages/gageData") | |
48358a25 | 1265 | (synopsis "Auxiliary data for the gage package") |
eb2f1a7d MIP |
1266 | (description |
1267 | "This is a supportive data package for the software package @code{gage}. | |
1268 | However, the data supplied here are also useful for gene set or pathway | |
1269 | analysis or microarray data analysis in general. In this package, we provide | |
1270 | two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and | |
1271 | BMP6 (originally published as an demo dataset for GAGE, also registered as | |
1272 | GSE13604 in GEO). This package also includes commonly used gene set data based | |
1273 | on KEGG pathways and GO terms for major research species, including human, | |
1274 | mouse, rat and budding yeast. Mapping data between common gene IDs for budding | |
1275 | yeast are also included.") | |
1276 | (license license:gpl2+))) | |
1277 | ||
ff1146b9 RW |
1278 | (define-public r-curatedtcgadata |
1279 | (package | |
1280 | (name "r-curatedtcgadata") | |
1281 | (version "1.8.0") | |
1282 | (source | |
1283 | (origin | |
1284 | (method url-fetch) | |
1285 | (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) | |
1286 | (sha256 | |
1287 | (base32 | |
1288 | "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) | |
1289 | (properties | |
1290 | `((upstream-name . "curatedTCGAData"))) | |
1291 | (build-system r-build-system) | |
1292 | (propagated-inputs | |
1293 | `(("r-annotationhub" ,r-annotationhub) | |
1294 | ("r-experimenthub" ,r-experimenthub) | |
1295 | ("r-hdf5array" ,r-hdf5array) | |
1296 | ("r-multiassayexperiment" ,r-multiassayexperiment) | |
1297 | ("r-s4vectors" ,r-s4vectors) | |
1298 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1299 | (home-page "https://bioconductor.org/packages/curatedTCGAData/") | |
1300 | (synopsis "Curated data from The Cancer Genome Atlas") | |
1301 | (description | |
1302 | "This package provides publicly available data from The Cancer Genome | |
1303 | Atlas (TCGA) as @code{MultiAssayExperiment} objects. | |
1304 | @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy | |
1305 | number, mutation, microRNA, protein, and others) with clinical / pathological | |
1306 | data. It also links assay barcodes with patient identifiers, enabling | |
1307 | harmonized subsetting of rows (features) and columns (patients / samples) | |
1308 | across the entire multi-'omics experiment.") | |
1309 | (license license:artistic2.0))) | |
1310 | ||
557a1089 RW |
1311 | \f |
1312 | ;;; Packages | |
1313 | ||
e5d722fb RW |
1314 | (define-public r-biocversion |
1315 | (package | |
1316 | (name "r-biocversion") | |
70ab9909 | 1317 | (version "3.12.0") |
e5d722fb RW |
1318 | (source |
1319 | (origin | |
1320 | (method url-fetch) | |
1321 | (uri (bioconductor-uri "BiocVersion" version)) | |
1322 | (sha256 | |
1323 | (base32 | |
70ab9909 | 1324 | "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk")))) |
e5d722fb RW |
1325 | (properties `((upstream-name . "BiocVersion"))) |
1326 | (build-system r-build-system) | |
1327 | (home-page "https://bioconductor.org/packages/BiocVersion/") | |
1328 | (synopsis "Set the appropriate version of Bioconductor packages") | |
1329 | (description | |
1330 | "This package provides repository information for the appropriate version | |
1331 | of Bioconductor.") | |
1332 | (license license:artistic2.0))) | |
1333 | ||
14bba460 RW |
1334 | (define-public r-biocgenerics |
1335 | (package | |
1336 | (name "r-biocgenerics") | |
8bd3170b | 1337 | (version "0.36.1") |
14bba460 RW |
1338 | (source (origin |
1339 | (method url-fetch) | |
1340 | (uri (bioconductor-uri "BiocGenerics" version)) | |
1341 | (sha256 | |
1342 | (base32 | |
8bd3170b | 1343 | "0x8cllriayrs99wd5l003iq6i28rb1mci23qcn13ga85578f5lz5")))) |
14bba460 RW |
1344 | (properties |
1345 | `((upstream-name . "BiocGenerics"))) | |
1346 | (build-system r-build-system) | |
1347 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
1348 | (synopsis "S4 generic functions for Bioconductor") | |
1349 | (description | |
1350 | "This package provides S4 generic functions needed by many Bioconductor | |
1351 | packages.") | |
1352 | (license license:artistic2.0))) | |
1353 | ||
17d95689 RW |
1354 | (define-public r-coverageview |
1355 | (package | |
1356 | (name "r-coverageview") | |
1357 | (version "1.28.0") | |
1358 | (source (origin | |
1359 | (method url-fetch) | |
1360 | (uri (bioconductor-uri "CoverageView" version)) | |
1361 | (sha256 | |
1362 | (base32 | |
1363 | "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj")))) | |
1364 | (build-system r-build-system) | |
1365 | (propagated-inputs | |
1366 | `(("r-s4vectors" ,r-s4vectors) | |
1367 | ("r-iranges" ,r-iranges) | |
1368 | ("r-genomicranges" ,r-genomicranges) | |
1369 | ("r-genomicalignments" ,r-genomicalignments) | |
1370 | ("r-rtracklayer" ,r-rtracklayer) | |
1371 | ("r-rsamtools" ,r-rsamtools))) | |
1372 | (home-page "https://bioconductor.org/packages/CoverageView/") | |
1373 | (synopsis "Coverage visualization package for R") | |
1374 | (description "This package provides a framework for the visualization of | |
1375 | genome coverage profiles. It can be used for ChIP-seq experiments, but it can | |
1376 | be also used for genome-wide nucleosome positioning experiments or other | |
1377 | experiment types where it is important to have a framework in order to inspect | |
1378 | how the coverage distributed across the genome.") | |
1379 | (license license:artistic2.0))) | |
1380 | ||
1abb6a2a RW |
1381 | (define-public r-cummerbund |
1382 | (package | |
1383 | (name "r-cummerbund") | |
1384 | (version "2.32.0") | |
1385 | (source (origin | |
1386 | (method url-fetch) | |
1387 | (uri (bioconductor-uri "cummeRbund" version)) | |
1388 | (sha256 | |
1389 | (base32 | |
1390 | "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj")))) | |
1391 | (build-system r-build-system) | |
1392 | (propagated-inputs | |
1393 | `(("r-biobase" ,r-biobase) | |
1394 | ("r-biocgenerics" ,r-biocgenerics) | |
1395 | ("r-fastcluster" ,r-fastcluster) | |
1396 | ("r-ggplot2" ,r-ggplot2) | |
1397 | ("r-gviz" ,r-gviz) | |
1398 | ("r-plyr" ,r-plyr) | |
1399 | ("r-reshape2" ,r-reshape2) | |
1400 | ("r-rsqlite" ,r-rsqlite) | |
1401 | ("r-rtracklayer" ,r-rtracklayer) | |
1402 | ("r-s4vectors" ,r-s4vectors))) | |
1403 | (home-page "https://bioconductor.org/packages/cummeRbund/") | |
1404 | (synopsis "Analyze Cufflinks high-throughput sequencing data") | |
1405 | (description "This package allows for persistent storage, access, | |
1406 | exploration, and manipulation of Cufflinks high-throughput sequencing | |
1407 | data. In addition, provides numerous plotting functions for commonly | |
1408 | used visualizations.") | |
1409 | (license license:artistic2.0))) | |
1410 | ||
23686ba3 | 1411 | (define-public r-delayedarray |
1412 | (package | |
1413 | (name "r-delayedarray") | |
fb73d7d1 | 1414 | (version "0.16.3") |
23686ba3 | 1415 | (source (origin |
1416 | (method url-fetch) | |
1417 | (uri (bioconductor-uri "DelayedArray" version)) | |
1418 | (sha256 | |
1419 | (base32 | |
fb73d7d1 | 1420 | "0w1wppy6m2iv41852dscg3y19sq84ahdx3m7c2p2pxjcznmv6hys")))) |
23686ba3 | 1421 | (properties |
1422 | `((upstream-name . "DelayedArray"))) | |
1423 | (build-system r-build-system) | |
1424 | (propagated-inputs | |
1425 | `(("r-biocgenerics" ,r-biocgenerics) | |
1426 | ("r-s4vectors" ,r-s4vectors) | |
1427 | ("r-iranges" ,r-iranges) | |
1428 | ("r-matrix" ,r-matrix) | |
1429 | ("r-matrixgenerics" ,r-matrixgenerics))) | |
1430 | (native-inputs | |
1431 | `(("r-knitr" ,r-knitr))) | |
1432 | (home-page "https://bioconductor.org/packages/DelayedArray") | |
1433 | (synopsis "Delayed operations on array-like objects") | |
1434 | (description | |
1435 | "Wrapping an array-like object (typically an on-disk object) in a | |
1436 | @code{DelayedArray} object allows one to perform common array operations on it | |
1437 | without loading the object in memory. In order to reduce memory usage and | |
1438 | optimize performance, operations on the object are either delayed or executed | |
1439 | using a block processing mechanism. Note that this also works on in-memory | |
1440 | array-like objects like @code{DataFrame} objects (typically with Rle columns), | |
1441 | @code{Matrix} objects, and ordinary arrays and data frames.") | |
1442 | (license license:artistic2.0))) | |
1443 | ||
30a4bd3b RW |
1444 | (define-public r-bluster |
1445 | (package | |
1446 | (name "r-bluster") | |
1447 | (version "1.0.0") | |
1448 | (source (origin | |
1449 | (method url-fetch) | |
1450 | (uri (bioconductor-uri "bluster" version)) | |
1451 | (sha256 | |
1452 | (base32 | |
1453 | "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61")))) | |
1454 | (properties `((upstream-name . "bluster"))) | |
1455 | (build-system r-build-system) | |
1456 | (propagated-inputs | |
1457 | `(("r-biocneighbors" ,r-biocneighbors) | |
1458 | ("r-biocparallel" ,r-biocparallel) | |
1459 | ("r-igraph" ,r-igraph) | |
1460 | ("r-matrix" ,r-matrix) | |
1461 | ("r-rcpp" ,r-rcpp) | |
1462 | ("r-s4vectors" ,r-s4vectors))) | |
1463 | (native-inputs | |
1464 | `(("r-knitr" ,r-knitr))) | |
1465 | (home-page "https://bioconductor.org/packages/bluster") | |
1466 | (synopsis "Clustering algorithms for Bioconductor") | |
1467 | (description"This package wraps common clustering algorithms in an easily | |
1468 | extended S4 framework. Backends are implemented for hierarchical, k-means | |
1469 | and graph-based clustering. Several utilities are also provided to compare | |
1470 | and evaluate clustering results.") | |
1471 | (license license:gpl3))) | |
1472 | ||
cc54848a RW |
1473 | (define-public r-ideoviz |
1474 | (package | |
1475 | (name "r-ideoviz") | |
1476 | (version "1.26.0") | |
1477 | (source (origin | |
1478 | (method url-fetch) | |
1479 | (uri (bioconductor-uri "IdeoViz" version)) | |
1480 | (sha256 | |
1481 | (base32 | |
1482 | "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq")))) | |
1483 | (build-system r-build-system) | |
1484 | (propagated-inputs | |
1485 | `(("r-biobase" ,r-biobase) | |
1486 | ("r-iranges" ,r-iranges) | |
1487 | ("r-genomicranges" ,r-genomicranges) | |
1488 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
1489 | ("r-rtracklayer" ,r-rtracklayer) | |
1490 | ("r-genomeinfodb" ,r-genomeinfodb))) | |
1491 | (home-page "https://bioconductor.org/packages/IdeoViz/") | |
1492 | (synopsis "Plots data along a chromosomal ideogram") | |
1493 | (description "This package provides functions to plot data associated with | |
1494 | arbitrary genomic intervals along chromosomal ideogram.") | |
1495 | (license license:gpl2))) | |
1496 | ||
9949f459 | 1497 | (define-public r-iranges |
1498 | (package | |
1499 | (name "r-iranges") | |
1500 | (version "2.24.1") | |
1501 | (source (origin | |
1502 | (method url-fetch) | |
1503 | (uri (bioconductor-uri "IRanges" version)) | |
1504 | (sha256 | |
1505 | (base32 | |
1506 | "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) | |
1507 | (properties | |
1508 | `((upstream-name . "IRanges"))) | |
1509 | (build-system r-build-system) | |
1510 | (propagated-inputs | |
1511 | `(("r-biocgenerics" ,r-biocgenerics) | |
1512 | ("r-s4vectors" ,r-s4vectors))) | |
1513 | (home-page "https://bioconductor.org/packages/IRanges") | |
1514 | (synopsis "Infrastructure for manipulating intervals on sequences") | |
1515 | (description | |
1516 | "This package provides efficient low-level and highly reusable S4 classes | |
1517 | for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more | |
1518 | generally, data that can be organized sequentially (formally defined as | |
1519 | @code{Vector} objects), as well as views on these @code{Vector} objects. | |
1520 | Efficient list-like classes are also provided for storing big collections of | |
1521 | instances of the basic classes. All classes in the package use consistent | |
1522 | naming and share the same rich and consistent \"Vector API\" as much as | |
1523 | possible.") | |
1524 | (license license:artistic2.0))) | |
1525 | ||
92822185 | 1526 | ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor. |
1527 | (define-public r-absfiltergsea | |
1528 | (package | |
1529 | (name "r-absfiltergsea") | |
1530 | (version "1.5.1") | |
1531 | (source | |
1532 | (origin | |
1533 | (method url-fetch) | |
1534 | (uri (cran-uri "AbsFilterGSEA" version)) | |
1535 | (sha256 | |
1536 | (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) | |
1537 | (properties `((upstream-name . "AbsFilterGSEA"))) | |
1538 | (build-system r-build-system) | |
1539 | (propagated-inputs | |
1540 | `(("r-biobase" ,r-biobase) | |
1541 | ("r-deseq" ,r-deseq) | |
1542 | ("r-limma" ,r-limma) | |
1543 | ("r-rcpp" ,r-rcpp) | |
1544 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
1545 | (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") | |
1546 | (synopsis "Improved false positive control of gene-permuting with absolute filtering") | |
1547 | (description | |
1548 | "This package provides a function that performs gene-permuting of a gene-set | |
1549 | enrichment analysis (GSEA) calculation with or without the absolute filtering. | |
1550 | Without filtering, users can perform (original) two-tailed or one-tailed | |
1551 | absolute GSEA.") | |
1552 | (license license:gpl2))) | |
1553 | ||
172b85aa | 1554 | ;; This is a CRAN package, but it depends on r-biobase from Bioconductor. |
1555 | (define-public r-bisquerna | |
1556 | (package | |
1557 | (name "r-bisquerna") | |
1558 | (version "1.0.4") | |
1559 | (source (origin | |
1560 | (method url-fetch) | |
1561 | (uri (cran-uri "BisqueRNA" version)) | |
1562 | (sha256 | |
1563 | (base32 | |
1564 | "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) | |
1565 | (properties `((upstream-name . "BisqueRNA"))) | |
1566 | (build-system r-build-system) | |
1567 | (propagated-inputs | |
1568 | `(("r-biobase" ,r-biobase) | |
1569 | ("r-limsolve" ,r-limsolve))) | |
1570 | (home-page "https://www.biorxiv.org/content/10.1101/669911v1") | |
1571 | (synopsis "Decomposition of bulk expression with single-cell sequencing") | |
1572 | (description "This package provides tools to accurately estimate cell type | |
1573 | abundances from heterogeneous bulk expression. A reference-based method | |
1574 | utilizes single-cell information to generate a signature matrix and | |
1575 | transformation of bulk expression for accurate regression based estimates. | |
1576 | A marker-based method utilizes known cell-specific marker genes to measure | |
1577 | relative abundances across samples.") | |
1578 | (license license:gpl3))) | |
1579 | ||
eb3c1051 RW |
1580 | ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 |
1581 | ;; from Bioconductor. | |
1582 | (define-public r-deconstructsigs | |
1583 | (package | |
1584 | (name "r-deconstructsigs") | |
1585 | (version "1.8.0") | |
1586 | (source (origin | |
1587 | (method url-fetch) | |
1588 | (uri (cran-uri "deconstructSigs" version)) | |
1589 | (sha256 | |
1590 | (base32 | |
1591 | "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) | |
1592 | (properties | |
1593 | `((upstream-name . "deconstructSigs"))) | |
1594 | (build-system r-build-system) | |
1595 | (propagated-inputs | |
1596 | `(("r-bsgenome" ,r-bsgenome) | |
1597 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
1598 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1599 | ("r-reshape2" ,r-reshape2))) | |
1600 | (home-page "https://github.com/raerose01/deconstructSigs") | |
1601 | (synopsis "Identifies signatures present in a tumor sample") | |
1602 | (description "This package takes sample information in the form of the | |
1603 | fraction of mutations in each of 96 trinucleotide contexts and identifies | |
1604 | the weighted combination of published signatures that, when summed, most | |
1605 | closely reconstructs the mutational profile.") | |
1606 | (license license:gpl2+))) | |
1607 | ||
17235ec2 RW |
1608 | ;; This is a CRAN package, but it depends on Bioconductor packages. |
1609 | (define-public r-nmf | |
1610 | (package | |
1611 | (name "r-nmf") | |
1612 | (version "0.23.0") | |
1613 | (source | |
1614 | (origin | |
1615 | (method url-fetch) | |
1616 | (uri (cran-uri "NMF" version)) | |
1617 | (sha256 | |
1618 | (base32 | |
1619 | "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g")))) | |
1620 | (properties `((upstream-name . "NMF"))) | |
1621 | (build-system r-build-system) | |
1622 | (propagated-inputs | |
1623 | `(("r-cluster" ,r-cluster) | |
1624 | ("r-biobase" ,r-biobase) | |
1625 | ("r-biocmanager" ,r-biocmanager) | |
1626 | ("r-bigmemory" ,r-bigmemory) ; suggested | |
1627 | ("r-synchronicity" ,r-synchronicity) ; suggested | |
1628 | ("r-colorspace" ,r-colorspace) | |
1629 | ("r-digest" ,r-digest) | |
1630 | ("r-doparallel" ,r-doparallel) | |
1631 | ("r-foreach" ,r-foreach) | |
1632 | ("r-ggplot2" ,r-ggplot2) | |
1633 | ("r-gridbase" ,r-gridbase) | |
1634 | ("r-pkgmaker" ,r-pkgmaker) | |
1635 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
1636 | ("r-registry" ,r-registry) | |
1637 | ("r-reshape2" ,r-reshape2) | |
1638 | ("r-rngtools" ,r-rngtools) | |
1639 | ("r-stringr" ,r-stringr))) | |
1640 | (native-inputs | |
1641 | `(("r-knitr" ,r-knitr))) | |
1642 | (home-page "http://renozao.github.io/NMF") | |
1643 | (synopsis "Algorithms and framework for nonnegative matrix factorization") | |
1644 | (description | |
1645 | "This package provides a framework to perform Non-negative Matrix | |
1646 | Factorization (NMF). The package implements a set of already published | |
1647 | algorithms and seeding methods, and provides a framework to test, develop and | |
1648 | plug new or custom algorithms. Most of the built-in algorithms have been | |
1649 | optimized in C++, and the main interface function provides an easy way of | |
1650 | performing parallel computations on multicore machines.") | |
1651 | (license license:gpl2+))) | |
1652 | ||
5cf940de RW |
1653 | (define-public r-affycomp |
1654 | (package | |
1655 | (name "r-affycomp") | |
c472549f | 1656 | (version "1.66.0") |
5cf940de RW |
1657 | (source |
1658 | (origin | |
1659 | (method url-fetch) | |
1660 | (uri (bioconductor-uri "affycomp" version)) | |
1661 | (sha256 | |
1662 | (base32 | |
c472549f | 1663 | "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk")))) |
5cf940de RW |
1664 | (properties `((upstream-name . "affycomp"))) |
1665 | (build-system r-build-system) | |
1666 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
1667 | (home-page "https://bioconductor.org/packages/affycomp/") | |
1668 | (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") | |
1669 | (description | |
1670 | "The package contains functions that can be used to compare expression | |
1671 | measures for Affymetrix Oligonucleotide Arrays.") | |
1672 | (license license:gpl2+))) | |
1673 | ||
5094aa94 RW |
1674 | (define-public r-affycompatible |
1675 | (package | |
1676 | (name "r-affycompatible") | |
fa2d16cc | 1677 | (version "1.50.0") |
5094aa94 RW |
1678 | (source |
1679 | (origin | |
1680 | (method url-fetch) | |
1681 | (uri (bioconductor-uri "AffyCompatible" version)) | |
1682 | (sha256 | |
1683 | (base32 | |
fa2d16cc | 1684 | "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x")))) |
5094aa94 RW |
1685 | (properties |
1686 | `((upstream-name . "AffyCompatible"))) | |
1687 | (build-system r-build-system) | |
1688 | (propagated-inputs | |
1689 | `(("r-biostrings" ,r-biostrings) | |
1690 | ("r-rcurl" ,r-rcurl) | |
1691 | ("r-xml" ,r-xml))) | |
1692 | (home-page "https://bioconductor.org/packages/AffyCompatible/") | |
1693 | (synopsis "Work with Affymetrix GeneChip files") | |
1694 | (description | |
1695 | "This package provides an interface to Affymetrix chip annotation and | |
1696 | sample attribute files. The package allows an easy way for users to download | |
1697 | and manage local data bases of Affynmetrix NetAffx annotation files. It also | |
1698 | provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip | |
1699 | Command Console} (AGCC)-compatible sample annotation files.") | |
1700 | (license license:artistic2.0))) | |
1701 | ||
4ca2d6c1 RW |
1702 | (define-public r-affycontam |
1703 | (package | |
1704 | (name "r-affycontam") | |
3e82f9cc | 1705 | (version "1.48.0") |
4ca2d6c1 RW |
1706 | (source |
1707 | (origin | |
1708 | (method url-fetch) | |
1709 | (uri (bioconductor-uri "affyContam" version)) | |
1710 | (sha256 | |
1711 | (base32 | |
3e82f9cc | 1712 | "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b")))) |
4ca2d6c1 RW |
1713 | (properties `((upstream-name . "affyContam"))) |
1714 | (build-system r-build-system) | |
1715 | (propagated-inputs | |
1716 | `(("r-affy" ,r-affy) | |
1717 | ("r-affydata" ,r-affydata) | |
1718 | ("r-biobase" ,r-biobase))) | |
1719 | (home-page "https://bioconductor.org/packages/affyContam/") | |
1720 | (synopsis "Structured corruption of Affymetrix CEL file data") | |
1721 | (description | |
1722 | "Microarray quality assessment is a major concern of microarray analysts. | |
1723 | This package provides some simple approaches to in silico creation of quality | |
1724 | problems in CEL-level data to help evaluate performance of quality metrics.") | |
1725 | (license license:artistic2.0))) | |
1726 | ||
12105c6c RW |
1727 | (define-public r-affycoretools |
1728 | (package | |
1729 | (name "r-affycoretools") | |
a92219b4 | 1730 | (version "1.62.0") |
12105c6c RW |
1731 | (source |
1732 | (origin | |
1733 | (method url-fetch) | |
1734 | (uri (bioconductor-uri "affycoretools" version)) | |
1735 | (sha256 | |
1736 | (base32 | |
a92219b4 | 1737 | "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0")))) |
12105c6c RW |
1738 | (properties `((upstream-name . "affycoretools"))) |
1739 | (build-system r-build-system) | |
1740 | (propagated-inputs | |
1741 | `(("r-affy" ,r-affy) | |
1742 | ("r-annotationdbi" ,r-annotationdbi) | |
1743 | ("r-biobase" ,r-biobase) | |
1744 | ("r-biocgenerics" ,r-biocgenerics) | |
1745 | ("r-dbi" ,r-dbi) | |
1746 | ("r-edger" ,r-edger) | |
1747 | ("r-gcrma" ,r-gcrma) | |
f8f181ae | 1748 | ("r-glimma" ,r-glimma) |
12105c6c RW |
1749 | ("r-ggplot2" ,r-ggplot2) |
1750 | ("r-gostats" ,r-gostats) | |
1751 | ("r-gplots" ,r-gplots) | |
1752 | ("r-hwriter" ,r-hwriter) | |
1753 | ("r-lattice" ,r-lattice) | |
1754 | ("r-limma" ,r-limma) | |
1755 | ("r-oligoclasses" ,r-oligoclasses) | |
1756 | ("r-reportingtools" ,r-reportingtools) | |
1757 | ("r-rsqlite" ,r-rsqlite) | |
1758 | ("r-s4vectors" ,r-s4vectors) | |
1759 | ("r-xtable" ,r-xtable))) | |
fa610697 RW |
1760 | (native-inputs |
1761 | `(("r-knitr" ,r-knitr))) | |
12105c6c RW |
1762 | (home-page "https://bioconductor.org/packages/affycoretools/") |
1763 | (synopsis "Functions for analyses with Affymetrix GeneChips") | |
1764 | (description | |
1765 | "This package provides various wrapper functions that have been written | |
1766 | to streamline the more common analyses that a Biostatistician might see.") | |
1767 | (license license:artistic2.0))) | |
1768 | ||
d6a5d9b2 RW |
1769 | (define-public r-affxparser |
1770 | (package | |
1771 | (name "r-affxparser") | |
8e6a2c32 | 1772 | (version "1.62.0") |
d6a5d9b2 RW |
1773 | (source |
1774 | (origin | |
1775 | (method url-fetch) | |
1776 | (uri (bioconductor-uri "affxparser" version)) | |
1777 | (sha256 | |
1778 | (base32 | |
8e6a2c32 | 1779 | "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p")))) |
d6a5d9b2 RW |
1780 | (properties `((upstream-name . "affxparser"))) |
1781 | (build-system r-build-system) | |
1782 | (home-page "https://github.com/HenrikBengtsson/affxparser") | |
1783 | (synopsis "Affymetrix File Parsing SDK") | |
1784 | (description | |
1785 | "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, | |
1786 | BAR). It provides methods for fast and memory efficient parsing of Affymetrix | |
1787 | files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files | |
1788 | are supported. Currently, there are methods for reading @dfn{chip definition | |
1789 | file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read | |
1790 | either in full or in part. For example, probe signals from a few probesets | |
1791 | can be extracted very quickly from a set of CEL files into a convenient list | |
1792 | structure.") | |
1793 | ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is | |
1794 | ;; under LGPLv2+. | |
1795 | (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2)))) | |
1796 | ||
7097c700 RW |
1797 | (define-public r-annotate |
1798 | (package | |
1799 | (name "r-annotate") | |
7d563023 | 1800 | (version "1.68.0") |
7097c700 RW |
1801 | (source |
1802 | (origin | |
1803 | (method url-fetch) | |
1804 | (uri (bioconductor-uri "annotate" version)) | |
1805 | (sha256 | |
1806 | (base32 | |
7d563023 | 1807 | "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l")))) |
7097c700 RW |
1808 | (build-system r-build-system) |
1809 | (propagated-inputs | |
1810 | `(("r-annotationdbi" ,r-annotationdbi) | |
1811 | ("r-biobase" ,r-biobase) | |
1812 | ("r-biocgenerics" ,r-biocgenerics) | |
1813 | ("r-dbi" ,r-dbi) | |
7d563023 | 1814 | ("r-httr" ,r-httr) |
7097c700 RW |
1815 | ("r-xml" ,r-xml) |
1816 | ("r-xtable" ,r-xtable))) | |
1817 | (home-page | |
1818 | "https://bioconductor.org/packages/annotate") | |
1819 | (synopsis "Annotation for microarrays") | |
1820 | (description "This package provides R environments for the annotation of | |
1821 | microarrays.") | |
1822 | (license license:artistic2.0))) | |
1823 | ||
23686ba3 | 1824 | (define-public r-annotationdbi |
1825 | (package | |
1826 | (name "r-annotationdbi") | |
1827 | (version "1.52.0") | |
1828 | (source (origin | |
1829 | (method url-fetch) | |
1830 | (uri (bioconductor-uri "AnnotationDbi" version)) | |
1831 | (sha256 | |
1832 | (base32 | |
1833 | "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) | |
1834 | (properties | |
1835 | `((upstream-name . "AnnotationDbi"))) | |
1836 | (build-system r-build-system) | |
1837 | (propagated-inputs | |
1838 | `(("r-biobase" ,r-biobase) | |
1839 | ("r-biocgenerics" ,r-biocgenerics) | |
1840 | ("r-dbi" ,r-dbi) | |
1841 | ("r-iranges" ,r-iranges) | |
1842 | ("r-rsqlite" ,r-rsqlite) | |
1843 | ("r-s4vectors" ,r-s4vectors))) | |
1844 | (native-inputs | |
1845 | `(("r-knitr" ,r-knitr))) | |
1846 | (home-page "https://bioconductor.org/packages/AnnotationDbi") | |
1847 | (synopsis "Annotation database interface") | |
1848 | (description | |
1849 | "This package provides user interface and database connection code for | |
1850 | annotation data packages using SQLite data storage.") | |
1851 | (license license:artistic2.0))) | |
1852 | ||
ff92c287 | 1853 | (define-public r-annotationforge |
1854 | (package | |
1855 | (name "r-annotationforge") | |
1856 | (version "1.32.0") | |
1857 | (source | |
1858 | (origin | |
1859 | (method url-fetch) | |
1860 | (uri (bioconductor-uri "AnnotationForge" version)) | |
1861 | (sha256 | |
1862 | (base32 | |
1863 | "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) | |
1864 | (properties | |
1865 | `((upstream-name . "AnnotationForge"))) | |
1866 | (build-system r-build-system) | |
1867 | (propagated-inputs | |
1868 | `(("r-annotationdbi" ,r-annotationdbi) | |
1869 | ("r-biobase" ,r-biobase) | |
1870 | ("r-biocgenerics" ,r-biocgenerics) | |
1871 | ("r-dbi" ,r-dbi) | |
1872 | ("r-rcurl" ,r-rcurl) | |
1873 | ("r-rsqlite" ,r-rsqlite) | |
1874 | ("r-s4vectors" ,r-s4vectors) | |
1875 | ("r-xml" ,r-xml))) | |
1876 | (native-inputs | |
1877 | `(("r-knitr" ,r-knitr))) | |
1878 | (home-page "https://bioconductor.org/packages/AnnotationForge") | |
1879 | (synopsis "Code for building annotation database packages") | |
1880 | (description | |
1881 | "This package provides code for generating Annotation packages and their | |
1882 | databases. Packages produced are intended to be used with AnnotationDbi.") | |
1883 | (license license:artistic2.0))) | |
1884 | ||
23686ba3 | 1885 | (define-public r-biobase |
1886 | (package | |
1887 | (name "r-biobase") | |
1888 | (version "2.50.0") | |
1889 | (source (origin | |
1890 | (method url-fetch) | |
1891 | (uri (bioconductor-uri "Biobase" version)) | |
1892 | (sha256 | |
1893 | (base32 | |
1894 | "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) | |
1895 | (properties | |
1896 | `((upstream-name . "Biobase"))) | |
1897 | (build-system r-build-system) | |
1898 | (propagated-inputs | |
1899 | `(("r-biocgenerics" ,r-biocgenerics))) | |
1900 | (home-page "https://bioconductor.org/packages/Biobase") | |
1901 | (synopsis "Base functions for Bioconductor") | |
1902 | (description | |
1903 | "This package provides functions that are needed by many other packages | |
1904 | on Bioconductor or which replace R functions.") | |
1905 | (license license:artistic2.0))) | |
1906 | ||
1907 | (define-public r-biomart | |
1908 | (package | |
1909 | (name "r-biomart") | |
1910 | (version "2.46.3") | |
1911 | (source (origin | |
1912 | (method url-fetch) | |
1913 | (uri (bioconductor-uri "biomaRt" version)) | |
1914 | (sha256 | |
1915 | (base32 | |
1916 | "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) | |
1917 | (properties | |
1918 | `((upstream-name . "biomaRt"))) | |
1919 | (build-system r-build-system) | |
1920 | (propagated-inputs | |
1921 | `(("r-annotationdbi" ,r-annotationdbi) | |
1922 | ("r-biocfilecache" ,r-biocfilecache) | |
1923 | ("r-httr" ,r-httr) | |
1924 | ("r-openssl" ,r-openssl) | |
1925 | ("r-progress" ,r-progress) | |
1926 | ("r-rappdirs" ,r-rappdirs) | |
1927 | ("r-stringr" ,r-stringr) | |
1928 | ("r-xml" ,r-xml) | |
1929 | ("r-xml2" ,r-xml2))) | |
1930 | (native-inputs | |
1931 | `(("r-knitr" ,r-knitr))) | |
1932 | (home-page "https://bioconductor.org/packages/biomaRt") | |
1933 | (synopsis "Interface to BioMart databases") | |
1934 | (description | |
1935 | "biomaRt provides an interface to a growing collection of databases | |
1936 | implementing the @url{BioMart software suite, http://www.biomart.org}. The | |
1937 | package enables retrieval of large amounts of data in a uniform way without | |
1938 | the need to know the underlying database schemas or write complex SQL queries. | |
1939 | Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, | |
1940 | Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt | |
1941 | users direct access to a diverse set of data and enable a wide range of | |
1942 | powerful online queries from gene annotation to database mining.") | |
1943 | (license license:artistic2.0))) | |
1944 | ||
1945 | (define-public r-biocparallel | |
1946 | (package | |
1947 | (name "r-biocparallel") | |
1948 | (version "1.24.1") | |
1949 | (source (origin | |
1950 | (method url-fetch) | |
1951 | (uri (bioconductor-uri "BiocParallel" version)) | |
1952 | (sha256 | |
1953 | (base32 | |
1954 | "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) | |
1955 | (properties | |
1956 | `((upstream-name . "BiocParallel"))) | |
1957 | (build-system r-build-system) | |
1958 | (arguments | |
1959 | `(#:phases | |
1960 | (modify-phases %standard-phases | |
1961 | (add-after 'unpack 'make-reproducible | |
1962 | (lambda _ | |
1963 | ;; Remove generated documentation. | |
1964 | (for-each delete-file | |
1965 | '("inst/doc/BiocParallel_BatchtoolsParam.pdf" | |
1966 | "inst/doc/Introduction_To_BiocParallel.pdf" | |
1967 | "inst/doc/Errors_Logs_And_Debugging.pdf" | |
1968 | "inst/doc/BiocParallel_BatchtoolsParam.R" | |
1969 | "inst/doc/Introduction_To_BiocParallel.R" | |
1970 | "inst/doc/Errors_Logs_And_Debugging.R")) | |
1971 | ||
1972 | ;; Remove time-dependent macro | |
1973 | (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw" | |
1974 | "inst/doc/Introduction_To_BiocParallel.Rnw" | |
1975 | "inst/doc/Errors_Logs_And_Debugging.Rnw" | |
1976 | "vignettes/BiocParallel_BatchtoolsParam.Rnw" | |
1977 | "vignettes/Introduction_To_BiocParallel.Rnw" | |
1978 | "vignettes/Errors_Logs_And_Debugging.Rnw") | |
1979 | (("\\today") "later")) | |
1980 | ||
1981 | ;; Initialize the random number generator seed when building. | |
1982 | (substitute* "R/internal_rng_stream.R" | |
1983 | (("\"L'Ecuyer-CMRG\"\\)" m) | |
1984 | (string-append | |
1985 | m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) | |
1986 | (propagated-inputs | |
1987 | `(("r-futile-logger" ,r-futile-logger) | |
1988 | ("r-snow" ,r-snow) | |
1989 | ("r-bh" ,r-bh))) | |
1990 | (native-inputs | |
1991 | `(("r-knitr" ,r-knitr))) | |
1992 | (home-page "https://bioconductor.org/packages/BiocParallel") | |
1993 | (synopsis "Bioconductor facilities for parallel evaluation") | |
1994 | (description | |
1995 | "This package provides modified versions and novel implementation of | |
1996 | functions for parallel evaluation, tailored to use with Bioconductor | |
1997 | objects.") | |
1998 | (license (list license:gpl2+ license:gpl3+)))) | |
1999 | ||
2000 | (define-public r-biostrings | |
2001 | (package | |
2002 | (name "r-biostrings") | |
2003 | (version "2.58.0") | |
2004 | (source (origin | |
2005 | (method url-fetch) | |
2006 | (uri (bioconductor-uri "Biostrings" version)) | |
2007 | (sha256 | |
2008 | (base32 | |
2009 | "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) | |
2010 | (properties | |
2011 | `((upstream-name . "Biostrings"))) | |
2012 | (build-system r-build-system) | |
2013 | (propagated-inputs | |
2014 | `(("r-biocgenerics" ,r-biocgenerics) | |
2015 | ("r-crayon" ,r-crayon) | |
2016 | ("r-iranges" ,r-iranges) | |
2017 | ("r-s4vectors" ,r-s4vectors) | |
2018 | ("r-xvector" ,r-xvector))) | |
2019 | (home-page "https://bioconductor.org/packages/Biostrings") | |
2020 | (synopsis "String objects and algorithms for biological sequences") | |
2021 | (description | |
2022 | "This package provides memory efficient string containers, string | |
2023 | matching algorithms, and other utilities, for fast manipulation of large | |
2024 | biological sequences or sets of sequences.") | |
2025 | (license license:artistic2.0))) | |
2026 | ||
4e7cf96c | 2027 | (define-public r-category |
2028 | (package | |
2029 | (name "r-category") | |
2030 | (version "2.56.0") | |
2031 | (source | |
2032 | (origin | |
2033 | (method url-fetch) | |
2034 | (uri (bioconductor-uri "Category" version)) | |
2035 | (sha256 | |
2036 | (base32 | |
2037 | "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) | |
2038 | (properties `((upstream-name . "Category"))) | |
2039 | (build-system r-build-system) | |
2040 | (propagated-inputs | |
2041 | `(("r-annotate" ,r-annotate) | |
2042 | ("r-annotationdbi" ,r-annotationdbi) | |
2043 | ("r-biobase" ,r-biobase) | |
2044 | ("r-biocgenerics" ,r-biocgenerics) | |
2045 | ("r-genefilter" ,r-genefilter) | |
2046 | ("r-graph" ,r-graph) | |
2047 | ("r-gseabase" ,r-gseabase) | |
2048 | ("r-matrix" ,r-matrix) | |
2049 | ("r-rbgl" ,r-rbgl) | |
2050 | ("r-dbi" ,r-dbi))) | |
2051 | (home-page "https://bioconductor.org/packages/Category") | |
2052 | (synopsis "Category analysis") | |
2053 | (description | |
2054 | "This package provides a collection of tools for performing category | |
2055 | analysis.") | |
2056 | (license license:artistic2.0))) | |
2057 | ||
37354585 | 2058 | (define-public r-deseq2 |
2059 | (package | |
2060 | (name "r-deseq2") | |
b45c625f | 2061 | (version "1.30.1") |
37354585 | 2062 | (source |
2063 | (origin | |
2064 | (method url-fetch) | |
2065 | (uri (bioconductor-uri "DESeq2" version)) | |
2066 | (sha256 | |
2067 | (base32 | |
b45c625f | 2068 | "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19")))) |
37354585 | 2069 | (properties `((upstream-name . "DESeq2"))) |
2070 | (build-system r-build-system) | |
2071 | (propagated-inputs | |
2072 | `(("r-biobase" ,r-biobase) | |
2073 | ("r-biocgenerics" ,r-biocgenerics) | |
2074 | ("r-biocparallel" ,r-biocparallel) | |
2075 | ("r-genefilter" ,r-genefilter) | |
2076 | ("r-geneplotter" ,r-geneplotter) | |
2077 | ("r-genomicranges" ,r-genomicranges) | |
2078 | ("r-ggplot2" ,r-ggplot2) | |
2079 | ("r-iranges" ,r-iranges) | |
2080 | ("r-locfit" ,r-locfit) | |
2081 | ("r-rcpp" ,r-rcpp) | |
2082 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
2083 | ("r-s4vectors" ,r-s4vectors) | |
2084 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2085 | (native-inputs | |
2086 | `(("r-knitr" ,r-knitr))) | |
2087 | (home-page "https://bioconductor.org/packages/DESeq2") | |
2088 | (synopsis "Differential gene expression analysis") | |
2089 | (description | |
2090 | "This package provides functions to estimate variance-mean dependence in | |
2091 | count data from high-throughput nucleotide sequencing assays and test for | |
2092 | differential expression based on a model using the negative binomial | |
2093 | distribution.") | |
2094 | (license license:lgpl3+))) | |
2095 | ||
d769b107 | 2096 | (define-public r-dexseq |
2097 | (package | |
2098 | (name "r-dexseq") | |
2099 | (version "1.36.0") | |
2100 | (source | |
2101 | (origin | |
2102 | (method url-fetch) | |
2103 | (uri (bioconductor-uri "DEXSeq" version)) | |
2104 | (sha256 | |
2105 | (base32 | |
2106 | "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) | |
2107 | (properties `((upstream-name . "DEXSeq"))) | |
2108 | (build-system r-build-system) | |
2109 | (propagated-inputs | |
2110 | `(("r-annotationdbi" ,r-annotationdbi) | |
2111 | ("r-biobase" ,r-biobase) | |
2112 | ("r-biocgenerics" ,r-biocgenerics) | |
2113 | ("r-biocparallel" ,r-biocparallel) | |
2114 | ("r-biomart" ,r-biomart) | |
2115 | ("r-deseq2" ,r-deseq2) | |
2116 | ("r-genefilter" ,r-genefilter) | |
2117 | ("r-geneplotter" ,r-geneplotter) | |
2118 | ("r-genomicranges" ,r-genomicranges) | |
2119 | ("r-hwriter" ,r-hwriter) | |
2120 | ("r-iranges" ,r-iranges) | |
2121 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2122 | ("r-rsamtools" ,r-rsamtools) | |
2123 | ("r-s4vectors" ,r-s4vectors) | |
2124 | ("r-statmod" ,r-statmod) | |
2125 | ("r-stringr" ,r-stringr) | |
2126 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2127 | (native-inputs | |
2128 | `(("r-knitr" ,r-knitr))) | |
2129 | (home-page "https://bioconductor.org/packages/DEXSeq") | |
2130 | (synopsis "Inference of differential exon usage in RNA-Seq") | |
2131 | (description | |
2132 | "This package is focused on finding differential exon usage using RNA-seq | |
2133 | exon counts between samples with different experimental designs. It provides | |
2134 | functions that allows the user to make the necessary statistical tests based | |
2135 | on a model that uses the negative binomial distribution to estimate the | |
2136 | variance between biological replicates and generalized linear models for | |
2137 | testing. The package also provides functions for the visualization and | |
2138 | exploration of the results.") | |
2139 | (license license:gpl3+))) | |
2140 | ||
082f3c54 | 2141 | (define-public r-edger |
2142 | (package | |
2143 | (name "r-edger") | |
2144 | (version "3.32.1") | |
2145 | (source (origin | |
2146 | (method url-fetch) | |
2147 | (uri (bioconductor-uri "edgeR" version)) | |
2148 | (sha256 | |
2149 | (base32 | |
2150 | "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) | |
2151 | (properties `((upstream-name . "edgeR"))) | |
2152 | (build-system r-build-system) | |
2153 | (propagated-inputs | |
2154 | `(("r-limma" ,r-limma) | |
2155 | ("r-locfit" ,r-locfit) | |
2156 | ("r-rcpp" ,r-rcpp) | |
2157 | ("r-statmod" ,r-statmod))) ;for estimateDisp | |
2158 | (home-page "http://bioinf.wehi.edu.au/edgeR") | |
2159 | (synopsis "EdgeR does empirical analysis of digital gene expression data") | |
2160 | (description "This package can do differential expression analysis of | |
2161 | RNA-seq expression profiles with biological replication. It implements a range | |
2162 | of statistical methodology based on the negative binomial distributions, | |
2163 | including empirical Bayes estimation, exact tests, generalized linear models | |
2164 | and quasi-likelihood tests. It be applied to differential signal analysis of | |
2165 | other types of genomic data that produce counts, including ChIP-seq, SAGE and | |
2166 | CAGE.") | |
2167 | (license license:gpl2+))) | |
2168 | ||
a35ea5fe | 2169 | (define-public r-genefilter |
2170 | (package | |
2171 | (name "r-genefilter") | |
2172 | (version "1.72.1") | |
2173 | (source | |
2174 | (origin | |
2175 | (method url-fetch) | |
2176 | (uri (bioconductor-uri "genefilter" version)) | |
2177 | (sha256 | |
2178 | (base32 | |
2179 | "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) | |
2180 | (build-system r-build-system) | |
2181 | (native-inputs | |
2182 | `(("gfortran" ,gfortran) | |
2183 | ("r-knitr" ,r-knitr))) | |
2184 | (propagated-inputs | |
2185 | `(("r-annotate" ,r-annotate) | |
2186 | ("r-annotationdbi" ,r-annotationdbi) | |
2187 | ("r-biobase" ,r-biobase) | |
2188 | ("r-biocgenerics" ,r-biocgenerics) | |
2189 | ("r-survival" ,r-survival))) | |
2190 | (home-page "https://bioconductor.org/packages/genefilter") | |
2191 | (synopsis "Filter genes from high-throughput experiments") | |
2192 | (description | |
2193 | "This package provides basic functions for filtering genes from | |
2194 | high-throughput sequencing experiments.") | |
2195 | (license license:artistic2.0))) | |
2196 | ||
35b62c04 | 2197 | (define-public r-genomeinfodb |
2198 | (package | |
2199 | (name "r-genomeinfodb") | |
fc1aef2c | 2200 | (version "1.26.7") |
35b62c04 | 2201 | (source (origin |
2202 | (method url-fetch) | |
2203 | (uri (bioconductor-uri "GenomeInfoDb" version)) | |
2204 | (sha256 | |
2205 | (base32 | |
fc1aef2c | 2206 | "0fp7sp3jmc2a1hk4r624lfavx8gc2ik3lv43ksc2jmspg6cvh516")))) |
35b62c04 | 2207 | (properties |
2208 | `((upstream-name . "GenomeInfoDb"))) | |
2209 | (build-system r-build-system) | |
2210 | (propagated-inputs | |
2211 | `(("r-biocgenerics" ,r-biocgenerics) | |
2212 | ("r-genomeinfodbdata" ,r-genomeinfodbdata) | |
2213 | ("r-iranges" ,r-iranges) | |
2214 | ("r-rcurl" ,r-rcurl) | |
2215 | ("r-s4vectors" ,r-s4vectors))) | |
2216 | (native-inputs | |
2217 | `(("r-knitr" ,r-knitr))) | |
2218 | (home-page "https://bioconductor.org/packages/GenomeInfoDb") | |
2219 | (synopsis "Utilities for manipulating chromosome identifiers") | |
2220 | (description | |
2221 | "This package contains data and functions that define and allow | |
2222 | translation between different chromosome sequence naming conventions (e.g., | |
2223 | \"chr1\" versus \"1\"), including a function that attempts to place sequence | |
2224 | names in their natural, rather than lexicographic, order.") | |
2225 | (license license:artistic2.0))) | |
2226 | ||
23686ba3 | 2227 | (define-public r-genomicranges |
2228 | (package | |
2229 | (name "r-genomicranges") | |
2230 | (version "1.42.0") | |
2231 | (source (origin | |
2232 | (method url-fetch) | |
2233 | (uri (bioconductor-uri "GenomicRanges" version)) | |
2234 | (sha256 | |
2235 | (base32 | |
2236 | "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) | |
2237 | (properties | |
2238 | `((upstream-name . "GenomicRanges"))) | |
2239 | (build-system r-build-system) | |
2240 | (propagated-inputs | |
2241 | `(("r-biocgenerics" ,r-biocgenerics) | |
2242 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2243 | ("r-iranges" ,r-iranges) | |
2244 | ("r-s4vectors" ,r-s4vectors) | |
2245 | ("r-xvector" ,r-xvector))) | |
2246 | (native-inputs | |
2247 | `(("r-knitr" ,r-knitr))) | |
2248 | (home-page "https://bioconductor.org/packages/GenomicRanges") | |
2249 | (synopsis "Representation and manipulation of genomic intervals") | |
2250 | (description | |
2251 | "This package provides tools to efficiently represent and manipulate | |
2252 | genomic annotations and alignments is playing a central role when it comes to | |
2253 | analyzing high-throughput sequencing data (a.k.a. NGS data). The | |
2254 | GenomicRanges package defines general purpose containers for storing and | |
2255 | manipulating genomic intervals and variables defined along a genome.") | |
2256 | (license license:artistic2.0))) | |
2257 | ||
2a970576 | 2258 | (define-public r-gostats |
2259 | (package | |
2260 | (name "r-gostats") | |
2261 | (version "2.56.0") | |
2262 | (source | |
2263 | (origin | |
2264 | (method url-fetch) | |
2265 | (uri (bioconductor-uri "GOstats" version)) | |
2266 | (sha256 | |
2267 | (base32 | |
2268 | "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j")))) | |
2269 | (properties `((upstream-name . "GOstats"))) | |
2270 | (build-system r-build-system) | |
2271 | (propagated-inputs | |
2272 | `(("r-annotate" ,r-annotate) | |
2273 | ("r-annotationdbi" ,r-annotationdbi) | |
2274 | ("r-annotationforge" ,r-annotationforge) | |
2275 | ("r-biobase" ,r-biobase) | |
2276 | ("r-category" ,r-category) | |
2277 | ("r-go-db" ,r-go-db) | |
2278 | ("r-graph" ,r-graph) | |
2279 | ("r-rgraphviz" ,r-rgraphviz) | |
2280 | ("r-rbgl" ,r-rbgl))) | |
2281 | (home-page "https://bioconductor.org/packages/GOstats") | |
2282 | (synopsis "Tools for manipulating GO and microarrays") | |
2283 | (description | |
2284 | "This package provides a set of tools for interacting with GO and | |
2285 | microarray data. A variety of basic manipulation tools for graphs, hypothesis | |
2286 | testing and other simple calculations.") | |
2287 | (license license:artistic2.0))) | |
2288 | ||
031fdda4 | 2289 | (define-public r-gseabase |
2290 | (package | |
2291 | (name "r-gseabase") | |
2292 | (version "1.52.1") | |
2293 | (source | |
2294 | (origin | |
2295 | (method url-fetch) | |
2296 | (uri (bioconductor-uri "GSEABase" version)) | |
2297 | (sha256 | |
2298 | (base32 | |
2299 | "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) | |
2300 | (properties `((upstream-name . "GSEABase"))) | |
2301 | (build-system r-build-system) | |
2302 | (propagated-inputs | |
2303 | `(("r-annotate" ,r-annotate) | |
2304 | ("r-annotationdbi" ,r-annotationdbi) | |
2305 | ("r-biobase" ,r-biobase) | |
2306 | ("r-biocgenerics" ,r-biocgenerics) | |
2307 | ("r-graph" ,r-graph) | |
2308 | ("r-xml" ,r-xml))) | |
2309 | (native-inputs | |
2310 | `(("r-knitr" ,r-knitr))) | |
2311 | (home-page "https://bioconductor.org/packages/GSEABase") | |
2312 | (synopsis "Gene set enrichment data structures and methods") | |
2313 | (description | |
2314 | "This package provides classes and methods to support @dfn{Gene Set | |
2315 | Enrichment Analysis} (GSEA).") | |
2316 | (license license:artistic2.0))) | |
2317 | ||
fa596599 RW |
2318 | (define-public r-hpar |
2319 | (package | |
2320 | (name "r-hpar") | |
fa7578b3 | 2321 | (version "1.32.1") |
fa596599 RW |
2322 | (source |
2323 | (origin | |
2324 | (method url-fetch) | |
2325 | (uri (bioconductor-uri "hpar" version)) | |
2326 | (sha256 | |
2327 | (base32 | |
fa7578b3 | 2328 | "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr")))) |
fa596599 | 2329 | (build-system r-build-system) |
07bea010 RW |
2330 | (native-inputs |
2331 | `(("r-knitr" ,r-knitr))) | |
fa596599 RW |
2332 | (home-page "https://bioconductor.org/packages/hpar/") |
2333 | (synopsis "Human Protein Atlas in R") | |
2334 | (description "This package provides a simple interface to and data from | |
2335 | the Human Protein Atlas project.") | |
2336 | (license license:artistic2.0))) | |
f44079bc | 2337 | |
23686ba3 | 2338 | (define-public r-limma |
2339 | (package | |
2340 | (name "r-limma") | |
2341 | (version "3.46.0") | |
2342 | (source (origin | |
2343 | (method url-fetch) | |
2344 | (uri (bioconductor-uri "limma" version)) | |
2345 | (sha256 | |
2346 | (base32 | |
2347 | "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) | |
2348 | (build-system r-build-system) | |
2349 | (home-page "http://bioinf.wehi.edu.au/limma") | |
2350 | (synopsis "Package for linear models for microarray and RNA-seq data") | |
2351 | (description "This package can be used for the analysis of gene expression | |
2352 | studies, especially the use of linear models for analysing designed experiments | |
2353 | and the assessment of differential expression. The analysis methods apply to | |
2354 | different technologies, including microarrays, RNA-seq, and quantitative PCR.") | |
2355 | (license license:gpl2+))) | |
2356 | ||
f44079bc | 2357 | (define-public r-rbgl |
2358 | (package | |
2359 | (name "r-rbgl") | |
2360 | (version "1.66.0") | |
2361 | (source | |
2362 | (origin | |
2363 | (method url-fetch) | |
2364 | (uri (bioconductor-uri "RBGL" version)) | |
2365 | (sha256 | |
2366 | (base32 | |
2367 | "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz")))) | |
2368 | (properties `((upstream-name . "RBGL"))) | |
2369 | (build-system r-build-system) | |
2370 | (propagated-inputs | |
2371 | `(("r-bh" ,r-bh) | |
2372 | ("r-graph" ,r-graph))) | |
2373 | (home-page "https://www.bioconductor.org/packages/RBGL") | |
2374 | (synopsis "Interface to the Boost graph library") | |
2375 | (description | |
2376 | "This package provides a fairly extensive and comprehensive interface to | |
2377 | the graph algorithms contained in the Boost library.") | |
2378 | (license license:artistic2.0))) | |
183ce988 RJ |
2379 | |
2380 | (define-public r-regioner | |
2381 | (package | |
2382 | (name "r-regioner") | |
d1ff3604 | 2383 | (version "1.22.0") |
183ce988 RJ |
2384 | (source |
2385 | (origin | |
2386 | (method url-fetch) | |
2387 | (uri (bioconductor-uri "regioneR" version)) | |
2388 | (sha256 | |
2389 | (base32 | |
d1ff3604 | 2390 | "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi")))) |
183ce988 RJ |
2391 | (properties `((upstream-name . "regioneR"))) |
2392 | (build-system r-build-system) | |
2393 | (propagated-inputs | |
d639d888 | 2394 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 2395 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 2396 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 2397 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 2398 | ("r-iranges" ,r-iranges) |
d639d888 RW |
2399 | ("r-memoise" ,r-memoise) |
2400 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 2401 | ("r-s4vectors" ,r-s4vectors))) |
7f34dd58 RW |
2402 | (native-inputs |
2403 | `(("r-knitr" ,r-knitr))) | |
183ce988 RJ |
2404 | (home-page "https://bioconductor.org/packages/regioneR/") |
2405 | (synopsis "Association analysis of genomic regions") | |
2406 | (description "This package offers a statistical framework based on | |
2407 | customizable permutation tests to assess the association between genomic | |
2408 | region sets and other genomic features.") | |
2409 | (license license:artistic2.0))) | |
a5b56a53 | 2410 | |
15184fb3 RW |
2411 | (define-public r-reportingtools |
2412 | (package | |
2413 | (name "r-reportingtools") | |
ee61edb6 | 2414 | (version "2.30.2") |
15184fb3 RW |
2415 | (source |
2416 | (origin | |
2417 | (method url-fetch) | |
2418 | (uri (bioconductor-uri "ReportingTools" version)) | |
2419 | (sha256 | |
2420 | (base32 | |
ee61edb6 | 2421 | "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb")))) |
15184fb3 RW |
2422 | (properties |
2423 | `((upstream-name . "ReportingTools"))) | |
2424 | (build-system r-build-system) | |
2425 | (propagated-inputs | |
2426 | `(("r-annotate" ,r-annotate) | |
2427 | ("r-annotationdbi" ,r-annotationdbi) | |
2428 | ("r-biobase" ,r-biobase) | |
2429 | ("r-biocgenerics" ,r-biocgenerics) | |
2430 | ("r-category" ,r-category) | |
2431 | ("r-deseq2" ,r-deseq2) | |
2432 | ("r-edger" ,r-edger) | |
2433 | ("r-ggbio" ,r-ggbio) | |
2434 | ("r-ggplot2" ,r-ggplot2) | |
2435 | ("r-gostats" ,r-gostats) | |
2436 | ("r-gseabase" ,r-gseabase) | |
2437 | ("r-hwriter" ,r-hwriter) | |
2438 | ("r-iranges" ,r-iranges) | |
2439 | ("r-knitr" ,r-knitr) | |
2440 | ("r-lattice" ,r-lattice) | |
2441 | ("r-limma" ,r-limma) | |
2442 | ("r-pfam-db" ,r-pfam-db) | |
2443 | ("r-r-utils" ,r-r-utils) | |
2444 | ("r-xml" ,r-xml))) | |
7f94cf01 RW |
2445 | (native-inputs |
2446 | `(("r-knitr" ,r-knitr))) | |
15184fb3 RW |
2447 | (home-page "https://bioconductor.org/packages/ReportingTools/") |
2448 | (synopsis "Tools for making reports in various formats") | |
2449 | (description | |
2450 | "The ReportingTools package enables users to easily display reports of | |
2451 | analysis results generated from sources such as microarray and sequencing | |
2452 | data. The package allows users to create HTML pages that may be viewed on a | |
2453 | web browser, or in other formats. Users can generate tables with sortable and | |
2454 | filterable columns, make and display plots, and link table entries to other | |
2455 | data sources such as NCBI or larger plots within the HTML page. Using the | |
2456 | package, users can also produce a table of contents page to link various | |
2457 | reports together for a particular project that can be viewed in a web | |
2458 | browser.") | |
2459 | (license license:artistic2.0))) | |
2460 | ||
23686ba3 | 2461 | (define-public r-rsamtools |
2462 | (package | |
2463 | (name "r-rsamtools") | |
2464 | (version "2.6.0") | |
2465 | (source (origin | |
2466 | (method url-fetch) | |
2467 | (uri (bioconductor-uri "Rsamtools" version)) | |
2468 | (sha256 | |
2469 | (base32 | |
2470 | "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) | |
2471 | (properties | |
2472 | `((upstream-name . "Rsamtools"))) | |
2473 | (build-system r-build-system) | |
2474 | (arguments | |
2475 | `(#:phases | |
2476 | (modify-phases %standard-phases | |
2477 | (add-after 'unpack 'use-system-zlib | |
2478 | (lambda _ | |
2479 | (substitute* "DESCRIPTION" | |
2480 | (("zlibbioc, ") "")) | |
2481 | (substitute* "NAMESPACE" | |
2482 | (("import\\(zlibbioc\\)") "")) | |
2483 | #t))))) | |
2484 | (propagated-inputs | |
2485 | `(("r-biocgenerics" ,r-biocgenerics) | |
2486 | ("r-biocparallel" ,r-biocparallel) | |
2487 | ("r-biostrings" ,r-biostrings) | |
2488 | ("r-bitops" ,r-bitops) | |
2489 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2490 | ("r-genomicranges" ,r-genomicranges) | |
2491 | ("r-iranges" ,r-iranges) | |
2492 | ("r-rhtslib" ,r-rhtslib) | |
2493 | ("r-s4vectors" ,r-s4vectors) | |
2494 | ("r-xvector" ,r-xvector))) | |
2495 | (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") | |
2496 | (synopsis "Interface to samtools, bcftools, and tabix") | |
2497 | (description | |
2498 | "This package provides an interface to the @code{samtools}, | |
2499 | @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence | |
2500 | Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed | |
2501 | tab-delimited (tabix) files.") | |
2502 | (license license:expat))) | |
2503 | ||
8957efa8 | 2504 | (define-public r-shortread |
2505 | (package | |
2506 | (name "r-shortread") | |
2507 | (version "1.48.0") | |
2508 | (source | |
2509 | (origin | |
2510 | (method url-fetch) | |
2511 | (uri (bioconductor-uri "ShortRead" version)) | |
2512 | (sha256 | |
2513 | (base32 | |
2514 | "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) | |
2515 | (properties `((upstream-name . "ShortRead"))) | |
2516 | (build-system r-build-system) | |
2517 | (inputs | |
2518 | `(("zlib" ,zlib))) | |
2519 | (propagated-inputs | |
2520 | `(("r-biobase" ,r-biobase) | |
2521 | ("r-biocgenerics" ,r-biocgenerics) | |
2522 | ("r-biocparallel" ,r-biocparallel) | |
2523 | ("r-biostrings" ,r-biostrings) | |
2524 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2525 | ("r-genomicalignments" ,r-genomicalignments) | |
2526 | ("r-genomicranges" ,r-genomicranges) | |
2527 | ("r-rhtslib" ,r-rhtslib) | |
2528 | ("r-hwriter" ,r-hwriter) | |
2529 | ("r-iranges" ,r-iranges) | |
2530 | ("r-lattice" ,r-lattice) | |
2531 | ("r-latticeextra" ,r-latticeextra) | |
2532 | ("r-rsamtools" ,r-rsamtools) | |
2533 | ("r-s4vectors" ,r-s4vectors) | |
2534 | ("r-xvector" ,r-xvector) | |
2535 | ("r-zlibbioc" ,r-zlibbioc))) | |
2536 | (home-page "https://bioconductor.org/packages/ShortRead") | |
2537 | (synopsis "FASTQ input and manipulation tools") | |
2538 | (description | |
2539 | "This package implements sampling, iteration, and input of FASTQ files. | |
2540 | It includes functions for filtering and trimming reads, and for generating a | |
2541 | quality assessment report. Data are represented as | |
2542 | @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of | |
2543 | purposes. The package also contains legacy support for early single-end, | |
2544 | ungapped alignment formats.") | |
2545 | (license license:artistic2.0))) | |
2546 | ||
7694aceb RW |
2547 | (define-public r-summarizedexperiment |
2548 | (package | |
2549 | (name "r-summarizedexperiment") | |
2550 | (version "1.20.0") | |
2551 | (source (origin | |
2552 | (method url-fetch) | |
2553 | (uri (bioconductor-uri "SummarizedExperiment" version)) | |
2554 | (sha256 | |
2555 | (base32 | |
2556 | "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps")))) | |
2557 | (properties | |
2558 | `((upstream-name . "SummarizedExperiment"))) | |
2559 | (build-system r-build-system) | |
2560 | (propagated-inputs | |
2561 | `(("r-biobase" ,r-biobase) | |
2562 | ("r-biocgenerics" ,r-biocgenerics) | |
2563 | ("r-delayedarray" ,r-delayedarray) | |
2564 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2565 | ("r-genomicranges" ,r-genomicranges) | |
2566 | ("r-iranges" ,r-iranges) | |
2567 | ("r-matrix" ,r-matrix) | |
2568 | ("r-matrixgenerics" ,r-matrixgenerics) | |
2569 | ("r-s4vectors" ,r-s4vectors))) | |
2570 | (native-inputs | |
2571 | `(("r-knitr" ,r-knitr))) | |
2572 | (home-page "https://bioconductor.org/packages/SummarizedExperiment") | |
2573 | (synopsis "Container for representing genomic ranges by sample") | |
2574 | (description | |
2575 | "The SummarizedExperiment container contains one or more assays, each | |
2576 | represented by a matrix-like object of numeric or other mode. The rows | |
2577 | typically represent genomic ranges of interest and the columns represent | |
2578 | samples.") | |
2579 | (license license:artistic2.0))) | |
2580 | ||
df6b3c25 | 2581 | (define-public r-systempiper |
2582 | (package | |
2583 | (name "r-systempiper") | |
390098dd | 2584 | (version "1.24.6") |
df6b3c25 | 2585 | (source |
2586 | (origin | |
2587 | (method url-fetch) | |
2588 | (uri (bioconductor-uri "systemPipeR" version)) | |
2589 | (sha256 | |
2590 | (base32 | |
390098dd | 2591 | "05qnn105gm423fka4kb84vpgzjmz1py6mxpfa2agwwmc5v012qbp")))) |
df6b3c25 | 2592 | (properties `((upstream-name . "systemPipeR"))) |
2593 | (build-system r-build-system) | |
2594 | (propagated-inputs | |
2595 | `(("r-annotate" ,r-annotate) | |
2596 | ("r-assertthat" ,r-assertthat) | |
2597 | ("r-batchtools" ,r-batchtools) | |
2598 | ("r-biostrings" ,r-biostrings) | |
2599 | ("r-deseq2" ,r-deseq2) | |
2600 | ("r-dot" ,r-dot) | |
2601 | ("r-edger" ,r-edger) | |
2602 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2603 | ("r-genomicranges" ,r-genomicranges) | |
2604 | ("r-ggplot2" ,r-ggplot2) | |
2605 | ("r-go-db" ,r-go-db) | |
2606 | ("r-gostats" ,r-gostats) | |
2607 | ("r-iranges" ,r-iranges) | |
2608 | ("r-limma" ,r-limma) | |
2609 | ("r-magrittr" ,r-magrittr) | |
2610 | ("r-pheatmap" ,r-pheatmap) | |
2611 | ("r-rjson" ,r-rjson) | |
2612 | ("r-rsamtools" ,r-rsamtools) | |
2613 | ("r-rsvg" ,r-rsvg) | |
2614 | ("r-shortread" ,r-shortread) | |
2615 | ("r-stringr" ,r-stringr) | |
2616 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
2617 | ("r-yaml" ,r-yaml) | |
2618 | ("r-variantannotation" ,r-variantannotation))) | |
2619 | (native-inputs | |
2620 | `(("r-knitr" ,r-knitr))) | |
2621 | (home-page "https://github.com/tgirke/systemPipeR") | |
2622 | (synopsis "Next generation sequencing workflow and reporting environment") | |
2623 | (description | |
2624 | "This R package provides tools for building and running automated | |
2625 | end-to-end analysis workflows for a wide range of @dfn{next generation | |
2626 | sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. | |
2627 | Important features include a uniform workflow interface across different NGS | |
2628 | applications, automated report generation, and support for running both R and | |
2629 | command-line software, such as NGS aligners or peak/variant callers, on local | |
2630 | computers or compute clusters. Efficient handling of complex sample sets and | |
2631 | experimental designs is facilitated by a consistently implemented sample | |
2632 | annotation infrastructure.") | |
2633 | (license license:artistic2.0))) | |
2634 | ||
bf612ead | 2635 | (define-public r-variantannotation |
2636 | (package | |
2637 | (name "r-variantannotation") | |
2638 | (version "1.36.0") | |
2639 | (source (origin | |
2640 | (method url-fetch) | |
2641 | (uri (bioconductor-uri "VariantAnnotation" version)) | |
2642 | (sha256 | |
2643 | (base32 | |
2644 | "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) | |
2645 | (properties | |
2646 | `((upstream-name . "VariantAnnotation"))) | |
2647 | (propagated-inputs | |
2648 | `(("r-annotationdbi" ,r-annotationdbi) | |
2649 | ("r-biobase" ,r-biobase) | |
2650 | ("r-biocgenerics" ,r-biocgenerics) | |
2651 | ("r-biostrings" ,r-biostrings) | |
2652 | ("r-bsgenome" ,r-bsgenome) | |
2653 | ("r-dbi" ,r-dbi) | |
2654 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2655 | ("r-genomicfeatures" ,r-genomicfeatures) | |
2656 | ("r-genomicranges" ,r-genomicranges) | |
2657 | ("r-iranges" ,r-iranges) | |
2658 | ("r-matrixgenerics" ,r-matrixgenerics) | |
2659 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
2660 | ("r-rhtslib" ,r-rhtslib) | |
2661 | ("r-rsamtools" ,r-rsamtools) | |
2662 | ("r-rtracklayer" ,r-rtracklayer) | |
2663 | ("r-s4vectors" ,r-s4vectors) | |
2664 | ("r-xvector" ,r-xvector) | |
2665 | ("r-zlibbioc" ,r-zlibbioc))) | |
2666 | (build-system r-build-system) | |
2667 | (home-page "https://bioconductor.org/packages/VariantAnnotation") | |
2668 | (synopsis "Package for annotation of genetic variants") | |
2669 | (description "This R package can annotate variants, compute amino acid | |
2670 | coding changes and predict coding outcomes.") | |
2671 | (license license:artistic2.0))) | |
2672 | ||
23686ba3 | 2673 | (define-public r-xvector |
2674 | (package | |
2675 | (name "r-xvector") | |
2676 | (version "0.30.0") | |
2677 | (source (origin | |
2678 | (method url-fetch) | |
2679 | (uri (bioconductor-uri "XVector" version)) | |
2680 | (sha256 | |
2681 | (base32 | |
2682 | "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) | |
2683 | (properties | |
2684 | `((upstream-name . "XVector"))) | |
2685 | (build-system r-build-system) | |
2686 | (arguments | |
2687 | `(#:phases | |
2688 | (modify-phases %standard-phases | |
2689 | (add-after 'unpack 'use-system-zlib | |
2690 | (lambda _ | |
2691 | (substitute* "DESCRIPTION" | |
2692 | (("zlibbioc, ") "")) | |
2693 | (substitute* "NAMESPACE" | |
2694 | (("import\\(zlibbioc\\)") "")) | |
2695 | #t))))) | |
2696 | (inputs | |
2697 | `(("zlib" ,zlib))) | |
2698 | (propagated-inputs | |
2699 | `(("r-biocgenerics" ,r-biocgenerics) | |
2700 | ("r-iranges" ,r-iranges) | |
2701 | ("r-s4vectors" ,r-s4vectors))) | |
2702 | (home-page "https://bioconductor.org/packages/XVector") | |
2703 | (synopsis "Representation and manpulation of external sequences") | |
2704 | (description | |
2705 | "This package provides memory efficient S4 classes for storing sequences | |
2706 | \"externally\" (behind an R external pointer, or on disk).") | |
2707 | (license license:artistic2.0))) | |
2708 | ||
bfb93b48 RW |
2709 | (define-public r-geneplotter |
2710 | (package | |
2711 | (name "r-geneplotter") | |
d72c4c98 | 2712 | (version "1.68.0") |
bfb93b48 RW |
2713 | (source |
2714 | (origin | |
2715 | (method url-fetch) | |
2716 | (uri (bioconductor-uri "geneplotter" version)) | |
2717 | (sha256 | |
2718 | (base32 | |
d72c4c98 | 2719 | "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx")))) |
bfb93b48 RW |
2720 | (build-system r-build-system) |
2721 | (propagated-inputs | |
2722 | `(("r-annotate" ,r-annotate) | |
2723 | ("r-annotationdbi" ,r-annotationdbi) | |
2724 | ("r-biobase" ,r-biobase) | |
2725 | ("r-biocgenerics" ,r-biocgenerics) | |
2726 | ("r-lattice" ,r-lattice) | |
2727 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
2728 | (home-page "https://bioconductor.org/packages/geneplotter") | |
2729 | (synopsis "Graphics functions for genomic data") | |
2730 | (description | |
2731 | "This package provides functions for plotting genomic data.") | |
2732 | (license license:artistic2.0))) | |
2733 | ||
01c7ba99 RW |
2734 | (define-public r-oligoclasses |
2735 | (package | |
2736 | (name "r-oligoclasses") | |
464df5cc | 2737 | (version "1.52.0") |
01c7ba99 RW |
2738 | (source |
2739 | (origin | |
2740 | (method url-fetch) | |
2741 | (uri (bioconductor-uri "oligoClasses" version)) | |
2742 | (sha256 | |
2743 | (base32 | |
464df5cc | 2744 | "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy")))) |
01c7ba99 RW |
2745 | (properties `((upstream-name . "oligoClasses"))) |
2746 | (build-system r-build-system) | |
2747 | (propagated-inputs | |
2748 | `(("r-affyio" ,r-affyio) | |
2749 | ("r-biobase" ,r-biobase) | |
2750 | ("r-biocgenerics" ,r-biocgenerics) | |
2751 | ("r-biocmanager" ,r-biocmanager) | |
2752 | ("r-biostrings" ,r-biostrings) | |
2753 | ("r-dbi" ,r-dbi) | |
2754 | ("r-ff" ,r-ff) | |
2755 | ("r-foreach" ,r-foreach) | |
2756 | ("r-genomicranges" ,r-genomicranges) | |
2757 | ("r-iranges" ,r-iranges) | |
2758 | ("r-rsqlite" ,r-rsqlite) | |
2759 | ("r-s4vectors" ,r-s4vectors) | |
2760 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2761 | (home-page "https://bioconductor.org/packages/oligoClasses/") | |
2762 | (synopsis "Classes for high-throughput arrays") | |
2763 | (description | |
2764 | "This package contains class definitions, validity checks, and | |
2765 | initialization methods for classes used by the @code{oligo} and @code{crlmm} | |
2766 | packages.") | |
2767 | (license license:gpl2+))) | |
2768 | ||
4c63eeb8 RW |
2769 | (define-public r-oligo |
2770 | (package | |
2771 | (name "r-oligo") | |
9af6fdf8 | 2772 | (version "1.54.1") |
4c63eeb8 RW |
2773 | (source |
2774 | (origin | |
2775 | (method url-fetch) | |
2776 | (uri (bioconductor-uri "oligo" version)) | |
2777 | (sha256 | |
2778 | (base32 | |
9af6fdf8 | 2779 | "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3")))) |
4c63eeb8 RW |
2780 | (properties `((upstream-name . "oligo"))) |
2781 | (build-system r-build-system) | |
2782 | (inputs `(("zlib" ,zlib))) | |
2783 | (propagated-inputs | |
2784 | `(("r-affxparser" ,r-affxparser) | |
2785 | ("r-affyio" ,r-affyio) | |
2786 | ("r-biobase" ,r-biobase) | |
2787 | ("r-biocgenerics" ,r-biocgenerics) | |
2788 | ("r-biostrings" ,r-biostrings) | |
2789 | ("r-dbi" ,r-dbi) | |
2790 | ("r-ff" ,r-ff) | |
2791 | ("r-oligoclasses" ,r-oligoclasses) | |
2792 | ("r-preprocesscore" ,r-preprocesscore) | |
2793 | ("r-rsqlite" ,r-rsqlite) | |
2794 | ("r-zlibbioc" ,r-zlibbioc))) | |
ace82f80 RW |
2795 | (native-inputs |
2796 | `(("r-knitr" ,r-knitr))) | |
4c63eeb8 RW |
2797 | (home-page "https://bioconductor.org/packages/oligo/") |
2798 | (synopsis "Preprocessing tools for oligonucleotide arrays") | |
2799 | (description | |
2800 | "This package provides a package to analyze oligonucleotide | |
2801 | arrays (expression/SNP/tiling/exon) at probe-level. It currently supports | |
2802 | Affymetrix (CEL files) and NimbleGen arrays (XYS files).") | |
2803 | (license license:lgpl2.0+))) | |
2804 | ||
4dc2ecc2 RW |
2805 | (define-public r-qvalue |
2806 | (package | |
2807 | (name "r-qvalue") | |
e9b60a29 | 2808 | (version "2.22.0") |
4dc2ecc2 RW |
2809 | (source |
2810 | (origin | |
2811 | (method url-fetch) | |
2812 | (uri (bioconductor-uri "qvalue" version)) | |
2813 | (sha256 | |
2814 | (base32 | |
e9b60a29 | 2815 | "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5")))) |
4dc2ecc2 RW |
2816 | (build-system r-build-system) |
2817 | (propagated-inputs | |
2818 | `(("r-ggplot2" ,r-ggplot2) | |
2819 | ("r-reshape2" ,r-reshape2))) | |
f9a24759 RW |
2820 | (native-inputs |
2821 | `(("r-knitr" ,r-knitr))) | |
702a1012 | 2822 | (home-page "https://github.com/StoreyLab/qvalue") |
4dc2ecc2 RW |
2823 | (synopsis "Q-value estimation for false discovery rate control") |
2824 | (description | |
2825 | "This package takes a list of p-values resulting from the simultaneous | |
2826 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
2827 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
2828 | of false positives incurred when that particular test is called significant. | |
2829 | The local FDR measures the posterior probability the null hypothesis is true | |
2830 | given the test's p-value. Various plots are automatically generated, allowing | |
2831 | one to make sensible significance cut-offs. The software can be applied to | |
2832 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
2833 | ;; Any version of the LGPL. | |
2834 | (license license:lgpl3+))) | |
2835 | ||
a0df9b93 RJ |
2836 | (define r-rcppnumerical |
2837 | (package | |
2838 | (name "r-rcppnumerical") | |
2839 | (version "0.4-0") | |
2840 | (source (origin | |
2841 | (method url-fetch) | |
2842 | (uri (cran-uri "RcppNumerical" version)) | |
2843 | (sha256 | |
2844 | (base32 | |
2845 | "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) | |
2846 | (properties `((upstream-name . "RcppNumerical"))) | |
2847 | (build-system r-build-system) | |
2848 | (propagated-inputs | |
2849 | `(("r-rcpp" ,r-rcpp) | |
2850 | ("r-rcppeigen" ,r-rcppeigen))) | |
2851 | (native-inputs | |
2852 | `(("r-knitr" ,r-knitr))) | |
2853 | (home-page "https://github.com/yixuan/RcppNumerical") | |
2854 | (synopsis "Rcpp integration for numerical computing libraries") | |
2855 | (description "This package provides a collection of open source libraries | |
2856 | for numerical computing (numerical integration, optimization, etc.) and their | |
2857 | integration with @code{Rcpp}.") | |
2858 | (license license:gpl2+))) | |
2859 | ||
3b399e51 RJ |
2860 | (define-public r-apeglm |
2861 | (package | |
2862 | (name "r-apeglm") | |
2863 | (version "1.12.0") | |
2864 | (source (origin | |
2865 | (method url-fetch) | |
2866 | (uri (bioconductor-uri "apeglm" version)) | |
2867 | (sha256 | |
2868 | (base32 | |
2869 | "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2")))) | |
2870 | (properties `((upstream-name . "apeglm"))) | |
2871 | (build-system r-build-system) | |
2872 | (propagated-inputs | |
2873 | `(("r-emdbook" ,r-emdbook) | |
2874 | ("r-genomicranges" ,r-genomicranges) | |
2875 | ("r-rcpp" ,r-rcpp) | |
2876 | ("r-rcppeigen" ,r-rcppeigen) | |
2877 | ("r-rcppnumerical" ,r-rcppnumerical) | |
2878 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2879 | (native-inputs `(("r-knitr" ,r-knitr))) | |
2880 | (home-page "https://bioconductor.org/packages/apeglm") | |
2881 | (synopsis "Approximate posterior estimation for GLM coefficients") | |
2882 | (description "This package provides Bayesian shrinkage estimators for | |
2883 | effect sizes for a variety of GLM models, using approximation of the | |
2884 | posterior for individual coefficients.") | |
2885 | (license license:gpl2))) | |
2886 | ||
6e396c4b RJ |
2887 | (define-public r-greylistchip |
2888 | (package | |
2889 | (name "r-greylistchip") | |
2890 | (version "1.22.0") | |
2891 | (source (origin | |
2892 | (method url-fetch) | |
2893 | (uri (bioconductor-uri "GreyListChIP" version)) | |
2894 | (sha256 | |
2895 | (base32 | |
2896 | "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6")))) | |
2897 | (properties `((upstream-name . "GreyListChIP"))) | |
2898 | (build-system r-build-system) | |
2899 | (propagated-inputs | |
2900 | `(("r-bsgenome" ,r-bsgenome) | |
2901 | ("r-genomeinfodb" ,r-genomeinfodb) | |
2902 | ("r-genomicalignments" ,r-genomicalignments) | |
2903 | ("r-genomicranges" ,r-genomicranges) | |
2904 | ("r-mass" ,r-mass) | |
2905 | ("r-rsamtools" ,r-rsamtools) | |
2906 | ("r-rtracklayer" ,r-rtracklayer) | |
2907 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
2908 | (home-page "https://bioconductor.org/packages/GreyListChIP") | |
2909 | (synopsis "Greylist artefact regions based on ChIP inputs") | |
2910 | (description "This package identifies regions of ChIP experiments with high | |
2911 | signal in the input, that lead to spurious peaks during peak calling.") | |
2912 | (license license:artistic2.0))) | |
2913 | ||
a5b56a53 RJ |
2914 | (define-public r-diffbind |
2915 | (package | |
2916 | (name "r-diffbind") | |
55185f9b | 2917 | (version "3.0.15") |
a5b56a53 RJ |
2918 | (source |
2919 | (origin | |
2920 | (method url-fetch) | |
2921 | (uri (bioconductor-uri "DiffBind" version)) | |
2922 | (sha256 | |
2923 | (base32 | |
55185f9b | 2924 | "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi")))) |
a5b56a53 RJ |
2925 | (properties `((upstream-name . "DiffBind"))) |
2926 | (build-system r-build-system) | |
a5b56a53 RJ |
2927 | (propagated-inputs |
2928 | `(("r-amap" ,r-amap) | |
341ebaaa RJ |
2929 | ("r-apeglm" ,r-apeglm) |
2930 | ("r-ashr" ,r-ashr) | |
a5b56a53 RJ |
2931 | ("r-biocparallel" ,r-biocparallel) |
2932 | ("r-deseq2" ,r-deseq2) | |
2933 | ("r-dplyr" ,r-dplyr) | |
a5b56a53 | 2934 | ("r-genomicalignments" ,r-genomicalignments) |
45bbccf4 RW |
2935 | ("r-genomicranges" ,r-genomicranges) |
2936 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
2937 | ("r-ggrepel" ,r-ggrepel) |
2938 | ("r-gplots" ,r-gplots) | |
341ebaaa | 2939 | ("r-greylistchip" ,r-greylistchip) |
a5b56a53 RJ |
2940 | ("r-iranges" ,r-iranges) |
2941 | ("r-lattice" ,r-lattice) | |
2942 | ("r-limma" ,r-limma) | |
2943 | ("r-locfit" ,r-locfit) | |
2944 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
2945 | ("r-rcpp" ,r-rcpp) | |
4c221b3b | 2946 | ("r-rhtslib" ,r-rhtslib) |
a5b56a53 RJ |
2947 | ("r-rsamtools" ,r-rsamtools) |
2948 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 2949 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
4c221b3b | 2950 | ("r-systempiper" ,r-systempiper))) |
99db6db7 | 2951 | (home-page "https://bioconductor.org/packages/DiffBind") |
a5b56a53 RJ |
2952 | (synopsis "Differential binding analysis of ChIP-Seq peak data") |
2953 | (description | |
2954 | "This package computes differentially bound sites from multiple | |
2955 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
2956 | occupancy (overlap) analysis and plotting functions.") | |
2957 | (license license:artistic2.0))) | |
6d94bf6b RJ |
2958 | |
2959 | (define-public r-ripseeker | |
2960 | (package | |
2961 | (name "r-ripseeker") | |
ba74434f | 2962 | (version "1.26.0") |
6d94bf6b RJ |
2963 | (source |
2964 | (origin | |
2965 | (method url-fetch) | |
2966 | (uri (bioconductor-uri "RIPSeeker" version)) | |
2967 | (sha256 | |
2968 | (base32 | |
ba74434f | 2969 | "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) |
6d94bf6b RJ |
2970 | (properties `((upstream-name . "RIPSeeker"))) |
2971 | (build-system r-build-system) | |
2972 | (propagated-inputs | |
2973 | `(("r-s4vectors" ,r-s4vectors) | |
2974 | ("r-iranges" ,r-iranges) | |
2975 | ("r-genomicranges" ,r-genomicranges) | |
2976 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
2977 | ("r-rsamtools" ,r-rsamtools) | |
2978 | ("r-genomicalignments" ,r-genomicalignments) | |
2979 | ("r-rtracklayer" ,r-rtracklayer))) | |
99db6db7 | 2980 | (home-page "https://bioconductor.org/packages/RIPSeeker") |
6d94bf6b RJ |
2981 | (synopsis |
2982 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
2983 | (description | |
2984 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
2985 | using two-state HMM with negative binomial emission probability. While | |
2986 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
2987 | a suite of bioinformatics tools integrated within this self-contained software | |
2988 | package comprehensively addressing issues ranging from post-alignments | |
2989 | processing to visualization and annotation.") | |
2990 | (license license:gpl2))) | |
a6ae9ffd RJ |
2991 | |
2992 | (define-public r-multtest | |
2993 | (package | |
2994 | (name "r-multtest") | |
1e6920c5 | 2995 | (version "2.46.0") |
a6ae9ffd RJ |
2996 | (source |
2997 | (origin | |
2998 | (method url-fetch) | |
2999 | (uri (bioconductor-uri "multtest" version)) | |
3000 | (sha256 | |
3001 | (base32 | |
1e6920c5 | 3002 | "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q")))) |
a6ae9ffd RJ |
3003 | (build-system r-build-system) |
3004 | (propagated-inputs | |
3005 | `(("r-survival" ,r-survival) | |
3006 | ("r-biocgenerics" ,r-biocgenerics) | |
3007 | ("r-biobase" ,r-biobase) | |
3008 | ("r-mass" ,r-mass))) | |
99db6db7 | 3009 | (home-page "https://bioconductor.org/packages/multtest") |
a6ae9ffd RJ |
3010 | (synopsis "Resampling-based multiple hypothesis testing") |
3011 | (description | |
3012 | "This package can do non-parametric bootstrap and permutation | |
3013 | resampling-based multiple testing procedures (including empirical Bayes | |
3014 | methods) for controlling the family-wise error rate (FWER), generalized | |
3015 | family-wise error rate (gFWER), tail probability of the proportion of | |
3016 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
3017 | of bootstrap-based null distribution are implemented (centered, centered | |
3018 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
3019 | available. Tests based on a variety of T- and F-statistics (including | |
3020 | T-statistics based on regression parameters from linear and survival models | |
3021 | as well as those based on correlation parameters) are included. When probing | |
3022 | hypotheses with T-statistics, users may also select a potentially faster null | |
3023 | distribution which is multivariate normal with mean zero and variance | |
3024 | covariance matrix derived from the vector influence function. Results are | |
3025 | reported in terms of adjusted P-values, confidence regions and test statistic | |
3026 | cutoffs. The procedures are directly applicable to identifying differentially | |
3027 | expressed genes in DNA microarray experiments.") | |
3028 | (license license:lgpl3))) | |
793f83ef | 3029 | |
5dfe4912 RW |
3030 | (define-public r-graph |
3031 | (package | |
3032 | (name "r-graph") | |
f519b4dc | 3033 | (version "1.68.0") |
5dfe4912 RW |
3034 | (source (origin |
3035 | (method url-fetch) | |
3036 | (uri (bioconductor-uri "graph" version)) | |
3037 | (sha256 | |
3038 | (base32 | |
f519b4dc | 3039 | "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4")))) |
5dfe4912 RW |
3040 | (build-system r-build-system) |
3041 | (propagated-inputs | |
3042 | `(("r-biocgenerics" ,r-biocgenerics))) | |
3043 | (home-page "https://bioconductor.org/packages/graph") | |
3044 | (synopsis "Handle graph data structures in R") | |
3045 | (description | |
3046 | "This package implements some simple graph handling capabilities for R.") | |
3047 | (license license:artistic2.0))) | |
3048 | ||
8017eb0a RW |
3049 | ;; This is a CRAN package, but it depends on a Bioconductor package. |
3050 | (define-public r-ggm | |
3051 | (package | |
3052 | (name "r-ggm") | |
3053 | (version "2.5") | |
3054 | (source | |
3055 | (origin | |
3056 | (method url-fetch) | |
3057 | (uri (cran-uri "ggm" version)) | |
3058 | (sha256 | |
3059 | (base32 | |
3060 | "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) | |
3061 | (properties `((upstream-name . "ggm"))) | |
3062 | (build-system r-build-system) | |
3063 | (propagated-inputs | |
3064 | `(("r-graph" ,r-graph) | |
3065 | ("r-igraph" ,r-igraph))) | |
3066 | (home-page "https://cran.r-project.org/package=ggm") | |
3067 | (synopsis "Functions for graphical Markov models") | |
3068 | (description | |
3069 | "This package provides functions and datasets for maximum likelihood | |
3070 | fitting of some classes of graphical Markov models.") | |
3071 | (license license:gpl2+))) | |
3072 | ||
a07717cc RW |
3073 | ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph. |
3074 | (define-public r-perfmeas | |
3075 | (package | |
3076 | (name "r-perfmeas") | |
3077 | (version "1.2.1") | |
3078 | (source | |
3079 | (origin | |
3080 | (method url-fetch) | |
3081 | (uri (cran-uri "PerfMeas" version)) | |
3082 | (sha256 | |
3083 | (base32 | |
3084 | "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93")))) | |
3085 | (properties `((upstream-name . "PerfMeas"))) | |
3086 | (build-system r-build-system) | |
3087 | (propagated-inputs | |
3088 | `(("r-graph" ,r-graph) | |
3089 | ("r-limma" ,r-limma) | |
3090 | ("r-rbgl" ,r-rbgl))) | |
3091 | (home-page "https://cran.r-project.org/web/packages/PerfMeas/") | |
3092 | (synopsis "Performance measures for ranking and classification tasks") | |
3093 | (description | |
3094 | "This package implements different performance measures for | |
3095 | classification and ranking tasks. @dfn{Area under curve} (AUC), precision at | |
3096 | a given recall, F-score for single and multiple classes are available.") | |
3097 | (license license:gpl2+))) | |
3098 | ||
b17ace24 | 3099 | ;; This is a CRAN package, but it depends on a Bioconductor package. |
a207bca2 RW |
3100 | (define-public r-codedepends |
3101 | (package | |
3102 | (name "r-codedepends") | |
3103 | (version "0.6.5") | |
3104 | (source | |
3105 | (origin | |
3106 | (method url-fetch) | |
3107 | (uri (cran-uri "CodeDepends" version)) | |
3108 | (sha256 | |
3109 | (base32 | |
3110 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
3111 | (properties `((upstream-name . "CodeDepends"))) | |
3112 | (build-system r-build-system) | |
3113 | (propagated-inputs | |
3114 | `(("r-codetools" ,r-codetools) | |
3115 | ("r-graph" ,r-graph) | |
3116 | ("r-xml" ,r-xml))) | |
5e1f2362 | 3117 | (home-page "https://cran.r-project.org/web/packages/CodeDepends") |
a207bca2 RW |
3118 | (synopsis "Analysis of R code for reproducible research and code comprehension") |
3119 | (description | |
3120 | "This package provides tools for analyzing R expressions or blocks of | |
3121 | code and determining the dependencies between them. It focuses on R scripts, | |
3122 | but can be used on the bodies of functions. There are many facilities | |
3123 | including the ability to summarize or get a high-level view of code, | |
3124 | determining dependencies between variables, code improvement suggestions.") | |
3125 | ;; Any version of the GPL | |
3126 | (license (list license:gpl2+ license:gpl3+)))) | |
3127 | ||
793f83ef RJ |
3128 | (define-public r-chippeakanno |
3129 | (package | |
3130 | (name "r-chippeakanno") | |
215b0ced | 3131 | (version "3.24.2") |
793f83ef RJ |
3132 | (source |
3133 | (origin | |
3134 | (method url-fetch) | |
3135 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
3136 | (sha256 | |
3137 | (base32 | |
215b0ced | 3138 | "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw")))) |
793f83ef RJ |
3139 | (properties `((upstream-name . "ChIPpeakAnno"))) |
3140 | (build-system r-build-system) | |
3141 | (propagated-inputs | |
85c1d20f | 3142 | `(("r-annotationdbi" ,r-annotationdbi) |
85c1d20f | 3143 | ("r-biocgenerics" ,r-biocgenerics) |
793f83ef | 3144 | ("r-biomart" ,r-biomart) |
85c1d20f | 3145 | ("r-biostrings" ,r-biostrings) |
85c1d20f | 3146 | ("r-dbi" ,r-dbi) |
215b0ced | 3147 | ("r-dplyr" ,r-dplyr) |
85c1d20f RW |
3148 | ("r-ensembldb" ,r-ensembldb) |
3149 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3150 | ("r-genomicalignments" ,r-genomicalignments) | |
793f83ef | 3151 | ("r-genomicfeatures" ,r-genomicfeatures) |
f794e85d | 3152 | ("r-genomicranges" ,r-genomicranges) |
d068d967 | 3153 | ("r-ggplot2" ,r-ggplot2) |
85c1d20f | 3154 | ("r-graph" ,r-graph) |
f794e85d | 3155 | ("r-iranges" ,r-iranges) |
d068d967 | 3156 | ("r-keggrest" ,r-keggrest) |
85c1d20f | 3157 | ("r-matrixstats" ,r-matrixstats) |
793f83ef RJ |
3158 | ("r-multtest" ,r-multtest) |
3159 | ("r-rbgl" ,r-rbgl) | |
793f83ef | 3160 | ("r-regioner" ,r-regioner) |
85c1d20f RW |
3161 | ("r-rsamtools" ,r-rsamtools) |
3162 | ("r-rtracklayer" ,r-rtracklayer) | |
f794e85d | 3163 | ("r-s4vectors" ,r-s4vectors) |
793f83ef | 3164 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
793f83ef | 3165 | ("r-venndiagram" ,r-venndiagram))) |
dc24de46 RW |
3166 | (native-inputs |
3167 | `(("r-knitr" ,r-knitr))) | |
99db6db7 | 3168 | (home-page "https://bioconductor.org/packages/ChIPpeakAnno") |
793f83ef RJ |
3169 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") |
3170 | (description | |
3171 | "The package includes functions to retrieve the sequences around the peak, | |
3172 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
3173 | custom features such as most conserved elements and other transcription factor | |
3174 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
3175 | for finding the peaks with bi-directional promoters with summary statistics | |
3176 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
3177 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
3178 | enrichedGO (addGeneIDs).") | |
3179 | (license license:gpl2+))) | |
164502d8 | 3180 | |
c8da0137 RJ |
3181 | (define-public r-matrixgenerics |
3182 | (package | |
3183 | (name "r-matrixgenerics") | |
669ea5ab | 3184 | (version "1.2.1") |
c8da0137 RJ |
3185 | (source (origin |
3186 | (method url-fetch) | |
3187 | (uri (bioconductor-uri "MatrixGenerics" version)) | |
3188 | (sha256 | |
3189 | (base32 | |
669ea5ab | 3190 | "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb")))) |
c8da0137 RJ |
3191 | (properties |
3192 | `((upstream-name . "MatrixGenerics"))) | |
3193 | (build-system r-build-system) | |
3194 | (propagated-inputs | |
3195 | `(("r-matrixstats" ,r-matrixstats))) | |
3196 | (home-page "https://bioconductor.org/packages/MatrixGenerics") | |
3197 | (synopsis "S4 generic summary statistic functions for matrix-like objects") | |
3198 | (description | |
3199 | "This package provides S4 generic functions modeled after the | |
3200 | @code{matrixStats} API for alternative matrix implementations. Packages with | |
3201 | alternative matrix implementation can depend on this package and implement the | |
3202 | generic functions that are defined here for a useful set of row and column | |
3203 | summary statistics. Other package developers can import this package and | |
3204 | handle a different matrix implementations without worrying about | |
3205 | incompatibilities.") | |
3206 | (license license:artistic2.0))) | |
3207 | ||
164502d8 RJ |
3208 | (define-public r-marray |
3209 | (package | |
3210 | (name "r-marray") | |
6e6c6272 | 3211 | (version "1.68.0") |
164502d8 RJ |
3212 | (source (origin |
3213 | (method url-fetch) | |
3214 | (uri (bioconductor-uri "marray" version)) | |
3215 | (sha256 | |
6e6c6272 | 3216 | (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray")))) |
164502d8 RJ |
3217 | (build-system r-build-system) |
3218 | (propagated-inputs | |
67487088 | 3219 | `(("r-limma" ,r-limma))) |
99db6db7 | 3220 | (home-page "https://bioconductor.org/packages/marray") |
164502d8 RJ |
3221 | (synopsis "Exploratory analysis for two-color spotted microarray data") |
3222 | (description "This package contains class definitions for two-color spotted | |
ab8979fc | 3223 | microarray data. It also includes functions for data input, diagnostic plots, |
164502d8 RJ |
3224 | normalization and quality checking.") |
3225 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
3226 | |
3227 | (define-public r-cghbase | |
3228 | (package | |
3229 | (name "r-cghbase") | |
ee052d05 | 3230 | (version "1.50.0") |
0416a0d4 RJ |
3231 | (source (origin |
3232 | (method url-fetch) | |
3233 | (uri (bioconductor-uri "CGHbase" version)) | |
3234 | (sha256 | |
ee052d05 | 3235 | (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4")))) |
0416a0d4 RJ |
3236 | (properties `((upstream-name . "CGHbase"))) |
3237 | (build-system r-build-system) | |
3238 | (propagated-inputs | |
3239 | `(("r-biobase" ,r-biobase) | |
3240 | ("r-marray" ,r-marray))) | |
99db6db7 | 3241 | (home-page "https://bioconductor.org/packages/CGHbase") |
0416a0d4 RJ |
3242 | (synopsis "Base functions and classes for arrayCGH data analysis") |
3243 | (description "This package contains functions and classes that are needed by | |
3244 | the @code{arrayCGH} packages.") | |
3245 | (license license:gpl2+))) | |
67ee83d6 RJ |
3246 | |
3247 | (define-public r-cghcall | |
3248 | (package | |
3249 | (name "r-cghcall") | |
72400035 | 3250 | (version "2.52.0") |
67ee83d6 RJ |
3251 | (source (origin |
3252 | (method url-fetch) | |
3253 | (uri (bioconductor-uri "CGHcall" version)) | |
3254 | (sha256 | |
72400035 | 3255 | (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba")))) |
67ee83d6 RJ |
3256 | (properties `((upstream-name . "CGHcall"))) |
3257 | (build-system r-build-system) | |
3258 | (propagated-inputs | |
3259 | `(("r-biobase" ,r-biobase) | |
3260 | ("r-cghbase" ,r-cghbase) | |
3261 | ("r-impute" ,r-impute) | |
3262 | ("r-dnacopy" ,r-dnacopy) | |
3263 | ("r-snowfall" ,r-snowfall))) | |
99db6db7 | 3264 | (home-page "https://bioconductor.org/packages/CGHcall") |
67ee83d6 RJ |
3265 | (synopsis "Base functions and classes for arrayCGH data analysis") |
3266 | (description "This package contains functions and classes that are needed by | |
3267 | @code{arrayCGH} packages.") | |
3268 | (license license:gpl2+))) | |
0ef8cc9c RJ |
3269 | |
3270 | (define-public r-qdnaseq | |
3271 | (package | |
3272 | (name "r-qdnaseq") | |
3b648409 | 3273 | (version "1.26.0") |
0ef8cc9c RJ |
3274 | (source (origin |
3275 | (method url-fetch) | |
3276 | (uri (bioconductor-uri "QDNAseq" version)) | |
3277 | (sha256 | |
3b648409 | 3278 | (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph")))) |
0ef8cc9c RJ |
3279 | (properties `((upstream-name . "QDNAseq"))) |
3280 | (build-system r-build-system) | |
3281 | (propagated-inputs | |
3282 | `(("r-biobase" ,r-biobase) | |
3283 | ("r-cghbase" ,r-cghbase) | |
3284 | ("r-cghcall" ,r-cghcall) | |
3285 | ("r-dnacopy" ,r-dnacopy) | |
23ce5ad1 RW |
3286 | ("r-future" ,r-future) |
3287 | ("r-future-apply" ,r-future-apply) | |
0ef8cc9c RJ |
3288 | ("r-genomicranges" ,r-genomicranges) |
3289 | ("r-iranges" ,r-iranges) | |
3290 | ("r-matrixstats" ,r-matrixstats) | |
3291 | ("r-r-utils" ,r-r-utils) | |
3292 | ("r-rsamtools" ,r-rsamtools))) | |
99db6db7 | 3293 | (home-page "https://bioconductor.org/packages/QDNAseq") |
0ef8cc9c RJ |
3294 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") |
3295 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
3296 | number of sequence reads in each counted, adjusted with a simultaneous | |
3297 | two-dimensional loess correction for sequence mappability and GC content, and | |
3298 | filtered to remove spurious regions in the genome. Downstream steps of | |
3299 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
3300 | respectively.") | |
3301 | (license license:gpl2+))) | |
bb15b581 RW |
3302 | |
3303 | (define-public r-bayseq | |
3304 | (package | |
3305 | (name "r-bayseq") | |
63572b0c | 3306 | (version "2.24.0") |
bb15b581 RW |
3307 | (source |
3308 | (origin | |
3309 | (method url-fetch) | |
3310 | (uri (bioconductor-uri "baySeq" version)) | |
3311 | (sha256 | |
3312 | (base32 | |
63572b0c | 3313 | "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215")))) |
bb15b581 RW |
3314 | (properties `((upstream-name . "baySeq"))) |
3315 | (build-system r-build-system) | |
3316 | (propagated-inputs | |
3317 | `(("r-abind" ,r-abind) | |
3318 | ("r-edger" ,r-edger) | |
3319 | ("r-genomicranges" ,r-genomicranges))) | |
3320 | (home-page "https://bioconductor.org/packages/baySeq/") | |
3321 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
3322 | (description | |
3323 | "This package identifies differential expression in high-throughput count | |
3324 | data, such as that derived from next-generation sequencing machines, | |
3325 | calculating estimated posterior likelihoods of differential expression (or | |
3326 | more complex hypotheses) via empirical Bayesian methods.") | |
3327 | (license license:gpl3))) | |
609f4ad1 RW |
3328 | |
3329 | (define-public r-chipcomp | |
3330 | (package | |
3331 | (name "r-chipcomp") | |
3f04b816 | 3332 | (version "1.20.0") |
609f4ad1 RW |
3333 | (source |
3334 | (origin | |
3335 | (method url-fetch) | |
3336 | (uri (bioconductor-uri "ChIPComp" version)) | |
3337 | (sha256 | |
3338 | (base32 | |
3f04b816 | 3339 | "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7")))) |
609f4ad1 RW |
3340 | (properties `((upstream-name . "ChIPComp"))) |
3341 | (build-system r-build-system) | |
3342 | (propagated-inputs | |
3343 | `(("r-biocgenerics" ,r-biocgenerics) | |
3344 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
3345 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
3346 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3347 | ("r-genomicranges" ,r-genomicranges) | |
3348 | ("r-iranges" ,r-iranges) | |
3349 | ("r-limma" ,r-limma) | |
3350 | ("r-rsamtools" ,r-rsamtools) | |
3351 | ("r-rtracklayer" ,r-rtracklayer) | |
3352 | ("r-s4vectors" ,r-s4vectors))) | |
3353 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
3354 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
3355 | (description | |
3356 | "ChIPComp implements a statistical method for quantitative comparison of | |
3357 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
3358 | sites across multiple conditions considering matching control in ChIP-seq | |
3359 | datasets.") | |
3360 | ;; Any version of the GPL. | |
3361 | (license license:gpl3+))) | |
0490f9de RW |
3362 | |
3363 | (define-public r-riboprofiling | |
3364 | (package | |
3365 | (name "r-riboprofiling") | |
03b655c5 | 3366 | (version "1.20.0") |
0490f9de RW |
3367 | (source |
3368 | (origin | |
3369 | (method url-fetch) | |
3370 | (uri (bioconductor-uri "RiboProfiling" version)) | |
3371 | (sha256 | |
3372 | (base32 | |
03b655c5 | 3373 | "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg")))) |
0490f9de RW |
3374 | (properties `((upstream-name . "RiboProfiling"))) |
3375 | (build-system r-build-system) | |
3376 | (propagated-inputs | |
3377 | `(("r-biocgenerics" ,r-biocgenerics) | |
3378 | ("r-biostrings" ,r-biostrings) | |
3379 | ("r-data-table" ,r-data-table) | |
3380 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3381 | ("r-genomicalignments" ,r-genomicalignments) | |
3382 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3383 | ("r-genomicranges" ,r-genomicranges) | |
3384 | ("r-ggbio" ,r-ggbio) | |
3385 | ("r-ggplot2" ,r-ggplot2) | |
3386 | ("r-iranges" ,r-iranges) | |
3387 | ("r-plyr" ,r-plyr) | |
3388 | ("r-reshape2" ,r-reshape2) | |
3389 | ("r-rsamtools" ,r-rsamtools) | |
3390 | ("r-rtracklayer" ,r-rtracklayer) | |
3391 | ("r-s4vectors" ,r-s4vectors) | |
3392 | ("r-sqldf" ,r-sqldf))) | |
7aae05a9 RW |
3393 | (native-inputs |
3394 | `(("r-knitr" ,r-knitr))) | |
0490f9de RW |
3395 | (home-page "https://bioconductor.org/packages/RiboProfiling/") |
3396 | (synopsis "Ribosome profiling data analysis") | |
3397 | (description "Starting with a BAM file, this package provides the | |
3398 | necessary functions for quality assessment, read start position recalibration, | |
3399 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
3400 | of count data: pairs, log fold-change, codon frequency and coverage | |
3401 | assessment, principal component analysis on codon coverage.") | |
3402 | (license license:gpl3))) | |
6ffdfe6a RW |
3403 | |
3404 | (define-public r-riboseqr | |
3405 | (package | |
3406 | (name "r-riboseqr") | |
3813c9fe | 3407 | (version "1.24.0") |
6ffdfe6a RW |
3408 | (source |
3409 | (origin | |
3410 | (method url-fetch) | |
3411 | (uri (bioconductor-uri "riboSeqR" version)) | |
3412 | (sha256 | |
3413 | (base32 | |
3813c9fe | 3414 | "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr")))) |
6ffdfe6a RW |
3415 | (properties `((upstream-name . "riboSeqR"))) |
3416 | (build-system r-build-system) | |
3417 | (propagated-inputs | |
3418 | `(("r-abind" ,r-abind) | |
3419 | ("r-bayseq" ,r-bayseq) | |
3420 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3421 | ("r-genomicranges" ,r-genomicranges) | |
3422 | ("r-iranges" ,r-iranges) | |
3423 | ("r-rsamtools" ,r-rsamtools) | |
3424 | ("r-seqlogo" ,r-seqlogo))) | |
3425 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
3426 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
3427 | (description | |
3428 | "This package provides plotting functions, frameshift detection and | |
3429 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
3430 | (license license:gpl3))) | |
a32279ff RW |
3431 | |
3432 | (define-public r-interactionset | |
b2bdc2f1 | 3433 | (package |
a32279ff | 3434 | (name "r-interactionset") |
b2bdc2f1 | 3435 | (version "1.18.1") |
a32279ff RW |
3436 | (source |
3437 | (origin | |
3438 | (method url-fetch) | |
3439 | (uri (bioconductor-uri "InteractionSet" version)) | |
3440 | (sha256 | |
3441 | (base32 | |
b2bdc2f1 | 3442 | "0dx6yw6rxgkcidnnyjzv57vzd112nf9n2bj6dkv7r3a2d2wj6xh4")))) |
a32279ff RW |
3443 | (properties |
3444 | `((upstream-name . "InteractionSet"))) | |
3445 | (build-system r-build-system) | |
3446 | (propagated-inputs | |
3447 | `(("r-biocgenerics" ,r-biocgenerics) | |
3448 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3449 | ("r-genomicranges" ,r-genomicranges) | |
3450 | ("r-iranges" ,r-iranges) | |
3451 | ("r-matrix" ,r-matrix) | |
3452 | ("r-rcpp" ,r-rcpp) | |
3453 | ("r-s4vectors" ,r-s4vectors) | |
3454 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
861a903f RW |
3455 | (native-inputs |
3456 | `(("r-knitr" ,r-knitr))) | |
a32279ff RW |
3457 | (home-page "https://bioconductor.org/packages/InteractionSet") |
3458 | (synopsis "Base classes for storing genomic interaction data") | |
3459 | (description | |
02fe0976 | 3460 | "This package provides the @code{GInteractions}, |
a32279ff RW |
3461 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
3462 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
3463 | experiments.") | |
3464 | (license license:gpl3))) | |
cf9a29b2 RW |
3465 | |
3466 | (define-public r-genomicinteractions | |
3467 | (package | |
3468 | (name "r-genomicinteractions") | |
dd9341ff | 3469 | (version "1.24.0") |
cf9a29b2 RW |
3470 | (source |
3471 | (origin | |
3472 | (method url-fetch) | |
3473 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
3474 | (sha256 | |
3475 | (base32 | |
dd9341ff | 3476 | "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd")))) |
cf9a29b2 RW |
3477 | (properties |
3478 | `((upstream-name . "GenomicInteractions"))) | |
3479 | (build-system r-build-system) | |
3480 | (propagated-inputs | |
3481 | `(("r-biobase" ,r-biobase) | |
3482 | ("r-biocgenerics" ,r-biocgenerics) | |
3483 | ("r-data-table" ,r-data-table) | |
3484 | ("r-dplyr" ,r-dplyr) | |
3485 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3486 | ("r-genomicranges" ,r-genomicranges) | |
3487 | ("r-ggplot2" ,r-ggplot2) | |
3488 | ("r-gridextra" ,r-gridextra) | |
3489 | ("r-gviz" ,r-gviz) | |
3490 | ("r-igraph" ,r-igraph) | |
3491 | ("r-interactionset" ,r-interactionset) | |
3492 | ("r-iranges" ,r-iranges) | |
3493 | ("r-rsamtools" ,r-rsamtools) | |
3494 | ("r-rtracklayer" ,r-rtracklayer) | |
3495 | ("r-s4vectors" ,r-s4vectors) | |
3496 | ("r-stringr" ,r-stringr))) | |
81a37891 RW |
3497 | (native-inputs |
3498 | `(("r-knitr" ,r-knitr))) | |
cf9a29b2 RW |
3499 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") |
3500 | (synopsis "R package for handling genomic interaction data") | |
3501 | (description | |
3502 | "This R package provides tools for handling genomic interaction data, | |
3503 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
3504 | information and producing various plots and statistics.") | |
3505 | (license license:gpl3))) | |
27c51606 RW |
3506 | |
3507 | (define-public r-ctc | |
3508 | (package | |
3509 | (name "r-ctc") | |
d27dfbf7 | 3510 | (version "1.64.0") |
27c51606 RW |
3511 | (source |
3512 | (origin | |
3513 | (method url-fetch) | |
3514 | (uri (bioconductor-uri "ctc" version)) | |
3515 | (sha256 | |
3516 | (base32 | |
d27dfbf7 | 3517 | "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp")))) |
27c51606 RW |
3518 | (build-system r-build-system) |
3519 | (propagated-inputs `(("r-amap" ,r-amap))) | |
3520 | (home-page "https://bioconductor.org/packages/ctc/") | |
3521 | (synopsis "Cluster and tree conversion") | |
3522 | (description | |
3523 | "This package provides tools for exporting and importing classification | |
3524 | trees and clusters to other programs.") | |
3525 | (license license:gpl2))) | |
5da0e142 RW |
3526 | |
3527 | (define-public r-goseq | |
3528 | (package | |
3529 | (name "r-goseq") | |
c97bcfbd | 3530 | (version "1.42.0") |
5da0e142 RW |
3531 | (source |
3532 | (origin | |
3533 | (method url-fetch) | |
3534 | (uri (bioconductor-uri "goseq" version)) | |
3535 | (sha256 | |
3536 | (base32 | |
c97bcfbd | 3537 | "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509")))) |
5da0e142 RW |
3538 | (build-system r-build-system) |
3539 | (propagated-inputs | |
3540 | `(("r-annotationdbi" ,r-annotationdbi) | |
3541 | ("r-biasedurn" ,r-biasedurn) | |
3542 | ("r-biocgenerics" ,r-biocgenerics) | |
3543 | ("r-genelendatabase" ,r-genelendatabase) | |
3544 | ("r-go-db" ,r-go-db) | |
3545 | ("r-mgcv" ,r-mgcv))) | |
3546 | (home-page "https://bioconductor.org/packages/goseq/") | |
3547 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
3548 | (description | |
3549 | "This package provides tools to detect Gene Ontology and/or other user | |
3550 | defined categories which are over/under represented in RNA-seq data.") | |
3551 | (license license:lgpl2.0+))) | |
f4235c0e RW |
3552 | |
3553 | (define-public r-glimma | |
3554 | (package | |
3555 | (name "r-glimma") | |
3dab4570 | 3556 | (version "2.0.0") |
f4235c0e RW |
3557 | (source |
3558 | (origin | |
3559 | (method url-fetch) | |
3560 | (uri (bioconductor-uri "Glimma" version)) | |
3561 | (sha256 | |
3562 | (base32 | |
3dab4570 | 3563 | "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv")))) |
f4235c0e RW |
3564 | (properties `((upstream-name . "Glimma"))) |
3565 | (build-system r-build-system) | |
3566 | (propagated-inputs | |
3dab4570 | 3567 | `(("r-deseq2" ,r-deseq2) |
3568 | ("r-edger" ,r-edger) | |
3569 | ("r-htmlwidgets" ,r-htmlwidgets) | |
f4235c0e | 3570 | ("r-jsonlite" ,r-jsonlite) |
3dab4570 | 3571 | ("r-limma" ,r-limma) |
3572 | ("r-s4vectors" ,r-s4vectors) | |
3573 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
a6251d6e RW |
3574 | (native-inputs |
3575 | `(("r-knitr" ,r-knitr))) | |
f4235c0e RW |
3576 | (home-page "https://github.com/Shians/Glimma") |
3577 | (synopsis "Interactive HTML graphics") | |
3578 | (description | |
3579 | "This package generates interactive visualisations for analysis of | |
3580 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
3581 | HTML page. The interactions are built on top of the popular static | |
3582 | representations of analysis results in order to provide additional | |
3583 | information.") | |
3584 | (license license:lgpl3))) | |
aa388dc7 RW |
3585 | |
3586 | (define-public r-rots | |
3587 | (package | |
3588 | (name "r-rots") | |
0ef40b23 | 3589 | (version "1.18.0") |
aa388dc7 RW |
3590 | (source |
3591 | (origin | |
3592 | (method url-fetch) | |
3593 | (uri (bioconductor-uri "ROTS" version)) | |
3594 | (sha256 | |
3595 | (base32 | |
0ef40b23 | 3596 | "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n")))) |
aa388dc7 RW |
3597 | (properties `((upstream-name . "ROTS"))) |
3598 | (build-system r-build-system) | |
3599 | (propagated-inputs | |
3600 | `(("r-biobase" ,r-biobase) | |
3601 | ("r-rcpp" ,r-rcpp))) | |
3602 | (home-page "https://bioconductor.org/packages/ROTS/") | |
3603 | (synopsis "Reproducibility-Optimized Test Statistic") | |
3604 | (description | |
3605 | "This package provides tools for calculating the | |
3606 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
3607 | in omics data.") | |
3608 | (license license:gpl2+))) | |
b64ce4b7 | 3609 | |
cad6fb2d RW |
3610 | (define-public r-plgem |
3611 | (package | |
3612 | (name "r-plgem") | |
1c9bdfcf | 3613 | (version "1.62.0") |
cad6fb2d RW |
3614 | (source |
3615 | (origin | |
3616 | (method url-fetch) | |
3617 | (uri (bioconductor-uri "plgem" version)) | |
3618 | (sha256 | |
3619 | (base32 | |
1c9bdfcf | 3620 | "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a")))) |
cad6fb2d RW |
3621 | (build-system r-build-system) |
3622 | (propagated-inputs | |
3623 | `(("r-biobase" ,r-biobase) | |
3624 | ("r-mass" ,r-mass))) | |
3625 | (home-page "http://www.genopolis.it") | |
3626 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
3627 | (description | |
3628 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
3629 | model the variance-versus-mean dependence that exists in a variety of | |
3630 | genome-wide datasets, including microarray and proteomics data. The use of | |
3631 | PLGEM has been shown to improve the detection of differentially expressed | |
3632 | genes or proteins in these datasets.") | |
3633 | (license license:gpl2))) | |
3634 | ||
b64ce4b7 RW |
3635 | (define-public r-inspect |
3636 | (package | |
3637 | (name "r-inspect") | |
41d6b41f | 3638 | (version "1.20.0") |
b64ce4b7 RW |
3639 | (source |
3640 | (origin | |
3641 | (method url-fetch) | |
3642 | (uri (bioconductor-uri "INSPEcT" version)) | |
3643 | (sha256 | |
3644 | (base32 | |
41d6b41f | 3645 | "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483")))) |
b64ce4b7 RW |
3646 | (properties `((upstream-name . "INSPEcT"))) |
3647 | (build-system r-build-system) | |
3648 | (propagated-inputs | |
3649 | `(("r-biobase" ,r-biobase) | |
3650 | ("r-biocgenerics" ,r-biocgenerics) | |
3651 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 3652 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 | 3653 | ("r-desolve" ,r-desolve) |
bd824de3 | 3654 | ("r-gdata" ,r-gdata) |
74bb4cdf | 3655 | ("r-genomeinfodb" ,r-genomeinfodb) |
b64ce4b7 RW |
3656 | ("r-genomicalignments" ,r-genomicalignments) |
3657 | ("r-genomicfeatures" ,r-genomicfeatures) | |
3658 | ("r-genomicranges" ,r-genomicranges) | |
3659 | ("r-iranges" ,r-iranges) | |
74bb4cdf | 3660 | ("r-kernsmooth" ,r-kernsmooth) |
c86fc969 | 3661 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
3662 | ("r-proc" ,r-proc) |
3663 | ("r-rootsolve" ,r-rootsolve) | |
3664 | ("r-rsamtools" ,r-rsamtools) | |
437bc4dd | 3665 | ("r-rtracklayer" ,r-rtracklayer) |
c86fc969 RW |
3666 | ("r-s4vectors" ,r-s4vectors) |
3667 | ("r-shiny" ,r-shiny) | |
3668 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
3669 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
3670 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
437bc4dd RW |
3671 | (native-inputs |
3672 | `(("r-knitr" ,r-knitr))) | |
b64ce4b7 RW |
3673 | (home-page "https://bioconductor.org/packages/INSPEcT") |
3674 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
3675 | (description | |
3676 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
3677 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
3678 | order to evaluate synthesis, processing and degradation rates and assess via | |
3679 | modeling the rates that determines changes in mature mRNA levels.") | |
3680 | (license license:gpl2))) | |
f6e99763 RW |
3681 | |
3682 | (define-public r-dnabarcodes | |
3683 | (package | |
3684 | (name "r-dnabarcodes") | |
874a774f | 3685 | (version "1.20.0") |
f6e99763 RW |
3686 | (source |
3687 | (origin | |
3688 | (method url-fetch) | |
3689 | (uri (bioconductor-uri "DNABarcodes" version)) | |
3690 | (sha256 | |
3691 | (base32 | |
874a774f | 3692 | "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg")))) |
f6e99763 RW |
3693 | (properties `((upstream-name . "DNABarcodes"))) |
3694 | (build-system r-build-system) | |
3695 | (propagated-inputs | |
3696 | `(("r-bh" ,r-bh) | |
3697 | ("r-matrix" ,r-matrix) | |
3698 | ("r-rcpp" ,r-rcpp))) | |
14f40ae8 RW |
3699 | (native-inputs |
3700 | `(("r-knitr" ,r-knitr))) | |
f6e99763 RW |
3701 | (home-page "https://bioconductor.org/packages/DNABarcodes") |
3702 | (synopsis "Create and analyze DNA barcodes") | |
3703 | (description | |
3704 | "This package offers tools to create DNA barcode sets capable of | |
3705 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
3706 | can be analyzed regarding their minimal, maximal and average distances between | |
3707 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
3708 | demultiplexed, i.e. assigned to their original reference barcode.") | |
3709 | (license license:gpl2))) | |
09aa3d06 RW |
3710 | |
3711 | (define-public r-ruvseq | |
3712 | (package | |
3713 | (name "r-ruvseq") | |
a55b1622 | 3714 | (version "1.24.0") |
09aa3d06 RW |
3715 | (source |
3716 | (origin | |
3717 | (method url-fetch) | |
3718 | (uri (bioconductor-uri "RUVSeq" version)) | |
3719 | (sha256 | |
3720 | (base32 | |
a55b1622 | 3721 | "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh")))) |
09aa3d06 RW |
3722 | (properties `((upstream-name . "RUVSeq"))) |
3723 | (build-system r-build-system) | |
3724 | (propagated-inputs | |
3725 | `(("r-biobase" ,r-biobase) | |
3726 | ("r-edaseq" ,r-edaseq) | |
3727 | ("r-edger" ,r-edger) | |
3728 | ("r-mass" ,r-mass))) | |
ae0fcaa6 RW |
3729 | (native-inputs |
3730 | `(("r-knitr" ,r-knitr))) | |
09aa3d06 RW |
3731 | (home-page "https://github.com/drisso/RUVSeq") |
3732 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
3733 | (description | |
3734 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
3735 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
3736 | samples.") | |
3737 | (license license:artistic2.0))) | |
286157dc RW |
3738 | |
3739 | (define-public r-biocneighbors | |
3740 | (package | |
3741 | (name "r-biocneighbors") | |
47147877 | 3742 | (version "1.8.2") |
286157dc RW |
3743 | (source |
3744 | (origin | |
3745 | (method url-fetch) | |
3746 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
3747 | (sha256 | |
3748 | (base32 | |
47147877 | 3749 | "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7")))) |
286157dc RW |
3750 | (properties `((upstream-name . "BiocNeighbors"))) |
3751 | (build-system r-build-system) | |
3752 | (propagated-inputs | |
12e2aa96 RW |
3753 | `(("r-biocparallel" ,r-biocparallel) |
3754 | ("r-matrix" ,r-matrix) | |
286157dc | 3755 | ("r-rcpp" ,r-rcpp) |
6fc161fc | 3756 | ("r-rcpphnsw" ,r-rcpphnsw) |
286157dc | 3757 | ("r-s4vectors" ,r-s4vectors))) |
f5864c11 RW |
3758 | (native-inputs |
3759 | `(("r-knitr" ,r-knitr))) | |
286157dc RW |
3760 | (home-page "https://bioconductor.org/packages/BiocNeighbors") |
3761 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
3762 | (description | |
3763 | "This package implements exact and approximate methods for nearest | |
3764 | neighbor detection, in a framework that allows them to be easily switched | |
3765 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
3766 | using pre-clustering with the k-means algorithm. Functions are also provided | |
3767 | to search for all neighbors within a given distance. Parallelization is | |
3768 | achieved for all methods using the BiocParallel framework.") | |
3769 | (license license:gpl3))) | |
8a587c89 | 3770 | |
99391290 RW |
3771 | (define-public r-biocsingular |
3772 | (package | |
3773 | (name "r-biocsingular") | |
798ec289 | 3774 | (version "1.6.0") |
99391290 RW |
3775 | (source |
3776 | (origin | |
3777 | (method url-fetch) | |
3778 | (uri (bioconductor-uri "BiocSingular" version)) | |
3779 | (sha256 | |
3780 | (base32 | |
798ec289 | 3781 | "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni")))) |
99391290 RW |
3782 | (properties `((upstream-name . "BiocSingular"))) |
3783 | (build-system r-build-system) | |
3784 | (propagated-inputs | |
3785 | `(("r-beachmat" ,r-beachmat) | |
3786 | ("r-biocgenerics" ,r-biocgenerics) | |
3787 | ("r-biocparallel" ,r-biocparallel) | |
3788 | ("r-delayedarray" ,r-delayedarray) | |
3789 | ("r-irlba" ,r-irlba) | |
3790 | ("r-matrix" ,r-matrix) | |
3791 | ("r-rcpp" ,r-rcpp) | |
3792 | ("r-rsvd" ,r-rsvd) | |
3793 | ("r-s4vectors" ,r-s4vectors))) | |
a8351d46 RW |
3794 | (native-inputs |
3795 | `(("r-knitr" ,r-knitr))) | |
99391290 RW |
3796 | (home-page "https://github.com/LTLA/BiocSingular") |
3797 | (synopsis "Singular value decomposition for Bioconductor packages") | |
3798 | (description | |
3799 | "This package implements exact and approximate methods for singular value | |
3800 | decomposition and principal components analysis, in a framework that allows | |
3801 | them to be easily switched within Bioconductor packages or workflows. Where | |
3802 | possible, parallelization is achieved using the BiocParallel framework.") | |
3803 | (license license:gpl3))) | |
3804 | ||
a961ae46 RW |
3805 | (define-public r-destiny |
3806 | (package | |
3807 | (name "r-destiny") | |
4217307f | 3808 | (version "3.4.0") |
a961ae46 RW |
3809 | (source |
3810 | (origin | |
3811 | (method url-fetch) | |
3812 | (uri (bioconductor-uri "destiny" version)) | |
3813 | (sha256 | |
3814 | (base32 | |
4217307f | 3815 | "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) |
a961ae46 RW |
3816 | (build-system r-build-system) |
3817 | (propagated-inputs | |
3818 | `(("r-biobase" ,r-biobase) | |
3819 | ("r-biocgenerics" ,r-biocgenerics) | |
6e10ac07 | 3820 | ("r-ggplot-multistats" ,r-ggplot-multistats) |
0aa72f2d | 3821 | ("r-ggplot2" ,r-ggplot2) |
a961ae46 | 3822 | ("r-ggthemes" ,r-ggthemes) |
6e10ac07 RW |
3823 | ("r-irlba" ,r-irlba) |
3824 | ("r-knn-covertree" ,r-knn-covertree) | |
a961ae46 | 3825 | ("r-matrix" ,r-matrix) |
6e10ac07 | 3826 | ("r-pcamethods" ,r-pcamethods) |
a961ae46 RW |
3827 | ("r-proxy" ,r-proxy) |
3828 | ("r-rcpp" ,r-rcpp) | |
3829 | ("r-rcppeigen" ,r-rcppeigen) | |
6e10ac07 RW |
3830 | ("r-rcpphnsw" ,r-rcpphnsw) |
3831 | ("r-rspectra" ,r-rspectra) | |
a961ae46 RW |
3832 | ("r-scales" ,r-scales) |
3833 | ("r-scatterplot3d" ,r-scatterplot3d) | |
6e10ac07 | 3834 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
a961ae46 RW |
3835 | ("r-smoother" ,r-smoother) |
3836 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6e10ac07 RW |
3837 | ("r-tidyr" ,r-tidyr) |
3838 | ("r-tidyselect" ,r-tidyselect) | |
a961ae46 | 3839 | ("r-vim" ,r-vim))) |
3f782a6d RW |
3840 | (native-inputs |
3841 | `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes | |
a961ae46 RW |
3842 | (home-page "https://bioconductor.org/packages/destiny/") |
3843 | (synopsis "Create and plot diffusion maps") | |
3844 | (description "This package provides tools to create and plot diffusion | |
3845 | maps.") | |
3846 | ;; Any version of the GPL | |
3847 | (license license:gpl3+))) | |
3848 | ||
8a587c89 RW |
3849 | (define-public r-savr |
3850 | (package | |
3851 | (name "r-savr") | |
967fc583 | 3852 | (version "1.28.0") |
8a587c89 RW |
3853 | (source |
3854 | (origin | |
3855 | (method url-fetch) | |
3856 | (uri (bioconductor-uri "savR" version)) | |
3857 | (sha256 | |
3858 | (base32 | |
967fc583 | 3859 | "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic")))) |
8a587c89 RW |
3860 | (properties `((upstream-name . "savR"))) |
3861 | (build-system r-build-system) | |
3862 | (propagated-inputs | |
3863 | `(("r-ggplot2" ,r-ggplot2) | |
3864 | ("r-gridextra" ,r-gridextra) | |
3865 | ("r-reshape2" ,r-reshape2) | |
3866 | ("r-scales" ,r-scales) | |
3867 | ("r-xml" ,r-xml))) | |
3868 | (home-page "https://github.com/bcalder/savR") | |
3869 | (synopsis "Parse and analyze Illumina SAV files") | |
3870 | (description | |
3871 | "This package provides tools to parse Illumina Sequence Analysis | |
3872 | Viewer (SAV) files, access data, and generate QC plots.") | |
3873 | (license license:agpl3+))) | |
41ffc214 RW |
3874 | |
3875 | (define-public r-chipexoqual | |
3876 | (package | |
3877 | (name "r-chipexoqual") | |
ff4d0804 | 3878 | (version "1.14.0") |
41ffc214 RW |
3879 | (source |
3880 | (origin | |
3881 | (method url-fetch) | |
3882 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
3883 | (sha256 | |
3884 | (base32 | |
ff4d0804 | 3885 | "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag")))) |
41ffc214 RW |
3886 | (properties `((upstream-name . "ChIPexoQual"))) |
3887 | (build-system r-build-system) | |
3888 | (propagated-inputs | |
3889 | `(("r-biocparallel" ,r-biocparallel) | |
3890 | ("r-biovizbase" ,r-biovizbase) | |
3891 | ("r-broom" ,r-broom) | |
3892 | ("r-data-table" ,r-data-table) | |
3893 | ("r-dplyr" ,r-dplyr) | |
3894 | ("r-genomeinfodb" ,r-genomeinfodb) | |
3895 | ("r-genomicalignments" ,r-genomicalignments) | |
3896 | ("r-genomicranges" ,r-genomicranges) | |
3897 | ("r-ggplot2" ,r-ggplot2) | |
3898 | ("r-hexbin" ,r-hexbin) | |
3899 | ("r-iranges" ,r-iranges) | |
3900 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3901 | ("r-rmarkdown" ,r-rmarkdown) | |
3902 | ("r-rsamtools" ,r-rsamtools) | |
3903 | ("r-s4vectors" ,r-s4vectors) | |
3904 | ("r-scales" ,r-scales) | |
3905 | ("r-viridis" ,r-viridis))) | |
9697afb1 RW |
3906 | (native-inputs |
3907 | `(("r-knitr" ,r-knitr))) | |
41ffc214 RW |
3908 | (home-page "https://github.com/keleslab/ChIPexoQual") |
3909 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
3910 | (description | |
3911 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
3912 | sequencing data.") | |
3913 | (license license:gpl2+))) | |
c18dccff | 3914 | |
3d13b448 RW |
3915 | (define-public r-copynumber |
3916 | (package | |
3917 | (name "r-copynumber") | |
43d8db04 | 3918 | (version "1.30.0") |
3d13b448 RW |
3919 | (source (origin |
3920 | (method url-fetch) | |
3921 | (uri (bioconductor-uri "copynumber" version)) | |
3922 | (sha256 | |
3923 | (base32 | |
43d8db04 | 3924 | "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm")))) |
3d13b448 RW |
3925 | (build-system r-build-system) |
3926 | (propagated-inputs | |
3927 | `(("r-s4vectors" ,r-s4vectors) | |
3928 | ("r-iranges" ,r-iranges) | |
3929 | ("r-genomicranges" ,r-genomicranges) | |
3930 | ("r-biocgenerics" ,r-biocgenerics))) | |
3931 | (home-page "https://bioconductor.org/packages/copynumber") | |
3932 | (synopsis "Segmentation of single- and multi-track copy number data") | |
3933 | (description | |
3934 | "This package segments single- and multi-track copy number data by a | |
3935 | penalized least squares regression method.") | |
3936 | (license license:artistic2.0))) | |
3937 | ||
c18dccff RW |
3938 | (define-public r-dnacopy |
3939 | (package | |
3940 | (name "r-dnacopy") | |
850f4c2a | 3941 | (version "1.64.0") |
c18dccff RW |
3942 | (source |
3943 | (origin | |
3944 | (method url-fetch) | |
3945 | (uri (bioconductor-uri "DNAcopy" version)) | |
3946 | (sha256 | |
3947 | (base32 | |
850f4c2a | 3948 | "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc")))) |
c18dccff RW |
3949 | (properties `((upstream-name . "DNAcopy"))) |
3950 | (build-system r-build-system) | |
3951 | (native-inputs `(("gfortran" ,gfortran))) | |
3952 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
3953 | (synopsis "DNA copy number data analysis") | |
3954 | (description | |
3955 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
3956 | algorithm to segment DNA copy number data and identify genomic regions with | |
3957 | abnormal copy number.") | |
3958 | (license license:gpl2+))) | |
3a0babac RW |
3959 | |
3960 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
3961 | ;; Bioconductor package. | |
3962 | (define-public r-htscluster | |
3963 | (package | |
3964 | (name "r-htscluster") | |
3965 | (version "2.0.8") | |
3966 | (source | |
3967 | (origin | |
3968 | (method url-fetch) | |
3969 | (uri (cran-uri "HTSCluster" version)) | |
3970 | (sha256 | |
3971 | (base32 | |
3972 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
3973 | (properties `((upstream-name . "HTSCluster"))) | |
3974 | (build-system r-build-system) | |
3975 | (propagated-inputs | |
3976 | `(("r-capushe" ,r-capushe) | |
3977 | ("r-edger" ,r-edger) | |
3978 | ("r-plotrix" ,r-plotrix))) | |
3979 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
3980 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
3981 | (description | |
3982 | "This package provides a Poisson mixture model is implemented to cluster | |
3983 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
3984 | estimation is performed using either the EM or CEM algorithm, and the slope | |
3985 | heuristics are used for model selection (i.e., to choose the number of | |
3986 | clusters).") | |
3987 | (license license:gpl3+))) | |
173c9960 RW |
3988 | |
3989 | (define-public r-deds | |
3990 | (package | |
3991 | (name "r-deds") | |
96030bf7 | 3992 | (version "1.60.0") |
173c9960 RW |
3993 | (source |
3994 | (origin | |
3995 | (method url-fetch) | |
3996 | (uri (bioconductor-uri "DEDS" version)) | |
3997 | (sha256 | |
3998 | (base32 | |
96030bf7 | 3999 | "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8")))) |
173c9960 RW |
4000 | (properties `((upstream-name . "DEDS"))) |
4001 | (build-system r-build-system) | |
4002 | (home-page "https://bioconductor.org/packages/DEDS/") | |
4003 | (synopsis "Differential expression via distance summary for microarray data") | |
4004 | (description | |
4005 | "This library contains functions that calculate various statistics of | |
4006 | differential expression for microarray data, including t statistics, fold | |
4007 | change, F statistics, SAM, moderated t and F statistics and B statistics. It | |
4008 | also implements a new methodology called DEDS (Differential Expression via | |
4009 | Distance Summary), which selects differentially expressed genes by integrating | |
4010 | and summarizing a set of statistics using a weighted distance approach.") | |
4011 | ;; Any version of the LGPL. | |
4012 | (license license:lgpl3+))) | |
7ed869f7 RW |
4013 | |
4014 | ;; This is a CRAN package, but since it depends on a Bioconductor package we | |
4015 | ;; put it here. | |
4016 | (define-public r-nbpseq | |
4017 | (package | |
4018 | (name "r-nbpseq") | |
4019 | (version "0.3.0") | |
4020 | (source | |
4021 | (origin | |
4022 | (method url-fetch) | |
4023 | (uri (cran-uri "NBPSeq" version)) | |
4024 | (sha256 | |
4025 | (base32 | |
4026 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) | |
4027 | (properties `((upstream-name . "NBPSeq"))) | |
4028 | (build-system r-build-system) | |
4029 | (propagated-inputs | |
4030 | `(("r-qvalue" ,r-qvalue))) | |
4031 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") | |
4032 | (synopsis "Negative binomial models for RNA-Seq data") | |
4033 | (description | |
4034 | "This package provides negative binomial models for two-group comparisons | |
4035 | and regression inferences from RNA-sequencing data.") | |
4036 | (license license:gpl2))) | |
3087a2f3 RW |
4037 | |
4038 | (define-public r-ebseq | |
4039 | (package | |
4040 | (name "r-ebseq") | |
939c888d | 4041 | (version "1.30.0") |
3087a2f3 RW |
4042 | (source |
4043 | (origin | |
4044 | (method url-fetch) | |
4045 | (uri (bioconductor-uri "EBSeq" version)) | |
4046 | (sha256 | |
4047 | (base32 | |
939c888d | 4048 | "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny")))) |
3087a2f3 RW |
4049 | (properties `((upstream-name . "EBSeq"))) |
4050 | (build-system r-build-system) | |
4051 | (propagated-inputs | |
4052 | `(("r-blockmodeling" ,r-blockmodeling) | |
4053 | ("r-gplots" ,r-gplots) | |
4054 | ("r-testthat" ,r-testthat))) | |
4055 | (home-page "https://bioconductor.org/packages/EBSeq") | |
4056 | (synopsis "Differential expression analysis of RNA-seq data") | |
4057 | (description | |
4058 | "This package provides tools for differential expression analysis at both | |
4059 | gene and isoform level using RNA-seq data") | |
4060 | (license license:artistic2.0))) | |
cb1ab035 RJ |
4061 | |
4062 | (define-public r-karyoploter | |
4063 | (package | |
4064 | (name "r-karyoploter") | |
37da4513 | 4065 | (version "1.16.0") |
cb1ab035 RJ |
4066 | (source (origin |
4067 | (method url-fetch) | |
4068 | (uri (bioconductor-uri "karyoploteR" version)) | |
4069 | (sha256 | |
4070 | (base32 | |
37da4513 | 4071 | "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2")))) |
cb1ab035 RJ |
4072 | (build-system r-build-system) |
4073 | (propagated-inputs | |
6e2dc9e3 RW |
4074 | `(("r-annotationdbi" ,r-annotationdbi) |
4075 | ("r-bamsignals" ,r-bamsignals) | |
4076 | ("r-bezier" ,r-bezier) | |
4077 | ("r-biovizbase" ,r-biovizbase) | |
4078 | ("r-digest" ,r-digest) | |
4079 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4080 | ("r-genomicfeatures" ,r-genomicfeatures) | |
cb1ab035 RJ |
4081 | ("r-genomicranges" ,r-genomicranges) |
4082 | ("r-iranges" ,r-iranges) | |
cb1ab035 | 4083 | ("r-memoise" ,r-memoise) |
6e2dc9e3 RW |
4084 | ("r-regioner" ,r-regioner) |
4085 | ("r-rsamtools" ,r-rsamtools) | |
cb1ab035 | 4086 | ("r-rtracklayer" ,r-rtracklayer) |
cb1ab035 | 4087 | ("r-s4vectors" ,r-s4vectors) |
cb1ab035 | 4088 | ("r-variantannotation" ,r-variantannotation))) |
6e2dc9e3 RW |
4089 | (native-inputs |
4090 | `(("r-knitr" ,r-knitr))) | |
cb1ab035 RJ |
4091 | (home-page "https://bioconductor.org/packages/karyoploteR/") |
4092 | (synopsis "Plot customizable linear genomes displaying arbitrary data") | |
4093 | (description "This package creates karyotype plots of arbitrary genomes and | |
7230f6d5 | 4094 | offers a complete set of functions to plot arbitrary data on them. It mimics |
cb1ab035 RJ |
4095 | many R base graphics functions coupling them with a coordinate change function |
4096 | automatically mapping the chromosome and data coordinates into the plot | |
4097 | coordinates.") | |
4098 | (license license:artistic2.0))) | |
2cb71d81 RW |
4099 | |
4100 | (define-public r-lpsymphony | |
4101 | (package | |
4102 | (name "r-lpsymphony") | |
378d67c9 | 4103 | (version "1.18.0") |
2cb71d81 RW |
4104 | (source |
4105 | (origin | |
4106 | (method url-fetch) | |
4107 | (uri (bioconductor-uri "lpsymphony" version)) | |
4108 | (sha256 | |
4109 | (base32 | |
378d67c9 | 4110 | "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9")))) |
2cb71d81 RW |
4111 | (build-system r-build-system) |
4112 | (inputs | |
0653b8b0 | 4113 | `(("zlib" ,zlib))) |
2cb71d81 | 4114 | (native-inputs |
0653b8b0 RW |
4115 | `(("pkg-config" ,pkg-config) |
4116 | ("r-knitr" ,r-knitr))) | |
c756328e | 4117 | (home-page "https://r-forge.r-project.org/projects/rsymphony") |
2cb71d81 RW |
4118 | (synopsis "Symphony integer linear programming solver in R") |
4119 | (description | |
4120 | "This package was derived from Rsymphony. The package provides an R | |
4121 | interface to SYMPHONY, a linear programming solver written in C++. The main | |
4122 | difference between this package and Rsymphony is that it includes the solver | |
4123 | source code, while Rsymphony expects to find header and library files on the | |
4124 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy | |
4125 | to install interface to SYMPHONY.") | |
4126 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. | |
4127 | ;; lpsimphony is released under the same terms. | |
4128 | (license license:epl1.0))) | |
704de8f5 RW |
4129 | |
4130 | (define-public r-ihw | |
4131 | (package | |
4132 | (name "r-ihw") | |
95b1f350 | 4133 | (version "1.18.0") |
704de8f5 RW |
4134 | (source |
4135 | (origin | |
4136 | (method url-fetch) | |
4137 | (uri (bioconductor-uri "IHW" version)) | |
4138 | (sha256 | |
4139 | (base32 | |
95b1f350 | 4140 | "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0")))) |
704de8f5 RW |
4141 | (properties `((upstream-name . "IHW"))) |
4142 | (build-system r-build-system) | |
4143 | (propagated-inputs | |
4144 | `(("r-biocgenerics" ,r-biocgenerics) | |
4145 | ("r-fdrtool" ,r-fdrtool) | |
4146 | ("r-lpsymphony" ,r-lpsymphony) | |
4147 | ("r-slam" ,r-slam))) | |
359a084a RW |
4148 | (native-inputs |
4149 | `(("r-knitr" ,r-knitr))) | |
704de8f5 RW |
4150 | (home-page "https://bioconductor.org/packages/IHW") |
4151 | (synopsis "Independent hypothesis weighting") | |
4152 | (description | |
4153 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing | |
4154 | procedure that increases power compared to the method of Benjamini and | |
4155 | Hochberg by assigning data-driven weights to each hypothesis. The input to | |
4156 | IHW is a two-column table of p-values and covariates. The covariate can be | |
4157 | any continuous-valued or categorical variable that is thought to be | |
4158 | informative on the statistical properties of each hypothesis test, while it is | |
4159 | independent of the p-value under the null hypothesis.") | |
4160 | (license license:artistic2.0))) | |
251e0830 RW |
4161 | |
4162 | (define-public r-icobra | |
4163 | (package | |
4164 | (name "r-icobra") | |
b410f072 | 4165 | (version "1.18.1") |
251e0830 RW |
4166 | (source |
4167 | (origin | |
4168 | (method url-fetch) | |
4169 | (uri (bioconductor-uri "iCOBRA" version)) | |
4170 | (sha256 | |
4171 | (base32 | |
b410f072 | 4172 | "183asczy9v2v1vrzxb7n7pa2yfzym3l24r3737k0jg6hnp2bpw50")))) |
251e0830 RW |
4173 | (properties `((upstream-name . "iCOBRA"))) |
4174 | (build-system r-build-system) | |
4175 | (propagated-inputs | |
4176 | `(("r-dplyr" ,r-dplyr) | |
4177 | ("r-dt" ,r-dt) | |
4178 | ("r-ggplot2" ,r-ggplot2) | |
4179 | ("r-limma" ,r-limma) | |
4180 | ("r-reshape2" ,r-reshape2) | |
4181 | ("r-rocr" ,r-rocr) | |
4182 | ("r-scales" ,r-scales) | |
4183 | ("r-shiny" ,r-shiny) | |
4184 | ("r-shinybs" ,r-shinybs) | |
4185 | ("r-shinydashboard" ,r-shinydashboard) | |
4186 | ("r-upsetr" ,r-upsetr))) | |
ee1e8fee RW |
4187 | (native-inputs |
4188 | `(("r-knitr" ,r-knitr))) | |
251e0830 RW |
4189 | (home-page "https://bioconductor.org/packages/iCOBRA") |
4190 | (synopsis "Comparison and visualization of ranking and assignment methods") | |
4191 | (description | |
4192 | "This package provides functions for calculation and visualization of | |
4193 | performance metrics for evaluation of ranking and binary | |
4194 | classification (assignment) methods. It also contains a Shiny application for | |
4195 | interactive exploration of results.") | |
4196 | (license license:gpl2+))) | |
925fcdbb RW |
4197 | |
4198 | (define-public r-mast | |
4199 | (package | |
4200 | (name "r-mast") | |
532b1068 | 4201 | (version "1.16.0") |
925fcdbb RW |
4202 | (source |
4203 | (origin | |
4204 | (method url-fetch) | |
4205 | (uri (bioconductor-uri "MAST" version)) | |
4206 | (sha256 | |
4207 | (base32 | |
532b1068 | 4208 | "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn")))) |
925fcdbb RW |
4209 | (properties `((upstream-name . "MAST"))) |
4210 | (build-system r-build-system) | |
4211 | (propagated-inputs | |
4212 | `(("r-abind" ,r-abind) | |
4213 | ("r-biobase" ,r-biobase) | |
4214 | ("r-biocgenerics" ,r-biocgenerics) | |
4215 | ("r-data-table" ,r-data-table) | |
4216 | ("r-ggplot2" ,r-ggplot2) | |
4217 | ("r-plyr" ,r-plyr) | |
4218 | ("r-progress" ,r-progress) | |
4219 | ("r-reshape2" ,r-reshape2) | |
4220 | ("r-s4vectors" ,r-s4vectors) | |
4221 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
4222 | ("r-stringr" ,r-stringr) | |
4223 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
51d1a7a2 RW |
4224 | (native-inputs |
4225 | `(("r-knitr" ,r-knitr))) | |
925fcdbb RW |
4226 | (home-page "https://github.com/RGLab/MAST/") |
4227 | (synopsis "Model-based analysis of single cell transcriptomics") | |
4228 | (description | |
4229 | "This package provides methods and models for handling zero-inflated | |
4230 | single cell assay data.") | |
4231 | (license license:gpl2+))) | |
2d7627cf RW |
4232 | |
4233 | (define-public r-monocle | |
4234 | (package | |
4235 | (name "r-monocle") | |
38bc0bf8 | 4236 | (version "2.18.0") |
2d7627cf RW |
4237 | (source |
4238 | (origin | |
4239 | (method url-fetch) | |
4240 | (uri (bioconductor-uri "monocle" version)) | |
4241 | (sha256 | |
4242 | (base32 | |
38bc0bf8 | 4243 | "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx")))) |
2d7627cf RW |
4244 | (build-system r-build-system) |
4245 | (propagated-inputs | |
4246 | `(("r-biobase" ,r-biobase) | |
4247 | ("r-biocgenerics" ,r-biocgenerics) | |
4248 | ("r-biocviews" ,r-biocviews) | |
4249 | ("r-cluster" ,r-cluster) | |
4250 | ("r-combinat" ,r-combinat) | |
4251 | ("r-ddrtree" ,r-ddrtree) | |
4252 | ("r-densityclust" ,r-densityclust) | |
4253 | ("r-dplyr" ,r-dplyr) | |
4254 | ("r-fastica" ,r-fastica) | |
4255 | ("r-ggplot2" ,r-ggplot2) | |
4256 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) | |
4257 | ("r-igraph" ,r-igraph) | |
4258 | ("r-irlba" ,r-irlba) | |
4259 | ("r-limma" ,r-limma) | |
4260 | ("r-mass" ,r-mass) | |
4261 | ("r-matrix" ,r-matrix) | |
4262 | ("r-matrixstats" ,r-matrixstats) | |
4263 | ("r-pheatmap" ,r-pheatmap) | |
4264 | ("r-plyr" ,r-plyr) | |
4265 | ("r-proxy" ,r-proxy) | |
4266 | ("r-qlcmatrix" ,r-qlcmatrix) | |
4267 | ("r-rann" ,r-rann) | |
4268 | ("r-rcpp" ,r-rcpp) | |
4269 | ("r-reshape2" ,r-reshape2) | |
4270 | ("r-rtsne" ,r-rtsne) | |
4271 | ("r-slam" ,r-slam) | |
4272 | ("r-stringr" ,r-stringr) | |
4273 | ("r-tibble" ,r-tibble) | |
4274 | ("r-vgam" ,r-vgam) | |
4275 | ("r-viridis" ,r-viridis))) | |
d1f3c371 RW |
4276 | (native-inputs |
4277 | `(("r-knitr" ,r-knitr))) | |
2d7627cf RW |
4278 | (home-page "https://bioconductor.org/packages/monocle") |
4279 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") | |
4280 | (description | |
4281 | "Monocle performs differential expression and time-series analysis for | |
4282 | single-cell expression experiments. It orders individual cells according to | |
4283 | progress through a biological process, without knowing ahead of time which | |
4284 | genes define progress through that process. Monocle also performs | |
4285 | differential expression analysis, clustering, visualization, and other useful | |
4286 | tasks on single cell expression data. It is designed to work with RNA-Seq and | |
4287 | qPCR data, but could be used with other types as well.") | |
4288 | (license license:artistic2.0))) | |
6213e441 | 4289 | |
b2dce6b5 RW |
4290 | (define-public r-monocle3 |
4291 | (package | |
4292 | (name "r-monocle3") | |
4293 | (version "0.1.2") | |
4294 | (source | |
4295 | (origin | |
4296 | (method git-fetch) | |
4297 | (uri (git-reference | |
b0e7b699 | 4298 | (url "https://github.com/cole-trapnell-lab/monocle3") |
b2dce6b5 RW |
4299 | (commit version))) |
4300 | (file-name (git-file-name name version)) | |
4301 | (sha256 | |
4302 | (base32 | |
4303 | "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) | |
4304 | (build-system r-build-system) | |
4305 | (propagated-inputs | |
4306 | `(("r-biobase" ,r-biobase) | |
4307 | ("r-biocgenerics" ,r-biocgenerics) | |
4308 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
4309 | ("r-dplyr" ,r-dplyr) | |
4310 | ("r-ggplot2" ,r-ggplot2) | |
4311 | ("r-ggrepel" ,r-ggrepel) | |
4312 | ("r-grr" ,r-grr) | |
4313 | ("r-htmlwidgets" ,r-htmlwidgets) | |
4314 | ("r-igraph" ,r-igraph) | |
4315 | ("r-irlba" ,r-irlba) | |
4316 | ("r-limma" ,r-limma) | |
4317 | ("r-lmtest" ,r-lmtest) | |
4318 | ("r-mass" ,r-mass) | |
4319 | ("r-matrix" ,r-matrix) | |
4320 | ("r-matrix-utils" ,r-matrix-utils) | |
4321 | ("r-pbapply" ,r-pbapply) | |
4322 | ("r-pbmcapply" ,r-pbmcapply) | |
4323 | ("r-pheatmap" ,r-pheatmap) | |
4324 | ("r-plotly" ,r-plotly) | |
4325 | ("r-pryr" ,r-pryr) | |
4326 | ("r-proxy" ,r-proxy) | |
4327 | ("r-pscl" ,r-pscl) | |
4328 | ("r-purrr" ,r-purrr) | |
4329 | ("r-rann" ,r-rann) | |
4330 | ("r-rcpp" ,r-rcpp) | |
4331 | ("r-rcppparallel" ,r-rcppparallel) | |
4332 | ("r-reshape2" ,r-reshape2) | |
4333 | ("r-reticulate" ,r-reticulate) | |
4334 | ("r-rhpcblasctl" ,r-rhpcblasctl) | |
4335 | ("r-rtsne" ,r-rtsne) | |
4336 | ("r-shiny" ,r-shiny) | |
4337 | ("r-slam" ,r-slam) | |
4338 | ("r-spdep" ,r-spdep) | |
4339 | ("r-speedglm" ,r-speedglm) | |
4340 | ("r-stringr" ,r-stringr) | |
4341 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
4342 | ("r-tibble" ,r-tibble) | |
4343 | ("r-tidyr" ,r-tidyr) | |
4344 | ("r-uwot" ,r-uwot) | |
4345 | ("r-viridis" ,r-viridis))) | |
4346 | (home-page "https://github.com/cole-trapnell-lab/monocle3") | |
4347 | (synopsis "Analysis toolkit for single-cell RNA-Seq data") | |
4348 | (description | |
4349 | "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") | |
4350 | (license license:expat))) | |
4351 | ||
6213e441 RW |
4352 | (define-public r-noiseq |
4353 | (package | |
4354 | (name "r-noiseq") | |
8396c45e | 4355 | (version "2.34.0") |
6213e441 RW |
4356 | (source |
4357 | (origin | |
4358 | (method url-fetch) | |
4359 | (uri (bioconductor-uri "NOISeq" version)) | |
4360 | (sha256 | |
4361 | (base32 | |
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6213e441 RW |
4363 | (properties `((upstream-name . "NOISeq"))) |
4364 | (build-system r-build-system) | |
4365 | (propagated-inputs | |
4366 | `(("r-biobase" ,r-biobase) | |
4367 | ("r-matrix" ,r-matrix))) | |
4368 | (home-page "https://bioconductor.org/packages/NOISeq") | |
4369 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") | |
4370 | (description | |
4371 | "This package provides tools to support the analysis of RNA-seq | |
4372 | expression data or other similar kind of data. It provides exploratory plots | |
4373 | to evaluate saturation, count distribution, expression per chromosome, type of | |
4374 | detected features, features length, etc. It also supports the analysis of | |
4375 | differential expression between two experimental conditions with no parametric | |
4376 | assumptions.") | |
4377 | (license license:artistic2.0))) | |
b409c357 RW |
4378 | |
4379 | (define-public r-scdd | |
4380 | (package | |
4381 | (name "r-scdd") | |
b856a487 | 4382 | (version "1.14.0") |
b409c357 RW |
4383 | (source |
4384 | (origin | |
4385 | (method url-fetch) | |
4386 | (uri (bioconductor-uri "scDD" version)) | |
4387 | (sha256 | |
4388 | (base32 | |
b856a487 | 4389 | "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g")))) |
b409c357 RW |
4390 | (properties `((upstream-name . "scDD"))) |
4391 | (build-system r-build-system) | |
4392 | (propagated-inputs | |
4393 | `(("r-arm" ,r-arm) | |
4394 | ("r-biocparallel" ,r-biocparallel) | |
4395 | ("r-ebseq" ,r-ebseq) | |
4396 | ("r-fields" ,r-fields) | |
4397 | ("r-ggplot2" ,r-ggplot2) | |
4398 | ("r-mclust" ,r-mclust) | |
4399 | ("r-outliers" ,r-outliers) | |
4400 | ("r-s4vectors" ,r-s4vectors) | |
4401 | ("r-scran" ,r-scran) | |
4402 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
4403 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
ce9e19bc RW |
4404 | (native-inputs |
4405 | `(("r-knitr" ,r-knitr))) | |
b409c357 RW |
4406 | (home-page "https://github.com/kdkorthauer/scDD") |
4407 | (synopsis "Mixture modeling of single-cell RNA-seq data") | |
4408 | (description | |
4409 | "This package implements a method to analyze single-cell RNA-seq data | |
4410 | utilizing flexible Dirichlet Process mixture models. Genes with differential | |
4411 | distributions of expression are classified into several interesting patterns | |
4412 | of differences between two conditions. The package also includes functions | |
4413 | for simulating data with these patterns from negative binomial | |
4414 | distributions.") | |
4415 | (license license:gpl2))) | |
f0887757 RW |
4416 | |
4417 | (define-public r-scone | |
4418 | (package | |
4419 | (name "r-scone") | |
bde9dc5b | 4420 | (version "1.14.0") |
f0887757 RW |
4421 | (source |
4422 | (origin | |
4423 | (method url-fetch) | |
4424 | (uri (bioconductor-uri "scone" version)) | |
4425 | (sha256 | |
4426 | (base32 | |
bde9dc5b | 4427 | "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73")))) |
f0887757 RW |
4428 | (build-system r-build-system) |
4429 | (propagated-inputs | |
4430 | `(("r-aroma-light" ,r-aroma-light) | |
4431 | ("r-biocparallel" ,r-biocparallel) | |
4432 | ("r-boot" ,r-boot) | |
4433 | ("r-class" ,r-class) | |
4434 | ("r-cluster" ,r-cluster) | |
4435 | ("r-compositions" ,r-compositions) | |
4436 | ("r-diptest" ,r-diptest) | |
4437 | ("r-edger" ,r-edger) | |
4438 | ("r-fpc" ,r-fpc) | |
4439 | ("r-gplots" ,r-gplots) | |
4440 | ("r-hexbin" ,r-hexbin) | |
4441 | ("r-limma" ,r-limma) | |
4442 | ("r-matrixstats" ,r-matrixstats) | |
4443 | ("r-mixtools" ,r-mixtools) | |
4444 | ("r-rarpack" ,r-rarpack) | |
4445 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4446 | ("r-rhdf5" ,r-rhdf5) | |
4447 | ("r-ruvseq" ,r-ruvseq) | |
4448 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
3fc1e039 RW |
4449 | (native-inputs |
4450 | `(("r-knitr" ,r-knitr))) | |
f0887757 RW |
4451 | (home-page "https://bioconductor.org/packages/scone") |
4452 | (synopsis "Single cell overview of normalized expression data") | |
4453 | (description | |
4454 | "SCONE is an R package for comparing and ranking the performance of | |
4455 | different normalization schemes for single-cell RNA-seq and other | |
4456 | high-throughput analyses.") | |
4457 | (license license:artistic2.0))) | |
f9201d67 RW |
4458 | |
4459 | (define-public r-geoquery | |
4460 | (package | |
4461 | (name "r-geoquery") | |
5c4edeef | 4462 | (version "2.58.0") |
f9201d67 RW |
4463 | (source |
4464 | (origin | |
4465 | (method url-fetch) | |
4466 | (uri (bioconductor-uri "GEOquery" version)) | |
4467 | (sha256 | |
4468 | (base32 | |
5c4edeef | 4469 | "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4")))) |
f9201d67 RW |
4470 | (properties `((upstream-name . "GEOquery"))) |
4471 | (build-system r-build-system) | |
4472 | (propagated-inputs | |
4473 | `(("r-biobase" ,r-biobase) | |
4474 | ("r-dplyr" ,r-dplyr) | |
4475 | ("r-httr" ,r-httr) | |
4476 | ("r-limma" ,r-limma) | |
4477 | ("r-magrittr" ,r-magrittr) | |
4478 | ("r-readr" ,r-readr) | |
4479 | ("r-tidyr" ,r-tidyr) | |
4480 | ("r-xml2" ,r-xml2))) | |
159e427c RW |
4481 | (native-inputs |
4482 | `(("r-knitr" ,r-knitr))) | |
f9201d67 RW |
4483 | (home-page "https://github.com/seandavi/GEOquery/") |
4484 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") | |
4485 | (description | |
4486 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of | |
4487 | microarray data. Given the rich and varied nature of this resource, it is | |
4488 | only natural to want to apply BioConductor tools to these data. GEOquery is | |
4489 | the bridge between GEO and BioConductor.") | |
4490 | (license license:gpl2))) | |
eed6ff03 RW |
4491 | |
4492 | (define-public r-illuminaio | |
4493 | (package | |
4494 | (name "r-illuminaio") | |
e89966e9 | 4495 | (version "0.32.0") |
eed6ff03 RW |
4496 | (source |
4497 | (origin | |
4498 | (method url-fetch) | |
4499 | (uri (bioconductor-uri "illuminaio" version)) | |
4500 | (sha256 | |
4501 | (base32 | |
e89966e9 | 4502 | "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay")))) |
eed6ff03 RW |
4503 | (build-system r-build-system) |
4504 | (propagated-inputs | |
4505 | `(("r-base64" ,r-base64))) | |
4506 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") | |
4507 | (synopsis "Parse Illumina microarray output files") | |
4508 | (description | |
4509 | "This package provides tools for parsing Illumina's microarray output | |
4510 | files, including IDAT.") | |
4511 | (license license:gpl2))) | |
f4eac096 RW |
4512 | |
4513 | (define-public r-siggenes | |
4514 | (package | |
4515 | (name "r-siggenes") | |
0fd830fe | 4516 | (version "1.64.0") |
f4eac096 RW |
4517 | (source |
4518 | (origin | |
4519 | (method url-fetch) | |
4520 | (uri (bioconductor-uri "siggenes" version)) | |
4521 | (sha256 | |
4522 | (base32 | |
0fd830fe | 4523 | "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w")))) |
f4eac096 RW |
4524 | (build-system r-build-system) |
4525 | (propagated-inputs | |
4526 | `(("r-biobase" ,r-biobase) | |
409f4dd6 RW |
4527 | ("r-multtest" ,r-multtest) |
4528 | ("r-scrime" ,r-scrime))) | |
f4eac096 RW |
4529 | (home-page "https://bioconductor.org/packages/siggenes/") |
4530 | (synopsis | |
4531 | "Multiple testing using SAM and Efron's empirical Bayes approaches") | |
4532 | (description | |
4533 | "This package provides tools for the identification of differentially | |
4534 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using | |
4535 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical | |
4536 | Bayes Analyses of Microarrays} (EBAM).") | |
4537 | (license license:lgpl2.0+))) | |
34a24f95 RW |
4538 | |
4539 | (define-public r-bumphunter | |
4540 | (package | |
4541 | (name "r-bumphunter") | |
50c5fee6 | 4542 | (version "1.32.0") |
34a24f95 RW |
4543 | (source |
4544 | (origin | |
4545 | (method url-fetch) | |
4546 | (uri (bioconductor-uri "bumphunter" version)) | |
4547 | (sha256 | |
4548 | (base32 | |
50c5fee6 | 4549 | "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk")))) |
34a24f95 RW |
4550 | (build-system r-build-system) |
4551 | (propagated-inputs | |
4552 | `(("r-annotationdbi" ,r-annotationdbi) | |
4553 | ("r-biocgenerics" ,r-biocgenerics) | |
4554 | ("r-dorng" ,r-dorng) | |
4555 | ("r-foreach" ,r-foreach) | |
4556 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4557 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4558 | ("r-genomicranges" ,r-genomicranges) | |
4559 | ("r-iranges" ,r-iranges) | |
4560 | ("r-iterators" ,r-iterators) | |
4561 | ("r-limma" ,r-limma) | |
4562 | ("r-locfit" ,r-locfit) | |
4563 | ("r-matrixstats" ,r-matrixstats) | |
4564 | ("r-s4vectors" ,r-s4vectors))) | |
4565 | (home-page "https://github.com/ririzarr/bumphunter") | |
4566 | (synopsis "Find bumps in genomic data") | |
4567 | (description | |
4568 | "This package provides tools for finding bumps in genomic data in order | |
4569 | to identify differentially methylated regions in epigenetic epidemiology | |
4570 | studies.") | |
4571 | (license license:artistic2.0))) | |
0fbaf195 RW |
4572 | |
4573 | (define-public r-minfi | |
4574 | (package | |
4575 | (name "r-minfi") | |
e5a4198b | 4576 | (version "1.36.0") |
0fbaf195 RW |
4577 | (source |
4578 | (origin | |
4579 | (method url-fetch) | |
4580 | (uri (bioconductor-uri "minfi" version)) | |
4581 | (sha256 | |
4582 | (base32 | |
e5a4198b | 4583 | "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi")))) |
0fbaf195 RW |
4584 | (build-system r-build-system) |
4585 | (propagated-inputs | |
4586 | `(("r-beanplot" ,r-beanplot) | |
4587 | ("r-biobase" ,r-biobase) | |
4588 | ("r-biocgenerics" ,r-biocgenerics) | |
4589 | ("r-biocparallel" ,r-biocparallel) | |
4590 | ("r-biostrings" ,r-biostrings) | |
4591 | ("r-bumphunter" ,r-bumphunter) | |
4592 | ("r-data-table" ,r-data-table) | |
4593 | ("r-delayedarray" ,r-delayedarray) | |
4594 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
4595 | ("r-genefilter" ,r-genefilter) | |
4596 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4597 | ("r-genomicranges" ,r-genomicranges) | |
4598 | ("r-geoquery" ,r-geoquery) | |
4599 | ("r-hdf5array" ,r-hdf5array) | |
4600 | ("r-illuminaio" ,r-illuminaio) | |
4601 | ("r-iranges" ,r-iranges) | |
4602 | ("r-lattice" ,r-lattice) | |
4603 | ("r-limma" ,r-limma) | |
4604 | ("r-mass" ,r-mass) | |
4605 | ("r-mclust" ,r-mclust) | |
4606 | ("r-nlme" ,r-nlme) | |
4607 | ("r-nor1mix" ,r-nor1mix) | |
4608 | ("r-preprocesscore" ,r-preprocesscore) | |
4609 | ("r-quadprog" ,r-quadprog) | |
4610 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4611 | ("r-reshape" ,r-reshape) | |
4612 | ("r-s4vectors" ,r-s4vectors) | |
4613 | ("r-siggenes" ,r-siggenes) | |
4614 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
83e6ffda RW |
4615 | (native-inputs |
4616 | `(("r-knitr" ,r-knitr))) | |
0fbaf195 RW |
4617 | (home-page "https://github.com/hansenlab/minfi") |
4618 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") | |
4619 | (description | |
4620 | "This package provides tools to analyze and visualize Illumina Infinium | |
4621 | methylation arrays.") | |
4622 | (license license:artistic2.0))) | |
5ec5ba02 RW |
4623 | |
4624 | (define-public r-methylumi | |
4625 | (package | |
4626 | (name "r-methylumi") | |
0b7dd447 | 4627 | (version "2.36.0") |
5ec5ba02 RW |
4628 | (source |
4629 | (origin | |
4630 | (method url-fetch) | |
4631 | (uri (bioconductor-uri "methylumi" version)) | |
4632 | (sha256 | |
4633 | (base32 | |
0b7dd447 | 4634 | "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh")))) |
5ec5ba02 RW |
4635 | (build-system r-build-system) |
4636 | (propagated-inputs | |
4637 | `(("r-annotate" ,r-annotate) | |
4638 | ("r-annotationdbi" ,r-annotationdbi) | |
4639 | ("r-biobase" ,r-biobase) | |
4640 | ("r-biocgenerics" ,r-biocgenerics) | |
4641 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) | |
4642 | ("r-genefilter" ,r-genefilter) | |
4643 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4644 | ("r-genomicranges" ,r-genomicranges) | |
4645 | ("r-ggplot2" ,r-ggplot2) | |
4646 | ("r-illuminaio" ,r-illuminaio) | |
4647 | ("r-iranges" ,r-iranges) | |
4648 | ("r-lattice" ,r-lattice) | |
4649 | ("r-matrixstats" ,r-matrixstats) | |
4650 | ("r-minfi" ,r-minfi) | |
4651 | ("r-reshape2" ,r-reshape2) | |
4652 | ("r-s4vectors" ,r-s4vectors) | |
4653 | ("r-scales" ,r-scales) | |
4654 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5f25d5f8 RW |
4655 | (native-inputs |
4656 | `(("r-knitr" ,r-knitr))) | |
5ec5ba02 RW |
4657 | (home-page "https://bioconductor.org/packages/methylumi") |
4658 | (synopsis "Handle Illumina methylation data") | |
4659 | (description | |
4660 | "This package provides classes for holding and manipulating Illumina | |
4661 | methylation data. Based on eSet, it can contain MIAME information, sample | |
4662 | information, feature information, and multiple matrices of data. An | |
4663 | \"intelligent\" import function, methylumiR can read the Illumina text files | |
4664 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from | |
4665 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, | |
4666 | background correction, and quality control features for GoldenGate, Infinium, | |
4667 | and Infinium HD arrays are also included.") | |
4668 | (license license:gpl2))) | |
09605cb2 RW |
4669 | |
4670 | (define-public r-lumi | |
4671 | (package | |
4672 | (name "r-lumi") | |
4eeaa159 | 4673 | (version "2.42.0") |
09605cb2 RW |
4674 | (source |
4675 | (origin | |
4676 | (method url-fetch) | |
4677 | (uri (bioconductor-uri "lumi" version)) | |
4678 | (sha256 | |
4679 | (base32 | |
4eeaa159 | 4680 | "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3")))) |
09605cb2 RW |
4681 | (build-system r-build-system) |
4682 | (propagated-inputs | |
4683 | `(("r-affy" ,r-affy) | |
4684 | ("r-annotate" ,r-annotate) | |
4685 | ("r-annotationdbi" ,r-annotationdbi) | |
4686 | ("r-biobase" ,r-biobase) | |
4687 | ("r-dbi" ,r-dbi) | |
4688 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4689 | ("r-genomicranges" ,r-genomicranges) | |
4690 | ("r-kernsmooth" ,r-kernsmooth) | |
4691 | ("r-lattice" ,r-lattice) | |
4692 | ("r-mass" ,r-mass) | |
4693 | ("r-methylumi" ,r-methylumi) | |
4694 | ("r-mgcv" ,r-mgcv) | |
4695 | ("r-nleqslv" ,r-nleqslv) | |
4696 | ("r-preprocesscore" ,r-preprocesscore) | |
4697 | ("r-rsqlite" ,r-rsqlite))) | |
4698 | (home-page "https://bioconductor.org/packages/lumi") | |
4699 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") | |
4700 | (description | |
4701 | "The lumi package provides an integrated solution for the Illumina | |
4702 | microarray data analysis. It includes functions of Illumina | |
4703 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific | |
4704 | variance stabilization, normalization and gene annotation at the probe level. | |
4705 | It also includes the functions of processing Illumina methylation microarrays, | |
4706 | especially Illumina Infinium methylation microarrays.") | |
4707 | (license license:lgpl2.0+))) | |
4291f36a RW |
4708 | |
4709 | (define-public r-linnorm | |
4710 | (package | |
4711 | (name "r-linnorm") | |
37e09611 | 4712 | (version "2.14.0") |
4291f36a RW |
4713 | (source |
4714 | (origin | |
4715 | (method url-fetch) | |
4716 | (uri (bioconductor-uri "Linnorm" version)) | |
4717 | (sha256 | |
4718 | (base32 | |
37e09611 | 4719 | "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3")))) |
4291f36a RW |
4720 | (properties `((upstream-name . "Linnorm"))) |
4721 | (build-system r-build-system) | |
4722 | (propagated-inputs | |
4723 | `(("r-amap" ,r-amap) | |
4724 | ("r-apcluster" ,r-apcluster) | |
4725 | ("r-ellipse" ,r-ellipse) | |
4726 | ("r-fastcluster" ,r-fastcluster) | |
4727 | ("r-fpc" ,r-fpc) | |
4728 | ("r-ggdendro" ,r-ggdendro) | |
4729 | ("r-ggplot2" ,r-ggplot2) | |
4730 | ("r-gmodels" ,r-gmodels) | |
4731 | ("r-igraph" ,r-igraph) | |
4732 | ("r-limma" ,r-limma) | |
4733 | ("r-mass" ,r-mass) | |
4734 | ("r-mclust" ,r-mclust) | |
4735 | ("r-rcpp" ,r-rcpp) | |
4736 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
4737 | ("r-rtsne" ,r-rtsne) | |
4738 | ("r-statmod" ,r-statmod) | |
4739 | ("r-vegan" ,r-vegan) | |
4740 | ("r-zoo" ,r-zoo))) | |
1465873c RW |
4741 | (native-inputs |
4742 | `(("r-knitr" ,r-knitr))) | |
4291f36a RW |
4743 | (home-page "http://www.jjwanglab.org/Linnorm/") |
4744 | (synopsis "Linear model and normality based transformation method") | |
4745 | (description | |
4746 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq | |
4747 | count data or any large scale count data. It transforms such datasets for | |
4748 | parametric tests. In addition to the transformtion function (@code{Linnorm}), | |
4749 | the following pipelines are implemented: | |
4750 | ||
4751 | @enumerate | |
4752 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) | |
4753 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means | |
4754 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, | |
4755 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) | |
4756 | @item Differential expression analysis or differential peak detection using | |
4757 | limma (@code{Linnorm.limma}) | |
4758 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) | |
4759 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) | |
4760 | @item Stable gene selection for scRNA-seq data; for users without or who do | |
4761 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) | |
4762 | @item Data imputation (@code{Linnorm.DataImput}). | |
4763 | @end enumerate | |
4764 | ||
4765 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the | |
4766 | @code{RnaXSim} function is included for simulating RNA-seq data for the | |
4767 | evaluation of DEG analysis methods.") | |
4768 | (license license:expat))) | |
e4a17532 RW |
4769 | |
4770 | (define-public r-ioniser | |
4771 | (package | |
4772 | (name "r-ioniser") | |
2a1a6d74 | 4773 | (version "2.14.0") |
e4a17532 RW |
4774 | (source |
4775 | (origin | |
4776 | (method url-fetch) | |
4777 | (uri (bioconductor-uri "IONiseR" version)) | |
4778 | (sha256 | |
4779 | (base32 | |
2a1a6d74 | 4780 | "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx")))) |
e4a17532 RW |
4781 | (properties `((upstream-name . "IONiseR"))) |
4782 | (build-system r-build-system) | |
4783 | (propagated-inputs | |
4784 | `(("r-biocgenerics" ,r-biocgenerics) | |
4785 | ("r-biocparallel" ,r-biocparallel) | |
4786 | ("r-biostrings" ,r-biostrings) | |
4787 | ("r-bit64" ,r-bit64) | |
4788 | ("r-dplyr" ,r-dplyr) | |
4789 | ("r-ggplot2" ,r-ggplot2) | |
4790 | ("r-magrittr" ,r-magrittr) | |
4791 | ("r-rhdf5" ,r-rhdf5) | |
4792 | ("r-shortread" ,r-shortread) | |
4793 | ("r-stringr" ,r-stringr) | |
4794 | ("r-tibble" ,r-tibble) | |
4795 | ("r-tidyr" ,r-tidyr) | |
4796 | ("r-xvector" ,r-xvector))) | |
293fb8a1 RW |
4797 | (native-inputs |
4798 | `(("r-knitr" ,r-knitr))) | |
e4a17532 RW |
4799 | (home-page "https://bioconductor.org/packages/IONiseR/") |
4800 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") | |
4801 | (description | |
4802 | "IONiseR provides tools for the quality assessment of Oxford Nanopore | |
4803 | MinION data. It extracts summary statistics from a set of fast5 files and can | |
4804 | be used either before or after base calling. In addition to standard | |
4805 | summaries of the read-types produced, it provides a number of plots for | |
4806 | visualising metrics relative to experiment run time or spatially over the | |
4807 | surface of a flowcell.") | |
4808 | (license license:expat))) | |
80eb01c7 | 4809 | |
f2114762 RW |
4810 | ;; This is a CRAN package, but it depends on multtest from Bioconductor. |
4811 | (define-public r-mutoss | |
4812 | (package | |
4813 | (name "r-mutoss") | |
4814 | (version "0.1-12") | |
4815 | (source | |
4816 | (origin | |
4817 | (method url-fetch) | |
4818 | (uri (cran-uri "mutoss" version)) | |
4819 | (sha256 | |
4820 | (base32 | |
4821 | "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298")))) | |
4822 | (properties `((upstream-name . "mutoss"))) | |
4823 | (build-system r-build-system) | |
4824 | (propagated-inputs | |
4825 | `(("r-multcomp" ,r-multcomp) | |
4826 | ("r-multtest" ,r-multtest) | |
4827 | ("r-mvtnorm" ,r-mvtnorm) | |
4828 | ("r-plotrix" ,r-plotrix))) | |
4829 | (home-page "https://github.com/kornl/mutoss/") | |
4830 | (synopsis "Unified multiple testing procedures") | |
4831 | (description | |
4832 | "This package is designed to ease the application and comparison of | |
4833 | multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods | |
4834 | are standardized and usable by the accompanying mutossGUI package.") | |
4835 | ;; Any version of the GPL. | |
4836 | (license (list license:gpl2+ license:gpl3+)))) | |
4837 | ||
bf770d92 RW |
4838 | ;; This is a CRAN package, but it depends on mutoss, which depends on multtest |
4839 | ;; from Bioconductor, so we put it here. | |
4840 | (define-public r-metap | |
4841 | (package | |
4842 | (name "r-metap") | |
fd6412cd | 4843 | (version "1.3") |
bf770d92 RW |
4844 | (source |
4845 | (origin | |
4846 | (method url-fetch) | |
4847 | (uri (cran-uri "metap" version)) | |
4848 | (sha256 | |
4849 | (base32 | |
fd6412cd | 4850 | "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) |
bf770d92 RW |
4851 | (build-system r-build-system) |
4852 | (propagated-inputs | |
4853 | `(("r-lattice" ,r-lattice) | |
4854 | ("r-mutoss" ,r-mutoss) | |
4855 | ("r-rdpack" ,r-rdpack) | |
4856 | ("r-tfisher" ,r-tfisher))) | |
4857 | (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") | |
4858 | (synopsis "Meta-analysis of significance values") | |
4859 | (description | |
4860 | "The canonical way to perform meta-analysis involves using effect sizes. | |
4861 | When they are not available this package provides a number of methods for | |
4862 | meta-analysis of significance values including the methods of Edgington, | |
4863 | Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate | |
4864 | published results; and a routine for graphical display.") | |
4865 | (license license:gpl2))) | |
4866 | ||
8a5460b4 RW |
4867 | (define-public r-triform |
4868 | (package | |
4869 | (name "r-triform") | |
ecb4e165 | 4870 | (version "1.29.0") |
8a5460b4 RW |
4871 | (source |
4872 | (origin | |
4873 | (method url-fetch) | |
4874 | (uri (bioconductor-uri "triform" version)) | |
4875 | (sha256 | |
4876 | (base32 | |
ecb4e165 | 4877 | "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) |
8a5460b4 RW |
4878 | (build-system r-build-system) |
4879 | (propagated-inputs | |
4880 | `(("r-biocgenerics" ,r-biocgenerics) | |
4881 | ("r-iranges" ,r-iranges) | |
4882 | ("r-yaml" ,r-yaml))) | |
4883 | (home-page "https://bioconductor.org/packages/triform/") | |
4884 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") | |
4885 | (description | |
4886 | "The Triform algorithm uses model-free statistics to identify peak-like | |
4887 | distributions of TF ChIP sequencing reads, taking advantage of an improved | |
4888 | peak definition in combination with known profile characteristics.") | |
4889 | (license license:gpl2))) | |
c538bcdd RW |
4890 | |
4891 | (define-public r-varianttools | |
4892 | (package | |
4893 | (name "r-varianttools") | |
67837d4a | 4894 | (version "1.32.0") |
c538bcdd RW |
4895 | (source |
4896 | (origin | |
4897 | (method url-fetch) | |
4898 | (uri (bioconductor-uri "VariantTools" version)) | |
4899 | (sha256 | |
4900 | (base32 | |
67837d4a | 4901 | "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89")))) |
c538bcdd RW |
4902 | (properties `((upstream-name . "VariantTools"))) |
4903 | (build-system r-build-system) | |
4904 | (propagated-inputs | |
4905 | `(("r-biobase" ,r-biobase) | |
4906 | ("r-biocgenerics" ,r-biocgenerics) | |
4907 | ("r-biocparallel" ,r-biocparallel) | |
4908 | ("r-biostrings" ,r-biostrings) | |
4909 | ("r-bsgenome" ,r-bsgenome) | |
4910 | ("r-genomeinfodb" ,r-genomeinfodb) | |
4911 | ("r-genomicfeatures" ,r-genomicfeatures) | |
4912 | ("r-genomicranges" ,r-genomicranges) | |
4913 | ("r-iranges" ,r-iranges) | |
4914 | ("r-matrix" ,r-matrix) | |
4915 | ("r-rsamtools" ,r-rsamtools) | |
4916 | ("r-rtracklayer" ,r-rtracklayer) | |
4917 | ("r-s4vectors" ,r-s4vectors) | |
4918 | ("r-variantannotation" ,r-variantannotation))) | |
4919 | (home-page "https://bioconductor.org/packages/VariantTools/") | |
4920 | (synopsis "Tools for exploratory analysis of variant calls") | |
4921 | (description | |
4922 | "Explore, diagnose, and compare variant calls using filters. The | |
4923 | VariantTools package supports a workflow for loading data, calling single | |
4924 | sample variants and tumor-specific somatic mutations or other sample-specific | |
4925 | variant types (e.g., RNA editing). Most of the functions operate on | |
4926 | alignments (BAM files) or datasets of called variants. The user is expected | |
4927 | to have already aligned the reads with a separate tool, e.g., GSNAP via | |
4928 | gmapR.") | |
4929 | (license license:artistic2.0))) | |
3e41919d RW |
4930 | |
4931 | (define-public r-heatplus | |
4932 | (package | |
4933 | (name "r-heatplus") | |
9813d24d | 4934 | (version "2.36.0") |
3e41919d RW |
4935 | (source |
4936 | (origin | |
4937 | (method url-fetch) | |
4938 | (uri (bioconductor-uri "Heatplus" version)) | |
4939 | (sha256 | |
4940 | (base32 | |
9813d24d | 4941 | "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n")))) |
3e41919d RW |
4942 | (properties `((upstream-name . "Heatplus"))) |
4943 | (build-system r-build-system) | |
4944 | (propagated-inputs | |
4945 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) | |
4946 | (home-page "https://github.com/alexploner/Heatplus") | |
4947 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") | |
4948 | (description | |
4949 | "This package provides tools to display a rectangular heatmap (intensity | |
4950 | plot) of a data matrix. By default, both samples (columns) and features (row) | |
4951 | of the matrix are sorted according to a hierarchical clustering, and the | |
4952 | corresponding dendrogram is plotted. Optionally, panels with additional | |
4953 | information about samples and features can be added to the plot.") | |
4954 | (license license:gpl2+))) | |
c04f230e RW |
4955 | |
4956 | (define-public r-gosemsim | |
4957 | (package | |
4958 | (name "r-gosemsim") | |
b2084e4d | 4959 | (version "2.16.1") |
c04f230e RW |
4960 | (source |
4961 | (origin | |
4962 | (method url-fetch) | |
4963 | (uri (bioconductor-uri "GOSemSim" version)) | |
4964 | (sha256 | |
4965 | (base32 | |
b2084e4d | 4966 | "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs")))) |
c04f230e RW |
4967 | (properties `((upstream-name . "GOSemSim"))) |
4968 | (build-system r-build-system) | |
4969 | (propagated-inputs | |
4970 | `(("r-annotationdbi" ,r-annotationdbi) | |
4971 | ("r-go-db" ,r-go-db) | |
4972 | ("r-rcpp" ,r-rcpp))) | |
d5951dc4 RW |
4973 | (native-inputs |
4974 | `(("r-knitr" ,r-knitr))) | |
c04f230e RW |
4975 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") |
4976 | (synopsis "GO-terms semantic similarity measures") | |
4977 | (description | |
4978 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide | |
4979 | quantitative ways to compute similarities between genes and gene groups, and | |
4980 | have became important basis for many bioinformatics analysis approaches. | |
4981 | GOSemSim is an R package for semantic similarity computation among GO terms, | |
4982 | sets of GO terms, gene products and gene clusters.") | |
4983 | (license license:artistic2.0))) | |
9d0f7942 RW |
4984 | |
4985 | (define-public r-anota | |
4986 | (package | |
4987 | (name "r-anota") | |
33c905b9 | 4988 | (version "1.38.0") |
9d0f7942 RW |
4989 | (source |
4990 | (origin | |
4991 | (method url-fetch) | |
4992 | (uri (bioconductor-uri "anota" version)) | |
4993 | (sha256 | |
4994 | (base32 | |
33c905b9 | 4995 | "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x")))) |
9d0f7942 RW |
4996 | (build-system r-build-system) |
4997 | (propagated-inputs | |
4998 | `(("r-multtest" ,r-multtest) | |
4999 | ("r-qvalue" ,r-qvalue))) | |
5000 | (home-page "https://bioconductor.org/packages/anota/") | |
5001 | (synopsis "Analysis of translational activity") | |
5002 | (description | |
5003 | "Genome wide studies of translational control is emerging as a tool to | |
0cea26bd | 5004 | study various biological conditions. The output from such analysis is both |
7230f6d5 | 5005 | the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively |
9d0f7942 RW |
5006 | involved in translation (the actively translating mRNA level) for each mRNA. |
5007 | The standard analysis of such data strives towards identifying differential | |
5008 | translational between two or more sample classes - i.e. differences in | |
5009 | actively translated mRNA levels that are independent of underlying differences | |
5010 | in cytosolic mRNA levels. This package allows for such analysis using partial | |
5011 | variances and the random variance model. As 10s of thousands of mRNAs are | |
4f664004 | 5012 | analyzed in parallel the library performs a number of tests to assure that |
9d0f7942 RW |
5013 | the data set is suitable for such analysis.") |
5014 | (license license:gpl3))) | |
a6d867fe RW |
5015 | |
5016 | (define-public r-sigpathway | |
5017 | (package | |
5018 | (name "r-sigpathway") | |
7dabc629 | 5019 | (version "1.58.0") |
a6d867fe RW |
5020 | (source |
5021 | (origin | |
5022 | (method url-fetch) | |
5023 | (uri (bioconductor-uri "sigPathway" version)) | |
5024 | (sha256 | |
5025 | (base32 | |
7dabc629 | 5026 | "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l")))) |
a6d867fe RW |
5027 | (properties `((upstream-name . "sigPathway"))) |
5028 | (build-system r-build-system) | |
5029 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") | |
5030 | (synopsis "Pathway analysis") | |
5031 | (description | |
5032 | "This package is used to conduct pathway analysis by calculating the NT_k | |
5033 | and NE_k statistics in a statistical framework for determining whether a | |
5034 | specified group of genes for a pathway has a coordinated association with a | |
5035 | phenotype of interest.") | |
5036 | (license license:gpl2))) | |
af26c7ae RW |
5037 | |
5038 | (define-public r-fgsea | |
5039 | (package | |
5040 | (name "r-fgsea") | |
d68a9ffa | 5041 | (version "1.16.0") |
af26c7ae RW |
5042 | (source |
5043 | (origin | |
5044 | (method url-fetch) | |
5045 | (uri (bioconductor-uri "fgsea" version)) | |
5046 | (sha256 | |
5047 | (base32 | |
d68a9ffa | 5048 | "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n")))) |
af26c7ae RW |
5049 | (build-system r-build-system) |
5050 | (propagated-inputs | |
ebffd24c RW |
5051 | `(("r-bh" ,r-bh) |
5052 | ("r-biocparallel" ,r-biocparallel) | |
af26c7ae RW |
5053 | ("r-data-table" ,r-data-table) |
5054 | ("r-fastmatch" ,r-fastmatch) | |
5055 | ("r-ggplot2" ,r-ggplot2) | |
5056 | ("r-gridextra" ,r-gridextra) | |
5057 | ("r-matrix" ,r-matrix) | |
5058 | ("r-rcpp" ,r-rcpp))) | |
1dec455c RW |
5059 | (native-inputs |
5060 | `(("r-knitr" ,r-knitr))) | |
af26c7ae RW |
5061 | (home-page "https://github.com/ctlab/fgsea/") |
5062 | (synopsis "Fast gene set enrichment analysis") | |
5063 | (description | |
5064 | "The package implements an algorithm for fast gene set enrichment | |
23c8ef71 VC |
5065 | analysis. Using the fast algorithm makes more permutations and gets |
5066 | more fine grained p-values, which allows using accurate standard approaches | |
af26c7ae RW |
5067 | to multiple hypothesis correction.") |
5068 | (license license:expat))) | |
305050b5 RW |
5069 | |
5070 | (define-public r-dose | |
5071 | (package | |
5072 | (name "r-dose") | |
aeb1d56f | 5073 | (version "3.16.0") |
305050b5 RW |
5074 | (source |
5075 | (origin | |
5076 | (method url-fetch) | |
5077 | (uri (bioconductor-uri "DOSE" version)) | |
5078 | (sha256 | |
5079 | (base32 | |
aeb1d56f | 5080 | "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4")))) |
305050b5 RW |
5081 | (properties `((upstream-name . "DOSE"))) |
5082 | (build-system r-build-system) | |
5083 | (propagated-inputs | |
5084 | `(("r-annotationdbi" ,r-annotationdbi) | |
5085 | ("r-biocparallel" ,r-biocparallel) | |
5086 | ("r-do-db" ,r-do-db) | |
5087 | ("r-fgsea" ,r-fgsea) | |
5088 | ("r-ggplot2" ,r-ggplot2) | |
5089 | ("r-gosemsim" ,r-gosemsim) | |
5090 | ("r-qvalue" ,r-qvalue) | |
3a80f1cf | 5091 | ("r-reshape2" ,r-reshape2))) |
5ef2b749 RW |
5092 | (native-inputs |
5093 | `(("r-knitr" ,r-knitr))) | |
305050b5 RW |
5094 | (home-page "https://guangchuangyu.github.io/software/DOSE/") |
5095 | (synopsis "Disease ontology semantic and enrichment analysis") | |
5096 | (description | |
5097 | "This package implements five methods proposed by Resnik, Schlicker, | |
5098 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among | |
5099 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses | |
5100 | including hypergeometric model and gene set enrichment analysis are also | |
5101 | implemented for discovering disease associations of high-throughput biological | |
5102 | data.") | |
5103 | (license license:artistic2.0))) | |
9c30cf65 RW |
5104 | |
5105 | (define-public r-enrichplot | |
5106 | (package | |
5107 | (name "r-enrichplot") | |
ebf9ad79 | 5108 | (version "1.10.2") |
9c30cf65 RW |
5109 | (source |
5110 | (origin | |
5111 | (method url-fetch) | |
5112 | (uri (bioconductor-uri "enrichplot" version)) | |
5113 | (sha256 | |
5114 | (base32 | |
ebf9ad79 | 5115 | "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv")))) |
9c30cf65 RW |
5116 | (build-system r-build-system) |
5117 | (propagated-inputs | |
eb3d17eb | 5118 | `(("r-cowplot" ,r-cowplot) |
9c30cf65 | 5119 | ("r-dose" ,r-dose) |
9c30cf65 | 5120 | ("r-ggplot2" ,r-ggplot2) |
9c30cf65 | 5121 | ("r-ggraph" ,r-ggraph) |
9c30cf65 | 5122 | ("r-gosemsim" ,r-gosemsim) |
9c30cf65 | 5123 | ("r-igraph" ,r-igraph) |
eb3d17eb | 5124 | ("r-magrittr" ,r-magrittr) |
43fb14ce | 5125 | ("r-plyr" ,r-plyr) |
9c30cf65 RW |
5126 | ("r-purrr" ,r-purrr) |
5127 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
43fb14ce | 5128 | ("r-reshape2" ,r-reshape2) |
eb3d17eb RJ |
5129 | ("r-scatterpie" ,r-scatterpie) |
5130 | ("r-shadowtext" ,r-shadowtext))) | |
43fb14ce RW |
5131 | (native-inputs |
5132 | `(("r-knitr" ,r-knitr))) | |
9c30cf65 RW |
5133 | (home-page "https://github.com/GuangchuangYu/enrichplot") |
5134 | (synopsis "Visualization of functional enrichment result") | |
5135 | (description | |
5136 | "The enrichplot package implements several visualization methods for | |
5137 | interpreting functional enrichment results obtained from ORA or GSEA analyses. | |
5138 | All the visualization methods are developed based on ggplot2 graphics.") | |
5139 | (license license:artistic2.0))) | |
f8295ee6 RW |
5140 | |
5141 | (define-public r-clusterprofiler | |
5142 | (package | |
5143 | (name "r-clusterprofiler") | |
6d070923 | 5144 | (version "3.18.1") |
f8295ee6 RW |
5145 | (source |
5146 | (origin | |
5147 | (method url-fetch) | |
5148 | (uri (bioconductor-uri "clusterProfiler" version)) | |
5149 | (sha256 | |
5150 | (base32 | |
6d070923 | 5151 | "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si")))) |
f8295ee6 RW |
5152 | (properties |
5153 | `((upstream-name . "clusterProfiler"))) | |
5154 | (build-system r-build-system) | |
5155 | (propagated-inputs | |
5156 | `(("r-annotationdbi" ,r-annotationdbi) | |
5157 | ("r-dose" ,r-dose) | |
63c8323a RW |
5158 | ("r-downloader" ,r-downloader) |
5159 | ("r-dplyr" ,r-dplyr) | |
f8295ee6 | 5160 | ("r-enrichplot" ,r-enrichplot) |
f8295ee6 RW |
5161 | ("r-go-db" ,r-go-db) |
5162 | ("r-gosemsim" ,r-gosemsim) | |
5163 | ("r-magrittr" ,r-magrittr) | |
5164 | ("r-plyr" ,r-plyr) | |
5165 | ("r-qvalue" ,r-qvalue) | |
69f3b278 | 5166 | ("r-rlang" ,r-rlang) |
f8295ee6 RW |
5167 | ("r-rvcheck" ,r-rvcheck) |
5168 | ("r-tidyr" ,r-tidyr))) | |
63c8323a RW |
5169 | (native-inputs |
5170 | `(("r-knitr" ,r-knitr))) | |
f8295ee6 RW |
5171 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") |
5172 | (synopsis "Analysis and visualization of functional profiles for gene clusters") | |
5173 | (description | |
5174 | "This package implements methods to analyze and visualize functional | |
5175 | profiles (GO and KEGG) of gene and gene clusters.") | |
5176 | (license license:artistic2.0))) | |
ce77562a RW |
5177 | |
5178 | (define-public r-mlinterfaces | |
5179 | (package | |
5180 | (name "r-mlinterfaces") | |
4f82931d | 5181 | (version "1.70.0") |
ce77562a RW |
5182 | (source |
5183 | (origin | |
5184 | (method url-fetch) | |
5185 | (uri (bioconductor-uri "MLInterfaces" version)) | |
5186 | (sha256 | |
5187 | (base32 | |
4f82931d | 5188 | "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r")))) |
ce77562a RW |
5189 | (properties `((upstream-name . "MLInterfaces"))) |
5190 | (build-system r-build-system) | |
5191 | (propagated-inputs | |
5192 | `(("r-annotate" ,r-annotate) | |
5193 | ("r-biobase" ,r-biobase) | |
5194 | ("r-biocgenerics" ,r-biocgenerics) | |
5195 | ("r-cluster" ,r-cluster) | |
5196 | ("r-fpc" ,r-fpc) | |
5197 | ("r-gbm" ,r-gbm) | |
5198 | ("r-gdata" ,r-gdata) | |
5199 | ("r-genefilter" ,r-genefilter) | |
5200 | ("r-ggvis" ,r-ggvis) | |
5201 | ("r-hwriter" ,r-hwriter) | |
5202 | ("r-mass" ,r-mass) | |
5203 | ("r-mlbench" ,r-mlbench) | |
5204 | ("r-pls" ,r-pls) | |
5205 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
500f7df8 | 5206 | ("r-rcpp" ,r-rcpp) |
ce77562a RW |
5207 | ("r-rpart" ,r-rpart) |
5208 | ("r-sfsmisc" ,r-sfsmisc) | |
5209 | ("r-shiny" ,r-shiny) | |
5210 | ("r-threejs" ,r-threejs))) | |
5211 | (home-page "https://bioconductor.org/packages/MLInterfaces/") | |
5212 | (synopsis "Interfaces to R machine learning procedures") | |
5213 | (description | |
5214 | "This package provides uniform interfaces to machine learning code for | |
5215 | data in R and Bioconductor containers.") | |
5216 | ;; Any version of the LGPL. | |
5217 | (license license:lgpl2.1+))) | |
a793e88c RW |
5218 | |
5219 | (define-public r-annaffy | |
5220 | (package | |
5221 | (name "r-annaffy") | |
aca4ebe4 | 5222 | (version "1.62.0") |
a793e88c RW |
5223 | (source |
5224 | (origin | |
5225 | (method url-fetch) | |
5226 | (uri (bioconductor-uri "annaffy" version)) | |
5227 | (sha256 | |
5228 | (base32 | |
aca4ebe4 | 5229 | "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i")))) |
a793e88c RW |
5230 | (build-system r-build-system) |
5231 | (arguments | |
5232 | `(#:phases | |
5233 | (modify-phases %standard-phases | |
5234 | (add-after 'unpack 'remove-reference-to-non-free-data | |
5235 | (lambda _ | |
5236 | (substitute* "DESCRIPTION" | |
5237 | ((", KEGG.db") "")) | |
5238 | #t))))) | |
5239 | (propagated-inputs | |
5240 | `(("r-annotationdbi" ,r-annotationdbi) | |
5241 | ("r-biobase" ,r-biobase) | |
5242 | ("r-dbi" ,r-dbi) | |
5243 | ("r-go-db" ,r-go-db))) | |
5244 | (home-page "https://bioconductor.org/packages/annaffy/") | |
5245 | (synopsis "Annotation tools for Affymetrix biological metadata") | |
5246 | (description | |
5247 | "This package provides functions for handling data from Bioconductor | |
5248 | Affymetrix annotation data packages. It produces compact HTML and text | |
5249 | reports including experimental data and URL links to many online databases. | |
5250 | It allows searching of biological metadata using various criteria.") | |
5251 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of | |
5252 | ;; the LGPL 2.1 is included. | |
5253 | (license license:lgpl2.1+))) | |
0ec0a5ec RW |
5254 | |
5255 | (define-public r-a4core | |
5256 | (package | |
5257 | (name "r-a4core") | |
c47a8cd9 | 5258 | (version "1.38.0") |
0ec0a5ec RW |
5259 | (source |
5260 | (origin | |
5261 | (method url-fetch) | |
5262 | (uri (bioconductor-uri "a4Core" version)) | |
5263 | (sha256 | |
5264 | (base32 | |
c47a8cd9 | 5265 | "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2")))) |
0ec0a5ec RW |
5266 | (properties `((upstream-name . "a4Core"))) |
5267 | (build-system r-build-system) | |
5268 | (propagated-inputs | |
5269 | `(("r-biobase" ,r-biobase) | |
5270 | ("r-glmnet" ,r-glmnet))) | |
c47a8cd9 | 5271 | (native-inputs |
5272 | `(("r-knitr" ,r-knitr))) | |
0ec0a5ec RW |
5273 | (home-page "https://bioconductor.org/packages/a4Core") |
5274 | (synopsis "Automated Affymetrix array analysis core package") | |
5275 | (description | |
5276 | "This is the core package for the automated analysis of Affymetrix | |
5277 | arrays.") | |
5278 | (license license:gpl3))) | |
9ae37581 RW |
5279 | |
5280 | (define-public r-a4classif | |
5281 | (package | |
5282 | (name "r-a4classif") | |
fa51705f | 5283 | (version "1.38.0") |
9ae37581 RW |
5284 | (source |
5285 | (origin | |
5286 | (method url-fetch) | |
5287 | (uri (bioconductor-uri "a4Classif" version)) | |
5288 | (sha256 | |
5289 | (base32 | |
fa51705f | 5290 | "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz")))) |
9ae37581 RW |
5291 | (properties `((upstream-name . "a4Classif"))) |
5292 | (build-system r-build-system) | |
5293 | (propagated-inputs | |
5294 | `(("r-a4core" ,r-a4core) | |
5295 | ("r-a4preproc" ,r-a4preproc) | |
fa51705f | 5296 | ("r-biobase" ,r-biobase) |
9ae37581 | 5297 | ("r-glmnet" ,r-glmnet) |
9ae37581 RW |
5298 | ("r-pamr" ,r-pamr) |
5299 | ("r-rocr" ,r-rocr) | |
5300 | ("r-varselrf" ,r-varselrf))) | |
fa51705f | 5301 | (native-inputs |
5302 | `(("r-knitr" ,r-knitr))) | |
9ae37581 RW |
5303 | (home-page "https://bioconductor.org/packages/a4Classif/") |
5304 | (synopsis "Automated Affymetrix array analysis classification package") | |
5305 | (description | |
5306 | "This is the classification package for the automated analysis of | |
5307 | Affymetrix arrays.") | |
5308 | (license license:gpl3))) | |
b8d13e2c RW |
5309 | |
5310 | (define-public r-a4preproc | |
5311 | (package | |
5312 | (name "r-a4preproc") | |
85155e2e | 5313 | (version "1.38.0") |
b8d13e2c RW |
5314 | (source |
5315 | (origin | |
5316 | (method url-fetch) | |
5317 | (uri (bioconductor-uri "a4Preproc" version)) | |
5318 | (sha256 | |
5319 | (base32 | |
85155e2e | 5320 | "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i")))) |
b8d13e2c RW |
5321 | (properties `((upstream-name . "a4Preproc"))) |
5322 | (build-system r-build-system) | |
5323 | (propagated-inputs | |
85155e2e | 5324 | `(("r-biobase" ,r-biobase) |
5325 | ("r-biocgenerics" ,r-biocgenerics))) | |
5326 | (native-inputs | |
5327 | `(("r-knitr" ,r-knitr))) | |
b8d13e2c RW |
5328 | (home-page "https://bioconductor.org/packages/a4Preproc/") |
5329 | (synopsis "Automated Affymetrix array analysis preprocessing package") | |
5330 | (description | |
5331 | "This is a package for the automated analysis of Affymetrix arrays. It | |
5332 | is used for preprocessing the arrays.") | |
5333 | (license license:gpl3))) | |
8e15f861 RW |
5334 | |
5335 | (define-public r-a4reporting | |
5336 | (package | |
5337 | (name "r-a4reporting") | |
2fb8298c | 5338 | (version "1.38.0") |
8e15f861 RW |
5339 | (source |
5340 | (origin | |
5341 | (method url-fetch) | |
5342 | (uri (bioconductor-uri "a4Reporting" version)) | |
5343 | (sha256 | |
5344 | (base32 | |
2fb8298c | 5345 | "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy")))) |
8e15f861 RW |
5346 | (properties `((upstream-name . "a4Reporting"))) |
5347 | (build-system r-build-system) | |
5348 | (propagated-inputs | |
2fb8298c | 5349 | `(("r-xtable" ,r-xtable))) |
5350 | (native-inputs | |
5351 | `(("r-knitr" ,r-knitr))) | |
8e15f861 RW |
5352 | (home-page "https://bioconductor.org/packages/a4Reporting/") |
5353 | (synopsis "Automated Affymetrix array analysis reporting package") | |
5354 | (description | |
5355 | "This is a package for the automated analysis of Affymetrix arrays. It | |
5356 | provides reporting features.") | |
5357 | (license license:gpl3))) | |
dbfe3375 RW |
5358 | |
5359 | (define-public r-a4base | |
5360 | (package | |
5361 | (name "r-a4base") | |
564d4279 | 5362 | (version "1.38.0") |
dbfe3375 RW |
5363 | (source |
5364 | (origin | |
5365 | (method url-fetch) | |
5366 | (uri (bioconductor-uri "a4Base" version)) | |
5367 | (sha256 | |
5368 | (base32 | |
564d4279 | 5369 | "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp")))) |
dbfe3375 RW |
5370 | (properties `((upstream-name . "a4Base"))) |
5371 | (build-system r-build-system) | |
5372 | (propagated-inputs | |
5373 | `(("r-a4core" ,r-a4core) | |
5374 | ("r-a4preproc" ,r-a4preproc) | |
5375 | ("r-annaffy" ,r-annaffy) | |
dbfe3375 RW |
5376 | ("r-biobase" ,r-biobase) |
5377 | ("r-genefilter" ,r-genefilter) | |
5378 | ("r-glmnet" ,r-glmnet) | |
5379 | ("r-gplots" ,r-gplots) | |
5380 | ("r-limma" ,r-limma) | |
5381 | ("r-mpm" ,r-mpm) | |
5382 | ("r-multtest" ,r-multtest))) | |
5383 | (home-page "https://bioconductor.org/packages/a4Base/") | |
5384 | (synopsis "Automated Affymetrix array analysis base package") | |
5385 | (description | |
5386 | "This package provides basic features for the automated analysis of | |
5387 | Affymetrix arrays.") | |
5388 | (license license:gpl3))) | |
84ad024e RW |
5389 | |
5390 | (define-public r-a4 | |
5391 | (package | |
5392 | (name "r-a4") | |
68efaafe | 5393 | (version "1.38.0") |
84ad024e RW |
5394 | (source |
5395 | (origin | |
5396 | (method url-fetch) | |
5397 | (uri (bioconductor-uri "a4" version)) | |
5398 | (sha256 | |
5399 | (base32 | |
68efaafe | 5400 | "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79")))) |
84ad024e RW |
5401 | (build-system r-build-system) |
5402 | (propagated-inputs | |
5403 | `(("r-a4base" ,r-a4base) | |
5404 | ("r-a4classif" ,r-a4classif) | |
5405 | ("r-a4core" ,r-a4core) | |
5406 | ("r-a4preproc" ,r-a4preproc) | |
5407 | ("r-a4reporting" ,r-a4reporting))) | |
5408 | (home-page "https://bioconductor.org/packages/a4/") | |
5409 | (synopsis "Automated Affymetrix array analysis umbrella package") | |
5410 | (description | |
5411 | "This package provides a software suite for the automated analysis of | |
5412 | Affymetrix arrays.") | |
5413 | (license license:gpl3))) | |
59d331f1 RW |
5414 | |
5415 | (define-public r-abseqr | |
5416 | (package | |
5417 | (name "r-abseqr") | |
8816139e | 5418 | (version "1.8.0") |
59d331f1 RW |
5419 | (source |
5420 | (origin | |
5421 | (method url-fetch) | |
5422 | (uri (bioconductor-uri "abseqR" version)) | |
5423 | (sha256 | |
5424 | (base32 | |
8816139e | 5425 | "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f")))) |
59d331f1 RW |
5426 | (properties `((upstream-name . "abseqR"))) |
5427 | (build-system r-build-system) | |
5428 | (inputs | |
8816139e | 5429 | `(("pandoc" ,pandoc))) |
59d331f1 RW |
5430 | (propagated-inputs |
5431 | `(("r-biocparallel" ,r-biocparallel) | |
5432 | ("r-biocstyle" ,r-biocstyle) | |
5433 | ("r-circlize" ,r-circlize) | |
5434 | ("r-flexdashboard" ,r-flexdashboard) | |
5435 | ("r-ggcorrplot" ,r-ggcorrplot) | |
5436 | ("r-ggdendro" ,r-ggdendro) | |
5437 | ("r-ggplot2" ,r-ggplot2) | |
5438 | ("r-gridextra" ,r-gridextra) | |
5439 | ("r-knitr" ,r-knitr) | |
5440 | ("r-plotly" ,r-plotly) | |
5441 | ("r-plyr" ,r-plyr) | |
5442 | ("r-png" ,r-png) | |
5443 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
5444 | ("r-reshape2" ,r-reshape2) | |
5445 | ("r-rmarkdown" ,r-rmarkdown) | |
5446 | ("r-stringr" ,r-stringr) | |
5447 | ("r-vegan" ,r-vegan) | |
5448 | ("r-venndiagram" ,r-venndiagram))) | |
35bcfaef RW |
5449 | (native-inputs |
5450 | `(("r-knitr" ,r-knitr))) | |
59d331f1 RW |
5451 | (home-page "https://github.com/malhamdoosh/abseqR") |
5452 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") | |
5453 | (description | |
5454 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of | |
5455 | sequencing datasets generated from antibody libraries and abseqR is one of its | |
5456 | packages. AbseqR empowers the users of abseqPy with plotting and reporting | |
5457 | capabilities and allows them to generate interactive HTML reports for the | |
5458 | convenience of viewing and sharing with other researchers. Additionally, | |
5459 | abseqR extends abseqPy to compare multiple repertoire analyses and perform | |
5460 | further downstream analysis on its output.") | |
5461 | (license license:gpl3))) | |
41aab7d1 RW |
5462 | |
5463 | (define-public r-bacon | |
5464 | (package | |
5465 | (name "r-bacon") | |
d5dcf1bb | 5466 | (version "1.18.0") |
41aab7d1 RW |
5467 | (source |
5468 | (origin | |
5469 | (method url-fetch) | |
5470 | (uri (bioconductor-uri "bacon" version)) | |
5471 | (sha256 | |
5472 | (base32 | |
d5dcf1bb | 5473 | "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47")))) |
41aab7d1 RW |
5474 | (build-system r-build-system) |
5475 | (propagated-inputs | |
5476 | `(("r-biocparallel" ,r-biocparallel) | |
5477 | ("r-ellipse" ,r-ellipse) | |
5478 | ("r-ggplot2" ,r-ggplot2))) | |
506cbeab RW |
5479 | (native-inputs |
5480 | `(("r-knitr" ,r-knitr))) | |
41aab7d1 RW |
5481 | (home-page "https://bioconductor.org/packages/bacon/") |
5482 | (synopsis "Controlling bias and inflation in association studies") | |
5483 | (description | |
5484 | "Bacon can be used to remove inflation and bias often observed in | |
5485 | epigenome- and transcriptome-wide association studies. To this end bacon | |
5486 | constructs an empirical null distribution using a Gibbs Sampling algorithm by | |
5487 | fitting a three-component normal mixture on z-scores.") | |
5488 | (license license:gpl2+))) | |
051e8e1a RW |
5489 | |
5490 | (define-public r-rgadem | |
5491 | (package | |
5492 | (name "r-rgadem") | |
41071edc | 5493 | (version "2.38.0") |
051e8e1a RW |
5494 | (source |
5495 | (origin | |
5496 | (method url-fetch) | |
5497 | (uri (bioconductor-uri "rGADEM" version)) | |
5498 | (sha256 | |
5499 | (base32 | |
41071edc | 5500 | "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw")))) |
051e8e1a RW |
5501 | (properties `((upstream-name . "rGADEM"))) |
5502 | (build-system r-build-system) | |
5503 | (propagated-inputs | |
5504 | `(("r-biostrings" ,r-biostrings) | |
5505 | ("r-bsgenome" ,r-bsgenome) | |
07189489 | 5506 | ("r-genomicranges" ,r-genomicranges) |
051e8e1a RW |
5507 | ("r-iranges" ,r-iranges) |
5508 | ("r-seqlogo" ,r-seqlogo))) | |
5509 | (home-page "https://bioconductor.org/packages/rGADEM/") | |
5510 | (synopsis "De novo sequence motif discovery") | |
5511 | (description | |
5512 | "rGADEM is an efficient de novo motif discovery tool for large-scale | |
5513 | genomic sequence data.") | |
5514 | (license license:artistic2.0))) | |
229f97c3 RW |
5515 | |
5516 | (define-public r-motiv | |
5517 | (package | |
5518 | (name "r-motiv") | |
352cfa34 | 5519 | (version "1.43.0") |
229f97c3 RW |
5520 | (source |
5521 | (origin | |
5522 | (method url-fetch) | |
5523 | (uri (bioconductor-uri "MotIV" version)) | |
5524 | (sha256 | |
5525 | (base32 | |
352cfa34 | 5526 | "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6")))) |
229f97c3 RW |
5527 | (properties `((upstream-name . "MotIV"))) |
5528 | (build-system r-build-system) | |
5529 | (inputs | |
5530 | `(("gsl" ,gsl))) | |
5531 | (propagated-inputs | |
5532 | `(("r-biocgenerics" ,r-biocgenerics) | |
5533 | ("r-biostrings" ,r-biostrings) | |
35a1b3ec | 5534 | ("r-genomicranges" ,r-genomicranges) |
229f97c3 RW |
5535 | ("r-iranges" ,r-iranges) |
5536 | ("r-lattice" ,r-lattice) | |
5537 | ("r-rgadem" ,r-rgadem) | |
5538 | ("r-s4vectors" ,r-s4vectors))) | |
5539 | (home-page "https://bioconductor.org/packages/MotIV/") | |
5540 | (synopsis "Motif identification and validation") | |
5541 | (description | |
5542 | "This package is used for the identification and validation of sequence | |
5543 | motifs. It makes use of STAMP for comparing a set of motifs to a given | |
5544 | database (e.g. JASPAR). It can also be used to visualize motifs, motif | |
5545 | distributions, modules and filter motifs.") | |
5546 | (license license:gpl2))) | |
2a72ef56 | 5547 | |
3699bcf5 RJ |
5548 | (define-public r-motifdb |
5549 | (package | |
5550 | (name "r-motifdb") | |
a2bae167 | 5551 | (version "1.32.0") |
3699bcf5 RJ |
5552 | (source (origin |
5553 | (method url-fetch) | |
5554 | (uri (bioconductor-uri "MotifDb" version)) | |
5555 | (sha256 | |
a2bae167 | 5556 | (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5")))) |
3699bcf5 RJ |
5557 | (properties `((upstream-name . "MotifDb"))) |
5558 | (build-system r-build-system) | |
5559 | (propagated-inputs | |
5560 | `(("r-biocgenerics" ,r-biocgenerics) | |
5561 | ("r-biostrings" ,r-biostrings) | |
da6a75fe | 5562 | ("r-genomicranges" ,r-genomicranges) |
3699bcf5 RJ |
5563 | ("r-iranges" ,r-iranges) |
5564 | ("r-rtracklayer" ,r-rtracklayer) | |
5565 | ("r-s4vectors" ,r-s4vectors) | |
5566 | ("r-splitstackshape" ,r-splitstackshape))) | |
da6a75fe RW |
5567 | (native-inputs |
5568 | `(("r-knitr" ,r-knitr))) | |
3699bcf5 RJ |
5569 | (home-page "https://www.bioconductor.org/packages/MotifDb/") |
5570 | (synopsis "Annotated collection of protein-DNA binding sequence motifs") | |
5571 | (description "This package provides more than 2000 annotated position | |
5572 | frequency matrices from nine public sources, for multiple organisms.") | |
5573 | (license license:artistic2.0))) | |
5574 | ||
886125d7 RJ |
5575 | (define-public r-motifbreakr |
5576 | (package | |
5577 | (name "r-motifbreakr") | |
301e549c | 5578 | (version "2.4.0") |
886125d7 RJ |
5579 | (source (origin |
5580 | (method url-fetch) | |
5581 | (uri (bioconductor-uri "motifbreakR" version)) | |
5582 | (sha256 | |
301e549c | 5583 | (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7")))) |
886125d7 RJ |
5584 | (properties `((upstream-name . "motifbreakR"))) |
5585 | (build-system r-build-system) | |
5586 | (propagated-inputs | |
e65783e0 RW |
5587 | `(("r-biocgenerics" ,r-biocgenerics) |
5588 | ("r-biocparallel" ,r-biocparallel) | |
886125d7 RJ |
5589 | ("r-biostrings" ,r-biostrings) |
5590 | ("r-bsgenome" ,r-bsgenome) | |
e65783e0 RW |
5591 | ("r-genomeinfodb" ,r-genomeinfodb) |
5592 | ("r-genomicranges" ,r-genomicranges) | |
5593 | ("r-grimport" ,r-grimport) | |
886125d7 | 5594 | ("r-gviz" ,r-gviz) |
e65783e0 | 5595 | ("r-iranges" ,r-iranges) |
886125d7 | 5596 | ("r-matrixstats" ,r-matrixstats) |
e65783e0 RW |
5597 | ("r-motifdb" ,r-motifdb) |
5598 | ("r-motifstack" ,r-motifstack) | |
5599 | ("r-rtracklayer" ,r-rtracklayer) | |
5600 | ("r-s4vectors" ,r-s4vectors) | |
5601 | ("r-stringr" ,r-stringr) | |
5602 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
886125d7 | 5603 | ("r-tfmpvalue" ,r-tfmpvalue) |
e65783e0 RW |
5604 | ("r-variantannotation" ,r-variantannotation))) |
5605 | (native-inputs | |
5606 | `(("r-knitr" ,r-knitr))) | |
886125d7 RJ |
5607 | (home-page "https://www.bioconductor.org/packages/motifbreakR/") |
5608 | (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") | |
5609 | (description "This package allows biologists to judge in the first place | |
5610 | whether the sequence surrounding the polymorphism is a good match, and in | |
5611 | the second place how much information is gained or lost in one allele of | |
5612 | the polymorphism relative to another. This package gives a choice of | |
5613 | algorithms for interrogation of genomes with motifs from public sources: | |
5614 | @enumerate | |
5615 | @item a weighted-sum probability matrix; | |
5616 | @item log-probabilities; | |
5617 | @item weighted by relative entropy. | |
5618 | @end enumerate | |
5619 | ||
5620 | This package can predict effects for novel or previously described variants in | |
5621 | public databases, making it suitable for tasks beyond the scope of its original | |
5622 | design. Lastly, it can be used to interrogate any genome curated within | |
5623 | Bioconductor.") | |
5624 | (license license:gpl2+))) | |
5625 | ||
2a72ef56 RW |
5626 | (define-public r-motifstack |
5627 | (package | |
5628 | (name "r-motifstack") | |
4b4cd2b8 | 5629 | (version "1.34.0") |
2a72ef56 RW |
5630 | (source |
5631 | (origin | |
5632 | (method url-fetch) | |
5633 | (uri (bioconductor-uri "motifStack" version)) | |
5634 | (sha256 | |
5635 | (base32 | |
4b4cd2b8 | 5636 | "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb")))) |
2a72ef56 RW |
5637 | (properties `((upstream-name . "motifStack"))) |
5638 | (build-system r-build-system) | |
5639 | (propagated-inputs | |
5640 | `(("r-ade4" ,r-ade4) | |
5641 | ("r-biostrings" ,r-biostrings) | |
dda936ca | 5642 | ("r-ggplot2" ,r-ggplot2) |
2a72ef56 | 5643 | ("r-htmlwidgets" ,r-htmlwidgets) |
2a72ef56 | 5644 | ("r-xml" ,r-xml))) |
e6fbaf0c RW |
5645 | (native-inputs |
5646 | `(("r-knitr" ,r-knitr))) | |
2a72ef56 RW |
5647 | (home-page "https://bioconductor.org/packages/motifStack/") |
5648 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") | |
5649 | (description | |
5650 | "The motifStack package is designed for graphic representation of | |
5651 | multiple motifs with different similarity scores. It works with both DNA/RNA | |
5652 | sequence motifs and amino acid sequence motifs. In addition, it provides the | |
5653 | flexibility for users to customize the graphic parameters such as the font | |
5654 | type and symbol colors.") | |
5655 | (license license:gpl2+))) | |
e5bff307 RW |
5656 | |
5657 | (define-public r-genomicscores | |
5658 | (package | |
5659 | (name "r-genomicscores") | |
39280618 | 5660 | (version "2.2.0") |
e5bff307 RW |
5661 | (source |
5662 | (origin | |
5663 | (method url-fetch) | |
5664 | (uri (bioconductor-uri "GenomicScores" version)) | |
5665 | (sha256 | |
5666 | (base32 | |
39280618 | 5667 | "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr")))) |
e5bff307 RW |
5668 | (properties `((upstream-name . "GenomicScores"))) |
5669 | (build-system r-build-system) | |
5670 | (propagated-inputs | |
5671 | `(("r-annotationhub" ,r-annotationhub) | |
5672 | ("r-biobase" ,r-biobase) | |
39280618 | 5673 | ("r-biocfilecache" ,r-biocfilecache) |
e5bff307 | 5674 | ("r-biocgenerics" ,r-biocgenerics) |
39280618 | 5675 | ("r-biocmanager" ,r-biocmanager) |
e5bff307 | 5676 | ("r-biostrings" ,r-biostrings) |
785c7596 | 5677 | ("r-delayedarray" ,r-delayedarray) |
e5bff307 RW |
5678 | ("r-genomeinfodb" ,r-genomeinfodb) |
5679 | ("r-genomicranges" ,r-genomicranges) | |
785c7596 | 5680 | ("r-hdf5array" ,r-hdf5array) |
e5bff307 | 5681 | ("r-iranges" ,r-iranges) |
785c7596 | 5682 | ("r-rhdf5" ,r-rhdf5) |
e5bff307 RW |
5683 | ("r-s4vectors" ,r-s4vectors) |
5684 | ("r-xml" ,r-xml))) | |
785c7596 RW |
5685 | (native-inputs |
5686 | `(("r-knitr" ,r-knitr))) | |
e5bff307 RW |
5687 | (home-page "https://github.com/rcastelo/GenomicScores/") |
5688 | (synopsis "Work with genome-wide position-specific scores") | |
5689 | (description | |
5690 | "This package provides infrastructure to store and access genome-wide | |
5691 | position-specific scores within R and Bioconductor.") | |
5692 | (license license:artistic2.0))) | |
32e0f906 RW |
5693 | |
5694 | (define-public r-atacseqqc | |
5695 | (package | |
5696 | (name "r-atacseqqc") | |
2ba61c67 | 5697 | (version "1.14.4") |
32e0f906 RW |
5698 | (source |
5699 | (origin | |
5700 | (method url-fetch) | |
5701 | (uri (bioconductor-uri "ATACseqQC" version)) | |
5702 | (sha256 | |
5703 | (base32 | |
2ba61c67 | 5704 | "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9")))) |
32e0f906 RW |
5705 | (properties `((upstream-name . "ATACseqQC"))) |
5706 | (build-system r-build-system) | |
5707 | (propagated-inputs | |
5708 | `(("r-biocgenerics" ,r-biocgenerics) | |
5709 | ("r-biostrings" ,r-biostrings) | |
5710 | ("r-bsgenome" ,r-bsgenome) | |
5711 | ("r-chippeakanno" ,r-chippeakanno) | |
bcc233c1 | 5712 | ("r-edger" ,r-edger) |
32e0f906 RW |
5713 | ("r-genomeinfodb" ,r-genomeinfodb) |
5714 | ("r-genomicalignments" ,r-genomicalignments) | |
5715 | ("r-genomicranges" ,r-genomicranges) | |
5716 | ("r-genomicscores" ,r-genomicscores) | |
5717 | ("r-iranges" ,r-iranges) | |
5718 | ("r-kernsmooth" ,r-kernsmooth) | |
5719 | ("r-limma" ,r-limma) | |
5720 | ("r-motifstack" ,r-motifstack) | |
5721 | ("r-preseqr" ,r-preseqr) | |
5722 | ("r-randomforest" ,r-randomforest) | |
5723 | ("r-rsamtools" ,r-rsamtools) | |
5724 | ("r-rtracklayer" ,r-rtracklayer) | |
5725 | ("r-s4vectors" ,r-s4vectors))) | |
dc30cc03 RW |
5726 | (native-inputs |
5727 | `(("r-knitr" ,r-knitr))) | |
32e0f906 RW |
5728 | (home-page "https://bioconductor.org/packages/ATACseqQC/") |
5729 | (synopsis "ATAC-seq quality control") | |
5730 | (description | |
5731 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using | |
5732 | sequencing, is a rapid and sensitive method for chromatin accessibility | |
5733 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq | |
5734 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly | |
5735 | assess whether their ATAC-seq experiment is successful. It includes | |
5736 | diagnostic plots of fragment size distribution, proportion of mitochondria | |
5737 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor | |
5738 | footprints.") | |
5739 | (license license:gpl2+))) | |
3972cfce RW |
5740 | |
5741 | (define-public r-gofuncr | |
5742 | (package | |
5743 | (name "r-gofuncr") | |
c3b69d63 | 5744 | (version "1.10.0") |
3972cfce RW |
5745 | (source |
5746 | (origin | |
5747 | (method url-fetch) | |
5748 | (uri (bioconductor-uri "GOfuncR" version)) | |
5749 | (sha256 | |
5750 | (base32 | |
c3b69d63 | 5751 | "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq")))) |
3972cfce RW |
5752 | (properties `((upstream-name . "GOfuncR"))) |
5753 | (build-system r-build-system) | |
5754 | (propagated-inputs | |
5755 | `(("r-annotationdbi" ,r-annotationdbi) | |
5756 | ("r-genomicranges" ,r-genomicranges) | |
5757 | ("r-gtools" ,r-gtools) | |
5758 | ("r-iranges" ,r-iranges) | |
5759 | ("r-mapplots" ,r-mapplots) | |
5760 | ("r-rcpp" ,r-rcpp) | |
5761 | ("r-vioplot" ,r-vioplot))) | |
028fd6f7 RW |
5762 | (native-inputs |
5763 | `(("r-knitr" ,r-knitr))) | |
3972cfce RW |
5764 | (home-page "https://bioconductor.org/packages/GOfuncR/") |
5765 | (synopsis "Gene ontology enrichment using FUNC") | |
5766 | (description | |
5767 | "GOfuncR performs a gene ontology enrichment analysis based on the | |
5768 | ontology enrichment software FUNC. GO-annotations are obtained from | |
5769 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is | |
5770 | included in the package and updated regularly. GOfuncR provides the standard | |
5771 | candidate vs background enrichment analysis using the hypergeometric test, as | |
5772 | well as three additional tests: | |
5773 | ||
5774 | @enumerate | |
5775 | @item the Wilcoxon rank-sum test that is used when genes are ranked, | |
5776 | @item a binomial test that is used when genes are associated with two counts, | |
5777 | and | |
5778 | @item a Chi-square or Fisher's exact test that is used in cases when genes are | |
5779 | associated with four counts. | |
5780 | @end enumerate | |
5781 | ||
5782 | To correct for multiple testing and interdependency of the tests, family-wise | |
5783 | error rates are computed based on random permutations of the gene-associated | |
5784 | variables. GOfuncR also provides tools for exploring the ontology graph and | |
5785 | the annotations, and options to take gene-length or spatial clustering of | |
5786 | genes into account. It is also possible to provide custom gene coordinates, | |
5787 | annotations and ontologies.") | |
5788 | (license license:gpl2+))) | |
9bf4bb19 RW |
5789 | |
5790 | (define-public r-abaenrichment | |
5791 | (package | |
5792 | (name "r-abaenrichment") | |
8a7f7112 | 5793 | (version "1.20.0") |
9bf4bb19 RW |
5794 | (source |
5795 | (origin | |
5796 | (method url-fetch) | |
5797 | (uri (bioconductor-uri "ABAEnrichment" version)) | |
5798 | (sha256 | |
5799 | (base32 | |
8a7f7112 | 5800 | "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c")))) |
9bf4bb19 RW |
5801 | (properties `((upstream-name . "ABAEnrichment"))) |
5802 | (build-system r-build-system) | |
5803 | (propagated-inputs | |
5804 | `(("r-abadata" ,r-abadata) | |
5805 | ("r-data-table" ,r-data-table) | |
5806 | ("r-gofuncr" ,r-gofuncr) | |
5807 | ("r-gplots" ,r-gplots) | |
5808 | ("r-gtools" ,r-gtools) | |
5809 | ("r-rcpp" ,r-rcpp))) | |
6a65ac15 RW |
5810 | (native-inputs |
5811 | `(("r-knitr" ,r-knitr))) | |
9bf4bb19 RW |
5812 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") |
5813 | (synopsis "Gene expression enrichment in human brain regions") | |
5814 | (description | |
5815 | "The package ABAEnrichment is designed to test for enrichment of user | |
5816 | defined candidate genes in the set of expressed genes in different human brain | |
5817 | regions. The core function @code{aba_enrich} integrates the expression of the | |
5818 | candidate gene set (averaged across donors) and the structural information of | |
5819 | the brain using an ontology, both provided by the Allen Brain Atlas project.") | |
5820 | (license license:gpl2+))) | |
0b91b7b9 RW |
5821 | |
5822 | (define-public r-annotationfuncs | |
5823 | (package | |
5824 | (name "r-annotationfuncs") | |
bc12a4b6 | 5825 | (version "1.40.0") |
0b91b7b9 RW |
5826 | (source |
5827 | (origin | |
5828 | (method url-fetch) | |
5829 | (uri (bioconductor-uri "AnnotationFuncs" version)) | |
5830 | (sha256 | |
5831 | (base32 | |
bc12a4b6 | 5832 | "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr")))) |
0b91b7b9 RW |
5833 | (properties |
5834 | `((upstream-name . "AnnotationFuncs"))) | |
5835 | (build-system r-build-system) | |
5836 | (propagated-inputs | |
5837 | `(("r-annotationdbi" ,r-annotationdbi) | |
5838 | ("r-dbi" ,r-dbi))) | |
5839 | (home-page "https://www.iysik.com/r/annotationfuncs") | |
5840 | (synopsis "Annotation translation functions") | |
5841 | (description | |
5842 | "This package provides functions for handling translating between | |
5843 | different identifieres using the Biocore Data Team data-packages (e.g. | |
5844 | @code{org.Bt.eg.db}).") | |
5845 | (license license:gpl2))) | |
adf7d813 RW |
5846 | |
5847 | (define-public r-annotationtools | |
5848 | (package | |
5849 | (name "r-annotationtools") | |
57791542 | 5850 | (version "1.64.0") |
adf7d813 RW |
5851 | (source |
5852 | (origin | |
5853 | (method url-fetch) | |
5854 | (uri (bioconductor-uri "annotationTools" version)) | |
5855 | (sha256 | |
5856 | (base32 | |
57791542 | 5857 | "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224")))) |
adf7d813 RW |
5858 | (properties |
5859 | `((upstream-name . "annotationTools"))) | |
5860 | (build-system r-build-system) | |
5861 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
5862 | (home-page "https://bioconductor.org/packages/annotationTools/") | |
5863 | (synopsis "Annotate microarrays and perform gene expression analyses") | |
5864 | (description | |
5865 | "This package provides functions to annotate microarrays, find orthologs, | |
5866 | and integrate heterogeneous gene expression profiles using annotation and | |
5867 | other molecular biology information available as flat file database (plain | |
5868 | text files).") | |
5869 | ;; Any version of the GPL. | |
5870 | (license (list license:gpl2+)))) | |
f31e10f8 RW |
5871 | |
5872 | (define-public r-allelicimbalance | |
5873 | (package | |
5874 | (name "r-allelicimbalance") | |
85c6636b | 5875 | (version "1.28.0") |
f31e10f8 RW |
5876 | (source |
5877 | (origin | |
5878 | (method url-fetch) | |
5879 | (uri (bioconductor-uri "AllelicImbalance" version)) | |
5880 | (sha256 | |
5881 | (base32 | |
85c6636b | 5882 | "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl")))) |
f31e10f8 RW |
5883 | (properties |
5884 | `((upstream-name . "AllelicImbalance"))) | |
5885 | (build-system r-build-system) | |
5886 | (propagated-inputs | |
5887 | `(("r-annotationdbi" ,r-annotationdbi) | |
5888 | ("r-biocgenerics" ,r-biocgenerics) | |
5889 | ("r-biostrings" ,r-biostrings) | |
5890 | ("r-bsgenome" ,r-bsgenome) | |
5891 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5892 | ("r-genomicalignments" ,r-genomicalignments) | |
5893 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5894 | ("r-genomicranges" ,r-genomicranges) | |
5895 | ("r-gridextra" ,r-gridextra) | |
5896 | ("r-gviz" ,r-gviz) | |
5897 | ("r-iranges" ,r-iranges) | |
5898 | ("r-lattice" ,r-lattice) | |
5899 | ("r-latticeextra" ,r-latticeextra) | |
5900 | ("r-nlme" ,r-nlme) | |
5901 | ("r-rsamtools" ,r-rsamtools) | |
5902 | ("r-s4vectors" ,r-s4vectors) | |
5903 | ("r-seqinr" ,r-seqinr) | |
5904 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
5905 | ("r-variantannotation" ,r-variantannotation))) | |
63149388 RW |
5906 | (native-inputs |
5907 | `(("r-knitr" ,r-knitr))) | |
f31e10f8 RW |
5908 | (home-page "https://github.com/pappewaio/AllelicImbalance") |
5909 | (synopsis "Investigate allele-specific expression") | |
5910 | (description | |
5911 | "This package provides a framework for allele-specific expression | |
5912 | investigation using RNA-seq data.") | |
5913 | (license license:gpl3))) | |
ffe7029b RW |
5914 | |
5915 | (define-public r-aucell | |
5916 | (package | |
5917 | (name "r-aucell") | |
ff8b9153 | 5918 | (version "1.12.0") |
ffe7029b RW |
5919 | (source |
5920 | (origin | |
5921 | (method url-fetch) | |
5922 | (uri (bioconductor-uri "AUCell" version)) | |
5923 | (sha256 | |
5924 | (base32 | |
ff8b9153 | 5925 | "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx")))) |
ffe7029b RW |
5926 | (properties `((upstream-name . "AUCell"))) |
5927 | (build-system r-build-system) | |
5928 | (propagated-inputs | |
3a35d274 RW |
5929 | `(("r-biocgenerics" ,r-biocgenerics) |
5930 | ("r-data-table" ,r-data-table) | |
ffe7029b RW |
5931 | ("r-gseabase" ,r-gseabase) |
5932 | ("r-mixtools" ,r-mixtools) | |
5933 | ("r-r-utils" ,r-r-utils) | |
3a35d274 | 5934 | ("r-s4vectors" ,r-s4vectors) |
ffe7029b RW |
5935 | ("r-shiny" ,r-shiny) |
5936 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
e059ab25 RW |
5937 | (native-inputs |
5938 | `(("r-knitr" ,r-knitr))) | |
ffe7029b RW |
5939 | (home-page "https://bioconductor.org/packages/AUCell/") |
5940 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") | |
5941 | (description | |
8c4bf6c2 | 5942 | "AUCell identifies cells with active gene sets (e.g. signatures, |
ffe7029b RW |
5943 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area |
5944 | Under the Curve} (AUC) to calculate whether a critical subset of the input | |
5945 | gene set is enriched within the expressed genes for each cell. The | |
5946 | distribution of AUC scores across all the cells allows exploring the relative | |
5947 | expression of the signature. Since the scoring method is ranking-based, | |
5948 | AUCell is independent of the gene expression units and the normalization | |
5949 | procedure. In addition, since the cells are evaluated individually, it can | |
5950 | easily be applied to bigger datasets, subsetting the expression matrix if | |
5951 | needed.") | |
5952 | (license license:gpl3))) | |
5cfa4bff RW |
5953 | |
5954 | (define-public r-ebimage | |
5955 | (package | |
5956 | (name "r-ebimage") | |
ba0bf98d | 5957 | (version "4.32.0") |
5cfa4bff RW |
5958 | (source |
5959 | (origin | |
5960 | (method url-fetch) | |
5961 | (uri (bioconductor-uri "EBImage" version)) | |
5962 | (sha256 | |
5963 | (base32 | |
ba0bf98d | 5964 | "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww")))) |
5cfa4bff RW |
5965 | (properties `((upstream-name . "EBImage"))) |
5966 | (build-system r-build-system) | |
5967 | (propagated-inputs | |
5968 | `(("r-abind" ,r-abind) | |
5969 | ("r-biocgenerics" ,r-biocgenerics) | |
5970 | ("r-fftwtools" ,r-fftwtools) | |
5971 | ("r-htmltools" ,r-htmltools) | |
5972 | ("r-htmlwidgets" ,r-htmlwidgets) | |
5973 | ("r-jpeg" ,r-jpeg) | |
5974 | ("r-locfit" ,r-locfit) | |
5975 | ("r-png" ,r-png) | |
5976 | ("r-rcurl" ,r-rcurl) | |
5977 | ("r-tiff" ,r-tiff))) | |
5978 | (native-inputs | |
5979 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
5980 | (home-page "https://github.com/aoles/EBImage") | |
5981 | (synopsis "Image processing and analysis toolbox for R") | |
5982 | (description | |
5983 | "EBImage provides general purpose functionality for image processing and | |
5984 | analysis. In the context of (high-throughput) microscopy-based cellular | |
5985 | assays, EBImage offers tools to segment cells and extract quantitative | |
5986 | cellular descriptors. This allows the automation of such tasks using the R | |
5987 | programming language and facilitates the use of other tools in the R | |
5988 | environment for signal processing, statistical modeling, machine learning and | |
5989 | visualization with image data.") | |
5990 | ;; Any version of the LGPL. | |
5991 | (license license:lgpl2.1+))) | |
51e98f7e RW |
5992 | |
5993 | (define-public r-yamss | |
5994 | (package | |
5995 | (name "r-yamss") | |
65ba4ba5 | 5996 | (version "1.16.0") |
51e98f7e RW |
5997 | (source |
5998 | (origin | |
5999 | (method url-fetch) | |
6000 | (uri (bioconductor-uri "yamss" version)) | |
6001 | (sha256 | |
6002 | (base32 | |
65ba4ba5 | 6003 | "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w")))) |
51e98f7e RW |
6004 | (build-system r-build-system) |
6005 | (propagated-inputs | |
6006 | `(("r-biocgenerics" ,r-biocgenerics) | |
6007 | ("r-data-table" ,r-data-table) | |
6008 | ("r-ebimage" ,r-ebimage) | |
6009 | ("r-iranges" ,r-iranges) | |
6010 | ("r-limma" ,r-limma) | |
6011 | ("r-matrix" ,r-matrix) | |
6012 | ("r-mzr" ,r-mzr) | |
6013 | ("r-s4vectors" ,r-s4vectors) | |
6014 | ("r-summarizedexperiment" | |
6015 | ,r-summarizedexperiment))) | |
6e397aad RW |
6016 | (native-inputs |
6017 | `(("r-knitr" ,r-knitr))) | |
51e98f7e RW |
6018 | (home-page "https://github.com/hansenlab/yamss") |
6019 | (synopsis "Tools for high-throughput metabolomics") | |
6020 | (description | |
6021 | "This package provides tools to analyze and visualize high-throughput | |
9b19734c | 6022 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
51e98f7e RW |
6023 | preprocess data in a way that enables reliable and powerful differential |
6024 | analysis.") | |
6025 | (license license:artistic2.0))) | |
398c4a93 RW |
6026 | |
6027 | (define-public r-gtrellis | |
6028 | (package | |
6029 | (name "r-gtrellis") | |
0836ef6b | 6030 | (version "1.22.0") |
398c4a93 RW |
6031 | (source |
6032 | (origin | |
6033 | (method url-fetch) | |
6034 | (uri (bioconductor-uri "gtrellis" version)) | |
6035 | (sha256 | |
6036 | (base32 | |
0836ef6b | 6037 | "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw")))) |
398c4a93 RW |
6038 | (build-system r-build-system) |
6039 | (propagated-inputs | |
6040 | `(("r-circlize" ,r-circlize) | |
6041 | ("r-genomicranges" ,r-genomicranges) | |
6042 | ("r-getoptlong" ,r-getoptlong) | |
6043 | ("r-iranges" ,r-iranges))) | |
a471def0 RW |
6044 | (native-inputs |
6045 | `(("r-knitr" ,r-knitr))) | |
398c4a93 RW |
6046 | (home-page "https://github.com/jokergoo/gtrellis") |
6047 | (synopsis "Genome level Trellis layout") | |
6048 | (description | |
6049 | "Genome level Trellis graph visualizes genomic data conditioned by | |
6050 | genomic categories (e.g. chromosomes). For each genomic category, multiple | |
6051 | dimensional data which are represented as tracks describe different features | |
6052 | from different aspects. This package provides high flexibility to arrange | |
6053 | genomic categories and to add self-defined graphics in the plot.") | |
6054 | (license license:expat))) | |
28098414 RW |
6055 | |
6056 | (define-public r-somaticsignatures | |
6057 | (package | |
6058 | (name "r-somaticsignatures") | |
36f3a19a | 6059 | (version "2.26.0") |
28098414 RW |
6060 | (source |
6061 | (origin | |
6062 | (method url-fetch) | |
6063 | (uri (bioconductor-uri "SomaticSignatures" version)) | |
6064 | (sha256 | |
6065 | (base32 | |
36f3a19a | 6066 | "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801")))) |
28098414 RW |
6067 | (properties |
6068 | `((upstream-name . "SomaticSignatures"))) | |
6069 | (build-system r-build-system) | |
6070 | (propagated-inputs | |
6071 | `(("r-biobase" ,r-biobase) | |
6072 | ("r-biostrings" ,r-biostrings) | |
6073 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6074 | ("r-genomicranges" ,r-genomicranges) | |
6075 | ("r-ggbio" ,r-ggbio) | |
6076 | ("r-ggplot2" ,r-ggplot2) | |
6077 | ("r-iranges" ,r-iranges) | |
6078 | ("r-nmf" ,r-nmf) | |
6079 | ("r-pcamethods" ,r-pcamethods) | |
6080 | ("r-proxy" ,r-proxy) | |
6081 | ("r-reshape2" ,r-reshape2) | |
6082 | ("r-s4vectors" ,r-s4vectors) | |
6083 | ("r-variantannotation" ,r-variantannotation))) | |
63c14717 RW |
6084 | (native-inputs |
6085 | `(("r-knitr" ,r-knitr))) | |
28098414 RW |
6086 | (home-page "https://github.com/juliangehring/SomaticSignatures") |
6087 | (synopsis "Somatic signatures") | |
6088 | (description | |
6089 | "This package identifies mutational signatures of @dfn{single nucleotide | |
6090 | variants} (SNVs). It provides a infrastructure related to the methodology | |
6091 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix | |
6092 | decomposition algorithms.") | |
6093 | (license license:expat))) | |
303f2ed1 RW |
6094 | |
6095 | (define-public r-yapsa | |
6096 | (package | |
6097 | (name "r-yapsa") | |
d0db04fc | 6098 | (version "1.16.0") |
303f2ed1 RW |
6099 | (source |
6100 | (origin | |
6101 | (method url-fetch) | |
6102 | (uri (bioconductor-uri "YAPSA" version)) | |
6103 | (sha256 | |
6104 | (base32 | |
d0db04fc | 6105 | "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb")))) |
303f2ed1 RW |
6106 | (properties `((upstream-name . "YAPSA"))) |
6107 | (build-system r-build-system) | |
6108 | (propagated-inputs | |
8a5abc62 RW |
6109 | `(("r-biostrings" ,r-biostrings) |
6110 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
6111 | ("r-circlize" ,r-circlize) | |
303f2ed1 RW |
6112 | ("r-complexheatmap" ,r-complexheatmap) |
6113 | ("r-corrplot" ,r-corrplot) | |
6114 | ("r-dendextend" ,r-dendextend) | |
8a5abc62 RW |
6115 | ("r-doparallel" ,r-doparallel) |
6116 | ("r-dplyr" ,r-dplyr) | |
303f2ed1 RW |
6117 | ("r-genomeinfodb" ,r-genomeinfodb) |
6118 | ("r-genomicranges" ,r-genomicranges) | |
6119 | ("r-getoptlong" ,r-getoptlong) | |
8a5abc62 | 6120 | ("r-ggbeeswarm" ,r-ggbeeswarm) |
303f2ed1 RW |
6121 | ("r-ggplot2" ,r-ggplot2) |
6122 | ("r-gridextra" ,r-gridextra) | |
6123 | ("r-gtrellis" ,r-gtrellis) | |
6124 | ("r-keggrest" ,r-keggrest) | |
d0db04fc | 6125 | ("r-limsolve" ,r-limsolve) |
8a5abc62 | 6126 | ("r-magrittr" ,r-magrittr) |
303f2ed1 | 6127 | ("r-pmcmr" ,r-pmcmr) |
8a5abc62 | 6128 | ("r-pracma" ,r-pracma) |
303f2ed1 RW |
6129 | ("r-reshape2" ,r-reshape2) |
6130 | ("r-somaticsignatures" ,r-somaticsignatures) | |
6131 | ("r-variantannotation" ,r-variantannotation))) | |
8a5abc62 RW |
6132 | (native-inputs |
6133 | `(("r-knitr" ,r-knitr))) | |
303f2ed1 RW |
6134 | (home-page "https://bioconductor.org/packages/YAPSA/") |
6135 | (synopsis "Yet another package for signature analysis") | |
6136 | (description | |
6137 | "This package provides functions and routines useful in the analysis of | |
6138 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, | |
6139 | functions to perform a signature analysis with known signatures and a | |
6140 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are | |
6141 | provided.") | |
6142 | (license license:gpl3))) | |
e99380d6 RW |
6143 | |
6144 | (define-public r-gcrma | |
6145 | (package | |
6146 | (name "r-gcrma") | |
3d41f0c2 | 6147 | (version "2.62.0") |
e99380d6 RW |
6148 | (source |
6149 | (origin | |
6150 | (method url-fetch) | |
6151 | (uri (bioconductor-uri "gcrma" version)) | |
6152 | (sha256 | |
6153 | (base32 | |
3d41f0c2 | 6154 | "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00")))) |
e99380d6 RW |
6155 | (build-system r-build-system) |
6156 | (propagated-inputs | |
6157 | `(("r-affy" ,r-affy) | |
6158 | ("r-affyio" ,r-affyio) | |
6159 | ("r-biobase" ,r-biobase) | |
6160 | ("r-biocmanager" ,r-biocmanager) | |
6161 | ("r-biostrings" ,r-biostrings) | |
6162 | ("r-xvector" ,r-xvector))) | |
6163 | (home-page "https://bioconductor.org/packages/gcrma/") | |
6164 | (synopsis "Background adjustment using sequence information") | |
6165 | (description | |
6166 | "Gcrma adjusts for background intensities in Affymetrix array data which | |
6167 | include optical noise and @dfn{non-specific binding} (NSB). The main function | |
6168 | @code{gcrma} converts background adjusted probe intensities to expression | |
6169 | measures using the same normalization and summarization methods as a | |
6170 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information | |
6171 | to estimate probe affinity to NSB. The sequence information is summarized in | |
6172 | a more complex way than the simple GC content. Instead, the base types (A, T, | |
6173 | G or C) at each position along the probe determine the affinity of each probe. | |
6174 | The parameters of the position-specific base contributions to the probe | |
6175 | affinity is estimated in an NSB experiment in which only NSB but no | |
7230f6d5 | 6176 | gene-specific binding is expected.") |
e99380d6 RW |
6177 | ;; Any version of the LGPL |
6178 | (license license:lgpl2.1+))) | |
4675b3cf RW |
6179 | |
6180 | (define-public r-simpleaffy | |
6181 | (package | |
6182 | (name "r-simpleaffy") | |
48aaef23 | 6183 | (version "2.66.0") |
4675b3cf RW |
6184 | (source |
6185 | (origin | |
6186 | (method url-fetch) | |
6187 | (uri (bioconductor-uri "simpleaffy" version)) | |
6188 | (sha256 | |
6189 | (base32 | |
48aaef23 | 6190 | "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb")))) |
4675b3cf RW |
6191 | (build-system r-build-system) |
6192 | (propagated-inputs | |
6193 | `(("r-affy" ,r-affy) | |
6194 | ("r-biobase" ,r-biobase) | |
6195 | ("r-biocgenerics" ,r-biocgenerics) | |
6196 | ("r-gcrma" ,r-gcrma) | |
6197 | ("r-genefilter" ,r-genefilter))) | |
6198 | (home-page "https://bioconductor.org/packages/simpleaffy/") | |
6199 | (synopsis "Very simple high level analysis of Affymetrix data") | |
6200 | (description | |
6201 | "This package provides high level functions for reading Affy @file{.CEL} | |
6202 | files, phenotypic data, and then computing simple things with it, such as | |
6203 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} | |
6204 | library. It also has some basic scatter plot functions and mechanisms for | |
6205 | generating high resolution journal figures.") | |
6206 | (license license:gpl2+))) | |
f562c90a RW |
6207 | |
6208 | (define-public r-yaqcaffy | |
6209 | (package | |
6210 | (name "r-yaqcaffy") | |
94dee0af | 6211 | (version "1.50.0") |
f562c90a RW |
6212 | (source |
6213 | (origin | |
6214 | (method url-fetch) | |
6215 | (uri (bioconductor-uri "yaqcaffy" version)) | |
6216 | (sha256 | |
6217 | (base32 | |
94dee0af | 6218 | "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96")))) |
f562c90a RW |
6219 | (build-system r-build-system) |
6220 | (propagated-inputs | |
6221 | `(("r-simpleaffy" ,r-simpleaffy))) | |
6222 | (home-page "https://bioconductor.org/packages/yaqcaffy/") | |
6223 | (synopsis "Affymetrix quality control and reproducibility analysis") | |
6224 | (description | |
6225 | "This is a package that can be used for quality control of Affymetrix | |
6226 | GeneChip expression data and reproducibility analysis of human whole genome | |
6227 | chips with the MAQC reference datasets.") | |
6228 | (license license:artistic2.0))) | |
59cf2629 RW |
6229 | |
6230 | (define-public r-quantro | |
6231 | (package | |
6232 | (name "r-quantro") | |
adf6edc7 | 6233 | (version "1.24.0") |
59cf2629 RW |
6234 | (source |
6235 | (origin | |
6236 | (method url-fetch) | |
6237 | (uri (bioconductor-uri "quantro" version)) | |
6238 | (sha256 | |
6239 | (base32 | |
adf6edc7 | 6240 | "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2")))) |
59cf2629 RW |
6241 | (build-system r-build-system) |
6242 | (propagated-inputs | |
6243 | `(("r-biobase" ,r-biobase) | |
6244 | ("r-doparallel" ,r-doparallel) | |
6245 | ("r-foreach" ,r-foreach) | |
6246 | ("r-ggplot2" ,r-ggplot2) | |
6247 | ("r-iterators" ,r-iterators) | |
6248 | ("r-minfi" ,r-minfi) | |
6249 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
70d90ae7 RW |
6250 | (native-inputs |
6251 | `(("r-knitr" ,r-knitr))) | |
59cf2629 RW |
6252 | (home-page "https://bioconductor.org/packages/quantro/") |
6253 | (synopsis "Test for when to use quantile normalization") | |
6254 | (description | |
6255 | "This package provides a data-driven test for the assumptions of quantile | |
6256 | normalization using raw data such as objects that inherit eSets (e.g. | |
6257 | ExpressionSet, MethylSet). Group level information about each sample (such as | |
6258 | Tumor / Normal status) must also be provided because the test assesses if | |
6259 | there are global differences in the distributions between the user-defined | |
6260 | groups.") | |
6261 | (license license:gpl3+))) | |
98a2af31 RW |
6262 | |
6263 | (define-public r-yarn | |
6264 | (package | |
6265 | (name "r-yarn") | |
8db36c1f | 6266 | (version "1.16.0") |
98a2af31 RW |
6267 | (source |
6268 | (origin | |
6269 | (method url-fetch) | |
6270 | (uri (bioconductor-uri "yarn" version)) | |
6271 | (sha256 | |
6272 | (base32 | |
8db36c1f | 6273 | "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp")))) |
98a2af31 RW |
6274 | (build-system r-build-system) |
6275 | (propagated-inputs | |
6276 | `(("r-biobase" ,r-biobase) | |
6277 | ("r-biomart" ,r-biomart) | |
6278 | ("r-downloader" ,r-downloader) | |
6279 | ("r-edger" ,r-edger) | |
6280 | ("r-gplots" ,r-gplots) | |
6281 | ("r-limma" ,r-limma) | |
6282 | ("r-matrixstats" ,r-matrixstats) | |
6283 | ("r-preprocesscore" ,r-preprocesscore) | |
6284 | ("r-quantro" ,r-quantro) | |
6285 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6286 | ("r-readr" ,r-readr))) | |
a37a6ffb RW |
6287 | (native-inputs |
6288 | `(("r-knitr" ,r-knitr))) | |
98a2af31 RW |
6289 | (home-page "https://bioconductor.org/packages/yarn/") |
6290 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") | |
6291 | (description | |
6292 | "Expedite large RNA-Seq analyses using a combination of previously | |
6293 | developed tools. YARN is meant to make it easier for the user in performing | |
6294 | basic mis-annotation quality control, filtering, and condition-aware | |
6295 | normalization. YARN leverages many Bioconductor tools and statistical | |
6296 | techniques to account for the large heterogeneity and sparsity found in very | |
6297 | large RNA-seq experiments.") | |
6298 | (license license:artistic2.0))) | |
a6e1eb1a RW |
6299 | |
6300 | (define-public r-roar | |
6301 | (package | |
6302 | (name "r-roar") | |
72476ade | 6303 | (version "1.26.0") |
a6e1eb1a RW |
6304 | (source |
6305 | (origin | |
6306 | (method url-fetch) | |
6307 | (uri (bioconductor-uri "roar" version)) | |
6308 | (sha256 | |
6309 | (base32 | |
72476ade | 6310 | "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw")))) |
a6e1eb1a RW |
6311 | (build-system r-build-system) |
6312 | (propagated-inputs | |
6313 | `(("r-biocgenerics" ,r-biocgenerics) | |
6314 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6315 | ("r-genomicalignments" ,r-genomicalignments) | |
6316 | ("r-genomicranges" ,r-genomicranges) | |
6317 | ("r-iranges" ,r-iranges) | |
6318 | ("r-rtracklayer" ,r-rtracklayer) | |
6319 | ("r-s4vectors" ,r-s4vectors) | |
6320 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
6321 | (home-page "https://github.com/vodkatad/roar/") | |
6322 | (synopsis "Identify differential APA usage from RNA-seq alignments") | |
6323 | (description | |
6324 | "This package provides tools for identifying preferential usage of APA | |
6325 | sites, comparing two biological conditions, starting from known alternative | |
6326 | sites and alignments obtained from standard RNA-seq experiments.") | |
6327 | (license license:gpl3))) | |
50d91770 RW |
6328 | |
6329 | (define-public r-xbseq | |
6330 | (package | |
6331 | (name "r-xbseq") | |
7f71341e | 6332 | (version "1.22.0") |
50d91770 RW |
6333 | (source |
6334 | (origin | |
6335 | (method url-fetch) | |
6336 | (uri (bioconductor-uri "XBSeq" version)) | |
6337 | (sha256 | |
6338 | (base32 | |
7f71341e | 6339 | "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz")))) |
50d91770 RW |
6340 | (properties `((upstream-name . "XBSeq"))) |
6341 | (build-system r-build-system) | |
6342 | (propagated-inputs | |
6343 | `(("r-biobase" ,r-biobase) | |
6344 | ("r-deseq2" ,r-deseq2) | |
6345 | ("r-dplyr" ,r-dplyr) | |
6346 | ("r-ggplot2" ,r-ggplot2) | |
6347 | ("r-locfit" ,r-locfit) | |
6348 | ("r-magrittr" ,r-magrittr) | |
6349 | ("r-matrixstats" ,r-matrixstats) | |
6350 | ("r-pracma" ,r-pracma) | |
6351 | ("r-roar" ,r-roar))) | |
bcd06bdb RW |
6352 | (native-inputs |
6353 | `(("r-knitr" ,r-knitr))) | |
50d91770 RW |
6354 | (home-page "https://github.com/Liuy12/XBSeq") |
6355 | (synopsis "Test for differential expression for RNA-seq data") | |
6356 | (description | |
6357 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential | |
6358 | expression} (DE), where a statistical model was established based on the | |
6359 | assumption that observed signals are the convolution of true expression | |
6360 | signals and sequencing noises. The mapped reads in non-exonic regions are | |
6361 | considered as sequencing noises, which follows a Poisson distribution. Given | |
6362 | measurable observed signal and background noise from RNA-seq data, true | |
6363 | expression signals, assuming governed by the negative binomial distribution, | |
6364 | can be delineated and thus the accurate detection of differential expressed | |
6365 | genes.") | |
6366 | (license license:gpl3+))) | |
c8310056 RW |
6367 | |
6368 | (define-public r-massspecwavelet | |
6369 | (package | |
6370 | (name "r-massspecwavelet") | |
f4e19e62 | 6371 | (version "1.56.0") |
c8310056 RW |
6372 | (source |
6373 | (origin | |
6374 | (method url-fetch) | |
6375 | (uri (bioconductor-uri "MassSpecWavelet" version)) | |
6376 | (sha256 | |
6377 | (base32 | |
f4e19e62 | 6378 | "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3")))) |
c8310056 RW |
6379 | (properties |
6380 | `((upstream-name . "MassSpecWavelet"))) | |
6381 | (build-system r-build-system) | |
6382 | (propagated-inputs | |
6383 | `(("r-waveslim" ,r-waveslim))) | |
6384 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") | |
6385 | (synopsis "Mass spectrum processing by wavelet-based algorithms") | |
6386 | (description | |
6387 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) | |
6388 | data mainly through the use of wavelet transforms. It supports peak detection | |
6389 | based on @dfn{Continuous Wavelet Transform} (CWT).") | |
6390 | (license license:lgpl2.0+))) | |
ec12e537 RW |
6391 | |
6392 | (define-public r-xcms | |
6393 | (package | |
6394 | (name "r-xcms") | |
a3af40ea | 6395 | (version "3.12.0") |
ec12e537 RW |
6396 | (source |
6397 | (origin | |
6398 | (method url-fetch) | |
6399 | (uri (bioconductor-uri "xcms" version)) | |
6400 | (sha256 | |
6401 | (base32 | |
a3af40ea | 6402 | "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv")))) |
ec12e537 RW |
6403 | (build-system r-build-system) |
6404 | (propagated-inputs | |
6405 | `(("r-biobase" ,r-biobase) | |
6406 | ("r-biocgenerics" ,r-biocgenerics) | |
6407 | ("r-biocparallel" ,r-biocparallel) | |
4fb52345 | 6408 | ("r-iranges" ,r-iranges) |
ec12e537 RW |
6409 | ("r-lattice" ,r-lattice) |
6410 | ("r-massspecwavelet" ,r-massspecwavelet) | |
a3af40ea | 6411 | ("r-mscoreutils" ,r-mscoreutils) |
ec12e537 | 6412 | ("r-msnbase" ,r-msnbase) |
ec12e537 RW |
6413 | ("r-mzr" ,r-mzr) |
6414 | ("r-plyr" ,r-plyr) | |
6415 | ("r-protgenerics" ,r-protgenerics) | |
6416 | ("r-rann" ,r-rann) | |
6417 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6418 | ("r-robustbase" ,r-robustbase) | |
ff9f179a RW |
6419 | ("r-s4vectors" ,r-s4vectors) |
6420 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
6421 | (native-inputs | |
6422 | `(("r-knitr" ,r-knitr))) | |
ec12e537 RW |
6423 | (home-page "https://bioconductor.org/packages/xcms/") |
6424 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") | |
6425 | (description | |
6426 | "This package provides a framework for processing and visualization of | |
6427 | chromatographically separated and single-spectra mass spectral data. It | |
6428 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses | |
6429 | data for high-throughput, untargeted analyte profiling.") | |
6430 | (license license:gpl2+))) | |
8830664d RW |
6431 | |
6432 | (define-public r-wrench | |
6433 | (package | |
6434 | (name "r-wrench") | |
dc7c6368 | 6435 | (version "1.8.0") |
8830664d RW |
6436 | (source |
6437 | (origin | |
6438 | (method url-fetch) | |
6439 | (uri (bioconductor-uri "Wrench" version)) | |
6440 | (sha256 | |
6441 | (base32 | |
dc7c6368 | 6442 | "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx")))) |
8830664d RW |
6443 | (properties `((upstream-name . "Wrench"))) |
6444 | (build-system r-build-system) | |
6445 | (propagated-inputs | |
6446 | `(("r-limma" ,r-limma) | |
6447 | ("r-locfit" ,r-locfit) | |
6448 | ("r-matrixstats" ,r-matrixstats))) | |
996f07b5 RW |
6449 | (native-inputs |
6450 | `(("r-knitr" ,r-knitr))) | |
8830664d RW |
6451 | (home-page "https://github.com/HCBravoLab/Wrench") |
6452 | (synopsis "Wrench normalization for sparse count data") | |
6453 | (description | |
6454 | "Wrench is a package for normalization sparse genomic count data, like | |
6455 | that arising from 16s metagenomic surveys.") | |
6456 | (license license:artistic2.0))) | |
b9b8b447 RW |
6457 | |
6458 | (define-public r-wiggleplotr | |
6459 | (package | |
6460 | (name "r-wiggleplotr") | |
397bcd2c | 6461 | (version "1.14.0") |
b9b8b447 RW |
6462 | (source |
6463 | (origin | |
6464 | (method url-fetch) | |
6465 | (uri (bioconductor-uri "wiggleplotr" version)) | |
6466 | (sha256 | |
6467 | (base32 | |
397bcd2c | 6468 | "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad")))) |
b9b8b447 RW |
6469 | (build-system r-build-system) |
6470 | (propagated-inputs | |
6471 | `(("r-assertthat" ,r-assertthat) | |
6472 | ("r-cowplot" ,r-cowplot) | |
6473 | ("r-dplyr" ,r-dplyr) | |
6474 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6475 | ("r-genomicranges" ,r-genomicranges) | |
6476 | ("r-ggplot2" ,r-ggplot2) | |
6477 | ("r-iranges" ,r-iranges) | |
6478 | ("r-purrr" ,r-purrr) | |
6479 | ("r-rtracklayer" ,r-rtracklayer) | |
6480 | ("r-s4vectors" ,r-s4vectors))) | |
ee0f7460 RW |
6481 | (native-inputs |
6482 | `(("r-knitr" ,r-knitr))) | |
b9b8b447 RW |
6483 | (home-page "https://bioconductor.org/packages/wiggleplotr/") |
6484 | (synopsis "Make read coverage plots from BigWig files") | |
6485 | (description | |
6486 | "This package provides tools to visualize read coverage from sequencing | |
6487 | experiments together with genomic annotations (genes, transcripts, peaks). | |
6488 | Introns of long transcripts can be rescaled to a fixed length for better | |
6489 | visualization of exonic read coverage.") | |
6490 | (license license:asl2.0))) | |
7b5101c5 RW |
6491 | |
6492 | (define-public r-widgettools | |
6493 | (package | |
6494 | (name "r-widgettools") | |
ba53681a | 6495 | (version "1.68.0") |
7b5101c5 RW |
6496 | (source |
6497 | (origin | |
6498 | (method url-fetch) | |
6499 | (uri (bioconductor-uri "widgetTools" version)) | |
6500 | (sha256 | |
6501 | (base32 | |
ba53681a | 6502 | "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w")))) |
7b5101c5 RW |
6503 | (properties `((upstream-name . "widgetTools"))) |
6504 | (build-system r-build-system) | |
6505 | (home-page "https://bioconductor.org/packages/widgetTools/") | |
6506 | (synopsis "Tools for creating interactive tcltk widgets") | |
6507 | (description | |
337bdc17 | 6508 | "This package contains tools to support the construction of tcltk |
7b5101c5 RW |
6509 | widgets in R.") |
6510 | ;; Any version of the LGPL. | |
6511 | (license license:lgpl3+))) | |
6b12f213 RW |
6512 | |
6513 | (define-public r-webbioc | |
6514 | (package | |
6515 | (name "r-webbioc") | |
d176ad34 | 6516 | (version "1.62.0") |
6b12f213 RW |
6517 | (source |
6518 | (origin | |
6519 | (method url-fetch) | |
6520 | (uri (bioconductor-uri "webbioc" version)) | |
6521 | (sha256 | |
6522 | (base32 | |
d176ad34 | 6523 | "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj")))) |
6b12f213 RW |
6524 | (build-system r-build-system) |
6525 | (inputs | |
6526 | `(("netpbm" ,netpbm) | |
6527 | ("perl" ,perl))) | |
6528 | (propagated-inputs | |
6529 | `(("r-affy" ,r-affy) | |
6530 | ("r-annaffy" ,r-annaffy) | |
6531 | ("r-biobase" ,r-biobase) | |
6532 | ("r-biocmanager" ,r-biocmanager) | |
6533 | ("r-gcrma" ,r-gcrma) | |
6534 | ("r-multtest" ,r-multtest) | |
6535 | ("r-qvalue" ,r-qvalue) | |
6536 | ("r-vsn" ,r-vsn))) | |
6537 | (home-page "https://www.bioconductor.org/") | |
6538 | (synopsis "Bioconductor web interface") | |
6539 | (description | |
6540 | "This package provides an integrated web interface for doing microarray | |
6541 | analysis using several of the Bioconductor packages. It is intended to be | |
6542 | deployed as a centralized bioinformatics resource for use by many users. | |
6543 | Currently only Affymetrix oligonucleotide analysis is supported.") | |
6544 | (license license:gpl2+))) | |
9800d859 RW |
6545 | |
6546 | (define-public r-zfpkm | |
6547 | (package | |
6548 | (name "r-zfpkm") | |
59fafa19 | 6549 | (version "1.12.0") |
9800d859 RW |
6550 | (source |
6551 | (origin | |
6552 | (method url-fetch) | |
6553 | (uri (bioconductor-uri "zFPKM" version)) | |
6554 | (sha256 | |
6555 | (base32 | |
59fafa19 | 6556 | "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm")))) |
9800d859 RW |
6557 | (properties `((upstream-name . "zFPKM"))) |
6558 | (build-system r-build-system) | |
6559 | (propagated-inputs | |
6560 | `(("r-checkmate" ,r-checkmate) | |
6561 | ("r-dplyr" ,r-dplyr) | |
6562 | ("r-ggplot2" ,r-ggplot2) | |
6563 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6564 | ("r-tidyr" ,r-tidyr))) | |
8fdca89b RW |
6565 | (native-inputs |
6566 | `(("r-knitr" ,r-knitr))) | |
9800d859 RW |
6567 | (home-page "https://github.com/ronammar/zFPKM/") |
6568 | (synopsis "Functions to facilitate zFPKM transformations") | |
6569 | (description | |
6570 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. | |
6571 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID | |
6572 | 24215113).") | |
6573 | (license license:gpl3))) | |
2bdc88fc RW |
6574 | |
6575 | (define-public r-rbowtie2 | |
6576 | (package | |
6577 | (name "r-rbowtie2") | |
9834d1ab | 6578 | (version "1.12.0") |
2bdc88fc RW |
6579 | (source |
6580 | (origin | |
6581 | (method url-fetch) | |
6582 | (uri (bioconductor-uri "Rbowtie2" version)) | |
6583 | (sha256 | |
6584 | (base32 | |
9834d1ab | 6585 | "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5")))) |
2bdc88fc RW |
6586 | (properties `((upstream-name . "Rbowtie2"))) |
6587 | (build-system r-build-system) | |
6588 | (inputs | |
6589 | `(("zlib" ,zlib))) | |
297854e6 RW |
6590 | (native-inputs |
6591 | `(("r-knitr" ,r-knitr))) | |
2bdc88fc RW |
6592 | (home-page "https://bioconductor.org/packages/Rbowtie2/") |
6593 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") | |
6594 | (description | |
6595 | "This package provides an R wrapper of the popular @code{bowtie2} | |
6596 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for | |
6597 | rapid adapter trimming, identification, and read merging.") | |
6598 | (license license:gpl3+))) | |
5622628f RW |
6599 | |
6600 | (define-public r-progeny | |
6601 | (package | |
6602 | (name "r-progeny") | |
d115db7f | 6603 | (version "1.12.0") |
5622628f RW |
6604 | (source |
6605 | (origin | |
6606 | (method url-fetch) | |
6607 | (uri (bioconductor-uri "progeny" version)) | |
6608 | (sha256 | |
6609 | (base32 | |
d115db7f | 6610 | "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7")))) |
5622628f | 6611 | (build-system r-build-system) |
8e5933a8 RW |
6612 | (propagated-inputs |
6613 | `(("r-biobase" ,r-biobase) | |
6614 | ("r-dplyr" ,r-dplyr) | |
6615 | ("r-ggplot2" ,r-ggplot2) | |
6616 | ("r-ggrepel" ,r-ggrepel) | |
6617 | ("r-gridextra" ,r-gridextra) | |
6618 | ("r-tidyr" ,r-tidyr))) | |
6619 | (native-inputs | |
6620 | `(("r-knitr" ,r-knitr))) | |
5622628f RW |
6621 | (home-page "https://github.com/saezlab/progeny") |
6622 | (synopsis "Pathway responsive gene activity inference") | |
6623 | (description | |
6624 | "This package provides a function to infer pathway activity from gene | |
6625 | expression. It contains the linear model inferred in the publication | |
6626 | \"Perturbation-response genes reveal signaling footprints in cancer gene | |
6627 | expression\".") | |
6628 | (license license:asl2.0))) | |
307586c1 RW |
6629 | |
6630 | (define-public r-arrmnormalization | |
6631 | (package | |
6632 | (name "r-arrmnormalization") | |
0067589a | 6633 | (version "1.30.0") |
307586c1 RW |
6634 | (source |
6635 | (origin | |
6636 | (method url-fetch) | |
6637 | (uri (bioconductor-uri "ARRmNormalization" version)) | |
6638 | (sha256 | |
6639 | (base32 | |
0067589a | 6640 | "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95")))) |
307586c1 RW |
6641 | (properties |
6642 | `((upstream-name . "ARRmNormalization"))) | |
6643 | (build-system r-build-system) | |
6644 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) | |
6645 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") | |
6646 | (synopsis "Adaptive robust regression normalization for methylation data") | |
6647 | (description | |
6648 | "This is a package to perform the @dfn{Adaptive Robust Regression | |
6649 | method} (ARRm) for the normalization of methylation data from the Illumina | |
6650 | Infinium HumanMethylation 450k assay.") | |
6651 | (license license:artistic2.0))) | |
fbf34949 RW |
6652 | |
6653 | (define-public r-biocfilecache | |
6654 | (package | |
6655 | (name "r-biocfilecache") | |
e65e81d2 | 6656 | (version "1.14.0") |
fbf34949 RW |
6657 | (source |
6658 | (origin | |
6659 | (method url-fetch) | |
6660 | (uri (bioconductor-uri "BiocFileCache" version)) | |
6661 | (sha256 | |
6662 | (base32 | |
e65e81d2 | 6663 | "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1")))) |
fbf34949 RW |
6664 | (properties `((upstream-name . "BiocFileCache"))) |
6665 | (build-system r-build-system) | |
6666 | (propagated-inputs | |
6667 | `(("r-curl" ,r-curl) | |
6668 | ("r-dbi" ,r-dbi) | |
6669 | ("r-dbplyr" ,r-dbplyr) | |
6670 | ("r-dplyr" ,r-dplyr) | |
6671 | ("r-httr" ,r-httr) | |
6672 | ("r-rappdirs" ,r-rappdirs) | |
6673 | ("r-rsqlite" ,r-rsqlite))) | |
173844fc RW |
6674 | (native-inputs |
6675 | `(("r-knitr" ,r-knitr))) | |
fbf34949 RW |
6676 | (home-page "https://bioconductor.org/packages/BiocFileCache/") |
6677 | (synopsis "Manage files across sessions") | |
6678 | (description | |
6679 | "This package creates a persistent on-disk cache of files that the user | |
6680 | can add, update, and retrieve. It is useful for managing resources (such as | |
6681 | custom Txdb objects) that are costly or difficult to create, web resources, | |
6682 | and data files used across sessions.") | |
6683 | (license license:artistic2.0))) | |
8c42f8f6 RW |
6684 | |
6685 | (define-public r-iclusterplus | |
6686 | (package | |
6687 | (name "r-iclusterplus") | |
4bc0675d | 6688 | (version "1.26.0") |
8c42f8f6 RW |
6689 | (source |
6690 | (origin | |
6691 | (method url-fetch) | |
6692 | (uri (bioconductor-uri "iClusterPlus" version)) | |
6693 | (sha256 | |
6694 | (base32 | |
4bc0675d | 6695 | "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q")))) |
8c42f8f6 RW |
6696 | (properties `((upstream-name . "iClusterPlus"))) |
6697 | (build-system r-build-system) | |
6698 | (native-inputs `(("gfortran" ,gfortran))) | |
6699 | (home-page "https://bioconductor.org/packages/iClusterPlus/") | |
6700 | (synopsis "Integrative clustering of multi-type genomic data") | |
6701 | (description | |
6702 | "iClusterPlus is developed for integrative clustering analysis of | |
6703 | multi-type genomic data and is an enhanced version of iCluster proposed and | |
6704 | developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise | |
6705 | from the experiments where biological samples (e.g. tumor samples) are | |
6706 | analyzed by multiple techniques, for instance, @dfn{array comparative genomic | |
6707 | hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so | |
6708 | on. In the iClusterPlus model, binary observations such as somatic mutation | |
6709 | are modeled as Binomial processes; categorical observations such as copy | |
6710 | number states are realizations of Multinomial random variables; counts are | |
6711 | modeled as Poisson random processes; and continuous measures are modeled by | |
6712 | Gaussian distributions.") | |
6713 | (license license:gpl2+))) | |
4d06ef4b RW |
6714 | |
6715 | (define-public r-rbowtie | |
6716 | (package | |
6717 | (name "r-rbowtie") | |
ea86d93e | 6718 | (version "1.30.0") |
4d06ef4b RW |
6719 | (source |
6720 | (origin | |
6721 | (method url-fetch) | |
6722 | (uri (bioconductor-uri "Rbowtie" version)) | |
6723 | (sha256 | |
6724 | (base32 | |
ea86d93e | 6725 | "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507")))) |
4d06ef4b RW |
6726 | (properties `((upstream-name . "Rbowtie"))) |
6727 | (build-system r-build-system) | |
6728 | (inputs | |
6729 | `(("zlib" ,zlib))) | |
568c3929 RW |
6730 | (native-inputs |
6731 | `(("r-knitr" ,r-knitr))) | |
4d06ef4b RW |
6732 | (home-page "https://bioconductor.org/packages/Rbowtie/") |
6733 | (synopsis "R bowtie wrapper") | |
6734 | (description | |
6735 | "This package provides an R wrapper around the popular bowtie short read | |
6736 | aligner and around SpliceMap, a de novo splice junction discovery and | |
6737 | alignment tool.") | |
6738 | (license license:artistic2.0))) | |
14441539 RW |
6739 | |
6740 | (define-public r-sgseq | |
6741 | (package | |
6742 | (name "r-sgseq") | |
ca0271c5 | 6743 | (version "1.24.0") |
14441539 RW |
6744 | (source |
6745 | (origin | |
6746 | (method url-fetch) | |
6747 | (uri (bioconductor-uri "SGSeq" version)) | |
6748 | (sha256 | |
6749 | (base32 | |
ca0271c5 | 6750 | "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx")))) |
14441539 RW |
6751 | (properties `((upstream-name . "SGSeq"))) |
6752 | (build-system r-build-system) | |
6753 | (propagated-inputs | |
6754 | `(("r-annotationdbi" ,r-annotationdbi) | |
6755 | ("r-biocgenerics" ,r-biocgenerics) | |
6756 | ("r-biostrings" ,r-biostrings) | |
6757 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6758 | ("r-genomicalignments" ,r-genomicalignments) | |
6759 | ("r-genomicfeatures" ,r-genomicfeatures) | |
6760 | ("r-genomicranges" ,r-genomicranges) | |
6761 | ("r-igraph" ,r-igraph) | |
6762 | ("r-iranges" ,r-iranges) | |
6763 | ("r-rsamtools" ,r-rsamtools) | |
6764 | ("r-rtracklayer" ,r-rtracklayer) | |
6765 | ("r-runit" ,r-runit) | |
6766 | ("r-s4vectors" ,r-s4vectors) | |
6767 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
201902bc RW |
6768 | (native-inputs |
6769 | `(("r-knitr" ,r-knitr))) | |
14441539 RW |
6770 | (home-page "https://bioconductor.org/packages/SGSeq/") |
6771 | (synopsis "Splice event prediction and quantification from RNA-seq data") | |
6772 | (description | |
6773 | "SGSeq is a package for analyzing splice events from RNA-seq data. Input | |
6774 | data are RNA-seq reads mapped to a reference genome in BAM format. Genes are | |
6775 | represented as a splice graph, which can be obtained from existing annotation | |
6776 | or predicted from the mapped sequence reads. Splice events are identified | |
6777 | from the graph and are quantified locally using structurally compatible reads | |
6778 | at the start or end of each splice variant. The software includes functions | |
6779 | for splice event prediction, quantification, visualization and | |
6780 | interpretation.") | |
6781 | (license license:artistic2.0))) | |
58656064 RW |
6782 | |
6783 | (define-public r-rhisat2 | |
6784 | (package | |
6785 | (name "r-rhisat2") | |
c36d888f | 6786 | (version "1.6.0") |
58656064 RW |
6787 | (source |
6788 | (origin | |
6789 | (method url-fetch) | |
6790 | (uri (bioconductor-uri "Rhisat2" version)) | |
6791 | (sha256 | |
6792 | (base32 | |
c36d888f | 6793 | "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb")))) |
58656064 RW |
6794 | (properties `((upstream-name . "Rhisat2"))) |
6795 | (build-system r-build-system) | |
3dd2450e RW |
6796 | (arguments |
6797 | `(#:phases | |
6798 | (modify-phases %standard-phases | |
6799 | (add-after 'unpack 'make-reproducible | |
6800 | (lambda _ | |
6801 | (substitute* "src/Makefile" | |
6802 | (("`hostname`") "guix") | |
6803 | (("`date`") "0") | |
6804 | ;; Avoid shelling out to "which". | |
6805 | (("^CC =.*") (which "gcc")) | |
6806 | (("^CPP =.*") (which "g++"))) | |
6807 | #t))))) | |
58656064 RW |
6808 | (propagated-inputs |
6809 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
6810 | ("r-genomicranges" ,r-genomicranges) | |
6811 | ("r-sgseq" ,r-sgseq))) | |
2aff2724 RW |
6812 | (native-inputs |
6813 | `(("r-knitr" ,r-knitr))) | |
58656064 RW |
6814 | (home-page "https://github.com/fmicompbio/Rhisat2") |
6815 | (synopsis "R Wrapper for HISAT2 sequence aligner") | |
6816 | (description | |
6817 | "This package provides an R interface to the HISAT2 spliced short-read | |
6818 | aligner by Kim et al. (2015). The package contains wrapper functions to | |
6819 | create a genome index and to perform the read alignment to the generated | |
6820 | index.") | |
6821 | (license license:gpl3))) | |
5e0241db RW |
6822 | |
6823 | (define-public r-quasr | |
6824 | (package | |
6825 | (name "r-quasr") | |
1b4c2719 | 6826 | (version "1.30.0") |
5e0241db RW |
6827 | (source |
6828 | (origin | |
6829 | (method url-fetch) | |
6830 | (uri (bioconductor-uri "QuasR" version)) | |
6831 | (sha256 | |
6832 | (base32 | |
1b4c2719 | 6833 | "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8")))) |
5e0241db RW |
6834 | (properties `((upstream-name . "QuasR"))) |
6835 | (build-system r-build-system) | |
5e0241db RW |
6836 | (propagated-inputs |
6837 | `(("r-annotationdbi" ,r-annotationdbi) | |
6838 | ("r-biobase" ,r-biobase) | |
6839 | ("r-biocgenerics" ,r-biocgenerics) | |
6840 | ("r-biocmanager" ,r-biocmanager) | |
6841 | ("r-biocparallel" ,r-biocparallel) | |
6842 | ("r-biostrings" ,r-biostrings) | |
6843 | ("r-bsgenome" ,r-bsgenome) | |
6844 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6845 | ("r-genomicalignments" ,r-genomicalignments) | |
6846 | ("r-genomicfeatures" ,r-genomicfeatures) | |
6847 | ("r-genomicfiles" ,r-genomicfiles) | |
6848 | ("r-genomicranges" ,r-genomicranges) | |
6849 | ("r-iranges" ,r-iranges) | |
6850 | ("r-rbowtie" ,r-rbowtie) | |
6851 | ("r-rhisat2" ,r-rhisat2) | |
6852 | ("r-rhtslib" ,r-rhtslib) | |
6853 | ("r-rsamtools" ,r-rsamtools) | |
6854 | ("r-rtracklayer" ,r-rtracklayer) | |
6855 | ("r-s4vectors" ,r-s4vectors) | |
6856 | ("r-shortread" ,r-shortread))) | |
a84abf43 RW |
6857 | (native-inputs |
6858 | `(("r-knitr" ,r-knitr))) | |
5e0241db RW |
6859 | (home-page "https://bioconductor.org/packages/QuasR/") |
6860 | (synopsis "Quantify and annotate short reads in R") | |
6861 | (description | |
6862 | "This package provides a framework for the quantification and analysis of | |
6863 | short genomic reads. It covers a complete workflow starting from raw sequence | |
6864 | reads, over creation of alignments and quality control plots, to the | |
6865 | quantification of genomic regions of interest.") | |
6866 | (license license:gpl2))) | |
496b024f RW |
6867 | |
6868 | (define-public r-rqc | |
6869 | (package | |
6870 | (name "r-rqc") | |
d8a7bf76 | 6871 | (version "1.24.0") |
496b024f RW |
6872 | (source |
6873 | (origin | |
6874 | (method url-fetch) | |
6875 | (uri (bioconductor-uri "Rqc" version)) | |
6876 | (sha256 | |
6877 | (base32 | |
d8a7bf76 | 6878 | "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9")))) |
496b024f RW |
6879 | (properties `((upstream-name . "Rqc"))) |
6880 | (build-system r-build-system) | |
6881 | (propagated-inputs | |
6882 | `(("r-biocgenerics" ,r-biocgenerics) | |
6883 | ("r-biocparallel" ,r-biocparallel) | |
6884 | ("r-biocstyle" ,r-biocstyle) | |
6885 | ("r-biostrings" ,r-biostrings) | |
6886 | ("r-biovizbase" ,r-biovizbase) | |
6887 | ("r-genomicalignments" ,r-genomicalignments) | |
6888 | ("r-genomicfiles" ,r-genomicfiles) | |
6889 | ("r-ggplot2" ,r-ggplot2) | |
6890 | ("r-iranges" ,r-iranges) | |
6891 | ("r-knitr" ,r-knitr) | |
6892 | ("r-markdown" ,r-markdown) | |
6893 | ("r-plyr" ,r-plyr) | |
6894 | ("r-rcpp" ,r-rcpp) | |
6895 | ("r-reshape2" ,r-reshape2) | |
6896 | ("r-rsamtools" ,r-rsamtools) | |
6897 | ("r-s4vectors" ,r-s4vectors) | |
6898 | ("r-shiny" ,r-shiny) | |
6899 | ("r-shortread" ,r-shortread))) | |
1c5360ac RW |
6900 | (native-inputs |
6901 | `(("r-knitr" ,r-knitr))) | |
496b024f RW |
6902 | (home-page "https://github.com/labbcb/Rqc") |
6903 | (synopsis "Quality control tool for high-throughput sequencing data") | |
6904 | (description | |
6905 | "Rqc is an optimized tool designed for quality control and assessment of | |
6906 | high-throughput sequencing data. It performs parallel processing of entire | |
6907 | files and produces a report which contains a set of high-resolution | |
6908 | graphics.") | |
6909 | (license license:gpl2+))) | |
81e3de01 RW |
6910 | |
6911 | (define-public r-birewire | |
6912 | (package | |
6913 | (name "r-birewire") | |
979b1edc | 6914 | (version "3.22.0") |
81e3de01 RW |
6915 | (source |
6916 | (origin | |
6917 | (method url-fetch) | |
6918 | (uri (bioconductor-uri "BiRewire" version)) | |
6919 | (sha256 | |
6920 | (base32 | |
979b1edc | 6921 | "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw")))) |
81e3de01 RW |
6922 | (properties `((upstream-name . "BiRewire"))) |
6923 | (build-system r-build-system) | |
6924 | (propagated-inputs | |
6925 | `(("r-igraph" ,r-igraph) | |
6926 | ("r-matrix" ,r-matrix) | |
6927 | ("r-slam" ,r-slam) | |
6928 | ("r-tsne" ,r-tsne))) | |
6929 | (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") | |
6930 | (synopsis "Tools for randomization of bipartite graphs") | |
6931 | (description | |
6932 | "This package provides functions for bipartite network rewiring through N | |
6933 | consecutive switching steps and for the computation of the minimal number of | |
6934 | switching steps to be performed in order to maximise the dissimilarity with | |
6935 | respect to the original network. It includes functions for the analysis of | |
6936 | the introduced randomness across the switching steps and several other | |
6937 | routines to analyse the resulting networks and their natural projections.") | |
6938 | (license license:gpl3))) | |
1a24f855 RW |
6939 | |
6940 | (define-public r-birta | |
6941 | (package | |
6942 | (name "r-birta") | |
cb941ca0 | 6943 | (version "1.31.0") |
1a24f855 RW |
6944 | (source |
6945 | (origin | |
6946 | (method url-fetch) | |
6947 | (uri (bioconductor-uri "birta" version)) | |
6948 | (sha256 | |
6949 | (base32 | |
cb941ca0 | 6950 | "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) |
1a24f855 RW |
6951 | (build-system r-build-system) |
6952 | (propagated-inputs | |
6953 | `(("r-biobase" ,r-biobase) | |
6954 | ("r-limma" ,r-limma) | |
6955 | ("r-mass" ,r-mass))) | |
6956 | (home-page "https://bioconductor.org/packages/birta") | |
6957 | (synopsis "Bayesian inference of regulation of transcriptional activity") | |
6958 | (description | |
6959 | "Expression levels of mRNA molecules are regulated by different | |
6960 | processes, comprising inhibition or activation by transcription factors and | |
6961 | post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian | |
6962 | Inference of Regulation of Transcriptional Activity) uses the regulatory | |
6963 | networks of transcription factors and miRNAs together with mRNA and miRNA | |
6964 | expression data to predict switches in regulatory activity between two | |
6965 | conditions. A Bayesian network is used to model the regulatory structure and | |
6966 | Markov-Chain-Monte-Carlo is applied to sample the activity states.") | |
6967 | (license license:gpl2+))) | |
a9fac3f4 | 6968 | |
b4a22cca RW |
6969 | (define-public r-multidataset |
6970 | (package | |
6971 | (name "r-multidataset") | |
1d747087 | 6972 | (version "1.18.2") |
b4a22cca RW |
6973 | (source |
6974 | (origin | |
6975 | (method url-fetch) | |
6976 | (uri (bioconductor-uri "MultiDataSet" version)) | |
6977 | (sha256 | |
6978 | (base32 | |
1d747087 | 6979 | "1wzhxgprriicw6lx1h91z4r9d5yaxar859scp83bm8pr9aznqk2z")))) |
b4a22cca RW |
6980 | (properties `((upstream-name . "MultiDataSet"))) |
6981 | (build-system r-build-system) | |
6982 | (propagated-inputs | |
6983 | `(("r-biobase" ,r-biobase) | |
6984 | ("r-biocgenerics" ,r-biocgenerics) | |
6985 | ("r-genomicranges" ,r-genomicranges) | |
6986 | ("r-ggplot2" ,r-ggplot2) | |
6987 | ("r-ggrepel" ,r-ggrepel) | |
6988 | ("r-iranges" ,r-iranges) | |
6989 | ("r-limma" ,r-limma) | |
6990 | ("r-qqman" ,r-qqman) | |
6991 | ("r-s4vectors" ,r-s4vectors) | |
6992 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
905bbb13 RW |
6993 | (native-inputs |
6994 | `(("r-knitr" ,r-knitr))) | |
b4a22cca RW |
6995 | (home-page "https://bioconductor.org/packages/MultiDataSet/") |
6996 | (synopsis "Implementation of MultiDataSet and ResultSet") | |
6997 | (description | |
6998 | "This package provides an implementation of the BRGE's (Bioinformatic | |
6999 | Research Group in Epidemiology from Center for Research in Environmental | |
7000 | Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for | |
7001 | integrating multi omics data sets and ResultSet is a container for omics | |
7002 | results. This package contains base classes for MEAL and rexposome | |
7003 | packages.") | |
7004 | (license license:expat))) | |
7005 | ||
a9fac3f4 RW |
7006 | (define-public r-ropls |
7007 | (package | |
7008 | (name "r-ropls") | |
59daf6ed | 7009 | (version "1.22.0") |
a9fac3f4 RW |
7010 | (source |
7011 | (origin | |
7012 | (method url-fetch) | |
7013 | (uri (bioconductor-uri "ropls" version)) | |
7014 | (sha256 | |
7015 | (base32 | |
59daf6ed | 7016 | "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5")))) |
a9fac3f4 | 7017 | (build-system r-build-system) |
643aaf7e RW |
7018 | (propagated-inputs |
7019 | `(("r-biobase" ,r-biobase) | |
7020 | ("r-multidataset" ,r-multidataset))) | |
a9fac3f4 RW |
7021 | (native-inputs |
7022 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
7023 | (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") | |
7024 | (synopsis "Multivariate analysis and feature selection of omics data") | |
7025 | (description | |
7026 | "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) | |
7027 | and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, | |
7028 | regression, classification, and feature selection of omics data where the | |
7029 | number of variables exceeds the number of samples and with multicollinearity | |
7030 | among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to | |
7031 | separately model the variation correlated (predictive) to the factor of | |
7032 | interest and the uncorrelated (orthogonal) variation. While performing | |
7033 | similarly to PLS, OPLS facilitates interpretation. | |
7034 | ||
7035 | This package provides imlementations of PCA, PLS, and OPLS for multivariate | |
7036 | analysis and feature selection of omics data. In addition to scores, loadings | |
7037 | and weights plots, the package provides metrics and graphics to determine the | |
7038 | optimal number of components (e.g. with the R2 and Q2 coefficients), check the | |
7039 | validity of the model by permutation testing, detect outliers, and perform | |
7040 | feature selection (e.g. with Variable Importance in Projection or regression | |
7041 | coefficients).") | |
7042 | (license license:cecill))) | |
075a9094 RW |
7043 | |
7044 | (define-public r-biosigner | |
7045 | (package | |
7046 | (name "r-biosigner") | |
7cda2d41 | 7047 | (version "1.18.2") |
075a9094 RW |
7048 | (source |
7049 | (origin | |
7050 | (method url-fetch) | |
7051 | (uri (bioconductor-uri "biosigner" version)) | |
7052 | (sha256 | |
7053 | (base32 | |
7cda2d41 | 7054 | "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn")))) |
075a9094 RW |
7055 | (build-system r-build-system) |
7056 | (propagated-inputs | |
7057 | `(("r-biobase" ,r-biobase) | |
7058 | ("r-e1071" ,r-e1071) | |
7d29dc9c | 7059 | ("r-multidataset" ,r-multidataset) |
075a9094 RW |
7060 | ("r-randomforest" ,r-randomforest) |
7061 | ("r-ropls" ,r-ropls))) | |
7062 | (native-inputs | |
f7100eda | 7063 | `(("r-knitr" ,r-knitr))) |
075a9094 RW |
7064 | (home-page "https://bioconductor.org/packages/biosigner/") |
7065 | (synopsis "Signature discovery from omics data") | |
7066 | (description | |
7067 | "Feature selection is critical in omics data analysis to extract | |
7068 | restricted and meaningful molecular signatures from complex and high-dimension | |
7069 | data, and to build robust classifiers. This package implements a method to | |
7070 | assess the relevance of the variables for the prediction performances of the | |
7071 | classifier. The approach can be run in parallel with the PLS-DA, Random | |
7072 | Forest, and SVM binary classifiers. The signatures and the corresponding | |
7073 | 'restricted' models are returned, enabling future predictions on new | |
7074 | datasets.") | |
7075 | (license license:cecill))) | |
ae6fa185 RW |
7076 | |
7077 | (define-public r-annotatr | |
7078 | (package | |
7079 | (name "r-annotatr") | |
458aa446 | 7080 | (version "1.16.0") |
ae6fa185 RW |
7081 | (source |
7082 | (origin | |
7083 | (method url-fetch) | |
7084 | (uri (bioconductor-uri "annotatr" version)) | |
7085 | (sha256 | |
7086 | (base32 | |
458aa446 | 7087 | "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9")))) |
ae6fa185 RW |
7088 | (build-system r-build-system) |
7089 | (propagated-inputs | |
7090 | `(("r-annotationdbi" ,r-annotationdbi) | |
7091 | ("r-annotationhub" ,r-annotationhub) | |
7092 | ("r-dplyr" ,r-dplyr) | |
7093 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7094 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7095 | ("r-genomicranges" ,r-genomicranges) | |
7096 | ("r-ggplot2" ,r-ggplot2) | |
7097 | ("r-iranges" ,r-iranges) | |
7098 | ("r-readr" ,r-readr) | |
7099 | ("r-regioner" ,r-regioner) | |
7100 | ("r-reshape2" ,r-reshape2) | |
7101 | ("r-rtracklayer" ,r-rtracklayer) | |
7102 | ("r-s4vectors" ,r-s4vectors))) | |
5ca991bf RW |
7103 | (native-inputs |
7104 | `(("r-knitr" ,r-knitr))) | |
ae6fa185 RW |
7105 | (home-page "https://bioconductor.org/packages/annotatr/") |
7106 | (synopsis "Annotation of genomic regions to genomic annotations") | |
7107 | (description | |
7108 | "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, | |
7109 | differentially methylated CpGs or regions, SNPs, etc.) it is often of interest | |
7110 | to investigate the intersecting genomic annotations. Such annotations include | |
7111 | those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), | |
7112 | CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as | |
7113 | enhancers. The annotatr package provides an easy way to summarize and | |
7114 | visualize the intersection of genomic sites/regions with genomic | |
7115 | annotations.") | |
7116 | (license license:gpl3))) | |
2cb738a6 RW |
7117 | |
7118 | (define-public r-rsubread | |
7119 | (package | |
7120 | (name "r-rsubread") | |
8a7933f3 | 7121 | (version "2.4.3") |
2cb738a6 RW |
7122 | (source |
7123 | (origin | |
7124 | (method url-fetch) | |
7125 | (uri (bioconductor-uri "Rsubread" version)) | |
7126 | (sha256 | |
7127 | (base32 | |
8a7933f3 | 7128 | "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba")))) |
2cb738a6 RW |
7129 | (properties `((upstream-name . "Rsubread"))) |
7130 | (build-system r-build-system) | |
7131 | (inputs `(("zlib" ,zlib))) | |
5d63f69b RW |
7132 | (propagated-inputs |
7133 | `(("r-matrix" ,r-matrix))) | |
2cb738a6 RW |
7134 | (home-page "https://bioconductor.org/packages/Rsubread/") |
7135 | (synopsis "Subread sequence alignment and counting for R") | |
7136 | (description | |
7137 | "This package provides tools for alignment, quantification and analysis | |
7138 | of second and third generation sequencing data. It includes functionality for | |
7139 | read mapping, read counting, SNP calling, structural variant detection and | |
7140 | gene fusion discovery. It can be applied to all major sequencing techologies | |
7141 | and to both short and long sequence reads.") | |
7142 | (license license:gpl3))) | |
a6fedf1f | 7143 | |
a0422d18 | 7144 | (define-public r-flowutils |
7145 | (package | |
7146 | (name "r-flowutils") | |
d361222d | 7147 | (version "1.54.0") |
a0422d18 | 7148 | (source |
7149 | (origin | |
7150 | (method url-fetch) | |
7151 | (uri (bioconductor-uri "flowUtils" version)) | |
7152 | (sha256 | |
7153 | (base32 | |
d361222d | 7154 | "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09")))) |
a0422d18 | 7155 | (properties `((upstream-name . "flowUtils"))) |
7156 | (build-system r-build-system) | |
7157 | (propagated-inputs | |
7158 | `(("r-biobase" ,r-biobase) | |
7159 | ("r-corpcor" ,r-corpcor) | |
7160 | ("r-flowcore" ,r-flowcore) | |
7161 | ("r-graph" ,r-graph) | |
7162 | ("r-runit" ,r-runit) | |
7163 | ("r-xml" ,r-xml))) | |
7164 | (home-page "https://github.com/jspidlen/flowUtils") | |
7165 | (synopsis "Utilities for flow cytometry") | |
7166 | (description | |
7167 | "This package provides utilities for flow cytometry data.") | |
7168 | (license license:artistic2.0))) | |
7169 | ||
ed6f49fc | 7170 | (define-public r-consensusclusterplus |
7171 | (package | |
7172 | (name "r-consensusclusterplus") | |
a49024e6 | 7173 | (version "1.54.0") |
ed6f49fc | 7174 | (source |
7175 | (origin | |
7176 | (method url-fetch) | |
7177 | (uri (bioconductor-uri "ConsensusClusterPlus" version)) | |
7178 | (sha256 | |
7179 | (base32 | |
a49024e6 | 7180 | "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp")))) |
ed6f49fc | 7181 | (properties |
7182 | `((upstream-name . "ConsensusClusterPlus"))) | |
7183 | (build-system r-build-system) | |
7184 | (propagated-inputs | |
7185 | `(("r-all" ,r-all) | |
7186 | ("r-biobase" ,r-biobase) | |
7187 | ("r-cluster" ,r-cluster))) | |
7188 | (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") | |
7189 | (synopsis "Clustering algorithm") | |
7190 | (description | |
7191 | "This package provides an implementation of an algorithm for determining | |
7192 | cluster count and membership by stability evidence in unsupervised analysis.") | |
7193 | (license license:gpl2))) | |
7194 | ||
b4aee31d RW |
7195 | (define-public r-cytolib |
7196 | (package | |
7197 | (name "r-cytolib") | |
9470f901 | 7198 | (version "2.2.1") |
b4aee31d RW |
7199 | (source |
7200 | (origin | |
7201 | (method url-fetch) | |
7202 | (uri (bioconductor-uri "cytolib" version)) | |
7203 | (sha256 | |
7204 | (base32 | |
9470f901 | 7205 | "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r")))) |
b4aee31d RW |
7206 | (properties `((upstream-name . "cytolib"))) |
7207 | (build-system r-build-system) | |
b58c4e76 | 7208 | (arguments |
7209 | `(#:phases | |
7210 | (modify-phases %standard-phases | |
7211 | (add-after 'unpack 'fix-linking | |
7212 | (lambda _ | |
7213 | (substitute* "src/Makevars.in" | |
7214 | ;; This is to avoid having a plain directory on the list of | |
7215 | ;; libraries to link. | |
7216 | (("\\(RHDF5_LIBS\\)" match) | |
7217 | (string-append match "/libhdf5.a"))) | |
7218 | #t))))) | |
3c73d7c5 | 7219 | (native-inputs |
c6ccd4fc | 7220 | `(("r-knitr" ,r-knitr) |
7221 | ("pkg-config" ,pkg-config))) | |
3c73d7c5 RW |
7222 | (propagated-inputs |
7223 | `(("r-bh" ,r-bh) | |
7224 | ("r-rcpp" ,r-rcpp) | |
7225 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
7226 | ("r-rcppparallel" ,r-rcppparallel) | |
7227 | ("r-rhdf5lib" ,r-rhdf5lib) | |
7228 | ("r-rprotobuflib" ,r-rprotobuflib))) | |
b4aee31d RW |
7229 | (home-page "https://bioconductor.org/packages/cytolib/") |
7230 | (synopsis "C++ infrastructure for working with gated cytometry") | |
7231 | (description | |
7232 | "This package provides the core data structure and API to represent and | |
7233 | interact with gated cytometry data.") | |
7234 | (license license:artistic2.0))) | |
7235 | ||
a6fedf1f | 7236 | (define-public r-flowcore |
7237 | (package | |
7238 | (name "r-flowcore") | |
3f0e93b4 | 7239 | (version "2.2.0") |
a6fedf1f | 7240 | (source |
7241 | (origin | |
7242 | (method url-fetch) | |
7243 | (uri (bioconductor-uri "flowCore" version)) | |
7244 | (sha256 | |
7245 | (base32 | |
3f0e93b4 | 7246 | "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8")))) |
a6fedf1f | 7247 | (properties `((upstream-name . "flowCore"))) |
7248 | (build-system r-build-system) | |
7249 | (propagated-inputs | |
7250 | `(("r-bh" ,r-bh) | |
7251 | ("r-biobase" ,r-biobase) | |
7252 | ("r-biocgenerics" ,r-biocgenerics) | |
b2a2f321 | 7253 | ("r-cytolib" ,r-cytolib) |
a6fedf1f | 7254 | ("r-matrixstats" ,r-matrixstats) |
faff2de0 RW |
7255 | ("r-rcpp" ,r-rcpp) |
7256 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
3f0e93b4 | 7257 | ("r-rprotobuflib" ,r-rprotobuflib) |
7258 | ("r-s4vectors" ,r-s4vectors))) | |
faff2de0 RW |
7259 | (native-inputs |
7260 | `(("r-knitr" ,r-knitr))) | |
a6fedf1f | 7261 | (home-page "https://bioconductor.org/packages/flowCore") |
7262 | (synopsis "Basic structures for flow cytometry data") | |
7263 | (description | |
7264 | "This package provides S4 data structures and basic functions to deal | |
7265 | with flow cytometry data.") | |
7266 | (license license:artistic2.0))) | |
e0cb053e | 7267 | |
7268 | (define-public r-flowmeans | |
7269 | (package | |
7270 | (name "r-flowmeans") | |
2cd78131 | 7271 | (version "1.50.0") |
e0cb053e | 7272 | (source |
7273 | (origin | |
7274 | (method url-fetch) | |
7275 | (uri (bioconductor-uri "flowMeans" version)) | |
7276 | (sha256 | |
7277 | (base32 | |
2cd78131 | 7278 | "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734")))) |
e0cb053e | 7279 | (properties `((upstream-name . "flowMeans"))) |
7280 | (build-system r-build-system) | |
7281 | (propagated-inputs | |
7282 | `(("r-biobase" ,r-biobase) | |
7283 | ("r-feature" ,r-feature) | |
7284 | ("r-flowcore" ,r-flowcore) | |
7285 | ("r-rrcov" ,r-rrcov))) | |
7286 | (home-page "https://bioconductor.org/packages/flowMeans") | |
7287 | (synopsis "Non-parametric flow cytometry data gating") | |
7288 | (description | |
7289 | "This package provides tools to identify cell populations in Flow | |
7290 | Cytometry data using non-parametric clustering and segmented-regression-based | |
7291 | change point detection.") | |
7292 | (license license:artistic2.0))) | |
1502751b | 7293 | |
15ac0c19 RW |
7294 | (define-public r-ncdfflow |
7295 | (package | |
7296 | (name "r-ncdfflow") | |
eac1eaaa | 7297 | (version "2.36.0") |
15ac0c19 RW |
7298 | (source |
7299 | (origin | |
7300 | (method url-fetch) | |
7301 | (uri (bioconductor-uri "ncdfFlow" version)) | |
7302 | (sha256 | |
7303 | (base32 | |
eac1eaaa | 7304 | "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac")))) |
15ac0c19 RW |
7305 | (properties `((upstream-name . "ncdfFlow"))) |
7306 | (build-system r-build-system) | |
0022e9f4 | 7307 | (arguments |
7308 | `(#:phases | |
7309 | (modify-phases %standard-phases | |
7310 | (add-after 'unpack 'fix-linking | |
7311 | (lambda _ | |
7312 | (substitute* "src/Makevars" | |
7313 | ;; This is to avoid having a plain directory on the list of | |
7314 | ;; libraries to link. | |
7315 | (("\\(RHDF5_LIBS\\)" match) | |
7316 | (string-append match "/libhdf5.a"))) | |
7317 | #t))))) | |
15ac0c19 RW |
7318 | (propagated-inputs |
7319 | `(("r-bh" ,r-bh) | |
7320 | ("r-biobase" ,r-biobase) | |
7321 | ("r-biocgenerics" ,r-biocgenerics) | |
7322 | ("r-flowcore" ,r-flowcore) | |
7323 | ("r-rcpp" ,r-rcpp) | |
7324 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
7325 | ("r-rhdf5lib" ,r-rhdf5lib) | |
7326 | ("r-zlibbioc" ,r-zlibbioc))) | |
631b12ca RW |
7327 | (native-inputs |
7328 | `(("r-knitr" ,r-knitr))) | |
15ac0c19 RW |
7329 | (home-page "https://bioconductor.org/packages/ncdfFlow/") |
7330 | (synopsis "HDF5 based storage for flow cytometry data") | |
7331 | (description | |
7332 | "This package provides HDF5 storage based methods and functions for | |
7333 | manipulation of flow cytometry data.") | |
7334 | (license license:artistic2.0))) | |
7335 | ||
f5f44031 RW |
7336 | (define-public r-ggcyto |
7337 | (package | |
7338 | (name "r-ggcyto") | |
43bf50ec | 7339 | (version "1.18.0") |
f5f44031 RW |
7340 | (source |
7341 | (origin | |
7342 | (method url-fetch) | |
7343 | (uri (bioconductor-uri "ggcyto" version)) | |
7344 | (sha256 | |
7345 | (base32 | |
43bf50ec | 7346 | "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m")))) |
f5f44031 RW |
7347 | (properties `((upstream-name . "ggcyto"))) |
7348 | (build-system r-build-system) | |
7349 | (propagated-inputs | |
7350 | `(("r-data-table" ,r-data-table) | |
7351 | ("r-flowcore" ,r-flowcore) | |
7352 | ("r-flowworkspace" ,r-flowworkspace) | |
7353 | ("r-ggplot2" ,r-ggplot2) | |
7354 | ("r-gridextra" ,r-gridextra) | |
3407dfa6 | 7355 | ("r-hexbin" ,r-hexbin) |
f5f44031 RW |
7356 | ("r-ncdfflow" ,r-ncdfflow) |
7357 | ("r-plyr" ,r-plyr) | |
7358 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
7359 | ("r-rlang" ,r-rlang) | |
7360 | ("r-scales" ,r-scales))) | |
0754fefb RW |
7361 | (native-inputs |
7362 | `(("r-knitr" ,r-knitr))) | |
f5f44031 RW |
7363 | (home-page "https://github.com/RGLab/ggcyto/issues") |
7364 | (synopsis "Visualize Cytometry data with ggplot") | |
7365 | (description | |
7366 | "With the dedicated fortify method implemented for @code{flowSet}, | |
7367 | @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow | |
7368 | cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper | |
7369 | and some custom layers also make it easy to add gates and population | |
7370 | statistics to the plot.") | |
7371 | (license license:artistic2.0))) | |
7372 | ||
0dd4b7d7 RW |
7373 | (define-public r-flowviz |
7374 | (package | |
7375 | (name "r-flowviz") | |
d5a53ab7 | 7376 | (version "1.54.0") |
0dd4b7d7 RW |
7377 | (source |
7378 | (origin | |
7379 | (method url-fetch) | |
7380 | (uri (bioconductor-uri "flowViz" version)) | |
7381 | (sha256 | |
7382 | (base32 | |
d5a53ab7 | 7383 | "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k")))) |
0dd4b7d7 RW |
7384 | (properties `((upstream-name . "flowViz"))) |
7385 | (build-system r-build-system) | |
7386 | (propagated-inputs | |
7387 | `(("r-biobase" ,r-biobase) | |
7388 | ("r-flowcore" ,r-flowcore) | |
7389 | ("r-hexbin" ,r-hexbin) | |
7390 | ("r-idpmisc" ,r-idpmisc) | |
7391 | ("r-kernsmooth" ,r-kernsmooth) | |
7392 | ("r-lattice" ,r-lattice) | |
7393 | ("r-latticeextra" ,r-latticeextra) | |
7394 | ("r-mass" ,r-mass) | |
7395 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
062789b8 RW |
7396 | (native-inputs |
7397 | `(("r-knitr" ,r-knitr))) | |
0dd4b7d7 RW |
7398 | (home-page "https://bioconductor.org/packages/flowViz/") |
7399 | (synopsis "Visualization for flow cytometry") | |
7400 | (description | |
7401 | "This package provides visualization tools for flow cytometry data.") | |
7402 | (license license:artistic2.0))) | |
7403 | ||
c8ab9eb1 RW |
7404 | (define-public r-flowclust |
7405 | (package | |
7406 | (name "r-flowclust") | |
33c5b6d7 | 7407 | (version "3.28.0") |
c8ab9eb1 RW |
7408 | (source |
7409 | (origin | |
7410 | (method url-fetch) | |
7411 | (uri (bioconductor-uri "flowClust" version)) | |
7412 | (sha256 | |
7413 | (base32 | |
33c5b6d7 | 7414 | "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq")))) |
c8ab9eb1 RW |
7415 | (properties `((upstream-name . "flowClust"))) |
7416 | (build-system r-build-system) | |
7417 | (arguments | |
7418 | `(#:configure-flags | |
7419 | (list "--configure-args=--enable-bundled-gsl=no"))) | |
7420 | (propagated-inputs | |
7421 | `(("r-biobase" ,r-biobase) | |
7422 | ("r-biocgenerics" ,r-biocgenerics) | |
7423 | ("r-clue" ,r-clue) | |
7424 | ("r-corpcor" ,r-corpcor) | |
7425 | ("r-ellipse" ,r-ellipse) | |
7426 | ("r-flowcore" ,r-flowcore) | |
7427 | ("r-flowviz" ,r-flowviz) | |
7428 | ("r-graph" ,r-graph) | |
7429 | ("r-mnormt" ,r-mnormt))) | |
7430 | (inputs | |
7431 | `(("gsl" ,gsl))) | |
7432 | (native-inputs | |
b347d6c3 RW |
7433 | `(("pkg-config" ,pkg-config) |
7434 | ("r-knitr" ,r-knitr))) | |
c8ab9eb1 RW |
7435 | (home-page "https://bioconductor.org/packages/flowClust") |
7436 | (synopsis "Clustering for flow cytometry") | |
7437 | (description | |
7438 | "This package provides robust model-based clustering using a t-mixture | |
7439 | model with Box-Cox transformation.") | |
7440 | (license license:artistic2.0))) | |
7441 | ||
f1964519 RW |
7442 | ;; TODO: this package bundles an old version of protobuf. It's not easy to |
7443 | ;; make it use our protobuf package instead. | |
7444 | (define-public r-rprotobuflib | |
7445 | (package | |
7446 | (name "r-rprotobuflib") | |
5bab0b7e | 7447 | (version "2.2.0") |
f1964519 RW |
7448 | (source |
7449 | (origin | |
7450 | (method url-fetch) | |
7451 | (uri (bioconductor-uri "RProtoBufLib" version)) | |
7452 | (sha256 | |
7453 | (base32 | |
5bab0b7e | 7454 | "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz")))) |
f1964519 RW |
7455 | (properties `((upstream-name . "RProtoBufLib"))) |
7456 | (build-system r-build-system) | |
7457 | (arguments | |
7458 | `(#:phases | |
7459 | (modify-phases %standard-phases | |
7460 | (add-after 'unpack 'unpack-bundled-sources | |
7461 | (lambda _ | |
7462 | (with-directory-excursion "src" | |
bafade83 | 7463 | (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) |
f1964519 | 7464 | #t))))) |
bafade83 RW |
7465 | (native-inputs |
7466 | `(("r-knitr" ,r-knitr))) | |
f1964519 RW |
7467 | (home-page "https://bioconductor.org/packages/RProtoBufLib/") |
7468 | (synopsis "C++ headers and static libraries of Protocol buffers") | |
7469 | (description | |
7470 | "This package provides the headers and static library of Protocol buffers | |
7471 | for other R packages to compile and link against.") | |
7472 | (license license:bsd-3))) | |
7473 | ||
82c11117 RW |
7474 | (define-public r-flowworkspace |
7475 | (package | |
7476 | (name "r-flowworkspace") | |
1b347814 | 7477 | (version "4.2.0") |
82c11117 RW |
7478 | (source |
7479 | (origin | |
7480 | (method url-fetch) | |
7481 | (uri (bioconductor-uri "flowWorkspace" version)) | |
7482 | (sha256 | |
7483 | (base32 | |
1b347814 | 7484 | "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag")))) |
82c11117 RW |
7485 | (properties `((upstream-name . "flowWorkspace"))) |
7486 | (build-system r-build-system) | |
ece564f0 | 7487 | (arguments |
7488 | `(#:phases | |
7489 | (modify-phases %standard-phases | |
7490 | (add-after 'unpack 'fix-linking | |
7491 | (lambda _ | |
7492 | (substitute* "src/Makevars" | |
7493 | ;; This is to avoid having a plain directory on the list of | |
7494 | ;; libraries to link. | |
7495 | (("\\{h5lib\\}" match) | |
7496 | (string-append match "/libhdf5.a"))) | |
7497 | #t))))) | |
82c11117 | 7498 | (propagated-inputs |
1b347814 | 7499 | `(("r-aws-s3" ,r-aws-s3) |
7500 | ("r-aws-signature" ,r-aws-signature) | |
7501 | ("r-bh" ,r-bh) | |
82c11117 RW |
7502 | ("r-biobase" ,r-biobase) |
7503 | ("r-biocgenerics" ,r-biocgenerics) | |
7504 | ("r-cytolib" ,r-cytolib) | |
7505 | ("r-data-table" ,r-data-table) | |
7506 | ("r-digest" ,r-digest) | |
7507 | ("r-dplyr" ,r-dplyr) | |
7508 | ("r-flowcore" ,r-flowcore) | |
a9af09df | 7509 | ("r-ggplot2" ,r-ggplot2) |
82c11117 | 7510 | ("r-graph" ,r-graph) |
82c11117 RW |
7511 | ("r-lattice" ,r-lattice) |
7512 | ("r-latticeextra" ,r-latticeextra) | |
7513 | ("r-matrixstats" ,r-matrixstats) | |
7514 | ("r-ncdfflow" ,r-ncdfflow) | |
7515 | ("r-rbgl" ,r-rbgl) | |
82c11117 | 7516 | ("r-rcpp" ,r-rcpp) |
a9af09df | 7517 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
82c11117 RW |
7518 | ("r-rcppparallel" ,r-rcppparallel) |
7519 | ("r-rgraphviz" ,r-rgraphviz) | |
a9af09df | 7520 | ("r-rhdf5lib" ,r-rhdf5lib) |
82c11117 RW |
7521 | ("r-rprotobuflib" ,r-rprotobuflib) |
7522 | ("r-scales" ,r-scales) | |
a9af09df RW |
7523 | ("r-xml" ,r-xml))) |
7524 | (native-inputs | |
7525 | `(("r-knitr" ,r-knitr))) | |
82c11117 RW |
7526 | (home-page "https://bioconductor.org/packages/flowWorkspace/") |
7527 | (synopsis "Infrastructure for working with cytometry data") | |
7528 | (description | |
7529 | "This package is designed to facilitate comparison of automated gating | |
7530 | methods against manual gating done in flowJo. This package allows you to | |
7531 | import basic flowJo workspaces into BioConductor and replicate the gating from | |
7532 | flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of | |
7533 | samples, compensation, and transformation are performed so that the output | |
7534 | matches the flowJo analysis.") | |
7535 | (license license:artistic2.0))) | |
7536 | ||
b700b9ec RW |
7537 | (define-public r-flowstats |
7538 | (package | |
7539 | (name "r-flowstats") | |
fd11c7b8 | 7540 | (version "4.2.0") |
b700b9ec RW |
7541 | (source |
7542 | (origin | |
7543 | (method url-fetch) | |
7544 | (uri (bioconductor-uri "flowStats" version)) | |
7545 | (sha256 | |
7546 | (base32 | |
fd11c7b8 | 7547 | "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x")))) |
b700b9ec RW |
7548 | (properties `((upstream-name . "flowStats"))) |
7549 | (build-system r-build-system) | |
7550 | (propagated-inputs | |
7551 | `(("r-biobase" ,r-biobase) | |
7552 | ("r-biocgenerics" ,r-biocgenerics) | |
7553 | ("r-cluster" ,r-cluster) | |
7554 | ("r-fda" ,r-fda) | |
7555 | ("r-flowcore" ,r-flowcore) | |
7556 | ("r-flowviz" ,r-flowviz) | |
7557 | ("r-flowworkspace" ,r-flowworkspace) | |
7558 | ("r-kernsmooth" ,r-kernsmooth) | |
7559 | ("r-ks" ,r-ks) | |
7560 | ("r-lattice" ,r-lattice) | |
7561 | ("r-mass" ,r-mass) | |
7562 | ("r-ncdfflow" ,r-ncdfflow) | |
7563 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
7564 | ("r-rrcov" ,r-rrcov))) | |
7565 | (home-page "http://www.github.com/RGLab/flowStats") | |
7566 | (synopsis "Statistical methods for the analysis of flow cytometry data") | |
7567 | (description | |
7568 | "This package provides methods and functionality to analyze flow data | |
7569 | that is beyond the basic infrastructure provided by the @code{flowCore} | |
7570 | package.") | |
7571 | (license license:artistic2.0))) | |
7572 | ||
6aedc805 RW |
7573 | (define-public r-opencyto |
7574 | (package | |
7575 | (name "r-opencyto") | |
5abf0a0d | 7576 | (version "2.2.0") |
6aedc805 RW |
7577 | (source |
7578 | (origin | |
7579 | (method url-fetch) | |
7580 | (uri (bioconductor-uri "openCyto" version)) | |
7581 | (sha256 | |
7582 | (base32 | |
5abf0a0d | 7583 | "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v")))) |
6aedc805 RW |
7584 | (properties `((upstream-name . "openCyto"))) |
7585 | (build-system r-build-system) | |
7586 | (propagated-inputs | |
7587 | `(("r-biobase" ,r-biobase) | |
7588 | ("r-biocgenerics" ,r-biocgenerics) | |
7589 | ("r-clue" ,r-clue) | |
7590 | ("r-data-table" ,r-data-table) | |
7591 | ("r-flowclust" ,r-flowclust) | |
7592 | ("r-flowcore" ,r-flowcore) | |
7593 | ("r-flowstats" ,r-flowstats) | |
7594 | ("r-flowviz" ,r-flowviz) | |
7595 | ("r-flowworkspace" ,r-flowworkspace) | |
7596 | ("r-graph" ,r-graph) | |
7597 | ("r-gtools" ,r-gtools) | |
7598 | ("r-ks" ,r-ks) | |
7599 | ("r-lattice" ,r-lattice) | |
7600 | ("r-mass" ,r-mass) | |
7601 | ("r-ncdfflow" ,r-ncdfflow) | |
7602 | ("r-plyr" ,r-plyr) | |
7603 | ("r-r-utils" ,r-r-utils) | |
7604 | ("r-rbgl" ,r-rbgl) | |
7605 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
7606 | ("r-rcpp" ,r-rcpp) | |
7607 | ("r-rrcov" ,r-rrcov))) | |
8f5e1674 RW |
7608 | (native-inputs |
7609 | `(("r-knitr" ,r-knitr))) | |
6aedc805 RW |
7610 | (home-page "https://bioconductor.org/packages/openCyto") |
7611 | (synopsis "Hierarchical gating pipeline for flow cytometry data") | |
7612 | (description | |
7613 | "This package is designed to facilitate the automated gating methods in a | |
7614 | sequential way to mimic the manual gating strategy.") | |
7615 | (license license:artistic2.0))) | |
7616 | ||
7a62d5e0 RW |
7617 | (define-public r-cytoml |
7618 | (package | |
7619 | (name "r-cytoml") | |
fa6bb614 | 7620 | (version "2.2.2") |
7a62d5e0 RW |
7621 | (source |
7622 | (origin | |
7623 | (method url-fetch) | |
7624 | (uri (bioconductor-uri "CytoML" version)) | |
7625 | (sha256 | |
7626 | (base32 | |
fa6bb614 | 7627 | "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1")))) |
7a62d5e0 RW |
7628 | (properties `((upstream-name . "CytoML"))) |
7629 | (build-system r-build-system) | |
2b224f90 | 7630 | (arguments |
7631 | `(#:phases | |
7632 | (modify-phases %standard-phases | |
7633 | (add-after 'unpack 'fix-linking | |
7634 | (lambda _ | |
7635 | (substitute* "src/Makevars.in" | |
7636 | ;; This is to avoid having a plain directory on the list of | |
7637 | ;; libraries to link. | |
7638 | (("\\{h5lib\\}" match) | |
7639 | (string-append match "/libhdf5.a"))) | |
7640 | #t))))) | |
7a62d5e0 | 7641 | (inputs |
fa6bb614 RW |
7642 | `(("libxml2" ,libxml2) |
7643 | ("zlib" ,zlib))) | |
7a62d5e0 RW |
7644 | (propagated-inputs |
7645 | `(("r-base64enc" ,r-base64enc) | |
7646 | ("r-bh" ,r-bh) | |
7647 | ("r-biobase" ,r-biobase) | |
7648 | ("r-corpcor" ,r-corpcor) | |
7649 | ("r-cytolib" ,r-cytolib) | |
7650 | ("r-data-table" ,r-data-table) | |
7651 | ("r-dplyr" ,r-dplyr) | |
7652 | ("r-flowcore" ,r-flowcore) | |
7653 | ("r-flowworkspace" ,r-flowworkspace) | |
7654 | ("r-ggcyto" ,r-ggcyto) | |
7655 | ("r-graph" ,r-graph) | |
7656 | ("r-jsonlite" ,r-jsonlite) | |
7657 | ("r-lattice" ,r-lattice) | |
7a62d5e0 RW |
7658 | ("r-opencyto" ,r-opencyto) |
7659 | ("r-plyr" ,r-plyr) | |
7660 | ("r-rbgl" ,r-rbgl) | |
7661 | ("r-rcpp" ,r-rcpp) | |
8d5a83b7 | 7662 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
7a62d5e0 RW |
7663 | ("r-rcppparallel" ,r-rcppparallel) |
7664 | ("r-rgraphviz" ,r-rgraphviz) | |
8d5a83b7 | 7665 | ("r-rhdf5lib" ,r-rhdf5lib) |
7a62d5e0 RW |
7666 | ("r-rprotobuflib" ,r-rprotobuflib) |
7667 | ("r-runit" ,r-runit) | |
8d5a83b7 | 7668 | ("r-tibble" ,r-tibble) |
7a62d5e0 | 7669 | ("r-xml" ,r-xml) |
ef588757 | 7670 | ("r-xml2" ,r-xml2) |
7a62d5e0 | 7671 | ("r-yaml" ,r-yaml))) |
d49e3f01 RW |
7672 | (native-inputs |
7673 | `(("r-knitr" ,r-knitr))) | |
7a62d5e0 RW |
7674 | (home-page "https://github.com/RGLab/CytoML") |
7675 | (synopsis "GatingML interface for cross platform cytometry data sharing") | |
7676 | (description | |
7677 | "This package provides an interface to implementations of the GatingML2.0 | |
7678 | standard to exchange gated cytometry data with other software platforms.") | |
7679 | (license license:artistic2.0))) | |
7680 | ||
1502751b | 7681 | (define-public r-flowsom |
7682 | (package | |
7683 | (name "r-flowsom") | |
1f7ddaf0 | 7684 | (version "1.22.0") |
1502751b | 7685 | (source |
7686 | (origin | |
7687 | (method url-fetch) | |
7688 | (uri (bioconductor-uri "FlowSOM" version)) | |
7689 | (sha256 | |
7690 | (base32 | |
1f7ddaf0 | 7691 | "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf")))) |
1502751b | 7692 | (properties `((upstream-name . "FlowSOM"))) |
7693 | (build-system r-build-system) | |
7694 | (propagated-inputs | |
7695 | `(("r-biocgenerics" ,r-biocgenerics) | |
7696 | ("r-consensusclusterplus" ,r-consensusclusterplus) | |
ba71567a | 7697 | ("r-cytoml" ,r-cytoml) |
1502751b | 7698 | ("r-flowcore" ,r-flowcore) |
ba71567a | 7699 | ("r-flowworkspace" ,r-flowworkspace) |
1502751b | 7700 | ("r-igraph" ,r-igraph) |
ba71567a | 7701 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
1502751b | 7702 | ("r-tsne" ,r-tsne) |
7703 | ("r-xml" ,r-xml))) | |
7704 | (home-page "https://bioconductor.org/packages/FlowSOM/") | |
7705 | (synopsis "Visualize and interpret cytometry data") | |
7706 | (description | |
7707 | "FlowSOM offers visualization options for cytometry data, by using | |
7708 | self-organizing map clustering and minimal spanning trees.") | |
7709 | (license license:gpl2+))) | |
1adb9cbc | 7710 | |
7711 | (define-public r-mixomics | |
7712 | (package | |
7713 | (name "r-mixomics") | |
b602ec9f | 7714 | (version "6.14.1") |
1adb9cbc | 7715 | (source |
7716 | (origin | |
7717 | (method url-fetch) | |
7718 | (uri (bioconductor-uri "mixOmics" version)) | |
7719 | (sha256 | |
7720 | (base32 | |
b602ec9f | 7721 | "07d1z33bc3bym1jwp1qqfhs18w4v9axk0ycnmldmj6piswvp44wk")))) |
1adb9cbc | 7722 | (properties `((upstream-name . "mixOmics"))) |
7723 | (build-system r-build-system) | |
7724 | (propagated-inputs | |
b602ec9f RW |
7725 | `(("r-biocparallel" ,r-biocparallel) |
7726 | ("r-corpcor" ,r-corpcor) | |
1adb9cbc | 7727 | ("r-dplyr" ,r-dplyr) |
7728 | ("r-ellipse" ,r-ellipse) | |
0e78ce36 | 7729 | ("r-ggrepel" ,r-ggrepel) |
1adb9cbc | 7730 | ("r-ggplot2" ,r-ggplot2) |
7731 | ("r-gridextra" ,r-gridextra) | |
7732 | ("r-igraph" ,r-igraph) | |
7733 | ("r-lattice" ,r-lattice) | |
7734 | ("r-mass" ,r-mass) | |
7735 | ("r-matrixstats" ,r-matrixstats) | |
7736 | ("r-rarpack" ,r-rarpack) | |
7737 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
7738 | ("r-reshape2" ,r-reshape2) | |
7739 | ("r-tidyr" ,r-tidyr))) | |
9669bc17 RW |
7740 | (native-inputs |
7741 | `(("r-knitr" ,r-knitr))) | |
1adb9cbc | 7742 | (home-page "http://www.mixOmics.org") |
7743 | (synopsis "Multivariate methods for exploration of biological datasets") | |
7744 | (description | |
7745 | "mixOmics offers a wide range of multivariate methods for the exploration | |
7746 | and integration of biological datasets with a particular focus on variable | |
7747 | selection. The package proposes several sparse multivariate models we have | |
7748 | developed to identify the key variables that are highly correlated, and/or | |
7749 | explain the biological outcome of interest. The data that can be analysed | |
7750 | with mixOmics may come from high throughput sequencing technologies, such as | |
7751 | omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but | |
7752 | also beyond the realm of omics (e.g. spectral imaging). The methods | |
7753 | implemented in mixOmics can also handle missing values without having to | |
7754 | delete entire rows with missing data.") | |
7755 | (license license:gpl2+))) | |
a0efa069 | 7756 | |
7757 | (define-public r-depecher | |
fafaeab4 | 7758 | (package ;Source/Weave error |
a0efa069 | 7759 | (name "r-depecher") |
fafaeab4 | 7760 | (version "1.6.0") |
a0efa069 | 7761 | (source |
7762 | (origin | |
7763 | (method url-fetch) | |
7764 | (uri (bioconductor-uri "DepecheR" version)) | |
7765 | (sha256 | |
7766 | (base32 | |
fafaeab4 | 7767 | "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469")))) |
a0efa069 | 7768 | (properties `((upstream-name . "DepecheR"))) |
7769 | (build-system r-build-system) | |
a0efa069 | 7770 | (propagated-inputs |
7771 | `(("r-beanplot" ,r-beanplot) | |
a0efa069 | 7772 | ("r-dosnow" ,r-dosnow) |
7773 | ("r-dplyr" ,r-dplyr) | |
2c8433ca | 7774 | ("r-fnn" ,r-fnn) |
a0efa069 | 7775 | ("r-foreach" ,r-foreach) |
7776 | ("r-ggplot2" ,r-ggplot2) | |
fafaeab4 | 7777 | ("r-gmodels" ,r-gmodels) |
a0efa069 | 7778 | ("r-gplots" ,r-gplots) |
7779 | ("r-mass" ,r-mass) | |
7780 | ("r-matrixstats" ,r-matrixstats) | |
7781 | ("r-mixomics" ,r-mixomics) | |
7782 | ("r-moments" ,r-moments) | |
7783 | ("r-rcpp" ,r-rcpp) | |
7784 | ("r-rcppeigen" ,r-rcppeigen) | |
7785 | ("r-reshape2" ,r-reshape2) | |
2c8433ca | 7786 | ("r-robustbase" ,r-robustbase) |
a0efa069 | 7787 | ("r-viridis" ,r-viridis))) |
bf3722f9 RW |
7788 | (native-inputs |
7789 | `(("r-knitr" ,r-knitr))) | |
a0efa069 | 7790 | (home-page "https://bioconductor.org/packages/DepecheR/") |
7791 | (synopsis "Identify traits of clusters in high-dimensional entities") | |
7792 | (description | |
7793 | "The purpose of this package is to identify traits in a dataset that can | |
7794 | separate groups. This is done on two levels. First, clustering is performed, | |
7795 | using an implementation of sparse K-means. Secondly, the generated clusters | |
7796 | are used to predict outcomes of groups of individuals based on their | |
7797 | distribution of observations in the different clusters. As certain clusters | |
7798 | with separating information will be identified, and these clusters are defined | |
7799 | by a sparse number of variables, this method can reduce the complexity of | |
7800 | data, to only emphasize the data that actually matters.") | |
7801 | (license license:expat))) | |
b46a0ee7 | 7802 | |
bb88417f RW |
7803 | (define-public r-rcistarget |
7804 | (package | |
7805 | (name "r-rcistarget") | |
64813573 | 7806 | (version "1.10.0") |
bb88417f RW |
7807 | (source |
7808 | (origin | |
7809 | (method url-fetch) | |
7810 | (uri (bioconductor-uri "RcisTarget" version)) | |
7811 | (sha256 | |
7812 | (base32 | |
64813573 | 7813 | "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf")))) |
bb88417f RW |
7814 | (properties `((upstream-name . "RcisTarget"))) |
7815 | (build-system r-build-system) | |
7816 | (propagated-inputs | |
7817 | `(("r-aucell" ,r-aucell) | |
7818 | ("r-biocgenerics" ,r-biocgenerics) | |
7819 | ("r-data-table" ,r-data-table) | |
7820 | ("r-feather" ,r-feather) | |
7821 | ("r-gseabase" ,r-gseabase) | |
7822 | ("r-r-utils" ,r-r-utils) | |
7823 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
93235b1e RW |
7824 | (native-inputs |
7825 | `(("r-knitr" ,r-knitr))) | |
bb88417f RW |
7826 | (home-page "https://aertslab.org/#scenic") |
7827 | (synopsis "Identify transcription factor binding motifs enriched on a gene list") | |
7828 | (description | |
7829 | "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) | |
7830 | over-represented on a gene list. In a first step, RcisTarget selects DNA | |
7831 | motifs that are significantly over-represented in the surroundings of the | |
7832 | @dfn{transcription start site} (TSS) of the genes in the gene-set. This is | |
7833 | achieved by using a database that contains genome-wide cross-species rankings | |
7834 | for each motif. The motifs that are then annotated to TFs and those that have | |
7835 | a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for | |
7836 | each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. | |
7837 | genes in the gene-set that are ranked above the leading edge).") | |
7838 | (license license:gpl3))) | |
7839 | ||
b46a0ee7 RW |
7840 | (define-public r-cicero |
7841 | (package | |
7842 | (name "r-cicero") | |
589ac422 | 7843 | (version "1.8.1") |
b46a0ee7 RW |
7844 | (source |
7845 | (origin | |
7846 | (method url-fetch) | |
7847 | (uri (bioconductor-uri "cicero" version)) | |
7848 | (sha256 | |
7849 | (base32 | |
589ac422 | 7850 | "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr")))) |
b46a0ee7 RW |
7851 | (build-system r-build-system) |
7852 | (propagated-inputs | |
7853 | `(("r-assertthat" ,r-assertthat) | |
7854 | ("r-biobase" ,r-biobase) | |
7855 | ("r-biocgenerics" ,r-biocgenerics) | |
7856 | ("r-data-table" ,r-data-table) | |
7857 | ("r-dplyr" ,r-dplyr) | |
7858 | ("r-fnn" ,r-fnn) | |
7859 | ("r-genomicranges" ,r-genomicranges) | |
7860 | ("r-ggplot2" ,r-ggplot2) | |
7861 | ("r-glasso" ,r-glasso) | |
7862 | ("r-gviz" ,r-gviz) | |
7863 | ("r-igraph" ,r-igraph) | |
7864 | ("r-iranges" ,r-iranges) | |
7865 | ("r-matrix" ,r-matrix) | |
7866 | ("r-monocle" ,r-monocle) | |
7867 | ("r-plyr" ,r-plyr) | |
7868 | ("r-reshape2" ,r-reshape2) | |
7869 | ("r-s4vectors" ,r-s4vectors) | |
1893092d | 7870 | ("r-stringi" ,r-stringi) |
b46a0ee7 RW |
7871 | ("r-stringr" ,r-stringr) |
7872 | ("r-tibble" ,r-tibble) | |
5ea4f604 | 7873 | ("r-tidyr" ,r-tidyr) |
b46a0ee7 | 7874 | ("r-vgam" ,r-vgam))) |
6bd6097e RW |
7875 | (native-inputs |
7876 | `(("r-knitr" ,r-knitr))) | |
b46a0ee7 RW |
7877 | (home-page "https://bioconductor.org/packages/cicero/") |
7878 | (synopsis "Predict cis-co-accessibility from single-cell data") | |
7879 | (description | |
7880 | "Cicero computes putative cis-regulatory maps from single-cell chromatin | |
7881 | accessibility data. It also extends the monocle package for use in chromatin | |
7882 | accessibility data.") | |
7883 | (license license:expat))) | |
14bb1c48 RW |
7884 | |
7885 | ;; This is the latest commit on the "monocle3" branch. | |
7886 | (define-public r-cicero-monocle3 | |
7887 | (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") | |
7888 | (revision "1")) | |
7889 | (package (inherit r-cicero) | |
7890 | (name "r-cicero-monocle3") | |
7891 | (version (git-version "1.3.2" revision commit)) | |
7892 | (source | |
7893 | (origin | |
7894 | (method git-fetch) | |
7895 | (uri (git-reference | |
b0e7b699 | 7896 | (url "https://github.com/cole-trapnell-lab/cicero-release") |
14bb1c48 RW |
7897 | (commit commit))) |
7898 | (file-name (git-file-name name version)) | |
7899 | (sha256 | |
7900 | (base32 | |
7901 | "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) | |
7902 | (propagated-inputs | |
7903 | `(("r-monocle3" ,r-monocle3) | |
7904 | ,@(alist-delete "r-monocle" | |
7905 | (package-propagated-inputs r-cicero))))))) | |
a9815a6c | 7906 | |
297531ef MIP |
7907 | (define-public r-circrnaprofiler |
7908 | (package | |
7909 | (name "r-circrnaprofiler") | |
4f617bfb | 7910 | (version "1.4.2") |
297531ef MIP |
7911 | (source |
7912 | (origin | |
7913 | (method url-fetch) | |
7914 | (uri (bioconductor-uri "circRNAprofiler" version)) | |
7915 | (sha256 | |
7916 | (base32 | |
4f617bfb | 7917 | "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8")))) |
297531ef MIP |
7918 | (properties |
7919 | `((upstream-name . "circRNAprofiler"))) | |
7920 | (build-system r-build-system) | |
7921 | (propagated-inputs | |
7922 | `(("r-annotationhub" ,r-annotationhub) | |
7923 | ("r-biostrings" ,r-biostrings) | |
7924 | ("r-bsgenome" ,r-bsgenome) | |
7925 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
7926 | ("r-deseq2" ,r-deseq2) | |
7927 | ("r-dplyr" ,r-dplyr) | |
7928 | ("r-edger" ,r-edger) | |
7929 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7930 | ("r-genomicranges" ,r-genomicranges) | |
7931 | ("r-ggplot2" ,r-ggplot2) | |
7932 | ("r-gwascat" ,r-gwascat) | |
7933 | ("r-iranges" ,r-iranges) | |
7934 | ("r-magrittr" ,r-magrittr) | |
7935 | ("r-r-utils" ,r-r-utils) | |
7936 | ("r-readr" ,r-readr) | |
7937 | ("r-reshape2" ,r-reshape2) | |
7938 | ("r-rlang" ,r-rlang) | |
7939 | ("r-rtracklayer" ,r-rtracklayer) | |
7940 | ("r-s4vectors" ,r-s4vectors) | |
7941 | ("r-seqinr" ,r-seqinr) | |
7942 | ("r-stringi" ,r-stringi) | |
7943 | ("r-stringr" ,r-stringr) | |
7944 | ("r-universalmotif" ,r-universalmotif))) | |
7945 | (native-inputs | |
7946 | `(("r-knitr" ,r-knitr))) | |
7947 | (home-page | |
7948 | "https://github.com/Aufiero/circRNAprofiler") | |
7949 | (synopsis | |
7950 | "Computational framework for the downstream analysis of circular RNA's") | |
7951 | (description | |
7952 | "@code{r-circrnaprofiler} is a computational framework for a comprehensive | |
7953 | in silico analysis of @dfn{circular RNA} (circRNAs). This computational | |
eb34afe1 | 7954 | framework allows combining and analyzing circRNAs previously detected by |
297531ef MIP |
7955 | multiple publicly available annotation-based circRNA detection tools. It |
7956 | covers different aspects of circRNAs analysis from differential expression | |
7957 | analysis, evolutionary conservation, biogenesis to functional analysis.") | |
7958 | (license license:gpl3))) | |
7959 | ||
a9815a6c RW |
7960 | (define-public r-cistopic |
7961 | (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") | |
7962 | (revision "0")) | |
7963 | (package | |
7964 | (name "r-cistopic") | |
7965 | (version (git-version "0.2.1" revision commit)) | |
7966 | (source | |
7967 | (origin | |
7968 | (method git-fetch) | |
7969 | (uri (git-reference | |
b0e7b699 | 7970 | (url "https://github.com/aertslab/cisTopic") |
a9815a6c RW |
7971 | (commit commit))) |
7972 | (file-name (git-file-name name version)) | |
7973 | (sha256 | |
7974 | (base32 | |
7975 | "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) | |
7976 | (build-system r-build-system) | |
7977 | (propagated-inputs | |
7978 | `(("r-aucell" ,r-aucell) | |
7979 | ("r-data-table" ,r-data-table) | |
7980 | ("r-dplyr" ,r-dplyr) | |
7981 | ("r-dosnow" ,r-dosnow) | |
7982 | ("r-dt" ,r-dt) | |
7983 | ("r-feather" ,r-feather) | |
7984 | ("r-fitdistrplus" ,r-fitdistrplus) | |
7985 | ("r-genomicranges" ,r-genomicranges) | |
7986 | ("r-ggplot2" ,r-ggplot2) | |
7987 | ("r-lda" ,r-lda) | |
7988 | ("r-matrix" ,r-matrix) | |
7989 | ("r-plyr" ,r-plyr) | |
7990 | ("r-rcistarget" ,r-rcistarget) | |
7991 | ("r-rtracklayer" ,r-rtracklayer) | |
7992 | ("r-s4vectors" ,r-s4vectors))) | |
7993 | (home-page "https://github.com/aertslab/cisTopic") | |
7994 | (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") | |
7995 | (description | |
7996 | "The sparse nature of single cell epigenomics data can be overruled using | |
7997 | probabilistic modelling methods such as @dfn{Latent Dirichlet | |
7998 | Allocation} (LDA). This package allows the probabilistic modelling of | |
7999 | cis-regulatory topics (cisTopics) from single cell epigenomics data, and | |
8000 | includes functionalities to identify cell states based on the contribution of | |
8001 | cisTopics and explore the nature and regulatory proteins driving them.") | |
8002 | (license license:gpl3)))) | |
d85c0f98 RW |
8003 | |
8004 | (define-public r-genie3 | |
8005 | (package | |
8006 | (name "r-genie3") | |
5d1bd611 | 8007 | (version "1.12.0") |
d85c0f98 RW |
8008 | (source |
8009 | (origin | |
8010 | (method url-fetch) | |
8011 | (uri (bioconductor-uri "GENIE3" version)) | |
8012 | (sha256 | |
8013 | (base32 | |
5d1bd611 | 8014 | "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5")))) |
d85c0f98 RW |
8015 | (properties `((upstream-name . "GENIE3"))) |
8016 | (build-system r-build-system) | |
8017 | (propagated-inputs `(("r-reshape2" ,r-reshape2))) | |
b3280883 RW |
8018 | (native-inputs |
8019 | `(("r-knitr" ,r-knitr))) | |
d85c0f98 RW |
8020 | (home-page "https://bioconductor.org/packages/GENIE3") |
8021 | (synopsis "Gene network inference with ensemble of trees") | |
8022 | (description | |
8023 | "This package implements the GENIE3 algorithm for inferring gene | |
8024 | regulatory networks from expression data.") | |
8025 | (license license:gpl2+))) | |
db316d73 RW |
8026 | |
8027 | (define-public r-roc | |
8028 | (package | |
8029 | (name "r-roc") | |
e7b61ba7 | 8030 | (version "1.66.0") |
db316d73 RW |
8031 | (source |
8032 | (origin | |
8033 | (method url-fetch) | |
8034 | (uri (bioconductor-uri "ROC" version)) | |
8035 | (sha256 | |
8036 | (base32 | |
e7b61ba7 | 8037 | "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9")))) |
db316d73 RW |
8038 | (properties `((upstream-name . "ROC"))) |
8039 | (build-system r-build-system) | |
3672b74f RW |
8040 | (propagated-inputs |
8041 | `(("r-knitr" ,r-knitr))) | |
db316d73 RW |
8042 | (home-page "https://www.bioconductor.org/packages/ROC/") |
8043 | (synopsis "Utilities for ROC curves") | |
8044 | (description | |
8045 | "This package provides utilities for @dfn{Receiver Operating | |
8046 | Characteristic} (ROC) curves, with a focus on micro arrays.") | |
8047 | (license license:artistic2.0))) | |
46721dea RW |
8048 | |
8049 | (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 | |
8050 | (package | |
8051 | (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") | |
8052 | (version "0.6.0") | |
8053 | (source | |
8054 | (origin | |
8055 | (method url-fetch) | |
8056 | (uri (bioconductor-uri | |
8057 | "IlluminaHumanMethylation450kanno.ilmn12.hg19" | |
8058 | version 'annotation)) | |
8059 | (sha256 | |
8060 | (base32 | |
8061 | "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) | |
8062 | (properties | |
8063 | `((upstream-name | |
8064 | . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) | |
8065 | (build-system r-build-system) | |
8066 | (propagated-inputs `(("r-minfi" ,r-minfi))) | |
8067 | (home-page | |
8068 | "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") | |
8069 | (synopsis "Annotation for Illumina's 450k methylation arrays") | |
8070 | (description | |
8071 | "This package provides manifests and annotation for Illumina's 450k array | |
8072 | data.") | |
8073 | (license license:artistic2.0))) | |
38babeaa RW |
8074 | |
8075 | (define-public r-watermelon | |
8076 | (package | |
8077 | (name "r-watermelon") | |
9f6e2bfe | 8078 | (version "1.34.0") |
38babeaa RW |
8079 | (source |
8080 | (origin | |
8081 | (method url-fetch) | |
8082 | (uri (bioconductor-uri "wateRmelon" version)) | |
8083 | (sha256 | |
8084 | (base32 | |
9f6e2bfe | 8085 | "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f")))) |
38babeaa RW |
8086 | (properties `((upstream-name . "wateRmelon"))) |
8087 | (build-system r-build-system) | |
8088 | (propagated-inputs | |
8089 | `(("r-biobase" ,r-biobase) | |
8090 | ("r-illuminahumanmethylation450kanno-ilmn12-hg19" | |
8091 | ,r-illuminahumanmethylation450kanno-ilmn12-hg19) | |
8092 | ("r-illuminaio" ,r-illuminaio) | |
8093 | ("r-limma" ,r-limma) | |
8094 | ("r-lumi" ,r-lumi) | |
8095 | ("r-matrixstats" ,r-matrixstats) | |
8096 | ("r-methylumi" ,r-methylumi) | |
8097 | ("r-roc" ,r-roc))) | |
8098 | (home-page "https://bioconductor.org/packages/wateRmelon/") | |
8099 | (synopsis "Illumina 450 methylation array normalization and metrics") | |
8100 | (description | |
8101 | "The standard index of DNA methylation (beta) is computed from methylated | |
8102 | and unmethylated signal intensities. Betas calculated from raw signal | |
8103 | intensities perform well, but using 11 methylomic datasets we demonstrate that | |
8104 | quantile normalization methods produce marked improvement. The commonly used | |
8105 | procedure of normalizing betas is inferior to the separate normalization of M | |
8106 | and U, and it is also advantageous to normalize Type I and Type II assays | |
8107 | separately. This package provides 15 flavours of betas and three performance | |
8108 | metrics, with methods for objects produced by the @code{methylumi} and | |
8109 | @code{minfi} packages.") | |
8110 | (license license:gpl3))) | |
7d2cb646 RW |
8111 | |
8112 | (define-public r-gdsfmt | |
8113 | (package | |
8114 | (name "r-gdsfmt") | |
6f37c3ea | 8115 | (version "1.26.1") |
7d2cb646 RW |
8116 | (source |
8117 | (origin | |
8118 | (method url-fetch) | |
8119 | (uri (bioconductor-uri "gdsfmt" version)) | |
8120 | (sha256 | |
8121 | (base32 | |
6f37c3ea | 8122 | "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n")) |
7d2cb646 RW |
8123 | (modules '((guix build utils))) |
8124 | ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build | |
8125 | ;; them and link with system libraries instead. | |
8126 | (snippet | |
8127 | '(begin | |
8128 | (for-each delete-file-recursively | |
8129 | '("src/LZ4" | |
8130 | "src/XZ" | |
8131 | "src/ZLIB")) | |
8132 | (substitute* "src/Makevars" | |
8133 | (("all: \\$\\(SHLIB\\)") "all:") | |
8134 | (("\\$\\(SHLIB\\): liblzma.a") "") | |
8135 | (("(ZLIB|LZ4)/.*") "") | |
8136 | (("CoreArray/dVLIntGDS.cpp.*") | |
8137 | "CoreArray/dVLIntGDS.cpp") | |
8138 | (("CoreArray/dVLIntGDS.o.*") | |
8139 | "CoreArray/dVLIntGDS.o") | |
8140 | (("PKG_LIBS = ./liblzma.a") | |
8141 | "PKG_LIBS = -llz4")) | |
8142 | (substitute* "src/CoreArray/dStream.h" | |
8143 | (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) | |
8144 | (string-append "include <" header ">"))) | |
8145 | #t)))) | |
8146 | (properties `((upstream-name . "gdsfmt"))) | |
8147 | (build-system r-build-system) | |
8148 | (inputs | |
8149 | `(("lz4" ,lz4) | |
8150 | ("xz" ,xz) | |
8151 | ("zlib" ,zlib))) | |
f4954b0b RW |
8152 | (native-inputs |
8153 | `(("r-knitr" ,r-knitr))) | |
7d2cb646 RW |
8154 | (home-page "http://corearray.sourceforge.net/") |
8155 | (synopsis | |
8156 | "R Interface to CoreArray Genomic Data Structure (GDS) Files") | |
8157 | (description | |
8158 | "This package provides a high-level R interface to CoreArray @dfn{Genomic | |
8159 | Data Structure} (GDS) data files, which are portable across platforms with | |
8160 | hierarchical structure to store multiple scalable array-oriented data sets | |
8161 | with metadata information. It is suited for large-scale datasets, especially | |
8162 | for data which are much larger than the available random-access memory. The | |
8163 | @code{gdsfmt} package offers efficient operations specifically designed for | |
8164 | integers of less than 8 bits, since a diploid genotype, like | |
8165 | @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a | |
8166 | byte. Data compression and decompression are available with relatively | |
8167 | efficient random access. It is also allowed to read a GDS file in parallel | |
8168 | with multiple R processes supported by the package @code{parallel}.") | |
8169 | (license license:lgpl3))) | |
6b5f59c7 RW |
8170 | |
8171 | (define-public r-bigmelon | |
8172 | (package | |
8173 | (name "r-bigmelon") | |
64f9fb30 | 8174 | (version "1.16.0") |
6b5f59c7 RW |
8175 | (source |
8176 | (origin | |
8177 | (method url-fetch) | |
8178 | (uri (bioconductor-uri "bigmelon" version)) | |
8179 | (sha256 | |
8180 | (base32 | |
64f9fb30 | 8181 | "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7")))) |
6b5f59c7 RW |
8182 | (properties `((upstream-name . "bigmelon"))) |
8183 | (build-system r-build-system) | |
8184 | (propagated-inputs | |
8185 | `(("r-biobase" ,r-biobase) | |
8186 | ("r-biocgenerics" ,r-biocgenerics) | |
8187 | ("r-gdsfmt" ,r-gdsfmt) | |
8188 | ("r-geoquery" ,r-geoquery) | |
8189 | ("r-methylumi" ,r-methylumi) | |
8190 | ("r-minfi" ,r-minfi) | |
8191 | ("r-watermelon" ,r-watermelon))) | |
8192 | (home-page "https://bioconductor.org/packages/bigmelon/") | |
8193 | (synopsis "Illumina methylation array analysis for large experiments") | |
8194 | (description | |
8195 | "This package provides methods for working with Illumina arrays using the | |
8196 | @code{gdsfmt} package.") | |
8197 | (license license:gpl3))) | |
739b2d10 | 8198 | |
e5dfcd8e RW |
8199 | (define-public r-seqbias |
8200 | (package | |
8201 | (name "r-seqbias") | |
42e00c09 | 8202 | (version "1.38.0") |
e5dfcd8e RW |
8203 | (source |
8204 | (origin | |
8205 | (method url-fetch) | |
8206 | (uri (bioconductor-uri "seqbias" version)) | |
8207 | (sha256 | |
8208 | (base32 | |
42e00c09 | 8209 | "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2")))) |
e5dfcd8e RW |
8210 | (properties `((upstream-name . "seqbias"))) |
8211 | (build-system r-build-system) | |
8212 | (propagated-inputs | |
8213 | `(("r-biostrings" ,r-biostrings) | |
8214 | ("r-genomicranges" ,r-genomicranges) | |
8215 | ("r-rhtslib" ,r-rhtslib))) | |
e5dfcd8e RW |
8216 | (home-page "https://bioconductor.org/packages/seqbias/") |
8217 | (synopsis "Estimation of per-position bias in high-throughput sequencing data") | |
8218 | (description | |
8219 | "This package implements a model of per-position sequencing bias in | |
8220 | high-throughput sequencing data using a simple Bayesian network, the structure | |
8221 | and parameters of which are trained on a set of aligned reads and a reference | |
8222 | genome sequence.") | |
8223 | (license license:lgpl3))) | |
8224 | ||
63daca1e RJ |
8225 | (define-public r-snplocs-hsapiens-dbsnp144-grch37 |
8226 | (package | |
8227 | (name "r-snplocs-hsapiens-dbsnp144-grch37") | |
8228 | (version "0.99.20") | |
8229 | (source (origin | |
8230 | (method url-fetch) | |
8231 | (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" | |
8232 | version 'annotation)) | |
8233 | (sha256 | |
8234 | (base32 | |
8235 | "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) | |
8236 | (build-system r-build-system) | |
8237 | ;; As this package provides little more than a very large data file it | |
8238 | ;; doesn't make sense to build substitutes. | |
8239 | (arguments `(#:substitutable? #f)) | |
8240 | (propagated-inputs | |
8241 | `(("r-biocgenerics" ,r-biocgenerics) | |
8242 | ("r-s4vectors" ,r-s4vectors) | |
8243 | ("r-iranges" ,r-iranges) | |
8244 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8245 | ("r-genomicranges" ,r-genomicranges) | |
8246 | ("r-bsgenome" ,r-bsgenome) | |
8247 | ("r-biostrings" ,r-biostrings))) | |
8248 | (home-page | |
8249 | "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") | |
8250 | (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") | |
8251 | (description "This package provides SNP locations and alleles for Homo | |
8252 | sapiens extracted from NCBI dbSNP Build 144. The source data files used for | |
8253 | this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped | |
8254 | to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a | |
8255 | patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, | |
1408e2ab | 8256 | X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for |
63daca1e RJ |
8257 | the mitochondrion chromosome. Therefore, the SNPs in this package can be |
8258 | injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the | |
8259 | correct position but this injection will exclude chrM (i.e. nothing will be | |
8260 | injected in that sequence).") | |
8261 | (license license:artistic2.0))) | |
8262 | ||
bb0024dc RW |
8263 | (define-public r-reqon |
8264 | (package | |
8265 | (name "r-reqon") | |
0c53f27d | 8266 | (version "1.36.0") |
bb0024dc RW |
8267 | (source |
8268 | (origin | |
8269 | (method url-fetch) | |
8270 | (uri (bioconductor-uri "ReQON" version)) | |
8271 | (sha256 | |
8272 | (base32 | |
0c53f27d | 8273 | "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq")))) |
bb0024dc RW |
8274 | (properties `((upstream-name . "ReQON"))) |
8275 | (build-system r-build-system) | |
8276 | (propagated-inputs | |
8277 | `(("r-rjava" ,r-rjava) | |
8278 | ("r-rsamtools" ,r-rsamtools) | |
8279 | ("r-seqbias" ,r-seqbias))) | |
8280 | (home-page "https://bioconductor.org/packages/ReQON/") | |
8281 | (synopsis "Recalibrating quality of nucleotides") | |
8282 | (description | |
8283 | "This package provides an implementation of an algorithm for | |
8284 | recalibrating the base quality scores for aligned sequencing data in BAM | |
8285 | format.") | |
8286 | (license license:gpl2))) | |
8287 | ||
739b2d10 RW |
8288 | (define-public r-wavcluster |
8289 | (package | |
8290 | (name "r-wavcluster") | |
fd7e23b5 | 8291 | (version "2.24.0") |
739b2d10 RW |
8292 | (source |
8293 | (origin | |
8294 | (method url-fetch) | |
8295 | (uri (bioconductor-uri "wavClusteR" version)) | |
8296 | (sha256 | |
8297 | (base32 | |
fd7e23b5 | 8298 | "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi")))) |
739b2d10 RW |
8299 | (properties `((upstream-name . "wavClusteR"))) |
8300 | (build-system r-build-system) | |
8301 | (propagated-inputs | |
8302 | `(("r-biocgenerics" ,r-biocgenerics) | |
8303 | ("r-biostrings" ,r-biostrings) | |
8304 | ("r-foreach" ,r-foreach) | |
8305 | ("r-genomicfeatures" ,r-genomicfeatures) | |
8306 | ("r-genomicranges" ,r-genomicranges) | |
8307 | ("r-ggplot2" ,r-ggplot2) | |
8308 | ("r-hmisc" ,r-hmisc) | |
8309 | ("r-iranges" ,r-iranges) | |
8310 | ("r-mclust" ,r-mclust) | |
8311 | ("r-rsamtools" ,r-rsamtools) | |
8312 | ("r-rtracklayer" ,r-rtracklayer) | |
8313 | ("r-s4vectors" ,r-s4vectors) | |
8314 | ("r-seqinr" ,r-seqinr) | |
fd7e23b5 | 8315 | ("r-stringr" ,r-stringr))) |
12b255f2 RW |
8316 | (native-inputs |
8317 | `(("r-knitr" ,r-knitr))) | |
739b2d10 RW |
8318 | (home-page "https://bioconductor.org/packages/wavClusteR/") |
8319 | (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") | |
8320 | (description | |
8321 | "This package provides an integrated pipeline for the analysis of | |
8322 | PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from | |
8323 | sequencing errors, SNPs and additional non-experimental sources by a non- | |
8324 | parametric mixture model. The protein binding sites (clusters) are then | |
8325 | resolved at high resolution and cluster statistics are estimated using a | |
8326 | rigorous Bayesian framework. Post-processing of the results, data export for | |
8327 | UCSC genome browser visualization and motif search analysis are provided. In | |
e40ecf8a | 8328 | addition, the package integrates RNA-Seq data to estimate the False |
739b2d10 RW |
8329 | Discovery Rate of cluster detection. Key functions support parallel multicore |
8330 | computing. While wavClusteR was designed for PAR-CLIP data analysis, it can | |
8331 | be applied to the analysis of other NGS data obtained from experimental | |
8332 | procedures that induce nucleotide substitutions (e.g. BisSeq).") | |
8333 | (license license:gpl2))) | |
853211a5 RW |
8334 | |
8335 | (define-public r-timeseriesexperiment | |
8336 | (package | |
8337 | (name "r-timeseriesexperiment") | |
87f704b4 | 8338 | (version "1.8.0") |
853211a5 RW |
8339 | (source |
8340 | (origin | |
8341 | (method url-fetch) | |
8342 | (uri (bioconductor-uri "TimeSeriesExperiment" version)) | |
8343 | (sha256 | |
8344 | (base32 | |
87f704b4 | 8345 | "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn")))) |
853211a5 RW |
8346 | (properties |
8347 | `((upstream-name . "TimeSeriesExperiment"))) | |
8348 | (build-system r-build-system) | |
8349 | (propagated-inputs | |
8350 | `(("r-deseq2" ,r-deseq2) | |
8351 | ("r-dplyr" ,r-dplyr) | |
8352 | ("r-dynamictreecut" ,r-dynamictreecut) | |
8353 | ("r-edger" ,r-edger) | |
8354 | ("r-ggplot2" ,r-ggplot2) | |
8355 | ("r-hmisc" ,r-hmisc) | |
8356 | ("r-limma" ,r-limma) | |
8357 | ("r-magrittr" ,r-magrittr) | |
8358 | ("r-proxy" ,r-proxy) | |
8359 | ("r-s4vectors" ,r-s4vectors) | |
8360 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
8361 | ("r-tibble" ,r-tibble) | |
8362 | ("r-tidyr" ,r-tidyr) | |
8363 | ("r-vegan" ,r-vegan) | |
8364 | ("r-viridis" ,r-viridis))) | |
49dd5041 RW |
8365 | (native-inputs |
8366 | `(("r-knitr" ,r-knitr))) | |
853211a5 RW |
8367 | (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") |
8368 | (synopsis "Analysis for short time-series data") | |
8369 | (description | |
8370 | "This package is a visualization and analysis toolbox for short time | |
8371 | course data which includes dimensionality reduction, clustering, two-sample | |
8372 | differential expression testing and gene ranking techniques. The package also | |
8373 | provides methods for retrieving enriched pathways.") | |
8374 | (license license:lgpl3+))) | |
df8576e5 RW |
8375 | |
8376 | (define-public r-variantfiltering | |
8377 | (package | |
8378 | (name "r-variantfiltering") | |
45ea773f | 8379 | (version "1.26.0") |
df8576e5 RW |
8380 | (source |
8381 | (origin | |
8382 | (method url-fetch) | |
8383 | (uri (bioconductor-uri "VariantFiltering" version)) | |
8384 | (sha256 | |
8385 | (base32 | |
45ea773f | 8386 | "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5")))) |
df8576e5 RW |
8387 | (properties |
8388 | `((upstream-name . "VariantFiltering"))) | |
8389 | (build-system r-build-system) | |
8390 | (propagated-inputs | |
8391 | `(("r-annotationdbi" ,r-annotationdbi) | |
8392 | ("r-biobase" ,r-biobase) | |
8393 | ("r-biocgenerics" ,r-biocgenerics) | |
8394 | ("r-biocparallel" ,r-biocparallel) | |
8395 | ("r-biostrings" ,r-biostrings) | |
8396 | ("r-bsgenome" ,r-bsgenome) | |
8397 | ("r-dt" ,r-dt) | |
8398 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8399 | ("r-genomicfeatures" ,r-genomicfeatures) | |
8400 | ("r-genomicranges" ,r-genomicranges) | |
8401 | ("r-genomicscores" ,r-genomicscores) | |
8402 | ("r-graph" ,r-graph) | |
8403 | ("r-gviz" ,r-gviz) | |
8404 | ("r-iranges" ,r-iranges) | |
8405 | ("r-rbgl" ,r-rbgl) | |
8406 | ("r-rsamtools" ,r-rsamtools) | |
8407 | ("r-s4vectors" ,r-s4vectors) | |
8408 | ("r-shiny" ,r-shiny) | |
8409 | ("r-shinyjs" ,r-shinyjs) | |
8410 | ("r-shinythemes" ,r-shinythemes) | |
8411 | ("r-shinytree" ,r-shinytree) | |
8412 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
8413 | ("r-variantannotation" ,r-variantannotation) | |
8414 | ("r-xvector" ,r-xvector))) | |
8415 | (home-page "https://github.com/rcastelo/VariantFiltering") | |
8416 | (synopsis "Filtering of coding and non-coding genetic variants") | |
8417 | (description | |
8418 | "Filter genetic variants using different criteria such as inheritance | |
8419 | model, amino acid change consequence, minor allele frequencies across human | |
8420 | populations, splice site strength, conservation, etc.") | |
8421 | (license license:artistic2.0))) | |
f5349b4d RW |
8422 | |
8423 | (define-public r-genomegraphs | |
8424 | (package | |
8425 | (name "r-genomegraphs") | |
053a2127 | 8426 | (version "1.46.0") |
f5349b4d RW |
8427 | (source |
8428 | (origin | |
8429 | (method url-fetch) | |
8430 | (uri (bioconductor-uri "GenomeGraphs" version)) | |
8431 | (sha256 | |
8432 | (base32 | |
053a2127 | 8433 | "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) |
f5349b4d RW |
8434 | (properties `((upstream-name . "GenomeGraphs"))) |
8435 | (build-system r-build-system) | |
8436 | (propagated-inputs | |
8437 | `(("r-biomart" ,r-biomart))) | |
8438 | (home-page "https://bioconductor.org/packages/GenomeGraphs/") | |
8439 | (synopsis "Plotting genomic information from Ensembl") | |
8440 | (description | |
8441 | "Genomic data analyses requires integrated visualization of known genomic | |
8442 | information and new experimental data. GenomeGraphs uses the biomaRt package | |
8443 | to perform live annotation queries to Ensembl and translates this to e.g. | |
8444 | gene/transcript structures in viewports of the grid graphics package. This | |
8445 | results in genomic information plotted together with your data. Another | |
8446 | strength of GenomeGraphs is to plot different data types such as array CGH, | |
8447 | gene expression, sequencing and other data, together in one plot using the | |
8448 | same genome coordinate system.") | |
8449 | (license license:artistic2.0))) | |
2a360cf6 RW |
8450 | |
8451 | (define-public r-wavetiling | |
8452 | (package | |
8453 | (name "r-wavetiling") | |
e13f9773 | 8454 | (version "1.28.0") |
2a360cf6 RW |
8455 | (source |
8456 | (origin | |
8457 | (method url-fetch) | |
8458 | (uri (bioconductor-uri "waveTiling" version)) | |
8459 | (sha256 | |
8460 | (base32 | |
e13f9773 | 8461 | "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) |
2a360cf6 RW |
8462 | (properties `((upstream-name . "waveTiling"))) |
8463 | (build-system r-build-system) | |
8464 | (propagated-inputs | |
8465 | `(("r-affy" ,r-affy) | |
8466 | ("r-biobase" ,r-biobase) | |
8467 | ("r-biostrings" ,r-biostrings) | |
8468 | ("r-genomegraphs" ,r-genomegraphs) | |
8469 | ("r-genomicranges" ,r-genomicranges) | |
8470 | ("r-iranges" ,r-iranges) | |
8471 | ("r-oligo" ,r-oligo) | |
8472 | ("r-oligoclasses" ,r-oligoclasses) | |
8473 | ("r-preprocesscore" ,r-preprocesscore) | |
8474 | ("r-waveslim" ,r-waveslim))) | |
8475 | (home-page "https://r-forge.r-project.org/projects/wavetiling/") | |
8476 | (synopsis "Wavelet-based models for tiling array transcriptome analysis") | |
8477 | (description | |
8478 | "This package is designed to conduct transcriptome analysis for tiling | |
8479 | arrays based on fast wavelet-based functional models.") | |
8480 | (license license:gpl2+))) | |
d80a1569 RW |
8481 | |
8482 | (define-public r-variancepartition | |
8483 | (package | |
8484 | (name "r-variancepartition") | |
44ecd5f7 | 8485 | (version "1.20.0") |
d80a1569 RW |
8486 | (source |
8487 | (origin | |
8488 | (method url-fetch) | |
8489 | (uri (bioconductor-uri "variancePartition" version)) | |
8490 | (sha256 | |
8491 | (base32 | |
44ecd5f7 | 8492 | "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah")))) |
d80a1569 RW |
8493 | (properties |
8494 | `((upstream-name . "variancePartition"))) | |
8495 | (build-system r-build-system) | |
8496 | (propagated-inputs | |
8497 | `(("r-biobase" ,r-biobase) | |
326746e1 | 8498 | ("r-biocparallel" ,r-biocparallel) |
d80a1569 RW |
8499 | ("r-colorramps" ,r-colorramps) |
8500 | ("r-doparallel" ,r-doparallel) | |
8501 | ("r-foreach" ,r-foreach) | |
8502 | ("r-ggplot2" ,r-ggplot2) | |
8503 | ("r-gplots" ,r-gplots) | |
8504 | ("r-iterators" ,r-iterators) | |
8505 | ("r-limma" ,r-limma) | |
8506 | ("r-lme4" ,r-lme4) | |
8507 | ("r-lmertest" ,r-lmertest) | |
8508 | ("r-mass" ,r-mass) | |
8509 | ("r-pbkrtest" ,r-pbkrtest) | |
8510 | ("r-progress" ,r-progress) | |
8511 | ("r-reshape2" ,r-reshape2) | |
8512 | ("r-scales" ,r-scales))) | |
fbbaf5ae RW |
8513 | (native-inputs |
8514 | `(("r-knitr" ,r-knitr))) | |
d80a1569 RW |
8515 | (home-page "https://bioconductor.org/packages/variancePartition/") |
8516 | (synopsis "Analyze variation in gene expression experiments") | |
8517 | (description | |
8518 | "This is a package providing tools to quantify and interpret multiple | |
8519 | sources of biological and technical variation in gene expression experiments. | |
8520 | It uses a linear mixed model to quantify variation in gene expression | |
8521 | attributable to individual, tissue, time point, or technical variables. The | |
8522 | package includes dream differential expression analysis for repeated | |
8523 | measures.") | |
8524 | (license license:gpl2+))) | |
16e2e4f2 | 8525 | |
8526 | (define-public r-htqpcr | |
8527 | (package | |
8528 | (name "r-htqpcr") | |
949626f2 | 8529 | (version "1.44.0") |
16e2e4f2 | 8530 | (source |
8531 | (origin | |
8532 | (method url-fetch) | |
8533 | (uri (bioconductor-uri "HTqPCR" version)) | |
8534 | (sha256 | |
8535 | (base32 | |
949626f2 | 8536 | "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji")))) |
16e2e4f2 | 8537 | (properties `((upstream-name . "HTqPCR"))) |
8538 | (build-system r-build-system) | |
8539 | (propagated-inputs | |
8540 | `(("r-affy" ,r-affy) | |
8541 | ("r-biobase" ,r-biobase) | |
8542 | ("r-gplots" ,r-gplots) | |
8543 | ("r-limma" ,r-limma) | |
8544 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
486a0800 TGR |
8545 | (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" |
8546 | "groups/bertone/software/HTqPCR.pdf")) | |
16e2e4f2 | 8547 | (synopsis "Automated analysis of high-throughput qPCR data") |
8548 | (description | |
8549 | "Analysis of Ct values from high throughput quantitative real-time | |
8550 | PCR (qPCR) assays across multiple conditions or replicates. The input data | |
8551 | can be from spatially-defined formats such ABI TaqMan Low Density Arrays or | |
8552 | OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad | |
8553 | Laboratories; conventional 96- or 384-well plates; or microfluidic devices | |
8554 | such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data | |
8555 | loading, quality assessment, normalization, visualization and parametric or | |
8556 | non-parametric testing for statistical significance in Ct values between | |
8557 | features (e.g. genes, microRNAs).") | |
8558 | (license license:artistic2.0))) | |
86fb2c63 | 8559 | |
8560 | (define-public r-unifiedwmwqpcr | |
8561 | (package | |
8562 | (name "r-unifiedwmwqpcr") | |
fa7e2429 | 8563 | (version "1.26.0") |
86fb2c63 | 8564 | (source |
8565 | (origin | |
8566 | (method url-fetch) | |
8567 | (uri (bioconductor-uri "unifiedWMWqPCR" version)) | |
8568 | (sha256 | |
8569 | (base32 | |
fa7e2429 | 8570 | "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv")))) |
86fb2c63 | 8571 | (properties |
8572 | `((upstream-name . "unifiedWMWqPCR"))) | |
8573 | (build-system r-build-system) | |
8574 | (propagated-inputs | |
8575 | `(("r-biocgenerics" ,r-biocgenerics) | |
8576 | ("r-htqpcr" ,r-htqpcr))) | |
8577 | (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") | |
8578 | (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") | |
8579 | (description | |
b5b0ee3b | 8580 | "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR |
86fb2c63 | 8581 | data. This modified test allows for testing differential expression in qPCR |
8582 | data.") | |
8583 | (license license:gpl2+))) | |
72b67e0b | 8584 | |
1353e536 MIP |
8585 | (define-public r-universalmotif |
8586 | (package | |
8587 | (name "r-universalmotif") | |
5bd5f755 | 8588 | (version "1.8.5") |
1353e536 MIP |
8589 | (source |
8590 | (origin | |
8591 | (method url-fetch) | |
8592 | (uri (bioconductor-uri "universalmotif" version)) | |
8593 | (sha256 | |
8594 | (base32 | |
5bd5f755 | 8595 | "07862bs771xldmdnq0zr8926dr299ach8nrgci14p5bbrc88l3ly")))) |
1353e536 MIP |
8596 | (properties |
8597 | `((upstream-name . "universalmotif"))) | |
8598 | (build-system r-build-system) | |
8599 | (arguments | |
8600 | `(#:phases | |
8601 | (modify-phases %standard-phases | |
8602 | (add-after 'unpack 'fix-reference-to-strip | |
8603 | (lambda _ | |
8604 | (substitute* "src/Makevars" | |
8605 | (("/usr/bin/strip") (which "strip")))))))) | |
8606 | (propagated-inputs | |
8607 | `(("r-biocgenerics" ,r-biocgenerics) | |
8608 | ("r-biostrings" ,r-biostrings) | |
8609 | ("r-ggplot2" ,r-ggplot2) | |
8610 | ("r-ggseqlogo" ,r-ggseqlogo) | |
8611 | ("r-iranges" ,r-iranges) | |
8612 | ("r-mass" ,r-mass) | |
8613 | ("r-rcpp" ,r-rcpp) | |
8614 | ("r-rcppthread" ,r-rcppthread) | |
8615 | ("r-rdpack" ,r-rdpack) | |
8616 | ("r-rlang" ,r-rlang) | |
8617 | ("r-s4vectors" ,r-s4vectors) | |
8618 | ("r-yaml" ,r-yaml))) | |
8619 | (native-inputs | |
8620 | `(("r-knitr" ,r-knitr))) | |
8621 | (home-page | |
8622 | "https://bioconductor.org/packages/universalmotif/") | |
8623 | (synopsis | |
8624 | "Specific structures importer, modifier, and exporter for R") | |
8625 | (description | |
8626 | "This package allows importing most common @dfn{specific structure} | |
8627 | (motif) types into R for use by functions provided by other Bioconductor | |
8628 | motif-related packages. Motifs can be exported into most major motif formats | |
8629 | from various classes as defined by other Bioconductor packages. A suite of | |
8630 | motif and sequence manipulation and analysis functions are included, including | |
8631 | enrichment, comparison, P-value calculation, shuffling, trimming, higher-order | |
8632 | motifs, and others.") | |
8633 | (license license:gpl3))) | |
8634 | ||
72b67e0b RW |
8635 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put |
8636 | ;; it here. | |
8637 | (define-public r-activedriverwgs | |
8638 | (package | |
8639 | (name "r-activedriverwgs") | |
5412da84 | 8640 | (version "1.1.1") |
72b67e0b RW |
8641 | (source |
8642 | (origin | |
8643 | (method url-fetch) | |
8644 | (uri (cran-uri "ActiveDriverWGS" version)) | |
8645 | (sha256 | |
8646 | (base32 | |
5412da84 | 8647 | "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say")))) |
72b67e0b RW |
8648 | (properties |
8649 | `((upstream-name . "ActiveDriverWGS"))) | |
8650 | (build-system r-build-system) | |
8651 | (propagated-inputs | |
8652 | `(("r-biostrings" ,r-biostrings) | |
8653 | ("r-bsgenome" ,r-bsgenome) | |
8654 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
8655 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8656 | ("r-genomicranges" ,r-genomicranges) | |
8657 | ("r-iranges" ,r-iranges) | |
72b67e0b | 8658 | ("r-s4vectors" ,r-s4vectors))) |
e1ce10e3 RW |
8659 | (native-inputs |
8660 | `(("r-knitr" ,r-knitr))) | |
72b67e0b RW |
8661 | (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") |
8662 | (synopsis "Driver discovery tool for cancer whole genomes") | |
8663 | (description | |
8664 | "This package provides a method for finding an enrichment of cancer | |
8665 | simple somatic mutations (SNVs and Indels) in functional elements across the | |
8666 | human genome. ActiveDriverWGS detects coding and noncoding driver elements | |
8667 | using whole genome sequencing data.") | |
8668 | (license license:gpl3))) | |
8e6f63dd RW |
8669 | |
8670 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put | |
8671 | ;; it here. | |
8672 | (define-public r-activepathways | |
8673 | (package | |
8674 | (name "r-activepathways") | |
a9a91280 | 8675 | (version "1.0.2") |
8e6f63dd RW |
8676 | (source |
8677 | (origin | |
8678 | (method url-fetch) | |
8679 | (uri (cran-uri "ActivePathways" version)) | |
8680 | (sha256 | |
8681 | (base32 | |
a9a91280 | 8682 | "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l")))) |
8e6f63dd RW |
8683 | (properties |
8684 | `((upstream-name . "ActivePathways"))) | |
8685 | (build-system r-build-system) | |
8686 | (propagated-inputs | |
8687 | `(("r-data-table" ,r-data-table) | |
a9a91280 | 8688 | ("r-ggplot2" ,r-ggplot2))) |
229736aa RW |
8689 | (native-inputs |
8690 | `(("r-knitr" ,r-knitr))) | |
8e6f63dd RW |
8691 | (home-page "https://cran.r-project.org/web/packages/ActivePathways/") |
8692 | (synopsis "Multivariate pathway enrichment analysis") | |
8693 | (description | |
8694 | "This package represents an integrative method of analyzing multi omics | |
8695 | data that conducts enrichment analysis of annotated gene sets. ActivePathways | |
8696 | uses a statistical data fusion approach, rationalizes contributing evidence | |
8697 | and highlights associated genes, improving systems-level understanding of | |
8698 | cellular organization in health and disease.") | |
8699 | (license license:gpl3))) | |
d11d6fea RW |
8700 | |
8701 | (define-public r-bgmix | |
8702 | (package | |
8703 | (name "r-bgmix") | |
fad5da32 | 8704 | (version "1.50.0") |
d11d6fea RW |
8705 | (source |
8706 | (origin | |
8707 | (method url-fetch) | |
8708 | (uri (bioconductor-uri "BGmix" version)) | |
8709 | (sha256 | |
8710 | (base32 | |
fad5da32 | 8711 | "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50")))) |
d11d6fea RW |
8712 | (properties `((upstream-name . "BGmix"))) |
8713 | (build-system r-build-system) | |
8714 | (propagated-inputs | |
8715 | `(("r-kernsmooth" ,r-kernsmooth))) | |
8716 | (home-page "https://bioconductor.org/packages/BGmix/") | |
8717 | (synopsis "Bayesian models for differential gene expression") | |
8718 | (description | |
8719 | "This package provides fully Bayesian mixture models for differential | |
8720 | gene expression.") | |
8721 | (license license:gpl2))) | |
75eb1149 RW |
8722 | |
8723 | (define-public r-bgx | |
8724 | (package | |
8725 | (name "r-bgx") | |
3cebe274 | 8726 | (version "1.56.0") |
75eb1149 RW |
8727 | (source |
8728 | (origin | |
8729 | (method url-fetch) | |
8730 | (uri (bioconductor-uri "bgx" version)) | |
8731 | (sha256 | |
8732 | (base32 | |
3cebe274 | 8733 | "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im")))) |
75eb1149 RW |
8734 | (properties `((upstream-name . "bgx"))) |
8735 | (build-system r-build-system) | |
8736 | (propagated-inputs | |
8737 | `(("r-affy" ,r-affy) | |
8738 | ("r-biobase" ,r-biobase) | |
8739 | ("r-gcrma" ,r-gcrma) | |
8740 | ("r-rcpp" ,r-rcpp))) | |
8741 | (home-page "https://bioconductor.org/packages/bgx/") | |
8742 | (synopsis "Bayesian gene expression") | |
8743 | (description | |
8744 | "This package provides tools for Bayesian integrated analysis of | |
8745 | Affymetrix GeneChips.") | |
8746 | (license license:gpl2))) | |
6bd50acf RW |
8747 | |
8748 | (define-public r-bhc | |
8749 | (package | |
8750 | (name "r-bhc") | |
2219bef1 | 8751 | (version "1.42.0") |
6bd50acf RW |
8752 | (source |
8753 | (origin | |
8754 | (method url-fetch) | |
8755 | (uri (bioconductor-uri "BHC" version)) | |
8756 | (sha256 | |
8757 | (base32 | |
2219bef1 | 8758 | "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn")))) |
6bd50acf RW |
8759 | (properties `((upstream-name . "BHC"))) |
8760 | (build-system r-build-system) | |
8761 | (home-page "https://bioconductor.org/packages/BHC/") | |
8762 | (synopsis "Bayesian hierarchical clustering") | |
8763 | (description | |
8764 | "The method implemented in this package performs bottom-up hierarchical | |
8765 | clustering, using a Dirichlet Process (infinite mixture) to model uncertainty | |
8766 | in the data and Bayesian model selection to decide at each step which clusters | |
8767 | to merge. This avoids several limitations of traditional methods, for example | |
8768 | how many clusters there should be and how to choose a principled distance | |
8769 | metric. This implementation accepts multinomial (i.e. discrete, with 2+ | |
8770 | categories) or time-series data. This version also includes a randomised | |
8771 | algorithm which is more efficient for larger data sets.") | |
8772 | (license license:gpl3))) | |
de9374b7 RW |
8773 | |
8774 | (define-public r-bicare | |
8775 | (package | |
8776 | (name "r-bicare") | |
4ec66569 | 8777 | (version "1.48.0") |
de9374b7 RW |
8778 | (source |
8779 | (origin | |
8780 | (method url-fetch) | |
8781 | (uri (bioconductor-uri "BicARE" version)) | |
8782 | (sha256 | |
8783 | (base32 | |
4ec66569 | 8784 | "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k")))) |
de9374b7 RW |
8785 | (properties `((upstream-name . "BicARE"))) |
8786 | (build-system r-build-system) | |
8787 | (propagated-inputs | |
8788 | `(("r-biobase" ,r-biobase) | |
8789 | ("r-gseabase" ,r-gseabase) | |
8790 | ("r-multtest" ,r-multtest))) | |
8791 | (home-page "http://bioinfo.curie.fr") | |
8792 | (synopsis "Biclustering analysis and results exploration") | |
8793 | (description | |
8794 | "This is a package for biclustering analysis and exploration of | |
8795 | results.") | |
8796 | (license license:gpl2))) | |
40fe63ad RW |
8797 | |
8798 | (define-public r-bifet | |
8799 | (package | |
8800 | (name "r-bifet") | |
d57be633 | 8801 | (version "1.10.0") |
40fe63ad RW |
8802 | (source |
8803 | (origin | |
8804 | (method url-fetch) | |
8805 | (uri (bioconductor-uri "BiFET" version)) | |
8806 | (sha256 | |
8807 | (base32 | |
d57be633 | 8808 | "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a")))) |
40fe63ad RW |
8809 | (properties `((upstream-name . "BiFET"))) |
8810 | (build-system r-build-system) | |
8811 | (propagated-inputs | |
8812 | `(("r-genomicranges" ,r-genomicranges) | |
8813 | ("r-poibin" ,r-poibin))) | |
a54fd409 RW |
8814 | (native-inputs |
8815 | `(("r-knitr" ,r-knitr))) | |
40fe63ad RW |
8816 | (home-page "https://bioconductor.org/packages/BiFET") |
8817 | (synopsis "Bias-free footprint enrichment test") | |
8818 | (description | |
8819 | "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are | |
8820 | over-represented in target regions compared to background regions after | |
8821 | correcting for the bias arising from the imbalance in read counts and GC | |
8822 | contents between the target and background regions. For a given TF k, BiFET | |
8823 | tests the null hypothesis that the target regions have the same probability of | |
8824 | having footprints for the TF k as the background regions while correcting for | |
8825 | the read count and GC content bias.") | |
8826 | (license license:gpl3))) | |
e823337c RW |
8827 | |
8828 | (define-public r-rsbml | |
8829 | (package | |
8830 | (name "r-rsbml") | |
3320f044 | 8831 | (version "2.48.0") |
e823337c RW |
8832 | (source |
8833 | (origin | |
8834 | (method url-fetch) | |
8835 | (uri (bioconductor-uri "rsbml" version)) | |
8836 | (sha256 | |
8837 | (base32 | |
3320f044 | 8838 | "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61")))) |
e823337c RW |
8839 | (properties `((upstream-name . "rsbml"))) |
8840 | (build-system r-build-system) | |
8841 | (inputs | |
8842 | `(("libsbml" ,libsbml) | |
8843 | ("zlib" ,zlib))) | |
8844 | (propagated-inputs | |
8845 | `(("r-biocgenerics" ,r-biocgenerics) | |
8846 | ("r-graph" ,r-graph))) | |
8847 | (native-inputs | |
8848 | `(("pkg-config" ,pkg-config))) | |
8849 | (home-page "http://www.sbml.org") | |
8850 | (synopsis "R support for SBML") | |
8851 | (description | |
8852 | "This package provides an R interface to libsbml for SBML parsing, | |
8853 | validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") | |
8854 | (license license:artistic2.0))) | |
75a8bb31 RW |
8855 | |
8856 | (define-public r-hypergraph | |
8857 | (package | |
8858 | (name "r-hypergraph") | |
294fd58a | 8859 | (version "1.62.0") |
75a8bb31 RW |
8860 | (source |
8861 | (origin | |
8862 | (method url-fetch) | |
8863 | (uri (bioconductor-uri "hypergraph" version)) | |
8864 | (sha256 | |
8865 | (base32 | |
294fd58a | 8866 | "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97")))) |
75a8bb31 RW |
8867 | (properties `((upstream-name . "hypergraph"))) |
8868 | (build-system r-build-system) | |
8869 | (propagated-inputs | |
8870 | `(("r-graph" ,r-graph))) | |
8871 | (home-page "https://bioconductor.org/packages/hypergraph") | |
8872 | (synopsis "Hypergraph data structures") | |
8873 | (description | |
8874 | "This package implements some simple capabilities for representing and | |
8875 | manipulating hypergraphs.") | |
8876 | (license license:artistic2.0))) | |
5aef09bd RW |
8877 | |
8878 | (define-public r-hyperdraw | |
8879 | (package | |
8880 | (name "r-hyperdraw") | |
249b7030 | 8881 | (version "1.42.0") |
5aef09bd RW |
8882 | (source |
8883 | (origin | |
8884 | (method url-fetch) | |
8885 | (uri (bioconductor-uri "hyperdraw" version)) | |
8886 | (sha256 | |
8887 | (base32 | |
249b7030 | 8888 | "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz")))) |
5aef09bd RW |
8889 | (properties `((upstream-name . "hyperdraw"))) |
8890 | (build-system r-build-system) | |
8891 | (inputs `(("graphviz" ,graphviz))) | |
8892 | (propagated-inputs | |
8893 | `(("r-graph" ,r-graph) | |
8894 | ("r-hypergraph" ,r-hypergraph) | |
8895 | ("r-rgraphviz" ,r-rgraphviz))) | |
8896 | (home-page "https://bioconductor.org/packages/hyperdraw") | |
8897 | (synopsis "Visualizing hypergraphs") | |
8898 | (description | |
8899 | "This package provides functions for visualizing hypergraphs.") | |
8900 | (license license:gpl2+))) | |
6ca6f866 RW |
8901 | |
8902 | (define-public r-biggr | |
8903 | (package | |
8904 | (name "r-biggr") | |
0f94a9ed | 8905 | (version "1.26.0") |
6ca6f866 RW |
8906 | (source |
8907 | (origin | |
8908 | (method url-fetch) | |
8909 | (uri (bioconductor-uri "BiGGR" version)) | |
8910 | (sha256 | |
8911 | (base32 | |
0f94a9ed | 8912 | "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y")))) |
6ca6f866 RW |
8913 | (properties `((upstream-name . "BiGGR"))) |
8914 | (build-system r-build-system) | |
8915 | (propagated-inputs | |
8916 | `(("r-hyperdraw" ,r-hyperdraw) | |
8917 | ("r-hypergraph" ,r-hypergraph) | |
8918 | ("r-lim" ,r-lim) | |
8919 | ("r-limsolve" ,r-limsolve) | |
8920 | ("r-rsbml" ,r-rsbml) | |
8921 | ("r-stringr" ,r-stringr))) | |
8922 | (home-page "https://bioconductor.org/packages/BiGGR/") | |
8923 | (synopsis "Constraint based modeling using metabolic reconstruction databases") | |
8924 | (description | |
8925 | "This package provides an interface to simulate metabolic reconstruction | |
8926 | from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic | |
8927 | reconstruction databases. The package facilitates @dfn{flux balance | |
8928 | analysis} (FBA) and the sampling of feasible flux distributions. Metabolic | |
8929 | networks and estimated fluxes can be visualized with hypergraphs.") | |
8930 | (license license:gpl3+))) | |
820373db RW |
8931 | |
8932 | (define-public r-bigmemoryextras | |
8933 | (package | |
8934 | (name "r-bigmemoryextras") | |
e80f8262 | 8935 | (version "1.38.0") |
820373db RW |
8936 | (source |
8937 | (origin | |
8938 | (method url-fetch) | |
8939 | (uri (bioconductor-uri "bigmemoryExtras" version)) | |
8940 | (sha256 | |
8941 | (base32 | |
e80f8262 | 8942 | "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj")))) |
820373db RW |
8943 | (properties |
8944 | `((upstream-name . "bigmemoryExtras"))) | |
8945 | (build-system r-build-system) | |
8946 | (propagated-inputs | |
8947 | `(("r-bigmemory" ,r-bigmemory))) | |
eef9c99c RW |
8948 | (native-inputs |
8949 | `(("r-knitr" ,r-knitr))) | |
820373db RW |
8950 | (home-page "https://github.com/phaverty/bigmemoryExtras") |
8951 | (synopsis "Extension of the bigmemory package") | |
8952 | (description | |
8953 | "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds | |
8954 | safety and convenience features to the @code{filebacked.big.matrix} class from | |
8955 | the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by | |
8956 | monitoring and gracefully restoring the connection to on-disk data and it also | |
7230f6d5 | 8957 | protects against accidental data modification with a file-system-based |
820373db RW |
8958 | permissions system. Utilities are provided for using @code{BigMatrix}-derived |
8959 | classes as @code{assayData} matrices within the @code{Biobase} package's | |
8960 | @code{eSet} family of classes. @code{BigMatrix} provides some optimizations | |
8961 | related to attaching to, and indexing into, file-backed matrices with | |
8962 | dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, | |
8963 | a file-backed matrix with factor properties.") | |
8964 | (license license:artistic2.0))) | |
d38775b1 RW |
8965 | |
8966 | (define-public r-bigpint | |
8967 | (package | |
8968 | (name "r-bigpint") | |
1e288678 | 8969 | (version "1.6.0") |
d38775b1 RW |
8970 | (source |
8971 | (origin | |
8972 | (method url-fetch) | |
8973 | (uri (bioconductor-uri "bigPint" version)) | |
8974 | (sha256 | |
8975 | (base32 | |
1e288678 | 8976 | "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis")))) |
d38775b1 RW |
8977 | (properties `((upstream-name . "bigPint"))) |
8978 | (build-system r-build-system) | |
8979 | (propagated-inputs | |
d0badcc1 RW |
8980 | `(("r-delayedarray" ,r-delayedarray) |
8981 | ("r-dplyr" ,r-dplyr) | |
d38775b1 RW |
8982 | ("r-ggally" ,r-ggally) |
8983 | ("r-ggplot2" ,r-ggplot2) | |
8984 | ("r-gridextra" ,r-gridextra) | |
8985 | ("r-hexbin" ,r-hexbin) | |
8986 | ("r-hmisc" ,r-hmisc) | |
8987 | ("r-htmlwidgets" ,r-htmlwidgets) | |
8988 | ("r-plotly" ,r-plotly) | |
8989 | ("r-plyr" ,r-plyr) | |
8990 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
8991 | ("r-reshape" ,r-reshape) | |
8992 | ("r-shiny" ,r-shiny) | |
8993 | ("r-shinycssloaders" ,r-shinycssloaders) | |
8994 | ("r-shinydashboard" ,r-shinydashboard) | |
8995 | ("r-stringr" ,r-stringr) | |
d0badcc1 | 8996 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
d38775b1 | 8997 | ("r-tidyr" ,r-tidyr))) |
1f2f01ae RW |
8998 | (native-inputs |
8999 | `(("r-knitr" ,r-knitr))) | |
d38775b1 RW |
9000 | (home-page "https://github.com/lindsayrutter/bigPint") |
9001 | (synopsis "Big multivariate data plotted interactively") | |
9002 | (description | |
9003 | "This package provides methods for visualizing large multivariate | |
9004 | datasets using static and interactive scatterplot matrices, parallel | |
9005 | coordinate plots, volcano plots, and litre plots. It includes examples for | |
9006 | visualizing RNA-sequencing datasets and differentially expressed genes.") | |
9007 | (license license:gpl3))) | |
991554fc RW |
9008 | |
9009 | (define-public r-chemminer | |
9010 | (package | |
9011 | (name "r-chemminer") | |
8c8d365c | 9012 | (version "3.42.2") |
991554fc RW |
9013 | (source |
9014 | (origin | |
9015 | (method url-fetch) | |
9016 | (uri (bioconductor-uri "ChemmineR" version)) | |
9017 | (sha256 | |
9018 | (base32 | |
8c8d365c | 9019 | "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9")))) |
991554fc RW |
9020 | (properties `((upstream-name . "ChemmineR"))) |
9021 | (build-system r-build-system) | |
9022 | (propagated-inputs | |
9023 | `(("r-base64enc" ,r-base64enc) | |
9024 | ("r-bh" ,r-bh) | |
9025 | ("r-biocgenerics" ,r-biocgenerics) | |
9026 | ("r-dbi" ,r-dbi) | |
9027 | ("r-digest" ,r-digest) | |
9028 | ("r-dt" ,r-dt) | |
9029 | ("r-ggplot2" ,r-ggplot2) | |
9030 | ("r-gridextra" ,r-gridextra) | |
9031 | ("r-png" ,r-png) | |
9032 | ("r-rcpp" ,r-rcpp) | |
9033 | ("r-rcurl" ,r-rcurl) | |
9034 | ("r-rjson" ,r-rjson) | |
9035 | ("r-rsvg" ,r-rsvg))) | |
06908a73 RW |
9036 | (native-inputs |
9037 | `(("r-knitr" ,r-knitr))) | |
991554fc RW |
9038 | (home-page "https://github.com/girke-lab/ChemmineR") |
9039 | (synopsis "Cheminformatics toolkit for R") | |
9040 | (description | |
9041 | "ChemmineR is a cheminformatics package for analyzing drug-like small | |
9042 | molecule data in R. It contains functions for efficient processing of large | |
9043 | numbers of molecules, physicochemical/structural property predictions, | |
9044 | structural similarity searching, classification and clustering of compound | |
9045 | libraries with a wide spectrum of algorithms. In addition, it offers | |
9046 | visualization functions for compound clustering results and chemical | |
9047 | structures.") | |
9048 | (license license:artistic2.0))) | |
48bcbef0 RW |
9049 | |
9050 | (define-public r-bioassayr | |
9051 | (package | |
9052 | (name "r-bioassayr") | |
c1942727 | 9053 | (version "1.28.3") |
48bcbef0 RW |
9054 | (source |
9055 | (origin | |
9056 | (method url-fetch) | |
9057 | (uri (bioconductor-uri "bioassayR" version)) | |
9058 | (sha256 | |
9059 | (base32 | |
c1942727 | 9060 | "03pdb76j7c28b1h1flb40ahq7i9iha22kblq6mkl3x4xmrdgaw5y")))) |
48bcbef0 RW |
9061 | (properties `((upstream-name . "bioassayR"))) |
9062 | (build-system r-build-system) | |
9063 | (propagated-inputs | |
9064 | `(("r-biocgenerics" ,r-biocgenerics) | |
9065 | ("r-chemminer" ,r-chemminer) | |
9066 | ("r-dbi" ,r-dbi) | |
9067 | ("r-matrix" ,r-matrix) | |
9068 | ("r-rjson" ,r-rjson) | |
9069 | ("r-rsqlite" ,r-rsqlite) | |
9070 | ("r-xml" ,r-xml))) | |
faaf2b35 RW |
9071 | (native-inputs |
9072 | `(("r-knitr" ,r-knitr))) | |
323aec6a | 9073 | (home-page "https://github.com/girke-lab/bioassayR") |
48bcbef0 RW |
9074 | (synopsis "Cross-target analysis of small molecule bioactivity") |
9075 | (description | |
9076 | "bioassayR is a computational tool that enables simultaneous analysis of | |
9077 | thousands of bioassay experiments performed over a diverse set of compounds | |
9078 | and biological targets. Unique features include support for large-scale | |
9079 | cross-target analyses of both public and custom bioassays, generation of | |
9080 | @dfn{high throughput screening fingerprints} (HTSFPs), and an optional | |
9081 | preloaded database that provides access to a substantial portion of publicly | |
9082 | available bioactivity data.") | |
9083 | (license license:artistic2.0))) | |
29fd736a RW |
9084 | |
9085 | (define-public r-biobroom | |
9086 | (package | |
9087 | (name "r-biobroom") | |
95e30d8f | 9088 | (version "1.22.0") |
29fd736a RW |
9089 | (source |
9090 | (origin | |
9091 | (method url-fetch) | |
9092 | (uri (bioconductor-uri "biobroom" version)) | |
9093 | (sha256 | |
9094 | (base32 | |
95e30d8f | 9095 | "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv")))) |
29fd736a RW |
9096 | (properties `((upstream-name . "biobroom"))) |
9097 | (build-system r-build-system) | |
9098 | (propagated-inputs | |
9099 | `(("r-biobase" ,r-biobase) | |
9100 | ("r-broom" ,r-broom) | |
9101 | ("r-dplyr" ,r-dplyr) | |
9102 | ("r-tidyr" ,r-tidyr))) | |
e09ca033 RW |
9103 | (native-inputs |
9104 | `(("r-knitr" ,r-knitr))) | |
29fd736a RW |
9105 | (home-page "https://github.com/StoreyLab/biobroom") |
9106 | (synopsis "Turn Bioconductor objects into tidy data frames") | |
9107 | (description | |
9108 | "This package contains methods for converting standard objects | |
9109 | constructed by bioinformatics packages, especially those in Bioconductor, and | |
9110 | converting them to @code{tidy} data. It thus serves as a complement to the | |
9111 | @code{broom} package, and follows the same tidy, augment, glance division of | |
9112 | tidying methods. Tidying data makes it easy to recombine, reshape and | |
9113 | visualize bioinformatics analyses.") | |
9114 | ;; Any version of the LGPL. | |
9115 | (license license:lgpl3+))) | |
c373223e RW |
9116 | |
9117 | (define-public r-graphite | |
9118 | (package | |
9119 | (name "r-graphite") | |
26224e09 | 9120 | (version "1.36.0") |
c373223e RW |
9121 | (source |
9122 | (origin | |
9123 | (method url-fetch) | |
9124 | (uri (bioconductor-uri "graphite" version)) | |
9125 | (sha256 | |
9126 | (base32 | |
26224e09 | 9127 | "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk")))) |
c373223e RW |
9128 | (properties `((upstream-name . "graphite"))) |
9129 | (build-system r-build-system) | |
9130 | (propagated-inputs | |
9131 | `(("r-annotationdbi" ,r-annotationdbi) | |
9132 | ("r-checkmate" ,r-checkmate) | |
9133 | ("r-graph" ,r-graph) | |
9134 | ("r-httr" ,r-httr) | |
9135 | ("r-rappdirs" ,r-rappdirs))) | |
9136 | (home-page "https://bioconductor.org/packages/graphite/") | |
9137 | (synopsis "Networks from pathway databases") | |
9138 | (description | |
9139 | "Graphite provides networks derived from eight public pathway databases, | |
9140 | and automates the conversion of node identifiers (e.g. from Entrez IDs to gene | |
9141 | symbols).") | |
9142 | (license license:agpl3+))) | |
f388834e RW |
9143 | |
9144 | (define-public r-reactomepa | |
9145 | (package | |
9146 | (name "r-reactomepa") | |
a4f4a552 | 9147 | (version "1.34.0") |
f388834e RW |
9148 | (source |
9149 | (origin | |
9150 | (method url-fetch) | |
9151 | (uri (bioconductor-uri "ReactomePA" version)) | |
9152 | (sha256 | |
9153 | (base32 | |
a4f4a552 | 9154 | "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m")))) |
f388834e RW |
9155 | (properties `((upstream-name . "ReactomePA"))) |
9156 | (build-system r-build-system) | |
9157 | (propagated-inputs | |
9158 | `(("r-annotationdbi" ,r-annotationdbi) | |
9159 | ("r-dose" ,r-dose) | |
9160 | ("r-enrichplot" ,r-enrichplot) | |
9161 | ("r-ggplot2" ,r-ggplot2) | |
9162 | ("r-ggraph" ,r-ggraph) | |
9163 | ("r-graphite" ,r-graphite) | |
9164 | ("r-igraph" ,r-igraph) | |
9165 | ("r-reactome-db" ,r-reactome-db))) | |
affb4ab3 RW |
9166 | (native-inputs |
9167 | `(("r-knitr" ,r-knitr))) | |
f388834e RW |
9168 | (home-page "https://guangchuangyu.github.io/software/ReactomePA") |
9169 | (synopsis "Reactome pathway analysis") | |
9170 | (description | |
9171 | "This package provides functions for pathway analysis based on the | |
9172 | REACTOME pathway database. It implements enrichment analysis, gene set | |
9173 | enrichment analysis and several functions for visualization.") | |
9174 | (license license:gpl2))) | |
21afe920 RW |
9175 | |
9176 | (define-public r-ebarrays | |
9177 | (package | |
9178 | (name "r-ebarrays") | |
b0f3bfe4 | 9179 | (version "2.54.0") |
21afe920 RW |
9180 | (source |
9181 | (origin | |
9182 | (method url-fetch) | |
9183 | (uri (bioconductor-uri "EBarrays" version)) | |
9184 | (sha256 | |
9185 | (base32 | |
b0f3bfe4 | 9186 | "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd")))) |
21afe920 RW |
9187 | (properties `((upstream-name . "EBarrays"))) |
9188 | (build-system r-build-system) | |
9189 | (propagated-inputs | |
9190 | `(("r-biobase" ,r-biobase) | |
9191 | ("r-cluster" ,r-cluster) | |
9192 | ("r-lattice" ,r-lattice))) | |
9193 | (home-page "https://bioconductor.org/packages/EBarrays/") | |
9194 | (synopsis "Gene clustering and differential expression identification") | |
9195 | (description | |
9196 | "EBarrays provides tools for the analysis of replicated/unreplicated | |
9197 | microarray data.") | |
9198 | (license license:gpl2+))) | |
f180be29 RW |
9199 | |
9200 | (define-public r-bioccasestudies | |
9201 | (package | |
9202 | (name "r-bioccasestudies") | |
7dced9ad | 9203 | (version "1.52.0") |
f180be29 RW |
9204 | (source |
9205 | (origin | |
9206 | (method url-fetch) | |
9207 | (uri (bioconductor-uri "BiocCaseStudies" version)) | |
9208 | (sha256 | |
9209 | (base32 | |
7dced9ad | 9210 | "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1")))) |
f180be29 RW |
9211 | (properties |
9212 | `((upstream-name . "BiocCaseStudies"))) | |
9213 | (build-system r-build-system) | |
9214 | (propagated-inputs `(("r-biobase" ,r-biobase))) | |
9215 | (home-page "https://bioconductor.org/packages/BiocCaseStudies") | |
9216 | (synopsis "Support for the case studies monograph") | |
9217 | (description | |
9218 | "This package provides software and data to support the case studies | |
9219 | monograph.") | |
9220 | (license license:artistic2.0))) | |
49f0860b | 9221 | |
852fa82d | 9222 | (define-public r-bioccheck |
9223 | (package | |
9224 | (name "r-bioccheck") | |
9225 | (version "1.26.0") | |
9226 | (source (origin | |
9227 | (method url-fetch) | |
9228 | (uri (bioconductor-uri "BiocCheck" version)) | |
9229 | (sha256 | |
9230 | (base32 | |
9231 | "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) | |
9232 | (properties | |
9233 | `((upstream-name . "BiocCheck"))) | |
9234 | (build-system r-build-system) | |
9235 | (arguments | |
9236 | '(#:phases | |
9237 | (modify-phases %standard-phases | |
9238 | ;; This package can be used by calling BiocCheck(<package>) from | |
9239 | ;; within R, or by running R CMD BiocCheck <package>. This phase | |
9240 | ;; makes sure the latter works. For this to work, the BiocCheck | |
9241 | ;; script must be somewhere on the PATH (not the R bin directory). | |
9242 | (add-after 'install 'install-bioccheck-subcommand | |
9243 | (lambda* (#:key outputs #:allow-other-keys) | |
9244 | (let* ((out (assoc-ref outputs "out")) | |
9245 | (dest-dir (string-append out "/bin")) | |
9246 | (script-dir | |
9247 | (string-append out "/site-library/BiocCheck/script/"))) | |
9248 | (mkdir-p dest-dir) | |
9249 | (symlink (string-append script-dir "/checkBadDeps.R") | |
9250 | (string-append dest-dir "/checkBadDeps.R")) | |
9251 | (symlink (string-append script-dir "/BiocCheck") | |
9252 | (string-append dest-dir "/BiocCheck"))) | |
9253 | #t))))) | |
9254 | (propagated-inputs | |
9255 | `(("r-codetools" ,r-codetools) | |
9256 | ("r-graph" ,r-graph) | |
9257 | ("r-httr" ,r-httr) | |
9258 | ("r-knitr" ,r-knitr) | |
9259 | ("r-optparse" ,r-optparse) | |
9260 | ("r-biocmanager" ,r-biocmanager) | |
9261 | ("r-biocviews" ,r-biocviews) | |
9262 | ("r-stringdist" ,r-stringdist))) | |
9263 | (native-inputs | |
9264 | `(("r-knitr" ,r-knitr))) | |
9265 | (home-page "https://bioconductor.org/packages/BiocCheck") | |
9266 | (synopsis "Executes Bioconductor-specific package checks") | |
9267 | (description "This package contains tools to perform additional quality | |
9268 | checks on R packages that are to be submitted to the Bioconductor repository.") | |
9269 | (license license:artistic2.0))) | |
9270 | ||
49f0860b RW |
9271 | (define-public r-biocgraph |
9272 | (package | |
9273 | (name "r-biocgraph") | |
abc18fc5 | 9274 | (version "1.52.0") |
49f0860b RW |
9275 | (source |
9276 | (origin | |
9277 | (method url-fetch) | |
9278 | (uri (bioconductor-uri "biocGraph" version)) | |
9279 | (sha256 | |
9280 | (base32 | |
abc18fc5 | 9281 | "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75")))) |
49f0860b RW |
9282 | (properties `((upstream-name . "biocGraph"))) |
9283 | (build-system r-build-system) | |
9284 | (propagated-inputs | |
9285 | `(("r-biocgenerics" ,r-biocgenerics) | |
9286 | ("r-geneplotter" ,r-geneplotter) | |
9287 | ("r-graph" ,r-graph) | |
9288 | ("r-rgraphviz" ,r-rgraphviz))) | |
9289 | (home-page "https://bioconductor.org/packages/biocGraph/") | |
9290 | (synopsis "Graph examples and use cases in Bioinformatics") | |
9291 | (description | |
9292 | "This package provides examples and code that make use of the | |
9293 | different graph related packages produced by Bioconductor.") | |
9294 | (license license:artistic2.0))) | |
244270e6 | 9295 | |
5ac55aea | 9296 | (define-public r-biocstyle |
9297 | (package | |
9298 | (name "r-biocstyle") | |
9299 | (version "2.18.1") | |
9300 | (source (origin | |
9301 | (method url-fetch) | |
9302 | (uri (bioconductor-uri "BiocStyle" version)) | |
9303 | (sha256 | |
9304 | (base32 | |
9305 | "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp")))) | |
9306 | (properties | |
9307 | `((upstream-name . "BiocStyle"))) | |
9308 | (build-system r-build-system) | |
9309 | (propagated-inputs | |
9310 | `(("r-biocmanager" ,r-biocmanager) | |
9311 | ("r-bookdown" ,r-bookdown) | |
9312 | ("r-knitr" ,r-knitr) | |
9313 | ("r-rmarkdown" ,r-rmarkdown) | |
9314 | ("r-yaml" ,r-yaml))) | |
9315 | (native-inputs | |
9316 | `(("r-knitr" ,r-knitr))) | |
9317 | (home-page "https://bioconductor.org/packages/BiocStyle") | |
9318 | (synopsis "Bioconductor formatting styles") | |
9319 | (description "This package provides standard formatting styles for | |
9320 | Bioconductor PDF and HTML documents. Package vignettes illustrate use and | |
9321 | functionality.") | |
9322 | (license license:artistic2.0))) | |
9323 | ||
134404b4 | 9324 | (define-public r-biocviews |
9325 | (package | |
9326 | (name "r-biocviews") | |
9327 | (version "1.58.1") | |
9328 | (source (origin | |
9329 | (method url-fetch) | |
9330 | (uri (bioconductor-uri "biocViews" version)) | |
9331 | (sha256 | |
9332 | (base32 | |
9333 | "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4")))) | |
9334 | (properties | |
9335 | `((upstream-name . "biocViews"))) | |
9336 | (build-system r-build-system) | |
9337 | (propagated-inputs | |
9338 | `(("r-biobase" ,r-biobase) | |
9339 | ("r-biocmanager" ,r-biocmanager) | |
9340 | ("r-graph" ,r-graph) | |
9341 | ("r-rbgl" ,r-rbgl) | |
9342 | ("r-rcurl" ,r-rcurl) | |
9343 | ("r-xml" ,r-xml) | |
9344 | ("r-runit" ,r-runit))) | |
9345 | (home-page "https://bioconductor.org/packages/biocViews") | |
9346 | (synopsis "Bioconductor package categorization helper") | |
9347 | (description "The purpose of biocViews is to create HTML pages that | |
9348 | categorize packages in a Bioconductor package repository according to keywords, | |
9349 | also known as views, in a controlled vocabulary.") | |
9350 | (license license:artistic2.0))) | |
9351 | ||
244270e6 RW |
9352 | (define-public r-experimenthub |
9353 | (package | |
9354 | (name "r-experimenthub") | |
b75b3ba2 | 9355 | (version "1.16.1") |
244270e6 RW |
9356 | (source |
9357 | (origin | |
9358 | (method url-fetch) | |
9359 | (uri (bioconductor-uri "ExperimentHub" version)) | |
9360 | (sha256 | |
9361 | (base32 | |
b75b3ba2 | 9362 | "1iyf052hh2dhlwzwwrj571cwr3hd9wp2j915sqg77x6jn40wjr1g")))) |
244270e6 RW |
9363 | (properties `((upstream-name . "ExperimentHub"))) |
9364 | (build-system r-build-system) | |
9365 | (propagated-inputs | |
9366 | `(("r-annotationhub" ,r-annotationhub) | |
9367 | ("r-biocfilecache" ,r-biocfilecache) | |
9368 | ("r-biocgenerics" ,r-biocgenerics) | |
9369 | ("r-biocmanager" ,r-biocmanager) | |
9370 | ("r-curl" ,r-curl) | |
9371 | ("r-rappdirs" ,r-rappdirs) | |
9372 | ("r-s4vectors" ,r-s4vectors))) | |
b56a3462 RW |
9373 | (native-inputs |
9374 | `(("r-knitr" ,r-knitr))) | |
244270e6 RW |
9375 | (home-page "https://bioconductor.org/packages/ExperimentHub/") |
9376 | (synopsis "Client to access ExperimentHub resources") | |
9377 | (description | |
9378 | "This package provides a client for the Bioconductor ExperimentHub web | |
9379 | resource. ExperimentHub provides a central location where curated data from | |
9380 | experiments, publications or training courses can be accessed. Each resource | |
9381 | has associated metadata, tags and date of modification. The client creates | |
9382 | and manages a local cache of files retrieved enabling quick and reproducible | |
9383 | access.") | |
9384 | (license license:artistic2.0))) | |
06784793 | 9385 | |
d5576b6e | 9386 | (define-public r-grohmm |
9387 | (package | |
9388 | (name "r-grohmm") | |
9389 | (version "1.24.0") | |
9390 | (source | |
9391 | (origin | |
9392 | (method url-fetch) | |
9393 | (uri (bioconductor-uri "groHMM" version)) | |
9394 | (sha256 | |
9395 | (base32 | |
9396 | "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx")))) | |
9397 | (properties `((upstream-name . "groHMM"))) | |
9398 | (build-system r-build-system) | |
9399 | (propagated-inputs | |
9400 | `(("r-genomeinfodb" ,r-genomeinfodb) | |
9401 | ("r-genomicalignments" ,r-genomicalignments) | |
9402 | ("r-genomicranges" ,r-genomicranges) | |
9403 | ("r-iranges" ,r-iranges) | |
9404 | ("r-mass" ,r-mass) | |
9405 | ("r-rtracklayer" ,r-rtracklayer) | |
9406 | ("r-s4vectors" ,r-s4vectors))) | |
9407 | (home-page "https://github.com/Kraus-Lab/groHMM") | |
9408 | (synopsis "GRO-seq analysis pipeline") | |
9409 | (description | |
9410 | "This package provides a pipeline for the analysis of GRO-seq data.") | |
9411 | (license license:gpl3+))) | |
9412 | ||
06784793 RW |
9413 | (define-public r-multiassayexperiment |
9414 | (package | |
9415 | (name "r-multiassayexperiment") | |
13d0b780 | 9416 | (version "1.16.0") |
06784793 RW |
9417 | (source |
9418 | (origin | |
9419 | (method url-fetch) | |
9420 | (uri (bioconductor-uri "MultiAssayExperiment" version)) | |
9421 | (sha256 | |
9422 | (base32 | |
13d0b780 | 9423 | "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs")))) |
06784793 RW |
9424 | (properties |
9425 | `((upstream-name . "MultiAssayExperiment"))) | |
9426 | (build-system r-build-system) | |
9427 | (propagated-inputs | |
9428 | `(("r-biobase" ,r-biobase) | |
9429 | ("r-biocgenerics" ,r-biocgenerics) | |
9430 | ("r-genomicranges" ,r-genomicranges) | |
9431 | ("r-iranges" ,r-iranges) | |
9432 | ("r-s4vectors" ,r-s4vectors) | |
9433 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
9434 | ("r-tidyr" ,r-tidyr))) | |
5d45d711 RW |
9435 | (native-inputs |
9436 | `(("r-knitr" ,r-knitr))) | |
798ca8d0 | 9437 | (home-page "https://waldronlab.io/MultiAssayExperiment/") |
06784793 RW |
9438 | (synopsis "Integration of multi-omics experiments in Bioconductor") |
9439 | (description | |
9440 | "MultiAssayExperiment harmonizes data management of multiple assays | |
9441 | performed on an overlapping set of specimens. It provides a familiar | |
9442 | Bioconductor user experience by extending concepts from | |
9443 | @code{SummarizedExperiment}, supporting an open-ended mix of standard data | |
9444 | classes for individual assays, and allowing subsetting by genomic ranges or | |
9445 | rownames.") | |
9446 | (license license:artistic2.0))) | |
c2b36a04 RW |
9447 | |
9448 | (define-public r-bioconcotk | |
9449 | (package | |
9450 | (name "r-bioconcotk") | |
e29b15ee | 9451 | (version "1.10.0") |
c2b36a04 RW |
9452 | (source |
9453 | (origin | |
9454 | (method url-fetch) | |
9455 | (uri (bioconductor-uri "BiocOncoTK" version)) | |
9456 | (sha256 | |
9457 | (base32 | |
e29b15ee | 9458 | "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108")))) |
c2b36a04 RW |
9459 | (properties `((upstream-name . "BiocOncoTK"))) |
9460 | (build-system r-build-system) | |
9461 | (propagated-inputs | |
9462 | `(("r-bigrquery" ,r-bigrquery) | |
9463 | ("r-car" ,r-car) | |
9464 | ("r-complexheatmap" ,r-complexheatmap) | |
9465 | ("r-curatedtcgadata" ,r-curatedtcgadata) | |
9466 | ("r-dbi" ,r-dbi) | |
9467 | ("r-dplyr" ,r-dplyr) | |
9468 | ("r-dt" ,r-dt) | |
9469 | ("r-genomicfeatures" ,r-genomicfeatures) | |
9470 | ("r-genomicranges" ,r-genomicranges) | |
9471 | ("r-ggplot2" ,r-ggplot2) | |
9472 | ("r-ggpubr" ,r-ggpubr) | |
9473 | ("r-graph" ,r-graph) | |
9474 | ("r-httr" ,r-httr) | |
9475 | ("r-iranges" ,r-iranges) | |
9476 | ("r-magrittr" ,r-magrittr) | |
9477 | ("r-plyr" ,r-plyr) | |
9478 | ("r-rgraphviz" ,r-rgraphviz) | |
9479 | ("r-rjson" ,r-rjson) | |
9480 | ("r-s4vectors" ,r-s4vectors) | |
9481 | ("r-scales" ,r-scales) | |
9482 | ("r-shiny" ,r-shiny) | |
9483 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
1c518215 RW |
9484 | (native-inputs |
9485 | `(("r-knitr" ,r-knitr))) | |
c2b36a04 RW |
9486 | (home-page "https://bioconductor.org/packages/BiocOncoTK") |
9487 | (synopsis "Bioconductor components for general cancer genomics") | |
9488 | (description | |
9489 | "The purpose of this package is to provide a central interface to various | |
9490 | tools for genome-scale analysis of cancer studies.") | |
9491 | (license license:artistic2.0))) | |
4d12c1e3 RW |
9492 | |
9493 | (define-public r-biocor | |
9494 | (package | |
9495 | (name "r-biocor") | |
072f722f | 9496 | (version "1.14.0") |
4d12c1e3 RW |
9497 | (source |
9498 | (origin | |
9499 | (method url-fetch) | |
9500 | (uri (bioconductor-uri "BioCor" version)) | |
9501 | (sha256 | |
9502 | (base32 | |
072f722f | 9503 | "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19")))) |
4d12c1e3 RW |
9504 | (properties `((upstream-name . "BioCor"))) |
9505 | (build-system r-build-system) | |
9506 | (propagated-inputs | |
9507 | `(("r-biocparallel" ,r-biocparallel) | |
9508 | ("r-gseabase" ,r-gseabase) | |
9509 | ("r-matrix" ,r-matrix))) | |
132abe5f RW |
9510 | (native-inputs |
9511 | `(("r-knitr" ,r-knitr))) | |
4d12c1e3 RW |
9512 | (home-page "https://llrs.github.io/BioCor/") |
9513 | (synopsis "Functional similarities") | |
9514 | (description | |
9515 | "This package provides tools to calculate functional similarities based | |
9516 | on the pathways described on KEGG and REACTOME or in gene sets. These | |
9517 | similarities can be calculated for pathways or gene sets, genes, or clusters | |
9518 | and combined with other similarities. They can be used to improve networks, | |
9519 | gene selection, testing relationships, and so on.") | |
9520 | (license license:expat))) | |
4a18112d RW |
9521 | |
9522 | (define-public r-biocpkgtools | |
9523 | (package | |
9524 | (name "r-biocpkgtools") | |
3c59d341 | 9525 | (version "1.8.2") |
4a18112d RW |
9526 | (source |
9527 | (origin | |
9528 | (method url-fetch) | |
9529 | (uri (bioconductor-uri "BiocPkgTools" version)) | |
9530 | (sha256 | |
9531 | (base32 | |
3c59d341 | 9532 | "18m816mh1ic0znp38wax8xppai77lkym3w84x4x30x2mf0vriqfw")))) |
4a18112d RW |
9533 | (properties `((upstream-name . "BiocPkgTools"))) |
9534 | (build-system r-build-system) | |
9535 | (propagated-inputs | |
2d6a7bca RW |
9536 | `(("r-biocfilecache" ,r-biocfilecache) |
9537 | ("r-biocmanager" ,r-biocmanager) | |
4a18112d RW |
9538 | ("r-biocviews" ,r-biocviews) |
9539 | ("r-dplyr" ,r-dplyr) | |
9540 | ("r-dt" ,r-dt) | |
9541 | ("r-gh" ,r-gh) | |
9542 | ("r-graph" ,r-graph) | |
9543 | ("r-htmltools" ,r-htmltools) | |
9544 | ("r-htmlwidgets" ,r-htmlwidgets) | |
9545 | ("r-httr" ,r-httr) | |
9546 | ("r-igraph" ,r-igraph) | |
9547 | ("r-jsonlite" ,r-jsonlite) | |
9548 | ("r-magrittr" ,r-magrittr) | |
2d6a7bca | 9549 | ("r-rappdirs" ,r-rappdirs) |
4a18112d RW |
9550 | ("r-rbgl" ,r-rbgl) |
9551 | ("r-readr" ,r-readr) | |
9552 | ("r-rex" ,r-rex) | |
2d6a7bca | 9553 | ("r-rlang" ,r-rlang) |
4a18112d RW |
9554 | ("r-rvest" ,r-rvest) |
9555 | ("r-stringr" ,r-stringr) | |
9556 | ("r-tibble" ,r-tibble) | |
9557 | ("r-tidyr" ,r-tidyr) | |
2d6a7bca | 9558 | ("r-tidyselect" ,r-tidyselect) |
4a18112d | 9559 | ("r-xml2" ,r-xml2))) |
2d6a7bca RW |
9560 | (native-inputs |
9561 | `(("r-knitr" ,r-knitr))) | |
4a18112d RW |
9562 | (home-page "https://github.com/seandavi/BiocPkgTools") |
9563 | (synopsis "Collection of tools for learning about Bioconductor packages") | |
9564 | (description | |
9565 | "Bioconductor has a rich ecosystem of metadata around packages, usage, | |
9566 | and build status. This package is a simple collection of functions to access | |
9567 | that metadata from R. The goal is to expose metadata for data mining and | |
9568 | value-added functionality such as package searching, text mining, and | |
9569 | analytics on packages.") | |
9570 | (license license:expat))) | |
43b66e3f RW |
9571 | |
9572 | (define-public r-biocset | |
9573 | (package | |
9574 | (name "r-biocset") | |
feb0cbf4 | 9575 | (version "1.4.0") |
43b66e3f RW |
9576 | (source |
9577 | (origin | |
9578 | (method url-fetch) | |
9579 | (uri (bioconductor-uri "BiocSet" version)) | |
9580 | (sha256 | |
9581 | (base32 | |
feb0cbf4 | 9582 | "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg")))) |
43b66e3f RW |
9583 | (properties `((upstream-name . "BiocSet"))) |
9584 | (build-system r-build-system) | |
9585 | (propagated-inputs | |
9586 | `(("r-annotationdbi" ,r-annotationdbi) | |
feb0cbf4 | 9587 | ("r-biocio" ,r-biocio) |
43b66e3f RW |
9588 | ("r-dplyr" ,r-dplyr) |
9589 | ("r-keggrest" ,r-keggrest) | |
feb0cbf4 | 9590 | ("r-ontologyindex" ,r-ontologyindex) |
43b66e3f RW |
9591 | ("r-plyr" ,r-plyr) |
9592 | ("r-rlang" ,r-rlang) | |
feb0cbf4 | 9593 | ("r-s4vectors" ,r-s4vectors) |
9594 | ("r-tibble" ,r-tibble) | |
9595 | ("r-tidyr" ,r-tidyr))) | |
723fa00d RW |
9596 | (native-inputs |
9597 | `(("r-knitr" ,r-knitr))) | |
43b66e3f RW |
9598 | (home-page |
9599 | "https://bioconductor.org/packages/BiocSet") | |
9600 | (synopsis | |
9601 | "Representing Different Biological Sets") | |
9602 | (description | |
9603 | "BiocSet displays different biological sets in a triple tibble format. | |
9604 | These three tibbles are @code{element}, @code{set}, and @code{elementset}. | |
5b98473a | 9605 | The user has the ability to activate one of these three tibbles to perform |
43b66e3f RW |
9606 | common functions from the @code{dplyr} package. Mapping functionality and |
9607 | accessing web references for elements/sets are also available in BiocSet.") | |
9608 | (license license:artistic2.0))) | |
0156297f RW |
9609 | |
9610 | (define-public r-biocworkflowtools | |
9611 | (package | |
9612 | (name "r-biocworkflowtools") | |
7891c83c | 9613 | (version "1.16.0") |
0156297f RW |
9614 | (source |
9615 | (origin | |
9616 | (method url-fetch) | |
9617 | (uri (bioconductor-uri "BiocWorkflowTools" version)) | |
9618 | (sha256 | |
9619 | (base32 | |
7891c83c | 9620 | "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6")))) |
0156297f RW |
9621 | (properties |
9622 | `((upstream-name . "BiocWorkflowTools"))) | |
9623 | (build-system r-build-system) | |
9624 | (propagated-inputs | |
9625 | `(("r-biocstyle" ,r-biocstyle) | |
9626 | ("r-bookdown" ,r-bookdown) | |
9627 | ("r-git2r" ,r-git2r) | |
9628 | ("r-httr" ,r-httr) | |
9629 | ("r-knitr" ,r-knitr) | |
9630 | ("r-rmarkdown" ,r-rmarkdown) | |
9631 | ("r-rstudioapi" ,r-rstudioapi) | |
9632 | ("r-stringr" ,r-stringr) | |
9633 | ("r-usethis" ,r-usethis))) | |
4ecba230 RW |
9634 | (native-inputs |
9635 | `(("r-knitr" ,r-knitr))) | |
0156297f RW |
9636 | (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") |
9637 | (synopsis "Tools to aid the development of Bioconductor Workflow packages") | |
9638 | (description | |
9639 | "This package provides functions to ease the transition between | |
9640 | Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") | |
9641 | (license license:expat))) | |
77e2de36 RW |
9642 | |
9643 | (define-public r-biodist | |
9644 | (package | |
9645 | (name "r-biodist") | |
15be98c1 | 9646 | (version "1.62.0") |
77e2de36 RW |
9647 | (source |
9648 | (origin | |
9649 | (method url-fetch) | |
9650 | (uri (bioconductor-uri "bioDist" version)) | |
9651 | (sha256 | |
9652 | (base32 | |
15be98c1 | 9653 | "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap")))) |
77e2de36 RW |
9654 | (properties `((upstream-name . "bioDist"))) |
9655 | (build-system r-build-system) | |
9656 | (propagated-inputs | |
9657 | `(("r-biobase" ,r-biobase) | |
9658 | ("r-kernsmooth" ,r-kernsmooth))) | |
9659 | (home-page "https://bioconductor.org/packages/bioDist/") | |
9660 | (synopsis "Different distance measures") | |
9661 | (description | |
9662 | "This package provides a collection of software tools for calculating | |
9663 | distance measures.") | |
9664 | (license license:artistic2.0))) | |
9bc516ba RW |
9665 | |
9666 | (define-public r-pcatools | |
9667 | (package | |
9668 | (name "r-pcatools") | |
1174317e | 9669 | (version "2.2.0") |
9bc516ba RW |
9670 | (source |
9671 | (origin | |
9672 | (method url-fetch) | |
9673 | (uri (bioconductor-uri "PCAtools" version)) | |
9674 | (sha256 | |
9675 | (base32 | |
1174317e | 9676 | "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb")))) |
9bc516ba RW |
9677 | (properties `((upstream-name . "PCAtools"))) |
9678 | (build-system r-build-system) | |
9679 | (propagated-inputs | |
9680 | `(("r-beachmat" ,r-beachmat) | |
9681 | ("r-bh" ,r-bh) | |
9682 | ("r-biocparallel" ,r-biocparallel) | |
9683 | ("r-biocsingular" ,r-biocsingular) | |
9684 | ("r-cowplot" ,r-cowplot) | |
9685 | ("r-delayedarray" ,r-delayedarray) | |
9686 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
9687 | ("r-dqrng" ,r-dqrng) | |
9688 | ("r-ggplot2" ,r-ggplot2) | |
9689 | ("r-ggrepel" ,r-ggrepel) | |
9690 | ("r-lattice" ,r-lattice) | |
9691 | ("r-matrix" ,r-matrix) | |
9692 | ("r-rcpp" ,r-rcpp) | |
9693 | ("r-reshape2" ,r-reshape2))) | |
9694 | (native-inputs `(("r-knitr" ,r-knitr))) | |
9695 | (home-page "https://github.com/kevinblighe/PCAtools") | |
9696 | (synopsis "PCAtools: everything Principal Components Analysis") | |
9697 | (description | |
9698 | "@dfn{Principal Component Analysis} (PCA) extracts the fundamental | |
9699 | structure of the data without the need to build any model to represent it. | |
9700 | This \"summary\" of the data is arrived at through a process of reduction that | |
9701 | can transform the large number of variables into a lesser number that are | |
9702 | uncorrelated (i.e. the 'principal components'), while at the same time being | |
9703 | capable of easy interpretation on the original data. PCAtools provides | |
9704 | functions for data exploration via PCA, and allows the user to generate | |
9705 | publication-ready figures. PCA is performed via @code{BiocSingular}; users | |
9706 | can also identify an optimal number of principal components via different | |
9707 | metrics, such as the elbow method and Horn's parallel analysis, which has | |
9708 | relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high | |
9709 | dimensional mass cytometry data.") | |
9710 | (license license:gpl3))) | |
c89afe75 RW |
9711 | |
9712 | (define-public r-rgreat | |
9713 | (package | |
9714 | (name "r-rgreat") | |
7a242042 | 9715 | (version "1.22.0") |
c89afe75 RW |
9716 | (source |
9717 | (origin | |
9718 | (method url-fetch) | |
9719 | (uri (bioconductor-uri "rGREAT" version)) | |
9720 | (sha256 | |
9721 | (base32 | |
7a242042 | 9722 | "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj")))) |
c89afe75 RW |
9723 | (properties `((upstream-name . "rGREAT"))) |
9724 | (build-system r-build-system) | |
9725 | (propagated-inputs | |
9726 | `(("r-genomicranges" ,r-genomicranges) | |
9727 | ("r-getoptlong" ,r-getoptlong) | |
9728 | ("r-iranges" ,r-iranges) | |
9729 | ("r-rcurl" ,r-rcurl) | |
9730 | ("r-rjson" ,r-rjson))) | |
9731 | (native-inputs `(("r-knitr" ,r-knitr))) | |
9732 | (home-page "https://github.com/jokergoo/rGREAT") | |
9733 | (synopsis "Client for GREAT analysis") | |
9734 | (description | |
9735 | "This package makes GREAT (Genomic Regions Enrichment of Annotations | |
9736 | Tool) analysis automatic by constructing a HTTP POST request according to | |
9737 | user's input and automatically retrieving results from GREAT web server.") | |
9738 | (license license:expat))) | |
0b8c7e4b RW |
9739 | |
9740 | (define-public r-m3c | |
9741 | (package | |
9742 | (name "r-m3c") | |
126846a0 | 9743 | (version "1.12.0") |
0b8c7e4b RW |
9744 | (source |
9745 | (origin | |
9746 | (method url-fetch) | |
9747 | (uri (bioconductor-uri "M3C" version)) | |
9748 | (sha256 | |
9749 | (base32 | |
126846a0 | 9750 | "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5")))) |
0b8c7e4b RW |
9751 | (properties `((upstream-name . "M3C"))) |
9752 | (build-system r-build-system) | |
9753 | (propagated-inputs | |
9754 | `(("r-cluster" ,r-cluster) | |
9755 | ("r-corpcor" ,r-corpcor) | |
9756 | ("r-doparallel" ,r-doparallel) | |
9757 | ("r-dosnow" ,r-dosnow) | |
9758 | ("r-foreach" ,r-foreach) | |
9759 | ("r-ggplot2" ,r-ggplot2) | |
9760 | ("r-matrix" ,r-matrix) | |
9761 | ("r-matrixcalc" ,r-matrixcalc) | |
9762 | ("r-rtsne" ,r-rtsne) | |
9763 | ("r-umap" ,r-umap))) | |
9764 | (native-inputs `(("r-knitr" ,r-knitr))) | |
9765 | (home-page "https://bioconductor.org/packages/M3C") | |
9766 | (synopsis "Monte Carlo reference-based consensus clustering") | |
9767 | (description | |
9768 | "M3C is a consensus clustering algorithm that uses a Monte Carlo | |
9769 | simulation to eliminate overestimation of @code{K} and can reject the null | |
9770 | hypothesis @code{K=1}.") | |
9771 | (license license:agpl3+))) | |
488001eb PL |
9772 | |
9773 | (define-public r-icens | |
9774 | (package | |
9775 | (name "r-icens") | |
3cacc3bd | 9776 | (version "1.62.0") |
488001eb PL |
9777 | (source |
9778 | (origin | |
9779 | (method url-fetch) | |
9780 | (uri (bioconductor-uri "Icens" version)) | |
9781 | (sha256 | |
9782 | (base32 | |
3cacc3bd | 9783 | "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr")))) |
488001eb PL |
9784 | (properties `((upstream-name . "Icens"))) |
9785 | (build-system r-build-system) | |
9786 | (propagated-inputs | |
9787 | `(("r-survival" ,r-survival))) | |
9788 | (home-page "https://bioconductor.org/packages/Icens") | |
9789 | (synopsis "NPMLE for censored and truncated data") | |
9790 | (description | |
9791 | "This package provides many functions for computing the | |
9792 | @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and | |
9793 | truncated data.") | |
9794 | (license license:artistic2.0))) | |
655c4bb2 PL |
9795 | |
9796 | ;; This is a CRAN package but it depends on r-icens, which is published on | |
9797 | ;; Bioconductor. | |
9798 | (define-public r-interval | |
9799 | (package | |
9800 | (name "r-interval") | |
65e361f9 | 9801 | (version "1.1-0.7") |
655c4bb2 PL |
9802 | (source |
9803 | (origin | |
9804 | (method url-fetch) | |
9805 | (uri (cran-uri "interval" version)) | |
9806 | (sha256 | |
9807 | (base32 | |
65e361f9 | 9808 | "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9")))) |
655c4bb2 PL |
9809 | (properties `((upstream-name . "interval"))) |
9810 | (build-system r-build-system) | |
9811 | (propagated-inputs | |
9812 | `(("r-icens" ,r-icens) | |
9813 | ("r-mlecens" ,r-mlecens) | |
9814 | ("r-perm" ,r-perm) | |
9815 | ("r-survival" ,r-survival))) | |
9816 | (home-page "https://cran.r-project.org/web/packages/interval/") | |
9817 | (synopsis "Weighted Logrank tests and NPMLE for interval censored data") | |
9818 | (description | |
9819 | "This package provides functions to fit nonparametric survival curves, | |
9820 | plot them, and perform logrank or Wilcoxon type tests.") | |
9821 | (license license:gpl2+))) | |
7e88ee9f PL |
9822 | |
9823 | ;; This is a CRAN package, but it depends on r-interval, which depends on a | |
9824 | ;; Bioconductor package. | |
9825 | (define-public r-fhtest | |
9826 | (package | |
9827 | (name "r-fhtest") | |
d7cfdc12 | 9828 | (version "1.5") |
7e88ee9f PL |
9829 | (source |
9830 | (origin | |
9831 | (method url-fetch) | |
9832 | (uri (cran-uri "FHtest" version)) | |
9833 | (sha256 | |
9834 | (base32 | |
d7cfdc12 | 9835 | "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q")))) |
7e88ee9f PL |
9836 | (properties `((upstream-name . "FHtest"))) |
9837 | (build-system r-build-system) | |
9838 | (propagated-inputs | |
9839 | `(("r-interval" ,r-interval) | |
9840 | ("r-kmsurv" ,r-kmsurv) | |
9841 | ("r-mass" ,r-mass) | |
9842 | ("r-perm" ,r-perm) | |
9843 | ("r-survival" ,r-survival))) | |
9844 | (home-page "https://cran.r-project.org/web/packages/FHtest/") | |
9845 | (synopsis "Tests for survival data based on the Fleming-Harrington class") | |
9846 | (description | |
9847 | "This package provides functions to compare two or more survival curves | |
9848 | with: | |
9849 | ||
9850 | @itemize | |
9851 | @item The Fleming-Harrington test for right-censored data based on | |
9852 | permutations and on counting processes. | |
9853 | @item An extension of the Fleming-Harrington test for interval-censored data | |
9854 | based on a permutation distribution and on a score vector distribution. | |
9855 | @end itemize | |
9856 | ") | |
9857 | (license license:gpl2+))) | |
f4d920b9 | 9858 | |
9859 | (define-public r-fourcseq | |
9860 | (package | |
9861 | (name "r-fourcseq") | |
e5b2c80d | 9862 | (version "1.24.0") |
f4d920b9 | 9863 | (source |
9864 | (origin | |
9865 | (method url-fetch) | |
9866 | (uri (bioconductor-uri "FourCSeq" version)) | |
9867 | (sha256 | |
e5b2c80d | 9868 | (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb")))) |
f4d920b9 | 9869 | (properties `((upstream-name . "FourCSeq"))) |
9870 | (build-system r-build-system) | |
9871 | (propagated-inputs | |
9872 | `(("r-biobase" ,r-biobase) | |
9873 | ("r-biostrings" ,r-biostrings) | |
9874 | ("r-deseq2" ,r-deseq2) | |
9875 | ("r-fda" ,r-fda) | |
9876 | ("r-genomicalignments" ,r-genomicalignments) | |
9877 | ("r-genomicranges" ,r-genomicranges) | |
9878 | ("r-ggbio" ,r-ggbio) | |
9879 | ("r-ggplot2" ,r-ggplot2) | |
9880 | ("r-gtools" ,r-gtools) | |
9881 | ("r-lsd" ,r-lsd) | |
9882 | ("r-matrix" ,r-matrix) | |
9883 | ("r-reshape2" ,r-reshape2) | |
9884 | ("r-rsamtools" ,r-rsamtools) | |
9885 | ("r-rtracklayer" ,r-rtracklayer) | |
9886 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
9887 | (native-inputs | |
9888 | `(("r-knitr" ,r-knitr))) | |
9889 | (home-page | |
9890 | "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") | |
9891 | (synopsis "Analysis of multiplexed 4C sequencing data") | |
9892 | (description | |
9893 | "This package is an R package dedicated to the analysis of (multiplexed) | |
9894 | 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific | |
9895 | interactions between DNA elements and identify differential interactions | |
9896 | between conditions. The statistical analysis in R starts with individual bam | |
9897 | files for each sample as inputs. To obtain these files, the package contains | |
9898 | a Python script to demultiplex libraries and trim off primer sequences. With | |
9899 | a standard alignment software the required bam files can be then be | |
9900 | generated.") | |
9901 | (license license:gpl3+))) | |
6e0ab26f | 9902 | |
9903 | (define-public r-preprocesscore | |
9904 | (package | |
9905 | (name "r-preprocesscore") | |
18ebacaa | 9906 | (version "1.52.1") |
6e0ab26f | 9907 | (source |
9908 | (origin | |
9909 | (method url-fetch) | |
9910 | (uri (bioconductor-uri "preprocessCore" version)) | |
9911 | (sha256 | |
9912 | (base32 | |
18ebacaa | 9913 | "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll")))) |
6e0ab26f | 9914 | (properties |
9915 | `((upstream-name . "preprocessCore"))) | |
9916 | (build-system r-build-system) | |
9917 | (home-page "https://github.com/bmbolstad/preprocessCore") | |
9918 | (synopsis "Collection of pre-processing functions") | |
9919 | (description | |
9920 | "This package provides a library of core pre-processing and normalization | |
9921 | routines.") | |
9922 | (license license:lgpl2.0+))) | |
b3a99837 | 9923 | |
d64e3a48 | 9924 | (define-public r-s4vectors |
9925 | (package | |
9926 | (name "r-s4vectors") | |
9927 | (version "0.28.1") | |
9928 | (source (origin | |
9929 | (method url-fetch) | |
9930 | (uri (bioconductor-uri "S4Vectors" version)) | |
9931 | (sha256 | |
9932 | (base32 | |
9933 | "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) | |
9934 | (properties | |
9935 | `((upstream-name . "S4Vectors"))) | |
9936 | (build-system r-build-system) | |
9937 | (propagated-inputs | |
9938 | `(("r-biocgenerics" ,r-biocgenerics))) | |
9939 | (home-page "https://bioconductor.org/packages/S4Vectors") | |
9940 | (synopsis "S4 implementation of vectors and lists") | |
9941 | (description | |
9942 | "The S4Vectors package defines the @code{Vector} and @code{List} virtual | |
9943 | classes and a set of generic functions that extend the semantic of ordinary | |
9944 | vectors and lists in R. Package developers can easily implement vector-like | |
9945 | or list-like objects as concrete subclasses of @code{Vector} or @code{List}. | |
9946 | In addition, a few low-level concrete subclasses of general interest (e.g. | |
9947 | @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the | |
9948 | S4Vectors package itself.") | |
9949 | (license license:artistic2.0))) | |
9950 | ||
3159fcf1 RW |
9951 | ;; This is a CRAN package, but it depends on preprocessorcore, which is a |
9952 | ;; Bioconductor package. | |
9953 | (define-public r-wgcna | |
9954 | (package | |
9955 | (name "r-wgcna") | |
ef8e4f41 | 9956 | (version "1.70-3") |
3159fcf1 RW |
9957 | (source |
9958 | (origin | |
9959 | (method url-fetch) | |
9960 | (uri (cran-uri "WGCNA" version)) | |
9961 | (sha256 | |
9962 | (base32 | |
ef8e4f41 | 9963 | "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r")))) |
3159fcf1 RW |
9964 | (properties `((upstream-name . "WGCNA"))) |
9965 | (build-system r-build-system) | |
9966 | (propagated-inputs | |
9967 | `(("r-annotationdbi" ,r-annotationdbi) | |
9968 | ("r-doparallel" ,r-doparallel) | |
9969 | ("r-dynamictreecut" ,r-dynamictreecut) | |
9970 | ("r-fastcluster" ,r-fastcluster) | |
9971 | ("r-foreach" ,r-foreach) | |
9972 | ("r-go-db" ,r-go-db) | |
9973 | ("r-hmisc" ,r-hmisc) | |
9974 | ("r-impute" ,r-impute) | |
9975 | ("r-rcpp" ,r-rcpp) | |
9976 | ("r-survival" ,r-survival) | |
9977 | ("r-matrixstats" ,r-matrixstats) | |
9978 | ("r-preprocesscore" ,r-preprocesscore))) | |
9979 | (home-page | |
9980 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") | |
9981 | (synopsis "Weighted correlation network analysis") | |
9982 | (description | |
9983 | "This package provides functions necessary to perform Weighted | |
9984 | Correlation Network Analysis on high-dimensional data. It includes functions | |
9985 | for rudimentary data cleaning, construction and summarization of correlation | |
9986 | networks, module identification and functions for relating both variables and | |
9987 | modules to sample traits. It also includes a number of utility functions for | |
9988 | data manipulation and visualization.") | |
9989 | (license license:gpl2+))) | |
9990 | ||
b3a99837 | 9991 | (define-public r-rgraphviz |
9992 | (package | |
9993 | (name "r-rgraphviz") | |
b6348b0e | 9994 | (version "2.34.0") |
b3a99837 | 9995 | (source |
9996 | (origin | |
9997 | (method url-fetch) | |
9998 | (uri (bioconductor-uri "Rgraphviz" version)) | |
9999 | (sha256 | |
10000 | (base32 | |
b6348b0e | 10001 | "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77")))) |
b3a99837 | 10002 | (properties `((upstream-name . "Rgraphviz"))) |
10003 | (build-system r-build-system) | |
10004 | (arguments | |
10005 | `(#:phases | |
10006 | (modify-phases %standard-phases | |
10007 | (add-after 'unpack 'make-reproducible | |
10008 | (lambda _ | |
10009 | ;; The replacement value is taken from src/graphviz/builddate.h | |
10010 | (substitute* "src/graphviz/configure" | |
10011 | (("VERSION_DATE=.*") | |
10012 | "VERSION_DATE=20200427.2341\n")) | |
10013 | #t))))) | |
10014 | ;; FIXME: Rgraphviz bundles the sources of an older variant of | |
10015 | ;; graphviz. It does not build with the latest version of graphviz, so | |
10016 | ;; we do not add graphviz to the inputs. | |
10017 | (inputs `(("zlib" ,zlib))) | |
10018 | (propagated-inputs | |
10019 | `(("r-graph" ,r-graph))) | |
10020 | (native-inputs | |
10021 | `(("pkg-config" ,pkg-config))) | |
10022 | (home-page "https://bioconductor.org/packages/Rgraphviz") | |
10023 | (synopsis "Plotting capabilities for R graph objects") | |
10024 | (description | |
10025 | "This package interfaces R with the graphviz library for plotting R graph | |
10026 | objects from the @code{graph} package.") | |
10027 | (license license:epl1.0))) | |
8c7c6db4 | 10028 | |
3292f6ed | 10029 | (define-public r-fithic |
10030 | (package | |
10031 | (name "r-fithic") | |
7105658e | 10032 | (version "1.16.0") |
3292f6ed | 10033 | (source (origin |
10034 | (method url-fetch) | |
10035 | (uri (bioconductor-uri "FitHiC" version)) | |
10036 | (sha256 | |
10037 | (base32 | |
7105658e | 10038 | "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2")))) |
3292f6ed | 10039 | (properties `((upstream-name . "FitHiC"))) |
10040 | (build-system r-build-system) | |
10041 | (propagated-inputs | |
10042 | `(("r-data-table" ,r-data-table) | |
10043 | ("r-fdrtool" ,r-fdrtool) | |
10044 | ("r-rcpp" ,r-rcpp))) | |
10045 | (native-inputs | |
10046 | `(("r-knitr" ,r-knitr))) | |
10047 | (home-page "https://bioconductor.org/packages/FitHiC") | |
10048 | (synopsis "Confidence estimation for intra-chromosomal contact maps") | |
10049 | (description | |
10050 | "Fit-Hi-C is a tool for assigning statistical confidence estimates to | |
10051 | intra-chromosomal contact maps produced by genome-wide genome architecture | |
10052 | assays such as Hi-C.") | |
10053 | (license license:gpl2+))) | |
10054 | ||
7df42d37 | 10055 | (define-public r-hitc |
10056 | (package | |
10057 | (name "r-hitc") | |
ed44a72a | 10058 | (version "1.34.0") |
7df42d37 | 10059 | (source (origin |
10060 | (method url-fetch) | |
10061 | (uri (bioconductor-uri "HiTC" version)) | |
10062 | (sha256 | |
10063 | (base32 | |
ed44a72a | 10064 | "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy")))) |
7df42d37 | 10065 | (properties `((upstream-name . "HiTC"))) |
10066 | (build-system r-build-system) | |
10067 | (propagated-inputs | |
10068 | `(("r-biostrings" ,r-biostrings) | |
10069 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10070 | ("r-genomicranges" ,r-genomicranges) | |
10071 | ("r-iranges" ,r-iranges) | |
10072 | ("r-matrix" ,r-matrix) | |
10073 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
10074 | ("r-rtracklayer" ,r-rtracklayer))) | |
10075 | (home-page "https://bioconductor.org/packages/HiTC") | |
10076 | (synopsis "High throughput chromosome conformation capture analysis") | |
10077 | (description | |
10078 | "The HiTC package was developed to explore high-throughput \"C\" data | |
10079 | such as 5C or Hi-C. Dedicated R classes as well as standard methods for | |
10080 | quality controls, normalization, visualization, and further analysis are also | |
10081 | provided.") | |
10082 | (license license:artistic2.0))) | |
10083 | ||
63b75c01 | 10084 | (define-public r-hdf5array |
10085 | (package | |
10086 | (name "r-hdf5array") | |
f7947f89 | 10087 | (version "1.18.1") |
63b75c01 | 10088 | (source |
10089 | (origin | |
10090 | (method url-fetch) | |
10091 | (uri (bioconductor-uri "HDF5Array" version)) | |
10092 | (sha256 | |
10093 | (base32 | |
f7947f89 | 10094 | "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g")))) |
63b75c01 | 10095 | (properties `((upstream-name . "HDF5Array"))) |
10096 | (build-system r-build-system) | |
26cf5eb5 | 10097 | (arguments |
10098 | `(#:phases | |
10099 | (modify-phases %standard-phases | |
10100 | (add-after 'unpack 'fix-linking | |
10101 | (lambda _ | |
10102 | (substitute* "src/Makevars" | |
10103 | ;; This is to avoid having a plain directory on the list of | |
10104 | ;; libraries to link. | |
10105 | (("\\(RHDF5LIB_LIBS\\)" match) | |
10106 | (string-append match "/libhdf5.a"))) | |
10107 | #t))))) | |
63b75c01 | 10108 | (inputs |
10109 | `(("zlib" ,zlib))) | |
10110 | (propagated-inputs | |
10111 | `(("r-biocgenerics" ,r-biocgenerics) | |
10112 | ("r-delayedarray" ,r-delayedarray) | |
10113 | ("r-iranges" ,r-iranges) | |
10114 | ("r-matrix" ,r-matrix) | |
10115 | ("r-rhdf5" ,r-rhdf5) | |
10116 | ("r-rhdf5lib" ,r-rhdf5lib) | |
10117 | ("r-s4vectors" ,r-s4vectors))) | |
10118 | (home-page "https://bioconductor.org/packages/HDF5Array") | |
10119 | (synopsis "HDF5 back end for DelayedArray objects") | |
10120 | (description "This package provides an array-like container for convenient | |
10121 | access and manipulation of HDF5 datasets. It supports delayed operations and | |
10122 | block processing.") | |
10123 | (license license:artistic2.0))) | |
10124 | ||
c61268c1 | 10125 | (define-public r-rhdf5lib |
10126 | (package | |
10127 | (name "r-rhdf5lib") | |
a1357422 | 10128 | (version "1.12.1") |
c61268c1 | 10129 | (source |
10130 | (origin | |
10131 | (method url-fetch) | |
10132 | (uri (bioconductor-uri "Rhdf5lib" version)) | |
10133 | (sha256 | |
10134 | (base32 | |
a1357422 | 10135 | "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28")) |
c61268c1 | 10136 | (modules '((guix build utils))) |
10137 | (snippet | |
10138 | '(begin | |
10139 | ;; Delete bundled binaries | |
10140 | (delete-file-recursively "src/wininclude/") | |
10141 | (delete-file-recursively "src/winlib-4.9.3/") | |
10142 | (delete-file-recursively "src/winlib-8.3.0/") | |
10143 | (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") | |
10144 | #t)))) | |
10145 | (properties `((upstream-name . "Rhdf5lib"))) | |
10146 | (build-system r-build-system) | |
10147 | (arguments | |
10148 | `(#:phases | |
10149 | (modify-phases %standard-phases | |
10150 | (add-after 'unpack 'do-not-use-bundled-hdf5 | |
10151 | (lambda* (#:key inputs #:allow-other-keys) | |
10152 | (for-each delete-file '("configure" "configure.ac")) | |
10153 | ;; Do not make other packages link with the proprietary libsz. | |
10154 | (substitute* "R/zzz.R" | |
10155 | ((" \"%s/libsz.a\"") "")) | |
10156 | (with-directory-excursion "src" | |
10157 | (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) | |
10158 | (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) | |
10159 | "hdf5") | |
10160 | ;; Remove timestamp and host system information to make | |
10161 | ;; the build reproducible. | |
10162 | (substitute* "hdf5/src/libhdf5.settings.in" | |
10163 | (("Configured on: @CONFIG_DATE@") | |
10164 | "Configured on: Guix") | |
10165 | (("Uname information:.*") | |
10166 | "Uname information: Linux\n") | |
10167 | ;; Remove unnecessary store reference. | |
10168 | (("C Compiler:.*") | |
10169 | "C Compiler: GCC\n")) | |
c5ae5c1c RJ |
10170 | (rename-file "hdf5/src/libhdf5.settings.in" |
10171 | "hdf5/src/libhdf5.settings") | |
c61268c1 | 10172 | (rename-file "Makevars.in" "Makevars") |
10173 | (substitute* "Makevars" | |
10174 | (("@ZLIB_LIB@") "-lz") | |
10175 | (("@ZLIB_INCLUDE@") "") | |
10176 | (("HDF5_CXX_LIB=.*") | |
10177 | (string-append "HDF5_CXX_LIB=" | |
10178 | (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) | |
10179 | (("HDF5_LIB=.*") | |
10180 | (string-append "HDF5_LIB=" | |
10181 | (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) | |
10182 | (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") | |
10183 | (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") | |
10184 | (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") | |
10185 | (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") | |
10186 | (("HDF5_HL_LIB=.*") | |
10187 | (string-append "HDF5_HL_LIB=" | |
10188 | (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) | |
10189 | (("HDF5_HL_CXX_LIB=.*") | |
10190 | (string-append "HDF5_HL_CXX_LIB=" | |
10191 | (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) | |
10192 | ;; szip is non-free software | |
10193 | (("cp \"\\$\\{SZIP_LIB\\}.*") "") | |
10194 | (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) | |
10195 | #t))))) | |
10196 | (inputs | |
10197 | `(("zlib" ,zlib))) | |
10198 | (propagated-inputs | |
10199 | `(("hdf5" ,hdf5-1.10))) | |
10200 | (native-inputs | |
10201 | `(("hdf5-source" ,(package-source hdf5-1.10)) | |
10202 | ("r-knitr" ,r-knitr))) | |
10203 | (home-page "https://bioconductor.org/packages/Rhdf5lib") | |
10204 | (synopsis "HDF5 library as an R package") | |
10205 | (description "This package provides C and C++ HDF5 libraries for use in R | |
10206 | packages.") | |
10207 | (license license:artistic2.0))) | |
10208 | ||
8863c14c | 10209 | (define-public r-beachmat |
10210 | (package | |
10211 | (name "r-beachmat") | |
79d51ffe | 10212 | (version "2.6.4") |
8863c14c | 10213 | (source |
10214 | (origin | |
10215 | (method url-fetch) | |
10216 | (uri (bioconductor-uri "beachmat" version)) | |
10217 | (sha256 | |
10218 | (base32 | |
79d51ffe | 10219 | "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji")))) |
8863c14c | 10220 | (build-system r-build-system) |
10221 | (propagated-inputs | |
10222 | `(("r-biocgenerics" ,r-biocgenerics) | |
10223 | ("r-delayedarray" ,r-delayedarray) | |
10224 | ("r-matrix" ,r-matrix))) | |
10225 | (native-inputs | |
10226 | `(("r-knitr" ,r-knitr))) | |
10227 | (home-page "https://bioconductor.org/packages/beachmat") | |
10228 | (synopsis "Compiling Bioconductor to handle each matrix type") | |
10229 | (description "This package provides a consistent C++ class interface for a | |
10230 | variety of commonly used matrix types, including sparse and HDF5-backed | |
10231 | matrices.") | |
10232 | (license license:gpl3))) | |
10233 | ||
e6bc150b RW |
10234 | ;; This package includes files that have been taken from kentutils. Some |
10235 | ;; parts of kentutils are not released under a free license, but this package | |
10236 | ;; only uses files that are also found in the free parts of kentutils. | |
10237 | (define-public r-cner | |
10238 | (package | |
10239 | (name "r-cner") | |
10240 | (version "1.26.0") | |
10241 | (source | |
10242 | (origin | |
10243 | (method url-fetch) | |
10244 | (uri (bioconductor-uri "CNEr" version)) | |
10245 | (sha256 | |
10246 | (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c")))) | |
10247 | (properties `((upstream-name . "CNEr"))) | |
10248 | (build-system r-build-system) | |
10249 | (inputs `(("zlib" ,zlib))) | |
10250 | (propagated-inputs | |
10251 | `(("r-annotate" ,r-annotate) | |
10252 | ("r-biocgenerics" ,r-biocgenerics) | |
10253 | ("r-biostrings" ,r-biostrings) | |
10254 | ("r-dbi" ,r-dbi) | |
10255 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10256 | ("r-genomicalignments" ,r-genomicalignments) | |
10257 | ("r-genomicranges" ,r-genomicranges) | |
10258 | ("r-ggplot2" ,r-ggplot2) | |
10259 | ("r-go-db" ,r-go-db) | |
10260 | ("r-iranges" ,r-iranges) | |
10261 | ("r-keggrest" ,r-keggrest) | |
10262 | ("r-powerlaw" ,r-powerlaw) | |
10263 | ("r-r-utils" ,r-r-utils) | |
10264 | ("r-readr" ,r-readr) | |
10265 | ("r-reshape2" ,r-reshape2) | |
10266 | ("r-rsqlite" ,r-rsqlite) | |
10267 | ("r-rtracklayer" ,r-rtracklayer) | |
10268 | ("r-s4vectors" ,r-s4vectors) | |
10269 | ("r-xvector" ,r-xvector))) | |
10270 | (native-inputs | |
10271 | `(("r-knitr" ,r-knitr))) | |
10272 | (home-page "https://github.com/ge11232002/CNEr") | |
10273 | (synopsis "CNE Detection and Visualization") | |
10274 | (description | |
10275 | "This package provides tools for large-scale identification and | |
10276 | advanced visualization of sets of conserved noncoding elements.") | |
10277 | ;; For all files in src/ucsc "license is hereby granted for all use - | |
10278 | ;; public, private or commercial"; this includes those files that don't | |
10279 | ;; have a license header, because they are included in the free parts of | |
10280 | ;; the kentutils package. | |
10281 | (license (list license:gpl2 | |
10282 | (license:non-copyleft | |
10283 | "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE"))))) | |
10284 | ||
2def2e20 RW |
10285 | (define-public r-tfbstools |
10286 | (package | |
10287 | (name "r-tfbstools") | |
10288 | (version "1.28.0") | |
10289 | (source | |
10290 | (origin | |
10291 | (method url-fetch) | |
10292 | (uri (bioconductor-uri "TFBSTools" version)) | |
10293 | (sha256 | |
10294 | (base32 | |
10295 | "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha")))) | |
10296 | (properties `((upstream-name . "TFBSTools"))) | |
10297 | (build-system r-build-system) | |
10298 | (propagated-inputs | |
10299 | `(("r-biobase" ,r-biobase) | |
10300 | ("r-biocgenerics" ,r-biocgenerics) | |
10301 | ("r-biocparallel" ,r-biocparallel) | |
10302 | ("r-biostrings" ,r-biostrings) | |
10303 | ("r-bsgenome" ,r-bsgenome) | |
10304 | ("r-catools" ,r-catools) | |
10305 | ("r-cner" ,r-cner) | |
10306 | ("r-dbi" ,r-dbi) | |
10307 | ("r-dirichletmultinomial" ,r-dirichletmultinomial) | |
10308 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10309 | ("r-genomicranges" ,r-genomicranges) | |
10310 | ("r-gtools" ,r-gtools) | |
10311 | ("r-iranges" ,r-iranges) | |
10312 | ("r-rsqlite" ,r-rsqlite) | |
10313 | ("r-rtracklayer" ,r-rtracklayer) | |
10314 | ("r-s4vectors" ,r-s4vectors) | |
10315 | ("r-seqlogo" ,r-seqlogo) | |
10316 | ("r-tfmpvalue" ,r-tfmpvalue) | |
10317 | ("r-xml" ,r-xml) | |
10318 | ("r-xvector" ,r-xvector))) | |
10319 | (native-inputs `(("r-knitr" ,r-knitr))) | |
10320 | (home-page "https://github.com/ge11232002/TFBSTools") | |
10321 | (synopsis "Transcription factor binding site (TFBS) analysis") | |
10322 | (description | |
10323 | "TFBSTools is a package for the analysis and manipulation of | |
10324 | transcription factor binding sites. It includes matrices conversion | |
10325 | between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight | |
10326 | Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also | |
10327 | scan putative TFBS from sequence/alignment, query JASPAR database and | |
10328 | provides a wrapper of de novo motif discovery software.") | |
10329 | (license license:gpl2))) | |
10330 | ||
9a38f39e RW |
10331 | (define-public r-motifmatchr |
10332 | (package | |
10333 | (name "r-motifmatchr") | |
10334 | (version "1.12.0") | |
10335 | (source | |
10336 | (origin | |
10337 | (method url-fetch) | |
10338 | (uri (bioconductor-uri "motifmatchr" version)) | |
10339 | (sha256 | |
10340 | (base32 | |
10341 | "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z")))) | |
10342 | (properties `((upstream-name . "motifmatchr"))) | |
10343 | (build-system r-build-system) | |
10344 | (propagated-inputs | |
10345 | `(("r-biostrings" ,r-biostrings) | |
10346 | ("r-bsgenome" ,r-bsgenome) | |
10347 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10348 | ("r-genomicranges" ,r-genomicranges) | |
10349 | ("r-iranges" ,r-iranges) | |
10350 | ("r-matrix" ,r-matrix) | |
10351 | ("r-rcpp" ,r-rcpp) | |
10352 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
10353 | ("r-rsamtools" ,r-rsamtools) | |
10354 | ("r-s4vectors" ,r-s4vectors) | |
10355 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10356 | ("r-tfbstools" ,r-tfbstools))) | |
10357 | (native-inputs `(("r-knitr" ,r-knitr))) | |
10358 | (home-page "https://bioconductor.org/packages/motifmatchr") | |
10359 | (synopsis "Fast motif matching in R") | |
10360 | (description | |
10361 | "Quickly find motif matches for many motifs and many sequences. | |
10362 | This package wraps C++ code from the MOODS motif calling library.") | |
10363 | (license license:gpl3))) | |
10364 | ||
89d7c8ef RW |
10365 | (define-public r-chromvar |
10366 | (package | |
10367 | (name "r-chromvar") | |
10368 | (version "1.12.0") | |
10369 | (source | |
10370 | (origin | |
10371 | (method url-fetch) | |
10372 | (uri (bioconductor-uri "chromVAR" version)) | |
10373 | (sha256 | |
10374 | (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819")))) | |
10375 | (properties `((upstream-name . "chromVAR"))) | |
10376 | (build-system r-build-system) | |
10377 | (propagated-inputs | |
10378 | `(("r-biocgenerics" ,r-biocgenerics) | |
10379 | ("r-biocparallel" ,r-biocparallel) | |
10380 | ("r-biostrings" ,r-biostrings) | |
10381 | ("r-bsgenome" ,r-bsgenome) | |
10382 | ("r-dt" ,r-dt) | |
10383 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10384 | ("r-genomicranges" ,r-genomicranges) | |
10385 | ("r-ggplot2" ,r-ggplot2) | |
10386 | ("r-iranges" ,r-iranges) | |
10387 | ("r-matrix" ,r-matrix) | |
10388 | ("r-miniui" ,r-miniui) | |
10389 | ("r-nabor" ,r-nabor) | |
10390 | ("r-plotly" ,r-plotly) | |
10391 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
10392 | ("r-rcpp" ,r-rcpp) | |
10393 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
10394 | ("r-rsamtools" ,r-rsamtools) | |
10395 | ("r-rtsne" ,r-rtsne) | |
10396 | ("r-s4vectors" ,r-s4vectors) | |
10397 | ("r-shiny" ,r-shiny) | |
10398 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10399 | ("r-tfbstools" ,r-tfbstools))) | |
10400 | (native-inputs `(("r-knitr" ,r-knitr))) | |
10401 | (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html") | |
10402 | (synopsis "Determine chromatin variation across regions") | |
10403 | (description | |
10404 | "This package @code{r-chromvar} determines variation in chromatin | |
10405 | accessibility across sets of annotations or peaks. @code{r-chromvar} is | |
10406 | designed primarily for single-cell or sparse chromatin accessibility data like | |
10407 | single cell assay for transposase-accessible chromatin using | |
10408 | sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease | |
10409 | sequence (@code{DNAse-seq}) experiments.") | |
10410 | (license license:expat))) | |
10411 | ||
916a3e59 | 10412 | (define-public r-singlecellexperiment |
10413 | (package | |
10414 | (name "r-singlecellexperiment") | |
4ef898d4 | 10415 | (version "1.12.0") |
916a3e59 | 10416 | (source |
10417 | (origin | |
10418 | (method url-fetch) | |
10419 | (uri (bioconductor-uri "SingleCellExperiment" version)) | |
10420 | (sha256 | |
10421 | (base32 | |
4ef898d4 | 10422 | "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2")))) |
916a3e59 | 10423 | (properties |
10424 | `((upstream-name . "SingleCellExperiment"))) | |
10425 | (build-system r-build-system) | |
10426 | (propagated-inputs | |
10427 | `(("r-biocgenerics" ,r-biocgenerics) | |
10428 | ("r-s4vectors" ,r-s4vectors) | |
10429 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10430 | (native-inputs | |
10431 | `(("r-knitr" ,r-knitr))) | |
10432 | (home-page "https://bioconductor.org/packages/SingleCellExperiment") | |
10433 | (synopsis "S4 classes for single cell data") | |
10434 | (description "This package defines an S4 class for storing data from | |
10435 | single-cell experiments. This includes specialized methods to store and | |
10436 | retrieve spike-in information, dimensionality reduction coordinates and size | |
10437 | factors for each cell, along with the usual metadata for genes and | |
10438 | libraries.") | |
10439 | (license license:gpl3))) | |
10440 | ||
0e60dda0 RW |
10441 | (define-public r-scuttle |
10442 | (package | |
10443 | (name "r-scuttle") | |
cf3e7038 | 10444 | (version "1.0.4") |
0e60dda0 RW |
10445 | (source |
10446 | (origin | |
10447 | (method url-fetch) | |
10448 | (uri (bioconductor-uri "scuttle" version)) | |
10449 | (sha256 | |
10450 | (base32 | |
cf3e7038 | 10451 | "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8")))) |
0e60dda0 RW |
10452 | (properties `((upstream-name . "scuttle"))) |
10453 | (build-system r-build-system) | |
10454 | (propagated-inputs | |
10455 | `(("r-beachmat" ,r-beachmat) | |
10456 | ("r-biocgenerics" ,r-biocgenerics) | |
10457 | ("r-biocparallel" ,r-biocparallel) | |
10458 | ("r-delayedarray" ,r-delayedarray) | |
10459 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
3872153a | 10460 | ("r-genomicranges" ,r-genomicranges) |
0e60dda0 RW |
10461 | ("r-matrix" ,r-matrix) |
10462 | ("r-rcpp" ,r-rcpp) | |
10463 | ("r-s4vectors" ,r-s4vectors) | |
10464 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
10465 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10466 | (native-inputs `(("r-knitr" ,r-knitr))) | |
10467 | (home-page "https://bioconductor.org/packages/scuttle") | |
10468 | (synopsis "Single-cell RNA-Seq analysis utilities") | |
10469 | (description | |
10470 | "This package provides basic utility functions for performing single-cell | |
10471 | analyses, focusing on simple normalization, quality control and data | |
10472 | transformations. It also provides some helper functions to assist development | |
10473 | of other packages.") | |
10474 | (license license:gpl3))) | |
10475 | ||
6b1946b3 | 10476 | (define-public r-scater |
10477 | (package | |
10478 | (name "r-scater") | |
1ada8ea9 | 10479 | (version "1.18.6") |
6b1946b3 | 10480 | (source (origin |
10481 | (method url-fetch) | |
10482 | (uri (bioconductor-uri "scater" version)) | |
10483 | (sha256 | |
10484 | (base32 | |
1ada8ea9 | 10485 | "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609")))) |
6b1946b3 | 10486 | (build-system r-build-system) |
10487 | (propagated-inputs | |
d4b5d186 | 10488 | `(("r-biocgenerics" ,r-biocgenerics) |
6b1946b3 | 10489 | ("r-biocneighbors" ,r-biocneighbors) |
10490 | ("r-biocparallel" ,r-biocparallel) | |
10491 | ("r-biocsingular" ,r-biocsingular) | |
10492 | ("r-delayedarray" ,r-delayedarray) | |
10493 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
10494 | ("r-ggbeeswarm" ,r-ggbeeswarm) | |
10495 | ("r-ggplot2" ,r-ggplot2) | |
d4b5d186 | 10496 | ("r-gridextra" ,r-gridextra) |
6b1946b3 | 10497 | ("r-matrix" ,r-matrix) |
6b1946b3 | 10498 | ("r-rlang" ,r-rlang) |
10499 | ("r-s4vectors" ,r-s4vectors) | |
d4b5d186 | 10500 | ("r-scuttle" ,r-scuttle) |
6b1946b3 | 10501 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
10502 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10503 | ("r-viridis" ,r-viridis))) | |
10504 | (native-inputs | |
10505 | `(("r-knitr" ,r-knitr))) | |
10506 | (home-page "https://github.com/davismcc/scater") | |
10507 | (synopsis "Single-cell analysis toolkit for gene expression data in R") | |
10508 | (description "This package provides a collection of tools for doing | |
10509 | various analyses of single-cell RNA-seq gene expression data, with a focus on | |
10510 | quality control.") | |
10511 | (license license:gpl2+))) | |
10512 | ||
1193b77e | 10513 | (define-public r-scran |
10514 | (package | |
10515 | (name "r-scran") | |
2191a414 | 10516 | (version "1.18.7") |
1193b77e | 10517 | (source |
10518 | (origin | |
10519 | (method url-fetch) | |
10520 | (uri (bioconductor-uri "scran" version)) | |
10521 | (sha256 | |
10522 | (base32 | |
2191a414 | 10523 | "0hsr58b7xj2cqdkyjdpzyifg5wrl1lbylq2h91zbjh5861qjv2n4")))) |
1193b77e | 10524 | (build-system r-build-system) |
10525 | (propagated-inputs | |
10526 | `(("r-beachmat" ,r-beachmat) | |
10527 | ("r-bh" ,r-bh) | |
10528 | ("r-biocgenerics" ,r-biocgenerics) | |
10529 | ("r-biocneighbors" ,r-biocneighbors) | |
10530 | ("r-biocparallel" ,r-biocparallel) | |
10531 | ("r-biocsingular" ,r-biocsingular) | |
b03c955c | 10532 | ("r-bluster" ,r-bluster) |
1193b77e | 10533 | ("r-delayedarray" ,r-delayedarray) |
10534 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
10535 | ("r-dqrng" ,r-dqrng) | |
10536 | ("r-edger" ,r-edger) | |
10537 | ("r-igraph" ,r-igraph) | |
1193b77e | 10538 | ("r-limma" ,r-limma) |
10539 | ("r-matrix" ,r-matrix) | |
10540 | ("r-rcpp" ,r-rcpp) | |
10541 | ("r-s4vectors" ,r-s4vectors) | |
b03c955c | 10542 | ("r-scuttle" ,r-scuttle) |
1193b77e | 10543 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
10544 | ("r-statmod" ,r-statmod) | |
10545 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10546 | (native-inputs | |
10547 | `(("r-knitr" ,r-knitr))) | |
10548 | (home-page "https://bioconductor.org/packages/scran") | |
10549 | (synopsis "Methods for single-cell RNA-Seq data analysis") | |
10550 | (description "This package implements a variety of low-level analyses of | |
10551 | single-cell RNA-seq data. Methods are provided for normalization of | |
10552 | cell-specific biases, assignment of cell cycle phase, and detection of highly | |
10553 | variable and significantly correlated genes.") | |
10554 | (license license:gpl3))) | |
10555 | ||
5e719988 RW |
10556 | (define-public r-sparsematrixstats |
10557 | (package | |
10558 | (name "r-sparsematrixstats") | |
8acfd9f3 | 10559 | (version "1.2.1") |
5e719988 RW |
10560 | (source |
10561 | (origin | |
10562 | (method url-fetch) | |
10563 | (uri (bioconductor-uri "sparseMatrixStats" version)) | |
10564 | (sha256 | |
10565 | (base32 | |
8acfd9f3 | 10566 | "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii")))) |
5e719988 RW |
10567 | (properties |
10568 | `((upstream-name . "sparseMatrixStats"))) | |
10569 | (build-system r-build-system) | |
10570 | (propagated-inputs | |
10571 | `(("r-matrix" ,r-matrix) | |
10572 | ("r-matrixgenerics" ,r-matrixgenerics) | |
10573 | ("r-matrixstats" ,r-matrixstats) | |
10574 | ("r-rcpp" ,r-rcpp))) | |
10575 | (native-inputs `(("r-knitr" ,r-knitr))) | |
10576 | (home-page "https://bioconductor.org/packages/sparseMatrixStats/") | |
10577 | (synopsis "Summary statistics for rows and columns of sparse matrices") | |
10578 | (description | |
10579 | "This package provides high performance functions for row and column | |
10580 | operations on sparse matrices. Currently, the optimizations are limited to | |
10581 | data in the column sparse format.") | |
10582 | (license license:expat))) | |
10583 | ||
8c7c6db4 | 10584 | (define-public r-delayedmatrixstats |
10585 | (package | |
10586 | (name "r-delayedmatrixstats") | |
311bb4bc | 10587 | (version "1.12.3") |
8c7c6db4 | 10588 | (source |
10589 | (origin | |
10590 | (method url-fetch) | |
10591 | (uri (bioconductor-uri "DelayedMatrixStats" version)) | |
10592 | (sha256 | |
10593 | (base32 | |
311bb4bc | 10594 | "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h")))) |
8c7c6db4 | 10595 | (properties |
10596 | `((upstream-name . "DelayedMatrixStats"))) | |
10597 | (build-system r-build-system) | |
10598 | (propagated-inputs | |
10599 | `(("r-biocparallel" ,r-biocparallel) | |
10600 | ("r-delayedarray" ,r-delayedarray) | |
10601 | ("r-hdf5array" ,r-hdf5array) | |
10602 | ("r-iranges" ,r-iranges) | |
10603 | ("r-matrix" ,r-matrix) | |
7601015f | 10604 | ("r-matrixgenerics" ,r-matrixgenerics) |
8c7c6db4 | 10605 | ("r-matrixstats" ,r-matrixstats) |
10c87ecf | 10606 | ("r-s4vectors" ,r-s4vectors) |
10607 | ("r-sparsematrixstats" ,r-sparsematrixstats))) | |
8c7c6db4 | 10608 | (native-inputs |
10609 | `(("r-knitr" ,r-knitr))) | |
10610 | (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") | |
10611 | (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") | |
10612 | (description | |
10613 | "This package provides a port of the @code{matrixStats} API for use with | |
10614 | @code{DelayedMatrix} objects from the @code{DelayedArray} package. It | |
10615 | contains high-performing functions operating on rows and columns of | |
10616 | @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, | |
10617 | @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions | |
10618 | are optimized per data type and for subsetted calculations such that both | |
10619 | memory usage and processing time is minimized.") | |
10620 | (license license:expat))) | |
fa2201c1 | 10621 | |
10622 | (define-public r-mscoreutils | |
10623 | (package | |
10624 | (name "r-mscoreutils") | |
10625 | (version "1.2.0") | |
10626 | (source | |
10627 | (origin | |
10628 | (method url-fetch) | |
10629 | (uri (bioconductor-uri "MsCoreUtils" version)) | |
10630 | (sha256 | |
10631 | (base32 | |
10632 | "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630")))) | |
10633 | (properties `((upstream-name . "MsCoreUtils"))) | |
10634 | (build-system r-build-system) | |
10635 | (propagated-inputs | |
10636 | `(("r-mass" ,r-mass) | |
10637 | ("r-rcpp" ,r-rcpp) | |
10638 | ("r-s4vectors" ,r-s4vectors))) | |
10639 | (native-inputs | |
10640 | `(("r-knitr" ,r-knitr))) | |
10641 | (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils") | |
10642 | (synopsis "Core utils for mass spectrometry data") | |
10643 | (description | |
10644 | "This package defines low-level functions for mass spectrometry data and | |
10645 | is independent of any high-level data structures. These functions include | |
10646 | mass spectra processing functions (noise estimation, smoothing, binning), | |
10647 | quantitative aggregation functions (median polish, robust summarisation, | |
10648 | etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as | |
10649 | well as misc helper functions, that are used across high-level data structure | |
10650 | within the R for Mass Spectrometry packages.") | |
10651 | (license license:artistic2.0))) | |
ff4834c0 | 10652 | |
10653 | (define-public r-biocio | |
10654 | (package | |
10655 | (name "r-biocio") | |
10656 | (version "1.0.1") | |
10657 | (source | |
10658 | (origin | |
10659 | (method url-fetch) | |
10660 | (uri (bioconductor-uri "BiocIO" version)) | |
10661 | (sha256 | |
10662 | (base32 | |
10663 | "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18")))) | |
10664 | (properties `((upstream-name . "BiocIO"))) | |
10665 | (build-system r-build-system) | |
10666 | (propagated-inputs | |
10667 | `(("r-biocgenerics" ,r-biocgenerics) | |
10668 | ("r-genomicranges" ,r-genomicranges) | |
10669 | ("r-rcurl" ,r-rcurl) | |
10670 | ("r-s4vectors" ,r-s4vectors))) | |
10671 | (native-inputs | |
10672 | `(("r-knitr" ,r-knitr))) | |
10673 | (home-page "https://bioconductor.org/packages/BiocIO") | |
10674 | (synopsis "Standard input and output for Bioconductor packages") | |
10675 | (description | |
10676 | "This package implements `import()` and `export()` standard generics for | |
10677 | importing and exporting biological data formats. `import()` supports | |
10678 | whole-file as well as chunk-wise iterative import. The `import()` interface | |
10679 | optionally provides a standard mechanism for 'lazy' access via `filter()` (on | |
10680 | row or element-like components of the file resource), `select()` (on | |
10681 | column-like components of the file resource) and `collect()`. The `import()` | |
10682 | interface optionally provides transparent access to remote (e.g. via https) | |
10683 | as well as local access. Developers can register a file extension, e.g., | |
10684 | `.loom` for dispatch from character-based URIs to specific `import()` / | |
10685 | `export()` methods based on classes representing file types, e.g., | |
10686 | `LoomFile()`.") | |
10687 | (license license:artistic2.0))) | |
e520c68f | 10688 | |
10689 | (define-public r-msmseda | |
10690 | (package | |
10691 | (name "r-msmseda") | |
10692 | (version "1.28.0") | |
10693 | (source | |
10694 | (origin | |
10695 | (method url-fetch) | |
10696 | (uri (bioconductor-uri "msmsEDA" version)) | |
10697 | (sha256 | |
10698 | (base32 | |
10699 | "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx")))) | |
10700 | (properties `((upstream-name . "msmsEDA"))) | |
10701 | (build-system r-build-system) | |
10702 | (propagated-inputs | |
10703 | `(("r-gplots" ,r-gplots) | |
10704 | ("r-mass" ,r-mass) | |
10705 | ("r-msnbase" ,r-msnbase) | |
10706 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
10707 | (home-page | |
10708 | "https://bioconductor.org/packages/msmsEDA") | |
10709 | (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts") | |
10710 | (description | |
10711 | "Exploratory data analysis to assess the quality of a set of LC-MS/MS | |
10712 | experiments, and visualize de influence of the involved factors.") | |
10713 | (license license:gpl2))) | |
16f16b5e | 10714 | |
10715 | (define-public r-msmstests | |
10716 | (package | |
10717 | (name "r-msmstests") | |
10718 | (version "1.28.0") | |
10719 | (source | |
10720 | (origin | |
10721 | (method url-fetch) | |
10722 | (uri (bioconductor-uri "msmsTests" version)) | |
10723 | (sha256 | |
10724 | (base32 | |
10725 | "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j")))) | |
10726 | (properties `((upstream-name . "msmsTests"))) | |
10727 | (build-system r-build-system) | |
10728 | (propagated-inputs | |
10729 | `(("r-edger" ,r-edger) | |
10730 | ("r-msmseda" ,r-msmseda) | |
10731 | ("r-msnbase" ,r-msnbase) | |
10732 | ("r-qvalue" ,r-qvalue))) | |
10733 | (home-page | |
10734 | "https://bioconductor.org/packages/msmsTests") | |
10735 | (synopsis "Differential LC-MS/MS expression tests") | |
10736 | (description | |
0e434dad | 10737 | "This package provides statistical tests for label-free LC-MS/MS data |
16f16b5e | 10738 | by spectral counts, to discover differentially expressed proteins between two |
10739 | biological conditions. Three tests are available: Poisson GLM regression, | |
10740 | quasi-likelihood GLM regression, and the negative binomial of the edgeR | |
37d47061 TGR |
10741 | package. The three models admit blocking factors to control for nuisance |
10742 | variables. To assure a good level of reproducibility a post-test filter is | |
16f16b5e | 10743 | available, where we may set the minimum effect size considered biologicaly |
10744 | relevant, and the minimum expression of the most abundant condition.") | |
10745 | (license license:gpl2))) | |
45dfb751 | 10746 | |
10747 | (define-public r-catalyst | |
10748 | (package | |
10749 | (name "r-catalyst") | |
4286233e | 10750 | (version "1.14.1") |
45dfb751 | 10751 | (source |
10752 | (origin | |
10753 | (method url-fetch) | |
10754 | (uri (bioconductor-uri "CATALYST" version)) | |
10755 | (sha256 | |
10756 | (base32 | |
4286233e | 10757 | "04b5kcvkfiw4ina11x3qf5kwrb7056zihm7xp1919bqm8k7nl3mn")))) |
45dfb751 | 10758 | (properties `((upstream-name . "CATALYST"))) |
10759 | (build-system r-build-system) | |
10760 | (propagated-inputs | |
10761 | `(("r-circlize" ,r-circlize) | |
10762 | ("r-complexheatmap" ,r-complexheatmap) | |
10763 | ("r-consensusclusterplus" ,r-consensusclusterplus) | |
10764 | ("r-cowplot" ,r-cowplot) | |
10765 | ("r-data-table" ,r-data-table) | |
10766 | ("r-dplyr" ,r-dplyr) | |
10767 | ("r-drc" ,r-drc) | |
10768 | ("r-flowcore" ,r-flowcore) | |
10769 | ("r-flowsom" ,r-flowsom) | |
10770 | ("r-ggplot2" ,r-ggplot2) | |
10771 | ("r-ggrepel" ,r-ggrepel) | |
10772 | ("r-ggridges" ,r-ggridges) | |
10773 | ("r-gridextra" ,r-gridextra) | |
10774 | ("r-magrittr" ,r-magrittr) | |
10775 | ("r-matrix" ,r-matrix) | |
10776 | ("r-matrixstats" ,r-matrixstats) | |
10777 | ("r-nnls" ,r-nnls) | |
10778 | ("r-purrr" ,r-purrr) | |
10779 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
10780 | ("r-reshape2" ,r-reshape2) | |
10781 | ("r-rtsne" ,r-rtsne) | |
10782 | ("r-s4vectors" ,r-s4vectors) | |
10783 | ("r-scales" ,r-scales) | |
10784 | ("r-scater" ,r-scater) | |
10785 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
10786 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10787 | (native-inputs | |
10788 | `(("r-knitr" ,r-knitr))) | |
10789 | (home-page | |
10790 | "https://github.com/HelenaLC/CATALYST") | |
10791 | (synopsis "Cytometry data analysis tools") | |
10792 | (description | |
10793 | "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass | |
10794 | cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as | |
10795 | reporters to label antibodies, thereby substantially decreasing spectral | |
10796 | overlap and allowing for examination of over 50 parameters at the single cell | |
10797 | level. While spectral overlap is significantly less pronounced in CyTOF than | |
10798 | flow cytometry, spillover due to detection sensitivity, isotopic impurities, | |
10799 | and oxide formation can impede data interpretability. We designed | |
10800 | CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for | |
10801 | preprocessing of cytometry data, including i) normalization using bead | |
10802 | standards, ii) single-cell deconvolution, and iii) bead-based compensation.") | |
10803 | (license license:gpl2+))) | |
7395458d | 10804 | |
8c2b7c9a | 10805 | (define-public r-erma |
10806 | (package | |
10807 | (name "r-erma") | |
10808 | (version "1.6.0") | |
10809 | (source | |
10810 | (origin | |
10811 | (method url-fetch) | |
10812 | (uri (bioconductor-uri "erma" version)) | |
10813 | (sha256 | |
10814 | (base32 | |
10815 | "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k")))) | |
10816 | (build-system r-build-system) | |
10817 | (propagated-inputs | |
10818 | `(("r-annotationdbi" ,r-annotationdbi) | |
10819 | ("r-biobase" ,r-biobase) | |
10820 | ("r-biocgenerics" ,r-biocgenerics) | |
10821 | ("r-biocparallel" ,r-biocparallel) | |
10822 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10823 | ("r-genomicfiles" ,r-genomicfiles) | |
10824 | ("r-genomicranges" ,r-genomicranges) | |
10825 | ("r-ggplot2" ,r-ggplot2) | |
10826 | ("r-homo-sapiens" ,r-homo-sapiens) | |
10827 | ("r-iranges" ,r-iranges) | |
10828 | ("r-rtracklayer" ,r-rtracklayer) | |
10829 | ("r-s4vectors" ,r-s4vectors) | |
10830 | ("r-shiny" ,r-shiny) | |
10831 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10832 | (native-inputs | |
10833 | `(("r-knitr" ,r-knitr))) | |
10834 | (home-page "https://bioconductor.org/packages/erma") | |
10835 | (synopsis "Epigenomic road map adventures") | |
10836 | (description | |
10837 | "The epigenomics road map describes locations of epigenetic marks in DNA | |
10838 | from a variety of cell types. Of interest are locations of histone | |
10839 | modifications, sites of DNA methylation, and regions of accessible chromatin. | |
10840 | This package presents a selection of elements of the road map including | |
10841 | metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines | |
10842 | by Ernst and Kellis.") | |
10843 | (license license:artistic2.0))) | |
10844 | ||
610cd6a1 | 10845 | (define-public r-ggbio |
10846 | (package | |
10847 | (name "r-ggbio") | |
10848 | (version "1.38.0") | |
10849 | (source | |
10850 | (origin | |
10851 | (method url-fetch) | |
10852 | (uri (bioconductor-uri "ggbio" version)) | |
10853 | (sha256 | |
10854 | (base32 | |
10855 | "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) | |
10856 | (build-system r-build-system) | |
10857 | (arguments | |
10858 | `(#:phases | |
10859 | (modify-phases %standard-phases | |
10860 | ;; See https://github.com/tengfei/ggbio/issues/117 | |
10861 | ;; This fix will be included in the next release. | |
10862 | (add-after 'unpack 'fix-typo | |
10863 | (lambda _ | |
10864 | (substitute* "R/GGbio-class.R" | |
10865 | (("fechable") "fetchable")) | |
10866 | #t))))) | |
10867 | (propagated-inputs | |
10868 | `(("r-annotationdbi" ,r-annotationdbi) | |
10869 | ("r-annotationfilter" ,r-annotationfilter) | |
10870 | ("r-biobase" ,r-biobase) | |
10871 | ("r-biocgenerics" ,r-biocgenerics) | |
10872 | ("r-biostrings" ,r-biostrings) | |
10873 | ("r-biovizbase" ,r-biovizbase) | |
10874 | ("r-bsgenome" ,r-bsgenome) | |
10875 | ("r-ensembldb" ,r-ensembldb) | |
10876 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10877 | ("r-genomicalignments" ,r-genomicalignments) | |
10878 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10879 | ("r-genomicranges" ,r-genomicranges) | |
10880 | ("r-ggally" ,r-ggally) | |
10881 | ("r-ggplot2" ,r-ggplot2) | |
10882 | ("r-gridextra" ,r-gridextra) | |
10883 | ("r-gtable" ,r-gtable) | |
10884 | ("r-hmisc" ,r-hmisc) | |
10885 | ("r-iranges" ,r-iranges) | |
10886 | ("r-organismdbi" ,r-organismdbi) | |
10887 | ("r-reshape2" ,r-reshape2) | |
10888 | ("r-rlang" ,r-rlang) | |
10889 | ("r-rsamtools" ,r-rsamtools) | |
10890 | ("r-rtracklayer" ,r-rtracklayer) | |
10891 | ("r-s4vectors" ,r-s4vectors) | |
10892 | ("r-scales" ,r-scales) | |
10893 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10894 | ("r-variantannotation" ,r-variantannotation))) | |
10895 | (native-inputs | |
10896 | `(("r-knitr" ,r-knitr))) | |
10897 | (home-page "http://www.tengfei.name/ggbio/") | |
10898 | (synopsis "Visualization tools for genomic data") | |
10899 | (description | |
10900 | "The ggbio package extends and specializes the grammar of graphics for | |
10901 | biological data. The graphics are designed to answer common scientific | |
10902 | questions, in particular those often asked of high throughput genomics data. | |
10903 | All core Bioconductor data structures are supported, where appropriate. The | |
10904 | package supports detailed views of particular genomic regions, as well as | |
10905 | genome-wide overviews. Supported overviews include ideograms and grand linear | |
10906 | views. High-level plots include sequence fragment length, edge-linked | |
10907 | interval to data view, mismatch pileup, and several splicing summaries.") | |
10908 | (license license:artistic2.0))) | |
10909 | ||
81f481d6 | 10910 | (define-public r-gqtlbase |
10911 | (package | |
10912 | (name "r-gqtlbase") | |
10913 | (version "1.21.1") | |
10914 | (source | |
10915 | (origin | |
10916 | (method url-fetch) | |
10917 | (uri (bioconductor-uri "gQTLBase" version)) | |
10918 | (sha256 | |
10919 | (base32 | |
10920 | "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh")))) | |
10921 | (properties `((upstream-name . "gQTLBase"))) | |
10922 | (build-system r-build-system) | |
10923 | (arguments | |
10924 | `(#:phases | |
10925 | (modify-phases %standard-phases | |
10926 | ;; This is an upstream bug. | |
10927 | (add-after 'unpack 'fix-imports | |
10928 | (lambda _ | |
10929 | (substitute* "NAMESPACE" | |
10930 | ((".*maxffmode.*") "") | |
10931 | (("importFrom\\(ff,.*") "import(ff)\n")) | |
10932 | #t))))) | |
10933 | (propagated-inputs | |
10934 | `(("r-batchjobs" ,r-batchjobs) | |
10935 | ("r-bbmisc" ,r-bbmisc) | |
10936 | ("r-biocgenerics" ,r-biocgenerics) | |
10937 | ("r-bit" ,r-bit) | |
10938 | ("r-doparallel" ,r-doparallel) | |
10939 | ("r-ff" ,r-ff) | |
10940 | ("r-ffbase" ,r-ffbase) | |
10941 | ("r-foreach" ,r-foreach) | |
10942 | ("r-genomicfiles" ,r-genomicfiles) | |
10943 | ("r-genomicranges" ,r-genomicranges) | |
10944 | ("r-rtracklayer" ,r-rtracklayer) | |
10945 | ("r-s4vectors" ,r-s4vectors) | |
10946 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10947 | (native-inputs | |
10948 | `(("r-knitr" ,r-knitr))) | |
10949 | (home-page "https://bioconductor.org/packages/gQTLBase") | |
10950 | (synopsis "Infrastructure for eQTL, mQTL and similar studies") | |
10951 | (description | |
10952 | "The purpose of this package is to simplify the storage and interrogation | |
10953 | of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, | |
10954 | and more.") | |
10955 | (license license:artistic2.0))) | |
10956 | ||
9534e7b7 | 10957 | (define-public r-gqtlstats |
10958 | (package | |
10959 | (name "r-gqtlstats") | |
10960 | (version "1.21.3") | |
10961 | (source | |
10962 | (origin | |
10963 | (method url-fetch) | |
10964 | (uri (bioconductor-uri "gQTLstats" version)) | |
10965 | (sha256 | |
10966 | (base32 | |
10967 | "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl")))) | |
10968 | (properties `((upstream-name . "gQTLstats"))) | |
10969 | (build-system r-build-system) | |
10970 | (propagated-inputs | |
10971 | `(("r-annotationdbi" ,r-annotationdbi) | |
10972 | ("r-batchjobs" ,r-batchjobs) | |
10973 | ("r-bbmisc" ,r-bbmisc) | |
10974 | ("r-beeswarm" ,r-beeswarm) | |
10975 | ("r-biobase" ,r-biobase) | |
10976 | ("r-biocgenerics" ,r-biocgenerics) | |
10977 | ("r-doparallel" ,r-doparallel) | |
10978 | ("r-dplyr" ,r-dplyr) | |
10979 | ("r-erma" ,r-erma) | |
10980 | ("r-ffbase" ,r-ffbase) | |
10981 | ("r-foreach" ,r-foreach) | |
10982 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10983 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10984 | ("r-genomicfiles" ,r-genomicfiles) | |
10985 | ("r-genomicranges" ,r-genomicranges) | |
10986 | ("r-ggbeeswarm" ,r-ggbeeswarm) | |
10987 | ("r-ggplot2" ,r-ggplot2) | |
10988 | ("r-gqtlbase" ,r-gqtlbase) | |
10989 | ("r-hardyweinberg" ,r-hardyweinberg) | |
10990 | ("r-homo-sapiens" ,r-homo-sapiens) | |
10991 | ("r-iranges" ,r-iranges) | |
10992 | ("r-limma" ,r-limma) | |
10993 | ("r-mgcv" ,r-mgcv) | |
10994 | ("r-plotly" ,r-plotly) | |
10995 | ("r-reshape2" ,r-reshape2) | |
10996 | ("r-s4vectors" ,r-s4vectors) | |
10997 | ("r-shiny" ,r-shiny) | |
10998 | ("r-snpstats" ,r-snpstats) | |
10999 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
11000 | ("r-variantannotation" ,r-variantannotation))) | |
11001 | (native-inputs | |
11002 | `(("r-knitr" ,r-knitr))) | |
11003 | (home-page "https://bioconductor.org/packages/gQTLstats") | |
11004 | (synopsis "Computationally efficient analysis for eQTL and allied studies") | |
11005 | (description | |
11006 | "This package provides tools for the computationally efficient analysis | |
11007 | of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc. | |
11008 | The software in this package aims to support refinements and functional | |
11009 | interpretation of members of a collection of association statistics on a | |
11010 | family of feature/genome hypotheses.") | |
11011 | (license license:artistic2.0))) | |
11012 | ||
2a4322f7 | 11013 | (define-public r-gviz |
11014 | (package | |
11015 | (name "r-gviz") | |
e0147aa4 | 11016 | (version "1.34.1") |
2a4322f7 | 11017 | (source |
11018 | (origin | |
11019 | (method url-fetch) | |
11020 | (uri (bioconductor-uri "Gviz" version)) | |
11021 | (sha256 | |
11022 | (base32 | |
e0147aa4 | 11023 | "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1")))) |
2a4322f7 | 11024 | (properties `((upstream-name . "Gviz"))) |
11025 | (build-system r-build-system) | |
11026 | (propagated-inputs | |
11027 | `(("r-annotationdbi" ,r-annotationdbi) | |
11028 | ("r-biobase" ,r-biobase) | |
11029 | ("r-biocgenerics" ,r-biocgenerics) | |
11030 | ("r-biomart" ,r-biomart) | |
11031 | ("r-biostrings" ,r-biostrings) | |
11032 | ("r-biovizbase" ,r-biovizbase) | |
11033 | ("r-bsgenome" ,r-bsgenome) | |
11034 | ("r-digest" ,r-digest) | |
11035 | ("r-ensembldb" ,r-ensembldb) | |
11036 | ("r-genomeinfodb" ,r-genomeinfodb) | |
11037 | ("r-genomicalignments" ,r-genomicalignments) | |
11038 | ("r-genomicfeatures" ,r-genomicfeatures) | |
11039 | ("r-genomicranges" ,r-genomicranges) | |
11040 | ("r-iranges" ,r-iranges) | |
11041 | ("r-lattice" ,r-lattice) | |
11042 | ("r-latticeextra" ,r-latticeextra) | |
11043 | ("r-matrixstats" ,r-matrixstats) | |
11044 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
11045 | ("r-rsamtools" ,r-rsamtools) | |
11046 | ("r-rtracklayer" ,r-rtracklayer) | |
11047 | ("r-s4vectors" ,r-s4vectors) | |
11048 | ("r-xvector" ,r-xvector))) | |
11049 | (native-inputs | |
11050 | `(("r-knitr" ,r-knitr))) | |
11051 | (home-page "https://bioconductor.org/packages/Gviz") | |
11052 | (synopsis "Plotting data and annotation information along genomic coordinates") | |
11053 | (description | |
11054 | "Genomic data analyses requires integrated visualization of known genomic | |
11055 | information and new experimental data. Gviz uses the biomaRt and the | |
11056 | rtracklayer packages to perform live annotation queries to Ensembl and UCSC | |
11057 | and translates this to e.g. gene/transcript structures in viewports of the | |
11058 | grid graphics package. This results in genomic information plotted together | |
11059 | with your data.") | |
11060 | (license license:artistic2.0))) | |
11061 | ||
69a5e066 | 11062 | (define-public r-gwascat |
11063 | (package | |
11064 | (name "r-gwascat") | |
11065 | (version "2.22.0") | |
11066 | (source | |
11067 | (origin | |
11068 | (method url-fetch) | |
11069 | (uri (bioconductor-uri "gwascat" version)) | |
11070 | (sha256 | |
11071 | (base32 | |
11072 | "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna")))) | |
11073 | (build-system r-build-system) | |
11074 | (propagated-inputs | |
11075 | `(("r-annotationdbi" ,r-annotationdbi) | |
11076 | ("r-biocfilecache" ,r-biocfilecache) | |
11077 | ("r-biostrings" ,r-biostrings) | |
11078 | ("r-genomeinfodb" ,r-genomeinfodb) | |
11079 | ("r-genomicfeatures" ,r-genomicfeatures) | |
11080 | ("r-genomicranges" ,r-genomicranges) | |
11081 | ("r-iranges" ,r-iranges) | |
11082 | ("r-readr" ,r-readr) | |
11083 | ("r-s4vectors" ,r-s4vectors) | |
11084 | ("r-snpstats" ,r-snpstats) | |
11085 | ("r-variantannotation" ,r-variantannotation))) | |
11086 | (native-inputs | |
11087 | `(("r-knitr" ,r-knitr))) | |
11088 | (home-page "https://bioconductor.org/packages/gwascat") | |
11089 | (synopsis "Tools for data in the EMBL-EBI GWAS catalog") | |
11090 | (description | |
11091 | "This package provides tools for representing and modeling data in the | |
11092 | EMBL-EBI GWAS catalog.") | |
11093 | (license license:artistic2.0))) | |
11094 | ||
7395458d MIP |
11095 | (define-public r-kegggraph |
11096 | (package | |
11097 | (name "r-kegggraph") | |
11098 | (version "1.50.0") | |
11099 | (source | |
11100 | (origin | |
11101 | (method url-fetch) | |
11102 | (uri (bioconductor-uri "KEGGgraph" version)) | |
11103 | (sha256 | |
11104 | (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v")))) | |
11105 | (properties `((upstream-name . "KEGGgraph"))) | |
11106 | (build-system r-build-system) | |
11107 | (propagated-inputs | |
11108 | `(("r-graph" ,r-graph) | |
11109 | ("r-rcurl" ,r-rcurl) | |
11110 | ("r-xml" ,r-xml))) | |
11111 | (home-page "https://bioconductor.org/packages/KEGGgraph") | |
11112 | (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") | |
11113 | (description | |
11114 | "@code{r-kegggraph} is an interface between Kegg Pathway database and graph | |
11115 | object as well as a collection of tools to analyze, dissect and visualize these | |
11116 | graphs. It parses the regularly updated kgml (Kegg XML) files into graph models | |
11117 | maintaining all essential pathway attributes. The package offers | |
11118 | functionalities including parsing, graph operation, visualization and etc.") | |
11119 | (license license:gpl2+))) | |
e4b0794e | 11120 | |
8f1237c3 | 11121 | (define-public r-ldblock |
11122 | (package | |
11123 | (name "r-ldblock") | |
11124 | (version "1.20.0") | |
11125 | (source | |
11126 | (origin | |
11127 | (method url-fetch) | |
11128 | (uri (bioconductor-uri "ldblock" version)) | |
11129 | (sha256 | |
11130 | (base32 | |
11131 | "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm")))) | |
11132 | (build-system r-build-system) | |
11133 | (propagated-inputs | |
11134 | `(("r-biocgenerics" ,r-biocgenerics) | |
11135 | ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) | |
11136 | ("r-ensembldb" ,r-ensembldb) | |
11137 | ("r-genomeinfodb" ,r-genomeinfodb) | |
11138 | ("r-genomicfiles" ,r-genomicfiles) | |
11139 | ("r-httr" ,r-httr) | |
11140 | ("r-matrix" ,r-matrix) | |
11141 | ("r-rsamtools" ,r-rsamtools) | |
11142 | ("r-snpstats" ,r-snpstats) | |
11143 | ("r-variantannotation" ,r-variantannotation))) | |
11144 | (native-inputs | |
11145 | `(("r-knitr" ,r-knitr))) | |
11146 | (home-page "https://bioconductor.org/packages/ldblock") | |
11147 | (synopsis "Data structures for linkage disequilibrium measures in populations") | |
11148 | (description | |
11149 | "This package defines data structures for @dfn{linkage | |
11150 | disequilibrium} (LD) measures in populations. Its purpose is to simplify | |
11151 | handling of existing population-level data for the purpose of flexibly | |
11152 | defining LD blocks.") | |
11153 | (license license:artistic2.0))) | |
11154 | ||
a7d6e1b6 RW |
11155 | ;; This is a CRAN package, but it depends on r-snpstats, which is a |
11156 | ;; Bioconductor package. | |
11157 | (define-public r-ldheatmap | |
11158 | (package | |
11159 | (name "r-ldheatmap") | |
11160 | (version "1.0-4") | |
11161 | (source | |
11162 | (origin | |
11163 | (method url-fetch) | |
11164 | (uri (cran-uri "LDheatmap" version)) | |
11165 | (sha256 | |
11166 | (base32 | |
11167 | "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7")))) | |
11168 | (properties `((upstream-name . "LDheatmap"))) | |
11169 | (build-system r-build-system) | |
11170 | (propagated-inputs | |
11171 | `(("r-genetics" ,r-genetics) | |
11172 | ("r-rcpp" ,r-rcpp) | |
11173 | ("r-snpstats" ,r-snpstats))) | |
11174 | (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") | |
11175 | (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") | |
11176 | (description | |
11177 | "This package provides tools to produce a graphical display, as a heat | |
11178 | map, of measures of pairwise linkage disequilibria between SNPs. Users may | |
11179 | optionally include the physical locations or genetic map distances of each SNP | |
11180 | on the plot.") | |
11181 | (license license:gpl3))) | |
11182 | ||
aa9a94bb RW |
11183 | ;; This is a CRAN package, but it depends on r-rgraphviz, which is a |
11184 | ;; Bioconductor package. | |
11185 | (define-public r-abn | |
11186 | (package | |
11187 | (name "r-abn") | |
11188 | (version "2.5-0") | |
11189 | (source | |
11190 | (origin | |
11191 | (method url-fetch) | |
11192 | (uri (cran-uri "abn" version)) | |
11193 | (sha256 | |
11194 | (base32 | |
11195 | "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw")))) | |
11196 | (build-system r-build-system) | |
11197 | (inputs | |
11198 | `(("gsl" ,gsl))) | |
11199 | (propagated-inputs | |
11200 | `(("r-lme4" ,r-lme4) | |
11201 | ("r-nnet" ,r-nnet) | |
11202 | ("r-rcpp" ,r-rcpp) | |
11203 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
11204 | ("r-rgraphviz" ,r-rgraphviz) | |
11205 | ("r-rjags" ,r-rjags))) | |
11206 | (home-page "https://r-bayesian-networks.org/") | |
11207 | (synopsis "Modelling multivariate data with additive bayesian networks") | |
11208 | (description | |
11209 | "Bayesian network analysis is a form of probabilistic graphical models | |
11210 | which derives from empirical data a directed acyclic graph, DAG, describing | |
11211 | the dependency structure between random variables. An additive Bayesian | |
11212 | network model consists of a form of a DAG where each node comprises a | |
11213 | @dfn{generalized linear model} (GLM). Additive Bayesian network models are | |
11214 | equivalent to Bayesian multivariate regression using graphical modelling, they | |
11215 | generalises the usual multivariable regression, GLM, to multiple dependent | |
11216 | variables. This package provides routines to help determine optimal Bayesian | |
11217 | network models for a given data set, where these models are used to identify | |
11218 | statistical dependencies in messy, complex data.") | |
11219 | (license license:gpl2+))) | |
11220 | ||
e4b0794e MIP |
11221 | (define-public r-pathview |
11222 | (package | |
11223 | (name "r-pathview") | |
11224 | (version "1.30.1") | |
11225 | (source | |
11226 | (origin | |
11227 | (method url-fetch) | |
11228 | (uri (bioconductor-uri "pathview" version)) | |
11229 | (sha256 | |
11230 | (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4")))) | |
11231 | (properties `((upstream-name . "pathview"))) | |
11232 | (build-system r-build-system) | |
11233 | (propagated-inputs | |
11234 | `(("r-annotationdbi" ,r-annotationdbi) | |
11235 | ("r-graph" ,r-graph) | |
11236 | ("r-kegggraph" ,r-kegggraph) | |
11237 | ("r-keggrest" ,r-keggrest) | |
11238 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
11239 | ("r-png" ,r-png) | |
11240 | ("r-rgraphviz" ,r-rgraphviz) | |
11241 | ("r-xml" ,r-xml))) | |
11242 | (home-page "https://pathview.uncc.edu/") | |
11243 | (synopsis "Tool set for pathway based data integration and visualization") | |
11244 | (description | |
11245 | "@code{r-pathview} is a tool set for pathway based data integration and | |
11246 | visualization. It maps and renders a wide variety of biological data on | |
11247 | relevant pathway graphs. All users need is to supply their data and specify | |
11248 | the target pathway. This package automatically downloads the pathway graph | |
11249 | data, parses the data file, maps user data to the pathway, and render pathway | |
11250 | graph with the mapped data. In addition, @code{r-pathview} also seamlessly | |
11251 | integrates with pathway and gene set (enrichment) analysis tools for | |
11252 | large-scale and fully automated analysis.") | |
11253 | (license license:gpl3+))) | |
838db0de | 11254 | |
61ec8928 | 11255 | (define-public r-snpstats |
11256 | (package | |
11257 | (name "r-snpstats") | |
11258 | (version "1.40.0") | |
11259 | (source | |
11260 | (origin | |
11261 | (method url-fetch) | |
11262 | (uri (bioconductor-uri "snpStats" version)) | |
11263 | (sha256 | |
11264 | (base32 | |
11265 | "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24")))) | |
11266 | (properties `((upstream-name . "snpStats"))) | |
11267 | (build-system r-build-system) | |
11268 | (inputs `(("zlib" ,zlib))) | |
11269 | (propagated-inputs | |
11270 | `(("r-biocgenerics" ,r-biocgenerics) | |
11271 | ("r-matrix" ,r-matrix) | |
11272 | ("r-survival" ,r-survival) | |
11273 | ("r-zlibbioc" ,r-zlibbioc))) | |
11274 | (home-page "https://bioconductor.org/packages/snpStats") | |
11275 | (synopsis "Methods for SNP association studies") | |
11276 | (description | |
11277 | "This package provides classes and statistical methods for large | |
11278 | @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends | |
11279 | the earlier snpMatrix package, allowing for uncertainty in genotypes.") | |
11280 | (license license:gpl3))) | |
11281 | ||
0ff88810 HL |
11282 | (define-public r-chromstar |
11283 | (package | |
11284 | (name "r-chromstar") | |
11285 | (version "1.16.0") | |
11286 | (source | |
11287 | (origin | |
11288 | (method url-fetch) | |
11289 | (uri (bioconductor-uri "chromstaR" version)) | |
11290 | (sha256 | |
11291 | (base32 | |
11292 | "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1")))) | |
11293 | (properties `((upstream-name . "chromstaR"))) | |
11294 | (build-system r-build-system) | |
11295 | (propagated-inputs | |
11296 | `(("r-bamsignals" ,r-bamsignals) | |
11297 | ("r-biocgenerics" ,r-biocgenerics) | |
11298 | ("r-chromstardata" ,r-chromstardata) | |
11299 | ("r-doparallel" ,r-doparallel) | |
11300 | ("r-foreach" ,r-foreach) | |
11301 | ("r-genomeinfodb" ,r-genomeinfodb) | |
11302 | ("r-genomicalignments" ,r-genomicalignments) | |
11303 | ("r-genomicranges" ,r-genomicranges) | |
11304 | ("r-ggplot2" ,r-ggplot2) | |
11305 | ("r-iranges" ,r-iranges) | |
11306 | ("r-mvtnorm" ,r-mvtnorm) | |
11307 | ("r-reshape2" ,r-reshape2) | |
11308 | ("r-rsamtools" ,r-rsamtools) | |
11309 | ("r-s4vectors" ,r-s4vectors))) | |
11310 | (native-inputs `(("r-knitr" ,r-knitr))) | |
11311 | (home-page "https://github.com/ataudt/chromstaR") | |
11312 | (synopsis "Chromatin state analysis for ChIP-Seq data") | |
11313 | (description | |
11314 | "This package implements functions for combinatorial and differential | |
11315 | analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, | |
04a5e791 | 11316 | export to genome browser viewable files, and functions for enrichment |
0ff88810 HL |
11317 | analyses.") |
11318 | (license license:artistic2.0))) | |
11319 | ||
bee797fa RW |
11320 | (define-public r-guitar |
11321 | (package | |
11322 | (name "r-guitar") | |
11323 | (version "2.6.0") | |
11324 | (source | |
11325 | (origin | |
11326 | (method url-fetch) | |
11327 | (uri (bioconductor-uri "Guitar" version)) | |
11328 | (sha256 | |
11329 | (base32 | |
11330 | "0lvfrpgrvmrz4f4qmsii70hw10h72zh1g1alv2sf6a6ixhndm0mz")))) | |
11331 | (properties `((upstream-name . "Guitar"))) | |
11332 | (build-system r-build-system) | |
11333 | (propagated-inputs | |
11334 | `(("r-annotationdbi" ,r-annotationdbi) | |
11335 | ("r-dplyr" ,r-dplyr) | |
11336 | ("r-genomicfeatures" ,r-genomicfeatures) | |
11337 | ("r-genomicranges" ,r-genomicranges) | |
11338 | ("r-ggplot2" ,r-ggplot2) | |
11339 | ("r-knitr" ,r-knitr) | |
11340 | ("r-magrittr" ,r-magrittr) | |
11341 | ("r-rtracklayer" ,r-rtracklayer))) | |
11342 | (native-inputs | |
11343 | `(("r-knitr" ,r-knitr))) | |
11344 | (home-page "https://bioconductor.org/packages/Guitar") | |
11345 | (synopsis "Visualize genomic features") | |
11346 | (description | |
11347 | "This package is designed for visualization of RNA-related genomic | |
11348 | features with respect to the landmarks of RNA transcripts, i.e., transcription | |
11349 | starting site, start codon, stop codon and transcription ending site.") | |
11350 | (license license:gpl2))) | |
11351 | ||
838db0de | 11352 | (define-public r-sushi |
11353 | (package | |
11354 | (name "r-sushi") | |
11355 | (version "1.28.0") | |
11356 | (source (origin | |
11357 | (method url-fetch) | |
11358 | (uri (bioconductor-uri "Sushi" version)) | |
11359 | (sha256 | |
11360 | (base32 | |
11361 | "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p")))) | |
11362 | (properties `((upstream-name . "Sushi"))) | |
11363 | (build-system r-build-system) | |
11364 | (propagated-inputs | |
11365 | `(("r-biomart" ,r-biomart) | |
11366 | ("r-zoo" ,r-zoo))) | |
11367 | (home-page "https://bioconductor.org/packages/Sushi") | |
11368 | (synopsis "Tools for visualizing genomics data") | |
11369 | (description | |
11370 | "This package provides flexible, quantitative, and integrative genomic | |
11371 | visualizations for publication-quality multi-panel figures.") | |
11372 | (license license:gpl2+))) |