Commit | Line | Data |
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fa596599 | 1 | ;;; GNU Guix --- Functional package management for GNU |
add2b195 | 2 | ;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net> |
7097c700 | 3 | ;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org> |
f39938b1 | 4 | ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> |
fa596599 RW |
5 | ;;; |
6 | ;;; This file is part of GNU Guix. | |
7 | ;;; | |
8 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
9 | ;;; under the terms of the GNU General Public License as published by | |
10 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
11 | ;;; your option) any later version. | |
12 | ;;; | |
13 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
14 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
16 | ;;; GNU General Public License for more details. | |
17 | ;;; | |
18 | ;;; You should have received a copy of the GNU General Public License | |
19 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
20 | ||
21 | (define-module (gnu packages bioconductor) | |
22 | #:use-module ((guix licenses) #:prefix license:) | |
23 | #:use-module (guix packages) | |
24 | #:use-module (guix download) | |
25 | #:use-module (guix build-system r) | |
183ce988 | 26 | #:use-module (gnu packages) |
cf9a29b2 | 27 | #:use-module (gnu packages bioinformatics) |
a5b56a53 RJ |
28 | #:use-module (gnu packages cran) |
29 | #:use-module (gnu packages compression) | |
c18dccff | 30 | #:use-module (gnu packages gcc) |
cf9a29b2 | 31 | #:use-module (gnu packages graph) |
b64ce4b7 | 32 | #:use-module (gnu packages maths) |
f4235c0e RW |
33 | #:use-module (gnu packages statistics) |
34 | #:use-module (gnu packages web)) | |
fa596599 | 35 | |
183db725 RW |
36 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
37 | (package | |
38 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
39 | (version "1.4.1") | |
40 | (source (origin | |
41 | (method url-fetch) | |
42 | ;; We cannot use bioconductor-uri here because this tarball is | |
43 | ;; located under "data/annotation/" instead of "bioc/". | |
44 | (uri (string-append "https://www.bioconductor.org/packages/" | |
45 | "release/data/annotation/src/contrib/" | |
46 | "BSgenome.Dmelanogaster.UCSC.dm6_" | |
47 | version ".tar.gz")) | |
48 | (sha256 | |
49 | (base32 | |
50 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
51 | (properties | |
52 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
53 | (build-system r-build-system) | |
54 | ;; As this package provides little more than a very large data file it | |
55 | ;; doesn't make sense to build substitutes. | |
56 | (arguments `(#:substitutable? #f)) | |
57 | (propagated-inputs | |
58 | `(("r-bsgenome" ,r-bsgenome))) | |
59 | (home-page | |
60 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
61 | (synopsis "Full genome sequences for Fly") | |
62 | (description | |
63 | "This package provides full genome sequences for Drosophila | |
64 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
65 | objects.") | |
66 | (license license:artistic2.0))) | |
67 | ||
dfac7eb9 RW |
68 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
69 | (package | |
70 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
71 | (version "1.3.99") | |
72 | (source (origin | |
73 | (method url-fetch) | |
74 | ;; We cannot use bioconductor-uri here because this tarball is | |
75 | ;; located under "data/annotation/" instead of "bioc/". | |
76 | (uri (string-append "http://www.bioconductor.org/packages/" | |
77 | "release/data/annotation/src/contrib/" | |
78 | "BSgenome.Dmelanogaster.UCSC.dm3.masked_" | |
79 | version ".tar.gz")) | |
80 | (sha256 | |
81 | (base32 | |
82 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
83 | (properties | |
84 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
85 | (build-system r-build-system) | |
86 | (propagated-inputs | |
87 | `(("r-bsgenome" ,r-bsgenome) | |
88 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
89 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
90 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
91 | (synopsis "Full masked genome sequences for Fly") | |
92 | (description | |
93 | "This package provides full masked genome sequences for Drosophila | |
94 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
95 | Biostrings objects. The sequences are the same as in | |
96 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
97 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
98 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
99 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
100 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
101 | (license license:artistic2.0))) | |
102 | ||
6fbd759b RW |
103 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
104 | (package | |
105 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
106 | (version "1.3.99") | |
107 | (source (origin | |
108 | (method url-fetch) | |
109 | ;; We cannot use bioconductor-uri here because this tarball is | |
110 | ;; located under "data/annotation/" instead of "bioc/". | |
111 | (uri (string-append "http://www.bioconductor.org/packages/" | |
112 | "release/data/annotation/src/contrib/" | |
113 | "BSgenome.Hsapiens.UCSC.hg19.masked_" | |
114 | version ".tar.gz")) | |
115 | (sha256 | |
116 | (base32 | |
117 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
118 | (properties | |
119 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
120 | (build-system r-build-system) | |
121 | (propagated-inputs | |
122 | `(("r-bsgenome" ,r-bsgenome) | |
123 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
124 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
125 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
126 | (synopsis "Full masked genome sequences for Homo sapiens") | |
127 | (description | |
128 | "This package provides full genome sequences for Homo sapiens (Human) as | |
129 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
130 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
131 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
132 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
133 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
134 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
135 | default.") | |
136 | (license license:artistic2.0))) | |
137 | ||
2bece692 RW |
138 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
139 | (package | |
140 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
141 | (version "1.3.99") | |
142 | (source (origin | |
143 | (method url-fetch) | |
144 | ;; We cannot use bioconductor-uri here because this tarball is | |
145 | ;; located under "data/annotation/" instead of "bioc/". | |
146 | (uri (string-append "http://www.bioconductor.org/packages/" | |
147 | "release/data/annotation/src/contrib/" | |
148 | "BSgenome.Mmusculus.UCSC.mm9.masked_" | |
149 | version ".tar.gz")) | |
150 | (sha256 | |
151 | (base32 | |
152 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
153 | (properties | |
154 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
155 | (build-system r-build-system) | |
156 | (propagated-inputs | |
157 | `(("r-bsgenome" ,r-bsgenome) | |
158 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
159 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
160 | (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") | |
161 | (synopsis "Full masked genome sequences for Mouse") | |
162 | (description | |
163 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
164 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
165 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
166 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
167 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
168 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
169 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
170 | default." ) | |
171 | (license license:artistic2.0))) | |
172 | ||
2cc51108 RW |
173 | (define-public r-genelendatabase |
174 | (package | |
175 | (name "r-genelendatabase") | |
176 | (version "1.16.0") | |
177 | (source | |
178 | (origin | |
179 | (method url-fetch) | |
180 | ;; We cannot use bioconductor-uri here because this tarball is | |
181 | ;; located under "data/experiment/" instead of "bioc/". | |
182 | (uri (string-append "https://bioconductor.org/packages/" | |
183 | "release/data/experiment/src/contrib" | |
184 | "/geneLenDataBase_" version ".tar.gz")) | |
185 | (sha256 | |
186 | (base32 | |
187 | "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5")))) | |
188 | (properties | |
189 | `((upstream-name . "geneLenDataBase"))) | |
190 | (build-system r-build-system) | |
191 | (propagated-inputs | |
192 | `(("r-rtracklayer" ,r-rtracklayer) | |
193 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
194 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
195 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
196 | (description | |
197 | "This package provides the lengths of mRNA transcripts for a number of | |
198 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
199 | (license license:lgpl2.0+))) | |
200 | ||
d220babf RW |
201 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
202 | (package | |
203 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") | |
204 | (version "3.2.2") | |
205 | (source (origin | |
206 | (method url-fetch) | |
207 | ;; We cannot use bioconductor-uri here because this tarball is | |
208 | ;; located under "data/annotation/" instead of "bioc/". | |
209 | (uri (string-append "https://bioconductor.org/packages/" | |
210 | "release/data/annotation/src/contrib" | |
211 | "/TxDb.Mmusculus.UCSC.mm9.knownGene_" | |
212 | version ".tar.gz")) | |
213 | (sha256 | |
214 | (base32 | |
215 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) | |
216 | (properties | |
217 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) | |
218 | (build-system r-build-system) | |
219 | (propagated-inputs | |
220 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
221 | ("r-annotationdbi" ,r-annotationdbi))) | |
222 | (home-page | |
223 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") | |
224 | (synopsis "Annotation package for mouse genome in TxDb format") | |
225 | (description | |
226 | "This package provides an annotation database of Mouse genome data. It | |
227 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The | |
228 | database is exposed as a @code{TxDb} object.") | |
229 | (license license:artistic2.0))) | |
230 | ||
2cc51108 | 231 | \f |
14bba460 RW |
232 | (define-public r-biocgenerics |
233 | (package | |
234 | (name "r-biocgenerics") | |
235 | (version "0.28.0") | |
236 | (source (origin | |
237 | (method url-fetch) | |
238 | (uri (bioconductor-uri "BiocGenerics" version)) | |
239 | (sha256 | |
240 | (base32 | |
241 | "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8")))) | |
242 | (properties | |
243 | `((upstream-name . "BiocGenerics"))) | |
244 | (build-system r-build-system) | |
245 | (home-page "https://bioconductor.org/packages/BiocGenerics") | |
246 | (synopsis "S4 generic functions for Bioconductor") | |
247 | (description | |
248 | "This package provides S4 generic functions needed by many Bioconductor | |
249 | packages.") | |
250 | (license license:artistic2.0))) | |
251 | ||
7097c700 RW |
252 | (define-public r-annotate |
253 | (package | |
254 | (name "r-annotate") | |
255 | (version "1.60.0") | |
256 | (source | |
257 | (origin | |
258 | (method url-fetch) | |
259 | (uri (bioconductor-uri "annotate" version)) | |
260 | (sha256 | |
261 | (base32 | |
262 | "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n")))) | |
263 | (build-system r-build-system) | |
264 | (propagated-inputs | |
265 | `(("r-annotationdbi" ,r-annotationdbi) | |
266 | ("r-biobase" ,r-biobase) | |
267 | ("r-biocgenerics" ,r-biocgenerics) | |
268 | ("r-dbi" ,r-dbi) | |
269 | ("r-rcurl" ,r-rcurl) | |
270 | ("r-xml" ,r-xml) | |
271 | ("r-xtable" ,r-xtable))) | |
272 | (home-page | |
273 | "https://bioconductor.org/packages/annotate") | |
274 | (synopsis "Annotation for microarrays") | |
275 | (description "This package provides R environments for the annotation of | |
276 | microarrays.") | |
277 | (license license:artistic2.0))) | |
278 | ||
fa596599 RW |
279 | (define-public r-hpar |
280 | (package | |
281 | (name "r-hpar") | |
61686921 | 282 | (version "1.24.0") |
fa596599 RW |
283 | (source |
284 | (origin | |
285 | (method url-fetch) | |
286 | (uri (bioconductor-uri "hpar" version)) | |
287 | (sha256 | |
288 | (base32 | |
61686921 | 289 | "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn")))) |
fa596599 RW |
290 | (build-system r-build-system) |
291 | (home-page "https://bioconductor.org/packages/hpar/") | |
292 | (synopsis "Human Protein Atlas in R") | |
293 | (description "This package provides a simple interface to and data from | |
294 | the Human Protein Atlas project.") | |
295 | (license license:artistic2.0))) | |
183ce988 RJ |
296 | |
297 | (define-public r-regioner | |
298 | (package | |
299 | (name "r-regioner") | |
d639d888 | 300 | (version "1.14.0") |
183ce988 RJ |
301 | (source |
302 | (origin | |
303 | (method url-fetch) | |
304 | (uri (bioconductor-uri "regioneR" version)) | |
305 | (sha256 | |
306 | (base32 | |
d639d888 | 307 | "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd")))) |
183ce988 RJ |
308 | (properties `((upstream-name . "regioneR"))) |
309 | (build-system r-build-system) | |
310 | (propagated-inputs | |
d639d888 | 311 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 312 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 313 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 314 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 315 | ("r-iranges" ,r-iranges) |
d639d888 RW |
316 | ("r-memoise" ,r-memoise) |
317 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 318 | ("r-s4vectors" ,r-s4vectors))) |
183ce988 RJ |
319 | (home-page "https://bioconductor.org/packages/regioneR/") |
320 | (synopsis "Association analysis of genomic regions") | |
321 | (description "This package offers a statistical framework based on | |
322 | customizable permutation tests to assess the association between genomic | |
323 | region sets and other genomic features.") | |
324 | (license license:artistic2.0))) | |
a5b56a53 RJ |
325 | |
326 | (define-public r-diffbind | |
327 | (package | |
328 | (name "r-diffbind") | |
98652568 | 329 | (version "2.10.0") |
a5b56a53 RJ |
330 | (source |
331 | (origin | |
332 | (method url-fetch) | |
333 | (uri (bioconductor-uri "DiffBind" version)) | |
334 | (sha256 | |
335 | (base32 | |
98652568 | 336 | "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5")))) |
a5b56a53 RJ |
337 | (properties `((upstream-name . "DiffBind"))) |
338 | (build-system r-build-system) | |
339 | (inputs | |
340 | `(("zlib" ,zlib))) | |
341 | (propagated-inputs | |
342 | `(("r-amap" ,r-amap) | |
343 | ("r-biocparallel" ,r-biocparallel) | |
344 | ("r-deseq2" ,r-deseq2) | |
345 | ("r-dplyr" ,r-dplyr) | |
346 | ("r-edger" ,r-edger) | |
347 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
348 | ("r-genomicranges" ,r-genomicranges) |
349 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
350 | ("r-ggrepel" ,r-ggrepel) |
351 | ("r-gplots" ,r-gplots) | |
352 | ("r-iranges" ,r-iranges) | |
353 | ("r-lattice" ,r-lattice) | |
354 | ("r-limma" ,r-limma) | |
355 | ("r-locfit" ,r-locfit) | |
356 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
357 | ("r-rcpp" ,r-rcpp) | |
358 | ("r-rsamtools" ,r-rsamtools) | |
359 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 360 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
a5b56a53 RJ |
361 | ("r-systempiper" ,r-systempiper) |
362 | ("r-zlibbioc" ,r-zlibbioc))) | |
363 | (home-page "http://bioconductor.org/packages/DiffBind") | |
364 | (synopsis "Differential binding analysis of ChIP-Seq peak data") | |
365 | (description | |
366 | "This package computes differentially bound sites from multiple | |
367 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
368 | occupancy (overlap) analysis and plotting functions.") | |
369 | (license license:artistic2.0))) | |
6d94bf6b RJ |
370 | |
371 | (define-public r-ripseeker | |
372 | (package | |
373 | (name "r-ripseeker") | |
e9427b2c | 374 | (version "1.22.0") |
6d94bf6b RJ |
375 | (source |
376 | (origin | |
377 | (method url-fetch) | |
378 | (uri (bioconductor-uri "RIPSeeker" version)) | |
379 | (sha256 | |
380 | (base32 | |
e9427b2c | 381 | "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i")))) |
6d94bf6b RJ |
382 | (properties `((upstream-name . "RIPSeeker"))) |
383 | (build-system r-build-system) | |
384 | (propagated-inputs | |
385 | `(("r-s4vectors" ,r-s4vectors) | |
386 | ("r-iranges" ,r-iranges) | |
387 | ("r-genomicranges" ,r-genomicranges) | |
388 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
389 | ("r-rsamtools" ,r-rsamtools) | |
390 | ("r-genomicalignments" ,r-genomicalignments) | |
391 | ("r-rtracklayer" ,r-rtracklayer))) | |
392 | (home-page "http://bioconductor.org/packages/RIPSeeker") | |
393 | (synopsis | |
394 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
395 | (description | |
396 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
397 | using two-state HMM with negative binomial emission probability. While | |
398 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
399 | a suite of bioinformatics tools integrated within this self-contained software | |
400 | package comprehensively addressing issues ranging from post-alignments | |
401 | processing to visualization and annotation.") | |
402 | (license license:gpl2))) | |
a6ae9ffd RJ |
403 | |
404 | (define-public r-multtest | |
405 | (package | |
406 | (name "r-multtest") | |
95ee4a46 | 407 | (version "2.38.0") |
a6ae9ffd RJ |
408 | (source |
409 | (origin | |
410 | (method url-fetch) | |
411 | (uri (bioconductor-uri "multtest" version)) | |
412 | (sha256 | |
413 | (base32 | |
95ee4a46 | 414 | "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k")))) |
a6ae9ffd RJ |
415 | (build-system r-build-system) |
416 | (propagated-inputs | |
417 | `(("r-survival" ,r-survival) | |
418 | ("r-biocgenerics" ,r-biocgenerics) | |
419 | ("r-biobase" ,r-biobase) | |
420 | ("r-mass" ,r-mass))) | |
421 | (home-page "http://bioconductor.org/packages/multtest") | |
422 | (synopsis "Resampling-based multiple hypothesis testing") | |
423 | (description | |
424 | "This package can do non-parametric bootstrap and permutation | |
425 | resampling-based multiple testing procedures (including empirical Bayes | |
426 | methods) for controlling the family-wise error rate (FWER), generalized | |
427 | family-wise error rate (gFWER), tail probability of the proportion of | |
428 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
429 | of bootstrap-based null distribution are implemented (centered, centered | |
430 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
431 | available. Tests based on a variety of T- and F-statistics (including | |
432 | T-statistics based on regression parameters from linear and survival models | |
433 | as well as those based on correlation parameters) are included. When probing | |
434 | hypotheses with T-statistics, users may also select a potentially faster null | |
435 | distribution which is multivariate normal with mean zero and variance | |
436 | covariance matrix derived from the vector influence function. Results are | |
437 | reported in terms of adjusted P-values, confidence regions and test statistic | |
438 | cutoffs. The procedures are directly applicable to identifying differentially | |
439 | expressed genes in DNA microarray experiments.") | |
440 | (license license:lgpl3))) | |
793f83ef | 441 | |
5dfe4912 RW |
442 | (define-public r-graph |
443 | (package | |
444 | (name "r-graph") | |
14520b64 | 445 | (version "1.60.0") |
5dfe4912 RW |
446 | (source (origin |
447 | (method url-fetch) | |
448 | (uri (bioconductor-uri "graph" version)) | |
449 | (sha256 | |
450 | (base32 | |
14520b64 | 451 | "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i")))) |
5dfe4912 RW |
452 | (build-system r-build-system) |
453 | (propagated-inputs | |
454 | `(("r-biocgenerics" ,r-biocgenerics))) | |
455 | (home-page "https://bioconductor.org/packages/graph") | |
456 | (synopsis "Handle graph data structures in R") | |
457 | (description | |
458 | "This package implements some simple graph handling capabilities for R.") | |
459 | (license license:artistic2.0))) | |
460 | ||
a207bca2 RW |
461 | (define-public r-codedepends |
462 | (package | |
463 | (name "r-codedepends") | |
464 | (version "0.6.5") | |
465 | (source | |
466 | (origin | |
467 | (method url-fetch) | |
468 | (uri (cran-uri "CodeDepends" version)) | |
469 | (sha256 | |
470 | (base32 | |
471 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
472 | (properties `((upstream-name . "CodeDepends"))) | |
473 | (build-system r-build-system) | |
474 | (propagated-inputs | |
475 | `(("r-codetools" ,r-codetools) | |
476 | ("r-graph" ,r-graph) | |
477 | ("r-xml" ,r-xml))) | |
478 | (home-page "http://cran.r-project.org/web/packages/CodeDepends") | |
479 | (synopsis "Analysis of R code for reproducible research and code comprehension") | |
480 | (description | |
481 | "This package provides tools for analyzing R expressions or blocks of | |
482 | code and determining the dependencies between them. It focuses on R scripts, | |
483 | but can be used on the bodies of functions. There are many facilities | |
484 | including the ability to summarize or get a high-level view of code, | |
485 | determining dependencies between variables, code improvement suggestions.") | |
486 | ;; Any version of the GPL | |
487 | (license (list license:gpl2+ license:gpl3+)))) | |
488 | ||
793f83ef RJ |
489 | (define-public r-chippeakanno |
490 | (package | |
491 | (name "r-chippeakanno") | |
add2b195 | 492 | (version "3.16.1") |
793f83ef RJ |
493 | (source |
494 | (origin | |
495 | (method url-fetch) | |
496 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
497 | (sha256 | |
498 | (base32 | |
add2b195 | 499 | "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3")))) |
793f83ef RJ |
500 | (properties `((upstream-name . "ChIPpeakAnno"))) |
501 | (build-system r-build-system) | |
502 | (propagated-inputs | |
503 | `(("r-biocgenerics" ,r-biocgenerics) | |
57d2fcd9 | 504 | ("r-biocmanager" ,r-biocmanager) |
f794e85d RW |
505 | ("r-biostrings" ,r-biostrings) |
506 | ("r-delayedarray" ,r-delayedarray) | |
793f83ef RJ |
507 | ("r-go-db" ,r-go-db) |
508 | ("r-biomart" ,r-biomart) | |
509 | ("r-bsgenome" ,r-bsgenome) | |
510 | ("r-genomicfeatures" ,r-genomicfeatures) | |
f794e85d | 511 | ("r-genomicranges" ,r-genomicranges) |
793f83ef | 512 | ("r-genomeinfodb" ,r-genomeinfodb) |
f794e85d | 513 | ("r-iranges" ,r-iranges) |
793f83ef RJ |
514 | ("r-matrixstats" ,r-matrixstats) |
515 | ("r-annotationdbi" ,r-annotationdbi) | |
516 | ("r-limma" ,r-limma) | |
517 | ("r-multtest" ,r-multtest) | |
518 | ("r-rbgl" ,r-rbgl) | |
519 | ("r-graph" ,r-graph) | |
793f83ef RJ |
520 | ("r-regioner" ,r-regioner) |
521 | ("r-dbi" ,r-dbi) | |
522 | ("r-ensembldb" ,r-ensembldb) | |
523 | ("r-biobase" ,r-biobase) | |
f794e85d | 524 | ("r-s4vectors" ,r-s4vectors) |
793f83ef RJ |
525 | ("r-seqinr" ,r-seqinr) |
526 | ("r-idr" ,r-idr) | |
527 | ("r-genomicalignments" ,r-genomicalignments) | |
528 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
529 | ("r-rsamtools" ,r-rsamtools) | |
530 | ("r-venndiagram" ,r-venndiagram))) | |
531 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") | |
532 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") | |
533 | (description | |
534 | "The package includes functions to retrieve the sequences around the peak, | |
535 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
536 | custom features such as most conserved elements and other transcription factor | |
537 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
538 | for finding the peaks with bi-directional promoters with summary statistics | |
539 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
540 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
541 | enrichedGO (addGeneIDs).") | |
542 | (license license:gpl2+))) | |
164502d8 RJ |
543 | |
544 | (define-public r-marray | |
545 | (package | |
546 | (name "r-marray") | |
f1c606ce | 547 | (version "1.60.0") |
164502d8 RJ |
548 | (source (origin |
549 | (method url-fetch) | |
550 | (uri (bioconductor-uri "marray" version)) | |
551 | (sha256 | |
f1c606ce | 552 | (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky")))) |
164502d8 RJ |
553 | (build-system r-build-system) |
554 | (propagated-inputs | |
67487088 | 555 | `(("r-limma" ,r-limma))) |
164502d8 RJ |
556 | (home-page "http://bioconductor.org/packages/marray") |
557 | (synopsis "Exploratory analysis for two-color spotted microarray data") | |
558 | (description "This package contains class definitions for two-color spotted | |
559 | microarray data. It also includes fuctions for data input, diagnostic plots, | |
560 | normalization and quality checking.") | |
561 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
562 | |
563 | (define-public r-cghbase | |
564 | (package | |
565 | (name "r-cghbase") | |
46cdceef | 566 | (version "1.42.0") |
0416a0d4 RJ |
567 | (source (origin |
568 | (method url-fetch) | |
569 | (uri (bioconductor-uri "CGHbase" version)) | |
570 | (sha256 | |
46cdceef | 571 | (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc")))) |
0416a0d4 RJ |
572 | (properties `((upstream-name . "CGHbase"))) |
573 | (build-system r-build-system) | |
574 | (propagated-inputs | |
575 | `(("r-biobase" ,r-biobase) | |
576 | ("r-marray" ,r-marray))) | |
577 | (home-page "http://bioconductor.org/packages/CGHbase") | |
578 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
579 | (description "This package contains functions and classes that are needed by | |
580 | the @code{arrayCGH} packages.") | |
581 | (license license:gpl2+))) | |
67ee83d6 RJ |
582 | |
583 | (define-public r-cghcall | |
584 | (package | |
585 | (name "r-cghcall") | |
9add0933 | 586 | (version "2.44.0") |
67ee83d6 RJ |
587 | (source (origin |
588 | (method url-fetch) | |
589 | (uri (bioconductor-uri "CGHcall" version)) | |
590 | (sha256 | |
9add0933 | 591 | (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi")))) |
67ee83d6 RJ |
592 | (properties `((upstream-name . "CGHcall"))) |
593 | (build-system r-build-system) | |
594 | (propagated-inputs | |
595 | `(("r-biobase" ,r-biobase) | |
596 | ("r-cghbase" ,r-cghbase) | |
597 | ("r-impute" ,r-impute) | |
598 | ("r-dnacopy" ,r-dnacopy) | |
599 | ("r-snowfall" ,r-snowfall))) | |
600 | (home-page "http://bioconductor.org/packages/CGHcall") | |
601 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
602 | (description "This package contains functions and classes that are needed by | |
603 | @code{arrayCGH} packages.") | |
604 | (license license:gpl2+))) | |
0ef8cc9c RJ |
605 | |
606 | (define-public r-qdnaseq | |
607 | (package | |
608 | (name "r-qdnaseq") | |
a92f5230 | 609 | (version "1.18.0") |
0ef8cc9c RJ |
610 | (source (origin |
611 | (method url-fetch) | |
612 | (uri (bioconductor-uri "QDNAseq" version)) | |
613 | (sha256 | |
a92f5230 | 614 | (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2")))) |
0ef8cc9c RJ |
615 | (properties `((upstream-name . "QDNAseq"))) |
616 | (build-system r-build-system) | |
617 | (propagated-inputs | |
618 | `(("r-biobase" ,r-biobase) | |
81b0181b | 619 | ("r-biocparallel" ,r-biocparallel) |
0ef8cc9c RJ |
620 | ("r-cghbase" ,r-cghbase) |
621 | ("r-cghcall" ,r-cghcall) | |
622 | ("r-dnacopy" ,r-dnacopy) | |
623 | ("r-genomicranges" ,r-genomicranges) | |
624 | ("r-iranges" ,r-iranges) | |
625 | ("r-matrixstats" ,r-matrixstats) | |
626 | ("r-r-utils" ,r-r-utils) | |
627 | ("r-rsamtools" ,r-rsamtools))) | |
628 | (home-page "http://bioconductor.org/packages/QDNAseq") | |
629 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") | |
630 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
631 | number of sequence reads in each counted, adjusted with a simultaneous | |
632 | two-dimensional loess correction for sequence mappability and GC content, and | |
633 | filtered to remove spurious regions in the genome. Downstream steps of | |
634 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
635 | respectively.") | |
636 | (license license:gpl2+))) | |
bb15b581 RW |
637 | |
638 | (define-public r-bayseq | |
639 | (package | |
640 | (name "r-bayseq") | |
4728e275 | 641 | (version "2.16.0") |
bb15b581 RW |
642 | (source |
643 | (origin | |
644 | (method url-fetch) | |
645 | (uri (bioconductor-uri "baySeq" version)) | |
646 | (sha256 | |
647 | (base32 | |
4728e275 | 648 | "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5")))) |
bb15b581 RW |
649 | (properties `((upstream-name . "baySeq"))) |
650 | (build-system r-build-system) | |
651 | (propagated-inputs | |
652 | `(("r-abind" ,r-abind) | |
653 | ("r-edger" ,r-edger) | |
654 | ("r-genomicranges" ,r-genomicranges))) | |
655 | (home-page "https://bioconductor.org/packages/baySeq/") | |
656 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
657 | (description | |
658 | "This package identifies differential expression in high-throughput count | |
659 | data, such as that derived from next-generation sequencing machines, | |
660 | calculating estimated posterior likelihoods of differential expression (or | |
661 | more complex hypotheses) via empirical Bayesian methods.") | |
662 | (license license:gpl3))) | |
609f4ad1 RW |
663 | |
664 | (define-public r-chipcomp | |
665 | (package | |
666 | (name "r-chipcomp") | |
aa802eaf | 667 | (version "1.12.0") |
609f4ad1 RW |
668 | (source |
669 | (origin | |
670 | (method url-fetch) | |
671 | (uri (bioconductor-uri "ChIPComp" version)) | |
672 | (sha256 | |
673 | (base32 | |
aa802eaf | 674 | "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85")))) |
609f4ad1 RW |
675 | (properties `((upstream-name . "ChIPComp"))) |
676 | (build-system r-build-system) | |
677 | (propagated-inputs | |
678 | `(("r-biocgenerics" ,r-biocgenerics) | |
679 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
680 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
681 | ("r-genomeinfodb" ,r-genomeinfodb) | |
682 | ("r-genomicranges" ,r-genomicranges) | |
683 | ("r-iranges" ,r-iranges) | |
684 | ("r-limma" ,r-limma) | |
685 | ("r-rsamtools" ,r-rsamtools) | |
686 | ("r-rtracklayer" ,r-rtracklayer) | |
687 | ("r-s4vectors" ,r-s4vectors))) | |
688 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
689 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
690 | (description | |
691 | "ChIPComp implements a statistical method for quantitative comparison of | |
692 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
693 | sites across multiple conditions considering matching control in ChIP-seq | |
694 | datasets.") | |
695 | ;; Any version of the GPL. | |
696 | (license license:gpl3+))) | |
0490f9de RW |
697 | |
698 | (define-public r-riboprofiling | |
699 | (package | |
700 | (name "r-riboprofiling") | |
e22e462b | 701 | (version "1.12.0") |
0490f9de RW |
702 | (source |
703 | (origin | |
704 | (method url-fetch) | |
705 | (uri (bioconductor-uri "RiboProfiling" version)) | |
706 | (sha256 | |
707 | (base32 | |
e22e462b | 708 | "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z")))) |
0490f9de RW |
709 | (properties `((upstream-name . "RiboProfiling"))) |
710 | (build-system r-build-system) | |
711 | (propagated-inputs | |
712 | `(("r-biocgenerics" ,r-biocgenerics) | |
713 | ("r-biostrings" ,r-biostrings) | |
714 | ("r-data-table" ,r-data-table) | |
715 | ("r-genomeinfodb" ,r-genomeinfodb) | |
716 | ("r-genomicalignments" ,r-genomicalignments) | |
717 | ("r-genomicfeatures" ,r-genomicfeatures) | |
718 | ("r-genomicranges" ,r-genomicranges) | |
719 | ("r-ggbio" ,r-ggbio) | |
720 | ("r-ggplot2" ,r-ggplot2) | |
721 | ("r-iranges" ,r-iranges) | |
722 | ("r-plyr" ,r-plyr) | |
723 | ("r-reshape2" ,r-reshape2) | |
724 | ("r-rsamtools" ,r-rsamtools) | |
725 | ("r-rtracklayer" ,r-rtracklayer) | |
726 | ("r-s4vectors" ,r-s4vectors) | |
727 | ("r-sqldf" ,r-sqldf))) | |
728 | (home-page "https://bioconductor.org/packages/RiboProfiling/") | |
729 | (synopsis "Ribosome profiling data analysis") | |
730 | (description "Starting with a BAM file, this package provides the | |
731 | necessary functions for quality assessment, read start position recalibration, | |
732 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
733 | of count data: pairs, log fold-change, codon frequency and coverage | |
734 | assessment, principal component analysis on codon coverage.") | |
735 | (license license:gpl3))) | |
6ffdfe6a RW |
736 | |
737 | (define-public r-riboseqr | |
738 | (package | |
739 | (name "r-riboseqr") | |
c4fed658 | 740 | (version "1.16.0") |
6ffdfe6a RW |
741 | (source |
742 | (origin | |
743 | (method url-fetch) | |
744 | (uri (bioconductor-uri "riboSeqR" version)) | |
745 | (sha256 | |
746 | (base32 | |
c4fed658 | 747 | "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb")))) |
6ffdfe6a RW |
748 | (properties `((upstream-name . "riboSeqR"))) |
749 | (build-system r-build-system) | |
750 | (propagated-inputs | |
751 | `(("r-abind" ,r-abind) | |
752 | ("r-bayseq" ,r-bayseq) | |
753 | ("r-genomeinfodb" ,r-genomeinfodb) | |
754 | ("r-genomicranges" ,r-genomicranges) | |
755 | ("r-iranges" ,r-iranges) | |
756 | ("r-rsamtools" ,r-rsamtools) | |
757 | ("r-seqlogo" ,r-seqlogo))) | |
758 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
759 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
760 | (description | |
761 | "This package provides plotting functions, frameshift detection and | |
762 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
763 | (license license:gpl3))) | |
a32279ff RW |
764 | |
765 | (define-public r-interactionset | |
766 | (package | |
767 | (name "r-interactionset") | |
bbc4787c | 768 | (version "1.10.0") |
a32279ff RW |
769 | (source |
770 | (origin | |
771 | (method url-fetch) | |
772 | (uri (bioconductor-uri "InteractionSet" version)) | |
773 | (sha256 | |
774 | (base32 | |
bbc4787c | 775 | "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb")))) |
a32279ff RW |
776 | (properties |
777 | `((upstream-name . "InteractionSet"))) | |
778 | (build-system r-build-system) | |
779 | (propagated-inputs | |
780 | `(("r-biocgenerics" ,r-biocgenerics) | |
781 | ("r-genomeinfodb" ,r-genomeinfodb) | |
782 | ("r-genomicranges" ,r-genomicranges) | |
783 | ("r-iranges" ,r-iranges) | |
784 | ("r-matrix" ,r-matrix) | |
785 | ("r-rcpp" ,r-rcpp) | |
786 | ("r-s4vectors" ,r-s4vectors) | |
787 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
788 | (home-page "https://bioconductor.org/packages/InteractionSet") | |
789 | (synopsis "Base classes for storing genomic interaction data") | |
790 | (description | |
791 | "This packages provides the @code{GInteractions}, | |
792 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods | |
793 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
794 | experiments.") | |
795 | (license license:gpl3))) | |
cf9a29b2 RW |
796 | |
797 | (define-public r-genomicinteractions | |
798 | (package | |
799 | (name "r-genomicinteractions") | |
5f2d0e63 | 800 | (version "1.16.0") |
cf9a29b2 RW |
801 | (source |
802 | (origin | |
803 | (method url-fetch) | |
804 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
805 | (sha256 | |
806 | (base32 | |
5f2d0e63 | 807 | "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q")))) |
cf9a29b2 RW |
808 | (properties |
809 | `((upstream-name . "GenomicInteractions"))) | |
810 | (build-system r-build-system) | |
811 | (propagated-inputs | |
812 | `(("r-biobase" ,r-biobase) | |
813 | ("r-biocgenerics" ,r-biocgenerics) | |
814 | ("r-data-table" ,r-data-table) | |
815 | ("r-dplyr" ,r-dplyr) | |
816 | ("r-genomeinfodb" ,r-genomeinfodb) | |
817 | ("r-genomicranges" ,r-genomicranges) | |
818 | ("r-ggplot2" ,r-ggplot2) | |
819 | ("r-gridextra" ,r-gridextra) | |
820 | ("r-gviz" ,r-gviz) | |
821 | ("r-igraph" ,r-igraph) | |
822 | ("r-interactionset" ,r-interactionset) | |
823 | ("r-iranges" ,r-iranges) | |
824 | ("r-rsamtools" ,r-rsamtools) | |
825 | ("r-rtracklayer" ,r-rtracklayer) | |
826 | ("r-s4vectors" ,r-s4vectors) | |
827 | ("r-stringr" ,r-stringr))) | |
828 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") | |
829 | (synopsis "R package for handling genomic interaction data") | |
830 | (description | |
831 | "This R package provides tools for handling genomic interaction data, | |
832 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
833 | information and producing various plots and statistics.") | |
834 | (license license:gpl3))) | |
27c51606 RW |
835 | |
836 | (define-public r-ctc | |
837 | (package | |
838 | (name "r-ctc") | |
b858338c | 839 | (version "1.56.0") |
27c51606 RW |
840 | (source |
841 | (origin | |
842 | (method url-fetch) | |
843 | (uri (bioconductor-uri "ctc" version)) | |
844 | (sha256 | |
845 | (base32 | |
b858338c | 846 | "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2")))) |
27c51606 RW |
847 | (build-system r-build-system) |
848 | (propagated-inputs `(("r-amap" ,r-amap))) | |
849 | (home-page "https://bioconductor.org/packages/ctc/") | |
850 | (synopsis "Cluster and tree conversion") | |
851 | (description | |
852 | "This package provides tools for exporting and importing classification | |
853 | trees and clusters to other programs.") | |
854 | (license license:gpl2))) | |
5da0e142 RW |
855 | |
856 | (define-public r-goseq | |
857 | (package | |
858 | (name "r-goseq") | |
7f2b1c4a | 859 | (version "1.34.1") |
5da0e142 RW |
860 | (source |
861 | (origin | |
862 | (method url-fetch) | |
863 | (uri (bioconductor-uri "goseq" version)) | |
864 | (sha256 | |
865 | (base32 | |
7f2b1c4a | 866 | "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn")))) |
5da0e142 RW |
867 | (build-system r-build-system) |
868 | (propagated-inputs | |
869 | `(("r-annotationdbi" ,r-annotationdbi) | |
870 | ("r-biasedurn" ,r-biasedurn) | |
871 | ("r-biocgenerics" ,r-biocgenerics) | |
872 | ("r-genelendatabase" ,r-genelendatabase) | |
873 | ("r-go-db" ,r-go-db) | |
874 | ("r-mgcv" ,r-mgcv))) | |
875 | (home-page "https://bioconductor.org/packages/goseq/") | |
876 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
877 | (description | |
878 | "This package provides tools to detect Gene Ontology and/or other user | |
879 | defined categories which are over/under represented in RNA-seq data.") | |
880 | (license license:lgpl2.0+))) | |
f4235c0e RW |
881 | |
882 | (define-public r-glimma | |
883 | (package | |
884 | (name "r-glimma") | |
0b469ee2 | 885 | (version "1.10.1") |
f4235c0e RW |
886 | (source |
887 | (origin | |
888 | (method url-fetch) | |
889 | (uri (bioconductor-uri "Glimma" version)) | |
890 | (sha256 | |
891 | (base32 | |
0b469ee2 | 892 | "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv")))) |
f4235c0e RW |
893 | (properties `((upstream-name . "Glimma"))) |
894 | (build-system r-build-system) | |
895 | (propagated-inputs | |
896 | `(("r-edger" ,r-edger) | |
897 | ("r-jsonlite" ,r-jsonlite) | |
898 | ("r-s4vectors" ,r-s4vectors))) | |
899 | (home-page "https://github.com/Shians/Glimma") | |
900 | (synopsis "Interactive HTML graphics") | |
901 | (description | |
902 | "This package generates interactive visualisations for analysis of | |
903 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
904 | HTML page. The interactions are built on top of the popular static | |
905 | representations of analysis results in order to provide additional | |
906 | information.") | |
907 | (license license:lgpl3))) | |
aa388dc7 RW |
908 | |
909 | (define-public r-rots | |
910 | (package | |
911 | (name "r-rots") | |
45dcd7dc | 912 | (version "1.10.1") |
aa388dc7 RW |
913 | (source |
914 | (origin | |
915 | (method url-fetch) | |
916 | (uri (bioconductor-uri "ROTS" version)) | |
917 | (sha256 | |
918 | (base32 | |
45dcd7dc | 919 | "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6")))) |
aa388dc7 RW |
920 | (properties `((upstream-name . "ROTS"))) |
921 | (build-system r-build-system) | |
922 | (propagated-inputs | |
923 | `(("r-biobase" ,r-biobase) | |
924 | ("r-rcpp" ,r-rcpp))) | |
925 | (home-page "https://bioconductor.org/packages/ROTS/") | |
926 | (synopsis "Reproducibility-Optimized Test Statistic") | |
927 | (description | |
928 | "This package provides tools for calculating the | |
929 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
930 | in omics data.") | |
931 | (license license:gpl2+))) | |
b64ce4b7 | 932 | |
cad6fb2d RW |
933 | (define-public r-plgem |
934 | (package | |
935 | (name "r-plgem") | |
936 | (version "1.54.1") | |
937 | (source | |
938 | (origin | |
939 | (method url-fetch) | |
940 | (uri (bioconductor-uri "plgem" version)) | |
941 | (sha256 | |
942 | (base32 | |
943 | "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg")))) | |
944 | (build-system r-build-system) | |
945 | (propagated-inputs | |
946 | `(("r-biobase" ,r-biobase) | |
947 | ("r-mass" ,r-mass))) | |
948 | (home-page "http://www.genopolis.it") | |
949 | (synopsis "Detect differential expression in microarray and proteomics datasets") | |
950 | (description | |
951 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully | |
952 | model the variance-versus-mean dependence that exists in a variety of | |
953 | genome-wide datasets, including microarray and proteomics data. The use of | |
954 | PLGEM has been shown to improve the detection of differentially expressed | |
955 | genes or proteins in these datasets.") | |
956 | (license license:gpl2))) | |
957 | ||
b64ce4b7 RW |
958 | (define-public r-inspect |
959 | (package | |
960 | (name "r-inspect") | |
c86fc969 | 961 | (version "1.12.1") |
b64ce4b7 RW |
962 | (source |
963 | (origin | |
964 | (method url-fetch) | |
965 | (uri (bioconductor-uri "INSPEcT" version)) | |
966 | (sha256 | |
967 | (base32 | |
c86fc969 | 968 | "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp")))) |
b64ce4b7 RW |
969 | (properties `((upstream-name . "INSPEcT"))) |
970 | (build-system r-build-system) | |
971 | (propagated-inputs | |
972 | `(("r-biobase" ,r-biobase) | |
973 | ("r-biocgenerics" ,r-biocgenerics) | |
974 | ("r-biocparallel" ,r-biocparallel) | |
c86fc969 | 975 | ("r-deseq2" ,r-deseq2) |
b64ce4b7 RW |
976 | ("r-desolve" ,r-desolve) |
977 | ("r-genomicalignments" ,r-genomicalignments) | |
978 | ("r-genomicfeatures" ,r-genomicfeatures) | |
979 | ("r-genomicranges" ,r-genomicranges) | |
980 | ("r-iranges" ,r-iranges) | |
c86fc969 | 981 | ("r-plgem" ,r-plgem) |
b64ce4b7 RW |
982 | ("r-preprocesscore" ,r-preprocesscore) |
983 | ("r-proc" ,r-proc) | |
984 | ("r-rootsolve" ,r-rootsolve) | |
985 | ("r-rsamtools" ,r-rsamtools) | |
c86fc969 RW |
986 | ("r-s4vectors" ,r-s4vectors) |
987 | ("r-shiny" ,r-shiny) | |
988 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
989 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" | |
990 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) | |
b64ce4b7 RW |
991 | (home-page "https://bioconductor.org/packages/INSPEcT") |
992 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
993 | (description | |
994 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
995 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
996 | order to evaluate synthesis, processing and degradation rates and assess via | |
997 | modeling the rates that determines changes in mature mRNA levels.") | |
998 | (license license:gpl2))) | |
f6e99763 RW |
999 | |
1000 | (define-public r-dnabarcodes | |
1001 | (package | |
1002 | (name "r-dnabarcodes") | |
318bcbc4 | 1003 | (version "1.12.0") |
f6e99763 RW |
1004 | (source |
1005 | (origin | |
1006 | (method url-fetch) | |
1007 | (uri (bioconductor-uri "DNABarcodes" version)) | |
1008 | (sha256 | |
1009 | (base32 | |
318bcbc4 | 1010 | "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0")))) |
f6e99763 RW |
1011 | (properties `((upstream-name . "DNABarcodes"))) |
1012 | (build-system r-build-system) | |
1013 | (propagated-inputs | |
1014 | `(("r-bh" ,r-bh) | |
1015 | ("r-matrix" ,r-matrix) | |
1016 | ("r-rcpp" ,r-rcpp))) | |
1017 | (home-page "https://bioconductor.org/packages/DNABarcodes") | |
1018 | (synopsis "Create and analyze DNA barcodes") | |
1019 | (description | |
1020 | "This package offers tools to create DNA barcode sets capable of | |
1021 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
1022 | can be analyzed regarding their minimal, maximal and average distances between | |
1023 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
1024 | demultiplexed, i.e. assigned to their original reference barcode.") | |
1025 | (license license:gpl2))) | |
09aa3d06 RW |
1026 | |
1027 | (define-public r-ruvseq | |
1028 | (package | |
1029 | (name "r-ruvseq") | |
c6e9b494 | 1030 | (version "1.16.1") |
09aa3d06 RW |
1031 | (source |
1032 | (origin | |
1033 | (method url-fetch) | |
1034 | (uri (bioconductor-uri "RUVSeq" version)) | |
1035 | (sha256 | |
1036 | (base32 | |
c6e9b494 | 1037 | "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv")))) |
09aa3d06 RW |
1038 | (properties `((upstream-name . "RUVSeq"))) |
1039 | (build-system r-build-system) | |
1040 | (propagated-inputs | |
1041 | `(("r-biobase" ,r-biobase) | |
1042 | ("r-edaseq" ,r-edaseq) | |
1043 | ("r-edger" ,r-edger) | |
1044 | ("r-mass" ,r-mass))) | |
1045 | (home-page "https://github.com/drisso/RUVSeq") | |
1046 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
1047 | (description | |
1048 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
1049 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
1050 | samples.") | |
1051 | (license license:artistic2.0))) | |
286157dc RW |
1052 | |
1053 | (define-public r-biocneighbors | |
1054 | (package | |
1055 | (name "r-biocneighbors") | |
1056 | (version "1.0.0") | |
1057 | (source | |
1058 | (origin | |
1059 | (method url-fetch) | |
1060 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
1061 | (sha256 | |
1062 | (base32 | |
1063 | "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll")))) | |
1064 | (properties `((upstream-name . "BiocNeighbors"))) | |
1065 | (build-system r-build-system) | |
1066 | (propagated-inputs | |
1067 | `(("r-biocparallel" ,r-biocparallel) | |
1068 | ("r-rcpp" ,r-rcpp) | |
1069 | ("r-rcppannoy" ,r-rcppannoy) | |
1070 | ("r-s4vectors" ,r-s4vectors))) | |
1071 | (home-page "https://bioconductor.org/packages/BiocNeighbors") | |
1072 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
1073 | (description | |
1074 | "This package implements exact and approximate methods for nearest | |
1075 | neighbor detection, in a framework that allows them to be easily switched | |
1076 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
1077 | using pre-clustering with the k-means algorithm. Functions are also provided | |
1078 | to search for all neighbors within a given distance. Parallelization is | |
1079 | achieved for all methods using the BiocParallel framework.") | |
1080 | (license license:gpl3))) | |
8a587c89 | 1081 | |
a961ae46 RW |
1082 | (define-public r-destiny |
1083 | (package | |
1084 | (name "r-destiny") | |
1085 | (version "2.12.0") | |
1086 | (source | |
1087 | (origin | |
1088 | (method url-fetch) | |
1089 | (uri (bioconductor-uri "destiny" version)) | |
1090 | (sha256 | |
1091 | (base32 | |
1092 | "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67")))) | |
1093 | (build-system r-build-system) | |
1094 | (propagated-inputs | |
1095 | `(("r-biobase" ,r-biobase) | |
1096 | ("r-biocgenerics" ,r-biocgenerics) | |
1097 | ("r-fnn" ,r-fnn) | |
1098 | ("r-ggthemes" ,r-ggthemes) | |
1099 | ("r-hmisc" ,r-hmisc) | |
1100 | ("r-igraph" ,r-igraph) | |
1101 | ("r-matrix" ,r-matrix) | |
1102 | ("r-proxy" ,r-proxy) | |
1103 | ("r-rcpp" ,r-rcpp) | |
1104 | ("r-rcppeigen" ,r-rcppeigen) | |
1105 | ("r-scales" ,r-scales) | |
1106 | ("r-scatterplot3d" ,r-scatterplot3d) | |
1107 | ("r-smoother" ,r-smoother) | |
1108 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1109 | ("r-vim" ,r-vim))) | |
1110 | (home-page "https://bioconductor.org/packages/destiny/") | |
1111 | (synopsis "Create and plot diffusion maps") | |
1112 | (description "This package provides tools to create and plot diffusion | |
1113 | maps.") | |
1114 | ;; Any version of the GPL | |
1115 | (license license:gpl3+))) | |
1116 | ||
8a587c89 RW |
1117 | (define-public r-savr |
1118 | (package | |
1119 | (name "r-savr") | |
1120 | (version "1.20.0") | |
1121 | (source | |
1122 | (origin | |
1123 | (method url-fetch) | |
1124 | (uri (bioconductor-uri "savR" version)) | |
1125 | (sha256 | |
1126 | (base32 | |
1127 | "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7")))) | |
1128 | (properties `((upstream-name . "savR"))) | |
1129 | (build-system r-build-system) | |
1130 | (propagated-inputs | |
1131 | `(("r-ggplot2" ,r-ggplot2) | |
1132 | ("r-gridextra" ,r-gridextra) | |
1133 | ("r-reshape2" ,r-reshape2) | |
1134 | ("r-scales" ,r-scales) | |
1135 | ("r-xml" ,r-xml))) | |
1136 | (home-page "https://github.com/bcalder/savR") | |
1137 | (synopsis "Parse and analyze Illumina SAV files") | |
1138 | (description | |
1139 | "This package provides tools to parse Illumina Sequence Analysis | |
1140 | Viewer (SAV) files, access data, and generate QC plots.") | |
1141 | (license license:agpl3+))) | |
41ffc214 RW |
1142 | |
1143 | (define-public r-chipexoqual | |
1144 | (package | |
1145 | (name "r-chipexoqual") | |
1146 | (version "1.6.0") | |
1147 | (source | |
1148 | (origin | |
1149 | (method url-fetch) | |
1150 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
1151 | (sha256 | |
1152 | (base32 | |
1153 | "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp")))) | |
1154 | (properties `((upstream-name . "ChIPexoQual"))) | |
1155 | (build-system r-build-system) | |
1156 | (propagated-inputs | |
1157 | `(("r-biocparallel" ,r-biocparallel) | |
1158 | ("r-biovizbase" ,r-biovizbase) | |
1159 | ("r-broom" ,r-broom) | |
1160 | ("r-data-table" ,r-data-table) | |
1161 | ("r-dplyr" ,r-dplyr) | |
1162 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1163 | ("r-genomicalignments" ,r-genomicalignments) | |
1164 | ("r-genomicranges" ,r-genomicranges) | |
1165 | ("r-ggplot2" ,r-ggplot2) | |
1166 | ("r-hexbin" ,r-hexbin) | |
1167 | ("r-iranges" ,r-iranges) | |
1168 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
1169 | ("r-rmarkdown" ,r-rmarkdown) | |
1170 | ("r-rsamtools" ,r-rsamtools) | |
1171 | ("r-s4vectors" ,r-s4vectors) | |
1172 | ("r-scales" ,r-scales) | |
1173 | ("r-viridis" ,r-viridis))) | |
1174 | (home-page "https://github.com/keleslab/ChIPexoQual") | |
1175 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
1176 | (description | |
1177 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
1178 | sequencing data.") | |
1179 | (license license:gpl2+))) | |
c18dccff RW |
1180 | |
1181 | (define-public r-dnacopy | |
1182 | (package | |
1183 | (name "r-dnacopy") | |
1184 | (version "1.56.0") | |
1185 | (source | |
1186 | (origin | |
1187 | (method url-fetch) | |
1188 | (uri (bioconductor-uri "DNAcopy" version)) | |
1189 | (sha256 | |
1190 | (base32 | |
1191 | "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82")))) | |
1192 | (properties `((upstream-name . "DNAcopy"))) | |
1193 | (build-system r-build-system) | |
1194 | (native-inputs `(("gfortran" ,gfortran))) | |
1195 | (home-page "https://bioconductor.org/packages/DNAcopy") | |
1196 | (synopsis "DNA copy number data analysis") | |
1197 | (description | |
1198 | "This package implements the @dfn{circular binary segmentation} (CBS) | |
1199 | algorithm to segment DNA copy number data and identify genomic regions with | |
1200 | abnormal copy number.") | |
1201 | (license license:gpl2+))) | |
3a0babac RW |
1202 | |
1203 | ;; This is a CRAN package, but it uncharacteristically depends on a | |
1204 | ;; Bioconductor package. | |
1205 | (define-public r-htscluster | |
1206 | (package | |
1207 | (name "r-htscluster") | |
1208 | (version "2.0.8") | |
1209 | (source | |
1210 | (origin | |
1211 | (method url-fetch) | |
1212 | (uri (cran-uri "HTSCluster" version)) | |
1213 | (sha256 | |
1214 | (base32 | |
1215 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) | |
1216 | (properties `((upstream-name . "HTSCluster"))) | |
1217 | (build-system r-build-system) | |
1218 | (propagated-inputs | |
1219 | `(("r-capushe" ,r-capushe) | |
1220 | ("r-edger" ,r-edger) | |
1221 | ("r-plotrix" ,r-plotrix))) | |
1222 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") | |
1223 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") | |
1224 | (description | |
1225 | "This package provides a Poisson mixture model is implemented to cluster | |
1226 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter | |
1227 | estimation is performed using either the EM or CEM algorithm, and the slope | |
1228 | heuristics are used for model selection (i.e., to choose the number of | |
1229 | clusters).") | |
1230 | (license license:gpl3+))) |