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fa596599 RW |
1 | ;;; GNU Guix --- Functional package management for GNU |
2 | ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> | |
183ce988 | 3 | ;;; Copyright © 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) | |
cf9a29b2 | 30 | #:use-module (gnu packages graph) |
f4235c0e RW |
31 | #:use-module (gnu packages statistics) |
32 | #:use-module (gnu packages web)) | |
fa596599 | 33 | |
183db725 RW |
34 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
35 | (package | |
36 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
37 | (version "1.4.1") | |
38 | (source (origin | |
39 | (method url-fetch) | |
40 | ;; We cannot use bioconductor-uri here because this tarball is | |
41 | ;; located under "data/annotation/" instead of "bioc/". | |
42 | (uri (string-append "https://www.bioconductor.org/packages/" | |
43 | "release/data/annotation/src/contrib/" | |
44 | "BSgenome.Dmelanogaster.UCSC.dm6_" | |
45 | version ".tar.gz")) | |
46 | (sha256 | |
47 | (base32 | |
48 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
49 | (properties | |
50 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
51 | (build-system r-build-system) | |
52 | ;; As this package provides little more than a very large data file it | |
53 | ;; doesn't make sense to build substitutes. | |
54 | (arguments `(#:substitutable? #f)) | |
55 | (propagated-inputs | |
56 | `(("r-bsgenome" ,r-bsgenome))) | |
57 | (home-page | |
58 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
59 | (synopsis "Full genome sequences for Fly") | |
60 | (description | |
61 | "This package provides full genome sequences for Drosophila | |
62 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
63 | objects.") | |
64 | (license license:artistic2.0))) | |
65 | ||
dfac7eb9 RW |
66 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
67 | (package | |
68 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
69 | (version "1.3.99") | |
70 | (source (origin | |
71 | (method url-fetch) | |
72 | ;; We cannot use bioconductor-uri here because this tarball is | |
73 | ;; located under "data/annotation/" instead of "bioc/". | |
74 | (uri (string-append "http://www.bioconductor.org/packages/" | |
75 | "release/data/annotation/src/contrib/" | |
76 | "BSgenome.Dmelanogaster.UCSC.dm3.masked_" | |
77 | version ".tar.gz")) | |
78 | (sha256 | |
79 | (base32 | |
80 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
81 | (properties | |
82 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
83 | (build-system r-build-system) | |
84 | (propagated-inputs | |
85 | `(("r-bsgenome" ,r-bsgenome) | |
86 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
87 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
88 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
89 | (synopsis "Full masked genome sequences for Fly") | |
90 | (description | |
91 | "This package provides full masked genome sequences for Drosophila | |
92 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
93 | Biostrings objects. The sequences are the same as in | |
94 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
95 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
96 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
97 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
98 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
99 | (license license:artistic2.0))) | |
100 | ||
6fbd759b RW |
101 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
102 | (package | |
103 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
104 | (version "1.3.99") | |
105 | (source (origin | |
106 | (method url-fetch) | |
107 | ;; We cannot use bioconductor-uri here because this tarball is | |
108 | ;; located under "data/annotation/" instead of "bioc/". | |
109 | (uri (string-append "http://www.bioconductor.org/packages/" | |
110 | "release/data/annotation/src/contrib/" | |
111 | "BSgenome.Hsapiens.UCSC.hg19.masked_" | |
112 | version ".tar.gz")) | |
113 | (sha256 | |
114 | (base32 | |
115 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
116 | (properties | |
117 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
118 | (build-system r-build-system) | |
119 | (propagated-inputs | |
120 | `(("r-bsgenome" ,r-bsgenome) | |
121 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
122 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
123 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
124 | (synopsis "Full masked genome sequences for Homo sapiens") | |
125 | (description | |
126 | "This package provides full genome sequences for Homo sapiens (Human) as | |
127 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
128 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
129 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
130 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
131 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
132 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
133 | default.") | |
134 | (license license:artistic2.0))) | |
135 | ||
2bece692 RW |
136 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
137 | (package | |
138 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
139 | (version "1.3.99") | |
140 | (source (origin | |
141 | (method url-fetch) | |
142 | ;; We cannot use bioconductor-uri here because this tarball is | |
143 | ;; located under "data/annotation/" instead of "bioc/". | |
144 | (uri (string-append "http://www.bioconductor.org/packages/" | |
145 | "release/data/annotation/src/contrib/" | |
146 | "BSgenome.Mmusculus.UCSC.mm9.masked_" | |
147 | version ".tar.gz")) | |
148 | (sha256 | |
149 | (base32 | |
150 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
151 | (properties | |
152 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
153 | (build-system r-build-system) | |
154 | (propagated-inputs | |
155 | `(("r-bsgenome" ,r-bsgenome) | |
156 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
157 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
158 | (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") | |
159 | (synopsis "Full masked genome sequences for Mouse") | |
160 | (description | |
161 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
162 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
163 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
164 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
165 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
166 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
167 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
168 | default." ) | |
169 | (license license:artistic2.0))) | |
170 | ||
2cc51108 RW |
171 | (define-public r-genelendatabase |
172 | (package | |
173 | (name "r-genelendatabase") | |
174 | (version "1.16.0") | |
175 | (source | |
176 | (origin | |
177 | (method url-fetch) | |
178 | ;; We cannot use bioconductor-uri here because this tarball is | |
179 | ;; located under "data/experiment/" instead of "bioc/". | |
180 | (uri (string-append "https://bioconductor.org/packages/" | |
181 | "release/data/experiment/src/contrib" | |
182 | "/geneLenDataBase_" version ".tar.gz")) | |
183 | (sha256 | |
184 | (base32 | |
185 | "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5")))) | |
186 | (properties | |
187 | `((upstream-name . "geneLenDataBase"))) | |
188 | (build-system r-build-system) | |
189 | (propagated-inputs | |
190 | `(("r-rtracklayer" ,r-rtracklayer) | |
191 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
192 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
193 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
194 | (description | |
195 | "This package provides the lengths of mRNA transcripts for a number of | |
196 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
197 | (license license:lgpl2.0+))) | |
198 | ||
199 | \f | |
fa596599 RW |
200 | (define-public r-hpar |
201 | (package | |
202 | (name "r-hpar") | |
2f5b3d8e | 203 | (version "1.22.2") |
fa596599 RW |
204 | (source |
205 | (origin | |
206 | (method url-fetch) | |
207 | (uri (bioconductor-uri "hpar" version)) | |
208 | (sha256 | |
209 | (base32 | |
2f5b3d8e | 210 | "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388")))) |
fa596599 RW |
211 | (build-system r-build-system) |
212 | (home-page "https://bioconductor.org/packages/hpar/") | |
213 | (synopsis "Human Protein Atlas in R") | |
214 | (description "This package provides a simple interface to and data from | |
215 | the Human Protein Atlas project.") | |
216 | (license license:artistic2.0))) | |
183ce988 RJ |
217 | |
218 | (define-public r-regioner | |
219 | (package | |
220 | (name "r-regioner") | |
72427c72 | 221 | (version "1.12.0") |
183ce988 RJ |
222 | (source |
223 | (origin | |
224 | (method url-fetch) | |
225 | (uri (bioconductor-uri "regioneR" version)) | |
226 | (sha256 | |
227 | (base32 | |
72427c72 | 228 | "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb")))) |
183ce988 RJ |
229 | (properties `((upstream-name . "regioneR"))) |
230 | (build-system r-build-system) | |
231 | (propagated-inputs | |
232 | `(("r-memoise" ,r-memoise) | |
233 | ("r-genomicranges" ,r-genomicranges) | |
234 | ("r-bsgenome" ,r-bsgenome) | |
235 | ("r-rtracklayer" ,r-rtracklayer) | |
236 | ("r-genomeinfodb" ,r-genomeinfodb) | |
72427c72 RW |
237 | ("r-iranges" ,r-iranges) |
238 | ("r-s4vectors" ,r-s4vectors))) | |
183ce988 RJ |
239 | (home-page "https://bioconductor.org/packages/regioneR/") |
240 | (synopsis "Association analysis of genomic regions") | |
241 | (description "This package offers a statistical framework based on | |
242 | customizable permutation tests to assess the association between genomic | |
243 | region sets and other genomic features.") | |
244 | (license license:artistic2.0))) | |
a5b56a53 RJ |
245 | |
246 | (define-public r-diffbind | |
247 | (package | |
248 | (name "r-diffbind") | |
45bbccf4 | 249 | (version "2.8.0") |
a5b56a53 RJ |
250 | (source |
251 | (origin | |
252 | (method url-fetch) | |
253 | (uri (bioconductor-uri "DiffBind" version)) | |
254 | (sha256 | |
255 | (base32 | |
45bbccf4 | 256 | "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish")))) |
a5b56a53 RJ |
257 | (properties `((upstream-name . "DiffBind"))) |
258 | (build-system r-build-system) | |
259 | (inputs | |
260 | `(("zlib" ,zlib))) | |
261 | (propagated-inputs | |
262 | `(("r-amap" ,r-amap) | |
263 | ("r-biocparallel" ,r-biocparallel) | |
264 | ("r-deseq2" ,r-deseq2) | |
265 | ("r-dplyr" ,r-dplyr) | |
266 | ("r-edger" ,r-edger) | |
267 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
268 | ("r-genomicranges" ,r-genomicranges) |
269 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
270 | ("r-ggrepel" ,r-ggrepel) |
271 | ("r-gplots" ,r-gplots) | |
272 | ("r-iranges" ,r-iranges) | |
273 | ("r-lattice" ,r-lattice) | |
274 | ("r-limma" ,r-limma) | |
275 | ("r-locfit" ,r-locfit) | |
276 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
277 | ("r-rcpp" ,r-rcpp) | |
278 | ("r-rsamtools" ,r-rsamtools) | |
279 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 280 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
a5b56a53 RJ |
281 | ("r-systempiper" ,r-systempiper) |
282 | ("r-zlibbioc" ,r-zlibbioc))) | |
283 | (home-page "http://bioconductor.org/packages/DiffBind") | |
284 | (synopsis "Differential binding analysis of ChIP-Seq peak data") | |
285 | (description | |
286 | "This package computes differentially bound sites from multiple | |
287 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
288 | occupancy (overlap) analysis and plotting functions.") | |
289 | (license license:artistic2.0))) | |
6d94bf6b RJ |
290 | |
291 | (define-public r-ripseeker | |
292 | (package | |
293 | (name "r-ripseeker") | |
43734b47 | 294 | (version "1.20.0") |
6d94bf6b RJ |
295 | (source |
296 | (origin | |
297 | (method url-fetch) | |
298 | (uri (bioconductor-uri "RIPSeeker" version)) | |
299 | (sha256 | |
300 | (base32 | |
43734b47 | 301 | "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi")))) |
6d94bf6b RJ |
302 | (properties `((upstream-name . "RIPSeeker"))) |
303 | (build-system r-build-system) | |
304 | (propagated-inputs | |
305 | `(("r-s4vectors" ,r-s4vectors) | |
306 | ("r-iranges" ,r-iranges) | |
307 | ("r-genomicranges" ,r-genomicranges) | |
308 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
309 | ("r-rsamtools" ,r-rsamtools) | |
310 | ("r-genomicalignments" ,r-genomicalignments) | |
311 | ("r-rtracklayer" ,r-rtracklayer))) | |
312 | (home-page "http://bioconductor.org/packages/RIPSeeker") | |
313 | (synopsis | |
314 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
315 | (description | |
316 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
317 | using two-state HMM with negative binomial emission probability. While | |
318 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
319 | a suite of bioinformatics tools integrated within this self-contained software | |
320 | package comprehensively addressing issues ranging from post-alignments | |
321 | processing to visualization and annotation.") | |
322 | (license license:gpl2))) | |
a6ae9ffd RJ |
323 | |
324 | (define-public r-multtest | |
325 | (package | |
326 | (name "r-multtest") | |
f39938b1 | 327 | (version "2.36.0") |
a6ae9ffd RJ |
328 | (source |
329 | (origin | |
330 | (method url-fetch) | |
331 | (uri (bioconductor-uri "multtest" version)) | |
332 | (sha256 | |
333 | (base32 | |
f39938b1 | 334 | "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0")))) |
a6ae9ffd RJ |
335 | (build-system r-build-system) |
336 | (propagated-inputs | |
337 | `(("r-survival" ,r-survival) | |
338 | ("r-biocgenerics" ,r-biocgenerics) | |
339 | ("r-biobase" ,r-biobase) | |
340 | ("r-mass" ,r-mass))) | |
341 | (home-page "http://bioconductor.org/packages/multtest") | |
342 | (synopsis "Resampling-based multiple hypothesis testing") | |
343 | (description | |
344 | "This package can do non-parametric bootstrap and permutation | |
345 | resampling-based multiple testing procedures (including empirical Bayes | |
346 | methods) for controlling the family-wise error rate (FWER), generalized | |
347 | family-wise error rate (gFWER), tail probability of the proportion of | |
348 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
349 | of bootstrap-based null distribution are implemented (centered, centered | |
350 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
351 | available. Tests based on a variety of T- and F-statistics (including | |
352 | T-statistics based on regression parameters from linear and survival models | |
353 | as well as those based on correlation parameters) are included. When probing | |
354 | hypotheses with T-statistics, users may also select a potentially faster null | |
355 | distribution which is multivariate normal with mean zero and variance | |
356 | covariance matrix derived from the vector influence function. Results are | |
357 | reported in terms of adjusted P-values, confidence regions and test statistic | |
358 | cutoffs. The procedures are directly applicable to identifying differentially | |
359 | expressed genes in DNA microarray experiments.") | |
360 | (license license:lgpl3))) | |
793f83ef RJ |
361 | |
362 | (define-public r-chippeakanno | |
363 | (package | |
364 | (name "r-chippeakanno") | |
f794e85d | 365 | (version "3.14.0") |
793f83ef RJ |
366 | (source |
367 | (origin | |
368 | (method url-fetch) | |
369 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
370 | (sha256 | |
371 | (base32 | |
f794e85d | 372 | "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0")))) |
793f83ef RJ |
373 | (properties `((upstream-name . "ChIPpeakAnno"))) |
374 | (build-system r-build-system) | |
375 | (propagated-inputs | |
376 | `(("r-biocgenerics" ,r-biocgenerics) | |
f794e85d RW |
377 | ("r-biostrings" ,r-biostrings) |
378 | ("r-delayedarray" ,r-delayedarray) | |
793f83ef RJ |
379 | ("r-go-db" ,r-go-db) |
380 | ("r-biomart" ,r-biomart) | |
381 | ("r-bsgenome" ,r-bsgenome) | |
382 | ("r-genomicfeatures" ,r-genomicfeatures) | |
f794e85d | 383 | ("r-genomicranges" ,r-genomicranges) |
793f83ef | 384 | ("r-genomeinfodb" ,r-genomeinfodb) |
f794e85d | 385 | ("r-iranges" ,r-iranges) |
793f83ef RJ |
386 | ("r-matrixstats" ,r-matrixstats) |
387 | ("r-annotationdbi" ,r-annotationdbi) | |
388 | ("r-limma" ,r-limma) | |
389 | ("r-multtest" ,r-multtest) | |
390 | ("r-rbgl" ,r-rbgl) | |
391 | ("r-graph" ,r-graph) | |
392 | ("r-biocinstaller" ,r-biocinstaller) | |
393 | ("r-regioner" ,r-regioner) | |
394 | ("r-dbi" ,r-dbi) | |
395 | ("r-ensembldb" ,r-ensembldb) | |
396 | ("r-biobase" ,r-biobase) | |
f794e85d | 397 | ("r-s4vectors" ,r-s4vectors) |
793f83ef RJ |
398 | ("r-seqinr" ,r-seqinr) |
399 | ("r-idr" ,r-idr) | |
400 | ("r-genomicalignments" ,r-genomicalignments) | |
401 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
402 | ("r-rsamtools" ,r-rsamtools) | |
403 | ("r-venndiagram" ,r-venndiagram))) | |
404 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") | |
405 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") | |
406 | (description | |
407 | "The package includes functions to retrieve the sequences around the peak, | |
408 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
409 | custom features such as most conserved elements and other transcription factor | |
410 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
411 | for finding the peaks with bi-directional promoters with summary statistics | |
412 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
413 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
414 | enrichedGO (addGeneIDs).") | |
415 | (license license:gpl2+))) | |
164502d8 RJ |
416 | |
417 | (define-public r-marray | |
418 | (package | |
419 | (name "r-marray") | |
67487088 | 420 | (version "1.58.0") |
164502d8 RJ |
421 | (source (origin |
422 | (method url-fetch) | |
423 | (uri (bioconductor-uri "marray" version)) | |
424 | (sha256 | |
67487088 | 425 | (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d")))) |
164502d8 RJ |
426 | (build-system r-build-system) |
427 | (propagated-inputs | |
67487088 | 428 | `(("r-limma" ,r-limma))) |
164502d8 RJ |
429 | (home-page "http://bioconductor.org/packages/marray") |
430 | (synopsis "Exploratory analysis for two-color spotted microarray data") | |
431 | (description "This package contains class definitions for two-color spotted | |
432 | microarray data. It also includes fuctions for data input, diagnostic plots, | |
433 | normalization and quality checking.") | |
434 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
435 | |
436 | (define-public r-cghbase | |
437 | (package | |
438 | (name "r-cghbase") | |
205df4a4 | 439 | (version "1.40.0") |
0416a0d4 RJ |
440 | (source (origin |
441 | (method url-fetch) | |
442 | (uri (bioconductor-uri "CGHbase" version)) | |
443 | (sha256 | |
205df4a4 | 444 | (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq")))) |
0416a0d4 RJ |
445 | (properties `((upstream-name . "CGHbase"))) |
446 | (build-system r-build-system) | |
447 | (propagated-inputs | |
448 | `(("r-biobase" ,r-biobase) | |
449 | ("r-marray" ,r-marray))) | |
450 | (home-page "http://bioconductor.org/packages/CGHbase") | |
451 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
452 | (description "This package contains functions and classes that are needed by | |
453 | the @code{arrayCGH} packages.") | |
454 | (license license:gpl2+))) | |
67ee83d6 RJ |
455 | |
456 | (define-public r-cghcall | |
457 | (package | |
458 | (name "r-cghcall") | |
5c0df206 | 459 | (version "2.42.0") |
67ee83d6 RJ |
460 | (source (origin |
461 | (method url-fetch) | |
462 | (uri (bioconductor-uri "CGHcall" version)) | |
463 | (sha256 | |
5c0df206 | 464 | (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz")))) |
67ee83d6 RJ |
465 | (properties `((upstream-name . "CGHcall"))) |
466 | (build-system r-build-system) | |
467 | (propagated-inputs | |
468 | `(("r-biobase" ,r-biobase) | |
469 | ("r-cghbase" ,r-cghbase) | |
470 | ("r-impute" ,r-impute) | |
471 | ("r-dnacopy" ,r-dnacopy) | |
472 | ("r-snowfall" ,r-snowfall))) | |
473 | (home-page "http://bioconductor.org/packages/CGHcall") | |
474 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
475 | (description "This package contains functions and classes that are needed by | |
476 | @code{arrayCGH} packages.") | |
477 | (license license:gpl2+))) | |
0ef8cc9c RJ |
478 | |
479 | (define-public r-qdnaseq | |
480 | (package | |
481 | (name "r-qdnaseq") | |
81b0181b | 482 | (version "1.16.0") |
0ef8cc9c RJ |
483 | (source (origin |
484 | (method url-fetch) | |
485 | (uri (bioconductor-uri "QDNAseq" version)) | |
486 | (sha256 | |
81b0181b | 487 | (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd")))) |
0ef8cc9c RJ |
488 | (properties `((upstream-name . "QDNAseq"))) |
489 | (build-system r-build-system) | |
490 | (propagated-inputs | |
491 | `(("r-biobase" ,r-biobase) | |
81b0181b | 492 | ("r-biocparallel" ,r-biocparallel) |
0ef8cc9c RJ |
493 | ("r-cghbase" ,r-cghbase) |
494 | ("r-cghcall" ,r-cghcall) | |
495 | ("r-dnacopy" ,r-dnacopy) | |
496 | ("r-genomicranges" ,r-genomicranges) | |
497 | ("r-iranges" ,r-iranges) | |
498 | ("r-matrixstats" ,r-matrixstats) | |
499 | ("r-r-utils" ,r-r-utils) | |
500 | ("r-rsamtools" ,r-rsamtools))) | |
501 | (home-page "http://bioconductor.org/packages/QDNAseq") | |
502 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") | |
503 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
504 | number of sequence reads in each counted, adjusted with a simultaneous | |
505 | two-dimensional loess correction for sequence mappability and GC content, and | |
506 | filtered to remove spurious regions in the genome. Downstream steps of | |
507 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
508 | respectively.") | |
509 | (license license:gpl2+))) | |
bb15b581 RW |
510 | |
511 | (define-public r-bayseq | |
512 | (package | |
513 | (name "r-bayseq") | |
514 | (version "2.14.0") | |
515 | (source | |
516 | (origin | |
517 | (method url-fetch) | |
518 | (uri (bioconductor-uri "baySeq" version)) | |
519 | (sha256 | |
520 | (base32 | |
521 | "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg")))) | |
522 | (properties `((upstream-name . "baySeq"))) | |
523 | (build-system r-build-system) | |
524 | (propagated-inputs | |
525 | `(("r-abind" ,r-abind) | |
526 | ("r-edger" ,r-edger) | |
527 | ("r-genomicranges" ,r-genomicranges))) | |
528 | (home-page "https://bioconductor.org/packages/baySeq/") | |
529 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
530 | (description | |
531 | "This package identifies differential expression in high-throughput count | |
532 | data, such as that derived from next-generation sequencing machines, | |
533 | calculating estimated posterior likelihoods of differential expression (or | |
534 | more complex hypotheses) via empirical Bayesian methods.") | |
535 | (license license:gpl3))) | |
609f4ad1 RW |
536 | |
537 | (define-public r-chipcomp | |
538 | (package | |
539 | (name "r-chipcomp") | |
540 | (version "1.10.0") | |
541 | (source | |
542 | (origin | |
543 | (method url-fetch) | |
544 | (uri (bioconductor-uri "ChIPComp" version)) | |
545 | (sha256 | |
546 | (base32 | |
547 | "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs")))) | |
548 | (properties `((upstream-name . "ChIPComp"))) | |
549 | (build-system r-build-system) | |
550 | (propagated-inputs | |
551 | `(("r-biocgenerics" ,r-biocgenerics) | |
552 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
553 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
554 | ("r-genomeinfodb" ,r-genomeinfodb) | |
555 | ("r-genomicranges" ,r-genomicranges) | |
556 | ("r-iranges" ,r-iranges) | |
557 | ("r-limma" ,r-limma) | |
558 | ("r-rsamtools" ,r-rsamtools) | |
559 | ("r-rtracklayer" ,r-rtracklayer) | |
560 | ("r-s4vectors" ,r-s4vectors))) | |
561 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
562 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
563 | (description | |
564 | "ChIPComp implements a statistical method for quantitative comparison of | |
565 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
566 | sites across multiple conditions considering matching control in ChIP-seq | |
567 | datasets.") | |
568 | ;; Any version of the GPL. | |
569 | (license license:gpl3+))) | |
0490f9de RW |
570 | |
571 | (define-public r-riboprofiling | |
572 | (package | |
573 | (name "r-riboprofiling") | |
574 | (version "1.10.0") | |
575 | (source | |
576 | (origin | |
577 | (method url-fetch) | |
578 | (uri (bioconductor-uri "RiboProfiling" version)) | |
579 | (sha256 | |
580 | (base32 | |
581 | "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0")))) | |
582 | (properties `((upstream-name . "RiboProfiling"))) | |
583 | (build-system r-build-system) | |
584 | (propagated-inputs | |
585 | `(("r-biocgenerics" ,r-biocgenerics) | |
586 | ("r-biostrings" ,r-biostrings) | |
587 | ("r-data-table" ,r-data-table) | |
588 | ("r-genomeinfodb" ,r-genomeinfodb) | |
589 | ("r-genomicalignments" ,r-genomicalignments) | |
590 | ("r-genomicfeatures" ,r-genomicfeatures) | |
591 | ("r-genomicranges" ,r-genomicranges) | |
592 | ("r-ggbio" ,r-ggbio) | |
593 | ("r-ggplot2" ,r-ggplot2) | |
594 | ("r-iranges" ,r-iranges) | |
595 | ("r-plyr" ,r-plyr) | |
596 | ("r-reshape2" ,r-reshape2) | |
597 | ("r-rsamtools" ,r-rsamtools) | |
598 | ("r-rtracklayer" ,r-rtracklayer) | |
599 | ("r-s4vectors" ,r-s4vectors) | |
600 | ("r-sqldf" ,r-sqldf))) | |
601 | (home-page "https://bioconductor.org/packages/RiboProfiling/") | |
602 | (synopsis "Ribosome profiling data analysis") | |
603 | (description "Starting with a BAM file, this package provides the | |
604 | necessary functions for quality assessment, read start position recalibration, | |
605 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
606 | of count data: pairs, log fold-change, codon frequency and coverage | |
607 | assessment, principal component analysis on codon coverage.") | |
608 | (license license:gpl3))) | |
6ffdfe6a RW |
609 | |
610 | (define-public r-riboseqr | |
611 | (package | |
612 | (name "r-riboseqr") | |
613 | (version "1.14.0") | |
614 | (source | |
615 | (origin | |
616 | (method url-fetch) | |
617 | (uri (bioconductor-uri "riboSeqR" version)) | |
618 | (sha256 | |
619 | (base32 | |
620 | "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn")))) | |
621 | (properties `((upstream-name . "riboSeqR"))) | |
622 | (build-system r-build-system) | |
623 | (propagated-inputs | |
624 | `(("r-abind" ,r-abind) | |
625 | ("r-bayseq" ,r-bayseq) | |
626 | ("r-genomeinfodb" ,r-genomeinfodb) | |
627 | ("r-genomicranges" ,r-genomicranges) | |
628 | ("r-iranges" ,r-iranges) | |
629 | ("r-rsamtools" ,r-rsamtools) | |
630 | ("r-seqlogo" ,r-seqlogo))) | |
631 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
632 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
633 | (description | |
634 | "This package provides plotting functions, frameshift detection and | |
635 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
636 | (license license:gpl3))) | |
a32279ff RW |
637 | |
638 | (define-public r-interactionset | |
639 | (package | |
640 | (name "r-interactionset") | |
641 | (version "1.8.0") | |
642 | (source | |
643 | (origin | |
644 | (method url-fetch) | |
645 | (uri (bioconductor-uri "InteractionSet" version)) | |
646 | (sha256 | |
647 | (base32 | |
648 | "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n")))) | |
649 | (properties | |
650 | `((upstream-name . "InteractionSet"))) | |
651 | (build-system r-build-system) | |
652 | (propagated-inputs | |
653 | `(("r-biocgenerics" ,r-biocgenerics) | |
654 | ("r-genomeinfodb" ,r-genomeinfodb) | |
655 | ("r-genomicranges" ,r-genomicranges) | |
656 | ("r-iranges" ,r-iranges) | |
657 | ("r-matrix" ,r-matrix) | |
658 | ("r-rcpp" ,r-rcpp) | |
659 | ("r-s4vectors" ,r-s4vectors) | |
660 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
661 | (home-page "https://bioconductor.org/packages/InteractionSet") | |
662 | (synopsis "Base classes for storing genomic interaction data") | |
663 | (description | |
664 | "This packages provides the @code{GInteractions}, | |
665 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods | |
666 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
667 | experiments.") | |
668 | (license license:gpl3))) | |
cf9a29b2 RW |
669 | |
670 | (define-public r-genomicinteractions | |
671 | (package | |
672 | (name "r-genomicinteractions") | |
673 | (version "1.14.0") | |
674 | (source | |
675 | (origin | |
676 | (method url-fetch) | |
677 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
678 | (sha256 | |
679 | (base32 | |
680 | "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q")))) | |
681 | (properties | |
682 | `((upstream-name . "GenomicInteractions"))) | |
683 | (build-system r-build-system) | |
684 | (propagated-inputs | |
685 | `(("r-biobase" ,r-biobase) | |
686 | ("r-biocgenerics" ,r-biocgenerics) | |
687 | ("r-data-table" ,r-data-table) | |
688 | ("r-dplyr" ,r-dplyr) | |
689 | ("r-genomeinfodb" ,r-genomeinfodb) | |
690 | ("r-genomicranges" ,r-genomicranges) | |
691 | ("r-ggplot2" ,r-ggplot2) | |
692 | ("r-gridextra" ,r-gridextra) | |
693 | ("r-gviz" ,r-gviz) | |
694 | ("r-igraph" ,r-igraph) | |
695 | ("r-interactionset" ,r-interactionset) | |
696 | ("r-iranges" ,r-iranges) | |
697 | ("r-rsamtools" ,r-rsamtools) | |
698 | ("r-rtracklayer" ,r-rtracklayer) | |
699 | ("r-s4vectors" ,r-s4vectors) | |
700 | ("r-stringr" ,r-stringr))) | |
701 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") | |
702 | (synopsis "R package for handling genomic interaction data") | |
703 | (description | |
704 | "This R package provides tools for handling genomic interaction data, | |
705 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
706 | information and producing various plots and statistics.") | |
707 | (license license:gpl3))) | |
27c51606 RW |
708 | |
709 | (define-public r-ctc | |
710 | (package | |
711 | (name "r-ctc") | |
712 | (version "1.54.0") | |
713 | (source | |
714 | (origin | |
715 | (method url-fetch) | |
716 | (uri (bioconductor-uri "ctc" version)) | |
717 | (sha256 | |
718 | (base32 | |
719 | "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9")))) | |
720 | (build-system r-build-system) | |
721 | (propagated-inputs `(("r-amap" ,r-amap))) | |
722 | (home-page "https://bioconductor.org/packages/ctc/") | |
723 | (synopsis "Cluster and tree conversion") | |
724 | (description | |
725 | "This package provides tools for exporting and importing classification | |
726 | trees and clusters to other programs.") | |
727 | (license license:gpl2))) | |
5da0e142 RW |
728 | |
729 | (define-public r-goseq | |
730 | (package | |
731 | (name "r-goseq") | |
732 | (version "1.32.0") | |
733 | (source | |
734 | (origin | |
735 | (method url-fetch) | |
736 | (uri (bioconductor-uri "goseq" version)) | |
737 | (sha256 | |
738 | (base32 | |
739 | "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l")))) | |
740 | (build-system r-build-system) | |
741 | (propagated-inputs | |
742 | `(("r-annotationdbi" ,r-annotationdbi) | |
743 | ("r-biasedurn" ,r-biasedurn) | |
744 | ("r-biocgenerics" ,r-biocgenerics) | |
745 | ("r-genelendatabase" ,r-genelendatabase) | |
746 | ("r-go-db" ,r-go-db) | |
747 | ("r-mgcv" ,r-mgcv))) | |
748 | (home-page "https://bioconductor.org/packages/goseq/") | |
749 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
750 | (description | |
751 | "This package provides tools to detect Gene Ontology and/or other user | |
752 | defined categories which are over/under represented in RNA-seq data.") | |
753 | (license license:lgpl2.0+))) | |
f4235c0e RW |
754 | |
755 | (define-public r-glimma | |
756 | (package | |
757 | (name "r-glimma") | |
758 | (version "1.8.2") | |
759 | (source | |
760 | (origin | |
761 | (method url-fetch) | |
762 | (uri (bioconductor-uri "Glimma" version)) | |
763 | (sha256 | |
764 | (base32 | |
765 | "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s")))) | |
766 | (properties `((upstream-name . "Glimma"))) | |
767 | (build-system r-build-system) | |
768 | (propagated-inputs | |
769 | `(("r-edger" ,r-edger) | |
770 | ("r-jsonlite" ,r-jsonlite) | |
771 | ("r-s4vectors" ,r-s4vectors))) | |
772 | (home-page "https://github.com/Shians/Glimma") | |
773 | (synopsis "Interactive HTML graphics") | |
774 | (description | |
775 | "This package generates interactive visualisations for analysis of | |
776 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
777 | HTML page. The interactions are built on top of the popular static | |
778 | representations of analysis results in order to provide additional | |
779 | information.") | |
780 | (license license:lgpl3))) | |
aa388dc7 RW |
781 | |
782 | (define-public r-rots | |
783 | (package | |
784 | (name "r-rots") | |
785 | (version "1.8.0") | |
786 | (source | |
787 | (origin | |
788 | (method url-fetch) | |
789 | (uri (bioconductor-uri "ROTS" version)) | |
790 | (sha256 | |
791 | (base32 | |
792 | "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3")))) | |
793 | (properties `((upstream-name . "ROTS"))) | |
794 | (build-system r-build-system) | |
795 | (propagated-inputs | |
796 | `(("r-biobase" ,r-biobase) | |
797 | ("r-rcpp" ,r-rcpp))) | |
798 | (home-page "https://bioconductor.org/packages/ROTS/") | |
799 | (synopsis "Reproducibility-Optimized Test Statistic") | |
800 | (description | |
801 | "This package provides tools for calculating the | |
802 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
803 | in omics data.") | |
804 | (license license:gpl2+))) |