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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) |
a5b56a53 RJ |
27 | #:use-module (gnu packages cran) |
28 | #:use-module (gnu packages compression) | |
183ce988 RJ |
29 | #:use-module (gnu packages statistics) |
30 | #:use-module (gnu packages bioinformatics)) | |
fa596599 | 31 | |
183db725 RW |
32 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
33 | (package | |
34 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
35 | (version "1.4.1") | |
36 | (source (origin | |
37 | (method url-fetch) | |
38 | ;; We cannot use bioconductor-uri here because this tarball is | |
39 | ;; located under "data/annotation/" instead of "bioc/". | |
40 | (uri (string-append "https://www.bioconductor.org/packages/" | |
41 | "release/data/annotation/src/contrib/" | |
42 | "BSgenome.Dmelanogaster.UCSC.dm6_" | |
43 | version ".tar.gz")) | |
44 | (sha256 | |
45 | (base32 | |
46 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
47 | (properties | |
48 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
49 | (build-system r-build-system) | |
50 | ;; As this package provides little more than a very large data file it | |
51 | ;; doesn't make sense to build substitutes. | |
52 | (arguments `(#:substitutable? #f)) | |
53 | (propagated-inputs | |
54 | `(("r-bsgenome" ,r-bsgenome))) | |
55 | (home-page | |
56 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
57 | (synopsis "Full genome sequences for Fly") | |
58 | (description | |
59 | "This package provides full genome sequences for Drosophila | |
60 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
61 | objects.") | |
62 | (license license:artistic2.0))) | |
63 | ||
fa596599 RW |
64 | (define-public r-hpar |
65 | (package | |
66 | (name "r-hpar") | |
2f5b3d8e | 67 | (version "1.22.2") |
fa596599 RW |
68 | (source |
69 | (origin | |
70 | (method url-fetch) | |
71 | (uri (bioconductor-uri "hpar" version)) | |
72 | (sha256 | |
73 | (base32 | |
2f5b3d8e | 74 | "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388")))) |
fa596599 RW |
75 | (build-system r-build-system) |
76 | (home-page "https://bioconductor.org/packages/hpar/") | |
77 | (synopsis "Human Protein Atlas in R") | |
78 | (description "This package provides a simple interface to and data from | |
79 | the Human Protein Atlas project.") | |
80 | (license license:artistic2.0))) | |
183ce988 RJ |
81 | |
82 | (define-public r-regioner | |
83 | (package | |
84 | (name "r-regioner") | |
72427c72 | 85 | (version "1.12.0") |
183ce988 RJ |
86 | (source |
87 | (origin | |
88 | (method url-fetch) | |
89 | (uri (bioconductor-uri "regioneR" version)) | |
90 | (sha256 | |
91 | (base32 | |
72427c72 | 92 | "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb")))) |
183ce988 RJ |
93 | (properties `((upstream-name . "regioneR"))) |
94 | (build-system r-build-system) | |
95 | (propagated-inputs | |
96 | `(("r-memoise" ,r-memoise) | |
97 | ("r-genomicranges" ,r-genomicranges) | |
98 | ("r-bsgenome" ,r-bsgenome) | |
99 | ("r-rtracklayer" ,r-rtracklayer) | |
100 | ("r-genomeinfodb" ,r-genomeinfodb) | |
72427c72 RW |
101 | ("r-iranges" ,r-iranges) |
102 | ("r-s4vectors" ,r-s4vectors))) | |
183ce988 RJ |
103 | (home-page "https://bioconductor.org/packages/regioneR/") |
104 | (synopsis "Association analysis of genomic regions") | |
105 | (description "This package offers a statistical framework based on | |
106 | customizable permutation tests to assess the association between genomic | |
107 | region sets and other genomic features.") | |
108 | (license license:artistic2.0))) | |
a5b56a53 RJ |
109 | |
110 | (define-public r-diffbind | |
111 | (package | |
112 | (name "r-diffbind") | |
45bbccf4 | 113 | (version "2.8.0") |
a5b56a53 RJ |
114 | (source |
115 | (origin | |
116 | (method url-fetch) | |
117 | (uri (bioconductor-uri "DiffBind" version)) | |
118 | (sha256 | |
119 | (base32 | |
45bbccf4 | 120 | "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish")))) |
a5b56a53 RJ |
121 | (properties `((upstream-name . "DiffBind"))) |
122 | (build-system r-build-system) | |
123 | (inputs | |
124 | `(("zlib" ,zlib))) | |
125 | (propagated-inputs | |
126 | `(("r-amap" ,r-amap) | |
127 | ("r-biocparallel" ,r-biocparallel) | |
128 | ("r-deseq2" ,r-deseq2) | |
129 | ("r-dplyr" ,r-dplyr) | |
130 | ("r-edger" ,r-edger) | |
131 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
132 | ("r-genomicranges" ,r-genomicranges) |
133 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
134 | ("r-ggrepel" ,r-ggrepel) |
135 | ("r-gplots" ,r-gplots) | |
136 | ("r-iranges" ,r-iranges) | |
137 | ("r-lattice" ,r-lattice) | |
138 | ("r-limma" ,r-limma) | |
139 | ("r-locfit" ,r-locfit) | |
140 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
141 | ("r-rcpp" ,r-rcpp) | |
142 | ("r-rsamtools" ,r-rsamtools) | |
143 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 144 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
a5b56a53 RJ |
145 | ("r-systempiper" ,r-systempiper) |
146 | ("r-zlibbioc" ,r-zlibbioc))) | |
147 | (home-page "http://bioconductor.org/packages/DiffBind") | |
148 | (synopsis "Differential binding analysis of ChIP-Seq peak data") | |
149 | (description | |
150 | "This package computes differentially bound sites from multiple | |
151 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
152 | occupancy (overlap) analysis and plotting functions.") | |
153 | (license license:artistic2.0))) | |
6d94bf6b RJ |
154 | |
155 | (define-public r-ripseeker | |
156 | (package | |
157 | (name "r-ripseeker") | |
43734b47 | 158 | (version "1.20.0") |
6d94bf6b RJ |
159 | (source |
160 | (origin | |
161 | (method url-fetch) | |
162 | (uri (bioconductor-uri "RIPSeeker" version)) | |
163 | (sha256 | |
164 | (base32 | |
43734b47 | 165 | "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi")))) |
6d94bf6b RJ |
166 | (properties `((upstream-name . "RIPSeeker"))) |
167 | (build-system r-build-system) | |
168 | (propagated-inputs | |
169 | `(("r-s4vectors" ,r-s4vectors) | |
170 | ("r-iranges" ,r-iranges) | |
171 | ("r-genomicranges" ,r-genomicranges) | |
172 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
173 | ("r-rsamtools" ,r-rsamtools) | |
174 | ("r-genomicalignments" ,r-genomicalignments) | |
175 | ("r-rtracklayer" ,r-rtracklayer))) | |
176 | (home-page "http://bioconductor.org/packages/RIPSeeker") | |
177 | (synopsis | |
178 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
179 | (description | |
180 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
181 | using two-state HMM with negative binomial emission probability. While | |
182 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
183 | a suite of bioinformatics tools integrated within this self-contained software | |
184 | package comprehensively addressing issues ranging from post-alignments | |
185 | processing to visualization and annotation.") | |
186 | (license license:gpl2))) | |
a6ae9ffd RJ |
187 | |
188 | (define-public r-multtest | |
189 | (package | |
190 | (name "r-multtest") | |
f39938b1 | 191 | (version "2.36.0") |
a6ae9ffd RJ |
192 | (source |
193 | (origin | |
194 | (method url-fetch) | |
195 | (uri (bioconductor-uri "multtest" version)) | |
196 | (sha256 | |
197 | (base32 | |
f39938b1 | 198 | "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0")))) |
a6ae9ffd RJ |
199 | (build-system r-build-system) |
200 | (propagated-inputs | |
201 | `(("r-survival" ,r-survival) | |
202 | ("r-biocgenerics" ,r-biocgenerics) | |
203 | ("r-biobase" ,r-biobase) | |
204 | ("r-mass" ,r-mass))) | |
205 | (home-page "http://bioconductor.org/packages/multtest") | |
206 | (synopsis "Resampling-based multiple hypothesis testing") | |
207 | (description | |
208 | "This package can do non-parametric bootstrap and permutation | |
209 | resampling-based multiple testing procedures (including empirical Bayes | |
210 | methods) for controlling the family-wise error rate (FWER), generalized | |
211 | family-wise error rate (gFWER), tail probability of the proportion of | |
212 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
213 | of bootstrap-based null distribution are implemented (centered, centered | |
214 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
215 | available. Tests based on a variety of T- and F-statistics (including | |
216 | T-statistics based on regression parameters from linear and survival models | |
217 | as well as those based on correlation parameters) are included. When probing | |
218 | hypotheses with T-statistics, users may also select a potentially faster null | |
219 | distribution which is multivariate normal with mean zero and variance | |
220 | covariance matrix derived from the vector influence function. Results are | |
221 | reported in terms of adjusted P-values, confidence regions and test statistic | |
222 | cutoffs. The procedures are directly applicable to identifying differentially | |
223 | expressed genes in DNA microarray experiments.") | |
224 | (license license:lgpl3))) | |
793f83ef RJ |
225 | |
226 | (define-public r-chippeakanno | |
227 | (package | |
228 | (name "r-chippeakanno") | |
f794e85d | 229 | (version "3.14.0") |
793f83ef RJ |
230 | (source |
231 | (origin | |
232 | (method url-fetch) | |
233 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
234 | (sha256 | |
235 | (base32 | |
f794e85d | 236 | "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0")))) |
793f83ef RJ |
237 | (properties `((upstream-name . "ChIPpeakAnno"))) |
238 | (build-system r-build-system) | |
239 | (propagated-inputs | |
240 | `(("r-biocgenerics" ,r-biocgenerics) | |
f794e85d RW |
241 | ("r-biostrings" ,r-biostrings) |
242 | ("r-delayedarray" ,r-delayedarray) | |
793f83ef RJ |
243 | ("r-go-db" ,r-go-db) |
244 | ("r-biomart" ,r-biomart) | |
245 | ("r-bsgenome" ,r-bsgenome) | |
246 | ("r-genomicfeatures" ,r-genomicfeatures) | |
f794e85d | 247 | ("r-genomicranges" ,r-genomicranges) |
793f83ef | 248 | ("r-genomeinfodb" ,r-genomeinfodb) |
f794e85d | 249 | ("r-iranges" ,r-iranges) |
793f83ef RJ |
250 | ("r-matrixstats" ,r-matrixstats) |
251 | ("r-annotationdbi" ,r-annotationdbi) | |
252 | ("r-limma" ,r-limma) | |
253 | ("r-multtest" ,r-multtest) | |
254 | ("r-rbgl" ,r-rbgl) | |
255 | ("r-graph" ,r-graph) | |
256 | ("r-biocinstaller" ,r-biocinstaller) | |
257 | ("r-regioner" ,r-regioner) | |
258 | ("r-dbi" ,r-dbi) | |
259 | ("r-ensembldb" ,r-ensembldb) | |
260 | ("r-biobase" ,r-biobase) | |
f794e85d | 261 | ("r-s4vectors" ,r-s4vectors) |
793f83ef RJ |
262 | ("r-seqinr" ,r-seqinr) |
263 | ("r-idr" ,r-idr) | |
264 | ("r-genomicalignments" ,r-genomicalignments) | |
265 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
266 | ("r-rsamtools" ,r-rsamtools) | |
267 | ("r-venndiagram" ,r-venndiagram))) | |
268 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") | |
269 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") | |
270 | (description | |
271 | "The package includes functions to retrieve the sequences around the peak, | |
272 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
273 | custom features such as most conserved elements and other transcription factor | |
274 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
275 | for finding the peaks with bi-directional promoters with summary statistics | |
276 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
277 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
278 | enrichedGO (addGeneIDs).") | |
279 | (license license:gpl2+))) | |
164502d8 RJ |
280 | |
281 | (define-public r-marray | |
282 | (package | |
283 | (name "r-marray") | |
67487088 | 284 | (version "1.58.0") |
164502d8 RJ |
285 | (source (origin |
286 | (method url-fetch) | |
287 | (uri (bioconductor-uri "marray" version)) | |
288 | (sha256 | |
67487088 | 289 | (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d")))) |
164502d8 RJ |
290 | (build-system r-build-system) |
291 | (propagated-inputs | |
67487088 | 292 | `(("r-limma" ,r-limma))) |
164502d8 RJ |
293 | (home-page "http://bioconductor.org/packages/marray") |
294 | (synopsis "Exploratory analysis for two-color spotted microarray data") | |
295 | (description "This package contains class definitions for two-color spotted | |
296 | microarray data. It also includes fuctions for data input, diagnostic plots, | |
297 | normalization and quality checking.") | |
298 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
299 | |
300 | (define-public r-cghbase | |
301 | (package | |
302 | (name "r-cghbase") | |
205df4a4 | 303 | (version "1.40.0") |
0416a0d4 RJ |
304 | (source (origin |
305 | (method url-fetch) | |
306 | (uri (bioconductor-uri "CGHbase" version)) | |
307 | (sha256 | |
205df4a4 | 308 | (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq")))) |
0416a0d4 RJ |
309 | (properties `((upstream-name . "CGHbase"))) |
310 | (build-system r-build-system) | |
311 | (propagated-inputs | |
312 | `(("r-biobase" ,r-biobase) | |
313 | ("r-marray" ,r-marray))) | |
314 | (home-page "http://bioconductor.org/packages/CGHbase") | |
315 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
316 | (description "This package contains functions and classes that are needed by | |
317 | the @code{arrayCGH} packages.") | |
318 | (license license:gpl2+))) | |
67ee83d6 RJ |
319 | |
320 | (define-public r-cghcall | |
321 | (package | |
322 | (name "r-cghcall") | |
5c0df206 | 323 | (version "2.42.0") |
67ee83d6 RJ |
324 | (source (origin |
325 | (method url-fetch) | |
326 | (uri (bioconductor-uri "CGHcall" version)) | |
327 | (sha256 | |
5c0df206 | 328 | (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz")))) |
67ee83d6 RJ |
329 | (properties `((upstream-name . "CGHcall"))) |
330 | (build-system r-build-system) | |
331 | (propagated-inputs | |
332 | `(("r-biobase" ,r-biobase) | |
333 | ("r-cghbase" ,r-cghbase) | |
334 | ("r-impute" ,r-impute) | |
335 | ("r-dnacopy" ,r-dnacopy) | |
336 | ("r-snowfall" ,r-snowfall))) | |
337 | (home-page "http://bioconductor.org/packages/CGHcall") | |
338 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
339 | (description "This package contains functions and classes that are needed by | |
340 | @code{arrayCGH} packages.") | |
341 | (license license:gpl2+))) | |
0ef8cc9c RJ |
342 | |
343 | (define-public r-qdnaseq | |
344 | (package | |
345 | (name "r-qdnaseq") | |
81b0181b | 346 | (version "1.16.0") |
0ef8cc9c RJ |
347 | (source (origin |
348 | (method url-fetch) | |
349 | (uri (bioconductor-uri "QDNAseq" version)) | |
350 | (sha256 | |
81b0181b | 351 | (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd")))) |
0ef8cc9c RJ |
352 | (properties `((upstream-name . "QDNAseq"))) |
353 | (build-system r-build-system) | |
354 | (propagated-inputs | |
355 | `(("r-biobase" ,r-biobase) | |
81b0181b | 356 | ("r-biocparallel" ,r-biocparallel) |
0ef8cc9c RJ |
357 | ("r-cghbase" ,r-cghbase) |
358 | ("r-cghcall" ,r-cghcall) | |
359 | ("r-dnacopy" ,r-dnacopy) | |
360 | ("r-genomicranges" ,r-genomicranges) | |
361 | ("r-iranges" ,r-iranges) | |
362 | ("r-matrixstats" ,r-matrixstats) | |
363 | ("r-r-utils" ,r-r-utils) | |
364 | ("r-rsamtools" ,r-rsamtools))) | |
365 | (home-page "http://bioconductor.org/packages/QDNAseq") | |
366 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") | |
367 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
368 | number of sequence reads in each counted, adjusted with a simultaneous | |
369 | two-dimensional loess correction for sequence mappability and GC content, and | |
370 | filtered to remove spurious regions in the genome. Downstream steps of | |
371 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
372 | respectively.") | |
373 | (license license:gpl2+))) |