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> |
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) |
b64ce4b7 | 31 | #:use-module (gnu packages maths) |
f4235c0e RW |
32 | #:use-module (gnu packages statistics) |
33 | #:use-module (gnu packages web)) | |
fa596599 | 34 | |
183db725 RW |
35 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
36 | (package | |
37 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") | |
38 | (version "1.4.1") | |
39 | (source (origin | |
40 | (method url-fetch) | |
41 | ;; We cannot use bioconductor-uri here because this tarball is | |
42 | ;; located under "data/annotation/" instead of "bioc/". | |
43 | (uri (string-append "https://www.bioconductor.org/packages/" | |
44 | "release/data/annotation/src/contrib/" | |
45 | "BSgenome.Dmelanogaster.UCSC.dm6_" | |
46 | version ".tar.gz")) | |
47 | (sha256 | |
48 | (base32 | |
49 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) | |
50 | (properties | |
51 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) | |
52 | (build-system r-build-system) | |
53 | ;; As this package provides little more than a very large data file it | |
54 | ;; doesn't make sense to build substitutes. | |
55 | (arguments `(#:substitutable? #f)) | |
56 | (propagated-inputs | |
57 | `(("r-bsgenome" ,r-bsgenome))) | |
58 | (home-page | |
59 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") | |
60 | (synopsis "Full genome sequences for Fly") | |
61 | (description | |
62 | "This package provides full genome sequences for Drosophila | |
63 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings | |
64 | objects.") | |
65 | (license license:artistic2.0))) | |
66 | ||
dfac7eb9 RW |
67 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
68 | (package | |
69 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") | |
70 | (version "1.3.99") | |
71 | (source (origin | |
72 | (method url-fetch) | |
73 | ;; We cannot use bioconductor-uri here because this tarball is | |
74 | ;; located under "data/annotation/" instead of "bioc/". | |
75 | (uri (string-append "http://www.bioconductor.org/packages/" | |
76 | "release/data/annotation/src/contrib/" | |
77 | "BSgenome.Dmelanogaster.UCSC.dm3.masked_" | |
78 | version ".tar.gz")) | |
79 | (sha256 | |
80 | (base32 | |
81 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) | |
82 | (properties | |
83 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) | |
84 | (build-system r-build-system) | |
85 | (propagated-inputs | |
86 | `(("r-bsgenome" ,r-bsgenome) | |
87 | ("r-bsgenome-dmelanogaster-ucsc-dm3" | |
88 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) | |
89 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") | |
90 | (synopsis "Full masked genome sequences for Fly") | |
91 | (description | |
92 | "This package provides full masked genome sequences for Drosophila | |
93 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
94 | Biostrings objects. The sequences are the same as in | |
95 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following | |
96 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of | |
97 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from | |
98 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats | |
99 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") | |
100 | (license license:artistic2.0))) | |
101 | ||
6fbd759b RW |
102 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
103 | (package | |
104 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") | |
105 | (version "1.3.99") | |
106 | (source (origin | |
107 | (method url-fetch) | |
108 | ;; We cannot use bioconductor-uri here because this tarball is | |
109 | ;; located under "data/annotation/" instead of "bioc/". | |
110 | (uri (string-append "http://www.bioconductor.org/packages/" | |
111 | "release/data/annotation/src/contrib/" | |
112 | "BSgenome.Hsapiens.UCSC.hg19.masked_" | |
113 | version ".tar.gz")) | |
114 | (sha256 | |
115 | (base32 | |
116 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) | |
117 | (properties | |
118 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) | |
119 | (build-system r-build-system) | |
120 | (propagated-inputs | |
121 | `(("r-bsgenome" ,r-bsgenome) | |
122 | ("r-bsgenome-hsapiens-ucsc-hg19" | |
123 | ,r-bsgenome-hsapiens-ucsc-hg19))) | |
124 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") | |
125 | (synopsis "Full masked genome sequences for Homo sapiens") | |
126 | (description | |
127 | "This package provides full genome sequences for Homo sapiens (Human) as | |
128 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The | |
129 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of | |
130 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
131 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
132 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
133 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
134 | default.") | |
135 | (license license:artistic2.0))) | |
136 | ||
2bece692 RW |
137 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
138 | (package | |
139 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") | |
140 | (version "1.3.99") | |
141 | (source (origin | |
142 | (method url-fetch) | |
143 | ;; We cannot use bioconductor-uri here because this tarball is | |
144 | ;; located under "data/annotation/" instead of "bioc/". | |
145 | (uri (string-append "http://www.bioconductor.org/packages/" | |
146 | "release/data/annotation/src/contrib/" | |
147 | "BSgenome.Mmusculus.UCSC.mm9.masked_" | |
148 | version ".tar.gz")) | |
149 | (sha256 | |
150 | (base32 | |
151 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) | |
152 | (properties | |
153 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) | |
154 | (build-system r-build-system) | |
155 | (propagated-inputs | |
156 | `(("r-bsgenome" ,r-bsgenome) | |
157 | ("r-bsgenome-mmusculus-ucsc-mm9" | |
158 | ,r-bsgenome-mmusculus-ucsc-mm9))) | |
159 | (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") | |
160 | (synopsis "Full masked genome sequences for Mouse") | |
161 | (description | |
162 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
163 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The | |
164 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of | |
165 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS | |
166 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of | |
167 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem | |
168 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by | |
169 | default." ) | |
170 | (license license:artistic2.0))) | |
171 | ||
2cc51108 RW |
172 | (define-public r-genelendatabase |
173 | (package | |
174 | (name "r-genelendatabase") | |
175 | (version "1.16.0") | |
176 | (source | |
177 | (origin | |
178 | (method url-fetch) | |
179 | ;; We cannot use bioconductor-uri here because this tarball is | |
180 | ;; located under "data/experiment/" instead of "bioc/". | |
181 | (uri (string-append "https://bioconductor.org/packages/" | |
182 | "release/data/experiment/src/contrib" | |
183 | "/geneLenDataBase_" version ".tar.gz")) | |
184 | (sha256 | |
185 | (base32 | |
186 | "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5")))) | |
187 | (properties | |
188 | `((upstream-name . "geneLenDataBase"))) | |
189 | (build-system r-build-system) | |
190 | (propagated-inputs | |
191 | `(("r-rtracklayer" ,r-rtracklayer) | |
192 | ("r-genomicfeatures" ,r-genomicfeatures))) | |
193 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") | |
194 | (synopsis "Lengths of mRNA transcripts for a number of genomes") | |
195 | (description | |
196 | "This package provides the lengths of mRNA transcripts for a number of | |
197 | genomes and gene ID formats, largely based on the UCSC table browser.") | |
198 | (license license:lgpl2.0+))) | |
199 | ||
200 | \f | |
fa596599 RW |
201 | (define-public r-hpar |
202 | (package | |
203 | (name "r-hpar") | |
61686921 | 204 | (version "1.24.0") |
fa596599 RW |
205 | (source |
206 | (origin | |
207 | (method url-fetch) | |
208 | (uri (bioconductor-uri "hpar" version)) | |
209 | (sha256 | |
210 | (base32 | |
61686921 | 211 | "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn")))) |
fa596599 RW |
212 | (build-system r-build-system) |
213 | (home-page "https://bioconductor.org/packages/hpar/") | |
214 | (synopsis "Human Protein Atlas in R") | |
215 | (description "This package provides a simple interface to and data from | |
216 | the Human Protein Atlas project.") | |
217 | (license license:artistic2.0))) | |
183ce988 RJ |
218 | |
219 | (define-public r-regioner | |
220 | (package | |
221 | (name "r-regioner") | |
d639d888 | 222 | (version "1.14.0") |
183ce988 RJ |
223 | (source |
224 | (origin | |
225 | (method url-fetch) | |
226 | (uri (bioconductor-uri "regioneR" version)) | |
227 | (sha256 | |
228 | (base32 | |
d639d888 | 229 | "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd")))) |
183ce988 RJ |
230 | (properties `((upstream-name . "regioneR"))) |
231 | (build-system r-build-system) | |
232 | (propagated-inputs | |
d639d888 | 233 | `(("r-biostrings" ,r-biostrings) |
183ce988 | 234 | ("r-bsgenome" ,r-bsgenome) |
183ce988 | 235 | ("r-genomeinfodb" ,r-genomeinfodb) |
d639d888 | 236 | ("r-genomicranges" ,r-genomicranges) |
72427c72 | 237 | ("r-iranges" ,r-iranges) |
d639d888 RW |
238 | ("r-memoise" ,r-memoise) |
239 | ("r-rtracklayer" ,r-rtracklayer) | |
72427c72 | 240 | ("r-s4vectors" ,r-s4vectors))) |
183ce988 RJ |
241 | (home-page "https://bioconductor.org/packages/regioneR/") |
242 | (synopsis "Association analysis of genomic regions") | |
243 | (description "This package offers a statistical framework based on | |
244 | customizable permutation tests to assess the association between genomic | |
245 | region sets and other genomic features.") | |
246 | (license license:artistic2.0))) | |
a5b56a53 RJ |
247 | |
248 | (define-public r-diffbind | |
249 | (package | |
250 | (name "r-diffbind") | |
98652568 | 251 | (version "2.10.0") |
a5b56a53 RJ |
252 | (source |
253 | (origin | |
254 | (method url-fetch) | |
255 | (uri (bioconductor-uri "DiffBind" version)) | |
256 | (sha256 | |
257 | (base32 | |
98652568 | 258 | "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5")))) |
a5b56a53 RJ |
259 | (properties `((upstream-name . "DiffBind"))) |
260 | (build-system r-build-system) | |
261 | (inputs | |
262 | `(("zlib" ,zlib))) | |
263 | (propagated-inputs | |
264 | `(("r-amap" ,r-amap) | |
265 | ("r-biocparallel" ,r-biocparallel) | |
266 | ("r-deseq2" ,r-deseq2) | |
267 | ("r-dplyr" ,r-dplyr) | |
268 | ("r-edger" ,r-edger) | |
269 | ("r-genomicalignments" ,r-genomicalignments) | |
45bbccf4 RW |
270 | ("r-genomicranges" ,r-genomicranges) |
271 | ("r-ggplot2" ,r-ggplot2) | |
a5b56a53 RJ |
272 | ("r-ggrepel" ,r-ggrepel) |
273 | ("r-gplots" ,r-gplots) | |
274 | ("r-iranges" ,r-iranges) | |
275 | ("r-lattice" ,r-lattice) | |
276 | ("r-limma" ,r-limma) | |
277 | ("r-locfit" ,r-locfit) | |
278 | ("r-rcolorbrewer" , r-rcolorbrewer) | |
279 | ("r-rcpp" ,r-rcpp) | |
280 | ("r-rsamtools" ,r-rsamtools) | |
281 | ("r-s4vectors" ,r-s4vectors) | |
45bbccf4 | 282 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
a5b56a53 RJ |
283 | ("r-systempiper" ,r-systempiper) |
284 | ("r-zlibbioc" ,r-zlibbioc))) | |
285 | (home-page "http://bioconductor.org/packages/DiffBind") | |
286 | (synopsis "Differential binding analysis of ChIP-Seq peak data") | |
287 | (description | |
288 | "This package computes differentially bound sites from multiple | |
289 | ChIP-seq experiments using affinity (quantitative) data. Also enables | |
290 | occupancy (overlap) analysis and plotting functions.") | |
291 | (license license:artistic2.0))) | |
6d94bf6b RJ |
292 | |
293 | (define-public r-ripseeker | |
294 | (package | |
295 | (name "r-ripseeker") | |
e9427b2c | 296 | (version "1.22.0") |
6d94bf6b RJ |
297 | (source |
298 | (origin | |
299 | (method url-fetch) | |
300 | (uri (bioconductor-uri "RIPSeeker" version)) | |
301 | (sha256 | |
302 | (base32 | |
e9427b2c | 303 | "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i")))) |
6d94bf6b RJ |
304 | (properties `((upstream-name . "RIPSeeker"))) |
305 | (build-system r-build-system) | |
306 | (propagated-inputs | |
307 | `(("r-s4vectors" ,r-s4vectors) | |
308 | ("r-iranges" ,r-iranges) | |
309 | ("r-genomicranges" ,r-genomicranges) | |
310 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
311 | ("r-rsamtools" ,r-rsamtools) | |
312 | ("r-genomicalignments" ,r-genomicalignments) | |
313 | ("r-rtracklayer" ,r-rtracklayer))) | |
314 | (home-page "http://bioconductor.org/packages/RIPSeeker") | |
315 | (synopsis | |
316 | "Identifying protein-associated transcripts from RIP-seq experiments") | |
317 | (description | |
318 | "This package infers and discriminates RIP peaks from RIP-seq alignments | |
319 | using two-state HMM with negative binomial emission probability. While | |
320 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides | |
321 | a suite of bioinformatics tools integrated within this self-contained software | |
322 | package comprehensively addressing issues ranging from post-alignments | |
323 | processing to visualization and annotation.") | |
324 | (license license:gpl2))) | |
a6ae9ffd RJ |
325 | |
326 | (define-public r-multtest | |
327 | (package | |
328 | (name "r-multtest") | |
95ee4a46 | 329 | (version "2.38.0") |
a6ae9ffd RJ |
330 | (source |
331 | (origin | |
332 | (method url-fetch) | |
333 | (uri (bioconductor-uri "multtest" version)) | |
334 | (sha256 | |
335 | (base32 | |
95ee4a46 | 336 | "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k")))) |
a6ae9ffd RJ |
337 | (build-system r-build-system) |
338 | (propagated-inputs | |
339 | `(("r-survival" ,r-survival) | |
340 | ("r-biocgenerics" ,r-biocgenerics) | |
341 | ("r-biobase" ,r-biobase) | |
342 | ("r-mass" ,r-mass))) | |
343 | (home-page "http://bioconductor.org/packages/multtest") | |
344 | (synopsis "Resampling-based multiple hypothesis testing") | |
345 | (description | |
346 | "This package can do non-parametric bootstrap and permutation | |
347 | resampling-based multiple testing procedures (including empirical Bayes | |
348 | methods) for controlling the family-wise error rate (FWER), generalized | |
349 | family-wise error rate (gFWER), tail probability of the proportion of | |
350 | false positives (TPPFP), and false discovery rate (FDR). Several choices | |
351 | of bootstrap-based null distribution are implemented (centered, centered | |
352 | and scaled, quantile-transformed). Single-step and step-wise methods are | |
353 | available. Tests based on a variety of T- and F-statistics (including | |
354 | T-statistics based on regression parameters from linear and survival models | |
355 | as well as those based on correlation parameters) are included. When probing | |
356 | hypotheses with T-statistics, users may also select a potentially faster null | |
357 | distribution which is multivariate normal with mean zero and variance | |
358 | covariance matrix derived from the vector influence function. Results are | |
359 | reported in terms of adjusted P-values, confidence regions and test statistic | |
360 | cutoffs. The procedures are directly applicable to identifying differentially | |
361 | expressed genes in DNA microarray experiments.") | |
362 | (license license:lgpl3))) | |
793f83ef | 363 | |
5dfe4912 RW |
364 | (define-public r-graph |
365 | (package | |
366 | (name "r-graph") | |
14520b64 | 367 | (version "1.60.0") |
5dfe4912 RW |
368 | (source (origin |
369 | (method url-fetch) | |
370 | (uri (bioconductor-uri "graph" version)) | |
371 | (sha256 | |
372 | (base32 | |
14520b64 | 373 | "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i")))) |
5dfe4912 RW |
374 | (build-system r-build-system) |
375 | (propagated-inputs | |
376 | `(("r-biocgenerics" ,r-biocgenerics))) | |
377 | (home-page "https://bioconductor.org/packages/graph") | |
378 | (synopsis "Handle graph data structures in R") | |
379 | (description | |
380 | "This package implements some simple graph handling capabilities for R.") | |
381 | (license license:artistic2.0))) | |
382 | ||
a207bca2 RW |
383 | (define-public r-codedepends |
384 | (package | |
385 | (name "r-codedepends") | |
386 | (version "0.6.5") | |
387 | (source | |
388 | (origin | |
389 | (method url-fetch) | |
390 | (uri (cran-uri "CodeDepends" version)) | |
391 | (sha256 | |
392 | (base32 | |
393 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) | |
394 | (properties `((upstream-name . "CodeDepends"))) | |
395 | (build-system r-build-system) | |
396 | (propagated-inputs | |
397 | `(("r-codetools" ,r-codetools) | |
398 | ("r-graph" ,r-graph) | |
399 | ("r-xml" ,r-xml))) | |
400 | (home-page "http://cran.r-project.org/web/packages/CodeDepends") | |
401 | (synopsis "Analysis of R code for reproducible research and code comprehension") | |
402 | (description | |
403 | "This package provides tools for analyzing R expressions or blocks of | |
404 | code and determining the dependencies between them. It focuses on R scripts, | |
405 | but can be used on the bodies of functions. There are many facilities | |
406 | including the ability to summarize or get a high-level view of code, | |
407 | determining dependencies between variables, code improvement suggestions.") | |
408 | ;; Any version of the GPL | |
409 | (license (list license:gpl2+ license:gpl3+)))) | |
410 | ||
793f83ef RJ |
411 | (define-public r-chippeakanno |
412 | (package | |
413 | (name "r-chippeakanno") | |
add2b195 | 414 | (version "3.16.1") |
793f83ef RJ |
415 | (source |
416 | (origin | |
417 | (method url-fetch) | |
418 | (uri (bioconductor-uri "ChIPpeakAnno" version)) | |
419 | (sha256 | |
420 | (base32 | |
add2b195 | 421 | "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3")))) |
793f83ef RJ |
422 | (properties `((upstream-name . "ChIPpeakAnno"))) |
423 | (build-system r-build-system) | |
424 | (propagated-inputs | |
425 | `(("r-biocgenerics" ,r-biocgenerics) | |
57d2fcd9 | 426 | ("r-biocmanager" ,r-biocmanager) |
f794e85d RW |
427 | ("r-biostrings" ,r-biostrings) |
428 | ("r-delayedarray" ,r-delayedarray) | |
793f83ef RJ |
429 | ("r-go-db" ,r-go-db) |
430 | ("r-biomart" ,r-biomart) | |
431 | ("r-bsgenome" ,r-bsgenome) | |
432 | ("r-genomicfeatures" ,r-genomicfeatures) | |
f794e85d | 433 | ("r-genomicranges" ,r-genomicranges) |
793f83ef | 434 | ("r-genomeinfodb" ,r-genomeinfodb) |
f794e85d | 435 | ("r-iranges" ,r-iranges) |
793f83ef RJ |
436 | ("r-matrixstats" ,r-matrixstats) |
437 | ("r-annotationdbi" ,r-annotationdbi) | |
438 | ("r-limma" ,r-limma) | |
439 | ("r-multtest" ,r-multtest) | |
440 | ("r-rbgl" ,r-rbgl) | |
441 | ("r-graph" ,r-graph) | |
793f83ef RJ |
442 | ("r-regioner" ,r-regioner) |
443 | ("r-dbi" ,r-dbi) | |
444 | ("r-ensembldb" ,r-ensembldb) | |
445 | ("r-biobase" ,r-biobase) | |
f794e85d | 446 | ("r-s4vectors" ,r-s4vectors) |
793f83ef RJ |
447 | ("r-seqinr" ,r-seqinr) |
448 | ("r-idr" ,r-idr) | |
449 | ("r-genomicalignments" ,r-genomicalignments) | |
450 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
451 | ("r-rsamtools" ,r-rsamtools) | |
452 | ("r-venndiagram" ,r-venndiagram))) | |
453 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") | |
454 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") | |
455 | (description | |
456 | "The package includes functions to retrieve the sequences around the peak, | |
457 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or | |
458 | custom features such as most conserved elements and other transcription factor | |
459 | binding sites supplied by users. Starting 2.0.5, new functions have been added | |
460 | for finding the peaks with bi-directional promoters with summary statistics | |
461 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks | |
462 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or | |
463 | enrichedGO (addGeneIDs).") | |
464 | (license license:gpl2+))) | |
164502d8 RJ |
465 | |
466 | (define-public r-marray | |
467 | (package | |
468 | (name "r-marray") | |
f1c606ce | 469 | (version "1.60.0") |
164502d8 RJ |
470 | (source (origin |
471 | (method url-fetch) | |
472 | (uri (bioconductor-uri "marray" version)) | |
473 | (sha256 | |
f1c606ce | 474 | (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky")))) |
164502d8 RJ |
475 | (build-system r-build-system) |
476 | (propagated-inputs | |
67487088 | 477 | `(("r-limma" ,r-limma))) |
164502d8 RJ |
478 | (home-page "http://bioconductor.org/packages/marray") |
479 | (synopsis "Exploratory analysis for two-color spotted microarray data") | |
480 | (description "This package contains class definitions for two-color spotted | |
481 | microarray data. It also includes fuctions for data input, diagnostic plots, | |
482 | normalization and quality checking.") | |
483 | (license license:lgpl2.0+))) | |
0416a0d4 RJ |
484 | |
485 | (define-public r-cghbase | |
486 | (package | |
487 | (name "r-cghbase") | |
46cdceef | 488 | (version "1.42.0") |
0416a0d4 RJ |
489 | (source (origin |
490 | (method url-fetch) | |
491 | (uri (bioconductor-uri "CGHbase" version)) | |
492 | (sha256 | |
46cdceef | 493 | (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc")))) |
0416a0d4 RJ |
494 | (properties `((upstream-name . "CGHbase"))) |
495 | (build-system r-build-system) | |
496 | (propagated-inputs | |
497 | `(("r-biobase" ,r-biobase) | |
498 | ("r-marray" ,r-marray))) | |
499 | (home-page "http://bioconductor.org/packages/CGHbase") | |
500 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
501 | (description "This package contains functions and classes that are needed by | |
502 | the @code{arrayCGH} packages.") | |
503 | (license license:gpl2+))) | |
67ee83d6 RJ |
504 | |
505 | (define-public r-cghcall | |
506 | (package | |
507 | (name "r-cghcall") | |
9add0933 | 508 | (version "2.44.0") |
67ee83d6 RJ |
509 | (source (origin |
510 | (method url-fetch) | |
511 | (uri (bioconductor-uri "CGHcall" version)) | |
512 | (sha256 | |
9add0933 | 513 | (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi")))) |
67ee83d6 RJ |
514 | (properties `((upstream-name . "CGHcall"))) |
515 | (build-system r-build-system) | |
516 | (propagated-inputs | |
517 | `(("r-biobase" ,r-biobase) | |
518 | ("r-cghbase" ,r-cghbase) | |
519 | ("r-impute" ,r-impute) | |
520 | ("r-dnacopy" ,r-dnacopy) | |
521 | ("r-snowfall" ,r-snowfall))) | |
522 | (home-page "http://bioconductor.org/packages/CGHcall") | |
523 | (synopsis "Base functions and classes for arrayCGH data analysis") | |
524 | (description "This package contains functions and classes that are needed by | |
525 | @code{arrayCGH} packages.") | |
526 | (license license:gpl2+))) | |
0ef8cc9c RJ |
527 | |
528 | (define-public r-qdnaseq | |
529 | (package | |
530 | (name "r-qdnaseq") | |
a92f5230 | 531 | (version "1.18.0") |
0ef8cc9c RJ |
532 | (source (origin |
533 | (method url-fetch) | |
534 | (uri (bioconductor-uri "QDNAseq" version)) | |
535 | (sha256 | |
a92f5230 | 536 | (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2")))) |
0ef8cc9c RJ |
537 | (properties `((upstream-name . "QDNAseq"))) |
538 | (build-system r-build-system) | |
539 | (propagated-inputs | |
540 | `(("r-biobase" ,r-biobase) | |
81b0181b | 541 | ("r-biocparallel" ,r-biocparallel) |
0ef8cc9c RJ |
542 | ("r-cghbase" ,r-cghbase) |
543 | ("r-cghcall" ,r-cghcall) | |
544 | ("r-dnacopy" ,r-dnacopy) | |
545 | ("r-genomicranges" ,r-genomicranges) | |
546 | ("r-iranges" ,r-iranges) | |
547 | ("r-matrixstats" ,r-matrixstats) | |
548 | ("r-r-utils" ,r-r-utils) | |
549 | ("r-rsamtools" ,r-rsamtools))) | |
550 | (home-page "http://bioconductor.org/packages/QDNAseq") | |
551 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") | |
552 | (description "The genome is divided into non-overlapping fixed-sized bins, | |
553 | number of sequence reads in each counted, adjusted with a simultaneous | |
554 | two-dimensional loess correction for sequence mappability and GC content, and | |
555 | filtered to remove spurious regions in the genome. Downstream steps of | |
556 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, | |
557 | respectively.") | |
558 | (license license:gpl2+))) | |
bb15b581 RW |
559 | |
560 | (define-public r-bayseq | |
561 | (package | |
562 | (name "r-bayseq") | |
4728e275 | 563 | (version "2.16.0") |
bb15b581 RW |
564 | (source |
565 | (origin | |
566 | (method url-fetch) | |
567 | (uri (bioconductor-uri "baySeq" version)) | |
568 | (sha256 | |
569 | (base32 | |
4728e275 | 570 | "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5")))) |
bb15b581 RW |
571 | (properties `((upstream-name . "baySeq"))) |
572 | (build-system r-build-system) | |
573 | (propagated-inputs | |
574 | `(("r-abind" ,r-abind) | |
575 | ("r-edger" ,r-edger) | |
576 | ("r-genomicranges" ,r-genomicranges))) | |
577 | (home-page "https://bioconductor.org/packages/baySeq/") | |
578 | (synopsis "Bayesian analysis of differential expression patterns in count data") | |
579 | (description | |
580 | "This package identifies differential expression in high-throughput count | |
581 | data, such as that derived from next-generation sequencing machines, | |
582 | calculating estimated posterior likelihoods of differential expression (or | |
583 | more complex hypotheses) via empirical Bayesian methods.") | |
584 | (license license:gpl3))) | |
609f4ad1 RW |
585 | |
586 | (define-public r-chipcomp | |
587 | (package | |
588 | (name "r-chipcomp") | |
aa802eaf | 589 | (version "1.12.0") |
609f4ad1 RW |
590 | (source |
591 | (origin | |
592 | (method url-fetch) | |
593 | (uri (bioconductor-uri "ChIPComp" version)) | |
594 | (sha256 | |
595 | (base32 | |
aa802eaf | 596 | "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85")))) |
609f4ad1 RW |
597 | (properties `((upstream-name . "ChIPComp"))) |
598 | (build-system r-build-system) | |
599 | (propagated-inputs | |
600 | `(("r-biocgenerics" ,r-biocgenerics) | |
601 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
602 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
603 | ("r-genomeinfodb" ,r-genomeinfodb) | |
604 | ("r-genomicranges" ,r-genomicranges) | |
605 | ("r-iranges" ,r-iranges) | |
606 | ("r-limma" ,r-limma) | |
607 | ("r-rsamtools" ,r-rsamtools) | |
608 | ("r-rtracklayer" ,r-rtracklayer) | |
609 | ("r-s4vectors" ,r-s4vectors))) | |
610 | (home-page "https://bioconductor.org/packages/ChIPComp") | |
611 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") | |
612 | (description | |
613 | "ChIPComp implements a statistical method for quantitative comparison of | |
614 | multiple ChIP-seq datasets. It detects differentially bound sharp binding | |
615 | sites across multiple conditions considering matching control in ChIP-seq | |
616 | datasets.") | |
617 | ;; Any version of the GPL. | |
618 | (license license:gpl3+))) | |
0490f9de RW |
619 | |
620 | (define-public r-riboprofiling | |
621 | (package | |
622 | (name "r-riboprofiling") | |
e22e462b | 623 | (version "1.12.0") |
0490f9de RW |
624 | (source |
625 | (origin | |
626 | (method url-fetch) | |
627 | (uri (bioconductor-uri "RiboProfiling" version)) | |
628 | (sha256 | |
629 | (base32 | |
e22e462b | 630 | "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z")))) |
0490f9de RW |
631 | (properties `((upstream-name . "RiboProfiling"))) |
632 | (build-system r-build-system) | |
633 | (propagated-inputs | |
634 | `(("r-biocgenerics" ,r-biocgenerics) | |
635 | ("r-biostrings" ,r-biostrings) | |
636 | ("r-data-table" ,r-data-table) | |
637 | ("r-genomeinfodb" ,r-genomeinfodb) | |
638 | ("r-genomicalignments" ,r-genomicalignments) | |
639 | ("r-genomicfeatures" ,r-genomicfeatures) | |
640 | ("r-genomicranges" ,r-genomicranges) | |
641 | ("r-ggbio" ,r-ggbio) | |
642 | ("r-ggplot2" ,r-ggplot2) | |
643 | ("r-iranges" ,r-iranges) | |
644 | ("r-plyr" ,r-plyr) | |
645 | ("r-reshape2" ,r-reshape2) | |
646 | ("r-rsamtools" ,r-rsamtools) | |
647 | ("r-rtracklayer" ,r-rtracklayer) | |
648 | ("r-s4vectors" ,r-s4vectors) | |
649 | ("r-sqldf" ,r-sqldf))) | |
650 | (home-page "https://bioconductor.org/packages/RiboProfiling/") | |
651 | (synopsis "Ribosome profiling data analysis") | |
652 | (description "Starting with a BAM file, this package provides the | |
653 | necessary functions for quality assessment, read start position recalibration, | |
654 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting | |
655 | of count data: pairs, log fold-change, codon frequency and coverage | |
656 | assessment, principal component analysis on codon coverage.") | |
657 | (license license:gpl3))) | |
6ffdfe6a RW |
658 | |
659 | (define-public r-riboseqr | |
660 | (package | |
661 | (name "r-riboseqr") | |
c4fed658 | 662 | (version "1.16.0") |
6ffdfe6a RW |
663 | (source |
664 | (origin | |
665 | (method url-fetch) | |
666 | (uri (bioconductor-uri "riboSeqR" version)) | |
667 | (sha256 | |
668 | (base32 | |
c4fed658 | 669 | "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb")))) |
6ffdfe6a RW |
670 | (properties `((upstream-name . "riboSeqR"))) |
671 | (build-system r-build-system) | |
672 | (propagated-inputs | |
673 | `(("r-abind" ,r-abind) | |
674 | ("r-bayseq" ,r-bayseq) | |
675 | ("r-genomeinfodb" ,r-genomeinfodb) | |
676 | ("r-genomicranges" ,r-genomicranges) | |
677 | ("r-iranges" ,r-iranges) | |
678 | ("r-rsamtools" ,r-rsamtools) | |
679 | ("r-seqlogo" ,r-seqlogo))) | |
680 | (home-page "https://bioconductor.org/packages/riboSeqR/") | |
681 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") | |
682 | (description | |
683 | "This package provides plotting functions, frameshift detection and | |
684 | parsing of genetic sequencing data from ribosome profiling experiments.") | |
685 | (license license:gpl3))) | |
a32279ff RW |
686 | |
687 | (define-public r-interactionset | |
688 | (package | |
689 | (name "r-interactionset") | |
bbc4787c | 690 | (version "1.10.0") |
a32279ff RW |
691 | (source |
692 | (origin | |
693 | (method url-fetch) | |
694 | (uri (bioconductor-uri "InteractionSet" version)) | |
695 | (sha256 | |
696 | (base32 | |
bbc4787c | 697 | "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb")))) |
a32279ff RW |
698 | (properties |
699 | `((upstream-name . "InteractionSet"))) | |
700 | (build-system r-build-system) | |
701 | (propagated-inputs | |
702 | `(("r-biocgenerics" ,r-biocgenerics) | |
703 | ("r-genomeinfodb" ,r-genomeinfodb) | |
704 | ("r-genomicranges" ,r-genomicranges) | |
705 | ("r-iranges" ,r-iranges) | |
706 | ("r-matrix" ,r-matrix) | |
707 | ("r-rcpp" ,r-rcpp) | |
708 | ("r-s4vectors" ,r-s4vectors) | |
709 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
710 | (home-page "https://bioconductor.org/packages/InteractionSet") | |
711 | (synopsis "Base classes for storing genomic interaction data") | |
712 | (description | |
713 | "This packages provides the @code{GInteractions}, | |
714 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods | |
715 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET | |
716 | experiments.") | |
717 | (license license:gpl3))) | |
cf9a29b2 RW |
718 | |
719 | (define-public r-genomicinteractions | |
720 | (package | |
721 | (name "r-genomicinteractions") | |
5f2d0e63 | 722 | (version "1.16.0") |
cf9a29b2 RW |
723 | (source |
724 | (origin | |
725 | (method url-fetch) | |
726 | (uri (bioconductor-uri "GenomicInteractions" version)) | |
727 | (sha256 | |
728 | (base32 | |
5f2d0e63 | 729 | "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q")))) |
cf9a29b2 RW |
730 | (properties |
731 | `((upstream-name . "GenomicInteractions"))) | |
732 | (build-system r-build-system) | |
733 | (propagated-inputs | |
734 | `(("r-biobase" ,r-biobase) | |
735 | ("r-biocgenerics" ,r-biocgenerics) | |
736 | ("r-data-table" ,r-data-table) | |
737 | ("r-dplyr" ,r-dplyr) | |
738 | ("r-genomeinfodb" ,r-genomeinfodb) | |
739 | ("r-genomicranges" ,r-genomicranges) | |
740 | ("r-ggplot2" ,r-ggplot2) | |
741 | ("r-gridextra" ,r-gridextra) | |
742 | ("r-gviz" ,r-gviz) | |
743 | ("r-igraph" ,r-igraph) | |
744 | ("r-interactionset" ,r-interactionset) | |
745 | ("r-iranges" ,r-iranges) | |
746 | ("r-rsamtools" ,r-rsamtools) | |
747 | ("r-rtracklayer" ,r-rtracklayer) | |
748 | ("r-s4vectors" ,r-s4vectors) | |
749 | ("r-stringr" ,r-stringr))) | |
750 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") | |
751 | (synopsis "R package for handling genomic interaction data") | |
752 | (description | |
753 | "This R package provides tools for handling genomic interaction data, | |
754 | such as ChIA-PET/Hi-C, annotating genomic features with interaction | |
755 | information and producing various plots and statistics.") | |
756 | (license license:gpl3))) | |
27c51606 RW |
757 | |
758 | (define-public r-ctc | |
759 | (package | |
760 | (name "r-ctc") | |
b858338c | 761 | (version "1.56.0") |
27c51606 RW |
762 | (source |
763 | (origin | |
764 | (method url-fetch) | |
765 | (uri (bioconductor-uri "ctc" version)) | |
766 | (sha256 | |
767 | (base32 | |
b858338c | 768 | "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2")))) |
27c51606 RW |
769 | (build-system r-build-system) |
770 | (propagated-inputs `(("r-amap" ,r-amap))) | |
771 | (home-page "https://bioconductor.org/packages/ctc/") | |
772 | (synopsis "Cluster and tree conversion") | |
773 | (description | |
774 | "This package provides tools for exporting and importing classification | |
775 | trees and clusters to other programs.") | |
776 | (license license:gpl2))) | |
5da0e142 RW |
777 | |
778 | (define-public r-goseq | |
779 | (package | |
780 | (name "r-goseq") | |
7f2b1c4a | 781 | (version "1.34.1") |
5da0e142 RW |
782 | (source |
783 | (origin | |
784 | (method url-fetch) | |
785 | (uri (bioconductor-uri "goseq" version)) | |
786 | (sha256 | |
787 | (base32 | |
7f2b1c4a | 788 | "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn")))) |
5da0e142 RW |
789 | (build-system r-build-system) |
790 | (propagated-inputs | |
791 | `(("r-annotationdbi" ,r-annotationdbi) | |
792 | ("r-biasedurn" ,r-biasedurn) | |
793 | ("r-biocgenerics" ,r-biocgenerics) | |
794 | ("r-genelendatabase" ,r-genelendatabase) | |
795 | ("r-go-db" ,r-go-db) | |
796 | ("r-mgcv" ,r-mgcv))) | |
797 | (home-page "https://bioconductor.org/packages/goseq/") | |
798 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") | |
799 | (description | |
800 | "This package provides tools to detect Gene Ontology and/or other user | |
801 | defined categories which are over/under represented in RNA-seq data.") | |
802 | (license license:lgpl2.0+))) | |
f4235c0e RW |
803 | |
804 | (define-public r-glimma | |
805 | (package | |
806 | (name "r-glimma") | |
0b469ee2 | 807 | (version "1.10.1") |
f4235c0e RW |
808 | (source |
809 | (origin | |
810 | (method url-fetch) | |
811 | (uri (bioconductor-uri "Glimma" version)) | |
812 | (sha256 | |
813 | (base32 | |
0b469ee2 | 814 | "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv")))) |
f4235c0e RW |
815 | (properties `((upstream-name . "Glimma"))) |
816 | (build-system r-build-system) | |
817 | (propagated-inputs | |
818 | `(("r-edger" ,r-edger) | |
819 | ("r-jsonlite" ,r-jsonlite) | |
820 | ("r-s4vectors" ,r-s4vectors))) | |
821 | (home-page "https://github.com/Shians/Glimma") | |
822 | (synopsis "Interactive HTML graphics") | |
823 | (description | |
824 | "This package generates interactive visualisations for analysis of | |
825 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an | |
826 | HTML page. The interactions are built on top of the popular static | |
827 | representations of analysis results in order to provide additional | |
828 | information.") | |
829 | (license license:lgpl3))) | |
aa388dc7 RW |
830 | |
831 | (define-public r-rots | |
832 | (package | |
833 | (name "r-rots") | |
c348cfed | 834 | (version "1.10.0") |
aa388dc7 RW |
835 | (source |
836 | (origin | |
837 | (method url-fetch) | |
838 | (uri (bioconductor-uri "ROTS" version)) | |
839 | (sha256 | |
840 | (base32 | |
c348cfed | 841 | "137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5")))) |
aa388dc7 RW |
842 | (properties `((upstream-name . "ROTS"))) |
843 | (build-system r-build-system) | |
844 | (propagated-inputs | |
845 | `(("r-biobase" ,r-biobase) | |
846 | ("r-rcpp" ,r-rcpp))) | |
847 | (home-page "https://bioconductor.org/packages/ROTS/") | |
848 | (synopsis "Reproducibility-Optimized Test Statistic") | |
849 | (description | |
850 | "This package provides tools for calculating the | |
851 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing | |
852 | in omics data.") | |
853 | (license license:gpl2+))) | |
b64ce4b7 RW |
854 | |
855 | (define-public r-inspect | |
856 | (package | |
857 | (name "r-inspect") | |
6f1e1d0f | 858 | (version "1.12.0") |
b64ce4b7 RW |
859 | (source |
860 | (origin | |
861 | (method url-fetch) | |
862 | (uri (bioconductor-uri "INSPEcT" version)) | |
863 | (sha256 | |
864 | (base32 | |
6f1e1d0f | 865 | "0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2")))) |
b64ce4b7 RW |
866 | (properties `((upstream-name . "INSPEcT"))) |
867 | (build-system r-build-system) | |
868 | (propagated-inputs | |
869 | `(("r-biobase" ,r-biobase) | |
870 | ("r-biocgenerics" ,r-biocgenerics) | |
871 | ("r-biocparallel" ,r-biocparallel) | |
872 | ("r-desolve" ,r-desolve) | |
873 | ("r-genomicalignments" ,r-genomicalignments) | |
874 | ("r-genomicfeatures" ,r-genomicfeatures) | |
875 | ("r-genomicranges" ,r-genomicranges) | |
876 | ("r-iranges" ,r-iranges) | |
877 | ("r-preprocesscore" ,r-preprocesscore) | |
878 | ("r-proc" ,r-proc) | |
879 | ("r-rootsolve" ,r-rootsolve) | |
880 | ("r-rsamtools" ,r-rsamtools) | |
881 | ("r-s4vectors" ,r-s4vectors))) | |
882 | (home-page "https://bioconductor.org/packages/INSPEcT") | |
883 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") | |
884 | (description | |
885 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in | |
886 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in | |
887 | order to evaluate synthesis, processing and degradation rates and assess via | |
888 | modeling the rates that determines changes in mature mRNA levels.") | |
889 | (license license:gpl2))) | |
f6e99763 RW |
890 | |
891 | (define-public r-dnabarcodes | |
892 | (package | |
893 | (name "r-dnabarcodes") | |
318bcbc4 | 894 | (version "1.12.0") |
f6e99763 RW |
895 | (source |
896 | (origin | |
897 | (method url-fetch) | |
898 | (uri (bioconductor-uri "DNABarcodes" version)) | |
899 | (sha256 | |
900 | (base32 | |
318bcbc4 | 901 | "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0")))) |
f6e99763 RW |
902 | (properties `((upstream-name . "DNABarcodes"))) |
903 | (build-system r-build-system) | |
904 | (propagated-inputs | |
905 | `(("r-bh" ,r-bh) | |
906 | ("r-matrix" ,r-matrix) | |
907 | ("r-rcpp" ,r-rcpp))) | |
908 | (home-page "https://bioconductor.org/packages/DNABarcodes") | |
909 | (synopsis "Create and analyze DNA barcodes") | |
910 | (description | |
911 | "This package offers tools to create DNA barcode sets capable of | |
912 | correcting insertion, deletion, and substitution errors. Existing barcodes | |
913 | can be analyzed regarding their minimal, maximal and average distances between | |
914 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be | |
915 | demultiplexed, i.e. assigned to their original reference barcode.") | |
916 | (license license:gpl2))) | |
09aa3d06 RW |
917 | |
918 | (define-public r-ruvseq | |
919 | (package | |
920 | (name "r-ruvseq") | |
ed35d7ca | 921 | (version "1.16.0") |
09aa3d06 RW |
922 | (source |
923 | (origin | |
924 | (method url-fetch) | |
925 | (uri (bioconductor-uri "RUVSeq" version)) | |
926 | (sha256 | |
927 | (base32 | |
ed35d7ca | 928 | "0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m")))) |
09aa3d06 RW |
929 | (properties `((upstream-name . "RUVSeq"))) |
930 | (build-system r-build-system) | |
931 | (propagated-inputs | |
932 | `(("r-biobase" ,r-biobase) | |
933 | ("r-edaseq" ,r-edaseq) | |
934 | ("r-edger" ,r-edger) | |
935 | ("r-mass" ,r-mass))) | |
936 | (home-page "https://github.com/drisso/RUVSeq") | |
937 | (synopsis "Remove unwanted variation from RNA-Seq data") | |
938 | (description | |
939 | "This package implements methods to @dfn{remove unwanted variation} (RUV) | |
940 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between | |
941 | samples.") | |
942 | (license license:artistic2.0))) | |
286157dc RW |
943 | |
944 | (define-public r-biocneighbors | |
945 | (package | |
946 | (name "r-biocneighbors") | |
947 | (version "1.0.0") | |
948 | (source | |
949 | (origin | |
950 | (method url-fetch) | |
951 | (uri (bioconductor-uri "BiocNeighbors" version)) | |
952 | (sha256 | |
953 | (base32 | |
954 | "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll")))) | |
955 | (properties `((upstream-name . "BiocNeighbors"))) | |
956 | (build-system r-build-system) | |
957 | (propagated-inputs | |
958 | `(("r-biocparallel" ,r-biocparallel) | |
959 | ("r-rcpp" ,r-rcpp) | |
960 | ("r-rcppannoy" ,r-rcppannoy) | |
961 | ("r-s4vectors" ,r-s4vectors))) | |
962 | (home-page "https://bioconductor.org/packages/BiocNeighbors") | |
963 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") | |
964 | (description | |
965 | "This package implements exact and approximate methods for nearest | |
966 | neighbor detection, in a framework that allows them to be easily switched | |
967 | within Bioconductor packages or workflows. The exact algorithm is implemented | |
968 | using pre-clustering with the k-means algorithm. Functions are also provided | |
969 | to search for all neighbors within a given distance. Parallelization is | |
970 | achieved for all methods using the BiocParallel framework.") | |
971 | (license license:gpl3))) | |
8a587c89 | 972 | |
a961ae46 RW |
973 | (define-public r-destiny |
974 | (package | |
975 | (name "r-destiny") | |
976 | (version "2.12.0") | |
977 | (source | |
978 | (origin | |
979 | (method url-fetch) | |
980 | (uri (bioconductor-uri "destiny" version)) | |
981 | (sha256 | |
982 | (base32 | |
983 | "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67")))) | |
984 | (build-system r-build-system) | |
985 | (propagated-inputs | |
986 | `(("r-biobase" ,r-biobase) | |
987 | ("r-biocgenerics" ,r-biocgenerics) | |
988 | ("r-fnn" ,r-fnn) | |
989 | ("r-ggthemes" ,r-ggthemes) | |
990 | ("r-hmisc" ,r-hmisc) | |
991 | ("r-igraph" ,r-igraph) | |
992 | ("r-matrix" ,r-matrix) | |
993 | ("r-proxy" ,r-proxy) | |
994 | ("r-rcpp" ,r-rcpp) | |
995 | ("r-rcppeigen" ,r-rcppeigen) | |
996 | ("r-scales" ,r-scales) | |
997 | ("r-scatterplot3d" ,r-scatterplot3d) | |
998 | ("r-smoother" ,r-smoother) | |
999 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
1000 | ("r-vim" ,r-vim))) | |
1001 | (home-page "https://bioconductor.org/packages/destiny/") | |
1002 | (synopsis "Create and plot diffusion maps") | |
1003 | (description "This package provides tools to create and plot diffusion | |
1004 | maps.") | |
1005 | ;; Any version of the GPL | |
1006 | (license license:gpl3+))) | |
1007 | ||
8a587c89 RW |
1008 | (define-public r-savr |
1009 | (package | |
1010 | (name "r-savr") | |
1011 | (version "1.20.0") | |
1012 | (source | |
1013 | (origin | |
1014 | (method url-fetch) | |
1015 | (uri (bioconductor-uri "savR" version)) | |
1016 | (sha256 | |
1017 | (base32 | |
1018 | "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7")))) | |
1019 | (properties `((upstream-name . "savR"))) | |
1020 | (build-system r-build-system) | |
1021 | (propagated-inputs | |
1022 | `(("r-ggplot2" ,r-ggplot2) | |
1023 | ("r-gridextra" ,r-gridextra) | |
1024 | ("r-reshape2" ,r-reshape2) | |
1025 | ("r-scales" ,r-scales) | |
1026 | ("r-xml" ,r-xml))) | |
1027 | (home-page "https://github.com/bcalder/savR") | |
1028 | (synopsis "Parse and analyze Illumina SAV files") | |
1029 | (description | |
1030 | "This package provides tools to parse Illumina Sequence Analysis | |
1031 | Viewer (SAV) files, access data, and generate QC plots.") | |
1032 | (license license:agpl3+))) | |
41ffc214 RW |
1033 | |
1034 | (define-public r-chipexoqual | |
1035 | (package | |
1036 | (name "r-chipexoqual") | |
1037 | (version "1.6.0") | |
1038 | (source | |
1039 | (origin | |
1040 | (method url-fetch) | |
1041 | (uri (bioconductor-uri "ChIPexoQual" version)) | |
1042 | (sha256 | |
1043 | (base32 | |
1044 | "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp")))) | |
1045 | (properties `((upstream-name . "ChIPexoQual"))) | |
1046 | (build-system r-build-system) | |
1047 | (propagated-inputs | |
1048 | `(("r-biocparallel" ,r-biocparallel) | |
1049 | ("r-biovizbase" ,r-biovizbase) | |
1050 | ("r-broom" ,r-broom) | |
1051 | ("r-data-table" ,r-data-table) | |
1052 | ("r-dplyr" ,r-dplyr) | |
1053 | ("r-genomeinfodb" ,r-genomeinfodb) | |
1054 | ("r-genomicalignments" ,r-genomicalignments) | |
1055 | ("r-genomicranges" ,r-genomicranges) | |
1056 | ("r-ggplot2" ,r-ggplot2) | |
1057 | ("r-hexbin" ,r-hexbin) | |
1058 | ("r-iranges" ,r-iranges) | |
1059 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
1060 | ("r-rmarkdown" ,r-rmarkdown) | |
1061 | ("r-rsamtools" ,r-rsamtools) | |
1062 | ("r-s4vectors" ,r-s4vectors) | |
1063 | ("r-scales" ,r-scales) | |
1064 | ("r-viridis" ,r-viridis))) | |
1065 | (home-page "https://github.com/keleslab/ChIPexoQual") | |
1066 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") | |
1067 | (description | |
1068 | "This package provides a quality control pipeline for ChIP-exo/nexus | |
1069 | sequencing data.") | |
1070 | (license license:gpl2+))) |