gnu: r-graph: Move from bioinformatics to bioconductor.
[jackhill/guix/guix.git] / gnu / packages / bioconductor.scm
1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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)
26 #:use-module (gnu packages)
27 #:use-module (gnu packages bioinformatics)
28 #:use-module (gnu packages cran)
29 #:use-module (gnu packages compression)
30 #:use-module (gnu packages graph)
31 #:use-module (gnu packages maths)
32 #:use-module (gnu packages statistics)
33 #:use-module (gnu packages web))
34
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
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
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
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
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
201 (define-public r-hpar
202 (package
203 (name "r-hpar")
204 (version "1.22.2")
205 (source
206 (origin
207 (method url-fetch)
208 (uri (bioconductor-uri "hpar" version))
209 (sha256
210 (base32
211 "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
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)))
218
219 (define-public r-regioner
220 (package
221 (name "r-regioner")
222 (version "1.12.0")
223 (source
224 (origin
225 (method url-fetch)
226 (uri (bioconductor-uri "regioneR" version))
227 (sha256
228 (base32
229 "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
230 (properties `((upstream-name . "regioneR")))
231 (build-system r-build-system)
232 (propagated-inputs
233 `(("r-memoise" ,r-memoise)
234 ("r-genomicranges" ,r-genomicranges)
235 ("r-bsgenome" ,r-bsgenome)
236 ("r-rtracklayer" ,r-rtracklayer)
237 ("r-genomeinfodb" ,r-genomeinfodb)
238 ("r-iranges" ,r-iranges)
239 ("r-s4vectors" ,r-s4vectors)))
240 (home-page "https://bioconductor.org/packages/regioneR/")
241 (synopsis "Association analysis of genomic regions")
242 (description "This package offers a statistical framework based on
243 customizable permutation tests to assess the association between genomic
244 region sets and other genomic features.")
245 (license license:artistic2.0)))
246
247 (define-public r-diffbind
248 (package
249 (name "r-diffbind")
250 (version "2.8.0")
251 (source
252 (origin
253 (method url-fetch)
254 (uri (bioconductor-uri "DiffBind" version))
255 (sha256
256 (base32
257 "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
258 (properties `((upstream-name . "DiffBind")))
259 (build-system r-build-system)
260 (inputs
261 `(("zlib" ,zlib)))
262 (propagated-inputs
263 `(("r-amap" ,r-amap)
264 ("r-biocparallel" ,r-biocparallel)
265 ("r-deseq2" ,r-deseq2)
266 ("r-dplyr" ,r-dplyr)
267 ("r-edger" ,r-edger)
268 ("r-genomicalignments" ,r-genomicalignments)
269 ("r-genomicranges" ,r-genomicranges)
270 ("r-ggplot2" ,r-ggplot2)
271 ("r-ggrepel" ,r-ggrepel)
272 ("r-gplots" ,r-gplots)
273 ("r-iranges" ,r-iranges)
274 ("r-lattice" ,r-lattice)
275 ("r-limma" ,r-limma)
276 ("r-locfit" ,r-locfit)
277 ("r-rcolorbrewer" , r-rcolorbrewer)
278 ("r-rcpp" ,r-rcpp)
279 ("r-rsamtools" ,r-rsamtools)
280 ("r-s4vectors" ,r-s4vectors)
281 ("r-summarizedexperiment" ,r-summarizedexperiment)
282 ("r-systempiper" ,r-systempiper)
283 ("r-zlibbioc" ,r-zlibbioc)))
284 (home-page "http://bioconductor.org/packages/DiffBind")
285 (synopsis "Differential binding analysis of ChIP-Seq peak data")
286 (description
287 "This package computes differentially bound sites from multiple
288 ChIP-seq experiments using affinity (quantitative) data. Also enables
289 occupancy (overlap) analysis and plotting functions.")
290 (license license:artistic2.0)))
291
292 (define-public r-ripseeker
293 (package
294 (name "r-ripseeker")
295 (version "1.20.0")
296 (source
297 (origin
298 (method url-fetch)
299 (uri (bioconductor-uri "RIPSeeker" version))
300 (sha256
301 (base32
302 "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
303 (properties `((upstream-name . "RIPSeeker")))
304 (build-system r-build-system)
305 (propagated-inputs
306 `(("r-s4vectors" ,r-s4vectors)
307 ("r-iranges" ,r-iranges)
308 ("r-genomicranges" ,r-genomicranges)
309 ("r-summarizedexperiment" ,r-summarizedexperiment)
310 ("r-rsamtools" ,r-rsamtools)
311 ("r-genomicalignments" ,r-genomicalignments)
312 ("r-rtracklayer" ,r-rtracklayer)))
313 (home-page "http://bioconductor.org/packages/RIPSeeker")
314 (synopsis
315 "Identifying protein-associated transcripts from RIP-seq experiments")
316 (description
317 "This package infers and discriminates RIP peaks from RIP-seq alignments
318 using two-state HMM with negative binomial emission probability. While
319 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
320 a suite of bioinformatics tools integrated within this self-contained software
321 package comprehensively addressing issues ranging from post-alignments
322 processing to visualization and annotation.")
323 (license license:gpl2)))
324
325 (define-public r-multtest
326 (package
327 (name "r-multtest")
328 (version "2.36.0")
329 (source
330 (origin
331 (method url-fetch)
332 (uri (bioconductor-uri "multtest" version))
333 (sha256
334 (base32
335 "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
336 (build-system r-build-system)
337 (propagated-inputs
338 `(("r-survival" ,r-survival)
339 ("r-biocgenerics" ,r-biocgenerics)
340 ("r-biobase" ,r-biobase)
341 ("r-mass" ,r-mass)))
342 (home-page "http://bioconductor.org/packages/multtest")
343 (synopsis "Resampling-based multiple hypothesis testing")
344 (description
345 "This package can do non-parametric bootstrap and permutation
346 resampling-based multiple testing procedures (including empirical Bayes
347 methods) for controlling the family-wise error rate (FWER), generalized
348 family-wise error rate (gFWER), tail probability of the proportion of
349 false positives (TPPFP), and false discovery rate (FDR). Several choices
350 of bootstrap-based null distribution are implemented (centered, centered
351 and scaled, quantile-transformed). Single-step and step-wise methods are
352 available. Tests based on a variety of T- and F-statistics (including
353 T-statistics based on regression parameters from linear and survival models
354 as well as those based on correlation parameters) are included. When probing
355 hypotheses with T-statistics, users may also select a potentially faster null
356 distribution which is multivariate normal with mean zero and variance
357 covariance matrix derived from the vector influence function. Results are
358 reported in terms of adjusted P-values, confidence regions and test statistic
359 cutoffs. The procedures are directly applicable to identifying differentially
360 expressed genes in DNA microarray experiments.")
361 (license license:lgpl3)))
362
363 (define-public r-graph
364 (package
365 (name "r-graph")
366 (version "1.58.0")
367 (source (origin
368 (method url-fetch)
369 (uri (bioconductor-uri "graph" version))
370 (sha256
371 (base32
372 "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
373 (build-system r-build-system)
374 (propagated-inputs
375 `(("r-biocgenerics" ,r-biocgenerics)))
376 (home-page "https://bioconductor.org/packages/graph")
377 (synopsis "Handle graph data structures in R")
378 (description
379 "This package implements some simple graph handling capabilities for R.")
380 (license license:artistic2.0)))
381
382 (define-public r-chippeakanno
383 (package
384 (name "r-chippeakanno")
385 (version "3.14.1")
386 (source
387 (origin
388 (method url-fetch)
389 (uri (bioconductor-uri "ChIPpeakAnno" version))
390 (sha256
391 (base32
392 "1cn1hfc3nvsf2n3563lkmvwjxfbiygx7f84zk683p89gy7zi1gyj"))))
393 (properties `((upstream-name . "ChIPpeakAnno")))
394 (build-system r-build-system)
395 (propagated-inputs
396 `(("r-biocgenerics" ,r-biocgenerics)
397 ("r-biostrings" ,r-biostrings)
398 ("r-delayedarray" ,r-delayedarray)
399 ("r-go-db" ,r-go-db)
400 ("r-biomart" ,r-biomart)
401 ("r-bsgenome" ,r-bsgenome)
402 ("r-genomicfeatures" ,r-genomicfeatures)
403 ("r-genomicranges" ,r-genomicranges)
404 ("r-genomeinfodb" ,r-genomeinfodb)
405 ("r-iranges" ,r-iranges)
406 ("r-matrixstats" ,r-matrixstats)
407 ("r-annotationdbi" ,r-annotationdbi)
408 ("r-limma" ,r-limma)
409 ("r-multtest" ,r-multtest)
410 ("r-rbgl" ,r-rbgl)
411 ("r-graph" ,r-graph)
412 ("r-biocinstaller" ,r-biocinstaller)
413 ("r-regioner" ,r-regioner)
414 ("r-dbi" ,r-dbi)
415 ("r-ensembldb" ,r-ensembldb)
416 ("r-biobase" ,r-biobase)
417 ("r-s4vectors" ,r-s4vectors)
418 ("r-seqinr" ,r-seqinr)
419 ("r-idr" ,r-idr)
420 ("r-genomicalignments" ,r-genomicalignments)
421 ("r-summarizedexperiment" ,r-summarizedexperiment)
422 ("r-rsamtools" ,r-rsamtools)
423 ("r-venndiagram" ,r-venndiagram)))
424 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
425 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
426 (description
427 "The package includes functions to retrieve the sequences around the peak,
428 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
429 custom features such as most conserved elements and other transcription factor
430 binding sites supplied by users. Starting 2.0.5, new functions have been added
431 for finding the peaks with bi-directional promoters with summary statistics
432 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
433 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
434 enrichedGO (addGeneIDs).")
435 (license license:gpl2+)))
436
437 (define-public r-marray
438 (package
439 (name "r-marray")
440 (version "1.58.0")
441 (source (origin
442 (method url-fetch)
443 (uri (bioconductor-uri "marray" version))
444 (sha256
445 (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
446 (build-system r-build-system)
447 (propagated-inputs
448 `(("r-limma" ,r-limma)))
449 (home-page "http://bioconductor.org/packages/marray")
450 (synopsis "Exploratory analysis for two-color spotted microarray data")
451 (description "This package contains class definitions for two-color spotted
452 microarray data. It also includes fuctions for data input, diagnostic plots,
453 normalization and quality checking.")
454 (license license:lgpl2.0+)))
455
456 (define-public r-cghbase
457 (package
458 (name "r-cghbase")
459 (version "1.40.0")
460 (source (origin
461 (method url-fetch)
462 (uri (bioconductor-uri "CGHbase" version))
463 (sha256
464 (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
465 (properties `((upstream-name . "CGHbase")))
466 (build-system r-build-system)
467 (propagated-inputs
468 `(("r-biobase" ,r-biobase)
469 ("r-marray" ,r-marray)))
470 (home-page "http://bioconductor.org/packages/CGHbase")
471 (synopsis "Base functions and classes for arrayCGH data analysis")
472 (description "This package contains functions and classes that are needed by
473 the @code{arrayCGH} packages.")
474 (license license:gpl2+)))
475
476 (define-public r-cghcall
477 (package
478 (name "r-cghcall")
479 (version "2.42.0")
480 (source (origin
481 (method url-fetch)
482 (uri (bioconductor-uri "CGHcall" version))
483 (sha256
484 (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
485 (properties `((upstream-name . "CGHcall")))
486 (build-system r-build-system)
487 (propagated-inputs
488 `(("r-biobase" ,r-biobase)
489 ("r-cghbase" ,r-cghbase)
490 ("r-impute" ,r-impute)
491 ("r-dnacopy" ,r-dnacopy)
492 ("r-snowfall" ,r-snowfall)))
493 (home-page "http://bioconductor.org/packages/CGHcall")
494 (synopsis "Base functions and classes for arrayCGH data analysis")
495 (description "This package contains functions and classes that are needed by
496 @code{arrayCGH} packages.")
497 (license license:gpl2+)))
498
499 (define-public r-qdnaseq
500 (package
501 (name "r-qdnaseq")
502 (version "1.16.0")
503 (source (origin
504 (method url-fetch)
505 (uri (bioconductor-uri "QDNAseq" version))
506 (sha256
507 (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
508 (properties `((upstream-name . "QDNAseq")))
509 (build-system r-build-system)
510 (propagated-inputs
511 `(("r-biobase" ,r-biobase)
512 ("r-biocparallel" ,r-biocparallel)
513 ("r-cghbase" ,r-cghbase)
514 ("r-cghcall" ,r-cghcall)
515 ("r-dnacopy" ,r-dnacopy)
516 ("r-genomicranges" ,r-genomicranges)
517 ("r-iranges" ,r-iranges)
518 ("r-matrixstats" ,r-matrixstats)
519 ("r-r-utils" ,r-r-utils)
520 ("r-rsamtools" ,r-rsamtools)))
521 (home-page "http://bioconductor.org/packages/QDNAseq")
522 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
523 (description "The genome is divided into non-overlapping fixed-sized bins,
524 number of sequence reads in each counted, adjusted with a simultaneous
525 two-dimensional loess correction for sequence mappability and GC content, and
526 filtered to remove spurious regions in the genome. Downstream steps of
527 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
528 respectively.")
529 (license license:gpl2+)))
530
531 (define-public r-bayseq
532 (package
533 (name "r-bayseq")
534 (version "2.14.0")
535 (source
536 (origin
537 (method url-fetch)
538 (uri (bioconductor-uri "baySeq" version))
539 (sha256
540 (base32
541 "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
542 (properties `((upstream-name . "baySeq")))
543 (build-system r-build-system)
544 (propagated-inputs
545 `(("r-abind" ,r-abind)
546 ("r-edger" ,r-edger)
547 ("r-genomicranges" ,r-genomicranges)))
548 (home-page "https://bioconductor.org/packages/baySeq/")
549 (synopsis "Bayesian analysis of differential expression patterns in count data")
550 (description
551 "This package identifies differential expression in high-throughput count
552 data, such as that derived from next-generation sequencing machines,
553 calculating estimated posterior likelihoods of differential expression (or
554 more complex hypotheses) via empirical Bayesian methods.")
555 (license license:gpl3)))
556
557 (define-public r-chipcomp
558 (package
559 (name "r-chipcomp")
560 (version "1.10.0")
561 (source
562 (origin
563 (method url-fetch)
564 (uri (bioconductor-uri "ChIPComp" version))
565 (sha256
566 (base32
567 "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
568 (properties `((upstream-name . "ChIPComp")))
569 (build-system r-build-system)
570 (propagated-inputs
571 `(("r-biocgenerics" ,r-biocgenerics)
572 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
573 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
574 ("r-genomeinfodb" ,r-genomeinfodb)
575 ("r-genomicranges" ,r-genomicranges)
576 ("r-iranges" ,r-iranges)
577 ("r-limma" ,r-limma)
578 ("r-rsamtools" ,r-rsamtools)
579 ("r-rtracklayer" ,r-rtracklayer)
580 ("r-s4vectors" ,r-s4vectors)))
581 (home-page "https://bioconductor.org/packages/ChIPComp")
582 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
583 (description
584 "ChIPComp implements a statistical method for quantitative comparison of
585 multiple ChIP-seq datasets. It detects differentially bound sharp binding
586 sites across multiple conditions considering matching control in ChIP-seq
587 datasets.")
588 ;; Any version of the GPL.
589 (license license:gpl3+)))
590
591 (define-public r-riboprofiling
592 (package
593 (name "r-riboprofiling")
594 (version "1.10.0")
595 (source
596 (origin
597 (method url-fetch)
598 (uri (bioconductor-uri "RiboProfiling" version))
599 (sha256
600 (base32
601 "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
602 (properties `((upstream-name . "RiboProfiling")))
603 (build-system r-build-system)
604 (propagated-inputs
605 `(("r-biocgenerics" ,r-biocgenerics)
606 ("r-biostrings" ,r-biostrings)
607 ("r-data-table" ,r-data-table)
608 ("r-genomeinfodb" ,r-genomeinfodb)
609 ("r-genomicalignments" ,r-genomicalignments)
610 ("r-genomicfeatures" ,r-genomicfeatures)
611 ("r-genomicranges" ,r-genomicranges)
612 ("r-ggbio" ,r-ggbio)
613 ("r-ggplot2" ,r-ggplot2)
614 ("r-iranges" ,r-iranges)
615 ("r-plyr" ,r-plyr)
616 ("r-reshape2" ,r-reshape2)
617 ("r-rsamtools" ,r-rsamtools)
618 ("r-rtracklayer" ,r-rtracklayer)
619 ("r-s4vectors" ,r-s4vectors)
620 ("r-sqldf" ,r-sqldf)))
621 (home-page "https://bioconductor.org/packages/RiboProfiling/")
622 (synopsis "Ribosome profiling data analysis")
623 (description "Starting with a BAM file, this package provides the
624 necessary functions for quality assessment, read start position recalibration,
625 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
626 of count data: pairs, log fold-change, codon frequency and coverage
627 assessment, principal component analysis on codon coverage.")
628 (license license:gpl3)))
629
630 (define-public r-riboseqr
631 (package
632 (name "r-riboseqr")
633 (version "1.14.0")
634 (source
635 (origin
636 (method url-fetch)
637 (uri (bioconductor-uri "riboSeqR" version))
638 (sha256
639 (base32
640 "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
641 (properties `((upstream-name . "riboSeqR")))
642 (build-system r-build-system)
643 (propagated-inputs
644 `(("r-abind" ,r-abind)
645 ("r-bayseq" ,r-bayseq)
646 ("r-genomeinfodb" ,r-genomeinfodb)
647 ("r-genomicranges" ,r-genomicranges)
648 ("r-iranges" ,r-iranges)
649 ("r-rsamtools" ,r-rsamtools)
650 ("r-seqlogo" ,r-seqlogo)))
651 (home-page "https://bioconductor.org/packages/riboSeqR/")
652 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
653 (description
654 "This package provides plotting functions, frameshift detection and
655 parsing of genetic sequencing data from ribosome profiling experiments.")
656 (license license:gpl3)))
657
658 (define-public r-interactionset
659 (package
660 (name "r-interactionset")
661 (version "1.8.0")
662 (source
663 (origin
664 (method url-fetch)
665 (uri (bioconductor-uri "InteractionSet" version))
666 (sha256
667 (base32
668 "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
669 (properties
670 `((upstream-name . "InteractionSet")))
671 (build-system r-build-system)
672 (propagated-inputs
673 `(("r-biocgenerics" ,r-biocgenerics)
674 ("r-genomeinfodb" ,r-genomeinfodb)
675 ("r-genomicranges" ,r-genomicranges)
676 ("r-iranges" ,r-iranges)
677 ("r-matrix" ,r-matrix)
678 ("r-rcpp" ,r-rcpp)
679 ("r-s4vectors" ,r-s4vectors)
680 ("r-summarizedexperiment" ,r-summarizedexperiment)))
681 (home-page "https://bioconductor.org/packages/InteractionSet")
682 (synopsis "Base classes for storing genomic interaction data")
683 (description
684 "This packages provides the @code{GInteractions},
685 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
686 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
687 experiments.")
688 (license license:gpl3)))
689
690 (define-public r-genomicinteractions
691 (package
692 (name "r-genomicinteractions")
693 (version "1.14.0")
694 (source
695 (origin
696 (method url-fetch)
697 (uri (bioconductor-uri "GenomicInteractions" version))
698 (sha256
699 (base32
700 "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
701 (properties
702 `((upstream-name . "GenomicInteractions")))
703 (build-system r-build-system)
704 (propagated-inputs
705 `(("r-biobase" ,r-biobase)
706 ("r-biocgenerics" ,r-biocgenerics)
707 ("r-data-table" ,r-data-table)
708 ("r-dplyr" ,r-dplyr)
709 ("r-genomeinfodb" ,r-genomeinfodb)
710 ("r-genomicranges" ,r-genomicranges)
711 ("r-ggplot2" ,r-ggplot2)
712 ("r-gridextra" ,r-gridextra)
713 ("r-gviz" ,r-gviz)
714 ("r-igraph" ,r-igraph)
715 ("r-interactionset" ,r-interactionset)
716 ("r-iranges" ,r-iranges)
717 ("r-rsamtools" ,r-rsamtools)
718 ("r-rtracklayer" ,r-rtracklayer)
719 ("r-s4vectors" ,r-s4vectors)
720 ("r-stringr" ,r-stringr)))
721 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
722 (synopsis "R package for handling genomic interaction data")
723 (description
724 "This R package provides tools for handling genomic interaction data,
725 such as ChIA-PET/Hi-C, annotating genomic features with interaction
726 information and producing various plots and statistics.")
727 (license license:gpl3)))
728
729 (define-public r-ctc
730 (package
731 (name "r-ctc")
732 (version "1.54.0")
733 (source
734 (origin
735 (method url-fetch)
736 (uri (bioconductor-uri "ctc" version))
737 (sha256
738 (base32
739 "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9"))))
740 (build-system r-build-system)
741 (propagated-inputs `(("r-amap" ,r-amap)))
742 (home-page "https://bioconductor.org/packages/ctc/")
743 (synopsis "Cluster and tree conversion")
744 (description
745 "This package provides tools for exporting and importing classification
746 trees and clusters to other programs.")
747 (license license:gpl2)))
748
749 (define-public r-goseq
750 (package
751 (name "r-goseq")
752 (version "1.32.0")
753 (source
754 (origin
755 (method url-fetch)
756 (uri (bioconductor-uri "goseq" version))
757 (sha256
758 (base32
759 "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l"))))
760 (build-system r-build-system)
761 (propagated-inputs
762 `(("r-annotationdbi" ,r-annotationdbi)
763 ("r-biasedurn" ,r-biasedurn)
764 ("r-biocgenerics" ,r-biocgenerics)
765 ("r-genelendatabase" ,r-genelendatabase)
766 ("r-go-db" ,r-go-db)
767 ("r-mgcv" ,r-mgcv)))
768 (home-page "https://bioconductor.org/packages/goseq/")
769 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
770 (description
771 "This package provides tools to detect Gene Ontology and/or other user
772 defined categories which are over/under represented in RNA-seq data.")
773 (license license:lgpl2.0+)))
774
775 (define-public r-glimma
776 (package
777 (name "r-glimma")
778 (version "1.8.2")
779 (source
780 (origin
781 (method url-fetch)
782 (uri (bioconductor-uri "Glimma" version))
783 (sha256
784 (base32
785 "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s"))))
786 (properties `((upstream-name . "Glimma")))
787 (build-system r-build-system)
788 (propagated-inputs
789 `(("r-edger" ,r-edger)
790 ("r-jsonlite" ,r-jsonlite)
791 ("r-s4vectors" ,r-s4vectors)))
792 (home-page "https://github.com/Shians/Glimma")
793 (synopsis "Interactive HTML graphics")
794 (description
795 "This package generates interactive visualisations for analysis of
796 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
797 HTML page. The interactions are built on top of the popular static
798 representations of analysis results in order to provide additional
799 information.")
800 (license license:lgpl3)))
801
802 (define-public r-rots
803 (package
804 (name "r-rots")
805 (version "1.8.0")
806 (source
807 (origin
808 (method url-fetch)
809 (uri (bioconductor-uri "ROTS" version))
810 (sha256
811 (base32
812 "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3"))))
813 (properties `((upstream-name . "ROTS")))
814 (build-system r-build-system)
815 (propagated-inputs
816 `(("r-biobase" ,r-biobase)
817 ("r-rcpp" ,r-rcpp)))
818 (home-page "https://bioconductor.org/packages/ROTS/")
819 (synopsis "Reproducibility-Optimized Test Statistic")
820 (description
821 "This package provides tools for calculating the
822 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
823 in omics data.")
824 (license license:gpl2+)))
825
826 (define-public r-inspect
827 (package
828 (name "r-inspect")
829 (version "1.10.0")
830 (source
831 (origin
832 (method url-fetch)
833 (uri (bioconductor-uri "INSPEcT" version))
834 (sha256
835 (base32
836 "1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p"))))
837 (properties `((upstream-name . "INSPEcT")))
838 (build-system r-build-system)
839 (propagated-inputs
840 `(("r-biobase" ,r-biobase)
841 ("r-biocgenerics" ,r-biocgenerics)
842 ("r-biocparallel" ,r-biocparallel)
843 ("r-desolve" ,r-desolve)
844 ("r-genomicalignments" ,r-genomicalignments)
845 ("r-genomicfeatures" ,r-genomicfeatures)
846 ("r-genomicranges" ,r-genomicranges)
847 ("r-iranges" ,r-iranges)
848 ("r-preprocesscore" ,r-preprocesscore)
849 ("r-proc" ,r-proc)
850 ("r-rootsolve" ,r-rootsolve)
851 ("r-rsamtools" ,r-rsamtools)
852 ("r-s4vectors" ,r-s4vectors)))
853 (home-page "https://bioconductor.org/packages/INSPEcT")
854 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
855 (description
856 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
857 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
858 order to evaluate synthesis, processing and degradation rates and assess via
859 modeling the rates that determines changes in mature mRNA levels.")
860 (license license:gpl2)))