1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
6 ;;; This file is part of GNU Guix.
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.
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.
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/>.
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 gcc)
31 #:use-module (gnu packages graph)
32 #:use-module (gnu packages maths)
33 #:use-module (gnu packages statistics)
34 #:use-module (gnu packages web))
36 (define-public r-bsgenome-celegans-ucsc-ce6
38 (name "r-bsgenome-celegans-ucsc-ce6")
42 ;; We cannot use bioconductor-uri here because this tarball is
43 ;; located under "data/annotation/" instead of "bioc/".
44 (uri (string-append "https://www.bioconductor.org/packages/"
45 "release/data/annotation/src/contrib/"
46 "BSgenome.Celegans.UCSC.ce6_"
50 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
52 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
53 (build-system r-build-system)
54 ;; As this package provides little more than a very large data file it
55 ;; doesn't make sense to build substitutes.
56 (arguments `(#:substitutable? #f))
58 `(("r-bsgenome" ,r-bsgenome)))
60 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
61 (synopsis "Full genome sequences for Worm")
63 "This package provides full genome sequences for Caenorhabditis
64 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
66 (license license:artistic2.0)))
68 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
70 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
74 ;; We cannot use bioconductor-uri here because this tarball is
75 ;; located under "data/annotation/" instead of "bioc/".
76 (uri (string-append "https://www.bioconductor.org/packages/"
77 "release/data/annotation/src/contrib/"
78 "BSgenome.Dmelanogaster.UCSC.dm6_"
82 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
84 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
85 (build-system r-build-system)
86 ;; As this package provides little more than a very large data file it
87 ;; doesn't make sense to build substitutes.
88 (arguments `(#:substitutable? #f))
90 `(("r-bsgenome" ,r-bsgenome)))
92 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
93 (synopsis "Full genome sequences for Fly")
95 "This package provides full genome sequences for Drosophila
96 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
98 (license license:artistic2.0)))
100 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
102 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
106 ;; We cannot use bioconductor-uri here because this tarball is
107 ;; located under "data/annotation/" instead of "bioc/".
108 (uri (string-append "http://www.bioconductor.org/packages/"
109 "release/data/annotation/src/contrib/"
110 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
114 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
116 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
117 (build-system r-build-system)
119 `(("r-bsgenome" ,r-bsgenome)
120 ("r-bsgenome-dmelanogaster-ucsc-dm3"
121 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
122 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
123 (synopsis "Full masked genome sequences for Fly")
125 "This package provides full masked genome sequences for Drosophila
126 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
127 Biostrings objects. The sequences are the same as in
128 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
129 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
130 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
131 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
132 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
133 (license license:artistic2.0)))
135 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
137 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
141 ;; We cannot use bioconductor-uri here because this tarball is
142 ;; located under "data/annotation/" instead of "bioc/".
143 (uri (string-append "https://www.bioconductor.org/packages/"
144 "release/data/annotation/src/contrib/"
145 "BSgenome.Hsapiens.1000genomes.hs37d5_"
149 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
151 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
152 (build-system r-build-system)
153 ;; As this package provides little more than a very large data file it
154 ;; doesn't make sense to build substitutes.
155 (arguments `(#:substitutable? #f))
157 `(("r-bsgenome" ,r-bsgenome)))
159 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
160 (synopsis "Full genome sequences for Homo sapiens")
162 "This package provides full genome sequences for Homo sapiens from
163 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
164 (license license:artistic2.0)))
166 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
168 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
172 ;; We cannot use bioconductor-uri here because this tarball is
173 ;; located under "data/annotation/" instead of "bioc/".
174 (uri (string-append "http://www.bioconductor.org/packages/"
175 "release/data/annotation/src/contrib/"
176 "BSgenome.Hsapiens.UCSC.hg19.masked_"
180 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
182 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
183 (build-system r-build-system)
185 `(("r-bsgenome" ,r-bsgenome)
186 ("r-bsgenome-hsapiens-ucsc-hg19"
187 ,r-bsgenome-hsapiens-ucsc-hg19)))
188 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
189 (synopsis "Full masked genome sequences for Homo sapiens")
191 "This package provides full genome sequences for Homo sapiens (Human) as
192 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
193 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
194 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
195 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
196 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
197 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
199 (license license:artistic2.0)))
201 (define-public r-bsgenome-mmusculus-ucsc-mm9
203 (name "r-bsgenome-mmusculus-ucsc-mm9")
207 ;; We cannot use bioconductor-uri here because this tarball is
208 ;; located under "data/annotation/" instead of "bioc/".
209 (uri (string-append "https://www.bioconductor.org/packages/"
210 "release/data/annotation/src/contrib/"
211 "BSgenome.Mmusculus.UCSC.mm9_"
215 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
217 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
218 (build-system r-build-system)
219 ;; As this package provides little more than a very large data file it
220 ;; doesn't make sense to build substitutes.
221 (arguments `(#:substitutable? #f))
223 `(("r-bsgenome" ,r-bsgenome)))
225 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
226 (synopsis "Full genome sequences for Mouse")
228 "This package provides full genome sequences for Mus musculus (Mouse) as
229 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
230 (license license:artistic2.0)))
232 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
234 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
238 ;; We cannot use bioconductor-uri here because this tarball is
239 ;; located under "data/annotation/" instead of "bioc/".
240 (uri (string-append "http://www.bioconductor.org/packages/"
241 "release/data/annotation/src/contrib/"
242 "BSgenome.Mmusculus.UCSC.mm9.masked_"
246 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
248 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
249 (build-system r-build-system)
251 `(("r-bsgenome" ,r-bsgenome)
252 ("r-bsgenome-mmusculus-ucsc-mm9"
253 ,r-bsgenome-mmusculus-ucsc-mm9)))
254 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
255 (synopsis "Full masked genome sequences for Mouse")
257 "This package provides full genome sequences for Mus musculus (Mouse) as
258 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
259 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
260 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
261 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
262 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
263 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
265 (license license:artistic2.0)))
267 (define-public r-bsgenome-mmusculus-ucsc-mm10
269 (name "r-bsgenome-mmusculus-ucsc-mm10")
273 ;; We cannot use bioconductor-uri here because this tarball is
274 ;; located under "data/annotation/" instead of "bioc/".
275 (uri (string-append "https://www.bioconductor.org/packages/"
276 "release/data/annotation/src/contrib/"
277 "BSgenome.Mmusculus.UCSC.mm10_"
281 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
283 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
284 (build-system r-build-system)
285 ;; As this package provides little more than a very large data file it
286 ;; doesn't make sense to build substitutes.
287 (arguments `(#:substitutable? #f))
289 `(("r-bsgenome" ,r-bsgenome)))
291 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
292 (synopsis "Full genome sequences for Mouse")
294 "This package provides full genome sequences for Mus
295 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
296 in Biostrings objects.")
297 (license license:artistic2.0)))
299 (define-public r-org-dr-eg-db
301 (name "r-org-dr-eg-db")
305 ;; We cannot use bioconductor-uri here because this tarball is
306 ;; located under "data/annotation/" instead of "bioc/".
307 (uri (string-append "https://www.bioconductor.org/packages/"
308 "release/data/annotation/src/contrib/"
309 "org.Dr.eg.db_" version ".tar.gz"))
312 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
314 `((upstream-name . "org.Dr.eg.db")))
315 (build-system r-build-system)
317 `(("r-annotationdbi" ,r-annotationdbi)))
318 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
319 (synopsis "Annotation for Zebrafish")
321 "This package provides genome wide annotations for Zebrafish, primarily
322 based on mapping using Entrez Gene identifiers.")
323 (license license:artistic2.0)))
325 (define-public r-bsgenome-hsapiens-ucsc-hg19
327 (name "r-bsgenome-hsapiens-ucsc-hg19")
331 ;; We cannot use bioconductor-uri here because this tarball is
332 ;; located under "data/annotation/" instead of "bioc/".
333 (uri (string-append "https://www.bioconductor.org/packages/"
334 "release/data/annotation/src/contrib/"
335 "BSgenome.Hsapiens.UCSC.hg19_"
339 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
341 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
342 (build-system r-build-system)
343 ;; As this package provides little more than a very large data file it
344 ;; doesn't make sense to build substitutes.
345 (arguments `(#:substitutable? #f))
347 `(("r-bsgenome" ,r-bsgenome)))
349 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
350 (synopsis "Full genome sequences for Homo sapiens")
352 "This package provides full genome sequences for Homo sapiens as provided
353 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
354 (license license:artistic2.0)))
356 (define-public r-genelendatabase
358 (name "r-genelendatabase")
363 ;; We cannot use bioconductor-uri here because this tarball is
364 ;; located under "data/experiment/" instead of "bioc/".
365 (uri (string-append "https://bioconductor.org/packages/"
366 "release/data/experiment/src/contrib"
367 "/geneLenDataBase_" version ".tar.gz"))
370 "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5"))))
372 `((upstream-name . "geneLenDataBase")))
373 (build-system r-build-system)
375 `(("r-rtracklayer" ,r-rtracklayer)
376 ("r-genomicfeatures" ,r-genomicfeatures)))
377 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
378 (synopsis "Lengths of mRNA transcripts for a number of genomes")
380 "This package provides the lengths of mRNA transcripts for a number of
381 genomes and gene ID formats, largely based on the UCSC table browser.")
382 (license license:lgpl2.0+)))
384 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
386 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
390 ;; We cannot use bioconductor-uri here because this tarball is
391 ;; located under "data/annotation/" instead of "bioc/".
392 (uri (string-append "https://bioconductor.org/packages/"
393 "release/data/annotation/src/contrib"
394 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
398 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
400 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
401 (build-system r-build-system)
402 ;; As this package provides little more than a very large data file it
403 ;; doesn't make sense to build substitutes.
404 (arguments `(#:substitutable? #f))
406 `(("r-genomicfeatures" ,r-genomicfeatures)))
408 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
409 (synopsis "Annotation package for human genome in TxDb format")
411 "This package provides an annotation database of Homo sapiens genome
412 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
413 track. The database is exposed as a @code{TxDb} object.")
414 (license license:artistic2.0)))
416 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
418 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
422 ;; We cannot use bioconductor-uri here because this tarball is
423 ;; located under "data/annotation/" instead of "bioc/".
424 (uri (string-append "https://bioconductor.org/packages/"
425 "release/data/annotation/src/contrib"
426 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
430 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
432 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
433 (build-system r-build-system)
435 `(("r-genomicfeatures" ,r-genomicfeatures)
436 ("r-annotationdbi" ,r-annotationdbi)))
438 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
439 (synopsis "Annotation package for mouse genome in TxDb format")
441 "This package provides an annotation database of Mouse genome data. It
442 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
443 database is exposed as a @code{TxDb} object.")
444 (license license:artistic2.0)))
447 (define-public r-biocgenerics
449 (name "r-biocgenerics")
453 (uri (bioconductor-uri "BiocGenerics" version))
456 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
458 `((upstream-name . "BiocGenerics")))
459 (build-system r-build-system)
460 (home-page "https://bioconductor.org/packages/BiocGenerics")
461 (synopsis "S4 generic functions for Bioconductor")
463 "This package provides S4 generic functions needed by many Bioconductor
465 (license license:artistic2.0)))
467 (define-public r-annotate
474 (uri (bioconductor-uri "annotate" version))
477 "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
478 (build-system r-build-system)
480 `(("r-annotationdbi" ,r-annotationdbi)
481 ("r-biobase" ,r-biobase)
482 ("r-biocgenerics" ,r-biocgenerics)
486 ("r-xtable" ,r-xtable)))
488 "https://bioconductor.org/packages/annotate")
489 (synopsis "Annotation for microarrays")
490 (description "This package provides R environments for the annotation of
492 (license license:artistic2.0)))
494 (define-public r-hpar
501 (uri (bioconductor-uri "hpar" version))
504 "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
505 (build-system r-build-system)
506 (home-page "https://bioconductor.org/packages/hpar/")
507 (synopsis "Human Protein Atlas in R")
508 (description "This package provides a simple interface to and data from
509 the Human Protein Atlas project.")
510 (license license:artistic2.0)))
512 (define-public r-regioner
519 (uri (bioconductor-uri "regioneR" version))
522 "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
523 (properties `((upstream-name . "regioneR")))
524 (build-system r-build-system)
526 `(("r-biostrings" ,r-biostrings)
527 ("r-bsgenome" ,r-bsgenome)
528 ("r-genomeinfodb" ,r-genomeinfodb)
529 ("r-genomicranges" ,r-genomicranges)
530 ("r-iranges" ,r-iranges)
531 ("r-memoise" ,r-memoise)
532 ("r-rtracklayer" ,r-rtracklayer)
533 ("r-s4vectors" ,r-s4vectors)))
534 (home-page "https://bioconductor.org/packages/regioneR/")
535 (synopsis "Association analysis of genomic regions")
536 (description "This package offers a statistical framework based on
537 customizable permutation tests to assess the association between genomic
538 region sets and other genomic features.")
539 (license license:artistic2.0)))
541 (define-public r-geneplotter
543 (name "r-geneplotter")
548 (uri (bioconductor-uri "geneplotter" version))
551 "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
552 (build-system r-build-system)
554 `(("r-annotate" ,r-annotate)
555 ("r-annotationdbi" ,r-annotationdbi)
556 ("r-biobase" ,r-biobase)
557 ("r-biocgenerics" ,r-biocgenerics)
558 ("r-lattice" ,r-lattice)
559 ("r-rcolorbrewer" ,r-rcolorbrewer)))
560 (home-page "https://bioconductor.org/packages/geneplotter")
561 (synopsis "Graphics functions for genomic data")
563 "This package provides functions for plotting genomic data.")
564 (license license:artistic2.0)))
566 (define-public r-diffbind
573 (uri (bioconductor-uri "DiffBind" version))
576 "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
577 (properties `((upstream-name . "DiffBind")))
578 (build-system r-build-system)
583 ("r-biocparallel" ,r-biocparallel)
584 ("r-deseq2" ,r-deseq2)
587 ("r-genomicalignments" ,r-genomicalignments)
588 ("r-genomicranges" ,r-genomicranges)
589 ("r-ggplot2" ,r-ggplot2)
590 ("r-ggrepel" ,r-ggrepel)
591 ("r-gplots" ,r-gplots)
592 ("r-iranges" ,r-iranges)
593 ("r-lattice" ,r-lattice)
595 ("r-locfit" ,r-locfit)
596 ("r-rcolorbrewer" , r-rcolorbrewer)
598 ("r-rsamtools" ,r-rsamtools)
599 ("r-s4vectors" ,r-s4vectors)
600 ("r-summarizedexperiment" ,r-summarizedexperiment)
601 ("r-systempiper" ,r-systempiper)
602 ("r-zlibbioc" ,r-zlibbioc)))
603 (home-page "http://bioconductor.org/packages/DiffBind")
604 (synopsis "Differential binding analysis of ChIP-Seq peak data")
606 "This package computes differentially bound sites from multiple
607 ChIP-seq experiments using affinity (quantitative) data. Also enables
608 occupancy (overlap) analysis and plotting functions.")
609 (license license:artistic2.0)))
611 (define-public r-ripseeker
618 (uri (bioconductor-uri "RIPSeeker" version))
621 "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
622 (properties `((upstream-name . "RIPSeeker")))
623 (build-system r-build-system)
625 `(("r-s4vectors" ,r-s4vectors)
626 ("r-iranges" ,r-iranges)
627 ("r-genomicranges" ,r-genomicranges)
628 ("r-summarizedexperiment" ,r-summarizedexperiment)
629 ("r-rsamtools" ,r-rsamtools)
630 ("r-genomicalignments" ,r-genomicalignments)
631 ("r-rtracklayer" ,r-rtracklayer)))
632 (home-page "http://bioconductor.org/packages/RIPSeeker")
634 "Identifying protein-associated transcripts from RIP-seq experiments")
636 "This package infers and discriminates RIP peaks from RIP-seq alignments
637 using two-state HMM with negative binomial emission probability. While
638 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
639 a suite of bioinformatics tools integrated within this self-contained software
640 package comprehensively addressing issues ranging from post-alignments
641 processing to visualization and annotation.")
642 (license license:gpl2)))
644 (define-public r-multtest
651 (uri (bioconductor-uri "multtest" version))
654 "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
655 (build-system r-build-system)
657 `(("r-survival" ,r-survival)
658 ("r-biocgenerics" ,r-biocgenerics)
659 ("r-biobase" ,r-biobase)
661 (home-page "http://bioconductor.org/packages/multtest")
662 (synopsis "Resampling-based multiple hypothesis testing")
664 "This package can do non-parametric bootstrap and permutation
665 resampling-based multiple testing procedures (including empirical Bayes
666 methods) for controlling the family-wise error rate (FWER), generalized
667 family-wise error rate (gFWER), tail probability of the proportion of
668 false positives (TPPFP), and false discovery rate (FDR). Several choices
669 of bootstrap-based null distribution are implemented (centered, centered
670 and scaled, quantile-transformed). Single-step and step-wise methods are
671 available. Tests based on a variety of T- and F-statistics (including
672 T-statistics based on regression parameters from linear and survival models
673 as well as those based on correlation parameters) are included. When probing
674 hypotheses with T-statistics, users may also select a potentially faster null
675 distribution which is multivariate normal with mean zero and variance
676 covariance matrix derived from the vector influence function. Results are
677 reported in terms of adjusted P-values, confidence regions and test statistic
678 cutoffs. The procedures are directly applicable to identifying differentially
679 expressed genes in DNA microarray experiments.")
680 (license license:lgpl3)))
682 (define-public r-graph
688 (uri (bioconductor-uri "graph" version))
691 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
692 (build-system r-build-system)
694 `(("r-biocgenerics" ,r-biocgenerics)))
695 (home-page "https://bioconductor.org/packages/graph")
696 (synopsis "Handle graph data structures in R")
698 "This package implements some simple graph handling capabilities for R.")
699 (license license:artistic2.0)))
701 (define-public r-codedepends
703 (name "r-codedepends")
708 (uri (cran-uri "CodeDepends" version))
711 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
712 (properties `((upstream-name . "CodeDepends")))
713 (build-system r-build-system)
715 `(("r-codetools" ,r-codetools)
718 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
719 (synopsis "Analysis of R code for reproducible research and code comprehension")
721 "This package provides tools for analyzing R expressions or blocks of
722 code and determining the dependencies between them. It focuses on R scripts,
723 but can be used on the bodies of functions. There are many facilities
724 including the ability to summarize or get a high-level view of code,
725 determining dependencies between variables, code improvement suggestions.")
726 ;; Any version of the GPL
727 (license (list license:gpl2+ license:gpl3+))))
729 (define-public r-chippeakanno
731 (name "r-chippeakanno")
736 (uri (bioconductor-uri "ChIPpeakAnno" version))
739 "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
740 (properties `((upstream-name . "ChIPpeakAnno")))
741 (build-system r-build-system)
743 `(("r-biocgenerics" ,r-biocgenerics)
744 ("r-biocmanager" ,r-biocmanager)
745 ("r-biostrings" ,r-biostrings)
746 ("r-delayedarray" ,r-delayedarray)
748 ("r-biomart" ,r-biomart)
749 ("r-bsgenome" ,r-bsgenome)
750 ("r-genomicfeatures" ,r-genomicfeatures)
751 ("r-genomicranges" ,r-genomicranges)
752 ("r-genomeinfodb" ,r-genomeinfodb)
753 ("r-iranges" ,r-iranges)
754 ("r-matrixstats" ,r-matrixstats)
755 ("r-annotationdbi" ,r-annotationdbi)
757 ("r-multtest" ,r-multtest)
760 ("r-regioner" ,r-regioner)
762 ("r-ensembldb" ,r-ensembldb)
763 ("r-biobase" ,r-biobase)
764 ("r-s4vectors" ,r-s4vectors)
765 ("r-seqinr" ,r-seqinr)
767 ("r-genomicalignments" ,r-genomicalignments)
768 ("r-summarizedexperiment" ,r-summarizedexperiment)
769 ("r-rsamtools" ,r-rsamtools)
770 ("r-venndiagram" ,r-venndiagram)))
771 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
772 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
774 "The package includes functions to retrieve the sequences around the peak,
775 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
776 custom features such as most conserved elements and other transcription factor
777 binding sites supplied by users. Starting 2.0.5, new functions have been added
778 for finding the peaks with bi-directional promoters with summary statistics
779 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
780 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
781 enrichedGO (addGeneIDs).")
782 (license license:gpl2+)))
784 (define-public r-marray
790 (uri (bioconductor-uri "marray" version))
792 (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
793 (build-system r-build-system)
795 `(("r-limma" ,r-limma)))
796 (home-page "http://bioconductor.org/packages/marray")
797 (synopsis "Exploratory analysis for two-color spotted microarray data")
798 (description "This package contains class definitions for two-color spotted
799 microarray data. It also includes fuctions for data input, diagnostic plots,
800 normalization and quality checking.")
801 (license license:lgpl2.0+)))
803 (define-public r-cghbase
809 (uri (bioconductor-uri "CGHbase" version))
811 (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
812 (properties `((upstream-name . "CGHbase")))
813 (build-system r-build-system)
815 `(("r-biobase" ,r-biobase)
816 ("r-marray" ,r-marray)))
817 (home-page "http://bioconductor.org/packages/CGHbase")
818 (synopsis "Base functions and classes for arrayCGH data analysis")
819 (description "This package contains functions and classes that are needed by
820 the @code{arrayCGH} packages.")
821 (license license:gpl2+)))
823 (define-public r-cghcall
829 (uri (bioconductor-uri "CGHcall" version))
831 (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
832 (properties `((upstream-name . "CGHcall")))
833 (build-system r-build-system)
835 `(("r-biobase" ,r-biobase)
836 ("r-cghbase" ,r-cghbase)
837 ("r-impute" ,r-impute)
838 ("r-dnacopy" ,r-dnacopy)
839 ("r-snowfall" ,r-snowfall)))
840 (home-page "http://bioconductor.org/packages/CGHcall")
841 (synopsis "Base functions and classes for arrayCGH data analysis")
842 (description "This package contains functions and classes that are needed by
843 @code{arrayCGH} packages.")
844 (license license:gpl2+)))
846 (define-public r-qdnaseq
852 (uri (bioconductor-uri "QDNAseq" version))
854 (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
855 (properties `((upstream-name . "QDNAseq")))
856 (build-system r-build-system)
858 `(("r-biobase" ,r-biobase)
859 ("r-biocparallel" ,r-biocparallel)
860 ("r-cghbase" ,r-cghbase)
861 ("r-cghcall" ,r-cghcall)
862 ("r-dnacopy" ,r-dnacopy)
863 ("r-genomicranges" ,r-genomicranges)
864 ("r-iranges" ,r-iranges)
865 ("r-matrixstats" ,r-matrixstats)
866 ("r-r-utils" ,r-r-utils)
867 ("r-rsamtools" ,r-rsamtools)))
868 (home-page "http://bioconductor.org/packages/QDNAseq")
869 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
870 (description "The genome is divided into non-overlapping fixed-sized bins,
871 number of sequence reads in each counted, adjusted with a simultaneous
872 two-dimensional loess correction for sequence mappability and GC content, and
873 filtered to remove spurious regions in the genome. Downstream steps of
874 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
876 (license license:gpl2+)))
878 (define-public r-bayseq
885 (uri (bioconductor-uri "baySeq" version))
888 "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
889 (properties `((upstream-name . "baySeq")))
890 (build-system r-build-system)
892 `(("r-abind" ,r-abind)
894 ("r-genomicranges" ,r-genomicranges)))
895 (home-page "https://bioconductor.org/packages/baySeq/")
896 (synopsis "Bayesian analysis of differential expression patterns in count data")
898 "This package identifies differential expression in high-throughput count
899 data, such as that derived from next-generation sequencing machines,
900 calculating estimated posterior likelihoods of differential expression (or
901 more complex hypotheses) via empirical Bayesian methods.")
902 (license license:gpl3)))
904 (define-public r-chipcomp
911 (uri (bioconductor-uri "ChIPComp" version))
914 "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
915 (properties `((upstream-name . "ChIPComp")))
916 (build-system r-build-system)
918 `(("r-biocgenerics" ,r-biocgenerics)
919 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
920 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
921 ("r-genomeinfodb" ,r-genomeinfodb)
922 ("r-genomicranges" ,r-genomicranges)
923 ("r-iranges" ,r-iranges)
925 ("r-rsamtools" ,r-rsamtools)
926 ("r-rtracklayer" ,r-rtracklayer)
927 ("r-s4vectors" ,r-s4vectors)))
928 (home-page "https://bioconductor.org/packages/ChIPComp")
929 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
931 "ChIPComp implements a statistical method for quantitative comparison of
932 multiple ChIP-seq datasets. It detects differentially bound sharp binding
933 sites across multiple conditions considering matching control in ChIP-seq
935 ;; Any version of the GPL.
936 (license license:gpl3+)))
938 (define-public r-riboprofiling
940 (name "r-riboprofiling")
945 (uri (bioconductor-uri "RiboProfiling" version))
948 "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
949 (properties `((upstream-name . "RiboProfiling")))
950 (build-system r-build-system)
952 `(("r-biocgenerics" ,r-biocgenerics)
953 ("r-biostrings" ,r-biostrings)
954 ("r-data-table" ,r-data-table)
955 ("r-genomeinfodb" ,r-genomeinfodb)
956 ("r-genomicalignments" ,r-genomicalignments)
957 ("r-genomicfeatures" ,r-genomicfeatures)
958 ("r-genomicranges" ,r-genomicranges)
960 ("r-ggplot2" ,r-ggplot2)
961 ("r-iranges" ,r-iranges)
963 ("r-reshape2" ,r-reshape2)
964 ("r-rsamtools" ,r-rsamtools)
965 ("r-rtracklayer" ,r-rtracklayer)
966 ("r-s4vectors" ,r-s4vectors)
967 ("r-sqldf" ,r-sqldf)))
968 (home-page "https://bioconductor.org/packages/RiboProfiling/")
969 (synopsis "Ribosome profiling data analysis")
970 (description "Starting with a BAM file, this package provides the
971 necessary functions for quality assessment, read start position recalibration,
972 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
973 of count data: pairs, log fold-change, codon frequency and coverage
974 assessment, principal component analysis on codon coverage.")
975 (license license:gpl3)))
977 (define-public r-riboseqr
984 (uri (bioconductor-uri "riboSeqR" version))
987 "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
988 (properties `((upstream-name . "riboSeqR")))
989 (build-system r-build-system)
991 `(("r-abind" ,r-abind)
992 ("r-bayseq" ,r-bayseq)
993 ("r-genomeinfodb" ,r-genomeinfodb)
994 ("r-genomicranges" ,r-genomicranges)
995 ("r-iranges" ,r-iranges)
996 ("r-rsamtools" ,r-rsamtools)
997 ("r-seqlogo" ,r-seqlogo)))
998 (home-page "https://bioconductor.org/packages/riboSeqR/")
999 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1001 "This package provides plotting functions, frameshift detection and
1002 parsing of genetic sequencing data from ribosome profiling experiments.")
1003 (license license:gpl3)))
1005 (define-public r-interactionset
1007 (name "r-interactionset")
1012 (uri (bioconductor-uri "InteractionSet" version))
1015 "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
1017 `((upstream-name . "InteractionSet")))
1018 (build-system r-build-system)
1020 `(("r-biocgenerics" ,r-biocgenerics)
1021 ("r-genomeinfodb" ,r-genomeinfodb)
1022 ("r-genomicranges" ,r-genomicranges)
1023 ("r-iranges" ,r-iranges)
1024 ("r-matrix" ,r-matrix)
1026 ("r-s4vectors" ,r-s4vectors)
1027 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1028 (home-page "https://bioconductor.org/packages/InteractionSet")
1029 (synopsis "Base classes for storing genomic interaction data")
1031 "This packages provides the @code{GInteractions},
1032 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1033 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1035 (license license:gpl3)))
1037 (define-public r-genomicinteractions
1039 (name "r-genomicinteractions")
1044 (uri (bioconductor-uri "GenomicInteractions" version))
1047 "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
1049 `((upstream-name . "GenomicInteractions")))
1050 (build-system r-build-system)
1052 `(("r-biobase" ,r-biobase)
1053 ("r-biocgenerics" ,r-biocgenerics)
1054 ("r-data-table" ,r-data-table)
1055 ("r-dplyr" ,r-dplyr)
1056 ("r-genomeinfodb" ,r-genomeinfodb)
1057 ("r-genomicranges" ,r-genomicranges)
1058 ("r-ggplot2" ,r-ggplot2)
1059 ("r-gridextra" ,r-gridextra)
1061 ("r-igraph" ,r-igraph)
1062 ("r-interactionset" ,r-interactionset)
1063 ("r-iranges" ,r-iranges)
1064 ("r-rsamtools" ,r-rsamtools)
1065 ("r-rtracklayer" ,r-rtracklayer)
1066 ("r-s4vectors" ,r-s4vectors)
1067 ("r-stringr" ,r-stringr)))
1068 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1069 (synopsis "R package for handling genomic interaction data")
1071 "This R package provides tools for handling genomic interaction data,
1072 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1073 information and producing various plots and statistics.")
1074 (license license:gpl3)))
1076 (define-public r-ctc
1083 (uri (bioconductor-uri "ctc" version))
1086 "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
1087 (build-system r-build-system)
1088 (propagated-inputs `(("r-amap" ,r-amap)))
1089 (home-page "https://bioconductor.org/packages/ctc/")
1090 (synopsis "Cluster and tree conversion")
1092 "This package provides tools for exporting and importing classification
1093 trees and clusters to other programs.")
1094 (license license:gpl2)))
1096 (define-public r-goseq
1103 (uri (bioconductor-uri "goseq" version))
1106 "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
1107 (build-system r-build-system)
1109 `(("r-annotationdbi" ,r-annotationdbi)
1110 ("r-biasedurn" ,r-biasedurn)
1111 ("r-biocgenerics" ,r-biocgenerics)
1112 ("r-genelendatabase" ,r-genelendatabase)
1113 ("r-go-db" ,r-go-db)
1114 ("r-mgcv" ,r-mgcv)))
1115 (home-page "https://bioconductor.org/packages/goseq/")
1116 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1118 "This package provides tools to detect Gene Ontology and/or other user
1119 defined categories which are over/under represented in RNA-seq data.")
1120 (license license:lgpl2.0+)))
1122 (define-public r-glimma
1129 (uri (bioconductor-uri "Glimma" version))
1132 "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
1133 (properties `((upstream-name . "Glimma")))
1134 (build-system r-build-system)
1136 `(("r-edger" ,r-edger)
1137 ("r-jsonlite" ,r-jsonlite)
1138 ("r-s4vectors" ,r-s4vectors)))
1139 (home-page "https://github.com/Shians/Glimma")
1140 (synopsis "Interactive HTML graphics")
1142 "This package generates interactive visualisations for analysis of
1143 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1144 HTML page. The interactions are built on top of the popular static
1145 representations of analysis results in order to provide additional
1147 (license license:lgpl3)))
1149 (define-public r-rots
1156 (uri (bioconductor-uri "ROTS" version))
1159 "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
1160 (properties `((upstream-name . "ROTS")))
1161 (build-system r-build-system)
1163 `(("r-biobase" ,r-biobase)
1164 ("r-rcpp" ,r-rcpp)))
1165 (home-page "https://bioconductor.org/packages/ROTS/")
1166 (synopsis "Reproducibility-Optimized Test Statistic")
1168 "This package provides tools for calculating the
1169 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1171 (license license:gpl2+)))
1173 (define-public r-plgem
1180 (uri (bioconductor-uri "plgem" version))
1183 "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
1184 (build-system r-build-system)
1186 `(("r-biobase" ,r-biobase)
1187 ("r-mass" ,r-mass)))
1188 (home-page "http://www.genopolis.it")
1189 (synopsis "Detect differential expression in microarray and proteomics datasets")
1191 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1192 model the variance-versus-mean dependence that exists in a variety of
1193 genome-wide datasets, including microarray and proteomics data. The use of
1194 PLGEM has been shown to improve the detection of differentially expressed
1195 genes or proteins in these datasets.")
1196 (license license:gpl2)))
1198 (define-public r-inspect
1205 (uri (bioconductor-uri "INSPEcT" version))
1208 "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
1209 (properties `((upstream-name . "INSPEcT")))
1210 (build-system r-build-system)
1212 `(("r-biobase" ,r-biobase)
1213 ("r-biocgenerics" ,r-biocgenerics)
1214 ("r-biocparallel" ,r-biocparallel)
1215 ("r-deseq2" ,r-deseq2)
1216 ("r-desolve" ,r-desolve)
1217 ("r-genomicalignments" ,r-genomicalignments)
1218 ("r-genomicfeatures" ,r-genomicfeatures)
1219 ("r-genomicranges" ,r-genomicranges)
1220 ("r-iranges" ,r-iranges)
1221 ("r-plgem" ,r-plgem)
1222 ("r-preprocesscore" ,r-preprocesscore)
1224 ("r-rootsolve" ,r-rootsolve)
1225 ("r-rsamtools" ,r-rsamtools)
1226 ("r-s4vectors" ,r-s4vectors)
1227 ("r-shiny" ,r-shiny)
1228 ("r-summarizedexperiment" ,r-summarizedexperiment)
1229 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1230 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1231 (home-page "https://bioconductor.org/packages/INSPEcT")
1232 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1234 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1235 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1236 order to evaluate synthesis, processing and degradation rates and assess via
1237 modeling the rates that determines changes in mature mRNA levels.")
1238 (license license:gpl2)))
1240 (define-public r-dnabarcodes
1242 (name "r-dnabarcodes")
1247 (uri (bioconductor-uri "DNABarcodes" version))
1250 "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
1251 (properties `((upstream-name . "DNABarcodes")))
1252 (build-system r-build-system)
1255 ("r-matrix" ,r-matrix)
1256 ("r-rcpp" ,r-rcpp)))
1257 (home-page "https://bioconductor.org/packages/DNABarcodes")
1258 (synopsis "Create and analyze DNA barcodes")
1260 "This package offers tools to create DNA barcode sets capable of
1261 correcting insertion, deletion, and substitution errors. Existing barcodes
1262 can be analyzed regarding their minimal, maximal and average distances between
1263 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1264 demultiplexed, i.e. assigned to their original reference barcode.")
1265 (license license:gpl2)))
1267 (define-public r-ruvseq
1274 (uri (bioconductor-uri "RUVSeq" version))
1277 "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
1278 (properties `((upstream-name . "RUVSeq")))
1279 (build-system r-build-system)
1281 `(("r-biobase" ,r-biobase)
1282 ("r-edaseq" ,r-edaseq)
1283 ("r-edger" ,r-edger)
1284 ("r-mass" ,r-mass)))
1285 (home-page "https://github.com/drisso/RUVSeq")
1286 (synopsis "Remove unwanted variation from RNA-Seq data")
1288 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1289 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1291 (license license:artistic2.0)))
1293 (define-public r-biocneighbors
1295 (name "r-biocneighbors")
1300 (uri (bioconductor-uri "BiocNeighbors" version))
1303 "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
1304 (properties `((upstream-name . "BiocNeighbors")))
1305 (build-system r-build-system)
1307 `(("r-biocparallel" ,r-biocparallel)
1309 ("r-rcppannoy" ,r-rcppannoy)
1310 ("r-s4vectors" ,r-s4vectors)))
1311 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1312 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1314 "This package implements exact and approximate methods for nearest
1315 neighbor detection, in a framework that allows them to be easily switched
1316 within Bioconductor packages or workflows. The exact algorithm is implemented
1317 using pre-clustering with the k-means algorithm. Functions are also provided
1318 to search for all neighbors within a given distance. Parallelization is
1319 achieved for all methods using the BiocParallel framework.")
1320 (license license:gpl3)))
1322 (define-public r-destiny
1329 (uri (bioconductor-uri "destiny" version))
1332 "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
1333 (build-system r-build-system)
1335 `(("r-biobase" ,r-biobase)
1336 ("r-biocgenerics" ,r-biocgenerics)
1338 ("r-ggthemes" ,r-ggthemes)
1339 ("r-hmisc" ,r-hmisc)
1340 ("r-igraph" ,r-igraph)
1341 ("r-matrix" ,r-matrix)
1342 ("r-proxy" ,r-proxy)
1344 ("r-rcppeigen" ,r-rcppeigen)
1345 ("r-scales" ,r-scales)
1346 ("r-scatterplot3d" ,r-scatterplot3d)
1347 ("r-smoother" ,r-smoother)
1348 ("r-summarizedexperiment" ,r-summarizedexperiment)
1350 (home-page "https://bioconductor.org/packages/destiny/")
1351 (synopsis "Create and plot diffusion maps")
1352 (description "This package provides tools to create and plot diffusion
1354 ;; Any version of the GPL
1355 (license license:gpl3+)))
1357 (define-public r-savr
1364 (uri (bioconductor-uri "savR" version))
1367 "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
1368 (properties `((upstream-name . "savR")))
1369 (build-system r-build-system)
1371 `(("r-ggplot2" ,r-ggplot2)
1372 ("r-gridextra" ,r-gridextra)
1373 ("r-reshape2" ,r-reshape2)
1374 ("r-scales" ,r-scales)
1376 (home-page "https://github.com/bcalder/savR")
1377 (synopsis "Parse and analyze Illumina SAV files")
1379 "This package provides tools to parse Illumina Sequence Analysis
1380 Viewer (SAV) files, access data, and generate QC plots.")
1381 (license license:agpl3+)))
1383 (define-public r-chipexoqual
1385 (name "r-chipexoqual")
1390 (uri (bioconductor-uri "ChIPexoQual" version))
1393 "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
1394 (properties `((upstream-name . "ChIPexoQual")))
1395 (build-system r-build-system)
1397 `(("r-biocparallel" ,r-biocparallel)
1398 ("r-biovizbase" ,r-biovizbase)
1399 ("r-broom" ,r-broom)
1400 ("r-data-table" ,r-data-table)
1401 ("r-dplyr" ,r-dplyr)
1402 ("r-genomeinfodb" ,r-genomeinfodb)
1403 ("r-genomicalignments" ,r-genomicalignments)
1404 ("r-genomicranges" ,r-genomicranges)
1405 ("r-ggplot2" ,r-ggplot2)
1406 ("r-hexbin" ,r-hexbin)
1407 ("r-iranges" ,r-iranges)
1408 ("r-rcolorbrewer" ,r-rcolorbrewer)
1409 ("r-rmarkdown" ,r-rmarkdown)
1410 ("r-rsamtools" ,r-rsamtools)
1411 ("r-s4vectors" ,r-s4vectors)
1412 ("r-scales" ,r-scales)
1413 ("r-viridis" ,r-viridis)))
1414 (home-page "https://github.com/keleslab/ChIPexoQual")
1415 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1417 "This package provides a quality control pipeline for ChIP-exo/nexus
1419 (license license:gpl2+)))
1421 (define-public r-copynumber
1423 (name "r-copynumber")
1427 (uri (bioconductor-uri "copynumber" version))
1430 "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
1431 (build-system r-build-system)
1433 `(("r-s4vectors" ,r-s4vectors)
1434 ("r-iranges" ,r-iranges)
1435 ("r-genomicranges" ,r-genomicranges)
1436 ("r-biocgenerics" ,r-biocgenerics)))
1437 (home-page "https://bioconductor.org/packages/copynumber")
1438 (synopsis "Segmentation of single- and multi-track copy number data")
1440 "This package segments single- and multi-track copy number data by a
1441 penalized least squares regression method.")
1442 (license license:artistic2.0)))
1444 (define-public r-dnacopy
1451 (uri (bioconductor-uri "DNAcopy" version))
1454 "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
1455 (properties `((upstream-name . "DNAcopy")))
1456 (build-system r-build-system)
1457 (native-inputs `(("gfortran" ,gfortran)))
1458 (home-page "https://bioconductor.org/packages/DNAcopy")
1459 (synopsis "DNA copy number data analysis")
1461 "This package implements the @dfn{circular binary segmentation} (CBS)
1462 algorithm to segment DNA copy number data and identify genomic regions with
1463 abnormal copy number.")
1464 (license license:gpl2+)))
1466 ;; This is a CRAN package, but it uncharacteristically depends on a
1467 ;; Bioconductor package.
1468 (define-public r-htscluster
1470 (name "r-htscluster")
1475 (uri (cran-uri "HTSCluster" version))
1478 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1479 (properties `((upstream-name . "HTSCluster")))
1480 (build-system r-build-system)
1482 `(("r-capushe" ,r-capushe)
1483 ("r-edger" ,r-edger)
1484 ("r-plotrix" ,r-plotrix)))
1485 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1486 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1488 "This package provides a Poisson mixture model is implemented to cluster
1489 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
1490 estimation is performed using either the EM or CEM algorithm, and the slope
1491 heuristics are used for model selection (i.e., to choose the number of
1493 (license license:gpl3+)))