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 base)
28 #:use-module (gnu packages bioinformatics)
29 #:use-module (gnu packages cran)
30 #:use-module (gnu packages compression)
31 #:use-module (gnu packages gcc)
32 #:use-module (gnu packages graph)
33 #:use-module (gnu packages haskell)
34 #:use-module (gnu packages image)
35 #:use-module (gnu packages maths)
36 #:use-module (gnu packages netpbm)
37 #:use-module (gnu packages perl)
38 #:use-module (gnu packages pkg-config)
39 #:use-module (gnu packages statistics)
40 #:use-module (gnu packages web))
45 (define-public r-bsgenome-celegans-ucsc-ce6
47 (name "r-bsgenome-celegans-ucsc-ce6")
51 ;; We cannot use bioconductor-uri here because this tarball is
52 ;; located under "data/annotation/" instead of "bioc/".
53 (uri (string-append "https://www.bioconductor.org/packages/"
54 "release/data/annotation/src/contrib/"
55 "BSgenome.Celegans.UCSC.ce6_"
59 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
61 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
62 (build-system r-build-system)
63 ;; As this package provides little more than a very large data file it
64 ;; doesn't make sense to build substitutes.
65 (arguments `(#:substitutable? #f))
67 `(("r-bsgenome" ,r-bsgenome)))
69 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
70 (synopsis "Full genome sequences for Worm")
72 "This package provides full genome sequences for Caenorhabditis
73 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
75 (license license:artistic2.0)))
77 (define-public r-bsgenome-celegans-ucsc-ce10
79 (name "r-bsgenome-celegans-ucsc-ce10")
83 ;; We cannot use bioconductor-uri here because this tarball is
84 ;; located under "data/annotation/" instead of "bioc/".
85 (uri (string-append "https://www.bioconductor.org/packages/"
86 "release/data/annotation/src/contrib/"
87 "BSgenome.Celegans.UCSC.ce10_"
91 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
93 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
94 (build-system r-build-system)
95 ;; As this package provides little more than a very large data file it
96 ;; doesn't make sense to build substitutes.
97 (arguments `(#:substitutable? #f))
99 `(("r-bsgenome" ,r-bsgenome)))
101 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
102 (synopsis "Full genome sequences for Worm")
104 "This package provides full genome sequences for Caenorhabditis
105 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
107 (license license:artistic2.0)))
109 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
111 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
115 ;; We cannot use bioconductor-uri here because this tarball is
116 ;; located under "data/annotation/" instead of "bioc/".
117 (uri (string-append "https://www.bioconductor.org/packages/"
118 "release/data/annotation/src/contrib/"
119 "BSgenome.Dmelanogaster.UCSC.dm6_"
123 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
125 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
126 (build-system r-build-system)
127 ;; As this package provides little more than a very large data file it
128 ;; doesn't make sense to build substitutes.
129 (arguments `(#:substitutable? #f))
131 `(("r-bsgenome" ,r-bsgenome)))
133 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
134 (synopsis "Full genome sequences for Fly")
136 "This package provides full genome sequences for Drosophila
137 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
139 (license license:artistic2.0)))
141 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
143 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
147 ;; We cannot use bioconductor-uri here because this tarball is
148 ;; located under "data/annotation/" instead of "bioc/".
149 (uri (string-append "https://www.bioconductor.org/packages/"
150 "release/data/annotation/src/contrib/"
151 "BSgenome.Dmelanogaster.UCSC.dm3_"
155 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
157 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
158 (build-system r-build-system)
159 ;; As this package provides little more than a very large data file it
160 ;; doesn't make sense to build substitutes.
161 (arguments `(#:substitutable? #f))
163 `(("r-bsgenome" ,r-bsgenome)))
165 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
166 (synopsis "Full genome sequences for Fly")
168 "This package provides full genome sequences for Drosophila
169 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
170 Biostrings objects.")
171 (license license:artistic2.0)))
173 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
175 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
179 ;; We cannot use bioconductor-uri here because this tarball is
180 ;; located under "data/annotation/" instead of "bioc/".
181 (uri (string-append "http://www.bioconductor.org/packages/"
182 "release/data/annotation/src/contrib/"
183 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
187 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
189 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
190 (build-system r-build-system)
192 `(("r-bsgenome" ,r-bsgenome)
193 ("r-bsgenome-dmelanogaster-ucsc-dm3"
194 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
195 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
196 (synopsis "Full masked genome sequences for Fly")
198 "This package provides full masked genome sequences for Drosophila
199 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
200 Biostrings objects. The sequences are the same as in
201 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
202 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
203 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
204 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
205 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
206 (license license:artistic2.0)))
208 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
210 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
214 ;; We cannot use bioconductor-uri here because this tarball is
215 ;; located under "data/annotation/" instead of "bioc/".
216 (uri (string-append "https://www.bioconductor.org/packages/"
217 "release/data/annotation/src/contrib/"
218 "BSgenome.Hsapiens.1000genomes.hs37d5_"
222 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
224 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
225 (build-system r-build-system)
226 ;; As this package provides little more than a very large data file it
227 ;; doesn't make sense to build substitutes.
228 (arguments `(#:substitutable? #f))
230 `(("r-bsgenome" ,r-bsgenome)))
232 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
233 (synopsis "Full genome sequences for Homo sapiens")
235 "This package provides full genome sequences for Homo sapiens from
236 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
237 (license license:artistic2.0)))
239 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
241 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
245 ;; We cannot use bioconductor-uri here because this tarball is
246 ;; located under "data/annotation/" instead of "bioc/".
247 (uri (string-append "http://www.bioconductor.org/packages/"
248 "release/data/annotation/src/contrib/"
249 "BSgenome.Hsapiens.UCSC.hg19.masked_"
253 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
255 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
256 (build-system r-build-system)
258 `(("r-bsgenome" ,r-bsgenome)
259 ("r-bsgenome-hsapiens-ucsc-hg19"
260 ,r-bsgenome-hsapiens-ucsc-hg19)))
261 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
262 (synopsis "Full masked genome sequences for Homo sapiens")
264 "This package provides full genome sequences for Homo sapiens (Human) as
265 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
266 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
267 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
268 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
269 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
270 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
272 (license license:artistic2.0)))
274 (define-public r-bsgenome-mmusculus-ucsc-mm9
276 (name "r-bsgenome-mmusculus-ucsc-mm9")
280 ;; We cannot use bioconductor-uri here because this tarball is
281 ;; located under "data/annotation/" instead of "bioc/".
282 (uri (string-append "https://www.bioconductor.org/packages/"
283 "release/data/annotation/src/contrib/"
284 "BSgenome.Mmusculus.UCSC.mm9_"
288 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
290 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
291 (build-system r-build-system)
292 ;; As this package provides little more than a very large data file it
293 ;; doesn't make sense to build substitutes.
294 (arguments `(#:substitutable? #f))
296 `(("r-bsgenome" ,r-bsgenome)))
298 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
299 (synopsis "Full genome sequences for Mouse")
301 "This package provides full genome sequences for Mus musculus (Mouse) as
302 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
303 (license license:artistic2.0)))
305 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
307 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
311 ;; We cannot use bioconductor-uri here because this tarball is
312 ;; located under "data/annotation/" instead of "bioc/".
313 (uri (string-append "http://www.bioconductor.org/packages/"
314 "release/data/annotation/src/contrib/"
315 "BSgenome.Mmusculus.UCSC.mm9.masked_"
319 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
321 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
322 (build-system r-build-system)
324 `(("r-bsgenome" ,r-bsgenome)
325 ("r-bsgenome-mmusculus-ucsc-mm9"
326 ,r-bsgenome-mmusculus-ucsc-mm9)))
327 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
328 (synopsis "Full masked genome sequences for Mouse")
330 "This package provides full genome sequences for Mus musculus (Mouse) as
331 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
332 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
333 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
334 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
335 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
336 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
338 (license license:artistic2.0)))
340 (define-public r-bsgenome-mmusculus-ucsc-mm10
342 (name "r-bsgenome-mmusculus-ucsc-mm10")
346 ;; We cannot use bioconductor-uri here because this tarball is
347 ;; located under "data/annotation/" instead of "bioc/".
348 (uri (string-append "https://www.bioconductor.org/packages/"
349 "release/data/annotation/src/contrib/"
350 "BSgenome.Mmusculus.UCSC.mm10_"
354 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
356 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
357 (build-system r-build-system)
358 ;; As this package provides little more than a very large data file it
359 ;; doesn't make sense to build substitutes.
360 (arguments `(#:substitutable? #f))
362 `(("r-bsgenome" ,r-bsgenome)))
364 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
365 (synopsis "Full genome sequences for Mouse")
367 "This package provides full genome sequences for Mus
368 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
369 in Biostrings objects.")
370 (license license:artistic2.0)))
372 (define-public r-org-ce-eg-db
374 (name "r-org-ce-eg-db")
378 ;; We cannot use bioconductor-uri here because this tarball is
379 ;; located under "data/annotation/" instead of "bioc/".
380 (uri (string-append "https://www.bioconductor.org/packages/"
381 "release/data/annotation/src/contrib/"
382 "org.Ce.eg.db_" version ".tar.gz"))
385 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
387 `((upstream-name . "org.Ce.eg.db")))
388 (build-system r-build-system)
390 `(("r-annotationdbi" ,r-annotationdbi)))
391 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
392 (synopsis "Genome wide annotation for Worm")
394 "This package provides mappings from Entrez gene identifiers to various
395 annotations for the genome of the model worm Caenorhabditis elegans.")
396 (license license:artistic2.0)))
398 (define-public r-org-dm-eg-db
400 (name "r-org-dm-eg-db")
404 ;; We cannot use bioconductor-uri here because this tarball is
405 ;; located under "data/annotation/" instead of "bioc/".
406 (uri (string-append "https://www.bioconductor.org/packages/"
407 "release/data/annotation/src/contrib/"
408 "org.Dm.eg.db_" version ".tar.gz"))
411 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
413 `((upstream-name . "org.Dm.eg.db")))
414 (build-system r-build-system)
416 `(("r-annotationdbi" ,r-annotationdbi)))
417 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
418 (synopsis "Genome wide annotation for Fly")
420 "This package provides mappings from Entrez gene identifiers to various
421 annotations for the genome of the model fruit fly Drosophila melanogaster.")
422 (license license:artistic2.0)))
424 (define-public r-org-dr-eg-db
426 (name "r-org-dr-eg-db")
430 ;; We cannot use bioconductor-uri here because this tarball is
431 ;; located under "data/annotation/" instead of "bioc/".
432 (uri (string-append "https://www.bioconductor.org/packages/"
433 "release/data/annotation/src/contrib/"
434 "org.Dr.eg.db_" version ".tar.gz"))
437 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
439 `((upstream-name . "org.Dr.eg.db")))
440 (build-system r-build-system)
442 `(("r-annotationdbi" ,r-annotationdbi)))
443 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
444 (synopsis "Annotation for Zebrafish")
446 "This package provides genome wide annotations for Zebrafish, primarily
447 based on mapping using Entrez Gene identifiers.")
448 (license license:artistic2.0)))
450 (define-public r-org-hs-eg-db
452 (name "r-org-hs-eg-db")
456 ;; We cannot use bioconductor-uri here because this tarball is
457 ;; located under "data/annotation/" instead of "bioc/".
458 (uri (string-append "https://www.bioconductor.org/packages/"
459 "release/data/annotation/src/contrib/"
460 "org.Hs.eg.db_" version ".tar.gz"))
463 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
465 `((upstream-name . "org.Hs.eg.db")))
466 (build-system r-build-system)
468 `(("r-annotationdbi" ,r-annotationdbi)))
469 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
470 (synopsis "Genome wide annotation for Human")
472 "This package contains genome-wide annotations for Human, primarily based
473 on mapping using Entrez Gene identifiers.")
474 (license license:artistic2.0)))
476 (define-public r-org-mm-eg-db
478 (name "r-org-mm-eg-db")
482 ;; We cannot use bioconductor-uri here because this tarball is
483 ;; located under "data/annotation/" instead of "bioc/".
484 (uri (string-append "https://www.bioconductor.org/packages/"
485 "release/data/annotation/src/contrib/"
486 "org.Mm.eg.db_" version ".tar.gz"))
489 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
491 `((upstream-name . "org.Mm.eg.db")))
492 (build-system r-build-system)
494 `(("r-annotationdbi" ,r-annotationdbi)))
495 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
496 (synopsis "Genome wide annotation for Mouse")
498 "This package provides mappings from Entrez gene identifiers to various
499 annotations for the genome of the model mouse Mus musculus.")
500 (license license:artistic2.0)))
502 (define-public r-bsgenome-hsapiens-ucsc-hg19
504 (name "r-bsgenome-hsapiens-ucsc-hg19")
508 ;; We cannot use bioconductor-uri here because this tarball is
509 ;; located under "data/annotation/" instead of "bioc/".
510 (uri (string-append "https://www.bioconductor.org/packages/"
511 "release/data/annotation/src/contrib/"
512 "BSgenome.Hsapiens.UCSC.hg19_"
516 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
518 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
519 (build-system r-build-system)
520 ;; As this package provides little more than a very large data file it
521 ;; doesn't make sense to build substitutes.
522 (arguments `(#:substitutable? #f))
524 `(("r-bsgenome" ,r-bsgenome)))
526 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
527 (synopsis "Full genome sequences for Homo sapiens")
529 "This package provides full genome sequences for Homo sapiens as provided
530 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
531 (license license:artistic2.0)))
533 (define-public r-genelendatabase
535 (name "r-genelendatabase")
540 ;; We cannot use bioconductor-uri here because this tarball is
541 ;; located under "data/experiment/" instead of "bioc/".
542 (uri (string-append "https://bioconductor.org/packages/"
543 "release/data/experiment/src/contrib"
544 "/geneLenDataBase_" version ".tar.gz"))
547 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
549 `((upstream-name . "geneLenDataBase")))
550 (build-system r-build-system)
552 `(("r-rtracklayer" ,r-rtracklayer)
553 ("r-genomicfeatures" ,r-genomicfeatures)))
554 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
555 (synopsis "Lengths of mRNA transcripts for a number of genomes")
557 "This package provides the lengths of mRNA transcripts for a number of
558 genomes and gene ID formats, largely based on the UCSC table browser.")
559 (license license:lgpl2.0+)))
561 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
563 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
567 ;; We cannot use bioconductor-uri here because this tarball is
568 ;; located under "data/annotation/" instead of "bioc/".
569 (uri (string-append "https://bioconductor.org/packages/"
570 "release/data/annotation/src/contrib"
571 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
575 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
577 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
578 (build-system r-build-system)
579 ;; As this package provides little more than a very large data file it
580 ;; doesn't make sense to build substitutes.
581 (arguments `(#:substitutable? #f))
583 `(("r-genomicfeatures" ,r-genomicfeatures)))
585 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
586 (synopsis "Annotation package for human genome in TxDb format")
588 "This package provides an annotation database of Homo sapiens genome
589 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
590 track. The database is exposed as a @code{TxDb} object.")
591 (license license:artistic2.0)))
593 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
595 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
599 ;; We cannot use bioconductor-uri here because this tarball is
600 ;; located under "data/annotation/" instead of "bioc/".
601 (uri (string-append "https://bioconductor.org/packages/"
602 "release/data/annotation/src/contrib"
603 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
607 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
609 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
610 (build-system r-build-system)
612 `(("r-genomicfeatures" ,r-genomicfeatures)
613 ("r-annotationdbi" ,r-annotationdbi)))
615 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
616 (synopsis "Annotation package for mouse genome in TxDb format")
618 "This package provides an annotation database of Mouse genome data. It
619 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
620 database is exposed as a @code{TxDb} object.")
621 (license license:artistic2.0)))
623 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
625 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
629 ;; We cannot use bioconductor-uri here because this tarball is
630 ;; located under "data/annotation/" instead of "bioc/".
631 (uri (string-append "https://www.bioconductor.org/packages/"
632 "release/data/annotation/src/contrib/"
633 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
637 "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
639 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
640 (build-system r-build-system)
641 ;; As this package provides little more than a very large data file it
642 ;; doesn't make sense to build substitutes.
643 (arguments `(#:substitutable? #f))
645 `(("r-bsgenome" ,r-bsgenome)
646 ("r-genomicfeatures" ,r-genomicfeatures)
647 ("r-annotationdbi" ,r-annotationdbi)))
649 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
650 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
652 "This package loads a TxDb object, which is an R interface to
653 prefabricated databases contained in this package. This package provides
654 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
655 based on the knownGene track.")
656 (license license:artistic2.0)))
658 (define-public r-fdb-infiniummethylation-hg19
660 (name "r-fdb-infiniummethylation-hg19")
664 ;; We cannot use bioconductor-uri here because this tarball is
665 ;; located under "data/annotation/" instead of "bioc/".
666 (uri (string-append "https://www.bioconductor.org/packages/"
667 "release/data/annotation/src/contrib/"
668 "FDb.InfiniumMethylation.hg19_"
672 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
674 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
675 (build-system r-build-system)
677 `(("r-biostrings" ,r-biostrings)
678 ("r-genomicfeatures" ,r-genomicfeatures)
679 ("r-annotationdbi" ,r-annotationdbi)
680 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
681 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
682 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
683 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
685 "This is an annotation package for Illumina Infinium DNA methylation
686 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
688 (license license:artistic2.0)))
690 (define-public r-illuminahumanmethylationepicmanifest
692 (name "r-illuminahumanmethylationepicmanifest")
696 ;; We cannot use bioconductor-uri here because this tarball is
697 ;; located under "data/annotation/" instead of "bioc/".
698 (uri (string-append "https://www.bioconductor.org/packages/"
699 "release/data/annotation/src/contrib/"
700 "IlluminaHumanMethylationEPICmanifest_"
704 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
706 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
707 (build-system r-build-system)
709 `(("r-minfi" ,r-minfi)))
710 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
711 (synopsis "Manifest for Illumina's EPIC methylation arrays")
713 "This is a manifest package for Illumina's EPIC methylation arrays.")
714 (license license:artistic2.0)))
716 (define-public r-do-db
722 ;; We cannot use bioconductor-uri here because this tarball is
723 ;; located under "data/annotation/" instead of "bioc/".
724 (uri (string-append "https://www.bioconductor.org/packages/"
725 "release/data/annotation/src/contrib/"
726 "DO.db_" version ".tar.gz"))
729 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
731 `((upstream-name . "DO.db")))
732 (build-system r-build-system)
734 `(("r-annotationdbi" ,r-annotationdbi)))
735 (home-page "https://www.bioconductor.org/packages/DO.db/")
736 (synopsis "Annotation maps describing the entire Disease Ontology")
738 "This package provides a set of annotation maps describing the entire
740 (license license:artistic2.0)))
745 (define-public r-abadata
751 ;; We cannot use bioconductor-uri here because this tarball is
752 ;; located under "data/experiment/" instead of "bioc/".
753 (uri (string-append "https://www.bioconductor.org/packages/"
754 "release/data/experiment/src/contrib/"
755 "ABAData_" version ".tar.gz"))
758 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
760 `((upstream-name . "ABAData")))
761 (build-system r-build-system)
763 `(("r-annotationdbi" ,r-annotationdbi)))
764 (home-page "https://www.bioconductor.org/packages/ABAData/")
765 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
767 "This package provides the data for the gene expression enrichment
768 analysis conducted in the package ABAEnrichment. The package includes three
769 datasets which are derived from the Allen Brain Atlas:
772 @item Gene expression data from Human Brain (adults) averaged across donors,
773 @item Gene expression data from the Developing Human Brain pooled into five
774 age categories and averaged across donors, and
775 @item a developmental effect score based on the Developing Human Brain
779 All datasets are restricted to protein coding genes.")
780 (license license:gpl2+)))
782 (define-public r-arrmdata
788 ;; We cannot use bioconductor-uri here because this tarball is
789 ;; located under "data/experiment/" instead of "bioc/".
790 (uri (string-append "https://www.bioconductor.org/packages/"
791 "release/data/experiment/src/contrib/"
792 "ARRmData_" version ".tar.gz"))
795 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
797 `((upstream-name . "ARRmData")))
798 (build-system r-build-system)
799 (home-page "https://www.bioconductor.org/packages/ARRmData/")
800 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
802 "This package provides raw beta values from 36 samples across 3 groups
803 from Illumina 450k methylation arrays.")
804 (license license:artistic2.0)))
806 (define-public r-hsmmsinglecell
808 (name "r-hsmmsinglecell")
812 ;; We cannot use bioconductor-uri here because this tarball is
813 ;; located under "data/experiment/" instead of "bioc/".
814 (uri (string-append "https://www.bioconductor.org/packages/"
815 "release/data/experiment/src/contrib/"
816 "HSMMSingleCell_" version ".tar.gz"))
819 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
821 `((upstream-name . "HSMMSingleCell")))
822 (build-system r-build-system)
823 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
824 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
826 "Skeletal myoblasts undergo a well-characterized sequence of
827 morphological and transcriptional changes during differentiation. In this
828 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
829 under high mitogen conditions (GM) and then differentiated by switching to
830 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
831 hundred cells taken over a time-course of serum-induced differentiation.
832 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
833 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
834 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
835 which were then sequenced to a depth of ~4 million reads per library,
836 resulting in a complete gene expression profile for each cell.")
837 (license license:artistic2.0)))
842 (define-public r-biocgenerics
844 (name "r-biocgenerics")
848 (uri (bioconductor-uri "BiocGenerics" version))
851 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
853 `((upstream-name . "BiocGenerics")))
854 (build-system r-build-system)
855 (home-page "https://bioconductor.org/packages/BiocGenerics")
856 (synopsis "S4 generic functions for Bioconductor")
858 "This package provides S4 generic functions needed by many Bioconductor
860 (license license:artistic2.0)))
862 (define-public r-annotate
869 (uri (bioconductor-uri "annotate" version))
872 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
873 (build-system r-build-system)
875 `(("r-annotationdbi" ,r-annotationdbi)
876 ("r-biobase" ,r-biobase)
877 ("r-biocgenerics" ,r-biocgenerics)
881 ("r-xtable" ,r-xtable)))
883 "https://bioconductor.org/packages/annotate")
884 (synopsis "Annotation for microarrays")
885 (description "This package provides R environments for the annotation of
887 (license license:artistic2.0)))
889 (define-public r-hpar
896 (uri (bioconductor-uri "hpar" version))
899 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
900 (build-system r-build-system)
901 (home-page "https://bioconductor.org/packages/hpar/")
902 (synopsis "Human Protein Atlas in R")
903 (description "This package provides a simple interface to and data from
904 the Human Protein Atlas project.")
905 (license license:artistic2.0)))
907 (define-public r-regioner
914 (uri (bioconductor-uri "regioneR" version))
917 "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q"))))
918 (properties `((upstream-name . "regioneR")))
919 (build-system r-build-system)
921 `(("r-biostrings" ,r-biostrings)
922 ("r-bsgenome" ,r-bsgenome)
923 ("r-genomeinfodb" ,r-genomeinfodb)
924 ("r-genomicranges" ,r-genomicranges)
925 ("r-iranges" ,r-iranges)
926 ("r-memoise" ,r-memoise)
927 ("r-rtracklayer" ,r-rtracklayer)
928 ("r-s4vectors" ,r-s4vectors)))
929 (home-page "https://bioconductor.org/packages/regioneR/")
930 (synopsis "Association analysis of genomic regions")
931 (description "This package offers a statistical framework based on
932 customizable permutation tests to assess the association between genomic
933 region sets and other genomic features.")
934 (license license:artistic2.0)))
936 (define-public r-geneplotter
938 (name "r-geneplotter")
943 (uri (bioconductor-uri "geneplotter" version))
946 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
947 (build-system r-build-system)
949 `(("r-annotate" ,r-annotate)
950 ("r-annotationdbi" ,r-annotationdbi)
951 ("r-biobase" ,r-biobase)
952 ("r-biocgenerics" ,r-biocgenerics)
953 ("r-lattice" ,r-lattice)
954 ("r-rcolorbrewer" ,r-rcolorbrewer)))
955 (home-page "https://bioconductor.org/packages/geneplotter")
956 (synopsis "Graphics functions for genomic data")
958 "This package provides functions for plotting genomic data.")
959 (license license:artistic2.0)))
961 (define-public r-qvalue
968 (uri (bioconductor-uri "qvalue" version))
971 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
972 (build-system r-build-system)
974 `(("r-ggplot2" ,r-ggplot2)
975 ("r-reshape2" ,r-reshape2)))
976 (home-page "http://github.com/jdstorey/qvalue")
977 (synopsis "Q-value estimation for false discovery rate control")
979 "This package takes a list of p-values resulting from the simultaneous
980 testing of many hypotheses and estimates their q-values and local @dfn{false
981 discovery rate} (FDR) values. The q-value of a test measures the proportion
982 of false positives incurred when that particular test is called significant.
983 The local FDR measures the posterior probability the null hypothesis is true
984 given the test's p-value. Various plots are automatically generated, allowing
985 one to make sensible significance cut-offs. The software can be applied to
986 problems in genomics, brain imaging, astrophysics, and data mining.")
987 ;; Any version of the LGPL.
988 (license license:lgpl3+)))
990 (define-public r-diffbind
997 (uri (bioconductor-uri "DiffBind" version))
1000 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1001 (properties `((upstream-name . "DiffBind")))
1002 (build-system r-build-system)
1006 `(("r-amap" ,r-amap)
1007 ("r-biocparallel" ,r-biocparallel)
1008 ("r-deseq2" ,r-deseq2)
1009 ("r-dplyr" ,r-dplyr)
1010 ("r-edger" ,r-edger)
1011 ("r-genomicalignments" ,r-genomicalignments)
1012 ("r-genomicranges" ,r-genomicranges)
1013 ("r-ggplot2" ,r-ggplot2)
1014 ("r-ggrepel" ,r-ggrepel)
1015 ("r-gplots" ,r-gplots)
1016 ("r-iranges" ,r-iranges)
1017 ("r-lattice" ,r-lattice)
1018 ("r-limma" ,r-limma)
1019 ("r-locfit" ,r-locfit)
1020 ("r-rcolorbrewer" , r-rcolorbrewer)
1022 ("r-rhtslib" ,r-rhtslib)
1023 ("r-rsamtools" ,r-rsamtools)
1024 ("r-s4vectors" ,r-s4vectors)
1025 ("r-summarizedexperiment" ,r-summarizedexperiment)
1026 ("r-systempiper" ,r-systempiper)))
1027 (home-page "http://bioconductor.org/packages/DiffBind")
1028 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1030 "This package computes differentially bound sites from multiple
1031 ChIP-seq experiments using affinity (quantitative) data. Also enables
1032 occupancy (overlap) analysis and plotting functions.")
1033 (license license:artistic2.0)))
1035 (define-public r-ripseeker
1037 (name "r-ripseeker")
1042 (uri (bioconductor-uri "RIPSeeker" version))
1045 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1046 (properties `((upstream-name . "RIPSeeker")))
1047 (build-system r-build-system)
1049 `(("r-s4vectors" ,r-s4vectors)
1050 ("r-iranges" ,r-iranges)
1051 ("r-genomicranges" ,r-genomicranges)
1052 ("r-summarizedexperiment" ,r-summarizedexperiment)
1053 ("r-rsamtools" ,r-rsamtools)
1054 ("r-genomicalignments" ,r-genomicalignments)
1055 ("r-rtracklayer" ,r-rtracklayer)))
1056 (home-page "http://bioconductor.org/packages/RIPSeeker")
1058 "Identifying protein-associated transcripts from RIP-seq experiments")
1060 "This package infers and discriminates RIP peaks from RIP-seq alignments
1061 using two-state HMM with negative binomial emission probability. While
1062 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1063 a suite of bioinformatics tools integrated within this self-contained software
1064 package comprehensively addressing issues ranging from post-alignments
1065 processing to visualization and annotation.")
1066 (license license:gpl2)))
1068 (define-public r-multtest
1075 (uri (bioconductor-uri "multtest" version))
1078 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1079 (build-system r-build-system)
1081 `(("r-survival" ,r-survival)
1082 ("r-biocgenerics" ,r-biocgenerics)
1083 ("r-biobase" ,r-biobase)
1084 ("r-mass" ,r-mass)))
1085 (home-page "http://bioconductor.org/packages/multtest")
1086 (synopsis "Resampling-based multiple hypothesis testing")
1088 "This package can do non-parametric bootstrap and permutation
1089 resampling-based multiple testing procedures (including empirical Bayes
1090 methods) for controlling the family-wise error rate (FWER), generalized
1091 family-wise error rate (gFWER), tail probability of the proportion of
1092 false positives (TPPFP), and false discovery rate (FDR). Several choices
1093 of bootstrap-based null distribution are implemented (centered, centered
1094 and scaled, quantile-transformed). Single-step and step-wise methods are
1095 available. Tests based on a variety of T- and F-statistics (including
1096 T-statistics based on regression parameters from linear and survival models
1097 as well as those based on correlation parameters) are included. When probing
1098 hypotheses with T-statistics, users may also select a potentially faster null
1099 distribution which is multivariate normal with mean zero and variance
1100 covariance matrix derived from the vector influence function. Results are
1101 reported in terms of adjusted P-values, confidence regions and test statistic
1102 cutoffs. The procedures are directly applicable to identifying differentially
1103 expressed genes in DNA microarray experiments.")
1104 (license license:lgpl3)))
1106 (define-public r-graph
1112 (uri (bioconductor-uri "graph" version))
1115 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1116 (build-system r-build-system)
1118 `(("r-biocgenerics" ,r-biocgenerics)))
1119 (home-page "https://bioconductor.org/packages/graph")
1120 (synopsis "Handle graph data structures in R")
1122 "This package implements some simple graph handling capabilities for R.")
1123 (license license:artistic2.0)))
1125 (define-public r-codedepends
1127 (name "r-codedepends")
1132 (uri (cran-uri "CodeDepends" version))
1135 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1136 (properties `((upstream-name . "CodeDepends")))
1137 (build-system r-build-system)
1139 `(("r-codetools" ,r-codetools)
1140 ("r-graph" ,r-graph)
1142 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1143 (synopsis "Analysis of R code for reproducible research and code comprehension")
1145 "This package provides tools for analyzing R expressions or blocks of
1146 code and determining the dependencies between them. It focuses on R scripts,
1147 but can be used on the bodies of functions. There are many facilities
1148 including the ability to summarize or get a high-level view of code,
1149 determining dependencies between variables, code improvement suggestions.")
1150 ;; Any version of the GPL
1151 (license (list license:gpl2+ license:gpl3+))))
1153 (define-public r-chippeakanno
1155 (name "r-chippeakanno")
1160 (uri (bioconductor-uri "ChIPpeakAnno" version))
1163 "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
1164 (properties `((upstream-name . "ChIPpeakAnno")))
1165 (build-system r-build-system)
1167 `(("r-annotationdbi" ,r-annotationdbi)
1168 ("r-biobase" ,r-biobase)
1169 ("r-biocgenerics" ,r-biocgenerics)
1170 ("r-biocmanager" ,r-biocmanager)
1171 ("r-biomart" ,r-biomart)
1172 ("r-biostrings" ,r-biostrings)
1173 ("r-bsgenome" ,r-bsgenome)
1175 ("r-delayedarray" ,r-delayedarray)
1176 ("r-ensembldb" ,r-ensembldb)
1177 ("r-genomeinfodb" ,r-genomeinfodb)
1178 ("r-genomicalignments" ,r-genomicalignments)
1179 ("r-genomicfeatures" ,r-genomicfeatures)
1180 ("r-genomicranges" ,r-genomicranges)
1181 ("r-go-db" ,r-go-db)
1182 ("r-graph" ,r-graph)
1184 ("r-iranges" ,r-iranges)
1185 ("r-limma" ,r-limma)
1186 ("r-matrixstats" ,r-matrixstats)
1187 ("r-multtest" ,r-multtest)
1189 ("r-regioner" ,r-regioner)
1190 ("r-rsamtools" ,r-rsamtools)
1191 ("r-rtracklayer" ,r-rtracklayer)
1192 ("r-s4vectors" ,r-s4vectors)
1193 ("r-seqinr" ,r-seqinr)
1194 ("r-summarizedexperiment" ,r-summarizedexperiment)
1195 ("r-venndiagram" ,r-venndiagram)))
1196 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1197 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1199 "The package includes functions to retrieve the sequences around the peak,
1200 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1201 custom features such as most conserved elements and other transcription factor
1202 binding sites supplied by users. Starting 2.0.5, new functions have been added
1203 for finding the peaks with bi-directional promoters with summary statistics
1204 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1205 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1206 enrichedGO (addGeneIDs).")
1207 (license license:gpl2+)))
1209 (define-public r-marray
1215 (uri (bioconductor-uri "marray" version))
1217 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1218 (build-system r-build-system)
1220 `(("r-limma" ,r-limma)))
1221 (home-page "http://bioconductor.org/packages/marray")
1222 (synopsis "Exploratory analysis for two-color spotted microarray data")
1223 (description "This package contains class definitions for two-color spotted
1224 microarray data. It also includes functions for data input, diagnostic plots,
1225 normalization and quality checking.")
1226 (license license:lgpl2.0+)))
1228 (define-public r-cghbase
1234 (uri (bioconductor-uri "CGHbase" version))
1236 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1237 (properties `((upstream-name . "CGHbase")))
1238 (build-system r-build-system)
1240 `(("r-biobase" ,r-biobase)
1241 ("r-marray" ,r-marray)))
1242 (home-page "http://bioconductor.org/packages/CGHbase")
1243 (synopsis "Base functions and classes for arrayCGH data analysis")
1244 (description "This package contains functions and classes that are needed by
1245 the @code{arrayCGH} packages.")
1246 (license license:gpl2+)))
1248 (define-public r-cghcall
1254 (uri (bioconductor-uri "CGHcall" version))
1256 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1257 (properties `((upstream-name . "CGHcall")))
1258 (build-system r-build-system)
1260 `(("r-biobase" ,r-biobase)
1261 ("r-cghbase" ,r-cghbase)
1262 ("r-impute" ,r-impute)
1263 ("r-dnacopy" ,r-dnacopy)
1264 ("r-snowfall" ,r-snowfall)))
1265 (home-page "http://bioconductor.org/packages/CGHcall")
1266 (synopsis "Base functions and classes for arrayCGH data analysis")
1267 (description "This package contains functions and classes that are needed by
1268 @code{arrayCGH} packages.")
1269 (license license:gpl2+)))
1271 (define-public r-qdnaseq
1277 (uri (bioconductor-uri "QDNAseq" version))
1279 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1280 (properties `((upstream-name . "QDNAseq")))
1281 (build-system r-build-system)
1283 `(("r-biobase" ,r-biobase)
1284 ("r-biocparallel" ,r-biocparallel)
1285 ("r-cghbase" ,r-cghbase)
1286 ("r-cghcall" ,r-cghcall)
1287 ("r-dnacopy" ,r-dnacopy)
1288 ("r-genomicranges" ,r-genomicranges)
1289 ("r-iranges" ,r-iranges)
1290 ("r-matrixstats" ,r-matrixstats)
1291 ("r-r-utils" ,r-r-utils)
1292 ("r-rsamtools" ,r-rsamtools)))
1293 (home-page "http://bioconductor.org/packages/QDNAseq")
1294 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1295 (description "The genome is divided into non-overlapping fixed-sized bins,
1296 number of sequence reads in each counted, adjusted with a simultaneous
1297 two-dimensional loess correction for sequence mappability and GC content, and
1298 filtered to remove spurious regions in the genome. Downstream steps of
1299 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1301 (license license:gpl2+)))
1303 (define-public r-bayseq
1310 (uri (bioconductor-uri "baySeq" version))
1313 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1314 (properties `((upstream-name . "baySeq")))
1315 (build-system r-build-system)
1317 `(("r-abind" ,r-abind)
1318 ("r-edger" ,r-edger)
1319 ("r-genomicranges" ,r-genomicranges)))
1320 (home-page "https://bioconductor.org/packages/baySeq/")
1321 (synopsis "Bayesian analysis of differential expression patterns in count data")
1323 "This package identifies differential expression in high-throughput count
1324 data, such as that derived from next-generation sequencing machines,
1325 calculating estimated posterior likelihoods of differential expression (or
1326 more complex hypotheses) via empirical Bayesian methods.")
1327 (license license:gpl3)))
1329 (define-public r-chipcomp
1336 (uri (bioconductor-uri "ChIPComp" version))
1339 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1340 (properties `((upstream-name . "ChIPComp")))
1341 (build-system r-build-system)
1343 `(("r-biocgenerics" ,r-biocgenerics)
1344 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1345 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1346 ("r-genomeinfodb" ,r-genomeinfodb)
1347 ("r-genomicranges" ,r-genomicranges)
1348 ("r-iranges" ,r-iranges)
1349 ("r-limma" ,r-limma)
1350 ("r-rsamtools" ,r-rsamtools)
1351 ("r-rtracklayer" ,r-rtracklayer)
1352 ("r-s4vectors" ,r-s4vectors)))
1353 (home-page "https://bioconductor.org/packages/ChIPComp")
1354 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1356 "ChIPComp implements a statistical method for quantitative comparison of
1357 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1358 sites across multiple conditions considering matching control in ChIP-seq
1360 ;; Any version of the GPL.
1361 (license license:gpl3+)))
1363 (define-public r-riboprofiling
1365 (name "r-riboprofiling")
1370 (uri (bioconductor-uri "RiboProfiling" version))
1373 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1374 (properties `((upstream-name . "RiboProfiling")))
1375 (build-system r-build-system)
1377 `(("r-biocgenerics" ,r-biocgenerics)
1378 ("r-biostrings" ,r-biostrings)
1379 ("r-data-table" ,r-data-table)
1380 ("r-genomeinfodb" ,r-genomeinfodb)
1381 ("r-genomicalignments" ,r-genomicalignments)
1382 ("r-genomicfeatures" ,r-genomicfeatures)
1383 ("r-genomicranges" ,r-genomicranges)
1384 ("r-ggbio" ,r-ggbio)
1385 ("r-ggplot2" ,r-ggplot2)
1386 ("r-iranges" ,r-iranges)
1388 ("r-reshape2" ,r-reshape2)
1389 ("r-rsamtools" ,r-rsamtools)
1390 ("r-rtracklayer" ,r-rtracklayer)
1391 ("r-s4vectors" ,r-s4vectors)
1392 ("r-sqldf" ,r-sqldf)))
1393 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1394 (synopsis "Ribosome profiling data analysis")
1395 (description "Starting with a BAM file, this package provides the
1396 necessary functions for quality assessment, read start position recalibration,
1397 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1398 of count data: pairs, log fold-change, codon frequency and coverage
1399 assessment, principal component analysis on codon coverage.")
1400 (license license:gpl3)))
1402 (define-public r-riboseqr
1409 (uri (bioconductor-uri "riboSeqR" version))
1412 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1413 (properties `((upstream-name . "riboSeqR")))
1414 (build-system r-build-system)
1416 `(("r-abind" ,r-abind)
1417 ("r-bayseq" ,r-bayseq)
1418 ("r-genomeinfodb" ,r-genomeinfodb)
1419 ("r-genomicranges" ,r-genomicranges)
1420 ("r-iranges" ,r-iranges)
1421 ("r-rsamtools" ,r-rsamtools)
1422 ("r-seqlogo" ,r-seqlogo)))
1423 (home-page "https://bioconductor.org/packages/riboSeqR/")
1424 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1426 "This package provides plotting functions, frameshift detection and
1427 parsing of genetic sequencing data from ribosome profiling experiments.")
1428 (license license:gpl3)))
1430 (define-public r-interactionset
1432 (name "r-interactionset")
1437 (uri (bioconductor-uri "InteractionSet" version))
1440 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1442 `((upstream-name . "InteractionSet")))
1443 (build-system r-build-system)
1445 `(("r-biocgenerics" ,r-biocgenerics)
1446 ("r-genomeinfodb" ,r-genomeinfodb)
1447 ("r-genomicranges" ,r-genomicranges)
1448 ("r-iranges" ,r-iranges)
1449 ("r-matrix" ,r-matrix)
1451 ("r-s4vectors" ,r-s4vectors)
1452 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1453 (home-page "https://bioconductor.org/packages/InteractionSet")
1454 (synopsis "Base classes for storing genomic interaction data")
1456 "This package provides the @code{GInteractions},
1457 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1458 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1460 (license license:gpl3)))
1462 (define-public r-genomicinteractions
1464 (name "r-genomicinteractions")
1469 (uri (bioconductor-uri "GenomicInteractions" version))
1472 "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
1474 `((upstream-name . "GenomicInteractions")))
1475 (build-system r-build-system)
1477 `(("r-biobase" ,r-biobase)
1478 ("r-biocgenerics" ,r-biocgenerics)
1479 ("r-data-table" ,r-data-table)
1480 ("r-dplyr" ,r-dplyr)
1481 ("r-genomeinfodb" ,r-genomeinfodb)
1482 ("r-genomicranges" ,r-genomicranges)
1483 ("r-ggplot2" ,r-ggplot2)
1484 ("r-gridextra" ,r-gridextra)
1486 ("r-igraph" ,r-igraph)
1487 ("r-interactionset" ,r-interactionset)
1488 ("r-iranges" ,r-iranges)
1489 ("r-rsamtools" ,r-rsamtools)
1490 ("r-rtracklayer" ,r-rtracklayer)
1491 ("r-s4vectors" ,r-s4vectors)
1492 ("r-stringr" ,r-stringr)))
1493 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1494 (synopsis "R package for handling genomic interaction data")
1496 "This R package provides tools for handling genomic interaction data,
1497 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1498 information and producing various plots and statistics.")
1499 (license license:gpl3)))
1501 (define-public r-ctc
1508 (uri (bioconductor-uri "ctc" version))
1511 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1512 (build-system r-build-system)
1513 (propagated-inputs `(("r-amap" ,r-amap)))
1514 (home-page "https://bioconductor.org/packages/ctc/")
1515 (synopsis "Cluster and tree conversion")
1517 "This package provides tools for exporting and importing classification
1518 trees and clusters to other programs.")
1519 (license license:gpl2)))
1521 (define-public r-goseq
1528 (uri (bioconductor-uri "goseq" version))
1531 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1532 (build-system r-build-system)
1534 `(("r-annotationdbi" ,r-annotationdbi)
1535 ("r-biasedurn" ,r-biasedurn)
1536 ("r-biocgenerics" ,r-biocgenerics)
1537 ("r-genelendatabase" ,r-genelendatabase)
1538 ("r-go-db" ,r-go-db)
1539 ("r-mgcv" ,r-mgcv)))
1540 (home-page "https://bioconductor.org/packages/goseq/")
1541 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1543 "This package provides tools to detect Gene Ontology and/or other user
1544 defined categories which are over/under represented in RNA-seq data.")
1545 (license license:lgpl2.0+)))
1547 (define-public r-glimma
1554 (uri (bioconductor-uri "Glimma" version))
1557 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1558 (properties `((upstream-name . "Glimma")))
1559 (build-system r-build-system)
1561 `(("r-edger" ,r-edger)
1562 ("r-jsonlite" ,r-jsonlite)
1563 ("r-s4vectors" ,r-s4vectors)))
1564 (home-page "https://github.com/Shians/Glimma")
1565 (synopsis "Interactive HTML graphics")
1567 "This package generates interactive visualisations for analysis of
1568 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1569 HTML page. The interactions are built on top of the popular static
1570 representations of analysis results in order to provide additional
1572 (license license:lgpl3)))
1574 (define-public r-rots
1581 (uri (bioconductor-uri "ROTS" version))
1584 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
1585 (properties `((upstream-name . "ROTS")))
1586 (build-system r-build-system)
1588 `(("r-biobase" ,r-biobase)
1589 ("r-rcpp" ,r-rcpp)))
1590 (home-page "https://bioconductor.org/packages/ROTS/")
1591 (synopsis "Reproducibility-Optimized Test Statistic")
1593 "This package provides tools for calculating the
1594 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1596 (license license:gpl2+)))
1598 (define-public r-plgem
1605 (uri (bioconductor-uri "plgem" version))
1608 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
1609 (build-system r-build-system)
1611 `(("r-biobase" ,r-biobase)
1612 ("r-mass" ,r-mass)))
1613 (home-page "http://www.genopolis.it")
1614 (synopsis "Detect differential expression in microarray and proteomics datasets")
1616 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1617 model the variance-versus-mean dependence that exists in a variety of
1618 genome-wide datasets, including microarray and proteomics data. The use of
1619 PLGEM has been shown to improve the detection of differentially expressed
1620 genes or proteins in these datasets.")
1621 (license license:gpl2)))
1623 (define-public r-inspect
1630 (uri (bioconductor-uri "INSPEcT" version))
1633 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
1634 (properties `((upstream-name . "INSPEcT")))
1635 (build-system r-build-system)
1637 `(("r-biobase" ,r-biobase)
1638 ("r-biocgenerics" ,r-biocgenerics)
1639 ("r-biocparallel" ,r-biocparallel)
1640 ("r-deseq2" ,r-deseq2)
1641 ("r-desolve" ,r-desolve)
1642 ("r-genomicalignments" ,r-genomicalignments)
1643 ("r-genomicfeatures" ,r-genomicfeatures)
1644 ("r-genomicranges" ,r-genomicranges)
1645 ("r-iranges" ,r-iranges)
1646 ("r-plgem" ,r-plgem)
1647 ("r-preprocesscore" ,r-preprocesscore)
1649 ("r-rootsolve" ,r-rootsolve)
1650 ("r-rsamtools" ,r-rsamtools)
1651 ("r-s4vectors" ,r-s4vectors)
1652 ("r-shiny" ,r-shiny)
1653 ("r-summarizedexperiment" ,r-summarizedexperiment)
1654 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1655 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1656 (home-page "https://bioconductor.org/packages/INSPEcT")
1657 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1659 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1660 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1661 order to evaluate synthesis, processing and degradation rates and assess via
1662 modeling the rates that determines changes in mature mRNA levels.")
1663 (license license:gpl2)))
1665 (define-public r-dnabarcodes
1667 (name "r-dnabarcodes")
1672 (uri (bioconductor-uri "DNABarcodes" version))
1675 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
1676 (properties `((upstream-name . "DNABarcodes")))
1677 (build-system r-build-system)
1680 ("r-matrix" ,r-matrix)
1681 ("r-rcpp" ,r-rcpp)))
1682 (home-page "https://bioconductor.org/packages/DNABarcodes")
1683 (synopsis "Create and analyze DNA barcodes")
1685 "This package offers tools to create DNA barcode sets capable of
1686 correcting insertion, deletion, and substitution errors. Existing barcodes
1687 can be analyzed regarding their minimal, maximal and average distances between
1688 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1689 demultiplexed, i.e. assigned to their original reference barcode.")
1690 (license license:gpl2)))
1692 (define-public r-ruvseq
1699 (uri (bioconductor-uri "RUVSeq" version))
1702 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
1703 (properties `((upstream-name . "RUVSeq")))
1704 (build-system r-build-system)
1706 `(("r-biobase" ,r-biobase)
1707 ("r-edaseq" ,r-edaseq)
1708 ("r-edger" ,r-edger)
1709 ("r-mass" ,r-mass)))
1710 (home-page "https://github.com/drisso/RUVSeq")
1711 (synopsis "Remove unwanted variation from RNA-Seq data")
1713 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1714 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1716 (license license:artistic2.0)))
1718 (define-public r-biocneighbors
1720 (name "r-biocneighbors")
1725 (uri (bioconductor-uri "BiocNeighbors" version))
1728 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
1729 (properties `((upstream-name . "BiocNeighbors")))
1730 (build-system r-build-system)
1732 `(("r-biocgenerics" ,r-biocgenerics)
1733 ("r-biocparallel" ,r-biocparallel)
1735 ("r-rcppannoy" ,r-rcppannoy)
1736 ("r-rcpphnsw" ,r-rcpphnsw)
1737 ("r-s4vectors" ,r-s4vectors)))
1738 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1739 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1741 "This package implements exact and approximate methods for nearest
1742 neighbor detection, in a framework that allows them to be easily switched
1743 within Bioconductor packages or workflows. The exact algorithm is implemented
1744 using pre-clustering with the k-means algorithm. Functions are also provided
1745 to search for all neighbors within a given distance. Parallelization is
1746 achieved for all methods using the BiocParallel framework.")
1747 (license license:gpl3)))
1749 (define-public r-biocsingular
1751 (name "r-biocsingular")
1756 (uri (bioconductor-uri "BiocSingular" version))
1759 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
1760 (properties `((upstream-name . "BiocSingular")))
1761 (build-system r-build-system)
1763 `(("r-beachmat" ,r-beachmat)
1764 ("r-biocgenerics" ,r-biocgenerics)
1765 ("r-biocparallel" ,r-biocparallel)
1766 ("r-delayedarray" ,r-delayedarray)
1767 ("r-irlba" ,r-irlba)
1768 ("r-matrix" ,r-matrix)
1771 ("r-s4vectors" ,r-s4vectors)))
1772 (home-page "https://github.com/LTLA/BiocSingular")
1773 (synopsis "Singular value decomposition for Bioconductor packages")
1775 "This package implements exact and approximate methods for singular value
1776 decomposition and principal components analysis, in a framework that allows
1777 them to be easily switched within Bioconductor packages or workflows. Where
1778 possible, parallelization is achieved using the BiocParallel framework.")
1779 (license license:gpl3)))
1781 (define-public r-destiny
1788 (uri (bioconductor-uri "destiny" version))
1791 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
1792 (build-system r-build-system)
1794 `(("r-biobase" ,r-biobase)
1795 ("r-biocgenerics" ,r-biocgenerics)
1796 ("r-ggplot2" ,r-ggplot2)
1797 ("r-ggthemes" ,r-ggthemes)
1798 ("r-igraph" ,r-igraph)
1799 ("r-matrix" ,r-matrix)
1800 ("r-proxy" ,r-proxy)
1802 ("r-rcppeigen" ,r-rcppeigen)
1803 ("r-scales" ,r-scales)
1804 ("r-scatterplot3d" ,r-scatterplot3d)
1805 ("r-smoother" ,r-smoother)
1806 ("r-summarizedexperiment" ,r-summarizedexperiment)
1808 (home-page "https://bioconductor.org/packages/destiny/")
1809 (synopsis "Create and plot diffusion maps")
1810 (description "This package provides tools to create and plot diffusion
1812 ;; Any version of the GPL
1813 (license license:gpl3+)))
1815 (define-public r-savr
1822 (uri (bioconductor-uri "savR" version))
1825 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
1826 (properties `((upstream-name . "savR")))
1827 (build-system r-build-system)
1829 `(("r-ggplot2" ,r-ggplot2)
1830 ("r-gridextra" ,r-gridextra)
1831 ("r-reshape2" ,r-reshape2)
1832 ("r-scales" ,r-scales)
1834 (home-page "https://github.com/bcalder/savR")
1835 (synopsis "Parse and analyze Illumina SAV files")
1837 "This package provides tools to parse Illumina Sequence Analysis
1838 Viewer (SAV) files, access data, and generate QC plots.")
1839 (license license:agpl3+)))
1841 (define-public r-chipexoqual
1843 (name "r-chipexoqual")
1848 (uri (bioconductor-uri "ChIPexoQual" version))
1851 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
1852 (properties `((upstream-name . "ChIPexoQual")))
1853 (build-system r-build-system)
1855 `(("r-biocparallel" ,r-biocparallel)
1856 ("r-biovizbase" ,r-biovizbase)
1857 ("r-broom" ,r-broom)
1858 ("r-data-table" ,r-data-table)
1859 ("r-dplyr" ,r-dplyr)
1860 ("r-genomeinfodb" ,r-genomeinfodb)
1861 ("r-genomicalignments" ,r-genomicalignments)
1862 ("r-genomicranges" ,r-genomicranges)
1863 ("r-ggplot2" ,r-ggplot2)
1864 ("r-hexbin" ,r-hexbin)
1865 ("r-iranges" ,r-iranges)
1866 ("r-rcolorbrewer" ,r-rcolorbrewer)
1867 ("r-rmarkdown" ,r-rmarkdown)
1868 ("r-rsamtools" ,r-rsamtools)
1869 ("r-s4vectors" ,r-s4vectors)
1870 ("r-scales" ,r-scales)
1871 ("r-viridis" ,r-viridis)))
1872 (home-page "https://github.com/keleslab/ChIPexoQual")
1873 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1875 "This package provides a quality control pipeline for ChIP-exo/nexus
1877 (license license:gpl2+)))
1879 (define-public r-copynumber
1881 (name "r-copynumber")
1885 (uri (bioconductor-uri "copynumber" version))
1888 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
1889 (build-system r-build-system)
1891 `(("r-s4vectors" ,r-s4vectors)
1892 ("r-iranges" ,r-iranges)
1893 ("r-genomicranges" ,r-genomicranges)
1894 ("r-biocgenerics" ,r-biocgenerics)))
1895 (home-page "https://bioconductor.org/packages/copynumber")
1896 (synopsis "Segmentation of single- and multi-track copy number data")
1898 "This package segments single- and multi-track copy number data by a
1899 penalized least squares regression method.")
1900 (license license:artistic2.0)))
1902 (define-public r-dnacopy
1909 (uri (bioconductor-uri "DNAcopy" version))
1912 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
1913 (properties `((upstream-name . "DNAcopy")))
1914 (build-system r-build-system)
1915 (native-inputs `(("gfortran" ,gfortran)))
1916 (home-page "https://bioconductor.org/packages/DNAcopy")
1917 (synopsis "DNA copy number data analysis")
1919 "This package implements the @dfn{circular binary segmentation} (CBS)
1920 algorithm to segment DNA copy number data and identify genomic regions with
1921 abnormal copy number.")
1922 (license license:gpl2+)))
1924 ;; This is a CRAN package, but it uncharacteristically depends on a
1925 ;; Bioconductor package.
1926 (define-public r-htscluster
1928 (name "r-htscluster")
1933 (uri (cran-uri "HTSCluster" version))
1936 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1937 (properties `((upstream-name . "HTSCluster")))
1938 (build-system r-build-system)
1940 `(("r-capushe" ,r-capushe)
1941 ("r-edger" ,r-edger)
1942 ("r-plotrix" ,r-plotrix)))
1943 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1944 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1946 "This package provides a Poisson mixture model is implemented to cluster
1947 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
1948 estimation is performed using either the EM or CEM algorithm, and the slope
1949 heuristics are used for model selection (i.e., to choose the number of
1951 (license license:gpl3+)))
1953 (define-public r-deds
1960 (uri (bioconductor-uri "DEDS" version))
1963 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
1964 (properties `((upstream-name . "DEDS")))
1965 (build-system r-build-system)
1966 (home-page "https://bioconductor.org/packages/DEDS/")
1967 (synopsis "Differential expression via distance summary for microarray data")
1969 "This library contains functions that calculate various statistics of
1970 differential expression for microarray data, including t statistics, fold
1971 change, F statistics, SAM, moderated t and F statistics and B statistics. It
1972 also implements a new methodology called DEDS (Differential Expression via
1973 Distance Summary), which selects differentially expressed genes by integrating
1974 and summarizing a set of statistics using a weighted distance approach.")
1975 ;; Any version of the LGPL.
1976 (license license:lgpl3+)))
1978 ;; This is a CRAN package, but since it depends on a Bioconductor package we
1980 (define-public r-nbpseq
1987 (uri (cran-uri "NBPSeq" version))
1990 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
1991 (properties `((upstream-name . "NBPSeq")))
1992 (build-system r-build-system)
1994 `(("r-qvalue" ,r-qvalue)))
1995 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
1996 (synopsis "Negative binomial models for RNA-Seq data")
1998 "This package provides negative binomial models for two-group comparisons
1999 and regression inferences from RNA-sequencing data.")
2000 (license license:gpl2)))
2002 (define-public r-ebseq
2009 (uri (bioconductor-uri "EBSeq" version))
2012 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2013 (properties `((upstream-name . "EBSeq")))
2014 (build-system r-build-system)
2016 `(("r-blockmodeling" ,r-blockmodeling)
2017 ("r-gplots" ,r-gplots)
2018 ("r-testthat" ,r-testthat)))
2019 (home-page "https://bioconductor.org/packages/EBSeq")
2020 (synopsis "Differential expression analysis of RNA-seq data")
2022 "This package provides tools for differential expression analysis at both
2023 gene and isoform level using RNA-seq data")
2024 (license license:artistic2.0)))
2026 (define-public r-lpsymphony
2028 (name "r-lpsymphony")
2033 (uri (bioconductor-uri "lpsymphony" version))
2036 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2037 (build-system r-build-system)
2039 `(("gfortran" ,gfortran)
2042 `(("pkg-config" ,pkg-config)))
2043 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2044 (synopsis "Symphony integer linear programming solver in R")
2046 "This package was derived from Rsymphony. The package provides an R
2047 interface to SYMPHONY, a linear programming solver written in C++. The main
2048 difference between this package and Rsymphony is that it includes the solver
2049 source code, while Rsymphony expects to find header and library files on the
2050 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2051 to install interface to SYMPHONY.")
2052 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2053 ;; lpsimphony is released under the same terms.
2054 (license license:epl1.0)))
2056 (define-public r-ihw
2063 (uri (bioconductor-uri "IHW" version))
2066 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2067 (properties `((upstream-name . "IHW")))
2068 (build-system r-build-system)
2070 `(("r-biocgenerics" ,r-biocgenerics)
2071 ("r-fdrtool" ,r-fdrtool)
2072 ("r-lpsymphony" ,r-lpsymphony)
2073 ("r-slam" ,r-slam)))
2074 (home-page "https://bioconductor.org/packages/IHW")
2075 (synopsis "Independent hypothesis weighting")
2077 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2078 procedure that increases power compared to the method of Benjamini and
2079 Hochberg by assigning data-driven weights to each hypothesis. The input to
2080 IHW is a two-column table of p-values and covariates. The covariate can be
2081 any continuous-valued or categorical variable that is thought to be
2082 informative on the statistical properties of each hypothesis test, while it is
2083 independent of the p-value under the null hypothesis.")
2084 (license license:artistic2.0)))
2086 (define-public r-icobra
2093 (uri (bioconductor-uri "iCOBRA" version))
2096 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2097 (properties `((upstream-name . "iCOBRA")))
2098 (build-system r-build-system)
2100 `(("r-dplyr" ,r-dplyr)
2102 ("r-ggplot2" ,r-ggplot2)
2103 ("r-limma" ,r-limma)
2104 ("r-reshape2" ,r-reshape2)
2106 ("r-scales" ,r-scales)
2107 ("r-shiny" ,r-shiny)
2108 ("r-shinybs" ,r-shinybs)
2109 ("r-shinydashboard" ,r-shinydashboard)
2110 ("r-upsetr" ,r-upsetr)))
2111 (home-page "https://bioconductor.org/packages/iCOBRA")
2112 (synopsis "Comparison and visualization of ranking and assignment methods")
2114 "This package provides functions for calculation and visualization of
2115 performance metrics for evaluation of ranking and binary
2116 classification (assignment) methods. It also contains a Shiny application for
2117 interactive exploration of results.")
2118 (license license:gpl2+)))
2120 (define-public r-mast
2127 (uri (bioconductor-uri "MAST" version))
2130 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2131 (properties `((upstream-name . "MAST")))
2132 (build-system r-build-system)
2134 `(("r-abind" ,r-abind)
2136 ("r-biobase" ,r-biobase)
2137 ("r-biocgenerics" ,r-biocgenerics)
2138 ("r-data-table" ,r-data-table)
2139 ("r-ggplot2" ,r-ggplot2)
2141 ("r-progress" ,r-progress)
2142 ("r-reshape2" ,r-reshape2)
2143 ("r-s4vectors" ,r-s4vectors)
2144 ("r-singlecellexperiment" ,r-singlecellexperiment)
2145 ("r-stringr" ,r-stringr)
2146 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2147 (home-page "https://github.com/RGLab/MAST/")
2148 (synopsis "Model-based analysis of single cell transcriptomics")
2150 "This package provides methods and models for handling zero-inflated
2151 single cell assay data.")
2152 (license license:gpl2+)))
2154 (define-public r-monocle
2161 (uri (bioconductor-uri "monocle" version))
2164 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2165 (build-system r-build-system)
2167 `(("r-biobase" ,r-biobase)
2168 ("r-biocgenerics" ,r-biocgenerics)
2169 ("r-biocviews" ,r-biocviews)
2170 ("r-cluster" ,r-cluster)
2171 ("r-combinat" ,r-combinat)
2172 ("r-ddrtree" ,r-ddrtree)
2173 ("r-densityclust" ,r-densityclust)
2174 ("r-dplyr" ,r-dplyr)
2175 ("r-fastica" ,r-fastica)
2176 ("r-ggplot2" ,r-ggplot2)
2177 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2178 ("r-igraph" ,r-igraph)
2179 ("r-irlba" ,r-irlba)
2180 ("r-limma" ,r-limma)
2182 ("r-matrix" ,r-matrix)
2183 ("r-matrixstats" ,r-matrixstats)
2184 ("r-pheatmap" ,r-pheatmap)
2186 ("r-proxy" ,r-proxy)
2187 ("r-qlcmatrix" ,r-qlcmatrix)
2190 ("r-reshape2" ,r-reshape2)
2191 ("r-rtsne" ,r-rtsne)
2193 ("r-stringr" ,r-stringr)
2194 ("r-tibble" ,r-tibble)
2196 ("r-viridis" ,r-viridis)))
2197 (home-page "https://bioconductor.org/packages/monocle")
2198 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2200 "Monocle performs differential expression and time-series analysis for
2201 single-cell expression experiments. It orders individual cells according to
2202 progress through a biological process, without knowing ahead of time which
2203 genes define progress through that process. Monocle also performs
2204 differential expression analysis, clustering, visualization, and other useful
2205 tasks on single cell expression data. It is designed to work with RNA-Seq and
2206 qPCR data, but could be used with other types as well.")
2207 (license license:artistic2.0)))
2209 (define-public r-noiseq
2216 (uri (bioconductor-uri "NOISeq" version))
2219 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2220 (properties `((upstream-name . "NOISeq")))
2221 (build-system r-build-system)
2223 `(("r-biobase" ,r-biobase)
2224 ("r-matrix" ,r-matrix)))
2225 (home-page "https://bioconductor.org/packages/NOISeq")
2226 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2228 "This package provides tools to support the analysis of RNA-seq
2229 expression data or other similar kind of data. It provides exploratory plots
2230 to evaluate saturation, count distribution, expression per chromosome, type of
2231 detected features, features length, etc. It also supports the analysis of
2232 differential expression between two experimental conditions with no parametric
2234 (license license:artistic2.0)))
2236 (define-public r-scdd
2243 (uri (bioconductor-uri "scDD" version))
2246 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2247 (properties `((upstream-name . "scDD")))
2248 (build-system r-build-system)
2251 ("r-biocparallel" ,r-biocparallel)
2252 ("r-ebseq" ,r-ebseq)
2253 ("r-fields" ,r-fields)
2254 ("r-ggplot2" ,r-ggplot2)
2255 ("r-mclust" ,r-mclust)
2256 ("r-outliers" ,r-outliers)
2257 ("r-s4vectors" ,r-s4vectors)
2258 ("r-scran" ,r-scran)
2259 ("r-singlecellexperiment" ,r-singlecellexperiment)
2260 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2261 (home-page "https://github.com/kdkorthauer/scDD")
2262 (synopsis "Mixture modeling of single-cell RNA-seq data")
2264 "This package implements a method to analyze single-cell RNA-seq data
2265 utilizing flexible Dirichlet Process mixture models. Genes with differential
2266 distributions of expression are classified into several interesting patterns
2267 of differences between two conditions. The package also includes functions
2268 for simulating data with these patterns from negative binomial
2270 (license license:gpl2)))
2272 (define-public r-scone
2279 (uri (bioconductor-uri "scone" version))
2282 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2283 (build-system r-build-system)
2285 `(("r-aroma-light" ,r-aroma-light)
2286 ("r-biocparallel" ,r-biocparallel)
2288 ("r-class" ,r-class)
2289 ("r-cluster" ,r-cluster)
2290 ("r-compositions" ,r-compositions)
2291 ("r-diptest" ,r-diptest)
2292 ("r-edger" ,r-edger)
2294 ("r-gplots" ,r-gplots)
2295 ("r-hexbin" ,r-hexbin)
2296 ("r-limma" ,r-limma)
2297 ("r-matrixstats" ,r-matrixstats)
2298 ("r-mixtools" ,r-mixtools)
2299 ("r-rarpack" ,r-rarpack)
2300 ("r-rcolorbrewer" ,r-rcolorbrewer)
2301 ("r-rhdf5" ,r-rhdf5)
2302 ("r-ruvseq" ,r-ruvseq)
2303 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2304 (home-page "https://bioconductor.org/packages/scone")
2305 (synopsis "Single cell overview of normalized expression data")
2307 "SCONE is an R package for comparing and ranking the performance of
2308 different normalization schemes for single-cell RNA-seq and other
2309 high-throughput analyses.")
2310 (license license:artistic2.0)))
2312 (define-public r-geoquery
2319 (uri (bioconductor-uri "GEOquery" version))
2322 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2323 (properties `((upstream-name . "GEOquery")))
2324 (build-system r-build-system)
2326 `(("r-biobase" ,r-biobase)
2327 ("r-dplyr" ,r-dplyr)
2329 ("r-limma" ,r-limma)
2330 ("r-magrittr" ,r-magrittr)
2331 ("r-readr" ,r-readr)
2332 ("r-tidyr" ,r-tidyr)
2333 ("r-xml2" ,r-xml2)))
2334 (home-page "https://github.com/seandavi/GEOquery/")
2335 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2337 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2338 microarray data. Given the rich and varied nature of this resource, it is
2339 only natural to want to apply BioConductor tools to these data. GEOquery is
2340 the bridge between GEO and BioConductor.")
2341 (license license:gpl2)))
2343 (define-public r-illuminaio
2345 (name "r-illuminaio")
2350 (uri (bioconductor-uri "illuminaio" version))
2353 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2354 (build-system r-build-system)
2356 `(("r-base64" ,r-base64)))
2357 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2358 (synopsis "Parse Illumina microarray output files")
2360 "This package provides tools for parsing Illumina's microarray output
2361 files, including IDAT.")
2362 (license license:gpl2)))
2364 (define-public r-siggenes
2371 (uri (bioconductor-uri "siggenes" version))
2374 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2375 (build-system r-build-system)
2377 `(("r-biobase" ,r-biobase)
2378 ("r-multtest" ,r-multtest)
2379 ("r-scrime" ,r-scrime)))
2380 (home-page "https://bioconductor.org/packages/siggenes/")
2382 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2384 "This package provides tools for the identification of differentially
2385 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2386 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2387 Bayes Analyses of Microarrays} (EBAM).")
2388 (license license:lgpl2.0+)))
2390 (define-public r-bumphunter
2392 (name "r-bumphunter")
2397 (uri (bioconductor-uri "bumphunter" version))
2400 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2401 (build-system r-build-system)
2403 `(("r-annotationdbi" ,r-annotationdbi)
2404 ("r-biocgenerics" ,r-biocgenerics)
2405 ("r-dorng" ,r-dorng)
2406 ("r-foreach" ,r-foreach)
2407 ("r-genomeinfodb" ,r-genomeinfodb)
2408 ("r-genomicfeatures" ,r-genomicfeatures)
2409 ("r-genomicranges" ,r-genomicranges)
2410 ("r-iranges" ,r-iranges)
2411 ("r-iterators" ,r-iterators)
2412 ("r-limma" ,r-limma)
2413 ("r-locfit" ,r-locfit)
2414 ("r-matrixstats" ,r-matrixstats)
2415 ("r-s4vectors" ,r-s4vectors)))
2416 (home-page "https://github.com/ririzarr/bumphunter")
2417 (synopsis "Find bumps in genomic data")
2419 "This package provides tools for finding bumps in genomic data in order
2420 to identify differentially methylated regions in epigenetic epidemiology
2422 (license license:artistic2.0)))
2424 (define-public r-minfi
2431 (uri (bioconductor-uri "minfi" version))
2434 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2435 (build-system r-build-system)
2437 `(("r-beanplot" ,r-beanplot)
2438 ("r-biobase" ,r-biobase)
2439 ("r-biocgenerics" ,r-biocgenerics)
2440 ("r-biocparallel" ,r-biocparallel)
2441 ("r-biostrings" ,r-biostrings)
2442 ("r-bumphunter" ,r-bumphunter)
2443 ("r-data-table" ,r-data-table)
2444 ("r-delayedarray" ,r-delayedarray)
2445 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2446 ("r-genefilter" ,r-genefilter)
2447 ("r-genomeinfodb" ,r-genomeinfodb)
2448 ("r-genomicranges" ,r-genomicranges)
2449 ("r-geoquery" ,r-geoquery)
2450 ("r-hdf5array" ,r-hdf5array)
2451 ("r-illuminaio" ,r-illuminaio)
2452 ("r-iranges" ,r-iranges)
2453 ("r-lattice" ,r-lattice)
2454 ("r-limma" ,r-limma)
2456 ("r-mclust" ,r-mclust)
2458 ("r-nor1mix" ,r-nor1mix)
2459 ("r-preprocesscore" ,r-preprocesscore)
2460 ("r-quadprog" ,r-quadprog)
2461 ("r-rcolorbrewer" ,r-rcolorbrewer)
2462 ("r-reshape" ,r-reshape)
2463 ("r-s4vectors" ,r-s4vectors)
2464 ("r-siggenes" ,r-siggenes)
2465 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2466 (home-page "https://github.com/hansenlab/minfi")
2467 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2469 "This package provides tools to analyze and visualize Illumina Infinium
2470 methylation arrays.")
2471 (license license:artistic2.0)))
2473 (define-public r-methylumi
2475 (name "r-methylumi")
2480 (uri (bioconductor-uri "methylumi" version))
2483 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2484 (build-system r-build-system)
2486 `(("r-annotate" ,r-annotate)
2487 ("r-annotationdbi" ,r-annotationdbi)
2488 ("r-biobase" ,r-biobase)
2489 ("r-biocgenerics" ,r-biocgenerics)
2490 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2491 ("r-genefilter" ,r-genefilter)
2492 ("r-genomeinfodb" ,r-genomeinfodb)
2493 ("r-genomicranges" ,r-genomicranges)
2494 ("r-ggplot2" ,r-ggplot2)
2495 ("r-illuminaio" ,r-illuminaio)
2496 ("r-iranges" ,r-iranges)
2497 ("r-lattice" ,r-lattice)
2498 ("r-matrixstats" ,r-matrixstats)
2499 ("r-minfi" ,r-minfi)
2500 ("r-reshape2" ,r-reshape2)
2501 ("r-s4vectors" ,r-s4vectors)
2502 ("r-scales" ,r-scales)
2503 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2504 (home-page "https://bioconductor.org/packages/methylumi")
2505 (synopsis "Handle Illumina methylation data")
2507 "This package provides classes for holding and manipulating Illumina
2508 methylation data. Based on eSet, it can contain MIAME information, sample
2509 information, feature information, and multiple matrices of data. An
2510 \"intelligent\" import function, methylumiR can read the Illumina text files
2511 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2512 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2513 background correction, and quality control features for GoldenGate, Infinium,
2514 and Infinium HD arrays are also included.")
2515 (license license:gpl2)))
2517 (define-public r-lumi
2524 (uri (bioconductor-uri "lumi" version))
2527 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2528 (build-system r-build-system)
2530 `(("r-affy" ,r-affy)
2531 ("r-annotate" ,r-annotate)
2532 ("r-annotationdbi" ,r-annotationdbi)
2533 ("r-biobase" ,r-biobase)
2535 ("r-genomicfeatures" ,r-genomicfeatures)
2536 ("r-genomicranges" ,r-genomicranges)
2537 ("r-kernsmooth" ,r-kernsmooth)
2538 ("r-lattice" ,r-lattice)
2540 ("r-methylumi" ,r-methylumi)
2542 ("r-nleqslv" ,r-nleqslv)
2543 ("r-preprocesscore" ,r-preprocesscore)
2544 ("r-rsqlite" ,r-rsqlite)))
2545 (home-page "https://bioconductor.org/packages/lumi")
2546 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2548 "The lumi package provides an integrated solution for the Illumina
2549 microarray data analysis. It includes functions of Illumina
2550 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2551 variance stabilization, normalization and gene annotation at the probe level.
2552 It also includes the functions of processing Illumina methylation microarrays,
2553 especially Illumina Infinium methylation microarrays.")
2554 (license license:lgpl2.0+)))
2556 (define-public r-linnorm
2563 (uri (bioconductor-uri "Linnorm" version))
2566 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
2567 (properties `((upstream-name . "Linnorm")))
2568 (build-system r-build-system)
2570 `(("r-amap" ,r-amap)
2571 ("r-apcluster" ,r-apcluster)
2572 ("r-ellipse" ,r-ellipse)
2573 ("r-fastcluster" ,r-fastcluster)
2575 ("r-ggdendro" ,r-ggdendro)
2576 ("r-ggplot2" ,r-ggplot2)
2577 ("r-gmodels" ,r-gmodels)
2578 ("r-igraph" ,r-igraph)
2579 ("r-limma" ,r-limma)
2581 ("r-mclust" ,r-mclust)
2583 ("r-rcpparmadillo" ,r-rcpparmadillo)
2584 ("r-rtsne" ,r-rtsne)
2585 ("r-statmod" ,r-statmod)
2586 ("r-vegan" ,r-vegan)
2588 (home-page "http://www.jjwanglab.org/Linnorm/")
2589 (synopsis "Linear model and normality based transformation method")
2591 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2592 count data or any large scale count data. It transforms such datasets for
2593 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2594 the following pipelines are implemented:
2597 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2598 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2599 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2600 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2601 @item Differential expression analysis or differential peak detection using
2602 limma (@code{Linnorm.limma})
2603 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2604 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2605 @item Stable gene selection for scRNA-seq data; for users without or who do
2606 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2607 @item Data imputation (@code{Linnorm.DataImput}).
2610 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2611 @code{RnaXSim} function is included for simulating RNA-seq data for the
2612 evaluation of DEG analysis methods.")
2613 (license license:expat)))
2615 (define-public r-ioniser
2622 (uri (bioconductor-uri "IONiseR" version))
2625 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
2626 (properties `((upstream-name . "IONiseR")))
2627 (build-system r-build-system)
2629 `(("r-biocgenerics" ,r-biocgenerics)
2630 ("r-biocparallel" ,r-biocparallel)
2631 ("r-biostrings" ,r-biostrings)
2632 ("r-bit64" ,r-bit64)
2633 ("r-dplyr" ,r-dplyr)
2634 ("r-ggplot2" ,r-ggplot2)
2635 ("r-magrittr" ,r-magrittr)
2636 ("r-rhdf5" ,r-rhdf5)
2637 ("r-shortread" ,r-shortread)
2638 ("r-stringr" ,r-stringr)
2639 ("r-tibble" ,r-tibble)
2640 ("r-tidyr" ,r-tidyr)
2641 ("r-xvector" ,r-xvector)))
2642 (home-page "https://bioconductor.org/packages/IONiseR/")
2643 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2645 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2646 MinION data. It extracts summary statistics from a set of fast5 files and can
2647 be used either before or after base calling. In addition to standard
2648 summaries of the read-types produced, it provides a number of plots for
2649 visualising metrics relative to experiment run time or spatially over the
2650 surface of a flowcell.")
2651 (license license:expat)))
2653 ;; This is a CRAN package, but it depends on packages from Bioconductor.
2654 (define-public r-gkmsvm
2661 (uri (cran-uri "gkmSVM" version))
2664 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2665 (properties `((upstream-name . "gkmSVM")))
2666 (build-system r-build-system)
2668 `(("r-biocgenerics" ,r-biocgenerics)
2669 ("r-biostrings" ,r-biostrings)
2670 ("r-genomeinfodb" ,r-genomeinfodb)
2671 ("r-genomicranges" ,r-genomicranges)
2672 ("r-iranges" ,r-iranges)
2673 ("r-kernlab" ,r-kernlab)
2676 ("r-rtracklayer" ,r-rtracklayer)
2677 ("r-s4vectors" ,r-s4vectors)
2678 ("r-seqinr" ,r-seqinr)))
2679 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2680 (synopsis "Gapped-kmer support vector machine")
2682 "This R package provides tools for training gapped-kmer SVM classifiers
2683 for DNA and protein sequences. This package supports several sequence
2684 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2685 (license license:gpl2+)))
2687 (define-public r-triform
2694 (uri (bioconductor-uri "triform" version))
2697 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
2698 (build-system r-build-system)
2700 `(("r-biocgenerics" ,r-biocgenerics)
2701 ("r-iranges" ,r-iranges)
2702 ("r-yaml" ,r-yaml)))
2703 (home-page "https://bioconductor.org/packages/triform/")
2704 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2706 "The Triform algorithm uses model-free statistics to identify peak-like
2707 distributions of TF ChIP sequencing reads, taking advantage of an improved
2708 peak definition in combination with known profile characteristics.")
2709 (license license:gpl2)))
2711 (define-public r-varianttools
2713 (name "r-varianttools")
2718 (uri (bioconductor-uri "VariantTools" version))
2721 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
2722 (properties `((upstream-name . "VariantTools")))
2723 (build-system r-build-system)
2725 `(("r-biobase" ,r-biobase)
2726 ("r-biocgenerics" ,r-biocgenerics)
2727 ("r-biocparallel" ,r-biocparallel)
2728 ("r-biostrings" ,r-biostrings)
2729 ("r-bsgenome" ,r-bsgenome)
2730 ("r-genomeinfodb" ,r-genomeinfodb)
2731 ("r-genomicfeatures" ,r-genomicfeatures)
2732 ("r-genomicranges" ,r-genomicranges)
2733 ("r-iranges" ,r-iranges)
2734 ("r-matrix" ,r-matrix)
2735 ("r-rsamtools" ,r-rsamtools)
2736 ("r-rtracklayer" ,r-rtracklayer)
2737 ("r-s4vectors" ,r-s4vectors)
2738 ("r-variantannotation" ,r-variantannotation)))
2739 (home-page "https://bioconductor.org/packages/VariantTools/")
2740 (synopsis "Tools for exploratory analysis of variant calls")
2742 "Explore, diagnose, and compare variant calls using filters. The
2743 VariantTools package supports a workflow for loading data, calling single
2744 sample variants and tumor-specific somatic mutations or other sample-specific
2745 variant types (e.g., RNA editing). Most of the functions operate on
2746 alignments (BAM files) or datasets of called variants. The user is expected
2747 to have already aligned the reads with a separate tool, e.g., GSNAP via
2749 (license license:artistic2.0)))
2751 (define-public r-heatplus
2758 (uri (bioconductor-uri "Heatplus" version))
2761 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
2762 (properties `((upstream-name . "Heatplus")))
2763 (build-system r-build-system)
2765 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2766 (home-page "https://github.com/alexploner/Heatplus")
2767 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2769 "This package provides tools to display a rectangular heatmap (intensity
2770 plot) of a data matrix. By default, both samples (columns) and features (row)
2771 of the matrix are sorted according to a hierarchical clustering, and the
2772 corresponding dendrogram is plotted. Optionally, panels with additional
2773 information about samples and features can be added to the plot.")
2774 (license license:gpl2+)))
2776 (define-public r-gosemsim
2783 (uri (bioconductor-uri "GOSemSim" version))
2786 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
2787 (properties `((upstream-name . "GOSemSim")))
2788 (build-system r-build-system)
2790 `(("r-annotationdbi" ,r-annotationdbi)
2791 ("r-go-db" ,r-go-db)
2792 ("r-rcpp" ,r-rcpp)))
2793 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2794 (synopsis "GO-terms semantic similarity measures")
2796 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2797 quantitative ways to compute similarities between genes and gene groups, and
2798 have became important basis for many bioinformatics analysis approaches.
2799 GOSemSim is an R package for semantic similarity computation among GO terms,
2800 sets of GO terms, gene products and gene clusters.")
2801 (license license:artistic2.0)))
2803 (define-public r-anota
2810 (uri (bioconductor-uri "anota" version))
2813 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
2814 (build-system r-build-system)
2816 `(("r-multtest" ,r-multtest)
2817 ("r-qvalue" ,r-qvalue)))
2818 (home-page "https://bioconductor.org/packages/anota/")
2819 (synopsis "Analysis of translational activity")
2821 "Genome wide studies of translational control is emerging as a tool to
2822 study various biological conditions. The output from such analysis is both
2823 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2824 involved in translation (the actively translating mRNA level) for each mRNA.
2825 The standard analysis of such data strives towards identifying differential
2826 translational between two or more sample classes - i.e. differences in
2827 actively translated mRNA levels that are independent of underlying differences
2828 in cytosolic mRNA levels. This package allows for such analysis using partial
2829 variances and the random variance model. As 10s of thousands of mRNAs are
2830 analyzed in parallel the library performs a number of tests to assure that
2831 the data set is suitable for such analysis.")
2832 (license license:gpl3)))
2834 (define-public r-sigpathway
2836 (name "r-sigpathway")
2841 (uri (bioconductor-uri "sigPathway" version))
2844 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
2845 (properties `((upstream-name . "sigPathway")))
2846 (build-system r-build-system)
2847 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
2848 (synopsis "Pathway analysis")
2850 "This package is used to conduct pathway analysis by calculating the NT_k
2851 and NE_k statistics in a statistical framework for determining whether a
2852 specified group of genes for a pathway has a coordinated association with a
2853 phenotype of interest.")
2854 (license license:gpl2)))
2856 (define-public r-fgsea
2863 (uri (bioconductor-uri "fgsea" version))
2866 "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c"))))
2867 (build-system r-build-system)
2870 ("r-biocparallel" ,r-biocparallel)
2871 ("r-data-table" ,r-data-table)
2872 ("r-fastmatch" ,r-fastmatch)
2873 ("r-ggplot2" ,r-ggplot2)
2874 ("r-gridextra" ,r-gridextra)
2875 ("r-matrix" ,r-matrix)
2876 ("r-rcpp" ,r-rcpp)))
2877 (home-page "https://github.com/ctlab/fgsea/")
2878 (synopsis "Fast gene set enrichment analysis")
2880 "The package implements an algorithm for fast gene set enrichment
2881 analysis. Using the fast algorithm allows to make more permutations and get
2882 more fine grained p-values, which allows to use accurate stantard approaches
2883 to multiple hypothesis correction.")
2884 (license license:expat)))
2886 (define-public r-dose
2893 (uri (bioconductor-uri "DOSE" version))
2896 "0dvhnfhzhhzcxm8zhdwrkif7sak4p888sjqfd3a0p77h0hs6g8pv"))))
2897 (properties `((upstream-name . "DOSE")))
2898 (build-system r-build-system)
2900 `(("r-annotationdbi" ,r-annotationdbi)
2901 ("r-biocparallel" ,r-biocparallel)
2902 ("r-do-db" ,r-do-db)
2903 ("r-fgsea" ,r-fgsea)
2904 ("r-ggplot2" ,r-ggplot2)
2905 ("r-gosemsim" ,r-gosemsim)
2906 ("r-qvalue" ,r-qvalue)
2907 ("r-reshape2" ,r-reshape2)
2908 ("r-s4vectors" ,r-s4vectors)))
2909 (home-page "https://guangchuangyu.github.io/software/DOSE/")
2910 (synopsis "Disease ontology semantic and enrichment analysis")
2912 "This package implements five methods proposed by Resnik, Schlicker,
2913 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
2914 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
2915 including hypergeometric model and gene set enrichment analysis are also
2916 implemented for discovering disease associations of high-throughput biological
2918 (license license:artistic2.0)))
2920 (define-public r-enrichplot
2922 (name "r-enrichplot")
2927 (uri (bioconductor-uri "enrichplot" version))
2930 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
2931 (build-system r-build-system)
2933 `(("r-annotationdbi" ,r-annotationdbi)
2934 ("r-cowplot" ,r-cowplot)
2936 ("r-europepmc" ,r-europepmc)
2937 ("r-ggplot2" ,r-ggplot2)
2938 ("r-ggplotify" ,r-ggplotify)
2939 ("r-ggraph" ,r-ggraph)
2940 ("r-ggridges" ,r-ggridges)
2941 ("r-gosemsim" ,r-gosemsim)
2942 ("r-gridextra" ,r-gridextra)
2943 ("r-igraph" ,r-igraph)
2944 ("r-purrr" ,r-purrr)
2945 ("r-rcolorbrewer" ,r-rcolorbrewer)
2946 ("r-reshape2" ,r-reshape2)
2947 ("r-upsetr" ,r-upsetr)))
2948 (home-page "https://github.com/GuangchuangYu/enrichplot")
2949 (synopsis "Visualization of functional enrichment result")
2951 "The enrichplot package implements several visualization methods for
2952 interpreting functional enrichment results obtained from ORA or GSEA analyses.
2953 All the visualization methods are developed based on ggplot2 graphics.")
2954 (license license:artistic2.0)))
2956 (define-public r-clusterprofiler
2958 (name "r-clusterprofiler")
2963 (uri (bioconductor-uri "clusterProfiler" version))
2966 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
2968 `((upstream-name . "clusterProfiler")))
2969 (build-system r-build-system)
2971 `(("r-annotationdbi" ,r-annotationdbi)
2973 ("r-enrichplot" ,r-enrichplot)
2974 ("r-ggplot2" ,r-ggplot2)
2975 ("r-go-db" ,r-go-db)
2976 ("r-gosemsim" ,r-gosemsim)
2977 ("r-magrittr" ,r-magrittr)
2979 ("r-qvalue" ,r-qvalue)
2980 ("r-rvcheck" ,r-rvcheck)
2981 ("r-tidyr" ,r-tidyr)))
2982 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
2983 (synopsis "Analysis and visualization of functional profiles for gene clusters")
2985 "This package implements methods to analyze and visualize functional
2986 profiles (GO and KEGG) of gene and gene clusters.")
2987 (license license:artistic2.0)))
2989 (define-public r-mlinterfaces
2991 (name "r-mlinterfaces")
2996 (uri (bioconductor-uri "MLInterfaces" version))
2999 "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
3000 (properties `((upstream-name . "MLInterfaces")))
3001 (build-system r-build-system)
3003 `(("r-annotate" ,r-annotate)
3004 ("r-biobase" ,r-biobase)
3005 ("r-biocgenerics" ,r-biocgenerics)
3006 ("r-cluster" ,r-cluster)
3009 ("r-gdata" ,r-gdata)
3010 ("r-genefilter" ,r-genefilter)
3011 ("r-ggvis" ,r-ggvis)
3012 ("r-hwriter" ,r-hwriter)
3014 ("r-mlbench" ,r-mlbench)
3016 ("r-rcolorbrewer" ,r-rcolorbrewer)
3018 ("r-rpart" ,r-rpart)
3019 ("r-sfsmisc" ,r-sfsmisc)
3020 ("r-shiny" ,r-shiny)
3021 ("r-threejs" ,r-threejs)))
3022 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3023 (synopsis "Interfaces to R machine learning procedures")
3025 "This package provides uniform interfaces to machine learning code for
3026 data in R and Bioconductor containers.")
3027 ;; Any version of the LGPL.
3028 (license license:lgpl2.1+)))
3030 (define-public r-annaffy
3037 (uri (bioconductor-uri "annaffy" version))
3040 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3041 (build-system r-build-system)
3044 (modify-phases %standard-phases
3045 (add-after 'unpack 'remove-reference-to-non-free-data
3047 (substitute* "DESCRIPTION"
3051 `(("r-annotationdbi" ,r-annotationdbi)
3052 ("r-biobase" ,r-biobase)
3054 ("r-go-db" ,r-go-db)))
3055 (home-page "https://bioconductor.org/packages/annaffy/")
3056 (synopsis "Annotation tools for Affymetrix biological metadata")
3058 "This package provides functions for handling data from Bioconductor
3059 Affymetrix annotation data packages. It produces compact HTML and text
3060 reports including experimental data and URL links to many online databases.
3061 It allows searching of biological metadata using various criteria.")
3062 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3063 ;; the LGPL 2.1 is included.
3064 (license license:lgpl2.1+)))
3066 (define-public r-a4core
3073 (uri (bioconductor-uri "a4Core" version))
3076 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3077 (properties `((upstream-name . "a4Core")))
3078 (build-system r-build-system)
3080 `(("r-biobase" ,r-biobase)
3081 ("r-glmnet" ,r-glmnet)))
3082 (home-page "https://bioconductor.org/packages/a4Core")
3083 (synopsis "Automated Affymetrix array analysis core package")
3085 "This is the core package for the automated analysis of Affymetrix
3087 (license license:gpl3)))
3089 (define-public r-a4classif
3091 (name "r-a4classif")
3096 (uri (bioconductor-uri "a4Classif" version))
3099 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3100 (properties `((upstream-name . "a4Classif")))
3101 (build-system r-build-system)
3103 `(("r-a4core" ,r-a4core)
3104 ("r-a4preproc" ,r-a4preproc)
3105 ("r-glmnet" ,r-glmnet)
3106 ("r-mlinterfaces" ,r-mlinterfaces)
3109 ("r-varselrf" ,r-varselrf)))
3110 (home-page "https://bioconductor.org/packages/a4Classif/")
3111 (synopsis "Automated Affymetrix array analysis classification package")
3113 "This is the classification package for the automated analysis of
3114 Affymetrix arrays.")
3115 (license license:gpl3)))
3117 (define-public r-a4preproc
3119 (name "r-a4preproc")
3124 (uri (bioconductor-uri "a4Preproc" version))
3127 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3128 (properties `((upstream-name . "a4Preproc")))
3129 (build-system r-build-system)
3131 `(("r-annotationdbi" ,r-annotationdbi)))
3132 (home-page "https://bioconductor.org/packages/a4Preproc/")
3133 (synopsis "Automated Affymetrix array analysis preprocessing package")
3135 "This is a package for the automated analysis of Affymetrix arrays. It
3136 is used for preprocessing the arrays.")
3137 (license license:gpl3)))
3139 (define-public r-a4reporting
3141 (name "r-a4reporting")
3146 (uri (bioconductor-uri "a4Reporting" version))
3149 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3150 (properties `((upstream-name . "a4Reporting")))
3151 (build-system r-build-system)
3153 `(("r-annaffy" ,r-annaffy)
3154 ("r-xtable" ,r-xtable)))
3155 (home-page "https://bioconductor.org/packages/a4Reporting/")
3156 (synopsis "Automated Affymetrix array analysis reporting package")
3158 "This is a package for the automated analysis of Affymetrix arrays. It
3159 provides reporting features.")
3160 (license license:gpl3)))
3162 (define-public r-a4base
3169 (uri (bioconductor-uri "a4Base" version))
3172 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3173 (properties `((upstream-name . "a4Base")))
3174 (build-system r-build-system)
3176 `(("r-a4core" ,r-a4core)
3177 ("r-a4preproc" ,r-a4preproc)
3178 ("r-annaffy" ,r-annaffy)
3179 ("r-annotationdbi" ,r-annotationdbi)
3180 ("r-biobase" ,r-biobase)
3181 ("r-genefilter" ,r-genefilter)
3182 ("r-glmnet" ,r-glmnet)
3183 ("r-gplots" ,r-gplots)
3184 ("r-limma" ,r-limma)
3186 ("r-multtest" ,r-multtest)))
3187 (home-page "https://bioconductor.org/packages/a4Base/")
3188 (synopsis "Automated Affymetrix array analysis base package")
3190 "This package provides basic features for the automated analysis of
3191 Affymetrix arrays.")
3192 (license license:gpl3)))
3201 (uri (bioconductor-uri "a4" version))
3204 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3205 (build-system r-build-system)
3207 `(("r-a4base" ,r-a4base)
3208 ("r-a4classif" ,r-a4classif)
3209 ("r-a4core" ,r-a4core)
3210 ("r-a4preproc" ,r-a4preproc)
3211 ("r-a4reporting" ,r-a4reporting)))
3212 (home-page "https://bioconductor.org/packages/a4/")
3213 (synopsis "Automated Affymetrix array analysis umbrella package")
3215 "This package provides a software suite for the automated analysis of
3216 Affymetrix arrays.")
3217 (license license:gpl3)))
3219 (define-public r-abseqr
3226 (uri (bioconductor-uri "abseqR" version))
3229 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3230 (properties `((upstream-name . "abseqR")))
3231 (build-system r-build-system)
3233 `(("pandoc" ,ghc-pandoc)))
3235 `(("r-biocparallel" ,r-biocparallel)
3236 ("r-biocstyle" ,r-biocstyle)
3237 ("r-circlize" ,r-circlize)
3238 ("r-flexdashboard" ,r-flexdashboard)
3239 ("r-ggcorrplot" ,r-ggcorrplot)
3240 ("r-ggdendro" ,r-ggdendro)
3241 ("r-ggplot2" ,r-ggplot2)
3242 ("r-gridextra" ,r-gridextra)
3243 ("r-knitr" ,r-knitr)
3244 ("r-plotly" ,r-plotly)
3247 ("r-rcolorbrewer" ,r-rcolorbrewer)
3248 ("r-reshape2" ,r-reshape2)
3249 ("r-rmarkdown" ,r-rmarkdown)
3250 ("r-stringr" ,r-stringr)
3251 ("r-vegan" ,r-vegan)
3252 ("r-venndiagram" ,r-venndiagram)))
3253 (home-page "https://github.com/malhamdoosh/abseqR")
3254 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3256 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3257 sequencing datasets generated from antibody libraries and abseqR is one of its
3258 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3259 capabilities and allows them to generate interactive HTML reports for the
3260 convenience of viewing and sharing with other researchers. Additionally,
3261 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3262 further downstream analysis on its output.")
3263 (license license:gpl3)))
3265 (define-public r-bacon
3272 (uri (bioconductor-uri "bacon" version))
3275 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3276 (build-system r-build-system)
3278 `(("r-biocparallel" ,r-biocparallel)
3279 ("r-ellipse" ,r-ellipse)
3280 ("r-ggplot2" ,r-ggplot2)))
3281 (home-page "https://bioconductor.org/packages/bacon/")
3282 (synopsis "Controlling bias and inflation in association studies")
3284 "Bacon can be used to remove inflation and bias often observed in
3285 epigenome- and transcriptome-wide association studies. To this end bacon
3286 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3287 fitting a three-component normal mixture on z-scores.")
3288 (license license:gpl2+)))
3290 (define-public r-rgadem
3297 (uri (bioconductor-uri "rGADEM" version))
3300 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3301 (properties `((upstream-name . "rGADEM")))
3302 (build-system r-build-system)
3304 `(("r-biostrings" ,r-biostrings)
3305 ("r-bsgenome" ,r-bsgenome)
3306 ("r-iranges" ,r-iranges)
3307 ("r-seqlogo" ,r-seqlogo)))
3308 (home-page "https://bioconductor.org/packages/rGADEM/")
3309 (synopsis "De novo sequence motif discovery")
3311 "rGADEM is an efficient de novo motif discovery tool for large-scale
3312 genomic sequence data.")
3313 (license license:artistic2.0)))
3315 (define-public r-motiv
3322 (uri (bioconductor-uri "MotIV" version))
3325 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3326 (properties `((upstream-name . "MotIV")))
3327 (build-system r-build-system)
3331 `(("r-biocgenerics" ,r-biocgenerics)
3332 ("r-biostrings" ,r-biostrings)
3333 ("r-iranges" ,r-iranges)
3334 ("r-lattice" ,r-lattice)
3335 ("r-rgadem" ,r-rgadem)
3336 ("r-s4vectors" ,r-s4vectors)))
3337 (home-page "https://bioconductor.org/packages/MotIV/")
3338 (synopsis "Motif identification and validation")
3340 "This package is used for the identification and validation of sequence
3341 motifs. It makes use of STAMP for comparing a set of motifs to a given
3342 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3343 distributions, modules and filter motifs.")
3344 (license license:gpl2)))
3346 (define-public r-motifstack
3348 (name "r-motifstack")
3353 (uri (bioconductor-uri "motifStack" version))
3356 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3357 (properties `((upstream-name . "motifStack")))
3358 (build-system r-build-system)
3360 `(("r-ade4" ,r-ade4)
3361 ("r-biostrings" ,r-biostrings)
3362 ("r-grimport2" ,r-grimport2)
3363 ("r-htmlwidgets" ,r-htmlwidgets)
3364 ("r-motiv" ,r-motiv)
3365 ("r-scales" ,r-scales)
3367 (home-page "https://bioconductor.org/packages/motifStack/")
3368 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3370 "The motifStack package is designed for graphic representation of
3371 multiple motifs with different similarity scores. It works with both DNA/RNA
3372 sequence motifs and amino acid sequence motifs. In addition, it provides the
3373 flexibility for users to customize the graphic parameters such as the font
3374 type and symbol colors.")
3375 (license license:gpl2+)))
3377 (define-public r-genomicscores
3379 (name "r-genomicscores")
3384 (uri (bioconductor-uri "GenomicScores" version))
3387 "17bd61icfycc61b5dij1968h026w7vfd9miwdcbppak1j6s08idq"))))
3388 (properties `((upstream-name . "GenomicScores")))
3389 (build-system r-build-system)
3391 `(("r-annotationhub" ,r-annotationhub)
3392 ("r-biobase" ,r-biobase)
3393 ("r-biocgenerics" ,r-biocgenerics)
3394 ("r-biostrings" ,r-biostrings)
3395 ("r-bsgenome" ,r-bsgenome)
3396 ("r-genomeinfodb" ,r-genomeinfodb)
3397 ("r-genomicranges" ,r-genomicranges)
3398 ("r-iranges" ,r-iranges)
3399 ("r-s4vectors" ,r-s4vectors)
3401 (home-page "https://github.com/rcastelo/GenomicScores/")
3402 (synopsis "Work with genome-wide position-specific scores")
3404 "This package provides infrastructure to store and access genome-wide
3405 position-specific scores within R and Bioconductor.")
3406 (license license:artistic2.0)))
3408 (define-public r-atacseqqc
3410 (name "r-atacseqqc")
3415 (uri (bioconductor-uri "ATACseqQC" version))
3418 "03f130vcd6hd3fv2pg60id0ddd6qkwsyx73gm907xaayf42ar2pj"))))
3419 (properties `((upstream-name . "ATACseqQC")))
3420 (build-system r-build-system)
3422 `(("r-biocgenerics" ,r-biocgenerics)
3423 ("r-biostrings" ,r-biostrings)
3424 ("r-bsgenome" ,r-bsgenome)
3425 ("r-chippeakanno" ,r-chippeakanno)
3426 ("r-edger" ,r-edger)
3427 ("r-genomeinfodb" ,r-genomeinfodb)
3428 ("r-genomicalignments" ,r-genomicalignments)
3429 ("r-genomicranges" ,r-genomicranges)
3430 ("r-genomicscores" ,r-genomicscores)
3431 ("r-iranges" ,r-iranges)
3432 ("r-kernsmooth" ,r-kernsmooth)
3433 ("r-limma" ,r-limma)
3434 ("r-motifstack" ,r-motifstack)
3435 ("r-preseqr" ,r-preseqr)
3436 ("r-randomforest" ,r-randomforest)
3437 ("r-rsamtools" ,r-rsamtools)
3438 ("r-rtracklayer" ,r-rtracklayer)
3439 ("r-s4vectors" ,r-s4vectors)))
3440 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3441 (synopsis "ATAC-seq quality control")
3443 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3444 sequencing, is a rapid and sensitive method for chromatin accessibility
3445 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3446 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3447 assess whether their ATAC-seq experiment is successful. It includes
3448 diagnostic plots of fragment size distribution, proportion of mitochondria
3449 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3451 (license license:gpl2+)))
3453 (define-public r-gofuncr
3460 (uri (bioconductor-uri "GOfuncR" version))
3463 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3464 (properties `((upstream-name . "GOfuncR")))
3465 (build-system r-build-system)
3467 `(("r-annotationdbi" ,r-annotationdbi)
3468 ("r-genomicranges" ,r-genomicranges)
3469 ("r-gtools" ,r-gtools)
3470 ("r-iranges" ,r-iranges)
3471 ("r-mapplots" ,r-mapplots)
3473 ("r-vioplot" ,r-vioplot)))
3474 (home-page "https://bioconductor.org/packages/GOfuncR/")
3475 (synopsis "Gene ontology enrichment using FUNC")
3477 "GOfuncR performs a gene ontology enrichment analysis based on the
3478 ontology enrichment software FUNC. GO-annotations are obtained from
3479 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3480 included in the package and updated regularly. GOfuncR provides the standard
3481 candidate vs background enrichment analysis using the hypergeometric test, as
3482 well as three additional tests:
3485 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3486 @item a binomial test that is used when genes are associated with two counts,
3488 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3489 associated with four counts.
3492 To correct for multiple testing and interdependency of the tests, family-wise
3493 error rates are computed based on random permutations of the gene-associated
3494 variables. GOfuncR also provides tools for exploring the ontology graph and
3495 the annotations, and options to take gene-length or spatial clustering of
3496 genes into account. It is also possible to provide custom gene coordinates,
3497 annotations and ontologies.")
3498 (license license:gpl2+)))
3500 (define-public r-abaenrichment
3502 (name "r-abaenrichment")
3507 (uri (bioconductor-uri "ABAEnrichment" version))
3510 "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
3511 (properties `((upstream-name . "ABAEnrichment")))
3512 (build-system r-build-system)
3514 `(("r-abadata" ,r-abadata)
3515 ("r-data-table" ,r-data-table)
3516 ("r-gofuncr" ,r-gofuncr)
3517 ("r-gplots" ,r-gplots)
3518 ("r-gtools" ,r-gtools)
3519 ("r-rcpp" ,r-rcpp)))
3520 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3521 (synopsis "Gene expression enrichment in human brain regions")
3523 "The package ABAEnrichment is designed to test for enrichment of user
3524 defined candidate genes in the set of expressed genes in different human brain
3525 regions. The core function @code{aba_enrich} integrates the expression of the
3526 candidate gene set (averaged across donors) and the structural information of
3527 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3528 (license license:gpl2+)))
3530 (define-public r-annotationfuncs
3532 (name "r-annotationfuncs")
3537 (uri (bioconductor-uri "AnnotationFuncs" version))
3540 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3542 `((upstream-name . "AnnotationFuncs")))
3543 (build-system r-build-system)
3545 `(("r-annotationdbi" ,r-annotationdbi)
3547 (home-page "https://www.iysik.com/r/annotationfuncs")
3548 (synopsis "Annotation translation functions")
3550 "This package provides functions for handling translating between
3551 different identifieres using the Biocore Data Team data-packages (e.g.
3552 @code{org.Bt.eg.db}).")
3553 (license license:gpl2)))
3555 (define-public r-annotationtools
3557 (name "r-annotationtools")
3562 (uri (bioconductor-uri "annotationTools" version))
3565 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
3567 `((upstream-name . "annotationTools")))
3568 (build-system r-build-system)
3569 (propagated-inputs `(("r-biobase" ,r-biobase)))
3570 (home-page "https://bioconductor.org/packages/annotationTools/")
3571 (synopsis "Annotate microarrays and perform gene expression analyses")
3573 "This package provides functions to annotate microarrays, find orthologs,
3574 and integrate heterogeneous gene expression profiles using annotation and
3575 other molecular biology information available as flat file database (plain
3577 ;; Any version of the GPL.
3578 (license (list license:gpl2+))))
3580 (define-public r-allelicimbalance
3582 (name "r-allelicimbalance")
3587 (uri (bioconductor-uri "AllelicImbalance" version))
3590 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
3592 `((upstream-name . "AllelicImbalance")))
3593 (build-system r-build-system)
3595 `(("r-annotationdbi" ,r-annotationdbi)
3596 ("r-biocgenerics" ,r-biocgenerics)
3597 ("r-biostrings" ,r-biostrings)
3598 ("r-bsgenome" ,r-bsgenome)
3599 ("r-genomeinfodb" ,r-genomeinfodb)
3600 ("r-genomicalignments" ,r-genomicalignments)
3601 ("r-genomicfeatures" ,r-genomicfeatures)
3602 ("r-genomicranges" ,r-genomicranges)
3603 ("r-gridextra" ,r-gridextra)
3605 ("r-iranges" ,r-iranges)
3606 ("r-lattice" ,r-lattice)
3607 ("r-latticeextra" ,r-latticeextra)
3609 ("r-rsamtools" ,r-rsamtools)
3610 ("r-s4vectors" ,r-s4vectors)
3611 ("r-seqinr" ,r-seqinr)
3612 ("r-summarizedexperiment" ,r-summarizedexperiment)
3613 ("r-variantannotation" ,r-variantannotation)))
3614 (home-page "https://github.com/pappewaio/AllelicImbalance")
3615 (synopsis "Investigate allele-specific expression")
3617 "This package provides a framework for allele-specific expression
3618 investigation using RNA-seq data.")
3619 (license license:gpl3)))
3621 (define-public r-aucell
3628 (uri (bioconductor-uri "AUCell" version))
3631 "025q1as9pifbxa7hidlz634q6d7l73zx8mqy4rjbfrk7d5615xvm"))))
3632 (properties `((upstream-name . "AUCell")))
3633 (build-system r-build-system)
3635 `(("r-data-table" ,r-data-table)
3636 ("r-gseabase" ,r-gseabase)
3637 ("r-mixtools" ,r-mixtools)
3638 ("r-r-utils" ,r-r-utils)
3639 ("r-shiny" ,r-shiny)
3640 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3641 (home-page "https://bioconductor.org/packages/AUCell/")
3642 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
3644 "AUCell allows to identify cells with active gene sets (e.g. signatures,
3645 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
3646 Under the Curve} (AUC) to calculate whether a critical subset of the input
3647 gene set is enriched within the expressed genes for each cell. The
3648 distribution of AUC scores across all the cells allows exploring the relative
3649 expression of the signature. Since the scoring method is ranking-based,
3650 AUCell is independent of the gene expression units and the normalization
3651 procedure. In addition, since the cells are evaluated individually, it can
3652 easily be applied to bigger datasets, subsetting the expression matrix if
3654 (license license:gpl3)))
3656 (define-public r-ebimage
3663 (uri (bioconductor-uri "EBImage" version))
3666 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
3667 (properties `((upstream-name . "EBImage")))
3668 (build-system r-build-system)
3670 `(("r-abind" ,r-abind)
3671 ("r-biocgenerics" ,r-biocgenerics)
3672 ("r-fftwtools" ,r-fftwtools)
3673 ("r-htmltools" ,r-htmltools)
3674 ("r-htmlwidgets" ,r-htmlwidgets)
3676 ("r-locfit" ,r-locfit)
3678 ("r-rcurl" ,r-rcurl)
3679 ("r-tiff" ,r-tiff)))
3681 `(("r-knitr" ,r-knitr))) ; for vignettes
3682 (home-page "https://github.com/aoles/EBImage")
3683 (synopsis "Image processing and analysis toolbox for R")
3685 "EBImage provides general purpose functionality for image processing and
3686 analysis. In the context of (high-throughput) microscopy-based cellular
3687 assays, EBImage offers tools to segment cells and extract quantitative
3688 cellular descriptors. This allows the automation of such tasks using the R
3689 programming language and facilitates the use of other tools in the R
3690 environment for signal processing, statistical modeling, machine learning and
3691 visualization with image data.")
3692 ;; Any version of the LGPL.
3693 (license license:lgpl2.1+)))
3695 (define-public r-yamss
3702 (uri (bioconductor-uri "yamss" version))
3705 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
3706 (build-system r-build-system)
3708 `(("r-biocgenerics" ,r-biocgenerics)
3709 ("r-data-table" ,r-data-table)
3710 ("r-ebimage" ,r-ebimage)
3711 ("r-iranges" ,r-iranges)
3712 ("r-limma" ,r-limma)
3713 ("r-matrix" ,r-matrix)
3715 ("r-s4vectors" ,r-s4vectors)
3716 ("r-summarizedexperiment"
3717 ,r-summarizedexperiment)))
3718 (home-page "https://github.com/hansenlab/yamss")
3719 (synopsis "Tools for high-throughput metabolomics")
3721 "This package provides tools to analyze and visualize high-throughput
3722 metabolomics data acquired using chromatography-mass spectrometry. These tools
3723 preprocess data in a way that enables reliable and powerful differential
3725 (license license:artistic2.0)))
3727 (define-public r-gtrellis
3734 (uri (bioconductor-uri "gtrellis" version))
3737 "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y"))))
3738 (build-system r-build-system)
3740 `(("r-circlize" ,r-circlize)
3741 ("r-genomicranges" ,r-genomicranges)
3742 ("r-getoptlong" ,r-getoptlong)
3743 ("r-iranges" ,r-iranges)))
3744 (home-page "https://github.com/jokergoo/gtrellis")
3745 (synopsis "Genome level Trellis layout")
3747 "Genome level Trellis graph visualizes genomic data conditioned by
3748 genomic categories (e.g. chromosomes). For each genomic category, multiple
3749 dimensional data which are represented as tracks describe different features
3750 from different aspects. This package provides high flexibility to arrange
3751 genomic categories and to add self-defined graphics in the plot.")
3752 (license license:expat)))
3754 (define-public r-somaticsignatures
3756 (name "r-somaticsignatures")
3761 (uri (bioconductor-uri "SomaticSignatures" version))
3764 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
3766 `((upstream-name . "SomaticSignatures")))
3767 (build-system r-build-system)
3769 `(("r-biobase" ,r-biobase)
3770 ("r-biostrings" ,r-biostrings)
3771 ("r-genomeinfodb" ,r-genomeinfodb)
3772 ("r-genomicranges" ,r-genomicranges)
3773 ("r-ggbio" ,r-ggbio)
3774 ("r-ggplot2" ,r-ggplot2)
3775 ("r-iranges" ,r-iranges)
3777 ("r-pcamethods" ,r-pcamethods)
3778 ("r-proxy" ,r-proxy)
3779 ("r-reshape2" ,r-reshape2)
3780 ("r-s4vectors" ,r-s4vectors)
3781 ("r-variantannotation" ,r-variantannotation)))
3782 (home-page "https://github.com/juliangehring/SomaticSignatures")
3783 (synopsis "Somatic signatures")
3785 "This package identifies mutational signatures of @dfn{single nucleotide
3786 variants} (SNVs). It provides a infrastructure related to the methodology
3787 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
3788 decomposition algorithms.")
3789 (license license:expat)))
3791 (define-public r-yapsa
3798 (uri (bioconductor-uri "YAPSA" version))
3801 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
3802 (properties `((upstream-name . "YAPSA")))
3803 (build-system r-build-system)
3805 `(("r-circlize" ,r-circlize)
3806 ("r-complexheatmap" ,r-complexheatmap)
3807 ("r-corrplot" ,r-corrplot)
3808 ("r-dendextend" ,r-dendextend)
3809 ("r-genomeinfodb" ,r-genomeinfodb)
3810 ("r-genomicranges" ,r-genomicranges)
3811 ("r-getoptlong" ,r-getoptlong)
3812 ("r-ggplot2" ,r-ggplot2)
3813 ("r-gridextra" ,r-gridextra)
3814 ("r-gtrellis" ,r-gtrellis)
3815 ("r-keggrest" ,r-keggrest)
3817 ("r-pmcmr" ,r-pmcmr)
3818 ("r-reshape2" ,r-reshape2)
3819 ("r-somaticsignatures" ,r-somaticsignatures)
3820 ("r-variantannotation" ,r-variantannotation)))
3821 (home-page "https://bioconductor.org/packages/YAPSA/")
3822 (synopsis "Yet another package for signature analysis")
3824 "This package provides functions and routines useful in the analysis of
3825 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
3826 functions to perform a signature analysis with known signatures and a
3827 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
3829 (license license:gpl3)))
3831 (define-public r-gcrma
3838 (uri (bioconductor-uri "gcrma" version))
3841 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
3842 (build-system r-build-system)
3844 `(("r-affy" ,r-affy)
3845 ("r-affyio" ,r-affyio)
3846 ("r-biobase" ,r-biobase)
3847 ("r-biocmanager" ,r-biocmanager)
3848 ("r-biostrings" ,r-biostrings)
3849 ("r-xvector" ,r-xvector)))
3850 (home-page "https://bioconductor.org/packages/gcrma/")
3851 (synopsis "Background adjustment using sequence information")
3853 "Gcrma adjusts for background intensities in Affymetrix array data which
3854 include optical noise and @dfn{non-specific binding} (NSB). The main function
3855 @code{gcrma} converts background adjusted probe intensities to expression
3856 measures using the same normalization and summarization methods as a
3857 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
3858 to estimate probe affinity to NSB. The sequence information is summarized in
3859 a more complex way than the simple GC content. Instead, the base types (A, T,
3860 G or C) at each position along the probe determine the affinity of each probe.
3861 The parameters of the position-specific base contributions to the probe
3862 affinity is estimated in an NSB experiment in which only NSB but no
3863 gene-specific bidning is expected.")
3864 ;; Any version of the LGPL
3865 (license license:lgpl2.1+)))
3867 (define-public r-simpleaffy
3869 (name "r-simpleaffy")
3874 (uri (bioconductor-uri "simpleaffy" version))
3877 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
3878 (build-system r-build-system)
3880 `(("r-affy" ,r-affy)
3881 ("r-biobase" ,r-biobase)
3882 ("r-biocgenerics" ,r-biocgenerics)
3883 ("r-gcrma" ,r-gcrma)
3884 ("r-genefilter" ,r-genefilter)))
3885 (home-page "https://bioconductor.org/packages/simpleaffy/")
3886 (synopsis "Very simple high level analysis of Affymetrix data")
3888 "This package provides high level functions for reading Affy @file{.CEL}
3889 files, phenotypic data, and then computing simple things with it, such as
3890 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
3891 library. It also has some basic scatter plot functions and mechanisms for
3892 generating high resolution journal figures.")
3893 (license license:gpl2+)))
3895 (define-public r-yaqcaffy
3902 (uri (bioconductor-uri "yaqcaffy" version))
3905 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
3906 (build-system r-build-system)
3908 `(("r-simpleaffy" ,r-simpleaffy)))
3909 (home-page "https://bioconductor.org/packages/yaqcaffy/")
3910 (synopsis "Affymetrix quality control and reproducibility analysis")
3912 "This is a package that can be used for quality control of Affymetrix
3913 GeneChip expression data and reproducibility analysis of human whole genome
3914 chips with the MAQC reference datasets.")
3915 (license license:artistic2.0)))
3917 (define-public r-quantro
3924 (uri (bioconductor-uri "quantro" version))
3927 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
3928 (build-system r-build-system)
3930 `(("r-biobase" ,r-biobase)
3931 ("r-doparallel" ,r-doparallel)
3932 ("r-foreach" ,r-foreach)
3933 ("r-ggplot2" ,r-ggplot2)
3934 ("r-iterators" ,r-iterators)
3935 ("r-minfi" ,r-minfi)
3936 ("r-rcolorbrewer" ,r-rcolorbrewer)))
3937 (home-page "https://bioconductor.org/packages/quantro/")
3938 (synopsis "Test for when to use quantile normalization")
3940 "This package provides a data-driven test for the assumptions of quantile
3941 normalization using raw data such as objects that inherit eSets (e.g.
3942 ExpressionSet, MethylSet). Group level information about each sample (such as
3943 Tumor / Normal status) must also be provided because the test assesses if
3944 there are global differences in the distributions between the user-defined
3946 (license license:gpl3+)))
3948 (define-public r-yarn
3955 (uri (bioconductor-uri "yarn" version))
3958 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
3959 (build-system r-build-system)
3961 `(("r-biobase" ,r-biobase)
3962 ("r-biomart" ,r-biomart)
3963 ("r-downloader" ,r-downloader)
3964 ("r-edger" ,r-edger)
3965 ("r-gplots" ,r-gplots)
3966 ("r-limma" ,r-limma)
3967 ("r-matrixstats" ,r-matrixstats)
3968 ("r-preprocesscore" ,r-preprocesscore)
3969 ("r-quantro" ,r-quantro)
3970 ("r-rcolorbrewer" ,r-rcolorbrewer)
3971 ("r-readr" ,r-readr)))
3972 (home-page "https://bioconductor.org/packages/yarn/")
3973 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
3975 "Expedite large RNA-Seq analyses using a combination of previously
3976 developed tools. YARN is meant to make it easier for the user in performing
3977 basic mis-annotation quality control, filtering, and condition-aware
3978 normalization. YARN leverages many Bioconductor tools and statistical
3979 techniques to account for the large heterogeneity and sparsity found in very
3980 large RNA-seq experiments.")
3981 (license license:artistic2.0)))
3983 (define-public r-roar
3990 (uri (bioconductor-uri "roar" version))
3993 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
3994 (build-system r-build-system)
3996 `(("r-biocgenerics" ,r-biocgenerics)
3997 ("r-genomeinfodb" ,r-genomeinfodb)
3998 ("r-genomicalignments" ,r-genomicalignments)
3999 ("r-genomicranges" ,r-genomicranges)
4000 ("r-iranges" ,r-iranges)
4001 ("r-rtracklayer" ,r-rtracklayer)
4002 ("r-s4vectors" ,r-s4vectors)
4003 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4004 (home-page "https://github.com/vodkatad/roar/")
4005 (synopsis "Identify differential APA usage from RNA-seq alignments")
4007 "This package provides tools for identifying preferential usage of APA
4008 sites, comparing two biological conditions, starting from known alternative
4009 sites and alignments obtained from standard RNA-seq experiments.")
4010 (license license:gpl3)))
4012 (define-public r-xbseq
4019 (uri (bioconductor-uri "XBSeq" version))
4022 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4023 (properties `((upstream-name . "XBSeq")))
4024 (build-system r-build-system)
4026 `(("r-biobase" ,r-biobase)
4027 ("r-deseq2" ,r-deseq2)
4028 ("r-dplyr" ,r-dplyr)
4029 ("r-ggplot2" ,r-ggplot2)
4030 ("r-locfit" ,r-locfit)
4031 ("r-magrittr" ,r-magrittr)
4032 ("r-matrixstats" ,r-matrixstats)
4033 ("r-pracma" ,r-pracma)
4034 ("r-roar" ,r-roar)))
4035 (home-page "https://github.com/Liuy12/XBSeq")
4036 (synopsis "Test for differential expression for RNA-seq data")
4038 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4039 expression} (DE), where a statistical model was established based on the
4040 assumption that observed signals are the convolution of true expression
4041 signals and sequencing noises. The mapped reads in non-exonic regions are
4042 considered as sequencing noises, which follows a Poisson distribution. Given
4043 measurable observed signal and background noise from RNA-seq data, true
4044 expression signals, assuming governed by the negative binomial distribution,
4045 can be delineated and thus the accurate detection of differential expressed
4047 (license license:gpl3+)))
4049 (define-public r-massspecwavelet
4051 (name "r-massspecwavelet")
4056 (uri (bioconductor-uri "MassSpecWavelet" version))
4059 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4061 `((upstream-name . "MassSpecWavelet")))
4062 (build-system r-build-system)
4064 `(("r-waveslim" ,r-waveslim)))
4065 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4066 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4068 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4069 data mainly through the use of wavelet transforms. It supports peak detection
4070 based on @dfn{Continuous Wavelet Transform} (CWT).")
4071 (license license:lgpl2.0+)))
4073 (define-public r-xcms
4080 (uri (bioconductor-uri "xcms" version))
4083 "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
4084 (build-system r-build-system)
4086 `(("r-biobase" ,r-biobase)
4087 ("r-biocgenerics" ,r-biocgenerics)
4088 ("r-biocparallel" ,r-biocparallel)
4089 ("r-lattice" ,r-lattice)
4090 ("r-massspecwavelet" ,r-massspecwavelet)
4091 ("r-msnbase" ,r-msnbase)
4092 ("r-multtest" ,r-multtest)
4095 ("r-protgenerics" ,r-protgenerics)
4097 ("r-rcolorbrewer" ,r-rcolorbrewer)
4098 ("r-robustbase" ,r-robustbase)
4099 ("r-s4vectors" ,r-s4vectors)))
4100 (home-page "https://bioconductor.org/packages/xcms/")
4101 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4103 "This package provides a framework for processing and visualization of
4104 chromatographically separated and single-spectra mass spectral data. It
4105 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4106 data for high-throughput, untargeted analyte profiling.")
4107 (license license:gpl2+)))
4109 (define-public r-wrench
4116 (uri (bioconductor-uri "Wrench" version))
4119 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4120 (properties `((upstream-name . "Wrench")))
4121 (build-system r-build-system)
4123 `(("r-limma" ,r-limma)
4124 ("r-locfit" ,r-locfit)
4125 ("r-matrixstats" ,r-matrixstats)))
4126 (home-page "https://github.com/HCBravoLab/Wrench")
4127 (synopsis "Wrench normalization for sparse count data")
4129 "Wrench is a package for normalization sparse genomic count data, like
4130 that arising from 16s metagenomic surveys.")
4131 (license license:artistic2.0)))
4133 (define-public r-wiggleplotr
4135 (name "r-wiggleplotr")
4140 (uri (bioconductor-uri "wiggleplotr" version))
4143 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4144 (build-system r-build-system)
4146 `(("r-assertthat" ,r-assertthat)
4147 ("r-cowplot" ,r-cowplot)
4148 ("r-dplyr" ,r-dplyr)
4149 ("r-genomeinfodb" ,r-genomeinfodb)
4150 ("r-genomicranges" ,r-genomicranges)
4151 ("r-ggplot2" ,r-ggplot2)
4152 ("r-iranges" ,r-iranges)
4153 ("r-purrr" ,r-purrr)
4154 ("r-rtracklayer" ,r-rtracklayer)
4155 ("r-s4vectors" ,r-s4vectors)))
4156 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4157 (synopsis "Make read coverage plots from BigWig files")
4159 "This package provides tools to visualize read coverage from sequencing
4160 experiments together with genomic annotations (genes, transcripts, peaks).
4161 Introns of long transcripts can be rescaled to a fixed length for better
4162 visualization of exonic read coverage.")
4163 (license license:asl2.0)))
4165 (define-public r-widgettools
4167 (name "r-widgettools")
4172 (uri (bioconductor-uri "widgetTools" version))
4175 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4176 (properties `((upstream-name . "widgetTools")))
4177 (build-system r-build-system)
4178 (home-page "https://bioconductor.org/packages/widgetTools/")
4179 (synopsis "Tools for creating interactive tcltk widgets")
4181 "This package contains tools to support the construction of tcltk
4183 ;; Any version of the LGPL.
4184 (license license:lgpl3+)))
4186 (define-public r-webbioc
4193 (uri (bioconductor-uri "webbioc" version))
4196 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4197 (build-system r-build-system)
4199 `(("netpbm" ,netpbm)
4202 `(("r-affy" ,r-affy)
4203 ("r-annaffy" ,r-annaffy)
4204 ("r-biobase" ,r-biobase)
4205 ("r-biocmanager" ,r-biocmanager)
4206 ("r-gcrma" ,r-gcrma)
4207 ("r-multtest" ,r-multtest)
4208 ("r-qvalue" ,r-qvalue)
4210 (home-page "https://www.bioconductor.org/")
4211 (synopsis "Bioconductor web interface")
4213 "This package provides an integrated web interface for doing microarray
4214 analysis using several of the Bioconductor packages. It is intended to be
4215 deployed as a centralized bioinformatics resource for use by many users.
4216 Currently only Affymetrix oligonucleotide analysis is supported.")
4217 (license license:gpl2+)))
4219 (define-public r-zfpkm
4226 (uri (bioconductor-uri "zFPKM" version))
4229 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4230 (properties `((upstream-name . "zFPKM")))
4231 (build-system r-build-system)
4233 `(("r-checkmate" ,r-checkmate)
4234 ("r-dplyr" ,r-dplyr)
4235 ("r-ggplot2" ,r-ggplot2)
4236 ("r-summarizedexperiment" ,r-summarizedexperiment)
4237 ("r-tidyr" ,r-tidyr)))
4238 (home-page "https://github.com/ronammar/zFPKM/")
4239 (synopsis "Functions to facilitate zFPKM transformations")
4241 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4242 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4244 (license license:gpl3)))
4246 (define-public r-rbowtie2
4253 (uri (bioconductor-uri "Rbowtie2" version))
4256 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4257 (properties `((upstream-name . "Rbowtie2")))
4258 (build-system r-build-system)
4261 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4262 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4264 "This package provides an R wrapper of the popular @code{bowtie2}
4265 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4266 rapid adapter trimming, identification, and read merging.")
4267 (license license:gpl3+)))
4269 (define-public r-progeny
4276 (uri (bioconductor-uri "progeny" version))
4279 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4280 (build-system r-build-system)
4281 (propagated-inputs `(("r-biobase" ,r-biobase)))
4282 (home-page "https://github.com/saezlab/progeny")
4283 (synopsis "Pathway responsive gene activity inference")
4285 "This package provides a function to infer pathway activity from gene
4286 expression. It contains the linear model inferred in the publication
4287 \"Perturbation-response genes reveal signaling footprints in cancer gene
4289 (license license:asl2.0)))
4291 (define-public r-arrmnormalization
4293 (name "r-arrmnormalization")
4298 (uri (bioconductor-uri "ARRmNormalization" version))
4301 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4303 `((upstream-name . "ARRmNormalization")))
4304 (build-system r-build-system)
4305 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4306 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4307 (synopsis "Adaptive robust regression normalization for methylation data")
4309 "This is a package to perform the @dfn{Adaptive Robust Regression
4310 method} (ARRm) for the normalization of methylation data from the Illumina
4311 Infinium HumanMethylation 450k assay.")
4312 (license license:artistic2.0)))
4314 (define-public r-biocfilecache
4316 (name "r-biocfilecache")
4321 (uri (bioconductor-uri "BiocFileCache" version))
4324 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4325 (properties `((upstream-name . "BiocFileCache")))
4326 (build-system r-build-system)
4328 `(("r-curl" ,r-curl)
4330 ("r-dbplyr" ,r-dbplyr)
4331 ("r-dplyr" ,r-dplyr)
4333 ("r-rappdirs" ,r-rappdirs)
4334 ("r-rsqlite" ,r-rsqlite)))
4335 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4336 (synopsis "Manage files across sessions")
4338 "This package creates a persistent on-disk cache of files that the user
4339 can add, update, and retrieve. It is useful for managing resources (such as
4340 custom Txdb objects) that are costly or difficult to create, web resources,
4341 and data files used across sessions.")
4342 (license license:artistic2.0)))
4344 (define-public r-iclusterplus
4346 (name "r-iclusterplus")
4351 (uri (bioconductor-uri "iClusterPlus" version))
4354 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4355 (properties `((upstream-name . "iClusterPlus")))
4356 (build-system r-build-system)
4357 (native-inputs `(("gfortran" ,gfortran)))
4358 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4359 (synopsis "Integrative clustering of multi-type genomic data")
4361 "iClusterPlus is developed for integrative clustering analysis of
4362 multi-type genomic data and is an enhanced version of iCluster proposed and
4363 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4364 from the experiments where biological samples (e.g. tumor samples) are
4365 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4366 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4367 on. In the iClusterPlus model, binary observations such as somatic mutation
4368 are modeled as Binomial processes; categorical observations such as copy
4369 number states are realizations of Multinomial random variables; counts are
4370 modeled as Poisson random processes; and continuous measures are modeled by
4371 Gaussian distributions.")
4372 (license license:gpl2+)))
4374 (define-public r-rbowtie
4381 (uri (bioconductor-uri "Rbowtie" version))
4384 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4385 (properties `((upstream-name . "Rbowtie")))
4386 (build-system r-build-system)
4389 (home-page "https://bioconductor.org/packages/Rbowtie/")
4390 (synopsis "R bowtie wrapper")
4392 "This package provides an R wrapper around the popular bowtie short read
4393 aligner and around SpliceMap, a de novo splice junction discovery and
4395 (license license:artistic2.0)))
4397 (define-public r-sgseq
4404 (uri (bioconductor-uri "SGSeq" version))
4407 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4408 (properties `((upstream-name . "SGSeq")))
4409 (build-system r-build-system)
4411 `(("r-annotationdbi" ,r-annotationdbi)
4412 ("r-biocgenerics" ,r-biocgenerics)
4413 ("r-biostrings" ,r-biostrings)
4414 ("r-genomeinfodb" ,r-genomeinfodb)
4415 ("r-genomicalignments" ,r-genomicalignments)
4416 ("r-genomicfeatures" ,r-genomicfeatures)
4417 ("r-genomicranges" ,r-genomicranges)
4418 ("r-igraph" ,r-igraph)
4419 ("r-iranges" ,r-iranges)
4420 ("r-rsamtools" ,r-rsamtools)
4421 ("r-rtracklayer" ,r-rtracklayer)
4422 ("r-runit" ,r-runit)
4423 ("r-s4vectors" ,r-s4vectors)
4424 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4425 (home-page "https://bioconductor.org/packages/SGSeq/")
4426 (synopsis "Splice event prediction and quantification from RNA-seq data")
4428 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4429 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4430 represented as a splice graph, which can be obtained from existing annotation
4431 or predicted from the mapped sequence reads. Splice events are identified
4432 from the graph and are quantified locally using structurally compatible reads
4433 at the start or end of each splice variant. The software includes functions
4434 for splice event prediction, quantification, visualization and
4436 (license license:artistic2.0)))
4438 (define-public r-rhisat2
4445 (uri (bioconductor-uri "Rhisat2" version))
4448 "01jhj5vvfl4n2d0nl3nd1iw9nii85mgw2adnrmxb8wwlxgy240vr"))))
4449 (properties `((upstream-name . "Rhisat2")))
4450 (build-system r-build-system)
4452 `(("which" ,which)))
4454 `(("r-genomicfeatures" ,r-genomicfeatures)
4455 ("r-genomicranges" ,r-genomicranges)
4456 ("r-sgseq" ,r-sgseq)))
4457 (home-page "https://github.com/fmicompbio/Rhisat2")
4458 (synopsis "R Wrapper for HISAT2 sequence aligner")
4460 "This package provides an R interface to the HISAT2 spliced short-read
4461 aligner by Kim et al. (2015). The package contains wrapper functions to
4462 create a genome index and to perform the read alignment to the generated
4464 (license license:gpl3)))
4466 (define-public r-quasr
4473 (uri (bioconductor-uri "QuasR" version))
4476 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4477 (properties `((upstream-name . "QuasR")))
4478 (build-system r-build-system)
4482 `(("r-annotationdbi" ,r-annotationdbi)
4483 ("r-biobase" ,r-biobase)
4484 ("r-biocgenerics" ,r-biocgenerics)
4485 ("r-biocmanager" ,r-biocmanager)
4486 ("r-biocparallel" ,r-biocparallel)
4487 ("r-biostrings" ,r-biostrings)
4488 ("r-bsgenome" ,r-bsgenome)
4489 ("r-genomeinfodb" ,r-genomeinfodb)
4490 ("r-genomicalignments" ,r-genomicalignments)
4491 ("r-genomicfeatures" ,r-genomicfeatures)
4492 ("r-genomicfiles" ,r-genomicfiles)
4493 ("r-genomicranges" ,r-genomicranges)
4494 ("r-iranges" ,r-iranges)
4495 ("r-rbowtie" ,r-rbowtie)
4496 ("r-rhisat2" ,r-rhisat2)
4497 ("r-rhtslib" ,r-rhtslib)
4498 ("r-rsamtools" ,r-rsamtools)
4499 ("r-rtracklayer" ,r-rtracklayer)
4500 ("r-s4vectors" ,r-s4vectors)
4501 ("r-shortread" ,r-shortread)))
4502 (home-page "https://bioconductor.org/packages/QuasR/")
4503 (synopsis "Quantify and annotate short reads in R")
4505 "This package provides a framework for the quantification and analysis of
4506 short genomic reads. It covers a complete workflow starting from raw sequence
4507 reads, over creation of alignments and quality control plots, to the
4508 quantification of genomic regions of interest.")
4509 (license license:gpl2)))
4511 (define-public r-rqc
4518 (uri (bioconductor-uri "Rqc" version))
4521 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
4522 (properties `((upstream-name . "Rqc")))
4523 (build-system r-build-system)
4525 `(("r-biocgenerics" ,r-biocgenerics)
4526 ("r-biocparallel" ,r-biocparallel)
4527 ("r-biocstyle" ,r-biocstyle)
4528 ("r-biostrings" ,r-biostrings)
4529 ("r-biovizbase" ,r-biovizbase)
4530 ("r-genomicalignments" ,r-genomicalignments)
4531 ("r-genomicfiles" ,r-genomicfiles)
4532 ("r-ggplot2" ,r-ggplot2)
4533 ("r-iranges" ,r-iranges)
4534 ("r-knitr" ,r-knitr)
4535 ("r-markdown" ,r-markdown)
4538 ("r-reshape2" ,r-reshape2)
4539 ("r-rsamtools" ,r-rsamtools)
4540 ("r-s4vectors" ,r-s4vectors)
4541 ("r-shiny" ,r-shiny)
4542 ("r-shortread" ,r-shortread)))
4543 (home-page "https://github.com/labbcb/Rqc")
4544 (synopsis "Quality control tool for high-throughput sequencing data")
4546 "Rqc is an optimized tool designed for quality control and assessment of
4547 high-throughput sequencing data. It performs parallel processing of entire
4548 files and produces a report which contains a set of high-resolution
4550 (license license:gpl2+)))