1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
6 ;;; This file is part of GNU Guix.
8 ;;; GNU Guix is free software; you can redistribute it and/or modify it
9 ;;; under the terms of the GNU General Public License as published by
10 ;;; the Free Software Foundation; either version 3 of the License, or (at
11 ;;; your option) any later version.
13 ;;; GNU Guix is distributed in the hope that it will be useful, but
14 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
15 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 ;;; GNU General Public License for more details.
18 ;;; You should have received a copy of the GNU General Public License
19 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
21 (define-module (gnu packages bioconductor)
22 #:use-module ((guix licenses) #:prefix license:)
23 #:use-module (guix packages)
24 #:use-module (guix download)
25 #:use-module (guix build-system r)
26 #:use-module (gnu packages)
27 #:use-module (gnu packages bioinformatics)
28 #:use-module (gnu packages cran)
29 #:use-module (gnu packages compression)
30 #:use-module (gnu packages gcc)
31 #:use-module (gnu packages graph)
32 #:use-module (gnu packages haskell)
33 #:use-module (gnu packages image)
34 #:use-module (gnu packages maths)
35 #:use-module (gnu packages pkg-config)
36 #:use-module (gnu packages statistics)
37 #:use-module (gnu packages web))
42 (define-public r-bsgenome-celegans-ucsc-ce6
44 (name "r-bsgenome-celegans-ucsc-ce6")
48 ;; We cannot use bioconductor-uri here because this tarball is
49 ;; located under "data/annotation/" instead of "bioc/".
50 (uri (string-append "https://www.bioconductor.org/packages/"
51 "release/data/annotation/src/contrib/"
52 "BSgenome.Celegans.UCSC.ce6_"
56 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
58 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
59 (build-system r-build-system)
60 ;; As this package provides little more than a very large data file it
61 ;; doesn't make sense to build substitutes.
62 (arguments `(#:substitutable? #f))
64 `(("r-bsgenome" ,r-bsgenome)))
66 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
67 (synopsis "Full genome sequences for Worm")
69 "This package provides full genome sequences for Caenorhabditis
70 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
72 (license license:artistic2.0)))
74 (define-public r-bsgenome-celegans-ucsc-ce10
76 (name "r-bsgenome-celegans-ucsc-ce10")
80 ;; We cannot use bioconductor-uri here because this tarball is
81 ;; located under "data/annotation/" instead of "bioc/".
82 (uri (string-append "https://www.bioconductor.org/packages/"
83 "release/data/annotation/src/contrib/"
84 "BSgenome.Celegans.UCSC.ce10_"
88 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
90 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
91 (build-system r-build-system)
92 ;; As this package provides little more than a very large data file it
93 ;; doesn't make sense to build substitutes.
94 (arguments `(#:substitutable? #f))
96 `(("r-bsgenome" ,r-bsgenome)))
98 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
99 (synopsis "Full genome sequences for Worm")
101 "This package provides full genome sequences for Caenorhabditis
102 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
104 (license license:artistic2.0)))
106 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
108 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
112 ;; We cannot use bioconductor-uri here because this tarball is
113 ;; located under "data/annotation/" instead of "bioc/".
114 (uri (string-append "https://www.bioconductor.org/packages/"
115 "release/data/annotation/src/contrib/"
116 "BSgenome.Dmelanogaster.UCSC.dm6_"
120 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
122 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
123 (build-system r-build-system)
124 ;; As this package provides little more than a very large data file it
125 ;; doesn't make sense to build substitutes.
126 (arguments `(#:substitutable? #f))
128 `(("r-bsgenome" ,r-bsgenome)))
130 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
131 (synopsis "Full genome sequences for Fly")
133 "This package provides full genome sequences for Drosophila
134 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
136 (license license:artistic2.0)))
138 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
140 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
144 ;; We cannot use bioconductor-uri here because this tarball is
145 ;; located under "data/annotation/" instead of "bioc/".
146 (uri (string-append "https://www.bioconductor.org/packages/"
147 "release/data/annotation/src/contrib/"
148 "BSgenome.Dmelanogaster.UCSC.dm3_"
152 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
154 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
155 (build-system r-build-system)
156 ;; As this package provides little more than a very large data file it
157 ;; doesn't make sense to build substitutes.
158 (arguments `(#:substitutable? #f))
160 `(("r-bsgenome" ,r-bsgenome)))
162 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
163 (synopsis "Full genome sequences for Fly")
165 "This package provides full genome sequences for Drosophila
166 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
167 Biostrings objects.")
168 (license license:artistic2.0)))
170 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
172 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
176 ;; We cannot use bioconductor-uri here because this tarball is
177 ;; located under "data/annotation/" instead of "bioc/".
178 (uri (string-append "http://www.bioconductor.org/packages/"
179 "release/data/annotation/src/contrib/"
180 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
184 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
186 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
187 (build-system r-build-system)
189 `(("r-bsgenome" ,r-bsgenome)
190 ("r-bsgenome-dmelanogaster-ucsc-dm3"
191 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
192 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
193 (synopsis "Full masked genome sequences for Fly")
195 "This package provides full masked genome sequences for Drosophila
196 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
197 Biostrings objects. The sequences are the same as in
198 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
199 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
200 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
201 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
202 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
203 (license license:artistic2.0)))
205 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
207 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
211 ;; We cannot use bioconductor-uri here because this tarball is
212 ;; located under "data/annotation/" instead of "bioc/".
213 (uri (string-append "https://www.bioconductor.org/packages/"
214 "release/data/annotation/src/contrib/"
215 "BSgenome.Hsapiens.1000genomes.hs37d5_"
219 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
221 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
222 (build-system r-build-system)
223 ;; As this package provides little more than a very large data file it
224 ;; doesn't make sense to build substitutes.
225 (arguments `(#:substitutable? #f))
227 `(("r-bsgenome" ,r-bsgenome)))
229 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
230 (synopsis "Full genome sequences for Homo sapiens")
232 "This package provides full genome sequences for Homo sapiens from
233 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
234 (license license:artistic2.0)))
236 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
238 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
242 ;; We cannot use bioconductor-uri here because this tarball is
243 ;; located under "data/annotation/" instead of "bioc/".
244 (uri (string-append "http://www.bioconductor.org/packages/"
245 "release/data/annotation/src/contrib/"
246 "BSgenome.Hsapiens.UCSC.hg19.masked_"
250 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
252 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
253 (build-system r-build-system)
255 `(("r-bsgenome" ,r-bsgenome)
256 ("r-bsgenome-hsapiens-ucsc-hg19"
257 ,r-bsgenome-hsapiens-ucsc-hg19)))
258 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
259 (synopsis "Full masked genome sequences for Homo sapiens")
261 "This package provides full genome sequences for Homo sapiens (Human) as
262 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
263 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
264 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
265 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
266 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
267 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
269 (license license:artistic2.0)))
271 (define-public r-bsgenome-mmusculus-ucsc-mm9
273 (name "r-bsgenome-mmusculus-ucsc-mm9")
277 ;; We cannot use bioconductor-uri here because this tarball is
278 ;; located under "data/annotation/" instead of "bioc/".
279 (uri (string-append "https://www.bioconductor.org/packages/"
280 "release/data/annotation/src/contrib/"
281 "BSgenome.Mmusculus.UCSC.mm9_"
285 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
287 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
288 (build-system r-build-system)
289 ;; As this package provides little more than a very large data file it
290 ;; doesn't make sense to build substitutes.
291 (arguments `(#:substitutable? #f))
293 `(("r-bsgenome" ,r-bsgenome)))
295 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
296 (synopsis "Full genome sequences for Mouse")
298 "This package provides full genome sequences for Mus musculus (Mouse) as
299 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
300 (license license:artistic2.0)))
302 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
304 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
308 ;; We cannot use bioconductor-uri here because this tarball is
309 ;; located under "data/annotation/" instead of "bioc/".
310 (uri (string-append "http://www.bioconductor.org/packages/"
311 "release/data/annotation/src/contrib/"
312 "BSgenome.Mmusculus.UCSC.mm9.masked_"
316 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
318 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
319 (build-system r-build-system)
321 `(("r-bsgenome" ,r-bsgenome)
322 ("r-bsgenome-mmusculus-ucsc-mm9"
323 ,r-bsgenome-mmusculus-ucsc-mm9)))
324 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
325 (synopsis "Full masked genome sequences for Mouse")
327 "This package provides full genome sequences for Mus musculus (Mouse) as
328 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
329 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
330 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
331 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
332 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
333 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
335 (license license:artistic2.0)))
337 (define-public r-bsgenome-mmusculus-ucsc-mm10
339 (name "r-bsgenome-mmusculus-ucsc-mm10")
343 ;; We cannot use bioconductor-uri here because this tarball is
344 ;; located under "data/annotation/" instead of "bioc/".
345 (uri (string-append "https://www.bioconductor.org/packages/"
346 "release/data/annotation/src/contrib/"
347 "BSgenome.Mmusculus.UCSC.mm10_"
351 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
353 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
354 (build-system r-build-system)
355 ;; As this package provides little more than a very large data file it
356 ;; doesn't make sense to build substitutes.
357 (arguments `(#:substitutable? #f))
359 `(("r-bsgenome" ,r-bsgenome)))
361 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
362 (synopsis "Full genome sequences for Mouse")
364 "This package provides full genome sequences for Mus
365 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
366 in Biostrings objects.")
367 (license license:artistic2.0)))
369 (define-public r-org-ce-eg-db
371 (name "r-org-ce-eg-db")
375 ;; We cannot use bioconductor-uri here because this tarball is
376 ;; located under "data/annotation/" instead of "bioc/".
377 (uri (string-append "https://www.bioconductor.org/packages/"
378 "release/data/annotation/src/contrib/"
379 "org.Ce.eg.db_" version ".tar.gz"))
382 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
384 `((upstream-name . "org.Ce.eg.db")))
385 (build-system r-build-system)
387 `(("r-annotationdbi" ,r-annotationdbi)))
388 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
389 (synopsis "Genome wide annotation for Worm")
391 "This package provides mappings from Entrez gene identifiers to various
392 annotations for the genome of the model worm Caenorhabditis elegans.")
393 (license license:artistic2.0)))
395 (define-public r-org-dm-eg-db
397 (name "r-org-dm-eg-db")
401 ;; We cannot use bioconductor-uri here because this tarball is
402 ;; located under "data/annotation/" instead of "bioc/".
403 (uri (string-append "https://www.bioconductor.org/packages/"
404 "release/data/annotation/src/contrib/"
405 "org.Dm.eg.db_" version ".tar.gz"))
408 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
410 `((upstream-name . "org.Dm.eg.db")))
411 (build-system r-build-system)
413 `(("r-annotationdbi" ,r-annotationdbi)))
414 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
415 (synopsis "Genome wide annotation for Fly")
417 "This package provides mappings from Entrez gene identifiers to various
418 annotations for the genome of the model fruit fly Drosophila melanogaster.")
419 (license license:artistic2.0)))
421 (define-public r-org-dr-eg-db
423 (name "r-org-dr-eg-db")
427 ;; We cannot use bioconductor-uri here because this tarball is
428 ;; located under "data/annotation/" instead of "bioc/".
429 (uri (string-append "https://www.bioconductor.org/packages/"
430 "release/data/annotation/src/contrib/"
431 "org.Dr.eg.db_" version ".tar.gz"))
434 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
436 `((upstream-name . "org.Dr.eg.db")))
437 (build-system r-build-system)
439 `(("r-annotationdbi" ,r-annotationdbi)))
440 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
441 (synopsis "Annotation for Zebrafish")
443 "This package provides genome wide annotations for Zebrafish, primarily
444 based on mapping using Entrez Gene identifiers.")
445 (license license:artistic2.0)))
447 (define-public r-org-hs-eg-db
449 (name "r-org-hs-eg-db")
453 ;; We cannot use bioconductor-uri here because this tarball is
454 ;; located under "data/annotation/" instead of "bioc/".
455 (uri (string-append "https://www.bioconductor.org/packages/"
456 "release/data/annotation/src/contrib/"
457 "org.Hs.eg.db_" version ".tar.gz"))
460 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
462 `((upstream-name . "org.Hs.eg.db")))
463 (build-system r-build-system)
465 `(("r-annotationdbi" ,r-annotationdbi)))
466 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
467 (synopsis "Genome wide annotation for Human")
469 "This package contains genome-wide annotations for Human, primarily based
470 on mapping using Entrez Gene identifiers.")
471 (license license:artistic2.0)))
473 (define-public r-org-mm-eg-db
475 (name "r-org-mm-eg-db")
479 ;; We cannot use bioconductor-uri here because this tarball is
480 ;; located under "data/annotation/" instead of "bioc/".
481 (uri (string-append "https://www.bioconductor.org/packages/"
482 "release/data/annotation/src/contrib/"
483 "org.Mm.eg.db_" version ".tar.gz"))
486 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
488 `((upstream-name . "org.Mm.eg.db")))
489 (build-system r-build-system)
491 `(("r-annotationdbi" ,r-annotationdbi)))
492 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
493 (synopsis "Genome wide annotation for Mouse")
495 "This package provides mappings from Entrez gene identifiers to various
496 annotations for the genome of the model mouse Mus musculus.")
497 (license license:artistic2.0)))
499 (define-public r-bsgenome-hsapiens-ucsc-hg19
501 (name "r-bsgenome-hsapiens-ucsc-hg19")
505 ;; We cannot use bioconductor-uri here because this tarball is
506 ;; located under "data/annotation/" instead of "bioc/".
507 (uri (string-append "https://www.bioconductor.org/packages/"
508 "release/data/annotation/src/contrib/"
509 "BSgenome.Hsapiens.UCSC.hg19_"
513 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
515 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
516 (build-system r-build-system)
517 ;; As this package provides little more than a very large data file it
518 ;; doesn't make sense to build substitutes.
519 (arguments `(#:substitutable? #f))
521 `(("r-bsgenome" ,r-bsgenome)))
523 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
524 (synopsis "Full genome sequences for Homo sapiens")
526 "This package provides full genome sequences for Homo sapiens as provided
527 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
528 (license license:artistic2.0)))
530 (define-public r-genelendatabase
532 (name "r-genelendatabase")
537 ;; We cannot use bioconductor-uri here because this tarball is
538 ;; located under "data/experiment/" instead of "bioc/".
539 (uri (string-append "https://bioconductor.org/packages/"
540 "release/data/experiment/src/contrib"
541 "/geneLenDataBase_" version ".tar.gz"))
544 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
546 `((upstream-name . "geneLenDataBase")))
547 (build-system r-build-system)
549 `(("r-rtracklayer" ,r-rtracklayer)
550 ("r-genomicfeatures" ,r-genomicfeatures)))
551 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
552 (synopsis "Lengths of mRNA transcripts for a number of genomes")
554 "This package provides the lengths of mRNA transcripts for a number of
555 genomes and gene ID formats, largely based on the UCSC table browser.")
556 (license license:lgpl2.0+)))
558 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
560 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
564 ;; We cannot use bioconductor-uri here because this tarball is
565 ;; located under "data/annotation/" instead of "bioc/".
566 (uri (string-append "https://bioconductor.org/packages/"
567 "release/data/annotation/src/contrib"
568 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
572 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
574 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
575 (build-system r-build-system)
576 ;; As this package provides little more than a very large data file it
577 ;; doesn't make sense to build substitutes.
578 (arguments `(#:substitutable? #f))
580 `(("r-genomicfeatures" ,r-genomicfeatures)))
582 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
583 (synopsis "Annotation package for human genome in TxDb format")
585 "This package provides an annotation database of Homo sapiens genome
586 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
587 track. The database is exposed as a @code{TxDb} object.")
588 (license license:artistic2.0)))
590 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
592 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
596 ;; We cannot use bioconductor-uri here because this tarball is
597 ;; located under "data/annotation/" instead of "bioc/".
598 (uri (string-append "https://bioconductor.org/packages/"
599 "release/data/annotation/src/contrib"
600 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
604 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
606 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
607 (build-system r-build-system)
609 `(("r-genomicfeatures" ,r-genomicfeatures)
610 ("r-annotationdbi" ,r-annotationdbi)))
612 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
613 (synopsis "Annotation package for mouse genome in TxDb format")
615 "This package provides an annotation database of Mouse genome data. It
616 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
617 database is exposed as a @code{TxDb} object.")
618 (license license:artistic2.0)))
620 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
622 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
626 ;; We cannot use bioconductor-uri here because this tarball is
627 ;; located under "data/annotation/" instead of "bioc/".
628 (uri (string-append "https://www.bioconductor.org/packages/"
629 "release/data/annotation/src/contrib/"
630 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
634 "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
636 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
637 (build-system r-build-system)
638 ;; As this package provides little more than a very large data file it
639 ;; doesn't make sense to build substitutes.
640 (arguments `(#:substitutable? #f))
642 `(("r-bsgenome" ,r-bsgenome)
643 ("r-genomicfeatures" ,r-genomicfeatures)
644 ("r-annotationdbi" ,r-annotationdbi)))
646 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
647 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
649 "This package loads a TxDb object, which is an R interface to
650 prefabricated databases contained in this package. This package provides
651 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
652 based on the knownGene track.")
653 (license license:artistic2.0)))
655 (define-public r-fdb-infiniummethylation-hg19
657 (name "r-fdb-infiniummethylation-hg19")
661 ;; We cannot use bioconductor-uri here because this tarball is
662 ;; located under "data/annotation/" instead of "bioc/".
663 (uri (string-append "https://www.bioconductor.org/packages/"
664 "release/data/annotation/src/contrib/"
665 "FDb.InfiniumMethylation.hg19_"
669 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
671 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
672 (build-system r-build-system)
674 `(("r-biostrings" ,r-biostrings)
675 ("r-genomicfeatures" ,r-genomicfeatures)
676 ("r-annotationdbi" ,r-annotationdbi)
677 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
678 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
679 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
680 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
682 "This is an annotation package for Illumina Infinium DNA methylation
683 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
685 (license license:artistic2.0)))
687 (define-public r-illuminahumanmethylationepicmanifest
689 (name "r-illuminahumanmethylationepicmanifest")
693 ;; We cannot use bioconductor-uri here because this tarball is
694 ;; located under "data/annotation/" instead of "bioc/".
695 (uri (string-append "https://www.bioconductor.org/packages/"
696 "release/data/annotation/src/contrib/"
697 "IlluminaHumanMethylationEPICmanifest_"
701 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
703 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
704 (build-system r-build-system)
706 `(("r-minfi" ,r-minfi)))
707 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
708 (synopsis "Manifest for Illumina's EPIC methylation arrays")
710 "This is a manifest package for Illumina's EPIC methylation arrays.")
711 (license license:artistic2.0)))
713 (define-public r-do-db
719 ;; We cannot use bioconductor-uri here because this tarball is
720 ;; located under "data/annotation/" instead of "bioc/".
721 (uri (string-append "https://www.bioconductor.org/packages/"
722 "release/data/annotation/src/contrib/"
723 "DO.db_" version ".tar.gz"))
726 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
728 `((upstream-name . "DO.db")))
729 (build-system r-build-system)
731 `(("r-annotationdbi" ,r-annotationdbi)))
732 (home-page "https://www.bioconductor.org/packages/DO.db/")
733 (synopsis "Annotation maps describing the entire Disease Ontology")
735 "This package provides a set of annotation maps describing the entire
737 (license license:artistic2.0)))
742 (define-public r-abadata
748 ;; We cannot use bioconductor-uri here because this tarball is
749 ;; located under "data/experiment/" instead of "bioc/".
750 (uri (string-append "https://www.bioconductor.org/packages/"
751 "release/data/experiment/src/contrib/"
752 "ABAData_" version ".tar.gz"))
755 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
757 `((upstream-name . "ABAData")))
758 (build-system r-build-system)
760 `(("r-annotationdbi" ,r-annotationdbi)))
761 (home-page "https://www.bioconductor.org/packages/ABAData/")
762 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
764 "This package provides the data for the gene expression enrichment
765 analysis conducted in the package ABAEnrichment. The package includes three
766 datasets which are derived from the Allen Brain Atlas:
769 @item Gene expression data from Human Brain (adults) averaged across donors,
770 @item Gene expression data from the Developing Human Brain pooled into five
771 age categories and averaged across donors, and
772 @item a developmental effect score based on the Developing Human Brain
776 All datasets are restricted to protein coding genes.")
777 (license license:gpl2+)))
779 (define-public r-hsmmsinglecell
781 (name "r-hsmmsinglecell")
785 ;; We cannot use bioconductor-uri here because this tarball is
786 ;; located under "data/experiment/" instead of "bioc/".
787 (uri (string-append "https://www.bioconductor.org/packages/"
788 "release/data/experiment/src/contrib/"
789 "HSMMSingleCell_" version ".tar.gz"))
792 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
794 `((upstream-name . "HSMMSingleCell")))
795 (build-system r-build-system)
796 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
797 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
799 "Skeletal myoblasts undergo a well-characterized sequence of
800 morphological and transcriptional changes during differentiation. In this
801 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
802 under high mitogen conditions (GM) and then differentiated by switching to
803 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
804 hundred cells taken over a time-course of serum-induced differentiation.
805 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
806 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
807 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
808 which were then sequenced to a depth of ~4 million reads per library,
809 resulting in a complete gene expression profile for each cell.")
810 (license license:artistic2.0)))
815 (define-public r-biocgenerics
817 (name "r-biocgenerics")
821 (uri (bioconductor-uri "BiocGenerics" version))
824 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
826 `((upstream-name . "BiocGenerics")))
827 (build-system r-build-system)
828 (home-page "https://bioconductor.org/packages/BiocGenerics")
829 (synopsis "S4 generic functions for Bioconductor")
831 "This package provides S4 generic functions needed by many Bioconductor
833 (license license:artistic2.0)))
835 (define-public r-annotate
842 (uri (bioconductor-uri "annotate" version))
845 "0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"))))
846 (build-system r-build-system)
848 `(("r-annotationdbi" ,r-annotationdbi)
849 ("r-biobase" ,r-biobase)
850 ("r-biocgenerics" ,r-biocgenerics)
854 ("r-xtable" ,r-xtable)))
856 "https://bioconductor.org/packages/annotate")
857 (synopsis "Annotation for microarrays")
858 (description "This package provides R environments for the annotation of
860 (license license:artistic2.0)))
862 (define-public r-hpar
869 (uri (bioconductor-uri "hpar" version))
872 "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
873 (build-system r-build-system)
874 (home-page "https://bioconductor.org/packages/hpar/")
875 (synopsis "Human Protein Atlas in R")
876 (description "This package provides a simple interface to and data from
877 the Human Protein Atlas project.")
878 (license license:artistic2.0)))
880 (define-public r-regioner
887 (uri (bioconductor-uri "regioneR" version))
890 "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
891 (properties `((upstream-name . "regioneR")))
892 (build-system r-build-system)
894 `(("r-biostrings" ,r-biostrings)
895 ("r-bsgenome" ,r-bsgenome)
896 ("r-genomeinfodb" ,r-genomeinfodb)
897 ("r-genomicranges" ,r-genomicranges)
898 ("r-iranges" ,r-iranges)
899 ("r-memoise" ,r-memoise)
900 ("r-rtracklayer" ,r-rtracklayer)
901 ("r-s4vectors" ,r-s4vectors)))
902 (home-page "https://bioconductor.org/packages/regioneR/")
903 (synopsis "Association analysis of genomic regions")
904 (description "This package offers a statistical framework based on
905 customizable permutation tests to assess the association between genomic
906 region sets and other genomic features.")
907 (license license:artistic2.0)))
909 (define-public r-geneplotter
911 (name "r-geneplotter")
916 (uri (bioconductor-uri "geneplotter" version))
919 "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
920 (build-system r-build-system)
922 `(("r-annotate" ,r-annotate)
923 ("r-annotationdbi" ,r-annotationdbi)
924 ("r-biobase" ,r-biobase)
925 ("r-biocgenerics" ,r-biocgenerics)
926 ("r-lattice" ,r-lattice)
927 ("r-rcolorbrewer" ,r-rcolorbrewer)))
928 (home-page "https://bioconductor.org/packages/geneplotter")
929 (synopsis "Graphics functions for genomic data")
931 "This package provides functions for plotting genomic data.")
932 (license license:artistic2.0)))
934 (define-public r-qvalue
941 (uri (bioconductor-uri "qvalue" version))
944 "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
945 (build-system r-build-system)
947 `(("r-ggplot2" ,r-ggplot2)
948 ("r-reshape2" ,r-reshape2)))
949 (home-page "http://github.com/jdstorey/qvalue")
950 (synopsis "Q-value estimation for false discovery rate control")
952 "This package takes a list of p-values resulting from the simultaneous
953 testing of many hypotheses and estimates their q-values and local @dfn{false
954 discovery rate} (FDR) values. The q-value of a test measures the proportion
955 of false positives incurred when that particular test is called significant.
956 The local FDR measures the posterior probability the null hypothesis is true
957 given the test's p-value. Various plots are automatically generated, allowing
958 one to make sensible significance cut-offs. The software can be applied to
959 problems in genomics, brain imaging, astrophysics, and data mining.")
960 ;; Any version of the LGPL.
961 (license license:lgpl3+)))
963 (define-public r-diffbind
970 (uri (bioconductor-uri "DiffBind" version))
973 "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
974 (properties `((upstream-name . "DiffBind")))
975 (build-system r-build-system)
980 ("r-biocparallel" ,r-biocparallel)
981 ("r-deseq2" ,r-deseq2)
984 ("r-genomicalignments" ,r-genomicalignments)
985 ("r-genomicranges" ,r-genomicranges)
986 ("r-ggplot2" ,r-ggplot2)
987 ("r-ggrepel" ,r-ggrepel)
988 ("r-gplots" ,r-gplots)
989 ("r-iranges" ,r-iranges)
990 ("r-lattice" ,r-lattice)
992 ("r-locfit" ,r-locfit)
993 ("r-rcolorbrewer" , r-rcolorbrewer)
995 ("r-rsamtools" ,r-rsamtools)
996 ("r-s4vectors" ,r-s4vectors)
997 ("r-summarizedexperiment" ,r-summarizedexperiment)
998 ("r-systempiper" ,r-systempiper)
999 ("r-zlibbioc" ,r-zlibbioc)))
1000 (home-page "http://bioconductor.org/packages/DiffBind")
1001 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1003 "This package computes differentially bound sites from multiple
1004 ChIP-seq experiments using affinity (quantitative) data. Also enables
1005 occupancy (overlap) analysis and plotting functions.")
1006 (license license:artistic2.0)))
1008 (define-public r-ripseeker
1010 (name "r-ripseeker")
1015 (uri (bioconductor-uri "RIPSeeker" version))
1018 "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
1019 (properties `((upstream-name . "RIPSeeker")))
1020 (build-system r-build-system)
1022 `(("r-s4vectors" ,r-s4vectors)
1023 ("r-iranges" ,r-iranges)
1024 ("r-genomicranges" ,r-genomicranges)
1025 ("r-summarizedexperiment" ,r-summarizedexperiment)
1026 ("r-rsamtools" ,r-rsamtools)
1027 ("r-genomicalignments" ,r-genomicalignments)
1028 ("r-rtracklayer" ,r-rtracklayer)))
1029 (home-page "http://bioconductor.org/packages/RIPSeeker")
1031 "Identifying protein-associated transcripts from RIP-seq experiments")
1033 "This package infers and discriminates RIP peaks from RIP-seq alignments
1034 using two-state HMM with negative binomial emission probability. While
1035 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1036 a suite of bioinformatics tools integrated within this self-contained software
1037 package comprehensively addressing issues ranging from post-alignments
1038 processing to visualization and annotation.")
1039 (license license:gpl2)))
1041 (define-public r-multtest
1048 (uri (bioconductor-uri "multtest" version))
1051 "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
1052 (build-system r-build-system)
1054 `(("r-survival" ,r-survival)
1055 ("r-biocgenerics" ,r-biocgenerics)
1056 ("r-biobase" ,r-biobase)
1057 ("r-mass" ,r-mass)))
1058 (home-page "http://bioconductor.org/packages/multtest")
1059 (synopsis "Resampling-based multiple hypothesis testing")
1061 "This package can do non-parametric bootstrap and permutation
1062 resampling-based multiple testing procedures (including empirical Bayes
1063 methods) for controlling the family-wise error rate (FWER), generalized
1064 family-wise error rate (gFWER), tail probability of the proportion of
1065 false positives (TPPFP), and false discovery rate (FDR). Several choices
1066 of bootstrap-based null distribution are implemented (centered, centered
1067 and scaled, quantile-transformed). Single-step and step-wise methods are
1068 available. Tests based on a variety of T- and F-statistics (including
1069 T-statistics based on regression parameters from linear and survival models
1070 as well as those based on correlation parameters) are included. When probing
1071 hypotheses with T-statistics, users may also select a potentially faster null
1072 distribution which is multivariate normal with mean zero and variance
1073 covariance matrix derived from the vector influence function. Results are
1074 reported in terms of adjusted P-values, confidence regions and test statistic
1075 cutoffs. The procedures are directly applicable to identifying differentially
1076 expressed genes in DNA microarray experiments.")
1077 (license license:lgpl3)))
1079 (define-public r-graph
1085 (uri (bioconductor-uri "graph" version))
1088 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
1089 (build-system r-build-system)
1091 `(("r-biocgenerics" ,r-biocgenerics)))
1092 (home-page "https://bioconductor.org/packages/graph")
1093 (synopsis "Handle graph data structures in R")
1095 "This package implements some simple graph handling capabilities for R.")
1096 (license license:artistic2.0)))
1098 (define-public r-codedepends
1100 (name "r-codedepends")
1105 (uri (cran-uri "CodeDepends" version))
1108 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1109 (properties `((upstream-name . "CodeDepends")))
1110 (build-system r-build-system)
1112 `(("r-codetools" ,r-codetools)
1113 ("r-graph" ,r-graph)
1115 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1116 (synopsis "Analysis of R code for reproducible research and code comprehension")
1118 "This package provides tools for analyzing R expressions or blocks of
1119 code and determining the dependencies between them. It focuses on R scripts,
1120 but can be used on the bodies of functions. There are many facilities
1121 including the ability to summarize or get a high-level view of code,
1122 determining dependencies between variables, code improvement suggestions.")
1123 ;; Any version of the GPL
1124 (license (list license:gpl2+ license:gpl3+))))
1126 (define-public r-chippeakanno
1128 (name "r-chippeakanno")
1133 (uri (bioconductor-uri "ChIPpeakAnno" version))
1136 "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
1137 (properties `((upstream-name . "ChIPpeakAnno")))
1138 (build-system r-build-system)
1140 `(("r-biocgenerics" ,r-biocgenerics)
1141 ("r-biocmanager" ,r-biocmanager)
1142 ("r-biostrings" ,r-biostrings)
1143 ("r-delayedarray" ,r-delayedarray)
1144 ("r-go-db" ,r-go-db)
1145 ("r-biomart" ,r-biomart)
1146 ("r-bsgenome" ,r-bsgenome)
1147 ("r-genomicfeatures" ,r-genomicfeatures)
1148 ("r-genomicranges" ,r-genomicranges)
1149 ("r-genomeinfodb" ,r-genomeinfodb)
1150 ("r-iranges" ,r-iranges)
1151 ("r-matrixstats" ,r-matrixstats)
1152 ("r-annotationdbi" ,r-annotationdbi)
1153 ("r-limma" ,r-limma)
1154 ("r-multtest" ,r-multtest)
1156 ("r-graph" ,r-graph)
1157 ("r-regioner" ,r-regioner)
1159 ("r-ensembldb" ,r-ensembldb)
1160 ("r-biobase" ,r-biobase)
1161 ("r-s4vectors" ,r-s4vectors)
1162 ("r-seqinr" ,r-seqinr)
1164 ("r-genomicalignments" ,r-genomicalignments)
1165 ("r-summarizedexperiment" ,r-summarizedexperiment)
1166 ("r-rsamtools" ,r-rsamtools)
1167 ("r-venndiagram" ,r-venndiagram)))
1168 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1169 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1171 "The package includes functions to retrieve the sequences around the peak,
1172 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1173 custom features such as most conserved elements and other transcription factor
1174 binding sites supplied by users. Starting 2.0.5, new functions have been added
1175 for finding the peaks with bi-directional promoters with summary statistics
1176 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1177 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1178 enrichedGO (addGeneIDs).")
1179 (license license:gpl2+)))
1181 (define-public r-marray
1187 (uri (bioconductor-uri "marray" version))
1189 (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
1190 (build-system r-build-system)
1192 `(("r-limma" ,r-limma)))
1193 (home-page "http://bioconductor.org/packages/marray")
1194 (synopsis "Exploratory analysis for two-color spotted microarray data")
1195 (description "This package contains class definitions for two-color spotted
1196 microarray data. It also includes fuctions for data input, diagnostic plots,
1197 normalization and quality checking.")
1198 (license license:lgpl2.0+)))
1200 (define-public r-cghbase
1206 (uri (bioconductor-uri "CGHbase" version))
1208 (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
1209 (properties `((upstream-name . "CGHbase")))
1210 (build-system r-build-system)
1212 `(("r-biobase" ,r-biobase)
1213 ("r-marray" ,r-marray)))
1214 (home-page "http://bioconductor.org/packages/CGHbase")
1215 (synopsis "Base functions and classes for arrayCGH data analysis")
1216 (description "This package contains functions and classes that are needed by
1217 the @code{arrayCGH} packages.")
1218 (license license:gpl2+)))
1220 (define-public r-cghcall
1226 (uri (bioconductor-uri "CGHcall" version))
1228 (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
1229 (properties `((upstream-name . "CGHcall")))
1230 (build-system r-build-system)
1232 `(("r-biobase" ,r-biobase)
1233 ("r-cghbase" ,r-cghbase)
1234 ("r-impute" ,r-impute)
1235 ("r-dnacopy" ,r-dnacopy)
1236 ("r-snowfall" ,r-snowfall)))
1237 (home-page "http://bioconductor.org/packages/CGHcall")
1238 (synopsis "Base functions and classes for arrayCGH data analysis")
1239 (description "This package contains functions and classes that are needed by
1240 @code{arrayCGH} packages.")
1241 (license license:gpl2+)))
1243 (define-public r-qdnaseq
1249 (uri (bioconductor-uri "QDNAseq" version))
1251 (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
1252 (properties `((upstream-name . "QDNAseq")))
1253 (build-system r-build-system)
1255 `(("r-biobase" ,r-biobase)
1256 ("r-biocparallel" ,r-biocparallel)
1257 ("r-cghbase" ,r-cghbase)
1258 ("r-cghcall" ,r-cghcall)
1259 ("r-dnacopy" ,r-dnacopy)
1260 ("r-genomicranges" ,r-genomicranges)
1261 ("r-iranges" ,r-iranges)
1262 ("r-matrixstats" ,r-matrixstats)
1263 ("r-r-utils" ,r-r-utils)
1264 ("r-rsamtools" ,r-rsamtools)))
1265 (home-page "http://bioconductor.org/packages/QDNAseq")
1266 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1267 (description "The genome is divided into non-overlapping fixed-sized bins,
1268 number of sequence reads in each counted, adjusted with a simultaneous
1269 two-dimensional loess correction for sequence mappability and GC content, and
1270 filtered to remove spurious regions in the genome. Downstream steps of
1271 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1273 (license license:gpl2+)))
1275 (define-public r-bayseq
1282 (uri (bioconductor-uri "baySeq" version))
1285 "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
1286 (properties `((upstream-name . "baySeq")))
1287 (build-system r-build-system)
1289 `(("r-abind" ,r-abind)
1290 ("r-edger" ,r-edger)
1291 ("r-genomicranges" ,r-genomicranges)))
1292 (home-page "https://bioconductor.org/packages/baySeq/")
1293 (synopsis "Bayesian analysis of differential expression patterns in count data")
1295 "This package identifies differential expression in high-throughput count
1296 data, such as that derived from next-generation sequencing machines,
1297 calculating estimated posterior likelihoods of differential expression (or
1298 more complex hypotheses) via empirical Bayesian methods.")
1299 (license license:gpl3)))
1301 (define-public r-chipcomp
1308 (uri (bioconductor-uri "ChIPComp" version))
1311 "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
1312 (properties `((upstream-name . "ChIPComp")))
1313 (build-system r-build-system)
1315 `(("r-biocgenerics" ,r-biocgenerics)
1316 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1317 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1318 ("r-genomeinfodb" ,r-genomeinfodb)
1319 ("r-genomicranges" ,r-genomicranges)
1320 ("r-iranges" ,r-iranges)
1321 ("r-limma" ,r-limma)
1322 ("r-rsamtools" ,r-rsamtools)
1323 ("r-rtracklayer" ,r-rtracklayer)
1324 ("r-s4vectors" ,r-s4vectors)))
1325 (home-page "https://bioconductor.org/packages/ChIPComp")
1326 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1328 "ChIPComp implements a statistical method for quantitative comparison of
1329 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1330 sites across multiple conditions considering matching control in ChIP-seq
1332 ;; Any version of the GPL.
1333 (license license:gpl3+)))
1335 (define-public r-riboprofiling
1337 (name "r-riboprofiling")
1342 (uri (bioconductor-uri "RiboProfiling" version))
1345 "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
1346 (properties `((upstream-name . "RiboProfiling")))
1347 (build-system r-build-system)
1349 `(("r-biocgenerics" ,r-biocgenerics)
1350 ("r-biostrings" ,r-biostrings)
1351 ("r-data-table" ,r-data-table)
1352 ("r-genomeinfodb" ,r-genomeinfodb)
1353 ("r-genomicalignments" ,r-genomicalignments)
1354 ("r-genomicfeatures" ,r-genomicfeatures)
1355 ("r-genomicranges" ,r-genomicranges)
1356 ("r-ggbio" ,r-ggbio)
1357 ("r-ggplot2" ,r-ggplot2)
1358 ("r-iranges" ,r-iranges)
1360 ("r-reshape2" ,r-reshape2)
1361 ("r-rsamtools" ,r-rsamtools)
1362 ("r-rtracklayer" ,r-rtracklayer)
1363 ("r-s4vectors" ,r-s4vectors)
1364 ("r-sqldf" ,r-sqldf)))
1365 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1366 (synopsis "Ribosome profiling data analysis")
1367 (description "Starting with a BAM file, this package provides the
1368 necessary functions for quality assessment, read start position recalibration,
1369 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1370 of count data: pairs, log fold-change, codon frequency and coverage
1371 assessment, principal component analysis on codon coverage.")
1372 (license license:gpl3)))
1374 (define-public r-riboseqr
1381 (uri (bioconductor-uri "riboSeqR" version))
1384 "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
1385 (properties `((upstream-name . "riboSeqR")))
1386 (build-system r-build-system)
1388 `(("r-abind" ,r-abind)
1389 ("r-bayseq" ,r-bayseq)
1390 ("r-genomeinfodb" ,r-genomeinfodb)
1391 ("r-genomicranges" ,r-genomicranges)
1392 ("r-iranges" ,r-iranges)
1393 ("r-rsamtools" ,r-rsamtools)
1394 ("r-seqlogo" ,r-seqlogo)))
1395 (home-page "https://bioconductor.org/packages/riboSeqR/")
1396 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1398 "This package provides plotting functions, frameshift detection and
1399 parsing of genetic sequencing data from ribosome profiling experiments.")
1400 (license license:gpl3)))
1402 (define-public r-interactionset
1404 (name "r-interactionset")
1409 (uri (bioconductor-uri "InteractionSet" version))
1412 "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
1414 `((upstream-name . "InteractionSet")))
1415 (build-system r-build-system)
1417 `(("r-biocgenerics" ,r-biocgenerics)
1418 ("r-genomeinfodb" ,r-genomeinfodb)
1419 ("r-genomicranges" ,r-genomicranges)
1420 ("r-iranges" ,r-iranges)
1421 ("r-matrix" ,r-matrix)
1423 ("r-s4vectors" ,r-s4vectors)
1424 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1425 (home-page "https://bioconductor.org/packages/InteractionSet")
1426 (synopsis "Base classes for storing genomic interaction data")
1428 "This packages provides the @code{GInteractions},
1429 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1430 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1432 (license license:gpl3)))
1434 (define-public r-genomicinteractions
1436 (name "r-genomicinteractions")
1441 (uri (bioconductor-uri "GenomicInteractions" version))
1444 "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
1446 `((upstream-name . "GenomicInteractions")))
1447 (build-system r-build-system)
1449 `(("r-biobase" ,r-biobase)
1450 ("r-biocgenerics" ,r-biocgenerics)
1451 ("r-data-table" ,r-data-table)
1452 ("r-dplyr" ,r-dplyr)
1453 ("r-genomeinfodb" ,r-genomeinfodb)
1454 ("r-genomicranges" ,r-genomicranges)
1455 ("r-ggplot2" ,r-ggplot2)
1456 ("r-gridextra" ,r-gridextra)
1458 ("r-igraph" ,r-igraph)
1459 ("r-interactionset" ,r-interactionset)
1460 ("r-iranges" ,r-iranges)
1461 ("r-rsamtools" ,r-rsamtools)
1462 ("r-rtracklayer" ,r-rtracklayer)
1463 ("r-s4vectors" ,r-s4vectors)
1464 ("r-stringr" ,r-stringr)))
1465 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1466 (synopsis "R package for handling genomic interaction data")
1468 "This R package provides tools for handling genomic interaction data,
1469 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1470 information and producing various plots and statistics.")
1471 (license license:gpl3)))
1473 (define-public r-ctc
1480 (uri (bioconductor-uri "ctc" version))
1483 "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
1484 (build-system r-build-system)
1485 (propagated-inputs `(("r-amap" ,r-amap)))
1486 (home-page "https://bioconductor.org/packages/ctc/")
1487 (synopsis "Cluster and tree conversion")
1489 "This package provides tools for exporting and importing classification
1490 trees and clusters to other programs.")
1491 (license license:gpl2)))
1493 (define-public r-goseq
1500 (uri (bioconductor-uri "goseq" version))
1503 "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
1504 (build-system r-build-system)
1506 `(("r-annotationdbi" ,r-annotationdbi)
1507 ("r-biasedurn" ,r-biasedurn)
1508 ("r-biocgenerics" ,r-biocgenerics)
1509 ("r-genelendatabase" ,r-genelendatabase)
1510 ("r-go-db" ,r-go-db)
1511 ("r-mgcv" ,r-mgcv)))
1512 (home-page "https://bioconductor.org/packages/goseq/")
1513 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1515 "This package provides tools to detect Gene Ontology and/or other user
1516 defined categories which are over/under represented in RNA-seq data.")
1517 (license license:lgpl2.0+)))
1519 (define-public r-glimma
1526 (uri (bioconductor-uri "Glimma" version))
1529 "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
1530 (properties `((upstream-name . "Glimma")))
1531 (build-system r-build-system)
1533 `(("r-edger" ,r-edger)
1534 ("r-jsonlite" ,r-jsonlite)
1535 ("r-s4vectors" ,r-s4vectors)))
1536 (home-page "https://github.com/Shians/Glimma")
1537 (synopsis "Interactive HTML graphics")
1539 "This package generates interactive visualisations for analysis of
1540 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1541 HTML page. The interactions are built on top of the popular static
1542 representations of analysis results in order to provide additional
1544 (license license:lgpl3)))
1546 (define-public r-rots
1553 (uri (bioconductor-uri "ROTS" version))
1556 "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
1557 (properties `((upstream-name . "ROTS")))
1558 (build-system r-build-system)
1560 `(("r-biobase" ,r-biobase)
1561 ("r-rcpp" ,r-rcpp)))
1562 (home-page "https://bioconductor.org/packages/ROTS/")
1563 (synopsis "Reproducibility-Optimized Test Statistic")
1565 "This package provides tools for calculating the
1566 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1568 (license license:gpl2+)))
1570 (define-public r-plgem
1577 (uri (bioconductor-uri "plgem" version))
1580 "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
1581 (build-system r-build-system)
1583 `(("r-biobase" ,r-biobase)
1584 ("r-mass" ,r-mass)))
1585 (home-page "http://www.genopolis.it")
1586 (synopsis "Detect differential expression in microarray and proteomics datasets")
1588 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1589 model the variance-versus-mean dependence that exists in a variety of
1590 genome-wide datasets, including microarray and proteomics data. The use of
1591 PLGEM has been shown to improve the detection of differentially expressed
1592 genes or proteins in these datasets.")
1593 (license license:gpl2)))
1595 (define-public r-inspect
1602 (uri (bioconductor-uri "INSPEcT" version))
1605 "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
1606 (properties `((upstream-name . "INSPEcT")))
1607 (build-system r-build-system)
1609 `(("r-biobase" ,r-biobase)
1610 ("r-biocgenerics" ,r-biocgenerics)
1611 ("r-biocparallel" ,r-biocparallel)
1612 ("r-deseq2" ,r-deseq2)
1613 ("r-desolve" ,r-desolve)
1614 ("r-genomicalignments" ,r-genomicalignments)
1615 ("r-genomicfeatures" ,r-genomicfeatures)
1616 ("r-genomicranges" ,r-genomicranges)
1617 ("r-iranges" ,r-iranges)
1618 ("r-plgem" ,r-plgem)
1619 ("r-preprocesscore" ,r-preprocesscore)
1621 ("r-rootsolve" ,r-rootsolve)
1622 ("r-rsamtools" ,r-rsamtools)
1623 ("r-s4vectors" ,r-s4vectors)
1624 ("r-shiny" ,r-shiny)
1625 ("r-summarizedexperiment" ,r-summarizedexperiment)
1626 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1627 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1628 (home-page "https://bioconductor.org/packages/INSPEcT")
1629 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1631 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1632 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1633 order to evaluate synthesis, processing and degradation rates and assess via
1634 modeling the rates that determines changes in mature mRNA levels.")
1635 (license license:gpl2)))
1637 (define-public r-dnabarcodes
1639 (name "r-dnabarcodes")
1644 (uri (bioconductor-uri "DNABarcodes" version))
1647 "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
1648 (properties `((upstream-name . "DNABarcodes")))
1649 (build-system r-build-system)
1652 ("r-matrix" ,r-matrix)
1653 ("r-rcpp" ,r-rcpp)))
1654 (home-page "https://bioconductor.org/packages/DNABarcodes")
1655 (synopsis "Create and analyze DNA barcodes")
1657 "This package offers tools to create DNA barcode sets capable of
1658 correcting insertion, deletion, and substitution errors. Existing barcodes
1659 can be analyzed regarding their minimal, maximal and average distances between
1660 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1661 demultiplexed, i.e. assigned to their original reference barcode.")
1662 (license license:gpl2)))
1664 (define-public r-ruvseq
1671 (uri (bioconductor-uri "RUVSeq" version))
1674 "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
1675 (properties `((upstream-name . "RUVSeq")))
1676 (build-system r-build-system)
1678 `(("r-biobase" ,r-biobase)
1679 ("r-edaseq" ,r-edaseq)
1680 ("r-edger" ,r-edger)
1681 ("r-mass" ,r-mass)))
1682 (home-page "https://github.com/drisso/RUVSeq")
1683 (synopsis "Remove unwanted variation from RNA-Seq data")
1685 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1686 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1688 (license license:artistic2.0)))
1690 (define-public r-biocneighbors
1692 (name "r-biocneighbors")
1697 (uri (bioconductor-uri "BiocNeighbors" version))
1700 "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
1701 (properties `((upstream-name . "BiocNeighbors")))
1702 (build-system r-build-system)
1704 `(("r-biocparallel" ,r-biocparallel)
1706 ("r-rcppannoy" ,r-rcppannoy)
1707 ("r-s4vectors" ,r-s4vectors)))
1708 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1709 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1711 "This package implements exact and approximate methods for nearest
1712 neighbor detection, in a framework that allows them to be easily switched
1713 within Bioconductor packages or workflows. The exact algorithm is implemented
1714 using pre-clustering with the k-means algorithm. Functions are also provided
1715 to search for all neighbors within a given distance. Parallelization is
1716 achieved for all methods using the BiocParallel framework.")
1717 (license license:gpl3)))
1719 (define-public r-destiny
1726 (uri (bioconductor-uri "destiny" version))
1729 "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
1730 (build-system r-build-system)
1732 `(("r-biobase" ,r-biobase)
1733 ("r-biocgenerics" ,r-biocgenerics)
1735 ("r-ggthemes" ,r-ggthemes)
1736 ("r-hmisc" ,r-hmisc)
1737 ("r-igraph" ,r-igraph)
1738 ("r-matrix" ,r-matrix)
1739 ("r-proxy" ,r-proxy)
1741 ("r-rcppeigen" ,r-rcppeigen)
1742 ("r-scales" ,r-scales)
1743 ("r-scatterplot3d" ,r-scatterplot3d)
1744 ("r-smoother" ,r-smoother)
1745 ("r-summarizedexperiment" ,r-summarizedexperiment)
1747 (home-page "https://bioconductor.org/packages/destiny/")
1748 (synopsis "Create and plot diffusion maps")
1749 (description "This package provides tools to create and plot diffusion
1751 ;; Any version of the GPL
1752 (license license:gpl3+)))
1754 (define-public r-savr
1761 (uri (bioconductor-uri "savR" version))
1764 "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
1765 (properties `((upstream-name . "savR")))
1766 (build-system r-build-system)
1768 `(("r-ggplot2" ,r-ggplot2)
1769 ("r-gridextra" ,r-gridextra)
1770 ("r-reshape2" ,r-reshape2)
1771 ("r-scales" ,r-scales)
1773 (home-page "https://github.com/bcalder/savR")
1774 (synopsis "Parse and analyze Illumina SAV files")
1776 "This package provides tools to parse Illumina Sequence Analysis
1777 Viewer (SAV) files, access data, and generate QC plots.")
1778 (license license:agpl3+)))
1780 (define-public r-chipexoqual
1782 (name "r-chipexoqual")
1787 (uri (bioconductor-uri "ChIPexoQual" version))
1790 "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
1791 (properties `((upstream-name . "ChIPexoQual")))
1792 (build-system r-build-system)
1794 `(("r-biocparallel" ,r-biocparallel)
1795 ("r-biovizbase" ,r-biovizbase)
1796 ("r-broom" ,r-broom)
1797 ("r-data-table" ,r-data-table)
1798 ("r-dplyr" ,r-dplyr)
1799 ("r-genomeinfodb" ,r-genomeinfodb)
1800 ("r-genomicalignments" ,r-genomicalignments)
1801 ("r-genomicranges" ,r-genomicranges)
1802 ("r-ggplot2" ,r-ggplot2)
1803 ("r-hexbin" ,r-hexbin)
1804 ("r-iranges" ,r-iranges)
1805 ("r-rcolorbrewer" ,r-rcolorbrewer)
1806 ("r-rmarkdown" ,r-rmarkdown)
1807 ("r-rsamtools" ,r-rsamtools)
1808 ("r-s4vectors" ,r-s4vectors)
1809 ("r-scales" ,r-scales)
1810 ("r-viridis" ,r-viridis)))
1811 (home-page "https://github.com/keleslab/ChIPexoQual")
1812 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1814 "This package provides a quality control pipeline for ChIP-exo/nexus
1816 (license license:gpl2+)))
1818 (define-public r-copynumber
1820 (name "r-copynumber")
1824 (uri (bioconductor-uri "copynumber" version))
1827 "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
1828 (build-system r-build-system)
1830 `(("r-s4vectors" ,r-s4vectors)
1831 ("r-iranges" ,r-iranges)
1832 ("r-genomicranges" ,r-genomicranges)
1833 ("r-biocgenerics" ,r-biocgenerics)))
1834 (home-page "https://bioconductor.org/packages/copynumber")
1835 (synopsis "Segmentation of single- and multi-track copy number data")
1837 "This package segments single- and multi-track copy number data by a
1838 penalized least squares regression method.")
1839 (license license:artistic2.0)))
1841 (define-public r-dnacopy
1848 (uri (bioconductor-uri "DNAcopy" version))
1851 "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
1852 (properties `((upstream-name . "DNAcopy")))
1853 (build-system r-build-system)
1854 (native-inputs `(("gfortran" ,gfortran)))
1855 (home-page "https://bioconductor.org/packages/DNAcopy")
1856 (synopsis "DNA copy number data analysis")
1858 "This package implements the @dfn{circular binary segmentation} (CBS)
1859 algorithm to segment DNA copy number data and identify genomic regions with
1860 abnormal copy number.")
1861 (license license:gpl2+)))
1863 ;; This is a CRAN package, but it uncharacteristically depends on a
1864 ;; Bioconductor package.
1865 (define-public r-htscluster
1867 (name "r-htscluster")
1872 (uri (cran-uri "HTSCluster" version))
1875 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1876 (properties `((upstream-name . "HTSCluster")))
1877 (build-system r-build-system)
1879 `(("r-capushe" ,r-capushe)
1880 ("r-edger" ,r-edger)
1881 ("r-plotrix" ,r-plotrix)))
1882 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1883 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1885 "This package provides a Poisson mixture model is implemented to cluster
1886 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
1887 estimation is performed using either the EM or CEM algorithm, and the slope
1888 heuristics are used for model selection (i.e., to choose the number of
1890 (license license:gpl3+)))
1892 (define-public r-deds
1899 (uri (bioconductor-uri "DEDS" version))
1902 "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
1903 (properties `((upstream-name . "DEDS")))
1904 (build-system r-build-system)
1905 (home-page "https://bioconductor.org/packages/DEDS/")
1906 (synopsis "Differential expression via distance summary for microarray data")
1908 "This library contains functions that calculate various statistics of
1909 differential expression for microarray data, including t statistics, fold
1910 change, F statistics, SAM, moderated t and F statistics and B statistics. It
1911 also implements a new methodology called DEDS (Differential Expression via
1912 Distance Summary), which selects differentially expressed genes by integrating
1913 and summarizing a set of statistics using a weighted distance approach.")
1914 ;; Any version of the LGPL.
1915 (license license:lgpl3+)))
1917 ;; This is a CRAN package, but since it depends on a Bioconductor package we
1919 (define-public r-nbpseq
1926 (uri (cran-uri "NBPSeq" version))
1929 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
1930 (properties `((upstream-name . "NBPSeq")))
1931 (build-system r-build-system)
1933 `(("r-qvalue" ,r-qvalue)))
1934 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
1935 (synopsis "Negative binomial models for RNA-Seq data")
1937 "This package provides negative binomial models for two-group comparisons
1938 and regression inferences from RNA-sequencing data.")
1939 (license license:gpl2)))
1941 (define-public r-ebseq
1948 (uri (bioconductor-uri "EBSeq" version))
1951 "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
1952 (properties `((upstream-name . "EBSeq")))
1953 (build-system r-build-system)
1955 `(("r-blockmodeling" ,r-blockmodeling)
1956 ("r-gplots" ,r-gplots)
1957 ("r-testthat" ,r-testthat)))
1958 (home-page "https://bioconductor.org/packages/EBSeq")
1959 (synopsis "Differential expression analysis of RNA-seq data")
1961 "This package provides tools for differential expression analysis at both
1962 gene and isoform level using RNA-seq data")
1963 (license license:artistic2.0)))
1965 (define-public r-lpsymphony
1967 (name "r-lpsymphony")
1972 (uri (bioconductor-uri "lpsymphony" version))
1975 "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
1976 (build-system r-build-system)
1978 `(("gfortran" ,gfortran)
1981 `(("pkg-config" ,pkg-config)))
1982 (home-page "http://r-forge.r-project.org/projects/rsymphony")
1983 (synopsis "Symphony integer linear programming solver in R")
1985 "This package was derived from Rsymphony. The package provides an R
1986 interface to SYMPHONY, a linear programming solver written in C++. The main
1987 difference between this package and Rsymphony is that it includes the solver
1988 source code, while Rsymphony expects to find header and library files on the
1989 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
1990 to install interface to SYMPHONY.")
1991 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
1992 ;; lpsimphony is released under the same terms.
1993 (license license:epl1.0)))
1995 (define-public r-ihw
2002 (uri (bioconductor-uri "IHW" version))
2005 "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
2006 (properties `((upstream-name . "IHW")))
2007 (build-system r-build-system)
2009 `(("r-biocgenerics" ,r-biocgenerics)
2010 ("r-fdrtool" ,r-fdrtool)
2011 ("r-lpsymphony" ,r-lpsymphony)
2012 ("r-slam" ,r-slam)))
2013 (home-page "https://bioconductor.org/packages/IHW")
2014 (synopsis "Independent hypothesis weighting")
2016 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2017 procedure that increases power compared to the method of Benjamini and
2018 Hochberg by assigning data-driven weights to each hypothesis. The input to
2019 IHW is a two-column table of p-values and covariates. The covariate can be
2020 any continuous-valued or categorical variable that is thought to be
2021 informative on the statistical properties of each hypothesis test, while it is
2022 independent of the p-value under the null hypothesis.")
2023 (license license:artistic2.0)))
2025 (define-public r-icobra
2032 (uri (bioconductor-uri "iCOBRA" version))
2035 "0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"))))
2036 (properties `((upstream-name . "iCOBRA")))
2037 (build-system r-build-system)
2039 `(("r-dplyr" ,r-dplyr)
2041 ("r-ggplot2" ,r-ggplot2)
2042 ("r-limma" ,r-limma)
2043 ("r-reshape2" ,r-reshape2)
2045 ("r-scales" ,r-scales)
2046 ("r-shiny" ,r-shiny)
2047 ("r-shinybs" ,r-shinybs)
2048 ("r-shinydashboard" ,r-shinydashboard)
2049 ("r-upsetr" ,r-upsetr)))
2050 (home-page "https://bioconductor.org/packages/iCOBRA")
2051 (synopsis "Comparison and visualization of ranking and assignment methods")
2053 "This package provides functions for calculation and visualization of
2054 performance metrics for evaluation of ranking and binary
2055 classification (assignment) methods. It also contains a Shiny application for
2056 interactive exploration of results.")
2057 (license license:gpl2+)))
2059 (define-public r-mast
2066 (uri (bioconductor-uri "MAST" version))
2069 "0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"))))
2070 (properties `((upstream-name . "MAST")))
2071 (build-system r-build-system)
2073 `(("r-abind" ,r-abind)
2074 ("r-biobase" ,r-biobase)
2075 ("r-biocgenerics" ,r-biocgenerics)
2076 ("r-data-table" ,r-data-table)
2077 ("r-ggplot2" ,r-ggplot2)
2079 ("r-progress" ,r-progress)
2080 ("r-reshape2" ,r-reshape2)
2081 ("r-s4vectors" ,r-s4vectors)
2082 ("r-singlecellexperiment" ,r-singlecellexperiment)
2083 ("r-stringr" ,r-stringr)
2084 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2085 (home-page "https://github.com/RGLab/MAST/")
2086 (synopsis "Model-based analysis of single cell transcriptomics")
2088 "This package provides methods and models for handling zero-inflated
2089 single cell assay data.")
2090 (license license:gpl2+)))
2092 (define-public r-monocle
2099 (uri (bioconductor-uri "monocle" version))
2102 "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
2103 (build-system r-build-system)
2105 `(("r-biobase" ,r-biobase)
2106 ("r-biocgenerics" ,r-biocgenerics)
2107 ("r-biocviews" ,r-biocviews)
2108 ("r-cluster" ,r-cluster)
2109 ("r-combinat" ,r-combinat)
2110 ("r-ddrtree" ,r-ddrtree)
2111 ("r-densityclust" ,r-densityclust)
2112 ("r-dplyr" ,r-dplyr)
2113 ("r-fastica" ,r-fastica)
2114 ("r-ggplot2" ,r-ggplot2)
2115 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2116 ("r-igraph" ,r-igraph)
2117 ("r-irlba" ,r-irlba)
2118 ("r-limma" ,r-limma)
2120 ("r-matrix" ,r-matrix)
2121 ("r-matrixstats" ,r-matrixstats)
2122 ("r-pheatmap" ,r-pheatmap)
2124 ("r-proxy" ,r-proxy)
2125 ("r-qlcmatrix" ,r-qlcmatrix)
2128 ("r-reshape2" ,r-reshape2)
2129 ("r-rtsne" ,r-rtsne)
2131 ("r-stringr" ,r-stringr)
2132 ("r-tibble" ,r-tibble)
2134 ("r-viridis" ,r-viridis)))
2135 (home-page "https://bioconductor.org/packages/monocle")
2136 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2138 "Monocle performs differential expression and time-series analysis for
2139 single-cell expression experiments. It orders individual cells according to
2140 progress through a biological process, without knowing ahead of time which
2141 genes define progress through that process. Monocle also performs
2142 differential expression analysis, clustering, visualization, and other useful
2143 tasks on single cell expression data. It is designed to work with RNA-Seq and
2144 qPCR data, but could be used with other types as well.")
2145 (license license:artistic2.0)))
2147 (define-public r-noiseq
2154 (uri (bioconductor-uri "NOISeq" version))
2157 "1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"))))
2158 (properties `((upstream-name . "NOISeq")))
2159 (build-system r-build-system)
2161 `(("r-biobase" ,r-biobase)
2162 ("r-matrix" ,r-matrix)))
2163 (home-page "https://bioconductor.org/packages/NOISeq")
2164 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2166 "This package provides tools to support the analysis of RNA-seq
2167 expression data or other similar kind of data. It provides exploratory plots
2168 to evaluate saturation, count distribution, expression per chromosome, type of
2169 detected features, features length, etc. It also supports the analysis of
2170 differential expression between two experimental conditions with no parametric
2172 (license license:artistic2.0)))
2174 (define-public r-scdd
2181 (uri (bioconductor-uri "scDD" version))
2184 "0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"))))
2185 (properties `((upstream-name . "scDD")))
2186 (build-system r-build-system)
2189 ("r-biocparallel" ,r-biocparallel)
2190 ("r-ebseq" ,r-ebseq)
2191 ("r-fields" ,r-fields)
2192 ("r-ggplot2" ,r-ggplot2)
2193 ("r-mclust" ,r-mclust)
2194 ("r-outliers" ,r-outliers)
2195 ("r-s4vectors" ,r-s4vectors)
2196 ("r-scran" ,r-scran)
2197 ("r-singlecellexperiment" ,r-singlecellexperiment)
2198 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2199 (home-page "https://github.com/kdkorthauer/scDD")
2200 (synopsis "Mixture modeling of single-cell RNA-seq data")
2202 "This package implements a method to analyze single-cell RNA-seq data
2203 utilizing flexible Dirichlet Process mixture models. Genes with differential
2204 distributions of expression are classified into several interesting patterns
2205 of differences between two conditions. The package also includes functions
2206 for simulating data with these patterns from negative binomial
2208 (license license:gpl2)))
2210 (define-public r-scone
2217 (uri (bioconductor-uri "scone" version))
2220 "0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"))))
2221 (build-system r-build-system)
2223 `(("r-aroma-light" ,r-aroma-light)
2224 ("r-biocparallel" ,r-biocparallel)
2226 ("r-class" ,r-class)
2227 ("r-cluster" ,r-cluster)
2228 ("r-compositions" ,r-compositions)
2229 ("r-diptest" ,r-diptest)
2230 ("r-edger" ,r-edger)
2232 ("r-gplots" ,r-gplots)
2233 ("r-hexbin" ,r-hexbin)
2234 ("r-limma" ,r-limma)
2235 ("r-matrixstats" ,r-matrixstats)
2236 ("r-mixtools" ,r-mixtools)
2237 ("r-rarpack" ,r-rarpack)
2238 ("r-rcolorbrewer" ,r-rcolorbrewer)
2239 ("r-rhdf5" ,r-rhdf5)
2240 ("r-ruvseq" ,r-ruvseq)
2241 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2242 (home-page "https://bioconductor.org/packages/scone")
2243 (synopsis "Single cell overview of normalized expression data")
2245 "SCONE is an R package for comparing and ranking the performance of
2246 different normalization schemes for single-cell RNA-seq and other
2247 high-throughput analyses.")
2248 (license license:artistic2.0)))
2250 (define-public r-geoquery
2257 (uri (bioconductor-uri "GEOquery" version))
2260 "074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"))))
2261 (properties `((upstream-name . "GEOquery")))
2262 (build-system r-build-system)
2264 `(("r-biobase" ,r-biobase)
2265 ("r-dplyr" ,r-dplyr)
2267 ("r-limma" ,r-limma)
2268 ("r-magrittr" ,r-magrittr)
2269 ("r-readr" ,r-readr)
2270 ("r-tidyr" ,r-tidyr)
2271 ("r-xml2" ,r-xml2)))
2272 (home-page "https://github.com/seandavi/GEOquery/")
2273 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2275 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2276 microarray data. Given the rich and varied nature of this resource, it is
2277 only natural to want to apply BioConductor tools to these data. GEOquery is
2278 the bridge between GEO and BioConductor.")
2279 (license license:gpl2)))
2281 (define-public r-illuminaio
2283 (name "r-illuminaio")
2288 (uri (bioconductor-uri "illuminaio" version))
2291 "1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"))))
2292 (build-system r-build-system)
2294 `(("r-base64" ,r-base64)))
2295 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2296 (synopsis "Parse Illumina microarray output files")
2298 "This package provides tools for parsing Illumina's microarray output
2299 files, including IDAT.")
2300 (license license:gpl2)))
2302 (define-public r-siggenes
2309 (uri (bioconductor-uri "siggenes" version))
2312 "0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"))))
2313 (build-system r-build-system)
2315 `(("r-biobase" ,r-biobase)
2316 ("r-multtest" ,r-multtest)))
2317 (home-page "https://bioconductor.org/packages/siggenes/")
2319 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2321 "This package provides tools for the identification of differentially
2322 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2323 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2324 Bayes Analyses of Microarrays} (EBAM).")
2325 (license license:lgpl2.0+)))
2327 (define-public r-bumphunter
2329 (name "r-bumphunter")
2334 (uri (bioconductor-uri "bumphunter" version))
2337 "1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"))))
2338 (build-system r-build-system)
2340 `(("r-annotationdbi" ,r-annotationdbi)
2341 ("r-biocgenerics" ,r-biocgenerics)
2342 ("r-dorng" ,r-dorng)
2343 ("r-foreach" ,r-foreach)
2344 ("r-genomeinfodb" ,r-genomeinfodb)
2345 ("r-genomicfeatures" ,r-genomicfeatures)
2346 ("r-genomicranges" ,r-genomicranges)
2347 ("r-iranges" ,r-iranges)
2348 ("r-iterators" ,r-iterators)
2349 ("r-limma" ,r-limma)
2350 ("r-locfit" ,r-locfit)
2351 ("r-matrixstats" ,r-matrixstats)
2352 ("r-s4vectors" ,r-s4vectors)))
2353 (home-page "https://github.com/ririzarr/bumphunter")
2354 (synopsis "Find bumps in genomic data")
2356 "This package provides tools for finding bumps in genomic data in order
2357 to identify differentially methylated regions in epigenetic epidemiology
2359 (license license:artistic2.0)))
2361 (define-public r-minfi
2368 (uri (bioconductor-uri "minfi" version))
2371 "1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"))))
2372 (build-system r-build-system)
2374 `(("r-beanplot" ,r-beanplot)
2375 ("r-biobase" ,r-biobase)
2376 ("r-biocgenerics" ,r-biocgenerics)
2377 ("r-biocparallel" ,r-biocparallel)
2378 ("r-biostrings" ,r-biostrings)
2379 ("r-bumphunter" ,r-bumphunter)
2380 ("r-data-table" ,r-data-table)
2381 ("r-delayedarray" ,r-delayedarray)
2382 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2383 ("r-genefilter" ,r-genefilter)
2384 ("r-genomeinfodb" ,r-genomeinfodb)
2385 ("r-genomicranges" ,r-genomicranges)
2386 ("r-geoquery" ,r-geoquery)
2387 ("r-hdf5array" ,r-hdf5array)
2388 ("r-illuminaio" ,r-illuminaio)
2389 ("r-iranges" ,r-iranges)
2390 ("r-lattice" ,r-lattice)
2391 ("r-limma" ,r-limma)
2393 ("r-mclust" ,r-mclust)
2395 ("r-nor1mix" ,r-nor1mix)
2396 ("r-preprocesscore" ,r-preprocesscore)
2397 ("r-quadprog" ,r-quadprog)
2398 ("r-rcolorbrewer" ,r-rcolorbrewer)
2399 ("r-reshape" ,r-reshape)
2400 ("r-s4vectors" ,r-s4vectors)
2401 ("r-siggenes" ,r-siggenes)
2402 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2403 (home-page "https://github.com/hansenlab/minfi")
2404 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2406 "This package provides tools to analyze and visualize Illumina Infinium
2407 methylation arrays.")
2408 (license license:artistic2.0)))
2410 (define-public r-methylumi
2412 (name "r-methylumi")
2417 (uri (bioconductor-uri "methylumi" version))
2420 "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"))))
2421 (build-system r-build-system)
2423 `(("r-annotate" ,r-annotate)
2424 ("r-annotationdbi" ,r-annotationdbi)
2425 ("r-biobase" ,r-biobase)
2426 ("r-biocgenerics" ,r-biocgenerics)
2427 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2428 ("r-genefilter" ,r-genefilter)
2429 ("r-genomeinfodb" ,r-genomeinfodb)
2430 ("r-genomicranges" ,r-genomicranges)
2431 ("r-ggplot2" ,r-ggplot2)
2432 ("r-illuminaio" ,r-illuminaio)
2433 ("r-iranges" ,r-iranges)
2434 ("r-lattice" ,r-lattice)
2435 ("r-matrixstats" ,r-matrixstats)
2436 ("r-minfi" ,r-minfi)
2437 ("r-reshape2" ,r-reshape2)
2438 ("r-s4vectors" ,r-s4vectors)
2439 ("r-scales" ,r-scales)
2440 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2441 (home-page "https://bioconductor.org/packages/methylumi")
2442 (synopsis "Handle Illumina methylation data")
2444 "This package provides classes for holding and manipulating Illumina
2445 methylation data. Based on eSet, it can contain MIAME information, sample
2446 information, feature information, and multiple matrices of data. An
2447 \"intelligent\" import function, methylumiR can read the Illumina text files
2448 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2449 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2450 background correction, and quality control features for GoldenGate, Infinium,
2451 and Infinium HD arrays are also included.")
2452 (license license:gpl2)))
2454 (define-public r-lumi
2461 (uri (bioconductor-uri "lumi" version))
2464 "1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"))))
2465 (build-system r-build-system)
2467 `(("r-affy" ,r-affy)
2468 ("r-annotate" ,r-annotate)
2469 ("r-annotationdbi" ,r-annotationdbi)
2470 ("r-biobase" ,r-biobase)
2472 ("r-genomicfeatures" ,r-genomicfeatures)
2473 ("r-genomicranges" ,r-genomicranges)
2474 ("r-kernsmooth" ,r-kernsmooth)
2475 ("r-lattice" ,r-lattice)
2477 ("r-methylumi" ,r-methylumi)
2479 ("r-nleqslv" ,r-nleqslv)
2480 ("r-preprocesscore" ,r-preprocesscore)
2481 ("r-rsqlite" ,r-rsqlite)))
2482 (home-page "https://bioconductor.org/packages/lumi")
2483 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2485 "The lumi package provides an integrated solution for the Illumina
2486 microarray data analysis. It includes functions of Illumina
2487 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2488 variance stabilization, normalization and gene annotation at the probe level.
2489 It also includes the functions of processing Illumina methylation microarrays,
2490 especially Illumina Infinium methylation microarrays.")
2491 (license license:lgpl2.0+)))
2493 (define-public r-linnorm
2500 (uri (bioconductor-uri "Linnorm" version))
2503 "1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"))))
2504 (properties `((upstream-name . "Linnorm")))
2505 (build-system r-build-system)
2507 `(("r-amap" ,r-amap)
2508 ("r-apcluster" ,r-apcluster)
2509 ("r-ellipse" ,r-ellipse)
2510 ("r-fastcluster" ,r-fastcluster)
2512 ("r-ggdendro" ,r-ggdendro)
2513 ("r-ggplot2" ,r-ggplot2)
2514 ("r-gmodels" ,r-gmodels)
2515 ("r-igraph" ,r-igraph)
2516 ("r-limma" ,r-limma)
2518 ("r-mclust" ,r-mclust)
2520 ("r-rcpparmadillo" ,r-rcpparmadillo)
2521 ("r-rtsne" ,r-rtsne)
2522 ("r-statmod" ,r-statmod)
2523 ("r-vegan" ,r-vegan)
2525 (home-page "http://www.jjwanglab.org/Linnorm/")
2526 (synopsis "Linear model and normality based transformation method")
2528 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2529 count data or any large scale count data. It transforms such datasets for
2530 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2531 the following pipelines are implemented:
2534 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2535 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2536 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2537 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2538 @item Differential expression analysis or differential peak detection using
2539 limma (@code{Linnorm.limma})
2540 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2541 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2542 @item Stable gene selection for scRNA-seq data; for users without or who do
2543 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2544 @item Data imputation (@code{Linnorm.DataImput}).
2547 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2548 @code{RnaXSim} function is included for simulating RNA-seq data for the
2549 evaluation of DEG analysis methods.")
2550 (license license:expat)))
2552 (define-public r-ioniser
2559 (uri (bioconductor-uri "IONiseR" version))
2562 "01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"))))
2563 (properties `((upstream-name . "IONiseR")))
2564 (build-system r-build-system)
2566 `(("r-biocgenerics" ,r-biocgenerics)
2567 ("r-biocparallel" ,r-biocparallel)
2568 ("r-biostrings" ,r-biostrings)
2569 ("r-bit64" ,r-bit64)
2570 ("r-dplyr" ,r-dplyr)
2571 ("r-ggplot2" ,r-ggplot2)
2572 ("r-magrittr" ,r-magrittr)
2573 ("r-rhdf5" ,r-rhdf5)
2574 ("r-shortread" ,r-shortread)
2575 ("r-stringr" ,r-stringr)
2576 ("r-tibble" ,r-tibble)
2577 ("r-tidyr" ,r-tidyr)
2578 ("r-xvector" ,r-xvector)))
2579 (home-page "https://bioconductor.org/packages/IONiseR/")
2580 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2582 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2583 MinION data. It extracts summary statistics from a set of fast5 files and can
2584 be used either before or after base calling. In addition to standard
2585 summaries of the read-types produced, it provides a number of plots for
2586 visualising metrics relative to experiment run time or spatially over the
2587 surface of a flowcell.")
2588 (license license:expat)))
2590 ;; This is a CRAN package, but it depends on packages from Bioconductor.
2591 (define-public r-gkmsvm
2598 (uri (cran-uri "gkmSVM" version))
2601 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2602 (properties `((upstream-name . "gkmSVM")))
2603 (build-system r-build-system)
2605 `(("r-biocgenerics" ,r-biocgenerics)
2606 ("r-biostrings" ,r-biostrings)
2607 ("r-genomeinfodb" ,r-genomeinfodb)
2608 ("r-genomicranges" ,r-genomicranges)
2609 ("r-iranges" ,r-iranges)
2610 ("r-kernlab" ,r-kernlab)
2613 ("r-rtracklayer" ,r-rtracklayer)
2614 ("r-s4vectors" ,r-s4vectors)
2615 ("r-seqinr" ,r-seqinr)))
2616 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2617 (synopsis "Gapped-kmer support vector machine")
2619 "This R package provides tools for training gapped-kmer SVM classifiers
2620 for DNA and protein sequences. This package supports several sequence
2621 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2622 (license license:gpl2+)))
2624 (define-public r-triform
2631 (uri (bioconductor-uri "triform" version))
2634 "12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s"))))
2635 (build-system r-build-system)
2637 `(("r-biocgenerics" ,r-biocgenerics)
2638 ("r-iranges" ,r-iranges)
2639 ("r-yaml" ,r-yaml)))
2640 (home-page "https://bioconductor.org/packages/triform/")
2641 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2643 "The Triform algorithm uses model-free statistics to identify peak-like
2644 distributions of TF ChIP sequencing reads, taking advantage of an improved
2645 peak definition in combination with known profile characteristics.")
2646 (license license:gpl2)))
2648 (define-public r-varianttools
2650 (name "r-varianttools")
2655 (uri (bioconductor-uri "VariantTools" version))
2658 "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
2659 (properties `((upstream-name . "VariantTools")))
2660 (build-system r-build-system)
2662 `(("r-biobase" ,r-biobase)
2663 ("r-biocgenerics" ,r-biocgenerics)
2664 ("r-biocparallel" ,r-biocparallel)
2665 ("r-biostrings" ,r-biostrings)
2666 ("r-bsgenome" ,r-bsgenome)
2667 ("r-genomeinfodb" ,r-genomeinfodb)
2668 ("r-genomicfeatures" ,r-genomicfeatures)
2669 ("r-genomicranges" ,r-genomicranges)
2670 ("r-iranges" ,r-iranges)
2671 ("r-matrix" ,r-matrix)
2672 ("r-rsamtools" ,r-rsamtools)
2673 ("r-rtracklayer" ,r-rtracklayer)
2674 ("r-s4vectors" ,r-s4vectors)
2675 ("r-variantannotation" ,r-variantannotation)))
2676 (home-page "https://bioconductor.org/packages/VariantTools/")
2677 (synopsis "Tools for exploratory analysis of variant calls")
2679 "Explore, diagnose, and compare variant calls using filters. The
2680 VariantTools package supports a workflow for loading data, calling single
2681 sample variants and tumor-specific somatic mutations or other sample-specific
2682 variant types (e.g., RNA editing). Most of the functions operate on
2683 alignments (BAM files) or datasets of called variants. The user is expected
2684 to have already aligned the reads with a separate tool, e.g., GSNAP via
2686 (license license:artistic2.0)))
2688 (define-public r-heatplus
2695 (uri (bioconductor-uri "Heatplus" version))
2698 "0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48"))))
2699 (properties `((upstream-name . "Heatplus")))
2700 (build-system r-build-system)
2702 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2703 (home-page "https://github.com/alexploner/Heatplus")
2704 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2706 "This package provides tools to display a rectangular heatmap (intensity
2707 plot) of a data matrix. By default, both samples (columns) and features (row)
2708 of the matrix are sorted according to a hierarchical clustering, and the
2709 corresponding dendrogram is plotted. Optionally, panels with additional
2710 information about samples and features can be added to the plot.")
2711 (license license:gpl2+)))
2713 (define-public r-gosemsim
2720 (uri (bioconductor-uri "GOSemSim" version))
2723 "0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib"))))
2724 (properties `((upstream-name . "GOSemSim")))
2725 (build-system r-build-system)
2727 `(("r-annotationdbi" ,r-annotationdbi)
2728 ("r-go-db" ,r-go-db)
2729 ("r-rcpp" ,r-rcpp)))
2730 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2731 (synopsis "GO-terms semantic similarity measures")
2733 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2734 quantitative ways to compute similarities between genes and gene groups, and
2735 have became important basis for many bioinformatics analysis approaches.
2736 GOSemSim is an R package for semantic similarity computation among GO terms,
2737 sets of GO terms, gene products and gene clusters.")
2738 (license license:artistic2.0)))
2740 (define-public r-anota
2747 (uri (bioconductor-uri "anota" version))
2750 "182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"))))
2751 (build-system r-build-system)
2753 `(("r-multtest" ,r-multtest)
2754 ("r-qvalue" ,r-qvalue)))
2755 (home-page "https://bioconductor.org/packages/anota/")
2756 (synopsis "Analysis of translational activity")
2758 "Genome wide studies of translational control is emerging as a tool to
2759 study verious biological conditions. The output from such analysis is both
2760 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2761 involved in translation (the actively translating mRNA level) for each mRNA.
2762 The standard analysis of such data strives towards identifying differential
2763 translational between two or more sample classes - i.e. differences in
2764 actively translated mRNA levels that are independent of underlying differences
2765 in cytosolic mRNA levels. This package allows for such analysis using partial
2766 variances and the random variance model. As 10s of thousands of mRNAs are
2767 analyzed in parallell the library performs a number of tests to assure that
2768 the data set is suitable for such analysis.")
2769 (license license:gpl3)))
2771 (define-public r-sigpathway
2773 (name "r-sigpathway")
2778 (uri (bioconductor-uri "sigPathway" version))
2781 "0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3"))))
2782 (properties `((upstream-name . "sigPathway")))
2783 (build-system r-build-system)
2784 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
2785 (synopsis "Pathway analysis")
2787 "This package is used to conduct pathway analysis by calculating the NT_k
2788 and NE_k statistics in a statistical framework for determining whether a
2789 specified group of genes for a pathway has a coordinated association with a
2790 phenotype of interest.")
2791 (license license:gpl2)))
2793 (define-public r-fgsea
2800 (uri (bioconductor-uri "fgsea" version))
2803 "0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"))))
2804 (build-system r-build-system)
2806 `(("r-biocparallel" ,r-biocparallel)
2807 ("r-data-table" ,r-data-table)
2808 ("r-fastmatch" ,r-fastmatch)
2809 ("r-ggplot2" ,r-ggplot2)
2810 ("r-gridextra" ,r-gridextra)
2811 ("r-matrix" ,r-matrix)
2812 ("r-rcpp" ,r-rcpp)))
2813 (home-page "https://github.com/ctlab/fgsea/")
2814 (synopsis "Fast gene set enrichment analysis")
2816 "The package implements an algorithm for fast gene set enrichment
2817 analysis. Using the fast algorithm allows to make more permutations and get
2818 more fine grained p-values, which allows to use accurate stantard approaches
2819 to multiple hypothesis correction.")
2820 (license license:expat)))
2822 (define-public r-dose
2829 (uri (bioconductor-uri "DOSE" version))
2832 "1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa"))))
2833 (properties `((upstream-name . "DOSE")))
2834 (build-system r-build-system)
2836 `(("r-annotationdbi" ,r-annotationdbi)
2837 ("r-biocparallel" ,r-biocparallel)
2838 ("r-do-db" ,r-do-db)
2839 ("r-fgsea" ,r-fgsea)
2840 ("r-ggplot2" ,r-ggplot2)
2841 ("r-gosemsim" ,r-gosemsim)
2842 ("r-qvalue" ,r-qvalue)
2843 ("r-reshape2" ,r-reshape2)
2844 ("r-s4vectors" ,r-s4vectors)))
2845 (home-page "https://guangchuangyu.github.io/software/DOSE/")
2846 (synopsis "Disease ontology semantic and enrichment analysis")
2848 "This package implements five methods proposed by Resnik, Schlicker,
2849 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
2850 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
2851 including hypergeometric model and gene set enrichment analysis are also
2852 implemented for discovering disease associations of high-throughput biological
2854 (license license:artistic2.0)))
2856 (define-public r-enrichplot
2858 (name "r-enrichplot")
2863 (uri (bioconductor-uri "enrichplot" version))
2866 "0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"))))
2867 (build-system r-build-system)
2869 `(("r-annotationdbi" ,r-annotationdbi)
2870 ("r-cowplot" ,r-cowplot)
2872 ("r-europepmc" ,r-europepmc)
2873 ("r-ggplot2" ,r-ggplot2)
2874 ("r-ggplotify" ,r-ggplotify)
2875 ("r-ggraph" ,r-ggraph)
2876 ("r-ggridges" ,r-ggridges)
2877 ("r-gosemsim" ,r-gosemsim)
2878 ("r-gridextra" ,r-gridextra)
2879 ("r-igraph" ,r-igraph)
2880 ("r-purrr" ,r-purrr)
2881 ("r-rcolorbrewer" ,r-rcolorbrewer)
2882 ("r-reshape2" ,r-reshape2)
2883 ("r-upsetr" ,r-upsetr)))
2884 (home-page "https://github.com/GuangchuangYu/enrichplot")
2885 (synopsis "Visualization of functional enrichment result")
2887 "The enrichplot package implements several visualization methods for
2888 interpreting functional enrichment results obtained from ORA or GSEA analyses.
2889 All the visualization methods are developed based on ggplot2 graphics.")
2890 (license license:artistic2.0)))
2892 (define-public r-clusterprofiler
2894 (name "r-clusterprofiler")
2899 (uri (bioconductor-uri "clusterProfiler" version))
2902 "1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm"))))
2904 `((upstream-name . "clusterProfiler")))
2905 (build-system r-build-system)
2907 `(("r-annotationdbi" ,r-annotationdbi)
2909 ("r-enrichplot" ,r-enrichplot)
2910 ("r-ggplot2" ,r-ggplot2)
2911 ("r-go-db" ,r-go-db)
2912 ("r-gosemsim" ,r-gosemsim)
2913 ("r-magrittr" ,r-magrittr)
2915 ("r-qvalue" ,r-qvalue)
2916 ("r-rvcheck" ,r-rvcheck)
2917 ("r-tidyr" ,r-tidyr)))
2918 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
2919 (synopsis "Analysis and visualization of functional profiles for gene clusters")
2921 "This package implements methods to analyze and visualize functional
2922 profiles (GO and KEGG) of gene and gene clusters.")
2923 (license license:artistic2.0)))
2925 (define-public r-mlinterfaces
2927 (name "r-mlinterfaces")
2932 (uri (bioconductor-uri "MLInterfaces" version))
2935 "12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8"))))
2936 (properties `((upstream-name . "MLInterfaces")))
2937 (build-system r-build-system)
2939 `(("r-annotate" ,r-annotate)
2940 ("r-biobase" ,r-biobase)
2941 ("r-biocgenerics" ,r-biocgenerics)
2942 ("r-cluster" ,r-cluster)
2945 ("r-gdata" ,r-gdata)
2946 ("r-genefilter" ,r-genefilter)
2947 ("r-ggvis" ,r-ggvis)
2948 ("r-hwriter" ,r-hwriter)
2950 ("r-mlbench" ,r-mlbench)
2952 ("r-rcolorbrewer" ,r-rcolorbrewer)
2954 ("r-rpart" ,r-rpart)
2955 ("r-sfsmisc" ,r-sfsmisc)
2956 ("r-shiny" ,r-shiny)
2957 ("r-threejs" ,r-threejs)))
2958 (home-page "https://bioconductor.org/packages/MLInterfaces/")
2959 (synopsis "Interfaces to R machine learning procedures")
2961 "This package provides uniform interfaces to machine learning code for
2962 data in R and Bioconductor containers.")
2963 ;; Any version of the LGPL.
2964 (license license:lgpl2.1+)))
2966 (define-public r-annaffy
2973 (uri (bioconductor-uri "annaffy" version))
2976 "16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5"))))
2977 (build-system r-build-system)
2980 (modify-phases %standard-phases
2981 (add-after 'unpack 'remove-reference-to-non-free-data
2983 (substitute* "DESCRIPTION"
2987 `(("r-annotationdbi" ,r-annotationdbi)
2988 ("r-biobase" ,r-biobase)
2990 ("r-go-db" ,r-go-db)))
2991 (home-page "https://bioconductor.org/packages/annaffy/")
2992 (synopsis "Annotation tools for Affymetrix biological metadata")
2994 "This package provides functions for handling data from Bioconductor
2995 Affymetrix annotation data packages. It produces compact HTML and text
2996 reports including experimental data and URL links to many online databases.
2997 It allows searching of biological metadata using various criteria.")
2998 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
2999 ;; the LGPL 2.1 is included.
3000 (license license:lgpl2.1+)))
3002 (define-public r-a4core
3009 (uri (bioconductor-uri "a4Core" version))
3012 "1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr"))))
3013 (properties `((upstream-name . "a4Core")))
3014 (build-system r-build-system)
3016 `(("r-biobase" ,r-biobase)
3017 ("r-glmnet" ,r-glmnet)))
3018 (home-page "https://bioconductor.org/packages/a4Core")
3019 (synopsis "Automated Affymetrix array analysis core package")
3021 "This is the core package for the automated analysis of Affymetrix
3023 (license license:gpl3)))
3025 (define-public r-a4classif
3027 (name "r-a4classif")
3032 (uri (bioconductor-uri "a4Classif" version))
3035 "02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j"))))
3036 (properties `((upstream-name . "a4Classif")))
3037 (build-system r-build-system)
3039 `(("r-a4core" ,r-a4core)
3040 ("r-a4preproc" ,r-a4preproc)
3041 ("r-glmnet" ,r-glmnet)
3042 ("r-mlinterfaces" ,r-mlinterfaces)
3045 ("r-varselrf" ,r-varselrf)))
3046 (home-page "https://bioconductor.org/packages/a4Classif/")
3047 (synopsis "Automated Affymetrix array analysis classification package")
3049 "This is the classification package for the automated analysis of
3050 Affymetrix arrays.")
3051 (license license:gpl3)))
3053 (define-public r-a4preproc
3055 (name "r-a4preproc")
3060 (uri (bioconductor-uri "a4Preproc" version))
3063 "1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp"))))
3064 (properties `((upstream-name . "a4Preproc")))
3065 (build-system r-build-system)
3067 `(("r-annotationdbi" ,r-annotationdbi)))
3068 (home-page "https://bioconductor.org/packages/a4Preproc/")
3069 (synopsis "Automated Affymetrix array analysis preprocessing package")
3071 "This is a package for the automated analysis of Affymetrix arrays. It
3072 is used for preprocessing the arrays.")
3073 (license license:gpl3)))
3075 (define-public r-a4reporting
3077 (name "r-a4reporting")
3082 (uri (bioconductor-uri "a4Reporting" version))
3085 "124774z3bfdjgxx2ad40795h92aam21yfx0rw0n01nk2wf6k7xc4"))))
3086 (properties `((upstream-name . "a4Reporting")))
3087 (build-system r-build-system)
3089 `(("r-annaffy" ,r-annaffy)
3090 ("r-xtable" ,r-xtable)))
3091 (home-page "https://bioconductor.org/packages/a4Reporting/")
3092 (synopsis "Automated Affymetrix array analysis reporting package")
3094 "This is a package for the automated analysis of Affymetrix arrays. It
3095 provides reporting features.")
3096 (license license:gpl3)))
3098 (define-public r-a4base
3105 (uri (bioconductor-uri "a4Base" version))
3108 "0k9k3bv99msbwf2y416cz316ssaha2dxvmaddbl7z9037p8mjr70"))))
3109 (properties `((upstream-name . "a4Base")))
3110 (build-system r-build-system)
3112 `(("r-a4core" ,r-a4core)
3113 ("r-a4preproc" ,r-a4preproc)
3114 ("r-annaffy" ,r-annaffy)
3115 ("r-annotationdbi" ,r-annotationdbi)
3116 ("r-biobase" ,r-biobase)
3117 ("r-genefilter" ,r-genefilter)
3118 ("r-glmnet" ,r-glmnet)
3119 ("r-gplots" ,r-gplots)
3120 ("r-limma" ,r-limma)
3122 ("r-multtest" ,r-multtest)))
3123 (home-page "https://bioconductor.org/packages/a4Base/")
3124 (synopsis "Automated Affymetrix array analysis base package")
3126 "This package provides basic features for the automated analysis of
3127 Affymetrix arrays.")
3128 (license license:gpl3)))
3137 (uri (bioconductor-uri "a4" version))
3140 "1iqjy35rqx3m2y0dm2bk4cnzdm1qvbi608bfmrid88w6wmwz3qlk"))))
3141 (build-system r-build-system)
3143 `(("r-a4base" ,r-a4base)
3144 ("r-a4classif" ,r-a4classif)
3145 ("r-a4core" ,r-a4core)
3146 ("r-a4preproc" ,r-a4preproc)
3147 ("r-a4reporting" ,r-a4reporting)))
3148 (home-page "https://bioconductor.org/packages/a4/")
3149 (synopsis "Automated Affymetrix array analysis umbrella package")
3151 "This package provides a software suite for the automated analysis of
3152 Affymetrix arrays.")
3153 (license license:gpl3)))
3155 (define-public r-abseqr
3162 (uri (bioconductor-uri "abseqR" version))
3165 "0w0ngxnilcrxlixsz7ls3zm99gyabxwn7w1r3r45n96d4aj075ry"))))
3166 (properties `((upstream-name . "abseqR")))
3167 (build-system r-build-system)
3169 `(("pandoc" ,ghc-pandoc)))
3171 `(("r-biocparallel" ,r-biocparallel)
3172 ("r-biocstyle" ,r-biocstyle)
3173 ("r-circlize" ,r-circlize)
3174 ("r-flexdashboard" ,r-flexdashboard)
3175 ("r-ggcorrplot" ,r-ggcorrplot)
3176 ("r-ggdendro" ,r-ggdendro)
3177 ("r-ggplot2" ,r-ggplot2)
3178 ("r-gridextra" ,r-gridextra)
3179 ("r-knitr" ,r-knitr)
3180 ("r-plotly" ,r-plotly)
3183 ("r-rcolorbrewer" ,r-rcolorbrewer)
3184 ("r-reshape2" ,r-reshape2)
3185 ("r-rmarkdown" ,r-rmarkdown)
3186 ("r-stringr" ,r-stringr)
3187 ("r-vegan" ,r-vegan)
3188 ("r-venndiagram" ,r-venndiagram)))
3189 (home-page "https://github.com/malhamdoosh/abseqR")
3190 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3192 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3193 sequencing datasets generated from antibody libraries and abseqR is one of its
3194 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3195 capabilities and allows them to generate interactive HTML reports for the
3196 convenience of viewing and sharing with other researchers. Additionally,
3197 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3198 further downstream analysis on its output.")
3199 (license license:gpl3)))
3201 (define-public r-bacon
3208 (uri (bioconductor-uri "bacon" version))
3211 "1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df"))))
3212 (build-system r-build-system)
3214 `(("r-biocparallel" ,r-biocparallel)
3215 ("r-ellipse" ,r-ellipse)
3216 ("r-ggplot2" ,r-ggplot2)))
3217 (home-page "https://bioconductor.org/packages/bacon/")
3218 (synopsis "Controlling bias and inflation in association studies")
3220 "Bacon can be used to remove inflation and bias often observed in
3221 epigenome- and transcriptome-wide association studies. To this end bacon
3222 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3223 fitting a three-component normal mixture on z-scores.")
3224 (license license:gpl2+)))
3226 (define-public r-rgadem
3233 (uri (bioconductor-uri "rGADEM" version))
3236 "1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2"))))
3237 (properties `((upstream-name . "rGADEM")))
3238 (build-system r-build-system)
3240 `(("r-biostrings" ,r-biostrings)
3241 ("r-bsgenome" ,r-bsgenome)
3242 ("r-iranges" ,r-iranges)
3243 ("r-seqlogo" ,r-seqlogo)))
3244 (home-page "https://bioconductor.org/packages/rGADEM/")
3245 (synopsis "De novo sequence motif discovery")
3247 "rGADEM is an efficient de novo motif discovery tool for large-scale
3248 genomic sequence data.")
3249 (license license:artistic2.0)))
3251 (define-public r-motiv
3258 (uri (bioconductor-uri "MotIV" version))
3261 "1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8"))))
3262 (properties `((upstream-name . "MotIV")))
3263 (build-system r-build-system)
3267 `(("r-biocgenerics" ,r-biocgenerics)
3268 ("r-biostrings" ,r-biostrings)
3269 ("r-iranges" ,r-iranges)
3270 ("r-lattice" ,r-lattice)
3271 ("r-rgadem" ,r-rgadem)
3272 ("r-s4vectors" ,r-s4vectors)))
3273 (home-page "https://bioconductor.org/packages/MotIV/")
3274 (synopsis "Motif identification and validation")
3276 "This package is used for the identification and validation of sequence
3277 motifs. It makes use of STAMP for comparing a set of motifs to a given
3278 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3279 distributions, modules and filter motifs.")
3280 (license license:gpl2)))
3282 (define-public r-motifstack
3284 (name "r-motifstack")
3289 (uri (bioconductor-uri "motifStack" version))
3292 "1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf"))))
3293 (properties `((upstream-name . "motifStack")))
3294 (build-system r-build-system)
3296 `(("r-ade4" ,r-ade4)
3297 ("r-biostrings" ,r-biostrings)
3298 ("r-grimport" ,r-grimport)
3299 ("r-htmlwidgets" ,r-htmlwidgets)
3300 ("r-motiv" ,r-motiv)
3301 ("r-scales" ,r-scales)
3303 (home-page "https://bioconductor.org/packages/motifStack/")
3304 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3306 "The motifStack package is designed for graphic representation of
3307 multiple motifs with different similarity scores. It works with both DNA/RNA
3308 sequence motifs and amino acid sequence motifs. In addition, it provides the
3309 flexibility for users to customize the graphic parameters such as the font
3310 type and symbol colors.")
3311 (license license:gpl2+)))
3313 (define-public r-genomicscores
3315 (name "r-genomicscores")
3320 (uri (bioconductor-uri "GenomicScores" version))
3323 "0lrhkcblvnki6kncwpavs01gbcz22yza6ma8zvfmbrrkfaxqzh8n"))))
3324 (properties `((upstream-name . "GenomicScores")))
3325 (build-system r-build-system)
3327 `(("r-annotationhub" ,r-annotationhub)
3328 ("r-biobase" ,r-biobase)
3329 ("r-biocgenerics" ,r-biocgenerics)
3330 ("r-biostrings" ,r-biostrings)
3331 ("r-bsgenome" ,r-bsgenome)
3332 ("r-genomeinfodb" ,r-genomeinfodb)
3333 ("r-genomicranges" ,r-genomicranges)
3334 ("r-iranges" ,r-iranges)
3335 ("r-s4vectors" ,r-s4vectors)
3337 (home-page "https://github.com/rcastelo/GenomicScores/")
3338 (synopsis "Work with genome-wide position-specific scores")
3340 "This package provides infrastructure to store and access genome-wide
3341 position-specific scores within R and Bioconductor.")
3342 (license license:artistic2.0)))
3344 (define-public r-atacseqqc
3346 (name "r-atacseqqc")
3351 (uri (bioconductor-uri "ATACseqQC" version))
3354 "1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn"))))
3355 (properties `((upstream-name . "ATACseqQC")))
3356 (build-system r-build-system)
3358 `(("r-biocgenerics" ,r-biocgenerics)
3359 ("r-biostrings" ,r-biostrings)
3360 ("r-bsgenome" ,r-bsgenome)
3361 ("r-chippeakanno" ,r-chippeakanno)
3362 ("r-genomeinfodb" ,r-genomeinfodb)
3363 ("r-genomicalignments" ,r-genomicalignments)
3364 ("r-genomicranges" ,r-genomicranges)
3365 ("r-genomicscores" ,r-genomicscores)
3366 ("r-iranges" ,r-iranges)
3367 ("r-kernsmooth" ,r-kernsmooth)
3368 ("r-limma" ,r-limma)
3369 ("r-motifstack" ,r-motifstack)
3370 ("r-preseqr" ,r-preseqr)
3371 ("r-randomforest" ,r-randomforest)
3372 ("r-rsamtools" ,r-rsamtools)
3373 ("r-rtracklayer" ,r-rtracklayer)
3374 ("r-s4vectors" ,r-s4vectors)))
3375 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3376 (synopsis "ATAC-seq quality control")
3378 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3379 sequencing, is a rapid and sensitive method for chromatin accessibility
3380 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3381 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3382 assess whether their ATAC-seq experiment is successful. It includes
3383 diagnostic plots of fragment size distribution, proportion of mitochondria
3384 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3386 (license license:gpl2+)))
3388 (define-public r-gofuncr
3395 (uri (bioconductor-uri "GOfuncR" version))
3398 "021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk"))))
3399 (properties `((upstream-name . "GOfuncR")))
3400 (build-system r-build-system)
3402 `(("r-annotationdbi" ,r-annotationdbi)
3403 ("r-genomicranges" ,r-genomicranges)
3404 ("r-gtools" ,r-gtools)
3405 ("r-iranges" ,r-iranges)
3406 ("r-mapplots" ,r-mapplots)
3408 ("r-vioplot" ,r-vioplot)))
3409 (home-page "https://bioconductor.org/packages/GOfuncR/")
3410 (synopsis "Gene ontology enrichment using FUNC")
3412 "GOfuncR performs a gene ontology enrichment analysis based on the
3413 ontology enrichment software FUNC. GO-annotations are obtained from
3414 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3415 included in the package and updated regularly. GOfuncR provides the standard
3416 candidate vs background enrichment analysis using the hypergeometric test, as
3417 well as three additional tests:
3420 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3421 @item a binomial test that is used when genes are associated with two counts,
3423 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3424 associated with four counts.
3427 To correct for multiple testing and interdependency of the tests, family-wise
3428 error rates are computed based on random permutations of the gene-associated
3429 variables. GOfuncR also provides tools for exploring the ontology graph and
3430 the annotations, and options to take gene-length or spatial clustering of
3431 genes into account. It is also possible to provide custom gene coordinates,
3432 annotations and ontologies.")
3433 (license license:gpl2+)))
3435 (define-public r-abaenrichment
3437 (name "r-abaenrichment")
3442 (uri (bioconductor-uri "ABAEnrichment" version))
3445 "0bvanqmg1smyckh16m2qn7d68zq4j7n74sgsnbgms5jngbp9158v"))))
3446 (properties `((upstream-name . "ABAEnrichment")))
3447 (build-system r-build-system)
3449 `(("r-abadata" ,r-abadata)
3450 ("r-data-table" ,r-data-table)
3451 ("r-gofuncr" ,r-gofuncr)
3452 ("r-gplots" ,r-gplots)
3453 ("r-gtools" ,r-gtools)
3454 ("r-rcpp" ,r-rcpp)))
3455 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3456 (synopsis "Gene expression enrichment in human brain regions")
3458 "The package ABAEnrichment is designed to test for enrichment of user
3459 defined candidate genes in the set of expressed genes in different human brain
3460 regions. The core function @code{aba_enrich} integrates the expression of the
3461 candidate gene set (averaged across donors) and the structural information of
3462 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3463 (license license:gpl2+)))
3465 (define-public r-annotationfuncs
3467 (name "r-annotationfuncs")
3472 (uri (bioconductor-uri "AnnotationFuncs" version))
3475 "1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss"))))
3477 `((upstream-name . "AnnotationFuncs")))
3478 (build-system r-build-system)
3480 `(("r-annotationdbi" ,r-annotationdbi)
3482 (home-page "https://www.iysik.com/r/annotationfuncs")
3483 (synopsis "Annotation translation functions")
3485 "This package provides functions for handling translating between
3486 different identifieres using the Biocore Data Team data-packages (e.g.
3487 @code{org.Bt.eg.db}).")
3488 (license license:gpl2)))
3490 (define-public r-annotationtools
3492 (name "r-annotationtools")
3497 (uri (bioconductor-uri "annotationTools" version))
3500 "0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z"))))
3502 `((upstream-name . "annotationTools")))
3503 (build-system r-build-system)
3504 (propagated-inputs `(("r-biobase" ,r-biobase)))
3505 (home-page "https://bioconductor.org/packages/annotationTools/")
3506 (synopsis "Annotate microarrays and perform gene expression analyses")
3508 "This package provides functions to annotate microarrays, find orthologs,
3509 and integrate heterogeneous gene expression profiles using annotation and
3510 other molecular biology information available as flat file database (plain
3512 ;; Any version of the GPL.
3513 (license (list license:gpl2+))))
3515 (define-public r-allelicimbalance
3517 (name "r-allelicimbalance")
3522 (uri (bioconductor-uri "AllelicImbalance" version))
3525 "03524lj6aw9cskbpxzjmi9g708x6p94mf26yz4j941g1d0mc3z91"))))
3527 `((upstream-name . "AllelicImbalance")))
3528 (build-system r-build-system)
3530 `(("r-annotationdbi" ,r-annotationdbi)
3531 ("r-biocgenerics" ,r-biocgenerics)
3532 ("r-biostrings" ,r-biostrings)
3533 ("r-bsgenome" ,r-bsgenome)
3534 ("r-genomeinfodb" ,r-genomeinfodb)
3535 ("r-genomicalignments" ,r-genomicalignments)
3536 ("r-genomicfeatures" ,r-genomicfeatures)
3537 ("r-genomicranges" ,r-genomicranges)
3538 ("r-gridextra" ,r-gridextra)
3540 ("r-iranges" ,r-iranges)
3541 ("r-lattice" ,r-lattice)
3542 ("r-latticeextra" ,r-latticeextra)
3544 ("r-rsamtools" ,r-rsamtools)
3545 ("r-s4vectors" ,r-s4vectors)
3546 ("r-seqinr" ,r-seqinr)
3547 ("r-summarizedexperiment" ,r-summarizedexperiment)
3548 ("r-variantannotation" ,r-variantannotation)))
3549 (home-page "https://github.com/pappewaio/AllelicImbalance")
3550 (synopsis "Investigate allele-specific expression")
3552 "This package provides a framework for allele-specific expression
3553 investigation using RNA-seq data.")
3554 (license license:gpl3)))
3556 (define-public r-aucell
3563 (uri (bioconductor-uri "AUCell" version))
3566 "1kdrs0521cyb8wlc4i3idfprrcy2f9w6kl56hfa94n0brmx62ya9"))))
3567 (properties `((upstream-name . "AUCell")))
3568 (build-system r-build-system)
3570 `(("r-data-table" ,r-data-table)
3571 ("r-gseabase" ,r-gseabase)
3572 ("r-mixtools" ,r-mixtools)
3573 ("r-r-utils" ,r-r-utils)
3574 ("r-shiny" ,r-shiny)
3575 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3576 (home-page "https://bioconductor.org/packages/AUCell/")
3577 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
3579 "AUCell allows to identify cells with active gene sets (e.g. signatures,
3580 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
3581 Under the Curve} (AUC) to calculate whether a critical subset of the input
3582 gene set is enriched within the expressed genes for each cell. The
3583 distribution of AUC scores across all the cells allows exploring the relative
3584 expression of the signature. Since the scoring method is ranking-based,
3585 AUCell is independent of the gene expression units and the normalization
3586 procedure. In addition, since the cells are evaluated individually, it can
3587 easily be applied to bigger datasets, subsetting the expression matrix if
3589 (license license:gpl3)))
3591 (define-public r-ebimage
3598 (uri (bioconductor-uri "EBImage" version))
3601 "18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx"))))
3602 (properties `((upstream-name . "EBImage")))
3603 (build-system r-build-system)
3605 `(("r-abind" ,r-abind)
3606 ("r-biocgenerics" ,r-biocgenerics)
3607 ("r-fftwtools" ,r-fftwtools)
3608 ("r-htmltools" ,r-htmltools)
3609 ("r-htmlwidgets" ,r-htmlwidgets)
3611 ("r-locfit" ,r-locfit)
3613 ("r-rcurl" ,r-rcurl)
3614 ("r-tiff" ,r-tiff)))
3616 `(("r-knitr" ,r-knitr))) ; for vignettes
3617 (home-page "https://github.com/aoles/EBImage")
3618 (synopsis "Image processing and analysis toolbox for R")
3620 "EBImage provides general purpose functionality for image processing and
3621 analysis. In the context of (high-throughput) microscopy-based cellular
3622 assays, EBImage offers tools to segment cells and extract quantitative
3623 cellular descriptors. This allows the automation of such tasks using the R
3624 programming language and facilitates the use of other tools in the R
3625 environment for signal processing, statistical modeling, machine learning and
3626 visualization with image data.")
3627 ;; Any version of the LGPL.
3628 (license license:lgpl2.1+)))
3630 (define-public r-yamss
3637 (uri (bioconductor-uri "yamss" version))
3640 "13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9"))))
3641 (build-system r-build-system)
3643 `(("r-biocgenerics" ,r-biocgenerics)
3644 ("r-data-table" ,r-data-table)
3645 ("r-ebimage" ,r-ebimage)
3646 ("r-iranges" ,r-iranges)
3647 ("r-limma" ,r-limma)
3648 ("r-matrix" ,r-matrix)
3650 ("r-s4vectors" ,r-s4vectors)
3651 ("r-summarizedexperiment"
3652 ,r-summarizedexperiment)))
3653 (home-page "https://github.com/hansenlab/yamss")
3654 (synopsis "Tools for high-throughput metabolomics")
3656 "This package provides tools to analyze and visualize high-throughput
3657 metabolomics data aquired using chromatography-mass spectrometry. These tools
3658 preprocess data in a way that enables reliable and powerful differential
3660 (license license:artistic2.0)))
3662 (define-public r-gtrellis
3669 (uri (bioconductor-uri "gtrellis" version))
3672 "17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v"))))
3673 (build-system r-build-system)
3675 `(("r-circlize" ,r-circlize)
3676 ("r-genomicranges" ,r-genomicranges)
3677 ("r-getoptlong" ,r-getoptlong)
3678 ("r-iranges" ,r-iranges)))
3679 (home-page "https://github.com/jokergoo/gtrellis")
3680 (synopsis "Genome level Trellis layout")
3682 "Genome level Trellis graph visualizes genomic data conditioned by
3683 genomic categories (e.g. chromosomes). For each genomic category, multiple
3684 dimensional data which are represented as tracks describe different features
3685 from different aspects. This package provides high flexibility to arrange
3686 genomic categories and to add self-defined graphics in the plot.")
3687 (license license:expat)))
3689 (define-public r-somaticsignatures
3691 (name "r-somaticsignatures")
3696 (uri (bioconductor-uri "SomaticSignatures" version))
3699 "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02"))))
3701 `((upstream-name . "SomaticSignatures")))
3702 (build-system r-build-system)
3704 `(("r-biobase" ,r-biobase)
3705 ("r-biostrings" ,r-biostrings)
3706 ("r-genomeinfodb" ,r-genomeinfodb)
3707 ("r-genomicranges" ,r-genomicranges)
3708 ("r-ggbio" ,r-ggbio)
3709 ("r-ggplot2" ,r-ggplot2)
3710 ("r-iranges" ,r-iranges)
3712 ("r-pcamethods" ,r-pcamethods)
3713 ("r-proxy" ,r-proxy)
3714 ("r-reshape2" ,r-reshape2)
3715 ("r-s4vectors" ,r-s4vectors)
3716 ("r-variantannotation" ,r-variantannotation)))
3717 (home-page "https://github.com/juliangehring/SomaticSignatures")
3718 (synopsis "Somatic signatures")
3720 "This package identifies mutational signatures of @dfn{single nucleotide
3721 variants} (SNVs). It provides a infrastructure related to the methodology
3722 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
3723 decomposition algorithms.")
3724 (license license:expat)))
3726 (define-public r-yapsa
3733 (uri (bioconductor-uri "YAPSA" version))
3736 "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j"))))
3737 (properties `((upstream-name . "YAPSA")))
3738 (build-system r-build-system)
3740 `(("r-circlize" ,r-circlize)
3741 ("r-complexheatmap" ,r-complexheatmap)
3742 ("r-corrplot" ,r-corrplot)
3743 ("r-dendextend" ,r-dendextend)
3744 ("r-genomeinfodb" ,r-genomeinfodb)
3745 ("r-genomicranges" ,r-genomicranges)
3746 ("r-getoptlong" ,r-getoptlong)
3747 ("r-ggplot2" ,r-ggplot2)
3748 ("r-gridextra" ,r-gridextra)
3749 ("r-gtrellis" ,r-gtrellis)
3750 ("r-keggrest" ,r-keggrest)
3752 ("r-pmcmr" ,r-pmcmr)
3753 ("r-reshape2" ,r-reshape2)
3754 ("r-somaticsignatures" ,r-somaticsignatures)
3755 ("r-variantannotation" ,r-variantannotation)))
3756 (home-page "https://bioconductor.org/packages/YAPSA/")
3757 (synopsis "Yet another package for signature analysis")
3759 "This package provides functions and routines useful in the analysis of
3760 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
3761 functions to perform a signature analysis with known signatures and a
3762 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
3764 (license license:gpl3)))
3766 (define-public r-gcrma
3773 (uri (bioconductor-uri "gcrma" version))
3776 "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim"))))
3777 (build-system r-build-system)
3779 `(("r-affy" ,r-affy)
3780 ("r-affyio" ,r-affyio)
3781 ("r-biobase" ,r-biobase)
3782 ("r-biocmanager" ,r-biocmanager)
3783 ("r-biostrings" ,r-biostrings)
3784 ("r-xvector" ,r-xvector)))
3785 (home-page "https://bioconductor.org/packages/gcrma/")
3786 (synopsis "Background adjustment using sequence information")
3788 "Gcrma adjusts for background intensities in Affymetrix array data which
3789 include optical noise and @dfn{non-specific binding} (NSB). The main function
3790 @code{gcrma} converts background adjusted probe intensities to expression
3791 measures using the same normalization and summarization methods as a
3792 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
3793 to estimate probe affinity to NSB. The sequence information is summarized in
3794 a more complex way than the simple GC content. Instead, the base types (A, T,
3795 G or C) at each position along the probe determine the affinity of each probe.
3796 The parameters of the position-specific base contributions to the probe
3797 affinity is estimated in an NSB experiment in which only NSB but no
3798 gene-specific bidning is expected.")
3799 ;; Any version of the LGPL
3800 (license license:lgpl2.1+)))
3802 (define-public r-simpleaffy
3804 (name "r-simpleaffy")
3809 (uri (bioconductor-uri "simpleaffy" version))
3812 "0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s"))))
3813 (build-system r-build-system)
3815 `(("r-affy" ,r-affy)
3816 ("r-biobase" ,r-biobase)
3817 ("r-biocgenerics" ,r-biocgenerics)
3818 ("r-gcrma" ,r-gcrma)
3819 ("r-genefilter" ,r-genefilter)))
3820 (home-page "https://bioconductor.org/packages/simpleaffy/")
3821 (synopsis "Very simple high level analysis of Affymetrix data")
3823 "This package provides high level functions for reading Affy @file{.CEL}
3824 files, phenotypic data, and then computing simple things with it, such as
3825 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
3826 library. It also has some basic scatter plot functions and mechanisms for
3827 generating high resolution journal figures.")
3828 (license license:gpl2+)))
3830 (define-public r-yaqcaffy
3837 (uri (bioconductor-uri "yaqcaffy" version))
3840 "192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk"))))
3841 (build-system r-build-system)
3843 `(("r-simpleaffy" ,r-simpleaffy)))
3844 (home-page "https://bioconductor.org/packages/yaqcaffy/")
3845 (synopsis "Affymetrix quality control and reproducibility analysis")
3847 "This is a package that can be used for quality control of Affymetrix
3848 GeneChip expression data and reproducibility analysis of human whole genome
3849 chips with the MAQC reference datasets.")
3850 (license license:artistic2.0)))
3852 (define-public r-quantro
3859 (uri (bioconductor-uri "quantro" version))
3862 "1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib"))))
3863 (build-system r-build-system)
3865 `(("r-biobase" ,r-biobase)
3866 ("r-doparallel" ,r-doparallel)
3867 ("r-foreach" ,r-foreach)
3868 ("r-ggplot2" ,r-ggplot2)
3869 ("r-iterators" ,r-iterators)
3870 ("r-minfi" ,r-minfi)
3871 ("r-rcolorbrewer" ,r-rcolorbrewer)))
3872 (home-page "https://bioconductor.org/packages/quantro/")
3873 (synopsis "Test for when to use quantile normalization")
3875 "This package provides a data-driven test for the assumptions of quantile
3876 normalization using raw data such as objects that inherit eSets (e.g.
3877 ExpressionSet, MethylSet). Group level information about each sample (such as
3878 Tumor / Normal status) must also be provided because the test assesses if
3879 there are global differences in the distributions between the user-defined
3881 (license license:gpl3+)))
3883 (define-public r-yarn
3890 (uri (bioconductor-uri "yarn" version))
3893 "0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s"))))
3894 (build-system r-build-system)
3896 `(("r-biobase" ,r-biobase)
3897 ("r-biomart" ,r-biomart)
3898 ("r-downloader" ,r-downloader)
3899 ("r-edger" ,r-edger)
3900 ("r-gplots" ,r-gplots)
3901 ("r-limma" ,r-limma)
3902 ("r-matrixstats" ,r-matrixstats)
3903 ("r-preprocesscore" ,r-preprocesscore)
3904 ("r-quantro" ,r-quantro)
3905 ("r-rcolorbrewer" ,r-rcolorbrewer)
3906 ("r-readr" ,r-readr)))
3907 (home-page "https://bioconductor.org/packages/yarn/")
3908 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
3910 "Expedite large RNA-Seq analyses using a combination of previously
3911 developed tools. YARN is meant to make it easier for the user in performing
3912 basic mis-annotation quality control, filtering, and condition-aware
3913 normalization. YARN leverages many Bioconductor tools and statistical
3914 techniques to account for the large heterogeneity and sparsity found in very
3915 large RNA-seq experiments.")
3916 (license license:artistic2.0)))
3918 (define-public r-roar
3925 (uri (bioconductor-uri "roar" version))
3928 "15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw"))))
3929 (build-system r-build-system)
3931 `(("r-biocgenerics" ,r-biocgenerics)
3932 ("r-genomeinfodb" ,r-genomeinfodb)
3933 ("r-genomicalignments" ,r-genomicalignments)
3934 ("r-genomicranges" ,r-genomicranges)
3935 ("r-iranges" ,r-iranges)
3936 ("r-rtracklayer" ,r-rtracklayer)
3937 ("r-s4vectors" ,r-s4vectors)
3938 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3939 (home-page "https://github.com/vodkatad/roar/")
3940 (synopsis "Identify differential APA usage from RNA-seq alignments")
3942 "This package provides tools for identifying preferential usage of APA
3943 sites, comparing two biological conditions, starting from known alternative
3944 sites and alignments obtained from standard RNA-seq experiments.")
3945 (license license:gpl3)))
3947 (define-public r-xbseq
3954 (uri (bioconductor-uri "XBSeq" version))
3957 "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph"))))
3958 (properties `((upstream-name . "XBSeq")))
3959 (build-system r-build-system)
3961 `(("r-biobase" ,r-biobase)
3962 ("r-deseq2" ,r-deseq2)
3963 ("r-dplyr" ,r-dplyr)
3964 ("r-ggplot2" ,r-ggplot2)
3965 ("r-locfit" ,r-locfit)
3966 ("r-magrittr" ,r-magrittr)
3967 ("r-matrixstats" ,r-matrixstats)
3968 ("r-pracma" ,r-pracma)
3969 ("r-roar" ,r-roar)))
3970 (home-page "https://github.com/Liuy12/XBSeq")
3971 (synopsis "Test for differential expression for RNA-seq data")
3973 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
3974 expression} (DE), where a statistical model was established based on the
3975 assumption that observed signals are the convolution of true expression
3976 signals and sequencing noises. The mapped reads in non-exonic regions are
3977 considered as sequencing noises, which follows a Poisson distribution. Given
3978 measurable observed signal and background noise from RNA-seq data, true
3979 expression signals, assuming governed by the negative binomial distribution,
3980 can be delineated and thus the accurate detection of differential expressed
3982 (license license:gpl3+)))
3984 (define-public r-massspecwavelet
3986 (name "r-massspecwavelet")
3991 (uri (bioconductor-uri "MassSpecWavelet" version))
3994 "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz"))))
3996 `((upstream-name . "MassSpecWavelet")))
3997 (build-system r-build-system)
3999 `(("r-waveslim" ,r-waveslim)))
4000 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4001 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4003 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4004 data mainly through the use of wavelet transforms. It supports peak detection
4005 based on @dfn{Continuous Wavelet Transform} (CWT).")
4006 (license license:lgpl2.0+)))
4008 (define-public r-xcms
4015 (uri (bioconductor-uri "xcms" version))
4018 "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww"))))
4019 (build-system r-build-system)
4021 `(("r-biobase" ,r-biobase)
4022 ("r-biocgenerics" ,r-biocgenerics)
4023 ("r-biocparallel" ,r-biocparallel)
4024 ("r-lattice" ,r-lattice)
4025 ("r-massspecwavelet" ,r-massspecwavelet)
4026 ("r-msnbase" ,r-msnbase)
4027 ("r-multtest" ,r-multtest)
4030 ("r-protgenerics" ,r-protgenerics)
4032 ("r-rcolorbrewer" ,r-rcolorbrewer)
4033 ("r-robustbase" ,r-robustbase)
4034 ("r-s4vectors" ,r-s4vectors)))
4035 (home-page "https://bioconductor.org/packages/xcms/")
4036 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4038 "This package provides a framework for processing and visualization of
4039 chromatographically separated and single-spectra mass spectral data. It
4040 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4041 data for high-throughput, untargeted analyte profiling.")
4042 (license license:gpl2+)))
4044 (define-public r-wrench
4051 (uri (bioconductor-uri "Wrench" version))
4054 "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg"))))
4055 (properties `((upstream-name . "Wrench")))
4056 (build-system r-build-system)
4058 `(("r-limma" ,r-limma)
4059 ("r-locfit" ,r-locfit)
4060 ("r-matrixstats" ,r-matrixstats)))
4061 (home-page "https://github.com/HCBravoLab/Wrench")
4062 (synopsis "Wrench normalization for sparse count data")
4064 "Wrench is a package for normalization sparse genomic count data, like
4065 that arising from 16s metagenomic surveys.")
4066 (license license:artistic2.0)))