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 netpbm)
36 #:use-module (gnu packages perl)
37 #:use-module (gnu packages pkg-config)
38 #:use-module (gnu packages statistics)
39 #:use-module (gnu packages web))
44 (define-public r-bsgenome-celegans-ucsc-ce6
46 (name "r-bsgenome-celegans-ucsc-ce6")
50 ;; We cannot use bioconductor-uri here because this tarball is
51 ;; located under "data/annotation/" instead of "bioc/".
52 (uri (string-append "https://www.bioconductor.org/packages/"
53 "release/data/annotation/src/contrib/"
54 "BSgenome.Celegans.UCSC.ce6_"
58 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
60 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
61 (build-system r-build-system)
62 ;; As this package provides little more than a very large data file it
63 ;; doesn't make sense to build substitutes.
64 (arguments `(#:substitutable? #f))
66 `(("r-bsgenome" ,r-bsgenome)))
68 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
69 (synopsis "Full genome sequences for Worm")
71 "This package provides full genome sequences for Caenorhabditis
72 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
74 (license license:artistic2.0)))
76 (define-public r-bsgenome-celegans-ucsc-ce10
78 (name "r-bsgenome-celegans-ucsc-ce10")
82 ;; We cannot use bioconductor-uri here because this tarball is
83 ;; located under "data/annotation/" instead of "bioc/".
84 (uri (string-append "https://www.bioconductor.org/packages/"
85 "release/data/annotation/src/contrib/"
86 "BSgenome.Celegans.UCSC.ce10_"
90 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
92 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
93 (build-system r-build-system)
94 ;; As this package provides little more than a very large data file it
95 ;; doesn't make sense to build substitutes.
96 (arguments `(#:substitutable? #f))
98 `(("r-bsgenome" ,r-bsgenome)))
100 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
101 (synopsis "Full genome sequences for Worm")
103 "This package provides full genome sequences for Caenorhabditis
104 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
106 (license license:artistic2.0)))
108 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
110 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
114 ;; We cannot use bioconductor-uri here because this tarball is
115 ;; located under "data/annotation/" instead of "bioc/".
116 (uri (string-append "https://www.bioconductor.org/packages/"
117 "release/data/annotation/src/contrib/"
118 "BSgenome.Dmelanogaster.UCSC.dm6_"
122 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
124 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
125 (build-system r-build-system)
126 ;; As this package provides little more than a very large data file it
127 ;; doesn't make sense to build substitutes.
128 (arguments `(#:substitutable? #f))
130 `(("r-bsgenome" ,r-bsgenome)))
132 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
133 (synopsis "Full genome sequences for Fly")
135 "This package provides full genome sequences for Drosophila
136 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
138 (license license:artistic2.0)))
140 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
142 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
146 ;; We cannot use bioconductor-uri here because this tarball is
147 ;; located under "data/annotation/" instead of "bioc/".
148 (uri (string-append "https://www.bioconductor.org/packages/"
149 "release/data/annotation/src/contrib/"
150 "BSgenome.Dmelanogaster.UCSC.dm3_"
154 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
156 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
157 (build-system r-build-system)
158 ;; As this package provides little more than a very large data file it
159 ;; doesn't make sense to build substitutes.
160 (arguments `(#:substitutable? #f))
162 `(("r-bsgenome" ,r-bsgenome)))
164 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
165 (synopsis "Full genome sequences for Fly")
167 "This package provides full genome sequences for Drosophila
168 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
169 Biostrings objects.")
170 (license license:artistic2.0)))
172 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
174 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
178 ;; We cannot use bioconductor-uri here because this tarball is
179 ;; located under "data/annotation/" instead of "bioc/".
180 (uri (string-append "http://www.bioconductor.org/packages/"
181 "release/data/annotation/src/contrib/"
182 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
186 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
188 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
189 (build-system r-build-system)
191 `(("r-bsgenome" ,r-bsgenome)
192 ("r-bsgenome-dmelanogaster-ucsc-dm3"
193 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
194 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
195 (synopsis "Full masked genome sequences for Fly")
197 "This package provides full masked genome sequences for Drosophila
198 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
199 Biostrings objects. The sequences are the same as in
200 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
201 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
202 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
203 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
204 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
205 (license license:artistic2.0)))
207 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
209 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
213 ;; We cannot use bioconductor-uri here because this tarball is
214 ;; located under "data/annotation/" instead of "bioc/".
215 (uri (string-append "https://www.bioconductor.org/packages/"
216 "release/data/annotation/src/contrib/"
217 "BSgenome.Hsapiens.1000genomes.hs37d5_"
221 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
223 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
224 (build-system r-build-system)
225 ;; As this package provides little more than a very large data file it
226 ;; doesn't make sense to build substitutes.
227 (arguments `(#:substitutable? #f))
229 `(("r-bsgenome" ,r-bsgenome)))
231 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
232 (synopsis "Full genome sequences for Homo sapiens")
234 "This package provides full genome sequences for Homo sapiens from
235 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
236 (license license:artistic2.0)))
238 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
240 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
244 ;; We cannot use bioconductor-uri here because this tarball is
245 ;; located under "data/annotation/" instead of "bioc/".
246 (uri (string-append "http://www.bioconductor.org/packages/"
247 "release/data/annotation/src/contrib/"
248 "BSgenome.Hsapiens.UCSC.hg19.masked_"
252 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
254 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
255 (build-system r-build-system)
257 `(("r-bsgenome" ,r-bsgenome)
258 ("r-bsgenome-hsapiens-ucsc-hg19"
259 ,r-bsgenome-hsapiens-ucsc-hg19)))
260 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
261 (synopsis "Full masked genome sequences for Homo sapiens")
263 "This package provides full genome sequences for Homo sapiens (Human) as
264 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
265 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
266 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
267 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
268 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
269 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
271 (license license:artistic2.0)))
273 (define-public r-bsgenome-mmusculus-ucsc-mm9
275 (name "r-bsgenome-mmusculus-ucsc-mm9")
279 ;; We cannot use bioconductor-uri here because this tarball is
280 ;; located under "data/annotation/" instead of "bioc/".
281 (uri (string-append "https://www.bioconductor.org/packages/"
282 "release/data/annotation/src/contrib/"
283 "BSgenome.Mmusculus.UCSC.mm9_"
287 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
289 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
290 (build-system r-build-system)
291 ;; As this package provides little more than a very large data file it
292 ;; doesn't make sense to build substitutes.
293 (arguments `(#:substitutable? #f))
295 `(("r-bsgenome" ,r-bsgenome)))
297 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
298 (synopsis "Full genome sequences for Mouse")
300 "This package provides full genome sequences for Mus musculus (Mouse) as
301 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
302 (license license:artistic2.0)))
304 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
306 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
310 ;; We cannot use bioconductor-uri here because this tarball is
311 ;; located under "data/annotation/" instead of "bioc/".
312 (uri (string-append "http://www.bioconductor.org/packages/"
313 "release/data/annotation/src/contrib/"
314 "BSgenome.Mmusculus.UCSC.mm9.masked_"
318 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
320 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
321 (build-system r-build-system)
323 `(("r-bsgenome" ,r-bsgenome)
324 ("r-bsgenome-mmusculus-ucsc-mm9"
325 ,r-bsgenome-mmusculus-ucsc-mm9)))
326 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
327 (synopsis "Full masked genome sequences for Mouse")
329 "This package provides full genome sequences for Mus musculus (Mouse) as
330 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
331 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
332 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
333 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
334 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
335 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
337 (license license:artistic2.0)))
339 (define-public r-bsgenome-mmusculus-ucsc-mm10
341 (name "r-bsgenome-mmusculus-ucsc-mm10")
345 ;; We cannot use bioconductor-uri here because this tarball is
346 ;; located under "data/annotation/" instead of "bioc/".
347 (uri (string-append "https://www.bioconductor.org/packages/"
348 "release/data/annotation/src/contrib/"
349 "BSgenome.Mmusculus.UCSC.mm10_"
353 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
355 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
356 (build-system r-build-system)
357 ;; As this package provides little more than a very large data file it
358 ;; doesn't make sense to build substitutes.
359 (arguments `(#:substitutable? #f))
361 `(("r-bsgenome" ,r-bsgenome)))
363 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
364 (synopsis "Full genome sequences for Mouse")
366 "This package provides full genome sequences for Mus
367 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
368 in Biostrings objects.")
369 (license license:artistic2.0)))
371 (define-public r-org-ce-eg-db
373 (name "r-org-ce-eg-db")
377 ;; We cannot use bioconductor-uri here because this tarball is
378 ;; located under "data/annotation/" instead of "bioc/".
379 (uri (string-append "https://www.bioconductor.org/packages/"
380 "release/data/annotation/src/contrib/"
381 "org.Ce.eg.db_" version ".tar.gz"))
384 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
386 `((upstream-name . "org.Ce.eg.db")))
387 (build-system r-build-system)
389 `(("r-annotationdbi" ,r-annotationdbi)))
390 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
391 (synopsis "Genome wide annotation for Worm")
393 "This package provides mappings from Entrez gene identifiers to various
394 annotations for the genome of the model worm Caenorhabditis elegans.")
395 (license license:artistic2.0)))
397 (define-public r-org-dm-eg-db
399 (name "r-org-dm-eg-db")
403 ;; We cannot use bioconductor-uri here because this tarball is
404 ;; located under "data/annotation/" instead of "bioc/".
405 (uri (string-append "https://www.bioconductor.org/packages/"
406 "release/data/annotation/src/contrib/"
407 "org.Dm.eg.db_" version ".tar.gz"))
410 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
412 `((upstream-name . "org.Dm.eg.db")))
413 (build-system r-build-system)
415 `(("r-annotationdbi" ,r-annotationdbi)))
416 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
417 (synopsis "Genome wide annotation for Fly")
419 "This package provides mappings from Entrez gene identifiers to various
420 annotations for the genome of the model fruit fly Drosophila melanogaster.")
421 (license license:artistic2.0)))
423 (define-public r-org-dr-eg-db
425 (name "r-org-dr-eg-db")
429 ;; We cannot use bioconductor-uri here because this tarball is
430 ;; located under "data/annotation/" instead of "bioc/".
431 (uri (string-append "https://www.bioconductor.org/packages/"
432 "release/data/annotation/src/contrib/"
433 "org.Dr.eg.db_" version ".tar.gz"))
436 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
438 `((upstream-name . "org.Dr.eg.db")))
439 (build-system r-build-system)
441 `(("r-annotationdbi" ,r-annotationdbi)))
442 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
443 (synopsis "Annotation for Zebrafish")
445 "This package provides genome wide annotations for Zebrafish, primarily
446 based on mapping using Entrez Gene identifiers.")
447 (license license:artistic2.0)))
449 (define-public r-org-hs-eg-db
451 (name "r-org-hs-eg-db")
455 ;; We cannot use bioconductor-uri here because this tarball is
456 ;; located under "data/annotation/" instead of "bioc/".
457 (uri (string-append "https://www.bioconductor.org/packages/"
458 "release/data/annotation/src/contrib/"
459 "org.Hs.eg.db_" version ".tar.gz"))
462 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
464 `((upstream-name . "org.Hs.eg.db")))
465 (build-system r-build-system)
467 `(("r-annotationdbi" ,r-annotationdbi)))
468 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
469 (synopsis "Genome wide annotation for Human")
471 "This package contains genome-wide annotations for Human, primarily based
472 on mapping using Entrez Gene identifiers.")
473 (license license:artistic2.0)))
475 (define-public r-org-mm-eg-db
477 (name "r-org-mm-eg-db")
481 ;; We cannot use bioconductor-uri here because this tarball is
482 ;; located under "data/annotation/" instead of "bioc/".
483 (uri (string-append "https://www.bioconductor.org/packages/"
484 "release/data/annotation/src/contrib/"
485 "org.Mm.eg.db_" version ".tar.gz"))
488 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
490 `((upstream-name . "org.Mm.eg.db")))
491 (build-system r-build-system)
493 `(("r-annotationdbi" ,r-annotationdbi)))
494 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
495 (synopsis "Genome wide annotation for Mouse")
497 "This package provides mappings from Entrez gene identifiers to various
498 annotations for the genome of the model mouse Mus musculus.")
499 (license license:artistic2.0)))
501 (define-public r-bsgenome-hsapiens-ucsc-hg19
503 (name "r-bsgenome-hsapiens-ucsc-hg19")
507 ;; We cannot use bioconductor-uri here because this tarball is
508 ;; located under "data/annotation/" instead of "bioc/".
509 (uri (string-append "https://www.bioconductor.org/packages/"
510 "release/data/annotation/src/contrib/"
511 "BSgenome.Hsapiens.UCSC.hg19_"
515 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
517 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
518 (build-system r-build-system)
519 ;; As this package provides little more than a very large data file it
520 ;; doesn't make sense to build substitutes.
521 (arguments `(#:substitutable? #f))
523 `(("r-bsgenome" ,r-bsgenome)))
525 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
526 (synopsis "Full genome sequences for Homo sapiens")
528 "This package provides full genome sequences for Homo sapiens as provided
529 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
530 (license license:artistic2.0)))
532 (define-public r-genelendatabase
534 (name "r-genelendatabase")
539 ;; We cannot use bioconductor-uri here because this tarball is
540 ;; located under "data/experiment/" instead of "bioc/".
541 (uri (string-append "https://bioconductor.org/packages/"
542 "release/data/experiment/src/contrib"
543 "/geneLenDataBase_" version ".tar.gz"))
546 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
548 `((upstream-name . "geneLenDataBase")))
549 (build-system r-build-system)
551 `(("r-rtracklayer" ,r-rtracklayer)
552 ("r-genomicfeatures" ,r-genomicfeatures)))
553 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
554 (synopsis "Lengths of mRNA transcripts for a number of genomes")
556 "This package provides the lengths of mRNA transcripts for a number of
557 genomes and gene ID formats, largely based on the UCSC table browser.")
558 (license license:lgpl2.0+)))
560 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
562 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
566 ;; We cannot use bioconductor-uri here because this tarball is
567 ;; located under "data/annotation/" instead of "bioc/".
568 (uri (string-append "https://bioconductor.org/packages/"
569 "release/data/annotation/src/contrib"
570 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
574 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
576 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
577 (build-system r-build-system)
578 ;; As this package provides little more than a very large data file it
579 ;; doesn't make sense to build substitutes.
580 (arguments `(#:substitutable? #f))
582 `(("r-genomicfeatures" ,r-genomicfeatures)))
584 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
585 (synopsis "Annotation package for human genome in TxDb format")
587 "This package provides an annotation database of Homo sapiens genome
588 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
589 track. The database is exposed as a @code{TxDb} object.")
590 (license license:artistic2.0)))
592 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
594 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
598 ;; We cannot use bioconductor-uri here because this tarball is
599 ;; located under "data/annotation/" instead of "bioc/".
600 (uri (string-append "https://bioconductor.org/packages/"
601 "release/data/annotation/src/contrib"
602 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
606 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
608 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
609 (build-system r-build-system)
611 `(("r-genomicfeatures" ,r-genomicfeatures)
612 ("r-annotationdbi" ,r-annotationdbi)))
614 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
615 (synopsis "Annotation package for mouse genome in TxDb format")
617 "This package provides an annotation database of Mouse genome data. It
618 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
619 database is exposed as a @code{TxDb} object.")
620 (license license:artistic2.0)))
622 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
624 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
628 ;; We cannot use bioconductor-uri here because this tarball is
629 ;; located under "data/annotation/" instead of "bioc/".
630 (uri (string-append "https://www.bioconductor.org/packages/"
631 "release/data/annotation/src/contrib/"
632 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
636 "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
638 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
639 (build-system r-build-system)
640 ;; As this package provides little more than a very large data file it
641 ;; doesn't make sense to build substitutes.
642 (arguments `(#:substitutable? #f))
644 `(("r-bsgenome" ,r-bsgenome)
645 ("r-genomicfeatures" ,r-genomicfeatures)
646 ("r-annotationdbi" ,r-annotationdbi)))
648 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
649 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
651 "This package loads a TxDb object, which is an R interface to
652 prefabricated databases contained in this package. This package provides
653 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
654 based on the knownGene track.")
655 (license license:artistic2.0)))
657 (define-public r-fdb-infiniummethylation-hg19
659 (name "r-fdb-infiniummethylation-hg19")
663 ;; We cannot use bioconductor-uri here because this tarball is
664 ;; located under "data/annotation/" instead of "bioc/".
665 (uri (string-append "https://www.bioconductor.org/packages/"
666 "release/data/annotation/src/contrib/"
667 "FDb.InfiniumMethylation.hg19_"
671 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
673 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
674 (build-system r-build-system)
676 `(("r-biostrings" ,r-biostrings)
677 ("r-genomicfeatures" ,r-genomicfeatures)
678 ("r-annotationdbi" ,r-annotationdbi)
679 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
680 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
681 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
682 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
684 "This is an annotation package for Illumina Infinium DNA methylation
685 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
687 (license license:artistic2.0)))
689 (define-public r-illuminahumanmethylationepicmanifest
691 (name "r-illuminahumanmethylationepicmanifest")
695 ;; We cannot use bioconductor-uri here because this tarball is
696 ;; located under "data/annotation/" instead of "bioc/".
697 (uri (string-append "https://www.bioconductor.org/packages/"
698 "release/data/annotation/src/contrib/"
699 "IlluminaHumanMethylationEPICmanifest_"
703 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
705 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
706 (build-system r-build-system)
708 `(("r-minfi" ,r-minfi)))
709 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
710 (synopsis "Manifest for Illumina's EPIC methylation arrays")
712 "This is a manifest package for Illumina's EPIC methylation arrays.")
713 (license license:artistic2.0)))
715 (define-public r-do-db
721 ;; We cannot use bioconductor-uri here because this tarball is
722 ;; located under "data/annotation/" instead of "bioc/".
723 (uri (string-append "https://www.bioconductor.org/packages/"
724 "release/data/annotation/src/contrib/"
725 "DO.db_" version ".tar.gz"))
728 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
730 `((upstream-name . "DO.db")))
731 (build-system r-build-system)
733 `(("r-annotationdbi" ,r-annotationdbi)))
734 (home-page "https://www.bioconductor.org/packages/DO.db/")
735 (synopsis "Annotation maps describing the entire Disease Ontology")
737 "This package provides a set of annotation maps describing the entire
739 (license license:artistic2.0)))
744 (define-public r-abadata
750 ;; We cannot use bioconductor-uri here because this tarball is
751 ;; located under "data/experiment/" instead of "bioc/".
752 (uri (string-append "https://www.bioconductor.org/packages/"
753 "release/data/experiment/src/contrib/"
754 "ABAData_" version ".tar.gz"))
757 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
759 `((upstream-name . "ABAData")))
760 (build-system r-build-system)
762 `(("r-annotationdbi" ,r-annotationdbi)))
763 (home-page "https://www.bioconductor.org/packages/ABAData/")
764 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
766 "This package provides the data for the gene expression enrichment
767 analysis conducted in the package ABAEnrichment. The package includes three
768 datasets which are derived from the Allen Brain Atlas:
771 @item Gene expression data from Human Brain (adults) averaged across donors,
772 @item Gene expression data from the Developing Human Brain pooled into five
773 age categories and averaged across donors, and
774 @item a developmental effect score based on the Developing Human Brain
778 All datasets are restricted to protein coding genes.")
779 (license license:gpl2+)))
781 (define-public r-arrmdata
787 ;; We cannot use bioconductor-uri here because this tarball is
788 ;; located under "data/experiment/" instead of "bioc/".
789 (uri (string-append "https://www.bioconductor.org/packages/"
790 "release/data/experiment/src/contrib/"
791 "ARRmData_" version ".tar.gz"))
794 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
796 `((upstream-name . "ARRmData")))
797 (build-system r-build-system)
798 (home-page "https://www.bioconductor.org/packages/ARRmData/")
799 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
801 "This package provides raw beta values from 36 samples across 3 groups
802 from Illumina 450k methylation arrays.")
803 (license license:artistic2.0)))
805 (define-public r-hsmmsinglecell
807 (name "r-hsmmsinglecell")
811 ;; We cannot use bioconductor-uri here because this tarball is
812 ;; located under "data/experiment/" instead of "bioc/".
813 (uri (string-append "https://www.bioconductor.org/packages/"
814 "release/data/experiment/src/contrib/"
815 "HSMMSingleCell_" version ".tar.gz"))
818 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
820 `((upstream-name . "HSMMSingleCell")))
821 (build-system r-build-system)
822 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
823 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
825 "Skeletal myoblasts undergo a well-characterized sequence of
826 morphological and transcriptional changes during differentiation. In this
827 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
828 under high mitogen conditions (GM) and then differentiated by switching to
829 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
830 hundred cells taken over a time-course of serum-induced differentiation.
831 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
832 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
833 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
834 which were then sequenced to a depth of ~4 million reads per library,
835 resulting in a complete gene expression profile for each cell.")
836 (license license:artistic2.0)))
841 (define-public r-biocgenerics
843 (name "r-biocgenerics")
847 (uri (bioconductor-uri "BiocGenerics" version))
850 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
852 `((upstream-name . "BiocGenerics")))
853 (build-system r-build-system)
854 (home-page "https://bioconductor.org/packages/BiocGenerics")
855 (synopsis "S4 generic functions for Bioconductor")
857 "This package provides S4 generic functions needed by many Bioconductor
859 (license license:artistic2.0)))
861 (define-public r-annotate
868 (uri (bioconductor-uri "annotate" version))
871 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
872 (build-system r-build-system)
874 `(("r-annotationdbi" ,r-annotationdbi)
875 ("r-biobase" ,r-biobase)
876 ("r-biocgenerics" ,r-biocgenerics)
880 ("r-xtable" ,r-xtable)))
882 "https://bioconductor.org/packages/annotate")
883 (synopsis "Annotation for microarrays")
884 (description "This package provides R environments for the annotation of
886 (license license:artistic2.0)))
888 (define-public r-hpar
895 (uri (bioconductor-uri "hpar" version))
898 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
899 (build-system r-build-system)
900 (home-page "https://bioconductor.org/packages/hpar/")
901 (synopsis "Human Protein Atlas in R")
902 (description "This package provides a simple interface to and data from
903 the Human Protein Atlas project.")
904 (license license:artistic2.0)))
906 (define-public r-regioner
913 (uri (bioconductor-uri "regioneR" version))
916 "014h2q346ynfdbpavh4p69cyv4j65hk934liq5892zznjzl73z7p"))))
917 (properties `((upstream-name . "regioneR")))
918 (build-system r-build-system)
920 `(("r-biostrings" ,r-biostrings)
921 ("r-bsgenome" ,r-bsgenome)
922 ("r-genomeinfodb" ,r-genomeinfodb)
923 ("r-genomicranges" ,r-genomicranges)
924 ("r-iranges" ,r-iranges)
925 ("r-memoise" ,r-memoise)
926 ("r-rtracklayer" ,r-rtracklayer)
927 ("r-s4vectors" ,r-s4vectors)))
928 (home-page "https://bioconductor.org/packages/regioneR/")
929 (synopsis "Association analysis of genomic regions")
930 (description "This package offers a statistical framework based on
931 customizable permutation tests to assess the association between genomic
932 region sets and other genomic features.")
933 (license license:artistic2.0)))
935 (define-public r-geneplotter
937 (name "r-geneplotter")
942 (uri (bioconductor-uri "geneplotter" version))
945 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
946 (build-system r-build-system)
948 `(("r-annotate" ,r-annotate)
949 ("r-annotationdbi" ,r-annotationdbi)
950 ("r-biobase" ,r-biobase)
951 ("r-biocgenerics" ,r-biocgenerics)
952 ("r-lattice" ,r-lattice)
953 ("r-rcolorbrewer" ,r-rcolorbrewer)))
954 (home-page "https://bioconductor.org/packages/geneplotter")
955 (synopsis "Graphics functions for genomic data")
957 "This package provides functions for plotting genomic data.")
958 (license license:artistic2.0)))
960 (define-public r-qvalue
967 (uri (bioconductor-uri "qvalue" version))
970 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
971 (build-system r-build-system)
973 `(("r-ggplot2" ,r-ggplot2)
974 ("r-reshape2" ,r-reshape2)))
975 (home-page "http://github.com/jdstorey/qvalue")
976 (synopsis "Q-value estimation for false discovery rate control")
978 "This package takes a list of p-values resulting from the simultaneous
979 testing of many hypotheses and estimates their q-values and local @dfn{false
980 discovery rate} (FDR) values. The q-value of a test measures the proportion
981 of false positives incurred when that particular test is called significant.
982 The local FDR measures the posterior probability the null hypothesis is true
983 given the test's p-value. Various plots are automatically generated, allowing
984 one to make sensible significance cut-offs. The software can be applied to
985 problems in genomics, brain imaging, astrophysics, and data mining.")
986 ;; Any version of the LGPL.
987 (license license:lgpl3+)))
989 (define-public r-diffbind
996 (uri (bioconductor-uri "DiffBind" version))
999 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1000 (properties `((upstream-name . "DiffBind")))
1001 (build-system r-build-system)
1005 `(("r-amap" ,r-amap)
1006 ("r-biocparallel" ,r-biocparallel)
1007 ("r-deseq2" ,r-deseq2)
1008 ("r-dplyr" ,r-dplyr)
1009 ("r-edger" ,r-edger)
1010 ("r-genomicalignments" ,r-genomicalignments)
1011 ("r-genomicranges" ,r-genomicranges)
1012 ("r-ggplot2" ,r-ggplot2)
1013 ("r-ggrepel" ,r-ggrepel)
1014 ("r-gplots" ,r-gplots)
1015 ("r-iranges" ,r-iranges)
1016 ("r-lattice" ,r-lattice)
1017 ("r-limma" ,r-limma)
1018 ("r-locfit" ,r-locfit)
1019 ("r-rcolorbrewer" , r-rcolorbrewer)
1021 ("r-rhtslib" ,r-rhtslib)
1022 ("r-rsamtools" ,r-rsamtools)
1023 ("r-s4vectors" ,r-s4vectors)
1024 ("r-summarizedexperiment" ,r-summarizedexperiment)
1025 ("r-systempiper" ,r-systempiper)))
1026 (home-page "http://bioconductor.org/packages/DiffBind")
1027 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1029 "This package computes differentially bound sites from multiple
1030 ChIP-seq experiments using affinity (quantitative) data. Also enables
1031 occupancy (overlap) analysis and plotting functions.")
1032 (license license:artistic2.0)))
1034 (define-public r-ripseeker
1036 (name "r-ripseeker")
1041 (uri (bioconductor-uri "RIPSeeker" version))
1044 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1045 (properties `((upstream-name . "RIPSeeker")))
1046 (build-system r-build-system)
1048 `(("r-s4vectors" ,r-s4vectors)
1049 ("r-iranges" ,r-iranges)
1050 ("r-genomicranges" ,r-genomicranges)
1051 ("r-summarizedexperiment" ,r-summarizedexperiment)
1052 ("r-rsamtools" ,r-rsamtools)
1053 ("r-genomicalignments" ,r-genomicalignments)
1054 ("r-rtracklayer" ,r-rtracklayer)))
1055 (home-page "http://bioconductor.org/packages/RIPSeeker")
1057 "Identifying protein-associated transcripts from RIP-seq experiments")
1059 "This package infers and discriminates RIP peaks from RIP-seq alignments
1060 using two-state HMM with negative binomial emission probability. While
1061 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1062 a suite of bioinformatics tools integrated within this self-contained software
1063 package comprehensively addressing issues ranging from post-alignments
1064 processing to visualization and annotation.")
1065 (license license:gpl2)))
1067 (define-public r-multtest
1074 (uri (bioconductor-uri "multtest" version))
1077 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1078 (build-system r-build-system)
1080 `(("r-survival" ,r-survival)
1081 ("r-biocgenerics" ,r-biocgenerics)
1082 ("r-biobase" ,r-biobase)
1083 ("r-mass" ,r-mass)))
1084 (home-page "http://bioconductor.org/packages/multtest")
1085 (synopsis "Resampling-based multiple hypothesis testing")
1087 "This package can do non-parametric bootstrap and permutation
1088 resampling-based multiple testing procedures (including empirical Bayes
1089 methods) for controlling the family-wise error rate (FWER), generalized
1090 family-wise error rate (gFWER), tail probability of the proportion of
1091 false positives (TPPFP), and false discovery rate (FDR). Several choices
1092 of bootstrap-based null distribution are implemented (centered, centered
1093 and scaled, quantile-transformed). Single-step and step-wise methods are
1094 available. Tests based on a variety of T- and F-statistics (including
1095 T-statistics based on regression parameters from linear and survival models
1096 as well as those based on correlation parameters) are included. When probing
1097 hypotheses with T-statistics, users may also select a potentially faster null
1098 distribution which is multivariate normal with mean zero and variance
1099 covariance matrix derived from the vector influence function. Results are
1100 reported in terms of adjusted P-values, confidence regions and test statistic
1101 cutoffs. The procedures are directly applicable to identifying differentially
1102 expressed genes in DNA microarray experiments.")
1103 (license license:lgpl3)))
1105 (define-public r-graph
1111 (uri (bioconductor-uri "graph" version))
1114 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1115 (build-system r-build-system)
1117 `(("r-biocgenerics" ,r-biocgenerics)))
1118 (home-page "https://bioconductor.org/packages/graph")
1119 (synopsis "Handle graph data structures in R")
1121 "This package implements some simple graph handling capabilities for R.")
1122 (license license:artistic2.0)))
1124 (define-public r-codedepends
1126 (name "r-codedepends")
1131 (uri (cran-uri "CodeDepends" version))
1134 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1135 (properties `((upstream-name . "CodeDepends")))
1136 (build-system r-build-system)
1138 `(("r-codetools" ,r-codetools)
1139 ("r-graph" ,r-graph)
1141 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1142 (synopsis "Analysis of R code for reproducible research and code comprehension")
1144 "This package provides tools for analyzing R expressions or blocks of
1145 code and determining the dependencies between them. It focuses on R scripts,
1146 but can be used on the bodies of functions. There are many facilities
1147 including the ability to summarize or get a high-level view of code,
1148 determining dependencies between variables, code improvement suggestions.")
1149 ;; Any version of the GPL
1150 (license (list license:gpl2+ license:gpl3+))))
1152 (define-public r-chippeakanno
1154 (name "r-chippeakanno")
1159 (uri (bioconductor-uri "ChIPpeakAnno" version))
1162 "089v16mm5m0rlyyyd0d6rz8gwb852zf3bcdrrw70wanlfjn258q7"))))
1163 (properties `((upstream-name . "ChIPpeakAnno")))
1164 (build-system r-build-system)
1166 `(("r-annotationdbi" ,r-annotationdbi)
1167 ("r-biobase" ,r-biobase)
1168 ("r-biocgenerics" ,r-biocgenerics)
1169 ("r-biocmanager" ,r-biocmanager)
1170 ("r-biomart" ,r-biomart)
1171 ("r-biostrings" ,r-biostrings)
1172 ("r-bsgenome" ,r-bsgenome)
1174 ("r-delayedarray" ,r-delayedarray)
1175 ("r-ensembldb" ,r-ensembldb)
1176 ("r-genomeinfodb" ,r-genomeinfodb)
1177 ("r-genomicalignments" ,r-genomicalignments)
1178 ("r-genomicfeatures" ,r-genomicfeatures)
1179 ("r-genomicranges" ,r-genomicranges)
1180 ("r-go-db" ,r-go-db)
1181 ("r-graph" ,r-graph)
1183 ("r-iranges" ,r-iranges)
1184 ("r-limma" ,r-limma)
1185 ("r-matrixstats" ,r-matrixstats)
1186 ("r-multtest" ,r-multtest)
1188 ("r-regioner" ,r-regioner)
1189 ("r-rsamtools" ,r-rsamtools)
1190 ("r-rtracklayer" ,r-rtracklayer)
1191 ("r-s4vectors" ,r-s4vectors)
1192 ("r-seqinr" ,r-seqinr)
1193 ("r-summarizedexperiment" ,r-summarizedexperiment)
1194 ("r-venndiagram" ,r-venndiagram)))
1195 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1196 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1198 "The package includes functions to retrieve the sequences around the peak,
1199 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1200 custom features such as most conserved elements and other transcription factor
1201 binding sites supplied by users. Starting 2.0.5, new functions have been added
1202 for finding the peaks with bi-directional promoters with summary statistics
1203 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1204 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1205 enrichedGO (addGeneIDs).")
1206 (license license:gpl2+)))
1208 (define-public r-marray
1214 (uri (bioconductor-uri "marray" version))
1216 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1217 (build-system r-build-system)
1219 `(("r-limma" ,r-limma)))
1220 (home-page "http://bioconductor.org/packages/marray")
1221 (synopsis "Exploratory analysis for two-color spotted microarray data")
1222 (description "This package contains class definitions for two-color spotted
1223 microarray data. It also includes fuctions for data input, diagnostic plots,
1224 normalization and quality checking.")
1225 (license license:lgpl2.0+)))
1227 (define-public r-cghbase
1233 (uri (bioconductor-uri "CGHbase" version))
1235 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1236 (properties `((upstream-name . "CGHbase")))
1237 (build-system r-build-system)
1239 `(("r-biobase" ,r-biobase)
1240 ("r-marray" ,r-marray)))
1241 (home-page "http://bioconductor.org/packages/CGHbase")
1242 (synopsis "Base functions and classes for arrayCGH data analysis")
1243 (description "This package contains functions and classes that are needed by
1244 the @code{arrayCGH} packages.")
1245 (license license:gpl2+)))
1247 (define-public r-cghcall
1253 (uri (bioconductor-uri "CGHcall" version))
1255 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1256 (properties `((upstream-name . "CGHcall")))
1257 (build-system r-build-system)
1259 `(("r-biobase" ,r-biobase)
1260 ("r-cghbase" ,r-cghbase)
1261 ("r-impute" ,r-impute)
1262 ("r-dnacopy" ,r-dnacopy)
1263 ("r-snowfall" ,r-snowfall)))
1264 (home-page "http://bioconductor.org/packages/CGHcall")
1265 (synopsis "Base functions and classes for arrayCGH data analysis")
1266 (description "This package contains functions and classes that are needed by
1267 @code{arrayCGH} packages.")
1268 (license license:gpl2+)))
1270 (define-public r-qdnaseq
1276 (uri (bioconductor-uri "QDNAseq" version))
1278 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1279 (properties `((upstream-name . "QDNAseq")))
1280 (build-system r-build-system)
1282 `(("r-biobase" ,r-biobase)
1283 ("r-biocparallel" ,r-biocparallel)
1284 ("r-cghbase" ,r-cghbase)
1285 ("r-cghcall" ,r-cghcall)
1286 ("r-dnacopy" ,r-dnacopy)
1287 ("r-genomicranges" ,r-genomicranges)
1288 ("r-iranges" ,r-iranges)
1289 ("r-matrixstats" ,r-matrixstats)
1290 ("r-r-utils" ,r-r-utils)
1291 ("r-rsamtools" ,r-rsamtools)))
1292 (home-page "http://bioconductor.org/packages/QDNAseq")
1293 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1294 (description "The genome is divided into non-overlapping fixed-sized bins,
1295 number of sequence reads in each counted, adjusted with a simultaneous
1296 two-dimensional loess correction for sequence mappability and GC content, and
1297 filtered to remove spurious regions in the genome. Downstream steps of
1298 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1300 (license license:gpl2+)))
1302 (define-public r-bayseq
1309 (uri (bioconductor-uri "baySeq" version))
1312 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1313 (properties `((upstream-name . "baySeq")))
1314 (build-system r-build-system)
1316 `(("r-abind" ,r-abind)
1317 ("r-edger" ,r-edger)
1318 ("r-genomicranges" ,r-genomicranges)))
1319 (home-page "https://bioconductor.org/packages/baySeq/")
1320 (synopsis "Bayesian analysis of differential expression patterns in count data")
1322 "This package identifies differential expression in high-throughput count
1323 data, such as that derived from next-generation sequencing machines,
1324 calculating estimated posterior likelihoods of differential expression (or
1325 more complex hypotheses) via empirical Bayesian methods.")
1326 (license license:gpl3)))
1328 (define-public r-chipcomp
1335 (uri (bioconductor-uri "ChIPComp" version))
1338 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1339 (properties `((upstream-name . "ChIPComp")))
1340 (build-system r-build-system)
1342 `(("r-biocgenerics" ,r-biocgenerics)
1343 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1344 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1345 ("r-genomeinfodb" ,r-genomeinfodb)
1346 ("r-genomicranges" ,r-genomicranges)
1347 ("r-iranges" ,r-iranges)
1348 ("r-limma" ,r-limma)
1349 ("r-rsamtools" ,r-rsamtools)
1350 ("r-rtracklayer" ,r-rtracklayer)
1351 ("r-s4vectors" ,r-s4vectors)))
1352 (home-page "https://bioconductor.org/packages/ChIPComp")
1353 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1355 "ChIPComp implements a statistical method for quantitative comparison of
1356 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1357 sites across multiple conditions considering matching control in ChIP-seq
1359 ;; Any version of the GPL.
1360 (license license:gpl3+)))
1362 (define-public r-riboprofiling
1364 (name "r-riboprofiling")
1369 (uri (bioconductor-uri "RiboProfiling" version))
1372 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1373 (properties `((upstream-name . "RiboProfiling")))
1374 (build-system r-build-system)
1376 `(("r-biocgenerics" ,r-biocgenerics)
1377 ("r-biostrings" ,r-biostrings)
1378 ("r-data-table" ,r-data-table)
1379 ("r-genomeinfodb" ,r-genomeinfodb)
1380 ("r-genomicalignments" ,r-genomicalignments)
1381 ("r-genomicfeatures" ,r-genomicfeatures)
1382 ("r-genomicranges" ,r-genomicranges)
1383 ("r-ggbio" ,r-ggbio)
1384 ("r-ggplot2" ,r-ggplot2)
1385 ("r-iranges" ,r-iranges)
1387 ("r-reshape2" ,r-reshape2)
1388 ("r-rsamtools" ,r-rsamtools)
1389 ("r-rtracklayer" ,r-rtracklayer)
1390 ("r-s4vectors" ,r-s4vectors)
1391 ("r-sqldf" ,r-sqldf)))
1392 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1393 (synopsis "Ribosome profiling data analysis")
1394 (description "Starting with a BAM file, this package provides the
1395 necessary functions for quality assessment, read start position recalibration,
1396 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1397 of count data: pairs, log fold-change, codon frequency and coverage
1398 assessment, principal component analysis on codon coverage.")
1399 (license license:gpl3)))
1401 (define-public r-riboseqr
1408 (uri (bioconductor-uri "riboSeqR" version))
1411 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1412 (properties `((upstream-name . "riboSeqR")))
1413 (build-system r-build-system)
1415 `(("r-abind" ,r-abind)
1416 ("r-bayseq" ,r-bayseq)
1417 ("r-genomeinfodb" ,r-genomeinfodb)
1418 ("r-genomicranges" ,r-genomicranges)
1419 ("r-iranges" ,r-iranges)
1420 ("r-rsamtools" ,r-rsamtools)
1421 ("r-seqlogo" ,r-seqlogo)))
1422 (home-page "https://bioconductor.org/packages/riboSeqR/")
1423 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1425 "This package provides plotting functions, frameshift detection and
1426 parsing of genetic sequencing data from ribosome profiling experiments.")
1427 (license license:gpl3)))
1429 (define-public r-interactionset
1431 (name "r-interactionset")
1436 (uri (bioconductor-uri "InteractionSet" version))
1439 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1441 `((upstream-name . "InteractionSet")))
1442 (build-system r-build-system)
1444 `(("r-biocgenerics" ,r-biocgenerics)
1445 ("r-genomeinfodb" ,r-genomeinfodb)
1446 ("r-genomicranges" ,r-genomicranges)
1447 ("r-iranges" ,r-iranges)
1448 ("r-matrix" ,r-matrix)
1450 ("r-s4vectors" ,r-s4vectors)
1451 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1452 (home-page "https://bioconductor.org/packages/InteractionSet")
1453 (synopsis "Base classes for storing genomic interaction data")
1455 "This packages provides the @code{GInteractions},
1456 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1457 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1459 (license license:gpl3)))
1461 (define-public r-genomicinteractions
1463 (name "r-genomicinteractions")
1468 (uri (bioconductor-uri "GenomicInteractions" version))
1471 "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
1473 `((upstream-name . "GenomicInteractions")))
1474 (build-system r-build-system)
1476 `(("r-biobase" ,r-biobase)
1477 ("r-biocgenerics" ,r-biocgenerics)
1478 ("r-data-table" ,r-data-table)
1479 ("r-dplyr" ,r-dplyr)
1480 ("r-genomeinfodb" ,r-genomeinfodb)
1481 ("r-genomicranges" ,r-genomicranges)
1482 ("r-ggplot2" ,r-ggplot2)
1483 ("r-gridextra" ,r-gridextra)
1485 ("r-igraph" ,r-igraph)
1486 ("r-interactionset" ,r-interactionset)
1487 ("r-iranges" ,r-iranges)
1488 ("r-rsamtools" ,r-rsamtools)
1489 ("r-rtracklayer" ,r-rtracklayer)
1490 ("r-s4vectors" ,r-s4vectors)
1491 ("r-stringr" ,r-stringr)))
1492 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1493 (synopsis "R package for handling genomic interaction data")
1495 "This R package provides tools for handling genomic interaction data,
1496 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1497 information and producing various plots and statistics.")
1498 (license license:gpl3)))
1500 (define-public r-ctc
1507 (uri (bioconductor-uri "ctc" version))
1510 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1511 (build-system r-build-system)
1512 (propagated-inputs `(("r-amap" ,r-amap)))
1513 (home-page "https://bioconductor.org/packages/ctc/")
1514 (synopsis "Cluster and tree conversion")
1516 "This package provides tools for exporting and importing classification
1517 trees and clusters to other programs.")
1518 (license license:gpl2)))
1520 (define-public r-goseq
1527 (uri (bioconductor-uri "goseq" version))
1530 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1531 (build-system r-build-system)
1533 `(("r-annotationdbi" ,r-annotationdbi)
1534 ("r-biasedurn" ,r-biasedurn)
1535 ("r-biocgenerics" ,r-biocgenerics)
1536 ("r-genelendatabase" ,r-genelendatabase)
1537 ("r-go-db" ,r-go-db)
1538 ("r-mgcv" ,r-mgcv)))
1539 (home-page "https://bioconductor.org/packages/goseq/")
1540 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1542 "This package provides tools to detect Gene Ontology and/or other user
1543 defined categories which are over/under represented in RNA-seq data.")
1544 (license license:lgpl2.0+)))
1546 (define-public r-glimma
1553 (uri (bioconductor-uri "Glimma" version))
1556 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1557 (properties `((upstream-name . "Glimma")))
1558 (build-system r-build-system)
1560 `(("r-edger" ,r-edger)
1561 ("r-jsonlite" ,r-jsonlite)
1562 ("r-s4vectors" ,r-s4vectors)))
1563 (home-page "https://github.com/Shians/Glimma")
1564 (synopsis "Interactive HTML graphics")
1566 "This package generates interactive visualisations for analysis of
1567 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1568 HTML page. The interactions are built on top of the popular static
1569 representations of analysis results in order to provide additional
1571 (license license:lgpl3)))
1573 (define-public r-rots
1580 (uri (bioconductor-uri "ROTS" version))
1583 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
1584 (properties `((upstream-name . "ROTS")))
1585 (build-system r-build-system)
1587 `(("r-biobase" ,r-biobase)
1588 ("r-rcpp" ,r-rcpp)))
1589 (home-page "https://bioconductor.org/packages/ROTS/")
1590 (synopsis "Reproducibility-Optimized Test Statistic")
1592 "This package provides tools for calculating the
1593 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1595 (license license:gpl2+)))
1597 (define-public r-plgem
1604 (uri (bioconductor-uri "plgem" version))
1607 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
1608 (build-system r-build-system)
1610 `(("r-biobase" ,r-biobase)
1611 ("r-mass" ,r-mass)))
1612 (home-page "http://www.genopolis.it")
1613 (synopsis "Detect differential expression in microarray and proteomics datasets")
1615 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1616 model the variance-versus-mean dependence that exists in a variety of
1617 genome-wide datasets, including microarray and proteomics data. The use of
1618 PLGEM has been shown to improve the detection of differentially expressed
1619 genes or proteins in these datasets.")
1620 (license license:gpl2)))
1622 (define-public r-inspect
1629 (uri (bioconductor-uri "INSPEcT" version))
1632 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
1633 (properties `((upstream-name . "INSPEcT")))
1634 (build-system r-build-system)
1636 `(("r-biobase" ,r-biobase)
1637 ("r-biocgenerics" ,r-biocgenerics)
1638 ("r-biocparallel" ,r-biocparallel)
1639 ("r-deseq2" ,r-deseq2)
1640 ("r-desolve" ,r-desolve)
1641 ("r-genomicalignments" ,r-genomicalignments)
1642 ("r-genomicfeatures" ,r-genomicfeatures)
1643 ("r-genomicranges" ,r-genomicranges)
1644 ("r-iranges" ,r-iranges)
1645 ("r-plgem" ,r-plgem)
1646 ("r-preprocesscore" ,r-preprocesscore)
1648 ("r-rootsolve" ,r-rootsolve)
1649 ("r-rsamtools" ,r-rsamtools)
1650 ("r-s4vectors" ,r-s4vectors)
1651 ("r-shiny" ,r-shiny)
1652 ("r-summarizedexperiment" ,r-summarizedexperiment)
1653 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1654 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1655 (home-page "https://bioconductor.org/packages/INSPEcT")
1656 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1658 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1659 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1660 order to evaluate synthesis, processing and degradation rates and assess via
1661 modeling the rates that determines changes in mature mRNA levels.")
1662 (license license:gpl2)))
1664 (define-public r-dnabarcodes
1666 (name "r-dnabarcodes")
1671 (uri (bioconductor-uri "DNABarcodes" version))
1674 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
1675 (properties `((upstream-name . "DNABarcodes")))
1676 (build-system r-build-system)
1679 ("r-matrix" ,r-matrix)
1680 ("r-rcpp" ,r-rcpp)))
1681 (home-page "https://bioconductor.org/packages/DNABarcodes")
1682 (synopsis "Create and analyze DNA barcodes")
1684 "This package offers tools to create DNA barcode sets capable of
1685 correcting insertion, deletion, and substitution errors. Existing barcodes
1686 can be analyzed regarding their minimal, maximal and average distances between
1687 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1688 demultiplexed, i.e. assigned to their original reference barcode.")
1689 (license license:gpl2)))
1691 (define-public r-ruvseq
1698 (uri (bioconductor-uri "RUVSeq" version))
1701 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
1702 (properties `((upstream-name . "RUVSeq")))
1703 (build-system r-build-system)
1705 `(("r-biobase" ,r-biobase)
1706 ("r-edaseq" ,r-edaseq)
1707 ("r-edger" ,r-edger)
1708 ("r-mass" ,r-mass)))
1709 (home-page "https://github.com/drisso/RUVSeq")
1710 (synopsis "Remove unwanted variation from RNA-Seq data")
1712 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1713 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1715 (license license:artistic2.0)))
1717 (define-public r-biocneighbors
1719 (name "r-biocneighbors")
1724 (uri (bioconductor-uri "BiocNeighbors" version))
1727 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
1728 (properties `((upstream-name . "BiocNeighbors")))
1729 (build-system r-build-system)
1731 `(("r-biocgenerics" ,r-biocgenerics)
1732 ("r-biocparallel" ,r-biocparallel)
1734 ("r-rcppannoy" ,r-rcppannoy)
1735 ("r-rcpphnsw" ,r-rcpphnsw)
1736 ("r-s4vectors" ,r-s4vectors)))
1737 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1738 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1740 "This package implements exact and approximate methods for nearest
1741 neighbor detection, in a framework that allows them to be easily switched
1742 within Bioconductor packages or workflows. The exact algorithm is implemented
1743 using pre-clustering with the k-means algorithm. Functions are also provided
1744 to search for all neighbors within a given distance. Parallelization is
1745 achieved for all methods using the BiocParallel framework.")
1746 (license license:gpl3)))
1748 (define-public r-biocsingular
1750 (name "r-biocsingular")
1755 (uri (bioconductor-uri "BiocSingular" version))
1758 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
1759 (properties `((upstream-name . "BiocSingular")))
1760 (build-system r-build-system)
1762 `(("r-beachmat" ,r-beachmat)
1763 ("r-biocgenerics" ,r-biocgenerics)
1764 ("r-biocparallel" ,r-biocparallel)
1765 ("r-delayedarray" ,r-delayedarray)
1766 ("r-irlba" ,r-irlba)
1767 ("r-matrix" ,r-matrix)
1770 ("r-s4vectors" ,r-s4vectors)))
1771 (home-page "https://github.com/LTLA/BiocSingular")
1772 (synopsis "Singular value decomposition for Bioconductor packages")
1774 "This package implements exact and approximate methods for singular value
1775 decomposition and principal components analysis, in a framework that allows
1776 them to be easily switched within Bioconductor packages or workflows. Where
1777 possible, parallelization is achieved using the BiocParallel framework.")
1778 (license license:gpl3)))
1780 (define-public r-destiny
1787 (uri (bioconductor-uri "destiny" version))
1790 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
1791 (build-system r-build-system)
1793 `(("r-biobase" ,r-biobase)
1794 ("r-biocgenerics" ,r-biocgenerics)
1795 ("r-ggplot2" ,r-ggplot2)
1796 ("r-ggthemes" ,r-ggthemes)
1797 ("r-igraph" ,r-igraph)
1798 ("r-matrix" ,r-matrix)
1799 ("r-proxy" ,r-proxy)
1801 ("r-rcppeigen" ,r-rcppeigen)
1802 ("r-scales" ,r-scales)
1803 ("r-scatterplot3d" ,r-scatterplot3d)
1804 ("r-smoother" ,r-smoother)
1805 ("r-summarizedexperiment" ,r-summarizedexperiment)
1807 (home-page "https://bioconductor.org/packages/destiny/")
1808 (synopsis "Create and plot diffusion maps")
1809 (description "This package provides tools to create and plot diffusion
1811 ;; Any version of the GPL
1812 (license license:gpl3+)))
1814 (define-public r-savr
1821 (uri (bioconductor-uri "savR" version))
1824 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
1825 (properties `((upstream-name . "savR")))
1826 (build-system r-build-system)
1828 `(("r-ggplot2" ,r-ggplot2)
1829 ("r-gridextra" ,r-gridextra)
1830 ("r-reshape2" ,r-reshape2)
1831 ("r-scales" ,r-scales)
1833 (home-page "https://github.com/bcalder/savR")
1834 (synopsis "Parse and analyze Illumina SAV files")
1836 "This package provides tools to parse Illumina Sequence Analysis
1837 Viewer (SAV) files, access data, and generate QC plots.")
1838 (license license:agpl3+)))
1840 (define-public r-chipexoqual
1842 (name "r-chipexoqual")
1847 (uri (bioconductor-uri "ChIPexoQual" version))
1850 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
1851 (properties `((upstream-name . "ChIPexoQual")))
1852 (build-system r-build-system)
1854 `(("r-biocparallel" ,r-biocparallel)
1855 ("r-biovizbase" ,r-biovizbase)
1856 ("r-broom" ,r-broom)
1857 ("r-data-table" ,r-data-table)
1858 ("r-dplyr" ,r-dplyr)
1859 ("r-genomeinfodb" ,r-genomeinfodb)
1860 ("r-genomicalignments" ,r-genomicalignments)
1861 ("r-genomicranges" ,r-genomicranges)
1862 ("r-ggplot2" ,r-ggplot2)
1863 ("r-hexbin" ,r-hexbin)
1864 ("r-iranges" ,r-iranges)
1865 ("r-rcolorbrewer" ,r-rcolorbrewer)
1866 ("r-rmarkdown" ,r-rmarkdown)
1867 ("r-rsamtools" ,r-rsamtools)
1868 ("r-s4vectors" ,r-s4vectors)
1869 ("r-scales" ,r-scales)
1870 ("r-viridis" ,r-viridis)))
1871 (home-page "https://github.com/keleslab/ChIPexoQual")
1872 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1874 "This package provides a quality control pipeline for ChIP-exo/nexus
1876 (license license:gpl2+)))
1878 (define-public r-copynumber
1880 (name "r-copynumber")
1884 (uri (bioconductor-uri "copynumber" version))
1887 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
1888 (build-system r-build-system)
1890 `(("r-s4vectors" ,r-s4vectors)
1891 ("r-iranges" ,r-iranges)
1892 ("r-genomicranges" ,r-genomicranges)
1893 ("r-biocgenerics" ,r-biocgenerics)))
1894 (home-page "https://bioconductor.org/packages/copynumber")
1895 (synopsis "Segmentation of single- and multi-track copy number data")
1897 "This package segments single- and multi-track copy number data by a
1898 penalized least squares regression method.")
1899 (license license:artistic2.0)))
1901 (define-public r-dnacopy
1908 (uri (bioconductor-uri "DNAcopy" version))
1911 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
1912 (properties `((upstream-name . "DNAcopy")))
1913 (build-system r-build-system)
1914 (native-inputs `(("gfortran" ,gfortran)))
1915 (home-page "https://bioconductor.org/packages/DNAcopy")
1916 (synopsis "DNA copy number data analysis")
1918 "This package implements the @dfn{circular binary segmentation} (CBS)
1919 algorithm to segment DNA copy number data and identify genomic regions with
1920 abnormal copy number.")
1921 (license license:gpl2+)))
1923 ;; This is a CRAN package, but it uncharacteristically depends on a
1924 ;; Bioconductor package.
1925 (define-public r-htscluster
1927 (name "r-htscluster")
1932 (uri (cran-uri "HTSCluster" version))
1935 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1936 (properties `((upstream-name . "HTSCluster")))
1937 (build-system r-build-system)
1939 `(("r-capushe" ,r-capushe)
1940 ("r-edger" ,r-edger)
1941 ("r-plotrix" ,r-plotrix)))
1942 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1943 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1945 "This package provides a Poisson mixture model is implemented to cluster
1946 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
1947 estimation is performed using either the EM or CEM algorithm, and the slope
1948 heuristics are used for model selection (i.e., to choose the number of
1950 (license license:gpl3+)))
1952 (define-public r-deds
1959 (uri (bioconductor-uri "DEDS" version))
1962 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
1963 (properties `((upstream-name . "DEDS")))
1964 (build-system r-build-system)
1965 (home-page "https://bioconductor.org/packages/DEDS/")
1966 (synopsis "Differential expression via distance summary for microarray data")
1968 "This library contains functions that calculate various statistics of
1969 differential expression for microarray data, including t statistics, fold
1970 change, F statistics, SAM, moderated t and F statistics and B statistics. It
1971 also implements a new methodology called DEDS (Differential Expression via
1972 Distance Summary), which selects differentially expressed genes by integrating
1973 and summarizing a set of statistics using a weighted distance approach.")
1974 ;; Any version of the LGPL.
1975 (license license:lgpl3+)))
1977 ;; This is a CRAN package, but since it depends on a Bioconductor package we
1979 (define-public r-nbpseq
1986 (uri (cran-uri "NBPSeq" version))
1989 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
1990 (properties `((upstream-name . "NBPSeq")))
1991 (build-system r-build-system)
1993 `(("r-qvalue" ,r-qvalue)))
1994 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
1995 (synopsis "Negative binomial models for RNA-Seq data")
1997 "This package provides negative binomial models for two-group comparisons
1998 and regression inferences from RNA-sequencing data.")
1999 (license license:gpl2)))
2001 (define-public r-ebseq
2008 (uri (bioconductor-uri "EBSeq" version))
2011 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2012 (properties `((upstream-name . "EBSeq")))
2013 (build-system r-build-system)
2015 `(("r-blockmodeling" ,r-blockmodeling)
2016 ("r-gplots" ,r-gplots)
2017 ("r-testthat" ,r-testthat)))
2018 (home-page "https://bioconductor.org/packages/EBSeq")
2019 (synopsis "Differential expression analysis of RNA-seq data")
2021 "This package provides tools for differential expression analysis at both
2022 gene and isoform level using RNA-seq data")
2023 (license license:artistic2.0)))
2025 (define-public r-lpsymphony
2027 (name "r-lpsymphony")
2032 (uri (bioconductor-uri "lpsymphony" version))
2035 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2036 (build-system r-build-system)
2038 `(("gfortran" ,gfortran)
2041 `(("pkg-config" ,pkg-config)))
2042 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2043 (synopsis "Symphony integer linear programming solver in R")
2045 "This package was derived from Rsymphony. The package provides an R
2046 interface to SYMPHONY, a linear programming solver written in C++. The main
2047 difference between this package and Rsymphony is that it includes the solver
2048 source code, while Rsymphony expects to find header and library files on the
2049 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2050 to install interface to SYMPHONY.")
2051 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2052 ;; lpsimphony is released under the same terms.
2053 (license license:epl1.0)))
2055 (define-public r-ihw
2062 (uri (bioconductor-uri "IHW" version))
2065 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2066 (properties `((upstream-name . "IHW")))
2067 (build-system r-build-system)
2069 `(("r-biocgenerics" ,r-biocgenerics)
2070 ("r-fdrtool" ,r-fdrtool)
2071 ("r-lpsymphony" ,r-lpsymphony)
2072 ("r-slam" ,r-slam)))
2073 (home-page "https://bioconductor.org/packages/IHW")
2074 (synopsis "Independent hypothesis weighting")
2076 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2077 procedure that increases power compared to the method of Benjamini and
2078 Hochberg by assigning data-driven weights to each hypothesis. The input to
2079 IHW is a two-column table of p-values and covariates. The covariate can be
2080 any continuous-valued or categorical variable that is thought to be
2081 informative on the statistical properties of each hypothesis test, while it is
2082 independent of the p-value under the null hypothesis.")
2083 (license license:artistic2.0)))
2085 (define-public r-icobra
2092 (uri (bioconductor-uri "iCOBRA" version))
2095 "1w9frnczgypzc2czbwrvlizqcqhbp6cdpyws7vkmnn9k0ggzxvfc"))))
2096 (properties `((upstream-name . "iCOBRA")))
2097 (build-system r-build-system)
2099 `(("r-dplyr" ,r-dplyr)
2101 ("r-ggplot2" ,r-ggplot2)
2102 ("r-limma" ,r-limma)
2103 ("r-reshape2" ,r-reshape2)
2105 ("r-scales" ,r-scales)
2106 ("r-shiny" ,r-shiny)
2107 ("r-shinybs" ,r-shinybs)
2108 ("r-shinydashboard" ,r-shinydashboard)
2109 ("r-upsetr" ,r-upsetr)))
2110 (home-page "https://bioconductor.org/packages/iCOBRA")
2111 (synopsis "Comparison and visualization of ranking and assignment methods")
2113 "This package provides functions for calculation and visualization of
2114 performance metrics for evaluation of ranking and binary
2115 classification (assignment) methods. It also contains a Shiny application for
2116 interactive exploration of results.")
2117 (license license:gpl2+)))
2119 (define-public r-mast
2126 (uri (bioconductor-uri "MAST" version))
2129 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2130 (properties `((upstream-name . "MAST")))
2131 (build-system r-build-system)
2133 `(("r-abind" ,r-abind)
2135 ("r-biobase" ,r-biobase)
2136 ("r-biocgenerics" ,r-biocgenerics)
2137 ("r-data-table" ,r-data-table)
2138 ("r-ggplot2" ,r-ggplot2)
2140 ("r-progress" ,r-progress)
2141 ("r-reshape2" ,r-reshape2)
2142 ("r-s4vectors" ,r-s4vectors)
2143 ("r-singlecellexperiment" ,r-singlecellexperiment)
2144 ("r-stringr" ,r-stringr)
2145 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2146 (home-page "https://github.com/RGLab/MAST/")
2147 (synopsis "Model-based analysis of single cell transcriptomics")
2149 "This package provides methods and models for handling zero-inflated
2150 single cell assay data.")
2151 (license license:gpl2+)))
2153 (define-public r-monocle
2160 (uri (bioconductor-uri "monocle" version))
2163 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2164 (build-system r-build-system)
2166 `(("r-biobase" ,r-biobase)
2167 ("r-biocgenerics" ,r-biocgenerics)
2168 ("r-biocviews" ,r-biocviews)
2169 ("r-cluster" ,r-cluster)
2170 ("r-combinat" ,r-combinat)
2171 ("r-ddrtree" ,r-ddrtree)
2172 ("r-densityclust" ,r-densityclust)
2173 ("r-dplyr" ,r-dplyr)
2174 ("r-fastica" ,r-fastica)
2175 ("r-ggplot2" ,r-ggplot2)
2176 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2177 ("r-igraph" ,r-igraph)
2178 ("r-irlba" ,r-irlba)
2179 ("r-limma" ,r-limma)
2181 ("r-matrix" ,r-matrix)
2182 ("r-matrixstats" ,r-matrixstats)
2183 ("r-pheatmap" ,r-pheatmap)
2185 ("r-proxy" ,r-proxy)
2186 ("r-qlcmatrix" ,r-qlcmatrix)
2189 ("r-reshape2" ,r-reshape2)
2190 ("r-rtsne" ,r-rtsne)
2192 ("r-stringr" ,r-stringr)
2193 ("r-tibble" ,r-tibble)
2195 ("r-viridis" ,r-viridis)))
2196 (home-page "https://bioconductor.org/packages/monocle")
2197 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2199 "Monocle performs differential expression and time-series analysis for
2200 single-cell expression experiments. It orders individual cells according to
2201 progress through a biological process, without knowing ahead of time which
2202 genes define progress through that process. Monocle also performs
2203 differential expression analysis, clustering, visualization, and other useful
2204 tasks on single cell expression data. It is designed to work with RNA-Seq and
2205 qPCR data, but could be used with other types as well.")
2206 (license license:artistic2.0)))
2208 (define-public r-noiseq
2215 (uri (bioconductor-uri "NOISeq" version))
2218 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2219 (properties `((upstream-name . "NOISeq")))
2220 (build-system r-build-system)
2222 `(("r-biobase" ,r-biobase)
2223 ("r-matrix" ,r-matrix)))
2224 (home-page "https://bioconductor.org/packages/NOISeq")
2225 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2227 "This package provides tools to support the analysis of RNA-seq
2228 expression data or other similar kind of data. It provides exploratory plots
2229 to evaluate saturation, count distribution, expression per chromosome, type of
2230 detected features, features length, etc. It also supports the analysis of
2231 differential expression between two experimental conditions with no parametric
2233 (license license:artistic2.0)))
2235 (define-public r-scdd
2242 (uri (bioconductor-uri "scDD" version))
2245 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2246 (properties `((upstream-name . "scDD")))
2247 (build-system r-build-system)
2250 ("r-biocparallel" ,r-biocparallel)
2251 ("r-ebseq" ,r-ebseq)
2252 ("r-fields" ,r-fields)
2253 ("r-ggplot2" ,r-ggplot2)
2254 ("r-mclust" ,r-mclust)
2255 ("r-outliers" ,r-outliers)
2256 ("r-s4vectors" ,r-s4vectors)
2257 ("r-scran" ,r-scran)
2258 ("r-singlecellexperiment" ,r-singlecellexperiment)
2259 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2260 (home-page "https://github.com/kdkorthauer/scDD")
2261 (synopsis "Mixture modeling of single-cell RNA-seq data")
2263 "This package implements a method to analyze single-cell RNA-seq data
2264 utilizing flexible Dirichlet Process mixture models. Genes with differential
2265 distributions of expression are classified into several interesting patterns
2266 of differences between two conditions. The package also includes functions
2267 for simulating data with these patterns from negative binomial
2269 (license license:gpl2)))
2271 (define-public r-scone
2278 (uri (bioconductor-uri "scone" version))
2281 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2282 (build-system r-build-system)
2284 `(("r-aroma-light" ,r-aroma-light)
2285 ("r-biocparallel" ,r-biocparallel)
2287 ("r-class" ,r-class)
2288 ("r-cluster" ,r-cluster)
2289 ("r-compositions" ,r-compositions)
2290 ("r-diptest" ,r-diptest)
2291 ("r-edger" ,r-edger)
2293 ("r-gplots" ,r-gplots)
2294 ("r-hexbin" ,r-hexbin)
2295 ("r-limma" ,r-limma)
2296 ("r-matrixstats" ,r-matrixstats)
2297 ("r-mixtools" ,r-mixtools)
2298 ("r-rarpack" ,r-rarpack)
2299 ("r-rcolorbrewer" ,r-rcolorbrewer)
2300 ("r-rhdf5" ,r-rhdf5)
2301 ("r-ruvseq" ,r-ruvseq)
2302 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2303 (home-page "https://bioconductor.org/packages/scone")
2304 (synopsis "Single cell overview of normalized expression data")
2306 "SCONE is an R package for comparing and ranking the performance of
2307 different normalization schemes for single-cell RNA-seq and other
2308 high-throughput analyses.")
2309 (license license:artistic2.0)))
2311 (define-public r-geoquery
2318 (uri (bioconductor-uri "GEOquery" version))
2321 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2322 (properties `((upstream-name . "GEOquery")))
2323 (build-system r-build-system)
2325 `(("r-biobase" ,r-biobase)
2326 ("r-dplyr" ,r-dplyr)
2328 ("r-limma" ,r-limma)
2329 ("r-magrittr" ,r-magrittr)
2330 ("r-readr" ,r-readr)
2331 ("r-tidyr" ,r-tidyr)
2332 ("r-xml2" ,r-xml2)))
2333 (home-page "https://github.com/seandavi/GEOquery/")
2334 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2336 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2337 microarray data. Given the rich and varied nature of this resource, it is
2338 only natural to want to apply BioConductor tools to these data. GEOquery is
2339 the bridge between GEO and BioConductor.")
2340 (license license:gpl2)))
2342 (define-public r-illuminaio
2344 (name "r-illuminaio")
2349 (uri (bioconductor-uri "illuminaio" version))
2352 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2353 (build-system r-build-system)
2355 `(("r-base64" ,r-base64)))
2356 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2357 (synopsis "Parse Illumina microarray output files")
2359 "This package provides tools for parsing Illumina's microarray output
2360 files, including IDAT.")
2361 (license license:gpl2)))
2363 (define-public r-siggenes
2370 (uri (bioconductor-uri "siggenes" version))
2373 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2374 (build-system r-build-system)
2376 `(("r-biobase" ,r-biobase)
2377 ("r-multtest" ,r-multtest)
2378 ("r-scrime" ,r-scrime)))
2379 (home-page "https://bioconductor.org/packages/siggenes/")
2381 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2383 "This package provides tools for the identification of differentially
2384 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2385 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2386 Bayes Analyses of Microarrays} (EBAM).")
2387 (license license:lgpl2.0+)))
2389 (define-public r-bumphunter
2391 (name "r-bumphunter")
2396 (uri (bioconductor-uri "bumphunter" version))
2399 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2400 (build-system r-build-system)
2402 `(("r-annotationdbi" ,r-annotationdbi)
2403 ("r-biocgenerics" ,r-biocgenerics)
2404 ("r-dorng" ,r-dorng)
2405 ("r-foreach" ,r-foreach)
2406 ("r-genomeinfodb" ,r-genomeinfodb)
2407 ("r-genomicfeatures" ,r-genomicfeatures)
2408 ("r-genomicranges" ,r-genomicranges)
2409 ("r-iranges" ,r-iranges)
2410 ("r-iterators" ,r-iterators)
2411 ("r-limma" ,r-limma)
2412 ("r-locfit" ,r-locfit)
2413 ("r-matrixstats" ,r-matrixstats)
2414 ("r-s4vectors" ,r-s4vectors)))
2415 (home-page "https://github.com/ririzarr/bumphunter")
2416 (synopsis "Find bumps in genomic data")
2418 "This package provides tools for finding bumps in genomic data in order
2419 to identify differentially methylated regions in epigenetic epidemiology
2421 (license license:artistic2.0)))
2423 (define-public r-minfi
2430 (uri (bioconductor-uri "minfi" version))
2433 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2434 (build-system r-build-system)
2436 `(("r-beanplot" ,r-beanplot)
2437 ("r-biobase" ,r-biobase)
2438 ("r-biocgenerics" ,r-biocgenerics)
2439 ("r-biocparallel" ,r-biocparallel)
2440 ("r-biostrings" ,r-biostrings)
2441 ("r-bumphunter" ,r-bumphunter)
2442 ("r-data-table" ,r-data-table)
2443 ("r-delayedarray" ,r-delayedarray)
2444 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2445 ("r-genefilter" ,r-genefilter)
2446 ("r-genomeinfodb" ,r-genomeinfodb)
2447 ("r-genomicranges" ,r-genomicranges)
2448 ("r-geoquery" ,r-geoquery)
2449 ("r-hdf5array" ,r-hdf5array)
2450 ("r-illuminaio" ,r-illuminaio)
2451 ("r-iranges" ,r-iranges)
2452 ("r-lattice" ,r-lattice)
2453 ("r-limma" ,r-limma)
2455 ("r-mclust" ,r-mclust)
2457 ("r-nor1mix" ,r-nor1mix)
2458 ("r-preprocesscore" ,r-preprocesscore)
2459 ("r-quadprog" ,r-quadprog)
2460 ("r-rcolorbrewer" ,r-rcolorbrewer)
2461 ("r-reshape" ,r-reshape)
2462 ("r-s4vectors" ,r-s4vectors)
2463 ("r-siggenes" ,r-siggenes)
2464 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2465 (home-page "https://github.com/hansenlab/minfi")
2466 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2468 "This package provides tools to analyze and visualize Illumina Infinium
2469 methylation arrays.")
2470 (license license:artistic2.0)))
2472 (define-public r-methylumi
2474 (name "r-methylumi")
2479 (uri (bioconductor-uri "methylumi" version))
2482 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2483 (build-system r-build-system)
2485 `(("r-annotate" ,r-annotate)
2486 ("r-annotationdbi" ,r-annotationdbi)
2487 ("r-biobase" ,r-biobase)
2488 ("r-biocgenerics" ,r-biocgenerics)
2489 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2490 ("r-genefilter" ,r-genefilter)
2491 ("r-genomeinfodb" ,r-genomeinfodb)
2492 ("r-genomicranges" ,r-genomicranges)
2493 ("r-ggplot2" ,r-ggplot2)
2494 ("r-illuminaio" ,r-illuminaio)
2495 ("r-iranges" ,r-iranges)
2496 ("r-lattice" ,r-lattice)
2497 ("r-matrixstats" ,r-matrixstats)
2498 ("r-minfi" ,r-minfi)
2499 ("r-reshape2" ,r-reshape2)
2500 ("r-s4vectors" ,r-s4vectors)
2501 ("r-scales" ,r-scales)
2502 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2503 (home-page "https://bioconductor.org/packages/methylumi")
2504 (synopsis "Handle Illumina methylation data")
2506 "This package provides classes for holding and manipulating Illumina
2507 methylation data. Based on eSet, it can contain MIAME information, sample
2508 information, feature information, and multiple matrices of data. An
2509 \"intelligent\" import function, methylumiR can read the Illumina text files
2510 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2511 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2512 background correction, and quality control features for GoldenGate, Infinium,
2513 and Infinium HD arrays are also included.")
2514 (license license:gpl2)))
2516 (define-public r-lumi
2523 (uri (bioconductor-uri "lumi" version))
2526 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2527 (build-system r-build-system)
2529 `(("r-affy" ,r-affy)
2530 ("r-annotate" ,r-annotate)
2531 ("r-annotationdbi" ,r-annotationdbi)
2532 ("r-biobase" ,r-biobase)
2534 ("r-genomicfeatures" ,r-genomicfeatures)
2535 ("r-genomicranges" ,r-genomicranges)
2536 ("r-kernsmooth" ,r-kernsmooth)
2537 ("r-lattice" ,r-lattice)
2539 ("r-methylumi" ,r-methylumi)
2541 ("r-nleqslv" ,r-nleqslv)
2542 ("r-preprocesscore" ,r-preprocesscore)
2543 ("r-rsqlite" ,r-rsqlite)))
2544 (home-page "https://bioconductor.org/packages/lumi")
2545 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2547 "The lumi package provides an integrated solution for the Illumina
2548 microarray data analysis. It includes functions of Illumina
2549 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2550 variance stabilization, normalization and gene annotation at the probe level.
2551 It also includes the functions of processing Illumina methylation microarrays,
2552 especially Illumina Infinium methylation microarrays.")
2553 (license license:lgpl2.0+)))
2555 (define-public r-linnorm
2562 (uri (bioconductor-uri "Linnorm" version))
2565 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
2566 (properties `((upstream-name . "Linnorm")))
2567 (build-system r-build-system)
2569 `(("r-amap" ,r-amap)
2570 ("r-apcluster" ,r-apcluster)
2571 ("r-ellipse" ,r-ellipse)
2572 ("r-fastcluster" ,r-fastcluster)
2574 ("r-ggdendro" ,r-ggdendro)
2575 ("r-ggplot2" ,r-ggplot2)
2576 ("r-gmodels" ,r-gmodels)
2577 ("r-igraph" ,r-igraph)
2578 ("r-limma" ,r-limma)
2580 ("r-mclust" ,r-mclust)
2582 ("r-rcpparmadillo" ,r-rcpparmadillo)
2583 ("r-rtsne" ,r-rtsne)
2584 ("r-statmod" ,r-statmod)
2585 ("r-vegan" ,r-vegan)
2587 (home-page "http://www.jjwanglab.org/Linnorm/")
2588 (synopsis "Linear model and normality based transformation method")
2590 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2591 count data or any large scale count data. It transforms such datasets for
2592 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2593 the following pipelines are implemented:
2596 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2597 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2598 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2599 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2600 @item Differential expression analysis or differential peak detection using
2601 limma (@code{Linnorm.limma})
2602 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2603 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2604 @item Stable gene selection for scRNA-seq data; for users without or who do
2605 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2606 @item Data imputation (@code{Linnorm.DataImput}).
2609 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2610 @code{RnaXSim} function is included for simulating RNA-seq data for the
2611 evaluation of DEG analysis methods.")
2612 (license license:expat)))
2614 (define-public r-ioniser
2621 (uri (bioconductor-uri "IONiseR" version))
2624 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
2625 (properties `((upstream-name . "IONiseR")))
2626 (build-system r-build-system)
2628 `(("r-biocgenerics" ,r-biocgenerics)
2629 ("r-biocparallel" ,r-biocparallel)
2630 ("r-biostrings" ,r-biostrings)
2631 ("r-bit64" ,r-bit64)
2632 ("r-dplyr" ,r-dplyr)
2633 ("r-ggplot2" ,r-ggplot2)
2634 ("r-magrittr" ,r-magrittr)
2635 ("r-rhdf5" ,r-rhdf5)
2636 ("r-shortread" ,r-shortread)
2637 ("r-stringr" ,r-stringr)
2638 ("r-tibble" ,r-tibble)
2639 ("r-tidyr" ,r-tidyr)
2640 ("r-xvector" ,r-xvector)))
2641 (home-page "https://bioconductor.org/packages/IONiseR/")
2642 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2644 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2645 MinION data. It extracts summary statistics from a set of fast5 files and can
2646 be used either before or after base calling. In addition to standard
2647 summaries of the read-types produced, it provides a number of plots for
2648 visualising metrics relative to experiment run time or spatially over the
2649 surface of a flowcell.")
2650 (license license:expat)))
2652 ;; This is a CRAN package, but it depends on packages from Bioconductor.
2653 (define-public r-gkmsvm
2660 (uri (cran-uri "gkmSVM" version))
2663 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2664 (properties `((upstream-name . "gkmSVM")))
2665 (build-system r-build-system)
2667 `(("r-biocgenerics" ,r-biocgenerics)
2668 ("r-biostrings" ,r-biostrings)
2669 ("r-genomeinfodb" ,r-genomeinfodb)
2670 ("r-genomicranges" ,r-genomicranges)
2671 ("r-iranges" ,r-iranges)
2672 ("r-kernlab" ,r-kernlab)
2675 ("r-rtracklayer" ,r-rtracklayer)
2676 ("r-s4vectors" ,r-s4vectors)
2677 ("r-seqinr" ,r-seqinr)))
2678 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2679 (synopsis "Gapped-kmer support vector machine")
2681 "This R package provides tools for training gapped-kmer SVM classifiers
2682 for DNA and protein sequences. This package supports several sequence
2683 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2684 (license license:gpl2+)))
2686 (define-public r-triform
2693 (uri (bioconductor-uri "triform" version))
2696 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
2697 (build-system r-build-system)
2699 `(("r-biocgenerics" ,r-biocgenerics)
2700 ("r-iranges" ,r-iranges)
2701 ("r-yaml" ,r-yaml)))
2702 (home-page "https://bioconductor.org/packages/triform/")
2703 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2705 "The Triform algorithm uses model-free statistics to identify peak-like
2706 distributions of TF ChIP sequencing reads, taking advantage of an improved
2707 peak definition in combination with known profile characteristics.")
2708 (license license:gpl2)))
2710 (define-public r-varianttools
2712 (name "r-varianttools")
2717 (uri (bioconductor-uri "VariantTools" version))
2720 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
2721 (properties `((upstream-name . "VariantTools")))
2722 (build-system r-build-system)
2724 `(("r-biobase" ,r-biobase)
2725 ("r-biocgenerics" ,r-biocgenerics)
2726 ("r-biocparallel" ,r-biocparallel)
2727 ("r-biostrings" ,r-biostrings)
2728 ("r-bsgenome" ,r-bsgenome)
2729 ("r-genomeinfodb" ,r-genomeinfodb)
2730 ("r-genomicfeatures" ,r-genomicfeatures)
2731 ("r-genomicranges" ,r-genomicranges)
2732 ("r-iranges" ,r-iranges)
2733 ("r-matrix" ,r-matrix)
2734 ("r-rsamtools" ,r-rsamtools)
2735 ("r-rtracklayer" ,r-rtracklayer)
2736 ("r-s4vectors" ,r-s4vectors)
2737 ("r-variantannotation" ,r-variantannotation)))
2738 (home-page "https://bioconductor.org/packages/VariantTools/")
2739 (synopsis "Tools for exploratory analysis of variant calls")
2741 "Explore, diagnose, and compare variant calls using filters. The
2742 VariantTools package supports a workflow for loading data, calling single
2743 sample variants and tumor-specific somatic mutations or other sample-specific
2744 variant types (e.g., RNA editing). Most of the functions operate on
2745 alignments (BAM files) or datasets of called variants. The user is expected
2746 to have already aligned the reads with a separate tool, e.g., GSNAP via
2748 (license license:artistic2.0)))
2750 (define-public r-heatplus
2757 (uri (bioconductor-uri "Heatplus" version))
2760 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
2761 (properties `((upstream-name . "Heatplus")))
2762 (build-system r-build-system)
2764 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2765 (home-page "https://github.com/alexploner/Heatplus")
2766 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2768 "This package provides tools to display a rectangular heatmap (intensity
2769 plot) of a data matrix. By default, both samples (columns) and features (row)
2770 of the matrix are sorted according to a hierarchical clustering, and the
2771 corresponding dendrogram is plotted. Optionally, panels with additional
2772 information about samples and features can be added to the plot.")
2773 (license license:gpl2+)))
2775 (define-public r-gosemsim
2782 (uri (bioconductor-uri "GOSemSim" version))
2785 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
2786 (properties `((upstream-name . "GOSemSim")))
2787 (build-system r-build-system)
2789 `(("r-annotationdbi" ,r-annotationdbi)
2790 ("r-go-db" ,r-go-db)
2791 ("r-rcpp" ,r-rcpp)))
2792 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2793 (synopsis "GO-terms semantic similarity measures")
2795 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2796 quantitative ways to compute similarities between genes and gene groups, and
2797 have became important basis for many bioinformatics analysis approaches.
2798 GOSemSim is an R package for semantic similarity computation among GO terms,
2799 sets of GO terms, gene products and gene clusters.")
2800 (license license:artistic2.0)))
2802 (define-public r-anota
2809 (uri (bioconductor-uri "anota" version))
2812 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
2813 (build-system r-build-system)
2815 `(("r-multtest" ,r-multtest)
2816 ("r-qvalue" ,r-qvalue)))
2817 (home-page "https://bioconductor.org/packages/anota/")
2818 (synopsis "Analysis of translational activity")
2820 "Genome wide studies of translational control is emerging as a tool to
2821 study verious biological conditions. The output from such analysis is both
2822 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2823 involved in translation (the actively translating mRNA level) for each mRNA.
2824 The standard analysis of such data strives towards identifying differential
2825 translational between two or more sample classes - i.e. differences in
2826 actively translated mRNA levels that are independent of underlying differences
2827 in cytosolic mRNA levels. This package allows for such analysis using partial
2828 variances and the random variance model. As 10s of thousands of mRNAs are
2829 analyzed in parallell the library performs a number of tests to assure that
2830 the data set is suitable for such analysis.")
2831 (license license:gpl3)))
2833 (define-public r-sigpathway
2835 (name "r-sigpathway")
2840 (uri (bioconductor-uri "sigPathway" version))
2843 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
2844 (properties `((upstream-name . "sigPathway")))
2845 (build-system r-build-system)
2846 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
2847 (synopsis "Pathway analysis")
2849 "This package is used to conduct pathway analysis by calculating the NT_k
2850 and NE_k statistics in a statistical framework for determining whether a
2851 specified group of genes for a pathway has a coordinated association with a
2852 phenotype of interest.")
2853 (license license:gpl2)))
2855 (define-public r-fgsea
2862 (uri (bioconductor-uri "fgsea" version))
2865 "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c"))))
2866 (build-system r-build-system)
2869 ("r-biocparallel" ,r-biocparallel)
2870 ("r-data-table" ,r-data-table)
2871 ("r-fastmatch" ,r-fastmatch)
2872 ("r-ggplot2" ,r-ggplot2)
2873 ("r-gridextra" ,r-gridextra)
2874 ("r-matrix" ,r-matrix)
2875 ("r-rcpp" ,r-rcpp)))
2876 (home-page "https://github.com/ctlab/fgsea/")
2877 (synopsis "Fast gene set enrichment analysis")
2879 "The package implements an algorithm for fast gene set enrichment
2880 analysis. Using the fast algorithm allows to make more permutations and get
2881 more fine grained p-values, which allows to use accurate stantard approaches
2882 to multiple hypothesis correction.")
2883 (license license:expat)))
2885 (define-public r-dose
2892 (uri (bioconductor-uri "DOSE" version))
2895 "0dvhnfhzhhzcxm8zhdwrkif7sak4p888sjqfd3a0p77h0hs6g8pv"))))
2896 (properties `((upstream-name . "DOSE")))
2897 (build-system r-build-system)
2899 `(("r-annotationdbi" ,r-annotationdbi)
2900 ("r-biocparallel" ,r-biocparallel)
2901 ("r-do-db" ,r-do-db)
2902 ("r-fgsea" ,r-fgsea)
2903 ("r-ggplot2" ,r-ggplot2)
2904 ("r-gosemsim" ,r-gosemsim)
2905 ("r-qvalue" ,r-qvalue)
2906 ("r-reshape2" ,r-reshape2)
2907 ("r-s4vectors" ,r-s4vectors)))
2908 (home-page "https://guangchuangyu.github.io/software/DOSE/")
2909 (synopsis "Disease ontology semantic and enrichment analysis")
2911 "This package implements five methods proposed by Resnik, Schlicker,
2912 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
2913 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
2914 including hypergeometric model and gene set enrichment analysis are also
2915 implemented for discovering disease associations of high-throughput biological
2917 (license license:artistic2.0)))
2919 (define-public r-enrichplot
2921 (name "r-enrichplot")
2926 (uri (bioconductor-uri "enrichplot" version))
2929 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
2930 (build-system r-build-system)
2932 `(("r-annotationdbi" ,r-annotationdbi)
2933 ("r-cowplot" ,r-cowplot)
2935 ("r-europepmc" ,r-europepmc)
2936 ("r-ggplot2" ,r-ggplot2)
2937 ("r-ggplotify" ,r-ggplotify)
2938 ("r-ggraph" ,r-ggraph)
2939 ("r-ggridges" ,r-ggridges)
2940 ("r-gosemsim" ,r-gosemsim)
2941 ("r-gridextra" ,r-gridextra)
2942 ("r-igraph" ,r-igraph)
2943 ("r-purrr" ,r-purrr)
2944 ("r-rcolorbrewer" ,r-rcolorbrewer)
2945 ("r-reshape2" ,r-reshape2)
2946 ("r-upsetr" ,r-upsetr)))
2947 (home-page "https://github.com/GuangchuangYu/enrichplot")
2948 (synopsis "Visualization of functional enrichment result")
2950 "The enrichplot package implements several visualization methods for
2951 interpreting functional enrichment results obtained from ORA or GSEA analyses.
2952 All the visualization methods are developed based on ggplot2 graphics.")
2953 (license license:artistic2.0)))
2955 (define-public r-clusterprofiler
2957 (name "r-clusterprofiler")
2962 (uri (bioconductor-uri "clusterProfiler" version))
2965 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
2967 `((upstream-name . "clusterProfiler")))
2968 (build-system r-build-system)
2970 `(("r-annotationdbi" ,r-annotationdbi)
2972 ("r-enrichplot" ,r-enrichplot)
2973 ("r-ggplot2" ,r-ggplot2)
2974 ("r-go-db" ,r-go-db)
2975 ("r-gosemsim" ,r-gosemsim)
2976 ("r-magrittr" ,r-magrittr)
2978 ("r-qvalue" ,r-qvalue)
2979 ("r-rvcheck" ,r-rvcheck)
2980 ("r-tidyr" ,r-tidyr)))
2981 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
2982 (synopsis "Analysis and visualization of functional profiles for gene clusters")
2984 "This package implements methods to analyze and visualize functional
2985 profiles (GO and KEGG) of gene and gene clusters.")
2986 (license license:artistic2.0)))
2988 (define-public r-mlinterfaces
2990 (name "r-mlinterfaces")
2995 (uri (bioconductor-uri "MLInterfaces" version))
2998 "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
2999 (properties `((upstream-name . "MLInterfaces")))
3000 (build-system r-build-system)
3002 `(("r-annotate" ,r-annotate)
3003 ("r-biobase" ,r-biobase)
3004 ("r-biocgenerics" ,r-biocgenerics)
3005 ("r-cluster" ,r-cluster)
3008 ("r-gdata" ,r-gdata)
3009 ("r-genefilter" ,r-genefilter)
3010 ("r-ggvis" ,r-ggvis)
3011 ("r-hwriter" ,r-hwriter)
3013 ("r-mlbench" ,r-mlbench)
3015 ("r-rcolorbrewer" ,r-rcolorbrewer)
3017 ("r-rpart" ,r-rpart)
3018 ("r-sfsmisc" ,r-sfsmisc)
3019 ("r-shiny" ,r-shiny)
3020 ("r-threejs" ,r-threejs)))
3021 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3022 (synopsis "Interfaces to R machine learning procedures")
3024 "This package provides uniform interfaces to machine learning code for
3025 data in R and Bioconductor containers.")
3026 ;; Any version of the LGPL.
3027 (license license:lgpl2.1+)))
3029 (define-public r-annaffy
3036 (uri (bioconductor-uri "annaffy" version))
3039 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3040 (build-system r-build-system)
3043 (modify-phases %standard-phases
3044 (add-after 'unpack 'remove-reference-to-non-free-data
3046 (substitute* "DESCRIPTION"
3050 `(("r-annotationdbi" ,r-annotationdbi)
3051 ("r-biobase" ,r-biobase)
3053 ("r-go-db" ,r-go-db)))
3054 (home-page "https://bioconductor.org/packages/annaffy/")
3055 (synopsis "Annotation tools for Affymetrix biological metadata")
3057 "This package provides functions for handling data from Bioconductor
3058 Affymetrix annotation data packages. It produces compact HTML and text
3059 reports including experimental data and URL links to many online databases.
3060 It allows searching of biological metadata using various criteria.")
3061 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3062 ;; the LGPL 2.1 is included.
3063 (license license:lgpl2.1+)))
3065 (define-public r-a4core
3072 (uri (bioconductor-uri "a4Core" version))
3075 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3076 (properties `((upstream-name . "a4Core")))
3077 (build-system r-build-system)
3079 `(("r-biobase" ,r-biobase)
3080 ("r-glmnet" ,r-glmnet)))
3081 (home-page "https://bioconductor.org/packages/a4Core")
3082 (synopsis "Automated Affymetrix array analysis core package")
3084 "This is the core package for the automated analysis of Affymetrix
3086 (license license:gpl3)))
3088 (define-public r-a4classif
3090 (name "r-a4classif")
3095 (uri (bioconductor-uri "a4Classif" version))
3098 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3099 (properties `((upstream-name . "a4Classif")))
3100 (build-system r-build-system)
3102 `(("r-a4core" ,r-a4core)
3103 ("r-a4preproc" ,r-a4preproc)
3104 ("r-glmnet" ,r-glmnet)
3105 ("r-mlinterfaces" ,r-mlinterfaces)
3108 ("r-varselrf" ,r-varselrf)))
3109 (home-page "https://bioconductor.org/packages/a4Classif/")
3110 (synopsis "Automated Affymetrix array analysis classification package")
3112 "This is the classification package for the automated analysis of
3113 Affymetrix arrays.")
3114 (license license:gpl3)))
3116 (define-public r-a4preproc
3118 (name "r-a4preproc")
3123 (uri (bioconductor-uri "a4Preproc" version))
3126 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3127 (properties `((upstream-name . "a4Preproc")))
3128 (build-system r-build-system)
3130 `(("r-annotationdbi" ,r-annotationdbi)))
3131 (home-page "https://bioconductor.org/packages/a4Preproc/")
3132 (synopsis "Automated Affymetrix array analysis preprocessing package")
3134 "This is a package for the automated analysis of Affymetrix arrays. It
3135 is used for preprocessing the arrays.")
3136 (license license:gpl3)))
3138 (define-public r-a4reporting
3140 (name "r-a4reporting")
3145 (uri (bioconductor-uri "a4Reporting" version))
3148 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3149 (properties `((upstream-name . "a4Reporting")))
3150 (build-system r-build-system)
3152 `(("r-annaffy" ,r-annaffy)
3153 ("r-xtable" ,r-xtable)))
3154 (home-page "https://bioconductor.org/packages/a4Reporting/")
3155 (synopsis "Automated Affymetrix array analysis reporting package")
3157 "This is a package for the automated analysis of Affymetrix arrays. It
3158 provides reporting features.")
3159 (license license:gpl3)))
3161 (define-public r-a4base
3168 (uri (bioconductor-uri "a4Base" version))
3171 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3172 (properties `((upstream-name . "a4Base")))
3173 (build-system r-build-system)
3175 `(("r-a4core" ,r-a4core)
3176 ("r-a4preproc" ,r-a4preproc)
3177 ("r-annaffy" ,r-annaffy)
3178 ("r-annotationdbi" ,r-annotationdbi)
3179 ("r-biobase" ,r-biobase)
3180 ("r-genefilter" ,r-genefilter)
3181 ("r-glmnet" ,r-glmnet)
3182 ("r-gplots" ,r-gplots)
3183 ("r-limma" ,r-limma)
3185 ("r-multtest" ,r-multtest)))
3186 (home-page "https://bioconductor.org/packages/a4Base/")
3187 (synopsis "Automated Affymetrix array analysis base package")
3189 "This package provides basic features for the automated analysis of
3190 Affymetrix arrays.")
3191 (license license:gpl3)))
3200 (uri (bioconductor-uri "a4" version))
3203 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3204 (build-system r-build-system)
3206 `(("r-a4base" ,r-a4base)
3207 ("r-a4classif" ,r-a4classif)
3208 ("r-a4core" ,r-a4core)
3209 ("r-a4preproc" ,r-a4preproc)
3210 ("r-a4reporting" ,r-a4reporting)))
3211 (home-page "https://bioconductor.org/packages/a4/")
3212 (synopsis "Automated Affymetrix array analysis umbrella package")
3214 "This package provides a software suite for the automated analysis of
3215 Affymetrix arrays.")
3216 (license license:gpl3)))
3218 (define-public r-abseqr
3225 (uri (bioconductor-uri "abseqR" version))
3228 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3229 (properties `((upstream-name . "abseqR")))
3230 (build-system r-build-system)
3232 `(("pandoc" ,ghc-pandoc)))
3234 `(("r-biocparallel" ,r-biocparallel)
3235 ("r-biocstyle" ,r-biocstyle)
3236 ("r-circlize" ,r-circlize)
3237 ("r-flexdashboard" ,r-flexdashboard)
3238 ("r-ggcorrplot" ,r-ggcorrplot)
3239 ("r-ggdendro" ,r-ggdendro)
3240 ("r-ggplot2" ,r-ggplot2)
3241 ("r-gridextra" ,r-gridextra)
3242 ("r-knitr" ,r-knitr)
3243 ("r-plotly" ,r-plotly)
3246 ("r-rcolorbrewer" ,r-rcolorbrewer)
3247 ("r-reshape2" ,r-reshape2)
3248 ("r-rmarkdown" ,r-rmarkdown)
3249 ("r-stringr" ,r-stringr)
3250 ("r-vegan" ,r-vegan)
3251 ("r-venndiagram" ,r-venndiagram)))
3252 (home-page "https://github.com/malhamdoosh/abseqR")
3253 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3255 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3256 sequencing datasets generated from antibody libraries and abseqR is one of its
3257 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3258 capabilities and allows them to generate interactive HTML reports for the
3259 convenience of viewing and sharing with other researchers. Additionally,
3260 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3261 further downstream analysis on its output.")
3262 (license license:gpl3)))
3264 (define-public r-bacon
3271 (uri (bioconductor-uri "bacon" version))
3274 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3275 (build-system r-build-system)
3277 `(("r-biocparallel" ,r-biocparallel)
3278 ("r-ellipse" ,r-ellipse)
3279 ("r-ggplot2" ,r-ggplot2)))
3280 (home-page "https://bioconductor.org/packages/bacon/")
3281 (synopsis "Controlling bias and inflation in association studies")
3283 "Bacon can be used to remove inflation and bias often observed in
3284 epigenome- and transcriptome-wide association studies. To this end bacon
3285 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3286 fitting a three-component normal mixture on z-scores.")
3287 (license license:gpl2+)))
3289 (define-public r-rgadem
3296 (uri (bioconductor-uri "rGADEM" version))
3299 "0mck3dsxzjxszfs1cl96kd83q7n85p3763s0y3gwws69jn7p6w5j"))))
3300 (properties `((upstream-name . "rGADEM")))
3301 (build-system r-build-system)
3303 `(("r-biostrings" ,r-biostrings)
3304 ("r-bsgenome" ,r-bsgenome)
3305 ("r-iranges" ,r-iranges)
3306 ("r-seqlogo" ,r-seqlogo)))
3307 (home-page "https://bioconductor.org/packages/rGADEM/")
3308 (synopsis "De novo sequence motif discovery")
3310 "rGADEM is an efficient de novo motif discovery tool for large-scale
3311 genomic sequence data.")
3312 (license license:artistic2.0)))
3314 (define-public r-motiv
3321 (uri (bioconductor-uri "MotIV" version))
3324 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3325 (properties `((upstream-name . "MotIV")))
3326 (build-system r-build-system)
3330 `(("r-biocgenerics" ,r-biocgenerics)
3331 ("r-biostrings" ,r-biostrings)
3332 ("r-iranges" ,r-iranges)
3333 ("r-lattice" ,r-lattice)
3334 ("r-rgadem" ,r-rgadem)
3335 ("r-s4vectors" ,r-s4vectors)))
3336 (home-page "https://bioconductor.org/packages/MotIV/")
3337 (synopsis "Motif identification and validation")
3339 "This package is used for the identification and validation of sequence
3340 motifs. It makes use of STAMP for comparing a set of motifs to a given
3341 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3342 distributions, modules and filter motifs.")
3343 (license license:gpl2)))
3345 (define-public r-motifstack
3347 (name "r-motifstack")
3352 (uri (bioconductor-uri "motifStack" version))
3355 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3356 (properties `((upstream-name . "motifStack")))
3357 (build-system r-build-system)
3359 `(("r-ade4" ,r-ade4)
3360 ("r-biostrings" ,r-biostrings)
3361 ("r-grimport2" ,r-grimport2)
3362 ("r-htmlwidgets" ,r-htmlwidgets)
3363 ("r-motiv" ,r-motiv)
3364 ("r-scales" ,r-scales)
3366 (home-page "https://bioconductor.org/packages/motifStack/")
3367 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3369 "The motifStack package is designed for graphic representation of
3370 multiple motifs with different similarity scores. It works with both DNA/RNA
3371 sequence motifs and amino acid sequence motifs. In addition, it provides the
3372 flexibility for users to customize the graphic parameters such as the font
3373 type and symbol colors.")
3374 (license license:gpl2+)))
3376 (define-public r-genomicscores
3378 (name "r-genomicscores")
3383 (uri (bioconductor-uri "GenomicScores" version))
3386 "17bd61icfycc61b5dij1968h026w7vfd9miwdcbppak1j6s08idq"))))
3387 (properties `((upstream-name . "GenomicScores")))
3388 (build-system r-build-system)
3390 `(("r-annotationhub" ,r-annotationhub)
3391 ("r-biobase" ,r-biobase)
3392 ("r-biocgenerics" ,r-biocgenerics)
3393 ("r-biostrings" ,r-biostrings)
3394 ("r-bsgenome" ,r-bsgenome)
3395 ("r-genomeinfodb" ,r-genomeinfodb)
3396 ("r-genomicranges" ,r-genomicranges)
3397 ("r-iranges" ,r-iranges)
3398 ("r-s4vectors" ,r-s4vectors)
3400 (home-page "https://github.com/rcastelo/GenomicScores/")
3401 (synopsis "Work with genome-wide position-specific scores")
3403 "This package provides infrastructure to store and access genome-wide
3404 position-specific scores within R and Bioconductor.")
3405 (license license:artistic2.0)))
3407 (define-public r-atacseqqc
3409 (name "r-atacseqqc")
3414 (uri (bioconductor-uri "ATACseqQC" version))
3417 "03f130vcd6hd3fv2pg60id0ddd6qkwsyx73gm907xaayf42ar2pj"))))
3418 (properties `((upstream-name . "ATACseqQC")))
3419 (build-system r-build-system)
3421 `(("r-biocgenerics" ,r-biocgenerics)
3422 ("r-biostrings" ,r-biostrings)
3423 ("r-bsgenome" ,r-bsgenome)
3424 ("r-chippeakanno" ,r-chippeakanno)
3425 ("r-edger" ,r-edger)
3426 ("r-genomeinfodb" ,r-genomeinfodb)
3427 ("r-genomicalignments" ,r-genomicalignments)
3428 ("r-genomicranges" ,r-genomicranges)
3429 ("r-genomicscores" ,r-genomicscores)
3430 ("r-iranges" ,r-iranges)
3431 ("r-kernsmooth" ,r-kernsmooth)
3432 ("r-limma" ,r-limma)
3433 ("r-motifstack" ,r-motifstack)
3434 ("r-preseqr" ,r-preseqr)
3435 ("r-randomforest" ,r-randomforest)
3436 ("r-rsamtools" ,r-rsamtools)
3437 ("r-rtracklayer" ,r-rtracklayer)
3438 ("r-s4vectors" ,r-s4vectors)))
3439 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3440 (synopsis "ATAC-seq quality control")
3442 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3443 sequencing, is a rapid and sensitive method for chromatin accessibility
3444 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3445 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3446 assess whether their ATAC-seq experiment is successful. It includes
3447 diagnostic plots of fragment size distribution, proportion of mitochondria
3448 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3450 (license license:gpl2+)))
3452 (define-public r-gofuncr
3459 (uri (bioconductor-uri "GOfuncR" version))
3462 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3463 (properties `((upstream-name . "GOfuncR")))
3464 (build-system r-build-system)
3466 `(("r-annotationdbi" ,r-annotationdbi)
3467 ("r-genomicranges" ,r-genomicranges)
3468 ("r-gtools" ,r-gtools)
3469 ("r-iranges" ,r-iranges)
3470 ("r-mapplots" ,r-mapplots)
3472 ("r-vioplot" ,r-vioplot)))
3473 (home-page "https://bioconductor.org/packages/GOfuncR/")
3474 (synopsis "Gene ontology enrichment using FUNC")
3476 "GOfuncR performs a gene ontology enrichment analysis based on the
3477 ontology enrichment software FUNC. GO-annotations are obtained from
3478 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3479 included in the package and updated regularly. GOfuncR provides the standard
3480 candidate vs background enrichment analysis using the hypergeometric test, as
3481 well as three additional tests:
3484 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3485 @item a binomial test that is used when genes are associated with two counts,
3487 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3488 associated with four counts.
3491 To correct for multiple testing and interdependency of the tests, family-wise
3492 error rates are computed based on random permutations of the gene-associated
3493 variables. GOfuncR also provides tools for exploring the ontology graph and
3494 the annotations, and options to take gene-length or spatial clustering of
3495 genes into account. It is also possible to provide custom gene coordinates,
3496 annotations and ontologies.")
3497 (license license:gpl2+)))
3499 (define-public r-abaenrichment
3501 (name "r-abaenrichment")
3506 (uri (bioconductor-uri "ABAEnrichment" version))
3509 "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
3510 (properties `((upstream-name . "ABAEnrichment")))
3511 (build-system r-build-system)
3513 `(("r-abadata" ,r-abadata)
3514 ("r-data-table" ,r-data-table)
3515 ("r-gofuncr" ,r-gofuncr)
3516 ("r-gplots" ,r-gplots)
3517 ("r-gtools" ,r-gtools)
3518 ("r-rcpp" ,r-rcpp)))
3519 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3520 (synopsis "Gene expression enrichment in human brain regions")
3522 "The package ABAEnrichment is designed to test for enrichment of user
3523 defined candidate genes in the set of expressed genes in different human brain
3524 regions. The core function @code{aba_enrich} integrates the expression of the
3525 candidate gene set (averaged across donors) and the structural information of
3526 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3527 (license license:gpl2+)))
3529 (define-public r-annotationfuncs
3531 (name "r-annotationfuncs")
3536 (uri (bioconductor-uri "AnnotationFuncs" version))
3539 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3541 `((upstream-name . "AnnotationFuncs")))
3542 (build-system r-build-system)
3544 `(("r-annotationdbi" ,r-annotationdbi)
3546 (home-page "https://www.iysik.com/r/annotationfuncs")
3547 (synopsis "Annotation translation functions")
3549 "This package provides functions for handling translating between
3550 different identifieres using the Biocore Data Team data-packages (e.g.
3551 @code{org.Bt.eg.db}).")
3552 (license license:gpl2)))
3554 (define-public r-annotationtools
3556 (name "r-annotationtools")
3561 (uri (bioconductor-uri "annotationTools" version))
3564 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
3566 `((upstream-name . "annotationTools")))
3567 (build-system r-build-system)
3568 (propagated-inputs `(("r-biobase" ,r-biobase)))
3569 (home-page "https://bioconductor.org/packages/annotationTools/")
3570 (synopsis "Annotate microarrays and perform gene expression analyses")
3572 "This package provides functions to annotate microarrays, find orthologs,
3573 and integrate heterogeneous gene expression profiles using annotation and
3574 other molecular biology information available as flat file database (plain
3576 ;; Any version of the GPL.
3577 (license (list license:gpl2+))))
3579 (define-public r-allelicimbalance
3581 (name "r-allelicimbalance")
3586 (uri (bioconductor-uri "AllelicImbalance" version))
3589 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
3591 `((upstream-name . "AllelicImbalance")))
3592 (build-system r-build-system)
3594 `(("r-annotationdbi" ,r-annotationdbi)
3595 ("r-biocgenerics" ,r-biocgenerics)
3596 ("r-biostrings" ,r-biostrings)
3597 ("r-bsgenome" ,r-bsgenome)
3598 ("r-genomeinfodb" ,r-genomeinfodb)
3599 ("r-genomicalignments" ,r-genomicalignments)
3600 ("r-genomicfeatures" ,r-genomicfeatures)
3601 ("r-genomicranges" ,r-genomicranges)
3602 ("r-gridextra" ,r-gridextra)
3604 ("r-iranges" ,r-iranges)
3605 ("r-lattice" ,r-lattice)
3606 ("r-latticeextra" ,r-latticeextra)
3608 ("r-rsamtools" ,r-rsamtools)
3609 ("r-s4vectors" ,r-s4vectors)
3610 ("r-seqinr" ,r-seqinr)
3611 ("r-summarizedexperiment" ,r-summarizedexperiment)
3612 ("r-variantannotation" ,r-variantannotation)))
3613 (home-page "https://github.com/pappewaio/AllelicImbalance")
3614 (synopsis "Investigate allele-specific expression")
3616 "This package provides a framework for allele-specific expression
3617 investigation using RNA-seq data.")
3618 (license license:gpl3)))
3620 (define-public r-aucell
3627 (uri (bioconductor-uri "AUCell" version))
3630 "025q1as9pifbxa7hidlz634q6d7l73zx8mqy4rjbfrk7d5615xvm"))))
3631 (properties `((upstream-name . "AUCell")))
3632 (build-system r-build-system)
3634 `(("r-data-table" ,r-data-table)
3635 ("r-gseabase" ,r-gseabase)
3636 ("r-mixtools" ,r-mixtools)
3637 ("r-r-utils" ,r-r-utils)
3638 ("r-shiny" ,r-shiny)
3639 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3640 (home-page "https://bioconductor.org/packages/AUCell/")
3641 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
3643 "AUCell allows to identify cells with active gene sets (e.g. signatures,
3644 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
3645 Under the Curve} (AUC) to calculate whether a critical subset of the input
3646 gene set is enriched within the expressed genes for each cell. The
3647 distribution of AUC scores across all the cells allows exploring the relative
3648 expression of the signature. Since the scoring method is ranking-based,
3649 AUCell is independent of the gene expression units and the normalization
3650 procedure. In addition, since the cells are evaluated individually, it can
3651 easily be applied to bigger datasets, subsetting the expression matrix if
3653 (license license:gpl3)))
3655 (define-public r-ebimage
3662 (uri (bioconductor-uri "EBImage" version))
3665 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
3666 (properties `((upstream-name . "EBImage")))
3667 (build-system r-build-system)
3669 `(("r-abind" ,r-abind)
3670 ("r-biocgenerics" ,r-biocgenerics)
3671 ("r-fftwtools" ,r-fftwtools)
3672 ("r-htmltools" ,r-htmltools)
3673 ("r-htmlwidgets" ,r-htmlwidgets)
3675 ("r-locfit" ,r-locfit)
3677 ("r-rcurl" ,r-rcurl)
3678 ("r-tiff" ,r-tiff)))
3680 `(("r-knitr" ,r-knitr))) ; for vignettes
3681 (home-page "https://github.com/aoles/EBImage")
3682 (synopsis "Image processing and analysis toolbox for R")
3684 "EBImage provides general purpose functionality for image processing and
3685 analysis. In the context of (high-throughput) microscopy-based cellular
3686 assays, EBImage offers tools to segment cells and extract quantitative
3687 cellular descriptors. This allows the automation of such tasks using the R
3688 programming language and facilitates the use of other tools in the R
3689 environment for signal processing, statistical modeling, machine learning and
3690 visualization with image data.")
3691 ;; Any version of the LGPL.
3692 (license license:lgpl2.1+)))
3694 (define-public r-yamss
3701 (uri (bioconductor-uri "yamss" version))
3704 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
3705 (build-system r-build-system)
3707 `(("r-biocgenerics" ,r-biocgenerics)
3708 ("r-data-table" ,r-data-table)
3709 ("r-ebimage" ,r-ebimage)
3710 ("r-iranges" ,r-iranges)
3711 ("r-limma" ,r-limma)
3712 ("r-matrix" ,r-matrix)
3714 ("r-s4vectors" ,r-s4vectors)
3715 ("r-summarizedexperiment"
3716 ,r-summarizedexperiment)))
3717 (home-page "https://github.com/hansenlab/yamss")
3718 (synopsis "Tools for high-throughput metabolomics")
3720 "This package provides tools to analyze and visualize high-throughput
3721 metabolomics data acquired using chromatography-mass spectrometry. These tools
3722 preprocess data in a way that enables reliable and powerful differential
3724 (license license:artistic2.0)))
3726 (define-public r-gtrellis
3733 (uri (bioconductor-uri "gtrellis" version))
3736 "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y"))))
3737 (build-system r-build-system)
3739 `(("r-circlize" ,r-circlize)
3740 ("r-genomicranges" ,r-genomicranges)
3741 ("r-getoptlong" ,r-getoptlong)
3742 ("r-iranges" ,r-iranges)))
3743 (home-page "https://github.com/jokergoo/gtrellis")
3744 (synopsis "Genome level Trellis layout")
3746 "Genome level Trellis graph visualizes genomic data conditioned by
3747 genomic categories (e.g. chromosomes). For each genomic category, multiple
3748 dimensional data which are represented as tracks describe different features
3749 from different aspects. This package provides high flexibility to arrange
3750 genomic categories and to add self-defined graphics in the plot.")
3751 (license license:expat)))
3753 (define-public r-somaticsignatures
3755 (name "r-somaticsignatures")
3760 (uri (bioconductor-uri "SomaticSignatures" version))
3763 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
3765 `((upstream-name . "SomaticSignatures")))
3766 (build-system r-build-system)
3768 `(("r-biobase" ,r-biobase)
3769 ("r-biostrings" ,r-biostrings)
3770 ("r-genomeinfodb" ,r-genomeinfodb)
3771 ("r-genomicranges" ,r-genomicranges)
3772 ("r-ggbio" ,r-ggbio)
3773 ("r-ggplot2" ,r-ggplot2)
3774 ("r-iranges" ,r-iranges)
3776 ("r-pcamethods" ,r-pcamethods)
3777 ("r-proxy" ,r-proxy)
3778 ("r-reshape2" ,r-reshape2)
3779 ("r-s4vectors" ,r-s4vectors)
3780 ("r-variantannotation" ,r-variantannotation)))
3781 (home-page "https://github.com/juliangehring/SomaticSignatures")
3782 (synopsis "Somatic signatures")
3784 "This package identifies mutational signatures of @dfn{single nucleotide
3785 variants} (SNVs). It provides a infrastructure related to the methodology
3786 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
3787 decomposition algorithms.")
3788 (license license:expat)))
3790 (define-public r-yapsa
3797 (uri (bioconductor-uri "YAPSA" version))
3800 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
3801 (properties `((upstream-name . "YAPSA")))
3802 (build-system r-build-system)
3804 `(("r-circlize" ,r-circlize)
3805 ("r-complexheatmap" ,r-complexheatmap)
3806 ("r-corrplot" ,r-corrplot)
3807 ("r-dendextend" ,r-dendextend)
3808 ("r-genomeinfodb" ,r-genomeinfodb)
3809 ("r-genomicranges" ,r-genomicranges)
3810 ("r-getoptlong" ,r-getoptlong)
3811 ("r-ggplot2" ,r-ggplot2)
3812 ("r-gridextra" ,r-gridextra)
3813 ("r-gtrellis" ,r-gtrellis)
3814 ("r-keggrest" ,r-keggrest)
3816 ("r-pmcmr" ,r-pmcmr)
3817 ("r-reshape2" ,r-reshape2)
3818 ("r-somaticsignatures" ,r-somaticsignatures)
3819 ("r-variantannotation" ,r-variantannotation)))
3820 (home-page "https://bioconductor.org/packages/YAPSA/")
3821 (synopsis "Yet another package for signature analysis")
3823 "This package provides functions and routines useful in the analysis of
3824 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
3825 functions to perform a signature analysis with known signatures and a
3826 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
3828 (license license:gpl3)))
3830 (define-public r-gcrma
3837 (uri (bioconductor-uri "gcrma" version))
3840 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
3841 (build-system r-build-system)
3843 `(("r-affy" ,r-affy)
3844 ("r-affyio" ,r-affyio)
3845 ("r-biobase" ,r-biobase)
3846 ("r-biocmanager" ,r-biocmanager)
3847 ("r-biostrings" ,r-biostrings)
3848 ("r-xvector" ,r-xvector)))
3849 (home-page "https://bioconductor.org/packages/gcrma/")
3850 (synopsis "Background adjustment using sequence information")
3852 "Gcrma adjusts for background intensities in Affymetrix array data which
3853 include optical noise and @dfn{non-specific binding} (NSB). The main function
3854 @code{gcrma} converts background adjusted probe intensities to expression
3855 measures using the same normalization and summarization methods as a
3856 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
3857 to estimate probe affinity to NSB. The sequence information is summarized in
3858 a more complex way than the simple GC content. Instead, the base types (A, T,
3859 G or C) at each position along the probe determine the affinity of each probe.
3860 The parameters of the position-specific base contributions to the probe
3861 affinity is estimated in an NSB experiment in which only NSB but no
3862 gene-specific bidning is expected.")
3863 ;; Any version of the LGPL
3864 (license license:lgpl2.1+)))
3866 (define-public r-simpleaffy
3868 (name "r-simpleaffy")
3873 (uri (bioconductor-uri "simpleaffy" version))
3876 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
3877 (build-system r-build-system)
3879 `(("r-affy" ,r-affy)
3880 ("r-biobase" ,r-biobase)
3881 ("r-biocgenerics" ,r-biocgenerics)
3882 ("r-gcrma" ,r-gcrma)
3883 ("r-genefilter" ,r-genefilter)))
3884 (home-page "https://bioconductor.org/packages/simpleaffy/")
3885 (synopsis "Very simple high level analysis of Affymetrix data")
3887 "This package provides high level functions for reading Affy @file{.CEL}
3888 files, phenotypic data, and then computing simple things with it, such as
3889 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
3890 library. It also has some basic scatter plot functions and mechanisms for
3891 generating high resolution journal figures.")
3892 (license license:gpl2+)))
3894 (define-public r-yaqcaffy
3901 (uri (bioconductor-uri "yaqcaffy" version))
3904 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
3905 (build-system r-build-system)
3907 `(("r-simpleaffy" ,r-simpleaffy)))
3908 (home-page "https://bioconductor.org/packages/yaqcaffy/")
3909 (synopsis "Affymetrix quality control and reproducibility analysis")
3911 "This is a package that can be used for quality control of Affymetrix
3912 GeneChip expression data and reproducibility analysis of human whole genome
3913 chips with the MAQC reference datasets.")
3914 (license license:artistic2.0)))
3916 (define-public r-quantro
3923 (uri (bioconductor-uri "quantro" version))
3926 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
3927 (build-system r-build-system)
3929 `(("r-biobase" ,r-biobase)
3930 ("r-doparallel" ,r-doparallel)
3931 ("r-foreach" ,r-foreach)
3932 ("r-ggplot2" ,r-ggplot2)
3933 ("r-iterators" ,r-iterators)
3934 ("r-minfi" ,r-minfi)
3935 ("r-rcolorbrewer" ,r-rcolorbrewer)))
3936 (home-page "https://bioconductor.org/packages/quantro/")
3937 (synopsis "Test for when to use quantile normalization")
3939 "This package provides a data-driven test for the assumptions of quantile
3940 normalization using raw data such as objects that inherit eSets (e.g.
3941 ExpressionSet, MethylSet). Group level information about each sample (such as
3942 Tumor / Normal status) must also be provided because the test assesses if
3943 there are global differences in the distributions between the user-defined
3945 (license license:gpl3+)))
3947 (define-public r-yarn
3954 (uri (bioconductor-uri "yarn" version))
3957 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
3958 (build-system r-build-system)
3960 `(("r-biobase" ,r-biobase)
3961 ("r-biomart" ,r-biomart)
3962 ("r-downloader" ,r-downloader)
3963 ("r-edger" ,r-edger)
3964 ("r-gplots" ,r-gplots)
3965 ("r-limma" ,r-limma)
3966 ("r-matrixstats" ,r-matrixstats)
3967 ("r-preprocesscore" ,r-preprocesscore)
3968 ("r-quantro" ,r-quantro)
3969 ("r-rcolorbrewer" ,r-rcolorbrewer)
3970 ("r-readr" ,r-readr)))
3971 (home-page "https://bioconductor.org/packages/yarn/")
3972 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
3974 "Expedite large RNA-Seq analyses using a combination of previously
3975 developed tools. YARN is meant to make it easier for the user in performing
3976 basic mis-annotation quality control, filtering, and condition-aware
3977 normalization. YARN leverages many Bioconductor tools and statistical
3978 techniques to account for the large heterogeneity and sparsity found in very
3979 large RNA-seq experiments.")
3980 (license license:artistic2.0)))
3982 (define-public r-roar
3989 (uri (bioconductor-uri "roar" version))
3992 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
3993 (build-system r-build-system)
3995 `(("r-biocgenerics" ,r-biocgenerics)
3996 ("r-genomeinfodb" ,r-genomeinfodb)
3997 ("r-genomicalignments" ,r-genomicalignments)
3998 ("r-genomicranges" ,r-genomicranges)
3999 ("r-iranges" ,r-iranges)
4000 ("r-rtracklayer" ,r-rtracklayer)
4001 ("r-s4vectors" ,r-s4vectors)
4002 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4003 (home-page "https://github.com/vodkatad/roar/")
4004 (synopsis "Identify differential APA usage from RNA-seq alignments")
4006 "This package provides tools for identifying preferential usage of APA
4007 sites, comparing two biological conditions, starting from known alternative
4008 sites and alignments obtained from standard RNA-seq experiments.")
4009 (license license:gpl3)))
4011 (define-public r-xbseq
4018 (uri (bioconductor-uri "XBSeq" version))
4021 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4022 (properties `((upstream-name . "XBSeq")))
4023 (build-system r-build-system)
4025 `(("r-biobase" ,r-biobase)
4026 ("r-deseq2" ,r-deseq2)
4027 ("r-dplyr" ,r-dplyr)
4028 ("r-ggplot2" ,r-ggplot2)
4029 ("r-locfit" ,r-locfit)
4030 ("r-magrittr" ,r-magrittr)
4031 ("r-matrixstats" ,r-matrixstats)
4032 ("r-pracma" ,r-pracma)
4033 ("r-roar" ,r-roar)))
4034 (home-page "https://github.com/Liuy12/XBSeq")
4035 (synopsis "Test for differential expression for RNA-seq data")
4037 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4038 expression} (DE), where a statistical model was established based on the
4039 assumption that observed signals are the convolution of true expression
4040 signals and sequencing noises. The mapped reads in non-exonic regions are
4041 considered as sequencing noises, which follows a Poisson distribution. Given
4042 measurable observed signal and background noise from RNA-seq data, true
4043 expression signals, assuming governed by the negative binomial distribution,
4044 can be delineated and thus the accurate detection of differential expressed
4046 (license license:gpl3+)))
4048 (define-public r-massspecwavelet
4050 (name "r-massspecwavelet")
4055 (uri (bioconductor-uri "MassSpecWavelet" version))
4058 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4060 `((upstream-name . "MassSpecWavelet")))
4061 (build-system r-build-system)
4063 `(("r-waveslim" ,r-waveslim)))
4064 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4065 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4067 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4068 data mainly through the use of wavelet transforms. It supports peak detection
4069 based on @dfn{Continuous Wavelet Transform} (CWT).")
4070 (license license:lgpl2.0+)))
4072 (define-public r-xcms
4079 (uri (bioconductor-uri "xcms" version))
4082 "0bpbsda38v7y9072ixslh4pnx1yq6s5cff4x7d4h9kgns3bskvcv"))))
4083 (build-system r-build-system)
4085 `(("r-biobase" ,r-biobase)
4086 ("r-biocgenerics" ,r-biocgenerics)
4087 ("r-biocparallel" ,r-biocparallel)
4088 ("r-lattice" ,r-lattice)
4089 ("r-massspecwavelet" ,r-massspecwavelet)
4090 ("r-msnbase" ,r-msnbase)
4091 ("r-multtest" ,r-multtest)
4094 ("r-protgenerics" ,r-protgenerics)
4096 ("r-rcolorbrewer" ,r-rcolorbrewer)
4097 ("r-robustbase" ,r-robustbase)
4098 ("r-s4vectors" ,r-s4vectors)))
4099 (home-page "https://bioconductor.org/packages/xcms/")
4100 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4102 "This package provides a framework for processing and visualization of
4103 chromatographically separated and single-spectra mass spectral data. It
4104 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4105 data for high-throughput, untargeted analyte profiling.")
4106 (license license:gpl2+)))
4108 (define-public r-wrench
4115 (uri (bioconductor-uri "Wrench" version))
4118 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4119 (properties `((upstream-name . "Wrench")))
4120 (build-system r-build-system)
4122 `(("r-limma" ,r-limma)
4123 ("r-locfit" ,r-locfit)
4124 ("r-matrixstats" ,r-matrixstats)))
4125 (home-page "https://github.com/HCBravoLab/Wrench")
4126 (synopsis "Wrench normalization for sparse count data")
4128 "Wrench is a package for normalization sparse genomic count data, like
4129 that arising from 16s metagenomic surveys.")
4130 (license license:artistic2.0)))
4132 (define-public r-wiggleplotr
4134 (name "r-wiggleplotr")
4139 (uri (bioconductor-uri "wiggleplotr" version))
4142 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4143 (build-system r-build-system)
4145 `(("r-assertthat" ,r-assertthat)
4146 ("r-cowplot" ,r-cowplot)
4147 ("r-dplyr" ,r-dplyr)
4148 ("r-genomeinfodb" ,r-genomeinfodb)
4149 ("r-genomicranges" ,r-genomicranges)
4150 ("r-ggplot2" ,r-ggplot2)
4151 ("r-iranges" ,r-iranges)
4152 ("r-purrr" ,r-purrr)
4153 ("r-rtracklayer" ,r-rtracklayer)
4154 ("r-s4vectors" ,r-s4vectors)))
4155 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4156 (synopsis "Make read coverage plots from BigWig files")
4158 "This package provides tools to visualize read coverage from sequencing
4159 experiments together with genomic annotations (genes, transcripts, peaks).
4160 Introns of long transcripts can be rescaled to a fixed length for better
4161 visualization of exonic read coverage.")
4162 (license license:asl2.0)))
4164 (define-public r-widgettools
4166 (name "r-widgettools")
4171 (uri (bioconductor-uri "widgetTools" version))
4174 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4175 (properties `((upstream-name . "widgetTools")))
4176 (build-system r-build-system)
4177 (home-page "https://bioconductor.org/packages/widgetTools/")
4178 (synopsis "Tools for creating interactive tcltk widgets")
4180 "This packages contains tools to support the construction of tcltk
4182 ;; Any version of the LGPL.
4183 (license license:lgpl3+)))
4185 (define-public r-webbioc
4192 (uri (bioconductor-uri "webbioc" version))
4195 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4196 (build-system r-build-system)
4198 `(("netpbm" ,netpbm)
4201 `(("r-affy" ,r-affy)
4202 ("r-annaffy" ,r-annaffy)
4203 ("r-biobase" ,r-biobase)
4204 ("r-biocmanager" ,r-biocmanager)
4205 ("r-gcrma" ,r-gcrma)
4206 ("r-multtest" ,r-multtest)
4207 ("r-qvalue" ,r-qvalue)
4209 (home-page "https://www.bioconductor.org/")
4210 (synopsis "Bioconductor web interface")
4212 "This package provides an integrated web interface for doing microarray
4213 analysis using several of the Bioconductor packages. It is intended to be
4214 deployed as a centralized bioinformatics resource for use by many users.
4215 Currently only Affymetrix oligonucleotide analysis is supported.")
4216 (license license:gpl2+)))
4218 (define-public r-zfpkm
4225 (uri (bioconductor-uri "zFPKM" version))
4228 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4229 (properties `((upstream-name . "zFPKM")))
4230 (build-system r-build-system)
4232 `(("r-checkmate" ,r-checkmate)
4233 ("r-dplyr" ,r-dplyr)
4234 ("r-ggplot2" ,r-ggplot2)
4235 ("r-summarizedexperiment" ,r-summarizedexperiment)
4236 ("r-tidyr" ,r-tidyr)))
4237 (home-page "https://github.com/ronammar/zFPKM/")
4238 (synopsis "Functions to facilitate zFPKM transformations")
4240 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4241 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4243 (license license:gpl3)))
4245 (define-public r-rbowtie2
4252 (uri (bioconductor-uri "Rbowtie2" version))
4255 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4256 (properties `((upstream-name . "Rbowtie2")))
4257 (build-system r-build-system)
4260 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4261 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4263 "This package provides an R wrapper of the popular @code{bowtie2}
4264 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4265 rapid adapter trimming, identification, and read merging.")
4266 (license license:gpl3+)))
4268 (define-public r-progeny
4275 (uri (bioconductor-uri "progeny" version))
4278 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4279 (build-system r-build-system)
4280 (propagated-inputs `(("r-biobase" ,r-biobase)))
4281 (home-page "https://github.com/saezlab/progeny")
4282 (synopsis "Pathway responsive gene activity inference")
4284 "This package provides a function to infer pathway activity from gene
4285 expression. It contains the linear model inferred in the publication
4286 \"Perturbation-response genes reveal signaling footprints in cancer gene
4288 (license license:asl2.0)))
4290 (define-public r-arrmnormalization
4292 (name "r-arrmnormalization")
4297 (uri (bioconductor-uri "ARRmNormalization" version))
4300 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4302 `((upstream-name . "ARRmNormalization")))
4303 (build-system r-build-system)
4304 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4305 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4306 (synopsis "Adaptive robust regression normalization for methylation data")
4308 "This is a package to perform the @dfn{Adaptive Robust Regression
4309 method} (ARRm) for the normalization of methylation data from the Illumina
4310 Infinium HumanMethylation 450k assay.")
4311 (license license:artistic2.0)))
4313 (define-public r-biocfilecache
4315 (name "r-biocfilecache")
4320 (uri (bioconductor-uri "BiocFileCache" version))
4323 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4324 (properties `((upstream-name . "BiocFileCache")))
4325 (build-system r-build-system)
4327 `(("r-curl" ,r-curl)
4329 ("r-dbplyr" ,r-dbplyr)
4330 ("r-dplyr" ,r-dplyr)
4332 ("r-rappdirs" ,r-rappdirs)
4333 ("r-rsqlite" ,r-rsqlite)))
4334 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4335 (synopsis "Manage files across sessions")
4337 "This package creates a persistent on-disk cache of files that the user
4338 can add, update, and retrieve. It is useful for managing resources (such as
4339 custom Txdb objects) that are costly or difficult to create, web resources,
4340 and data files used across sessions.")
4341 (license license:artistic2.0)))