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 maths)
34 #:use-module (gnu packages pkg-config)
35 #:use-module (gnu packages statistics)
36 #:use-module (gnu packages web))
41 (define-public r-bsgenome-celegans-ucsc-ce6
43 (name "r-bsgenome-celegans-ucsc-ce6")
47 ;; We cannot use bioconductor-uri here because this tarball is
48 ;; located under "data/annotation/" instead of "bioc/".
49 (uri (string-append "https://www.bioconductor.org/packages/"
50 "release/data/annotation/src/contrib/"
51 "BSgenome.Celegans.UCSC.ce6_"
55 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
57 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
58 (build-system r-build-system)
59 ;; As this package provides little more than a very large data file it
60 ;; doesn't make sense to build substitutes.
61 (arguments `(#:substitutable? #f))
63 `(("r-bsgenome" ,r-bsgenome)))
65 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
66 (synopsis "Full genome sequences for Worm")
68 "This package provides full genome sequences for Caenorhabditis
69 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
71 (license license:artistic2.0)))
73 (define-public r-bsgenome-celegans-ucsc-ce10
75 (name "r-bsgenome-celegans-ucsc-ce10")
79 ;; We cannot use bioconductor-uri here because this tarball is
80 ;; located under "data/annotation/" instead of "bioc/".
81 (uri (string-append "https://www.bioconductor.org/packages/"
82 "release/data/annotation/src/contrib/"
83 "BSgenome.Celegans.UCSC.ce10_"
87 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
89 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
90 (build-system r-build-system)
91 ;; As this package provides little more than a very large data file it
92 ;; doesn't make sense to build substitutes.
93 (arguments `(#:substitutable? #f))
95 `(("r-bsgenome" ,r-bsgenome)))
97 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
98 (synopsis "Full genome sequences for Worm")
100 "This package provides full genome sequences for Caenorhabditis
101 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
103 (license license:artistic2.0)))
105 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
107 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
111 ;; We cannot use bioconductor-uri here because this tarball is
112 ;; located under "data/annotation/" instead of "bioc/".
113 (uri (string-append "https://www.bioconductor.org/packages/"
114 "release/data/annotation/src/contrib/"
115 "BSgenome.Dmelanogaster.UCSC.dm6_"
119 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
121 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
122 (build-system r-build-system)
123 ;; As this package provides little more than a very large data file it
124 ;; doesn't make sense to build substitutes.
125 (arguments `(#:substitutable? #f))
127 `(("r-bsgenome" ,r-bsgenome)))
129 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
130 (synopsis "Full genome sequences for Fly")
132 "This package provides full genome sequences for Drosophila
133 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
135 (license license:artistic2.0)))
137 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
139 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
143 ;; We cannot use bioconductor-uri here because this tarball is
144 ;; located under "data/annotation/" instead of "bioc/".
145 (uri (string-append "https://www.bioconductor.org/packages/"
146 "release/data/annotation/src/contrib/"
147 "BSgenome.Dmelanogaster.UCSC.dm3_"
151 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
153 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
154 (build-system r-build-system)
155 ;; As this package provides little more than a very large data file it
156 ;; doesn't make sense to build substitutes.
157 (arguments `(#:substitutable? #f))
159 `(("r-bsgenome" ,r-bsgenome)))
161 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
162 (synopsis "Full genome sequences for Fly")
164 "This package provides full genome sequences for Drosophila
165 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
166 Biostrings objects.")
167 (license license:artistic2.0)))
169 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
171 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
175 ;; We cannot use bioconductor-uri here because this tarball is
176 ;; located under "data/annotation/" instead of "bioc/".
177 (uri (string-append "http://www.bioconductor.org/packages/"
178 "release/data/annotation/src/contrib/"
179 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
183 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
185 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
186 (build-system r-build-system)
188 `(("r-bsgenome" ,r-bsgenome)
189 ("r-bsgenome-dmelanogaster-ucsc-dm3"
190 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
191 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
192 (synopsis "Full masked genome sequences for Fly")
194 "This package provides full masked genome sequences for Drosophila
195 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
196 Biostrings objects. The sequences are the same as in
197 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
198 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
199 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
200 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
201 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
202 (license license:artistic2.0)))
204 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
206 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
210 ;; We cannot use bioconductor-uri here because this tarball is
211 ;; located under "data/annotation/" instead of "bioc/".
212 (uri (string-append "https://www.bioconductor.org/packages/"
213 "release/data/annotation/src/contrib/"
214 "BSgenome.Hsapiens.1000genomes.hs37d5_"
218 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
220 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
221 (build-system r-build-system)
222 ;; As this package provides little more than a very large data file it
223 ;; doesn't make sense to build substitutes.
224 (arguments `(#:substitutable? #f))
226 `(("r-bsgenome" ,r-bsgenome)))
228 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
229 (synopsis "Full genome sequences for Homo sapiens")
231 "This package provides full genome sequences for Homo sapiens from
232 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
233 (license license:artistic2.0)))
235 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
237 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
241 ;; We cannot use bioconductor-uri here because this tarball is
242 ;; located under "data/annotation/" instead of "bioc/".
243 (uri (string-append "http://www.bioconductor.org/packages/"
244 "release/data/annotation/src/contrib/"
245 "BSgenome.Hsapiens.UCSC.hg19.masked_"
249 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
251 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
252 (build-system r-build-system)
254 `(("r-bsgenome" ,r-bsgenome)
255 ("r-bsgenome-hsapiens-ucsc-hg19"
256 ,r-bsgenome-hsapiens-ucsc-hg19)))
257 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
258 (synopsis "Full masked genome sequences for Homo sapiens")
260 "This package provides full genome sequences for Homo sapiens (Human) as
261 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
262 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
263 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
264 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
265 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
266 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
268 (license license:artistic2.0)))
270 (define-public r-bsgenome-mmusculus-ucsc-mm9
272 (name "r-bsgenome-mmusculus-ucsc-mm9")
276 ;; We cannot use bioconductor-uri here because this tarball is
277 ;; located under "data/annotation/" instead of "bioc/".
278 (uri (string-append "https://www.bioconductor.org/packages/"
279 "release/data/annotation/src/contrib/"
280 "BSgenome.Mmusculus.UCSC.mm9_"
284 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
286 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
287 (build-system r-build-system)
288 ;; As this package provides little more than a very large data file it
289 ;; doesn't make sense to build substitutes.
290 (arguments `(#:substitutable? #f))
292 `(("r-bsgenome" ,r-bsgenome)))
294 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
295 (synopsis "Full genome sequences for Mouse")
297 "This package provides full genome sequences for Mus musculus (Mouse) as
298 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
299 (license license:artistic2.0)))
301 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
303 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
307 ;; We cannot use bioconductor-uri here because this tarball is
308 ;; located under "data/annotation/" instead of "bioc/".
309 (uri (string-append "http://www.bioconductor.org/packages/"
310 "release/data/annotation/src/contrib/"
311 "BSgenome.Mmusculus.UCSC.mm9.masked_"
315 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
317 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
318 (build-system r-build-system)
320 `(("r-bsgenome" ,r-bsgenome)
321 ("r-bsgenome-mmusculus-ucsc-mm9"
322 ,r-bsgenome-mmusculus-ucsc-mm9)))
323 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
324 (synopsis "Full masked genome sequences for Mouse")
326 "This package provides full genome sequences for Mus musculus (Mouse) as
327 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
328 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
329 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
330 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
331 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
332 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
334 (license license:artistic2.0)))
336 (define-public r-bsgenome-mmusculus-ucsc-mm10
338 (name "r-bsgenome-mmusculus-ucsc-mm10")
342 ;; We cannot use bioconductor-uri here because this tarball is
343 ;; located under "data/annotation/" instead of "bioc/".
344 (uri (string-append "https://www.bioconductor.org/packages/"
345 "release/data/annotation/src/contrib/"
346 "BSgenome.Mmusculus.UCSC.mm10_"
350 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
352 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
353 (build-system r-build-system)
354 ;; As this package provides little more than a very large data file it
355 ;; doesn't make sense to build substitutes.
356 (arguments `(#:substitutable? #f))
358 `(("r-bsgenome" ,r-bsgenome)))
360 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
361 (synopsis "Full genome sequences for Mouse")
363 "This package provides full genome sequences for Mus
364 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
365 in Biostrings objects.")
366 (license license:artistic2.0)))
368 (define-public r-org-ce-eg-db
370 (name "r-org-ce-eg-db")
374 ;; We cannot use bioconductor-uri here because this tarball is
375 ;; located under "data/annotation/" instead of "bioc/".
376 (uri (string-append "https://www.bioconductor.org/packages/"
377 "release/data/annotation/src/contrib/"
378 "org.Ce.eg.db_" version ".tar.gz"))
381 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
383 `((upstream-name . "org.Ce.eg.db")))
384 (build-system r-build-system)
386 `(("r-annotationdbi" ,r-annotationdbi)))
387 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
388 (synopsis "Genome wide annotation for Worm")
390 "This package provides mappings from Entrez gene identifiers to various
391 annotations for the genome of the model worm Caenorhabditis elegans.")
392 (license license:artistic2.0)))
394 (define-public r-org-dm-eg-db
396 (name "r-org-dm-eg-db")
400 ;; We cannot use bioconductor-uri here because this tarball is
401 ;; located under "data/annotation/" instead of "bioc/".
402 (uri (string-append "https://www.bioconductor.org/packages/"
403 "release/data/annotation/src/contrib/"
404 "org.Dm.eg.db_" version ".tar.gz"))
407 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
409 `((upstream-name . "org.Dm.eg.db")))
410 (build-system r-build-system)
412 `(("r-annotationdbi" ,r-annotationdbi)))
413 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
414 (synopsis "Genome wide annotation for Fly")
416 "This package provides mappings from Entrez gene identifiers to various
417 annotations for the genome of the model fruit fly Drosophila melanogaster.")
418 (license license:artistic2.0)))
420 (define-public r-org-dr-eg-db
422 (name "r-org-dr-eg-db")
426 ;; We cannot use bioconductor-uri here because this tarball is
427 ;; located under "data/annotation/" instead of "bioc/".
428 (uri (string-append "https://www.bioconductor.org/packages/"
429 "release/data/annotation/src/contrib/"
430 "org.Dr.eg.db_" version ".tar.gz"))
433 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
435 `((upstream-name . "org.Dr.eg.db")))
436 (build-system r-build-system)
438 `(("r-annotationdbi" ,r-annotationdbi)))
439 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
440 (synopsis "Annotation for Zebrafish")
442 "This package provides genome wide annotations for Zebrafish, primarily
443 based on mapping using Entrez Gene identifiers.")
444 (license license:artistic2.0)))
446 (define-public r-org-hs-eg-db
448 (name "r-org-hs-eg-db")
452 ;; We cannot use bioconductor-uri here because this tarball is
453 ;; located under "data/annotation/" instead of "bioc/".
454 (uri (string-append "https://www.bioconductor.org/packages/"
455 "release/data/annotation/src/contrib/"
456 "org.Hs.eg.db_" version ".tar.gz"))
459 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
461 `((upstream-name . "org.Hs.eg.db")))
462 (build-system r-build-system)
464 `(("r-annotationdbi" ,r-annotationdbi)))
465 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
466 (synopsis "Genome wide annotation for Human")
468 "This package contains genome-wide annotations for Human, primarily based
469 on mapping using Entrez Gene identifiers.")
470 (license license:artistic2.0)))
472 (define-public r-org-mm-eg-db
474 (name "r-org-mm-eg-db")
478 ;; We cannot use bioconductor-uri here because this tarball is
479 ;; located under "data/annotation/" instead of "bioc/".
480 (uri (string-append "https://www.bioconductor.org/packages/"
481 "release/data/annotation/src/contrib/"
482 "org.Mm.eg.db_" version ".tar.gz"))
485 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
487 `((upstream-name . "org.Mm.eg.db")))
488 (build-system r-build-system)
490 `(("r-annotationdbi" ,r-annotationdbi)))
491 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
492 (synopsis "Genome wide annotation for Mouse")
494 "This package provides mappings from Entrez gene identifiers to various
495 annotations for the genome of the model mouse Mus musculus.")
496 (license license:artistic2.0)))
498 (define-public r-bsgenome-hsapiens-ucsc-hg19
500 (name "r-bsgenome-hsapiens-ucsc-hg19")
504 ;; We cannot use bioconductor-uri here because this tarball is
505 ;; located under "data/annotation/" instead of "bioc/".
506 (uri (string-append "https://www.bioconductor.org/packages/"
507 "release/data/annotation/src/contrib/"
508 "BSgenome.Hsapiens.UCSC.hg19_"
512 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
514 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
515 (build-system r-build-system)
516 ;; As this package provides little more than a very large data file it
517 ;; doesn't make sense to build substitutes.
518 (arguments `(#:substitutable? #f))
520 `(("r-bsgenome" ,r-bsgenome)))
522 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
523 (synopsis "Full genome sequences for Homo sapiens")
525 "This package provides full genome sequences for Homo sapiens as provided
526 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
527 (license license:artistic2.0)))
529 (define-public r-genelendatabase
531 (name "r-genelendatabase")
536 ;; We cannot use bioconductor-uri here because this tarball is
537 ;; located under "data/experiment/" instead of "bioc/".
538 (uri (string-append "https://bioconductor.org/packages/"
539 "release/data/experiment/src/contrib"
540 "/geneLenDataBase_" version ".tar.gz"))
543 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
545 `((upstream-name . "geneLenDataBase")))
546 (build-system r-build-system)
548 `(("r-rtracklayer" ,r-rtracklayer)
549 ("r-genomicfeatures" ,r-genomicfeatures)))
550 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
551 (synopsis "Lengths of mRNA transcripts for a number of genomes")
553 "This package provides the lengths of mRNA transcripts for a number of
554 genomes and gene ID formats, largely based on the UCSC table browser.")
555 (license license:lgpl2.0+)))
557 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
559 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
563 ;; We cannot use bioconductor-uri here because this tarball is
564 ;; located under "data/annotation/" instead of "bioc/".
565 (uri (string-append "https://bioconductor.org/packages/"
566 "release/data/annotation/src/contrib"
567 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
571 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
573 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
574 (build-system r-build-system)
575 ;; As this package provides little more than a very large data file it
576 ;; doesn't make sense to build substitutes.
577 (arguments `(#:substitutable? #f))
579 `(("r-genomicfeatures" ,r-genomicfeatures)))
581 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
582 (synopsis "Annotation package for human genome in TxDb format")
584 "This package provides an annotation database of Homo sapiens genome
585 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
586 track. The database is exposed as a @code{TxDb} object.")
587 (license license:artistic2.0)))
589 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
591 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
595 ;; We cannot use bioconductor-uri here because this tarball is
596 ;; located under "data/annotation/" instead of "bioc/".
597 (uri (string-append "https://bioconductor.org/packages/"
598 "release/data/annotation/src/contrib"
599 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
603 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
605 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
606 (build-system r-build-system)
608 `(("r-genomicfeatures" ,r-genomicfeatures)
609 ("r-annotationdbi" ,r-annotationdbi)))
611 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
612 (synopsis "Annotation package for mouse genome in TxDb format")
614 "This package provides an annotation database of Mouse genome data. It
615 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
616 database is exposed as a @code{TxDb} object.")
617 (license license:artistic2.0)))
619 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
621 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
625 ;; We cannot use bioconductor-uri here because this tarball is
626 ;; located under "data/annotation/" instead of "bioc/".
627 (uri (string-append "https://www.bioconductor.org/packages/"
628 "release/data/annotation/src/contrib/"
629 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
633 "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
635 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
636 (build-system r-build-system)
637 ;; As this package provides little more than a very large data file it
638 ;; doesn't make sense to build substitutes.
639 (arguments `(#:substitutable? #f))
641 `(("r-bsgenome" ,r-bsgenome)
642 ("r-genomicfeatures" ,r-genomicfeatures)
643 ("r-annotationdbi" ,r-annotationdbi)))
645 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
646 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
648 "This package loads a TxDb object, which is an R interface to
649 prefabricated databases contained in this package. This package provides
650 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
651 based on the knownGene track.")
652 (license license:artistic2.0)))
654 (define-public r-fdb-infiniummethylation-hg19
656 (name "r-fdb-infiniummethylation-hg19")
660 ;; We cannot use bioconductor-uri here because this tarball is
661 ;; located under "data/annotation/" instead of "bioc/".
662 (uri (string-append "https://www.bioconductor.org/packages/"
663 "release/data/annotation/src/contrib/"
664 "FDb.InfiniumMethylation.hg19_"
668 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
670 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
671 (build-system r-build-system)
673 `(("r-biostrings" ,r-biostrings)
674 ("r-genomicfeatures" ,r-genomicfeatures)
675 ("r-annotationdbi" ,r-annotationdbi)
676 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
677 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
678 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
679 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
681 "This is an annotation package for Illumina Infinium DNA methylation
682 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
684 (license license:artistic2.0)))
686 (define-public r-illuminahumanmethylationepicmanifest
688 (name "r-illuminahumanmethylationepicmanifest")
692 ;; We cannot use bioconductor-uri here because this tarball is
693 ;; located under "data/annotation/" instead of "bioc/".
694 (uri (string-append "https://www.bioconductor.org/packages/"
695 "release/data/annotation/src/contrib/"
696 "IlluminaHumanMethylationEPICmanifest_"
700 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
702 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
703 (build-system r-build-system)
705 `(("r-minfi" ,r-minfi)))
706 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
707 (synopsis "Manifest for Illumina's EPIC methylation arrays")
709 "This is a manifest package for Illumina's EPIC methylation arrays.")
710 (license license:artistic2.0)))
712 (define-public r-do-db
718 ;; We cannot use bioconductor-uri here because this tarball is
719 ;; located under "data/annotation/" instead of "bioc/".
720 (uri (string-append "https://www.bioconductor.org/packages/"
721 "release/data/annotation/src/contrib/"
722 "DO.db_" version ".tar.gz"))
725 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
727 `((upstream-name . "DO.db")))
728 (build-system r-build-system)
730 `(("r-annotationdbi" ,r-annotationdbi)))
731 (home-page "https://www.bioconductor.org/packages/DO.db/")
732 (synopsis "Annotation maps describing the entire Disease Ontology")
734 "This package provides a set of annotation maps describing the entire
736 (license license:artistic2.0)))
741 (define-public r-hsmmsinglecell
743 (name "r-hsmmsinglecell")
747 ;; We cannot use bioconductor-uri here because this tarball is
748 ;; located under "data/experiment/" instead of "bioc/".
749 (uri (string-append "https://www.bioconductor.org/packages/"
750 "release/data/experiment/src/contrib/"
751 "HSMMSingleCell_" version ".tar.gz"))
754 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
756 `((upstream-name . "HSMMSingleCell")))
757 (build-system r-build-system)
758 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
759 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
761 "Skeletal myoblasts undergo a well-characterized sequence of
762 morphological and transcriptional changes during differentiation. In this
763 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
764 under high mitogen conditions (GM) and then differentiated by switching to
765 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
766 hundred cells taken over a time-course of serum-induced differentiation.
767 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
768 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
769 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
770 which were then sequenced to a depth of ~4 million reads per library,
771 resulting in a complete gene expression profile for each cell.")
772 (license license:artistic2.0)))
777 (define-public r-biocgenerics
779 (name "r-biocgenerics")
783 (uri (bioconductor-uri "BiocGenerics" version))
786 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
788 `((upstream-name . "BiocGenerics")))
789 (build-system r-build-system)
790 (home-page "https://bioconductor.org/packages/BiocGenerics")
791 (synopsis "S4 generic functions for Bioconductor")
793 "This package provides S4 generic functions needed by many Bioconductor
795 (license license:artistic2.0)))
797 (define-public r-annotate
804 (uri (bioconductor-uri "annotate" version))
807 "0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"))))
808 (build-system r-build-system)
810 `(("r-annotationdbi" ,r-annotationdbi)
811 ("r-biobase" ,r-biobase)
812 ("r-biocgenerics" ,r-biocgenerics)
816 ("r-xtable" ,r-xtable)))
818 "https://bioconductor.org/packages/annotate")
819 (synopsis "Annotation for microarrays")
820 (description "This package provides R environments for the annotation of
822 (license license:artistic2.0)))
824 (define-public r-hpar
831 (uri (bioconductor-uri "hpar" version))
834 "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
835 (build-system r-build-system)
836 (home-page "https://bioconductor.org/packages/hpar/")
837 (synopsis "Human Protein Atlas in R")
838 (description "This package provides a simple interface to and data from
839 the Human Protein Atlas project.")
840 (license license:artistic2.0)))
842 (define-public r-regioner
849 (uri (bioconductor-uri "regioneR" version))
852 "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
853 (properties `((upstream-name . "regioneR")))
854 (build-system r-build-system)
856 `(("r-biostrings" ,r-biostrings)
857 ("r-bsgenome" ,r-bsgenome)
858 ("r-genomeinfodb" ,r-genomeinfodb)
859 ("r-genomicranges" ,r-genomicranges)
860 ("r-iranges" ,r-iranges)
861 ("r-memoise" ,r-memoise)
862 ("r-rtracklayer" ,r-rtracklayer)
863 ("r-s4vectors" ,r-s4vectors)))
864 (home-page "https://bioconductor.org/packages/regioneR/")
865 (synopsis "Association analysis of genomic regions")
866 (description "This package offers a statistical framework based on
867 customizable permutation tests to assess the association between genomic
868 region sets and other genomic features.")
869 (license license:artistic2.0)))
871 (define-public r-geneplotter
873 (name "r-geneplotter")
878 (uri (bioconductor-uri "geneplotter" version))
881 "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
882 (build-system r-build-system)
884 `(("r-annotate" ,r-annotate)
885 ("r-annotationdbi" ,r-annotationdbi)
886 ("r-biobase" ,r-biobase)
887 ("r-biocgenerics" ,r-biocgenerics)
888 ("r-lattice" ,r-lattice)
889 ("r-rcolorbrewer" ,r-rcolorbrewer)))
890 (home-page "https://bioconductor.org/packages/geneplotter")
891 (synopsis "Graphics functions for genomic data")
893 "This package provides functions for plotting genomic data.")
894 (license license:artistic2.0)))
896 (define-public r-qvalue
903 (uri (bioconductor-uri "qvalue" version))
906 "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
907 (build-system r-build-system)
909 `(("r-ggplot2" ,r-ggplot2)
910 ("r-reshape2" ,r-reshape2)))
911 (home-page "http://github.com/jdstorey/qvalue")
912 (synopsis "Q-value estimation for false discovery rate control")
914 "This package takes a list of p-values resulting from the simultaneous
915 testing of many hypotheses and estimates their q-values and local @dfn{false
916 discovery rate} (FDR) values. The q-value of a test measures the proportion
917 of false positives incurred when that particular test is called significant.
918 The local FDR measures the posterior probability the null hypothesis is true
919 given the test's p-value. Various plots are automatically generated, allowing
920 one to make sensible significance cut-offs. The software can be applied to
921 problems in genomics, brain imaging, astrophysics, and data mining.")
922 ;; Any version of the LGPL.
923 (license license:lgpl3+)))
925 (define-public r-diffbind
932 (uri (bioconductor-uri "DiffBind" version))
935 "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
936 (properties `((upstream-name . "DiffBind")))
937 (build-system r-build-system)
942 ("r-biocparallel" ,r-biocparallel)
943 ("r-deseq2" ,r-deseq2)
946 ("r-genomicalignments" ,r-genomicalignments)
947 ("r-genomicranges" ,r-genomicranges)
948 ("r-ggplot2" ,r-ggplot2)
949 ("r-ggrepel" ,r-ggrepel)
950 ("r-gplots" ,r-gplots)
951 ("r-iranges" ,r-iranges)
952 ("r-lattice" ,r-lattice)
954 ("r-locfit" ,r-locfit)
955 ("r-rcolorbrewer" , r-rcolorbrewer)
957 ("r-rsamtools" ,r-rsamtools)
958 ("r-s4vectors" ,r-s4vectors)
959 ("r-summarizedexperiment" ,r-summarizedexperiment)
960 ("r-systempiper" ,r-systempiper)
961 ("r-zlibbioc" ,r-zlibbioc)))
962 (home-page "http://bioconductor.org/packages/DiffBind")
963 (synopsis "Differential binding analysis of ChIP-Seq peak data")
965 "This package computes differentially bound sites from multiple
966 ChIP-seq experiments using affinity (quantitative) data. Also enables
967 occupancy (overlap) analysis and plotting functions.")
968 (license license:artistic2.0)))
970 (define-public r-ripseeker
977 (uri (bioconductor-uri "RIPSeeker" version))
980 "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
981 (properties `((upstream-name . "RIPSeeker")))
982 (build-system r-build-system)
984 `(("r-s4vectors" ,r-s4vectors)
985 ("r-iranges" ,r-iranges)
986 ("r-genomicranges" ,r-genomicranges)
987 ("r-summarizedexperiment" ,r-summarizedexperiment)
988 ("r-rsamtools" ,r-rsamtools)
989 ("r-genomicalignments" ,r-genomicalignments)
990 ("r-rtracklayer" ,r-rtracklayer)))
991 (home-page "http://bioconductor.org/packages/RIPSeeker")
993 "Identifying protein-associated transcripts from RIP-seq experiments")
995 "This package infers and discriminates RIP peaks from RIP-seq alignments
996 using two-state HMM with negative binomial emission probability. While
997 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
998 a suite of bioinformatics tools integrated within this self-contained software
999 package comprehensively addressing issues ranging from post-alignments
1000 processing to visualization and annotation.")
1001 (license license:gpl2)))
1003 (define-public r-multtest
1010 (uri (bioconductor-uri "multtest" version))
1013 "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
1014 (build-system r-build-system)
1016 `(("r-survival" ,r-survival)
1017 ("r-biocgenerics" ,r-biocgenerics)
1018 ("r-biobase" ,r-biobase)
1019 ("r-mass" ,r-mass)))
1020 (home-page "http://bioconductor.org/packages/multtest")
1021 (synopsis "Resampling-based multiple hypothesis testing")
1023 "This package can do non-parametric bootstrap and permutation
1024 resampling-based multiple testing procedures (including empirical Bayes
1025 methods) for controlling the family-wise error rate (FWER), generalized
1026 family-wise error rate (gFWER), tail probability of the proportion of
1027 false positives (TPPFP), and false discovery rate (FDR). Several choices
1028 of bootstrap-based null distribution are implemented (centered, centered
1029 and scaled, quantile-transformed). Single-step and step-wise methods are
1030 available. Tests based on a variety of T- and F-statistics (including
1031 T-statistics based on regression parameters from linear and survival models
1032 as well as those based on correlation parameters) are included. When probing
1033 hypotheses with T-statistics, users may also select a potentially faster null
1034 distribution which is multivariate normal with mean zero and variance
1035 covariance matrix derived from the vector influence function. Results are
1036 reported in terms of adjusted P-values, confidence regions and test statistic
1037 cutoffs. The procedures are directly applicable to identifying differentially
1038 expressed genes in DNA microarray experiments.")
1039 (license license:lgpl3)))
1041 (define-public r-graph
1047 (uri (bioconductor-uri "graph" version))
1050 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
1051 (build-system r-build-system)
1053 `(("r-biocgenerics" ,r-biocgenerics)))
1054 (home-page "https://bioconductor.org/packages/graph")
1055 (synopsis "Handle graph data structures in R")
1057 "This package implements some simple graph handling capabilities for R.")
1058 (license license:artistic2.0)))
1060 (define-public r-codedepends
1062 (name "r-codedepends")
1067 (uri (cran-uri "CodeDepends" version))
1070 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1071 (properties `((upstream-name . "CodeDepends")))
1072 (build-system r-build-system)
1074 `(("r-codetools" ,r-codetools)
1075 ("r-graph" ,r-graph)
1077 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1078 (synopsis "Analysis of R code for reproducible research and code comprehension")
1080 "This package provides tools for analyzing R expressions or blocks of
1081 code and determining the dependencies between them. It focuses on R scripts,
1082 but can be used on the bodies of functions. There are many facilities
1083 including the ability to summarize or get a high-level view of code,
1084 determining dependencies between variables, code improvement suggestions.")
1085 ;; Any version of the GPL
1086 (license (list license:gpl2+ license:gpl3+))))
1088 (define-public r-chippeakanno
1090 (name "r-chippeakanno")
1095 (uri (bioconductor-uri "ChIPpeakAnno" version))
1098 "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
1099 (properties `((upstream-name . "ChIPpeakAnno")))
1100 (build-system r-build-system)
1102 `(("r-biocgenerics" ,r-biocgenerics)
1103 ("r-biocmanager" ,r-biocmanager)
1104 ("r-biostrings" ,r-biostrings)
1105 ("r-delayedarray" ,r-delayedarray)
1106 ("r-go-db" ,r-go-db)
1107 ("r-biomart" ,r-biomart)
1108 ("r-bsgenome" ,r-bsgenome)
1109 ("r-genomicfeatures" ,r-genomicfeatures)
1110 ("r-genomicranges" ,r-genomicranges)
1111 ("r-genomeinfodb" ,r-genomeinfodb)
1112 ("r-iranges" ,r-iranges)
1113 ("r-matrixstats" ,r-matrixstats)
1114 ("r-annotationdbi" ,r-annotationdbi)
1115 ("r-limma" ,r-limma)
1116 ("r-multtest" ,r-multtest)
1118 ("r-graph" ,r-graph)
1119 ("r-regioner" ,r-regioner)
1121 ("r-ensembldb" ,r-ensembldb)
1122 ("r-biobase" ,r-biobase)
1123 ("r-s4vectors" ,r-s4vectors)
1124 ("r-seqinr" ,r-seqinr)
1126 ("r-genomicalignments" ,r-genomicalignments)
1127 ("r-summarizedexperiment" ,r-summarizedexperiment)
1128 ("r-rsamtools" ,r-rsamtools)
1129 ("r-venndiagram" ,r-venndiagram)))
1130 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1131 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1133 "The package includes functions to retrieve the sequences around the peak,
1134 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1135 custom features such as most conserved elements and other transcription factor
1136 binding sites supplied by users. Starting 2.0.5, new functions have been added
1137 for finding the peaks with bi-directional promoters with summary statistics
1138 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1139 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1140 enrichedGO (addGeneIDs).")
1141 (license license:gpl2+)))
1143 (define-public r-marray
1149 (uri (bioconductor-uri "marray" version))
1151 (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
1152 (build-system r-build-system)
1154 `(("r-limma" ,r-limma)))
1155 (home-page "http://bioconductor.org/packages/marray")
1156 (synopsis "Exploratory analysis for two-color spotted microarray data")
1157 (description "This package contains class definitions for two-color spotted
1158 microarray data. It also includes fuctions for data input, diagnostic plots,
1159 normalization and quality checking.")
1160 (license license:lgpl2.0+)))
1162 (define-public r-cghbase
1168 (uri (bioconductor-uri "CGHbase" version))
1170 (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
1171 (properties `((upstream-name . "CGHbase")))
1172 (build-system r-build-system)
1174 `(("r-biobase" ,r-biobase)
1175 ("r-marray" ,r-marray)))
1176 (home-page "http://bioconductor.org/packages/CGHbase")
1177 (synopsis "Base functions and classes for arrayCGH data analysis")
1178 (description "This package contains functions and classes that are needed by
1179 the @code{arrayCGH} packages.")
1180 (license license:gpl2+)))
1182 (define-public r-cghcall
1188 (uri (bioconductor-uri "CGHcall" version))
1190 (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
1191 (properties `((upstream-name . "CGHcall")))
1192 (build-system r-build-system)
1194 `(("r-biobase" ,r-biobase)
1195 ("r-cghbase" ,r-cghbase)
1196 ("r-impute" ,r-impute)
1197 ("r-dnacopy" ,r-dnacopy)
1198 ("r-snowfall" ,r-snowfall)))
1199 (home-page "http://bioconductor.org/packages/CGHcall")
1200 (synopsis "Base functions and classes for arrayCGH data analysis")
1201 (description "This package contains functions and classes that are needed by
1202 @code{arrayCGH} packages.")
1203 (license license:gpl2+)))
1205 (define-public r-qdnaseq
1211 (uri (bioconductor-uri "QDNAseq" version))
1213 (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
1214 (properties `((upstream-name . "QDNAseq")))
1215 (build-system r-build-system)
1217 `(("r-biobase" ,r-biobase)
1218 ("r-biocparallel" ,r-biocparallel)
1219 ("r-cghbase" ,r-cghbase)
1220 ("r-cghcall" ,r-cghcall)
1221 ("r-dnacopy" ,r-dnacopy)
1222 ("r-genomicranges" ,r-genomicranges)
1223 ("r-iranges" ,r-iranges)
1224 ("r-matrixstats" ,r-matrixstats)
1225 ("r-r-utils" ,r-r-utils)
1226 ("r-rsamtools" ,r-rsamtools)))
1227 (home-page "http://bioconductor.org/packages/QDNAseq")
1228 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1229 (description "The genome is divided into non-overlapping fixed-sized bins,
1230 number of sequence reads in each counted, adjusted with a simultaneous
1231 two-dimensional loess correction for sequence mappability and GC content, and
1232 filtered to remove spurious regions in the genome. Downstream steps of
1233 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1235 (license license:gpl2+)))
1237 (define-public r-bayseq
1244 (uri (bioconductor-uri "baySeq" version))
1247 "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
1248 (properties `((upstream-name . "baySeq")))
1249 (build-system r-build-system)
1251 `(("r-abind" ,r-abind)
1252 ("r-edger" ,r-edger)
1253 ("r-genomicranges" ,r-genomicranges)))
1254 (home-page "https://bioconductor.org/packages/baySeq/")
1255 (synopsis "Bayesian analysis of differential expression patterns in count data")
1257 "This package identifies differential expression in high-throughput count
1258 data, such as that derived from next-generation sequencing machines,
1259 calculating estimated posterior likelihoods of differential expression (or
1260 more complex hypotheses) via empirical Bayesian methods.")
1261 (license license:gpl3)))
1263 (define-public r-chipcomp
1270 (uri (bioconductor-uri "ChIPComp" version))
1273 "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
1274 (properties `((upstream-name . "ChIPComp")))
1275 (build-system r-build-system)
1277 `(("r-biocgenerics" ,r-biocgenerics)
1278 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1279 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1280 ("r-genomeinfodb" ,r-genomeinfodb)
1281 ("r-genomicranges" ,r-genomicranges)
1282 ("r-iranges" ,r-iranges)
1283 ("r-limma" ,r-limma)
1284 ("r-rsamtools" ,r-rsamtools)
1285 ("r-rtracklayer" ,r-rtracklayer)
1286 ("r-s4vectors" ,r-s4vectors)))
1287 (home-page "https://bioconductor.org/packages/ChIPComp")
1288 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1290 "ChIPComp implements a statistical method for quantitative comparison of
1291 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1292 sites across multiple conditions considering matching control in ChIP-seq
1294 ;; Any version of the GPL.
1295 (license license:gpl3+)))
1297 (define-public r-riboprofiling
1299 (name "r-riboprofiling")
1304 (uri (bioconductor-uri "RiboProfiling" version))
1307 "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
1308 (properties `((upstream-name . "RiboProfiling")))
1309 (build-system r-build-system)
1311 `(("r-biocgenerics" ,r-biocgenerics)
1312 ("r-biostrings" ,r-biostrings)
1313 ("r-data-table" ,r-data-table)
1314 ("r-genomeinfodb" ,r-genomeinfodb)
1315 ("r-genomicalignments" ,r-genomicalignments)
1316 ("r-genomicfeatures" ,r-genomicfeatures)
1317 ("r-genomicranges" ,r-genomicranges)
1318 ("r-ggbio" ,r-ggbio)
1319 ("r-ggplot2" ,r-ggplot2)
1320 ("r-iranges" ,r-iranges)
1322 ("r-reshape2" ,r-reshape2)
1323 ("r-rsamtools" ,r-rsamtools)
1324 ("r-rtracklayer" ,r-rtracklayer)
1325 ("r-s4vectors" ,r-s4vectors)
1326 ("r-sqldf" ,r-sqldf)))
1327 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1328 (synopsis "Ribosome profiling data analysis")
1329 (description "Starting with a BAM file, this package provides the
1330 necessary functions for quality assessment, read start position recalibration,
1331 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1332 of count data: pairs, log fold-change, codon frequency and coverage
1333 assessment, principal component analysis on codon coverage.")
1334 (license license:gpl3)))
1336 (define-public r-riboseqr
1343 (uri (bioconductor-uri "riboSeqR" version))
1346 "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
1347 (properties `((upstream-name . "riboSeqR")))
1348 (build-system r-build-system)
1350 `(("r-abind" ,r-abind)
1351 ("r-bayseq" ,r-bayseq)
1352 ("r-genomeinfodb" ,r-genomeinfodb)
1353 ("r-genomicranges" ,r-genomicranges)
1354 ("r-iranges" ,r-iranges)
1355 ("r-rsamtools" ,r-rsamtools)
1356 ("r-seqlogo" ,r-seqlogo)))
1357 (home-page "https://bioconductor.org/packages/riboSeqR/")
1358 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1360 "This package provides plotting functions, frameshift detection and
1361 parsing of genetic sequencing data from ribosome profiling experiments.")
1362 (license license:gpl3)))
1364 (define-public r-interactionset
1366 (name "r-interactionset")
1371 (uri (bioconductor-uri "InteractionSet" version))
1374 "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
1376 `((upstream-name . "InteractionSet")))
1377 (build-system r-build-system)
1379 `(("r-biocgenerics" ,r-biocgenerics)
1380 ("r-genomeinfodb" ,r-genomeinfodb)
1381 ("r-genomicranges" ,r-genomicranges)
1382 ("r-iranges" ,r-iranges)
1383 ("r-matrix" ,r-matrix)
1385 ("r-s4vectors" ,r-s4vectors)
1386 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1387 (home-page "https://bioconductor.org/packages/InteractionSet")
1388 (synopsis "Base classes for storing genomic interaction data")
1390 "This packages provides the @code{GInteractions},
1391 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1392 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1394 (license license:gpl3)))
1396 (define-public r-genomicinteractions
1398 (name "r-genomicinteractions")
1403 (uri (bioconductor-uri "GenomicInteractions" version))
1406 "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
1408 `((upstream-name . "GenomicInteractions")))
1409 (build-system r-build-system)
1411 `(("r-biobase" ,r-biobase)
1412 ("r-biocgenerics" ,r-biocgenerics)
1413 ("r-data-table" ,r-data-table)
1414 ("r-dplyr" ,r-dplyr)
1415 ("r-genomeinfodb" ,r-genomeinfodb)
1416 ("r-genomicranges" ,r-genomicranges)
1417 ("r-ggplot2" ,r-ggplot2)
1418 ("r-gridextra" ,r-gridextra)
1420 ("r-igraph" ,r-igraph)
1421 ("r-interactionset" ,r-interactionset)
1422 ("r-iranges" ,r-iranges)
1423 ("r-rsamtools" ,r-rsamtools)
1424 ("r-rtracklayer" ,r-rtracklayer)
1425 ("r-s4vectors" ,r-s4vectors)
1426 ("r-stringr" ,r-stringr)))
1427 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1428 (synopsis "R package for handling genomic interaction data")
1430 "This R package provides tools for handling genomic interaction data,
1431 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1432 information and producing various plots and statistics.")
1433 (license license:gpl3)))
1435 (define-public r-ctc
1442 (uri (bioconductor-uri "ctc" version))
1445 "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
1446 (build-system r-build-system)
1447 (propagated-inputs `(("r-amap" ,r-amap)))
1448 (home-page "https://bioconductor.org/packages/ctc/")
1449 (synopsis "Cluster and tree conversion")
1451 "This package provides tools for exporting and importing classification
1452 trees and clusters to other programs.")
1453 (license license:gpl2)))
1455 (define-public r-goseq
1462 (uri (bioconductor-uri "goseq" version))
1465 "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
1466 (build-system r-build-system)
1468 `(("r-annotationdbi" ,r-annotationdbi)
1469 ("r-biasedurn" ,r-biasedurn)
1470 ("r-biocgenerics" ,r-biocgenerics)
1471 ("r-genelendatabase" ,r-genelendatabase)
1472 ("r-go-db" ,r-go-db)
1473 ("r-mgcv" ,r-mgcv)))
1474 (home-page "https://bioconductor.org/packages/goseq/")
1475 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1477 "This package provides tools to detect Gene Ontology and/or other user
1478 defined categories which are over/under represented in RNA-seq data.")
1479 (license license:lgpl2.0+)))
1481 (define-public r-glimma
1488 (uri (bioconductor-uri "Glimma" version))
1491 "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
1492 (properties `((upstream-name . "Glimma")))
1493 (build-system r-build-system)
1495 `(("r-edger" ,r-edger)
1496 ("r-jsonlite" ,r-jsonlite)
1497 ("r-s4vectors" ,r-s4vectors)))
1498 (home-page "https://github.com/Shians/Glimma")
1499 (synopsis "Interactive HTML graphics")
1501 "This package generates interactive visualisations for analysis of
1502 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1503 HTML page. The interactions are built on top of the popular static
1504 representations of analysis results in order to provide additional
1506 (license license:lgpl3)))
1508 (define-public r-rots
1515 (uri (bioconductor-uri "ROTS" version))
1518 "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
1519 (properties `((upstream-name . "ROTS")))
1520 (build-system r-build-system)
1522 `(("r-biobase" ,r-biobase)
1523 ("r-rcpp" ,r-rcpp)))
1524 (home-page "https://bioconductor.org/packages/ROTS/")
1525 (synopsis "Reproducibility-Optimized Test Statistic")
1527 "This package provides tools for calculating the
1528 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1530 (license license:gpl2+)))
1532 (define-public r-plgem
1539 (uri (bioconductor-uri "plgem" version))
1542 "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
1543 (build-system r-build-system)
1545 `(("r-biobase" ,r-biobase)
1546 ("r-mass" ,r-mass)))
1547 (home-page "http://www.genopolis.it")
1548 (synopsis "Detect differential expression in microarray and proteomics datasets")
1550 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1551 model the variance-versus-mean dependence that exists in a variety of
1552 genome-wide datasets, including microarray and proteomics data. The use of
1553 PLGEM has been shown to improve the detection of differentially expressed
1554 genes or proteins in these datasets.")
1555 (license license:gpl2)))
1557 (define-public r-inspect
1564 (uri (bioconductor-uri "INSPEcT" version))
1567 "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
1568 (properties `((upstream-name . "INSPEcT")))
1569 (build-system r-build-system)
1571 `(("r-biobase" ,r-biobase)
1572 ("r-biocgenerics" ,r-biocgenerics)
1573 ("r-biocparallel" ,r-biocparallel)
1574 ("r-deseq2" ,r-deseq2)
1575 ("r-desolve" ,r-desolve)
1576 ("r-genomicalignments" ,r-genomicalignments)
1577 ("r-genomicfeatures" ,r-genomicfeatures)
1578 ("r-genomicranges" ,r-genomicranges)
1579 ("r-iranges" ,r-iranges)
1580 ("r-plgem" ,r-plgem)
1581 ("r-preprocesscore" ,r-preprocesscore)
1583 ("r-rootsolve" ,r-rootsolve)
1584 ("r-rsamtools" ,r-rsamtools)
1585 ("r-s4vectors" ,r-s4vectors)
1586 ("r-shiny" ,r-shiny)
1587 ("r-summarizedexperiment" ,r-summarizedexperiment)
1588 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1589 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1590 (home-page "https://bioconductor.org/packages/INSPEcT")
1591 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1593 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1594 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1595 order to evaluate synthesis, processing and degradation rates and assess via
1596 modeling the rates that determines changes in mature mRNA levels.")
1597 (license license:gpl2)))
1599 (define-public r-dnabarcodes
1601 (name "r-dnabarcodes")
1606 (uri (bioconductor-uri "DNABarcodes" version))
1609 "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
1610 (properties `((upstream-name . "DNABarcodes")))
1611 (build-system r-build-system)
1614 ("r-matrix" ,r-matrix)
1615 ("r-rcpp" ,r-rcpp)))
1616 (home-page "https://bioconductor.org/packages/DNABarcodes")
1617 (synopsis "Create and analyze DNA barcodes")
1619 "This package offers tools to create DNA barcode sets capable of
1620 correcting insertion, deletion, and substitution errors. Existing barcodes
1621 can be analyzed regarding their minimal, maximal and average distances between
1622 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1623 demultiplexed, i.e. assigned to their original reference barcode.")
1624 (license license:gpl2)))
1626 (define-public r-ruvseq
1633 (uri (bioconductor-uri "RUVSeq" version))
1636 "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
1637 (properties `((upstream-name . "RUVSeq")))
1638 (build-system r-build-system)
1640 `(("r-biobase" ,r-biobase)
1641 ("r-edaseq" ,r-edaseq)
1642 ("r-edger" ,r-edger)
1643 ("r-mass" ,r-mass)))
1644 (home-page "https://github.com/drisso/RUVSeq")
1645 (synopsis "Remove unwanted variation from RNA-Seq data")
1647 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1648 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1650 (license license:artistic2.0)))
1652 (define-public r-biocneighbors
1654 (name "r-biocneighbors")
1659 (uri (bioconductor-uri "BiocNeighbors" version))
1662 "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
1663 (properties `((upstream-name . "BiocNeighbors")))
1664 (build-system r-build-system)
1666 `(("r-biocparallel" ,r-biocparallel)
1668 ("r-rcppannoy" ,r-rcppannoy)
1669 ("r-s4vectors" ,r-s4vectors)))
1670 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1671 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1673 "This package implements exact and approximate methods for nearest
1674 neighbor detection, in a framework that allows them to be easily switched
1675 within Bioconductor packages or workflows. The exact algorithm is implemented
1676 using pre-clustering with the k-means algorithm. Functions are also provided
1677 to search for all neighbors within a given distance. Parallelization is
1678 achieved for all methods using the BiocParallel framework.")
1679 (license license:gpl3)))
1681 (define-public r-destiny
1688 (uri (bioconductor-uri "destiny" version))
1691 "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
1692 (build-system r-build-system)
1694 `(("r-biobase" ,r-biobase)
1695 ("r-biocgenerics" ,r-biocgenerics)
1697 ("r-ggthemes" ,r-ggthemes)
1698 ("r-hmisc" ,r-hmisc)
1699 ("r-igraph" ,r-igraph)
1700 ("r-matrix" ,r-matrix)
1701 ("r-proxy" ,r-proxy)
1703 ("r-rcppeigen" ,r-rcppeigen)
1704 ("r-scales" ,r-scales)
1705 ("r-scatterplot3d" ,r-scatterplot3d)
1706 ("r-smoother" ,r-smoother)
1707 ("r-summarizedexperiment" ,r-summarizedexperiment)
1709 (home-page "https://bioconductor.org/packages/destiny/")
1710 (synopsis "Create and plot diffusion maps")
1711 (description "This package provides tools to create and plot diffusion
1713 ;; Any version of the GPL
1714 (license license:gpl3+)))
1716 (define-public r-savr
1723 (uri (bioconductor-uri "savR" version))
1726 "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
1727 (properties `((upstream-name . "savR")))
1728 (build-system r-build-system)
1730 `(("r-ggplot2" ,r-ggplot2)
1731 ("r-gridextra" ,r-gridextra)
1732 ("r-reshape2" ,r-reshape2)
1733 ("r-scales" ,r-scales)
1735 (home-page "https://github.com/bcalder/savR")
1736 (synopsis "Parse and analyze Illumina SAV files")
1738 "This package provides tools to parse Illumina Sequence Analysis
1739 Viewer (SAV) files, access data, and generate QC plots.")
1740 (license license:agpl3+)))
1742 (define-public r-chipexoqual
1744 (name "r-chipexoqual")
1749 (uri (bioconductor-uri "ChIPexoQual" version))
1752 "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
1753 (properties `((upstream-name . "ChIPexoQual")))
1754 (build-system r-build-system)
1756 `(("r-biocparallel" ,r-biocparallel)
1757 ("r-biovizbase" ,r-biovizbase)
1758 ("r-broom" ,r-broom)
1759 ("r-data-table" ,r-data-table)
1760 ("r-dplyr" ,r-dplyr)
1761 ("r-genomeinfodb" ,r-genomeinfodb)
1762 ("r-genomicalignments" ,r-genomicalignments)
1763 ("r-genomicranges" ,r-genomicranges)
1764 ("r-ggplot2" ,r-ggplot2)
1765 ("r-hexbin" ,r-hexbin)
1766 ("r-iranges" ,r-iranges)
1767 ("r-rcolorbrewer" ,r-rcolorbrewer)
1768 ("r-rmarkdown" ,r-rmarkdown)
1769 ("r-rsamtools" ,r-rsamtools)
1770 ("r-s4vectors" ,r-s4vectors)
1771 ("r-scales" ,r-scales)
1772 ("r-viridis" ,r-viridis)))
1773 (home-page "https://github.com/keleslab/ChIPexoQual")
1774 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1776 "This package provides a quality control pipeline for ChIP-exo/nexus
1778 (license license:gpl2+)))
1780 (define-public r-copynumber
1782 (name "r-copynumber")
1786 (uri (bioconductor-uri "copynumber" version))
1789 "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
1790 (build-system r-build-system)
1792 `(("r-s4vectors" ,r-s4vectors)
1793 ("r-iranges" ,r-iranges)
1794 ("r-genomicranges" ,r-genomicranges)
1795 ("r-biocgenerics" ,r-biocgenerics)))
1796 (home-page "https://bioconductor.org/packages/copynumber")
1797 (synopsis "Segmentation of single- and multi-track copy number data")
1799 "This package segments single- and multi-track copy number data by a
1800 penalized least squares regression method.")
1801 (license license:artistic2.0)))
1803 (define-public r-dnacopy
1810 (uri (bioconductor-uri "DNAcopy" version))
1813 "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
1814 (properties `((upstream-name . "DNAcopy")))
1815 (build-system r-build-system)
1816 (native-inputs `(("gfortran" ,gfortran)))
1817 (home-page "https://bioconductor.org/packages/DNAcopy")
1818 (synopsis "DNA copy number data analysis")
1820 "This package implements the @dfn{circular binary segmentation} (CBS)
1821 algorithm to segment DNA copy number data and identify genomic regions with
1822 abnormal copy number.")
1823 (license license:gpl2+)))
1825 ;; This is a CRAN package, but it uncharacteristically depends on a
1826 ;; Bioconductor package.
1827 (define-public r-htscluster
1829 (name "r-htscluster")
1834 (uri (cran-uri "HTSCluster" version))
1837 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1838 (properties `((upstream-name . "HTSCluster")))
1839 (build-system r-build-system)
1841 `(("r-capushe" ,r-capushe)
1842 ("r-edger" ,r-edger)
1843 ("r-plotrix" ,r-plotrix)))
1844 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1845 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1847 "This package provides a Poisson mixture model is implemented to cluster
1848 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
1849 estimation is performed using either the EM or CEM algorithm, and the slope
1850 heuristics are used for model selection (i.e., to choose the number of
1852 (license license:gpl3+)))
1854 (define-public r-deds
1861 (uri (bioconductor-uri "DEDS" version))
1864 "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
1865 (properties `((upstream-name . "DEDS")))
1866 (build-system r-build-system)
1867 (home-page "https://bioconductor.org/packages/DEDS/")
1868 (synopsis "Differential expression via distance summary for microarray data")
1870 "This library contains functions that calculate various statistics of
1871 differential expression for microarray data, including t statistics, fold
1872 change, F statistics, SAM, moderated t and F statistics and B statistics. It
1873 also implements a new methodology called DEDS (Differential Expression via
1874 Distance Summary), which selects differentially expressed genes by integrating
1875 and summarizing a set of statistics using a weighted distance approach.")
1876 ;; Any version of the LGPL.
1877 (license license:lgpl3+)))
1879 ;; This is a CRAN package, but since it depends on a Bioconductor package we
1881 (define-public r-nbpseq
1888 (uri (cran-uri "NBPSeq" version))
1891 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
1892 (properties `((upstream-name . "NBPSeq")))
1893 (build-system r-build-system)
1895 `(("r-qvalue" ,r-qvalue)))
1896 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
1897 (synopsis "Negative binomial models for RNA-Seq data")
1899 "This package provides negative binomial models for two-group comparisons
1900 and regression inferences from RNA-sequencing data.")
1901 (license license:gpl2)))
1903 (define-public r-ebseq
1910 (uri (bioconductor-uri "EBSeq" version))
1913 "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
1914 (properties `((upstream-name . "EBSeq")))
1915 (build-system r-build-system)
1917 `(("r-blockmodeling" ,r-blockmodeling)
1918 ("r-gplots" ,r-gplots)
1919 ("r-testthat" ,r-testthat)))
1920 (home-page "https://bioconductor.org/packages/EBSeq")
1921 (synopsis "Differential expression analysis of RNA-seq data")
1923 "This package provides tools for differential expression analysis at both
1924 gene and isoform level using RNA-seq data")
1925 (license license:artistic2.0)))
1927 (define-public r-lpsymphony
1929 (name "r-lpsymphony")
1934 (uri (bioconductor-uri "lpsymphony" version))
1937 "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
1938 (build-system r-build-system)
1940 `(("gfortran" ,gfortran)
1943 `(("pkg-config" ,pkg-config)))
1944 (home-page "http://r-forge.r-project.org/projects/rsymphony")
1945 (synopsis "Symphony integer linear programming solver in R")
1947 "This package was derived from Rsymphony. The package provides an R
1948 interface to SYMPHONY, a linear programming solver written in C++. The main
1949 difference between this package and Rsymphony is that it includes the solver
1950 source code, while Rsymphony expects to find header and library files on the
1951 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
1952 to install interface to SYMPHONY.")
1953 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
1954 ;; lpsimphony is released under the same terms.
1955 (license license:epl1.0)))
1957 (define-public r-ihw
1964 (uri (bioconductor-uri "IHW" version))
1967 "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
1968 (properties `((upstream-name . "IHW")))
1969 (build-system r-build-system)
1971 `(("r-biocgenerics" ,r-biocgenerics)
1972 ("r-fdrtool" ,r-fdrtool)
1973 ("r-lpsymphony" ,r-lpsymphony)
1974 ("r-slam" ,r-slam)))
1975 (home-page "https://bioconductor.org/packages/IHW")
1976 (synopsis "Independent hypothesis weighting")
1978 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
1979 procedure that increases power compared to the method of Benjamini and
1980 Hochberg by assigning data-driven weights to each hypothesis. The input to
1981 IHW is a two-column table of p-values and covariates. The covariate can be
1982 any continuous-valued or categorical variable that is thought to be
1983 informative on the statistical properties of each hypothesis test, while it is
1984 independent of the p-value under the null hypothesis.")
1985 (license license:artistic2.0)))
1987 (define-public r-icobra
1994 (uri (bioconductor-uri "iCOBRA" version))
1997 "0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"))))
1998 (properties `((upstream-name . "iCOBRA")))
1999 (build-system r-build-system)
2001 `(("r-dplyr" ,r-dplyr)
2003 ("r-ggplot2" ,r-ggplot2)
2004 ("r-limma" ,r-limma)
2005 ("r-reshape2" ,r-reshape2)
2007 ("r-scales" ,r-scales)
2008 ("r-shiny" ,r-shiny)
2009 ("r-shinybs" ,r-shinybs)
2010 ("r-shinydashboard" ,r-shinydashboard)
2011 ("r-upsetr" ,r-upsetr)))
2012 (home-page "https://bioconductor.org/packages/iCOBRA")
2013 (synopsis "Comparison and visualization of ranking and assignment methods")
2015 "This package provides functions for calculation and visualization of
2016 performance metrics for evaluation of ranking and binary
2017 classification (assignment) methods. It also contains a Shiny application for
2018 interactive exploration of results.")
2019 (license license:gpl2+)))
2021 (define-public r-mast
2028 (uri (bioconductor-uri "MAST" version))
2031 "0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"))))
2032 (properties `((upstream-name . "MAST")))
2033 (build-system r-build-system)
2035 `(("r-abind" ,r-abind)
2036 ("r-biobase" ,r-biobase)
2037 ("r-biocgenerics" ,r-biocgenerics)
2038 ("r-data-table" ,r-data-table)
2039 ("r-ggplot2" ,r-ggplot2)
2041 ("r-progress" ,r-progress)
2042 ("r-reshape2" ,r-reshape2)
2043 ("r-s4vectors" ,r-s4vectors)
2044 ("r-singlecellexperiment" ,r-singlecellexperiment)
2045 ("r-stringr" ,r-stringr)
2046 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2047 (home-page "https://github.com/RGLab/MAST/")
2048 (synopsis "Model-based analysis of single cell transcriptomics")
2050 "This package provides methods and models for handling zero-inflated
2051 single cell assay data.")
2052 (license license:gpl2+)))
2054 (define-public r-monocle
2061 (uri (bioconductor-uri "monocle" version))
2064 "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
2065 (build-system r-build-system)
2067 `(("r-biobase" ,r-biobase)
2068 ("r-biocgenerics" ,r-biocgenerics)
2069 ("r-biocviews" ,r-biocviews)
2070 ("r-cluster" ,r-cluster)
2071 ("r-combinat" ,r-combinat)
2072 ("r-ddrtree" ,r-ddrtree)
2073 ("r-densityclust" ,r-densityclust)
2074 ("r-dplyr" ,r-dplyr)
2075 ("r-fastica" ,r-fastica)
2076 ("r-ggplot2" ,r-ggplot2)
2077 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2078 ("r-igraph" ,r-igraph)
2079 ("r-irlba" ,r-irlba)
2080 ("r-limma" ,r-limma)
2082 ("r-matrix" ,r-matrix)
2083 ("r-matrixstats" ,r-matrixstats)
2084 ("r-pheatmap" ,r-pheatmap)
2086 ("r-proxy" ,r-proxy)
2087 ("r-qlcmatrix" ,r-qlcmatrix)
2090 ("r-reshape2" ,r-reshape2)
2091 ("r-rtsne" ,r-rtsne)
2093 ("r-stringr" ,r-stringr)
2094 ("r-tibble" ,r-tibble)
2096 ("r-viridis" ,r-viridis)))
2097 (home-page "https://bioconductor.org/packages/monocle")
2098 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2100 "Monocle performs differential expression and time-series analysis for
2101 single-cell expression experiments. It orders individual cells according to
2102 progress through a biological process, without knowing ahead of time which
2103 genes define progress through that process. Monocle also performs
2104 differential expression analysis, clustering, visualization, and other useful
2105 tasks on single cell expression data. It is designed to work with RNA-Seq and
2106 qPCR data, but could be used with other types as well.")
2107 (license license:artistic2.0)))
2109 (define-public r-noiseq
2116 (uri (bioconductor-uri "NOISeq" version))
2119 "1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"))))
2120 (properties `((upstream-name . "NOISeq")))
2121 (build-system r-build-system)
2123 `(("r-biobase" ,r-biobase)
2124 ("r-matrix" ,r-matrix)))
2125 (home-page "https://bioconductor.org/packages/NOISeq")
2126 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2128 "This package provides tools to support the analysis of RNA-seq
2129 expression data or other similar kind of data. It provides exploratory plots
2130 to evaluate saturation, count distribution, expression per chromosome, type of
2131 detected features, features length, etc. It also supports the analysis of
2132 differential expression between two experimental conditions with no parametric
2134 (license license:artistic2.0)))
2136 (define-public r-scdd
2143 (uri (bioconductor-uri "scDD" version))
2146 "0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"))))
2147 (properties `((upstream-name . "scDD")))
2148 (build-system r-build-system)
2151 ("r-biocparallel" ,r-biocparallel)
2152 ("r-ebseq" ,r-ebseq)
2153 ("r-fields" ,r-fields)
2154 ("r-ggplot2" ,r-ggplot2)
2155 ("r-mclust" ,r-mclust)
2156 ("r-outliers" ,r-outliers)
2157 ("r-s4vectors" ,r-s4vectors)
2158 ("r-scran" ,r-scran)
2159 ("r-singlecellexperiment" ,r-singlecellexperiment)
2160 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2161 (home-page "https://github.com/kdkorthauer/scDD")
2162 (synopsis "Mixture modeling of single-cell RNA-seq data")
2164 "This package implements a method to analyze single-cell RNA-seq data
2165 utilizing flexible Dirichlet Process mixture models. Genes with differential
2166 distributions of expression are classified into several interesting patterns
2167 of differences between two conditions. The package also includes functions
2168 for simulating data with these patterns from negative binomial
2170 (license license:gpl2)))
2172 (define-public r-scone
2179 (uri (bioconductor-uri "scone" version))
2182 "0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"))))
2183 (build-system r-build-system)
2185 `(("r-aroma-light" ,r-aroma-light)
2186 ("r-biocparallel" ,r-biocparallel)
2188 ("r-class" ,r-class)
2189 ("r-cluster" ,r-cluster)
2190 ("r-compositions" ,r-compositions)
2191 ("r-diptest" ,r-diptest)
2192 ("r-edger" ,r-edger)
2194 ("r-gplots" ,r-gplots)
2195 ("r-hexbin" ,r-hexbin)
2196 ("r-limma" ,r-limma)
2197 ("r-matrixstats" ,r-matrixstats)
2198 ("r-mixtools" ,r-mixtools)
2199 ("r-rarpack" ,r-rarpack)
2200 ("r-rcolorbrewer" ,r-rcolorbrewer)
2201 ("r-rhdf5" ,r-rhdf5)
2202 ("r-ruvseq" ,r-ruvseq)
2203 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2204 (home-page "https://bioconductor.org/packages/scone")
2205 (synopsis "Single cell overview of normalized expression data")
2207 "SCONE is an R package for comparing and ranking the performance of
2208 different normalization schemes for single-cell RNA-seq and other
2209 high-throughput analyses.")
2210 (license license:artistic2.0)))
2212 (define-public r-geoquery
2219 (uri (bioconductor-uri "GEOquery" version))
2222 "074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"))))
2223 (properties `((upstream-name . "GEOquery")))
2224 (build-system r-build-system)
2226 `(("r-biobase" ,r-biobase)
2227 ("r-dplyr" ,r-dplyr)
2229 ("r-limma" ,r-limma)
2230 ("r-magrittr" ,r-magrittr)
2231 ("r-readr" ,r-readr)
2232 ("r-tidyr" ,r-tidyr)
2233 ("r-xml2" ,r-xml2)))
2234 (home-page "https://github.com/seandavi/GEOquery/")
2235 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2237 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2238 microarray data. Given the rich and varied nature of this resource, it is
2239 only natural to want to apply BioConductor tools to these data. GEOquery is
2240 the bridge between GEO and BioConductor.")
2241 (license license:gpl2)))
2243 (define-public r-illuminaio
2245 (name "r-illuminaio")
2250 (uri (bioconductor-uri "illuminaio" version))
2253 "1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"))))
2254 (build-system r-build-system)
2256 `(("r-base64" ,r-base64)))
2257 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2258 (synopsis "Parse Illumina microarray output files")
2260 "This package provides tools for parsing Illumina's microarray output
2261 files, including IDAT.")
2262 (license license:gpl2)))
2264 (define-public r-siggenes
2271 (uri (bioconductor-uri "siggenes" version))
2274 "0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"))))
2275 (build-system r-build-system)
2277 `(("r-biobase" ,r-biobase)
2278 ("r-multtest" ,r-multtest)))
2279 (home-page "https://bioconductor.org/packages/siggenes/")
2281 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2283 "This package provides tools for the identification of differentially
2284 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2285 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2286 Bayes Analyses of Microarrays} (EBAM).")
2287 (license license:lgpl2.0+)))
2289 (define-public r-bumphunter
2291 (name "r-bumphunter")
2296 (uri (bioconductor-uri "bumphunter" version))
2299 "1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"))))
2300 (build-system r-build-system)
2302 `(("r-annotationdbi" ,r-annotationdbi)
2303 ("r-biocgenerics" ,r-biocgenerics)
2304 ("r-dorng" ,r-dorng)
2305 ("r-foreach" ,r-foreach)
2306 ("r-genomeinfodb" ,r-genomeinfodb)
2307 ("r-genomicfeatures" ,r-genomicfeatures)
2308 ("r-genomicranges" ,r-genomicranges)
2309 ("r-iranges" ,r-iranges)
2310 ("r-iterators" ,r-iterators)
2311 ("r-limma" ,r-limma)
2312 ("r-locfit" ,r-locfit)
2313 ("r-matrixstats" ,r-matrixstats)
2314 ("r-s4vectors" ,r-s4vectors)))
2315 (home-page "https://github.com/ririzarr/bumphunter")
2316 (synopsis "Find bumps in genomic data")
2318 "This package provides tools for finding bumps in genomic data in order
2319 to identify differentially methylated regions in epigenetic epidemiology
2321 (license license:artistic2.0)))
2323 (define-public r-minfi
2330 (uri (bioconductor-uri "minfi" version))
2333 "1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"))))
2334 (build-system r-build-system)
2336 `(("r-beanplot" ,r-beanplot)
2337 ("r-biobase" ,r-biobase)
2338 ("r-biocgenerics" ,r-biocgenerics)
2339 ("r-biocparallel" ,r-biocparallel)
2340 ("r-biostrings" ,r-biostrings)
2341 ("r-bumphunter" ,r-bumphunter)
2342 ("r-data-table" ,r-data-table)
2343 ("r-delayedarray" ,r-delayedarray)
2344 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2345 ("r-genefilter" ,r-genefilter)
2346 ("r-genomeinfodb" ,r-genomeinfodb)
2347 ("r-genomicranges" ,r-genomicranges)
2348 ("r-geoquery" ,r-geoquery)
2349 ("r-hdf5array" ,r-hdf5array)
2350 ("r-illuminaio" ,r-illuminaio)
2351 ("r-iranges" ,r-iranges)
2352 ("r-lattice" ,r-lattice)
2353 ("r-limma" ,r-limma)
2355 ("r-mclust" ,r-mclust)
2357 ("r-nor1mix" ,r-nor1mix)
2358 ("r-preprocesscore" ,r-preprocesscore)
2359 ("r-quadprog" ,r-quadprog)
2360 ("r-rcolorbrewer" ,r-rcolorbrewer)
2361 ("r-reshape" ,r-reshape)
2362 ("r-s4vectors" ,r-s4vectors)
2363 ("r-siggenes" ,r-siggenes)
2364 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2365 (home-page "https://github.com/hansenlab/minfi")
2366 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2368 "This package provides tools to analyze and visualize Illumina Infinium
2369 methylation arrays.")
2370 (license license:artistic2.0)))
2372 (define-public r-methylumi
2374 (name "r-methylumi")
2379 (uri (bioconductor-uri "methylumi" version))
2382 "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"))))
2383 (build-system r-build-system)
2385 `(("r-annotate" ,r-annotate)
2386 ("r-annotationdbi" ,r-annotationdbi)
2387 ("r-biobase" ,r-biobase)
2388 ("r-biocgenerics" ,r-biocgenerics)
2389 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2390 ("r-genefilter" ,r-genefilter)
2391 ("r-genomeinfodb" ,r-genomeinfodb)
2392 ("r-genomicranges" ,r-genomicranges)
2393 ("r-ggplot2" ,r-ggplot2)
2394 ("r-illuminaio" ,r-illuminaio)
2395 ("r-iranges" ,r-iranges)
2396 ("r-lattice" ,r-lattice)
2397 ("r-matrixstats" ,r-matrixstats)
2398 ("r-minfi" ,r-minfi)
2399 ("r-reshape2" ,r-reshape2)
2400 ("r-s4vectors" ,r-s4vectors)
2401 ("r-scales" ,r-scales)
2402 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2403 (home-page "https://bioconductor.org/packages/methylumi")
2404 (synopsis "Handle Illumina methylation data")
2406 "This package provides classes for holding and manipulating Illumina
2407 methylation data. Based on eSet, it can contain MIAME information, sample
2408 information, feature information, and multiple matrices of data. An
2409 \"intelligent\" import function, methylumiR can read the Illumina text files
2410 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2411 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2412 background correction, and quality control features for GoldenGate, Infinium,
2413 and Infinium HD arrays are also included.")
2414 (license license:gpl2)))
2416 (define-public r-lumi
2423 (uri (bioconductor-uri "lumi" version))
2426 "1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"))))
2427 (build-system r-build-system)
2429 `(("r-affy" ,r-affy)
2430 ("r-annotate" ,r-annotate)
2431 ("r-annotationdbi" ,r-annotationdbi)
2432 ("r-biobase" ,r-biobase)
2434 ("r-genomicfeatures" ,r-genomicfeatures)
2435 ("r-genomicranges" ,r-genomicranges)
2436 ("r-kernsmooth" ,r-kernsmooth)
2437 ("r-lattice" ,r-lattice)
2439 ("r-methylumi" ,r-methylumi)
2441 ("r-nleqslv" ,r-nleqslv)
2442 ("r-preprocesscore" ,r-preprocesscore)
2443 ("r-rsqlite" ,r-rsqlite)))
2444 (home-page "https://bioconductor.org/packages/lumi")
2445 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2447 "The lumi package provides an integrated solution for the Illumina
2448 microarray data analysis. It includes functions of Illumina
2449 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2450 variance stabilization, normalization and gene annotation at the probe level.
2451 It also includes the functions of processing Illumina methylation microarrays,
2452 especially Illumina Infinium methylation microarrays.")
2453 (license license:lgpl2.0+)))
2455 (define-public r-linnorm
2462 (uri (bioconductor-uri "Linnorm" version))
2465 "1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"))))
2466 (properties `((upstream-name . "Linnorm")))
2467 (build-system r-build-system)
2469 `(("r-amap" ,r-amap)
2470 ("r-apcluster" ,r-apcluster)
2471 ("r-ellipse" ,r-ellipse)
2472 ("r-fastcluster" ,r-fastcluster)
2474 ("r-ggdendro" ,r-ggdendro)
2475 ("r-ggplot2" ,r-ggplot2)
2476 ("r-gmodels" ,r-gmodels)
2477 ("r-igraph" ,r-igraph)
2478 ("r-limma" ,r-limma)
2480 ("r-mclust" ,r-mclust)
2482 ("r-rcpparmadillo" ,r-rcpparmadillo)
2483 ("r-rtsne" ,r-rtsne)
2484 ("r-statmod" ,r-statmod)
2485 ("r-vegan" ,r-vegan)
2487 (home-page "http://www.jjwanglab.org/Linnorm/")
2488 (synopsis "Linear model and normality based transformation method")
2490 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2491 count data or any large scale count data. It transforms such datasets for
2492 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2493 the following pipelines are implemented:
2496 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2497 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2498 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2499 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2500 @item Differential expression analysis or differential peak detection using
2501 limma (@code{Linnorm.limma})
2502 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2503 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2504 @item Stable gene selection for scRNA-seq data; for users without or who do
2505 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2506 @item Data imputation (@code{Linnorm.DataImput}).
2509 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2510 @code{RnaXSim} function is included for simulating RNA-seq data for the
2511 evaluation of DEG analysis methods.")
2512 (license license:expat)))
2514 (define-public r-ioniser
2521 (uri (bioconductor-uri "IONiseR" version))
2524 "01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"))))
2525 (properties `((upstream-name . "IONiseR")))
2526 (build-system r-build-system)
2528 `(("r-biocgenerics" ,r-biocgenerics)
2529 ("r-biocparallel" ,r-biocparallel)
2530 ("r-biostrings" ,r-biostrings)
2531 ("r-bit64" ,r-bit64)
2532 ("r-dplyr" ,r-dplyr)
2533 ("r-ggplot2" ,r-ggplot2)
2534 ("r-magrittr" ,r-magrittr)
2535 ("r-rhdf5" ,r-rhdf5)
2536 ("r-shortread" ,r-shortread)
2537 ("r-stringr" ,r-stringr)
2538 ("r-tibble" ,r-tibble)
2539 ("r-tidyr" ,r-tidyr)
2540 ("r-xvector" ,r-xvector)))
2541 (home-page "https://bioconductor.org/packages/IONiseR/")
2542 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2544 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2545 MinION data. It extracts summary statistics from a set of fast5 files and can
2546 be used either before or after base calling. In addition to standard
2547 summaries of the read-types produced, it provides a number of plots for
2548 visualising metrics relative to experiment run time or spatially over the
2549 surface of a flowcell.")
2550 (license license:expat)))
2552 ;; This is a CRAN package, but it depends on packages from Bioconductor.
2553 (define-public r-gkmsvm
2560 (uri (cran-uri "gkmSVM" version))
2563 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2564 (properties `((upstream-name . "gkmSVM")))
2565 (build-system r-build-system)
2567 `(("r-biocgenerics" ,r-biocgenerics)
2568 ("r-biostrings" ,r-biostrings)
2569 ("r-genomeinfodb" ,r-genomeinfodb)
2570 ("r-genomicranges" ,r-genomicranges)
2571 ("r-iranges" ,r-iranges)
2572 ("r-kernlab" ,r-kernlab)
2575 ("r-rtracklayer" ,r-rtracklayer)
2576 ("r-s4vectors" ,r-s4vectors)
2577 ("r-seqinr" ,r-seqinr)))
2578 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2579 (synopsis "Gapped-kmer support vector machine")
2581 "This R package provides tools for training gapped-kmer SVM classifiers
2582 for DNA and protein sequences. This package supports several sequence
2583 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2584 (license license:gpl2+)))
2586 (define-public r-triform
2593 (uri (bioconductor-uri "triform" version))
2596 "12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s"))))
2597 (build-system r-build-system)
2599 `(("r-biocgenerics" ,r-biocgenerics)
2600 ("r-iranges" ,r-iranges)
2601 ("r-yaml" ,r-yaml)))
2602 (home-page "https://bioconductor.org/packages/triform/")
2603 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2605 "The Triform algorithm uses model-free statistics to identify peak-like
2606 distributions of TF ChIP sequencing reads, taking advantage of an improved
2607 peak definition in combination with known profile characteristics.")
2608 (license license:gpl2)))
2610 (define-public r-varianttools
2612 (name "r-varianttools")
2617 (uri (bioconductor-uri "VariantTools" version))
2620 "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
2621 (properties `((upstream-name . "VariantTools")))
2622 (build-system r-build-system)
2624 `(("r-biobase" ,r-biobase)
2625 ("r-biocgenerics" ,r-biocgenerics)
2626 ("r-biocparallel" ,r-biocparallel)
2627 ("r-biostrings" ,r-biostrings)
2628 ("r-bsgenome" ,r-bsgenome)
2629 ("r-genomeinfodb" ,r-genomeinfodb)
2630 ("r-genomicfeatures" ,r-genomicfeatures)
2631 ("r-genomicranges" ,r-genomicranges)
2632 ("r-iranges" ,r-iranges)
2633 ("r-matrix" ,r-matrix)
2634 ("r-rsamtools" ,r-rsamtools)
2635 ("r-rtracklayer" ,r-rtracklayer)
2636 ("r-s4vectors" ,r-s4vectors)
2637 ("r-variantannotation" ,r-variantannotation)))
2638 (home-page "https://bioconductor.org/packages/VariantTools/")
2639 (synopsis "Tools for exploratory analysis of variant calls")
2641 "Explore, diagnose, and compare variant calls using filters. The
2642 VariantTools package supports a workflow for loading data, calling single
2643 sample variants and tumor-specific somatic mutations or other sample-specific
2644 variant types (e.g., RNA editing). Most of the functions operate on
2645 alignments (BAM files) or datasets of called variants. The user is expected
2646 to have already aligned the reads with a separate tool, e.g., GSNAP via
2648 (license license:artistic2.0)))
2650 (define-public r-heatplus
2657 (uri (bioconductor-uri "Heatplus" version))
2660 "0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48"))))
2661 (properties `((upstream-name . "Heatplus")))
2662 (build-system r-build-system)
2664 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2665 (home-page "https://github.com/alexploner/Heatplus")
2666 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2668 "This package provides tools to display a rectangular heatmap (intensity
2669 plot) of a data matrix. By default, both samples (columns) and features (row)
2670 of the matrix are sorted according to a hierarchical clustering, and the
2671 corresponding dendrogram is plotted. Optionally, panels with additional
2672 information about samples and features can be added to the plot.")
2673 (license license:gpl2+)))
2675 (define-public r-gosemsim
2682 (uri (bioconductor-uri "GOSemSim" version))
2685 "0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib"))))
2686 (properties `((upstream-name . "GOSemSim")))
2687 (build-system r-build-system)
2689 `(("r-annotationdbi" ,r-annotationdbi)
2690 ("r-go-db" ,r-go-db)
2691 ("r-rcpp" ,r-rcpp)))
2692 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2693 (synopsis "GO-terms semantic similarity measures")
2695 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2696 quantitative ways to compute similarities between genes and gene groups, and
2697 have became important basis for many bioinformatics analysis approaches.
2698 GOSemSim is an R package for semantic similarity computation among GO terms,
2699 sets of GO terms, gene products and gene clusters.")
2700 (license license:artistic2.0)))
2702 (define-public r-anota
2709 (uri (bioconductor-uri "anota" version))
2712 "182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"))))
2713 (build-system r-build-system)
2715 `(("r-multtest" ,r-multtest)
2716 ("r-qvalue" ,r-qvalue)))
2717 (home-page "https://bioconductor.org/packages/anota/")
2718 (synopsis "Analysis of translational activity")
2720 "Genome wide studies of translational control is emerging as a tool to
2721 study verious biological conditions. The output from such analysis is both
2722 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2723 involved in translation (the actively translating mRNA level) for each mRNA.
2724 The standard analysis of such data strives towards identifying differential
2725 translational between two or more sample classes - i.e. differences in
2726 actively translated mRNA levels that are independent of underlying differences
2727 in cytosolic mRNA levels. This package allows for such analysis using partial
2728 variances and the random variance model. As 10s of thousands of mRNAs are
2729 analyzed in parallell the library performs a number of tests to assure that
2730 the data set is suitable for such analysis.")
2731 (license license:gpl3)))
2733 (define-public r-sigpathway
2735 (name "r-sigpathway")
2740 (uri (bioconductor-uri "sigPathway" version))
2743 "0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3"))))
2744 (properties `((upstream-name . "sigPathway")))
2745 (build-system r-build-system)
2746 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
2747 (synopsis "Pathway analysis")
2749 "This package is used to conduct pathway analysis by calculating the NT_k
2750 and NE_k statistics in a statistical framework for determining whether a
2751 specified group of genes for a pathway has a coordinated association with a
2752 phenotype of interest.")
2753 (license license:gpl2)))
2755 (define-public r-fgsea
2762 (uri (bioconductor-uri "fgsea" version))
2765 "0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"))))
2766 (build-system r-build-system)
2768 `(("r-biocparallel" ,r-biocparallel)
2769 ("r-data-table" ,r-data-table)
2770 ("r-fastmatch" ,r-fastmatch)
2771 ("r-ggplot2" ,r-ggplot2)
2772 ("r-gridextra" ,r-gridextra)
2773 ("r-matrix" ,r-matrix)
2774 ("r-rcpp" ,r-rcpp)))
2775 (home-page "https://github.com/ctlab/fgsea/")
2776 (synopsis "Fast gene set enrichment analysis")
2778 "The package implements an algorithm for fast gene set enrichment
2779 analysis. Using the fast algorithm allows to make more permutations and get
2780 more fine grained p-values, which allows to use accurate stantard approaches
2781 to multiple hypothesis correction.")
2782 (license license:expat)))
2784 (define-public r-dose
2791 (uri (bioconductor-uri "DOSE" version))
2794 "1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa"))))
2795 (properties `((upstream-name . "DOSE")))
2796 (build-system r-build-system)
2798 `(("r-annotationdbi" ,r-annotationdbi)
2799 ("r-biocparallel" ,r-biocparallel)
2800 ("r-do-db" ,r-do-db)
2801 ("r-fgsea" ,r-fgsea)
2802 ("r-ggplot2" ,r-ggplot2)
2803 ("r-gosemsim" ,r-gosemsim)
2804 ("r-qvalue" ,r-qvalue)
2805 ("r-reshape2" ,r-reshape2)
2806 ("r-s4vectors" ,r-s4vectors)))
2807 (home-page "https://guangchuangyu.github.io/software/DOSE/")
2808 (synopsis "Disease ontology semantic and enrichment analysis")
2810 "This package implements five methods proposed by Resnik, Schlicker,
2811 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
2812 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
2813 including hypergeometric model and gene set enrichment analysis are also
2814 implemented for discovering disease associations of high-throughput biological
2816 (license license:artistic2.0)))
2818 (define-public r-enrichplot
2820 (name "r-enrichplot")
2825 (uri (bioconductor-uri "enrichplot" version))
2828 "0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"))))
2829 (build-system r-build-system)
2831 `(("r-annotationdbi" ,r-annotationdbi)
2832 ("r-cowplot" ,r-cowplot)
2834 ("r-europepmc" ,r-europepmc)
2835 ("r-ggplot2" ,r-ggplot2)
2836 ("r-ggplotify" ,r-ggplotify)
2837 ("r-ggraph" ,r-ggraph)
2838 ("r-ggridges" ,r-ggridges)
2839 ("r-gosemsim" ,r-gosemsim)
2840 ("r-gridextra" ,r-gridextra)
2841 ("r-igraph" ,r-igraph)
2842 ("r-purrr" ,r-purrr)
2843 ("r-rcolorbrewer" ,r-rcolorbrewer)
2844 ("r-reshape2" ,r-reshape2)
2845 ("r-upsetr" ,r-upsetr)))
2846 (home-page "https://github.com/GuangchuangYu/enrichplot")
2847 (synopsis "Visualization of functional enrichment result")
2849 "The enrichplot package implements several visualization methods for
2850 interpreting functional enrichment results obtained from ORA or GSEA analyses.
2851 All the visualization methods are developed based on ggplot2 graphics.")
2852 (license license:artistic2.0)))
2854 (define-public r-clusterprofiler
2856 (name "r-clusterprofiler")
2861 (uri (bioconductor-uri "clusterProfiler" version))
2864 "1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm"))))
2866 `((upstream-name . "clusterProfiler")))
2867 (build-system r-build-system)
2869 `(("r-annotationdbi" ,r-annotationdbi)
2871 ("r-enrichplot" ,r-enrichplot)
2872 ("r-ggplot2" ,r-ggplot2)
2873 ("r-go-db" ,r-go-db)
2874 ("r-gosemsim" ,r-gosemsim)
2875 ("r-magrittr" ,r-magrittr)
2877 ("r-qvalue" ,r-qvalue)
2878 ("r-rvcheck" ,r-rvcheck)
2879 ("r-tidyr" ,r-tidyr)))
2880 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
2881 (synopsis "Analysis and visualization of functional profiles for gene clusters")
2883 "This package implements methods to analyze and visualize functional
2884 profiles (GO and KEGG) of gene and gene clusters.")
2885 (license license:artistic2.0)))
2887 (define-public r-mlinterfaces
2889 (name "r-mlinterfaces")
2894 (uri (bioconductor-uri "MLInterfaces" version))
2897 "12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8"))))
2898 (properties `((upstream-name . "MLInterfaces")))
2899 (build-system r-build-system)
2901 `(("r-annotate" ,r-annotate)
2902 ("r-biobase" ,r-biobase)
2903 ("r-biocgenerics" ,r-biocgenerics)
2904 ("r-cluster" ,r-cluster)
2907 ("r-gdata" ,r-gdata)
2908 ("r-genefilter" ,r-genefilter)
2909 ("r-ggvis" ,r-ggvis)
2910 ("r-hwriter" ,r-hwriter)
2912 ("r-mlbench" ,r-mlbench)
2914 ("r-rcolorbrewer" ,r-rcolorbrewer)
2916 ("r-rpart" ,r-rpart)
2917 ("r-sfsmisc" ,r-sfsmisc)
2918 ("r-shiny" ,r-shiny)
2919 ("r-threejs" ,r-threejs)))
2920 (home-page "https://bioconductor.org/packages/MLInterfaces/")
2921 (synopsis "Interfaces to R machine learning procedures")
2923 "This package provides uniform interfaces to machine learning code for
2924 data in R and Bioconductor containers.")
2925 ;; Any version of the LGPL.
2926 (license license:lgpl2.1+)))
2928 (define-public r-annaffy
2935 (uri (bioconductor-uri "annaffy" version))
2938 "16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5"))))
2939 (build-system r-build-system)
2942 (modify-phases %standard-phases
2943 (add-after 'unpack 'remove-reference-to-non-free-data
2945 (substitute* "DESCRIPTION"
2949 `(("r-annotationdbi" ,r-annotationdbi)
2950 ("r-biobase" ,r-biobase)
2952 ("r-go-db" ,r-go-db)))
2953 (home-page "https://bioconductor.org/packages/annaffy/")
2954 (synopsis "Annotation tools for Affymetrix biological metadata")
2956 "This package provides functions for handling data from Bioconductor
2957 Affymetrix annotation data packages. It produces compact HTML and text
2958 reports including experimental data and URL links to many online databases.
2959 It allows searching of biological metadata using various criteria.")
2960 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
2961 ;; the LGPL 2.1 is included.
2962 (license license:lgpl2.1+)))
2964 (define-public r-a4core
2971 (uri (bioconductor-uri "a4Core" version))
2974 "1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr"))))
2975 (properties `((upstream-name . "a4Core")))
2976 (build-system r-build-system)
2978 `(("r-biobase" ,r-biobase)
2979 ("r-glmnet" ,r-glmnet)))
2980 (home-page "https://bioconductor.org/packages/a4Core")
2981 (synopsis "Automated Affymetrix array analysis core package")
2983 "This is the core package for the automated analysis of Affymetrix
2985 (license license:gpl3)))
2987 (define-public r-a4classif
2989 (name "r-a4classif")
2994 (uri (bioconductor-uri "a4Classif" version))
2997 "02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j"))))
2998 (properties `((upstream-name . "a4Classif")))
2999 (build-system r-build-system)
3001 `(("r-a4core" ,r-a4core)
3002 ("r-a4preproc" ,r-a4preproc)
3003 ("r-glmnet" ,r-glmnet)
3004 ("r-mlinterfaces" ,r-mlinterfaces)
3007 ("r-varselrf" ,r-varselrf)))
3008 (home-page "https://bioconductor.org/packages/a4Classif/")
3009 (synopsis "Automated Affymetrix array analysis classification package")
3011 "This is the classification package for the automated analysis of
3012 Affymetrix arrays.")
3013 (license license:gpl3)))
3015 (define-public r-a4preproc
3017 (name "r-a4preproc")
3022 (uri (bioconductor-uri "a4Preproc" version))
3025 "1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp"))))
3026 (properties `((upstream-name . "a4Preproc")))
3027 (build-system r-build-system)
3029 `(("r-annotationdbi" ,r-annotationdbi)))
3030 (home-page "https://bioconductor.org/packages/a4Preproc/")
3031 (synopsis "Automated Affymetrix array analysis preprocessing package")
3033 "This is a package for the automated analysis of Affymetrix arrays. It
3034 is used for preprocessing the arrays.")
3035 (license license:gpl3)))
3037 (define-public r-a4reporting
3039 (name "r-a4reporting")
3044 (uri (bioconductor-uri "a4Reporting" version))
3047 "124774z3bfdjgxx2ad40795h92aam21yfx0rw0n01nk2wf6k7xc4"))))
3048 (properties `((upstream-name . "a4Reporting")))
3049 (build-system r-build-system)
3051 `(("r-annaffy" ,r-annaffy)
3052 ("r-xtable" ,r-xtable)))
3053 (home-page "https://bioconductor.org/packages/a4Reporting/")
3054 (synopsis "Automated Affymetrix array analysis reporting package")
3056 "This is a package for the automated analysis of Affymetrix arrays. It
3057 provides reporting features.")
3058 (license license:gpl3)))
3060 (define-public r-a4base
3067 (uri (bioconductor-uri "a4Base" version))
3070 "0k9k3bv99msbwf2y416cz316ssaha2dxvmaddbl7z9037p8mjr70"))))
3071 (properties `((upstream-name . "a4Base")))
3072 (build-system r-build-system)
3074 `(("r-a4core" ,r-a4core)
3075 ("r-a4preproc" ,r-a4preproc)
3076 ("r-annaffy" ,r-annaffy)
3077 ("r-annotationdbi" ,r-annotationdbi)
3078 ("r-biobase" ,r-biobase)
3079 ("r-genefilter" ,r-genefilter)
3080 ("r-glmnet" ,r-glmnet)
3081 ("r-gplots" ,r-gplots)
3082 ("r-limma" ,r-limma)
3084 ("r-multtest" ,r-multtest)))
3085 (home-page "https://bioconductor.org/packages/a4Base/")
3086 (synopsis "Automated Affymetrix array analysis base package")
3088 "This package provides basic features for the automated analysis of
3089 Affymetrix arrays.")
3090 (license license:gpl3)))
3099 (uri (bioconductor-uri "a4" version))
3102 "1iqjy35rqx3m2y0dm2bk4cnzdm1qvbi608bfmrid88w6wmwz3qlk"))))
3103 (build-system r-build-system)
3105 `(("r-a4base" ,r-a4base)
3106 ("r-a4classif" ,r-a4classif)
3107 ("r-a4core" ,r-a4core)
3108 ("r-a4preproc" ,r-a4preproc)
3109 ("r-a4reporting" ,r-a4reporting)))
3110 (home-page "https://bioconductor.org/packages/a4/")
3111 (synopsis "Automated Affymetrix array analysis umbrella package")
3113 "This package provides a software suite for the automated analysis of
3114 Affymetrix arrays.")
3115 (license license:gpl3)))
3117 (define-public r-abseqr
3124 (uri (bioconductor-uri "abseqR" version))
3127 "0w0ngxnilcrxlixsz7ls3zm99gyabxwn7w1r3r45n96d4aj075ry"))))
3128 (properties `((upstream-name . "abseqR")))
3129 (build-system r-build-system)
3131 `(("pandoc" ,ghc-pandoc)))
3133 `(("r-biocparallel" ,r-biocparallel)
3134 ("r-biocstyle" ,r-biocstyle)
3135 ("r-circlize" ,r-circlize)
3136 ("r-flexdashboard" ,r-flexdashboard)
3137 ("r-ggcorrplot" ,r-ggcorrplot)
3138 ("r-ggdendro" ,r-ggdendro)
3139 ("r-ggplot2" ,r-ggplot2)
3140 ("r-gridextra" ,r-gridextra)
3141 ("r-knitr" ,r-knitr)
3142 ("r-plotly" ,r-plotly)
3145 ("r-rcolorbrewer" ,r-rcolorbrewer)
3146 ("r-reshape2" ,r-reshape2)
3147 ("r-rmarkdown" ,r-rmarkdown)
3148 ("r-stringr" ,r-stringr)
3149 ("r-vegan" ,r-vegan)
3150 ("r-venndiagram" ,r-venndiagram)))
3151 (home-page "https://github.com/malhamdoosh/abseqR")
3152 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3154 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3155 sequencing datasets generated from antibody libraries and abseqR is one of its
3156 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3157 capabilities and allows them to generate interactive HTML reports for the
3158 convenience of viewing and sharing with other researchers. Additionally,
3159 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3160 further downstream analysis on its output.")
3161 (license license:gpl3)))