1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
6 ;;; This file is part of GNU Guix.
8 ;;; GNU Guix is free software; you can redistribute it and/or modify it
9 ;;; under the terms of the GNU General Public License as published by
10 ;;; the Free Software Foundation; either version 3 of the License, or (at
11 ;;; your option) any later version.
13 ;;; GNU Guix is distributed in the hope that it will be useful, but
14 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
15 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 ;;; GNU General Public License for more details.
18 ;;; You should have received a copy of the GNU General Public License
19 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
21 (define-module (gnu packages bioconductor)
22 #:use-module ((guix licenses) #:prefix license:)
23 #:use-module (guix packages)
24 #:use-module (guix download)
25 #:use-module (guix build-system r)
26 #:use-module (gnu packages)
27 #:use-module (gnu packages bioinformatics)
28 #:use-module (gnu packages cran)
29 #:use-module (gnu packages compression)
30 #:use-module (gnu packages gcc)
31 #:use-module (gnu packages graph)
32 #:use-module (gnu packages maths)
33 #:use-module (gnu packages pkg-config)
34 #:use-module (gnu packages statistics)
35 #:use-module (gnu packages web))
40 (define-public r-bsgenome-celegans-ucsc-ce6
42 (name "r-bsgenome-celegans-ucsc-ce6")
46 ;; We cannot use bioconductor-uri here because this tarball is
47 ;; located under "data/annotation/" instead of "bioc/".
48 (uri (string-append "https://www.bioconductor.org/packages/"
49 "release/data/annotation/src/contrib/"
50 "BSgenome.Celegans.UCSC.ce6_"
54 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
56 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
57 (build-system r-build-system)
58 ;; As this package provides little more than a very large data file it
59 ;; doesn't make sense to build substitutes.
60 (arguments `(#:substitutable? #f))
62 `(("r-bsgenome" ,r-bsgenome)))
64 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
65 (synopsis "Full genome sequences for Worm")
67 "This package provides full genome sequences for Caenorhabditis
68 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
70 (license license:artistic2.0)))
72 (define-public r-bsgenome-celegans-ucsc-ce10
74 (name "r-bsgenome-celegans-ucsc-ce10")
78 ;; We cannot use bioconductor-uri here because this tarball is
79 ;; located under "data/annotation/" instead of "bioc/".
80 (uri (string-append "https://www.bioconductor.org/packages/"
81 "release/data/annotation/src/contrib/"
82 "BSgenome.Celegans.UCSC.ce10_"
86 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
88 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
89 (build-system r-build-system)
90 ;; As this package provides little more than a very large data file it
91 ;; doesn't make sense to build substitutes.
92 (arguments `(#:substitutable? #f))
94 `(("r-bsgenome" ,r-bsgenome)))
96 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
97 (synopsis "Full genome sequences for Worm")
99 "This package provides full genome sequences for Caenorhabditis
100 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
102 (license license:artistic2.0)))
104 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
106 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
110 ;; We cannot use bioconductor-uri here because this tarball is
111 ;; located under "data/annotation/" instead of "bioc/".
112 (uri (string-append "https://www.bioconductor.org/packages/"
113 "release/data/annotation/src/contrib/"
114 "BSgenome.Dmelanogaster.UCSC.dm6_"
118 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
120 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
121 (build-system r-build-system)
122 ;; As this package provides little more than a very large data file it
123 ;; doesn't make sense to build substitutes.
124 (arguments `(#:substitutable? #f))
126 `(("r-bsgenome" ,r-bsgenome)))
128 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
129 (synopsis "Full genome sequences for Fly")
131 "This package provides full genome sequences for Drosophila
132 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
134 (license license:artistic2.0)))
136 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
138 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
142 ;; We cannot use bioconductor-uri here because this tarball is
143 ;; located under "data/annotation/" instead of "bioc/".
144 (uri (string-append "https://www.bioconductor.org/packages/"
145 "release/data/annotation/src/contrib/"
146 "BSgenome.Dmelanogaster.UCSC.dm3_"
150 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
152 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
153 (build-system r-build-system)
154 ;; As this package provides little more than a very large data file it
155 ;; doesn't make sense to build substitutes.
156 (arguments `(#:substitutable? #f))
158 `(("r-bsgenome" ,r-bsgenome)))
160 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
161 (synopsis "Full genome sequences for Fly")
163 "This package provides full genome sequences for Drosophila
164 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
165 Biostrings objects.")
166 (license license:artistic2.0)))
168 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
170 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
174 ;; We cannot use bioconductor-uri here because this tarball is
175 ;; located under "data/annotation/" instead of "bioc/".
176 (uri (string-append "http://www.bioconductor.org/packages/"
177 "release/data/annotation/src/contrib/"
178 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
182 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
184 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
185 (build-system r-build-system)
187 `(("r-bsgenome" ,r-bsgenome)
188 ("r-bsgenome-dmelanogaster-ucsc-dm3"
189 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
190 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
191 (synopsis "Full masked genome sequences for Fly")
193 "This package provides full masked genome sequences for Drosophila
194 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
195 Biostrings objects. The sequences are the same as in
196 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
197 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
198 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
199 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
200 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
201 (license license:artistic2.0)))
203 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
205 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
209 ;; We cannot use bioconductor-uri here because this tarball is
210 ;; located under "data/annotation/" instead of "bioc/".
211 (uri (string-append "https://www.bioconductor.org/packages/"
212 "release/data/annotation/src/contrib/"
213 "BSgenome.Hsapiens.1000genomes.hs37d5_"
217 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
219 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
220 (build-system r-build-system)
221 ;; As this package provides little more than a very large data file it
222 ;; doesn't make sense to build substitutes.
223 (arguments `(#:substitutable? #f))
225 `(("r-bsgenome" ,r-bsgenome)))
227 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
228 (synopsis "Full genome sequences for Homo sapiens")
230 "This package provides full genome sequences for Homo sapiens from
231 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
232 (license license:artistic2.0)))
234 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
236 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
240 ;; We cannot use bioconductor-uri here because this tarball is
241 ;; located under "data/annotation/" instead of "bioc/".
242 (uri (string-append "http://www.bioconductor.org/packages/"
243 "release/data/annotation/src/contrib/"
244 "BSgenome.Hsapiens.UCSC.hg19.masked_"
248 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
250 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
251 (build-system r-build-system)
253 `(("r-bsgenome" ,r-bsgenome)
254 ("r-bsgenome-hsapiens-ucsc-hg19"
255 ,r-bsgenome-hsapiens-ucsc-hg19)))
256 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
257 (synopsis "Full masked genome sequences for Homo sapiens")
259 "This package provides full genome sequences for Homo sapiens (Human) as
260 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
261 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
262 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
263 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
264 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
265 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
267 (license license:artistic2.0)))
269 (define-public r-bsgenome-mmusculus-ucsc-mm9
271 (name "r-bsgenome-mmusculus-ucsc-mm9")
275 ;; We cannot use bioconductor-uri here because this tarball is
276 ;; located under "data/annotation/" instead of "bioc/".
277 (uri (string-append "https://www.bioconductor.org/packages/"
278 "release/data/annotation/src/contrib/"
279 "BSgenome.Mmusculus.UCSC.mm9_"
283 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
285 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
286 (build-system r-build-system)
287 ;; As this package provides little more than a very large data file it
288 ;; doesn't make sense to build substitutes.
289 (arguments `(#:substitutable? #f))
291 `(("r-bsgenome" ,r-bsgenome)))
293 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
294 (synopsis "Full genome sequences for Mouse")
296 "This package provides full genome sequences for Mus musculus (Mouse) as
297 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
298 (license license:artistic2.0)))
300 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
302 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
306 ;; We cannot use bioconductor-uri here because this tarball is
307 ;; located under "data/annotation/" instead of "bioc/".
308 (uri (string-append "http://www.bioconductor.org/packages/"
309 "release/data/annotation/src/contrib/"
310 "BSgenome.Mmusculus.UCSC.mm9.masked_"
314 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
316 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
317 (build-system r-build-system)
319 `(("r-bsgenome" ,r-bsgenome)
320 ("r-bsgenome-mmusculus-ucsc-mm9"
321 ,r-bsgenome-mmusculus-ucsc-mm9)))
322 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
323 (synopsis "Full masked genome sequences for Mouse")
325 "This package provides full genome sequences for Mus musculus (Mouse) as
326 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
327 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
328 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
329 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
330 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
331 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
333 (license license:artistic2.0)))
335 (define-public r-bsgenome-mmusculus-ucsc-mm10
337 (name "r-bsgenome-mmusculus-ucsc-mm10")
341 ;; We cannot use bioconductor-uri here because this tarball is
342 ;; located under "data/annotation/" instead of "bioc/".
343 (uri (string-append "https://www.bioconductor.org/packages/"
344 "release/data/annotation/src/contrib/"
345 "BSgenome.Mmusculus.UCSC.mm10_"
349 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
351 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
352 (build-system r-build-system)
353 ;; As this package provides little more than a very large data file it
354 ;; doesn't make sense to build substitutes.
355 (arguments `(#:substitutable? #f))
357 `(("r-bsgenome" ,r-bsgenome)))
359 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
360 (synopsis "Full genome sequences for Mouse")
362 "This package provides full genome sequences for Mus
363 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
364 in Biostrings objects.")
365 (license license:artistic2.0)))
367 (define-public r-org-ce-eg-db
369 (name "r-org-ce-eg-db")
373 ;; We cannot use bioconductor-uri here because this tarball is
374 ;; located under "data/annotation/" instead of "bioc/".
375 (uri (string-append "https://www.bioconductor.org/packages/"
376 "release/data/annotation/src/contrib/"
377 "org.Ce.eg.db_" version ".tar.gz"))
380 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
382 `((upstream-name . "org.Ce.eg.db")))
383 (build-system r-build-system)
385 `(("r-annotationdbi" ,r-annotationdbi)))
386 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
387 (synopsis "Genome wide annotation for Worm")
389 "This package provides mappings from Entrez gene identifiers to various
390 annotations for the genome of the model worm Caenorhabditis elegans.")
391 (license license:artistic2.0)))
393 (define-public r-org-dm-eg-db
395 (name "r-org-dm-eg-db")
399 ;; We cannot use bioconductor-uri here because this tarball is
400 ;; located under "data/annotation/" instead of "bioc/".
401 (uri (string-append "https://www.bioconductor.org/packages/"
402 "release/data/annotation/src/contrib/"
403 "org.Dm.eg.db_" version ".tar.gz"))
406 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
408 `((upstream-name . "org.Dm.eg.db")))
409 (build-system r-build-system)
411 `(("r-annotationdbi" ,r-annotationdbi)))
412 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
413 (synopsis "Genome wide annotation for Fly")
415 "This package provides mappings from Entrez gene identifiers to various
416 annotations for the genome of the model fruit fly Drosophila melanogaster.")
417 (license license:artistic2.0)))
419 (define-public r-org-dr-eg-db
421 (name "r-org-dr-eg-db")
425 ;; We cannot use bioconductor-uri here because this tarball is
426 ;; located under "data/annotation/" instead of "bioc/".
427 (uri (string-append "https://www.bioconductor.org/packages/"
428 "release/data/annotation/src/contrib/"
429 "org.Dr.eg.db_" version ".tar.gz"))
432 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
434 `((upstream-name . "org.Dr.eg.db")))
435 (build-system r-build-system)
437 `(("r-annotationdbi" ,r-annotationdbi)))
438 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
439 (synopsis "Annotation for Zebrafish")
441 "This package provides genome wide annotations for Zebrafish, primarily
442 based on mapping using Entrez Gene identifiers.")
443 (license license:artistic2.0)))
445 (define-public r-org-hs-eg-db
447 (name "r-org-hs-eg-db")
451 ;; We cannot use bioconductor-uri here because this tarball is
452 ;; located under "data/annotation/" instead of "bioc/".
453 (uri (string-append "https://www.bioconductor.org/packages/"
454 "release/data/annotation/src/contrib/"
455 "org.Hs.eg.db_" version ".tar.gz"))
458 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
460 `((upstream-name . "org.Hs.eg.db")))
461 (build-system r-build-system)
463 `(("r-annotationdbi" ,r-annotationdbi)))
464 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
465 (synopsis "Genome wide annotation for Human")
467 "This package contains genome-wide annotations for Human, primarily based
468 on mapping using Entrez Gene identifiers.")
469 (license license:artistic2.0)))
471 (define-public r-org-mm-eg-db
473 (name "r-org-mm-eg-db")
477 ;; We cannot use bioconductor-uri here because this tarball is
478 ;; located under "data/annotation/" instead of "bioc/".
479 (uri (string-append "https://www.bioconductor.org/packages/"
480 "release/data/annotation/src/contrib/"
481 "org.Mm.eg.db_" version ".tar.gz"))
484 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
486 `((upstream-name . "org.Mm.eg.db")))
487 (build-system r-build-system)
489 `(("r-annotationdbi" ,r-annotationdbi)))
490 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
491 (synopsis "Genome wide annotation for Mouse")
493 "This package provides mappings from Entrez gene identifiers to various
494 annotations for the genome of the model mouse Mus musculus.")
495 (license license:artistic2.0)))
497 (define-public r-bsgenome-hsapiens-ucsc-hg19
499 (name "r-bsgenome-hsapiens-ucsc-hg19")
503 ;; We cannot use bioconductor-uri here because this tarball is
504 ;; located under "data/annotation/" instead of "bioc/".
505 (uri (string-append "https://www.bioconductor.org/packages/"
506 "release/data/annotation/src/contrib/"
507 "BSgenome.Hsapiens.UCSC.hg19_"
511 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
513 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
514 (build-system r-build-system)
515 ;; As this package provides little more than a very large data file it
516 ;; doesn't make sense to build substitutes.
517 (arguments `(#:substitutable? #f))
519 `(("r-bsgenome" ,r-bsgenome)))
521 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
522 (synopsis "Full genome sequences for Homo sapiens")
524 "This package provides full genome sequences for Homo sapiens as provided
525 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
526 (license license:artistic2.0)))
528 (define-public r-genelendatabase
530 (name "r-genelendatabase")
535 ;; We cannot use bioconductor-uri here because this tarball is
536 ;; located under "data/experiment/" instead of "bioc/".
537 (uri (string-append "https://bioconductor.org/packages/"
538 "release/data/experiment/src/contrib"
539 "/geneLenDataBase_" version ".tar.gz"))
542 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
544 `((upstream-name . "geneLenDataBase")))
545 (build-system r-build-system)
547 `(("r-rtracklayer" ,r-rtracklayer)
548 ("r-genomicfeatures" ,r-genomicfeatures)))
549 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
550 (synopsis "Lengths of mRNA transcripts for a number of genomes")
552 "This package provides the lengths of mRNA transcripts for a number of
553 genomes and gene ID formats, largely based on the UCSC table browser.")
554 (license license:lgpl2.0+)))
556 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
558 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
562 ;; We cannot use bioconductor-uri here because this tarball is
563 ;; located under "data/annotation/" instead of "bioc/".
564 (uri (string-append "https://bioconductor.org/packages/"
565 "release/data/annotation/src/contrib"
566 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
570 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
572 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
573 (build-system r-build-system)
574 ;; As this package provides little more than a very large data file it
575 ;; doesn't make sense to build substitutes.
576 (arguments `(#:substitutable? #f))
578 `(("r-genomicfeatures" ,r-genomicfeatures)))
580 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
581 (synopsis "Annotation package for human genome in TxDb format")
583 "This package provides an annotation database of Homo sapiens genome
584 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
585 track. The database is exposed as a @code{TxDb} object.")
586 (license license:artistic2.0)))
588 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
590 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
594 ;; We cannot use bioconductor-uri here because this tarball is
595 ;; located under "data/annotation/" instead of "bioc/".
596 (uri (string-append "https://bioconductor.org/packages/"
597 "release/data/annotation/src/contrib"
598 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
602 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
604 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
605 (build-system r-build-system)
607 `(("r-genomicfeatures" ,r-genomicfeatures)
608 ("r-annotationdbi" ,r-annotationdbi)))
610 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
611 (synopsis "Annotation package for mouse genome in TxDb format")
613 "This package provides an annotation database of Mouse genome data. It
614 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
615 database is exposed as a @code{TxDb} object.")
616 (license license:artistic2.0)))
618 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
620 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
624 ;; We cannot use bioconductor-uri here because this tarball is
625 ;; located under "data/annotation/" instead of "bioc/".
626 (uri (string-append "https://www.bioconductor.org/packages/"
627 "release/data/annotation/src/contrib/"
628 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
632 "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
634 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
635 (build-system r-build-system)
636 ;; As this package provides little more than a very large data file it
637 ;; doesn't make sense to build substitutes.
638 (arguments `(#:substitutable? #f))
640 `(("r-bsgenome" ,r-bsgenome)
641 ("r-genomicfeatures" ,r-genomicfeatures)
642 ("r-annotationdbi" ,r-annotationdbi)))
644 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
645 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
647 "This package loads a TxDb object, which is an R interface to
648 prefabricated databases contained in this package. This package provides
649 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
650 based on the knownGene track.")
651 (license license:artistic2.0)))
653 (define-public r-fdb-infiniummethylation-hg19
655 (name "r-fdb-infiniummethylation-hg19")
659 ;; We cannot use bioconductor-uri here because this tarball is
660 ;; located under "data/annotation/" instead of "bioc/".
661 (uri (string-append "https://www.bioconductor.org/packages/"
662 "release/data/annotation/src/contrib/"
663 "FDb.InfiniumMethylation.hg19_"
667 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
669 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
670 (build-system r-build-system)
672 `(("r-biostrings" ,r-biostrings)
673 ("r-genomicfeatures" ,r-genomicfeatures)
674 ("r-annotationdbi" ,r-annotationdbi)
675 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
676 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
677 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
678 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
680 "This is an annotation package for Illumina Infinium DNA methylation
681 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
683 (license license:artistic2.0)))
685 (define-public r-illuminahumanmethylationepicmanifest
687 (name "r-illuminahumanmethylationepicmanifest")
691 ;; We cannot use bioconductor-uri here because this tarball is
692 ;; located under "data/annotation/" instead of "bioc/".
693 (uri (string-append "https://www.bioconductor.org/packages/"
694 "release/data/annotation/src/contrib/"
695 "IlluminaHumanMethylationEPICmanifest_"
699 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
701 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
702 (build-system r-build-system)
704 `(("r-minfi" ,r-minfi)))
705 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
706 (synopsis "Manifest for Illumina's EPIC methylation arrays")
708 "This is a manifest package for Illumina's EPIC methylation arrays.")
709 (license license:artistic2.0)))
711 (define-public r-do-db
717 ;; We cannot use bioconductor-uri here because this tarball is
718 ;; located under "data/annotation/" instead of "bioc/".
719 (uri (string-append "https://www.bioconductor.org/packages/"
720 "release/data/annotation/src/contrib/"
721 "DO.db_" version ".tar.gz"))
724 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
726 `((upstream-name . "DO.db")))
727 (build-system r-build-system)
729 `(("r-annotationdbi" ,r-annotationdbi)))
730 (home-page "https://www.bioconductor.org/packages/DO.db/")
731 (synopsis "Annotation maps describing the entire Disease Ontology")
733 "This package provides a set of annotation maps describing the entire
735 (license license:artistic2.0)))
740 (define-public r-hsmmsinglecell
742 (name "r-hsmmsinglecell")
746 ;; We cannot use bioconductor-uri here because this tarball is
747 ;; located under "data/experiment/" instead of "bioc/".
748 (uri (string-append "https://www.bioconductor.org/packages/"
749 "release/data/experiment/src/contrib/"
750 "HSMMSingleCell_" version ".tar.gz"))
753 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
755 `((upstream-name . "HSMMSingleCell")))
756 (build-system r-build-system)
757 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
758 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
760 "Skeletal myoblasts undergo a well-characterized sequence of
761 morphological and transcriptional changes during differentiation. In this
762 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
763 under high mitogen conditions (GM) and then differentiated by switching to
764 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
765 hundred cells taken over a time-course of serum-induced differentiation.
766 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
767 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
768 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
769 which were then sequenced to a depth of ~4 million reads per library,
770 resulting in a complete gene expression profile for each cell.")
771 (license license:artistic2.0)))
776 (define-public r-biocgenerics
778 (name "r-biocgenerics")
782 (uri (bioconductor-uri "BiocGenerics" version))
785 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
787 `((upstream-name . "BiocGenerics")))
788 (build-system r-build-system)
789 (home-page "https://bioconductor.org/packages/BiocGenerics")
790 (synopsis "S4 generic functions for Bioconductor")
792 "This package provides S4 generic functions needed by many Bioconductor
794 (license license:artistic2.0)))
796 (define-public r-annotate
803 (uri (bioconductor-uri "annotate" version))
806 "0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"))))
807 (build-system r-build-system)
809 `(("r-annotationdbi" ,r-annotationdbi)
810 ("r-biobase" ,r-biobase)
811 ("r-biocgenerics" ,r-biocgenerics)
815 ("r-xtable" ,r-xtable)))
817 "https://bioconductor.org/packages/annotate")
818 (synopsis "Annotation for microarrays")
819 (description "This package provides R environments for the annotation of
821 (license license:artistic2.0)))
823 (define-public r-hpar
830 (uri (bioconductor-uri "hpar" version))
833 "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
834 (build-system r-build-system)
835 (home-page "https://bioconductor.org/packages/hpar/")
836 (synopsis "Human Protein Atlas in R")
837 (description "This package provides a simple interface to and data from
838 the Human Protein Atlas project.")
839 (license license:artistic2.0)))
841 (define-public r-regioner
848 (uri (bioconductor-uri "regioneR" version))
851 "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
852 (properties `((upstream-name . "regioneR")))
853 (build-system r-build-system)
855 `(("r-biostrings" ,r-biostrings)
856 ("r-bsgenome" ,r-bsgenome)
857 ("r-genomeinfodb" ,r-genomeinfodb)
858 ("r-genomicranges" ,r-genomicranges)
859 ("r-iranges" ,r-iranges)
860 ("r-memoise" ,r-memoise)
861 ("r-rtracklayer" ,r-rtracklayer)
862 ("r-s4vectors" ,r-s4vectors)))
863 (home-page "https://bioconductor.org/packages/regioneR/")
864 (synopsis "Association analysis of genomic regions")
865 (description "This package offers a statistical framework based on
866 customizable permutation tests to assess the association between genomic
867 region sets and other genomic features.")
868 (license license:artistic2.0)))
870 (define-public r-geneplotter
872 (name "r-geneplotter")
877 (uri (bioconductor-uri "geneplotter" version))
880 "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
881 (build-system r-build-system)
883 `(("r-annotate" ,r-annotate)
884 ("r-annotationdbi" ,r-annotationdbi)
885 ("r-biobase" ,r-biobase)
886 ("r-biocgenerics" ,r-biocgenerics)
887 ("r-lattice" ,r-lattice)
888 ("r-rcolorbrewer" ,r-rcolorbrewer)))
889 (home-page "https://bioconductor.org/packages/geneplotter")
890 (synopsis "Graphics functions for genomic data")
892 "This package provides functions for plotting genomic data.")
893 (license license:artistic2.0)))
895 (define-public r-qvalue
902 (uri (bioconductor-uri "qvalue" version))
905 "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
906 (build-system r-build-system)
908 `(("r-ggplot2" ,r-ggplot2)
909 ("r-reshape2" ,r-reshape2)))
910 (home-page "http://github.com/jdstorey/qvalue")
911 (synopsis "Q-value estimation for false discovery rate control")
913 "This package takes a list of p-values resulting from the simultaneous
914 testing of many hypotheses and estimates their q-values and local @dfn{false
915 discovery rate} (FDR) values. The q-value of a test measures the proportion
916 of false positives incurred when that particular test is called significant.
917 The local FDR measures the posterior probability the null hypothesis is true
918 given the test's p-value. Various plots are automatically generated, allowing
919 one to make sensible significance cut-offs. The software can be applied to
920 problems in genomics, brain imaging, astrophysics, and data mining.")
921 ;; Any version of the LGPL.
922 (license license:lgpl3+)))
924 (define-public r-diffbind
931 (uri (bioconductor-uri "DiffBind" version))
934 "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
935 (properties `((upstream-name . "DiffBind")))
936 (build-system r-build-system)
941 ("r-biocparallel" ,r-biocparallel)
942 ("r-deseq2" ,r-deseq2)
945 ("r-genomicalignments" ,r-genomicalignments)
946 ("r-genomicranges" ,r-genomicranges)
947 ("r-ggplot2" ,r-ggplot2)
948 ("r-ggrepel" ,r-ggrepel)
949 ("r-gplots" ,r-gplots)
950 ("r-iranges" ,r-iranges)
951 ("r-lattice" ,r-lattice)
953 ("r-locfit" ,r-locfit)
954 ("r-rcolorbrewer" , r-rcolorbrewer)
956 ("r-rsamtools" ,r-rsamtools)
957 ("r-s4vectors" ,r-s4vectors)
958 ("r-summarizedexperiment" ,r-summarizedexperiment)
959 ("r-systempiper" ,r-systempiper)
960 ("r-zlibbioc" ,r-zlibbioc)))
961 (home-page "http://bioconductor.org/packages/DiffBind")
962 (synopsis "Differential binding analysis of ChIP-Seq peak data")
964 "This package computes differentially bound sites from multiple
965 ChIP-seq experiments using affinity (quantitative) data. Also enables
966 occupancy (overlap) analysis and plotting functions.")
967 (license license:artistic2.0)))
969 (define-public r-ripseeker
976 (uri (bioconductor-uri "RIPSeeker" version))
979 "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
980 (properties `((upstream-name . "RIPSeeker")))
981 (build-system r-build-system)
983 `(("r-s4vectors" ,r-s4vectors)
984 ("r-iranges" ,r-iranges)
985 ("r-genomicranges" ,r-genomicranges)
986 ("r-summarizedexperiment" ,r-summarizedexperiment)
987 ("r-rsamtools" ,r-rsamtools)
988 ("r-genomicalignments" ,r-genomicalignments)
989 ("r-rtracklayer" ,r-rtracklayer)))
990 (home-page "http://bioconductor.org/packages/RIPSeeker")
992 "Identifying protein-associated transcripts from RIP-seq experiments")
994 "This package infers and discriminates RIP peaks from RIP-seq alignments
995 using two-state HMM with negative binomial emission probability. While
996 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
997 a suite of bioinformatics tools integrated within this self-contained software
998 package comprehensively addressing issues ranging from post-alignments
999 processing to visualization and annotation.")
1000 (license license:gpl2)))
1002 (define-public r-multtest
1009 (uri (bioconductor-uri "multtest" version))
1012 "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
1013 (build-system r-build-system)
1015 `(("r-survival" ,r-survival)
1016 ("r-biocgenerics" ,r-biocgenerics)
1017 ("r-biobase" ,r-biobase)
1018 ("r-mass" ,r-mass)))
1019 (home-page "http://bioconductor.org/packages/multtest")
1020 (synopsis "Resampling-based multiple hypothesis testing")
1022 "This package can do non-parametric bootstrap and permutation
1023 resampling-based multiple testing procedures (including empirical Bayes
1024 methods) for controlling the family-wise error rate (FWER), generalized
1025 family-wise error rate (gFWER), tail probability of the proportion of
1026 false positives (TPPFP), and false discovery rate (FDR). Several choices
1027 of bootstrap-based null distribution are implemented (centered, centered
1028 and scaled, quantile-transformed). Single-step and step-wise methods are
1029 available. Tests based on a variety of T- and F-statistics (including
1030 T-statistics based on regression parameters from linear and survival models
1031 as well as those based on correlation parameters) are included. When probing
1032 hypotheses with T-statistics, users may also select a potentially faster null
1033 distribution which is multivariate normal with mean zero and variance
1034 covariance matrix derived from the vector influence function. Results are
1035 reported in terms of adjusted P-values, confidence regions and test statistic
1036 cutoffs. The procedures are directly applicable to identifying differentially
1037 expressed genes in DNA microarray experiments.")
1038 (license license:lgpl3)))
1040 (define-public r-graph
1046 (uri (bioconductor-uri "graph" version))
1049 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
1050 (build-system r-build-system)
1052 `(("r-biocgenerics" ,r-biocgenerics)))
1053 (home-page "https://bioconductor.org/packages/graph")
1054 (synopsis "Handle graph data structures in R")
1056 "This package implements some simple graph handling capabilities for R.")
1057 (license license:artistic2.0)))
1059 (define-public r-codedepends
1061 (name "r-codedepends")
1066 (uri (cran-uri "CodeDepends" version))
1069 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1070 (properties `((upstream-name . "CodeDepends")))
1071 (build-system r-build-system)
1073 `(("r-codetools" ,r-codetools)
1074 ("r-graph" ,r-graph)
1076 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1077 (synopsis "Analysis of R code for reproducible research and code comprehension")
1079 "This package provides tools for analyzing R expressions or blocks of
1080 code and determining the dependencies between them. It focuses on R scripts,
1081 but can be used on the bodies of functions. There are many facilities
1082 including the ability to summarize or get a high-level view of code,
1083 determining dependencies between variables, code improvement suggestions.")
1084 ;; Any version of the GPL
1085 (license (list license:gpl2+ license:gpl3+))))
1087 (define-public r-chippeakanno
1089 (name "r-chippeakanno")
1094 (uri (bioconductor-uri "ChIPpeakAnno" version))
1097 "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
1098 (properties `((upstream-name . "ChIPpeakAnno")))
1099 (build-system r-build-system)
1101 `(("r-biocgenerics" ,r-biocgenerics)
1102 ("r-biocmanager" ,r-biocmanager)
1103 ("r-biostrings" ,r-biostrings)
1104 ("r-delayedarray" ,r-delayedarray)
1105 ("r-go-db" ,r-go-db)
1106 ("r-biomart" ,r-biomart)
1107 ("r-bsgenome" ,r-bsgenome)
1108 ("r-genomicfeatures" ,r-genomicfeatures)
1109 ("r-genomicranges" ,r-genomicranges)
1110 ("r-genomeinfodb" ,r-genomeinfodb)
1111 ("r-iranges" ,r-iranges)
1112 ("r-matrixstats" ,r-matrixstats)
1113 ("r-annotationdbi" ,r-annotationdbi)
1114 ("r-limma" ,r-limma)
1115 ("r-multtest" ,r-multtest)
1117 ("r-graph" ,r-graph)
1118 ("r-regioner" ,r-regioner)
1120 ("r-ensembldb" ,r-ensembldb)
1121 ("r-biobase" ,r-biobase)
1122 ("r-s4vectors" ,r-s4vectors)
1123 ("r-seqinr" ,r-seqinr)
1125 ("r-genomicalignments" ,r-genomicalignments)
1126 ("r-summarizedexperiment" ,r-summarizedexperiment)
1127 ("r-rsamtools" ,r-rsamtools)
1128 ("r-venndiagram" ,r-venndiagram)))
1129 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1130 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1132 "The package includes functions to retrieve the sequences around the peak,
1133 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1134 custom features such as most conserved elements and other transcription factor
1135 binding sites supplied by users. Starting 2.0.5, new functions have been added
1136 for finding the peaks with bi-directional promoters with summary statistics
1137 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1138 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1139 enrichedGO (addGeneIDs).")
1140 (license license:gpl2+)))
1142 (define-public r-marray
1148 (uri (bioconductor-uri "marray" version))
1150 (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
1151 (build-system r-build-system)
1153 `(("r-limma" ,r-limma)))
1154 (home-page "http://bioconductor.org/packages/marray")
1155 (synopsis "Exploratory analysis for two-color spotted microarray data")
1156 (description "This package contains class definitions for two-color spotted
1157 microarray data. It also includes fuctions for data input, diagnostic plots,
1158 normalization and quality checking.")
1159 (license license:lgpl2.0+)))
1161 (define-public r-cghbase
1167 (uri (bioconductor-uri "CGHbase" version))
1169 (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
1170 (properties `((upstream-name . "CGHbase")))
1171 (build-system r-build-system)
1173 `(("r-biobase" ,r-biobase)
1174 ("r-marray" ,r-marray)))
1175 (home-page "http://bioconductor.org/packages/CGHbase")
1176 (synopsis "Base functions and classes for arrayCGH data analysis")
1177 (description "This package contains functions and classes that are needed by
1178 the @code{arrayCGH} packages.")
1179 (license license:gpl2+)))
1181 (define-public r-cghcall
1187 (uri (bioconductor-uri "CGHcall" version))
1189 (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
1190 (properties `((upstream-name . "CGHcall")))
1191 (build-system r-build-system)
1193 `(("r-biobase" ,r-biobase)
1194 ("r-cghbase" ,r-cghbase)
1195 ("r-impute" ,r-impute)
1196 ("r-dnacopy" ,r-dnacopy)
1197 ("r-snowfall" ,r-snowfall)))
1198 (home-page "http://bioconductor.org/packages/CGHcall")
1199 (synopsis "Base functions and classes for arrayCGH data analysis")
1200 (description "This package contains functions and classes that are needed by
1201 @code{arrayCGH} packages.")
1202 (license license:gpl2+)))
1204 (define-public r-qdnaseq
1210 (uri (bioconductor-uri "QDNAseq" version))
1212 (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
1213 (properties `((upstream-name . "QDNAseq")))
1214 (build-system r-build-system)
1216 `(("r-biobase" ,r-biobase)
1217 ("r-biocparallel" ,r-biocparallel)
1218 ("r-cghbase" ,r-cghbase)
1219 ("r-cghcall" ,r-cghcall)
1220 ("r-dnacopy" ,r-dnacopy)
1221 ("r-genomicranges" ,r-genomicranges)
1222 ("r-iranges" ,r-iranges)
1223 ("r-matrixstats" ,r-matrixstats)
1224 ("r-r-utils" ,r-r-utils)
1225 ("r-rsamtools" ,r-rsamtools)))
1226 (home-page "http://bioconductor.org/packages/QDNAseq")
1227 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1228 (description "The genome is divided into non-overlapping fixed-sized bins,
1229 number of sequence reads in each counted, adjusted with a simultaneous
1230 two-dimensional loess correction for sequence mappability and GC content, and
1231 filtered to remove spurious regions in the genome. Downstream steps of
1232 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1234 (license license:gpl2+)))
1236 (define-public r-bayseq
1243 (uri (bioconductor-uri "baySeq" version))
1246 "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
1247 (properties `((upstream-name . "baySeq")))
1248 (build-system r-build-system)
1250 `(("r-abind" ,r-abind)
1251 ("r-edger" ,r-edger)
1252 ("r-genomicranges" ,r-genomicranges)))
1253 (home-page "https://bioconductor.org/packages/baySeq/")
1254 (synopsis "Bayesian analysis of differential expression patterns in count data")
1256 "This package identifies differential expression in high-throughput count
1257 data, such as that derived from next-generation sequencing machines,
1258 calculating estimated posterior likelihoods of differential expression (or
1259 more complex hypotheses) via empirical Bayesian methods.")
1260 (license license:gpl3)))
1262 (define-public r-chipcomp
1269 (uri (bioconductor-uri "ChIPComp" version))
1272 "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
1273 (properties `((upstream-name . "ChIPComp")))
1274 (build-system r-build-system)
1276 `(("r-biocgenerics" ,r-biocgenerics)
1277 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1278 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1279 ("r-genomeinfodb" ,r-genomeinfodb)
1280 ("r-genomicranges" ,r-genomicranges)
1281 ("r-iranges" ,r-iranges)
1282 ("r-limma" ,r-limma)
1283 ("r-rsamtools" ,r-rsamtools)
1284 ("r-rtracklayer" ,r-rtracklayer)
1285 ("r-s4vectors" ,r-s4vectors)))
1286 (home-page "https://bioconductor.org/packages/ChIPComp")
1287 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1289 "ChIPComp implements a statistical method for quantitative comparison of
1290 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1291 sites across multiple conditions considering matching control in ChIP-seq
1293 ;; Any version of the GPL.
1294 (license license:gpl3+)))
1296 (define-public r-riboprofiling
1298 (name "r-riboprofiling")
1303 (uri (bioconductor-uri "RiboProfiling" version))
1306 "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
1307 (properties `((upstream-name . "RiboProfiling")))
1308 (build-system r-build-system)
1310 `(("r-biocgenerics" ,r-biocgenerics)
1311 ("r-biostrings" ,r-biostrings)
1312 ("r-data-table" ,r-data-table)
1313 ("r-genomeinfodb" ,r-genomeinfodb)
1314 ("r-genomicalignments" ,r-genomicalignments)
1315 ("r-genomicfeatures" ,r-genomicfeatures)
1316 ("r-genomicranges" ,r-genomicranges)
1317 ("r-ggbio" ,r-ggbio)
1318 ("r-ggplot2" ,r-ggplot2)
1319 ("r-iranges" ,r-iranges)
1321 ("r-reshape2" ,r-reshape2)
1322 ("r-rsamtools" ,r-rsamtools)
1323 ("r-rtracklayer" ,r-rtracklayer)
1324 ("r-s4vectors" ,r-s4vectors)
1325 ("r-sqldf" ,r-sqldf)))
1326 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1327 (synopsis "Ribosome profiling data analysis")
1328 (description "Starting with a BAM file, this package provides the
1329 necessary functions for quality assessment, read start position recalibration,
1330 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1331 of count data: pairs, log fold-change, codon frequency and coverage
1332 assessment, principal component analysis on codon coverage.")
1333 (license license:gpl3)))
1335 (define-public r-riboseqr
1342 (uri (bioconductor-uri "riboSeqR" version))
1345 "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
1346 (properties `((upstream-name . "riboSeqR")))
1347 (build-system r-build-system)
1349 `(("r-abind" ,r-abind)
1350 ("r-bayseq" ,r-bayseq)
1351 ("r-genomeinfodb" ,r-genomeinfodb)
1352 ("r-genomicranges" ,r-genomicranges)
1353 ("r-iranges" ,r-iranges)
1354 ("r-rsamtools" ,r-rsamtools)
1355 ("r-seqlogo" ,r-seqlogo)))
1356 (home-page "https://bioconductor.org/packages/riboSeqR/")
1357 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1359 "This package provides plotting functions, frameshift detection and
1360 parsing of genetic sequencing data from ribosome profiling experiments.")
1361 (license license:gpl3)))
1363 (define-public r-interactionset
1365 (name "r-interactionset")
1370 (uri (bioconductor-uri "InteractionSet" version))
1373 "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
1375 `((upstream-name . "InteractionSet")))
1376 (build-system r-build-system)
1378 `(("r-biocgenerics" ,r-biocgenerics)
1379 ("r-genomeinfodb" ,r-genomeinfodb)
1380 ("r-genomicranges" ,r-genomicranges)
1381 ("r-iranges" ,r-iranges)
1382 ("r-matrix" ,r-matrix)
1384 ("r-s4vectors" ,r-s4vectors)
1385 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1386 (home-page "https://bioconductor.org/packages/InteractionSet")
1387 (synopsis "Base classes for storing genomic interaction data")
1389 "This packages provides the @code{GInteractions},
1390 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1391 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1393 (license license:gpl3)))
1395 (define-public r-genomicinteractions
1397 (name "r-genomicinteractions")
1402 (uri (bioconductor-uri "GenomicInteractions" version))
1405 "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
1407 `((upstream-name . "GenomicInteractions")))
1408 (build-system r-build-system)
1410 `(("r-biobase" ,r-biobase)
1411 ("r-biocgenerics" ,r-biocgenerics)
1412 ("r-data-table" ,r-data-table)
1413 ("r-dplyr" ,r-dplyr)
1414 ("r-genomeinfodb" ,r-genomeinfodb)
1415 ("r-genomicranges" ,r-genomicranges)
1416 ("r-ggplot2" ,r-ggplot2)
1417 ("r-gridextra" ,r-gridextra)
1419 ("r-igraph" ,r-igraph)
1420 ("r-interactionset" ,r-interactionset)
1421 ("r-iranges" ,r-iranges)
1422 ("r-rsamtools" ,r-rsamtools)
1423 ("r-rtracklayer" ,r-rtracklayer)
1424 ("r-s4vectors" ,r-s4vectors)
1425 ("r-stringr" ,r-stringr)))
1426 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1427 (synopsis "R package for handling genomic interaction data")
1429 "This R package provides tools for handling genomic interaction data,
1430 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1431 information and producing various plots and statistics.")
1432 (license license:gpl3)))
1434 (define-public r-ctc
1441 (uri (bioconductor-uri "ctc" version))
1444 "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
1445 (build-system r-build-system)
1446 (propagated-inputs `(("r-amap" ,r-amap)))
1447 (home-page "https://bioconductor.org/packages/ctc/")
1448 (synopsis "Cluster and tree conversion")
1450 "This package provides tools for exporting and importing classification
1451 trees and clusters to other programs.")
1452 (license license:gpl2)))
1454 (define-public r-goseq
1461 (uri (bioconductor-uri "goseq" version))
1464 "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
1465 (build-system r-build-system)
1467 `(("r-annotationdbi" ,r-annotationdbi)
1468 ("r-biasedurn" ,r-biasedurn)
1469 ("r-biocgenerics" ,r-biocgenerics)
1470 ("r-genelendatabase" ,r-genelendatabase)
1471 ("r-go-db" ,r-go-db)
1472 ("r-mgcv" ,r-mgcv)))
1473 (home-page "https://bioconductor.org/packages/goseq/")
1474 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1476 "This package provides tools to detect Gene Ontology and/or other user
1477 defined categories which are over/under represented in RNA-seq data.")
1478 (license license:lgpl2.0+)))
1480 (define-public r-glimma
1487 (uri (bioconductor-uri "Glimma" version))
1490 "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
1491 (properties `((upstream-name . "Glimma")))
1492 (build-system r-build-system)
1494 `(("r-edger" ,r-edger)
1495 ("r-jsonlite" ,r-jsonlite)
1496 ("r-s4vectors" ,r-s4vectors)))
1497 (home-page "https://github.com/Shians/Glimma")
1498 (synopsis "Interactive HTML graphics")
1500 "This package generates interactive visualisations for analysis of
1501 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1502 HTML page. The interactions are built on top of the popular static
1503 representations of analysis results in order to provide additional
1505 (license license:lgpl3)))
1507 (define-public r-rots
1514 (uri (bioconductor-uri "ROTS" version))
1517 "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
1518 (properties `((upstream-name . "ROTS")))
1519 (build-system r-build-system)
1521 `(("r-biobase" ,r-biobase)
1522 ("r-rcpp" ,r-rcpp)))
1523 (home-page "https://bioconductor.org/packages/ROTS/")
1524 (synopsis "Reproducibility-Optimized Test Statistic")
1526 "This package provides tools for calculating the
1527 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1529 (license license:gpl2+)))
1531 (define-public r-plgem
1538 (uri (bioconductor-uri "plgem" version))
1541 "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
1542 (build-system r-build-system)
1544 `(("r-biobase" ,r-biobase)
1545 ("r-mass" ,r-mass)))
1546 (home-page "http://www.genopolis.it")
1547 (synopsis "Detect differential expression in microarray and proteomics datasets")
1549 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1550 model the variance-versus-mean dependence that exists in a variety of
1551 genome-wide datasets, including microarray and proteomics data. The use of
1552 PLGEM has been shown to improve the detection of differentially expressed
1553 genes or proteins in these datasets.")
1554 (license license:gpl2)))
1556 (define-public r-inspect
1563 (uri (bioconductor-uri "INSPEcT" version))
1566 "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
1567 (properties `((upstream-name . "INSPEcT")))
1568 (build-system r-build-system)
1570 `(("r-biobase" ,r-biobase)
1571 ("r-biocgenerics" ,r-biocgenerics)
1572 ("r-biocparallel" ,r-biocparallel)
1573 ("r-deseq2" ,r-deseq2)
1574 ("r-desolve" ,r-desolve)
1575 ("r-genomicalignments" ,r-genomicalignments)
1576 ("r-genomicfeatures" ,r-genomicfeatures)
1577 ("r-genomicranges" ,r-genomicranges)
1578 ("r-iranges" ,r-iranges)
1579 ("r-plgem" ,r-plgem)
1580 ("r-preprocesscore" ,r-preprocesscore)
1582 ("r-rootsolve" ,r-rootsolve)
1583 ("r-rsamtools" ,r-rsamtools)
1584 ("r-s4vectors" ,r-s4vectors)
1585 ("r-shiny" ,r-shiny)
1586 ("r-summarizedexperiment" ,r-summarizedexperiment)
1587 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1588 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1589 (home-page "https://bioconductor.org/packages/INSPEcT")
1590 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1592 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1593 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1594 order to evaluate synthesis, processing and degradation rates and assess via
1595 modeling the rates that determines changes in mature mRNA levels.")
1596 (license license:gpl2)))
1598 (define-public r-dnabarcodes
1600 (name "r-dnabarcodes")
1605 (uri (bioconductor-uri "DNABarcodes" version))
1608 "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
1609 (properties `((upstream-name . "DNABarcodes")))
1610 (build-system r-build-system)
1613 ("r-matrix" ,r-matrix)
1614 ("r-rcpp" ,r-rcpp)))
1615 (home-page "https://bioconductor.org/packages/DNABarcodes")
1616 (synopsis "Create and analyze DNA barcodes")
1618 "This package offers tools to create DNA barcode sets capable of
1619 correcting insertion, deletion, and substitution errors. Existing barcodes
1620 can be analyzed regarding their minimal, maximal and average distances between
1621 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1622 demultiplexed, i.e. assigned to their original reference barcode.")
1623 (license license:gpl2)))
1625 (define-public r-ruvseq
1632 (uri (bioconductor-uri "RUVSeq" version))
1635 "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
1636 (properties `((upstream-name . "RUVSeq")))
1637 (build-system r-build-system)
1639 `(("r-biobase" ,r-biobase)
1640 ("r-edaseq" ,r-edaseq)
1641 ("r-edger" ,r-edger)
1642 ("r-mass" ,r-mass)))
1643 (home-page "https://github.com/drisso/RUVSeq")
1644 (synopsis "Remove unwanted variation from RNA-Seq data")
1646 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1647 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1649 (license license:artistic2.0)))
1651 (define-public r-biocneighbors
1653 (name "r-biocneighbors")
1658 (uri (bioconductor-uri "BiocNeighbors" version))
1661 "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
1662 (properties `((upstream-name . "BiocNeighbors")))
1663 (build-system r-build-system)
1665 `(("r-biocparallel" ,r-biocparallel)
1667 ("r-rcppannoy" ,r-rcppannoy)
1668 ("r-s4vectors" ,r-s4vectors)))
1669 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1670 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1672 "This package implements exact and approximate methods for nearest
1673 neighbor detection, in a framework that allows them to be easily switched
1674 within Bioconductor packages or workflows. The exact algorithm is implemented
1675 using pre-clustering with the k-means algorithm. Functions are also provided
1676 to search for all neighbors within a given distance. Parallelization is
1677 achieved for all methods using the BiocParallel framework.")
1678 (license license:gpl3)))
1680 (define-public r-destiny
1687 (uri (bioconductor-uri "destiny" version))
1690 "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
1691 (build-system r-build-system)
1693 `(("r-biobase" ,r-biobase)
1694 ("r-biocgenerics" ,r-biocgenerics)
1696 ("r-ggthemes" ,r-ggthemes)
1697 ("r-hmisc" ,r-hmisc)
1698 ("r-igraph" ,r-igraph)
1699 ("r-matrix" ,r-matrix)
1700 ("r-proxy" ,r-proxy)
1702 ("r-rcppeigen" ,r-rcppeigen)
1703 ("r-scales" ,r-scales)
1704 ("r-scatterplot3d" ,r-scatterplot3d)
1705 ("r-smoother" ,r-smoother)
1706 ("r-summarizedexperiment" ,r-summarizedexperiment)
1708 (home-page "https://bioconductor.org/packages/destiny/")
1709 (synopsis "Create and plot diffusion maps")
1710 (description "This package provides tools to create and plot diffusion
1712 ;; Any version of the GPL
1713 (license license:gpl3+)))
1715 (define-public r-savr
1722 (uri (bioconductor-uri "savR" version))
1725 "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
1726 (properties `((upstream-name . "savR")))
1727 (build-system r-build-system)
1729 `(("r-ggplot2" ,r-ggplot2)
1730 ("r-gridextra" ,r-gridextra)
1731 ("r-reshape2" ,r-reshape2)
1732 ("r-scales" ,r-scales)
1734 (home-page "https://github.com/bcalder/savR")
1735 (synopsis "Parse and analyze Illumina SAV files")
1737 "This package provides tools to parse Illumina Sequence Analysis
1738 Viewer (SAV) files, access data, and generate QC plots.")
1739 (license license:agpl3+)))
1741 (define-public r-chipexoqual
1743 (name "r-chipexoqual")
1748 (uri (bioconductor-uri "ChIPexoQual" version))
1751 "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
1752 (properties `((upstream-name . "ChIPexoQual")))
1753 (build-system r-build-system)
1755 `(("r-biocparallel" ,r-biocparallel)
1756 ("r-biovizbase" ,r-biovizbase)
1757 ("r-broom" ,r-broom)
1758 ("r-data-table" ,r-data-table)
1759 ("r-dplyr" ,r-dplyr)
1760 ("r-genomeinfodb" ,r-genomeinfodb)
1761 ("r-genomicalignments" ,r-genomicalignments)
1762 ("r-genomicranges" ,r-genomicranges)
1763 ("r-ggplot2" ,r-ggplot2)
1764 ("r-hexbin" ,r-hexbin)
1765 ("r-iranges" ,r-iranges)
1766 ("r-rcolorbrewer" ,r-rcolorbrewer)
1767 ("r-rmarkdown" ,r-rmarkdown)
1768 ("r-rsamtools" ,r-rsamtools)
1769 ("r-s4vectors" ,r-s4vectors)
1770 ("r-scales" ,r-scales)
1771 ("r-viridis" ,r-viridis)))
1772 (home-page "https://github.com/keleslab/ChIPexoQual")
1773 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1775 "This package provides a quality control pipeline for ChIP-exo/nexus
1777 (license license:gpl2+)))
1779 (define-public r-copynumber
1781 (name "r-copynumber")
1785 (uri (bioconductor-uri "copynumber" version))
1788 "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
1789 (build-system r-build-system)
1791 `(("r-s4vectors" ,r-s4vectors)
1792 ("r-iranges" ,r-iranges)
1793 ("r-genomicranges" ,r-genomicranges)
1794 ("r-biocgenerics" ,r-biocgenerics)))
1795 (home-page "https://bioconductor.org/packages/copynumber")
1796 (synopsis "Segmentation of single- and multi-track copy number data")
1798 "This package segments single- and multi-track copy number data by a
1799 penalized least squares regression method.")
1800 (license license:artistic2.0)))
1802 (define-public r-dnacopy
1809 (uri (bioconductor-uri "DNAcopy" version))
1812 "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
1813 (properties `((upstream-name . "DNAcopy")))
1814 (build-system r-build-system)
1815 (native-inputs `(("gfortran" ,gfortran)))
1816 (home-page "https://bioconductor.org/packages/DNAcopy")
1817 (synopsis "DNA copy number data analysis")
1819 "This package implements the @dfn{circular binary segmentation} (CBS)
1820 algorithm to segment DNA copy number data and identify genomic regions with
1821 abnormal copy number.")
1822 (license license:gpl2+)))
1824 ;; This is a CRAN package, but it uncharacteristically depends on a
1825 ;; Bioconductor package.
1826 (define-public r-htscluster
1828 (name "r-htscluster")
1833 (uri (cran-uri "HTSCluster" version))
1836 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1837 (properties `((upstream-name . "HTSCluster")))
1838 (build-system r-build-system)
1840 `(("r-capushe" ,r-capushe)
1841 ("r-edger" ,r-edger)
1842 ("r-plotrix" ,r-plotrix)))
1843 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1844 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1846 "This package provides a Poisson mixture model is implemented to cluster
1847 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
1848 estimation is performed using either the EM or CEM algorithm, and the slope
1849 heuristics are used for model selection (i.e., to choose the number of
1851 (license license:gpl3+)))
1853 (define-public r-deds
1860 (uri (bioconductor-uri "DEDS" version))
1863 "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
1864 (properties `((upstream-name . "DEDS")))
1865 (build-system r-build-system)
1866 (home-page "https://bioconductor.org/packages/DEDS/")
1867 (synopsis "Differential expression via distance summary for microarray data")
1869 "This library contains functions that calculate various statistics of
1870 differential expression for microarray data, including t statistics, fold
1871 change, F statistics, SAM, moderated t and F statistics and B statistics. It
1872 also implements a new methodology called DEDS (Differential Expression via
1873 Distance Summary), which selects differentially expressed genes by integrating
1874 and summarizing a set of statistics using a weighted distance approach.")
1875 ;; Any version of the LGPL.
1876 (license license:lgpl3+)))
1878 ;; This is a CRAN package, but since it depends on a Bioconductor package we
1880 (define-public r-nbpseq
1887 (uri (cran-uri "NBPSeq" version))
1890 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
1891 (properties `((upstream-name . "NBPSeq")))
1892 (build-system r-build-system)
1894 `(("r-qvalue" ,r-qvalue)))
1895 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
1896 (synopsis "Negative binomial models for RNA-Seq data")
1898 "This package provides negative binomial models for two-group comparisons
1899 and regression inferences from RNA-sequencing data.")
1900 (license license:gpl2)))
1902 (define-public r-ebseq
1909 (uri (bioconductor-uri "EBSeq" version))
1912 "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
1913 (properties `((upstream-name . "EBSeq")))
1914 (build-system r-build-system)
1916 `(("r-blockmodeling" ,r-blockmodeling)
1917 ("r-gplots" ,r-gplots)
1918 ("r-testthat" ,r-testthat)))
1919 (home-page "https://bioconductor.org/packages/EBSeq")
1920 (synopsis "Differential expression analysis of RNA-seq data")
1922 "This package provides tools for differential expression analysis at both
1923 gene and isoform level using RNA-seq data")
1924 (license license:artistic2.0)))
1926 (define-public r-lpsymphony
1928 (name "r-lpsymphony")
1933 (uri (bioconductor-uri "lpsymphony" version))
1936 "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
1937 (build-system r-build-system)
1939 `(("gfortran" ,gfortran)
1942 `(("pkg-config" ,pkg-config)))
1943 (home-page "http://r-forge.r-project.org/projects/rsymphony")
1944 (synopsis "Symphony integer linear programming solver in R")
1946 "This package was derived from Rsymphony. The package provides an R
1947 interface to SYMPHONY, a linear programming solver written in C++. The main
1948 difference between this package and Rsymphony is that it includes the solver
1949 source code, while Rsymphony expects to find header and library files on the
1950 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
1951 to install interface to SYMPHONY.")
1952 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
1953 ;; lpsimphony is released under the same terms.
1954 (license license:epl1.0)))
1956 (define-public r-ihw
1963 (uri (bioconductor-uri "IHW" version))
1966 "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
1967 (properties `((upstream-name . "IHW")))
1968 (build-system r-build-system)
1970 `(("r-biocgenerics" ,r-biocgenerics)
1971 ("r-fdrtool" ,r-fdrtool)
1972 ("r-lpsymphony" ,r-lpsymphony)
1973 ("r-slam" ,r-slam)))
1974 (home-page "https://bioconductor.org/packages/IHW")
1975 (synopsis "Independent hypothesis weighting")
1977 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
1978 procedure that increases power compared to the method of Benjamini and
1979 Hochberg by assigning data-driven weights to each hypothesis. The input to
1980 IHW is a two-column table of p-values and covariates. The covariate can be
1981 any continuous-valued or categorical variable that is thought to be
1982 informative on the statistical properties of each hypothesis test, while it is
1983 independent of the p-value under the null hypothesis.")
1984 (license license:artistic2.0)))
1986 (define-public r-icobra
1993 (uri (bioconductor-uri "iCOBRA" version))
1996 "0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"))))
1997 (properties `((upstream-name . "iCOBRA")))
1998 (build-system r-build-system)
2000 `(("r-dplyr" ,r-dplyr)
2002 ("r-ggplot2" ,r-ggplot2)
2003 ("r-limma" ,r-limma)
2004 ("r-reshape2" ,r-reshape2)
2006 ("r-scales" ,r-scales)
2007 ("r-shiny" ,r-shiny)
2008 ("r-shinybs" ,r-shinybs)
2009 ("r-shinydashboard" ,r-shinydashboard)
2010 ("r-upsetr" ,r-upsetr)))
2011 (home-page "https://bioconductor.org/packages/iCOBRA")
2012 (synopsis "Comparison and visualization of ranking and assignment methods")
2014 "This package provides functions for calculation and visualization of
2015 performance metrics for evaluation of ranking and binary
2016 classification (assignment) methods. It also contains a Shiny application for
2017 interactive exploration of results.")
2018 (license license:gpl2+)))
2020 (define-public r-mast
2027 (uri (bioconductor-uri "MAST" version))
2030 "0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"))))
2031 (properties `((upstream-name . "MAST")))
2032 (build-system r-build-system)
2034 `(("r-abind" ,r-abind)
2035 ("r-biobase" ,r-biobase)
2036 ("r-biocgenerics" ,r-biocgenerics)
2037 ("r-data-table" ,r-data-table)
2038 ("r-ggplot2" ,r-ggplot2)
2040 ("r-progress" ,r-progress)
2041 ("r-reshape2" ,r-reshape2)
2042 ("r-s4vectors" ,r-s4vectors)
2043 ("r-singlecellexperiment" ,r-singlecellexperiment)
2044 ("r-stringr" ,r-stringr)
2045 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2046 (home-page "https://github.com/RGLab/MAST/")
2047 (synopsis "Model-based analysis of single cell transcriptomics")
2049 "This package provides methods and models for handling zero-inflated
2050 single cell assay data.")
2051 (license license:gpl2+)))
2053 (define-public r-monocle
2060 (uri (bioconductor-uri "monocle" version))
2063 "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
2064 (build-system r-build-system)
2066 `(("r-biobase" ,r-biobase)
2067 ("r-biocgenerics" ,r-biocgenerics)
2068 ("r-biocviews" ,r-biocviews)
2069 ("r-cluster" ,r-cluster)
2070 ("r-combinat" ,r-combinat)
2071 ("r-ddrtree" ,r-ddrtree)
2072 ("r-densityclust" ,r-densityclust)
2073 ("r-dplyr" ,r-dplyr)
2074 ("r-fastica" ,r-fastica)
2075 ("r-ggplot2" ,r-ggplot2)
2076 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2077 ("r-igraph" ,r-igraph)
2078 ("r-irlba" ,r-irlba)
2079 ("r-limma" ,r-limma)
2081 ("r-matrix" ,r-matrix)
2082 ("r-matrixstats" ,r-matrixstats)
2083 ("r-pheatmap" ,r-pheatmap)
2085 ("r-proxy" ,r-proxy)
2086 ("r-qlcmatrix" ,r-qlcmatrix)
2089 ("r-reshape2" ,r-reshape2)
2090 ("r-rtsne" ,r-rtsne)
2092 ("r-stringr" ,r-stringr)
2093 ("r-tibble" ,r-tibble)
2095 ("r-viridis" ,r-viridis)))
2096 (home-page "https://bioconductor.org/packages/monocle")
2097 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2099 "Monocle performs differential expression and time-series analysis for
2100 single-cell expression experiments. It orders individual cells according to
2101 progress through a biological process, without knowing ahead of time which
2102 genes define progress through that process. Monocle also performs
2103 differential expression analysis, clustering, visualization, and other useful
2104 tasks on single cell expression data. It is designed to work with RNA-Seq and
2105 qPCR data, but could be used with other types as well.")
2106 (license license:artistic2.0)))
2108 (define-public r-noiseq
2115 (uri (bioconductor-uri "NOISeq" version))
2118 "1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"))))
2119 (properties `((upstream-name . "NOISeq")))
2120 (build-system r-build-system)
2122 `(("r-biobase" ,r-biobase)
2123 ("r-matrix" ,r-matrix)))
2124 (home-page "https://bioconductor.org/packages/NOISeq")
2125 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2127 "This package provides tools to support the analysis of RNA-seq
2128 expression data or other similar kind of data. It provides exploratory plots
2129 to evaluate saturation, count distribution, expression per chromosome, type of
2130 detected features, features length, etc. It also supports the analysis of
2131 differential expression between two experimental conditions with no parametric
2133 (license license:artistic2.0)))
2135 (define-public r-scdd
2142 (uri (bioconductor-uri "scDD" version))
2145 "0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"))))
2146 (properties `((upstream-name . "scDD")))
2147 (build-system r-build-system)
2150 ("r-biocparallel" ,r-biocparallel)
2151 ("r-ebseq" ,r-ebseq)
2152 ("r-fields" ,r-fields)
2153 ("r-ggplot2" ,r-ggplot2)
2154 ("r-mclust" ,r-mclust)
2155 ("r-outliers" ,r-outliers)
2156 ("r-s4vectors" ,r-s4vectors)
2157 ("r-scran" ,r-scran)
2158 ("r-singlecellexperiment" ,r-singlecellexperiment)
2159 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2160 (home-page "https://github.com/kdkorthauer/scDD")
2161 (synopsis "Mixture modeling of single-cell RNA-seq data")
2163 "This package implements a method to analyze single-cell RNA-seq data
2164 utilizing flexible Dirichlet Process mixture models. Genes with differential
2165 distributions of expression are classified into several interesting patterns
2166 of differences between two conditions. The package also includes functions
2167 for simulating data with these patterns from negative binomial
2169 (license license:gpl2)))
2171 (define-public r-scone
2178 (uri (bioconductor-uri "scone" version))
2181 "0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"))))
2182 (build-system r-build-system)
2184 `(("r-aroma-light" ,r-aroma-light)
2185 ("r-biocparallel" ,r-biocparallel)
2187 ("r-class" ,r-class)
2188 ("r-cluster" ,r-cluster)
2189 ("r-compositions" ,r-compositions)
2190 ("r-diptest" ,r-diptest)
2191 ("r-edger" ,r-edger)
2193 ("r-gplots" ,r-gplots)
2194 ("r-hexbin" ,r-hexbin)
2195 ("r-limma" ,r-limma)
2196 ("r-matrixstats" ,r-matrixstats)
2197 ("r-mixtools" ,r-mixtools)
2198 ("r-rarpack" ,r-rarpack)
2199 ("r-rcolorbrewer" ,r-rcolorbrewer)
2200 ("r-rhdf5" ,r-rhdf5)
2201 ("r-ruvseq" ,r-ruvseq)
2202 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2203 (home-page "https://bioconductor.org/packages/scone")
2204 (synopsis "Single cell overview of normalized expression data")
2206 "SCONE is an R package for comparing and ranking the performance of
2207 different normalization schemes for single-cell RNA-seq and other
2208 high-throughput analyses.")
2209 (license license:artistic2.0)))
2211 (define-public r-geoquery
2218 (uri (bioconductor-uri "GEOquery" version))
2221 "074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"))))
2222 (properties `((upstream-name . "GEOquery")))
2223 (build-system r-build-system)
2225 `(("r-biobase" ,r-biobase)
2226 ("r-dplyr" ,r-dplyr)
2228 ("r-limma" ,r-limma)
2229 ("r-magrittr" ,r-magrittr)
2230 ("r-readr" ,r-readr)
2231 ("r-tidyr" ,r-tidyr)
2232 ("r-xml2" ,r-xml2)))
2233 (home-page "https://github.com/seandavi/GEOquery/")
2234 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2236 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2237 microarray data. Given the rich and varied nature of this resource, it is
2238 only natural to want to apply BioConductor tools to these data. GEOquery is
2239 the bridge between GEO and BioConductor.")
2240 (license license:gpl2)))
2242 (define-public r-illuminaio
2244 (name "r-illuminaio")
2249 (uri (bioconductor-uri "illuminaio" version))
2252 "1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"))))
2253 (build-system r-build-system)
2255 `(("r-base64" ,r-base64)))
2256 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2257 (synopsis "Parse Illumina microarray output files")
2259 "This package provides tools for parsing Illumina's microarray output
2260 files, including IDAT.")
2261 (license license:gpl2)))
2263 (define-public r-siggenes
2270 (uri (bioconductor-uri "siggenes" version))
2273 "0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"))))
2274 (build-system r-build-system)
2276 `(("r-biobase" ,r-biobase)
2277 ("r-multtest" ,r-multtest)))
2278 (home-page "https://bioconductor.org/packages/siggenes/")
2280 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2282 "This package provides tools for the identification of differentially
2283 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2284 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2285 Bayes Analyses of Microarrays} (EBAM).")
2286 (license license:lgpl2.0+)))
2288 (define-public r-bumphunter
2290 (name "r-bumphunter")
2295 (uri (bioconductor-uri "bumphunter" version))
2298 "1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"))))
2299 (build-system r-build-system)
2301 `(("r-annotationdbi" ,r-annotationdbi)
2302 ("r-biocgenerics" ,r-biocgenerics)
2303 ("r-dorng" ,r-dorng)
2304 ("r-foreach" ,r-foreach)
2305 ("r-genomeinfodb" ,r-genomeinfodb)
2306 ("r-genomicfeatures" ,r-genomicfeatures)
2307 ("r-genomicranges" ,r-genomicranges)
2308 ("r-iranges" ,r-iranges)
2309 ("r-iterators" ,r-iterators)
2310 ("r-limma" ,r-limma)
2311 ("r-locfit" ,r-locfit)
2312 ("r-matrixstats" ,r-matrixstats)
2313 ("r-s4vectors" ,r-s4vectors)))
2314 (home-page "https://github.com/ririzarr/bumphunter")
2315 (synopsis "Find bumps in genomic data")
2317 "This package provides tools for finding bumps in genomic data in order
2318 to identify differentially methylated regions in epigenetic epidemiology
2320 (license license:artistic2.0)))
2322 (define-public r-minfi
2329 (uri (bioconductor-uri "minfi" version))
2332 "1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"))))
2333 (build-system r-build-system)
2335 `(("r-beanplot" ,r-beanplot)
2336 ("r-biobase" ,r-biobase)
2337 ("r-biocgenerics" ,r-biocgenerics)
2338 ("r-biocparallel" ,r-biocparallel)
2339 ("r-biostrings" ,r-biostrings)
2340 ("r-bumphunter" ,r-bumphunter)
2341 ("r-data-table" ,r-data-table)
2342 ("r-delayedarray" ,r-delayedarray)
2343 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2344 ("r-genefilter" ,r-genefilter)
2345 ("r-genomeinfodb" ,r-genomeinfodb)
2346 ("r-genomicranges" ,r-genomicranges)
2347 ("r-geoquery" ,r-geoquery)
2348 ("r-hdf5array" ,r-hdf5array)
2349 ("r-illuminaio" ,r-illuminaio)
2350 ("r-iranges" ,r-iranges)
2351 ("r-lattice" ,r-lattice)
2352 ("r-limma" ,r-limma)
2354 ("r-mclust" ,r-mclust)
2356 ("r-nor1mix" ,r-nor1mix)
2357 ("r-preprocesscore" ,r-preprocesscore)
2358 ("r-quadprog" ,r-quadprog)
2359 ("r-rcolorbrewer" ,r-rcolorbrewer)
2360 ("r-reshape" ,r-reshape)
2361 ("r-s4vectors" ,r-s4vectors)
2362 ("r-siggenes" ,r-siggenes)
2363 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2364 (home-page "https://github.com/hansenlab/minfi")
2365 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2367 "This package provides tools to analyze and visualize Illumina Infinium
2368 methylation arrays.")
2369 (license license:artistic2.0)))
2371 (define-public r-methylumi
2373 (name "r-methylumi")
2378 (uri (bioconductor-uri "methylumi" version))
2381 "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"))))
2382 (build-system r-build-system)
2384 `(("r-annotate" ,r-annotate)
2385 ("r-annotationdbi" ,r-annotationdbi)
2386 ("r-biobase" ,r-biobase)
2387 ("r-biocgenerics" ,r-biocgenerics)
2388 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2389 ("r-genefilter" ,r-genefilter)
2390 ("r-genomeinfodb" ,r-genomeinfodb)
2391 ("r-genomicranges" ,r-genomicranges)
2392 ("r-ggplot2" ,r-ggplot2)
2393 ("r-illuminaio" ,r-illuminaio)
2394 ("r-iranges" ,r-iranges)
2395 ("r-lattice" ,r-lattice)
2396 ("r-matrixstats" ,r-matrixstats)
2397 ("r-minfi" ,r-minfi)
2398 ("r-reshape2" ,r-reshape2)
2399 ("r-s4vectors" ,r-s4vectors)
2400 ("r-scales" ,r-scales)
2401 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2402 (home-page "https://bioconductor.org/packages/methylumi")
2403 (synopsis "Handle Illumina methylation data")
2405 "This package provides classes for holding and manipulating Illumina
2406 methylation data. Based on eSet, it can contain MIAME information, sample
2407 information, feature information, and multiple matrices of data. An
2408 \"intelligent\" import function, methylumiR can read the Illumina text files
2409 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2410 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2411 background correction, and quality control features for GoldenGate, Infinium,
2412 and Infinium HD arrays are also included.")
2413 (license license:gpl2)))
2415 (define-public r-lumi
2422 (uri (bioconductor-uri "lumi" version))
2425 "1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"))))
2426 (build-system r-build-system)
2428 `(("r-affy" ,r-affy)
2429 ("r-annotate" ,r-annotate)
2430 ("r-annotationdbi" ,r-annotationdbi)
2431 ("r-biobase" ,r-biobase)
2433 ("r-genomicfeatures" ,r-genomicfeatures)
2434 ("r-genomicranges" ,r-genomicranges)
2435 ("r-kernsmooth" ,r-kernsmooth)
2436 ("r-lattice" ,r-lattice)
2438 ("r-methylumi" ,r-methylumi)
2440 ("r-nleqslv" ,r-nleqslv)
2441 ("r-preprocesscore" ,r-preprocesscore)
2442 ("r-rsqlite" ,r-rsqlite)))
2443 (home-page "https://bioconductor.org/packages/lumi")
2444 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2446 "The lumi package provides an integrated solution for the Illumina
2447 microarray data analysis. It includes functions of Illumina
2448 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2449 variance stabilization, normalization and gene annotation at the probe level.
2450 It also includes the functions of processing Illumina methylation microarrays,
2451 especially Illumina Infinium methylation microarrays.")
2452 (license license:lgpl2.0+)))
2454 (define-public r-linnorm
2461 (uri (bioconductor-uri "Linnorm" version))
2464 "1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"))))
2465 (properties `((upstream-name . "Linnorm")))
2466 (build-system r-build-system)
2468 `(("r-amap" ,r-amap)
2469 ("r-apcluster" ,r-apcluster)
2470 ("r-ellipse" ,r-ellipse)
2471 ("r-fastcluster" ,r-fastcluster)
2473 ("r-ggdendro" ,r-ggdendro)
2474 ("r-ggplot2" ,r-ggplot2)
2475 ("r-gmodels" ,r-gmodels)
2476 ("r-igraph" ,r-igraph)
2477 ("r-limma" ,r-limma)
2479 ("r-mclust" ,r-mclust)
2481 ("r-rcpparmadillo" ,r-rcpparmadillo)
2482 ("r-rtsne" ,r-rtsne)
2483 ("r-statmod" ,r-statmod)
2484 ("r-vegan" ,r-vegan)
2486 (home-page "http://www.jjwanglab.org/Linnorm/")
2487 (synopsis "Linear model and normality based transformation method")
2489 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2490 count data or any large scale count data. It transforms such datasets for
2491 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2492 the following pipelines are implemented:
2495 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2496 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2497 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2498 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2499 @item Differential expression analysis or differential peak detection using
2500 limma (@code{Linnorm.limma})
2501 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2502 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2503 @item Stable gene selection for scRNA-seq data; for users without or who do
2504 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2505 @item Data imputation (@code{Linnorm.DataImput}).
2508 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2509 @code{RnaXSim} function is included for simulating RNA-seq data for the
2510 evaluation of DEG analysis methods.")
2511 (license license:expat)))
2513 (define-public r-ioniser
2520 (uri (bioconductor-uri "IONiseR" version))
2523 "01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"))))
2524 (properties `((upstream-name . "IONiseR")))
2525 (build-system r-build-system)
2527 `(("r-biocgenerics" ,r-biocgenerics)
2528 ("r-biocparallel" ,r-biocparallel)
2529 ("r-biostrings" ,r-biostrings)
2530 ("r-bit64" ,r-bit64)
2531 ("r-dplyr" ,r-dplyr)
2532 ("r-ggplot2" ,r-ggplot2)
2533 ("r-magrittr" ,r-magrittr)
2534 ("r-rhdf5" ,r-rhdf5)
2535 ("r-shortread" ,r-shortread)
2536 ("r-stringr" ,r-stringr)
2537 ("r-tibble" ,r-tibble)
2538 ("r-tidyr" ,r-tidyr)
2539 ("r-xvector" ,r-xvector)))
2540 (home-page "https://bioconductor.org/packages/IONiseR/")
2541 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2543 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2544 MinION data. It extracts summary statistics from a set of fast5 files and can
2545 be used either before or after base calling. In addition to standard
2546 summaries of the read-types produced, it provides a number of plots for
2547 visualising metrics relative to experiment run time or spatially over the
2548 surface of a flowcell.")
2549 (license license:expat)))
2551 ;; This is a CRAN package, but it depends on packages from Bioconductor.
2552 (define-public r-gkmsvm
2559 (uri (cran-uri "gkmSVM" version))
2562 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2563 (properties `((upstream-name . "gkmSVM")))
2564 (build-system r-build-system)
2566 `(("r-biocgenerics" ,r-biocgenerics)
2567 ("r-biostrings" ,r-biostrings)
2568 ("r-genomeinfodb" ,r-genomeinfodb)
2569 ("r-genomicranges" ,r-genomicranges)
2570 ("r-iranges" ,r-iranges)
2571 ("r-kernlab" ,r-kernlab)
2574 ("r-rtracklayer" ,r-rtracklayer)
2575 ("r-s4vectors" ,r-s4vectors)
2576 ("r-seqinr" ,r-seqinr)))
2577 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2578 (synopsis "Gapped-kmer support vector machine")
2580 "This R package provides tools for training gapped-kmer SVM classifiers
2581 for DNA and protein sequences. This package supports several sequence
2582 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2583 (license license:gpl2+)))
2585 (define-public r-triform
2592 (uri (bioconductor-uri "triform" version))
2595 "12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s"))))
2596 (build-system r-build-system)
2598 `(("r-biocgenerics" ,r-biocgenerics)
2599 ("r-iranges" ,r-iranges)
2600 ("r-yaml" ,r-yaml)))
2601 (home-page "https://bioconductor.org/packages/triform/")
2602 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2604 "The Triform algorithm uses model-free statistics to identify peak-like
2605 distributions of TF ChIP sequencing reads, taking advantage of an improved
2606 peak definition in combination with known profile characteristics.")
2607 (license license:gpl2)))
2609 (define-public r-varianttools
2611 (name "r-varianttools")
2616 (uri (bioconductor-uri "VariantTools" version))
2619 "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
2620 (properties `((upstream-name . "VariantTools")))
2621 (build-system r-build-system)
2623 `(("r-biobase" ,r-biobase)
2624 ("r-biocgenerics" ,r-biocgenerics)
2625 ("r-biocparallel" ,r-biocparallel)
2626 ("r-biostrings" ,r-biostrings)
2627 ("r-bsgenome" ,r-bsgenome)
2628 ("r-genomeinfodb" ,r-genomeinfodb)
2629 ("r-genomicfeatures" ,r-genomicfeatures)
2630 ("r-genomicranges" ,r-genomicranges)
2631 ("r-iranges" ,r-iranges)
2632 ("r-matrix" ,r-matrix)
2633 ("r-rsamtools" ,r-rsamtools)
2634 ("r-rtracklayer" ,r-rtracklayer)
2635 ("r-s4vectors" ,r-s4vectors)
2636 ("r-variantannotation" ,r-variantannotation)))
2637 (home-page "https://bioconductor.org/packages/VariantTools/")
2638 (synopsis "Tools for exploratory analysis of variant calls")
2640 "Explore, diagnose, and compare variant calls using filters. The
2641 VariantTools package supports a workflow for loading data, calling single
2642 sample variants and tumor-specific somatic mutations or other sample-specific
2643 variant types (e.g., RNA editing). Most of the functions operate on
2644 alignments (BAM files) or datasets of called variants. The user is expected
2645 to have already aligned the reads with a separate tool, e.g., GSNAP via
2647 (license license:artistic2.0)))
2649 (define-public r-heatplus
2656 (uri (bioconductor-uri "Heatplus" version))
2659 "0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48"))))
2660 (properties `((upstream-name . "Heatplus")))
2661 (build-system r-build-system)
2663 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2664 (home-page "https://github.com/alexploner/Heatplus")
2665 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2667 "This package provides tools to display a rectangular heatmap (intensity
2668 plot) of a data matrix. By default, both samples (columns) and features (row)
2669 of the matrix are sorted according to a hierarchical clustering, and the
2670 corresponding dendrogram is plotted. Optionally, panels with additional
2671 information about samples and features can be added to the plot.")
2672 (license license:gpl2+)))
2674 (define-public r-gosemsim
2681 (uri (bioconductor-uri "GOSemSim" version))
2684 "0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib"))))
2685 (properties `((upstream-name . "GOSemSim")))
2686 (build-system r-build-system)
2688 `(("r-annotationdbi" ,r-annotationdbi)
2689 ("r-go-db" ,r-go-db)
2690 ("r-rcpp" ,r-rcpp)))
2691 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2692 (synopsis "GO-terms semantic similarity measures")
2694 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2695 quantitative ways to compute similarities between genes and gene groups, and
2696 have became important basis for many bioinformatics analysis approaches.
2697 GOSemSim is an R package for semantic similarity computation among GO terms,
2698 sets of GO terms, gene products and gene clusters.")
2699 (license license:artistic2.0)))
2701 (define-public r-anota
2708 (uri (bioconductor-uri "anota" version))
2711 "182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"))))
2712 (build-system r-build-system)
2714 `(("r-multtest" ,r-multtest)
2715 ("r-qvalue" ,r-qvalue)))
2716 (home-page "https://bioconductor.org/packages/anota/")
2717 (synopsis "Analysis of translational activity")
2719 "Genome wide studies of translational control is emerging as a tool to
2720 study verious biological conditions. The output from such analysis is both
2721 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2722 involved in translation (the actively translating mRNA level) for each mRNA.
2723 The standard analysis of such data strives towards identifying differential
2724 translational between two or more sample classes - i.e. differences in
2725 actively translated mRNA levels that are independent of underlying differences
2726 in cytosolic mRNA levels. This package allows for such analysis using partial
2727 variances and the random variance model. As 10s of thousands of mRNAs are
2728 analyzed in parallell the library performs a number of tests to assure that
2729 the data set is suitable for such analysis.")
2730 (license license:gpl3)))
2732 (define-public r-sigpathway
2734 (name "r-sigpathway")
2739 (uri (bioconductor-uri "sigPathway" version))
2742 "0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3"))))
2743 (properties `((upstream-name . "sigPathway")))
2744 (build-system r-build-system)
2745 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
2746 (synopsis "Pathway analysis")
2748 "This package is used to conduct pathway analysis by calculating the NT_k
2749 and NE_k statistics in a statistical framework for determining whether a
2750 specified group of genes for a pathway has a coordinated association with a
2751 phenotype of interest.")
2752 (license license:gpl2)))
2754 (define-public r-fgsea
2761 (uri (bioconductor-uri "fgsea" version))
2764 "0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"))))
2765 (build-system r-build-system)
2767 `(("r-biocparallel" ,r-biocparallel)
2768 ("r-data-table" ,r-data-table)
2769 ("r-fastmatch" ,r-fastmatch)
2770 ("r-ggplot2" ,r-ggplot2)
2771 ("r-gridextra" ,r-gridextra)
2772 ("r-matrix" ,r-matrix)
2773 ("r-rcpp" ,r-rcpp)))
2774 (home-page "https://github.com/ctlab/fgsea/")
2775 (synopsis "Fast gene set enrichment analysis")
2777 "The package implements an algorithm for fast gene set enrichment
2778 analysis. Using the fast algorithm allows to make more permutations and get
2779 more fine grained p-values, which allows to use accurate stantard approaches
2780 to multiple hypothesis correction.")
2781 (license license:expat)))
2783 (define-public r-dose
2790 (uri (bioconductor-uri "DOSE" version))
2793 "1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa"))))
2794 (properties `((upstream-name . "DOSE")))
2795 (build-system r-build-system)
2797 `(("r-annotationdbi" ,r-annotationdbi)
2798 ("r-biocparallel" ,r-biocparallel)
2799 ("r-do-db" ,r-do-db)
2800 ("r-fgsea" ,r-fgsea)
2801 ("r-ggplot2" ,r-ggplot2)
2802 ("r-gosemsim" ,r-gosemsim)
2803 ("r-qvalue" ,r-qvalue)
2804 ("r-reshape2" ,r-reshape2)
2805 ("r-s4vectors" ,r-s4vectors)))
2806 (home-page "https://guangchuangyu.github.io/software/DOSE/")
2807 (synopsis "Disease ontology semantic and enrichment analysis")
2809 "This package implements five methods proposed by Resnik, Schlicker,
2810 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
2811 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
2812 including hypergeometric model and gene set enrichment analysis are also
2813 implemented for discovering disease associations of high-throughput biological
2815 (license license:artistic2.0)))
2817 (define-public r-enrichplot
2819 (name "r-enrichplot")
2824 (uri (bioconductor-uri "enrichplot" version))
2827 "0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"))))
2828 (build-system r-build-system)
2830 `(("r-annotationdbi" ,r-annotationdbi)
2831 ("r-cowplot" ,r-cowplot)
2833 ("r-europepmc" ,r-europepmc)
2834 ("r-ggplot2" ,r-ggplot2)
2835 ("r-ggplotify" ,r-ggplotify)
2836 ("r-ggraph" ,r-ggraph)
2837 ("r-ggridges" ,r-ggridges)
2838 ("r-gosemsim" ,r-gosemsim)
2839 ("r-gridextra" ,r-gridextra)
2840 ("r-igraph" ,r-igraph)
2841 ("r-purrr" ,r-purrr)
2842 ("r-rcolorbrewer" ,r-rcolorbrewer)
2843 ("r-reshape2" ,r-reshape2)
2844 ("r-upsetr" ,r-upsetr)))
2845 (home-page "https://github.com/GuangchuangYu/enrichplot")
2846 (synopsis "Visualization of functional enrichment result")
2848 "The enrichplot package implements several visualization methods for
2849 interpreting functional enrichment results obtained from ORA or GSEA analyses.
2850 All the visualization methods are developed based on ggplot2 graphics.")
2851 (license license:artistic2.0)))
2853 (define-public r-clusterprofiler
2855 (name "r-clusterprofiler")
2860 (uri (bioconductor-uri "clusterProfiler" version))
2863 "1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm"))))
2865 `((upstream-name . "clusterProfiler")))
2866 (build-system r-build-system)
2868 `(("r-annotationdbi" ,r-annotationdbi)
2870 ("r-enrichplot" ,r-enrichplot)
2871 ("r-ggplot2" ,r-ggplot2)
2872 ("r-go-db" ,r-go-db)
2873 ("r-gosemsim" ,r-gosemsim)
2874 ("r-magrittr" ,r-magrittr)
2876 ("r-qvalue" ,r-qvalue)
2877 ("r-rvcheck" ,r-rvcheck)
2878 ("r-tidyr" ,r-tidyr)))
2879 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
2880 (synopsis "Analysis and visualization of functional profiles for gene clusters")
2882 "This package implements methods to analyze and visualize functional
2883 profiles (GO and KEGG) of gene and gene clusters.")
2884 (license license:artistic2.0)))
2886 (define-public r-mlinterfaces
2888 (name "r-mlinterfaces")
2893 (uri (bioconductor-uri "MLInterfaces" version))
2896 "12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8"))))
2897 (properties `((upstream-name . "MLInterfaces")))
2898 (build-system r-build-system)
2900 `(("r-annotate" ,r-annotate)
2901 ("r-biobase" ,r-biobase)
2902 ("r-biocgenerics" ,r-biocgenerics)
2903 ("r-cluster" ,r-cluster)
2906 ("r-gdata" ,r-gdata)
2907 ("r-genefilter" ,r-genefilter)
2908 ("r-ggvis" ,r-ggvis)
2909 ("r-hwriter" ,r-hwriter)
2911 ("r-mlbench" ,r-mlbench)
2913 ("r-rcolorbrewer" ,r-rcolorbrewer)
2915 ("r-rpart" ,r-rpart)
2916 ("r-sfsmisc" ,r-sfsmisc)
2917 ("r-shiny" ,r-shiny)
2918 ("r-threejs" ,r-threejs)))
2919 (home-page "https://bioconductor.org/packages/MLInterfaces/")
2920 (synopsis "Interfaces to R machine learning procedures")
2922 "This package provides uniform interfaces to machine learning code for
2923 data in R and Bioconductor containers.")
2924 ;; Any version of the LGPL.
2925 (license license:lgpl2.1+)))
2927 (define-public r-annaffy
2934 (uri (bioconductor-uri "annaffy" version))
2937 "16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5"))))
2938 (build-system r-build-system)
2941 (modify-phases %standard-phases
2942 (add-after 'unpack 'remove-reference-to-non-free-data
2944 (substitute* "DESCRIPTION"
2948 `(("r-annotationdbi" ,r-annotationdbi)
2949 ("r-biobase" ,r-biobase)
2951 ("r-go-db" ,r-go-db)))
2952 (home-page "https://bioconductor.org/packages/annaffy/")
2953 (synopsis "Annotation tools for Affymetrix biological metadata")
2955 "This package provides functions for handling data from Bioconductor
2956 Affymetrix annotation data packages. It produces compact HTML and text
2957 reports including experimental data and URL links to many online databases.
2958 It allows searching of biological metadata using various criteria.")
2959 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
2960 ;; the LGPL 2.1 is included.
2961 (license license:lgpl2.1+)))
2963 (define-public r-a4core
2970 (uri (bioconductor-uri "a4Core" version))
2973 "1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr"))))
2974 (properties `((upstream-name . "a4Core")))
2975 (build-system r-build-system)
2977 `(("r-biobase" ,r-biobase)
2978 ("r-glmnet" ,r-glmnet)))
2979 (home-page "https://bioconductor.org/packages/a4Core")
2980 (synopsis "Automated Affymetrix array analysis core package")
2982 "This is the core package for the automated analysis of Affymetrix
2984 (license license:gpl3)))
2986 (define-public r-a4classif
2988 (name "r-a4classif")
2993 (uri (bioconductor-uri "a4Classif" version))
2996 "02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j"))))
2997 (properties `((upstream-name . "a4Classif")))
2998 (build-system r-build-system)
3000 `(("r-a4core" ,r-a4core)
3001 ("r-a4preproc" ,r-a4preproc)
3002 ("r-glmnet" ,r-glmnet)
3003 ("r-mlinterfaces" ,r-mlinterfaces)
3006 ("r-varselrf" ,r-varselrf)))
3007 (home-page "https://bioconductor.org/packages/a4Classif/")
3008 (synopsis "Automated Affymetrix array analysis classification package")
3010 "This is the classification package for the automated analysis of
3011 Affymetrix arrays.")
3012 (license license:gpl3)))
3014 (define-public r-a4preproc
3016 (name "r-a4preproc")
3021 (uri (bioconductor-uri "a4Preproc" version))
3024 "1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp"))))
3025 (properties `((upstream-name . "a4Preproc")))
3026 (build-system r-build-system)
3028 `(("r-annotationdbi" ,r-annotationdbi)))
3029 (home-page "https://bioconductor.org/packages/a4Preproc/")
3030 (synopsis "Automated Affymetrix array analysis preprocessing package")
3032 "This is a package for the automated analysis of Affymetrix arrays. It
3033 is used for preprocessing the arrays.")
3034 (license license:gpl3)))