1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
7 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
9 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
10 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
11 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
12 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
14 ;;; This file is part of GNU Guix.
16 ;;; GNU Guix is free software; you can redistribute it and/or modify it
17 ;;; under the terms of the GNU General Public License as published by
18 ;;; the Free Software Foundation; either version 3 of the License, or (at
19 ;;; your option) any later version.
21 ;;; GNU Guix is distributed in the hope that it will be useful, but
22 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
23 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
24 ;;; GNU General Public License for more details.
26 ;;; You should have received a copy of the GNU General Public License
27 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
29 (define-module (gnu packages bioconductor)
30 #:use-module ((guix licenses) #:prefix license:)
31 #:use-module (guix packages)
32 #:use-module (guix download)
33 #:use-module (guix git-download)
34 #:use-module (guix build-system r)
35 #:use-module (gnu packages)
36 #:use-module (gnu packages base)
37 #:use-module (gnu packages bioinformatics)
38 #:use-module (gnu packages cran)
39 #:use-module (gnu packages compression)
40 #:use-module (gnu packages gcc)
41 #:use-module (gnu packages graph)
42 #:use-module (gnu packages graphviz)
43 #:use-module (gnu packages haskell-xyz)
44 #:use-module (gnu packages image)
45 #:use-module (gnu packages maths)
46 #:use-module (gnu packages netpbm)
47 #:use-module (gnu packages perl)
48 #:use-module (gnu packages pkg-config)
49 #:use-module (gnu packages statistics)
50 #:use-module (gnu packages web)
51 #:use-module (gnu packages xml)
52 #:use-module (srfi srfi-1))
57 (define-public r-org-eck12-eg-db
59 (name "r-org-eck12-eg-db")
64 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
66 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
68 `((upstream-name . "org.EcK12.eg.db")))
69 (build-system r-build-system)
71 `(("r-annotationdbi" ,r-annotationdbi)))
72 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
73 (synopsis "Genome wide annotation for E coli strain K12")
75 "This package provides genome wide annotation for E coli strain K12,
76 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
77 National Center for Biotechnology Information (NCBI)’s database for
78 gene-specific information. Entrez Gene maintains records from genomes which
79 have been completely sequenced, which have an active research community to
80 submit gene-specific information, or which are scheduled for intense sequence
82 (license license:artistic2.0)))
84 (define-public r-reactome-db
86 (name "r-reactome-db")
91 (uri (bioconductor-uri "reactome.db" version 'annotation))
94 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
95 (properties `((upstream-name . "reactome.db")))
96 (build-system r-build-system)
98 `(("r-annotationdbi" ,r-annotationdbi)))
99 (home-page "https://bioconductor.org/packages/reactome.db/")
100 (synopsis "Annotation maps for reactome")
102 "This package provides a set of annotation maps for the REACTOME
103 database, assembled using data from REACTOME.")
104 (license license:cc-by4.0)))
106 (define-public r-bsgenome-celegans-ucsc-ce6
108 (name "r-bsgenome-celegans-ucsc-ce6")
112 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
113 version 'annotation))
116 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
118 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
119 (build-system r-build-system)
121 `(("r-bsgenome" ,r-bsgenome)))
123 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
124 (synopsis "Full genome sequences for Worm")
126 "This package provides full genome sequences for Caenorhabditis
127 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
129 (license license:artistic2.0)))
131 (define-public r-bsgenome-celegans-ucsc-ce10
133 (name "r-bsgenome-celegans-ucsc-ce10")
137 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
138 version 'annotation))
141 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
143 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
144 (build-system r-build-system)
146 `(("r-bsgenome" ,r-bsgenome)))
148 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
149 (synopsis "Full genome sequences for Worm")
151 "This package provides full genome sequences for Caenorhabditis
152 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
154 (license license:artistic2.0)))
156 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
158 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
162 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
163 version 'annotation))
166 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
168 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
169 (build-system r-build-system)
171 `(("r-bsgenome" ,r-bsgenome)))
173 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
174 (synopsis "Full genome sequences for Fly")
176 "This package provides full genome sequences for Drosophila
177 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
179 (license license:artistic2.0)))
181 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
183 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
187 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
188 version 'annotation))
191 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
193 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
194 (build-system r-build-system)
196 `(("r-bsgenome" ,r-bsgenome)))
198 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
199 (synopsis "Full genome sequences for Fly")
201 "This package provides full genome sequences for Drosophila
202 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
203 Biostrings objects.")
204 (license license:artistic2.0)))
206 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
208 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
212 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
213 version 'annotation))
216 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
218 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
219 (build-system r-build-system)
221 `(("r-bsgenome" ,r-bsgenome)
222 ("r-bsgenome-dmelanogaster-ucsc-dm3"
223 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
224 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
225 (synopsis "Full masked genome sequences for Fly")
227 "This package provides full masked genome sequences for Drosophila
228 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
229 Biostrings objects. The sequences are the same as in
230 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
231 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
232 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
233 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
234 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
235 (license license:artistic2.0)))
237 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
239 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
243 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
244 version 'annotation))
247 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
249 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
250 (build-system r-build-system)
252 `(("r-bsgenome" ,r-bsgenome)))
254 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
255 (synopsis "Full genome sequences for Homo sapiens")
257 "This package provides full genome sequences for Homo sapiens from
258 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
259 (license license:artistic2.0)))
261 (define-public r-bsgenome-hsapiens-ncbi-grch38
263 (name "r-bsgenome-hsapiens-ncbi-grch38")
268 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
269 version 'annotation))
272 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
273 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
274 (build-system r-build-system)
275 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
277 "https://bioconductor.org/packages/release/data/annotation/html/\
278 BSgenome.Hsapiens.NCBI.GRCh38.html")
279 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
281 "This package provides full genome sequences for Homo sapiens (Human) as
282 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
283 (license license:artistic2.0)))
285 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
287 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
291 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
292 version 'annotation))
295 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
297 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
298 (build-system r-build-system)
300 `(("r-bsgenome" ,r-bsgenome)
301 ("r-bsgenome-hsapiens-ucsc-hg19"
302 ,r-bsgenome-hsapiens-ucsc-hg19)))
303 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
304 (synopsis "Full masked genome sequences for Homo sapiens")
306 "This package provides full genome sequences for Homo sapiens (Human) as
307 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
308 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
309 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
310 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
311 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
312 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
314 (license license:artistic2.0)))
316 (define-public r-bsgenome-mmusculus-ucsc-mm9
318 (name "r-bsgenome-mmusculus-ucsc-mm9")
322 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
323 version 'annotation))
326 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
328 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
329 (build-system r-build-system)
331 `(("r-bsgenome" ,r-bsgenome)))
333 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
334 (synopsis "Full genome sequences for Mouse")
336 "This package provides full genome sequences for Mus musculus (Mouse) as
337 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
338 (license license:artistic2.0)))
340 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
342 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
346 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
347 version 'annotation))
350 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
352 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
353 (build-system r-build-system)
355 `(("r-bsgenome" ,r-bsgenome)
356 ("r-bsgenome-mmusculus-ucsc-mm9"
357 ,r-bsgenome-mmusculus-ucsc-mm9)))
358 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
359 (synopsis "Full masked genome sequences for Mouse")
361 "This package provides full genome sequences for Mus musculus (Mouse) as
362 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
363 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
364 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
365 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
366 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
367 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
369 (license license:artistic2.0)))
371 (define-public r-bsgenome-mmusculus-ucsc-mm10
373 (name "r-bsgenome-mmusculus-ucsc-mm10")
377 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
378 version 'annotation))
381 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
383 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
384 (build-system r-build-system)
386 `(("r-bsgenome" ,r-bsgenome)))
388 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
389 (synopsis "Full genome sequences for Mouse")
391 "This package provides full genome sequences for Mus
392 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
393 in Biostrings objects.")
394 (license license:artistic2.0)))
396 (define-public r-genomeinfodbdata
398 (name "r-genomeinfodbdata")
402 (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
405 "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
407 `((upstream-name . "GenomeInfoDbData")))
408 (build-system r-build-system)
409 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
410 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
411 (description "This package contains data for mapping between NCBI taxonomy
412 ID and species. It is used by functions in the GenomeInfoDb package.")
413 (license license:artistic2.0)))
415 (define-public r-homo-sapiens
417 (name "r-homo-sapiens")
421 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
424 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
426 `((upstream-name . "Homo.sapiens")))
427 (build-system r-build-system)
429 `(("r-genomicfeatures" ,r-genomicfeatures)
431 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
432 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
433 ("r-organismdbi" ,r-organismdbi)
434 ("r-annotationdbi" ,r-annotationdbi)))
435 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
436 (synopsis "Annotation package for the Homo.sapiens object")
438 "This package contains the Homo.sapiens object to access data from
439 several related annotation packages.")
440 (license license:artistic2.0)))
442 (define-public r-org-ce-eg-db
444 (name "r-org-ce-eg-db")
448 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
451 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
453 `((upstream-name . "org.Ce.eg.db")))
454 (build-system r-build-system)
456 `(("r-annotationdbi" ,r-annotationdbi)))
457 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
458 (synopsis "Genome wide annotation for Worm")
460 "This package provides mappings from Entrez gene identifiers to various
461 annotations for the genome of the model worm Caenorhabditis elegans.")
462 (license license:artistic2.0)))
464 (define-public r-org-dm-eg-db
466 (name "r-org-dm-eg-db")
470 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
473 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
475 `((upstream-name . "org.Dm.eg.db")))
476 (build-system r-build-system)
478 `(("r-annotationdbi" ,r-annotationdbi)))
479 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
480 (synopsis "Genome wide annotation for Fly")
482 "This package provides mappings from Entrez gene identifiers to various
483 annotations for the genome of the model fruit fly Drosophila melanogaster.")
484 (license license:artistic2.0)))
486 (define-public r-org-dr-eg-db
488 (name "r-org-dr-eg-db")
492 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
495 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
497 `((upstream-name . "org.Dr.eg.db")))
498 (build-system r-build-system)
500 `(("r-annotationdbi" ,r-annotationdbi)))
501 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
502 (synopsis "Annotation for Zebrafish")
504 "This package provides genome wide annotations for Zebrafish, primarily
505 based on mapping using Entrez Gene identifiers.")
506 (license license:artistic2.0)))
508 (define-public r-org-hs-eg-db
510 (name "r-org-hs-eg-db")
514 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
517 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
519 `((upstream-name . "org.Hs.eg.db")))
520 (build-system r-build-system)
522 `(("r-annotationdbi" ,r-annotationdbi)))
523 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
524 (synopsis "Genome wide annotation for Human")
526 "This package contains genome-wide annotations for Human, primarily based
527 on mapping using Entrez Gene identifiers.")
528 (license license:artistic2.0)))
530 (define-public r-org-mm-eg-db
532 (name "r-org-mm-eg-db")
536 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
539 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
541 `((upstream-name . "org.Mm.eg.db")))
542 (build-system r-build-system)
544 `(("r-annotationdbi" ,r-annotationdbi)))
545 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
546 (synopsis "Genome wide annotation for Mouse")
548 "This package provides mappings from Entrez gene identifiers to various
549 annotations for the genome of the model mouse Mus musculus.")
550 (license license:artistic2.0)))
552 (define-public r-bsgenome-hsapiens-ucsc-hg19
554 (name "r-bsgenome-hsapiens-ucsc-hg19")
558 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
559 version 'annotation))
562 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
564 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
565 (build-system r-build-system)
567 `(("r-bsgenome" ,r-bsgenome)))
569 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
570 (synopsis "Full genome sequences for Homo sapiens")
572 "This package provides full genome sequences for Homo sapiens as provided
573 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
574 (license license:artistic2.0)))
576 (define-public r-bsgenome-hsapiens-ucsc-hg38
578 (name "r-bsgenome-hsapiens-ucsc-hg38")
582 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
583 version 'annotation))
586 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
588 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
589 (build-system r-build-system)
591 `(("r-bsgenome" ,r-bsgenome)))
593 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
594 (synopsis "Full genome sequences for Homo sapiens")
596 "This package provides full genome sequences for Homo sapiens (Human)
597 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
598 (license license:artistic2.0)))
600 (define-public r-ensdb-hsapiens-v75
602 (name "r-ensdb-hsapiens-v75")
607 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
610 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
612 `((upstream-name . "EnsDb.Hsapiens.v75")))
613 (build-system r-build-system)
615 `(("r-ensembldb" ,r-ensembldb)))
616 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
617 (synopsis "Ensembl based annotation package")
619 "This package exposes an annotation database generated from Ensembl.")
620 (license license:artistic2.0)))
622 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
624 (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
629 (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
630 version 'annotation))
633 "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
635 `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
636 (build-system r-build-system)
638 `(("r-annotationdbi" ,r-annotationdbi)
639 ("r-genomicfeatures" ,r-genomicfeatures)))
641 "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
642 (synopsis "Annotation package for TxDb object(s)")
644 "This package exposes an annotation databases generated from UCSC by
645 exposing these as TxDb objects.")
646 (license license:artistic2.0)))
648 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
650 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
654 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
655 version 'annotation))
658 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
660 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
661 (build-system r-build-system)
663 `(("r-genomicfeatures" ,r-genomicfeatures)))
665 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
666 (synopsis "Annotation package for human genome in TxDb format")
668 "This package provides an annotation database of Homo sapiens genome
669 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
670 track. The database is exposed as a @code{TxDb} object.")
671 (license license:artistic2.0)))
673 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
675 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
679 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
680 version 'annotation))
683 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
685 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
686 (build-system r-build-system)
688 `(("r-genomicfeatures" ,r-genomicfeatures)))
690 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
691 (synopsis "Annotation package for human genome in TxDb format")
693 "This package provides an annotation database of Homo sapiens genome
694 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
695 track. The database is exposed as a @code{TxDb} object.")
696 (license license:artistic2.0)))
698 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
700 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
704 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
705 version 'annotation))
708 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
710 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
711 (build-system r-build-system)
713 `(("r-genomicfeatures" ,r-genomicfeatures)
714 ("r-annotationdbi" ,r-annotationdbi)))
716 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
717 (synopsis "Annotation package for mouse genome in TxDb format")
719 "This package provides an annotation database of Mouse genome data. It
720 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
721 database is exposed as a @code{TxDb} object.")
722 (license license:artistic2.0)))
724 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
726 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
730 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
731 version 'annotation))
734 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
736 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
737 (build-system r-build-system)
739 `(("r-bsgenome" ,r-bsgenome)
740 ("r-genomicfeatures" ,r-genomicfeatures)
741 ("r-annotationdbi" ,r-annotationdbi)))
743 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
744 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
746 "This package loads a TxDb object, which is an R interface to
747 prefabricated databases contained in this package. This package provides
748 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
749 based on the knownGene track.")
750 (license license:artistic2.0)))
752 (define-public r-txdb-celegans-ucsc-ce6-ensgene
754 (name "r-txdb-celegans-ucsc-ce6-ensgene")
759 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
760 version 'annotation))
763 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
765 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
766 (build-system r-build-system)
768 `(("r-annotationdbi" ,r-annotationdbi)
769 ("r-genomicfeatures" ,r-genomicfeatures)))
770 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
771 (synopsis "Annotation package for C elegans TxDb objects")
773 "This package exposes a C elegans annotation database generated from UCSC
774 by exposing these as TxDb objects.")
775 (license license:artistic2.0)))
777 (define-public r-fdb-infiniummethylation-hg19
779 (name "r-fdb-infiniummethylation-hg19")
783 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
784 version 'annotation))
787 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
789 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
790 (build-system r-build-system)
792 `(("r-biostrings" ,r-biostrings)
793 ("r-genomicfeatures" ,r-genomicfeatures)
794 ("r-annotationdbi" ,r-annotationdbi)
795 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
796 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
797 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
798 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
800 "This is an annotation package for Illumina Infinium DNA methylation
801 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
803 (license license:artistic2.0)))
805 (define-public r-illuminahumanmethylationepicmanifest
807 (name "r-illuminahumanmethylationepicmanifest")
811 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
812 version 'annotation))
815 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
817 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
818 (build-system r-build-system)
820 `(("r-minfi" ,r-minfi)))
821 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
822 (synopsis "Manifest for Illumina's EPIC methylation arrays")
824 "This is a manifest package for Illumina's EPIC methylation arrays.")
825 (license license:artistic2.0)))
827 (define-public r-do-db
833 (uri (bioconductor-uri "DO.db" version 'annotation))
836 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
838 `((upstream-name . "DO.db")))
839 (build-system r-build-system)
841 `(("r-annotationdbi" ,r-annotationdbi)))
842 (home-page "https://www.bioconductor.org/packages/DO.db/")
843 (synopsis "Annotation maps describing the entire Disease Ontology")
845 "This package provides a set of annotation maps describing the entire
847 (license license:artistic2.0)))
849 (define-public r-pfam-db
856 (uri (bioconductor-uri "PFAM.db" version 'annotation))
859 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
860 (properties `((upstream-name . "PFAM.db")))
861 (build-system r-build-system)
863 `(("r-annotationdbi" ,r-annotationdbi)))
864 (home-page "https://bioconductor.org/packages/PFAM.db")
865 (synopsis "Set of protein ID mappings for PFAM")
867 "This package provides a set of protein ID mappings for PFAM, assembled
868 using data from public repositories.")
869 (license license:artistic2.0)))
871 (define-public r-phastcons100way-ucsc-hg19
873 (name "r-phastcons100way-ucsc-hg19")
878 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
879 version 'annotation))
882 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
884 `((upstream-name . "phastCons100way.UCSC.hg19")))
885 (build-system r-build-system)
887 `(("r-bsgenome" ,r-bsgenome)
888 ("r-genomeinfodb" ,r-genomeinfodb)
889 ("r-genomicranges" ,r-genomicranges)
890 ("r-genomicscores" ,r-genomicscores)
891 ("r-iranges" ,r-iranges)
892 ("r-s4vectors" ,r-s4vectors)))
893 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
894 (synopsis "UCSC phastCons conservation scores for hg19")
896 "This package provides UCSC phastCons conservation scores for the human
897 genome (hg19) calculated from multiple alignments with other 99 vertebrate
899 (license license:artistic2.0)))
904 (define-public r-abadata
910 (uri (bioconductor-uri "ABAData" version 'experiment))
913 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
915 `((upstream-name . "ABAData")))
916 (build-system r-build-system)
918 `(("r-annotationdbi" ,r-annotationdbi)))
919 (home-page "https://www.bioconductor.org/packages/ABAData/")
920 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
922 "This package provides the data for the gene expression enrichment
923 analysis conducted in the package ABAEnrichment. The package includes three
924 datasets which are derived from the Allen Brain Atlas:
927 @item Gene expression data from Human Brain (adults) averaged across donors,
928 @item Gene expression data from the Developing Human Brain pooled into five
929 age categories and averaged across donors, and
930 @item a developmental effect score based on the Developing Human Brain
934 All datasets are restricted to protein coding genes.")
935 (license license:gpl2+)))
937 (define-public r-arrmdata
943 (uri (bioconductor-uri "ARRmData" version 'experiment))
946 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
948 `((upstream-name . "ARRmData")))
949 (build-system r-build-system)
950 (home-page "https://www.bioconductor.org/packages/ARRmData/")
951 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
953 "This package provides raw beta values from 36 samples across 3 groups
954 from Illumina 450k methylation arrays.")
955 (license license:artistic2.0)))
957 (define-public r-chromstardata
959 (name "r-chromstardata")
964 (uri (bioconductor-uri "chromstaRData" version 'experiment))
967 "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
968 (properties `((upstream-name . "chromstaRData")))
969 (build-system r-build-system)
970 (home-page "https://bioconductor.org/packages/chromstaRData/")
971 (synopsis "ChIP-seq data for demonstration purposes")
973 "This package provides ChIP-seq data for demonstration purposes in the
975 (license license:gpl3)))
977 (define-public r-genelendatabase
979 (name "r-genelendatabase")
984 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
987 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
989 `((upstream-name . "geneLenDataBase")))
990 (build-system r-build-system)
992 `(("r-rtracklayer" ,r-rtracklayer)
993 ("r-genomicfeatures" ,r-genomicfeatures)))
994 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
995 (synopsis "Lengths of mRNA transcripts for a number of genomes")
997 "This package provides the lengths of mRNA transcripts for a number of
998 genomes and gene ID formats, largely based on the UCSC table browser.")
999 (license license:lgpl2.0+)))
1001 (define-public r-pasilla
1008 "http://bioconductor.org/packages/release/data/experiment"
1009 "/src/contrib/pasilla_" version ".tar.gz"))
1012 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
1013 (build-system r-build-system)
1015 `(("r-biocstyle" ,r-biocstyle)
1016 ("r-dexseq" ,r-dexseq)
1017 ("r-knitr" ,r-knitr)
1018 ("r-rmarkdown" ,r-rmarkdown)))
1019 (home-page "https://www.bioconductor.org/packages/pasilla/")
1020 (synopsis "Data package with per-exon and per-gene read counts")
1021 (description "This package provides per-exon and per-gene read counts
1022 computed for selected genes from RNA-seq data that were presented in the
1023 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
1024 by Brooks et al., Genome Research 2011.")
1025 (license license:lgpl2.1+)))
1027 (define-public r-hsmmsinglecell
1029 (name "r-hsmmsinglecell")
1033 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1036 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
1038 `((upstream-name . "HSMMSingleCell")))
1039 (build-system r-build-system)
1040 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1041 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1043 "Skeletal myoblasts undergo a well-characterized sequence of
1044 morphological and transcriptional changes during differentiation. In this
1045 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1046 under high mitogen conditions (GM) and then differentiated by switching to
1047 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1048 hundred cells taken over a time-course of serum-induced differentiation.
1049 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1050 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1051 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1052 which were then sequenced to a depth of ~4 million reads per library,
1053 resulting in a complete gene expression profile for each cell.")
1054 (license license:artistic2.0)))
1056 (define-public r-all
1062 (uri (bioconductor-uri "ALL" version 'experiment))
1065 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1066 (properties `((upstream-name . "ALL")))
1067 (build-system r-build-system)
1069 `(("r-biobase" ,r-biobase)))
1070 (home-page "https://bioconductor.org/packages/ALL")
1071 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1073 "The data consist of microarrays from 128 different individuals with
1074 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1075 are available. The data have been normalized (using rma) and it is the
1076 jointly normalized data that are available here. The data are presented in
1077 the form of an @code{exprSet} object.")
1078 (license license:artistic2.0)))
1080 (define-public r-affydata
1087 (uri (bioconductor-uri "affydata" version 'experiment))
1090 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1091 (properties `((upstream-name . "affydata")))
1092 (build-system r-build-system)
1094 `(("r-affy" ,r-affy)))
1095 (home-page "https://bioconductor.org/packages/affydata/")
1096 (synopsis "Affymetrix data for demonstration purposes")
1098 "This package provides example datasets that represent 'real world
1099 examples' of Affymetrix data, unlike the artificial examples included in the
1100 package @code{affy}.")
1101 (license license:gpl2+)))
1103 (define-public r-gagedata
1110 (uri (bioconductor-uri "gageData" version 'experiment))
1112 (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn"))))
1113 (properties `((upstream-name . "gageData")))
1114 (build-system r-build-system)
1115 (home-page "https://bioconductor.org/packages/gageData")
1116 (synopsis "Auxiliary data for the gage package")
1118 "This is a supportive data package for the software package @code{gage}.
1119 However, the data supplied here are also useful for gene set or pathway
1120 analysis or microarray data analysis in general. In this package, we provide
1121 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1122 BMP6 (originally published as an demo dataset for GAGE, also registered as
1123 GSE13604 in GEO). This package also includes commonly used gene set data based
1124 on KEGG pathways and GO terms for major research species, including human,
1125 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1126 yeast are also included.")
1127 (license license:gpl2+)))
1129 (define-public r-curatedtcgadata
1131 (name "r-curatedtcgadata")
1136 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1139 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1141 `((upstream-name . "curatedTCGAData")))
1142 (build-system r-build-system)
1144 `(("r-annotationhub" ,r-annotationhub)
1145 ("r-experimenthub" ,r-experimenthub)
1146 ("r-hdf5array" ,r-hdf5array)
1147 ("r-multiassayexperiment" ,r-multiassayexperiment)
1148 ("r-s4vectors" ,r-s4vectors)
1149 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1150 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1151 (synopsis "Curated data from The Cancer Genome Atlas")
1153 "This package provides publicly available data from The Cancer Genome
1154 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1155 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1156 number, mutation, microRNA, protein, and others) with clinical / pathological
1157 data. It also links assay barcodes with patient identifiers, enabling
1158 harmonized subsetting of rows (features) and columns (patients / samples)
1159 across the entire multi-'omics experiment.")
1160 (license license:artistic2.0)))
1165 (define-public r-biocversion
1167 (name "r-biocversion")
1172 (uri (bioconductor-uri "BiocVersion" version))
1175 "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
1176 (properties `((upstream-name . "BiocVersion")))
1177 (build-system r-build-system)
1178 (home-page "https://bioconductor.org/packages/BiocVersion/")
1179 (synopsis "Set the appropriate version of Bioconductor packages")
1181 "This package provides repository information for the appropriate version
1183 (license license:artistic2.0)))
1185 (define-public r-biocgenerics
1187 (name "r-biocgenerics")
1191 (uri (bioconductor-uri "BiocGenerics" version))
1194 "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
1196 `((upstream-name . "BiocGenerics")))
1197 (build-system r-build-system)
1198 (home-page "https://bioconductor.org/packages/BiocGenerics")
1199 (synopsis "S4 generic functions for Bioconductor")
1201 "This package provides S4 generic functions needed by many Bioconductor
1203 (license license:artistic2.0)))
1205 (define-public r-coverageview
1207 (name "r-coverageview")
1211 (uri (bioconductor-uri "CoverageView" version))
1214 "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
1215 (build-system r-build-system)
1217 `(("r-s4vectors" ,r-s4vectors)
1218 ("r-iranges" ,r-iranges)
1219 ("r-genomicranges" ,r-genomicranges)
1220 ("r-genomicalignments" ,r-genomicalignments)
1221 ("r-rtracklayer" ,r-rtracklayer)
1222 ("r-rsamtools" ,r-rsamtools)))
1223 (home-page "https://bioconductor.org/packages/CoverageView/")
1224 (synopsis "Coverage visualization package for R")
1225 (description "This package provides a framework for the visualization of
1226 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1227 be also used for genome-wide nucleosome positioning experiments or other
1228 experiment types where it is important to have a framework in order to inspect
1229 how the coverage distributed across the genome.")
1230 (license license:artistic2.0)))
1232 (define-public r-cummerbund
1234 (name "r-cummerbund")
1238 (uri (bioconductor-uri "cummeRbund" version))
1241 "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
1242 (build-system r-build-system)
1244 `(("r-biobase" ,r-biobase)
1245 ("r-biocgenerics" ,r-biocgenerics)
1246 ("r-fastcluster" ,r-fastcluster)
1247 ("r-ggplot2" ,r-ggplot2)
1250 ("r-reshape2" ,r-reshape2)
1251 ("r-rsqlite" ,r-rsqlite)
1252 ("r-rtracklayer" ,r-rtracklayer)
1253 ("r-s4vectors" ,r-s4vectors)))
1254 (home-page "https://bioconductor.org/packages/cummeRbund/")
1255 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1256 (description "This package allows for persistent storage, access,
1257 exploration, and manipulation of Cufflinks high-throughput sequencing
1258 data. In addition, provides numerous plotting functions for commonly
1259 used visualizations.")
1260 (license license:artistic2.0)))
1262 (define-public r-delayedarray
1264 (name "r-delayedarray")
1268 (uri (bioconductor-uri "DelayedArray" version))
1271 "0w1wppy6m2iv41852dscg3y19sq84ahdx3m7c2p2pxjcznmv6hys"))))
1273 `((upstream-name . "DelayedArray")))
1274 (build-system r-build-system)
1276 `(("r-biocgenerics" ,r-biocgenerics)
1277 ("r-s4vectors" ,r-s4vectors)
1278 ("r-iranges" ,r-iranges)
1279 ("r-matrix" ,r-matrix)
1280 ("r-matrixgenerics" ,r-matrixgenerics)))
1282 `(("r-knitr" ,r-knitr)))
1283 (home-page "https://bioconductor.org/packages/DelayedArray")
1284 (synopsis "Delayed operations on array-like objects")
1286 "Wrapping an array-like object (typically an on-disk object) in a
1287 @code{DelayedArray} object allows one to perform common array operations on it
1288 without loading the object in memory. In order to reduce memory usage and
1289 optimize performance, operations on the object are either delayed or executed
1290 using a block processing mechanism. Note that this also works on in-memory
1291 array-like objects like @code{DataFrame} objects (typically with Rle columns),
1292 @code{Matrix} objects, and ordinary arrays and data frames.")
1293 (license license:artistic2.0)))
1295 (define-public r-bluster
1301 (uri (bioconductor-uri "bluster" version))
1304 "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61"))))
1305 (properties `((upstream-name . "bluster")))
1306 (build-system r-build-system)
1308 `(("r-biocneighbors" ,r-biocneighbors)
1309 ("r-biocparallel" ,r-biocparallel)
1310 ("r-igraph" ,r-igraph)
1311 ("r-matrix" ,r-matrix)
1313 ("r-s4vectors" ,r-s4vectors)))
1315 `(("r-knitr" ,r-knitr)))
1316 (home-page "https://bioconductor.org/packages/bluster")
1317 (synopsis "Clustering algorithms for Bioconductor")
1318 (description"This package wraps common clustering algorithms in an easily
1319 extended S4 framework. Backends are implemented for hierarchical, k-means
1320 and graph-based clustering. Several utilities are also provided to compare
1321 and evaluate clustering results.")
1322 (license license:gpl3)))
1324 (define-public r-ideoviz
1330 (uri (bioconductor-uri "IdeoViz" version))
1333 "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
1334 (build-system r-build-system)
1336 `(("r-biobase" ,r-biobase)
1337 ("r-iranges" ,r-iranges)
1338 ("r-genomicranges" ,r-genomicranges)
1339 ("r-rcolorbrewer" ,r-rcolorbrewer)
1340 ("r-rtracklayer" ,r-rtracklayer)
1341 ("r-genomeinfodb" ,r-genomeinfodb)))
1342 (home-page "https://bioconductor.org/packages/IdeoViz/")
1343 (synopsis "Plots data along a chromosomal ideogram")
1344 (description "This package provides functions to plot data associated with
1345 arbitrary genomic intervals along chromosomal ideogram.")
1346 (license license:gpl2)))
1348 (define-public r-iranges
1354 (uri (bioconductor-uri "IRanges" version))
1357 "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52"))))
1359 `((upstream-name . "IRanges")))
1360 (build-system r-build-system)
1362 `(("r-biocgenerics" ,r-biocgenerics)
1363 ("r-s4vectors" ,r-s4vectors)))
1364 (home-page "https://bioconductor.org/packages/IRanges")
1365 (synopsis "Infrastructure for manipulating intervals on sequences")
1367 "This package provides efficient low-level and highly reusable S4 classes
1368 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
1369 generally, data that can be organized sequentially (formally defined as
1370 @code{Vector} objects), as well as views on these @code{Vector} objects.
1371 Efficient list-like classes are also provided for storing big collections of
1372 instances of the basic classes. All classes in the package use consistent
1373 naming and share the same rich and consistent \"Vector API\" as much as
1375 (license license:artistic2.0)))
1377 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
1378 (define-public r-absfiltergsea
1380 (name "r-absfiltergsea")
1385 (uri (cran-uri "AbsFilterGSEA" version))
1387 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
1388 (properties `((upstream-name . "AbsFilterGSEA")))
1389 (build-system r-build-system)
1391 `(("r-biobase" ,r-biobase)
1392 ("r-deseq" ,r-deseq)
1393 ("r-limma" ,r-limma)
1395 ("r-rcpparmadillo" ,r-rcpparmadillo)))
1396 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
1397 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
1399 "This package provides a function that performs gene-permuting of a gene-set
1400 enrichment analysis (GSEA) calculation with or without the absolute filtering.
1401 Without filtering, users can perform (original) two-tailed or one-tailed
1403 (license license:gpl2)))
1405 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
1406 (define-public r-bisquerna
1408 (name "r-bisquerna")
1412 (uri (cran-uri "BisqueRNA" version))
1415 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
1416 (properties `((upstream-name . "BisqueRNA")))
1417 (build-system r-build-system)
1419 `(("r-biobase" ,r-biobase)
1420 ("r-limsolve" ,r-limsolve)))
1421 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
1422 (synopsis "Decomposition of bulk expression with single-cell sequencing")
1423 (description "This package provides tools to accurately estimate cell type
1424 abundances from heterogeneous bulk expression. A reference-based method
1425 utilizes single-cell information to generate a signature matrix and
1426 transformation of bulk expression for accurate regression based estimates.
1427 A marker-based method utilizes known cell-specific marker genes to measure
1428 relative abundances across samples.")
1429 (license license:gpl3)))
1431 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
1432 ;; from Bioconductor.
1433 (define-public r-deconstructsigs
1435 (name "r-deconstructsigs")
1439 (uri (cran-uri "deconstructSigs" version))
1442 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
1444 `((upstream-name . "deconstructSigs")))
1445 (build-system r-build-system)
1447 `(("r-bsgenome" ,r-bsgenome)
1448 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1449 ("r-genomeinfodb" ,r-genomeinfodb)
1450 ("r-reshape2" ,r-reshape2)))
1451 (home-page "https://github.com/raerose01/deconstructSigs")
1452 (synopsis "Identifies signatures present in a tumor sample")
1453 (description "This package takes sample information in the form of the
1454 fraction of mutations in each of 96 trinucleotide contexts and identifies
1455 the weighted combination of published signatures that, when summed, most
1456 closely reconstructs the mutational profile.")
1457 (license license:gpl2+)))
1459 ;; This is a CRAN package, but it depends on Bioconductor packages.
1460 (define-public r-nmf
1467 (uri (cran-uri "NMF" version))
1470 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
1471 (properties `((upstream-name . "NMF")))
1472 (build-system r-build-system)
1474 `(("r-cluster" ,r-cluster)
1475 ("r-biobase" ,r-biobase)
1476 ("r-biocmanager" ,r-biocmanager)
1477 ("r-bigmemory" ,r-bigmemory) ; suggested
1478 ("r-synchronicity" ,r-synchronicity) ; suggested
1479 ("r-colorspace" ,r-colorspace)
1480 ("r-digest" ,r-digest)
1481 ("r-doparallel" ,r-doparallel)
1482 ("r-foreach" ,r-foreach)
1483 ("r-ggplot2" ,r-ggplot2)
1484 ("r-gridbase" ,r-gridbase)
1485 ("r-pkgmaker" ,r-pkgmaker)
1486 ("r-rcolorbrewer" ,r-rcolorbrewer)
1487 ("r-registry" ,r-registry)
1488 ("r-reshape2" ,r-reshape2)
1489 ("r-rngtools" ,r-rngtools)
1490 ("r-stringr" ,r-stringr)))
1492 `(("r-knitr" ,r-knitr)))
1493 (home-page "http://renozao.github.io/NMF")
1494 (synopsis "Algorithms and framework for nonnegative matrix factorization")
1496 "This package provides a framework to perform Non-negative Matrix
1497 Factorization (NMF). The package implements a set of already published
1498 algorithms and seeding methods, and provides a framework to test, develop and
1499 plug new or custom algorithms. Most of the built-in algorithms have been
1500 optimized in C++, and the main interface function provides an easy way of
1501 performing parallel computations on multicore machines.")
1502 (license license:gpl2+)))
1504 (define-public r-affycomp
1511 (uri (bioconductor-uri "affycomp" version))
1514 "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
1515 (properties `((upstream-name . "affycomp")))
1516 (build-system r-build-system)
1517 (propagated-inputs `(("r-biobase" ,r-biobase)))
1518 (home-page "https://bioconductor.org/packages/affycomp/")
1519 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1521 "The package contains functions that can be used to compare expression
1522 measures for Affymetrix Oligonucleotide Arrays.")
1523 (license license:gpl2+)))
1525 (define-public r-affycompatible
1527 (name "r-affycompatible")
1532 (uri (bioconductor-uri "AffyCompatible" version))
1535 "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
1537 `((upstream-name . "AffyCompatible")))
1538 (build-system r-build-system)
1540 `(("r-biostrings" ,r-biostrings)
1541 ("r-rcurl" ,r-rcurl)
1543 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1544 (synopsis "Work with Affymetrix GeneChip files")
1546 "This package provides an interface to Affymetrix chip annotation and
1547 sample attribute files. The package allows an easy way for users to download
1548 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1549 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1550 Command Console} (AGCC)-compatible sample annotation files.")
1551 (license license:artistic2.0)))
1553 (define-public r-affycontam
1555 (name "r-affycontam")
1560 (uri (bioconductor-uri "affyContam" version))
1563 "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
1564 (properties `((upstream-name . "affyContam")))
1565 (build-system r-build-system)
1567 `(("r-affy" ,r-affy)
1568 ("r-affydata" ,r-affydata)
1569 ("r-biobase" ,r-biobase)))
1570 (home-page "https://bioconductor.org/packages/affyContam/")
1571 (synopsis "Structured corruption of Affymetrix CEL file data")
1573 "Microarray quality assessment is a major concern of microarray analysts.
1574 This package provides some simple approaches to in silico creation of quality
1575 problems in CEL-level data to help evaluate performance of quality metrics.")
1576 (license license:artistic2.0)))
1578 (define-public r-affycoretools
1580 (name "r-affycoretools")
1585 (uri (bioconductor-uri "affycoretools" version))
1588 "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
1589 (properties `((upstream-name . "affycoretools")))
1590 (build-system r-build-system)
1592 `(("r-affy" ,r-affy)
1593 ("r-annotationdbi" ,r-annotationdbi)
1594 ("r-biobase" ,r-biobase)
1595 ("r-biocgenerics" ,r-biocgenerics)
1597 ("r-edger" ,r-edger)
1598 ("r-gcrma" ,r-gcrma)
1599 ("r-glimma" ,r-glimma)
1600 ("r-ggplot2" ,r-ggplot2)
1601 ("r-gostats" ,r-gostats)
1602 ("r-gplots" ,r-gplots)
1603 ("r-hwriter" ,r-hwriter)
1604 ("r-lattice" ,r-lattice)
1605 ("r-limma" ,r-limma)
1606 ("r-oligoclasses" ,r-oligoclasses)
1607 ("r-reportingtools" ,r-reportingtools)
1608 ("r-rsqlite" ,r-rsqlite)
1609 ("r-s4vectors" ,r-s4vectors)
1610 ("r-xtable" ,r-xtable)))
1612 `(("r-knitr" ,r-knitr)))
1613 (home-page "https://bioconductor.org/packages/affycoretools/")
1614 (synopsis "Functions for analyses with Affymetrix GeneChips")
1616 "This package provides various wrapper functions that have been written
1617 to streamline the more common analyses that a Biostatistician might see.")
1618 (license license:artistic2.0)))
1620 (define-public r-affxparser
1622 (name "r-affxparser")
1627 (uri (bioconductor-uri "affxparser" version))
1630 "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
1631 (properties `((upstream-name . "affxparser")))
1632 (build-system r-build-system)
1633 (home-page "https://github.com/HenrikBengtsson/affxparser")
1634 (synopsis "Affymetrix File Parsing SDK")
1636 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1637 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1638 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1639 are supported. Currently, there are methods for reading @dfn{chip definition
1640 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1641 either in full or in part. For example, probe signals from a few probesets
1642 can be extracted very quickly from a set of CEL files into a convenient list
1644 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1646 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1648 (define-public r-annotate
1655 (uri (bioconductor-uri "annotate" version))
1658 "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
1659 (build-system r-build-system)
1661 `(("r-annotationdbi" ,r-annotationdbi)
1662 ("r-biobase" ,r-biobase)
1663 ("r-biocgenerics" ,r-biocgenerics)
1667 ("r-xtable" ,r-xtable)))
1669 "https://bioconductor.org/packages/annotate")
1670 (synopsis "Annotation for microarrays")
1671 (description "This package provides R environments for the annotation of
1673 (license license:artistic2.0)))
1675 (define-public r-annotationdbi
1677 (name "r-annotationdbi")
1681 (uri (bioconductor-uri "AnnotationDbi" version))
1684 "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
1686 `((upstream-name . "AnnotationDbi")))
1687 (build-system r-build-system)
1689 `(("r-biobase" ,r-biobase)
1690 ("r-biocgenerics" ,r-biocgenerics)
1692 ("r-iranges" ,r-iranges)
1693 ("r-rsqlite" ,r-rsqlite)
1694 ("r-s4vectors" ,r-s4vectors)))
1696 `(("r-knitr" ,r-knitr)))
1697 (home-page "https://bioconductor.org/packages/AnnotationDbi")
1698 (synopsis "Annotation database interface")
1700 "This package provides user interface and database connection code for
1701 annotation data packages using SQLite data storage.")
1702 (license license:artistic2.0)))
1704 (define-public r-annotationforge
1706 (name "r-annotationforge")
1711 (uri (bioconductor-uri "AnnotationForge" version))
1714 "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
1716 `((upstream-name . "AnnotationForge")))
1717 (build-system r-build-system)
1719 `(("r-annotationdbi" ,r-annotationdbi)
1720 ("r-biobase" ,r-biobase)
1721 ("r-biocgenerics" ,r-biocgenerics)
1723 ("r-rcurl" ,r-rcurl)
1724 ("r-rsqlite" ,r-rsqlite)
1725 ("r-s4vectors" ,r-s4vectors)
1728 `(("r-knitr" ,r-knitr)))
1729 (home-page "https://bioconductor.org/packages/AnnotationForge")
1730 (synopsis "Code for building annotation database packages")
1732 "This package provides code for generating Annotation packages and their
1733 databases. Packages produced are intended to be used with AnnotationDbi.")
1734 (license license:artistic2.0)))
1736 (define-public r-biobase
1742 (uri (bioconductor-uri "Biobase" version))
1745 "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
1747 `((upstream-name . "Biobase")))
1748 (build-system r-build-system)
1750 `(("r-biocgenerics" ,r-biocgenerics)))
1751 (home-page "https://bioconductor.org/packages/Biobase")
1752 (synopsis "Base functions for Bioconductor")
1754 "This package provides functions that are needed by many other packages
1755 on Bioconductor or which replace R functions.")
1756 (license license:artistic2.0)))
1758 (define-public r-biomart
1764 (uri (bioconductor-uri "biomaRt" version))
1767 "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
1769 `((upstream-name . "biomaRt")))
1770 (build-system r-build-system)
1772 `(("r-annotationdbi" ,r-annotationdbi)
1773 ("r-biocfilecache" ,r-biocfilecache)
1775 ("r-openssl" ,r-openssl)
1776 ("r-progress" ,r-progress)
1777 ("r-rappdirs" ,r-rappdirs)
1778 ("r-stringr" ,r-stringr)
1780 ("r-xml2" ,r-xml2)))
1782 `(("r-knitr" ,r-knitr)))
1783 (home-page "https://bioconductor.org/packages/biomaRt")
1784 (synopsis "Interface to BioMart databases")
1786 "biomaRt provides an interface to a growing collection of databases
1787 implementing the @url{BioMart software suite, http://www.biomart.org}. The
1788 package enables retrieval of large amounts of data in a uniform way without
1789 the need to know the underlying database schemas or write complex SQL queries.
1790 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
1791 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
1792 users direct access to a diverse set of data and enable a wide range of
1793 powerful online queries from gene annotation to database mining.")
1794 (license license:artistic2.0)))
1796 (define-public r-biocparallel
1798 (name "r-biocparallel")
1802 (uri (bioconductor-uri "BiocParallel" version))
1805 "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
1807 `((upstream-name . "BiocParallel")))
1808 (build-system r-build-system)
1811 (modify-phases %standard-phases
1812 (add-after 'unpack 'make-reproducible
1814 ;; Remove generated documentation.
1815 (for-each delete-file
1816 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
1817 "inst/doc/Introduction_To_BiocParallel.pdf"
1818 "inst/doc/Errors_Logs_And_Debugging.pdf"
1819 "inst/doc/BiocParallel_BatchtoolsParam.R"
1820 "inst/doc/Introduction_To_BiocParallel.R"
1821 "inst/doc/Errors_Logs_And_Debugging.R"))
1823 ;; Remove time-dependent macro
1824 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
1825 "inst/doc/Introduction_To_BiocParallel.Rnw"
1826 "inst/doc/Errors_Logs_And_Debugging.Rnw"
1827 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
1828 "vignettes/Introduction_To_BiocParallel.Rnw"
1829 "vignettes/Errors_Logs_And_Debugging.Rnw")
1830 (("\\today") "later"))
1832 ;; Initialize the random number generator seed when building.
1833 (substitute* "R/internal_rng_stream.R"
1834 (("\"L'Ecuyer-CMRG\"\\)" m)
1836 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
1838 `(("r-futile-logger" ,r-futile-logger)
1842 `(("r-knitr" ,r-knitr)))
1843 (home-page "https://bioconductor.org/packages/BiocParallel")
1844 (synopsis "Bioconductor facilities for parallel evaluation")
1846 "This package provides modified versions and novel implementation of
1847 functions for parallel evaluation, tailored to use with Bioconductor
1849 (license (list license:gpl2+ license:gpl3+))))
1851 (define-public r-biostrings
1853 (name "r-biostrings")
1857 (uri (bioconductor-uri "Biostrings" version))
1860 "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
1862 `((upstream-name . "Biostrings")))
1863 (build-system r-build-system)
1865 `(("r-biocgenerics" ,r-biocgenerics)
1866 ("r-crayon" ,r-crayon)
1867 ("r-iranges" ,r-iranges)
1868 ("r-s4vectors" ,r-s4vectors)
1869 ("r-xvector" ,r-xvector)))
1870 (home-page "https://bioconductor.org/packages/Biostrings")
1871 (synopsis "String objects and algorithms for biological sequences")
1873 "This package provides memory efficient string containers, string
1874 matching algorithms, and other utilities, for fast manipulation of large
1875 biological sequences or sets of sequences.")
1876 (license license:artistic2.0)))
1878 (define-public r-category
1885 (uri (bioconductor-uri "Category" version))
1888 "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
1889 (properties `((upstream-name . "Category")))
1890 (build-system r-build-system)
1892 `(("r-annotate" ,r-annotate)
1893 ("r-annotationdbi" ,r-annotationdbi)
1894 ("r-biobase" ,r-biobase)
1895 ("r-biocgenerics" ,r-biocgenerics)
1896 ("r-genefilter" ,r-genefilter)
1897 ("r-graph" ,r-graph)
1898 ("r-gseabase" ,r-gseabase)
1899 ("r-matrix" ,r-matrix)
1902 (home-page "https://bioconductor.org/packages/Category")
1903 (synopsis "Category analysis")
1905 "This package provides a collection of tools for performing category
1907 (license license:artistic2.0)))
1909 (define-public r-deseq2
1916 (uri (bioconductor-uri "DESeq2" version))
1919 "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19"))))
1920 (properties `((upstream-name . "DESeq2")))
1921 (build-system r-build-system)
1923 `(("r-biobase" ,r-biobase)
1924 ("r-biocgenerics" ,r-biocgenerics)
1925 ("r-biocparallel" ,r-biocparallel)
1926 ("r-genefilter" ,r-genefilter)
1927 ("r-geneplotter" ,r-geneplotter)
1928 ("r-genomicranges" ,r-genomicranges)
1929 ("r-ggplot2" ,r-ggplot2)
1930 ("r-iranges" ,r-iranges)
1931 ("r-locfit" ,r-locfit)
1933 ("r-rcpparmadillo" ,r-rcpparmadillo)
1934 ("r-s4vectors" ,r-s4vectors)
1935 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1937 `(("r-knitr" ,r-knitr)))
1938 (home-page "https://bioconductor.org/packages/DESeq2")
1939 (synopsis "Differential gene expression analysis")
1941 "This package provides functions to estimate variance-mean dependence in
1942 count data from high-throughput nucleotide sequencing assays and test for
1943 differential expression based on a model using the negative binomial
1945 (license license:lgpl3+)))
1947 (define-public r-dexseq
1954 (uri (bioconductor-uri "DEXSeq" version))
1957 "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
1958 (properties `((upstream-name . "DEXSeq")))
1959 (build-system r-build-system)
1961 `(("r-annotationdbi" ,r-annotationdbi)
1962 ("r-biobase" ,r-biobase)
1963 ("r-biocgenerics" ,r-biocgenerics)
1964 ("r-biocparallel" ,r-biocparallel)
1965 ("r-biomart" ,r-biomart)
1966 ("r-deseq2" ,r-deseq2)
1967 ("r-genefilter" ,r-genefilter)
1968 ("r-geneplotter" ,r-geneplotter)
1969 ("r-genomicranges" ,r-genomicranges)
1970 ("r-hwriter" ,r-hwriter)
1971 ("r-iranges" ,r-iranges)
1972 ("r-rcolorbrewer" ,r-rcolorbrewer)
1973 ("r-rsamtools" ,r-rsamtools)
1974 ("r-s4vectors" ,r-s4vectors)
1975 ("r-statmod" ,r-statmod)
1976 ("r-stringr" ,r-stringr)
1977 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1979 `(("r-knitr" ,r-knitr)))
1980 (home-page "https://bioconductor.org/packages/DEXSeq")
1981 (synopsis "Inference of differential exon usage in RNA-Seq")
1983 "This package is focused on finding differential exon usage using RNA-seq
1984 exon counts between samples with different experimental designs. It provides
1985 functions that allows the user to make the necessary statistical tests based
1986 on a model that uses the negative binomial distribution to estimate the
1987 variance between biological replicates and generalized linear models for
1988 testing. The package also provides functions for the visualization and
1989 exploration of the results.")
1990 (license license:gpl3+)))
1992 (define-public r-edger
1998 (uri (bioconductor-uri "edgeR" version))
2001 "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
2002 (properties `((upstream-name . "edgeR")))
2003 (build-system r-build-system)
2005 `(("r-limma" ,r-limma)
2006 ("r-locfit" ,r-locfit)
2008 ("r-statmod" ,r-statmod))) ;for estimateDisp
2009 (home-page "http://bioinf.wehi.edu.au/edgeR")
2010 (synopsis "EdgeR does empirical analysis of digital gene expression data")
2011 (description "This package can do differential expression analysis of
2012 RNA-seq expression profiles with biological replication. It implements a range
2013 of statistical methodology based on the negative binomial distributions,
2014 including empirical Bayes estimation, exact tests, generalized linear models
2015 and quasi-likelihood tests. It be applied to differential signal analysis of
2016 other types of genomic data that produce counts, including ChIP-seq, SAGE and
2018 (license license:gpl2+)))
2020 (define-public r-genefilter
2022 (name "r-genefilter")
2027 (uri (bioconductor-uri "genefilter" version))
2030 "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
2031 (build-system r-build-system)
2033 `(("gfortran" ,gfortran)
2034 ("r-knitr" ,r-knitr)))
2036 `(("r-annotate" ,r-annotate)
2037 ("r-annotationdbi" ,r-annotationdbi)
2038 ("r-biobase" ,r-biobase)
2039 ("r-biocgenerics" ,r-biocgenerics)
2040 ("r-survival" ,r-survival)))
2041 (home-page "https://bioconductor.org/packages/genefilter")
2042 (synopsis "Filter genes from high-throughput experiments")
2044 "This package provides basic functions for filtering genes from
2045 high-throughput sequencing experiments.")
2046 (license license:artistic2.0)))
2048 (define-public r-genomeinfodb
2050 (name "r-genomeinfodb")
2054 (uri (bioconductor-uri "GenomeInfoDb" version))
2057 "1wy4dwiv0pgim975var802z565py4a0nakx6zdvbhry4c0dfczd1"))))
2059 `((upstream-name . "GenomeInfoDb")))
2060 (build-system r-build-system)
2062 `(("r-biocgenerics" ,r-biocgenerics)
2063 ("r-genomeinfodbdata" ,r-genomeinfodbdata)
2064 ("r-iranges" ,r-iranges)
2065 ("r-rcurl" ,r-rcurl)
2066 ("r-s4vectors" ,r-s4vectors)))
2068 `(("r-knitr" ,r-knitr)))
2069 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
2070 (synopsis "Utilities for manipulating chromosome identifiers")
2072 "This package contains data and functions that define and allow
2073 translation between different chromosome sequence naming conventions (e.g.,
2074 \"chr1\" versus \"1\"), including a function that attempts to place sequence
2075 names in their natural, rather than lexicographic, order.")
2076 (license license:artistic2.0)))
2078 (define-public r-genomicranges
2080 (name "r-genomicranges")
2084 (uri (bioconductor-uri "GenomicRanges" version))
2087 "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
2089 `((upstream-name . "GenomicRanges")))
2090 (build-system r-build-system)
2092 `(("r-biocgenerics" ,r-biocgenerics)
2093 ("r-genomeinfodb" ,r-genomeinfodb)
2094 ("r-iranges" ,r-iranges)
2095 ("r-s4vectors" ,r-s4vectors)
2096 ("r-xvector" ,r-xvector)))
2098 `(("r-knitr" ,r-knitr)))
2099 (home-page "https://bioconductor.org/packages/GenomicRanges")
2100 (synopsis "Representation and manipulation of genomic intervals")
2102 "This package provides tools to efficiently represent and manipulate
2103 genomic annotations and alignments is playing a central role when it comes to
2104 analyzing high-throughput sequencing data (a.k.a. NGS data). The
2105 GenomicRanges package defines general purpose containers for storing and
2106 manipulating genomic intervals and variables defined along a genome.")
2107 (license license:artistic2.0)))
2109 (define-public r-gostats
2116 (uri (bioconductor-uri "GOstats" version))
2119 "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
2120 (properties `((upstream-name . "GOstats")))
2121 (build-system r-build-system)
2123 `(("r-annotate" ,r-annotate)
2124 ("r-annotationdbi" ,r-annotationdbi)
2125 ("r-annotationforge" ,r-annotationforge)
2126 ("r-biobase" ,r-biobase)
2127 ("r-category" ,r-category)
2128 ("r-go-db" ,r-go-db)
2129 ("r-graph" ,r-graph)
2130 ("r-rgraphviz" ,r-rgraphviz)
2131 ("r-rbgl" ,r-rbgl)))
2132 (home-page "https://bioconductor.org/packages/GOstats")
2133 (synopsis "Tools for manipulating GO and microarrays")
2135 "This package provides a set of tools for interacting with GO and
2136 microarray data. A variety of basic manipulation tools for graphs, hypothesis
2137 testing and other simple calculations.")
2138 (license license:artistic2.0)))
2140 (define-public r-gseabase
2147 (uri (bioconductor-uri "GSEABase" version))
2150 "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
2151 (properties `((upstream-name . "GSEABase")))
2152 (build-system r-build-system)
2154 `(("r-annotate" ,r-annotate)
2155 ("r-annotationdbi" ,r-annotationdbi)
2156 ("r-biobase" ,r-biobase)
2157 ("r-biocgenerics" ,r-biocgenerics)
2158 ("r-graph" ,r-graph)
2161 `(("r-knitr" ,r-knitr)))
2162 (home-page "https://bioconductor.org/packages/GSEABase")
2163 (synopsis "Gene set enrichment data structures and methods")
2165 "This package provides classes and methods to support @dfn{Gene Set
2166 Enrichment Analysis} (GSEA).")
2167 (license license:artistic2.0)))
2169 (define-public r-hpar
2176 (uri (bioconductor-uri "hpar" version))
2179 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
2180 (build-system r-build-system)
2182 `(("r-knitr" ,r-knitr)))
2183 (home-page "https://bioconductor.org/packages/hpar/")
2184 (synopsis "Human Protein Atlas in R")
2185 (description "This package provides a simple interface to and data from
2186 the Human Protein Atlas project.")
2187 (license license:artistic2.0)))
2189 (define-public r-limma
2195 (uri (bioconductor-uri "limma" version))
2198 "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
2199 (build-system r-build-system)
2200 (home-page "http://bioinf.wehi.edu.au/limma")
2201 (synopsis "Package for linear models for microarray and RNA-seq data")
2202 (description "This package can be used for the analysis of gene expression
2203 studies, especially the use of linear models for analysing designed experiments
2204 and the assessment of differential expression. The analysis methods apply to
2205 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
2206 (license license:gpl2+)))
2208 (define-public r-rbgl
2215 (uri (bioconductor-uri "RBGL" version))
2218 "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
2219 (properties `((upstream-name . "RBGL")))
2220 (build-system r-build-system)
2223 ("r-graph" ,r-graph)))
2224 (home-page "https://www.bioconductor.org/packages/RBGL")
2225 (synopsis "Interface to the Boost graph library")
2227 "This package provides a fairly extensive and comprehensive interface to
2228 the graph algorithms contained in the Boost library.")
2229 (license license:artistic2.0)))
2231 (define-public r-regioner
2238 (uri (bioconductor-uri "regioneR" version))
2241 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
2242 (properties `((upstream-name . "regioneR")))
2243 (build-system r-build-system)
2245 `(("r-biostrings" ,r-biostrings)
2246 ("r-bsgenome" ,r-bsgenome)
2247 ("r-genomeinfodb" ,r-genomeinfodb)
2248 ("r-genomicranges" ,r-genomicranges)
2249 ("r-iranges" ,r-iranges)
2250 ("r-memoise" ,r-memoise)
2251 ("r-rtracklayer" ,r-rtracklayer)
2252 ("r-s4vectors" ,r-s4vectors)))
2254 `(("r-knitr" ,r-knitr)))
2255 (home-page "https://bioconductor.org/packages/regioneR/")
2256 (synopsis "Association analysis of genomic regions")
2257 (description "This package offers a statistical framework based on
2258 customizable permutation tests to assess the association between genomic
2259 region sets and other genomic features.")
2260 (license license:artistic2.0)))
2262 (define-public r-reportingtools
2264 (name "r-reportingtools")
2269 (uri (bioconductor-uri "ReportingTools" version))
2272 "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb"))))
2274 `((upstream-name . "ReportingTools")))
2275 (build-system r-build-system)
2277 `(("r-annotate" ,r-annotate)
2278 ("r-annotationdbi" ,r-annotationdbi)
2279 ("r-biobase" ,r-biobase)
2280 ("r-biocgenerics" ,r-biocgenerics)
2281 ("r-category" ,r-category)
2282 ("r-deseq2" ,r-deseq2)
2283 ("r-edger" ,r-edger)
2284 ("r-ggbio" ,r-ggbio)
2285 ("r-ggplot2" ,r-ggplot2)
2286 ("r-gostats" ,r-gostats)
2287 ("r-gseabase" ,r-gseabase)
2288 ("r-hwriter" ,r-hwriter)
2289 ("r-iranges" ,r-iranges)
2290 ("r-knitr" ,r-knitr)
2291 ("r-lattice" ,r-lattice)
2292 ("r-limma" ,r-limma)
2293 ("r-pfam-db" ,r-pfam-db)
2294 ("r-r-utils" ,r-r-utils)
2297 `(("r-knitr" ,r-knitr)))
2298 (home-page "https://bioconductor.org/packages/ReportingTools/")
2299 (synopsis "Tools for making reports in various formats")
2301 "The ReportingTools package enables users to easily display reports of
2302 analysis results generated from sources such as microarray and sequencing
2303 data. The package allows users to create HTML pages that may be viewed on a
2304 web browser, or in other formats. Users can generate tables with sortable and
2305 filterable columns, make and display plots, and link table entries to other
2306 data sources such as NCBI or larger plots within the HTML page. Using the
2307 package, users can also produce a table of contents page to link various
2308 reports together for a particular project that can be viewed in a web
2310 (license license:artistic2.0)))
2312 (define-public r-rsamtools
2314 (name "r-rsamtools")
2318 (uri (bioconductor-uri "Rsamtools" version))
2321 "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
2323 `((upstream-name . "Rsamtools")))
2324 (build-system r-build-system)
2327 (modify-phases %standard-phases
2328 (add-after 'unpack 'use-system-zlib
2330 (substitute* "DESCRIPTION"
2331 (("zlibbioc, ") ""))
2332 (substitute* "NAMESPACE"
2333 (("import\\(zlibbioc\\)") ""))
2336 `(("r-biocgenerics" ,r-biocgenerics)
2337 ("r-biocparallel" ,r-biocparallel)
2338 ("r-biostrings" ,r-biostrings)
2339 ("r-bitops" ,r-bitops)
2340 ("r-genomeinfodb" ,r-genomeinfodb)
2341 ("r-genomicranges" ,r-genomicranges)
2342 ("r-iranges" ,r-iranges)
2343 ("r-rhtslib" ,r-rhtslib)
2344 ("r-s4vectors" ,r-s4vectors)
2345 ("r-xvector" ,r-xvector)))
2346 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
2347 (synopsis "Interface to samtools, bcftools, and tabix")
2349 "This package provides an interface to the @code{samtools},
2350 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
2351 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
2352 tab-delimited (tabix) files.")
2353 (license license:expat)))
2355 (define-public r-shortread
2357 (name "r-shortread")
2362 (uri (bioconductor-uri "ShortRead" version))
2365 "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
2366 (properties `((upstream-name . "ShortRead")))
2367 (build-system r-build-system)
2371 `(("r-biobase" ,r-biobase)
2372 ("r-biocgenerics" ,r-biocgenerics)
2373 ("r-biocparallel" ,r-biocparallel)
2374 ("r-biostrings" ,r-biostrings)
2375 ("r-genomeinfodb" ,r-genomeinfodb)
2376 ("r-genomicalignments" ,r-genomicalignments)
2377 ("r-genomicranges" ,r-genomicranges)
2378 ("r-rhtslib" ,r-rhtslib)
2379 ("r-hwriter" ,r-hwriter)
2380 ("r-iranges" ,r-iranges)
2381 ("r-lattice" ,r-lattice)
2382 ("r-latticeextra" ,r-latticeextra)
2383 ("r-rsamtools" ,r-rsamtools)
2384 ("r-s4vectors" ,r-s4vectors)
2385 ("r-xvector" ,r-xvector)
2386 ("r-zlibbioc" ,r-zlibbioc)))
2387 (home-page "https://bioconductor.org/packages/ShortRead")
2388 (synopsis "FASTQ input and manipulation tools")
2390 "This package implements sampling, iteration, and input of FASTQ files.
2391 It includes functions for filtering and trimming reads, and for generating a
2392 quality assessment report. Data are represented as
2393 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
2394 purposes. The package also contains legacy support for early single-end,
2395 ungapped alignment formats.")
2396 (license license:artistic2.0)))
2398 (define-public r-systempiper
2400 (name "r-systempiper")
2405 (uri (bioconductor-uri "systemPipeR" version))
2408 "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
2409 (properties `((upstream-name . "systemPipeR")))
2410 (build-system r-build-system)
2412 `(("r-annotate" ,r-annotate)
2413 ("r-assertthat" ,r-assertthat)
2414 ("r-batchtools" ,r-batchtools)
2415 ("r-biostrings" ,r-biostrings)
2416 ("r-deseq2" ,r-deseq2)
2418 ("r-edger" ,r-edger)
2419 ("r-genomicfeatures" ,r-genomicfeatures)
2420 ("r-genomicranges" ,r-genomicranges)
2421 ("r-ggplot2" ,r-ggplot2)
2422 ("r-go-db" ,r-go-db)
2423 ("r-gostats" ,r-gostats)
2424 ("r-iranges" ,r-iranges)
2425 ("r-limma" ,r-limma)
2426 ("r-magrittr" ,r-magrittr)
2427 ("r-pheatmap" ,r-pheatmap)
2428 ("r-rjson" ,r-rjson)
2429 ("r-rsamtools" ,r-rsamtools)
2431 ("r-shortread" ,r-shortread)
2432 ("r-stringr" ,r-stringr)
2433 ("r-summarizedexperiment" ,r-summarizedexperiment)
2435 ("r-variantannotation" ,r-variantannotation)))
2437 `(("r-knitr" ,r-knitr)))
2438 (home-page "https://github.com/tgirke/systemPipeR")
2439 (synopsis "Next generation sequencing workflow and reporting environment")
2441 "This R package provides tools for building and running automated
2442 end-to-end analysis workflows for a wide range of @dfn{next generation
2443 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
2444 Important features include a uniform workflow interface across different NGS
2445 applications, automated report generation, and support for running both R and
2446 command-line software, such as NGS aligners or peak/variant callers, on local
2447 computers or compute clusters. Efficient handling of complex sample sets and
2448 experimental designs is facilitated by a consistently implemented sample
2449 annotation infrastructure.")
2450 (license license:artistic2.0)))
2452 (define-public r-variantannotation
2454 (name "r-variantannotation")
2458 (uri (bioconductor-uri "VariantAnnotation" version))
2461 "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
2463 `((upstream-name . "VariantAnnotation")))
2465 `(("r-annotationdbi" ,r-annotationdbi)
2466 ("r-biobase" ,r-biobase)
2467 ("r-biocgenerics" ,r-biocgenerics)
2468 ("r-biostrings" ,r-biostrings)
2469 ("r-bsgenome" ,r-bsgenome)
2471 ("r-genomeinfodb" ,r-genomeinfodb)
2472 ("r-genomicfeatures" ,r-genomicfeatures)
2473 ("r-genomicranges" ,r-genomicranges)
2474 ("r-iranges" ,r-iranges)
2475 ("r-matrixgenerics" ,r-matrixgenerics)
2476 ("r-summarizedexperiment" ,r-summarizedexperiment)
2477 ("r-rhtslib" ,r-rhtslib)
2478 ("r-rsamtools" ,r-rsamtools)
2479 ("r-rtracklayer" ,r-rtracklayer)
2480 ("r-s4vectors" ,r-s4vectors)
2481 ("r-xvector" ,r-xvector)
2482 ("r-zlibbioc" ,r-zlibbioc)))
2483 (build-system r-build-system)
2484 (home-page "https://bioconductor.org/packages/VariantAnnotation")
2485 (synopsis "Package for annotation of genetic variants")
2486 (description "This R package can annotate variants, compute amino acid
2487 coding changes and predict coding outcomes.")
2488 (license license:artistic2.0)))
2490 (define-public r-xvector
2496 (uri (bioconductor-uri "XVector" version))
2499 "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
2501 `((upstream-name . "XVector")))
2502 (build-system r-build-system)
2505 (modify-phases %standard-phases
2506 (add-after 'unpack 'use-system-zlib
2508 (substitute* "DESCRIPTION"
2509 (("zlibbioc, ") ""))
2510 (substitute* "NAMESPACE"
2511 (("import\\(zlibbioc\\)") ""))
2516 `(("r-biocgenerics" ,r-biocgenerics)
2517 ("r-iranges" ,r-iranges)
2518 ("r-s4vectors" ,r-s4vectors)))
2519 (home-page "https://bioconductor.org/packages/XVector")
2520 (synopsis "Representation and manpulation of external sequences")
2522 "This package provides memory efficient S4 classes for storing sequences
2523 \"externally\" (behind an R external pointer, or on disk).")
2524 (license license:artistic2.0)))
2526 (define-public r-geneplotter
2528 (name "r-geneplotter")
2533 (uri (bioconductor-uri "geneplotter" version))
2536 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
2537 (build-system r-build-system)
2539 `(("r-annotate" ,r-annotate)
2540 ("r-annotationdbi" ,r-annotationdbi)
2541 ("r-biobase" ,r-biobase)
2542 ("r-biocgenerics" ,r-biocgenerics)
2543 ("r-lattice" ,r-lattice)
2544 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2545 (home-page "https://bioconductor.org/packages/geneplotter")
2546 (synopsis "Graphics functions for genomic data")
2548 "This package provides functions for plotting genomic data.")
2549 (license license:artistic2.0)))
2551 (define-public r-oligoclasses
2553 (name "r-oligoclasses")
2558 (uri (bioconductor-uri "oligoClasses" version))
2561 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
2562 (properties `((upstream-name . "oligoClasses")))
2563 (build-system r-build-system)
2565 `(("r-affyio" ,r-affyio)
2566 ("r-biobase" ,r-biobase)
2567 ("r-biocgenerics" ,r-biocgenerics)
2568 ("r-biocmanager" ,r-biocmanager)
2569 ("r-biostrings" ,r-biostrings)
2572 ("r-foreach" ,r-foreach)
2573 ("r-genomicranges" ,r-genomicranges)
2574 ("r-iranges" ,r-iranges)
2575 ("r-rsqlite" ,r-rsqlite)
2576 ("r-s4vectors" ,r-s4vectors)
2577 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2578 (home-page "https://bioconductor.org/packages/oligoClasses/")
2579 (synopsis "Classes for high-throughput arrays")
2581 "This package contains class definitions, validity checks, and
2582 initialization methods for classes used by the @code{oligo} and @code{crlmm}
2584 (license license:gpl2+)))
2586 (define-public r-oligo
2593 (uri (bioconductor-uri "oligo" version))
2596 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
2597 (properties `((upstream-name . "oligo")))
2598 (build-system r-build-system)
2599 (inputs `(("zlib" ,zlib)))
2601 `(("r-affxparser" ,r-affxparser)
2602 ("r-affyio" ,r-affyio)
2603 ("r-biobase" ,r-biobase)
2604 ("r-biocgenerics" ,r-biocgenerics)
2605 ("r-biostrings" ,r-biostrings)
2608 ("r-oligoclasses" ,r-oligoclasses)
2609 ("r-preprocesscore" ,r-preprocesscore)
2610 ("r-rsqlite" ,r-rsqlite)
2611 ("r-zlibbioc" ,r-zlibbioc)))
2613 `(("r-knitr" ,r-knitr)))
2614 (home-page "https://bioconductor.org/packages/oligo/")
2615 (synopsis "Preprocessing tools for oligonucleotide arrays")
2617 "This package provides a package to analyze oligonucleotide
2618 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
2619 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
2620 (license license:lgpl2.0+)))
2622 (define-public r-qvalue
2629 (uri (bioconductor-uri "qvalue" version))
2632 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
2633 (build-system r-build-system)
2635 `(("r-ggplot2" ,r-ggplot2)
2636 ("r-reshape2" ,r-reshape2)))
2638 `(("r-knitr" ,r-knitr)))
2639 (home-page "https://github.com/StoreyLab/qvalue")
2640 (synopsis "Q-value estimation for false discovery rate control")
2642 "This package takes a list of p-values resulting from the simultaneous
2643 testing of many hypotheses and estimates their q-values and local @dfn{false
2644 discovery rate} (FDR) values. The q-value of a test measures the proportion
2645 of false positives incurred when that particular test is called significant.
2646 The local FDR measures the posterior probability the null hypothesis is true
2647 given the test's p-value. Various plots are automatically generated, allowing
2648 one to make sensible significance cut-offs. The software can be applied to
2649 problems in genomics, brain imaging, astrophysics, and data mining.")
2650 ;; Any version of the LGPL.
2651 (license license:lgpl3+)))
2653 (define r-rcppnumerical
2655 (name "r-rcppnumerical")
2659 (uri (cran-uri "RcppNumerical" version))
2662 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
2663 (properties `((upstream-name . "RcppNumerical")))
2664 (build-system r-build-system)
2666 `(("r-rcpp" ,r-rcpp)
2667 ("r-rcppeigen" ,r-rcppeigen)))
2669 `(("r-knitr" ,r-knitr)))
2670 (home-page "https://github.com/yixuan/RcppNumerical")
2671 (synopsis "Rcpp integration for numerical computing libraries")
2672 (description "This package provides a collection of open source libraries
2673 for numerical computing (numerical integration, optimization, etc.) and their
2674 integration with @code{Rcpp}.")
2675 (license license:gpl2+)))
2677 (define-public r-apeglm
2683 (uri (bioconductor-uri "apeglm" version))
2686 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
2687 (properties `((upstream-name . "apeglm")))
2688 (build-system r-build-system)
2690 `(("r-emdbook" ,r-emdbook)
2691 ("r-genomicranges" ,r-genomicranges)
2693 ("r-rcppeigen" ,r-rcppeigen)
2694 ("r-rcppnumerical" ,r-rcppnumerical)
2695 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2696 (native-inputs `(("r-knitr" ,r-knitr)))
2697 (home-page "https://bioconductor.org/packages/apeglm")
2698 (synopsis "Approximate posterior estimation for GLM coefficients")
2699 (description "This package provides Bayesian shrinkage estimators for
2700 effect sizes for a variety of GLM models, using approximation of the
2701 posterior for individual coefficients.")
2702 (license license:gpl2)))
2704 (define-public r-greylistchip
2706 (name "r-greylistchip")
2710 (uri (bioconductor-uri "GreyListChIP" version))
2713 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
2714 (properties `((upstream-name . "GreyListChIP")))
2715 (build-system r-build-system)
2717 `(("r-bsgenome" ,r-bsgenome)
2718 ("r-genomeinfodb" ,r-genomeinfodb)
2719 ("r-genomicalignments" ,r-genomicalignments)
2720 ("r-genomicranges" ,r-genomicranges)
2722 ("r-rsamtools" ,r-rsamtools)
2723 ("r-rtracklayer" ,r-rtracklayer)
2724 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2725 (home-page "https://bioconductor.org/packages/GreyListChIP")
2726 (synopsis "Greylist artefact regions based on ChIP inputs")
2727 (description "This package identifies regions of ChIP experiments with high
2728 signal in the input, that lead to spurious peaks during peak calling.")
2729 (license license:artistic2.0)))
2731 (define-public r-diffbind
2738 (uri (bioconductor-uri "DiffBind" version))
2741 "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi"))))
2742 (properties `((upstream-name . "DiffBind")))
2743 (build-system r-build-system)
2745 `(("r-amap" ,r-amap)
2746 ("r-apeglm" ,r-apeglm)
2748 ("r-biocparallel" ,r-biocparallel)
2749 ("r-deseq2" ,r-deseq2)
2750 ("r-dplyr" ,r-dplyr)
2751 ("r-genomicalignments" ,r-genomicalignments)
2752 ("r-genomicranges" ,r-genomicranges)
2753 ("r-ggplot2" ,r-ggplot2)
2754 ("r-ggrepel" ,r-ggrepel)
2755 ("r-gplots" ,r-gplots)
2756 ("r-greylistchip" ,r-greylistchip)
2757 ("r-iranges" ,r-iranges)
2758 ("r-lattice" ,r-lattice)
2759 ("r-limma" ,r-limma)
2760 ("r-locfit" ,r-locfit)
2761 ("r-rcolorbrewer" , r-rcolorbrewer)
2763 ("r-rhtslib" ,r-rhtslib)
2764 ("r-rsamtools" ,r-rsamtools)
2765 ("r-s4vectors" ,r-s4vectors)
2766 ("r-summarizedexperiment" ,r-summarizedexperiment)
2767 ("r-systempiper" ,r-systempiper)))
2768 (home-page "https://bioconductor.org/packages/DiffBind")
2769 (synopsis "Differential binding analysis of ChIP-Seq peak data")
2771 "This package computes differentially bound sites from multiple
2772 ChIP-seq experiments using affinity (quantitative) data. Also enables
2773 occupancy (overlap) analysis and plotting functions.")
2774 (license license:artistic2.0)))
2776 (define-public r-ripseeker
2778 (name "r-ripseeker")
2783 (uri (bioconductor-uri "RIPSeeker" version))
2786 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
2787 (properties `((upstream-name . "RIPSeeker")))
2788 (build-system r-build-system)
2790 `(("r-s4vectors" ,r-s4vectors)
2791 ("r-iranges" ,r-iranges)
2792 ("r-genomicranges" ,r-genomicranges)
2793 ("r-summarizedexperiment" ,r-summarizedexperiment)
2794 ("r-rsamtools" ,r-rsamtools)
2795 ("r-genomicalignments" ,r-genomicalignments)
2796 ("r-rtracklayer" ,r-rtracklayer)))
2797 (home-page "https://bioconductor.org/packages/RIPSeeker")
2799 "Identifying protein-associated transcripts from RIP-seq experiments")
2801 "This package infers and discriminates RIP peaks from RIP-seq alignments
2802 using two-state HMM with negative binomial emission probability. While
2803 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
2804 a suite of bioinformatics tools integrated within this self-contained software
2805 package comprehensively addressing issues ranging from post-alignments
2806 processing to visualization and annotation.")
2807 (license license:gpl2)))
2809 (define-public r-multtest
2816 (uri (bioconductor-uri "multtest" version))
2819 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
2820 (build-system r-build-system)
2822 `(("r-survival" ,r-survival)
2823 ("r-biocgenerics" ,r-biocgenerics)
2824 ("r-biobase" ,r-biobase)
2825 ("r-mass" ,r-mass)))
2826 (home-page "https://bioconductor.org/packages/multtest")
2827 (synopsis "Resampling-based multiple hypothesis testing")
2829 "This package can do non-parametric bootstrap and permutation
2830 resampling-based multiple testing procedures (including empirical Bayes
2831 methods) for controlling the family-wise error rate (FWER), generalized
2832 family-wise error rate (gFWER), tail probability of the proportion of
2833 false positives (TPPFP), and false discovery rate (FDR). Several choices
2834 of bootstrap-based null distribution are implemented (centered, centered
2835 and scaled, quantile-transformed). Single-step and step-wise methods are
2836 available. Tests based on a variety of T- and F-statistics (including
2837 T-statistics based on regression parameters from linear and survival models
2838 as well as those based on correlation parameters) are included. When probing
2839 hypotheses with T-statistics, users may also select a potentially faster null
2840 distribution which is multivariate normal with mean zero and variance
2841 covariance matrix derived from the vector influence function. Results are
2842 reported in terms of adjusted P-values, confidence regions and test statistic
2843 cutoffs. The procedures are directly applicable to identifying differentially
2844 expressed genes in DNA microarray experiments.")
2845 (license license:lgpl3)))
2847 (define-public r-graph
2853 (uri (bioconductor-uri "graph" version))
2856 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
2857 (build-system r-build-system)
2859 `(("r-biocgenerics" ,r-biocgenerics)))
2860 (home-page "https://bioconductor.org/packages/graph")
2861 (synopsis "Handle graph data structures in R")
2863 "This package implements some simple graph handling capabilities for R.")
2864 (license license:artistic2.0)))
2866 ;; This is a CRAN package, but it depends on a Bioconductor package.
2867 (define-public r-ggm
2874 (uri (cran-uri "ggm" version))
2877 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
2878 (properties `((upstream-name . "ggm")))
2879 (build-system r-build-system)
2881 `(("r-graph" ,r-graph)
2882 ("r-igraph" ,r-igraph)))
2883 (home-page "https://cran.r-project.org/package=ggm")
2884 (synopsis "Functions for graphical Markov models")
2886 "This package provides functions and datasets for maximum likelihood
2887 fitting of some classes of graphical Markov models.")
2888 (license license:gpl2+)))
2890 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
2891 (define-public r-perfmeas
2898 (uri (cran-uri "PerfMeas" version))
2901 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
2902 (properties `((upstream-name . "PerfMeas")))
2903 (build-system r-build-system)
2905 `(("r-graph" ,r-graph)
2906 ("r-limma" ,r-limma)
2907 ("r-rbgl" ,r-rbgl)))
2908 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
2909 (synopsis "Performance measures for ranking and classification tasks")
2911 "This package implements different performance measures for
2912 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
2913 a given recall, F-score for single and multiple classes are available.")
2914 (license license:gpl2+)))
2916 ;; This is a CRAN package, but it depends on a Bioconductor package.
2917 (define-public r-codedepends
2919 (name "r-codedepends")
2924 (uri (cran-uri "CodeDepends" version))
2927 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
2928 (properties `((upstream-name . "CodeDepends")))
2929 (build-system r-build-system)
2931 `(("r-codetools" ,r-codetools)
2932 ("r-graph" ,r-graph)
2934 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
2935 (synopsis "Analysis of R code for reproducible research and code comprehension")
2937 "This package provides tools for analyzing R expressions or blocks of
2938 code and determining the dependencies between them. It focuses on R scripts,
2939 but can be used on the bodies of functions. There are many facilities
2940 including the ability to summarize or get a high-level view of code,
2941 determining dependencies between variables, code improvement suggestions.")
2942 ;; Any version of the GPL
2943 (license (list license:gpl2+ license:gpl3+))))
2945 (define-public r-chippeakanno
2947 (name "r-chippeakanno")
2952 (uri (bioconductor-uri "ChIPpeakAnno" version))
2955 "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw"))))
2956 (properties `((upstream-name . "ChIPpeakAnno")))
2957 (build-system r-build-system)
2959 `(("r-annotationdbi" ,r-annotationdbi)
2960 ("r-biocgenerics" ,r-biocgenerics)
2961 ("r-biomart" ,r-biomart)
2962 ("r-biostrings" ,r-biostrings)
2964 ("r-dplyr" ,r-dplyr)
2965 ("r-ensembldb" ,r-ensembldb)
2966 ("r-genomeinfodb" ,r-genomeinfodb)
2967 ("r-genomicalignments" ,r-genomicalignments)
2968 ("r-genomicfeatures" ,r-genomicfeatures)
2969 ("r-genomicranges" ,r-genomicranges)
2970 ("r-ggplot2" ,r-ggplot2)
2971 ("r-graph" ,r-graph)
2972 ("r-iranges" ,r-iranges)
2973 ("r-keggrest" ,r-keggrest)
2974 ("r-matrixstats" ,r-matrixstats)
2975 ("r-multtest" ,r-multtest)
2977 ("r-regioner" ,r-regioner)
2978 ("r-rsamtools" ,r-rsamtools)
2979 ("r-rtracklayer" ,r-rtracklayer)
2980 ("r-s4vectors" ,r-s4vectors)
2981 ("r-summarizedexperiment" ,r-summarizedexperiment)
2982 ("r-venndiagram" ,r-venndiagram)))
2984 `(("r-knitr" ,r-knitr)))
2985 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
2986 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
2988 "The package includes functions to retrieve the sequences around the peak,
2989 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
2990 custom features such as most conserved elements and other transcription factor
2991 binding sites supplied by users. Starting 2.0.5, new functions have been added
2992 for finding the peaks with bi-directional promoters with summary statistics
2993 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
2994 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
2995 enrichedGO (addGeneIDs).")
2996 (license license:gpl2+)))
2998 (define-public r-matrixgenerics
3000 (name "r-matrixgenerics")
3004 (uri (bioconductor-uri "MatrixGenerics" version))
3007 "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
3009 `((upstream-name . "MatrixGenerics")))
3010 (build-system r-build-system)
3012 `(("r-matrixstats" ,r-matrixstats)))
3013 (home-page "https://bioconductor.org/packages/MatrixGenerics")
3014 (synopsis "S4 generic summary statistic functions for matrix-like objects")
3016 "This package provides S4 generic functions modeled after the
3017 @code{matrixStats} API for alternative matrix implementations. Packages with
3018 alternative matrix implementation can depend on this package and implement the
3019 generic functions that are defined here for a useful set of row and column
3020 summary statistics. Other package developers can import this package and
3021 handle a different matrix implementations without worrying about
3022 incompatibilities.")
3023 (license license:artistic2.0)))
3025 (define-public r-marray
3031 (uri (bioconductor-uri "marray" version))
3033 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
3034 (build-system r-build-system)
3036 `(("r-limma" ,r-limma)))
3037 (home-page "https://bioconductor.org/packages/marray")
3038 (synopsis "Exploratory analysis for two-color spotted microarray data")
3039 (description "This package contains class definitions for two-color spotted
3040 microarray data. It also includes functions for data input, diagnostic plots,
3041 normalization and quality checking.")
3042 (license license:lgpl2.0+)))
3044 (define-public r-cghbase
3050 (uri (bioconductor-uri "CGHbase" version))
3052 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
3053 (properties `((upstream-name . "CGHbase")))
3054 (build-system r-build-system)
3056 `(("r-biobase" ,r-biobase)
3057 ("r-marray" ,r-marray)))
3058 (home-page "https://bioconductor.org/packages/CGHbase")
3059 (synopsis "Base functions and classes for arrayCGH data analysis")
3060 (description "This package contains functions and classes that are needed by
3061 the @code{arrayCGH} packages.")
3062 (license license:gpl2+)))
3064 (define-public r-cghcall
3070 (uri (bioconductor-uri "CGHcall" version))
3072 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
3073 (properties `((upstream-name . "CGHcall")))
3074 (build-system r-build-system)
3076 `(("r-biobase" ,r-biobase)
3077 ("r-cghbase" ,r-cghbase)
3078 ("r-impute" ,r-impute)
3079 ("r-dnacopy" ,r-dnacopy)
3080 ("r-snowfall" ,r-snowfall)))
3081 (home-page "https://bioconductor.org/packages/CGHcall")
3082 (synopsis "Base functions and classes for arrayCGH data analysis")
3083 (description "This package contains functions and classes that are needed by
3084 @code{arrayCGH} packages.")
3085 (license license:gpl2+)))
3087 (define-public r-qdnaseq
3093 (uri (bioconductor-uri "QDNAseq" version))
3095 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
3096 (properties `((upstream-name . "QDNAseq")))
3097 (build-system r-build-system)
3099 `(("r-biobase" ,r-biobase)
3100 ("r-cghbase" ,r-cghbase)
3101 ("r-cghcall" ,r-cghcall)
3102 ("r-dnacopy" ,r-dnacopy)
3103 ("r-future" ,r-future)
3104 ("r-future-apply" ,r-future-apply)
3105 ("r-genomicranges" ,r-genomicranges)
3106 ("r-iranges" ,r-iranges)
3107 ("r-matrixstats" ,r-matrixstats)
3108 ("r-r-utils" ,r-r-utils)
3109 ("r-rsamtools" ,r-rsamtools)))
3110 (home-page "https://bioconductor.org/packages/QDNAseq")
3111 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
3112 (description "The genome is divided into non-overlapping fixed-sized bins,
3113 number of sequence reads in each counted, adjusted with a simultaneous
3114 two-dimensional loess correction for sequence mappability and GC content, and
3115 filtered to remove spurious regions in the genome. Downstream steps of
3116 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
3118 (license license:gpl2+)))
3120 (define-public r-bayseq
3127 (uri (bioconductor-uri "baySeq" version))
3130 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
3131 (properties `((upstream-name . "baySeq")))
3132 (build-system r-build-system)
3134 `(("r-abind" ,r-abind)
3135 ("r-edger" ,r-edger)
3136 ("r-genomicranges" ,r-genomicranges)))
3137 (home-page "https://bioconductor.org/packages/baySeq/")
3138 (synopsis "Bayesian analysis of differential expression patterns in count data")
3140 "This package identifies differential expression in high-throughput count
3141 data, such as that derived from next-generation sequencing machines,
3142 calculating estimated posterior likelihoods of differential expression (or
3143 more complex hypotheses) via empirical Bayesian methods.")
3144 (license license:gpl3)))
3146 (define-public r-chipcomp
3153 (uri (bioconductor-uri "ChIPComp" version))
3156 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
3157 (properties `((upstream-name . "ChIPComp")))
3158 (build-system r-build-system)
3160 `(("r-biocgenerics" ,r-biocgenerics)
3161 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
3162 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
3163 ("r-genomeinfodb" ,r-genomeinfodb)
3164 ("r-genomicranges" ,r-genomicranges)
3165 ("r-iranges" ,r-iranges)
3166 ("r-limma" ,r-limma)
3167 ("r-rsamtools" ,r-rsamtools)
3168 ("r-rtracklayer" ,r-rtracklayer)
3169 ("r-s4vectors" ,r-s4vectors)))
3170 (home-page "https://bioconductor.org/packages/ChIPComp")
3171 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
3173 "ChIPComp implements a statistical method for quantitative comparison of
3174 multiple ChIP-seq datasets. It detects differentially bound sharp binding
3175 sites across multiple conditions considering matching control in ChIP-seq
3177 ;; Any version of the GPL.
3178 (license license:gpl3+)))
3180 (define-public r-riboprofiling
3182 (name "r-riboprofiling")
3187 (uri (bioconductor-uri "RiboProfiling" version))
3190 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
3191 (properties `((upstream-name . "RiboProfiling")))
3192 (build-system r-build-system)
3194 `(("r-biocgenerics" ,r-biocgenerics)
3195 ("r-biostrings" ,r-biostrings)
3196 ("r-data-table" ,r-data-table)
3197 ("r-genomeinfodb" ,r-genomeinfodb)
3198 ("r-genomicalignments" ,r-genomicalignments)
3199 ("r-genomicfeatures" ,r-genomicfeatures)
3200 ("r-genomicranges" ,r-genomicranges)
3201 ("r-ggbio" ,r-ggbio)
3202 ("r-ggplot2" ,r-ggplot2)
3203 ("r-iranges" ,r-iranges)
3205 ("r-reshape2" ,r-reshape2)
3206 ("r-rsamtools" ,r-rsamtools)
3207 ("r-rtracklayer" ,r-rtracklayer)
3208 ("r-s4vectors" ,r-s4vectors)
3209 ("r-sqldf" ,r-sqldf)))
3211 `(("r-knitr" ,r-knitr)))
3212 (home-page "https://bioconductor.org/packages/RiboProfiling/")
3213 (synopsis "Ribosome profiling data analysis")
3214 (description "Starting with a BAM file, this package provides the
3215 necessary functions for quality assessment, read start position recalibration,
3216 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
3217 of count data: pairs, log fold-change, codon frequency and coverage
3218 assessment, principal component analysis on codon coverage.")
3219 (license license:gpl3)))
3221 (define-public r-riboseqr
3228 (uri (bioconductor-uri "riboSeqR" version))
3231 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
3232 (properties `((upstream-name . "riboSeqR")))
3233 (build-system r-build-system)
3235 `(("r-abind" ,r-abind)
3236 ("r-bayseq" ,r-bayseq)
3237 ("r-genomeinfodb" ,r-genomeinfodb)
3238 ("r-genomicranges" ,r-genomicranges)
3239 ("r-iranges" ,r-iranges)
3240 ("r-rsamtools" ,r-rsamtools)
3241 ("r-seqlogo" ,r-seqlogo)))
3242 (home-page "https://bioconductor.org/packages/riboSeqR/")
3243 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
3245 "This package provides plotting functions, frameshift detection and
3246 parsing of genetic sequencing data from ribosome profiling experiments.")
3247 (license license:gpl3)))
3249 (define-public r-interactionset
3251 (name "r-interactionset")
3256 (uri (bioconductor-uri "InteractionSet" version))
3259 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
3261 `((upstream-name . "InteractionSet")))
3262 (build-system r-build-system)
3264 `(("r-biocgenerics" ,r-biocgenerics)
3265 ("r-genomeinfodb" ,r-genomeinfodb)
3266 ("r-genomicranges" ,r-genomicranges)
3267 ("r-iranges" ,r-iranges)
3268 ("r-matrix" ,r-matrix)
3270 ("r-s4vectors" ,r-s4vectors)
3271 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3273 `(("r-knitr" ,r-knitr)))
3274 (home-page "https://bioconductor.org/packages/InteractionSet")
3275 (synopsis "Base classes for storing genomic interaction data")
3277 "This package provides the @code{GInteractions},
3278 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
3279 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
3281 (license license:gpl3)))
3283 (define-public r-genomicinteractions
3285 (name "r-genomicinteractions")
3290 (uri (bioconductor-uri "GenomicInteractions" version))
3293 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
3295 `((upstream-name . "GenomicInteractions")))
3296 (build-system r-build-system)
3298 `(("r-biobase" ,r-biobase)
3299 ("r-biocgenerics" ,r-biocgenerics)
3300 ("r-data-table" ,r-data-table)
3301 ("r-dplyr" ,r-dplyr)
3302 ("r-genomeinfodb" ,r-genomeinfodb)
3303 ("r-genomicranges" ,r-genomicranges)
3304 ("r-ggplot2" ,r-ggplot2)
3305 ("r-gridextra" ,r-gridextra)
3307 ("r-igraph" ,r-igraph)
3308 ("r-interactionset" ,r-interactionset)
3309 ("r-iranges" ,r-iranges)
3310 ("r-rsamtools" ,r-rsamtools)
3311 ("r-rtracklayer" ,r-rtracklayer)
3312 ("r-s4vectors" ,r-s4vectors)
3313 ("r-stringr" ,r-stringr)))
3315 `(("r-knitr" ,r-knitr)))
3316 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
3317 (synopsis "R package for handling genomic interaction data")
3319 "This R package provides tools for handling genomic interaction data,
3320 such as ChIA-PET/Hi-C, annotating genomic features with interaction
3321 information and producing various plots and statistics.")
3322 (license license:gpl3)))
3324 (define-public r-ctc
3331 (uri (bioconductor-uri "ctc" version))
3334 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
3335 (build-system r-build-system)
3336 (propagated-inputs `(("r-amap" ,r-amap)))
3337 (home-page "https://bioconductor.org/packages/ctc/")
3338 (synopsis "Cluster and tree conversion")
3340 "This package provides tools for exporting and importing classification
3341 trees and clusters to other programs.")
3342 (license license:gpl2)))
3344 (define-public r-goseq
3351 (uri (bioconductor-uri "goseq" version))
3354 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
3355 (build-system r-build-system)
3357 `(("r-annotationdbi" ,r-annotationdbi)
3358 ("r-biasedurn" ,r-biasedurn)
3359 ("r-biocgenerics" ,r-biocgenerics)
3360 ("r-genelendatabase" ,r-genelendatabase)
3361 ("r-go-db" ,r-go-db)
3362 ("r-mgcv" ,r-mgcv)))
3363 (home-page "https://bioconductor.org/packages/goseq/")
3364 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
3366 "This package provides tools to detect Gene Ontology and/or other user
3367 defined categories which are over/under represented in RNA-seq data.")
3368 (license license:lgpl2.0+)))
3370 (define-public r-glimma
3377 (uri (bioconductor-uri "Glimma" version))
3380 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
3381 (properties `((upstream-name . "Glimma")))
3382 (build-system r-build-system)
3384 `(("r-deseq2" ,r-deseq2)
3385 ("r-edger" ,r-edger)
3386 ("r-htmlwidgets" ,r-htmlwidgets)
3387 ("r-jsonlite" ,r-jsonlite)
3388 ("r-limma" ,r-limma)
3389 ("r-s4vectors" ,r-s4vectors)
3390 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3392 `(("r-knitr" ,r-knitr)))
3393 (home-page "https://github.com/Shians/Glimma")
3394 (synopsis "Interactive HTML graphics")
3396 "This package generates interactive visualisations for analysis of
3397 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
3398 HTML page. The interactions are built on top of the popular static
3399 representations of analysis results in order to provide additional
3401 (license license:lgpl3)))
3403 (define-public r-rots
3410 (uri (bioconductor-uri "ROTS" version))
3413 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
3414 (properties `((upstream-name . "ROTS")))
3415 (build-system r-build-system)
3417 `(("r-biobase" ,r-biobase)
3418 ("r-rcpp" ,r-rcpp)))
3419 (home-page "https://bioconductor.org/packages/ROTS/")
3420 (synopsis "Reproducibility-Optimized Test Statistic")
3422 "This package provides tools for calculating the
3423 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
3425 (license license:gpl2+)))
3427 (define-public r-plgem
3434 (uri (bioconductor-uri "plgem" version))
3437 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
3438 (build-system r-build-system)
3440 `(("r-biobase" ,r-biobase)
3441 ("r-mass" ,r-mass)))
3442 (home-page "http://www.genopolis.it")
3443 (synopsis "Detect differential expression in microarray and proteomics datasets")
3445 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
3446 model the variance-versus-mean dependence that exists in a variety of
3447 genome-wide datasets, including microarray and proteomics data. The use of
3448 PLGEM has been shown to improve the detection of differentially expressed
3449 genes or proteins in these datasets.")
3450 (license license:gpl2)))
3452 (define-public r-inspect
3459 (uri (bioconductor-uri "INSPEcT" version))
3462 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
3463 (properties `((upstream-name . "INSPEcT")))
3464 (build-system r-build-system)
3466 `(("r-biobase" ,r-biobase)
3467 ("r-biocgenerics" ,r-biocgenerics)
3468 ("r-biocparallel" ,r-biocparallel)
3469 ("r-deseq2" ,r-deseq2)
3470 ("r-desolve" ,r-desolve)
3471 ("r-gdata" ,r-gdata)
3472 ("r-genomeinfodb" ,r-genomeinfodb)
3473 ("r-genomicalignments" ,r-genomicalignments)
3474 ("r-genomicfeatures" ,r-genomicfeatures)
3475 ("r-genomicranges" ,r-genomicranges)
3476 ("r-iranges" ,r-iranges)
3477 ("r-kernsmooth" ,r-kernsmooth)
3478 ("r-plgem" ,r-plgem)
3480 ("r-rootsolve" ,r-rootsolve)
3481 ("r-rsamtools" ,r-rsamtools)
3482 ("r-rtracklayer" ,r-rtracklayer)
3483 ("r-s4vectors" ,r-s4vectors)
3484 ("r-shiny" ,r-shiny)
3485 ("r-summarizedexperiment" ,r-summarizedexperiment)
3486 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
3487 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
3489 `(("r-knitr" ,r-knitr)))
3490 (home-page "https://bioconductor.org/packages/INSPEcT")
3491 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
3493 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
3494 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
3495 order to evaluate synthesis, processing and degradation rates and assess via
3496 modeling the rates that determines changes in mature mRNA levels.")
3497 (license license:gpl2)))
3499 (define-public r-dnabarcodes
3501 (name "r-dnabarcodes")
3506 (uri (bioconductor-uri "DNABarcodes" version))
3509 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
3510 (properties `((upstream-name . "DNABarcodes")))
3511 (build-system r-build-system)
3514 ("r-matrix" ,r-matrix)
3515 ("r-rcpp" ,r-rcpp)))
3517 `(("r-knitr" ,r-knitr)))
3518 (home-page "https://bioconductor.org/packages/DNABarcodes")
3519 (synopsis "Create and analyze DNA barcodes")
3521 "This package offers tools to create DNA barcode sets capable of
3522 correcting insertion, deletion, and substitution errors. Existing barcodes
3523 can be analyzed regarding their minimal, maximal and average distances between
3524 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
3525 demultiplexed, i.e. assigned to their original reference barcode.")
3526 (license license:gpl2)))
3528 (define-public r-ruvseq
3535 (uri (bioconductor-uri "RUVSeq" version))
3538 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
3539 (properties `((upstream-name . "RUVSeq")))
3540 (build-system r-build-system)
3542 `(("r-biobase" ,r-biobase)
3543 ("r-edaseq" ,r-edaseq)
3544 ("r-edger" ,r-edger)
3545 ("r-mass" ,r-mass)))
3547 `(("r-knitr" ,r-knitr)))
3548 (home-page "https://github.com/drisso/RUVSeq")
3549 (synopsis "Remove unwanted variation from RNA-Seq data")
3551 "This package implements methods to @dfn{remove unwanted variation} (RUV)
3552 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
3554 (license license:artistic2.0)))
3556 (define-public r-biocneighbors
3558 (name "r-biocneighbors")
3563 (uri (bioconductor-uri "BiocNeighbors" version))
3566 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
3567 (properties `((upstream-name . "BiocNeighbors")))
3568 (build-system r-build-system)
3570 `(("r-biocparallel" ,r-biocparallel)
3571 ("r-matrix" ,r-matrix)
3573 ("r-rcpphnsw" ,r-rcpphnsw)
3574 ("r-s4vectors" ,r-s4vectors)))
3576 `(("r-knitr" ,r-knitr)))
3577 (home-page "https://bioconductor.org/packages/BiocNeighbors")
3578 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
3580 "This package implements exact and approximate methods for nearest
3581 neighbor detection, in a framework that allows them to be easily switched
3582 within Bioconductor packages or workflows. The exact algorithm is implemented
3583 using pre-clustering with the k-means algorithm. Functions are also provided
3584 to search for all neighbors within a given distance. Parallelization is
3585 achieved for all methods using the BiocParallel framework.")
3586 (license license:gpl3)))
3588 (define-public r-biocsingular
3590 (name "r-biocsingular")
3595 (uri (bioconductor-uri "BiocSingular" version))
3598 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
3599 (properties `((upstream-name . "BiocSingular")))
3600 (build-system r-build-system)
3602 `(("r-beachmat" ,r-beachmat)
3603 ("r-biocgenerics" ,r-biocgenerics)
3604 ("r-biocparallel" ,r-biocparallel)
3605 ("r-delayedarray" ,r-delayedarray)
3606 ("r-irlba" ,r-irlba)
3607 ("r-matrix" ,r-matrix)
3610 ("r-s4vectors" ,r-s4vectors)))
3612 `(("r-knitr" ,r-knitr)))
3613 (home-page "https://github.com/LTLA/BiocSingular")
3614 (synopsis "Singular value decomposition for Bioconductor packages")
3616 "This package implements exact and approximate methods for singular value
3617 decomposition and principal components analysis, in a framework that allows
3618 them to be easily switched within Bioconductor packages or workflows. Where
3619 possible, parallelization is achieved using the BiocParallel framework.")
3620 (license license:gpl3)))
3622 (define-public r-destiny
3629 (uri (bioconductor-uri "destiny" version))
3632 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
3633 (build-system r-build-system)
3635 `(("r-biobase" ,r-biobase)
3636 ("r-biocgenerics" ,r-biocgenerics)
3637 ("r-ggplot-multistats" ,r-ggplot-multistats)
3638 ("r-ggplot2" ,r-ggplot2)
3639 ("r-ggthemes" ,r-ggthemes)
3640 ("r-irlba" ,r-irlba)
3641 ("r-knn-covertree" ,r-knn-covertree)
3642 ("r-matrix" ,r-matrix)
3643 ("r-pcamethods" ,r-pcamethods)
3644 ("r-proxy" ,r-proxy)
3646 ("r-rcppeigen" ,r-rcppeigen)
3647 ("r-rcpphnsw" ,r-rcpphnsw)
3648 ("r-rspectra" ,r-rspectra)
3649 ("r-scales" ,r-scales)
3650 ("r-scatterplot3d" ,r-scatterplot3d)
3651 ("r-singlecellexperiment" ,r-singlecellexperiment)
3652 ("r-smoother" ,r-smoother)
3653 ("r-summarizedexperiment" ,r-summarizedexperiment)
3654 ("r-tidyr" ,r-tidyr)
3655 ("r-tidyselect" ,r-tidyselect)
3658 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
3659 (home-page "https://bioconductor.org/packages/destiny/")
3660 (synopsis "Create and plot diffusion maps")
3661 (description "This package provides tools to create and plot diffusion
3663 ;; Any version of the GPL
3664 (license license:gpl3+)))
3666 (define-public r-savr
3673 (uri (bioconductor-uri "savR" version))
3676 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
3677 (properties `((upstream-name . "savR")))
3678 (build-system r-build-system)
3680 `(("r-ggplot2" ,r-ggplot2)
3681 ("r-gridextra" ,r-gridextra)
3682 ("r-reshape2" ,r-reshape2)
3683 ("r-scales" ,r-scales)
3685 (home-page "https://github.com/bcalder/savR")
3686 (synopsis "Parse and analyze Illumina SAV files")
3688 "This package provides tools to parse Illumina Sequence Analysis
3689 Viewer (SAV) files, access data, and generate QC plots.")
3690 (license license:agpl3+)))
3692 (define-public r-chipexoqual
3694 (name "r-chipexoqual")
3699 (uri (bioconductor-uri "ChIPexoQual" version))
3702 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
3703 (properties `((upstream-name . "ChIPexoQual")))
3704 (build-system r-build-system)
3706 `(("r-biocparallel" ,r-biocparallel)
3707 ("r-biovizbase" ,r-biovizbase)
3708 ("r-broom" ,r-broom)
3709 ("r-data-table" ,r-data-table)
3710 ("r-dplyr" ,r-dplyr)
3711 ("r-genomeinfodb" ,r-genomeinfodb)
3712 ("r-genomicalignments" ,r-genomicalignments)
3713 ("r-genomicranges" ,r-genomicranges)
3714 ("r-ggplot2" ,r-ggplot2)
3715 ("r-hexbin" ,r-hexbin)
3716 ("r-iranges" ,r-iranges)
3717 ("r-rcolorbrewer" ,r-rcolorbrewer)
3718 ("r-rmarkdown" ,r-rmarkdown)
3719 ("r-rsamtools" ,r-rsamtools)
3720 ("r-s4vectors" ,r-s4vectors)
3721 ("r-scales" ,r-scales)
3722 ("r-viridis" ,r-viridis)))
3724 `(("r-knitr" ,r-knitr)))
3725 (home-page "https://github.com/keleslab/ChIPexoQual")
3726 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
3728 "This package provides a quality control pipeline for ChIP-exo/nexus
3730 (license license:gpl2+)))
3732 (define-public r-copynumber
3734 (name "r-copynumber")
3738 (uri (bioconductor-uri "copynumber" version))
3741 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
3742 (build-system r-build-system)
3744 `(("r-s4vectors" ,r-s4vectors)
3745 ("r-iranges" ,r-iranges)
3746 ("r-genomicranges" ,r-genomicranges)
3747 ("r-biocgenerics" ,r-biocgenerics)))
3748 (home-page "https://bioconductor.org/packages/copynumber")
3749 (synopsis "Segmentation of single- and multi-track copy number data")
3751 "This package segments single- and multi-track copy number data by a
3752 penalized least squares regression method.")
3753 (license license:artistic2.0)))
3755 (define-public r-dnacopy
3762 (uri (bioconductor-uri "DNAcopy" version))
3765 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
3766 (properties `((upstream-name . "DNAcopy")))
3767 (build-system r-build-system)
3768 (native-inputs `(("gfortran" ,gfortran)))
3769 (home-page "https://bioconductor.org/packages/DNAcopy")
3770 (synopsis "DNA copy number data analysis")
3772 "This package implements the @dfn{circular binary segmentation} (CBS)
3773 algorithm to segment DNA copy number data and identify genomic regions with
3774 abnormal copy number.")
3775 (license license:gpl2+)))
3777 ;; This is a CRAN package, but it uncharacteristically depends on a
3778 ;; Bioconductor package.
3779 (define-public r-htscluster
3781 (name "r-htscluster")
3786 (uri (cran-uri "HTSCluster" version))
3789 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
3790 (properties `((upstream-name . "HTSCluster")))
3791 (build-system r-build-system)
3793 `(("r-capushe" ,r-capushe)
3794 ("r-edger" ,r-edger)
3795 ("r-plotrix" ,r-plotrix)))
3796 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
3797 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
3799 "This package provides a Poisson mixture model is implemented to cluster
3800 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
3801 estimation is performed using either the EM or CEM algorithm, and the slope
3802 heuristics are used for model selection (i.e., to choose the number of
3804 (license license:gpl3+)))
3806 (define-public r-deds
3813 (uri (bioconductor-uri "DEDS" version))
3816 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
3817 (properties `((upstream-name . "DEDS")))
3818 (build-system r-build-system)
3819 (home-page "https://bioconductor.org/packages/DEDS/")
3820 (synopsis "Differential expression via distance summary for microarray data")
3822 "This library contains functions that calculate various statistics of
3823 differential expression for microarray data, including t statistics, fold
3824 change, F statistics, SAM, moderated t and F statistics and B statistics. It
3825 also implements a new methodology called DEDS (Differential Expression via
3826 Distance Summary), which selects differentially expressed genes by integrating
3827 and summarizing a set of statistics using a weighted distance approach.")
3828 ;; Any version of the LGPL.
3829 (license license:lgpl3+)))
3831 ;; This is a CRAN package, but since it depends on a Bioconductor package we
3833 (define-public r-nbpseq
3840 (uri (cran-uri "NBPSeq" version))
3843 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
3844 (properties `((upstream-name . "NBPSeq")))
3845 (build-system r-build-system)
3847 `(("r-qvalue" ,r-qvalue)))
3848 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
3849 (synopsis "Negative binomial models for RNA-Seq data")
3851 "This package provides negative binomial models for two-group comparisons
3852 and regression inferences from RNA-sequencing data.")
3853 (license license:gpl2)))
3855 (define-public r-ebseq
3862 (uri (bioconductor-uri "EBSeq" version))
3865 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
3866 (properties `((upstream-name . "EBSeq")))
3867 (build-system r-build-system)
3869 `(("r-blockmodeling" ,r-blockmodeling)
3870 ("r-gplots" ,r-gplots)
3871 ("r-testthat" ,r-testthat)))
3872 (home-page "https://bioconductor.org/packages/EBSeq")
3873 (synopsis "Differential expression analysis of RNA-seq data")
3875 "This package provides tools for differential expression analysis at both
3876 gene and isoform level using RNA-seq data")
3877 (license license:artistic2.0)))
3879 (define-public r-karyoploter
3881 (name "r-karyoploter")
3885 (uri (bioconductor-uri "karyoploteR" version))
3888 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
3889 (build-system r-build-system)
3891 `(("r-annotationdbi" ,r-annotationdbi)
3892 ("r-bamsignals" ,r-bamsignals)
3893 ("r-bezier" ,r-bezier)
3894 ("r-biovizbase" ,r-biovizbase)
3895 ("r-digest" ,r-digest)
3896 ("r-genomeinfodb" ,r-genomeinfodb)
3897 ("r-genomicfeatures" ,r-genomicfeatures)
3898 ("r-genomicranges" ,r-genomicranges)
3899 ("r-iranges" ,r-iranges)
3900 ("r-memoise" ,r-memoise)
3901 ("r-regioner" ,r-regioner)
3902 ("r-rsamtools" ,r-rsamtools)
3903 ("r-rtracklayer" ,r-rtracklayer)
3904 ("r-s4vectors" ,r-s4vectors)
3905 ("r-variantannotation" ,r-variantannotation)))
3907 `(("r-knitr" ,r-knitr)))
3908 (home-page "https://bioconductor.org/packages/karyoploteR/")
3909 (synopsis "Plot customizable linear genomes displaying arbitrary data")
3910 (description "This package creates karyotype plots of arbitrary genomes and
3911 offers a complete set of functions to plot arbitrary data on them. It mimics
3912 many R base graphics functions coupling them with a coordinate change function
3913 automatically mapping the chromosome and data coordinates into the plot
3915 (license license:artistic2.0)))
3917 (define-public r-lpsymphony
3919 (name "r-lpsymphony")
3924 (uri (bioconductor-uri "lpsymphony" version))
3927 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
3928 (build-system r-build-system)
3932 `(("pkg-config" ,pkg-config)
3933 ("r-knitr" ,r-knitr)))
3934 (home-page "https://r-forge.r-project.org/projects/rsymphony")
3935 (synopsis "Symphony integer linear programming solver in R")
3937 "This package was derived from Rsymphony. The package provides an R
3938 interface to SYMPHONY, a linear programming solver written in C++. The main
3939 difference between this package and Rsymphony is that it includes the solver
3940 source code, while Rsymphony expects to find header and library files on the
3941 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
3942 to install interface to SYMPHONY.")
3943 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
3944 ;; lpsimphony is released under the same terms.
3945 (license license:epl1.0)))
3947 (define-public r-ihw
3954 (uri (bioconductor-uri "IHW" version))
3957 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
3958 (properties `((upstream-name . "IHW")))
3959 (build-system r-build-system)
3961 `(("r-biocgenerics" ,r-biocgenerics)
3962 ("r-fdrtool" ,r-fdrtool)
3963 ("r-lpsymphony" ,r-lpsymphony)
3964 ("r-slam" ,r-slam)))
3966 `(("r-knitr" ,r-knitr)))
3967 (home-page "https://bioconductor.org/packages/IHW")
3968 (synopsis "Independent hypothesis weighting")
3970 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
3971 procedure that increases power compared to the method of Benjamini and
3972 Hochberg by assigning data-driven weights to each hypothesis. The input to
3973 IHW is a two-column table of p-values and covariates. The covariate can be
3974 any continuous-valued or categorical variable that is thought to be
3975 informative on the statistical properties of each hypothesis test, while it is
3976 independent of the p-value under the null hypothesis.")
3977 (license license:artistic2.0)))
3979 (define-public r-icobra
3986 (uri (bioconductor-uri "iCOBRA" version))
3989 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
3990 (properties `((upstream-name . "iCOBRA")))
3991 (build-system r-build-system)
3993 `(("r-dplyr" ,r-dplyr)
3995 ("r-ggplot2" ,r-ggplot2)
3996 ("r-limma" ,r-limma)
3997 ("r-reshape2" ,r-reshape2)
3999 ("r-scales" ,r-scales)
4000 ("r-shiny" ,r-shiny)
4001 ("r-shinybs" ,r-shinybs)
4002 ("r-shinydashboard" ,r-shinydashboard)
4003 ("r-upsetr" ,r-upsetr)))
4005 `(("r-knitr" ,r-knitr)))
4006 (home-page "https://bioconductor.org/packages/iCOBRA")
4007 (synopsis "Comparison and visualization of ranking and assignment methods")
4009 "This package provides functions for calculation and visualization of
4010 performance metrics for evaluation of ranking and binary
4011 classification (assignment) methods. It also contains a Shiny application for
4012 interactive exploration of results.")
4013 (license license:gpl2+)))
4015 (define-public r-mast
4022 (uri (bioconductor-uri "MAST" version))
4025 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
4026 (properties `((upstream-name . "MAST")))
4027 (build-system r-build-system)
4029 `(("r-abind" ,r-abind)
4030 ("r-biobase" ,r-biobase)
4031 ("r-biocgenerics" ,r-biocgenerics)
4032 ("r-data-table" ,r-data-table)
4033 ("r-ggplot2" ,r-ggplot2)
4035 ("r-progress" ,r-progress)
4036 ("r-reshape2" ,r-reshape2)
4037 ("r-s4vectors" ,r-s4vectors)
4038 ("r-singlecellexperiment" ,r-singlecellexperiment)
4039 ("r-stringr" ,r-stringr)
4040 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4042 `(("r-knitr" ,r-knitr)))
4043 (home-page "https://github.com/RGLab/MAST/")
4044 (synopsis "Model-based analysis of single cell transcriptomics")
4046 "This package provides methods and models for handling zero-inflated
4047 single cell assay data.")
4048 (license license:gpl2+)))
4050 (define-public r-monocle
4057 (uri (bioconductor-uri "monocle" version))
4060 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
4061 (build-system r-build-system)
4063 `(("r-biobase" ,r-biobase)
4064 ("r-biocgenerics" ,r-biocgenerics)
4065 ("r-biocviews" ,r-biocviews)
4066 ("r-cluster" ,r-cluster)
4067 ("r-combinat" ,r-combinat)
4068 ("r-ddrtree" ,r-ddrtree)
4069 ("r-densityclust" ,r-densityclust)
4070 ("r-dplyr" ,r-dplyr)
4071 ("r-fastica" ,r-fastica)
4072 ("r-ggplot2" ,r-ggplot2)
4073 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
4074 ("r-igraph" ,r-igraph)
4075 ("r-irlba" ,r-irlba)
4076 ("r-limma" ,r-limma)
4078 ("r-matrix" ,r-matrix)
4079 ("r-matrixstats" ,r-matrixstats)
4080 ("r-pheatmap" ,r-pheatmap)
4082 ("r-proxy" ,r-proxy)
4083 ("r-qlcmatrix" ,r-qlcmatrix)
4086 ("r-reshape2" ,r-reshape2)
4087 ("r-rtsne" ,r-rtsne)
4089 ("r-stringr" ,r-stringr)
4090 ("r-tibble" ,r-tibble)
4092 ("r-viridis" ,r-viridis)))
4094 `(("r-knitr" ,r-knitr)))
4095 (home-page "https://bioconductor.org/packages/monocle")
4096 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
4098 "Monocle performs differential expression and time-series analysis for
4099 single-cell expression experiments. It orders individual cells according to
4100 progress through a biological process, without knowing ahead of time which
4101 genes define progress through that process. Monocle also performs
4102 differential expression analysis, clustering, visualization, and other useful
4103 tasks on single cell expression data. It is designed to work with RNA-Seq and
4104 qPCR data, but could be used with other types as well.")
4105 (license license:artistic2.0)))
4107 (define-public r-monocle3
4115 (url "https://github.com/cole-trapnell-lab/monocle3")
4117 (file-name (git-file-name name version))
4120 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
4121 (build-system r-build-system)
4123 `(("r-biobase" ,r-biobase)
4124 ("r-biocgenerics" ,r-biocgenerics)
4125 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
4126 ("r-dplyr" ,r-dplyr)
4127 ("r-ggplot2" ,r-ggplot2)
4128 ("r-ggrepel" ,r-ggrepel)
4130 ("r-htmlwidgets" ,r-htmlwidgets)
4131 ("r-igraph" ,r-igraph)
4132 ("r-irlba" ,r-irlba)
4133 ("r-limma" ,r-limma)
4134 ("r-lmtest" ,r-lmtest)
4136 ("r-matrix" ,r-matrix)
4137 ("r-matrix-utils" ,r-matrix-utils)
4138 ("r-pbapply" ,r-pbapply)
4139 ("r-pbmcapply" ,r-pbmcapply)
4140 ("r-pheatmap" ,r-pheatmap)
4141 ("r-plotly" ,r-plotly)
4143 ("r-proxy" ,r-proxy)
4145 ("r-purrr" ,r-purrr)
4148 ("r-rcppparallel" ,r-rcppparallel)
4149 ("r-reshape2" ,r-reshape2)
4150 ("r-reticulate" ,r-reticulate)
4151 ("r-rhpcblasctl" ,r-rhpcblasctl)
4152 ("r-rtsne" ,r-rtsne)
4153 ("r-shiny" ,r-shiny)
4155 ("r-spdep" ,r-spdep)
4156 ("r-speedglm" ,r-speedglm)
4157 ("r-stringr" ,r-stringr)
4158 ("r-singlecellexperiment" ,r-singlecellexperiment)
4159 ("r-tibble" ,r-tibble)
4160 ("r-tidyr" ,r-tidyr)
4162 ("r-viridis" ,r-viridis)))
4163 (home-page "https://github.com/cole-trapnell-lab/monocle3")
4164 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
4166 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
4167 (license license:expat)))
4169 (define-public r-noiseq
4176 (uri (bioconductor-uri "NOISeq" version))
4179 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
4180 (properties `((upstream-name . "NOISeq")))
4181 (build-system r-build-system)
4183 `(("r-biobase" ,r-biobase)
4184 ("r-matrix" ,r-matrix)))
4185 (home-page "https://bioconductor.org/packages/NOISeq")
4186 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
4188 "This package provides tools to support the analysis of RNA-seq
4189 expression data or other similar kind of data. It provides exploratory plots
4190 to evaluate saturation, count distribution, expression per chromosome, type of
4191 detected features, features length, etc. It also supports the analysis of
4192 differential expression between two experimental conditions with no parametric
4194 (license license:artistic2.0)))
4196 (define-public r-scdd
4203 (uri (bioconductor-uri "scDD" version))
4206 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
4207 (properties `((upstream-name . "scDD")))
4208 (build-system r-build-system)
4211 ("r-biocparallel" ,r-biocparallel)
4212 ("r-ebseq" ,r-ebseq)
4213 ("r-fields" ,r-fields)
4214 ("r-ggplot2" ,r-ggplot2)
4215 ("r-mclust" ,r-mclust)
4216 ("r-outliers" ,r-outliers)
4217 ("r-s4vectors" ,r-s4vectors)
4218 ("r-scran" ,r-scran)
4219 ("r-singlecellexperiment" ,r-singlecellexperiment)
4220 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4222 `(("r-knitr" ,r-knitr)))
4223 (home-page "https://github.com/kdkorthauer/scDD")
4224 (synopsis "Mixture modeling of single-cell RNA-seq data")
4226 "This package implements a method to analyze single-cell RNA-seq data
4227 utilizing flexible Dirichlet Process mixture models. Genes with differential
4228 distributions of expression are classified into several interesting patterns
4229 of differences between two conditions. The package also includes functions
4230 for simulating data with these patterns from negative binomial
4232 (license license:gpl2)))
4234 (define-public r-scone
4241 (uri (bioconductor-uri "scone" version))
4244 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
4245 (build-system r-build-system)
4247 `(("r-aroma-light" ,r-aroma-light)
4248 ("r-biocparallel" ,r-biocparallel)
4250 ("r-class" ,r-class)
4251 ("r-cluster" ,r-cluster)
4252 ("r-compositions" ,r-compositions)
4253 ("r-diptest" ,r-diptest)
4254 ("r-edger" ,r-edger)
4256 ("r-gplots" ,r-gplots)
4257 ("r-hexbin" ,r-hexbin)
4258 ("r-limma" ,r-limma)
4259 ("r-matrixstats" ,r-matrixstats)
4260 ("r-mixtools" ,r-mixtools)
4261 ("r-rarpack" ,r-rarpack)
4262 ("r-rcolorbrewer" ,r-rcolorbrewer)
4263 ("r-rhdf5" ,r-rhdf5)
4264 ("r-ruvseq" ,r-ruvseq)
4265 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4267 `(("r-knitr" ,r-knitr)))
4268 (home-page "https://bioconductor.org/packages/scone")
4269 (synopsis "Single cell overview of normalized expression data")
4271 "SCONE is an R package for comparing and ranking the performance of
4272 different normalization schemes for single-cell RNA-seq and other
4273 high-throughput analyses.")
4274 (license license:artistic2.0)))
4276 (define-public r-geoquery
4283 (uri (bioconductor-uri "GEOquery" version))
4286 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
4287 (properties `((upstream-name . "GEOquery")))
4288 (build-system r-build-system)
4290 `(("r-biobase" ,r-biobase)
4291 ("r-dplyr" ,r-dplyr)
4293 ("r-limma" ,r-limma)
4294 ("r-magrittr" ,r-magrittr)
4295 ("r-readr" ,r-readr)
4296 ("r-tidyr" ,r-tidyr)
4297 ("r-xml2" ,r-xml2)))
4299 `(("r-knitr" ,r-knitr)))
4300 (home-page "https://github.com/seandavi/GEOquery/")
4301 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
4303 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
4304 microarray data. Given the rich and varied nature of this resource, it is
4305 only natural to want to apply BioConductor tools to these data. GEOquery is
4306 the bridge between GEO and BioConductor.")
4307 (license license:gpl2)))
4309 (define-public r-illuminaio
4311 (name "r-illuminaio")
4316 (uri (bioconductor-uri "illuminaio" version))
4319 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
4320 (build-system r-build-system)
4322 `(("r-base64" ,r-base64)))
4323 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
4324 (synopsis "Parse Illumina microarray output files")
4326 "This package provides tools for parsing Illumina's microarray output
4327 files, including IDAT.")
4328 (license license:gpl2)))
4330 (define-public r-siggenes
4337 (uri (bioconductor-uri "siggenes" version))
4340 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
4341 (build-system r-build-system)
4343 `(("r-biobase" ,r-biobase)
4344 ("r-multtest" ,r-multtest)
4345 ("r-scrime" ,r-scrime)))
4346 (home-page "https://bioconductor.org/packages/siggenes/")
4348 "Multiple testing using SAM and Efron's empirical Bayes approaches")
4350 "This package provides tools for the identification of differentially
4351 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
4352 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
4353 Bayes Analyses of Microarrays} (EBAM).")
4354 (license license:lgpl2.0+)))
4356 (define-public r-bumphunter
4358 (name "r-bumphunter")
4363 (uri (bioconductor-uri "bumphunter" version))
4366 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
4367 (build-system r-build-system)
4369 `(("r-annotationdbi" ,r-annotationdbi)
4370 ("r-biocgenerics" ,r-biocgenerics)
4371 ("r-dorng" ,r-dorng)
4372 ("r-foreach" ,r-foreach)
4373 ("r-genomeinfodb" ,r-genomeinfodb)
4374 ("r-genomicfeatures" ,r-genomicfeatures)
4375 ("r-genomicranges" ,r-genomicranges)
4376 ("r-iranges" ,r-iranges)
4377 ("r-iterators" ,r-iterators)
4378 ("r-limma" ,r-limma)
4379 ("r-locfit" ,r-locfit)
4380 ("r-matrixstats" ,r-matrixstats)
4381 ("r-s4vectors" ,r-s4vectors)))
4382 (home-page "https://github.com/ririzarr/bumphunter")
4383 (synopsis "Find bumps in genomic data")
4385 "This package provides tools for finding bumps in genomic data in order
4386 to identify differentially methylated regions in epigenetic epidemiology
4388 (license license:artistic2.0)))
4390 (define-public r-minfi
4397 (uri (bioconductor-uri "minfi" version))
4400 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
4401 (build-system r-build-system)
4403 `(("r-beanplot" ,r-beanplot)
4404 ("r-biobase" ,r-biobase)
4405 ("r-biocgenerics" ,r-biocgenerics)
4406 ("r-biocparallel" ,r-biocparallel)
4407 ("r-biostrings" ,r-biostrings)
4408 ("r-bumphunter" ,r-bumphunter)
4409 ("r-data-table" ,r-data-table)
4410 ("r-delayedarray" ,r-delayedarray)
4411 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
4412 ("r-genefilter" ,r-genefilter)
4413 ("r-genomeinfodb" ,r-genomeinfodb)
4414 ("r-genomicranges" ,r-genomicranges)
4415 ("r-geoquery" ,r-geoquery)
4416 ("r-hdf5array" ,r-hdf5array)
4417 ("r-illuminaio" ,r-illuminaio)
4418 ("r-iranges" ,r-iranges)
4419 ("r-lattice" ,r-lattice)
4420 ("r-limma" ,r-limma)
4422 ("r-mclust" ,r-mclust)
4424 ("r-nor1mix" ,r-nor1mix)
4425 ("r-preprocesscore" ,r-preprocesscore)
4426 ("r-quadprog" ,r-quadprog)
4427 ("r-rcolorbrewer" ,r-rcolorbrewer)
4428 ("r-reshape" ,r-reshape)
4429 ("r-s4vectors" ,r-s4vectors)
4430 ("r-siggenes" ,r-siggenes)
4431 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4433 `(("r-knitr" ,r-knitr)))
4434 (home-page "https://github.com/hansenlab/minfi")
4435 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
4437 "This package provides tools to analyze and visualize Illumina Infinium
4438 methylation arrays.")
4439 (license license:artistic2.0)))
4441 (define-public r-methylumi
4443 (name "r-methylumi")
4448 (uri (bioconductor-uri "methylumi" version))
4451 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
4452 (build-system r-build-system)
4454 `(("r-annotate" ,r-annotate)
4455 ("r-annotationdbi" ,r-annotationdbi)
4456 ("r-biobase" ,r-biobase)
4457 ("r-biocgenerics" ,r-biocgenerics)
4458 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
4459 ("r-genefilter" ,r-genefilter)
4460 ("r-genomeinfodb" ,r-genomeinfodb)
4461 ("r-genomicranges" ,r-genomicranges)
4462 ("r-ggplot2" ,r-ggplot2)
4463 ("r-illuminaio" ,r-illuminaio)
4464 ("r-iranges" ,r-iranges)
4465 ("r-lattice" ,r-lattice)
4466 ("r-matrixstats" ,r-matrixstats)
4467 ("r-minfi" ,r-minfi)
4468 ("r-reshape2" ,r-reshape2)
4469 ("r-s4vectors" ,r-s4vectors)
4470 ("r-scales" ,r-scales)
4471 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4473 `(("r-knitr" ,r-knitr)))
4474 (home-page "https://bioconductor.org/packages/methylumi")
4475 (synopsis "Handle Illumina methylation data")
4477 "This package provides classes for holding and manipulating Illumina
4478 methylation data. Based on eSet, it can contain MIAME information, sample
4479 information, feature information, and multiple matrices of data. An
4480 \"intelligent\" import function, methylumiR can read the Illumina text files
4481 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
4482 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
4483 background correction, and quality control features for GoldenGate, Infinium,
4484 and Infinium HD arrays are also included.")
4485 (license license:gpl2)))
4487 (define-public r-lumi
4494 (uri (bioconductor-uri "lumi" version))
4497 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
4498 (build-system r-build-system)
4500 `(("r-affy" ,r-affy)
4501 ("r-annotate" ,r-annotate)
4502 ("r-annotationdbi" ,r-annotationdbi)
4503 ("r-biobase" ,r-biobase)
4505 ("r-genomicfeatures" ,r-genomicfeatures)
4506 ("r-genomicranges" ,r-genomicranges)
4507 ("r-kernsmooth" ,r-kernsmooth)
4508 ("r-lattice" ,r-lattice)
4510 ("r-methylumi" ,r-methylumi)
4512 ("r-nleqslv" ,r-nleqslv)
4513 ("r-preprocesscore" ,r-preprocesscore)
4514 ("r-rsqlite" ,r-rsqlite)))
4515 (home-page "https://bioconductor.org/packages/lumi")
4516 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
4518 "The lumi package provides an integrated solution for the Illumina
4519 microarray data analysis. It includes functions of Illumina
4520 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
4521 variance stabilization, normalization and gene annotation at the probe level.
4522 It also includes the functions of processing Illumina methylation microarrays,
4523 especially Illumina Infinium methylation microarrays.")
4524 (license license:lgpl2.0+)))
4526 (define-public r-linnorm
4533 (uri (bioconductor-uri "Linnorm" version))
4536 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
4537 (properties `((upstream-name . "Linnorm")))
4538 (build-system r-build-system)
4540 `(("r-amap" ,r-amap)
4541 ("r-apcluster" ,r-apcluster)
4542 ("r-ellipse" ,r-ellipse)
4543 ("r-fastcluster" ,r-fastcluster)
4545 ("r-ggdendro" ,r-ggdendro)
4546 ("r-ggplot2" ,r-ggplot2)
4547 ("r-gmodels" ,r-gmodels)
4548 ("r-igraph" ,r-igraph)
4549 ("r-limma" ,r-limma)
4551 ("r-mclust" ,r-mclust)
4553 ("r-rcpparmadillo" ,r-rcpparmadillo)
4554 ("r-rtsne" ,r-rtsne)
4555 ("r-statmod" ,r-statmod)
4556 ("r-vegan" ,r-vegan)
4559 `(("r-knitr" ,r-knitr)))
4560 (home-page "http://www.jjwanglab.org/Linnorm/")
4561 (synopsis "Linear model and normality based transformation method")
4563 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
4564 count data or any large scale count data. It transforms such datasets for
4565 parametric tests. In addition to the transformtion function (@code{Linnorm}),
4566 the following pipelines are implemented:
4569 @item Library size/batch effect normalization (@code{Linnorm.Norm})
4570 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
4571 clustering or hierarchical clustering (@code{Linnorm.tSNE},
4572 @code{Linnorm.PCA}, @code{Linnorm.HClust})
4573 @item Differential expression analysis or differential peak detection using
4574 limma (@code{Linnorm.limma})
4575 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
4576 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
4577 @item Stable gene selection for scRNA-seq data; for users without or who do
4578 not want to rely on spike-in genes (@code{Linnorm.SGenes})
4579 @item Data imputation (@code{Linnorm.DataImput}).
4582 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
4583 @code{RnaXSim} function is included for simulating RNA-seq data for the
4584 evaluation of DEG analysis methods.")
4585 (license license:expat)))
4587 (define-public r-ioniser
4594 (uri (bioconductor-uri "IONiseR" version))
4597 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
4598 (properties `((upstream-name . "IONiseR")))
4599 (build-system r-build-system)
4601 `(("r-biocgenerics" ,r-biocgenerics)
4602 ("r-biocparallel" ,r-biocparallel)
4603 ("r-biostrings" ,r-biostrings)
4604 ("r-bit64" ,r-bit64)
4605 ("r-dplyr" ,r-dplyr)
4606 ("r-ggplot2" ,r-ggplot2)
4607 ("r-magrittr" ,r-magrittr)
4608 ("r-rhdf5" ,r-rhdf5)
4609 ("r-shortread" ,r-shortread)
4610 ("r-stringr" ,r-stringr)
4611 ("r-tibble" ,r-tibble)
4612 ("r-tidyr" ,r-tidyr)
4613 ("r-xvector" ,r-xvector)))
4615 `(("r-knitr" ,r-knitr)))
4616 (home-page "https://bioconductor.org/packages/IONiseR/")
4617 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
4619 "IONiseR provides tools for the quality assessment of Oxford Nanopore
4620 MinION data. It extracts summary statistics from a set of fast5 files and can
4621 be used either before or after base calling. In addition to standard
4622 summaries of the read-types produced, it provides a number of plots for
4623 visualising metrics relative to experiment run time or spatially over the
4624 surface of a flowcell.")
4625 (license license:expat)))
4627 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
4628 (define-public r-mutoss
4635 (uri (cran-uri "mutoss" version))
4638 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
4639 (properties `((upstream-name . "mutoss")))
4640 (build-system r-build-system)
4642 `(("r-multcomp" ,r-multcomp)
4643 ("r-multtest" ,r-multtest)
4644 ("r-mvtnorm" ,r-mvtnorm)
4645 ("r-plotrix" ,r-plotrix)))
4646 (home-page "https://github.com/kornl/mutoss/")
4647 (synopsis "Unified multiple testing procedures")
4649 "This package is designed to ease the application and comparison of
4650 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
4651 are standardized and usable by the accompanying mutossGUI package.")
4652 ;; Any version of the GPL.
4653 (license (list license:gpl2+ license:gpl3+))))
4655 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
4656 ;; from Bioconductor, so we put it here.
4657 (define-public r-metap
4664 (uri (cran-uri "metap" version))
4667 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
4668 (build-system r-build-system)
4670 `(("r-lattice" ,r-lattice)
4671 ("r-mutoss" ,r-mutoss)
4672 ("r-rdpack" ,r-rdpack)
4673 ("r-tfisher" ,r-tfisher)))
4674 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
4675 (synopsis "Meta-analysis of significance values")
4677 "The canonical way to perform meta-analysis involves using effect sizes.
4678 When they are not available this package provides a number of methods for
4679 meta-analysis of significance values including the methods of Edgington,
4680 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
4681 published results; and a routine for graphical display.")
4682 (license license:gpl2)))
4684 (define-public r-triform
4691 (uri (bioconductor-uri "triform" version))
4694 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
4695 (build-system r-build-system)
4697 `(("r-biocgenerics" ,r-biocgenerics)
4698 ("r-iranges" ,r-iranges)
4699 ("r-yaml" ,r-yaml)))
4700 (home-page "https://bioconductor.org/packages/triform/")
4701 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
4703 "The Triform algorithm uses model-free statistics to identify peak-like
4704 distributions of TF ChIP sequencing reads, taking advantage of an improved
4705 peak definition in combination with known profile characteristics.")
4706 (license license:gpl2)))
4708 (define-public r-varianttools
4710 (name "r-varianttools")
4715 (uri (bioconductor-uri "VariantTools" version))
4718 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
4719 (properties `((upstream-name . "VariantTools")))
4720 (build-system r-build-system)
4722 `(("r-biobase" ,r-biobase)
4723 ("r-biocgenerics" ,r-biocgenerics)
4724 ("r-biocparallel" ,r-biocparallel)
4725 ("r-biostrings" ,r-biostrings)
4726 ("r-bsgenome" ,r-bsgenome)
4727 ("r-genomeinfodb" ,r-genomeinfodb)
4728 ("r-genomicfeatures" ,r-genomicfeatures)
4729 ("r-genomicranges" ,r-genomicranges)
4730 ("r-iranges" ,r-iranges)
4731 ("r-matrix" ,r-matrix)
4732 ("r-rsamtools" ,r-rsamtools)
4733 ("r-rtracklayer" ,r-rtracklayer)
4734 ("r-s4vectors" ,r-s4vectors)
4735 ("r-variantannotation" ,r-variantannotation)))
4736 (home-page "https://bioconductor.org/packages/VariantTools/")
4737 (synopsis "Tools for exploratory analysis of variant calls")
4739 "Explore, diagnose, and compare variant calls using filters. The
4740 VariantTools package supports a workflow for loading data, calling single
4741 sample variants and tumor-specific somatic mutations or other sample-specific
4742 variant types (e.g., RNA editing). Most of the functions operate on
4743 alignments (BAM files) or datasets of called variants. The user is expected
4744 to have already aligned the reads with a separate tool, e.g., GSNAP via
4746 (license license:artistic2.0)))
4748 (define-public r-heatplus
4755 (uri (bioconductor-uri "Heatplus" version))
4758 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
4759 (properties `((upstream-name . "Heatplus")))
4760 (build-system r-build-system)
4762 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
4763 (home-page "https://github.com/alexploner/Heatplus")
4764 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
4766 "This package provides tools to display a rectangular heatmap (intensity
4767 plot) of a data matrix. By default, both samples (columns) and features (row)
4768 of the matrix are sorted according to a hierarchical clustering, and the
4769 corresponding dendrogram is plotted. Optionally, panels with additional
4770 information about samples and features can be added to the plot.")
4771 (license license:gpl2+)))
4773 (define-public r-gosemsim
4780 (uri (bioconductor-uri "GOSemSim" version))
4783 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
4784 (properties `((upstream-name . "GOSemSim")))
4785 (build-system r-build-system)
4787 `(("r-annotationdbi" ,r-annotationdbi)
4788 ("r-go-db" ,r-go-db)
4789 ("r-rcpp" ,r-rcpp)))
4791 `(("r-knitr" ,r-knitr)))
4792 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
4793 (synopsis "GO-terms semantic similarity measures")
4795 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
4796 quantitative ways to compute similarities between genes and gene groups, and
4797 have became important basis for many bioinformatics analysis approaches.
4798 GOSemSim is an R package for semantic similarity computation among GO terms,
4799 sets of GO terms, gene products and gene clusters.")
4800 (license license:artistic2.0)))
4802 (define-public r-anota
4809 (uri (bioconductor-uri "anota" version))
4812 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
4813 (build-system r-build-system)
4815 `(("r-multtest" ,r-multtest)
4816 ("r-qvalue" ,r-qvalue)))
4817 (home-page "https://bioconductor.org/packages/anota/")
4818 (synopsis "Analysis of translational activity")
4820 "Genome wide studies of translational control is emerging as a tool to
4821 study various biological conditions. The output from such analysis is both
4822 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
4823 involved in translation (the actively translating mRNA level) for each mRNA.
4824 The standard analysis of such data strives towards identifying differential
4825 translational between two or more sample classes - i.e. differences in
4826 actively translated mRNA levels that are independent of underlying differences
4827 in cytosolic mRNA levels. This package allows for such analysis using partial
4828 variances and the random variance model. As 10s of thousands of mRNAs are
4829 analyzed in parallel the library performs a number of tests to assure that
4830 the data set is suitable for such analysis.")
4831 (license license:gpl3)))
4833 (define-public r-sigpathway
4835 (name "r-sigpathway")
4840 (uri (bioconductor-uri "sigPathway" version))
4843 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
4844 (properties `((upstream-name . "sigPathway")))
4845 (build-system r-build-system)
4846 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
4847 (synopsis "Pathway analysis")
4849 "This package is used to conduct pathway analysis by calculating the NT_k
4850 and NE_k statistics in a statistical framework for determining whether a
4851 specified group of genes for a pathway has a coordinated association with a
4852 phenotype of interest.")
4853 (license license:gpl2)))
4855 (define-public r-fgsea
4862 (uri (bioconductor-uri "fgsea" version))
4865 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
4866 (build-system r-build-system)
4869 ("r-biocparallel" ,r-biocparallel)
4870 ("r-data-table" ,r-data-table)
4871 ("r-fastmatch" ,r-fastmatch)
4872 ("r-ggplot2" ,r-ggplot2)
4873 ("r-gridextra" ,r-gridextra)
4874 ("r-matrix" ,r-matrix)
4875 ("r-rcpp" ,r-rcpp)))
4877 `(("r-knitr" ,r-knitr)))
4878 (home-page "https://github.com/ctlab/fgsea/")
4879 (synopsis "Fast gene set enrichment analysis")
4881 "The package implements an algorithm for fast gene set enrichment
4882 analysis. Using the fast algorithm makes more permutations and gets
4883 more fine grained p-values, which allows using accurate standard approaches
4884 to multiple hypothesis correction.")
4885 (license license:expat)))
4887 (define-public r-dose
4894 (uri (bioconductor-uri "DOSE" version))
4897 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
4898 (properties `((upstream-name . "DOSE")))
4899 (build-system r-build-system)
4901 `(("r-annotationdbi" ,r-annotationdbi)
4902 ("r-biocparallel" ,r-biocparallel)
4903 ("r-do-db" ,r-do-db)
4904 ("r-fgsea" ,r-fgsea)
4905 ("r-ggplot2" ,r-ggplot2)
4906 ("r-gosemsim" ,r-gosemsim)
4907 ("r-qvalue" ,r-qvalue)
4908 ("r-reshape2" ,r-reshape2)))
4910 `(("r-knitr" ,r-knitr)))
4911 (home-page "https://guangchuangyu.github.io/software/DOSE/")
4912 (synopsis "Disease ontology semantic and enrichment analysis")
4914 "This package implements five methods proposed by Resnik, Schlicker,
4915 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
4916 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
4917 including hypergeometric model and gene set enrichment analysis are also
4918 implemented for discovering disease associations of high-throughput biological
4920 (license license:artistic2.0)))
4922 (define-public r-enrichplot
4924 (name "r-enrichplot")
4929 (uri (bioconductor-uri "enrichplot" version))
4932 "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
4933 (build-system r-build-system)
4935 `(("r-cowplot" ,r-cowplot)
4937 ("r-ggplot2" ,r-ggplot2)
4938 ("r-ggraph" ,r-ggraph)
4939 ("r-gosemsim" ,r-gosemsim)
4940 ("r-igraph" ,r-igraph)
4941 ("r-magrittr" ,r-magrittr)
4943 ("r-purrr" ,r-purrr)
4944 ("r-rcolorbrewer" ,r-rcolorbrewer)
4945 ("r-reshape2" ,r-reshape2)
4946 ("r-scatterpie" ,r-scatterpie)
4947 ("r-shadowtext" ,r-shadowtext)))
4949 `(("r-knitr" ,r-knitr)))
4950 (home-page "https://github.com/GuangchuangYu/enrichplot")
4951 (synopsis "Visualization of functional enrichment result")
4953 "The enrichplot package implements several visualization methods for
4954 interpreting functional enrichment results obtained from ORA or GSEA analyses.
4955 All the visualization methods are developed based on ggplot2 graphics.")
4956 (license license:artistic2.0)))
4958 (define-public r-clusterprofiler
4960 (name "r-clusterprofiler")
4965 (uri (bioconductor-uri "clusterProfiler" version))
4968 "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
4970 `((upstream-name . "clusterProfiler")))
4971 (build-system r-build-system)
4973 `(("r-annotationdbi" ,r-annotationdbi)
4975 ("r-downloader" ,r-downloader)
4976 ("r-dplyr" ,r-dplyr)
4977 ("r-enrichplot" ,r-enrichplot)
4978 ("r-go-db" ,r-go-db)
4979 ("r-gosemsim" ,r-gosemsim)
4980 ("r-magrittr" ,r-magrittr)
4982 ("r-qvalue" ,r-qvalue)
4983 ("r-rlang" ,r-rlang)
4984 ("r-rvcheck" ,r-rvcheck)
4985 ("r-tidyr" ,r-tidyr)))
4987 `(("r-knitr" ,r-knitr)))
4988 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
4989 (synopsis "Analysis and visualization of functional profiles for gene clusters")
4991 "This package implements methods to analyze and visualize functional
4992 profiles (GO and KEGG) of gene and gene clusters.")
4993 (license license:artistic2.0)))
4995 (define-public r-mlinterfaces
4997 (name "r-mlinterfaces")
5002 (uri (bioconductor-uri "MLInterfaces" version))
5005 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
5006 (properties `((upstream-name . "MLInterfaces")))
5007 (build-system r-build-system)
5009 `(("r-annotate" ,r-annotate)
5010 ("r-biobase" ,r-biobase)
5011 ("r-biocgenerics" ,r-biocgenerics)
5012 ("r-cluster" ,r-cluster)
5015 ("r-gdata" ,r-gdata)
5016 ("r-genefilter" ,r-genefilter)
5017 ("r-ggvis" ,r-ggvis)
5018 ("r-hwriter" ,r-hwriter)
5020 ("r-mlbench" ,r-mlbench)
5022 ("r-rcolorbrewer" ,r-rcolorbrewer)
5024 ("r-rpart" ,r-rpart)
5025 ("r-sfsmisc" ,r-sfsmisc)
5026 ("r-shiny" ,r-shiny)
5027 ("r-threejs" ,r-threejs)))
5028 (home-page "https://bioconductor.org/packages/MLInterfaces/")
5029 (synopsis "Interfaces to R machine learning procedures")
5031 "This package provides uniform interfaces to machine learning code for
5032 data in R and Bioconductor containers.")
5033 ;; Any version of the LGPL.
5034 (license license:lgpl2.1+)))
5036 (define-public r-annaffy
5043 (uri (bioconductor-uri "annaffy" version))
5046 "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
5047 (build-system r-build-system)
5050 (modify-phases %standard-phases
5051 (add-after 'unpack 'remove-reference-to-non-free-data
5053 (substitute* "DESCRIPTION"
5057 `(("r-annotationdbi" ,r-annotationdbi)
5058 ("r-biobase" ,r-biobase)
5060 ("r-go-db" ,r-go-db)))
5061 (home-page "https://bioconductor.org/packages/annaffy/")
5062 (synopsis "Annotation tools for Affymetrix biological metadata")
5064 "This package provides functions for handling data from Bioconductor
5065 Affymetrix annotation data packages. It produces compact HTML and text
5066 reports including experimental data and URL links to many online databases.
5067 It allows searching of biological metadata using various criteria.")
5068 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
5069 ;; the LGPL 2.1 is included.
5070 (license license:lgpl2.1+)))
5072 (define-public r-a4core
5079 (uri (bioconductor-uri "a4Core" version))
5082 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
5083 (properties `((upstream-name . "a4Core")))
5084 (build-system r-build-system)
5086 `(("r-biobase" ,r-biobase)
5087 ("r-glmnet" ,r-glmnet)))
5089 `(("r-knitr" ,r-knitr)))
5090 (home-page "https://bioconductor.org/packages/a4Core")
5091 (synopsis "Automated Affymetrix array analysis core package")
5093 "This is the core package for the automated analysis of Affymetrix
5095 (license license:gpl3)))
5097 (define-public r-a4classif
5099 (name "r-a4classif")
5104 (uri (bioconductor-uri "a4Classif" version))
5107 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
5108 (properties `((upstream-name . "a4Classif")))
5109 (build-system r-build-system)
5111 `(("r-a4core" ,r-a4core)
5112 ("r-a4preproc" ,r-a4preproc)
5113 ("r-biobase" ,r-biobase)
5114 ("r-glmnet" ,r-glmnet)
5117 ("r-varselrf" ,r-varselrf)))
5119 `(("r-knitr" ,r-knitr)))
5120 (home-page "https://bioconductor.org/packages/a4Classif/")
5121 (synopsis "Automated Affymetrix array analysis classification package")
5123 "This is the classification package for the automated analysis of
5124 Affymetrix arrays.")
5125 (license license:gpl3)))
5127 (define-public r-a4preproc
5129 (name "r-a4preproc")
5134 (uri (bioconductor-uri "a4Preproc" version))
5137 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
5138 (properties `((upstream-name . "a4Preproc")))
5139 (build-system r-build-system)
5141 `(("r-biobase" ,r-biobase)
5142 ("r-biocgenerics" ,r-biocgenerics)))
5144 `(("r-knitr" ,r-knitr)))
5145 (home-page "https://bioconductor.org/packages/a4Preproc/")
5146 (synopsis "Automated Affymetrix array analysis preprocessing package")
5148 "This is a package for the automated analysis of Affymetrix arrays. It
5149 is used for preprocessing the arrays.")
5150 (license license:gpl3)))
5152 (define-public r-a4reporting
5154 (name "r-a4reporting")
5159 (uri (bioconductor-uri "a4Reporting" version))
5162 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
5163 (properties `((upstream-name . "a4Reporting")))
5164 (build-system r-build-system)
5166 `(("r-xtable" ,r-xtable)))
5168 `(("r-knitr" ,r-knitr)))
5169 (home-page "https://bioconductor.org/packages/a4Reporting/")
5170 (synopsis "Automated Affymetrix array analysis reporting package")
5172 "This is a package for the automated analysis of Affymetrix arrays. It
5173 provides reporting features.")
5174 (license license:gpl3)))
5176 (define-public r-a4base
5183 (uri (bioconductor-uri "a4Base" version))
5186 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
5187 (properties `((upstream-name . "a4Base")))
5188 (build-system r-build-system)
5190 `(("r-a4core" ,r-a4core)
5191 ("r-a4preproc" ,r-a4preproc)
5192 ("r-annaffy" ,r-annaffy)
5193 ("r-biobase" ,r-biobase)
5194 ("r-genefilter" ,r-genefilter)
5195 ("r-glmnet" ,r-glmnet)
5196 ("r-gplots" ,r-gplots)
5197 ("r-limma" ,r-limma)
5199 ("r-multtest" ,r-multtest)))
5200 (home-page "https://bioconductor.org/packages/a4Base/")
5201 (synopsis "Automated Affymetrix array analysis base package")
5203 "This package provides basic features for the automated analysis of
5204 Affymetrix arrays.")
5205 (license license:gpl3)))
5214 (uri (bioconductor-uri "a4" version))
5217 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
5218 (build-system r-build-system)
5220 `(("r-a4base" ,r-a4base)
5221 ("r-a4classif" ,r-a4classif)
5222 ("r-a4core" ,r-a4core)
5223 ("r-a4preproc" ,r-a4preproc)
5224 ("r-a4reporting" ,r-a4reporting)))
5225 (home-page "https://bioconductor.org/packages/a4/")
5226 (synopsis "Automated Affymetrix array analysis umbrella package")
5228 "This package provides a software suite for the automated analysis of
5229 Affymetrix arrays.")
5230 (license license:gpl3)))
5232 (define-public r-abseqr
5239 (uri (bioconductor-uri "abseqR" version))
5242 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
5243 (properties `((upstream-name . "abseqR")))
5244 (build-system r-build-system)
5246 `(("pandoc" ,pandoc)))
5248 `(("r-biocparallel" ,r-biocparallel)
5249 ("r-biocstyle" ,r-biocstyle)
5250 ("r-circlize" ,r-circlize)
5251 ("r-flexdashboard" ,r-flexdashboard)
5252 ("r-ggcorrplot" ,r-ggcorrplot)
5253 ("r-ggdendro" ,r-ggdendro)
5254 ("r-ggplot2" ,r-ggplot2)
5255 ("r-gridextra" ,r-gridextra)
5256 ("r-knitr" ,r-knitr)
5257 ("r-plotly" ,r-plotly)
5260 ("r-rcolorbrewer" ,r-rcolorbrewer)
5261 ("r-reshape2" ,r-reshape2)
5262 ("r-rmarkdown" ,r-rmarkdown)
5263 ("r-stringr" ,r-stringr)
5264 ("r-vegan" ,r-vegan)
5265 ("r-venndiagram" ,r-venndiagram)))
5267 `(("r-knitr" ,r-knitr)))
5268 (home-page "https://github.com/malhamdoosh/abseqR")
5269 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
5271 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
5272 sequencing datasets generated from antibody libraries and abseqR is one of its
5273 packages. AbseqR empowers the users of abseqPy with plotting and reporting
5274 capabilities and allows them to generate interactive HTML reports for the
5275 convenience of viewing and sharing with other researchers. Additionally,
5276 abseqR extends abseqPy to compare multiple repertoire analyses and perform
5277 further downstream analysis on its output.")
5278 (license license:gpl3)))
5280 (define-public r-bacon
5287 (uri (bioconductor-uri "bacon" version))
5290 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
5291 (build-system r-build-system)
5293 `(("r-biocparallel" ,r-biocparallel)
5294 ("r-ellipse" ,r-ellipse)
5295 ("r-ggplot2" ,r-ggplot2)))
5297 `(("r-knitr" ,r-knitr)))
5298 (home-page "https://bioconductor.org/packages/bacon/")
5299 (synopsis "Controlling bias and inflation in association studies")
5301 "Bacon can be used to remove inflation and bias often observed in
5302 epigenome- and transcriptome-wide association studies. To this end bacon
5303 constructs an empirical null distribution using a Gibbs Sampling algorithm by
5304 fitting a three-component normal mixture on z-scores.")
5305 (license license:gpl2+)))
5307 (define-public r-rgadem
5314 (uri (bioconductor-uri "rGADEM" version))
5317 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
5318 (properties `((upstream-name . "rGADEM")))
5319 (build-system r-build-system)
5321 `(("r-biostrings" ,r-biostrings)
5322 ("r-bsgenome" ,r-bsgenome)
5323 ("r-genomicranges" ,r-genomicranges)
5324 ("r-iranges" ,r-iranges)
5325 ("r-seqlogo" ,r-seqlogo)))
5326 (home-page "https://bioconductor.org/packages/rGADEM/")
5327 (synopsis "De novo sequence motif discovery")
5329 "rGADEM is an efficient de novo motif discovery tool for large-scale
5330 genomic sequence data.")
5331 (license license:artistic2.0)))
5333 (define-public r-motiv
5340 (uri (bioconductor-uri "MotIV" version))
5343 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
5344 (properties `((upstream-name . "MotIV")))
5345 (build-system r-build-system)
5349 `(("r-biocgenerics" ,r-biocgenerics)
5350 ("r-biostrings" ,r-biostrings)
5351 ("r-genomicranges" ,r-genomicranges)
5352 ("r-iranges" ,r-iranges)
5353 ("r-lattice" ,r-lattice)
5354 ("r-rgadem" ,r-rgadem)
5355 ("r-s4vectors" ,r-s4vectors)))
5356 (home-page "https://bioconductor.org/packages/MotIV/")
5357 (synopsis "Motif identification and validation")
5359 "This package is used for the identification and validation of sequence
5360 motifs. It makes use of STAMP for comparing a set of motifs to a given
5361 database (e.g. JASPAR). It can also be used to visualize motifs, motif
5362 distributions, modules and filter motifs.")
5363 (license license:gpl2)))
5365 (define-public r-motifdb
5371 (uri (bioconductor-uri "MotifDb" version))
5373 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
5374 (properties `((upstream-name . "MotifDb")))
5375 (build-system r-build-system)
5377 `(("r-biocgenerics" ,r-biocgenerics)
5378 ("r-biostrings" ,r-biostrings)
5379 ("r-genomicranges" ,r-genomicranges)
5380 ("r-iranges" ,r-iranges)
5381 ("r-rtracklayer" ,r-rtracklayer)
5382 ("r-s4vectors" ,r-s4vectors)
5383 ("r-splitstackshape" ,r-splitstackshape)))
5385 `(("r-knitr" ,r-knitr)))
5386 (home-page "https://www.bioconductor.org/packages/MotifDb/")
5387 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
5388 (description "This package provides more than 2000 annotated position
5389 frequency matrices from nine public sources, for multiple organisms.")
5390 (license license:artistic2.0)))
5392 (define-public r-motifbreakr
5394 (name "r-motifbreakr")
5398 (uri (bioconductor-uri "motifbreakR" version))
5400 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
5401 (properties `((upstream-name . "motifbreakR")))
5402 (build-system r-build-system)
5404 `(("r-biocgenerics" ,r-biocgenerics)
5405 ("r-biocparallel" ,r-biocparallel)
5406 ("r-biostrings" ,r-biostrings)
5407 ("r-bsgenome" ,r-bsgenome)
5408 ("r-genomeinfodb" ,r-genomeinfodb)
5409 ("r-genomicranges" ,r-genomicranges)
5410 ("r-grimport" ,r-grimport)
5412 ("r-iranges" ,r-iranges)
5413 ("r-matrixstats" ,r-matrixstats)
5414 ("r-motifdb" ,r-motifdb)
5415 ("r-motifstack" ,r-motifstack)
5416 ("r-rtracklayer" ,r-rtracklayer)
5417 ("r-s4vectors" ,r-s4vectors)
5418 ("r-stringr" ,r-stringr)
5419 ("r-summarizedexperiment" ,r-summarizedexperiment)
5420 ("r-tfmpvalue" ,r-tfmpvalue)
5421 ("r-variantannotation" ,r-variantannotation)))
5423 `(("r-knitr" ,r-knitr)))
5424 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
5425 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
5426 (description "This package allows biologists to judge in the first place
5427 whether the sequence surrounding the polymorphism is a good match, and in
5428 the second place how much information is gained or lost in one allele of
5429 the polymorphism relative to another. This package gives a choice of
5430 algorithms for interrogation of genomes with motifs from public sources:
5432 @item a weighted-sum probability matrix;
5433 @item log-probabilities;
5434 @item weighted by relative entropy.
5437 This package can predict effects for novel or previously described variants in
5438 public databases, making it suitable for tasks beyond the scope of its original
5439 design. Lastly, it can be used to interrogate any genome curated within
5441 (license license:gpl2+)))
5443 (define-public r-motifstack
5445 (name "r-motifstack")
5450 (uri (bioconductor-uri "motifStack" version))
5453 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
5454 (properties `((upstream-name . "motifStack")))
5455 (build-system r-build-system)
5457 `(("r-ade4" ,r-ade4)
5458 ("r-biostrings" ,r-biostrings)
5459 ("r-ggplot2" ,r-ggplot2)
5460 ("r-htmlwidgets" ,r-htmlwidgets)
5463 `(("r-knitr" ,r-knitr)))
5464 (home-page "https://bioconductor.org/packages/motifStack/")
5465 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
5467 "The motifStack package is designed for graphic representation of
5468 multiple motifs with different similarity scores. It works with both DNA/RNA
5469 sequence motifs and amino acid sequence motifs. In addition, it provides the
5470 flexibility for users to customize the graphic parameters such as the font
5471 type and symbol colors.")
5472 (license license:gpl2+)))
5474 (define-public r-genomicscores
5476 (name "r-genomicscores")
5481 (uri (bioconductor-uri "GenomicScores" version))
5484 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
5485 (properties `((upstream-name . "GenomicScores")))
5486 (build-system r-build-system)
5488 `(("r-annotationhub" ,r-annotationhub)
5489 ("r-biobase" ,r-biobase)
5490 ("r-biocfilecache" ,r-biocfilecache)
5491 ("r-biocgenerics" ,r-biocgenerics)
5492 ("r-biocmanager" ,r-biocmanager)
5493 ("r-biostrings" ,r-biostrings)
5494 ("r-delayedarray" ,r-delayedarray)
5495 ("r-genomeinfodb" ,r-genomeinfodb)
5496 ("r-genomicranges" ,r-genomicranges)
5497 ("r-hdf5array" ,r-hdf5array)
5498 ("r-iranges" ,r-iranges)
5499 ("r-rhdf5" ,r-rhdf5)
5500 ("r-s4vectors" ,r-s4vectors)
5503 `(("r-knitr" ,r-knitr)))
5504 (home-page "https://github.com/rcastelo/GenomicScores/")
5505 (synopsis "Work with genome-wide position-specific scores")
5507 "This package provides infrastructure to store and access genome-wide
5508 position-specific scores within R and Bioconductor.")
5509 (license license:artistic2.0)))
5511 (define-public r-atacseqqc
5513 (name "r-atacseqqc")
5518 (uri (bioconductor-uri "ATACseqQC" version))
5521 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
5522 (properties `((upstream-name . "ATACseqQC")))
5523 (build-system r-build-system)
5525 `(("r-biocgenerics" ,r-biocgenerics)
5526 ("r-biostrings" ,r-biostrings)
5527 ("r-bsgenome" ,r-bsgenome)
5528 ("r-chippeakanno" ,r-chippeakanno)
5529 ("r-edger" ,r-edger)
5530 ("r-genomeinfodb" ,r-genomeinfodb)
5531 ("r-genomicalignments" ,r-genomicalignments)
5532 ("r-genomicranges" ,r-genomicranges)
5533 ("r-genomicscores" ,r-genomicscores)
5534 ("r-iranges" ,r-iranges)
5535 ("r-kernsmooth" ,r-kernsmooth)
5536 ("r-limma" ,r-limma)
5537 ("r-motifstack" ,r-motifstack)
5538 ("r-preseqr" ,r-preseqr)
5539 ("r-randomforest" ,r-randomforest)
5540 ("r-rsamtools" ,r-rsamtools)
5541 ("r-rtracklayer" ,r-rtracklayer)
5542 ("r-s4vectors" ,r-s4vectors)))
5544 `(("r-knitr" ,r-knitr)))
5545 (home-page "https://bioconductor.org/packages/ATACseqQC/")
5546 (synopsis "ATAC-seq quality control")
5548 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
5549 sequencing, is a rapid and sensitive method for chromatin accessibility
5550 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
5551 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
5552 assess whether their ATAC-seq experiment is successful. It includes
5553 diagnostic plots of fragment size distribution, proportion of mitochondria
5554 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
5556 (license license:gpl2+)))
5558 (define-public r-gofuncr
5565 (uri (bioconductor-uri "GOfuncR" version))
5568 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
5569 (properties `((upstream-name . "GOfuncR")))
5570 (build-system r-build-system)
5572 `(("r-annotationdbi" ,r-annotationdbi)
5573 ("r-genomicranges" ,r-genomicranges)
5574 ("r-gtools" ,r-gtools)
5575 ("r-iranges" ,r-iranges)
5576 ("r-mapplots" ,r-mapplots)
5578 ("r-vioplot" ,r-vioplot)))
5580 `(("r-knitr" ,r-knitr)))
5581 (home-page "https://bioconductor.org/packages/GOfuncR/")
5582 (synopsis "Gene ontology enrichment using FUNC")
5584 "GOfuncR performs a gene ontology enrichment analysis based on the
5585 ontology enrichment software FUNC. GO-annotations are obtained from
5586 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
5587 included in the package and updated regularly. GOfuncR provides the standard
5588 candidate vs background enrichment analysis using the hypergeometric test, as
5589 well as three additional tests:
5592 @item the Wilcoxon rank-sum test that is used when genes are ranked,
5593 @item a binomial test that is used when genes are associated with two counts,
5595 @item a Chi-square or Fisher's exact test that is used in cases when genes are
5596 associated with four counts.
5599 To correct for multiple testing and interdependency of the tests, family-wise
5600 error rates are computed based on random permutations of the gene-associated
5601 variables. GOfuncR also provides tools for exploring the ontology graph and
5602 the annotations, and options to take gene-length or spatial clustering of
5603 genes into account. It is also possible to provide custom gene coordinates,
5604 annotations and ontologies.")
5605 (license license:gpl2+)))
5607 (define-public r-abaenrichment
5609 (name "r-abaenrichment")
5614 (uri (bioconductor-uri "ABAEnrichment" version))
5617 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
5618 (properties `((upstream-name . "ABAEnrichment")))
5619 (build-system r-build-system)
5621 `(("r-abadata" ,r-abadata)
5622 ("r-data-table" ,r-data-table)
5623 ("r-gofuncr" ,r-gofuncr)
5624 ("r-gplots" ,r-gplots)
5625 ("r-gtools" ,r-gtools)
5626 ("r-rcpp" ,r-rcpp)))
5628 `(("r-knitr" ,r-knitr)))
5629 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
5630 (synopsis "Gene expression enrichment in human brain regions")
5632 "The package ABAEnrichment is designed to test for enrichment of user
5633 defined candidate genes in the set of expressed genes in different human brain
5634 regions. The core function @code{aba_enrich} integrates the expression of the
5635 candidate gene set (averaged across donors) and the structural information of
5636 the brain using an ontology, both provided by the Allen Brain Atlas project.")
5637 (license license:gpl2+)))
5639 (define-public r-annotationfuncs
5641 (name "r-annotationfuncs")
5646 (uri (bioconductor-uri "AnnotationFuncs" version))
5649 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
5651 `((upstream-name . "AnnotationFuncs")))
5652 (build-system r-build-system)
5654 `(("r-annotationdbi" ,r-annotationdbi)
5656 (home-page "https://www.iysik.com/r/annotationfuncs")
5657 (synopsis "Annotation translation functions")
5659 "This package provides functions for handling translating between
5660 different identifieres using the Biocore Data Team data-packages (e.g.
5661 @code{org.Bt.eg.db}).")
5662 (license license:gpl2)))
5664 (define-public r-annotationtools
5666 (name "r-annotationtools")
5671 (uri (bioconductor-uri "annotationTools" version))
5674 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
5676 `((upstream-name . "annotationTools")))
5677 (build-system r-build-system)
5678 (propagated-inputs `(("r-biobase" ,r-biobase)))
5679 (home-page "https://bioconductor.org/packages/annotationTools/")
5680 (synopsis "Annotate microarrays and perform gene expression analyses")
5682 "This package provides functions to annotate microarrays, find orthologs,
5683 and integrate heterogeneous gene expression profiles using annotation and
5684 other molecular biology information available as flat file database (plain
5686 ;; Any version of the GPL.
5687 (license (list license:gpl2+))))
5689 (define-public r-allelicimbalance
5691 (name "r-allelicimbalance")
5696 (uri (bioconductor-uri "AllelicImbalance" version))
5699 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
5701 `((upstream-name . "AllelicImbalance")))
5702 (build-system r-build-system)
5704 `(("r-annotationdbi" ,r-annotationdbi)
5705 ("r-biocgenerics" ,r-biocgenerics)
5706 ("r-biostrings" ,r-biostrings)
5707 ("r-bsgenome" ,r-bsgenome)
5708 ("r-genomeinfodb" ,r-genomeinfodb)
5709 ("r-genomicalignments" ,r-genomicalignments)
5710 ("r-genomicfeatures" ,r-genomicfeatures)
5711 ("r-genomicranges" ,r-genomicranges)
5712 ("r-gridextra" ,r-gridextra)
5714 ("r-iranges" ,r-iranges)
5715 ("r-lattice" ,r-lattice)
5716 ("r-latticeextra" ,r-latticeextra)
5718 ("r-rsamtools" ,r-rsamtools)
5719 ("r-s4vectors" ,r-s4vectors)
5720 ("r-seqinr" ,r-seqinr)
5721 ("r-summarizedexperiment" ,r-summarizedexperiment)
5722 ("r-variantannotation" ,r-variantannotation)))
5724 `(("r-knitr" ,r-knitr)))
5725 (home-page "https://github.com/pappewaio/AllelicImbalance")
5726 (synopsis "Investigate allele-specific expression")
5728 "This package provides a framework for allele-specific expression
5729 investigation using RNA-seq data.")
5730 (license license:gpl3)))
5732 (define-public r-aucell
5739 (uri (bioconductor-uri "AUCell" version))
5742 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
5743 (properties `((upstream-name . "AUCell")))
5744 (build-system r-build-system)
5746 `(("r-biocgenerics" ,r-biocgenerics)
5747 ("r-data-table" ,r-data-table)
5748 ("r-gseabase" ,r-gseabase)
5749 ("r-mixtools" ,r-mixtools)
5750 ("r-r-utils" ,r-r-utils)
5751 ("r-s4vectors" ,r-s4vectors)
5752 ("r-shiny" ,r-shiny)
5753 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5755 `(("r-knitr" ,r-knitr)))
5756 (home-page "https://bioconductor.org/packages/AUCell/")
5757 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
5759 "AUCell identifies cells with active gene sets (e.g. signatures,
5760 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
5761 Under the Curve} (AUC) to calculate whether a critical subset of the input
5762 gene set is enriched within the expressed genes for each cell. The
5763 distribution of AUC scores across all the cells allows exploring the relative
5764 expression of the signature. Since the scoring method is ranking-based,
5765 AUCell is independent of the gene expression units and the normalization
5766 procedure. In addition, since the cells are evaluated individually, it can
5767 easily be applied to bigger datasets, subsetting the expression matrix if
5769 (license license:gpl3)))
5771 (define-public r-ebimage
5778 (uri (bioconductor-uri "EBImage" version))
5781 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
5782 (properties `((upstream-name . "EBImage")))
5783 (build-system r-build-system)
5785 `(("r-abind" ,r-abind)
5786 ("r-biocgenerics" ,r-biocgenerics)
5787 ("r-fftwtools" ,r-fftwtools)
5788 ("r-htmltools" ,r-htmltools)
5789 ("r-htmlwidgets" ,r-htmlwidgets)
5791 ("r-locfit" ,r-locfit)
5793 ("r-rcurl" ,r-rcurl)
5794 ("r-tiff" ,r-tiff)))
5796 `(("r-knitr" ,r-knitr))) ; for vignettes
5797 (home-page "https://github.com/aoles/EBImage")
5798 (synopsis "Image processing and analysis toolbox for R")
5800 "EBImage provides general purpose functionality for image processing and
5801 analysis. In the context of (high-throughput) microscopy-based cellular
5802 assays, EBImage offers tools to segment cells and extract quantitative
5803 cellular descriptors. This allows the automation of such tasks using the R
5804 programming language and facilitates the use of other tools in the R
5805 environment for signal processing, statistical modeling, machine learning and
5806 visualization with image data.")
5807 ;; Any version of the LGPL.
5808 (license license:lgpl2.1+)))
5810 (define-public r-yamss
5817 (uri (bioconductor-uri "yamss" version))
5820 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
5821 (build-system r-build-system)
5823 `(("r-biocgenerics" ,r-biocgenerics)
5824 ("r-data-table" ,r-data-table)
5825 ("r-ebimage" ,r-ebimage)
5826 ("r-iranges" ,r-iranges)
5827 ("r-limma" ,r-limma)
5828 ("r-matrix" ,r-matrix)
5830 ("r-s4vectors" ,r-s4vectors)
5831 ("r-summarizedexperiment"
5832 ,r-summarizedexperiment)))
5834 `(("r-knitr" ,r-knitr)))
5835 (home-page "https://github.com/hansenlab/yamss")
5836 (synopsis "Tools for high-throughput metabolomics")
5838 "This package provides tools to analyze and visualize high-throughput
5839 metabolomics data acquired using chromatography-mass spectrometry. These tools
5840 preprocess data in a way that enables reliable and powerful differential
5842 (license license:artistic2.0)))
5844 (define-public r-gtrellis
5851 (uri (bioconductor-uri "gtrellis" version))
5854 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
5855 (build-system r-build-system)
5857 `(("r-circlize" ,r-circlize)
5858 ("r-genomicranges" ,r-genomicranges)
5859 ("r-getoptlong" ,r-getoptlong)
5860 ("r-iranges" ,r-iranges)))
5862 `(("r-knitr" ,r-knitr)))
5863 (home-page "https://github.com/jokergoo/gtrellis")
5864 (synopsis "Genome level Trellis layout")
5866 "Genome level Trellis graph visualizes genomic data conditioned by
5867 genomic categories (e.g. chromosomes). For each genomic category, multiple
5868 dimensional data which are represented as tracks describe different features
5869 from different aspects. This package provides high flexibility to arrange
5870 genomic categories and to add self-defined graphics in the plot.")
5871 (license license:expat)))
5873 (define-public r-somaticsignatures
5875 (name "r-somaticsignatures")
5880 (uri (bioconductor-uri "SomaticSignatures" version))
5883 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
5885 `((upstream-name . "SomaticSignatures")))
5886 (build-system r-build-system)
5888 `(("r-biobase" ,r-biobase)
5889 ("r-biostrings" ,r-biostrings)
5890 ("r-genomeinfodb" ,r-genomeinfodb)
5891 ("r-genomicranges" ,r-genomicranges)
5892 ("r-ggbio" ,r-ggbio)
5893 ("r-ggplot2" ,r-ggplot2)
5894 ("r-iranges" ,r-iranges)
5896 ("r-pcamethods" ,r-pcamethods)
5897 ("r-proxy" ,r-proxy)
5898 ("r-reshape2" ,r-reshape2)
5899 ("r-s4vectors" ,r-s4vectors)
5900 ("r-variantannotation" ,r-variantannotation)))
5902 `(("r-knitr" ,r-knitr)))
5903 (home-page "https://github.com/juliangehring/SomaticSignatures")
5904 (synopsis "Somatic signatures")
5906 "This package identifies mutational signatures of @dfn{single nucleotide
5907 variants} (SNVs). It provides a infrastructure related to the methodology
5908 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
5909 decomposition algorithms.")
5910 (license license:expat)))
5912 (define-public r-yapsa
5919 (uri (bioconductor-uri "YAPSA" version))
5922 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
5923 (properties `((upstream-name . "YAPSA")))
5924 (build-system r-build-system)
5926 `(("r-biostrings" ,r-biostrings)
5927 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
5928 ("r-circlize" ,r-circlize)
5929 ("r-complexheatmap" ,r-complexheatmap)
5930 ("r-corrplot" ,r-corrplot)
5931 ("r-dendextend" ,r-dendextend)
5932 ("r-doparallel" ,r-doparallel)
5933 ("r-dplyr" ,r-dplyr)
5934 ("r-genomeinfodb" ,r-genomeinfodb)
5935 ("r-genomicranges" ,r-genomicranges)
5936 ("r-getoptlong" ,r-getoptlong)
5937 ("r-ggbeeswarm" ,r-ggbeeswarm)
5938 ("r-ggplot2" ,r-ggplot2)
5939 ("r-gridextra" ,r-gridextra)
5940 ("r-gtrellis" ,r-gtrellis)
5941 ("r-keggrest" ,r-keggrest)
5942 ("r-limsolve" ,r-limsolve)
5943 ("r-magrittr" ,r-magrittr)
5944 ("r-pmcmr" ,r-pmcmr)
5945 ("r-pracma" ,r-pracma)
5946 ("r-reshape2" ,r-reshape2)
5947 ("r-somaticsignatures" ,r-somaticsignatures)
5948 ("r-variantannotation" ,r-variantannotation)))
5950 `(("r-knitr" ,r-knitr)))
5951 (home-page "https://bioconductor.org/packages/YAPSA/")
5952 (synopsis "Yet another package for signature analysis")
5954 "This package provides functions and routines useful in the analysis of
5955 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
5956 functions to perform a signature analysis with known signatures and a
5957 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
5959 (license license:gpl3)))
5961 (define-public r-gcrma
5968 (uri (bioconductor-uri "gcrma" version))
5971 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
5972 (build-system r-build-system)
5974 `(("r-affy" ,r-affy)
5975 ("r-affyio" ,r-affyio)
5976 ("r-biobase" ,r-biobase)
5977 ("r-biocmanager" ,r-biocmanager)
5978 ("r-biostrings" ,r-biostrings)
5979 ("r-xvector" ,r-xvector)))
5980 (home-page "https://bioconductor.org/packages/gcrma/")
5981 (synopsis "Background adjustment using sequence information")
5983 "Gcrma adjusts for background intensities in Affymetrix array data which
5984 include optical noise and @dfn{non-specific binding} (NSB). The main function
5985 @code{gcrma} converts background adjusted probe intensities to expression
5986 measures using the same normalization and summarization methods as a
5987 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
5988 to estimate probe affinity to NSB. The sequence information is summarized in
5989 a more complex way than the simple GC content. Instead, the base types (A, T,
5990 G or C) at each position along the probe determine the affinity of each probe.
5991 The parameters of the position-specific base contributions to the probe
5992 affinity is estimated in an NSB experiment in which only NSB but no
5993 gene-specific binding is expected.")
5994 ;; Any version of the LGPL
5995 (license license:lgpl2.1+)))
5997 (define-public r-simpleaffy
5999 (name "r-simpleaffy")
6004 (uri (bioconductor-uri "simpleaffy" version))
6007 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
6008 (build-system r-build-system)
6010 `(("r-affy" ,r-affy)
6011 ("r-biobase" ,r-biobase)
6012 ("r-biocgenerics" ,r-biocgenerics)
6013 ("r-gcrma" ,r-gcrma)
6014 ("r-genefilter" ,r-genefilter)))
6015 (home-page "https://bioconductor.org/packages/simpleaffy/")
6016 (synopsis "Very simple high level analysis of Affymetrix data")
6018 "This package provides high level functions for reading Affy @file{.CEL}
6019 files, phenotypic data, and then computing simple things with it, such as
6020 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
6021 library. It also has some basic scatter plot functions and mechanisms for
6022 generating high resolution journal figures.")
6023 (license license:gpl2+)))
6025 (define-public r-yaqcaffy
6032 (uri (bioconductor-uri "yaqcaffy" version))
6035 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
6036 (build-system r-build-system)
6038 `(("r-simpleaffy" ,r-simpleaffy)))
6039 (home-page "https://bioconductor.org/packages/yaqcaffy/")
6040 (synopsis "Affymetrix quality control and reproducibility analysis")
6042 "This is a package that can be used for quality control of Affymetrix
6043 GeneChip expression data and reproducibility analysis of human whole genome
6044 chips with the MAQC reference datasets.")
6045 (license license:artistic2.0)))
6047 (define-public r-quantro
6054 (uri (bioconductor-uri "quantro" version))
6057 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
6058 (build-system r-build-system)
6060 `(("r-biobase" ,r-biobase)
6061 ("r-doparallel" ,r-doparallel)
6062 ("r-foreach" ,r-foreach)
6063 ("r-ggplot2" ,r-ggplot2)
6064 ("r-iterators" ,r-iterators)
6065 ("r-minfi" ,r-minfi)
6066 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6068 `(("r-knitr" ,r-knitr)))
6069 (home-page "https://bioconductor.org/packages/quantro/")
6070 (synopsis "Test for when to use quantile normalization")
6072 "This package provides a data-driven test for the assumptions of quantile
6073 normalization using raw data such as objects that inherit eSets (e.g.
6074 ExpressionSet, MethylSet). Group level information about each sample (such as
6075 Tumor / Normal status) must also be provided because the test assesses if
6076 there are global differences in the distributions between the user-defined
6078 (license license:gpl3+)))
6080 (define-public r-yarn
6087 (uri (bioconductor-uri "yarn" version))
6090 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
6091 (build-system r-build-system)
6093 `(("r-biobase" ,r-biobase)
6094 ("r-biomart" ,r-biomart)
6095 ("r-downloader" ,r-downloader)
6096 ("r-edger" ,r-edger)
6097 ("r-gplots" ,r-gplots)
6098 ("r-limma" ,r-limma)
6099 ("r-matrixstats" ,r-matrixstats)
6100 ("r-preprocesscore" ,r-preprocesscore)
6101 ("r-quantro" ,r-quantro)
6102 ("r-rcolorbrewer" ,r-rcolorbrewer)
6103 ("r-readr" ,r-readr)))
6105 `(("r-knitr" ,r-knitr)))
6106 (home-page "https://bioconductor.org/packages/yarn/")
6107 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
6109 "Expedite large RNA-Seq analyses using a combination of previously
6110 developed tools. YARN is meant to make it easier for the user in performing
6111 basic mis-annotation quality control, filtering, and condition-aware
6112 normalization. YARN leverages many Bioconductor tools and statistical
6113 techniques to account for the large heterogeneity and sparsity found in very
6114 large RNA-seq experiments.")
6115 (license license:artistic2.0)))
6117 (define-public r-roar
6124 (uri (bioconductor-uri "roar" version))
6127 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
6128 (build-system r-build-system)
6130 `(("r-biocgenerics" ,r-biocgenerics)
6131 ("r-genomeinfodb" ,r-genomeinfodb)
6132 ("r-genomicalignments" ,r-genomicalignments)
6133 ("r-genomicranges" ,r-genomicranges)
6134 ("r-iranges" ,r-iranges)
6135 ("r-rtracklayer" ,r-rtracklayer)
6136 ("r-s4vectors" ,r-s4vectors)
6137 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6138 (home-page "https://github.com/vodkatad/roar/")
6139 (synopsis "Identify differential APA usage from RNA-seq alignments")
6141 "This package provides tools for identifying preferential usage of APA
6142 sites, comparing two biological conditions, starting from known alternative
6143 sites and alignments obtained from standard RNA-seq experiments.")
6144 (license license:gpl3)))
6146 (define-public r-xbseq
6153 (uri (bioconductor-uri "XBSeq" version))
6156 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
6157 (properties `((upstream-name . "XBSeq")))
6158 (build-system r-build-system)
6160 `(("r-biobase" ,r-biobase)
6161 ("r-deseq2" ,r-deseq2)
6162 ("r-dplyr" ,r-dplyr)
6163 ("r-ggplot2" ,r-ggplot2)
6164 ("r-locfit" ,r-locfit)
6165 ("r-magrittr" ,r-magrittr)
6166 ("r-matrixstats" ,r-matrixstats)
6167 ("r-pracma" ,r-pracma)
6168 ("r-roar" ,r-roar)))
6170 `(("r-knitr" ,r-knitr)))
6171 (home-page "https://github.com/Liuy12/XBSeq")
6172 (synopsis "Test for differential expression for RNA-seq data")
6174 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
6175 expression} (DE), where a statistical model was established based on the
6176 assumption that observed signals are the convolution of true expression
6177 signals and sequencing noises. The mapped reads in non-exonic regions are
6178 considered as sequencing noises, which follows a Poisson distribution. Given
6179 measurable observed signal and background noise from RNA-seq data, true
6180 expression signals, assuming governed by the negative binomial distribution,
6181 can be delineated and thus the accurate detection of differential expressed
6183 (license license:gpl3+)))
6185 (define-public r-massspecwavelet
6187 (name "r-massspecwavelet")
6192 (uri (bioconductor-uri "MassSpecWavelet" version))
6195 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
6197 `((upstream-name . "MassSpecWavelet")))
6198 (build-system r-build-system)
6200 `(("r-waveslim" ,r-waveslim)))
6201 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
6202 (synopsis "Mass spectrum processing by wavelet-based algorithms")
6204 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
6205 data mainly through the use of wavelet transforms. It supports peak detection
6206 based on @dfn{Continuous Wavelet Transform} (CWT).")
6207 (license license:lgpl2.0+)))
6209 (define-public r-xcms
6216 (uri (bioconductor-uri "xcms" version))
6219 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
6220 (build-system r-build-system)
6222 `(("r-biobase" ,r-biobase)
6223 ("r-biocgenerics" ,r-biocgenerics)
6224 ("r-biocparallel" ,r-biocparallel)
6225 ("r-iranges" ,r-iranges)
6226 ("r-lattice" ,r-lattice)
6227 ("r-massspecwavelet" ,r-massspecwavelet)
6228 ("r-mscoreutils" ,r-mscoreutils)
6229 ("r-msnbase" ,r-msnbase)
6232 ("r-protgenerics" ,r-protgenerics)
6234 ("r-rcolorbrewer" ,r-rcolorbrewer)
6235 ("r-robustbase" ,r-robustbase)
6236 ("r-s4vectors" ,r-s4vectors)
6237 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6239 `(("r-knitr" ,r-knitr)))
6240 (home-page "https://bioconductor.org/packages/xcms/")
6241 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
6243 "This package provides a framework for processing and visualization of
6244 chromatographically separated and single-spectra mass spectral data. It
6245 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
6246 data for high-throughput, untargeted analyte profiling.")
6247 (license license:gpl2+)))
6249 (define-public r-wrench
6256 (uri (bioconductor-uri "Wrench" version))
6259 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
6260 (properties `((upstream-name . "Wrench")))
6261 (build-system r-build-system)
6263 `(("r-limma" ,r-limma)
6264 ("r-locfit" ,r-locfit)
6265 ("r-matrixstats" ,r-matrixstats)))
6267 `(("r-knitr" ,r-knitr)))
6268 (home-page "https://github.com/HCBravoLab/Wrench")
6269 (synopsis "Wrench normalization for sparse count data")
6271 "Wrench is a package for normalization sparse genomic count data, like
6272 that arising from 16s metagenomic surveys.")
6273 (license license:artistic2.0)))
6275 (define-public r-wiggleplotr
6277 (name "r-wiggleplotr")
6282 (uri (bioconductor-uri "wiggleplotr" version))
6285 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
6286 (build-system r-build-system)
6288 `(("r-assertthat" ,r-assertthat)
6289 ("r-cowplot" ,r-cowplot)
6290 ("r-dplyr" ,r-dplyr)
6291 ("r-genomeinfodb" ,r-genomeinfodb)
6292 ("r-genomicranges" ,r-genomicranges)
6293 ("r-ggplot2" ,r-ggplot2)
6294 ("r-iranges" ,r-iranges)
6295 ("r-purrr" ,r-purrr)
6296 ("r-rtracklayer" ,r-rtracklayer)
6297 ("r-s4vectors" ,r-s4vectors)))
6299 `(("r-knitr" ,r-knitr)))
6300 (home-page "https://bioconductor.org/packages/wiggleplotr/")
6301 (synopsis "Make read coverage plots from BigWig files")
6303 "This package provides tools to visualize read coverage from sequencing
6304 experiments together with genomic annotations (genes, transcripts, peaks).
6305 Introns of long transcripts can be rescaled to a fixed length for better
6306 visualization of exonic read coverage.")
6307 (license license:asl2.0)))
6309 (define-public r-widgettools
6311 (name "r-widgettools")
6316 (uri (bioconductor-uri "widgetTools" version))
6319 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
6320 (properties `((upstream-name . "widgetTools")))
6321 (build-system r-build-system)
6322 (home-page "https://bioconductor.org/packages/widgetTools/")
6323 (synopsis "Tools for creating interactive tcltk widgets")
6325 "This package contains tools to support the construction of tcltk
6327 ;; Any version of the LGPL.
6328 (license license:lgpl3+)))
6330 (define-public r-webbioc
6337 (uri (bioconductor-uri "webbioc" version))
6340 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
6341 (build-system r-build-system)
6343 `(("netpbm" ,netpbm)
6346 `(("r-affy" ,r-affy)
6347 ("r-annaffy" ,r-annaffy)
6348 ("r-biobase" ,r-biobase)
6349 ("r-biocmanager" ,r-biocmanager)
6350 ("r-gcrma" ,r-gcrma)
6351 ("r-multtest" ,r-multtest)
6352 ("r-qvalue" ,r-qvalue)
6354 (home-page "https://www.bioconductor.org/")
6355 (synopsis "Bioconductor web interface")
6357 "This package provides an integrated web interface for doing microarray
6358 analysis using several of the Bioconductor packages. It is intended to be
6359 deployed as a centralized bioinformatics resource for use by many users.
6360 Currently only Affymetrix oligonucleotide analysis is supported.")
6361 (license license:gpl2+)))
6363 (define-public r-zfpkm
6370 (uri (bioconductor-uri "zFPKM" version))
6373 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
6374 (properties `((upstream-name . "zFPKM")))
6375 (build-system r-build-system)
6377 `(("r-checkmate" ,r-checkmate)
6378 ("r-dplyr" ,r-dplyr)
6379 ("r-ggplot2" ,r-ggplot2)
6380 ("r-summarizedexperiment" ,r-summarizedexperiment)
6381 ("r-tidyr" ,r-tidyr)))
6383 `(("r-knitr" ,r-knitr)))
6384 (home-page "https://github.com/ronammar/zFPKM/")
6385 (synopsis "Functions to facilitate zFPKM transformations")
6387 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
6388 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
6390 (license license:gpl3)))
6392 (define-public r-rbowtie2
6399 (uri (bioconductor-uri "Rbowtie2" version))
6402 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
6403 (properties `((upstream-name . "Rbowtie2")))
6404 (build-system r-build-system)
6408 `(("r-knitr" ,r-knitr)))
6409 (home-page "https://bioconductor.org/packages/Rbowtie2/")
6410 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
6412 "This package provides an R wrapper of the popular @code{bowtie2}
6413 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
6414 rapid adapter trimming, identification, and read merging.")
6415 (license license:gpl3+)))
6417 (define-public r-progeny
6424 (uri (bioconductor-uri "progeny" version))
6427 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
6428 (build-system r-build-system)
6430 `(("r-biobase" ,r-biobase)
6431 ("r-dplyr" ,r-dplyr)
6432 ("r-ggplot2" ,r-ggplot2)
6433 ("r-ggrepel" ,r-ggrepel)
6434 ("r-gridextra" ,r-gridextra)
6435 ("r-tidyr" ,r-tidyr)))
6437 `(("r-knitr" ,r-knitr)))
6438 (home-page "https://github.com/saezlab/progeny")
6439 (synopsis "Pathway responsive gene activity inference")
6441 "This package provides a function to infer pathway activity from gene
6442 expression. It contains the linear model inferred in the publication
6443 \"Perturbation-response genes reveal signaling footprints in cancer gene
6445 (license license:asl2.0)))
6447 (define-public r-arrmnormalization
6449 (name "r-arrmnormalization")
6454 (uri (bioconductor-uri "ARRmNormalization" version))
6457 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
6459 `((upstream-name . "ARRmNormalization")))
6460 (build-system r-build-system)
6461 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
6462 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
6463 (synopsis "Adaptive robust regression normalization for methylation data")
6465 "This is a package to perform the @dfn{Adaptive Robust Regression
6466 method} (ARRm) for the normalization of methylation data from the Illumina
6467 Infinium HumanMethylation 450k assay.")
6468 (license license:artistic2.0)))
6470 (define-public r-biocfilecache
6472 (name "r-biocfilecache")
6477 (uri (bioconductor-uri "BiocFileCache" version))
6480 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
6481 (properties `((upstream-name . "BiocFileCache")))
6482 (build-system r-build-system)
6484 `(("r-curl" ,r-curl)
6486 ("r-dbplyr" ,r-dbplyr)
6487 ("r-dplyr" ,r-dplyr)
6489 ("r-rappdirs" ,r-rappdirs)
6490 ("r-rsqlite" ,r-rsqlite)))
6492 `(("r-knitr" ,r-knitr)))
6493 (home-page "https://bioconductor.org/packages/BiocFileCache/")
6494 (synopsis "Manage files across sessions")
6496 "This package creates a persistent on-disk cache of files that the user
6497 can add, update, and retrieve. It is useful for managing resources (such as
6498 custom Txdb objects) that are costly or difficult to create, web resources,
6499 and data files used across sessions.")
6500 (license license:artistic2.0)))
6502 (define-public r-iclusterplus
6504 (name "r-iclusterplus")
6509 (uri (bioconductor-uri "iClusterPlus" version))
6512 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
6513 (properties `((upstream-name . "iClusterPlus")))
6514 (build-system r-build-system)
6515 (native-inputs `(("gfortran" ,gfortran)))
6516 (home-page "https://bioconductor.org/packages/iClusterPlus/")
6517 (synopsis "Integrative clustering of multi-type genomic data")
6519 "iClusterPlus is developed for integrative clustering analysis of
6520 multi-type genomic data and is an enhanced version of iCluster proposed and
6521 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
6522 from the experiments where biological samples (e.g. tumor samples) are
6523 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
6524 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
6525 on. In the iClusterPlus model, binary observations such as somatic mutation
6526 are modeled as Binomial processes; categorical observations such as copy
6527 number states are realizations of Multinomial random variables; counts are
6528 modeled as Poisson random processes; and continuous measures are modeled by
6529 Gaussian distributions.")
6530 (license license:gpl2+)))
6532 (define-public r-rbowtie
6539 (uri (bioconductor-uri "Rbowtie" version))
6542 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
6543 (properties `((upstream-name . "Rbowtie")))
6544 (build-system r-build-system)
6548 `(("r-knitr" ,r-knitr)))
6549 (home-page "https://bioconductor.org/packages/Rbowtie/")
6550 (synopsis "R bowtie wrapper")
6552 "This package provides an R wrapper around the popular bowtie short read
6553 aligner and around SpliceMap, a de novo splice junction discovery and
6555 (license license:artistic2.0)))
6557 (define-public r-sgseq
6564 (uri (bioconductor-uri "SGSeq" version))
6567 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
6568 (properties `((upstream-name . "SGSeq")))
6569 (build-system r-build-system)
6571 `(("r-annotationdbi" ,r-annotationdbi)
6572 ("r-biocgenerics" ,r-biocgenerics)
6573 ("r-biostrings" ,r-biostrings)
6574 ("r-genomeinfodb" ,r-genomeinfodb)
6575 ("r-genomicalignments" ,r-genomicalignments)
6576 ("r-genomicfeatures" ,r-genomicfeatures)
6577 ("r-genomicranges" ,r-genomicranges)
6578 ("r-igraph" ,r-igraph)
6579 ("r-iranges" ,r-iranges)
6580 ("r-rsamtools" ,r-rsamtools)
6581 ("r-rtracklayer" ,r-rtracklayer)
6582 ("r-runit" ,r-runit)
6583 ("r-s4vectors" ,r-s4vectors)
6584 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6586 `(("r-knitr" ,r-knitr)))
6587 (home-page "https://bioconductor.org/packages/SGSeq/")
6588 (synopsis "Splice event prediction and quantification from RNA-seq data")
6590 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
6591 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
6592 represented as a splice graph, which can be obtained from existing annotation
6593 or predicted from the mapped sequence reads. Splice events are identified
6594 from the graph and are quantified locally using structurally compatible reads
6595 at the start or end of each splice variant. The software includes functions
6596 for splice event prediction, quantification, visualization and
6598 (license license:artistic2.0)))
6600 (define-public r-rhisat2
6607 (uri (bioconductor-uri "Rhisat2" version))
6610 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
6611 (properties `((upstream-name . "Rhisat2")))
6612 (build-system r-build-system)
6615 (modify-phases %standard-phases
6616 (add-after 'unpack 'make-reproducible
6618 (substitute* "src/Makefile"
6619 (("`hostname`") "guix")
6621 ;; Avoid shelling out to "which".
6622 (("^CC =.*") (which "gcc"))
6623 (("^CPP =.*") (which "g++")))
6626 `(("r-genomicfeatures" ,r-genomicfeatures)
6627 ("r-genomicranges" ,r-genomicranges)
6628 ("r-sgseq" ,r-sgseq)))
6630 `(("r-knitr" ,r-knitr)))
6631 (home-page "https://github.com/fmicompbio/Rhisat2")
6632 (synopsis "R Wrapper for HISAT2 sequence aligner")
6634 "This package provides an R interface to the HISAT2 spliced short-read
6635 aligner by Kim et al. (2015). The package contains wrapper functions to
6636 create a genome index and to perform the read alignment to the generated
6638 (license license:gpl3)))
6640 (define-public r-quasr
6647 (uri (bioconductor-uri "QuasR" version))
6650 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
6651 (properties `((upstream-name . "QuasR")))
6652 (build-system r-build-system)
6654 `(("r-annotationdbi" ,r-annotationdbi)
6655 ("r-biobase" ,r-biobase)
6656 ("r-biocgenerics" ,r-biocgenerics)
6657 ("r-biocmanager" ,r-biocmanager)
6658 ("r-biocparallel" ,r-biocparallel)
6659 ("r-biostrings" ,r-biostrings)
6660 ("r-bsgenome" ,r-bsgenome)
6661 ("r-genomeinfodb" ,r-genomeinfodb)
6662 ("r-genomicalignments" ,r-genomicalignments)
6663 ("r-genomicfeatures" ,r-genomicfeatures)
6664 ("r-genomicfiles" ,r-genomicfiles)
6665 ("r-genomicranges" ,r-genomicranges)
6666 ("r-iranges" ,r-iranges)
6667 ("r-rbowtie" ,r-rbowtie)
6668 ("r-rhisat2" ,r-rhisat2)
6669 ("r-rhtslib" ,r-rhtslib)
6670 ("r-rsamtools" ,r-rsamtools)
6671 ("r-rtracklayer" ,r-rtracklayer)
6672 ("r-s4vectors" ,r-s4vectors)
6673 ("r-shortread" ,r-shortread)))
6675 `(("r-knitr" ,r-knitr)))
6676 (home-page "https://bioconductor.org/packages/QuasR/")
6677 (synopsis "Quantify and annotate short reads in R")
6679 "This package provides a framework for the quantification and analysis of
6680 short genomic reads. It covers a complete workflow starting from raw sequence
6681 reads, over creation of alignments and quality control plots, to the
6682 quantification of genomic regions of interest.")
6683 (license license:gpl2)))
6685 (define-public r-rqc
6692 (uri (bioconductor-uri "Rqc" version))
6695 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
6696 (properties `((upstream-name . "Rqc")))
6697 (build-system r-build-system)
6699 `(("r-biocgenerics" ,r-biocgenerics)
6700 ("r-biocparallel" ,r-biocparallel)
6701 ("r-biocstyle" ,r-biocstyle)
6702 ("r-biostrings" ,r-biostrings)
6703 ("r-biovizbase" ,r-biovizbase)
6704 ("r-genomicalignments" ,r-genomicalignments)
6705 ("r-genomicfiles" ,r-genomicfiles)
6706 ("r-ggplot2" ,r-ggplot2)
6707 ("r-iranges" ,r-iranges)
6708 ("r-knitr" ,r-knitr)
6709 ("r-markdown" ,r-markdown)
6712 ("r-reshape2" ,r-reshape2)
6713 ("r-rsamtools" ,r-rsamtools)
6714 ("r-s4vectors" ,r-s4vectors)
6715 ("r-shiny" ,r-shiny)
6716 ("r-shortread" ,r-shortread)))
6718 `(("r-knitr" ,r-knitr)))
6719 (home-page "https://github.com/labbcb/Rqc")
6720 (synopsis "Quality control tool for high-throughput sequencing data")
6722 "Rqc is an optimized tool designed for quality control and assessment of
6723 high-throughput sequencing data. It performs parallel processing of entire
6724 files and produces a report which contains a set of high-resolution
6726 (license license:gpl2+)))
6728 (define-public r-birewire
6735 (uri (bioconductor-uri "BiRewire" version))
6738 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
6739 (properties `((upstream-name . "BiRewire")))
6740 (build-system r-build-system)
6742 `(("r-igraph" ,r-igraph)
6743 ("r-matrix" ,r-matrix)
6745 ("r-tsne" ,r-tsne)))
6746 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
6747 (synopsis "Tools for randomization of bipartite graphs")
6749 "This package provides functions for bipartite network rewiring through N
6750 consecutive switching steps and for the computation of the minimal number of
6751 switching steps to be performed in order to maximise the dissimilarity with
6752 respect to the original network. It includes functions for the analysis of
6753 the introduced randomness across the switching steps and several other
6754 routines to analyse the resulting networks and their natural projections.")
6755 (license license:gpl3)))
6757 (define-public r-birta
6764 (uri (bioconductor-uri "birta" version))
6767 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
6768 (build-system r-build-system)
6770 `(("r-biobase" ,r-biobase)
6771 ("r-limma" ,r-limma)
6772 ("r-mass" ,r-mass)))
6773 (home-page "https://bioconductor.org/packages/birta")
6774 (synopsis "Bayesian inference of regulation of transcriptional activity")
6776 "Expression levels of mRNA molecules are regulated by different
6777 processes, comprising inhibition or activation by transcription factors and
6778 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
6779 Inference of Regulation of Transcriptional Activity) uses the regulatory
6780 networks of transcription factors and miRNAs together with mRNA and miRNA
6781 expression data to predict switches in regulatory activity between two
6782 conditions. A Bayesian network is used to model the regulatory structure and
6783 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
6784 (license license:gpl2+)))
6786 (define-public r-multidataset
6788 (name "r-multidataset")
6793 (uri (bioconductor-uri "MultiDataSet" version))
6796 "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4"))))
6797 (properties `((upstream-name . "MultiDataSet")))
6798 (build-system r-build-system)
6800 `(("r-biobase" ,r-biobase)
6801 ("r-biocgenerics" ,r-biocgenerics)
6802 ("r-genomicranges" ,r-genomicranges)
6803 ("r-ggplot2" ,r-ggplot2)
6804 ("r-ggrepel" ,r-ggrepel)
6805 ("r-iranges" ,r-iranges)
6806 ("r-limma" ,r-limma)
6807 ("r-qqman" ,r-qqman)
6808 ("r-s4vectors" ,r-s4vectors)
6809 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6811 `(("r-knitr" ,r-knitr)))
6812 (home-page "https://bioconductor.org/packages/MultiDataSet/")
6813 (synopsis "Implementation of MultiDataSet and ResultSet")
6815 "This package provides an implementation of the BRGE's (Bioinformatic
6816 Research Group in Epidemiology from Center for Research in Environmental
6817 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
6818 integrating multi omics data sets and ResultSet is a container for omics
6819 results. This package contains base classes for MEAL and rexposome
6821 (license license:expat)))
6823 (define-public r-ropls
6830 (uri (bioconductor-uri "ropls" version))
6833 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
6834 (build-system r-build-system)
6836 `(("r-biobase" ,r-biobase)
6837 ("r-multidataset" ,r-multidataset)))
6839 `(("r-knitr" ,r-knitr))) ; for vignettes
6840 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
6841 (synopsis "Multivariate analysis and feature selection of omics data")
6843 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
6844 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
6845 regression, classification, and feature selection of omics data where the
6846 number of variables exceeds the number of samples and with multicollinearity
6847 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
6848 separately model the variation correlated (predictive) to the factor of
6849 interest and the uncorrelated (orthogonal) variation. While performing
6850 similarly to PLS, OPLS facilitates interpretation.
6852 This package provides imlementations of PCA, PLS, and OPLS for multivariate
6853 analysis and feature selection of omics data. In addition to scores, loadings
6854 and weights plots, the package provides metrics and graphics to determine the
6855 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
6856 validity of the model by permutation testing, detect outliers, and perform
6857 feature selection (e.g. with Variable Importance in Projection or regression
6859 (license license:cecill)))
6861 (define-public r-biosigner
6863 (name "r-biosigner")
6868 (uri (bioconductor-uri "biosigner" version))
6871 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
6872 (build-system r-build-system)
6874 `(("r-biobase" ,r-biobase)
6875 ("r-e1071" ,r-e1071)
6876 ("r-multidataset" ,r-multidataset)
6877 ("r-randomforest" ,r-randomforest)
6878 ("r-ropls" ,r-ropls)))
6880 `(("r-knitr" ,r-knitr)))
6881 (home-page "https://bioconductor.org/packages/biosigner/")
6882 (synopsis "Signature discovery from omics data")
6884 "Feature selection is critical in omics data analysis to extract
6885 restricted and meaningful molecular signatures from complex and high-dimension
6886 data, and to build robust classifiers. This package implements a method to
6887 assess the relevance of the variables for the prediction performances of the
6888 classifier. The approach can be run in parallel with the PLS-DA, Random
6889 Forest, and SVM binary classifiers. The signatures and the corresponding
6890 'restricted' models are returned, enabling future predictions on new
6892 (license license:cecill)))
6894 (define-public r-annotatr
6901 (uri (bioconductor-uri "annotatr" version))
6904 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
6905 (build-system r-build-system)
6907 `(("r-annotationdbi" ,r-annotationdbi)
6908 ("r-annotationhub" ,r-annotationhub)
6909 ("r-dplyr" ,r-dplyr)
6910 ("r-genomeinfodb" ,r-genomeinfodb)
6911 ("r-genomicfeatures" ,r-genomicfeatures)
6912 ("r-genomicranges" ,r-genomicranges)
6913 ("r-ggplot2" ,r-ggplot2)
6914 ("r-iranges" ,r-iranges)
6915 ("r-readr" ,r-readr)
6916 ("r-regioner" ,r-regioner)
6917 ("r-reshape2" ,r-reshape2)
6918 ("r-rtracklayer" ,r-rtracklayer)
6919 ("r-s4vectors" ,r-s4vectors)))
6921 `(("r-knitr" ,r-knitr)))
6922 (home-page "https://bioconductor.org/packages/annotatr/")
6923 (synopsis "Annotation of genomic regions to genomic annotations")
6925 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
6926 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
6927 to investigate the intersecting genomic annotations. Such annotations include
6928 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
6929 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
6930 enhancers. The annotatr package provides an easy way to summarize and
6931 visualize the intersection of genomic sites/regions with genomic
6933 (license license:gpl3)))
6935 (define-public r-rsubread
6942 (uri (bioconductor-uri "Rsubread" version))
6945 "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba"))))
6946 (properties `((upstream-name . "Rsubread")))
6947 (build-system r-build-system)
6948 (inputs `(("zlib" ,zlib)))
6950 `(("r-matrix" ,r-matrix)))
6951 (home-page "https://bioconductor.org/packages/Rsubread/")
6952 (synopsis "Subread sequence alignment and counting for R")
6954 "This package provides tools for alignment, quantification and analysis
6955 of second and third generation sequencing data. It includes functionality for
6956 read mapping, read counting, SNP calling, structural variant detection and
6957 gene fusion discovery. It can be applied to all major sequencing techologies
6958 and to both short and long sequence reads.")
6959 (license license:gpl3)))
6961 (define-public r-flowutils
6963 (name "r-flowutils")
6968 (uri (bioconductor-uri "flowUtils" version))
6971 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
6972 (properties `((upstream-name . "flowUtils")))
6973 (build-system r-build-system)
6975 `(("r-biobase" ,r-biobase)
6976 ("r-corpcor" ,r-corpcor)
6977 ("r-flowcore" ,r-flowcore)
6978 ("r-graph" ,r-graph)
6979 ("r-runit" ,r-runit)
6981 (home-page "https://github.com/jspidlen/flowUtils")
6982 (synopsis "Utilities for flow cytometry")
6984 "This package provides utilities for flow cytometry data.")
6985 (license license:artistic2.0)))
6987 (define-public r-consensusclusterplus
6989 (name "r-consensusclusterplus")
6994 (uri (bioconductor-uri "ConsensusClusterPlus" version))
6997 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
6999 `((upstream-name . "ConsensusClusterPlus")))
7000 (build-system r-build-system)
7003 ("r-biobase" ,r-biobase)
7004 ("r-cluster" ,r-cluster)))
7005 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
7006 (synopsis "Clustering algorithm")
7008 "This package provides an implementation of an algorithm for determining
7009 cluster count and membership by stability evidence in unsupervised analysis.")
7010 (license license:gpl2)))
7012 (define-public r-cytolib
7019 (uri (bioconductor-uri "cytolib" version))
7022 "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
7023 (properties `((upstream-name . "cytolib")))
7024 (build-system r-build-system)
7027 (modify-phases %standard-phases
7028 (add-after 'unpack 'fix-linking
7030 (substitute* "src/Makevars.in"
7031 ;; This is to avoid having a plain directory on the list of
7032 ;; libraries to link.
7033 (("\\(RHDF5_LIBS\\)" match)
7034 (string-append match "/libhdf5.a")))
7037 `(("r-knitr" ,r-knitr)
7038 ("pkg-config" ,pkg-config)))
7042 ("r-rcpparmadillo" ,r-rcpparmadillo)
7043 ("r-rcppparallel" ,r-rcppparallel)
7044 ("r-rhdf5lib" ,r-rhdf5lib)
7045 ("r-rprotobuflib" ,r-rprotobuflib)))
7046 (home-page "https://bioconductor.org/packages/cytolib/")
7047 (synopsis "C++ infrastructure for working with gated cytometry")
7049 "This package provides the core data structure and API to represent and
7050 interact with gated cytometry data.")
7051 (license license:artistic2.0)))
7053 (define-public r-flowcore
7060 (uri (bioconductor-uri "flowCore" version))
7063 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
7064 (properties `((upstream-name . "flowCore")))
7065 (build-system r-build-system)
7068 ("r-biobase" ,r-biobase)
7069 ("r-biocgenerics" ,r-biocgenerics)
7070 ("r-cytolib" ,r-cytolib)
7071 ("r-matrixstats" ,r-matrixstats)
7073 ("r-rcpparmadillo" ,r-rcpparmadillo)
7074 ("r-rprotobuflib" ,r-rprotobuflib)
7075 ("r-s4vectors" ,r-s4vectors)))
7077 `(("r-knitr" ,r-knitr)))
7078 (home-page "https://bioconductor.org/packages/flowCore")
7079 (synopsis "Basic structures for flow cytometry data")
7081 "This package provides S4 data structures and basic functions to deal
7082 with flow cytometry data.")
7083 (license license:artistic2.0)))
7085 (define-public r-flowmeans
7087 (name "r-flowmeans")
7092 (uri (bioconductor-uri "flowMeans" version))
7095 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
7096 (properties `((upstream-name . "flowMeans")))
7097 (build-system r-build-system)
7099 `(("r-biobase" ,r-biobase)
7100 ("r-feature" ,r-feature)
7101 ("r-flowcore" ,r-flowcore)
7102 ("r-rrcov" ,r-rrcov)))
7103 (home-page "https://bioconductor.org/packages/flowMeans")
7104 (synopsis "Non-parametric flow cytometry data gating")
7106 "This package provides tools to identify cell populations in Flow
7107 Cytometry data using non-parametric clustering and segmented-regression-based
7108 change point detection.")
7109 (license license:artistic2.0)))
7111 (define-public r-ncdfflow
7118 (uri (bioconductor-uri "ncdfFlow" version))
7121 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
7122 (properties `((upstream-name . "ncdfFlow")))
7123 (build-system r-build-system)
7126 (modify-phases %standard-phases
7127 (add-after 'unpack 'fix-linking
7129 (substitute* "src/Makevars"
7130 ;; This is to avoid having a plain directory on the list of
7131 ;; libraries to link.
7132 (("\\(RHDF5_LIBS\\)" match)
7133 (string-append match "/libhdf5.a")))
7137 ("r-biobase" ,r-biobase)
7138 ("r-biocgenerics" ,r-biocgenerics)
7139 ("r-flowcore" ,r-flowcore)
7141 ("r-rcpparmadillo" ,r-rcpparmadillo)
7142 ("r-rhdf5lib" ,r-rhdf5lib)
7143 ("r-zlibbioc" ,r-zlibbioc)))
7145 `(("r-knitr" ,r-knitr)))
7146 (home-page "https://bioconductor.org/packages/ncdfFlow/")
7147 (synopsis "HDF5 based storage for flow cytometry data")
7149 "This package provides HDF5 storage based methods and functions for
7150 manipulation of flow cytometry data.")
7151 (license license:artistic2.0)))
7153 (define-public r-ggcyto
7160 (uri (bioconductor-uri "ggcyto" version))
7163 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
7164 (properties `((upstream-name . "ggcyto")))
7165 (build-system r-build-system)
7167 `(("r-data-table" ,r-data-table)
7168 ("r-flowcore" ,r-flowcore)
7169 ("r-flowworkspace" ,r-flowworkspace)
7170 ("r-ggplot2" ,r-ggplot2)
7171 ("r-gridextra" ,r-gridextra)
7172 ("r-hexbin" ,r-hexbin)
7173 ("r-ncdfflow" ,r-ncdfflow)
7175 ("r-rcolorbrewer" ,r-rcolorbrewer)
7176 ("r-rlang" ,r-rlang)
7177 ("r-scales" ,r-scales)))
7179 `(("r-knitr" ,r-knitr)))
7180 (home-page "https://github.com/RGLab/ggcyto/issues")
7181 (synopsis "Visualize Cytometry data with ggplot")
7183 "With the dedicated fortify method implemented for @code{flowSet},
7184 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
7185 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
7186 and some custom layers also make it easy to add gates and population
7187 statistics to the plot.")
7188 (license license:artistic2.0)))
7190 (define-public r-flowviz
7197 (uri (bioconductor-uri "flowViz" version))
7200 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
7201 (properties `((upstream-name . "flowViz")))
7202 (build-system r-build-system)
7204 `(("r-biobase" ,r-biobase)
7205 ("r-flowcore" ,r-flowcore)
7206 ("r-hexbin" ,r-hexbin)
7207 ("r-idpmisc" ,r-idpmisc)
7208 ("r-kernsmooth" ,r-kernsmooth)
7209 ("r-lattice" ,r-lattice)
7210 ("r-latticeextra" ,r-latticeextra)
7212 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7214 `(("r-knitr" ,r-knitr)))
7215 (home-page "https://bioconductor.org/packages/flowViz/")
7216 (synopsis "Visualization for flow cytometry")
7218 "This package provides visualization tools for flow cytometry data.")
7219 (license license:artistic2.0)))
7221 (define-public r-flowclust
7223 (name "r-flowclust")
7228 (uri (bioconductor-uri "flowClust" version))
7231 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
7232 (properties `((upstream-name . "flowClust")))
7233 (build-system r-build-system)
7236 (list "--configure-args=--enable-bundled-gsl=no")))
7238 `(("r-biobase" ,r-biobase)
7239 ("r-biocgenerics" ,r-biocgenerics)
7241 ("r-corpcor" ,r-corpcor)
7242 ("r-ellipse" ,r-ellipse)
7243 ("r-flowcore" ,r-flowcore)
7244 ("r-flowviz" ,r-flowviz)
7245 ("r-graph" ,r-graph)
7246 ("r-mnormt" ,r-mnormt)))
7250 `(("pkg-config" ,pkg-config)
7251 ("r-knitr" ,r-knitr)))
7252 (home-page "https://bioconductor.org/packages/flowClust")
7253 (synopsis "Clustering for flow cytometry")
7255 "This package provides robust model-based clustering using a t-mixture
7256 model with Box-Cox transformation.")
7257 (license license:artistic2.0)))
7259 ;; TODO: this package bundles an old version of protobuf. It's not easy to
7260 ;; make it use our protobuf package instead.
7261 (define-public r-rprotobuflib
7263 (name "r-rprotobuflib")
7268 (uri (bioconductor-uri "RProtoBufLib" version))
7271 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
7272 (properties `((upstream-name . "RProtoBufLib")))
7273 (build-system r-build-system)
7276 (modify-phases %standard-phases
7277 (add-after 'unpack 'unpack-bundled-sources
7279 (with-directory-excursion "src"
7280 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
7283 `(("r-knitr" ,r-knitr)))
7284 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
7285 (synopsis "C++ headers and static libraries of Protocol buffers")
7287 "This package provides the headers and static library of Protocol buffers
7288 for other R packages to compile and link against.")
7289 (license license:bsd-3)))
7291 (define-public r-flowworkspace
7293 (name "r-flowworkspace")
7298 (uri (bioconductor-uri "flowWorkspace" version))
7301 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
7302 (properties `((upstream-name . "flowWorkspace")))
7303 (build-system r-build-system)
7306 (modify-phases %standard-phases
7307 (add-after 'unpack 'fix-linking
7309 (substitute* "src/Makevars"
7310 ;; This is to avoid having a plain directory on the list of
7311 ;; libraries to link.
7312 (("\\{h5lib\\}" match)
7313 (string-append match "/libhdf5.a")))
7316 `(("r-aws-s3" ,r-aws-s3)
7317 ("r-aws-signature" ,r-aws-signature)
7319 ("r-biobase" ,r-biobase)
7320 ("r-biocgenerics" ,r-biocgenerics)
7321 ("r-cytolib" ,r-cytolib)
7322 ("r-data-table" ,r-data-table)
7323 ("r-digest" ,r-digest)
7324 ("r-dplyr" ,r-dplyr)
7325 ("r-flowcore" ,r-flowcore)
7326 ("r-ggplot2" ,r-ggplot2)
7327 ("r-graph" ,r-graph)
7328 ("r-lattice" ,r-lattice)
7329 ("r-latticeextra" ,r-latticeextra)
7330 ("r-matrixstats" ,r-matrixstats)
7331 ("r-ncdfflow" ,r-ncdfflow)
7334 ("r-rcpparmadillo" ,r-rcpparmadillo)
7335 ("r-rcppparallel" ,r-rcppparallel)
7336 ("r-rgraphviz" ,r-rgraphviz)
7337 ("r-rhdf5lib" ,r-rhdf5lib)
7338 ("r-rprotobuflib" ,r-rprotobuflib)
7339 ("r-scales" ,r-scales)
7342 `(("r-knitr" ,r-knitr)))
7343 (home-page "https://bioconductor.org/packages/flowWorkspace/")
7344 (synopsis "Infrastructure for working with cytometry data")
7346 "This package is designed to facilitate comparison of automated gating
7347 methods against manual gating done in flowJo. This package allows you to
7348 import basic flowJo workspaces into BioConductor and replicate the gating from
7349 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
7350 samples, compensation, and transformation are performed so that the output
7351 matches the flowJo analysis.")
7352 (license license:artistic2.0)))
7354 (define-public r-flowstats
7356 (name "r-flowstats")
7361 (uri (bioconductor-uri "flowStats" version))
7364 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
7365 (properties `((upstream-name . "flowStats")))
7366 (build-system r-build-system)
7368 `(("r-biobase" ,r-biobase)
7369 ("r-biocgenerics" ,r-biocgenerics)
7370 ("r-cluster" ,r-cluster)
7372 ("r-flowcore" ,r-flowcore)
7373 ("r-flowviz" ,r-flowviz)
7374 ("r-flowworkspace" ,r-flowworkspace)
7375 ("r-kernsmooth" ,r-kernsmooth)
7377 ("r-lattice" ,r-lattice)
7379 ("r-ncdfflow" ,r-ncdfflow)
7380 ("r-rcolorbrewer" ,r-rcolorbrewer)
7381 ("r-rrcov" ,r-rrcov)))
7382 (home-page "http://www.github.com/RGLab/flowStats")
7383 (synopsis "Statistical methods for the analysis of flow cytometry data")
7385 "This package provides methods and functionality to analyze flow data
7386 that is beyond the basic infrastructure provided by the @code{flowCore}
7388 (license license:artistic2.0)))
7390 (define-public r-opencyto
7397 (uri (bioconductor-uri "openCyto" version))
7400 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
7401 (properties `((upstream-name . "openCyto")))
7402 (build-system r-build-system)
7404 `(("r-biobase" ,r-biobase)
7405 ("r-biocgenerics" ,r-biocgenerics)
7407 ("r-data-table" ,r-data-table)
7408 ("r-flowclust" ,r-flowclust)
7409 ("r-flowcore" ,r-flowcore)
7410 ("r-flowstats" ,r-flowstats)
7411 ("r-flowviz" ,r-flowviz)
7412 ("r-flowworkspace" ,r-flowworkspace)
7413 ("r-graph" ,r-graph)
7414 ("r-gtools" ,r-gtools)
7416 ("r-lattice" ,r-lattice)
7418 ("r-ncdfflow" ,r-ncdfflow)
7420 ("r-r-utils" ,r-r-utils)
7422 ("r-rcolorbrewer" ,r-rcolorbrewer)
7424 ("r-rrcov" ,r-rrcov)))
7426 `(("r-knitr" ,r-knitr)))
7427 (home-page "https://bioconductor.org/packages/openCyto")
7428 (synopsis "Hierarchical gating pipeline for flow cytometry data")
7430 "This package is designed to facilitate the automated gating methods in a
7431 sequential way to mimic the manual gating strategy.")
7432 (license license:artistic2.0)))
7434 (define-public r-cytoml
7441 (uri (bioconductor-uri "CytoML" version))
7444 "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1"))))
7445 (properties `((upstream-name . "CytoML")))
7446 (build-system r-build-system)
7449 (modify-phases %standard-phases
7450 (add-after 'unpack 'fix-linking
7452 (substitute* "src/Makevars.in"
7453 ;; This is to avoid having a plain directory on the list of
7454 ;; libraries to link.
7455 (("\\{h5lib\\}" match)
7456 (string-append match "/libhdf5.a")))
7459 `(("libxml2" ,libxml2)
7462 `(("r-base64enc" ,r-base64enc)
7464 ("r-biobase" ,r-biobase)
7465 ("r-corpcor" ,r-corpcor)
7466 ("r-cytolib" ,r-cytolib)
7467 ("r-data-table" ,r-data-table)
7468 ("r-dplyr" ,r-dplyr)
7469 ("r-flowcore" ,r-flowcore)
7470 ("r-flowworkspace" ,r-flowworkspace)
7471 ("r-ggcyto" ,r-ggcyto)
7472 ("r-graph" ,r-graph)
7473 ("r-jsonlite" ,r-jsonlite)
7474 ("r-lattice" ,r-lattice)
7475 ("r-opencyto" ,r-opencyto)
7479 ("r-rcpparmadillo" ,r-rcpparmadillo)
7480 ("r-rcppparallel" ,r-rcppparallel)
7481 ("r-rgraphviz" ,r-rgraphviz)
7482 ("r-rhdf5lib" ,r-rhdf5lib)
7483 ("r-rprotobuflib" ,r-rprotobuflib)
7484 ("r-runit" ,r-runit)
7485 ("r-tibble" ,r-tibble)
7488 ("r-yaml" ,r-yaml)))
7490 `(("r-knitr" ,r-knitr)))
7491 (home-page "https://github.com/RGLab/CytoML")
7492 (synopsis "GatingML interface for cross platform cytometry data sharing")
7494 "This package provides an interface to implementations of the GatingML2.0
7495 standard to exchange gated cytometry data with other software platforms.")
7496 (license license:artistic2.0)))
7498 (define-public r-flowsom
7505 (uri (bioconductor-uri "FlowSOM" version))
7508 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
7509 (properties `((upstream-name . "FlowSOM")))
7510 (build-system r-build-system)
7512 `(("r-biocgenerics" ,r-biocgenerics)
7513 ("r-consensusclusterplus" ,r-consensusclusterplus)
7514 ("r-cytoml" ,r-cytoml)
7515 ("r-flowcore" ,r-flowcore)
7516 ("r-flowworkspace" ,r-flowworkspace)
7517 ("r-igraph" ,r-igraph)
7518 ("r-rcolorbrewer" ,r-rcolorbrewer)
7521 (home-page "https://bioconductor.org/packages/FlowSOM/")
7522 (synopsis "Visualize and interpret cytometry data")
7524 "FlowSOM offers visualization options for cytometry data, by using
7525 self-organizing map clustering and minimal spanning trees.")
7526 (license license:gpl2+)))
7528 (define-public r-mixomics
7535 (uri (bioconductor-uri "mixOmics" version))
7538 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
7539 (properties `((upstream-name . "mixOmics")))
7540 (build-system r-build-system)
7542 `(("r-corpcor" ,r-corpcor)
7543 ("r-dplyr" ,r-dplyr)
7544 ("r-ellipse" ,r-ellipse)
7545 ("r-ggrepel" ,r-ggrepel)
7546 ("r-ggplot2" ,r-ggplot2)
7547 ("r-gridextra" ,r-gridextra)
7548 ("r-igraph" ,r-igraph)
7549 ("r-lattice" ,r-lattice)
7551 ("r-matrixstats" ,r-matrixstats)
7552 ("r-rarpack" ,r-rarpack)
7553 ("r-rcolorbrewer" ,r-rcolorbrewer)
7554 ("r-reshape2" ,r-reshape2)
7555 ("r-tidyr" ,r-tidyr)))
7557 `(("r-knitr" ,r-knitr)))
7558 (home-page "http://www.mixOmics.org")
7559 (synopsis "Multivariate methods for exploration of biological datasets")
7561 "mixOmics offers a wide range of multivariate methods for the exploration
7562 and integration of biological datasets with a particular focus on variable
7563 selection. The package proposes several sparse multivariate models we have
7564 developed to identify the key variables that are highly correlated, and/or
7565 explain the biological outcome of interest. The data that can be analysed
7566 with mixOmics may come from high throughput sequencing technologies, such as
7567 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
7568 also beyond the realm of omics (e.g. spectral imaging). The methods
7569 implemented in mixOmics can also handle missing values without having to
7570 delete entire rows with missing data.")
7571 (license license:gpl2+)))
7573 (define-public r-depecher
7574 (package ;Source/Weave error
7580 (uri (bioconductor-uri "DepecheR" version))
7583 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
7584 (properties `((upstream-name . "DepecheR")))
7585 (build-system r-build-system)
7587 `(("r-beanplot" ,r-beanplot)
7588 ("r-dosnow" ,r-dosnow)
7589 ("r-dplyr" ,r-dplyr)
7591 ("r-foreach" ,r-foreach)
7592 ("r-ggplot2" ,r-ggplot2)
7593 ("r-gmodels" ,r-gmodels)
7594 ("r-gplots" ,r-gplots)
7596 ("r-matrixstats" ,r-matrixstats)
7597 ("r-mixomics" ,r-mixomics)
7598 ("r-moments" ,r-moments)
7600 ("r-rcppeigen" ,r-rcppeigen)
7601 ("r-reshape2" ,r-reshape2)
7602 ("r-robustbase" ,r-robustbase)
7603 ("r-viridis" ,r-viridis)))
7605 `(("r-knitr" ,r-knitr)))
7606 (home-page "https://bioconductor.org/packages/DepecheR/")
7607 (synopsis "Identify traits of clusters in high-dimensional entities")
7609 "The purpose of this package is to identify traits in a dataset that can
7610 separate groups. This is done on two levels. First, clustering is performed,
7611 using an implementation of sparse K-means. Secondly, the generated clusters
7612 are used to predict outcomes of groups of individuals based on their
7613 distribution of observations in the different clusters. As certain clusters
7614 with separating information will be identified, and these clusters are defined
7615 by a sparse number of variables, this method can reduce the complexity of
7616 data, to only emphasize the data that actually matters.")
7617 (license license:expat)))
7619 (define-public r-rcistarget
7621 (name "r-rcistarget")
7626 (uri (bioconductor-uri "RcisTarget" version))
7629 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
7630 (properties `((upstream-name . "RcisTarget")))
7631 (build-system r-build-system)
7633 `(("r-aucell" ,r-aucell)
7634 ("r-biocgenerics" ,r-biocgenerics)
7635 ("r-data-table" ,r-data-table)
7636 ("r-feather" ,r-feather)
7637 ("r-gseabase" ,r-gseabase)
7638 ("r-r-utils" ,r-r-utils)
7639 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7641 `(("r-knitr" ,r-knitr)))
7642 (home-page "https://aertslab.org/#scenic")
7643 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
7645 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
7646 over-represented on a gene list. In a first step, RcisTarget selects DNA
7647 motifs that are significantly over-represented in the surroundings of the
7648 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
7649 achieved by using a database that contains genome-wide cross-species rankings
7650 for each motif. The motifs that are then annotated to TFs and those that have
7651 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
7652 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
7653 genes in the gene-set that are ranked above the leading edge).")
7654 (license license:gpl3)))
7656 (define-public r-cicero
7663 (uri (bioconductor-uri "cicero" version))
7666 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
7667 (build-system r-build-system)
7669 `(("r-assertthat" ,r-assertthat)
7670 ("r-biobase" ,r-biobase)
7671 ("r-biocgenerics" ,r-biocgenerics)
7672 ("r-data-table" ,r-data-table)
7673 ("r-dplyr" ,r-dplyr)
7675 ("r-genomicranges" ,r-genomicranges)
7676 ("r-ggplot2" ,r-ggplot2)
7677 ("r-glasso" ,r-glasso)
7679 ("r-igraph" ,r-igraph)
7680 ("r-iranges" ,r-iranges)
7681 ("r-matrix" ,r-matrix)
7682 ("r-monocle" ,r-monocle)
7684 ("r-reshape2" ,r-reshape2)
7685 ("r-s4vectors" ,r-s4vectors)
7686 ("r-stringi" ,r-stringi)
7687 ("r-stringr" ,r-stringr)
7688 ("r-tibble" ,r-tibble)
7689 ("r-tidyr" ,r-tidyr)
7690 ("r-vgam" ,r-vgam)))
7692 `(("r-knitr" ,r-knitr)))
7693 (home-page "https://bioconductor.org/packages/cicero/")
7694 (synopsis "Predict cis-co-accessibility from single-cell data")
7696 "Cicero computes putative cis-regulatory maps from single-cell chromatin
7697 accessibility data. It also extends the monocle package for use in chromatin
7698 accessibility data.")
7699 (license license:expat)))
7701 ;; This is the latest commit on the "monocle3" branch.
7702 (define-public r-cicero-monocle3
7703 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
7705 (package (inherit r-cicero)
7706 (name "r-cicero-monocle3")
7707 (version (git-version "1.3.2" revision commit))
7712 (url "https://github.com/cole-trapnell-lab/cicero-release")
7714 (file-name (git-file-name name version))
7717 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
7719 `(("r-monocle3" ,r-monocle3)
7720 ,@(alist-delete "r-monocle"
7721 (package-propagated-inputs r-cicero)))))))
7723 (define-public r-circrnaprofiler
7725 (name "r-circrnaprofiler")
7730 (uri (bioconductor-uri "circRNAprofiler" version))
7733 "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
7735 `((upstream-name . "circRNAprofiler")))
7736 (build-system r-build-system)
7738 `(("r-annotationhub" ,r-annotationhub)
7739 ("r-biostrings" ,r-biostrings)
7740 ("r-bsgenome" ,r-bsgenome)
7741 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7742 ("r-deseq2" ,r-deseq2)
7743 ("r-dplyr" ,r-dplyr)
7744 ("r-edger" ,r-edger)
7745 ("r-genomeinfodb" ,r-genomeinfodb)
7746 ("r-genomicranges" ,r-genomicranges)
7747 ("r-ggplot2" ,r-ggplot2)
7748 ("r-gwascat" ,r-gwascat)
7749 ("r-iranges" ,r-iranges)
7750 ("r-magrittr" ,r-magrittr)
7751 ("r-r-utils" ,r-r-utils)
7752 ("r-readr" ,r-readr)
7753 ("r-reshape2" ,r-reshape2)
7754 ("r-rlang" ,r-rlang)
7755 ("r-rtracklayer" ,r-rtracklayer)
7756 ("r-s4vectors" ,r-s4vectors)
7757 ("r-seqinr" ,r-seqinr)
7758 ("r-stringi" ,r-stringi)
7759 ("r-stringr" ,r-stringr)
7760 ("r-universalmotif" ,r-universalmotif)))
7762 `(("r-knitr" ,r-knitr)))
7764 "https://github.com/Aufiero/circRNAprofiler")
7766 "Computational framework for the downstream analysis of circular RNA's")
7768 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
7769 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
7770 framework allows combining and analyzing circRNAs previously detected by
7771 multiple publicly available annotation-based circRNA detection tools. It
7772 covers different aspects of circRNAs analysis from differential expression
7773 analysis, evolutionary conservation, biogenesis to functional analysis.")
7774 (license license:gpl3)))
7776 (define-public r-cistopic
7777 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
7781 (version (git-version "0.2.1" revision commit))
7786 (url "https://github.com/aertslab/cisTopic")
7788 (file-name (git-file-name name version))
7791 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
7792 (build-system r-build-system)
7794 `(("r-aucell" ,r-aucell)
7795 ("r-data-table" ,r-data-table)
7796 ("r-dplyr" ,r-dplyr)
7797 ("r-dosnow" ,r-dosnow)
7799 ("r-feather" ,r-feather)
7800 ("r-fitdistrplus" ,r-fitdistrplus)
7801 ("r-genomicranges" ,r-genomicranges)
7802 ("r-ggplot2" ,r-ggplot2)
7804 ("r-matrix" ,r-matrix)
7806 ("r-rcistarget" ,r-rcistarget)
7807 ("r-rtracklayer" ,r-rtracklayer)
7808 ("r-s4vectors" ,r-s4vectors)))
7809 (home-page "https://github.com/aertslab/cisTopic")
7810 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
7812 "The sparse nature of single cell epigenomics data can be overruled using
7813 probabilistic modelling methods such as @dfn{Latent Dirichlet
7814 Allocation} (LDA). This package allows the probabilistic modelling of
7815 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
7816 includes functionalities to identify cell states based on the contribution of
7817 cisTopics and explore the nature and regulatory proteins driving them.")
7818 (license license:gpl3))))
7820 (define-public r-genie3
7827 (uri (bioconductor-uri "GENIE3" version))
7830 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
7831 (properties `((upstream-name . "GENIE3")))
7832 (build-system r-build-system)
7833 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
7835 `(("r-knitr" ,r-knitr)))
7836 (home-page "https://bioconductor.org/packages/GENIE3")
7837 (synopsis "Gene network inference with ensemble of trees")
7839 "This package implements the GENIE3 algorithm for inferring gene
7840 regulatory networks from expression data.")
7841 (license license:gpl2+)))
7843 (define-public r-roc
7850 (uri (bioconductor-uri "ROC" version))
7853 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
7854 (properties `((upstream-name . "ROC")))
7855 (build-system r-build-system)
7857 `(("r-knitr" ,r-knitr)))
7858 (home-page "https://www.bioconductor.org/packages/ROC/")
7859 (synopsis "Utilities for ROC curves")
7861 "This package provides utilities for @dfn{Receiver Operating
7862 Characteristic} (ROC) curves, with a focus on micro arrays.")
7863 (license license:artistic2.0)))
7865 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
7867 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
7872 (uri (bioconductor-uri
7873 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
7874 version 'annotation))
7877 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
7880 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
7881 (build-system r-build-system)
7882 (propagated-inputs `(("r-minfi" ,r-minfi)))
7884 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
7885 (synopsis "Annotation for Illumina's 450k methylation arrays")
7887 "This package provides manifests and annotation for Illumina's 450k array
7889 (license license:artistic2.0)))
7891 (define-public r-watermelon
7893 (name "r-watermelon")
7898 (uri (bioconductor-uri "wateRmelon" version))
7901 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
7902 (properties `((upstream-name . "wateRmelon")))
7903 (build-system r-build-system)
7905 `(("r-biobase" ,r-biobase)
7906 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
7907 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
7908 ("r-illuminaio" ,r-illuminaio)
7909 ("r-limma" ,r-limma)
7911 ("r-matrixstats" ,r-matrixstats)
7912 ("r-methylumi" ,r-methylumi)
7914 (home-page "https://bioconductor.org/packages/wateRmelon/")
7915 (synopsis "Illumina 450 methylation array normalization and metrics")
7917 "The standard index of DNA methylation (beta) is computed from methylated
7918 and unmethylated signal intensities. Betas calculated from raw signal
7919 intensities perform well, but using 11 methylomic datasets we demonstrate that
7920 quantile normalization methods produce marked improvement. The commonly used
7921 procedure of normalizing betas is inferior to the separate normalization of M
7922 and U, and it is also advantageous to normalize Type I and Type II assays
7923 separately. This package provides 15 flavours of betas and three performance
7924 metrics, with methods for objects produced by the @code{methylumi} and
7925 @code{minfi} packages.")
7926 (license license:gpl3)))
7928 (define-public r-gdsfmt
7935 (uri (bioconductor-uri "gdsfmt" version))
7938 "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
7939 (modules '((guix build utils)))
7940 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
7941 ;; them and link with system libraries instead.
7944 (for-each delete-file-recursively
7948 (substitute* "src/Makevars"
7949 (("all: \\$\\(SHLIB\\)") "all:")
7950 (("\\$\\(SHLIB\\): liblzma.a") "")
7951 (("(ZLIB|LZ4)/.*") "")
7952 (("CoreArray/dVLIntGDS.cpp.*")
7953 "CoreArray/dVLIntGDS.cpp")
7954 (("CoreArray/dVLIntGDS.o.*")
7955 "CoreArray/dVLIntGDS.o")
7956 (("PKG_LIBS = ./liblzma.a")
7957 "PKG_LIBS = -llz4"))
7958 (substitute* "src/CoreArray/dStream.h"
7959 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
7960 (string-append "include <" header ">")))
7962 (properties `((upstream-name . "gdsfmt")))
7963 (build-system r-build-system)
7969 `(("r-knitr" ,r-knitr)))
7970 (home-page "http://corearray.sourceforge.net/")
7972 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
7974 "This package provides a high-level R interface to CoreArray @dfn{Genomic
7975 Data Structure} (GDS) data files, which are portable across platforms with
7976 hierarchical structure to store multiple scalable array-oriented data sets
7977 with metadata information. It is suited for large-scale datasets, especially
7978 for data which are much larger than the available random-access memory. The
7979 @code{gdsfmt} package offers efficient operations specifically designed for
7980 integers of less than 8 bits, since a diploid genotype, like
7981 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
7982 byte. Data compression and decompression are available with relatively
7983 efficient random access. It is also allowed to read a GDS file in parallel
7984 with multiple R processes supported by the package @code{parallel}.")
7985 (license license:lgpl3)))
7987 (define-public r-bigmelon
7994 (uri (bioconductor-uri "bigmelon" version))
7997 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
7998 (properties `((upstream-name . "bigmelon")))
7999 (build-system r-build-system)
8001 `(("r-biobase" ,r-biobase)
8002 ("r-biocgenerics" ,r-biocgenerics)
8003 ("r-gdsfmt" ,r-gdsfmt)
8004 ("r-geoquery" ,r-geoquery)
8005 ("r-methylumi" ,r-methylumi)
8006 ("r-minfi" ,r-minfi)
8007 ("r-watermelon" ,r-watermelon)))
8008 (home-page "https://bioconductor.org/packages/bigmelon/")
8009 (synopsis "Illumina methylation array analysis for large experiments")
8011 "This package provides methods for working with Illumina arrays using the
8012 @code{gdsfmt} package.")
8013 (license license:gpl3)))
8015 (define-public r-seqbias
8022 (uri (bioconductor-uri "seqbias" version))
8025 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
8026 (properties `((upstream-name . "seqbias")))
8027 (build-system r-build-system)
8029 `(("r-biostrings" ,r-biostrings)
8030 ("r-genomicranges" ,r-genomicranges)
8031 ("r-rhtslib" ,r-rhtslib)))
8032 (home-page "https://bioconductor.org/packages/seqbias/")
8033 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
8035 "This package implements a model of per-position sequencing bias in
8036 high-throughput sequencing data using a simple Bayesian network, the structure
8037 and parameters of which are trained on a set of aligned reads and a reference
8039 (license license:lgpl3)))
8041 (define-public r-snplocs-hsapiens-dbsnp144-grch37
8043 (name "r-snplocs-hsapiens-dbsnp144-grch37")
8047 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
8048 version 'annotation))
8051 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
8052 (build-system r-build-system)
8053 ;; As this package provides little more than a very large data file it
8054 ;; doesn't make sense to build substitutes.
8055 (arguments `(#:substitutable? #f))
8057 `(("r-biocgenerics" ,r-biocgenerics)
8058 ("r-s4vectors" ,r-s4vectors)
8059 ("r-iranges" ,r-iranges)
8060 ("r-genomeinfodb" ,r-genomeinfodb)
8061 ("r-genomicranges" ,r-genomicranges)
8062 ("r-bsgenome" ,r-bsgenome)
8063 ("r-biostrings" ,r-biostrings)))
8065 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
8066 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
8067 (description "This package provides SNP locations and alleles for Homo
8068 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
8069 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
8070 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
8071 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
8072 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
8073 the mitochondrion chromosome. Therefore, the SNPs in this package can be
8074 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
8075 correct position but this injection will exclude chrM (i.e. nothing will be
8076 injected in that sequence).")
8077 (license license:artistic2.0)))
8079 (define-public r-reqon
8086 (uri (bioconductor-uri "ReQON" version))
8089 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
8090 (properties `((upstream-name . "ReQON")))
8091 (build-system r-build-system)
8093 `(("r-rjava" ,r-rjava)
8094 ("r-rsamtools" ,r-rsamtools)
8095 ("r-seqbias" ,r-seqbias)))
8096 (home-page "https://bioconductor.org/packages/ReQON/")
8097 (synopsis "Recalibrating quality of nucleotides")
8099 "This package provides an implementation of an algorithm for
8100 recalibrating the base quality scores for aligned sequencing data in BAM
8102 (license license:gpl2)))
8104 (define-public r-wavcluster
8106 (name "r-wavcluster")
8111 (uri (bioconductor-uri "wavClusteR" version))
8114 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
8115 (properties `((upstream-name . "wavClusteR")))
8116 (build-system r-build-system)
8118 `(("r-biocgenerics" ,r-biocgenerics)
8119 ("r-biostrings" ,r-biostrings)
8120 ("r-foreach" ,r-foreach)
8121 ("r-genomicfeatures" ,r-genomicfeatures)
8122 ("r-genomicranges" ,r-genomicranges)
8123 ("r-ggplot2" ,r-ggplot2)
8124 ("r-hmisc" ,r-hmisc)
8125 ("r-iranges" ,r-iranges)
8126 ("r-mclust" ,r-mclust)
8127 ("r-rsamtools" ,r-rsamtools)
8128 ("r-rtracklayer" ,r-rtracklayer)
8129 ("r-s4vectors" ,r-s4vectors)
8130 ("r-seqinr" ,r-seqinr)
8131 ("r-stringr" ,r-stringr)))
8133 `(("r-knitr" ,r-knitr)))
8134 (home-page "https://bioconductor.org/packages/wavClusteR/")
8135 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
8137 "This package provides an integrated pipeline for the analysis of
8138 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
8139 sequencing errors, SNPs and additional non-experimental sources by a non-
8140 parametric mixture model. The protein binding sites (clusters) are then
8141 resolved at high resolution and cluster statistics are estimated using a
8142 rigorous Bayesian framework. Post-processing of the results, data export for
8143 UCSC genome browser visualization and motif search analysis are provided. In
8144 addition, the package integrates RNA-Seq data to estimate the False
8145 Discovery Rate of cluster detection. Key functions support parallel multicore
8146 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
8147 be applied to the analysis of other NGS data obtained from experimental
8148 procedures that induce nucleotide substitutions (e.g. BisSeq).")
8149 (license license:gpl2)))
8151 (define-public r-timeseriesexperiment
8153 (name "r-timeseriesexperiment")
8158 (uri (bioconductor-uri "TimeSeriesExperiment" version))
8161 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
8163 `((upstream-name . "TimeSeriesExperiment")))
8164 (build-system r-build-system)
8166 `(("r-deseq2" ,r-deseq2)
8167 ("r-dplyr" ,r-dplyr)
8168 ("r-dynamictreecut" ,r-dynamictreecut)
8169 ("r-edger" ,r-edger)
8170 ("r-ggplot2" ,r-ggplot2)
8171 ("r-hmisc" ,r-hmisc)
8172 ("r-limma" ,r-limma)
8173 ("r-magrittr" ,r-magrittr)
8174 ("r-proxy" ,r-proxy)
8175 ("r-s4vectors" ,r-s4vectors)
8176 ("r-summarizedexperiment" ,r-summarizedexperiment)
8177 ("r-tibble" ,r-tibble)
8178 ("r-tidyr" ,r-tidyr)
8179 ("r-vegan" ,r-vegan)
8180 ("r-viridis" ,r-viridis)))
8182 `(("r-knitr" ,r-knitr)))
8183 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
8184 (synopsis "Analysis for short time-series data")
8186 "This package is a visualization and analysis toolbox for short time
8187 course data which includes dimensionality reduction, clustering, two-sample
8188 differential expression testing and gene ranking techniques. The package also
8189 provides methods for retrieving enriched pathways.")
8190 (license license:lgpl3+)))
8192 (define-public r-variantfiltering
8194 (name "r-variantfiltering")
8199 (uri (bioconductor-uri "VariantFiltering" version))
8202 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
8204 `((upstream-name . "VariantFiltering")))
8205 (build-system r-build-system)
8207 `(("r-annotationdbi" ,r-annotationdbi)
8208 ("r-biobase" ,r-biobase)
8209 ("r-biocgenerics" ,r-biocgenerics)
8210 ("r-biocparallel" ,r-biocparallel)
8211 ("r-biostrings" ,r-biostrings)
8212 ("r-bsgenome" ,r-bsgenome)
8214 ("r-genomeinfodb" ,r-genomeinfodb)
8215 ("r-genomicfeatures" ,r-genomicfeatures)
8216 ("r-genomicranges" ,r-genomicranges)
8217 ("r-genomicscores" ,r-genomicscores)
8218 ("r-graph" ,r-graph)
8220 ("r-iranges" ,r-iranges)
8222 ("r-rsamtools" ,r-rsamtools)
8223 ("r-s4vectors" ,r-s4vectors)
8224 ("r-shiny" ,r-shiny)
8225 ("r-shinyjs" ,r-shinyjs)
8226 ("r-shinythemes" ,r-shinythemes)
8227 ("r-shinytree" ,r-shinytree)
8228 ("r-summarizedexperiment" ,r-summarizedexperiment)
8229 ("r-variantannotation" ,r-variantannotation)
8230 ("r-xvector" ,r-xvector)))
8231 (home-page "https://github.com/rcastelo/VariantFiltering")
8232 (synopsis "Filtering of coding and non-coding genetic variants")
8234 "Filter genetic variants using different criteria such as inheritance
8235 model, amino acid change consequence, minor allele frequencies across human
8236 populations, splice site strength, conservation, etc.")
8237 (license license:artistic2.0)))
8239 (define-public r-genomegraphs
8241 (name "r-genomegraphs")
8246 (uri (bioconductor-uri "GenomeGraphs" version))
8249 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
8250 (properties `((upstream-name . "GenomeGraphs")))
8251 (build-system r-build-system)
8253 `(("r-biomart" ,r-biomart)))
8254 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
8255 (synopsis "Plotting genomic information from Ensembl")
8257 "Genomic data analyses requires integrated visualization of known genomic
8258 information and new experimental data. GenomeGraphs uses the biomaRt package
8259 to perform live annotation queries to Ensembl and translates this to e.g.
8260 gene/transcript structures in viewports of the grid graphics package. This
8261 results in genomic information plotted together with your data. Another
8262 strength of GenomeGraphs is to plot different data types such as array CGH,
8263 gene expression, sequencing and other data, together in one plot using the
8264 same genome coordinate system.")
8265 (license license:artistic2.0)))
8267 (define-public r-wavetiling
8269 (name "r-wavetiling")
8274 (uri (bioconductor-uri "waveTiling" version))
8277 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
8278 (properties `((upstream-name . "waveTiling")))
8279 (build-system r-build-system)
8281 `(("r-affy" ,r-affy)
8282 ("r-biobase" ,r-biobase)
8283 ("r-biostrings" ,r-biostrings)
8284 ("r-genomegraphs" ,r-genomegraphs)
8285 ("r-genomicranges" ,r-genomicranges)
8286 ("r-iranges" ,r-iranges)
8287 ("r-oligo" ,r-oligo)
8288 ("r-oligoclasses" ,r-oligoclasses)
8289 ("r-preprocesscore" ,r-preprocesscore)
8290 ("r-waveslim" ,r-waveslim)))
8291 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
8292 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
8294 "This package is designed to conduct transcriptome analysis for tiling
8295 arrays based on fast wavelet-based functional models.")
8296 (license license:gpl2+)))
8298 (define-public r-variancepartition
8300 (name "r-variancepartition")
8305 (uri (bioconductor-uri "variancePartition" version))
8308 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
8310 `((upstream-name . "variancePartition")))
8311 (build-system r-build-system)
8313 `(("r-biobase" ,r-biobase)
8314 ("r-biocparallel" ,r-biocparallel)
8315 ("r-colorramps" ,r-colorramps)
8316 ("r-doparallel" ,r-doparallel)
8317 ("r-foreach" ,r-foreach)
8318 ("r-ggplot2" ,r-ggplot2)
8319 ("r-gplots" ,r-gplots)
8320 ("r-iterators" ,r-iterators)
8321 ("r-limma" ,r-limma)
8323 ("r-lmertest" ,r-lmertest)
8325 ("r-pbkrtest" ,r-pbkrtest)
8326 ("r-progress" ,r-progress)
8327 ("r-reshape2" ,r-reshape2)
8328 ("r-scales" ,r-scales)))
8330 `(("r-knitr" ,r-knitr)))
8331 (home-page "https://bioconductor.org/packages/variancePartition/")
8332 (synopsis "Analyze variation in gene expression experiments")
8334 "This is a package providing tools to quantify and interpret multiple
8335 sources of biological and technical variation in gene expression experiments.
8336 It uses a linear mixed model to quantify variation in gene expression
8337 attributable to individual, tissue, time point, or technical variables. The
8338 package includes dream differential expression analysis for repeated
8340 (license license:gpl2+)))
8342 (define-public r-htqpcr
8349 (uri (bioconductor-uri "HTqPCR" version))
8352 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
8353 (properties `((upstream-name . "HTqPCR")))
8354 (build-system r-build-system)
8356 `(("r-affy" ,r-affy)
8357 ("r-biobase" ,r-biobase)
8358 ("r-gplots" ,r-gplots)
8359 ("r-limma" ,r-limma)
8360 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8361 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
8362 "groups/bertone/software/HTqPCR.pdf"))
8363 (synopsis "Automated analysis of high-throughput qPCR data")
8365 "Analysis of Ct values from high throughput quantitative real-time
8366 PCR (qPCR) assays across multiple conditions or replicates. The input data
8367 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
8368 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
8369 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
8370 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
8371 loading, quality assessment, normalization, visualization and parametric or
8372 non-parametric testing for statistical significance in Ct values between
8373 features (e.g. genes, microRNAs).")
8374 (license license:artistic2.0)))
8376 (define-public r-unifiedwmwqpcr
8378 (name "r-unifiedwmwqpcr")
8383 (uri (bioconductor-uri "unifiedWMWqPCR" version))
8386 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
8388 `((upstream-name . "unifiedWMWqPCR")))
8389 (build-system r-build-system)
8391 `(("r-biocgenerics" ,r-biocgenerics)
8392 ("r-htqpcr" ,r-htqpcr)))
8393 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
8394 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
8396 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
8397 data. This modified test allows for testing differential expression in qPCR
8399 (license license:gpl2+)))
8401 (define-public r-universalmotif
8403 (name "r-universalmotif")
8408 (uri (bioconductor-uri "universalmotif" version))
8411 "0pmi5mp5v0srr482vlkfmkp28bywq969fvv9g5kjl5rxki963zmr"))))
8413 `((upstream-name . "universalmotif")))
8414 (build-system r-build-system)
8417 (modify-phases %standard-phases
8418 (add-after 'unpack 'fix-reference-to-strip
8420 (substitute* "src/Makevars"
8421 (("/usr/bin/strip") (which "strip"))))))))
8423 `(("r-biocgenerics" ,r-biocgenerics)
8424 ("r-biostrings" ,r-biostrings)
8425 ("r-ggplot2" ,r-ggplot2)
8426 ("r-ggseqlogo" ,r-ggseqlogo)
8427 ("r-iranges" ,r-iranges)
8430 ("r-rcppthread" ,r-rcppthread)
8431 ("r-rdpack" ,r-rdpack)
8432 ("r-rlang" ,r-rlang)
8433 ("r-s4vectors" ,r-s4vectors)
8434 ("r-yaml" ,r-yaml)))
8436 `(("r-knitr" ,r-knitr)))
8438 "https://bioconductor.org/packages/universalmotif/")
8440 "Specific structures importer, modifier, and exporter for R")
8442 "This package allows importing most common @dfn{specific structure}
8443 (motif) types into R for use by functions provided by other Bioconductor
8444 motif-related packages. Motifs can be exported into most major motif formats
8445 from various classes as defined by other Bioconductor packages. A suite of
8446 motif and sequence manipulation and analysis functions are included, including
8447 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
8448 motifs, and others.")
8449 (license license:gpl3)))
8451 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
8453 (define-public r-activedriverwgs
8455 (name "r-activedriverwgs")
8460 (uri (cran-uri "ActiveDriverWGS" version))
8463 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
8465 `((upstream-name . "ActiveDriverWGS")))
8466 (build-system r-build-system)
8468 `(("r-biostrings" ,r-biostrings)
8469 ("r-bsgenome" ,r-bsgenome)
8470 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8471 ("r-genomeinfodb" ,r-genomeinfodb)
8472 ("r-genomicranges" ,r-genomicranges)
8473 ("r-iranges" ,r-iranges)
8474 ("r-s4vectors" ,r-s4vectors)))
8476 `(("r-knitr" ,r-knitr)))
8477 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
8478 (synopsis "Driver discovery tool for cancer whole genomes")
8480 "This package provides a method for finding an enrichment of cancer
8481 simple somatic mutations (SNVs and Indels) in functional elements across the
8482 human genome. ActiveDriverWGS detects coding and noncoding driver elements
8483 using whole genome sequencing data.")
8484 (license license:gpl3)))
8486 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
8488 (define-public r-activepathways
8490 (name "r-activepathways")
8495 (uri (cran-uri "ActivePathways" version))
8498 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
8500 `((upstream-name . "ActivePathways")))
8501 (build-system r-build-system)
8503 `(("r-data-table" ,r-data-table)
8504 ("r-ggplot2" ,r-ggplot2)))
8506 `(("r-knitr" ,r-knitr)))
8507 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
8508 (synopsis "Multivariate pathway enrichment analysis")
8510 "This package represents an integrative method of analyzing multi omics
8511 data that conducts enrichment analysis of annotated gene sets. ActivePathways
8512 uses a statistical data fusion approach, rationalizes contributing evidence
8513 and highlights associated genes, improving systems-level understanding of
8514 cellular organization in health and disease.")
8515 (license license:gpl3)))
8517 (define-public r-bgmix
8524 (uri (bioconductor-uri "BGmix" version))
8527 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
8528 (properties `((upstream-name . "BGmix")))
8529 (build-system r-build-system)
8531 `(("r-kernsmooth" ,r-kernsmooth)))
8532 (home-page "https://bioconductor.org/packages/BGmix/")
8533 (synopsis "Bayesian models for differential gene expression")
8535 "This package provides fully Bayesian mixture models for differential
8537 (license license:gpl2)))
8539 (define-public r-bgx
8546 (uri (bioconductor-uri "bgx" version))
8549 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
8550 (properties `((upstream-name . "bgx")))
8551 (build-system r-build-system)
8553 `(("r-affy" ,r-affy)
8554 ("r-biobase" ,r-biobase)
8555 ("r-gcrma" ,r-gcrma)
8556 ("r-rcpp" ,r-rcpp)))
8557 (home-page "https://bioconductor.org/packages/bgx/")
8558 (synopsis "Bayesian gene expression")
8560 "This package provides tools for Bayesian integrated analysis of
8561 Affymetrix GeneChips.")
8562 (license license:gpl2)))
8564 (define-public r-bhc
8571 (uri (bioconductor-uri "BHC" version))
8574 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
8575 (properties `((upstream-name . "BHC")))
8576 (build-system r-build-system)
8577 (home-page "https://bioconductor.org/packages/BHC/")
8578 (synopsis "Bayesian hierarchical clustering")
8580 "The method implemented in this package performs bottom-up hierarchical
8581 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
8582 in the data and Bayesian model selection to decide at each step which clusters
8583 to merge. This avoids several limitations of traditional methods, for example
8584 how many clusters there should be and how to choose a principled distance
8585 metric. This implementation accepts multinomial (i.e. discrete, with 2+
8586 categories) or time-series data. This version also includes a randomised
8587 algorithm which is more efficient for larger data sets.")
8588 (license license:gpl3)))
8590 (define-public r-bicare
8597 (uri (bioconductor-uri "BicARE" version))
8600 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
8601 (properties `((upstream-name . "BicARE")))
8602 (build-system r-build-system)
8604 `(("r-biobase" ,r-biobase)
8605 ("r-gseabase" ,r-gseabase)
8606 ("r-multtest" ,r-multtest)))
8607 (home-page "http://bioinfo.curie.fr")
8608 (synopsis "Biclustering analysis and results exploration")
8610 "This is a package for biclustering analysis and exploration of
8612 (license license:gpl2)))
8614 (define-public r-bifet
8621 (uri (bioconductor-uri "BiFET" version))
8624 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
8625 (properties `((upstream-name . "BiFET")))
8626 (build-system r-build-system)
8628 `(("r-genomicranges" ,r-genomicranges)
8629 ("r-poibin" ,r-poibin)))
8631 `(("r-knitr" ,r-knitr)))
8632 (home-page "https://bioconductor.org/packages/BiFET")
8633 (synopsis "Bias-free footprint enrichment test")
8635 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
8636 over-represented in target regions compared to background regions after
8637 correcting for the bias arising from the imbalance in read counts and GC
8638 contents between the target and background regions. For a given TF k, BiFET
8639 tests the null hypothesis that the target regions have the same probability of
8640 having footprints for the TF k as the background regions while correcting for
8641 the read count and GC content bias.")
8642 (license license:gpl3)))
8644 (define-public r-rsbml
8651 (uri (bioconductor-uri "rsbml" version))
8654 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
8655 (properties `((upstream-name . "rsbml")))
8656 (build-system r-build-system)
8658 `(("libsbml" ,libsbml)
8661 `(("r-biocgenerics" ,r-biocgenerics)
8662 ("r-graph" ,r-graph)))
8664 `(("pkg-config" ,pkg-config)))
8665 (home-page "http://www.sbml.org")
8666 (synopsis "R support for SBML")
8668 "This package provides an R interface to libsbml for SBML parsing,
8669 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
8670 (license license:artistic2.0)))
8672 (define-public r-hypergraph
8674 (name "r-hypergraph")
8679 (uri (bioconductor-uri "hypergraph" version))
8682 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
8683 (properties `((upstream-name . "hypergraph")))
8684 (build-system r-build-system)
8686 `(("r-graph" ,r-graph)))
8687 (home-page "https://bioconductor.org/packages/hypergraph")
8688 (synopsis "Hypergraph data structures")
8690 "This package implements some simple capabilities for representing and
8691 manipulating hypergraphs.")
8692 (license license:artistic2.0)))
8694 (define-public r-hyperdraw
8696 (name "r-hyperdraw")
8701 (uri (bioconductor-uri "hyperdraw" version))
8704 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
8705 (properties `((upstream-name . "hyperdraw")))
8706 (build-system r-build-system)
8707 (inputs `(("graphviz" ,graphviz)))
8709 `(("r-graph" ,r-graph)
8710 ("r-hypergraph" ,r-hypergraph)
8711 ("r-rgraphviz" ,r-rgraphviz)))
8712 (home-page "https://bioconductor.org/packages/hyperdraw")
8713 (synopsis "Visualizing hypergraphs")
8715 "This package provides functions for visualizing hypergraphs.")
8716 (license license:gpl2+)))
8718 (define-public r-biggr
8725 (uri (bioconductor-uri "BiGGR" version))
8728 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
8729 (properties `((upstream-name . "BiGGR")))
8730 (build-system r-build-system)
8732 `(("r-hyperdraw" ,r-hyperdraw)
8733 ("r-hypergraph" ,r-hypergraph)
8735 ("r-limsolve" ,r-limsolve)
8736 ("r-rsbml" ,r-rsbml)
8737 ("r-stringr" ,r-stringr)))
8738 (home-page "https://bioconductor.org/packages/BiGGR/")
8739 (synopsis "Constraint based modeling using metabolic reconstruction databases")
8741 "This package provides an interface to simulate metabolic reconstruction
8742 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
8743 reconstruction databases. The package facilitates @dfn{flux balance
8744 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
8745 networks and estimated fluxes can be visualized with hypergraphs.")
8746 (license license:gpl3+)))
8748 (define-public r-bigmemoryextras
8750 (name "r-bigmemoryextras")
8755 (uri (bioconductor-uri "bigmemoryExtras" version))
8758 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
8760 `((upstream-name . "bigmemoryExtras")))
8761 (build-system r-build-system)
8763 `(("r-bigmemory" ,r-bigmemory)))
8765 `(("r-knitr" ,r-knitr)))
8766 (home-page "https://github.com/phaverty/bigmemoryExtras")
8767 (synopsis "Extension of the bigmemory package")
8769 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
8770 safety and convenience features to the @code{filebacked.big.matrix} class from
8771 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
8772 monitoring and gracefully restoring the connection to on-disk data and it also
8773 protects against accidental data modification with a file-system-based
8774 permissions system. Utilities are provided for using @code{BigMatrix}-derived
8775 classes as @code{assayData} matrices within the @code{Biobase} package's
8776 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
8777 related to attaching to, and indexing into, file-backed matrices with
8778 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
8779 a file-backed matrix with factor properties.")
8780 (license license:artistic2.0)))
8782 (define-public r-bigpint
8789 (uri (bioconductor-uri "bigPint" version))
8792 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
8793 (properties `((upstream-name . "bigPint")))
8794 (build-system r-build-system)
8796 `(("r-delayedarray" ,r-delayedarray)
8797 ("r-dplyr" ,r-dplyr)
8798 ("r-ggally" ,r-ggally)
8799 ("r-ggplot2" ,r-ggplot2)
8800 ("r-gridextra" ,r-gridextra)
8801 ("r-hexbin" ,r-hexbin)
8802 ("r-hmisc" ,r-hmisc)
8803 ("r-htmlwidgets" ,r-htmlwidgets)
8804 ("r-plotly" ,r-plotly)
8806 ("r-rcolorbrewer" ,r-rcolorbrewer)
8807 ("r-reshape" ,r-reshape)
8808 ("r-shiny" ,r-shiny)
8809 ("r-shinycssloaders" ,r-shinycssloaders)
8810 ("r-shinydashboard" ,r-shinydashboard)
8811 ("r-stringr" ,r-stringr)
8812 ("r-summarizedexperiment" ,r-summarizedexperiment)
8813 ("r-tidyr" ,r-tidyr)))
8815 `(("r-knitr" ,r-knitr)))
8816 (home-page "https://github.com/lindsayrutter/bigPint")
8817 (synopsis "Big multivariate data plotted interactively")
8819 "This package provides methods for visualizing large multivariate
8820 datasets using static and interactive scatterplot matrices, parallel
8821 coordinate plots, volcano plots, and litre plots. It includes examples for
8822 visualizing RNA-sequencing datasets and differentially expressed genes.")
8823 (license license:gpl3)))
8825 (define-public r-chemminer
8827 (name "r-chemminer")
8832 (uri (bioconductor-uri "ChemmineR" version))
8835 "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
8836 (properties `((upstream-name . "ChemmineR")))
8837 (build-system r-build-system)
8839 `(("r-base64enc" ,r-base64enc)
8841 ("r-biocgenerics" ,r-biocgenerics)
8843 ("r-digest" ,r-digest)
8845 ("r-ggplot2" ,r-ggplot2)
8846 ("r-gridextra" ,r-gridextra)
8849 ("r-rcurl" ,r-rcurl)
8850 ("r-rjson" ,r-rjson)
8851 ("r-rsvg" ,r-rsvg)))
8853 `(("r-knitr" ,r-knitr)))
8854 (home-page "https://github.com/girke-lab/ChemmineR")
8855 (synopsis "Cheminformatics toolkit for R")
8857 "ChemmineR is a cheminformatics package for analyzing drug-like small
8858 molecule data in R. It contains functions for efficient processing of large
8859 numbers of molecules, physicochemical/structural property predictions,
8860 structural similarity searching, classification and clustering of compound
8861 libraries with a wide spectrum of algorithms. In addition, it offers
8862 visualization functions for compound clustering results and chemical
8864 (license license:artistic2.0)))
8866 (define-public r-bioassayr
8868 (name "r-bioassayr")
8873 (uri (bioconductor-uri "bioassayR" version))
8876 "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5"))))
8877 (properties `((upstream-name . "bioassayR")))
8878 (build-system r-build-system)
8880 `(("r-biocgenerics" ,r-biocgenerics)
8881 ("r-chemminer" ,r-chemminer)
8883 ("r-matrix" ,r-matrix)
8884 ("r-rjson" ,r-rjson)
8885 ("r-rsqlite" ,r-rsqlite)
8888 `(("r-knitr" ,r-knitr)))
8889 (home-page "https://github.com/girke-lab/bioassayR")
8890 (synopsis "Cross-target analysis of small molecule bioactivity")
8892 "bioassayR is a computational tool that enables simultaneous analysis of
8893 thousands of bioassay experiments performed over a diverse set of compounds
8894 and biological targets. Unique features include support for large-scale
8895 cross-target analyses of both public and custom bioassays, generation of
8896 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
8897 preloaded database that provides access to a substantial portion of publicly
8898 available bioactivity data.")
8899 (license license:artistic2.0)))
8901 (define-public r-biobroom
8908 (uri (bioconductor-uri "biobroom" version))
8911 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
8912 (properties `((upstream-name . "biobroom")))
8913 (build-system r-build-system)
8915 `(("r-biobase" ,r-biobase)
8916 ("r-broom" ,r-broom)
8917 ("r-dplyr" ,r-dplyr)
8918 ("r-tidyr" ,r-tidyr)))
8920 `(("r-knitr" ,r-knitr)))
8921 (home-page "https://github.com/StoreyLab/biobroom")
8922 (synopsis "Turn Bioconductor objects into tidy data frames")
8924 "This package contains methods for converting standard objects
8925 constructed by bioinformatics packages, especially those in Bioconductor, and
8926 converting them to @code{tidy} data. It thus serves as a complement to the
8927 @code{broom} package, and follows the same tidy, augment, glance division of
8928 tidying methods. Tidying data makes it easy to recombine, reshape and
8929 visualize bioinformatics analyses.")
8930 ;; Any version of the LGPL.
8931 (license license:lgpl3+)))
8933 (define-public r-graphite
8940 (uri (bioconductor-uri "graphite" version))
8943 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
8944 (properties `((upstream-name . "graphite")))
8945 (build-system r-build-system)
8947 `(("r-annotationdbi" ,r-annotationdbi)
8948 ("r-checkmate" ,r-checkmate)
8949 ("r-graph" ,r-graph)
8951 ("r-rappdirs" ,r-rappdirs)))
8952 (home-page "https://bioconductor.org/packages/graphite/")
8953 (synopsis "Networks from pathway databases")
8955 "Graphite provides networks derived from eight public pathway databases,
8956 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
8958 (license license:agpl3+)))
8960 (define-public r-reactomepa
8962 (name "r-reactomepa")
8967 (uri (bioconductor-uri "ReactomePA" version))
8970 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
8971 (properties `((upstream-name . "ReactomePA")))
8972 (build-system r-build-system)
8974 `(("r-annotationdbi" ,r-annotationdbi)
8976 ("r-enrichplot" ,r-enrichplot)
8977 ("r-ggplot2" ,r-ggplot2)
8978 ("r-ggraph" ,r-ggraph)
8979 ("r-graphite" ,r-graphite)
8980 ("r-igraph" ,r-igraph)
8981 ("r-reactome-db" ,r-reactome-db)))
8983 `(("r-knitr" ,r-knitr)))
8984 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
8985 (synopsis "Reactome pathway analysis")
8987 "This package provides functions for pathway analysis based on the
8988 REACTOME pathway database. It implements enrichment analysis, gene set
8989 enrichment analysis and several functions for visualization.")
8990 (license license:gpl2)))
8992 (define-public r-ebarrays
8999 (uri (bioconductor-uri "EBarrays" version))
9002 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
9003 (properties `((upstream-name . "EBarrays")))
9004 (build-system r-build-system)
9006 `(("r-biobase" ,r-biobase)
9007 ("r-cluster" ,r-cluster)
9008 ("r-lattice" ,r-lattice)))
9009 (home-page "https://bioconductor.org/packages/EBarrays/")
9010 (synopsis "Gene clustering and differential expression identification")
9012 "EBarrays provides tools for the analysis of replicated/unreplicated
9014 (license license:gpl2+)))
9016 (define-public r-bioccasestudies
9018 (name "r-bioccasestudies")
9023 (uri (bioconductor-uri "BiocCaseStudies" version))
9026 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
9028 `((upstream-name . "BiocCaseStudies")))
9029 (build-system r-build-system)
9030 (propagated-inputs `(("r-biobase" ,r-biobase)))
9031 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
9032 (synopsis "Support for the case studies monograph")
9034 "This package provides software and data to support the case studies
9036 (license license:artistic2.0)))
9038 (define-public r-bioccheck
9040 (name "r-bioccheck")
9044 (uri (bioconductor-uri "BiocCheck" version))
9047 "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
9049 `((upstream-name . "BiocCheck")))
9050 (build-system r-build-system)
9053 (modify-phases %standard-phases
9054 ;; This package can be used by calling BiocCheck(<package>) from
9055 ;; within R, or by running R CMD BiocCheck <package>. This phase
9056 ;; makes sure the latter works. For this to work, the BiocCheck
9057 ;; script must be somewhere on the PATH (not the R bin directory).
9058 (add-after 'install 'install-bioccheck-subcommand
9059 (lambda* (#:key outputs #:allow-other-keys)
9060 (let* ((out (assoc-ref outputs "out"))
9061 (dest-dir (string-append out "/bin"))
9063 (string-append out "/site-library/BiocCheck/script/")))
9065 (symlink (string-append script-dir "/checkBadDeps.R")
9066 (string-append dest-dir "/checkBadDeps.R"))
9067 (symlink (string-append script-dir "/BiocCheck")
9068 (string-append dest-dir "/BiocCheck")))
9071 `(("r-codetools" ,r-codetools)
9072 ("r-graph" ,r-graph)
9074 ("r-knitr" ,r-knitr)
9075 ("r-optparse" ,r-optparse)
9076 ("r-biocmanager" ,r-biocmanager)
9077 ("r-biocviews" ,r-biocviews)
9078 ("r-stringdist" ,r-stringdist)))
9080 `(("r-knitr" ,r-knitr)))
9081 (home-page "https://bioconductor.org/packages/BiocCheck")
9082 (synopsis "Executes Bioconductor-specific package checks")
9083 (description "This package contains tools to perform additional quality
9084 checks on R packages that are to be submitted to the Bioconductor repository.")
9085 (license license:artistic2.0)))
9087 (define-public r-biocgraph
9089 (name "r-biocgraph")
9094 (uri (bioconductor-uri "biocGraph" version))
9097 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
9098 (properties `((upstream-name . "biocGraph")))
9099 (build-system r-build-system)
9101 `(("r-biocgenerics" ,r-biocgenerics)
9102 ("r-geneplotter" ,r-geneplotter)
9103 ("r-graph" ,r-graph)
9104 ("r-rgraphviz" ,r-rgraphviz)))
9105 (home-page "https://bioconductor.org/packages/biocGraph/")
9106 (synopsis "Graph examples and use cases in Bioinformatics")
9108 "This package provides examples and code that make use of the
9109 different graph related packages produced by Bioconductor.")
9110 (license license:artistic2.0)))
9112 (define-public r-biocstyle
9114 (name "r-biocstyle")
9118 (uri (bioconductor-uri "BiocStyle" version))
9121 "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
9123 `((upstream-name . "BiocStyle")))
9124 (build-system r-build-system)
9126 `(("r-biocmanager" ,r-biocmanager)
9127 ("r-bookdown" ,r-bookdown)
9128 ("r-knitr" ,r-knitr)
9129 ("r-rmarkdown" ,r-rmarkdown)
9130 ("r-yaml" ,r-yaml)))
9132 `(("r-knitr" ,r-knitr)))
9133 (home-page "https://bioconductor.org/packages/BiocStyle")
9134 (synopsis "Bioconductor formatting styles")
9135 (description "This package provides standard formatting styles for
9136 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
9138 (license license:artistic2.0)))
9140 (define-public r-biocviews
9142 (name "r-biocviews")
9146 (uri (bioconductor-uri "biocViews" version))
9149 "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
9151 `((upstream-name . "biocViews")))
9152 (build-system r-build-system)
9154 `(("r-biobase" ,r-biobase)
9155 ("r-biocmanager" ,r-biocmanager)
9156 ("r-graph" ,r-graph)
9158 ("r-rcurl" ,r-rcurl)
9160 ("r-runit" ,r-runit)))
9161 (home-page "https://bioconductor.org/packages/biocViews")
9162 (synopsis "Bioconductor package categorization helper")
9163 (description "The purpose of biocViews is to create HTML pages that
9164 categorize packages in a Bioconductor package repository according to keywords,
9165 also known as views, in a controlled vocabulary.")
9166 (license license:artistic2.0)))
9168 (define-public r-experimenthub
9170 (name "r-experimenthub")
9175 (uri (bioconductor-uri "ExperimentHub" version))
9178 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
9179 (properties `((upstream-name . "ExperimentHub")))
9180 (build-system r-build-system)
9182 `(("r-annotationhub" ,r-annotationhub)
9183 ("r-biocfilecache" ,r-biocfilecache)
9184 ("r-biocgenerics" ,r-biocgenerics)
9185 ("r-biocmanager" ,r-biocmanager)
9187 ("r-rappdirs" ,r-rappdirs)
9188 ("r-s4vectors" ,r-s4vectors)))
9190 `(("r-knitr" ,r-knitr)))
9191 (home-page "https://bioconductor.org/packages/ExperimentHub/")
9192 (synopsis "Client to access ExperimentHub resources")
9194 "This package provides a client for the Bioconductor ExperimentHub web
9195 resource. ExperimentHub provides a central location where curated data from
9196 experiments, publications or training courses can be accessed. Each resource
9197 has associated metadata, tags and date of modification. The client creates
9198 and manages a local cache of files retrieved enabling quick and reproducible
9200 (license license:artistic2.0)))
9202 (define-public r-grohmm
9209 (uri (bioconductor-uri "groHMM" version))
9212 "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
9213 (properties `((upstream-name . "groHMM")))
9214 (build-system r-build-system)
9216 `(("r-genomeinfodb" ,r-genomeinfodb)
9217 ("r-genomicalignments" ,r-genomicalignments)
9218 ("r-genomicranges" ,r-genomicranges)
9219 ("r-iranges" ,r-iranges)
9221 ("r-rtracklayer" ,r-rtracklayer)
9222 ("r-s4vectors" ,r-s4vectors)))
9223 (home-page "https://github.com/Kraus-Lab/groHMM")
9224 (synopsis "GRO-seq analysis pipeline")
9226 "This package provides a pipeline for the analysis of GRO-seq data.")
9227 (license license:gpl3+)))
9229 (define-public r-multiassayexperiment
9231 (name "r-multiassayexperiment")
9236 (uri (bioconductor-uri "MultiAssayExperiment" version))
9239 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
9241 `((upstream-name . "MultiAssayExperiment")))
9242 (build-system r-build-system)
9244 `(("r-biobase" ,r-biobase)
9245 ("r-biocgenerics" ,r-biocgenerics)
9246 ("r-genomicranges" ,r-genomicranges)
9247 ("r-iranges" ,r-iranges)
9248 ("r-s4vectors" ,r-s4vectors)
9249 ("r-summarizedexperiment" ,r-summarizedexperiment)
9250 ("r-tidyr" ,r-tidyr)))
9252 `(("r-knitr" ,r-knitr)))
9253 (home-page "https://waldronlab.io/MultiAssayExperiment/")
9254 (synopsis "Integration of multi-omics experiments in Bioconductor")
9256 "MultiAssayExperiment harmonizes data management of multiple assays
9257 performed on an overlapping set of specimens. It provides a familiar
9258 Bioconductor user experience by extending concepts from
9259 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
9260 classes for individual assays, and allowing subsetting by genomic ranges or
9262 (license license:artistic2.0)))
9264 (define-public r-bioconcotk
9266 (name "r-bioconcotk")
9271 (uri (bioconductor-uri "BiocOncoTK" version))
9274 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
9275 (properties `((upstream-name . "BiocOncoTK")))
9276 (build-system r-build-system)
9278 `(("r-bigrquery" ,r-bigrquery)
9280 ("r-complexheatmap" ,r-complexheatmap)
9281 ("r-curatedtcgadata" ,r-curatedtcgadata)
9283 ("r-dplyr" ,r-dplyr)
9285 ("r-genomicfeatures" ,r-genomicfeatures)
9286 ("r-genomicranges" ,r-genomicranges)
9287 ("r-ggplot2" ,r-ggplot2)
9288 ("r-ggpubr" ,r-ggpubr)
9289 ("r-graph" ,r-graph)
9291 ("r-iranges" ,r-iranges)
9292 ("r-magrittr" ,r-magrittr)
9294 ("r-rgraphviz" ,r-rgraphviz)
9295 ("r-rjson" ,r-rjson)
9296 ("r-s4vectors" ,r-s4vectors)
9297 ("r-scales" ,r-scales)
9298 ("r-shiny" ,r-shiny)
9299 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9301 `(("r-knitr" ,r-knitr)))
9302 (home-page "https://bioconductor.org/packages/BiocOncoTK")
9303 (synopsis "Bioconductor components for general cancer genomics")
9305 "The purpose of this package is to provide a central interface to various
9306 tools for genome-scale analysis of cancer studies.")
9307 (license license:artistic2.0)))
9309 (define-public r-biocor
9316 (uri (bioconductor-uri "BioCor" version))
9319 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
9320 (properties `((upstream-name . "BioCor")))
9321 (build-system r-build-system)
9323 `(("r-biocparallel" ,r-biocparallel)
9324 ("r-gseabase" ,r-gseabase)
9325 ("r-matrix" ,r-matrix)))
9327 `(("r-knitr" ,r-knitr)))
9328 (home-page "https://llrs.github.io/BioCor/")
9329 (synopsis "Functional similarities")
9331 "This package provides tools to calculate functional similarities based
9332 on the pathways described on KEGG and REACTOME or in gene sets. These
9333 similarities can be calculated for pathways or gene sets, genes, or clusters
9334 and combined with other similarities. They can be used to improve networks,
9335 gene selection, testing relationships, and so on.")
9336 (license license:expat)))
9338 (define-public r-biocpkgtools
9340 (name "r-biocpkgtools")
9345 (uri (bioconductor-uri "BiocPkgTools" version))
9348 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
9349 (properties `((upstream-name . "BiocPkgTools")))
9350 (build-system r-build-system)
9352 `(("r-biocfilecache" ,r-biocfilecache)
9353 ("r-biocmanager" ,r-biocmanager)
9354 ("r-biocviews" ,r-biocviews)
9355 ("r-dplyr" ,r-dplyr)
9358 ("r-graph" ,r-graph)
9359 ("r-htmltools" ,r-htmltools)
9360 ("r-htmlwidgets" ,r-htmlwidgets)
9362 ("r-igraph" ,r-igraph)
9363 ("r-jsonlite" ,r-jsonlite)
9364 ("r-magrittr" ,r-magrittr)
9365 ("r-rappdirs" ,r-rappdirs)
9367 ("r-readr" ,r-readr)
9369 ("r-rlang" ,r-rlang)
9370 ("r-rvest" ,r-rvest)
9371 ("r-stringr" ,r-stringr)
9372 ("r-tibble" ,r-tibble)
9373 ("r-tidyr" ,r-tidyr)
9374 ("r-tidyselect" ,r-tidyselect)
9375 ("r-xml2" ,r-xml2)))
9377 `(("r-knitr" ,r-knitr)))
9378 (home-page "https://github.com/seandavi/BiocPkgTools")
9379 (synopsis "Collection of tools for learning about Bioconductor packages")
9381 "Bioconductor has a rich ecosystem of metadata around packages, usage,
9382 and build status. This package is a simple collection of functions to access
9383 that metadata from R. The goal is to expose metadata for data mining and
9384 value-added functionality such as package searching, text mining, and
9385 analytics on packages.")
9386 (license license:expat)))
9388 (define-public r-biocset
9395 (uri (bioconductor-uri "BiocSet" version))
9398 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
9399 (properties `((upstream-name . "BiocSet")))
9400 (build-system r-build-system)
9402 `(("r-annotationdbi" ,r-annotationdbi)
9403 ("r-biocio" ,r-biocio)
9404 ("r-dplyr" ,r-dplyr)
9405 ("r-keggrest" ,r-keggrest)
9406 ("r-ontologyindex" ,r-ontologyindex)
9408 ("r-rlang" ,r-rlang)
9409 ("r-s4vectors" ,r-s4vectors)
9410 ("r-tibble" ,r-tibble)
9411 ("r-tidyr" ,r-tidyr)))
9413 `(("r-knitr" ,r-knitr)))
9415 "https://bioconductor.org/packages/BiocSet")
9417 "Representing Different Biological Sets")
9419 "BiocSet displays different biological sets in a triple tibble format.
9420 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
9421 The user has the ability to activate one of these three tibbles to perform
9422 common functions from the @code{dplyr} package. Mapping functionality and
9423 accessing web references for elements/sets are also available in BiocSet.")
9424 (license license:artistic2.0)))
9426 (define-public r-biocworkflowtools
9428 (name "r-biocworkflowtools")
9433 (uri (bioconductor-uri "BiocWorkflowTools" version))
9436 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
9438 `((upstream-name . "BiocWorkflowTools")))
9439 (build-system r-build-system)
9441 `(("r-biocstyle" ,r-biocstyle)
9442 ("r-bookdown" ,r-bookdown)
9443 ("r-git2r" ,r-git2r)
9445 ("r-knitr" ,r-knitr)
9446 ("r-rmarkdown" ,r-rmarkdown)
9447 ("r-rstudioapi" ,r-rstudioapi)
9448 ("r-stringr" ,r-stringr)
9449 ("r-usethis" ,r-usethis)))
9451 `(("r-knitr" ,r-knitr)))
9452 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
9453 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
9455 "This package provides functions to ease the transition between
9456 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
9457 (license license:expat)))
9459 (define-public r-biodist
9466 (uri (bioconductor-uri "bioDist" version))
9469 "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
9470 (properties `((upstream-name . "bioDist")))
9471 (build-system r-build-system)
9473 `(("r-biobase" ,r-biobase)
9474 ("r-kernsmooth" ,r-kernsmooth)))
9475 (home-page "https://bioconductor.org/packages/bioDist/")
9476 (synopsis "Different distance measures")
9478 "This package provides a collection of software tools for calculating
9479 distance measures.")
9480 (license license:artistic2.0)))
9482 (define-public r-pcatools
9489 (uri (bioconductor-uri "PCAtools" version))
9492 "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
9493 (properties `((upstream-name . "PCAtools")))
9494 (build-system r-build-system)
9496 `(("r-beachmat" ,r-beachmat)
9498 ("r-biocparallel" ,r-biocparallel)
9499 ("r-biocsingular" ,r-biocsingular)
9500 ("r-cowplot" ,r-cowplot)
9501 ("r-delayedarray" ,r-delayedarray)
9502 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9503 ("r-dqrng" ,r-dqrng)
9504 ("r-ggplot2" ,r-ggplot2)
9505 ("r-ggrepel" ,r-ggrepel)
9506 ("r-lattice" ,r-lattice)
9507 ("r-matrix" ,r-matrix)
9509 ("r-reshape2" ,r-reshape2)))
9510 (native-inputs `(("r-knitr" ,r-knitr)))
9511 (home-page "https://github.com/kevinblighe/PCAtools")
9512 (synopsis "PCAtools: everything Principal Components Analysis")
9514 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
9515 structure of the data without the need to build any model to represent it.
9516 This \"summary\" of the data is arrived at through a process of reduction that
9517 can transform the large number of variables into a lesser number that are
9518 uncorrelated (i.e. the 'principal components'), while at the same time being
9519 capable of easy interpretation on the original data. PCAtools provides
9520 functions for data exploration via PCA, and allows the user to generate
9521 publication-ready figures. PCA is performed via @code{BiocSingular}; users
9522 can also identify an optimal number of principal components via different
9523 metrics, such as the elbow method and Horn's parallel analysis, which has
9524 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
9525 dimensional mass cytometry data.")
9526 (license license:gpl3)))
9528 (define-public r-rgreat
9535 (uri (bioconductor-uri "rGREAT" version))
9538 "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
9539 (properties `((upstream-name . "rGREAT")))
9540 (build-system r-build-system)
9542 `(("r-genomicranges" ,r-genomicranges)
9543 ("r-getoptlong" ,r-getoptlong)
9544 ("r-iranges" ,r-iranges)
9545 ("r-rcurl" ,r-rcurl)
9546 ("r-rjson" ,r-rjson)))
9547 (native-inputs `(("r-knitr" ,r-knitr)))
9548 (home-page "https://github.com/jokergoo/rGREAT")
9549 (synopsis "Client for GREAT analysis")
9551 "This package makes GREAT (Genomic Regions Enrichment of Annotations
9552 Tool) analysis automatic by constructing a HTTP POST request according to
9553 user's input and automatically retrieving results from GREAT web server.")
9554 (license license:expat)))
9556 (define-public r-m3c
9563 (uri (bioconductor-uri "M3C" version))
9566 "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
9567 (properties `((upstream-name . "M3C")))
9568 (build-system r-build-system)
9570 `(("r-cluster" ,r-cluster)
9571 ("r-corpcor" ,r-corpcor)
9572 ("r-doparallel" ,r-doparallel)
9573 ("r-dosnow" ,r-dosnow)
9574 ("r-foreach" ,r-foreach)
9575 ("r-ggplot2" ,r-ggplot2)
9576 ("r-matrix" ,r-matrix)
9577 ("r-matrixcalc" ,r-matrixcalc)
9578 ("r-rtsne" ,r-rtsne)
9579 ("r-umap" ,r-umap)))
9580 (native-inputs `(("r-knitr" ,r-knitr)))
9581 (home-page "https://bioconductor.org/packages/M3C")
9582 (synopsis "Monte Carlo reference-based consensus clustering")
9584 "M3C is a consensus clustering algorithm that uses a Monte Carlo
9585 simulation to eliminate overestimation of @code{K} and can reject the null
9586 hypothesis @code{K=1}.")
9587 (license license:agpl3+)))
9589 (define-public r-icens
9596 (uri (bioconductor-uri "Icens" version))
9599 "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
9600 (properties `((upstream-name . "Icens")))
9601 (build-system r-build-system)
9603 `(("r-survival" ,r-survival)))
9604 (home-page "https://bioconductor.org/packages/Icens")
9605 (synopsis "NPMLE for censored and truncated data")
9607 "This package provides many functions for computing the
9608 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
9610 (license license:artistic2.0)))
9612 ;; This is a CRAN package but it depends on r-icens, which is published on
9614 (define-public r-interval
9621 (uri (cran-uri "interval" version))
9624 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
9625 (properties `((upstream-name . "interval")))
9626 (build-system r-build-system)
9628 `(("r-icens" ,r-icens)
9629 ("r-mlecens" ,r-mlecens)
9631 ("r-survival" ,r-survival)))
9632 (home-page "https://cran.r-project.org/web/packages/interval/")
9633 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
9635 "This package provides functions to fit nonparametric survival curves,
9636 plot them, and perform logrank or Wilcoxon type tests.")
9637 (license license:gpl2+)))
9639 ;; This is a CRAN package, but it depends on r-interval, which depends on a
9640 ;; Bioconductor package.
9641 (define-public r-fhtest
9648 (uri (cran-uri "FHtest" version))
9651 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
9652 (properties `((upstream-name . "FHtest")))
9653 (build-system r-build-system)
9655 `(("r-interval" ,r-interval)
9656 ("r-kmsurv" ,r-kmsurv)
9659 ("r-survival" ,r-survival)))
9660 (home-page "https://cran.r-project.org/web/packages/FHtest/")
9661 (synopsis "Tests for survival data based on the Fleming-Harrington class")
9663 "This package provides functions to compare two or more survival curves
9667 @item The Fleming-Harrington test for right-censored data based on
9668 permutations and on counting processes.
9669 @item An extension of the Fleming-Harrington test for interval-censored data
9670 based on a permutation distribution and on a score vector distribution.
9673 (license license:gpl2+)))
9675 (define-public r-fourcseq
9682 (uri (bioconductor-uri "FourCSeq" version))
9684 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
9685 (properties `((upstream-name . "FourCSeq")))
9686 (build-system r-build-system)
9688 `(("r-biobase" ,r-biobase)
9689 ("r-biostrings" ,r-biostrings)
9690 ("r-deseq2" ,r-deseq2)
9692 ("r-genomicalignments" ,r-genomicalignments)
9693 ("r-genomicranges" ,r-genomicranges)
9694 ("r-ggbio" ,r-ggbio)
9695 ("r-ggplot2" ,r-ggplot2)
9696 ("r-gtools" ,r-gtools)
9698 ("r-matrix" ,r-matrix)
9699 ("r-reshape2" ,r-reshape2)
9700 ("r-rsamtools" ,r-rsamtools)
9701 ("r-rtracklayer" ,r-rtracklayer)
9702 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9704 `(("r-knitr" ,r-knitr)))
9706 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
9707 (synopsis "Analysis of multiplexed 4C sequencing data")
9709 "This package is an R package dedicated to the analysis of (multiplexed)
9710 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
9711 interactions between DNA elements and identify differential interactions
9712 between conditions. The statistical analysis in R starts with individual bam
9713 files for each sample as inputs. To obtain these files, the package contains
9714 a Python script to demultiplex libraries and trim off primer sequences. With
9715 a standard alignment software the required bam files can be then be
9717 (license license:gpl3+)))
9719 (define-public r-preprocesscore
9721 (name "r-preprocesscore")
9726 (uri (bioconductor-uri "preprocessCore" version))
9729 "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
9731 `((upstream-name . "preprocessCore")))
9732 (build-system r-build-system)
9733 (home-page "https://github.com/bmbolstad/preprocessCore")
9734 (synopsis "Collection of pre-processing functions")
9736 "This package provides a library of core pre-processing and normalization
9738 (license license:lgpl2.0+)))
9740 (define-public r-s4vectors
9742 (name "r-s4vectors")
9746 (uri (bioconductor-uri "S4Vectors" version))
9749 "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh"))))
9751 `((upstream-name . "S4Vectors")))
9752 (build-system r-build-system)
9754 `(("r-biocgenerics" ,r-biocgenerics)))
9755 (home-page "https://bioconductor.org/packages/S4Vectors")
9756 (synopsis "S4 implementation of vectors and lists")
9758 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
9759 classes and a set of generic functions that extend the semantic of ordinary
9760 vectors and lists in R. Package developers can easily implement vector-like
9761 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
9762 In addition, a few low-level concrete subclasses of general interest (e.g.
9763 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
9764 S4Vectors package itself.")
9765 (license license:artistic2.0)))
9767 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
9768 ;; Bioconductor package.
9769 (define-public r-wgcna
9776 (uri (cran-uri "WGCNA" version))
9779 "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
9780 (properties `((upstream-name . "WGCNA")))
9781 (build-system r-build-system)
9783 `(("r-annotationdbi" ,r-annotationdbi)
9784 ("r-doparallel" ,r-doparallel)
9785 ("r-dynamictreecut" ,r-dynamictreecut)
9786 ("r-fastcluster" ,r-fastcluster)
9787 ("r-foreach" ,r-foreach)
9788 ("r-go-db" ,r-go-db)
9789 ("r-hmisc" ,r-hmisc)
9790 ("r-impute" ,r-impute)
9792 ("r-survival" ,r-survival)
9793 ("r-matrixstats" ,r-matrixstats)
9794 ("r-preprocesscore" ,r-preprocesscore)))
9796 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
9797 (synopsis "Weighted correlation network analysis")
9799 "This package provides functions necessary to perform Weighted
9800 Correlation Network Analysis on high-dimensional data. It includes functions
9801 for rudimentary data cleaning, construction and summarization of correlation
9802 networks, module identification and functions for relating both variables and
9803 modules to sample traits. It also includes a number of utility functions for
9804 data manipulation and visualization.")
9805 (license license:gpl2+)))
9807 (define-public r-rgraphviz
9809 (name "r-rgraphviz")
9814 (uri (bioconductor-uri "Rgraphviz" version))
9817 "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
9818 (properties `((upstream-name . "Rgraphviz")))
9819 (build-system r-build-system)
9822 (modify-phases %standard-phases
9823 (add-after 'unpack 'make-reproducible
9825 ;; The replacement value is taken from src/graphviz/builddate.h
9826 (substitute* "src/graphviz/configure"
9827 (("VERSION_DATE=.*")
9828 "VERSION_DATE=20200427.2341\n"))
9830 ;; FIXME: Rgraphviz bundles the sources of an older variant of
9831 ;; graphviz. It does not build with the latest version of graphviz, so
9832 ;; we do not add graphviz to the inputs.
9833 (inputs `(("zlib" ,zlib)))
9835 `(("r-graph" ,r-graph)))
9837 `(("pkg-config" ,pkg-config)))
9838 (home-page "https://bioconductor.org/packages/Rgraphviz")
9839 (synopsis "Plotting capabilities for R graph objects")
9841 "This package interfaces R with the graphviz library for plotting R graph
9842 objects from the @code{graph} package.")
9843 (license license:epl1.0)))
9845 (define-public r-fithic
9851 (uri (bioconductor-uri "FitHiC" version))
9854 "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
9855 (properties `((upstream-name . "FitHiC")))
9856 (build-system r-build-system)
9858 `(("r-data-table" ,r-data-table)
9859 ("r-fdrtool" ,r-fdrtool)
9860 ("r-rcpp" ,r-rcpp)))
9862 `(("r-knitr" ,r-knitr)))
9863 (home-page "https://bioconductor.org/packages/FitHiC")
9864 (synopsis "Confidence estimation for intra-chromosomal contact maps")
9866 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
9867 intra-chromosomal contact maps produced by genome-wide genome architecture
9868 assays such as Hi-C.")
9869 (license license:gpl2+)))
9871 (define-public r-hitc
9877 (uri (bioconductor-uri "HiTC" version))
9880 "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
9881 (properties `((upstream-name . "HiTC")))
9882 (build-system r-build-system)
9884 `(("r-biostrings" ,r-biostrings)
9885 ("r-genomeinfodb" ,r-genomeinfodb)
9886 ("r-genomicranges" ,r-genomicranges)
9887 ("r-iranges" ,r-iranges)
9888 ("r-matrix" ,r-matrix)
9889 ("r-rcolorbrewer" ,r-rcolorbrewer)
9890 ("r-rtracklayer" ,r-rtracklayer)))
9891 (home-page "https://bioconductor.org/packages/HiTC")
9892 (synopsis "High throughput chromosome conformation capture analysis")
9894 "The HiTC package was developed to explore high-throughput \"C\" data
9895 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
9896 quality controls, normalization, visualization, and further analysis are also
9898 (license license:artistic2.0)))
9900 (define-public r-hdf5array
9902 (name "r-hdf5array")
9907 (uri (bioconductor-uri "HDF5Array" version))
9910 "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
9911 (properties `((upstream-name . "HDF5Array")))
9912 (build-system r-build-system)
9915 (modify-phases %standard-phases
9916 (add-after 'unpack 'fix-linking
9918 (substitute* "src/Makevars"
9919 ;; This is to avoid having a plain directory on the list of
9920 ;; libraries to link.
9921 (("\\(RHDF5LIB_LIBS\\)" match)
9922 (string-append match "/libhdf5.a")))
9927 `(("r-biocgenerics" ,r-biocgenerics)
9928 ("r-delayedarray" ,r-delayedarray)
9929 ("r-iranges" ,r-iranges)
9930 ("r-matrix" ,r-matrix)
9931 ("r-rhdf5" ,r-rhdf5)
9932 ("r-rhdf5lib" ,r-rhdf5lib)
9933 ("r-s4vectors" ,r-s4vectors)))
9934 (home-page "https://bioconductor.org/packages/HDF5Array")
9935 (synopsis "HDF5 back end for DelayedArray objects")
9936 (description "This package provides an array-like container for convenient
9937 access and manipulation of HDF5 datasets. It supports delayed operations and
9939 (license license:artistic2.0)))
9941 (define-public r-rhdf5lib
9948 (uri (bioconductor-uri "Rhdf5lib" version))
9951 "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
9952 (modules '((guix build utils)))
9955 ;; Delete bundled binaries
9956 (delete-file-recursively "src/wininclude/")
9957 (delete-file-recursively "src/winlib-4.9.3/")
9958 (delete-file-recursively "src/winlib-8.3.0/")
9959 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
9961 (properties `((upstream-name . "Rhdf5lib")))
9962 (build-system r-build-system)
9965 (modify-phases %standard-phases
9966 (add-after 'unpack 'do-not-use-bundled-hdf5
9967 (lambda* (#:key inputs #:allow-other-keys)
9968 (for-each delete-file '("configure" "configure.ac"))
9969 ;; Do not make other packages link with the proprietary libsz.
9970 (substitute* "R/zzz.R"
9971 ((" \"%s/libsz.a\"") ""))
9972 (with-directory-excursion "src"
9973 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
9974 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
9976 ;; Remove timestamp and host system information to make
9977 ;; the build reproducible.
9978 (substitute* "hdf5/src/libhdf5.settings.in"
9979 (("Configured on: @CONFIG_DATE@")
9980 "Configured on: Guix")
9981 (("Uname information:.*")
9982 "Uname information: Linux\n")
9983 ;; Remove unnecessary store reference.
9985 "C Compiler: GCC\n"))
9986 (rename-file "hdf5/src/libhdf5.settings.in"
9987 "hdf5/src/libhdf5.settings")
9988 (rename-file "Makevars.in" "Makevars")
9989 (substitute* "Makevars"
9990 (("@ZLIB_LIB@") "-lz")
9991 (("@ZLIB_INCLUDE@") "")
9992 (("HDF5_CXX_LIB=.*")
9993 (string-append "HDF5_CXX_LIB="
9994 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
9996 (string-append "HDF5_LIB="
9997 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
9998 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
9999 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
10000 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
10001 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
10002 (("HDF5_HL_LIB=.*")
10003 (string-append "HDF5_HL_LIB="
10004 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
10005 (("HDF5_HL_CXX_LIB=.*")
10006 (string-append "HDF5_HL_CXX_LIB="
10007 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
10008 ;; szip is non-free software
10009 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
10010 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
10015 `(("hdf5" ,hdf5-1.10)))
10017 `(("hdf5-source" ,(package-source hdf5-1.10))
10018 ("r-knitr" ,r-knitr)))
10019 (home-page "https://bioconductor.org/packages/Rhdf5lib")
10020 (synopsis "HDF5 library as an R package")
10021 (description "This package provides C and C++ HDF5 libraries for use in R
10023 (license license:artistic2.0)))
10025 (define-public r-beachmat
10027 (name "r-beachmat")
10032 (uri (bioconductor-uri "beachmat" version))
10035 "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
10036 (build-system r-build-system)
10038 `(("r-biocgenerics" ,r-biocgenerics)
10039 ("r-delayedarray" ,r-delayedarray)
10040 ("r-matrix" ,r-matrix)))
10042 `(("r-knitr" ,r-knitr)))
10043 (home-page "https://bioconductor.org/packages/beachmat")
10044 (synopsis "Compiling Bioconductor to handle each matrix type")
10045 (description "This package provides a consistent C++ class interface for a
10046 variety of commonly used matrix types, including sparse and HDF5-backed
10048 (license license:gpl3)))
10050 ;; This package includes files that have been taken from kentutils. Some
10051 ;; parts of kentutils are not released under a free license, but this package
10052 ;; only uses files that are also found in the free parts of kentutils.
10053 (define-public r-cner
10060 (uri (bioconductor-uri "CNEr" version))
10062 (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
10063 (properties `((upstream-name . "CNEr")))
10064 (build-system r-build-system)
10065 (inputs `(("zlib" ,zlib)))
10067 `(("r-annotate" ,r-annotate)
10068 ("r-biocgenerics" ,r-biocgenerics)
10069 ("r-biostrings" ,r-biostrings)
10071 ("r-genomeinfodb" ,r-genomeinfodb)
10072 ("r-genomicalignments" ,r-genomicalignments)
10073 ("r-genomicranges" ,r-genomicranges)
10074 ("r-ggplot2" ,r-ggplot2)
10075 ("r-go-db" ,r-go-db)
10076 ("r-iranges" ,r-iranges)
10077 ("r-keggrest" ,r-keggrest)
10078 ("r-powerlaw" ,r-powerlaw)
10079 ("r-r-utils" ,r-r-utils)
10080 ("r-readr" ,r-readr)
10081 ("r-reshape2" ,r-reshape2)
10082 ("r-rsqlite" ,r-rsqlite)
10083 ("r-rtracklayer" ,r-rtracklayer)
10084 ("r-s4vectors" ,r-s4vectors)
10085 ("r-xvector" ,r-xvector)))
10087 `(("r-knitr" ,r-knitr)))
10088 (home-page "https://github.com/ge11232002/CNEr")
10089 (synopsis "CNE Detection and Visualization")
10091 "This package provides tools for large-scale identification and
10092 advanced visualization of sets of conserved noncoding elements.")
10093 ;; For all files in src/ucsc "license is hereby granted for all use -
10094 ;; public, private or commercial"; this includes those files that don't
10095 ;; have a license header, because they are included in the free parts of
10096 ;; the kentutils package.
10097 (license (list license:gpl2
10098 (license:non-copyleft
10099 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
10101 (define-public r-tfbstools
10103 (name "r-tfbstools")
10108 (uri (bioconductor-uri "TFBSTools" version))
10111 "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
10112 (properties `((upstream-name . "TFBSTools")))
10113 (build-system r-build-system)
10115 `(("r-biobase" ,r-biobase)
10116 ("r-biocgenerics" ,r-biocgenerics)
10117 ("r-biocparallel" ,r-biocparallel)
10118 ("r-biostrings" ,r-biostrings)
10119 ("r-bsgenome" ,r-bsgenome)
10120 ("r-catools" ,r-catools)
10123 ("r-dirichletmultinomial" ,r-dirichletmultinomial)
10124 ("r-genomeinfodb" ,r-genomeinfodb)
10125 ("r-genomicranges" ,r-genomicranges)
10126 ("r-gtools" ,r-gtools)
10127 ("r-iranges" ,r-iranges)
10128 ("r-rsqlite" ,r-rsqlite)
10129 ("r-rtracklayer" ,r-rtracklayer)
10130 ("r-s4vectors" ,r-s4vectors)
10131 ("r-seqlogo" ,r-seqlogo)
10132 ("r-tfmpvalue" ,r-tfmpvalue)
10134 ("r-xvector" ,r-xvector)))
10135 (native-inputs `(("r-knitr" ,r-knitr)))
10136 (home-page "https://github.com/ge11232002/TFBSTools")
10137 (synopsis "Transcription factor binding site (TFBS) analysis")
10139 "TFBSTools is a package for the analysis and manipulation of
10140 transcription factor binding sites. It includes matrices conversion
10141 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
10142 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
10143 scan putative TFBS from sequence/alignment, query JASPAR database and
10144 provides a wrapper of de novo motif discovery software.")
10145 (license license:gpl2)))
10147 (define-public r-motifmatchr
10149 (name "r-motifmatchr")
10154 (uri (bioconductor-uri "motifmatchr" version))
10157 "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z"))))
10158 (properties `((upstream-name . "motifmatchr")))
10159 (build-system r-build-system)
10161 `(("r-biostrings" ,r-biostrings)
10162 ("r-bsgenome" ,r-bsgenome)
10163 ("r-genomeinfodb" ,r-genomeinfodb)
10164 ("r-genomicranges" ,r-genomicranges)
10165 ("r-iranges" ,r-iranges)
10166 ("r-matrix" ,r-matrix)
10168 ("r-rcpparmadillo" ,r-rcpparmadillo)
10169 ("r-rsamtools" ,r-rsamtools)
10170 ("r-s4vectors" ,r-s4vectors)
10171 ("r-summarizedexperiment" ,r-summarizedexperiment)
10172 ("r-tfbstools" ,r-tfbstools)))
10173 (native-inputs `(("r-knitr" ,r-knitr)))
10174 (home-page "https://bioconductor.org/packages/motifmatchr")
10175 (synopsis "Fast motif matching in R")
10177 "Quickly find motif matches for many motifs and many sequences.
10178 This package wraps C++ code from the MOODS motif calling library.")
10179 (license license:gpl3)))
10181 (define-public r-chromvar
10183 (name "r-chromvar")
10188 (uri (bioconductor-uri "chromVAR" version))
10190 (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819"))))
10191 (properties `((upstream-name . "chromVAR")))
10192 (build-system r-build-system)
10194 `(("r-biocgenerics" ,r-biocgenerics)
10195 ("r-biocparallel" ,r-biocparallel)
10196 ("r-biostrings" ,r-biostrings)
10197 ("r-bsgenome" ,r-bsgenome)
10199 ("r-genomeinfodb" ,r-genomeinfodb)
10200 ("r-genomicranges" ,r-genomicranges)
10201 ("r-ggplot2" ,r-ggplot2)
10202 ("r-iranges" ,r-iranges)
10203 ("r-matrix" ,r-matrix)
10204 ("r-miniui" ,r-miniui)
10205 ("r-nabor" ,r-nabor)
10206 ("r-plotly" ,r-plotly)
10207 ("r-rcolorbrewer" ,r-rcolorbrewer)
10209 ("r-rcpparmadillo" ,r-rcpparmadillo)
10210 ("r-rsamtools" ,r-rsamtools)
10211 ("r-rtsne" ,r-rtsne)
10212 ("r-s4vectors" ,r-s4vectors)
10213 ("r-shiny" ,r-shiny)
10214 ("r-summarizedexperiment" ,r-summarizedexperiment)
10215 ("r-tfbstools" ,r-tfbstools)))
10216 (native-inputs `(("r-knitr" ,r-knitr)))
10217 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
10218 (synopsis "Determine chromatin variation across regions")
10220 "This package @code{r-chromvar} determines variation in chromatin
10221 accessibility across sets of annotations or peaks. @code{r-chromvar} is
10222 designed primarily for single-cell or sparse chromatin accessibility data like
10223 single cell assay for transposase-accessible chromatin using
10224 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
10225 sequence (@code{DNAse-seq}) experiments.")
10226 (license license:expat)))
10228 (define-public r-singlecellexperiment
10230 (name "r-singlecellexperiment")
10235 (uri (bioconductor-uri "SingleCellExperiment" version))
10238 "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
10240 `((upstream-name . "SingleCellExperiment")))
10241 (build-system r-build-system)
10243 `(("r-biocgenerics" ,r-biocgenerics)
10244 ("r-s4vectors" ,r-s4vectors)
10245 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10247 `(("r-knitr" ,r-knitr)))
10248 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
10249 (synopsis "S4 classes for single cell data")
10250 (description "This package defines an S4 class for storing data from
10251 single-cell experiments. This includes specialized methods to store and
10252 retrieve spike-in information, dimensionality reduction coordinates and size
10253 factors for each cell, along with the usual metadata for genes and
10255 (license license:gpl3)))
10257 (define-public r-scuttle
10264 (uri (bioconductor-uri "scuttle" version))
10267 "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
10268 (properties `((upstream-name . "scuttle")))
10269 (build-system r-build-system)
10271 `(("r-beachmat" ,r-beachmat)
10272 ("r-biocgenerics" ,r-biocgenerics)
10273 ("r-biocparallel" ,r-biocparallel)
10274 ("r-delayedarray" ,r-delayedarray)
10275 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10276 ("r-genomicranges" ,r-genomicranges)
10277 ("r-matrix" ,r-matrix)
10279 ("r-s4vectors" ,r-s4vectors)
10280 ("r-singlecellexperiment" ,r-singlecellexperiment)
10281 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10282 (native-inputs `(("r-knitr" ,r-knitr)))
10283 (home-page "https://bioconductor.org/packages/scuttle")
10284 (synopsis "Single-cell RNA-Seq analysis utilities")
10286 "This package provides basic utility functions for performing single-cell
10287 analyses, focusing on simple normalization, quality control and data
10288 transformations. It also provides some helper functions to assist development
10289 of other packages.")
10290 (license license:gpl3)))
10292 (define-public r-scater
10298 (uri (bioconductor-uri "scater" version))
10301 "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609"))))
10302 (build-system r-build-system)
10304 `(("r-biocgenerics" ,r-biocgenerics)
10305 ("r-biocneighbors" ,r-biocneighbors)
10306 ("r-biocparallel" ,r-biocparallel)
10307 ("r-biocsingular" ,r-biocsingular)
10308 ("r-delayedarray" ,r-delayedarray)
10309 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10310 ("r-ggbeeswarm" ,r-ggbeeswarm)
10311 ("r-ggplot2" ,r-ggplot2)
10312 ("r-gridextra" ,r-gridextra)
10313 ("r-matrix" ,r-matrix)
10314 ("r-rlang" ,r-rlang)
10315 ("r-s4vectors" ,r-s4vectors)
10316 ("r-scuttle" ,r-scuttle)
10317 ("r-singlecellexperiment" ,r-singlecellexperiment)
10318 ("r-summarizedexperiment" ,r-summarizedexperiment)
10319 ("r-viridis" ,r-viridis)))
10321 `(("r-knitr" ,r-knitr)))
10322 (home-page "https://github.com/davismcc/scater")
10323 (synopsis "Single-cell analysis toolkit for gene expression data in R")
10324 (description "This package provides a collection of tools for doing
10325 various analyses of single-cell RNA-seq gene expression data, with a focus on
10327 (license license:gpl2+)))
10329 (define-public r-scran
10336 (uri (bioconductor-uri "scran" version))
10339 "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
10340 (build-system r-build-system)
10342 `(("r-beachmat" ,r-beachmat)
10344 ("r-biocgenerics" ,r-biocgenerics)
10345 ("r-biocneighbors" ,r-biocneighbors)
10346 ("r-biocparallel" ,r-biocparallel)
10347 ("r-biocsingular" ,r-biocsingular)
10348 ("r-bluster" ,r-bluster)
10349 ("r-delayedarray" ,r-delayedarray)
10350 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10351 ("r-dqrng" ,r-dqrng)
10352 ("r-edger" ,r-edger)
10353 ("r-igraph" ,r-igraph)
10354 ("r-limma" ,r-limma)
10355 ("r-matrix" ,r-matrix)
10357 ("r-s4vectors" ,r-s4vectors)
10358 ("r-scuttle" ,r-scuttle)
10359 ("r-singlecellexperiment" ,r-singlecellexperiment)
10360 ("r-statmod" ,r-statmod)
10361 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10363 `(("r-knitr" ,r-knitr)))
10364 (home-page "https://bioconductor.org/packages/scran")
10365 (synopsis "Methods for single-cell RNA-Seq data analysis")
10366 (description "This package implements a variety of low-level analyses of
10367 single-cell RNA-seq data. Methods are provided for normalization of
10368 cell-specific biases, assignment of cell cycle phase, and detection of highly
10369 variable and significantly correlated genes.")
10370 (license license:gpl3)))
10372 (define-public r-sparsematrixstats
10374 (name "r-sparsematrixstats")
10379 (uri (bioconductor-uri "sparseMatrixStats" version))
10382 "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
10384 `((upstream-name . "sparseMatrixStats")))
10385 (build-system r-build-system)
10387 `(("r-matrix" ,r-matrix)
10388 ("r-matrixgenerics" ,r-matrixgenerics)
10389 ("r-matrixstats" ,r-matrixstats)
10390 ("r-rcpp" ,r-rcpp)))
10391 (native-inputs `(("r-knitr" ,r-knitr)))
10392 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
10393 (synopsis "Summary statistics for rows and columns of sparse matrices")
10395 "This package provides high performance functions for row and column
10396 operations on sparse matrices. Currently, the optimizations are limited to
10397 data in the column sparse format.")
10398 (license license:expat)))
10400 (define-public r-delayedmatrixstats
10402 (name "r-delayedmatrixstats")
10407 (uri (bioconductor-uri "DelayedMatrixStats" version))
10410 "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
10412 `((upstream-name . "DelayedMatrixStats")))
10413 (build-system r-build-system)
10415 `(("r-biocparallel" ,r-biocparallel)
10416 ("r-delayedarray" ,r-delayedarray)
10417 ("r-hdf5array" ,r-hdf5array)
10418 ("r-iranges" ,r-iranges)
10419 ("r-matrix" ,r-matrix)
10420 ("r-matrixgenerics" ,r-matrixgenerics)
10421 ("r-matrixstats" ,r-matrixstats)
10422 ("r-s4vectors" ,r-s4vectors)
10423 ("r-sparsematrixstats" ,r-sparsematrixstats)))
10425 `(("r-knitr" ,r-knitr)))
10426 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
10427 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
10429 "This package provides a port of the @code{matrixStats} API for use with
10430 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
10431 contains high-performing functions operating on rows and columns of
10432 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
10433 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
10434 are optimized per data type and for subsetted calculations such that both
10435 memory usage and processing time is minimized.")
10436 (license license:expat)))
10438 (define-public r-mscoreutils
10440 (name "r-mscoreutils")
10445 (uri (bioconductor-uri "MsCoreUtils" version))
10448 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
10449 (properties `((upstream-name . "MsCoreUtils")))
10450 (build-system r-build-system)
10452 `(("r-mass" ,r-mass)
10454 ("r-s4vectors" ,r-s4vectors)))
10456 `(("r-knitr" ,r-knitr)))
10457 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
10458 (synopsis "Core utils for mass spectrometry data")
10460 "This package defines low-level functions for mass spectrometry data and
10461 is independent of any high-level data structures. These functions include
10462 mass spectra processing functions (noise estimation, smoothing, binning),
10463 quantitative aggregation functions (median polish, robust summarisation,
10464 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
10465 well as misc helper functions, that are used across high-level data structure
10466 within the R for Mass Spectrometry packages.")
10467 (license license:artistic2.0)))
10469 (define-public r-biocio
10476 (uri (bioconductor-uri "BiocIO" version))
10479 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
10480 (properties `((upstream-name . "BiocIO")))
10481 (build-system r-build-system)
10483 `(("r-biocgenerics" ,r-biocgenerics)
10484 ("r-genomicranges" ,r-genomicranges)
10485 ("r-rcurl" ,r-rcurl)
10486 ("r-s4vectors" ,r-s4vectors)))
10488 `(("r-knitr" ,r-knitr)))
10489 (home-page "https://bioconductor.org/packages/BiocIO")
10490 (synopsis "Standard input and output for Bioconductor packages")
10492 "This package implements `import()` and `export()` standard generics for
10493 importing and exporting biological data formats. `import()` supports
10494 whole-file as well as chunk-wise iterative import. The `import()` interface
10495 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
10496 row or element-like components of the file resource), `select()` (on
10497 column-like components of the file resource) and `collect()`. The `import()`
10498 interface optionally provides transparent access to remote (e.g. via https)
10499 as well as local access. Developers can register a file extension, e.g.,
10500 `.loom` for dispatch from character-based URIs to specific `import()` /
10501 `export()` methods based on classes representing file types, e.g.,
10503 (license license:artistic2.0)))
10505 (define-public r-msmseda
10512 (uri (bioconductor-uri "msmsEDA" version))
10515 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
10516 (properties `((upstream-name . "msmsEDA")))
10517 (build-system r-build-system)
10519 `(("r-gplots" ,r-gplots)
10521 ("r-msnbase" ,r-msnbase)
10522 ("r-rcolorbrewer" ,r-rcolorbrewer)))
10524 "https://bioconductor.org/packages/msmsEDA")
10525 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
10527 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
10528 experiments, and visualize de influence of the involved factors.")
10529 (license license:gpl2)))
10531 (define-public r-msmstests
10533 (name "r-msmstests")
10538 (uri (bioconductor-uri "msmsTests" version))
10541 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
10542 (properties `((upstream-name . "msmsTests")))
10543 (build-system r-build-system)
10545 `(("r-edger" ,r-edger)
10546 ("r-msmseda" ,r-msmseda)
10547 ("r-msnbase" ,r-msnbase)
10548 ("r-qvalue" ,r-qvalue)))
10550 "https://bioconductor.org/packages/msmsTests")
10551 (synopsis "Differential LC-MS/MS expression tests")
10553 "This package provides statistical tests for label-free LC-MS/MS data
10554 by spectral counts, to discover differentially expressed proteins between two
10555 biological conditions. Three tests are available: Poisson GLM regression,
10556 quasi-likelihood GLM regression, and the negative binomial of the edgeR
10557 package. The three models admit blocking factors to control for nuisance
10558 variables. To assure a good level of reproducibility a post-test filter is
10559 available, where we may set the minimum effect size considered biologicaly
10560 relevant, and the minimum expression of the most abundant condition.")
10561 (license license:gpl2)))
10563 (define-public r-catalyst
10565 (name "r-catalyst")
10570 (uri (bioconductor-uri "CATALYST" version))
10573 "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
10574 (properties `((upstream-name . "CATALYST")))
10575 (build-system r-build-system)
10577 `(("r-circlize" ,r-circlize)
10578 ("r-complexheatmap" ,r-complexheatmap)
10579 ("r-consensusclusterplus" ,r-consensusclusterplus)
10580 ("r-cowplot" ,r-cowplot)
10581 ("r-data-table" ,r-data-table)
10582 ("r-dplyr" ,r-dplyr)
10584 ("r-flowcore" ,r-flowcore)
10585 ("r-flowsom" ,r-flowsom)
10586 ("r-ggplot2" ,r-ggplot2)
10587 ("r-ggrepel" ,r-ggrepel)
10588 ("r-ggridges" ,r-ggridges)
10589 ("r-gridextra" ,r-gridextra)
10590 ("r-magrittr" ,r-magrittr)
10591 ("r-matrix" ,r-matrix)
10592 ("r-matrixstats" ,r-matrixstats)
10594 ("r-purrr" ,r-purrr)
10595 ("r-rcolorbrewer" ,r-rcolorbrewer)
10596 ("r-reshape2" ,r-reshape2)
10597 ("r-rtsne" ,r-rtsne)
10598 ("r-s4vectors" ,r-s4vectors)
10599 ("r-scales" ,r-scales)
10600 ("r-scater" ,r-scater)
10601 ("r-singlecellexperiment" ,r-singlecellexperiment)
10602 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10604 `(("r-knitr" ,r-knitr)))
10606 "https://github.com/HelenaLC/CATALYST")
10607 (synopsis "Cytometry data analysis tools")
10609 "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
10610 cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
10611 reporters to label antibodies, thereby substantially decreasing spectral
10612 overlap and allowing for examination of over 50 parameters at the single cell
10613 level. While spectral overlap is significantly less pronounced in CyTOF than
10614 flow cytometry, spillover due to detection sensitivity, isotopic impurities,
10615 and oxide formation can impede data interpretability. We designed
10616 CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
10617 preprocessing of cytometry data, including i) normalization using bead
10618 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
10619 (license license:gpl2+)))
10621 (define-public r-erma
10628 (uri (bioconductor-uri "erma" version))
10631 "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
10632 (build-system r-build-system)
10634 `(("r-annotationdbi" ,r-annotationdbi)
10635 ("r-biobase" ,r-biobase)
10636 ("r-biocgenerics" ,r-biocgenerics)
10637 ("r-biocparallel" ,r-biocparallel)
10638 ("r-genomeinfodb" ,r-genomeinfodb)
10639 ("r-genomicfiles" ,r-genomicfiles)
10640 ("r-genomicranges" ,r-genomicranges)
10641 ("r-ggplot2" ,r-ggplot2)
10642 ("r-homo-sapiens" ,r-homo-sapiens)
10643 ("r-iranges" ,r-iranges)
10644 ("r-rtracklayer" ,r-rtracklayer)
10645 ("r-s4vectors" ,r-s4vectors)
10646 ("r-shiny" ,r-shiny)
10647 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10649 `(("r-knitr" ,r-knitr)))
10650 (home-page "https://bioconductor.org/packages/erma")
10651 (synopsis "Epigenomic road map adventures")
10653 "The epigenomics road map describes locations of epigenetic marks in DNA
10654 from a variety of cell types. Of interest are locations of histone
10655 modifications, sites of DNA methylation, and regions of accessible chromatin.
10656 This package presents a selection of elements of the road map including
10657 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
10658 by Ernst and Kellis.")
10659 (license license:artistic2.0)))
10661 (define-public r-ggbio
10668 (uri (bioconductor-uri "ggbio" version))
10671 "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
10672 (build-system r-build-system)
10675 (modify-phases %standard-phases
10676 ;; See https://github.com/tengfei/ggbio/issues/117
10677 ;; This fix will be included in the next release.
10678 (add-after 'unpack 'fix-typo
10680 (substitute* "R/GGbio-class.R"
10681 (("fechable") "fetchable"))
10684 `(("r-annotationdbi" ,r-annotationdbi)
10685 ("r-annotationfilter" ,r-annotationfilter)
10686 ("r-biobase" ,r-biobase)
10687 ("r-biocgenerics" ,r-biocgenerics)
10688 ("r-biostrings" ,r-biostrings)
10689 ("r-biovizbase" ,r-biovizbase)
10690 ("r-bsgenome" ,r-bsgenome)
10691 ("r-ensembldb" ,r-ensembldb)
10692 ("r-genomeinfodb" ,r-genomeinfodb)
10693 ("r-genomicalignments" ,r-genomicalignments)
10694 ("r-genomicfeatures" ,r-genomicfeatures)
10695 ("r-genomicranges" ,r-genomicranges)
10696 ("r-ggally" ,r-ggally)
10697 ("r-ggplot2" ,r-ggplot2)
10698 ("r-gridextra" ,r-gridextra)
10699 ("r-gtable" ,r-gtable)
10700 ("r-hmisc" ,r-hmisc)
10701 ("r-iranges" ,r-iranges)
10702 ("r-organismdbi" ,r-organismdbi)
10703 ("r-reshape2" ,r-reshape2)
10704 ("r-rlang" ,r-rlang)
10705 ("r-rsamtools" ,r-rsamtools)
10706 ("r-rtracklayer" ,r-rtracklayer)
10707 ("r-s4vectors" ,r-s4vectors)
10708 ("r-scales" ,r-scales)
10709 ("r-summarizedexperiment" ,r-summarizedexperiment)
10710 ("r-variantannotation" ,r-variantannotation)))
10712 `(("r-knitr" ,r-knitr)))
10713 (home-page "http://www.tengfei.name/ggbio/")
10714 (synopsis "Visualization tools for genomic data")
10716 "The ggbio package extends and specializes the grammar of graphics for
10717 biological data. The graphics are designed to answer common scientific
10718 questions, in particular those often asked of high throughput genomics data.
10719 All core Bioconductor data structures are supported, where appropriate. The
10720 package supports detailed views of particular genomic regions, as well as
10721 genome-wide overviews. Supported overviews include ideograms and grand linear
10722 views. High-level plots include sequence fragment length, edge-linked
10723 interval to data view, mismatch pileup, and several splicing summaries.")
10724 (license license:artistic2.0)))
10726 (define-public r-gqtlbase
10728 (name "r-gqtlbase")
10733 (uri (bioconductor-uri "gQTLBase" version))
10736 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
10737 (properties `((upstream-name . "gQTLBase")))
10738 (build-system r-build-system)
10741 (modify-phases %standard-phases
10742 ;; This is an upstream bug.
10743 (add-after 'unpack 'fix-imports
10745 (substitute* "NAMESPACE"
10746 ((".*maxffmode.*") "")
10747 (("importFrom\\(ff,.*") "import(ff)\n"))
10750 `(("r-batchjobs" ,r-batchjobs)
10751 ("r-bbmisc" ,r-bbmisc)
10752 ("r-biocgenerics" ,r-biocgenerics)
10754 ("r-doparallel" ,r-doparallel)
10756 ("r-ffbase" ,r-ffbase)
10757 ("r-foreach" ,r-foreach)
10758 ("r-genomicfiles" ,r-genomicfiles)
10759 ("r-genomicranges" ,r-genomicranges)
10760 ("r-rtracklayer" ,r-rtracklayer)
10761 ("r-s4vectors" ,r-s4vectors)
10762 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10764 `(("r-knitr" ,r-knitr)))
10765 (home-page "https://bioconductor.org/packages/gQTLBase")
10766 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
10768 "The purpose of this package is to simplify the storage and interrogation
10769 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
10771 (license license:artistic2.0)))
10773 (define-public r-gqtlstats
10775 (name "r-gqtlstats")
10780 (uri (bioconductor-uri "gQTLstats" version))
10783 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
10784 (properties `((upstream-name . "gQTLstats")))
10785 (build-system r-build-system)
10787 `(("r-annotationdbi" ,r-annotationdbi)
10788 ("r-batchjobs" ,r-batchjobs)
10789 ("r-bbmisc" ,r-bbmisc)
10790 ("r-beeswarm" ,r-beeswarm)
10791 ("r-biobase" ,r-biobase)
10792 ("r-biocgenerics" ,r-biocgenerics)
10793 ("r-doparallel" ,r-doparallel)
10794 ("r-dplyr" ,r-dplyr)
10796 ("r-ffbase" ,r-ffbase)
10797 ("r-foreach" ,r-foreach)
10798 ("r-genomeinfodb" ,r-genomeinfodb)
10799 ("r-genomicfeatures" ,r-genomicfeatures)
10800 ("r-genomicfiles" ,r-genomicfiles)
10801 ("r-genomicranges" ,r-genomicranges)
10802 ("r-ggbeeswarm" ,r-ggbeeswarm)
10803 ("r-ggplot2" ,r-ggplot2)
10804 ("r-gqtlbase" ,r-gqtlbase)
10805 ("r-hardyweinberg" ,r-hardyweinberg)
10806 ("r-homo-sapiens" ,r-homo-sapiens)
10807 ("r-iranges" ,r-iranges)
10808 ("r-limma" ,r-limma)
10810 ("r-plotly" ,r-plotly)
10811 ("r-reshape2" ,r-reshape2)
10812 ("r-s4vectors" ,r-s4vectors)
10813 ("r-shiny" ,r-shiny)
10814 ("r-snpstats" ,r-snpstats)
10815 ("r-summarizedexperiment" ,r-summarizedexperiment)
10816 ("r-variantannotation" ,r-variantannotation)))
10818 `(("r-knitr" ,r-knitr)))
10819 (home-page "https://bioconductor.org/packages/gQTLstats")
10820 (synopsis "Computationally efficient analysis for eQTL and allied studies")
10822 "This package provides tools for the computationally efficient analysis
10823 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
10824 The software in this package aims to support refinements and functional
10825 interpretation of members of a collection of association statistics on a
10826 family of feature/genome hypotheses.")
10827 (license license:artistic2.0)))
10829 (define-public r-gviz
10836 (uri (bioconductor-uri "Gviz" version))
10839 "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1"))))
10840 (properties `((upstream-name . "Gviz")))
10841 (build-system r-build-system)
10843 `(("r-annotationdbi" ,r-annotationdbi)
10844 ("r-biobase" ,r-biobase)
10845 ("r-biocgenerics" ,r-biocgenerics)
10846 ("r-biomart" ,r-biomart)
10847 ("r-biostrings" ,r-biostrings)
10848 ("r-biovizbase" ,r-biovizbase)
10849 ("r-bsgenome" ,r-bsgenome)
10850 ("r-digest" ,r-digest)
10851 ("r-ensembldb" ,r-ensembldb)
10852 ("r-genomeinfodb" ,r-genomeinfodb)
10853 ("r-genomicalignments" ,r-genomicalignments)
10854 ("r-genomicfeatures" ,r-genomicfeatures)
10855 ("r-genomicranges" ,r-genomicranges)
10856 ("r-iranges" ,r-iranges)
10857 ("r-lattice" ,r-lattice)
10858 ("r-latticeextra" ,r-latticeextra)
10859 ("r-matrixstats" ,r-matrixstats)
10860 ("r-rcolorbrewer" ,r-rcolorbrewer)
10861 ("r-rsamtools" ,r-rsamtools)
10862 ("r-rtracklayer" ,r-rtracklayer)
10863 ("r-s4vectors" ,r-s4vectors)
10864 ("r-xvector" ,r-xvector)))
10866 `(("r-knitr" ,r-knitr)))
10867 (home-page "https://bioconductor.org/packages/Gviz")
10868 (synopsis "Plotting data and annotation information along genomic coordinates")
10870 "Genomic data analyses requires integrated visualization of known genomic
10871 information and new experimental data. Gviz uses the biomaRt and the
10872 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
10873 and translates this to e.g. gene/transcript structures in viewports of the
10874 grid graphics package. This results in genomic information plotted together
10876 (license license:artistic2.0)))
10878 (define-public r-gwascat
10885 (uri (bioconductor-uri "gwascat" version))
10888 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
10889 (build-system r-build-system)
10891 `(("r-annotationdbi" ,r-annotationdbi)
10892 ("r-biocfilecache" ,r-biocfilecache)
10893 ("r-biostrings" ,r-biostrings)
10894 ("r-genomeinfodb" ,r-genomeinfodb)
10895 ("r-genomicfeatures" ,r-genomicfeatures)
10896 ("r-genomicranges" ,r-genomicranges)
10897 ("r-iranges" ,r-iranges)
10898 ("r-readr" ,r-readr)
10899 ("r-s4vectors" ,r-s4vectors)
10900 ("r-snpstats" ,r-snpstats)
10901 ("r-variantannotation" ,r-variantannotation)))
10903 `(("r-knitr" ,r-knitr)))
10904 (home-page "https://bioconductor.org/packages/gwascat")
10905 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
10907 "This package provides tools for representing and modeling data in the
10908 EMBL-EBI GWAS catalog.")
10909 (license license:artistic2.0)))
10911 (define-public r-kegggraph
10913 (name "r-kegggraph")
10918 (uri (bioconductor-uri "KEGGgraph" version))
10920 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
10921 (properties `((upstream-name . "KEGGgraph")))
10922 (build-system r-build-system)
10924 `(("r-graph" ,r-graph)
10925 ("r-rcurl" ,r-rcurl)
10927 (home-page "https://bioconductor.org/packages/KEGGgraph")
10928 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
10930 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
10931 object as well as a collection of tools to analyze, dissect and visualize these
10932 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
10933 maintaining all essential pathway attributes. The package offers
10934 functionalities including parsing, graph operation, visualization and etc.")
10935 (license license:gpl2+)))
10937 (define-public r-ldblock
10944 (uri (bioconductor-uri "ldblock" version))
10947 "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
10948 (build-system r-build-system)
10950 `(("r-biocgenerics" ,r-biocgenerics)
10951 ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
10952 ("r-ensembldb" ,r-ensembldb)
10953 ("r-genomeinfodb" ,r-genomeinfodb)
10954 ("r-genomicfiles" ,r-genomicfiles)
10956 ("r-matrix" ,r-matrix)
10957 ("r-rsamtools" ,r-rsamtools)
10958 ("r-snpstats" ,r-snpstats)
10959 ("r-variantannotation" ,r-variantannotation)))
10961 `(("r-knitr" ,r-knitr)))
10962 (home-page "https://bioconductor.org/packages/ldblock")
10963 (synopsis "Data structures for linkage disequilibrium measures in populations")
10965 "This package defines data structures for @dfn{linkage
10966 disequilibrium} (LD) measures in populations. Its purpose is to simplify
10967 handling of existing population-level data for the purpose of flexibly
10968 defining LD blocks.")
10969 (license license:artistic2.0)))
10971 ;; This is a CRAN package, but it depends on r-snpstats, which is a
10972 ;; Bioconductor package.
10973 (define-public r-ldheatmap
10975 (name "r-ldheatmap")
10980 (uri (cran-uri "LDheatmap" version))
10983 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
10984 (properties `((upstream-name . "LDheatmap")))
10985 (build-system r-build-system)
10987 `(("r-genetics" ,r-genetics)
10989 ("r-snpstats" ,r-snpstats)))
10990 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
10991 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
10993 "This package provides tools to produce a graphical display, as a heat
10994 map, of measures of pairwise linkage disequilibria between SNPs. Users may
10995 optionally include the physical locations or genetic map distances of each SNP
10997 (license license:gpl3)))
10999 (define-public r-pathview
11001 (name "r-pathview")
11006 (uri (bioconductor-uri "pathview" version))
11008 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
11009 (properties `((upstream-name . "pathview")))
11010 (build-system r-build-system)
11012 `(("r-annotationdbi" ,r-annotationdbi)
11013 ("r-graph" ,r-graph)
11014 ("r-kegggraph" ,r-kegggraph)
11015 ("r-keggrest" ,r-keggrest)
11016 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
11018 ("r-rgraphviz" ,r-rgraphviz)
11020 (home-page "https://pathview.uncc.edu/")
11021 (synopsis "Tool set for pathway based data integration and visualization")
11023 "@code{r-pathview} is a tool set for pathway based data integration and
11024 visualization. It maps and renders a wide variety of biological data on
11025 relevant pathway graphs. All users need is to supply their data and specify
11026 the target pathway. This package automatically downloads the pathway graph
11027 data, parses the data file, maps user data to the pathway, and render pathway
11028 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
11029 integrates with pathway and gene set (enrichment) analysis tools for
11030 large-scale and fully automated analysis.")
11031 (license license:gpl3+)))
11033 (define-public r-snpstats
11035 (name "r-snpstats")
11040 (uri (bioconductor-uri "snpStats" version))
11043 "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
11044 (properties `((upstream-name . "snpStats")))
11045 (build-system r-build-system)
11046 (inputs `(("zlib" ,zlib)))
11048 `(("r-biocgenerics" ,r-biocgenerics)
11049 ("r-matrix" ,r-matrix)
11050 ("r-survival" ,r-survival)
11051 ("r-zlibbioc" ,r-zlibbioc)))
11052 (home-page "https://bioconductor.org/packages/snpStats")
11053 (synopsis "Methods for SNP association studies")
11055 "This package provides classes and statistical methods for large
11056 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
11057 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
11058 (license license:gpl3)))
11060 (define-public r-chromstar
11062 (name "r-chromstar")
11067 (uri (bioconductor-uri "chromstaR" version))
11070 "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1"))))
11071 (properties `((upstream-name . "chromstaR")))
11072 (build-system r-build-system)
11074 `(("r-bamsignals" ,r-bamsignals)
11075 ("r-biocgenerics" ,r-biocgenerics)
11076 ("r-chromstardata" ,r-chromstardata)
11077 ("r-doparallel" ,r-doparallel)
11078 ("r-foreach" ,r-foreach)
11079 ("r-genomeinfodb" ,r-genomeinfodb)
11080 ("r-genomicalignments" ,r-genomicalignments)
11081 ("r-genomicranges" ,r-genomicranges)
11082 ("r-ggplot2" ,r-ggplot2)
11083 ("r-iranges" ,r-iranges)
11084 ("r-mvtnorm" ,r-mvtnorm)
11085 ("r-reshape2" ,r-reshape2)
11086 ("r-rsamtools" ,r-rsamtools)
11087 ("r-s4vectors" ,r-s4vectors)))
11088 (native-inputs `(("r-knitr" ,r-knitr)))
11089 (home-page "https://github.com/ataudt/chromstaR")
11090 (synopsis "Chromatin state analysis for ChIP-Seq data")
11092 "This package implements functions for combinatorial and differential
11093 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
11094 export to genome browser viewable files, and functions for enrichment
11096 (license license:artistic2.0)))
11098 (define-public r-sushi
11104 (uri (bioconductor-uri "Sushi" version))
11107 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
11108 (properties `((upstream-name . "Sushi")))
11109 (build-system r-build-system)
11111 `(("r-biomart" ,r-biomart)
11113 (home-page "https://bioconductor.org/packages/Sushi")
11114 (synopsis "Tools for visualizing genomics data")
11116 "This package provides flexible, quantitative, and integrative genomic
11117 visualizations for publication-quality multi-panel figures.")
11118 (license license:gpl2+)))