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-hsapiens-ucsc-hg19-knowngene
624 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
628 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
629 version 'annotation))
632 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
634 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
635 (build-system r-build-system)
637 `(("r-genomicfeatures" ,r-genomicfeatures)))
639 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
640 (synopsis "Annotation package for human genome in TxDb format")
642 "This package provides an annotation database of Homo sapiens genome
643 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
644 track. The database is exposed as a @code{TxDb} object.")
645 (license license:artistic2.0)))
647 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
649 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
653 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
654 version 'annotation))
657 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
659 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
660 (build-system r-build-system)
662 `(("r-genomicfeatures" ,r-genomicfeatures)))
664 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
665 (synopsis "Annotation package for human genome in TxDb format")
667 "This package provides an annotation database of Homo sapiens genome
668 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
669 track. The database is exposed as a @code{TxDb} object.")
670 (license license:artistic2.0)))
672 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
674 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
678 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
679 version 'annotation))
682 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
684 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
685 (build-system r-build-system)
687 `(("r-genomicfeatures" ,r-genomicfeatures)
688 ("r-annotationdbi" ,r-annotationdbi)))
690 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
691 (synopsis "Annotation package for mouse genome in TxDb format")
693 "This package provides an annotation database of Mouse genome data. It
694 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
695 database is exposed as a @code{TxDb} object.")
696 (license license:artistic2.0)))
698 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
700 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
704 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
705 version 'annotation))
708 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
710 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
711 (build-system r-build-system)
713 `(("r-bsgenome" ,r-bsgenome)
714 ("r-genomicfeatures" ,r-genomicfeatures)
715 ("r-annotationdbi" ,r-annotationdbi)))
717 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
718 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
720 "This package loads a TxDb object, which is an R interface to
721 prefabricated databases contained in this package. This package provides
722 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
723 based on the knownGene track.")
724 (license license:artistic2.0)))
726 (define-public r-txdb-celegans-ucsc-ce6-ensgene
728 (name "r-txdb-celegans-ucsc-ce6-ensgene")
733 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
734 version 'annotation))
737 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
739 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
740 (build-system r-build-system)
742 `(("r-annotationdbi" ,r-annotationdbi)
743 ("r-genomicfeatures" ,r-genomicfeatures)))
744 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
745 (synopsis "Annotation package for C elegans TxDb objects")
747 "This package exposes a C elegans annotation database generated from UCSC
748 by exposing these as TxDb objects.")
749 (license license:artistic2.0)))
751 (define-public r-fdb-infiniummethylation-hg19
753 (name "r-fdb-infiniummethylation-hg19")
757 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
758 version 'annotation))
761 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
763 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
764 (build-system r-build-system)
766 `(("r-biostrings" ,r-biostrings)
767 ("r-genomicfeatures" ,r-genomicfeatures)
768 ("r-annotationdbi" ,r-annotationdbi)
769 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
770 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
771 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
772 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
774 "This is an annotation package for Illumina Infinium DNA methylation
775 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
777 (license license:artistic2.0)))
779 (define-public r-illuminahumanmethylationepicmanifest
781 (name "r-illuminahumanmethylationepicmanifest")
785 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
786 version 'annotation))
789 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
791 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
792 (build-system r-build-system)
794 `(("r-minfi" ,r-minfi)))
795 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
796 (synopsis "Manifest for Illumina's EPIC methylation arrays")
798 "This is a manifest package for Illumina's EPIC methylation arrays.")
799 (license license:artistic2.0)))
801 (define-public r-do-db
807 (uri (bioconductor-uri "DO.db" version 'annotation))
810 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
812 `((upstream-name . "DO.db")))
813 (build-system r-build-system)
815 `(("r-annotationdbi" ,r-annotationdbi)))
816 (home-page "https://www.bioconductor.org/packages/DO.db/")
817 (synopsis "Annotation maps describing the entire Disease Ontology")
819 "This package provides a set of annotation maps describing the entire
821 (license license:artistic2.0)))
823 (define-public r-pfam-db
830 (uri (bioconductor-uri "PFAM.db" version 'annotation))
833 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
834 (properties `((upstream-name . "PFAM.db")))
835 (build-system r-build-system)
837 `(("r-annotationdbi" ,r-annotationdbi)))
838 (home-page "https://bioconductor.org/packages/PFAM.db")
839 (synopsis "Set of protein ID mappings for PFAM")
841 "This package provides a set of protein ID mappings for PFAM, assembled
842 using data from public repositories.")
843 (license license:artistic2.0)))
845 (define-public r-phastcons100way-ucsc-hg19
847 (name "r-phastcons100way-ucsc-hg19")
852 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
853 version 'annotation))
856 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
858 `((upstream-name . "phastCons100way.UCSC.hg19")))
859 (build-system r-build-system)
861 `(("r-bsgenome" ,r-bsgenome)
862 ("r-genomeinfodb" ,r-genomeinfodb)
863 ("r-genomicranges" ,r-genomicranges)
864 ("r-genomicscores" ,r-genomicscores)
865 ("r-iranges" ,r-iranges)
866 ("r-s4vectors" ,r-s4vectors)))
867 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
868 (synopsis "UCSC phastCons conservation scores for hg19")
870 "This package provides UCSC phastCons conservation scores for the human
871 genome (hg19) calculated from multiple alignments with other 99 vertebrate
873 (license license:artistic2.0)))
878 (define-public r-abadata
884 (uri (bioconductor-uri "ABAData" version 'experiment))
887 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
889 `((upstream-name . "ABAData")))
890 (build-system r-build-system)
892 `(("r-annotationdbi" ,r-annotationdbi)))
893 (home-page "https://www.bioconductor.org/packages/ABAData/")
894 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
896 "This package provides the data for the gene expression enrichment
897 analysis conducted in the package ABAEnrichment. The package includes three
898 datasets which are derived from the Allen Brain Atlas:
901 @item Gene expression data from Human Brain (adults) averaged across donors,
902 @item Gene expression data from the Developing Human Brain pooled into five
903 age categories and averaged across donors, and
904 @item a developmental effect score based on the Developing Human Brain
908 All datasets are restricted to protein coding genes.")
909 (license license:gpl2+)))
911 (define-public r-arrmdata
917 (uri (bioconductor-uri "ARRmData" version 'experiment))
920 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
922 `((upstream-name . "ARRmData")))
923 (build-system r-build-system)
924 (home-page "https://www.bioconductor.org/packages/ARRmData/")
925 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
927 "This package provides raw beta values from 36 samples across 3 groups
928 from Illumina 450k methylation arrays.")
929 (license license:artistic2.0)))
931 (define-public r-chromstardata
933 (name "r-chromstardata")
938 (uri (bioconductor-uri "chromstaRData" version 'experiment))
941 "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
942 (properties `((upstream-name . "chromstaRData")))
943 (build-system r-build-system)
944 (home-page "https://bioconductor.org/packages/chromstaRData/")
945 (synopsis "ChIP-seq data for demonstration purposes")
947 "This package provides ChIP-seq data for demonstration purposes in the
949 (license license:gpl3)))
951 (define-public r-genelendatabase
953 (name "r-genelendatabase")
958 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
961 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
963 `((upstream-name . "geneLenDataBase")))
964 (build-system r-build-system)
966 `(("r-rtracklayer" ,r-rtracklayer)
967 ("r-genomicfeatures" ,r-genomicfeatures)))
968 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
969 (synopsis "Lengths of mRNA transcripts for a number of genomes")
971 "This package provides the lengths of mRNA transcripts for a number of
972 genomes and gene ID formats, largely based on the UCSC table browser.")
973 (license license:lgpl2.0+)))
975 (define-public r-pasilla
982 "http://bioconductor.org/packages/release/data/experiment"
983 "/src/contrib/pasilla_" version ".tar.gz"))
986 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
987 (build-system r-build-system)
989 `(("r-biocstyle" ,r-biocstyle)
990 ("r-dexseq" ,r-dexseq)
992 ("r-rmarkdown" ,r-rmarkdown)))
993 (home-page "https://www.bioconductor.org/packages/pasilla/")
994 (synopsis "Data package with per-exon and per-gene read counts")
995 (description "This package provides per-exon and per-gene read counts
996 computed for selected genes from RNA-seq data that were presented in the
997 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
998 by Brooks et al., Genome Research 2011.")
999 (license license:lgpl2.1+)))
1001 (define-public r-hsmmsinglecell
1003 (name "r-hsmmsinglecell")
1007 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1010 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
1012 `((upstream-name . "HSMMSingleCell")))
1013 (build-system r-build-system)
1014 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1015 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1017 "Skeletal myoblasts undergo a well-characterized sequence of
1018 morphological and transcriptional changes during differentiation. In this
1019 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1020 under high mitogen conditions (GM) and then differentiated by switching to
1021 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1022 hundred cells taken over a time-course of serum-induced differentiation.
1023 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1024 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1025 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1026 which were then sequenced to a depth of ~4 million reads per library,
1027 resulting in a complete gene expression profile for each cell.")
1028 (license license:artistic2.0)))
1030 (define-public r-all
1036 (uri (bioconductor-uri "ALL" version 'experiment))
1039 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1040 (properties `((upstream-name . "ALL")))
1041 (build-system r-build-system)
1043 `(("r-biobase" ,r-biobase)))
1044 (home-page "https://bioconductor.org/packages/ALL")
1045 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1047 "The data consist of microarrays from 128 different individuals with
1048 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1049 are available. The data have been normalized (using rma) and it is the
1050 jointly normalized data that are available here. The data are presented in
1051 the form of an @code{exprSet} object.")
1052 (license license:artistic2.0)))
1054 (define-public r-affydata
1061 (uri (bioconductor-uri "affydata" version 'experiment))
1064 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1065 (properties `((upstream-name . "affydata")))
1066 (build-system r-build-system)
1068 `(("r-affy" ,r-affy)))
1069 (home-page "https://bioconductor.org/packages/affydata/")
1070 (synopsis "Affymetrix data for demonstration purposes")
1072 "This package provides example datasets that represent 'real world
1073 examples' of Affymetrix data, unlike the artificial examples included in the
1074 package @code{affy}.")
1075 (license license:gpl2+)))
1077 (define-public r-gagedata
1084 (uri (bioconductor-uri "gageData" version 'experiment))
1086 (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn"))))
1087 (properties `((upstream-name . "gageData")))
1088 (build-system r-build-system)
1089 (home-page "https://bioconductor.org/packages/gageData")
1090 (synopsis "Auxillary data for gage package")
1092 "This is a supportive data package for the software package @code{gage}.
1093 However, the data supplied here are also useful for gene set or pathway
1094 analysis or microarray data analysis in general. In this package, we provide
1095 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1096 BMP6 (originally published as an demo dataset for GAGE, also registered as
1097 GSE13604 in GEO). This package also includes commonly used gene set data based
1098 on KEGG pathways and GO terms for major research species, including human,
1099 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1100 yeast are also included.")
1101 (license license:gpl2+)))
1103 (define-public r-curatedtcgadata
1105 (name "r-curatedtcgadata")
1110 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1113 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1115 `((upstream-name . "curatedTCGAData")))
1116 (build-system r-build-system)
1118 `(("r-annotationhub" ,r-annotationhub)
1119 ("r-experimenthub" ,r-experimenthub)
1120 ("r-hdf5array" ,r-hdf5array)
1121 ("r-multiassayexperiment" ,r-multiassayexperiment)
1122 ("r-s4vectors" ,r-s4vectors)
1123 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1124 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1125 (synopsis "Curated data from The Cancer Genome Atlas")
1127 "This package provides publicly available data from The Cancer Genome
1128 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1129 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1130 number, mutation, microRNA, protein, and others) with clinical / pathological
1131 data. It also links assay barcodes with patient identifiers, enabling
1132 harmonized subsetting of rows (features) and columns (patients / samples)
1133 across the entire multi-'omics experiment.")
1134 (license license:artistic2.0)))
1139 (define-public r-biocversion
1141 (name "r-biocversion")
1146 (uri (bioconductor-uri "BiocVersion" version))
1149 "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
1150 (properties `((upstream-name . "BiocVersion")))
1151 (build-system r-build-system)
1152 (home-page "https://bioconductor.org/packages/BiocVersion/")
1153 (synopsis "Set the appropriate version of Bioconductor packages")
1155 "This package provides repository information for the appropriate version
1157 (license license:artistic2.0)))
1159 (define-public r-biocgenerics
1161 (name "r-biocgenerics")
1165 (uri (bioconductor-uri "BiocGenerics" version))
1168 "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
1170 `((upstream-name . "BiocGenerics")))
1171 (build-system r-build-system)
1172 (home-page "https://bioconductor.org/packages/BiocGenerics")
1173 (synopsis "S4 generic functions for Bioconductor")
1175 "This package provides S4 generic functions needed by many Bioconductor
1177 (license license:artistic2.0)))
1179 (define-public r-coverageview
1181 (name "r-coverageview")
1185 (uri (bioconductor-uri "CoverageView" version))
1188 "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
1189 (build-system r-build-system)
1191 `(("r-s4vectors" ,r-s4vectors)
1192 ("r-iranges" ,r-iranges)
1193 ("r-genomicranges" ,r-genomicranges)
1194 ("r-genomicalignments" ,r-genomicalignments)
1195 ("r-rtracklayer" ,r-rtracklayer)
1196 ("r-rsamtools" ,r-rsamtools)))
1197 (home-page "https://bioconductor.org/packages/CoverageView/")
1198 (synopsis "Coverage visualization package for R")
1199 (description "This package provides a framework for the visualization of
1200 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1201 be also used for genome-wide nucleosome positioning experiments or other
1202 experiment types where it is important to have a framework in order to inspect
1203 how the coverage distributed across the genome.")
1204 (license license:artistic2.0)))
1206 (define-public r-cummerbund
1208 (name "r-cummerbund")
1212 (uri (bioconductor-uri "cummeRbund" version))
1215 "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
1216 (build-system r-build-system)
1218 `(("r-biobase" ,r-biobase)
1219 ("r-biocgenerics" ,r-biocgenerics)
1220 ("r-fastcluster" ,r-fastcluster)
1221 ("r-ggplot2" ,r-ggplot2)
1224 ("r-reshape2" ,r-reshape2)
1225 ("r-rsqlite" ,r-rsqlite)
1226 ("r-rtracklayer" ,r-rtracklayer)
1227 ("r-s4vectors" ,r-s4vectors)))
1228 (home-page "https://bioconductor.org/packages/cummeRbund/")
1229 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1230 (description "This package allows for persistent storage, access,
1231 exploration, and manipulation of Cufflinks high-throughput sequencing
1232 data. In addition, provides numerous plotting functions for commonly
1233 used visualizations.")
1234 (license license:artistic2.0)))
1236 (define-public r-delayedarray
1238 (name "r-delayedarray")
1242 (uri (bioconductor-uri "DelayedArray" version))
1245 "0w1wppy6m2iv41852dscg3y19sq84ahdx3m7c2p2pxjcznmv6hys"))))
1247 `((upstream-name . "DelayedArray")))
1248 (build-system r-build-system)
1250 `(("r-biocgenerics" ,r-biocgenerics)
1251 ("r-s4vectors" ,r-s4vectors)
1252 ("r-iranges" ,r-iranges)
1253 ("r-matrix" ,r-matrix)
1254 ("r-matrixgenerics" ,r-matrixgenerics)))
1256 `(("r-knitr" ,r-knitr)))
1257 (home-page "https://bioconductor.org/packages/DelayedArray")
1258 (synopsis "Delayed operations on array-like objects")
1260 "Wrapping an array-like object (typically an on-disk object) in a
1261 @code{DelayedArray} object allows one to perform common array operations on it
1262 without loading the object in memory. In order to reduce memory usage and
1263 optimize performance, operations on the object are either delayed or executed
1264 using a block processing mechanism. Note that this also works on in-memory
1265 array-like objects like @code{DataFrame} objects (typically with Rle columns),
1266 @code{Matrix} objects, and ordinary arrays and data frames.")
1267 (license license:artistic2.0)))
1269 (define-public r-bluster
1275 (uri (bioconductor-uri "bluster" version))
1278 "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61"))))
1279 (properties `((upstream-name . "bluster")))
1280 (build-system r-build-system)
1282 `(("r-biocneighbors" ,r-biocneighbors)
1283 ("r-biocparallel" ,r-biocparallel)
1284 ("r-igraph" ,r-igraph)
1285 ("r-matrix" ,r-matrix)
1287 ("r-s4vectors" ,r-s4vectors)))
1289 `(("r-knitr" ,r-knitr)))
1290 (home-page "https://bioconductor.org/packages/bluster")
1291 (synopsis "Clustering algorithms for Bioconductor")
1292 (description"This package wraps common clustering algorithms in an easily
1293 extended S4 framework. Backends are implemented for hierarchical, k-means
1294 and graph-based clustering. Several utilities are also provided to compare
1295 and evaluate clustering results.")
1296 (license license:gpl3)))
1298 (define-public r-ideoviz
1304 (uri (bioconductor-uri "IdeoViz" version))
1307 "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
1308 (build-system r-build-system)
1310 `(("r-biobase" ,r-biobase)
1311 ("r-iranges" ,r-iranges)
1312 ("r-genomicranges" ,r-genomicranges)
1313 ("r-rcolorbrewer" ,r-rcolorbrewer)
1314 ("r-rtracklayer" ,r-rtracklayer)
1315 ("r-genomeinfodb" ,r-genomeinfodb)))
1316 (home-page "https://bioconductor.org/packages/IdeoViz/")
1317 (synopsis "Plots data along a chromosomal ideogram")
1318 (description "This package provides functions to plot data associated with
1319 arbitrary genomic intervals along chromosomal ideogram.")
1320 (license license:gpl2)))
1322 (define-public r-iranges
1328 (uri (bioconductor-uri "IRanges" version))
1331 "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52"))))
1333 `((upstream-name . "IRanges")))
1334 (build-system r-build-system)
1336 `(("r-biocgenerics" ,r-biocgenerics)
1337 ("r-s4vectors" ,r-s4vectors)))
1338 (home-page "https://bioconductor.org/packages/IRanges")
1339 (synopsis "Infrastructure for manipulating intervals on sequences")
1341 "This package provides efficient low-level and highly reusable S4 classes
1342 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
1343 generally, data that can be organized sequentially (formally defined as
1344 @code{Vector} objects), as well as views on these @code{Vector} objects.
1345 Efficient list-like classes are also provided for storing big collections of
1346 instances of the basic classes. All classes in the package use consistent
1347 naming and share the same rich and consistent \"Vector API\" as much as
1349 (license license:artistic2.0)))
1351 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
1352 (define-public r-absfiltergsea
1354 (name "r-absfiltergsea")
1359 (uri (cran-uri "AbsFilterGSEA" version))
1361 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
1362 (properties `((upstream-name . "AbsFilterGSEA")))
1363 (build-system r-build-system)
1365 `(("r-biobase" ,r-biobase)
1366 ("r-deseq" ,r-deseq)
1367 ("r-limma" ,r-limma)
1369 ("r-rcpparmadillo" ,r-rcpparmadillo)))
1370 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
1371 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
1373 "This package provides a function that performs gene-permuting of a gene-set
1374 enrichment analysis (GSEA) calculation with or without the absolute filtering.
1375 Without filtering, users can perform (original) two-tailed or one-tailed
1377 (license license:gpl2)))
1379 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
1380 (define-public r-bisquerna
1382 (name "r-bisquerna")
1386 (uri (cran-uri "BisqueRNA" version))
1389 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
1390 (properties `((upstream-name . "BisqueRNA")))
1391 (build-system r-build-system)
1393 `(("r-biobase" ,r-biobase)
1394 ("r-limsolve" ,r-limsolve)))
1395 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
1396 (synopsis "Decomposition of bulk expression with single-cell sequencing")
1397 (description "This package provides tools to accurately estimate cell type
1398 abundances from heterogeneous bulk expression. A reference-based method
1399 utilizes single-cell information to generate a signature matrix and
1400 transformation of bulk expression for accurate regression based estimates.
1401 A marker-based method utilizes known cell-specific marker genes to measure
1402 relative abundances across samples.")
1403 (license license:gpl3)))
1405 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
1406 ;; from Bioconductor.
1407 (define-public r-deconstructsigs
1409 (name "r-deconstructsigs")
1413 (uri (cran-uri "deconstructSigs" version))
1416 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
1418 `((upstream-name . "deconstructSigs")))
1419 (build-system r-build-system)
1421 `(("r-bsgenome" ,r-bsgenome)
1422 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1423 ("r-genomeinfodb" ,r-genomeinfodb)
1424 ("r-reshape2" ,r-reshape2)))
1425 (home-page "https://github.com/raerose01/deconstructSigs")
1426 (synopsis "Identifies signatures present in a tumor sample")
1427 (description "This package takes sample information in the form of the
1428 fraction of mutations in each of 96 trinucleotide contexts and identifies
1429 the weighted combination of published signatures that, when summed, most
1430 closely reconstructs the mutational profile.")
1431 (license license:gpl2+)))
1433 ;; This is a CRAN package, but it depends on Bioconductor packages.
1434 (define-public r-nmf
1441 (uri (cran-uri "NMF" version))
1444 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
1445 (properties `((upstream-name . "NMF")))
1446 (build-system r-build-system)
1448 `(("r-cluster" ,r-cluster)
1449 ("r-biobase" ,r-biobase)
1450 ("r-biocmanager" ,r-biocmanager)
1451 ("r-bigmemory" ,r-bigmemory) ; suggested
1452 ("r-synchronicity" ,r-synchronicity) ; suggested
1453 ("r-colorspace" ,r-colorspace)
1454 ("r-digest" ,r-digest)
1455 ("r-doparallel" ,r-doparallel)
1456 ("r-foreach" ,r-foreach)
1457 ("r-ggplot2" ,r-ggplot2)
1458 ("r-gridbase" ,r-gridbase)
1459 ("r-pkgmaker" ,r-pkgmaker)
1460 ("r-rcolorbrewer" ,r-rcolorbrewer)
1461 ("r-registry" ,r-registry)
1462 ("r-reshape2" ,r-reshape2)
1463 ("r-rngtools" ,r-rngtools)
1464 ("r-stringr" ,r-stringr)))
1466 `(("r-knitr" ,r-knitr)))
1467 (home-page "http://renozao.github.io/NMF")
1468 (synopsis "Algorithms and framework for nonnegative matrix factorization")
1470 "This package provides a framework to perform Non-negative Matrix
1471 Factorization (NMF). The package implements a set of already published
1472 algorithms and seeding methods, and provides a framework to test, develop and
1473 plug new or custom algorithms. Most of the built-in algorithms have been
1474 optimized in C++, and the main interface function provides an easy way of
1475 performing parallel computations on multicore machines.")
1476 (license license:gpl2+)))
1478 (define-public r-affycomp
1485 (uri (bioconductor-uri "affycomp" version))
1488 "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
1489 (properties `((upstream-name . "affycomp")))
1490 (build-system r-build-system)
1491 (propagated-inputs `(("r-biobase" ,r-biobase)))
1492 (home-page "https://bioconductor.org/packages/affycomp/")
1493 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1495 "The package contains functions that can be used to compare expression
1496 measures for Affymetrix Oligonucleotide Arrays.")
1497 (license license:gpl2+)))
1499 (define-public r-affycompatible
1501 (name "r-affycompatible")
1506 (uri (bioconductor-uri "AffyCompatible" version))
1509 "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
1511 `((upstream-name . "AffyCompatible")))
1512 (build-system r-build-system)
1514 `(("r-biostrings" ,r-biostrings)
1515 ("r-rcurl" ,r-rcurl)
1517 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1518 (synopsis "Work with Affymetrix GeneChip files")
1520 "This package provides an interface to Affymetrix chip annotation and
1521 sample attribute files. The package allows an easy way for users to download
1522 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1523 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1524 Command Console} (AGCC)-compatible sample annotation files.")
1525 (license license:artistic2.0)))
1527 (define-public r-affycontam
1529 (name "r-affycontam")
1534 (uri (bioconductor-uri "affyContam" version))
1537 "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
1538 (properties `((upstream-name . "affyContam")))
1539 (build-system r-build-system)
1541 `(("r-affy" ,r-affy)
1542 ("r-affydata" ,r-affydata)
1543 ("r-biobase" ,r-biobase)))
1544 (home-page "https://bioconductor.org/packages/affyContam/")
1545 (synopsis "Structured corruption of Affymetrix CEL file data")
1547 "Microarray quality assessment is a major concern of microarray analysts.
1548 This package provides some simple approaches to in silico creation of quality
1549 problems in CEL-level data to help evaluate performance of quality metrics.")
1550 (license license:artistic2.0)))
1552 (define-public r-affycoretools
1554 (name "r-affycoretools")
1559 (uri (bioconductor-uri "affycoretools" version))
1562 "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
1563 (properties `((upstream-name . "affycoretools")))
1564 (build-system r-build-system)
1566 `(("r-affy" ,r-affy)
1567 ("r-annotationdbi" ,r-annotationdbi)
1568 ("r-biobase" ,r-biobase)
1569 ("r-biocgenerics" ,r-biocgenerics)
1571 ("r-edger" ,r-edger)
1572 ("r-gcrma" ,r-gcrma)
1573 ("r-glimma" ,r-glimma)
1574 ("r-ggplot2" ,r-ggplot2)
1575 ("r-gostats" ,r-gostats)
1576 ("r-gplots" ,r-gplots)
1577 ("r-hwriter" ,r-hwriter)
1578 ("r-lattice" ,r-lattice)
1579 ("r-limma" ,r-limma)
1580 ("r-oligoclasses" ,r-oligoclasses)
1581 ("r-reportingtools" ,r-reportingtools)
1582 ("r-rsqlite" ,r-rsqlite)
1583 ("r-s4vectors" ,r-s4vectors)
1584 ("r-xtable" ,r-xtable)))
1586 `(("r-knitr" ,r-knitr)))
1587 (home-page "https://bioconductor.org/packages/affycoretools/")
1588 (synopsis "Functions for analyses with Affymetrix GeneChips")
1590 "This package provides various wrapper functions that have been written
1591 to streamline the more common analyses that a Biostatistician might see.")
1592 (license license:artistic2.0)))
1594 (define-public r-affxparser
1596 (name "r-affxparser")
1601 (uri (bioconductor-uri "affxparser" version))
1604 "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
1605 (properties `((upstream-name . "affxparser")))
1606 (build-system r-build-system)
1607 (home-page "https://github.com/HenrikBengtsson/affxparser")
1608 (synopsis "Affymetrix File Parsing SDK")
1610 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1611 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1612 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1613 are supported. Currently, there are methods for reading @dfn{chip definition
1614 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1615 either in full or in part. For example, probe signals from a few probesets
1616 can be extracted very quickly from a set of CEL files into a convenient list
1618 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1620 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1622 (define-public r-annotate
1629 (uri (bioconductor-uri "annotate" version))
1632 "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
1633 (build-system r-build-system)
1635 `(("r-annotationdbi" ,r-annotationdbi)
1636 ("r-biobase" ,r-biobase)
1637 ("r-biocgenerics" ,r-biocgenerics)
1641 ("r-xtable" ,r-xtable)))
1643 "https://bioconductor.org/packages/annotate")
1644 (synopsis "Annotation for microarrays")
1645 (description "This package provides R environments for the annotation of
1647 (license license:artistic2.0)))
1649 (define-public r-annotationdbi
1651 (name "r-annotationdbi")
1655 (uri (bioconductor-uri "AnnotationDbi" version))
1658 "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
1660 `((upstream-name . "AnnotationDbi")))
1661 (build-system r-build-system)
1663 `(("r-biobase" ,r-biobase)
1664 ("r-biocgenerics" ,r-biocgenerics)
1666 ("r-iranges" ,r-iranges)
1667 ("r-rsqlite" ,r-rsqlite)
1668 ("r-s4vectors" ,r-s4vectors)))
1670 `(("r-knitr" ,r-knitr)))
1671 (home-page "https://bioconductor.org/packages/AnnotationDbi")
1672 (synopsis "Annotation database interface")
1674 "This package provides user interface and database connection code for
1675 annotation data packages using SQLite data storage.")
1676 (license license:artistic2.0)))
1678 (define-public r-annotationforge
1680 (name "r-annotationforge")
1685 (uri (bioconductor-uri "AnnotationForge" version))
1688 "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
1690 `((upstream-name . "AnnotationForge")))
1691 (build-system r-build-system)
1693 `(("r-annotationdbi" ,r-annotationdbi)
1694 ("r-biobase" ,r-biobase)
1695 ("r-biocgenerics" ,r-biocgenerics)
1697 ("r-rcurl" ,r-rcurl)
1698 ("r-rsqlite" ,r-rsqlite)
1699 ("r-s4vectors" ,r-s4vectors)
1702 `(("r-knitr" ,r-knitr)))
1703 (home-page "https://bioconductor.org/packages/AnnotationForge")
1704 (synopsis "Code for building annotation database packages")
1706 "This package provides code for generating Annotation packages and their
1707 databases. Packages produced are intended to be used with AnnotationDbi.")
1708 (license license:artistic2.0)))
1710 (define-public r-biobase
1716 (uri (bioconductor-uri "Biobase" version))
1719 "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
1721 `((upstream-name . "Biobase")))
1722 (build-system r-build-system)
1724 `(("r-biocgenerics" ,r-biocgenerics)))
1725 (home-page "https://bioconductor.org/packages/Biobase")
1726 (synopsis "Base functions for Bioconductor")
1728 "This package provides functions that are needed by many other packages
1729 on Bioconductor or which replace R functions.")
1730 (license license:artistic2.0)))
1732 (define-public r-biomart
1738 (uri (bioconductor-uri "biomaRt" version))
1741 "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
1743 `((upstream-name . "biomaRt")))
1744 (build-system r-build-system)
1746 `(("r-annotationdbi" ,r-annotationdbi)
1747 ("r-biocfilecache" ,r-biocfilecache)
1749 ("r-openssl" ,r-openssl)
1750 ("r-progress" ,r-progress)
1751 ("r-rappdirs" ,r-rappdirs)
1752 ("r-stringr" ,r-stringr)
1754 ("r-xml2" ,r-xml2)))
1756 `(("r-knitr" ,r-knitr)))
1757 (home-page "https://bioconductor.org/packages/biomaRt")
1758 (synopsis "Interface to BioMart databases")
1760 "biomaRt provides an interface to a growing collection of databases
1761 implementing the @url{BioMart software suite, http://www.biomart.org}. The
1762 package enables retrieval of large amounts of data in a uniform way without
1763 the need to know the underlying database schemas or write complex SQL queries.
1764 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
1765 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
1766 users direct access to a diverse set of data and enable a wide range of
1767 powerful online queries from gene annotation to database mining.")
1768 (license license:artistic2.0)))
1770 (define-public r-biocparallel
1772 (name "r-biocparallel")
1776 (uri (bioconductor-uri "BiocParallel" version))
1779 "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
1781 `((upstream-name . "BiocParallel")))
1782 (build-system r-build-system)
1785 (modify-phases %standard-phases
1786 (add-after 'unpack 'make-reproducible
1788 ;; Remove generated documentation.
1789 (for-each delete-file
1790 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
1791 "inst/doc/Introduction_To_BiocParallel.pdf"
1792 "inst/doc/Errors_Logs_And_Debugging.pdf"
1793 "inst/doc/BiocParallel_BatchtoolsParam.R"
1794 "inst/doc/Introduction_To_BiocParallel.R"
1795 "inst/doc/Errors_Logs_And_Debugging.R"))
1797 ;; Remove time-dependent macro
1798 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
1799 "inst/doc/Introduction_To_BiocParallel.Rnw"
1800 "inst/doc/Errors_Logs_And_Debugging.Rnw"
1801 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
1802 "vignettes/Introduction_To_BiocParallel.Rnw"
1803 "vignettes/Errors_Logs_And_Debugging.Rnw")
1804 (("\\today") "later"))
1806 ;; Initialize the random number generator seed when building.
1807 (substitute* "R/internal_rng_stream.R"
1808 (("\"L'Ecuyer-CMRG\"\\)" m)
1810 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
1812 `(("r-futile-logger" ,r-futile-logger)
1816 `(("r-knitr" ,r-knitr)))
1817 (home-page "https://bioconductor.org/packages/BiocParallel")
1818 (synopsis "Bioconductor facilities for parallel evaluation")
1820 "This package provides modified versions and novel implementation of
1821 functions for parallel evaluation, tailored to use with Bioconductor
1823 (license (list license:gpl2+ license:gpl3+))))
1825 (define-public r-biostrings
1827 (name "r-biostrings")
1831 (uri (bioconductor-uri "Biostrings" version))
1834 "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
1836 `((upstream-name . "Biostrings")))
1837 (build-system r-build-system)
1839 `(("r-biocgenerics" ,r-biocgenerics)
1840 ("r-crayon" ,r-crayon)
1841 ("r-iranges" ,r-iranges)
1842 ("r-s4vectors" ,r-s4vectors)
1843 ("r-xvector" ,r-xvector)))
1844 (home-page "https://bioconductor.org/packages/Biostrings")
1845 (synopsis "String objects and algorithms for biological sequences")
1847 "This package provides memory efficient string containers, string
1848 matching algorithms, and other utilities, for fast manipulation of large
1849 biological sequences or sets of sequences.")
1850 (license license:artistic2.0)))
1852 (define-public r-category
1859 (uri (bioconductor-uri "Category" version))
1862 "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
1863 (properties `((upstream-name . "Category")))
1864 (build-system r-build-system)
1866 `(("r-annotate" ,r-annotate)
1867 ("r-annotationdbi" ,r-annotationdbi)
1868 ("r-biobase" ,r-biobase)
1869 ("r-biocgenerics" ,r-biocgenerics)
1870 ("r-genefilter" ,r-genefilter)
1871 ("r-graph" ,r-graph)
1872 ("r-gseabase" ,r-gseabase)
1873 ("r-matrix" ,r-matrix)
1876 (home-page "https://bioconductor.org/packages/Category")
1877 (synopsis "Category analysis")
1879 "This package provides a collection of tools for performing category
1881 (license license:artistic2.0)))
1883 (define-public r-deseq2
1890 (uri (bioconductor-uri "DESeq2" version))
1893 "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19"))))
1894 (properties `((upstream-name . "DESeq2")))
1895 (build-system r-build-system)
1897 `(("r-biobase" ,r-biobase)
1898 ("r-biocgenerics" ,r-biocgenerics)
1899 ("r-biocparallel" ,r-biocparallel)
1900 ("r-genefilter" ,r-genefilter)
1901 ("r-geneplotter" ,r-geneplotter)
1902 ("r-genomicranges" ,r-genomicranges)
1903 ("r-ggplot2" ,r-ggplot2)
1904 ("r-iranges" ,r-iranges)
1905 ("r-locfit" ,r-locfit)
1907 ("r-rcpparmadillo" ,r-rcpparmadillo)
1908 ("r-s4vectors" ,r-s4vectors)
1909 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1911 `(("r-knitr" ,r-knitr)))
1912 (home-page "https://bioconductor.org/packages/DESeq2")
1913 (synopsis "Differential gene expression analysis")
1915 "This package provides functions to estimate variance-mean dependence in
1916 count data from high-throughput nucleotide sequencing assays and test for
1917 differential expression based on a model using the negative binomial
1919 (license license:lgpl3+)))
1921 (define-public r-dexseq
1928 (uri (bioconductor-uri "DEXSeq" version))
1931 "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
1932 (properties `((upstream-name . "DEXSeq")))
1933 (build-system r-build-system)
1935 `(("r-annotationdbi" ,r-annotationdbi)
1936 ("r-biobase" ,r-biobase)
1937 ("r-biocgenerics" ,r-biocgenerics)
1938 ("r-biocparallel" ,r-biocparallel)
1939 ("r-biomart" ,r-biomart)
1940 ("r-deseq2" ,r-deseq2)
1941 ("r-genefilter" ,r-genefilter)
1942 ("r-geneplotter" ,r-geneplotter)
1943 ("r-genomicranges" ,r-genomicranges)
1944 ("r-hwriter" ,r-hwriter)
1945 ("r-iranges" ,r-iranges)
1946 ("r-rcolorbrewer" ,r-rcolorbrewer)
1947 ("r-rsamtools" ,r-rsamtools)
1948 ("r-s4vectors" ,r-s4vectors)
1949 ("r-statmod" ,r-statmod)
1950 ("r-stringr" ,r-stringr)
1951 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1953 `(("r-knitr" ,r-knitr)))
1954 (home-page "https://bioconductor.org/packages/DEXSeq")
1955 (synopsis "Inference of differential exon usage in RNA-Seq")
1957 "This package is focused on finding differential exon usage using RNA-seq
1958 exon counts between samples with different experimental designs. It provides
1959 functions that allows the user to make the necessary statistical tests based
1960 on a model that uses the negative binomial distribution to estimate the
1961 variance between biological replicates and generalized linear models for
1962 testing. The package also provides functions for the visualization and
1963 exploration of the results.")
1964 (license license:gpl3+)))
1966 (define-public r-edger
1972 (uri (bioconductor-uri "edgeR" version))
1975 "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
1976 (properties `((upstream-name . "edgeR")))
1977 (build-system r-build-system)
1979 `(("r-limma" ,r-limma)
1980 ("r-locfit" ,r-locfit)
1982 ("r-statmod" ,r-statmod))) ;for estimateDisp
1983 (home-page "http://bioinf.wehi.edu.au/edgeR")
1984 (synopsis "EdgeR does empirical analysis of digital gene expression data")
1985 (description "This package can do differential expression analysis of
1986 RNA-seq expression profiles with biological replication. It implements a range
1987 of statistical methodology based on the negative binomial distributions,
1988 including empirical Bayes estimation, exact tests, generalized linear models
1989 and quasi-likelihood tests. It be applied to differential signal analysis of
1990 other types of genomic data that produce counts, including ChIP-seq, SAGE and
1992 (license license:gpl2+)))
1994 (define-public r-genefilter
1996 (name "r-genefilter")
2001 (uri (bioconductor-uri "genefilter" version))
2004 "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
2005 (build-system r-build-system)
2007 `(("gfortran" ,gfortran)
2008 ("r-knitr" ,r-knitr)))
2010 `(("r-annotate" ,r-annotate)
2011 ("r-annotationdbi" ,r-annotationdbi)
2012 ("r-biobase" ,r-biobase)
2013 ("r-biocgenerics" ,r-biocgenerics)
2014 ("r-survival" ,r-survival)))
2015 (home-page "https://bioconductor.org/packages/genefilter")
2016 (synopsis "Filter genes from high-throughput experiments")
2018 "This package provides basic functions for filtering genes from
2019 high-throughput sequencing experiments.")
2020 (license license:artistic2.0)))
2022 (define-public r-genomeinfodb
2024 (name "r-genomeinfodb")
2028 (uri (bioconductor-uri "GenomeInfoDb" version))
2031 "1wy4dwiv0pgim975var802z565py4a0nakx6zdvbhry4c0dfczd1"))))
2033 `((upstream-name . "GenomeInfoDb")))
2034 (build-system r-build-system)
2036 `(("r-biocgenerics" ,r-biocgenerics)
2037 ("r-genomeinfodbdata" ,r-genomeinfodbdata)
2038 ("r-iranges" ,r-iranges)
2039 ("r-rcurl" ,r-rcurl)
2040 ("r-s4vectors" ,r-s4vectors)))
2042 `(("r-knitr" ,r-knitr)))
2043 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
2044 (synopsis "Utilities for manipulating chromosome identifiers")
2046 "This package contains data and functions that define and allow
2047 translation between different chromosome sequence naming conventions (e.g.,
2048 \"chr1\" versus \"1\"), including a function that attempts to place sequence
2049 names in their natural, rather than lexicographic, order.")
2050 (license license:artistic2.0)))
2052 (define-public r-genomicranges
2054 (name "r-genomicranges")
2058 (uri (bioconductor-uri "GenomicRanges" version))
2061 "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
2063 `((upstream-name . "GenomicRanges")))
2064 (build-system r-build-system)
2066 `(("r-biocgenerics" ,r-biocgenerics)
2067 ("r-genomeinfodb" ,r-genomeinfodb)
2068 ("r-iranges" ,r-iranges)
2069 ("r-s4vectors" ,r-s4vectors)
2070 ("r-xvector" ,r-xvector)))
2072 `(("r-knitr" ,r-knitr)))
2073 (home-page "https://bioconductor.org/packages/GenomicRanges")
2074 (synopsis "Representation and manipulation of genomic intervals")
2076 "This package provides tools to efficiently represent and manipulate
2077 genomic annotations and alignments is playing a central role when it comes to
2078 analyzing high-throughput sequencing data (a.k.a. NGS data). The
2079 GenomicRanges package defines general purpose containers for storing and
2080 manipulating genomic intervals and variables defined along a genome.")
2081 (license license:artistic2.0)))
2083 (define-public r-gostats
2090 (uri (bioconductor-uri "GOstats" version))
2093 "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
2094 (properties `((upstream-name . "GOstats")))
2095 (build-system r-build-system)
2097 `(("r-annotate" ,r-annotate)
2098 ("r-annotationdbi" ,r-annotationdbi)
2099 ("r-annotationforge" ,r-annotationforge)
2100 ("r-biobase" ,r-biobase)
2101 ("r-category" ,r-category)
2102 ("r-go-db" ,r-go-db)
2103 ("r-graph" ,r-graph)
2104 ("r-rgraphviz" ,r-rgraphviz)
2105 ("r-rbgl" ,r-rbgl)))
2106 (home-page "https://bioconductor.org/packages/GOstats")
2107 (synopsis "Tools for manipulating GO and microarrays")
2109 "This package provides a set of tools for interacting with GO and
2110 microarray data. A variety of basic manipulation tools for graphs, hypothesis
2111 testing and other simple calculations.")
2112 (license license:artistic2.0)))
2114 (define-public r-gseabase
2121 (uri (bioconductor-uri "GSEABase" version))
2124 "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
2125 (properties `((upstream-name . "GSEABase")))
2126 (build-system r-build-system)
2128 `(("r-annotate" ,r-annotate)
2129 ("r-annotationdbi" ,r-annotationdbi)
2130 ("r-biobase" ,r-biobase)
2131 ("r-biocgenerics" ,r-biocgenerics)
2132 ("r-graph" ,r-graph)
2135 `(("r-knitr" ,r-knitr)))
2136 (home-page "https://bioconductor.org/packages/GSEABase")
2137 (synopsis "Gene set enrichment data structures and methods")
2139 "This package provides classes and methods to support @dfn{Gene Set
2140 Enrichment Analysis} (GSEA).")
2141 (license license:artistic2.0)))
2143 (define-public r-hpar
2150 (uri (bioconductor-uri "hpar" version))
2153 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
2154 (build-system r-build-system)
2156 `(("r-knitr" ,r-knitr)))
2157 (home-page "https://bioconductor.org/packages/hpar/")
2158 (synopsis "Human Protein Atlas in R")
2159 (description "This package provides a simple interface to and data from
2160 the Human Protein Atlas project.")
2161 (license license:artistic2.0)))
2163 (define-public r-limma
2169 (uri (bioconductor-uri "limma" version))
2172 "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
2173 (build-system r-build-system)
2174 (home-page "http://bioinf.wehi.edu.au/limma")
2175 (synopsis "Package for linear models for microarray and RNA-seq data")
2176 (description "This package can be used for the analysis of gene expression
2177 studies, especially the use of linear models for analysing designed experiments
2178 and the assessment of differential expression. The analysis methods apply to
2179 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
2180 (license license:gpl2+)))
2182 (define-public r-rbgl
2189 (uri (bioconductor-uri "RBGL" version))
2192 "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
2193 (properties `((upstream-name . "RBGL")))
2194 (build-system r-build-system)
2197 ("r-graph" ,r-graph)))
2198 (home-page "https://www.bioconductor.org/packages/RBGL")
2199 (synopsis "Interface to the Boost graph library")
2201 "This package provides a fairly extensive and comprehensive interface to
2202 the graph algorithms contained in the Boost library.")
2203 (license license:artistic2.0)))
2205 (define-public r-regioner
2212 (uri (bioconductor-uri "regioneR" version))
2215 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
2216 (properties `((upstream-name . "regioneR")))
2217 (build-system r-build-system)
2219 `(("r-biostrings" ,r-biostrings)
2220 ("r-bsgenome" ,r-bsgenome)
2221 ("r-genomeinfodb" ,r-genomeinfodb)
2222 ("r-genomicranges" ,r-genomicranges)
2223 ("r-iranges" ,r-iranges)
2224 ("r-memoise" ,r-memoise)
2225 ("r-rtracklayer" ,r-rtracklayer)
2226 ("r-s4vectors" ,r-s4vectors)))
2228 `(("r-knitr" ,r-knitr)))
2229 (home-page "https://bioconductor.org/packages/regioneR/")
2230 (synopsis "Association analysis of genomic regions")
2231 (description "This package offers a statistical framework based on
2232 customizable permutation tests to assess the association between genomic
2233 region sets and other genomic features.")
2234 (license license:artistic2.0)))
2236 (define-public r-reportingtools
2238 (name "r-reportingtools")
2243 (uri (bioconductor-uri "ReportingTools" version))
2246 "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb"))))
2248 `((upstream-name . "ReportingTools")))
2249 (build-system r-build-system)
2251 `(("r-annotate" ,r-annotate)
2252 ("r-annotationdbi" ,r-annotationdbi)
2253 ("r-biobase" ,r-biobase)
2254 ("r-biocgenerics" ,r-biocgenerics)
2255 ("r-category" ,r-category)
2256 ("r-deseq2" ,r-deseq2)
2257 ("r-edger" ,r-edger)
2258 ("r-ggbio" ,r-ggbio)
2259 ("r-ggplot2" ,r-ggplot2)
2260 ("r-gostats" ,r-gostats)
2261 ("r-gseabase" ,r-gseabase)
2262 ("r-hwriter" ,r-hwriter)
2263 ("r-iranges" ,r-iranges)
2264 ("r-knitr" ,r-knitr)
2265 ("r-lattice" ,r-lattice)
2266 ("r-limma" ,r-limma)
2267 ("r-pfam-db" ,r-pfam-db)
2268 ("r-r-utils" ,r-r-utils)
2271 `(("r-knitr" ,r-knitr)))
2272 (home-page "https://bioconductor.org/packages/ReportingTools/")
2273 (synopsis "Tools for making reports in various formats")
2275 "The ReportingTools package enables users to easily display reports of
2276 analysis results generated from sources such as microarray and sequencing
2277 data. The package allows users to create HTML pages that may be viewed on a
2278 web browser, or in other formats. Users can generate tables with sortable and
2279 filterable columns, make and display plots, and link table entries to other
2280 data sources such as NCBI or larger plots within the HTML page. Using the
2281 package, users can also produce a table of contents page to link various
2282 reports together for a particular project that can be viewed in a web
2284 (license license:artistic2.0)))
2286 (define-public r-rsamtools
2288 (name "r-rsamtools")
2292 (uri (bioconductor-uri "Rsamtools" version))
2295 "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
2297 `((upstream-name . "Rsamtools")))
2298 (build-system r-build-system)
2301 (modify-phases %standard-phases
2302 (add-after 'unpack 'use-system-zlib
2304 (substitute* "DESCRIPTION"
2305 (("zlibbioc, ") ""))
2306 (substitute* "NAMESPACE"
2307 (("import\\(zlibbioc\\)") ""))
2310 `(("r-biocgenerics" ,r-biocgenerics)
2311 ("r-biocparallel" ,r-biocparallel)
2312 ("r-biostrings" ,r-biostrings)
2313 ("r-bitops" ,r-bitops)
2314 ("r-genomeinfodb" ,r-genomeinfodb)
2315 ("r-genomicranges" ,r-genomicranges)
2316 ("r-iranges" ,r-iranges)
2317 ("r-rhtslib" ,r-rhtslib)
2318 ("r-s4vectors" ,r-s4vectors)
2319 ("r-xvector" ,r-xvector)))
2320 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
2321 (synopsis "Interface to samtools, bcftools, and tabix")
2323 "This package provides an interface to the @code{samtools},
2324 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
2325 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
2326 tab-delimited (tabix) files.")
2327 (license license:expat)))
2329 (define-public r-shortread
2331 (name "r-shortread")
2336 (uri (bioconductor-uri "ShortRead" version))
2339 "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
2340 (properties `((upstream-name . "ShortRead")))
2341 (build-system r-build-system)
2345 `(("r-biobase" ,r-biobase)
2346 ("r-biocgenerics" ,r-biocgenerics)
2347 ("r-biocparallel" ,r-biocparallel)
2348 ("r-biostrings" ,r-biostrings)
2349 ("r-genomeinfodb" ,r-genomeinfodb)
2350 ("r-genomicalignments" ,r-genomicalignments)
2351 ("r-genomicranges" ,r-genomicranges)
2352 ("r-rhtslib" ,r-rhtslib)
2353 ("r-hwriter" ,r-hwriter)
2354 ("r-iranges" ,r-iranges)
2355 ("r-lattice" ,r-lattice)
2356 ("r-latticeextra" ,r-latticeextra)
2357 ("r-rsamtools" ,r-rsamtools)
2358 ("r-s4vectors" ,r-s4vectors)
2359 ("r-xvector" ,r-xvector)
2360 ("r-zlibbioc" ,r-zlibbioc)))
2361 (home-page "https://bioconductor.org/packages/ShortRead")
2362 (synopsis "FASTQ input and manipulation tools")
2364 "This package implements sampling, iteration, and input of FASTQ files.
2365 It includes functions for filtering and trimming reads, and for generating a
2366 quality assessment report. Data are represented as
2367 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
2368 purposes. The package also contains legacy support for early single-end,
2369 ungapped alignment formats.")
2370 (license license:artistic2.0)))
2372 (define-public r-systempiper
2374 (name "r-systempiper")
2379 (uri (bioconductor-uri "systemPipeR" version))
2382 "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
2383 (properties `((upstream-name . "systemPipeR")))
2384 (build-system r-build-system)
2386 `(("r-annotate" ,r-annotate)
2387 ("r-assertthat" ,r-assertthat)
2388 ("r-batchtools" ,r-batchtools)
2389 ("r-biostrings" ,r-biostrings)
2390 ("r-deseq2" ,r-deseq2)
2392 ("r-edger" ,r-edger)
2393 ("r-genomicfeatures" ,r-genomicfeatures)
2394 ("r-genomicranges" ,r-genomicranges)
2395 ("r-ggplot2" ,r-ggplot2)
2396 ("r-go-db" ,r-go-db)
2397 ("r-gostats" ,r-gostats)
2398 ("r-iranges" ,r-iranges)
2399 ("r-limma" ,r-limma)
2400 ("r-magrittr" ,r-magrittr)
2401 ("r-pheatmap" ,r-pheatmap)
2402 ("r-rjson" ,r-rjson)
2403 ("r-rsamtools" ,r-rsamtools)
2405 ("r-shortread" ,r-shortread)
2406 ("r-stringr" ,r-stringr)
2407 ("r-summarizedexperiment" ,r-summarizedexperiment)
2409 ("r-variantannotation" ,r-variantannotation)))
2411 `(("r-knitr" ,r-knitr)))
2412 (home-page "https://github.com/tgirke/systemPipeR")
2413 (synopsis "Next generation sequencing workflow and reporting environment")
2415 "This R package provides tools for building and running automated
2416 end-to-end analysis workflows for a wide range of @dfn{next generation
2417 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
2418 Important features include a uniform workflow interface across different NGS
2419 applications, automated report generation, and support for running both R and
2420 command-line software, such as NGS aligners or peak/variant callers, on local
2421 computers or compute clusters. Efficient handling of complex sample sets and
2422 experimental designs is facilitated by a consistently implemented sample
2423 annotation infrastructure.")
2424 (license license:artistic2.0)))
2426 (define-public r-variantannotation
2428 (name "r-variantannotation")
2432 (uri (bioconductor-uri "VariantAnnotation" version))
2435 "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
2437 `((upstream-name . "VariantAnnotation")))
2439 `(("r-annotationdbi" ,r-annotationdbi)
2440 ("r-biobase" ,r-biobase)
2441 ("r-biocgenerics" ,r-biocgenerics)
2442 ("r-biostrings" ,r-biostrings)
2443 ("r-bsgenome" ,r-bsgenome)
2445 ("r-genomeinfodb" ,r-genomeinfodb)
2446 ("r-genomicfeatures" ,r-genomicfeatures)
2447 ("r-genomicranges" ,r-genomicranges)
2448 ("r-iranges" ,r-iranges)
2449 ("r-matrixgenerics" ,r-matrixgenerics)
2450 ("r-summarizedexperiment" ,r-summarizedexperiment)
2451 ("r-rhtslib" ,r-rhtslib)
2452 ("r-rsamtools" ,r-rsamtools)
2453 ("r-rtracklayer" ,r-rtracklayer)
2454 ("r-s4vectors" ,r-s4vectors)
2455 ("r-xvector" ,r-xvector)
2456 ("r-zlibbioc" ,r-zlibbioc)))
2457 (build-system r-build-system)
2458 (home-page "https://bioconductor.org/packages/VariantAnnotation")
2459 (synopsis "Package for annotation of genetic variants")
2460 (description "This R package can annotate variants, compute amino acid
2461 coding changes and predict coding outcomes.")
2462 (license license:artistic2.0)))
2464 (define-public r-xvector
2470 (uri (bioconductor-uri "XVector" version))
2473 "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
2475 `((upstream-name . "XVector")))
2476 (build-system r-build-system)
2479 (modify-phases %standard-phases
2480 (add-after 'unpack 'use-system-zlib
2482 (substitute* "DESCRIPTION"
2483 (("zlibbioc, ") ""))
2484 (substitute* "NAMESPACE"
2485 (("import\\(zlibbioc\\)") ""))
2490 `(("r-biocgenerics" ,r-biocgenerics)
2491 ("r-iranges" ,r-iranges)
2492 ("r-s4vectors" ,r-s4vectors)))
2493 (home-page "https://bioconductor.org/packages/XVector")
2494 (synopsis "Representation and manpulation of external sequences")
2496 "This package provides memory efficient S4 classes for storing sequences
2497 \"externally\" (behind an R external pointer, or on disk).")
2498 (license license:artistic2.0)))
2500 (define-public r-geneplotter
2502 (name "r-geneplotter")
2507 (uri (bioconductor-uri "geneplotter" version))
2510 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
2511 (build-system r-build-system)
2513 `(("r-annotate" ,r-annotate)
2514 ("r-annotationdbi" ,r-annotationdbi)
2515 ("r-biobase" ,r-biobase)
2516 ("r-biocgenerics" ,r-biocgenerics)
2517 ("r-lattice" ,r-lattice)
2518 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2519 (home-page "https://bioconductor.org/packages/geneplotter")
2520 (synopsis "Graphics functions for genomic data")
2522 "This package provides functions for plotting genomic data.")
2523 (license license:artistic2.0)))
2525 (define-public r-oligoclasses
2527 (name "r-oligoclasses")
2532 (uri (bioconductor-uri "oligoClasses" version))
2535 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
2536 (properties `((upstream-name . "oligoClasses")))
2537 (build-system r-build-system)
2539 `(("r-affyio" ,r-affyio)
2540 ("r-biobase" ,r-biobase)
2541 ("r-biocgenerics" ,r-biocgenerics)
2542 ("r-biocmanager" ,r-biocmanager)
2543 ("r-biostrings" ,r-biostrings)
2546 ("r-foreach" ,r-foreach)
2547 ("r-genomicranges" ,r-genomicranges)
2548 ("r-iranges" ,r-iranges)
2549 ("r-rsqlite" ,r-rsqlite)
2550 ("r-s4vectors" ,r-s4vectors)
2551 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2552 (home-page "https://bioconductor.org/packages/oligoClasses/")
2553 (synopsis "Classes for high-throughput arrays")
2555 "This package contains class definitions, validity checks, and
2556 initialization methods for classes used by the @code{oligo} and @code{crlmm}
2558 (license license:gpl2+)))
2560 (define-public r-oligo
2567 (uri (bioconductor-uri "oligo" version))
2570 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
2571 (properties `((upstream-name . "oligo")))
2572 (build-system r-build-system)
2573 (inputs `(("zlib" ,zlib)))
2575 `(("r-affxparser" ,r-affxparser)
2576 ("r-affyio" ,r-affyio)
2577 ("r-biobase" ,r-biobase)
2578 ("r-biocgenerics" ,r-biocgenerics)
2579 ("r-biostrings" ,r-biostrings)
2582 ("r-oligoclasses" ,r-oligoclasses)
2583 ("r-preprocesscore" ,r-preprocesscore)
2584 ("r-rsqlite" ,r-rsqlite)
2585 ("r-zlibbioc" ,r-zlibbioc)))
2587 `(("r-knitr" ,r-knitr)))
2588 (home-page "https://bioconductor.org/packages/oligo/")
2589 (synopsis "Preprocessing tools for oligonucleotide arrays")
2591 "This package provides a package to analyze oligonucleotide
2592 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
2593 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
2594 (license license:lgpl2.0+)))
2596 (define-public r-qvalue
2603 (uri (bioconductor-uri "qvalue" version))
2606 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
2607 (build-system r-build-system)
2609 `(("r-ggplot2" ,r-ggplot2)
2610 ("r-reshape2" ,r-reshape2)))
2612 `(("r-knitr" ,r-knitr)))
2613 (home-page "https://github.com/StoreyLab/qvalue")
2614 (synopsis "Q-value estimation for false discovery rate control")
2616 "This package takes a list of p-values resulting from the simultaneous
2617 testing of many hypotheses and estimates their q-values and local @dfn{false
2618 discovery rate} (FDR) values. The q-value of a test measures the proportion
2619 of false positives incurred when that particular test is called significant.
2620 The local FDR measures the posterior probability the null hypothesis is true
2621 given the test's p-value. Various plots are automatically generated, allowing
2622 one to make sensible significance cut-offs. The software can be applied to
2623 problems in genomics, brain imaging, astrophysics, and data mining.")
2624 ;; Any version of the LGPL.
2625 (license license:lgpl3+)))
2627 (define r-rcppnumerical
2629 (name "r-rcppnumerical")
2633 (uri (cran-uri "RcppNumerical" version))
2636 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
2637 (properties `((upstream-name . "RcppNumerical")))
2638 (build-system r-build-system)
2640 `(("r-rcpp" ,r-rcpp)
2641 ("r-rcppeigen" ,r-rcppeigen)))
2643 `(("r-knitr" ,r-knitr)))
2644 (home-page "https://github.com/yixuan/RcppNumerical")
2645 (synopsis "Rcpp integration for numerical computing libraries")
2646 (description "This package provides a collection of open source libraries
2647 for numerical computing (numerical integration, optimization, etc.) and their
2648 integration with @code{Rcpp}.")
2649 (license license:gpl2+)))
2651 (define-public r-apeglm
2657 (uri (bioconductor-uri "apeglm" version))
2660 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
2661 (properties `((upstream-name . "apeglm")))
2662 (build-system r-build-system)
2664 `(("r-emdbook" ,r-emdbook)
2665 ("r-genomicranges" ,r-genomicranges)
2667 ("r-rcppeigen" ,r-rcppeigen)
2668 ("r-rcppnumerical" ,r-rcppnumerical)
2669 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2670 (native-inputs `(("r-knitr" ,r-knitr)))
2671 (home-page "https://bioconductor.org/packages/apeglm")
2672 (synopsis "Approximate posterior estimation for GLM coefficients")
2673 (description "This package provides Bayesian shrinkage estimators for
2674 effect sizes for a variety of GLM models, using approximation of the
2675 posterior for individual coefficients.")
2676 (license license:gpl2)))
2678 (define-public r-greylistchip
2680 (name "r-greylistchip")
2684 (uri (bioconductor-uri "GreyListChIP" version))
2687 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
2688 (properties `((upstream-name . "GreyListChIP")))
2689 (build-system r-build-system)
2691 `(("r-bsgenome" ,r-bsgenome)
2692 ("r-genomeinfodb" ,r-genomeinfodb)
2693 ("r-genomicalignments" ,r-genomicalignments)
2694 ("r-genomicranges" ,r-genomicranges)
2696 ("r-rsamtools" ,r-rsamtools)
2697 ("r-rtracklayer" ,r-rtracklayer)
2698 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2699 (home-page "https://bioconductor.org/packages/GreyListChIP")
2700 (synopsis "Greylist artefact regions based on ChIP inputs")
2701 (description "This package identifies regions of ChIP experiments with high
2702 signal in the input, that lead to spurious peaks during peak calling.")
2703 (license license:artistic2.0)))
2705 (define-public r-diffbind
2712 (uri (bioconductor-uri "DiffBind" version))
2715 "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi"))))
2716 (properties `((upstream-name . "DiffBind")))
2717 (build-system r-build-system)
2719 `(("r-amap" ,r-amap)
2720 ("r-apeglm" ,r-apeglm)
2722 ("r-biocparallel" ,r-biocparallel)
2723 ("r-deseq2" ,r-deseq2)
2724 ("r-dplyr" ,r-dplyr)
2725 ("r-genomicalignments" ,r-genomicalignments)
2726 ("r-genomicranges" ,r-genomicranges)
2727 ("r-ggplot2" ,r-ggplot2)
2728 ("r-ggrepel" ,r-ggrepel)
2729 ("r-gplots" ,r-gplots)
2730 ("r-greylistchip" ,r-greylistchip)
2731 ("r-iranges" ,r-iranges)
2732 ("r-lattice" ,r-lattice)
2733 ("r-limma" ,r-limma)
2734 ("r-locfit" ,r-locfit)
2735 ("r-rcolorbrewer" , r-rcolorbrewer)
2737 ("r-rhtslib" ,r-rhtslib)
2738 ("r-rsamtools" ,r-rsamtools)
2739 ("r-s4vectors" ,r-s4vectors)
2740 ("r-summarizedexperiment" ,r-summarizedexperiment)
2741 ("r-systempiper" ,r-systempiper)))
2742 (home-page "https://bioconductor.org/packages/DiffBind")
2743 (synopsis "Differential binding analysis of ChIP-Seq peak data")
2745 "This package computes differentially bound sites from multiple
2746 ChIP-seq experiments using affinity (quantitative) data. Also enables
2747 occupancy (overlap) analysis and plotting functions.")
2748 (license license:artistic2.0)))
2750 (define-public r-ripseeker
2752 (name "r-ripseeker")
2757 (uri (bioconductor-uri "RIPSeeker" version))
2760 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
2761 (properties `((upstream-name . "RIPSeeker")))
2762 (build-system r-build-system)
2764 `(("r-s4vectors" ,r-s4vectors)
2765 ("r-iranges" ,r-iranges)
2766 ("r-genomicranges" ,r-genomicranges)
2767 ("r-summarizedexperiment" ,r-summarizedexperiment)
2768 ("r-rsamtools" ,r-rsamtools)
2769 ("r-genomicalignments" ,r-genomicalignments)
2770 ("r-rtracklayer" ,r-rtracklayer)))
2771 (home-page "https://bioconductor.org/packages/RIPSeeker")
2773 "Identifying protein-associated transcripts from RIP-seq experiments")
2775 "This package infers and discriminates RIP peaks from RIP-seq alignments
2776 using two-state HMM with negative binomial emission probability. While
2777 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
2778 a suite of bioinformatics tools integrated within this self-contained software
2779 package comprehensively addressing issues ranging from post-alignments
2780 processing to visualization and annotation.")
2781 (license license:gpl2)))
2783 (define-public r-multtest
2790 (uri (bioconductor-uri "multtest" version))
2793 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
2794 (build-system r-build-system)
2796 `(("r-survival" ,r-survival)
2797 ("r-biocgenerics" ,r-biocgenerics)
2798 ("r-biobase" ,r-biobase)
2799 ("r-mass" ,r-mass)))
2800 (home-page "https://bioconductor.org/packages/multtest")
2801 (synopsis "Resampling-based multiple hypothesis testing")
2803 "This package can do non-parametric bootstrap and permutation
2804 resampling-based multiple testing procedures (including empirical Bayes
2805 methods) for controlling the family-wise error rate (FWER), generalized
2806 family-wise error rate (gFWER), tail probability of the proportion of
2807 false positives (TPPFP), and false discovery rate (FDR). Several choices
2808 of bootstrap-based null distribution are implemented (centered, centered
2809 and scaled, quantile-transformed). Single-step and step-wise methods are
2810 available. Tests based on a variety of T- and F-statistics (including
2811 T-statistics based on regression parameters from linear and survival models
2812 as well as those based on correlation parameters) are included. When probing
2813 hypotheses with T-statistics, users may also select a potentially faster null
2814 distribution which is multivariate normal with mean zero and variance
2815 covariance matrix derived from the vector influence function. Results are
2816 reported in terms of adjusted P-values, confidence regions and test statistic
2817 cutoffs. The procedures are directly applicable to identifying differentially
2818 expressed genes in DNA microarray experiments.")
2819 (license license:lgpl3)))
2821 (define-public r-graph
2827 (uri (bioconductor-uri "graph" version))
2830 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
2831 (build-system r-build-system)
2833 `(("r-biocgenerics" ,r-biocgenerics)))
2834 (home-page "https://bioconductor.org/packages/graph")
2835 (synopsis "Handle graph data structures in R")
2837 "This package implements some simple graph handling capabilities for R.")
2838 (license license:artistic2.0)))
2840 ;; This is a CRAN package, but it depends on a Bioconductor package.
2841 (define-public r-ggm
2848 (uri (cran-uri "ggm" version))
2851 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
2852 (properties `((upstream-name . "ggm")))
2853 (build-system r-build-system)
2855 `(("r-graph" ,r-graph)
2856 ("r-igraph" ,r-igraph)))
2857 (home-page "https://cran.r-project.org/package=ggm")
2858 (synopsis "Functions for graphical Markov models")
2860 "This package provides functions and datasets for maximum likelihood
2861 fitting of some classes of graphical Markov models.")
2862 (license license:gpl2+)))
2864 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
2865 (define-public r-perfmeas
2872 (uri (cran-uri "PerfMeas" version))
2875 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
2876 (properties `((upstream-name . "PerfMeas")))
2877 (build-system r-build-system)
2879 `(("r-graph" ,r-graph)
2880 ("r-limma" ,r-limma)
2881 ("r-rbgl" ,r-rbgl)))
2882 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
2883 (synopsis "Performance measures for ranking and classification tasks")
2885 "This package implements different performance measures for
2886 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
2887 a given recall, F-score for single and multiple classes are available.")
2888 (license license:gpl2+)))
2890 ;; This is a CRAN package, but it depends on a Bioconductor package.
2891 (define-public r-codedepends
2893 (name "r-codedepends")
2898 (uri (cran-uri "CodeDepends" version))
2901 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
2902 (properties `((upstream-name . "CodeDepends")))
2903 (build-system r-build-system)
2905 `(("r-codetools" ,r-codetools)
2906 ("r-graph" ,r-graph)
2908 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
2909 (synopsis "Analysis of R code for reproducible research and code comprehension")
2911 "This package provides tools for analyzing R expressions or blocks of
2912 code and determining the dependencies between them. It focuses on R scripts,
2913 but can be used on the bodies of functions. There are many facilities
2914 including the ability to summarize or get a high-level view of code,
2915 determining dependencies between variables, code improvement suggestions.")
2916 ;; Any version of the GPL
2917 (license (list license:gpl2+ license:gpl3+))))
2919 (define-public r-chippeakanno
2921 (name "r-chippeakanno")
2926 (uri (bioconductor-uri "ChIPpeakAnno" version))
2929 "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw"))))
2930 (properties `((upstream-name . "ChIPpeakAnno")))
2931 (build-system r-build-system)
2933 `(("r-annotationdbi" ,r-annotationdbi)
2934 ("r-biocgenerics" ,r-biocgenerics)
2935 ("r-biomart" ,r-biomart)
2936 ("r-biostrings" ,r-biostrings)
2938 ("r-dplyr" ,r-dplyr)
2939 ("r-ensembldb" ,r-ensembldb)
2940 ("r-genomeinfodb" ,r-genomeinfodb)
2941 ("r-genomicalignments" ,r-genomicalignments)
2942 ("r-genomicfeatures" ,r-genomicfeatures)
2943 ("r-genomicranges" ,r-genomicranges)
2944 ("r-ggplot2" ,r-ggplot2)
2945 ("r-graph" ,r-graph)
2946 ("r-iranges" ,r-iranges)
2947 ("r-keggrest" ,r-keggrest)
2948 ("r-matrixstats" ,r-matrixstats)
2949 ("r-multtest" ,r-multtest)
2951 ("r-regioner" ,r-regioner)
2952 ("r-rsamtools" ,r-rsamtools)
2953 ("r-rtracklayer" ,r-rtracklayer)
2954 ("r-s4vectors" ,r-s4vectors)
2955 ("r-summarizedexperiment" ,r-summarizedexperiment)
2956 ("r-venndiagram" ,r-venndiagram)))
2958 `(("r-knitr" ,r-knitr)))
2959 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
2960 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
2962 "The package includes functions to retrieve the sequences around the peak,
2963 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
2964 custom features such as most conserved elements and other transcription factor
2965 binding sites supplied by users. Starting 2.0.5, new functions have been added
2966 for finding the peaks with bi-directional promoters with summary statistics
2967 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
2968 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
2969 enrichedGO (addGeneIDs).")
2970 (license license:gpl2+)))
2972 (define-public r-matrixgenerics
2974 (name "r-matrixgenerics")
2978 (uri (bioconductor-uri "MatrixGenerics" version))
2981 "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
2983 `((upstream-name . "MatrixGenerics")))
2984 (build-system r-build-system)
2986 `(("r-matrixstats" ,r-matrixstats)))
2987 (home-page "https://bioconductor.org/packages/MatrixGenerics")
2988 (synopsis "S4 generic summary statistic functions for matrix-like objects")
2990 "This package provides S4 generic functions modeled after the
2991 @code{matrixStats} API for alternative matrix implementations. Packages with
2992 alternative matrix implementation can depend on this package and implement the
2993 generic functions that are defined here for a useful set of row and column
2994 summary statistics. Other package developers can import this package and
2995 handle a different matrix implementations without worrying about
2996 incompatibilities.")
2997 (license license:artistic2.0)))
2999 (define-public r-marray
3005 (uri (bioconductor-uri "marray" version))
3007 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
3008 (build-system r-build-system)
3010 `(("r-limma" ,r-limma)))
3011 (home-page "https://bioconductor.org/packages/marray")
3012 (synopsis "Exploratory analysis for two-color spotted microarray data")
3013 (description "This package contains class definitions for two-color spotted
3014 microarray data. It also includes functions for data input, diagnostic plots,
3015 normalization and quality checking.")
3016 (license license:lgpl2.0+)))
3018 (define-public r-cghbase
3024 (uri (bioconductor-uri "CGHbase" version))
3026 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
3027 (properties `((upstream-name . "CGHbase")))
3028 (build-system r-build-system)
3030 `(("r-biobase" ,r-biobase)
3031 ("r-marray" ,r-marray)))
3032 (home-page "https://bioconductor.org/packages/CGHbase")
3033 (synopsis "Base functions and classes for arrayCGH data analysis")
3034 (description "This package contains functions and classes that are needed by
3035 the @code{arrayCGH} packages.")
3036 (license license:gpl2+)))
3038 (define-public r-cghcall
3044 (uri (bioconductor-uri "CGHcall" version))
3046 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
3047 (properties `((upstream-name . "CGHcall")))
3048 (build-system r-build-system)
3050 `(("r-biobase" ,r-biobase)
3051 ("r-cghbase" ,r-cghbase)
3052 ("r-impute" ,r-impute)
3053 ("r-dnacopy" ,r-dnacopy)
3054 ("r-snowfall" ,r-snowfall)))
3055 (home-page "https://bioconductor.org/packages/CGHcall")
3056 (synopsis "Base functions and classes for arrayCGH data analysis")
3057 (description "This package contains functions and classes that are needed by
3058 @code{arrayCGH} packages.")
3059 (license license:gpl2+)))
3061 (define-public r-qdnaseq
3067 (uri (bioconductor-uri "QDNAseq" version))
3069 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
3070 (properties `((upstream-name . "QDNAseq")))
3071 (build-system r-build-system)
3073 `(("r-biobase" ,r-biobase)
3074 ("r-cghbase" ,r-cghbase)
3075 ("r-cghcall" ,r-cghcall)
3076 ("r-dnacopy" ,r-dnacopy)
3077 ("r-future" ,r-future)
3078 ("r-future-apply" ,r-future-apply)
3079 ("r-genomicranges" ,r-genomicranges)
3080 ("r-iranges" ,r-iranges)
3081 ("r-matrixstats" ,r-matrixstats)
3082 ("r-r-utils" ,r-r-utils)
3083 ("r-rsamtools" ,r-rsamtools)))
3084 (home-page "https://bioconductor.org/packages/QDNAseq")
3085 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
3086 (description "The genome is divided into non-overlapping fixed-sized bins,
3087 number of sequence reads in each counted, adjusted with a simultaneous
3088 two-dimensional loess correction for sequence mappability and GC content, and
3089 filtered to remove spurious regions in the genome. Downstream steps of
3090 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
3092 (license license:gpl2+)))
3094 (define-public r-bayseq
3101 (uri (bioconductor-uri "baySeq" version))
3104 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
3105 (properties `((upstream-name . "baySeq")))
3106 (build-system r-build-system)
3108 `(("r-abind" ,r-abind)
3109 ("r-edger" ,r-edger)
3110 ("r-genomicranges" ,r-genomicranges)))
3111 (home-page "https://bioconductor.org/packages/baySeq/")
3112 (synopsis "Bayesian analysis of differential expression patterns in count data")
3114 "This package identifies differential expression in high-throughput count
3115 data, such as that derived from next-generation sequencing machines,
3116 calculating estimated posterior likelihoods of differential expression (or
3117 more complex hypotheses) via empirical Bayesian methods.")
3118 (license license:gpl3)))
3120 (define-public r-chipcomp
3127 (uri (bioconductor-uri "ChIPComp" version))
3130 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
3131 (properties `((upstream-name . "ChIPComp")))
3132 (build-system r-build-system)
3134 `(("r-biocgenerics" ,r-biocgenerics)
3135 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
3136 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
3137 ("r-genomeinfodb" ,r-genomeinfodb)
3138 ("r-genomicranges" ,r-genomicranges)
3139 ("r-iranges" ,r-iranges)
3140 ("r-limma" ,r-limma)
3141 ("r-rsamtools" ,r-rsamtools)
3142 ("r-rtracklayer" ,r-rtracklayer)
3143 ("r-s4vectors" ,r-s4vectors)))
3144 (home-page "https://bioconductor.org/packages/ChIPComp")
3145 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
3147 "ChIPComp implements a statistical method for quantitative comparison of
3148 multiple ChIP-seq datasets. It detects differentially bound sharp binding
3149 sites across multiple conditions considering matching control in ChIP-seq
3151 ;; Any version of the GPL.
3152 (license license:gpl3+)))
3154 (define-public r-riboprofiling
3156 (name "r-riboprofiling")
3161 (uri (bioconductor-uri "RiboProfiling" version))
3164 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
3165 (properties `((upstream-name . "RiboProfiling")))
3166 (build-system r-build-system)
3168 `(("r-biocgenerics" ,r-biocgenerics)
3169 ("r-biostrings" ,r-biostrings)
3170 ("r-data-table" ,r-data-table)
3171 ("r-genomeinfodb" ,r-genomeinfodb)
3172 ("r-genomicalignments" ,r-genomicalignments)
3173 ("r-genomicfeatures" ,r-genomicfeatures)
3174 ("r-genomicranges" ,r-genomicranges)
3175 ("r-ggbio" ,r-ggbio)
3176 ("r-ggplot2" ,r-ggplot2)
3177 ("r-iranges" ,r-iranges)
3179 ("r-reshape2" ,r-reshape2)
3180 ("r-rsamtools" ,r-rsamtools)
3181 ("r-rtracklayer" ,r-rtracklayer)
3182 ("r-s4vectors" ,r-s4vectors)
3183 ("r-sqldf" ,r-sqldf)))
3185 `(("r-knitr" ,r-knitr)))
3186 (home-page "https://bioconductor.org/packages/RiboProfiling/")
3187 (synopsis "Ribosome profiling data analysis")
3188 (description "Starting with a BAM file, this package provides the
3189 necessary functions for quality assessment, read start position recalibration,
3190 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
3191 of count data: pairs, log fold-change, codon frequency and coverage
3192 assessment, principal component analysis on codon coverage.")
3193 (license license:gpl3)))
3195 (define-public r-riboseqr
3202 (uri (bioconductor-uri "riboSeqR" version))
3205 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
3206 (properties `((upstream-name . "riboSeqR")))
3207 (build-system r-build-system)
3209 `(("r-abind" ,r-abind)
3210 ("r-bayseq" ,r-bayseq)
3211 ("r-genomeinfodb" ,r-genomeinfodb)
3212 ("r-genomicranges" ,r-genomicranges)
3213 ("r-iranges" ,r-iranges)
3214 ("r-rsamtools" ,r-rsamtools)
3215 ("r-seqlogo" ,r-seqlogo)))
3216 (home-page "https://bioconductor.org/packages/riboSeqR/")
3217 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
3219 "This package provides plotting functions, frameshift detection and
3220 parsing of genetic sequencing data from ribosome profiling experiments.")
3221 (license license:gpl3)))
3223 (define-public r-interactionset
3225 (name "r-interactionset")
3230 (uri (bioconductor-uri "InteractionSet" version))
3233 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
3235 `((upstream-name . "InteractionSet")))
3236 (build-system r-build-system)
3238 `(("r-biocgenerics" ,r-biocgenerics)
3239 ("r-genomeinfodb" ,r-genomeinfodb)
3240 ("r-genomicranges" ,r-genomicranges)
3241 ("r-iranges" ,r-iranges)
3242 ("r-matrix" ,r-matrix)
3244 ("r-s4vectors" ,r-s4vectors)
3245 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3247 `(("r-knitr" ,r-knitr)))
3248 (home-page "https://bioconductor.org/packages/InteractionSet")
3249 (synopsis "Base classes for storing genomic interaction data")
3251 "This package provides the @code{GInteractions},
3252 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
3253 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
3255 (license license:gpl3)))
3257 (define-public r-genomicinteractions
3259 (name "r-genomicinteractions")
3264 (uri (bioconductor-uri "GenomicInteractions" version))
3267 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
3269 `((upstream-name . "GenomicInteractions")))
3270 (build-system r-build-system)
3272 `(("r-biobase" ,r-biobase)
3273 ("r-biocgenerics" ,r-biocgenerics)
3274 ("r-data-table" ,r-data-table)
3275 ("r-dplyr" ,r-dplyr)
3276 ("r-genomeinfodb" ,r-genomeinfodb)
3277 ("r-genomicranges" ,r-genomicranges)
3278 ("r-ggplot2" ,r-ggplot2)
3279 ("r-gridextra" ,r-gridextra)
3281 ("r-igraph" ,r-igraph)
3282 ("r-interactionset" ,r-interactionset)
3283 ("r-iranges" ,r-iranges)
3284 ("r-rsamtools" ,r-rsamtools)
3285 ("r-rtracklayer" ,r-rtracklayer)
3286 ("r-s4vectors" ,r-s4vectors)
3287 ("r-stringr" ,r-stringr)))
3289 `(("r-knitr" ,r-knitr)))
3290 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
3291 (synopsis "R package for handling genomic interaction data")
3293 "This R package provides tools for handling genomic interaction data,
3294 such as ChIA-PET/Hi-C, annotating genomic features with interaction
3295 information and producing various plots and statistics.")
3296 (license license:gpl3)))
3298 (define-public r-ctc
3305 (uri (bioconductor-uri "ctc" version))
3308 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
3309 (build-system r-build-system)
3310 (propagated-inputs `(("r-amap" ,r-amap)))
3311 (home-page "https://bioconductor.org/packages/ctc/")
3312 (synopsis "Cluster and tree conversion")
3314 "This package provides tools for exporting and importing classification
3315 trees and clusters to other programs.")
3316 (license license:gpl2)))
3318 (define-public r-goseq
3325 (uri (bioconductor-uri "goseq" version))
3328 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
3329 (build-system r-build-system)
3331 `(("r-annotationdbi" ,r-annotationdbi)
3332 ("r-biasedurn" ,r-biasedurn)
3333 ("r-biocgenerics" ,r-biocgenerics)
3334 ("r-genelendatabase" ,r-genelendatabase)
3335 ("r-go-db" ,r-go-db)
3336 ("r-mgcv" ,r-mgcv)))
3337 (home-page "https://bioconductor.org/packages/goseq/")
3338 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
3340 "This package provides tools to detect Gene Ontology and/or other user
3341 defined categories which are over/under represented in RNA-seq data.")
3342 (license license:lgpl2.0+)))
3344 (define-public r-glimma
3351 (uri (bioconductor-uri "Glimma" version))
3354 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
3355 (properties `((upstream-name . "Glimma")))
3356 (build-system r-build-system)
3358 `(("r-deseq2" ,r-deseq2)
3359 ("r-edger" ,r-edger)
3360 ("r-htmlwidgets" ,r-htmlwidgets)
3361 ("r-jsonlite" ,r-jsonlite)
3362 ("r-limma" ,r-limma)
3363 ("r-s4vectors" ,r-s4vectors)
3364 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3366 `(("r-knitr" ,r-knitr)))
3367 (home-page "https://github.com/Shians/Glimma")
3368 (synopsis "Interactive HTML graphics")
3370 "This package generates interactive visualisations for analysis of
3371 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
3372 HTML page. The interactions are built on top of the popular static
3373 representations of analysis results in order to provide additional
3375 (license license:lgpl3)))
3377 (define-public r-rots
3384 (uri (bioconductor-uri "ROTS" version))
3387 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
3388 (properties `((upstream-name . "ROTS")))
3389 (build-system r-build-system)
3391 `(("r-biobase" ,r-biobase)
3392 ("r-rcpp" ,r-rcpp)))
3393 (home-page "https://bioconductor.org/packages/ROTS/")
3394 (synopsis "Reproducibility-Optimized Test Statistic")
3396 "This package provides tools for calculating the
3397 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
3399 (license license:gpl2+)))
3401 (define-public r-plgem
3408 (uri (bioconductor-uri "plgem" version))
3411 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
3412 (build-system r-build-system)
3414 `(("r-biobase" ,r-biobase)
3415 ("r-mass" ,r-mass)))
3416 (home-page "http://www.genopolis.it")
3417 (synopsis "Detect differential expression in microarray and proteomics datasets")
3419 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
3420 model the variance-versus-mean dependence that exists in a variety of
3421 genome-wide datasets, including microarray and proteomics data. The use of
3422 PLGEM has been shown to improve the detection of differentially expressed
3423 genes or proteins in these datasets.")
3424 (license license:gpl2)))
3426 (define-public r-inspect
3433 (uri (bioconductor-uri "INSPEcT" version))
3436 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
3437 (properties `((upstream-name . "INSPEcT")))
3438 (build-system r-build-system)
3440 `(("r-biobase" ,r-biobase)
3441 ("r-biocgenerics" ,r-biocgenerics)
3442 ("r-biocparallel" ,r-biocparallel)
3443 ("r-deseq2" ,r-deseq2)
3444 ("r-desolve" ,r-desolve)
3445 ("r-gdata" ,r-gdata)
3446 ("r-genomeinfodb" ,r-genomeinfodb)
3447 ("r-genomicalignments" ,r-genomicalignments)
3448 ("r-genomicfeatures" ,r-genomicfeatures)
3449 ("r-genomicranges" ,r-genomicranges)
3450 ("r-iranges" ,r-iranges)
3451 ("r-kernsmooth" ,r-kernsmooth)
3452 ("r-plgem" ,r-plgem)
3454 ("r-rootsolve" ,r-rootsolve)
3455 ("r-rsamtools" ,r-rsamtools)
3456 ("r-rtracklayer" ,r-rtracklayer)
3457 ("r-s4vectors" ,r-s4vectors)
3458 ("r-shiny" ,r-shiny)
3459 ("r-summarizedexperiment" ,r-summarizedexperiment)
3460 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
3461 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
3463 `(("r-knitr" ,r-knitr)))
3464 (home-page "https://bioconductor.org/packages/INSPEcT")
3465 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
3467 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
3468 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
3469 order to evaluate synthesis, processing and degradation rates and assess via
3470 modeling the rates that determines changes in mature mRNA levels.")
3471 (license license:gpl2)))
3473 (define-public r-dnabarcodes
3475 (name "r-dnabarcodes")
3480 (uri (bioconductor-uri "DNABarcodes" version))
3483 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
3484 (properties `((upstream-name . "DNABarcodes")))
3485 (build-system r-build-system)
3488 ("r-matrix" ,r-matrix)
3489 ("r-rcpp" ,r-rcpp)))
3491 `(("r-knitr" ,r-knitr)))
3492 (home-page "https://bioconductor.org/packages/DNABarcodes")
3493 (synopsis "Create and analyze DNA barcodes")
3495 "This package offers tools to create DNA barcode sets capable of
3496 correcting insertion, deletion, and substitution errors. Existing barcodes
3497 can be analyzed regarding their minimal, maximal and average distances between
3498 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
3499 demultiplexed, i.e. assigned to their original reference barcode.")
3500 (license license:gpl2)))
3502 (define-public r-ruvseq
3509 (uri (bioconductor-uri "RUVSeq" version))
3512 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
3513 (properties `((upstream-name . "RUVSeq")))
3514 (build-system r-build-system)
3516 `(("r-biobase" ,r-biobase)
3517 ("r-edaseq" ,r-edaseq)
3518 ("r-edger" ,r-edger)
3519 ("r-mass" ,r-mass)))
3521 `(("r-knitr" ,r-knitr)))
3522 (home-page "https://github.com/drisso/RUVSeq")
3523 (synopsis "Remove unwanted variation from RNA-Seq data")
3525 "This package implements methods to @dfn{remove unwanted variation} (RUV)
3526 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
3528 (license license:artistic2.0)))
3530 (define-public r-biocneighbors
3532 (name "r-biocneighbors")
3537 (uri (bioconductor-uri "BiocNeighbors" version))
3540 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
3541 (properties `((upstream-name . "BiocNeighbors")))
3542 (build-system r-build-system)
3544 `(("r-biocparallel" ,r-biocparallel)
3545 ("r-matrix" ,r-matrix)
3547 ("r-rcpphnsw" ,r-rcpphnsw)
3548 ("r-s4vectors" ,r-s4vectors)))
3550 `(("r-knitr" ,r-knitr)))
3551 (home-page "https://bioconductor.org/packages/BiocNeighbors")
3552 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
3554 "This package implements exact and approximate methods for nearest
3555 neighbor detection, in a framework that allows them to be easily switched
3556 within Bioconductor packages or workflows. The exact algorithm is implemented
3557 using pre-clustering with the k-means algorithm. Functions are also provided
3558 to search for all neighbors within a given distance. Parallelization is
3559 achieved for all methods using the BiocParallel framework.")
3560 (license license:gpl3)))
3562 (define-public r-biocsingular
3564 (name "r-biocsingular")
3569 (uri (bioconductor-uri "BiocSingular" version))
3572 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
3573 (properties `((upstream-name . "BiocSingular")))
3574 (build-system r-build-system)
3576 `(("r-beachmat" ,r-beachmat)
3577 ("r-biocgenerics" ,r-biocgenerics)
3578 ("r-biocparallel" ,r-biocparallel)
3579 ("r-delayedarray" ,r-delayedarray)
3580 ("r-irlba" ,r-irlba)
3581 ("r-matrix" ,r-matrix)
3584 ("r-s4vectors" ,r-s4vectors)))
3586 `(("r-knitr" ,r-knitr)))
3587 (home-page "https://github.com/LTLA/BiocSingular")
3588 (synopsis "Singular value decomposition for Bioconductor packages")
3590 "This package implements exact and approximate methods for singular value
3591 decomposition and principal components analysis, in a framework that allows
3592 them to be easily switched within Bioconductor packages or workflows. Where
3593 possible, parallelization is achieved using the BiocParallel framework.")
3594 (license license:gpl3)))
3596 (define-public r-destiny
3603 (uri (bioconductor-uri "destiny" version))
3606 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
3607 (build-system r-build-system)
3609 `(("r-biobase" ,r-biobase)
3610 ("r-biocgenerics" ,r-biocgenerics)
3611 ("r-ggplot-multistats" ,r-ggplot-multistats)
3612 ("r-ggplot2" ,r-ggplot2)
3613 ("r-ggthemes" ,r-ggthemes)
3614 ("r-irlba" ,r-irlba)
3615 ("r-knn-covertree" ,r-knn-covertree)
3616 ("r-matrix" ,r-matrix)
3617 ("r-pcamethods" ,r-pcamethods)
3618 ("r-proxy" ,r-proxy)
3620 ("r-rcppeigen" ,r-rcppeigen)
3621 ("r-rcpphnsw" ,r-rcpphnsw)
3622 ("r-rspectra" ,r-rspectra)
3623 ("r-scales" ,r-scales)
3624 ("r-scatterplot3d" ,r-scatterplot3d)
3625 ("r-singlecellexperiment" ,r-singlecellexperiment)
3626 ("r-smoother" ,r-smoother)
3627 ("r-summarizedexperiment" ,r-summarizedexperiment)
3628 ("r-tidyr" ,r-tidyr)
3629 ("r-tidyselect" ,r-tidyselect)
3632 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
3633 (home-page "https://bioconductor.org/packages/destiny/")
3634 (synopsis "Create and plot diffusion maps")
3635 (description "This package provides tools to create and plot diffusion
3637 ;; Any version of the GPL
3638 (license license:gpl3+)))
3640 (define-public r-savr
3647 (uri (bioconductor-uri "savR" version))
3650 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
3651 (properties `((upstream-name . "savR")))
3652 (build-system r-build-system)
3654 `(("r-ggplot2" ,r-ggplot2)
3655 ("r-gridextra" ,r-gridextra)
3656 ("r-reshape2" ,r-reshape2)
3657 ("r-scales" ,r-scales)
3659 (home-page "https://github.com/bcalder/savR")
3660 (synopsis "Parse and analyze Illumina SAV files")
3662 "This package provides tools to parse Illumina Sequence Analysis
3663 Viewer (SAV) files, access data, and generate QC plots.")
3664 (license license:agpl3+)))
3666 (define-public r-chipexoqual
3668 (name "r-chipexoqual")
3673 (uri (bioconductor-uri "ChIPexoQual" version))
3676 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
3677 (properties `((upstream-name . "ChIPexoQual")))
3678 (build-system r-build-system)
3680 `(("r-biocparallel" ,r-biocparallel)
3681 ("r-biovizbase" ,r-biovizbase)
3682 ("r-broom" ,r-broom)
3683 ("r-data-table" ,r-data-table)
3684 ("r-dplyr" ,r-dplyr)
3685 ("r-genomeinfodb" ,r-genomeinfodb)
3686 ("r-genomicalignments" ,r-genomicalignments)
3687 ("r-genomicranges" ,r-genomicranges)
3688 ("r-ggplot2" ,r-ggplot2)
3689 ("r-hexbin" ,r-hexbin)
3690 ("r-iranges" ,r-iranges)
3691 ("r-rcolorbrewer" ,r-rcolorbrewer)
3692 ("r-rmarkdown" ,r-rmarkdown)
3693 ("r-rsamtools" ,r-rsamtools)
3694 ("r-s4vectors" ,r-s4vectors)
3695 ("r-scales" ,r-scales)
3696 ("r-viridis" ,r-viridis)))
3698 `(("r-knitr" ,r-knitr)))
3699 (home-page "https://github.com/keleslab/ChIPexoQual")
3700 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
3702 "This package provides a quality control pipeline for ChIP-exo/nexus
3704 (license license:gpl2+)))
3706 (define-public r-copynumber
3708 (name "r-copynumber")
3712 (uri (bioconductor-uri "copynumber" version))
3715 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
3716 (build-system r-build-system)
3718 `(("r-s4vectors" ,r-s4vectors)
3719 ("r-iranges" ,r-iranges)
3720 ("r-genomicranges" ,r-genomicranges)
3721 ("r-biocgenerics" ,r-biocgenerics)))
3722 (home-page "https://bioconductor.org/packages/copynumber")
3723 (synopsis "Segmentation of single- and multi-track copy number data")
3725 "This package segments single- and multi-track copy number data by a
3726 penalized least squares regression method.")
3727 (license license:artistic2.0)))
3729 (define-public r-dnacopy
3736 (uri (bioconductor-uri "DNAcopy" version))
3739 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
3740 (properties `((upstream-name . "DNAcopy")))
3741 (build-system r-build-system)
3742 (native-inputs `(("gfortran" ,gfortran)))
3743 (home-page "https://bioconductor.org/packages/DNAcopy")
3744 (synopsis "DNA copy number data analysis")
3746 "This package implements the @dfn{circular binary segmentation} (CBS)
3747 algorithm to segment DNA copy number data and identify genomic regions with
3748 abnormal copy number.")
3749 (license license:gpl2+)))
3751 ;; This is a CRAN package, but it uncharacteristically depends on a
3752 ;; Bioconductor package.
3753 (define-public r-htscluster
3755 (name "r-htscluster")
3760 (uri (cran-uri "HTSCluster" version))
3763 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
3764 (properties `((upstream-name . "HTSCluster")))
3765 (build-system r-build-system)
3767 `(("r-capushe" ,r-capushe)
3768 ("r-edger" ,r-edger)
3769 ("r-plotrix" ,r-plotrix)))
3770 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
3771 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
3773 "This package provides a Poisson mixture model is implemented to cluster
3774 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
3775 estimation is performed using either the EM or CEM algorithm, and the slope
3776 heuristics are used for model selection (i.e., to choose the number of
3778 (license license:gpl3+)))
3780 (define-public r-deds
3787 (uri (bioconductor-uri "DEDS" version))
3790 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
3791 (properties `((upstream-name . "DEDS")))
3792 (build-system r-build-system)
3793 (home-page "https://bioconductor.org/packages/DEDS/")
3794 (synopsis "Differential expression via distance summary for microarray data")
3796 "This library contains functions that calculate various statistics of
3797 differential expression for microarray data, including t statistics, fold
3798 change, F statistics, SAM, moderated t and F statistics and B statistics. It
3799 also implements a new methodology called DEDS (Differential Expression via
3800 Distance Summary), which selects differentially expressed genes by integrating
3801 and summarizing a set of statistics using a weighted distance approach.")
3802 ;; Any version of the LGPL.
3803 (license license:lgpl3+)))
3805 ;; This is a CRAN package, but since it depends on a Bioconductor package we
3807 (define-public r-nbpseq
3814 (uri (cran-uri "NBPSeq" version))
3817 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
3818 (properties `((upstream-name . "NBPSeq")))
3819 (build-system r-build-system)
3821 `(("r-qvalue" ,r-qvalue)))
3822 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
3823 (synopsis "Negative binomial models for RNA-Seq data")
3825 "This package provides negative binomial models for two-group comparisons
3826 and regression inferences from RNA-sequencing data.")
3827 (license license:gpl2)))
3829 (define-public r-ebseq
3836 (uri (bioconductor-uri "EBSeq" version))
3839 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
3840 (properties `((upstream-name . "EBSeq")))
3841 (build-system r-build-system)
3843 `(("r-blockmodeling" ,r-blockmodeling)
3844 ("r-gplots" ,r-gplots)
3845 ("r-testthat" ,r-testthat)))
3846 (home-page "https://bioconductor.org/packages/EBSeq")
3847 (synopsis "Differential expression analysis of RNA-seq data")
3849 "This package provides tools for differential expression analysis at both
3850 gene and isoform level using RNA-seq data")
3851 (license license:artistic2.0)))
3853 (define-public r-karyoploter
3855 (name "r-karyoploter")
3859 (uri (bioconductor-uri "karyoploteR" version))
3862 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
3863 (build-system r-build-system)
3865 `(("r-annotationdbi" ,r-annotationdbi)
3866 ("r-bamsignals" ,r-bamsignals)
3867 ("r-bezier" ,r-bezier)
3868 ("r-biovizbase" ,r-biovizbase)
3869 ("r-digest" ,r-digest)
3870 ("r-genomeinfodb" ,r-genomeinfodb)
3871 ("r-genomicfeatures" ,r-genomicfeatures)
3872 ("r-genomicranges" ,r-genomicranges)
3873 ("r-iranges" ,r-iranges)
3874 ("r-memoise" ,r-memoise)
3875 ("r-regioner" ,r-regioner)
3876 ("r-rsamtools" ,r-rsamtools)
3877 ("r-rtracklayer" ,r-rtracklayer)
3878 ("r-s4vectors" ,r-s4vectors)
3879 ("r-variantannotation" ,r-variantannotation)))
3881 `(("r-knitr" ,r-knitr)))
3882 (home-page "https://bioconductor.org/packages/karyoploteR/")
3883 (synopsis "Plot customizable linear genomes displaying arbitrary data")
3884 (description "This package creates karyotype plots of arbitrary genomes and
3885 offers a complete set of functions to plot arbitrary data on them. It mimics
3886 many R base graphics functions coupling them with a coordinate change function
3887 automatically mapping the chromosome and data coordinates into the plot
3889 (license license:artistic2.0)))
3891 (define-public r-lpsymphony
3893 (name "r-lpsymphony")
3898 (uri (bioconductor-uri "lpsymphony" version))
3901 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
3902 (build-system r-build-system)
3906 `(("pkg-config" ,pkg-config)
3907 ("r-knitr" ,r-knitr)))
3908 (home-page "https://r-forge.r-project.org/projects/rsymphony")
3909 (synopsis "Symphony integer linear programming solver in R")
3911 "This package was derived from Rsymphony. The package provides an R
3912 interface to SYMPHONY, a linear programming solver written in C++. The main
3913 difference between this package and Rsymphony is that it includes the solver
3914 source code, while Rsymphony expects to find header and library files on the
3915 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
3916 to install interface to SYMPHONY.")
3917 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
3918 ;; lpsimphony is released under the same terms.
3919 (license license:epl1.0)))
3921 (define-public r-ihw
3928 (uri (bioconductor-uri "IHW" version))
3931 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
3932 (properties `((upstream-name . "IHW")))
3933 (build-system r-build-system)
3935 `(("r-biocgenerics" ,r-biocgenerics)
3936 ("r-fdrtool" ,r-fdrtool)
3937 ("r-lpsymphony" ,r-lpsymphony)
3938 ("r-slam" ,r-slam)))
3940 `(("r-knitr" ,r-knitr)))
3941 (home-page "https://bioconductor.org/packages/IHW")
3942 (synopsis "Independent hypothesis weighting")
3944 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
3945 procedure that increases power compared to the method of Benjamini and
3946 Hochberg by assigning data-driven weights to each hypothesis. The input to
3947 IHW is a two-column table of p-values and covariates. The covariate can be
3948 any continuous-valued or categorical variable that is thought to be
3949 informative on the statistical properties of each hypothesis test, while it is
3950 independent of the p-value under the null hypothesis.")
3951 (license license:artistic2.0)))
3953 (define-public r-icobra
3960 (uri (bioconductor-uri "iCOBRA" version))
3963 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
3964 (properties `((upstream-name . "iCOBRA")))
3965 (build-system r-build-system)
3967 `(("r-dplyr" ,r-dplyr)
3969 ("r-ggplot2" ,r-ggplot2)
3970 ("r-limma" ,r-limma)
3971 ("r-reshape2" ,r-reshape2)
3973 ("r-scales" ,r-scales)
3974 ("r-shiny" ,r-shiny)
3975 ("r-shinybs" ,r-shinybs)
3976 ("r-shinydashboard" ,r-shinydashboard)
3977 ("r-upsetr" ,r-upsetr)))
3979 `(("r-knitr" ,r-knitr)))
3980 (home-page "https://bioconductor.org/packages/iCOBRA")
3981 (synopsis "Comparison and visualization of ranking and assignment methods")
3983 "This package provides functions for calculation and visualization of
3984 performance metrics for evaluation of ranking and binary
3985 classification (assignment) methods. It also contains a Shiny application for
3986 interactive exploration of results.")
3987 (license license:gpl2+)))
3989 (define-public r-mast
3996 (uri (bioconductor-uri "MAST" version))
3999 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
4000 (properties `((upstream-name . "MAST")))
4001 (build-system r-build-system)
4003 `(("r-abind" ,r-abind)
4004 ("r-biobase" ,r-biobase)
4005 ("r-biocgenerics" ,r-biocgenerics)
4006 ("r-data-table" ,r-data-table)
4007 ("r-ggplot2" ,r-ggplot2)
4009 ("r-progress" ,r-progress)
4010 ("r-reshape2" ,r-reshape2)
4011 ("r-s4vectors" ,r-s4vectors)
4012 ("r-singlecellexperiment" ,r-singlecellexperiment)
4013 ("r-stringr" ,r-stringr)
4014 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4016 `(("r-knitr" ,r-knitr)))
4017 (home-page "https://github.com/RGLab/MAST/")
4018 (synopsis "Model-based analysis of single cell transcriptomics")
4020 "This package provides methods and models for handling zero-inflated
4021 single cell assay data.")
4022 (license license:gpl2+)))
4024 (define-public r-monocle
4031 (uri (bioconductor-uri "monocle" version))
4034 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
4035 (build-system r-build-system)
4037 `(("r-biobase" ,r-biobase)
4038 ("r-biocgenerics" ,r-biocgenerics)
4039 ("r-biocviews" ,r-biocviews)
4040 ("r-cluster" ,r-cluster)
4041 ("r-combinat" ,r-combinat)
4042 ("r-ddrtree" ,r-ddrtree)
4043 ("r-densityclust" ,r-densityclust)
4044 ("r-dplyr" ,r-dplyr)
4045 ("r-fastica" ,r-fastica)
4046 ("r-ggplot2" ,r-ggplot2)
4047 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
4048 ("r-igraph" ,r-igraph)
4049 ("r-irlba" ,r-irlba)
4050 ("r-limma" ,r-limma)
4052 ("r-matrix" ,r-matrix)
4053 ("r-matrixstats" ,r-matrixstats)
4054 ("r-pheatmap" ,r-pheatmap)
4056 ("r-proxy" ,r-proxy)
4057 ("r-qlcmatrix" ,r-qlcmatrix)
4060 ("r-reshape2" ,r-reshape2)
4061 ("r-rtsne" ,r-rtsne)
4063 ("r-stringr" ,r-stringr)
4064 ("r-tibble" ,r-tibble)
4066 ("r-viridis" ,r-viridis)))
4068 `(("r-knitr" ,r-knitr)))
4069 (home-page "https://bioconductor.org/packages/monocle")
4070 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
4072 "Monocle performs differential expression and time-series analysis for
4073 single-cell expression experiments. It orders individual cells according to
4074 progress through a biological process, without knowing ahead of time which
4075 genes define progress through that process. Monocle also performs
4076 differential expression analysis, clustering, visualization, and other useful
4077 tasks on single cell expression data. It is designed to work with RNA-Seq and
4078 qPCR data, but could be used with other types as well.")
4079 (license license:artistic2.0)))
4081 (define-public r-monocle3
4089 (url "https://github.com/cole-trapnell-lab/monocle3")
4091 (file-name (git-file-name name version))
4094 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
4095 (build-system r-build-system)
4097 `(("r-biobase" ,r-biobase)
4098 ("r-biocgenerics" ,r-biocgenerics)
4099 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
4100 ("r-dplyr" ,r-dplyr)
4101 ("r-ggplot2" ,r-ggplot2)
4102 ("r-ggrepel" ,r-ggrepel)
4104 ("r-htmlwidgets" ,r-htmlwidgets)
4105 ("r-igraph" ,r-igraph)
4106 ("r-irlba" ,r-irlba)
4107 ("r-limma" ,r-limma)
4108 ("r-lmtest" ,r-lmtest)
4110 ("r-matrix" ,r-matrix)
4111 ("r-matrix-utils" ,r-matrix-utils)
4112 ("r-pbapply" ,r-pbapply)
4113 ("r-pbmcapply" ,r-pbmcapply)
4114 ("r-pheatmap" ,r-pheatmap)
4115 ("r-plotly" ,r-plotly)
4117 ("r-proxy" ,r-proxy)
4119 ("r-purrr" ,r-purrr)
4122 ("r-rcppparallel" ,r-rcppparallel)
4123 ("r-reshape2" ,r-reshape2)
4124 ("r-reticulate" ,r-reticulate)
4125 ("r-rhpcblasctl" ,r-rhpcblasctl)
4126 ("r-rtsne" ,r-rtsne)
4127 ("r-shiny" ,r-shiny)
4129 ("r-spdep" ,r-spdep)
4130 ("r-speedglm" ,r-speedglm)
4131 ("r-stringr" ,r-stringr)
4132 ("r-singlecellexperiment" ,r-singlecellexperiment)
4133 ("r-tibble" ,r-tibble)
4134 ("r-tidyr" ,r-tidyr)
4136 ("r-viridis" ,r-viridis)))
4137 (home-page "https://github.com/cole-trapnell-lab/monocle3")
4138 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
4140 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
4141 (license license:expat)))
4143 (define-public r-noiseq
4150 (uri (bioconductor-uri "NOISeq" version))
4153 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
4154 (properties `((upstream-name . "NOISeq")))
4155 (build-system r-build-system)
4157 `(("r-biobase" ,r-biobase)
4158 ("r-matrix" ,r-matrix)))
4159 (home-page "https://bioconductor.org/packages/NOISeq")
4160 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
4162 "This package provides tools to support the analysis of RNA-seq
4163 expression data or other similar kind of data. It provides exploratory plots
4164 to evaluate saturation, count distribution, expression per chromosome, type of
4165 detected features, features length, etc. It also supports the analysis of
4166 differential expression between two experimental conditions with no parametric
4168 (license license:artistic2.0)))
4170 (define-public r-scdd
4177 (uri (bioconductor-uri "scDD" version))
4180 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
4181 (properties `((upstream-name . "scDD")))
4182 (build-system r-build-system)
4185 ("r-biocparallel" ,r-biocparallel)
4186 ("r-ebseq" ,r-ebseq)
4187 ("r-fields" ,r-fields)
4188 ("r-ggplot2" ,r-ggplot2)
4189 ("r-mclust" ,r-mclust)
4190 ("r-outliers" ,r-outliers)
4191 ("r-s4vectors" ,r-s4vectors)
4192 ("r-scran" ,r-scran)
4193 ("r-singlecellexperiment" ,r-singlecellexperiment)
4194 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4196 `(("r-knitr" ,r-knitr)))
4197 (home-page "https://github.com/kdkorthauer/scDD")
4198 (synopsis "Mixture modeling of single-cell RNA-seq data")
4200 "This package implements a method to analyze single-cell RNA-seq data
4201 utilizing flexible Dirichlet Process mixture models. Genes with differential
4202 distributions of expression are classified into several interesting patterns
4203 of differences between two conditions. The package also includes functions
4204 for simulating data with these patterns from negative binomial
4206 (license license:gpl2)))
4208 (define-public r-scone
4215 (uri (bioconductor-uri "scone" version))
4218 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
4219 (build-system r-build-system)
4221 `(("r-aroma-light" ,r-aroma-light)
4222 ("r-biocparallel" ,r-biocparallel)
4224 ("r-class" ,r-class)
4225 ("r-cluster" ,r-cluster)
4226 ("r-compositions" ,r-compositions)
4227 ("r-diptest" ,r-diptest)
4228 ("r-edger" ,r-edger)
4230 ("r-gplots" ,r-gplots)
4231 ("r-hexbin" ,r-hexbin)
4232 ("r-limma" ,r-limma)
4233 ("r-matrixstats" ,r-matrixstats)
4234 ("r-mixtools" ,r-mixtools)
4235 ("r-rarpack" ,r-rarpack)
4236 ("r-rcolorbrewer" ,r-rcolorbrewer)
4237 ("r-rhdf5" ,r-rhdf5)
4238 ("r-ruvseq" ,r-ruvseq)
4239 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4241 `(("r-knitr" ,r-knitr)))
4242 (home-page "https://bioconductor.org/packages/scone")
4243 (synopsis "Single cell overview of normalized expression data")
4245 "SCONE is an R package for comparing and ranking the performance of
4246 different normalization schemes for single-cell RNA-seq and other
4247 high-throughput analyses.")
4248 (license license:artistic2.0)))
4250 (define-public r-geoquery
4257 (uri (bioconductor-uri "GEOquery" version))
4260 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
4261 (properties `((upstream-name . "GEOquery")))
4262 (build-system r-build-system)
4264 `(("r-biobase" ,r-biobase)
4265 ("r-dplyr" ,r-dplyr)
4267 ("r-limma" ,r-limma)
4268 ("r-magrittr" ,r-magrittr)
4269 ("r-readr" ,r-readr)
4270 ("r-tidyr" ,r-tidyr)
4271 ("r-xml2" ,r-xml2)))
4273 `(("r-knitr" ,r-knitr)))
4274 (home-page "https://github.com/seandavi/GEOquery/")
4275 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
4277 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
4278 microarray data. Given the rich and varied nature of this resource, it is
4279 only natural to want to apply BioConductor tools to these data. GEOquery is
4280 the bridge between GEO and BioConductor.")
4281 (license license:gpl2)))
4283 (define-public r-illuminaio
4285 (name "r-illuminaio")
4290 (uri (bioconductor-uri "illuminaio" version))
4293 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
4294 (build-system r-build-system)
4296 `(("r-base64" ,r-base64)))
4297 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
4298 (synopsis "Parse Illumina microarray output files")
4300 "This package provides tools for parsing Illumina's microarray output
4301 files, including IDAT.")
4302 (license license:gpl2)))
4304 (define-public r-siggenes
4311 (uri (bioconductor-uri "siggenes" version))
4314 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
4315 (build-system r-build-system)
4317 `(("r-biobase" ,r-biobase)
4318 ("r-multtest" ,r-multtest)
4319 ("r-scrime" ,r-scrime)))
4320 (home-page "https://bioconductor.org/packages/siggenes/")
4322 "Multiple testing using SAM and Efron's empirical Bayes approaches")
4324 "This package provides tools for the identification of differentially
4325 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
4326 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
4327 Bayes Analyses of Microarrays} (EBAM).")
4328 (license license:lgpl2.0+)))
4330 (define-public r-bumphunter
4332 (name "r-bumphunter")
4337 (uri (bioconductor-uri "bumphunter" version))
4340 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
4341 (build-system r-build-system)
4343 `(("r-annotationdbi" ,r-annotationdbi)
4344 ("r-biocgenerics" ,r-biocgenerics)
4345 ("r-dorng" ,r-dorng)
4346 ("r-foreach" ,r-foreach)
4347 ("r-genomeinfodb" ,r-genomeinfodb)
4348 ("r-genomicfeatures" ,r-genomicfeatures)
4349 ("r-genomicranges" ,r-genomicranges)
4350 ("r-iranges" ,r-iranges)
4351 ("r-iterators" ,r-iterators)
4352 ("r-limma" ,r-limma)
4353 ("r-locfit" ,r-locfit)
4354 ("r-matrixstats" ,r-matrixstats)
4355 ("r-s4vectors" ,r-s4vectors)))
4356 (home-page "https://github.com/ririzarr/bumphunter")
4357 (synopsis "Find bumps in genomic data")
4359 "This package provides tools for finding bumps in genomic data in order
4360 to identify differentially methylated regions in epigenetic epidemiology
4362 (license license:artistic2.0)))
4364 (define-public r-minfi
4371 (uri (bioconductor-uri "minfi" version))
4374 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
4375 (build-system r-build-system)
4377 `(("r-beanplot" ,r-beanplot)
4378 ("r-biobase" ,r-biobase)
4379 ("r-biocgenerics" ,r-biocgenerics)
4380 ("r-biocparallel" ,r-biocparallel)
4381 ("r-biostrings" ,r-biostrings)
4382 ("r-bumphunter" ,r-bumphunter)
4383 ("r-data-table" ,r-data-table)
4384 ("r-delayedarray" ,r-delayedarray)
4385 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
4386 ("r-genefilter" ,r-genefilter)
4387 ("r-genomeinfodb" ,r-genomeinfodb)
4388 ("r-genomicranges" ,r-genomicranges)
4389 ("r-geoquery" ,r-geoquery)
4390 ("r-hdf5array" ,r-hdf5array)
4391 ("r-illuminaio" ,r-illuminaio)
4392 ("r-iranges" ,r-iranges)
4393 ("r-lattice" ,r-lattice)
4394 ("r-limma" ,r-limma)
4396 ("r-mclust" ,r-mclust)
4398 ("r-nor1mix" ,r-nor1mix)
4399 ("r-preprocesscore" ,r-preprocesscore)
4400 ("r-quadprog" ,r-quadprog)
4401 ("r-rcolorbrewer" ,r-rcolorbrewer)
4402 ("r-reshape" ,r-reshape)
4403 ("r-s4vectors" ,r-s4vectors)
4404 ("r-siggenes" ,r-siggenes)
4405 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4407 `(("r-knitr" ,r-knitr)))
4408 (home-page "https://github.com/hansenlab/minfi")
4409 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
4411 "This package provides tools to analyze and visualize Illumina Infinium
4412 methylation arrays.")
4413 (license license:artistic2.0)))
4415 (define-public r-methylumi
4417 (name "r-methylumi")
4422 (uri (bioconductor-uri "methylumi" version))
4425 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
4426 (build-system r-build-system)
4428 `(("r-annotate" ,r-annotate)
4429 ("r-annotationdbi" ,r-annotationdbi)
4430 ("r-biobase" ,r-biobase)
4431 ("r-biocgenerics" ,r-biocgenerics)
4432 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
4433 ("r-genefilter" ,r-genefilter)
4434 ("r-genomeinfodb" ,r-genomeinfodb)
4435 ("r-genomicranges" ,r-genomicranges)
4436 ("r-ggplot2" ,r-ggplot2)
4437 ("r-illuminaio" ,r-illuminaio)
4438 ("r-iranges" ,r-iranges)
4439 ("r-lattice" ,r-lattice)
4440 ("r-matrixstats" ,r-matrixstats)
4441 ("r-minfi" ,r-minfi)
4442 ("r-reshape2" ,r-reshape2)
4443 ("r-s4vectors" ,r-s4vectors)
4444 ("r-scales" ,r-scales)
4445 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4447 `(("r-knitr" ,r-knitr)))
4448 (home-page "https://bioconductor.org/packages/methylumi")
4449 (synopsis "Handle Illumina methylation data")
4451 "This package provides classes for holding and manipulating Illumina
4452 methylation data. Based on eSet, it can contain MIAME information, sample
4453 information, feature information, and multiple matrices of data. An
4454 \"intelligent\" import function, methylumiR can read the Illumina text files
4455 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
4456 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
4457 background correction, and quality control features for GoldenGate, Infinium,
4458 and Infinium HD arrays are also included.")
4459 (license license:gpl2)))
4461 (define-public r-lumi
4468 (uri (bioconductor-uri "lumi" version))
4471 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
4472 (build-system r-build-system)
4474 `(("r-affy" ,r-affy)
4475 ("r-annotate" ,r-annotate)
4476 ("r-annotationdbi" ,r-annotationdbi)
4477 ("r-biobase" ,r-biobase)
4479 ("r-genomicfeatures" ,r-genomicfeatures)
4480 ("r-genomicranges" ,r-genomicranges)
4481 ("r-kernsmooth" ,r-kernsmooth)
4482 ("r-lattice" ,r-lattice)
4484 ("r-methylumi" ,r-methylumi)
4486 ("r-nleqslv" ,r-nleqslv)
4487 ("r-preprocesscore" ,r-preprocesscore)
4488 ("r-rsqlite" ,r-rsqlite)))
4489 (home-page "https://bioconductor.org/packages/lumi")
4490 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
4492 "The lumi package provides an integrated solution for the Illumina
4493 microarray data analysis. It includes functions of Illumina
4494 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
4495 variance stabilization, normalization and gene annotation at the probe level.
4496 It also includes the functions of processing Illumina methylation microarrays,
4497 especially Illumina Infinium methylation microarrays.")
4498 (license license:lgpl2.0+)))
4500 (define-public r-linnorm
4507 (uri (bioconductor-uri "Linnorm" version))
4510 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
4511 (properties `((upstream-name . "Linnorm")))
4512 (build-system r-build-system)
4514 `(("r-amap" ,r-amap)
4515 ("r-apcluster" ,r-apcluster)
4516 ("r-ellipse" ,r-ellipse)
4517 ("r-fastcluster" ,r-fastcluster)
4519 ("r-ggdendro" ,r-ggdendro)
4520 ("r-ggplot2" ,r-ggplot2)
4521 ("r-gmodels" ,r-gmodels)
4522 ("r-igraph" ,r-igraph)
4523 ("r-limma" ,r-limma)
4525 ("r-mclust" ,r-mclust)
4527 ("r-rcpparmadillo" ,r-rcpparmadillo)
4528 ("r-rtsne" ,r-rtsne)
4529 ("r-statmod" ,r-statmod)
4530 ("r-vegan" ,r-vegan)
4533 `(("r-knitr" ,r-knitr)))
4534 (home-page "http://www.jjwanglab.org/Linnorm/")
4535 (synopsis "Linear model and normality based transformation method")
4537 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
4538 count data or any large scale count data. It transforms such datasets for
4539 parametric tests. In addition to the transformtion function (@code{Linnorm}),
4540 the following pipelines are implemented:
4543 @item Library size/batch effect normalization (@code{Linnorm.Norm})
4544 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
4545 clustering or hierarchical clustering (@code{Linnorm.tSNE},
4546 @code{Linnorm.PCA}, @code{Linnorm.HClust})
4547 @item Differential expression analysis or differential peak detection using
4548 limma (@code{Linnorm.limma})
4549 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
4550 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
4551 @item Stable gene selection for scRNA-seq data; for users without or who do
4552 not want to rely on spike-in genes (@code{Linnorm.SGenes})
4553 @item Data imputation (@code{Linnorm.DataImput}).
4556 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
4557 @code{RnaXSim} function is included for simulating RNA-seq data for the
4558 evaluation of DEG analysis methods.")
4559 (license license:expat)))
4561 (define-public r-ioniser
4568 (uri (bioconductor-uri "IONiseR" version))
4571 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
4572 (properties `((upstream-name . "IONiseR")))
4573 (build-system r-build-system)
4575 `(("r-biocgenerics" ,r-biocgenerics)
4576 ("r-biocparallel" ,r-biocparallel)
4577 ("r-biostrings" ,r-biostrings)
4578 ("r-bit64" ,r-bit64)
4579 ("r-dplyr" ,r-dplyr)
4580 ("r-ggplot2" ,r-ggplot2)
4581 ("r-magrittr" ,r-magrittr)
4582 ("r-rhdf5" ,r-rhdf5)
4583 ("r-shortread" ,r-shortread)
4584 ("r-stringr" ,r-stringr)
4585 ("r-tibble" ,r-tibble)
4586 ("r-tidyr" ,r-tidyr)
4587 ("r-xvector" ,r-xvector)))
4589 `(("r-knitr" ,r-knitr)))
4590 (home-page "https://bioconductor.org/packages/IONiseR/")
4591 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
4593 "IONiseR provides tools for the quality assessment of Oxford Nanopore
4594 MinION data. It extracts summary statistics from a set of fast5 files and can
4595 be used either before or after base calling. In addition to standard
4596 summaries of the read-types produced, it provides a number of plots for
4597 visualising metrics relative to experiment run time or spatially over the
4598 surface of a flowcell.")
4599 (license license:expat)))
4601 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
4602 (define-public r-mutoss
4609 (uri (cran-uri "mutoss" version))
4612 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
4613 (properties `((upstream-name . "mutoss")))
4614 (build-system r-build-system)
4616 `(("r-multcomp" ,r-multcomp)
4617 ("r-multtest" ,r-multtest)
4618 ("r-mvtnorm" ,r-mvtnorm)
4619 ("r-plotrix" ,r-plotrix)))
4620 (home-page "https://github.com/kornl/mutoss/")
4621 (synopsis "Unified multiple testing procedures")
4623 "This package is designed to ease the application and comparison of
4624 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
4625 are standardized and usable by the accompanying mutossGUI package.")
4626 ;; Any version of the GPL.
4627 (license (list license:gpl2+ license:gpl3+))))
4629 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
4630 ;; from Bioconductor, so we put it here.
4631 (define-public r-metap
4638 (uri (cran-uri "metap" version))
4641 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
4642 (build-system r-build-system)
4644 `(("r-lattice" ,r-lattice)
4645 ("r-mutoss" ,r-mutoss)
4646 ("r-rdpack" ,r-rdpack)
4647 ("r-tfisher" ,r-tfisher)))
4648 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
4649 (synopsis "Meta-analysis of significance values")
4651 "The canonical way to perform meta-analysis involves using effect sizes.
4652 When they are not available this package provides a number of methods for
4653 meta-analysis of significance values including the methods of Edgington,
4654 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
4655 published results; and a routine for graphical display.")
4656 (license license:gpl2)))
4658 (define-public r-triform
4665 (uri (bioconductor-uri "triform" version))
4668 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
4669 (build-system r-build-system)
4671 `(("r-biocgenerics" ,r-biocgenerics)
4672 ("r-iranges" ,r-iranges)
4673 ("r-yaml" ,r-yaml)))
4674 (home-page "https://bioconductor.org/packages/triform/")
4675 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
4677 "The Triform algorithm uses model-free statistics to identify peak-like
4678 distributions of TF ChIP sequencing reads, taking advantage of an improved
4679 peak definition in combination with known profile characteristics.")
4680 (license license:gpl2)))
4682 (define-public r-varianttools
4684 (name "r-varianttools")
4689 (uri (bioconductor-uri "VariantTools" version))
4692 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
4693 (properties `((upstream-name . "VariantTools")))
4694 (build-system r-build-system)
4696 `(("r-biobase" ,r-biobase)
4697 ("r-biocgenerics" ,r-biocgenerics)
4698 ("r-biocparallel" ,r-biocparallel)
4699 ("r-biostrings" ,r-biostrings)
4700 ("r-bsgenome" ,r-bsgenome)
4701 ("r-genomeinfodb" ,r-genomeinfodb)
4702 ("r-genomicfeatures" ,r-genomicfeatures)
4703 ("r-genomicranges" ,r-genomicranges)
4704 ("r-iranges" ,r-iranges)
4705 ("r-matrix" ,r-matrix)
4706 ("r-rsamtools" ,r-rsamtools)
4707 ("r-rtracklayer" ,r-rtracklayer)
4708 ("r-s4vectors" ,r-s4vectors)
4709 ("r-variantannotation" ,r-variantannotation)))
4710 (home-page "https://bioconductor.org/packages/VariantTools/")
4711 (synopsis "Tools for exploratory analysis of variant calls")
4713 "Explore, diagnose, and compare variant calls using filters. The
4714 VariantTools package supports a workflow for loading data, calling single
4715 sample variants and tumor-specific somatic mutations or other sample-specific
4716 variant types (e.g., RNA editing). Most of the functions operate on
4717 alignments (BAM files) or datasets of called variants. The user is expected
4718 to have already aligned the reads with a separate tool, e.g., GSNAP via
4720 (license license:artistic2.0)))
4722 (define-public r-heatplus
4729 (uri (bioconductor-uri "Heatplus" version))
4732 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
4733 (properties `((upstream-name . "Heatplus")))
4734 (build-system r-build-system)
4736 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
4737 (home-page "https://github.com/alexploner/Heatplus")
4738 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
4740 "This package provides tools to display a rectangular heatmap (intensity
4741 plot) of a data matrix. By default, both samples (columns) and features (row)
4742 of the matrix are sorted according to a hierarchical clustering, and the
4743 corresponding dendrogram is plotted. Optionally, panels with additional
4744 information about samples and features can be added to the plot.")
4745 (license license:gpl2+)))
4747 (define-public r-gosemsim
4754 (uri (bioconductor-uri "GOSemSim" version))
4757 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
4758 (properties `((upstream-name . "GOSemSim")))
4759 (build-system r-build-system)
4761 `(("r-annotationdbi" ,r-annotationdbi)
4762 ("r-go-db" ,r-go-db)
4763 ("r-rcpp" ,r-rcpp)))
4765 `(("r-knitr" ,r-knitr)))
4766 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
4767 (synopsis "GO-terms semantic similarity measures")
4769 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
4770 quantitative ways to compute similarities between genes and gene groups, and
4771 have became important basis for many bioinformatics analysis approaches.
4772 GOSemSim is an R package for semantic similarity computation among GO terms,
4773 sets of GO terms, gene products and gene clusters.")
4774 (license license:artistic2.0)))
4776 (define-public r-anota
4783 (uri (bioconductor-uri "anota" version))
4786 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
4787 (build-system r-build-system)
4789 `(("r-multtest" ,r-multtest)
4790 ("r-qvalue" ,r-qvalue)))
4791 (home-page "https://bioconductor.org/packages/anota/")
4792 (synopsis "Analysis of translational activity")
4794 "Genome wide studies of translational control is emerging as a tool to
4795 study various biological conditions. The output from such analysis is both
4796 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
4797 involved in translation (the actively translating mRNA level) for each mRNA.
4798 The standard analysis of such data strives towards identifying differential
4799 translational between two or more sample classes - i.e. differences in
4800 actively translated mRNA levels that are independent of underlying differences
4801 in cytosolic mRNA levels. This package allows for such analysis using partial
4802 variances and the random variance model. As 10s of thousands of mRNAs are
4803 analyzed in parallel the library performs a number of tests to assure that
4804 the data set is suitable for such analysis.")
4805 (license license:gpl3)))
4807 (define-public r-sigpathway
4809 (name "r-sigpathway")
4814 (uri (bioconductor-uri "sigPathway" version))
4817 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
4818 (properties `((upstream-name . "sigPathway")))
4819 (build-system r-build-system)
4820 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
4821 (synopsis "Pathway analysis")
4823 "This package is used to conduct pathway analysis by calculating the NT_k
4824 and NE_k statistics in a statistical framework for determining whether a
4825 specified group of genes for a pathway has a coordinated association with a
4826 phenotype of interest.")
4827 (license license:gpl2)))
4829 (define-public r-fgsea
4836 (uri (bioconductor-uri "fgsea" version))
4839 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
4840 (build-system r-build-system)
4843 ("r-biocparallel" ,r-biocparallel)
4844 ("r-data-table" ,r-data-table)
4845 ("r-fastmatch" ,r-fastmatch)
4846 ("r-ggplot2" ,r-ggplot2)
4847 ("r-gridextra" ,r-gridextra)
4848 ("r-matrix" ,r-matrix)
4849 ("r-rcpp" ,r-rcpp)))
4851 `(("r-knitr" ,r-knitr)))
4852 (home-page "https://github.com/ctlab/fgsea/")
4853 (synopsis "Fast gene set enrichment analysis")
4855 "The package implements an algorithm for fast gene set enrichment
4856 analysis. Using the fast algorithm makes more permutations and gets
4857 more fine grained p-values, which allows using accurate standard approaches
4858 to multiple hypothesis correction.")
4859 (license license:expat)))
4861 (define-public r-dose
4868 (uri (bioconductor-uri "DOSE" version))
4871 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
4872 (properties `((upstream-name . "DOSE")))
4873 (build-system r-build-system)
4875 `(("r-annotationdbi" ,r-annotationdbi)
4876 ("r-biocparallel" ,r-biocparallel)
4877 ("r-do-db" ,r-do-db)
4878 ("r-fgsea" ,r-fgsea)
4879 ("r-ggplot2" ,r-ggplot2)
4880 ("r-gosemsim" ,r-gosemsim)
4881 ("r-qvalue" ,r-qvalue)
4882 ("r-reshape2" ,r-reshape2)))
4884 `(("r-knitr" ,r-knitr)))
4885 (home-page "https://guangchuangyu.github.io/software/DOSE/")
4886 (synopsis "Disease ontology semantic and enrichment analysis")
4888 "This package implements five methods proposed by Resnik, Schlicker,
4889 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
4890 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
4891 including hypergeometric model and gene set enrichment analysis are also
4892 implemented for discovering disease associations of high-throughput biological
4894 (license license:artistic2.0)))
4896 (define-public r-enrichplot
4898 (name "r-enrichplot")
4903 (uri (bioconductor-uri "enrichplot" version))
4906 "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
4907 (build-system r-build-system)
4909 `(("r-cowplot" ,r-cowplot)
4911 ("r-ggplot2" ,r-ggplot2)
4912 ("r-ggraph" ,r-ggraph)
4913 ("r-gosemsim" ,r-gosemsim)
4914 ("r-igraph" ,r-igraph)
4915 ("r-magrittr" ,r-magrittr)
4917 ("r-purrr" ,r-purrr)
4918 ("r-rcolorbrewer" ,r-rcolorbrewer)
4919 ("r-reshape2" ,r-reshape2)
4920 ("r-scatterpie" ,r-scatterpie)
4921 ("r-shadowtext" ,r-shadowtext)))
4923 `(("r-knitr" ,r-knitr)))
4924 (home-page "https://github.com/GuangchuangYu/enrichplot")
4925 (synopsis "Visualization of functional enrichment result")
4927 "The enrichplot package implements several visualization methods for
4928 interpreting functional enrichment results obtained from ORA or GSEA analyses.
4929 All the visualization methods are developed based on ggplot2 graphics.")
4930 (license license:artistic2.0)))
4932 (define-public r-clusterprofiler
4934 (name "r-clusterprofiler")
4939 (uri (bioconductor-uri "clusterProfiler" version))
4942 "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
4944 `((upstream-name . "clusterProfiler")))
4945 (build-system r-build-system)
4947 `(("r-annotationdbi" ,r-annotationdbi)
4949 ("r-downloader" ,r-downloader)
4950 ("r-dplyr" ,r-dplyr)
4951 ("r-enrichplot" ,r-enrichplot)
4952 ("r-go-db" ,r-go-db)
4953 ("r-gosemsim" ,r-gosemsim)
4954 ("r-magrittr" ,r-magrittr)
4956 ("r-qvalue" ,r-qvalue)
4957 ("r-rlang" ,r-rlang)
4958 ("r-rvcheck" ,r-rvcheck)
4959 ("r-tidyr" ,r-tidyr)))
4961 `(("r-knitr" ,r-knitr)))
4962 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
4963 (synopsis "Analysis and visualization of functional profiles for gene clusters")
4965 "This package implements methods to analyze and visualize functional
4966 profiles (GO and KEGG) of gene and gene clusters.")
4967 (license license:artistic2.0)))
4969 (define-public r-mlinterfaces
4971 (name "r-mlinterfaces")
4976 (uri (bioconductor-uri "MLInterfaces" version))
4979 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
4980 (properties `((upstream-name . "MLInterfaces")))
4981 (build-system r-build-system)
4983 `(("r-annotate" ,r-annotate)
4984 ("r-biobase" ,r-biobase)
4985 ("r-biocgenerics" ,r-biocgenerics)
4986 ("r-cluster" ,r-cluster)
4989 ("r-gdata" ,r-gdata)
4990 ("r-genefilter" ,r-genefilter)
4991 ("r-ggvis" ,r-ggvis)
4992 ("r-hwriter" ,r-hwriter)
4994 ("r-mlbench" ,r-mlbench)
4996 ("r-rcolorbrewer" ,r-rcolorbrewer)
4998 ("r-rpart" ,r-rpart)
4999 ("r-sfsmisc" ,r-sfsmisc)
5000 ("r-shiny" ,r-shiny)
5001 ("r-threejs" ,r-threejs)))
5002 (home-page "https://bioconductor.org/packages/MLInterfaces/")
5003 (synopsis "Interfaces to R machine learning procedures")
5005 "This package provides uniform interfaces to machine learning code for
5006 data in R and Bioconductor containers.")
5007 ;; Any version of the LGPL.
5008 (license license:lgpl2.1+)))
5010 (define-public r-annaffy
5017 (uri (bioconductor-uri "annaffy" version))
5020 "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
5021 (build-system r-build-system)
5024 (modify-phases %standard-phases
5025 (add-after 'unpack 'remove-reference-to-non-free-data
5027 (substitute* "DESCRIPTION"
5031 `(("r-annotationdbi" ,r-annotationdbi)
5032 ("r-biobase" ,r-biobase)
5034 ("r-go-db" ,r-go-db)))
5035 (home-page "https://bioconductor.org/packages/annaffy/")
5036 (synopsis "Annotation tools for Affymetrix biological metadata")
5038 "This package provides functions for handling data from Bioconductor
5039 Affymetrix annotation data packages. It produces compact HTML and text
5040 reports including experimental data and URL links to many online databases.
5041 It allows searching of biological metadata using various criteria.")
5042 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
5043 ;; the LGPL 2.1 is included.
5044 (license license:lgpl2.1+)))
5046 (define-public r-a4core
5053 (uri (bioconductor-uri "a4Core" version))
5056 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
5057 (properties `((upstream-name . "a4Core")))
5058 (build-system r-build-system)
5060 `(("r-biobase" ,r-biobase)
5061 ("r-glmnet" ,r-glmnet)))
5063 `(("r-knitr" ,r-knitr)))
5064 (home-page "https://bioconductor.org/packages/a4Core")
5065 (synopsis "Automated Affymetrix array analysis core package")
5067 "This is the core package for the automated analysis of Affymetrix
5069 (license license:gpl3)))
5071 (define-public r-a4classif
5073 (name "r-a4classif")
5078 (uri (bioconductor-uri "a4Classif" version))
5081 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
5082 (properties `((upstream-name . "a4Classif")))
5083 (build-system r-build-system)
5085 `(("r-a4core" ,r-a4core)
5086 ("r-a4preproc" ,r-a4preproc)
5087 ("r-biobase" ,r-biobase)
5088 ("r-glmnet" ,r-glmnet)
5091 ("r-varselrf" ,r-varselrf)))
5093 `(("r-knitr" ,r-knitr)))
5094 (home-page "https://bioconductor.org/packages/a4Classif/")
5095 (synopsis "Automated Affymetrix array analysis classification package")
5097 "This is the classification package for the automated analysis of
5098 Affymetrix arrays.")
5099 (license license:gpl3)))
5101 (define-public r-a4preproc
5103 (name "r-a4preproc")
5108 (uri (bioconductor-uri "a4Preproc" version))
5111 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
5112 (properties `((upstream-name . "a4Preproc")))
5113 (build-system r-build-system)
5115 `(("r-biobase" ,r-biobase)
5116 ("r-biocgenerics" ,r-biocgenerics)))
5118 `(("r-knitr" ,r-knitr)))
5119 (home-page "https://bioconductor.org/packages/a4Preproc/")
5120 (synopsis "Automated Affymetrix array analysis preprocessing package")
5122 "This is a package for the automated analysis of Affymetrix arrays. It
5123 is used for preprocessing the arrays.")
5124 (license license:gpl3)))
5126 (define-public r-a4reporting
5128 (name "r-a4reporting")
5133 (uri (bioconductor-uri "a4Reporting" version))
5136 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
5137 (properties `((upstream-name . "a4Reporting")))
5138 (build-system r-build-system)
5140 `(("r-xtable" ,r-xtable)))
5142 `(("r-knitr" ,r-knitr)))
5143 (home-page "https://bioconductor.org/packages/a4Reporting/")
5144 (synopsis "Automated Affymetrix array analysis reporting package")
5146 "This is a package for the automated analysis of Affymetrix arrays. It
5147 provides reporting features.")
5148 (license license:gpl3)))
5150 (define-public r-a4base
5157 (uri (bioconductor-uri "a4Base" version))
5160 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
5161 (properties `((upstream-name . "a4Base")))
5162 (build-system r-build-system)
5164 `(("r-a4core" ,r-a4core)
5165 ("r-a4preproc" ,r-a4preproc)
5166 ("r-annaffy" ,r-annaffy)
5167 ("r-biobase" ,r-biobase)
5168 ("r-genefilter" ,r-genefilter)
5169 ("r-glmnet" ,r-glmnet)
5170 ("r-gplots" ,r-gplots)
5171 ("r-limma" ,r-limma)
5173 ("r-multtest" ,r-multtest)))
5174 (home-page "https://bioconductor.org/packages/a4Base/")
5175 (synopsis "Automated Affymetrix array analysis base package")
5177 "This package provides basic features for the automated analysis of
5178 Affymetrix arrays.")
5179 (license license:gpl3)))
5188 (uri (bioconductor-uri "a4" version))
5191 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
5192 (build-system r-build-system)
5194 `(("r-a4base" ,r-a4base)
5195 ("r-a4classif" ,r-a4classif)
5196 ("r-a4core" ,r-a4core)
5197 ("r-a4preproc" ,r-a4preproc)
5198 ("r-a4reporting" ,r-a4reporting)))
5199 (home-page "https://bioconductor.org/packages/a4/")
5200 (synopsis "Automated Affymetrix array analysis umbrella package")
5202 "This package provides a software suite for the automated analysis of
5203 Affymetrix arrays.")
5204 (license license:gpl3)))
5206 (define-public r-abseqr
5213 (uri (bioconductor-uri "abseqR" version))
5216 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
5217 (properties `((upstream-name . "abseqR")))
5218 (build-system r-build-system)
5220 `(("pandoc" ,pandoc)))
5222 `(("r-biocparallel" ,r-biocparallel)
5223 ("r-biocstyle" ,r-biocstyle)
5224 ("r-circlize" ,r-circlize)
5225 ("r-flexdashboard" ,r-flexdashboard)
5226 ("r-ggcorrplot" ,r-ggcorrplot)
5227 ("r-ggdendro" ,r-ggdendro)
5228 ("r-ggplot2" ,r-ggplot2)
5229 ("r-gridextra" ,r-gridextra)
5230 ("r-knitr" ,r-knitr)
5231 ("r-plotly" ,r-plotly)
5234 ("r-rcolorbrewer" ,r-rcolorbrewer)
5235 ("r-reshape2" ,r-reshape2)
5236 ("r-rmarkdown" ,r-rmarkdown)
5237 ("r-stringr" ,r-stringr)
5238 ("r-vegan" ,r-vegan)
5239 ("r-venndiagram" ,r-venndiagram)))
5241 `(("r-knitr" ,r-knitr)))
5242 (home-page "https://github.com/malhamdoosh/abseqR")
5243 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
5245 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
5246 sequencing datasets generated from antibody libraries and abseqR is one of its
5247 packages. AbseqR empowers the users of abseqPy with plotting and reporting
5248 capabilities and allows them to generate interactive HTML reports for the
5249 convenience of viewing and sharing with other researchers. Additionally,
5250 abseqR extends abseqPy to compare multiple repertoire analyses and perform
5251 further downstream analysis on its output.")
5252 (license license:gpl3)))
5254 (define-public r-bacon
5261 (uri (bioconductor-uri "bacon" version))
5264 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
5265 (build-system r-build-system)
5267 `(("r-biocparallel" ,r-biocparallel)
5268 ("r-ellipse" ,r-ellipse)
5269 ("r-ggplot2" ,r-ggplot2)))
5271 `(("r-knitr" ,r-knitr)))
5272 (home-page "https://bioconductor.org/packages/bacon/")
5273 (synopsis "Controlling bias and inflation in association studies")
5275 "Bacon can be used to remove inflation and bias often observed in
5276 epigenome- and transcriptome-wide association studies. To this end bacon
5277 constructs an empirical null distribution using a Gibbs Sampling algorithm by
5278 fitting a three-component normal mixture on z-scores.")
5279 (license license:gpl2+)))
5281 (define-public r-rgadem
5288 (uri (bioconductor-uri "rGADEM" version))
5291 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
5292 (properties `((upstream-name . "rGADEM")))
5293 (build-system r-build-system)
5295 `(("r-biostrings" ,r-biostrings)
5296 ("r-bsgenome" ,r-bsgenome)
5297 ("r-genomicranges" ,r-genomicranges)
5298 ("r-iranges" ,r-iranges)
5299 ("r-seqlogo" ,r-seqlogo)))
5300 (home-page "https://bioconductor.org/packages/rGADEM/")
5301 (synopsis "De novo sequence motif discovery")
5303 "rGADEM is an efficient de novo motif discovery tool for large-scale
5304 genomic sequence data.")
5305 (license license:artistic2.0)))
5307 (define-public r-motiv
5314 (uri (bioconductor-uri "MotIV" version))
5317 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
5318 (properties `((upstream-name . "MotIV")))
5319 (build-system r-build-system)
5323 `(("r-biocgenerics" ,r-biocgenerics)
5324 ("r-biostrings" ,r-biostrings)
5325 ("r-genomicranges" ,r-genomicranges)
5326 ("r-iranges" ,r-iranges)
5327 ("r-lattice" ,r-lattice)
5328 ("r-rgadem" ,r-rgadem)
5329 ("r-s4vectors" ,r-s4vectors)))
5330 (home-page "https://bioconductor.org/packages/MotIV/")
5331 (synopsis "Motif identification and validation")
5333 "This package is used for the identification and validation of sequence
5334 motifs. It makes use of STAMP for comparing a set of motifs to a given
5335 database (e.g. JASPAR). It can also be used to visualize motifs, motif
5336 distributions, modules and filter motifs.")
5337 (license license:gpl2)))
5339 (define-public r-motifdb
5345 (uri (bioconductor-uri "MotifDb" version))
5347 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
5348 (properties `((upstream-name . "MotifDb")))
5349 (build-system r-build-system)
5351 `(("r-biocgenerics" ,r-biocgenerics)
5352 ("r-biostrings" ,r-biostrings)
5353 ("r-genomicranges" ,r-genomicranges)
5354 ("r-iranges" ,r-iranges)
5355 ("r-rtracklayer" ,r-rtracklayer)
5356 ("r-s4vectors" ,r-s4vectors)
5357 ("r-splitstackshape" ,r-splitstackshape)))
5359 `(("r-knitr" ,r-knitr)))
5360 (home-page "https://www.bioconductor.org/packages/MotifDb/")
5361 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
5362 (description "This package provides more than 2000 annotated position
5363 frequency matrices from nine public sources, for multiple organisms.")
5364 (license license:artistic2.0)))
5366 (define-public r-motifbreakr
5368 (name "r-motifbreakr")
5372 (uri (bioconductor-uri "motifbreakR" version))
5374 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
5375 (properties `((upstream-name . "motifbreakR")))
5376 (build-system r-build-system)
5378 `(("r-biocgenerics" ,r-biocgenerics)
5379 ("r-biocparallel" ,r-biocparallel)
5380 ("r-biostrings" ,r-biostrings)
5381 ("r-bsgenome" ,r-bsgenome)
5382 ("r-genomeinfodb" ,r-genomeinfodb)
5383 ("r-genomicranges" ,r-genomicranges)
5384 ("r-grimport" ,r-grimport)
5386 ("r-iranges" ,r-iranges)
5387 ("r-matrixstats" ,r-matrixstats)
5388 ("r-motifdb" ,r-motifdb)
5389 ("r-motifstack" ,r-motifstack)
5390 ("r-rtracklayer" ,r-rtracklayer)
5391 ("r-s4vectors" ,r-s4vectors)
5392 ("r-stringr" ,r-stringr)
5393 ("r-summarizedexperiment" ,r-summarizedexperiment)
5394 ("r-tfmpvalue" ,r-tfmpvalue)
5395 ("r-variantannotation" ,r-variantannotation)))
5397 `(("r-knitr" ,r-knitr)))
5398 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
5399 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
5400 (description "This package allows biologists to judge in the first place
5401 whether the sequence surrounding the polymorphism is a good match, and in
5402 the second place how much information is gained or lost in one allele of
5403 the polymorphism relative to another. This package gives a choice of
5404 algorithms for interrogation of genomes with motifs from public sources:
5406 @item a weighted-sum probability matrix;
5407 @item log-probabilities;
5408 @item weighted by relative entropy.
5411 This package can predict effects for novel or previously described variants in
5412 public databases, making it suitable for tasks beyond the scope of its original
5413 design. Lastly, it can be used to interrogate any genome curated within
5415 (license license:gpl2+)))
5417 (define-public r-motifstack
5419 (name "r-motifstack")
5424 (uri (bioconductor-uri "motifStack" version))
5427 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
5428 (properties `((upstream-name . "motifStack")))
5429 (build-system r-build-system)
5431 `(("r-ade4" ,r-ade4)
5432 ("r-biostrings" ,r-biostrings)
5433 ("r-ggplot2" ,r-ggplot2)
5434 ("r-htmlwidgets" ,r-htmlwidgets)
5437 `(("r-knitr" ,r-knitr)))
5438 (home-page "https://bioconductor.org/packages/motifStack/")
5439 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
5441 "The motifStack package is designed for graphic representation of
5442 multiple motifs with different similarity scores. It works with both DNA/RNA
5443 sequence motifs and amino acid sequence motifs. In addition, it provides the
5444 flexibility for users to customize the graphic parameters such as the font
5445 type and symbol colors.")
5446 (license license:gpl2+)))
5448 (define-public r-genomicscores
5450 (name "r-genomicscores")
5455 (uri (bioconductor-uri "GenomicScores" version))
5458 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
5459 (properties `((upstream-name . "GenomicScores")))
5460 (build-system r-build-system)
5462 `(("r-annotationhub" ,r-annotationhub)
5463 ("r-biobase" ,r-biobase)
5464 ("r-biocfilecache" ,r-biocfilecache)
5465 ("r-biocgenerics" ,r-biocgenerics)
5466 ("r-biocmanager" ,r-biocmanager)
5467 ("r-biostrings" ,r-biostrings)
5468 ("r-delayedarray" ,r-delayedarray)
5469 ("r-genomeinfodb" ,r-genomeinfodb)
5470 ("r-genomicranges" ,r-genomicranges)
5471 ("r-hdf5array" ,r-hdf5array)
5472 ("r-iranges" ,r-iranges)
5473 ("r-rhdf5" ,r-rhdf5)
5474 ("r-s4vectors" ,r-s4vectors)
5477 `(("r-knitr" ,r-knitr)))
5478 (home-page "https://github.com/rcastelo/GenomicScores/")
5479 (synopsis "Work with genome-wide position-specific scores")
5481 "This package provides infrastructure to store and access genome-wide
5482 position-specific scores within R and Bioconductor.")
5483 (license license:artistic2.0)))
5485 (define-public r-atacseqqc
5487 (name "r-atacseqqc")
5492 (uri (bioconductor-uri "ATACseqQC" version))
5495 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
5496 (properties `((upstream-name . "ATACseqQC")))
5497 (build-system r-build-system)
5499 `(("r-biocgenerics" ,r-biocgenerics)
5500 ("r-biostrings" ,r-biostrings)
5501 ("r-bsgenome" ,r-bsgenome)
5502 ("r-chippeakanno" ,r-chippeakanno)
5503 ("r-edger" ,r-edger)
5504 ("r-genomeinfodb" ,r-genomeinfodb)
5505 ("r-genomicalignments" ,r-genomicalignments)
5506 ("r-genomicranges" ,r-genomicranges)
5507 ("r-genomicscores" ,r-genomicscores)
5508 ("r-iranges" ,r-iranges)
5509 ("r-kernsmooth" ,r-kernsmooth)
5510 ("r-limma" ,r-limma)
5511 ("r-motifstack" ,r-motifstack)
5512 ("r-preseqr" ,r-preseqr)
5513 ("r-randomforest" ,r-randomforest)
5514 ("r-rsamtools" ,r-rsamtools)
5515 ("r-rtracklayer" ,r-rtracklayer)
5516 ("r-s4vectors" ,r-s4vectors)))
5518 `(("r-knitr" ,r-knitr)))
5519 (home-page "https://bioconductor.org/packages/ATACseqQC/")
5520 (synopsis "ATAC-seq quality control")
5522 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
5523 sequencing, is a rapid and sensitive method for chromatin accessibility
5524 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
5525 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
5526 assess whether their ATAC-seq experiment is successful. It includes
5527 diagnostic plots of fragment size distribution, proportion of mitochondria
5528 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
5530 (license license:gpl2+)))
5532 (define-public r-gofuncr
5539 (uri (bioconductor-uri "GOfuncR" version))
5542 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
5543 (properties `((upstream-name . "GOfuncR")))
5544 (build-system r-build-system)
5546 `(("r-annotationdbi" ,r-annotationdbi)
5547 ("r-genomicranges" ,r-genomicranges)
5548 ("r-gtools" ,r-gtools)
5549 ("r-iranges" ,r-iranges)
5550 ("r-mapplots" ,r-mapplots)
5552 ("r-vioplot" ,r-vioplot)))
5554 `(("r-knitr" ,r-knitr)))
5555 (home-page "https://bioconductor.org/packages/GOfuncR/")
5556 (synopsis "Gene ontology enrichment using FUNC")
5558 "GOfuncR performs a gene ontology enrichment analysis based on the
5559 ontology enrichment software FUNC. GO-annotations are obtained from
5560 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
5561 included in the package and updated regularly. GOfuncR provides the standard
5562 candidate vs background enrichment analysis using the hypergeometric test, as
5563 well as three additional tests:
5566 @item the Wilcoxon rank-sum test that is used when genes are ranked,
5567 @item a binomial test that is used when genes are associated with two counts,
5569 @item a Chi-square or Fisher's exact test that is used in cases when genes are
5570 associated with four counts.
5573 To correct for multiple testing and interdependency of the tests, family-wise
5574 error rates are computed based on random permutations of the gene-associated
5575 variables. GOfuncR also provides tools for exploring the ontology graph and
5576 the annotations, and options to take gene-length or spatial clustering of
5577 genes into account. It is also possible to provide custom gene coordinates,
5578 annotations and ontologies.")
5579 (license license:gpl2+)))
5581 (define-public r-abaenrichment
5583 (name "r-abaenrichment")
5588 (uri (bioconductor-uri "ABAEnrichment" version))
5591 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
5592 (properties `((upstream-name . "ABAEnrichment")))
5593 (build-system r-build-system)
5595 `(("r-abadata" ,r-abadata)
5596 ("r-data-table" ,r-data-table)
5597 ("r-gofuncr" ,r-gofuncr)
5598 ("r-gplots" ,r-gplots)
5599 ("r-gtools" ,r-gtools)
5600 ("r-rcpp" ,r-rcpp)))
5602 `(("r-knitr" ,r-knitr)))
5603 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
5604 (synopsis "Gene expression enrichment in human brain regions")
5606 "The package ABAEnrichment is designed to test for enrichment of user
5607 defined candidate genes in the set of expressed genes in different human brain
5608 regions. The core function @code{aba_enrich} integrates the expression of the
5609 candidate gene set (averaged across donors) and the structural information of
5610 the brain using an ontology, both provided by the Allen Brain Atlas project.")
5611 (license license:gpl2+)))
5613 (define-public r-annotationfuncs
5615 (name "r-annotationfuncs")
5620 (uri (bioconductor-uri "AnnotationFuncs" version))
5623 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
5625 `((upstream-name . "AnnotationFuncs")))
5626 (build-system r-build-system)
5628 `(("r-annotationdbi" ,r-annotationdbi)
5630 (home-page "https://www.iysik.com/r/annotationfuncs")
5631 (synopsis "Annotation translation functions")
5633 "This package provides functions for handling translating between
5634 different identifieres using the Biocore Data Team data-packages (e.g.
5635 @code{org.Bt.eg.db}).")
5636 (license license:gpl2)))
5638 (define-public r-annotationtools
5640 (name "r-annotationtools")
5645 (uri (bioconductor-uri "annotationTools" version))
5648 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
5650 `((upstream-name . "annotationTools")))
5651 (build-system r-build-system)
5652 (propagated-inputs `(("r-biobase" ,r-biobase)))
5653 (home-page "https://bioconductor.org/packages/annotationTools/")
5654 (synopsis "Annotate microarrays and perform gene expression analyses")
5656 "This package provides functions to annotate microarrays, find orthologs,
5657 and integrate heterogeneous gene expression profiles using annotation and
5658 other molecular biology information available as flat file database (plain
5660 ;; Any version of the GPL.
5661 (license (list license:gpl2+))))
5663 (define-public r-allelicimbalance
5665 (name "r-allelicimbalance")
5670 (uri (bioconductor-uri "AllelicImbalance" version))
5673 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
5675 `((upstream-name . "AllelicImbalance")))
5676 (build-system r-build-system)
5678 `(("r-annotationdbi" ,r-annotationdbi)
5679 ("r-biocgenerics" ,r-biocgenerics)
5680 ("r-biostrings" ,r-biostrings)
5681 ("r-bsgenome" ,r-bsgenome)
5682 ("r-genomeinfodb" ,r-genomeinfodb)
5683 ("r-genomicalignments" ,r-genomicalignments)
5684 ("r-genomicfeatures" ,r-genomicfeatures)
5685 ("r-genomicranges" ,r-genomicranges)
5686 ("r-gridextra" ,r-gridextra)
5688 ("r-iranges" ,r-iranges)
5689 ("r-lattice" ,r-lattice)
5690 ("r-latticeextra" ,r-latticeextra)
5692 ("r-rsamtools" ,r-rsamtools)
5693 ("r-s4vectors" ,r-s4vectors)
5694 ("r-seqinr" ,r-seqinr)
5695 ("r-summarizedexperiment" ,r-summarizedexperiment)
5696 ("r-variantannotation" ,r-variantannotation)))
5698 `(("r-knitr" ,r-knitr)))
5699 (home-page "https://github.com/pappewaio/AllelicImbalance")
5700 (synopsis "Investigate allele-specific expression")
5702 "This package provides a framework for allele-specific expression
5703 investigation using RNA-seq data.")
5704 (license license:gpl3)))
5706 (define-public r-aucell
5713 (uri (bioconductor-uri "AUCell" version))
5716 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
5717 (properties `((upstream-name . "AUCell")))
5718 (build-system r-build-system)
5720 `(("r-biocgenerics" ,r-biocgenerics)
5721 ("r-data-table" ,r-data-table)
5722 ("r-gseabase" ,r-gseabase)
5723 ("r-mixtools" ,r-mixtools)
5724 ("r-r-utils" ,r-r-utils)
5725 ("r-s4vectors" ,r-s4vectors)
5726 ("r-shiny" ,r-shiny)
5727 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5729 `(("r-knitr" ,r-knitr)))
5730 (home-page "https://bioconductor.org/packages/AUCell/")
5731 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
5733 "AUCell identifies cells with active gene sets (e.g. signatures,
5734 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
5735 Under the Curve} (AUC) to calculate whether a critical subset of the input
5736 gene set is enriched within the expressed genes for each cell. The
5737 distribution of AUC scores across all the cells allows exploring the relative
5738 expression of the signature. Since the scoring method is ranking-based,
5739 AUCell is independent of the gene expression units and the normalization
5740 procedure. In addition, since the cells are evaluated individually, it can
5741 easily be applied to bigger datasets, subsetting the expression matrix if
5743 (license license:gpl3)))
5745 (define-public r-ebimage
5752 (uri (bioconductor-uri "EBImage" version))
5755 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
5756 (properties `((upstream-name . "EBImage")))
5757 (build-system r-build-system)
5759 `(("r-abind" ,r-abind)
5760 ("r-biocgenerics" ,r-biocgenerics)
5761 ("r-fftwtools" ,r-fftwtools)
5762 ("r-htmltools" ,r-htmltools)
5763 ("r-htmlwidgets" ,r-htmlwidgets)
5765 ("r-locfit" ,r-locfit)
5767 ("r-rcurl" ,r-rcurl)
5768 ("r-tiff" ,r-tiff)))
5770 `(("r-knitr" ,r-knitr))) ; for vignettes
5771 (home-page "https://github.com/aoles/EBImage")
5772 (synopsis "Image processing and analysis toolbox for R")
5774 "EBImage provides general purpose functionality for image processing and
5775 analysis. In the context of (high-throughput) microscopy-based cellular
5776 assays, EBImage offers tools to segment cells and extract quantitative
5777 cellular descriptors. This allows the automation of such tasks using the R
5778 programming language and facilitates the use of other tools in the R
5779 environment for signal processing, statistical modeling, machine learning and
5780 visualization with image data.")
5781 ;; Any version of the LGPL.
5782 (license license:lgpl2.1+)))
5784 (define-public r-yamss
5791 (uri (bioconductor-uri "yamss" version))
5794 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
5795 (build-system r-build-system)
5797 `(("r-biocgenerics" ,r-biocgenerics)
5798 ("r-data-table" ,r-data-table)
5799 ("r-ebimage" ,r-ebimage)
5800 ("r-iranges" ,r-iranges)
5801 ("r-limma" ,r-limma)
5802 ("r-matrix" ,r-matrix)
5804 ("r-s4vectors" ,r-s4vectors)
5805 ("r-summarizedexperiment"
5806 ,r-summarizedexperiment)))
5808 `(("r-knitr" ,r-knitr)))
5809 (home-page "https://github.com/hansenlab/yamss")
5810 (synopsis "Tools for high-throughput metabolomics")
5812 "This package provides tools to analyze and visualize high-throughput
5813 metabolomics data acquired using chromatography-mass spectrometry. These tools
5814 preprocess data in a way that enables reliable and powerful differential
5816 (license license:artistic2.0)))
5818 (define-public r-gtrellis
5825 (uri (bioconductor-uri "gtrellis" version))
5828 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
5829 (build-system r-build-system)
5831 `(("r-circlize" ,r-circlize)
5832 ("r-genomicranges" ,r-genomicranges)
5833 ("r-getoptlong" ,r-getoptlong)
5834 ("r-iranges" ,r-iranges)))
5836 `(("r-knitr" ,r-knitr)))
5837 (home-page "https://github.com/jokergoo/gtrellis")
5838 (synopsis "Genome level Trellis layout")
5840 "Genome level Trellis graph visualizes genomic data conditioned by
5841 genomic categories (e.g. chromosomes). For each genomic category, multiple
5842 dimensional data which are represented as tracks describe different features
5843 from different aspects. This package provides high flexibility to arrange
5844 genomic categories and to add self-defined graphics in the plot.")
5845 (license license:expat)))
5847 (define-public r-somaticsignatures
5849 (name "r-somaticsignatures")
5854 (uri (bioconductor-uri "SomaticSignatures" version))
5857 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
5859 `((upstream-name . "SomaticSignatures")))
5860 (build-system r-build-system)
5862 `(("r-biobase" ,r-biobase)
5863 ("r-biostrings" ,r-biostrings)
5864 ("r-genomeinfodb" ,r-genomeinfodb)
5865 ("r-genomicranges" ,r-genomicranges)
5866 ("r-ggbio" ,r-ggbio)
5867 ("r-ggplot2" ,r-ggplot2)
5868 ("r-iranges" ,r-iranges)
5870 ("r-pcamethods" ,r-pcamethods)
5871 ("r-proxy" ,r-proxy)
5872 ("r-reshape2" ,r-reshape2)
5873 ("r-s4vectors" ,r-s4vectors)
5874 ("r-variantannotation" ,r-variantannotation)))
5876 `(("r-knitr" ,r-knitr)))
5877 (home-page "https://github.com/juliangehring/SomaticSignatures")
5878 (synopsis "Somatic signatures")
5880 "This package identifies mutational signatures of @dfn{single nucleotide
5881 variants} (SNVs). It provides a infrastructure related to the methodology
5882 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
5883 decomposition algorithms.")
5884 (license license:expat)))
5886 (define-public r-yapsa
5893 (uri (bioconductor-uri "YAPSA" version))
5896 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
5897 (properties `((upstream-name . "YAPSA")))
5898 (build-system r-build-system)
5900 `(("r-biostrings" ,r-biostrings)
5901 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
5902 ("r-circlize" ,r-circlize)
5903 ("r-complexheatmap" ,r-complexheatmap)
5904 ("r-corrplot" ,r-corrplot)
5905 ("r-dendextend" ,r-dendextend)
5906 ("r-doparallel" ,r-doparallel)
5907 ("r-dplyr" ,r-dplyr)
5908 ("r-genomeinfodb" ,r-genomeinfodb)
5909 ("r-genomicranges" ,r-genomicranges)
5910 ("r-getoptlong" ,r-getoptlong)
5911 ("r-ggbeeswarm" ,r-ggbeeswarm)
5912 ("r-ggplot2" ,r-ggplot2)
5913 ("r-gridextra" ,r-gridextra)
5914 ("r-gtrellis" ,r-gtrellis)
5915 ("r-keggrest" ,r-keggrest)
5916 ("r-limsolve" ,r-limsolve)
5917 ("r-magrittr" ,r-magrittr)
5918 ("r-pmcmr" ,r-pmcmr)
5919 ("r-pracma" ,r-pracma)
5920 ("r-reshape2" ,r-reshape2)
5921 ("r-somaticsignatures" ,r-somaticsignatures)
5922 ("r-variantannotation" ,r-variantannotation)))
5924 `(("r-knitr" ,r-knitr)))
5925 (home-page "https://bioconductor.org/packages/YAPSA/")
5926 (synopsis "Yet another package for signature analysis")
5928 "This package provides functions and routines useful in the analysis of
5929 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
5930 functions to perform a signature analysis with known signatures and a
5931 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
5933 (license license:gpl3)))
5935 (define-public r-gcrma
5942 (uri (bioconductor-uri "gcrma" version))
5945 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
5946 (build-system r-build-system)
5948 `(("r-affy" ,r-affy)
5949 ("r-affyio" ,r-affyio)
5950 ("r-biobase" ,r-biobase)
5951 ("r-biocmanager" ,r-biocmanager)
5952 ("r-biostrings" ,r-biostrings)
5953 ("r-xvector" ,r-xvector)))
5954 (home-page "https://bioconductor.org/packages/gcrma/")
5955 (synopsis "Background adjustment using sequence information")
5957 "Gcrma adjusts for background intensities in Affymetrix array data which
5958 include optical noise and @dfn{non-specific binding} (NSB). The main function
5959 @code{gcrma} converts background adjusted probe intensities to expression
5960 measures using the same normalization and summarization methods as a
5961 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
5962 to estimate probe affinity to NSB. The sequence information is summarized in
5963 a more complex way than the simple GC content. Instead, the base types (A, T,
5964 G or C) at each position along the probe determine the affinity of each probe.
5965 The parameters of the position-specific base contributions to the probe
5966 affinity is estimated in an NSB experiment in which only NSB but no
5967 gene-specific binding is expected.")
5968 ;; Any version of the LGPL
5969 (license license:lgpl2.1+)))
5971 (define-public r-simpleaffy
5973 (name "r-simpleaffy")
5978 (uri (bioconductor-uri "simpleaffy" version))
5981 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
5982 (build-system r-build-system)
5984 `(("r-affy" ,r-affy)
5985 ("r-biobase" ,r-biobase)
5986 ("r-biocgenerics" ,r-biocgenerics)
5987 ("r-gcrma" ,r-gcrma)
5988 ("r-genefilter" ,r-genefilter)))
5989 (home-page "https://bioconductor.org/packages/simpleaffy/")
5990 (synopsis "Very simple high level analysis of Affymetrix data")
5992 "This package provides high level functions for reading Affy @file{.CEL}
5993 files, phenotypic data, and then computing simple things with it, such as
5994 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
5995 library. It also has some basic scatter plot functions and mechanisms for
5996 generating high resolution journal figures.")
5997 (license license:gpl2+)))
5999 (define-public r-yaqcaffy
6006 (uri (bioconductor-uri "yaqcaffy" version))
6009 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
6010 (build-system r-build-system)
6012 `(("r-simpleaffy" ,r-simpleaffy)))
6013 (home-page "https://bioconductor.org/packages/yaqcaffy/")
6014 (synopsis "Affymetrix quality control and reproducibility analysis")
6016 "This is a package that can be used for quality control of Affymetrix
6017 GeneChip expression data and reproducibility analysis of human whole genome
6018 chips with the MAQC reference datasets.")
6019 (license license:artistic2.0)))
6021 (define-public r-quantro
6028 (uri (bioconductor-uri "quantro" version))
6031 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
6032 (build-system r-build-system)
6034 `(("r-biobase" ,r-biobase)
6035 ("r-doparallel" ,r-doparallel)
6036 ("r-foreach" ,r-foreach)
6037 ("r-ggplot2" ,r-ggplot2)
6038 ("r-iterators" ,r-iterators)
6039 ("r-minfi" ,r-minfi)
6040 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6042 `(("r-knitr" ,r-knitr)))
6043 (home-page "https://bioconductor.org/packages/quantro/")
6044 (synopsis "Test for when to use quantile normalization")
6046 "This package provides a data-driven test for the assumptions of quantile
6047 normalization using raw data such as objects that inherit eSets (e.g.
6048 ExpressionSet, MethylSet). Group level information about each sample (such as
6049 Tumor / Normal status) must also be provided because the test assesses if
6050 there are global differences in the distributions between the user-defined
6052 (license license:gpl3+)))
6054 (define-public r-yarn
6061 (uri (bioconductor-uri "yarn" version))
6064 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
6065 (build-system r-build-system)
6067 `(("r-biobase" ,r-biobase)
6068 ("r-biomart" ,r-biomart)
6069 ("r-downloader" ,r-downloader)
6070 ("r-edger" ,r-edger)
6071 ("r-gplots" ,r-gplots)
6072 ("r-limma" ,r-limma)
6073 ("r-matrixstats" ,r-matrixstats)
6074 ("r-preprocesscore" ,r-preprocesscore)
6075 ("r-quantro" ,r-quantro)
6076 ("r-rcolorbrewer" ,r-rcolorbrewer)
6077 ("r-readr" ,r-readr)))
6079 `(("r-knitr" ,r-knitr)))
6080 (home-page "https://bioconductor.org/packages/yarn/")
6081 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
6083 "Expedite large RNA-Seq analyses using a combination of previously
6084 developed tools. YARN is meant to make it easier for the user in performing
6085 basic mis-annotation quality control, filtering, and condition-aware
6086 normalization. YARN leverages many Bioconductor tools and statistical
6087 techniques to account for the large heterogeneity and sparsity found in very
6088 large RNA-seq experiments.")
6089 (license license:artistic2.0)))
6091 (define-public r-roar
6098 (uri (bioconductor-uri "roar" version))
6101 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
6102 (build-system r-build-system)
6104 `(("r-biocgenerics" ,r-biocgenerics)
6105 ("r-genomeinfodb" ,r-genomeinfodb)
6106 ("r-genomicalignments" ,r-genomicalignments)
6107 ("r-genomicranges" ,r-genomicranges)
6108 ("r-iranges" ,r-iranges)
6109 ("r-rtracklayer" ,r-rtracklayer)
6110 ("r-s4vectors" ,r-s4vectors)
6111 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6112 (home-page "https://github.com/vodkatad/roar/")
6113 (synopsis "Identify differential APA usage from RNA-seq alignments")
6115 "This package provides tools for identifying preferential usage of APA
6116 sites, comparing two biological conditions, starting from known alternative
6117 sites and alignments obtained from standard RNA-seq experiments.")
6118 (license license:gpl3)))
6120 (define-public r-xbseq
6127 (uri (bioconductor-uri "XBSeq" version))
6130 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
6131 (properties `((upstream-name . "XBSeq")))
6132 (build-system r-build-system)
6134 `(("r-biobase" ,r-biobase)
6135 ("r-deseq2" ,r-deseq2)
6136 ("r-dplyr" ,r-dplyr)
6137 ("r-ggplot2" ,r-ggplot2)
6138 ("r-locfit" ,r-locfit)
6139 ("r-magrittr" ,r-magrittr)
6140 ("r-matrixstats" ,r-matrixstats)
6141 ("r-pracma" ,r-pracma)
6142 ("r-roar" ,r-roar)))
6144 `(("r-knitr" ,r-knitr)))
6145 (home-page "https://github.com/Liuy12/XBSeq")
6146 (synopsis "Test for differential expression for RNA-seq data")
6148 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
6149 expression} (DE), where a statistical model was established based on the
6150 assumption that observed signals are the convolution of true expression
6151 signals and sequencing noises. The mapped reads in non-exonic regions are
6152 considered as sequencing noises, which follows a Poisson distribution. Given
6153 measurable observed signal and background noise from RNA-seq data, true
6154 expression signals, assuming governed by the negative binomial distribution,
6155 can be delineated and thus the accurate detection of differential expressed
6157 (license license:gpl3+)))
6159 (define-public r-massspecwavelet
6161 (name "r-massspecwavelet")
6166 (uri (bioconductor-uri "MassSpecWavelet" version))
6169 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
6171 `((upstream-name . "MassSpecWavelet")))
6172 (build-system r-build-system)
6174 `(("r-waveslim" ,r-waveslim)))
6175 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
6176 (synopsis "Mass spectrum processing by wavelet-based algorithms")
6178 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
6179 data mainly through the use of wavelet transforms. It supports peak detection
6180 based on @dfn{Continuous Wavelet Transform} (CWT).")
6181 (license license:lgpl2.0+)))
6183 (define-public r-xcms
6190 (uri (bioconductor-uri "xcms" version))
6193 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
6194 (build-system r-build-system)
6196 `(("r-biobase" ,r-biobase)
6197 ("r-biocgenerics" ,r-biocgenerics)
6198 ("r-biocparallel" ,r-biocparallel)
6199 ("r-iranges" ,r-iranges)
6200 ("r-lattice" ,r-lattice)
6201 ("r-massspecwavelet" ,r-massspecwavelet)
6202 ("r-mscoreutils" ,r-mscoreutils)
6203 ("r-msnbase" ,r-msnbase)
6206 ("r-protgenerics" ,r-protgenerics)
6208 ("r-rcolorbrewer" ,r-rcolorbrewer)
6209 ("r-robustbase" ,r-robustbase)
6210 ("r-s4vectors" ,r-s4vectors)
6211 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6213 `(("r-knitr" ,r-knitr)))
6214 (home-page "https://bioconductor.org/packages/xcms/")
6215 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
6217 "This package provides a framework for processing and visualization of
6218 chromatographically separated and single-spectra mass spectral data. It
6219 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
6220 data for high-throughput, untargeted analyte profiling.")
6221 (license license:gpl2+)))
6223 (define-public r-wrench
6230 (uri (bioconductor-uri "Wrench" version))
6233 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
6234 (properties `((upstream-name . "Wrench")))
6235 (build-system r-build-system)
6237 `(("r-limma" ,r-limma)
6238 ("r-locfit" ,r-locfit)
6239 ("r-matrixstats" ,r-matrixstats)))
6241 `(("r-knitr" ,r-knitr)))
6242 (home-page "https://github.com/HCBravoLab/Wrench")
6243 (synopsis "Wrench normalization for sparse count data")
6245 "Wrench is a package for normalization sparse genomic count data, like
6246 that arising from 16s metagenomic surveys.")
6247 (license license:artistic2.0)))
6249 (define-public r-wiggleplotr
6251 (name "r-wiggleplotr")
6256 (uri (bioconductor-uri "wiggleplotr" version))
6259 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
6260 (build-system r-build-system)
6262 `(("r-assertthat" ,r-assertthat)
6263 ("r-cowplot" ,r-cowplot)
6264 ("r-dplyr" ,r-dplyr)
6265 ("r-genomeinfodb" ,r-genomeinfodb)
6266 ("r-genomicranges" ,r-genomicranges)
6267 ("r-ggplot2" ,r-ggplot2)
6268 ("r-iranges" ,r-iranges)
6269 ("r-purrr" ,r-purrr)
6270 ("r-rtracklayer" ,r-rtracklayer)
6271 ("r-s4vectors" ,r-s4vectors)))
6273 `(("r-knitr" ,r-knitr)))
6274 (home-page "https://bioconductor.org/packages/wiggleplotr/")
6275 (synopsis "Make read coverage plots from BigWig files")
6277 "This package provides tools to visualize read coverage from sequencing
6278 experiments together with genomic annotations (genes, transcripts, peaks).
6279 Introns of long transcripts can be rescaled to a fixed length for better
6280 visualization of exonic read coverage.")
6281 (license license:asl2.0)))
6283 (define-public r-widgettools
6285 (name "r-widgettools")
6290 (uri (bioconductor-uri "widgetTools" version))
6293 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
6294 (properties `((upstream-name . "widgetTools")))
6295 (build-system r-build-system)
6296 (home-page "https://bioconductor.org/packages/widgetTools/")
6297 (synopsis "Tools for creating interactive tcltk widgets")
6299 "This package contains tools to support the construction of tcltk
6301 ;; Any version of the LGPL.
6302 (license license:lgpl3+)))
6304 (define-public r-webbioc
6311 (uri (bioconductor-uri "webbioc" version))
6314 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
6315 (build-system r-build-system)
6317 `(("netpbm" ,netpbm)
6320 `(("r-affy" ,r-affy)
6321 ("r-annaffy" ,r-annaffy)
6322 ("r-biobase" ,r-biobase)
6323 ("r-biocmanager" ,r-biocmanager)
6324 ("r-gcrma" ,r-gcrma)
6325 ("r-multtest" ,r-multtest)
6326 ("r-qvalue" ,r-qvalue)
6328 (home-page "https://www.bioconductor.org/")
6329 (synopsis "Bioconductor web interface")
6331 "This package provides an integrated web interface for doing microarray
6332 analysis using several of the Bioconductor packages. It is intended to be
6333 deployed as a centralized bioinformatics resource for use by many users.
6334 Currently only Affymetrix oligonucleotide analysis is supported.")
6335 (license license:gpl2+)))
6337 (define-public r-zfpkm
6344 (uri (bioconductor-uri "zFPKM" version))
6347 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
6348 (properties `((upstream-name . "zFPKM")))
6349 (build-system r-build-system)
6351 `(("r-checkmate" ,r-checkmate)
6352 ("r-dplyr" ,r-dplyr)
6353 ("r-ggplot2" ,r-ggplot2)
6354 ("r-summarizedexperiment" ,r-summarizedexperiment)
6355 ("r-tidyr" ,r-tidyr)))
6357 `(("r-knitr" ,r-knitr)))
6358 (home-page "https://github.com/ronammar/zFPKM/")
6359 (synopsis "Functions to facilitate zFPKM transformations")
6361 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
6362 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
6364 (license license:gpl3)))
6366 (define-public r-rbowtie2
6373 (uri (bioconductor-uri "Rbowtie2" version))
6376 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
6377 (properties `((upstream-name . "Rbowtie2")))
6378 (build-system r-build-system)
6382 `(("r-knitr" ,r-knitr)))
6383 (home-page "https://bioconductor.org/packages/Rbowtie2/")
6384 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
6386 "This package provides an R wrapper of the popular @code{bowtie2}
6387 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
6388 rapid adapter trimming, identification, and read merging.")
6389 (license license:gpl3+)))
6391 (define-public r-progeny
6398 (uri (bioconductor-uri "progeny" version))
6401 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
6402 (build-system r-build-system)
6404 `(("r-biobase" ,r-biobase)
6405 ("r-dplyr" ,r-dplyr)
6406 ("r-ggplot2" ,r-ggplot2)
6407 ("r-ggrepel" ,r-ggrepel)
6408 ("r-gridextra" ,r-gridextra)
6409 ("r-tidyr" ,r-tidyr)))
6411 `(("r-knitr" ,r-knitr)))
6412 (home-page "https://github.com/saezlab/progeny")
6413 (synopsis "Pathway responsive gene activity inference")
6415 "This package provides a function to infer pathway activity from gene
6416 expression. It contains the linear model inferred in the publication
6417 \"Perturbation-response genes reveal signaling footprints in cancer gene
6419 (license license:asl2.0)))
6421 (define-public r-arrmnormalization
6423 (name "r-arrmnormalization")
6428 (uri (bioconductor-uri "ARRmNormalization" version))
6431 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
6433 `((upstream-name . "ARRmNormalization")))
6434 (build-system r-build-system)
6435 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
6436 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
6437 (synopsis "Adaptive robust regression normalization for methylation data")
6439 "This is a package to perform the @dfn{Adaptive Robust Regression
6440 method} (ARRm) for the normalization of methylation data from the Illumina
6441 Infinium HumanMethylation 450k assay.")
6442 (license license:artistic2.0)))
6444 (define-public r-biocfilecache
6446 (name "r-biocfilecache")
6451 (uri (bioconductor-uri "BiocFileCache" version))
6454 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
6455 (properties `((upstream-name . "BiocFileCache")))
6456 (build-system r-build-system)
6458 `(("r-curl" ,r-curl)
6460 ("r-dbplyr" ,r-dbplyr)
6461 ("r-dplyr" ,r-dplyr)
6463 ("r-rappdirs" ,r-rappdirs)
6464 ("r-rsqlite" ,r-rsqlite)))
6466 `(("r-knitr" ,r-knitr)))
6467 (home-page "https://bioconductor.org/packages/BiocFileCache/")
6468 (synopsis "Manage files across sessions")
6470 "This package creates a persistent on-disk cache of files that the user
6471 can add, update, and retrieve. It is useful for managing resources (such as
6472 custom Txdb objects) that are costly or difficult to create, web resources,
6473 and data files used across sessions.")
6474 (license license:artistic2.0)))
6476 (define-public r-iclusterplus
6478 (name "r-iclusterplus")
6483 (uri (bioconductor-uri "iClusterPlus" version))
6486 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
6487 (properties `((upstream-name . "iClusterPlus")))
6488 (build-system r-build-system)
6489 (native-inputs `(("gfortran" ,gfortran)))
6490 (home-page "https://bioconductor.org/packages/iClusterPlus/")
6491 (synopsis "Integrative clustering of multi-type genomic data")
6493 "iClusterPlus is developed for integrative clustering analysis of
6494 multi-type genomic data and is an enhanced version of iCluster proposed and
6495 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
6496 from the experiments where biological samples (e.g. tumor samples) are
6497 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
6498 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
6499 on. In the iClusterPlus model, binary observations such as somatic mutation
6500 are modeled as Binomial processes; categorical observations such as copy
6501 number states are realizations of Multinomial random variables; counts are
6502 modeled as Poisson random processes; and continuous measures are modeled by
6503 Gaussian distributions.")
6504 (license license:gpl2+)))
6506 (define-public r-rbowtie
6513 (uri (bioconductor-uri "Rbowtie" version))
6516 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
6517 (properties `((upstream-name . "Rbowtie")))
6518 (build-system r-build-system)
6522 `(("r-knitr" ,r-knitr)))
6523 (home-page "https://bioconductor.org/packages/Rbowtie/")
6524 (synopsis "R bowtie wrapper")
6526 "This package provides an R wrapper around the popular bowtie short read
6527 aligner and around SpliceMap, a de novo splice junction discovery and
6529 (license license:artistic2.0)))
6531 (define-public r-sgseq
6538 (uri (bioconductor-uri "SGSeq" version))
6541 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
6542 (properties `((upstream-name . "SGSeq")))
6543 (build-system r-build-system)
6545 `(("r-annotationdbi" ,r-annotationdbi)
6546 ("r-biocgenerics" ,r-biocgenerics)
6547 ("r-biostrings" ,r-biostrings)
6548 ("r-genomeinfodb" ,r-genomeinfodb)
6549 ("r-genomicalignments" ,r-genomicalignments)
6550 ("r-genomicfeatures" ,r-genomicfeatures)
6551 ("r-genomicranges" ,r-genomicranges)
6552 ("r-igraph" ,r-igraph)
6553 ("r-iranges" ,r-iranges)
6554 ("r-rsamtools" ,r-rsamtools)
6555 ("r-rtracklayer" ,r-rtracklayer)
6556 ("r-runit" ,r-runit)
6557 ("r-s4vectors" ,r-s4vectors)
6558 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6560 `(("r-knitr" ,r-knitr)))
6561 (home-page "https://bioconductor.org/packages/SGSeq/")
6562 (synopsis "Splice event prediction and quantification from RNA-seq data")
6564 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
6565 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
6566 represented as a splice graph, which can be obtained from existing annotation
6567 or predicted from the mapped sequence reads. Splice events are identified
6568 from the graph and are quantified locally using structurally compatible reads
6569 at the start or end of each splice variant. The software includes functions
6570 for splice event prediction, quantification, visualization and
6572 (license license:artistic2.0)))
6574 (define-public r-rhisat2
6581 (uri (bioconductor-uri "Rhisat2" version))
6584 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
6585 (properties `((upstream-name . "Rhisat2")))
6586 (build-system r-build-system)
6589 (modify-phases %standard-phases
6590 (add-after 'unpack 'make-reproducible
6592 (substitute* "src/Makefile"
6593 (("`hostname`") "guix")
6595 ;; Avoid shelling out to "which".
6596 (("^CC =.*") (which "gcc"))
6597 (("^CPP =.*") (which "g++")))
6600 `(("r-genomicfeatures" ,r-genomicfeatures)
6601 ("r-genomicranges" ,r-genomicranges)
6602 ("r-sgseq" ,r-sgseq)))
6604 `(("r-knitr" ,r-knitr)))
6605 (home-page "https://github.com/fmicompbio/Rhisat2")
6606 (synopsis "R Wrapper for HISAT2 sequence aligner")
6608 "This package provides an R interface to the HISAT2 spliced short-read
6609 aligner by Kim et al. (2015). The package contains wrapper functions to
6610 create a genome index and to perform the read alignment to the generated
6612 (license license:gpl3)))
6614 (define-public r-quasr
6621 (uri (bioconductor-uri "QuasR" version))
6624 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
6625 (properties `((upstream-name . "QuasR")))
6626 (build-system r-build-system)
6628 `(("r-annotationdbi" ,r-annotationdbi)
6629 ("r-biobase" ,r-biobase)
6630 ("r-biocgenerics" ,r-biocgenerics)
6631 ("r-biocmanager" ,r-biocmanager)
6632 ("r-biocparallel" ,r-biocparallel)
6633 ("r-biostrings" ,r-biostrings)
6634 ("r-bsgenome" ,r-bsgenome)
6635 ("r-genomeinfodb" ,r-genomeinfodb)
6636 ("r-genomicalignments" ,r-genomicalignments)
6637 ("r-genomicfeatures" ,r-genomicfeatures)
6638 ("r-genomicfiles" ,r-genomicfiles)
6639 ("r-genomicranges" ,r-genomicranges)
6640 ("r-iranges" ,r-iranges)
6641 ("r-rbowtie" ,r-rbowtie)
6642 ("r-rhisat2" ,r-rhisat2)
6643 ("r-rhtslib" ,r-rhtslib)
6644 ("r-rsamtools" ,r-rsamtools)
6645 ("r-rtracklayer" ,r-rtracklayer)
6646 ("r-s4vectors" ,r-s4vectors)
6647 ("r-shortread" ,r-shortread)))
6649 `(("r-knitr" ,r-knitr)))
6650 (home-page "https://bioconductor.org/packages/QuasR/")
6651 (synopsis "Quantify and annotate short reads in R")
6653 "This package provides a framework for the quantification and analysis of
6654 short genomic reads. It covers a complete workflow starting from raw sequence
6655 reads, over creation of alignments and quality control plots, to the
6656 quantification of genomic regions of interest.")
6657 (license license:gpl2)))
6659 (define-public r-rqc
6666 (uri (bioconductor-uri "Rqc" version))
6669 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
6670 (properties `((upstream-name . "Rqc")))
6671 (build-system r-build-system)
6673 `(("r-biocgenerics" ,r-biocgenerics)
6674 ("r-biocparallel" ,r-biocparallel)
6675 ("r-biocstyle" ,r-biocstyle)
6676 ("r-biostrings" ,r-biostrings)
6677 ("r-biovizbase" ,r-biovizbase)
6678 ("r-genomicalignments" ,r-genomicalignments)
6679 ("r-genomicfiles" ,r-genomicfiles)
6680 ("r-ggplot2" ,r-ggplot2)
6681 ("r-iranges" ,r-iranges)
6682 ("r-knitr" ,r-knitr)
6683 ("r-markdown" ,r-markdown)
6686 ("r-reshape2" ,r-reshape2)
6687 ("r-rsamtools" ,r-rsamtools)
6688 ("r-s4vectors" ,r-s4vectors)
6689 ("r-shiny" ,r-shiny)
6690 ("r-shortread" ,r-shortread)))
6692 `(("r-knitr" ,r-knitr)))
6693 (home-page "https://github.com/labbcb/Rqc")
6694 (synopsis "Quality control tool for high-throughput sequencing data")
6696 "Rqc is an optimized tool designed for quality control and assessment of
6697 high-throughput sequencing data. It performs parallel processing of entire
6698 files and produces a report which contains a set of high-resolution
6700 (license license:gpl2+)))
6702 (define-public r-birewire
6709 (uri (bioconductor-uri "BiRewire" version))
6712 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
6713 (properties `((upstream-name . "BiRewire")))
6714 (build-system r-build-system)
6716 `(("r-igraph" ,r-igraph)
6717 ("r-matrix" ,r-matrix)
6719 ("r-tsne" ,r-tsne)))
6720 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
6721 (synopsis "Tools for randomization of bipartite graphs")
6723 "This package provides functions for bipartite network rewiring through N
6724 consecutive switching steps and for the computation of the minimal number of
6725 switching steps to be performed in order to maximise the dissimilarity with
6726 respect to the original network. It includes functions for the analysis of
6727 the introduced randomness across the switching steps and several other
6728 routines to analyse the resulting networks and their natural projections.")
6729 (license license:gpl3)))
6731 (define-public r-birta
6738 (uri (bioconductor-uri "birta" version))
6741 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
6742 (build-system r-build-system)
6744 `(("r-biobase" ,r-biobase)
6745 ("r-limma" ,r-limma)
6746 ("r-mass" ,r-mass)))
6747 (home-page "https://bioconductor.org/packages/birta")
6748 (synopsis "Bayesian inference of regulation of transcriptional activity")
6750 "Expression levels of mRNA molecules are regulated by different
6751 processes, comprising inhibition or activation by transcription factors and
6752 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
6753 Inference of Regulation of Transcriptional Activity) uses the regulatory
6754 networks of transcription factors and miRNAs together with mRNA and miRNA
6755 expression data to predict switches in regulatory activity between two
6756 conditions. A Bayesian network is used to model the regulatory structure and
6757 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
6758 (license license:gpl2+)))
6760 (define-public r-multidataset
6762 (name "r-multidataset")
6767 (uri (bioconductor-uri "MultiDataSet" version))
6770 "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4"))))
6771 (properties `((upstream-name . "MultiDataSet")))
6772 (build-system r-build-system)
6774 `(("r-biobase" ,r-biobase)
6775 ("r-biocgenerics" ,r-biocgenerics)
6776 ("r-genomicranges" ,r-genomicranges)
6777 ("r-ggplot2" ,r-ggplot2)
6778 ("r-ggrepel" ,r-ggrepel)
6779 ("r-iranges" ,r-iranges)
6780 ("r-limma" ,r-limma)
6781 ("r-qqman" ,r-qqman)
6782 ("r-s4vectors" ,r-s4vectors)
6783 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6785 `(("r-knitr" ,r-knitr)))
6786 (home-page "https://bioconductor.org/packages/MultiDataSet/")
6787 (synopsis "Implementation of MultiDataSet and ResultSet")
6789 "This package provides an implementation of the BRGE's (Bioinformatic
6790 Research Group in Epidemiology from Center for Research in Environmental
6791 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
6792 integrating multi omics data sets and ResultSet is a container for omics
6793 results. This package contains base classes for MEAL and rexposome
6795 (license license:expat)))
6797 (define-public r-ropls
6804 (uri (bioconductor-uri "ropls" version))
6807 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
6808 (build-system r-build-system)
6810 `(("r-biobase" ,r-biobase)
6811 ("r-multidataset" ,r-multidataset)))
6813 `(("r-knitr" ,r-knitr))) ; for vignettes
6814 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
6815 (synopsis "Multivariate analysis and feature selection of omics data")
6817 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
6818 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
6819 regression, classification, and feature selection of omics data where the
6820 number of variables exceeds the number of samples and with multicollinearity
6821 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
6822 separately model the variation correlated (predictive) to the factor of
6823 interest and the uncorrelated (orthogonal) variation. While performing
6824 similarly to PLS, OPLS facilitates interpretation.
6826 This package provides imlementations of PCA, PLS, and OPLS for multivariate
6827 analysis and feature selection of omics data. In addition to scores, loadings
6828 and weights plots, the package provides metrics and graphics to determine the
6829 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
6830 validity of the model by permutation testing, detect outliers, and perform
6831 feature selection (e.g. with Variable Importance in Projection or regression
6833 (license license:cecill)))
6835 (define-public r-biosigner
6837 (name "r-biosigner")
6842 (uri (bioconductor-uri "biosigner" version))
6845 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
6846 (build-system r-build-system)
6848 `(("r-biobase" ,r-biobase)
6849 ("r-e1071" ,r-e1071)
6850 ("r-multidataset" ,r-multidataset)
6851 ("r-randomforest" ,r-randomforest)
6852 ("r-ropls" ,r-ropls)))
6854 `(("r-knitr" ,r-knitr)))
6855 (home-page "https://bioconductor.org/packages/biosigner/")
6856 (synopsis "Signature discovery from omics data")
6858 "Feature selection is critical in omics data analysis to extract
6859 restricted and meaningful molecular signatures from complex and high-dimension
6860 data, and to build robust classifiers. This package implements a method to
6861 assess the relevance of the variables for the prediction performances of the
6862 classifier. The approach can be run in parallel with the PLS-DA, Random
6863 Forest, and SVM binary classifiers. The signatures and the corresponding
6864 'restricted' models are returned, enabling future predictions on new
6866 (license license:cecill)))
6868 (define-public r-annotatr
6875 (uri (bioconductor-uri "annotatr" version))
6878 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
6879 (build-system r-build-system)
6881 `(("r-annotationdbi" ,r-annotationdbi)
6882 ("r-annotationhub" ,r-annotationhub)
6883 ("r-dplyr" ,r-dplyr)
6884 ("r-genomeinfodb" ,r-genomeinfodb)
6885 ("r-genomicfeatures" ,r-genomicfeatures)
6886 ("r-genomicranges" ,r-genomicranges)
6887 ("r-ggplot2" ,r-ggplot2)
6888 ("r-iranges" ,r-iranges)
6889 ("r-readr" ,r-readr)
6890 ("r-regioner" ,r-regioner)
6891 ("r-reshape2" ,r-reshape2)
6892 ("r-rtracklayer" ,r-rtracklayer)
6893 ("r-s4vectors" ,r-s4vectors)))
6895 `(("r-knitr" ,r-knitr)))
6896 (home-page "https://bioconductor.org/packages/annotatr/")
6897 (synopsis "Annotation of genomic regions to genomic annotations")
6899 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
6900 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
6901 to investigate the intersecting genomic annotations. Such annotations include
6902 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
6903 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
6904 enhancers. The annotatr package provides an easy way to summarize and
6905 visualize the intersection of genomic sites/regions with genomic
6907 (license license:gpl3)))
6909 (define-public r-rsubread
6916 (uri (bioconductor-uri "Rsubread" version))
6919 "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba"))))
6920 (properties `((upstream-name . "Rsubread")))
6921 (build-system r-build-system)
6922 (inputs `(("zlib" ,zlib)))
6924 `(("r-matrix" ,r-matrix)))
6925 (home-page "https://bioconductor.org/packages/Rsubread/")
6926 (synopsis "Subread sequence alignment and counting for R")
6928 "This package provides tools for alignment, quantification and analysis
6929 of second and third generation sequencing data. It includes functionality for
6930 read mapping, read counting, SNP calling, structural variant detection and
6931 gene fusion discovery. It can be applied to all major sequencing techologies
6932 and to both short and long sequence reads.")
6933 (license license:gpl3)))
6935 (define-public r-flowutils
6937 (name "r-flowutils")
6942 (uri (bioconductor-uri "flowUtils" version))
6945 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
6946 (properties `((upstream-name . "flowUtils")))
6947 (build-system r-build-system)
6949 `(("r-biobase" ,r-biobase)
6950 ("r-corpcor" ,r-corpcor)
6951 ("r-flowcore" ,r-flowcore)
6952 ("r-graph" ,r-graph)
6953 ("r-runit" ,r-runit)
6955 (home-page "https://github.com/jspidlen/flowUtils")
6956 (synopsis "Utilities for flow cytometry")
6958 "This package provides utilities for flow cytometry data.")
6959 (license license:artistic2.0)))
6961 (define-public r-consensusclusterplus
6963 (name "r-consensusclusterplus")
6968 (uri (bioconductor-uri "ConsensusClusterPlus" version))
6971 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
6973 `((upstream-name . "ConsensusClusterPlus")))
6974 (build-system r-build-system)
6977 ("r-biobase" ,r-biobase)
6978 ("r-cluster" ,r-cluster)))
6979 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
6980 (synopsis "Clustering algorithm")
6982 "This package provides an implementation of an algorithm for determining
6983 cluster count and membership by stability evidence in unsupervised analysis.")
6984 (license license:gpl2)))
6986 (define-public r-cytolib
6993 (uri (bioconductor-uri "cytolib" version))
6996 "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
6997 (properties `((upstream-name . "cytolib")))
6998 (build-system r-build-system)
7001 (modify-phases %standard-phases
7002 (add-after 'unpack 'fix-linking
7004 (substitute* "src/Makevars.in"
7005 ;; This is to avoid having a plain directory on the list of
7006 ;; libraries to link.
7007 (("\\(RHDF5_LIBS\\)" match)
7008 (string-append match "/libhdf5.a")))
7011 `(("r-knitr" ,r-knitr)
7012 ("pkg-config" ,pkg-config)))
7016 ("r-rcpparmadillo" ,r-rcpparmadillo)
7017 ("r-rcppparallel" ,r-rcppparallel)
7018 ("r-rhdf5lib" ,r-rhdf5lib)
7019 ("r-rprotobuflib" ,r-rprotobuflib)))
7020 (home-page "https://bioconductor.org/packages/cytolib/")
7021 (synopsis "C++ infrastructure for working with gated cytometry")
7023 "This package provides the core data structure and API to represent and
7024 interact with gated cytometry data.")
7025 (license license:artistic2.0)))
7027 (define-public r-flowcore
7034 (uri (bioconductor-uri "flowCore" version))
7037 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
7038 (properties `((upstream-name . "flowCore")))
7039 (build-system r-build-system)
7042 ("r-biobase" ,r-biobase)
7043 ("r-biocgenerics" ,r-biocgenerics)
7044 ("r-cytolib" ,r-cytolib)
7045 ("r-matrixstats" ,r-matrixstats)
7047 ("r-rcpparmadillo" ,r-rcpparmadillo)
7048 ("r-rprotobuflib" ,r-rprotobuflib)
7049 ("r-s4vectors" ,r-s4vectors)))
7051 `(("r-knitr" ,r-knitr)))
7052 (home-page "https://bioconductor.org/packages/flowCore")
7053 (synopsis "Basic structures for flow cytometry data")
7055 "This package provides S4 data structures and basic functions to deal
7056 with flow cytometry data.")
7057 (license license:artistic2.0)))
7059 (define-public r-flowmeans
7061 (name "r-flowmeans")
7066 (uri (bioconductor-uri "flowMeans" version))
7069 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
7070 (properties `((upstream-name . "flowMeans")))
7071 (build-system r-build-system)
7073 `(("r-biobase" ,r-biobase)
7074 ("r-feature" ,r-feature)
7075 ("r-flowcore" ,r-flowcore)
7076 ("r-rrcov" ,r-rrcov)))
7077 (home-page "https://bioconductor.org/packages/flowMeans")
7078 (synopsis "Non-parametric flow cytometry data gating")
7080 "This package provides tools to identify cell populations in Flow
7081 Cytometry data using non-parametric clustering and segmented-regression-based
7082 change point detection.")
7083 (license license:artistic2.0)))
7085 (define-public r-ncdfflow
7092 (uri (bioconductor-uri "ncdfFlow" version))
7095 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
7096 (properties `((upstream-name . "ncdfFlow")))
7097 (build-system r-build-system)
7100 (modify-phases %standard-phases
7101 (add-after 'unpack 'fix-linking
7103 (substitute* "src/Makevars"
7104 ;; This is to avoid having a plain directory on the list of
7105 ;; libraries to link.
7106 (("\\(RHDF5_LIBS\\)" match)
7107 (string-append match "/libhdf5.a")))
7111 ("r-biobase" ,r-biobase)
7112 ("r-biocgenerics" ,r-biocgenerics)
7113 ("r-flowcore" ,r-flowcore)
7115 ("r-rcpparmadillo" ,r-rcpparmadillo)
7116 ("r-rhdf5lib" ,r-rhdf5lib)
7117 ("r-zlibbioc" ,r-zlibbioc)))
7119 `(("r-knitr" ,r-knitr)))
7120 (home-page "https://bioconductor.org/packages/ncdfFlow/")
7121 (synopsis "HDF5 based storage for flow cytometry data")
7123 "This package provides HDF5 storage based methods and functions for
7124 manipulation of flow cytometry data.")
7125 (license license:artistic2.0)))
7127 (define-public r-ggcyto
7134 (uri (bioconductor-uri "ggcyto" version))
7137 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
7138 (properties `((upstream-name . "ggcyto")))
7139 (build-system r-build-system)
7141 `(("r-data-table" ,r-data-table)
7142 ("r-flowcore" ,r-flowcore)
7143 ("r-flowworkspace" ,r-flowworkspace)
7144 ("r-ggplot2" ,r-ggplot2)
7145 ("r-gridextra" ,r-gridextra)
7146 ("r-hexbin" ,r-hexbin)
7147 ("r-ncdfflow" ,r-ncdfflow)
7149 ("r-rcolorbrewer" ,r-rcolorbrewer)
7150 ("r-rlang" ,r-rlang)
7151 ("r-scales" ,r-scales)))
7153 `(("r-knitr" ,r-knitr)))
7154 (home-page "https://github.com/RGLab/ggcyto/issues")
7155 (synopsis "Visualize Cytometry data with ggplot")
7157 "With the dedicated fortify method implemented for @code{flowSet},
7158 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
7159 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
7160 and some custom layers also make it easy to add gates and population
7161 statistics to the plot.")
7162 (license license:artistic2.0)))
7164 (define-public r-flowviz
7171 (uri (bioconductor-uri "flowViz" version))
7174 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
7175 (properties `((upstream-name . "flowViz")))
7176 (build-system r-build-system)
7178 `(("r-biobase" ,r-biobase)
7179 ("r-flowcore" ,r-flowcore)
7180 ("r-hexbin" ,r-hexbin)
7181 ("r-idpmisc" ,r-idpmisc)
7182 ("r-kernsmooth" ,r-kernsmooth)
7183 ("r-lattice" ,r-lattice)
7184 ("r-latticeextra" ,r-latticeextra)
7186 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7188 `(("r-knitr" ,r-knitr)))
7189 (home-page "https://bioconductor.org/packages/flowViz/")
7190 (synopsis "Visualization for flow cytometry")
7192 "This package provides visualization tools for flow cytometry data.")
7193 (license license:artistic2.0)))
7195 (define-public r-flowclust
7197 (name "r-flowclust")
7202 (uri (bioconductor-uri "flowClust" version))
7205 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
7206 (properties `((upstream-name . "flowClust")))
7207 (build-system r-build-system)
7210 (list "--configure-args=--enable-bundled-gsl=no")))
7212 `(("r-biobase" ,r-biobase)
7213 ("r-biocgenerics" ,r-biocgenerics)
7215 ("r-corpcor" ,r-corpcor)
7216 ("r-ellipse" ,r-ellipse)
7217 ("r-flowcore" ,r-flowcore)
7218 ("r-flowviz" ,r-flowviz)
7219 ("r-graph" ,r-graph)
7220 ("r-mnormt" ,r-mnormt)))
7224 `(("pkg-config" ,pkg-config)
7225 ("r-knitr" ,r-knitr)))
7226 (home-page "https://bioconductor.org/packages/flowClust")
7227 (synopsis "Clustering for flow cytometry")
7229 "This package provides robust model-based clustering using a t-mixture
7230 model with Box-Cox transformation.")
7231 (license license:artistic2.0)))
7233 ;; TODO: this package bundles an old version of protobuf. It's not easy to
7234 ;; make it use our protobuf package instead.
7235 (define-public r-rprotobuflib
7237 (name "r-rprotobuflib")
7242 (uri (bioconductor-uri "RProtoBufLib" version))
7245 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
7246 (properties `((upstream-name . "RProtoBufLib")))
7247 (build-system r-build-system)
7250 (modify-phases %standard-phases
7251 (add-after 'unpack 'unpack-bundled-sources
7253 (with-directory-excursion "src"
7254 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
7257 `(("r-knitr" ,r-knitr)))
7258 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
7259 (synopsis "C++ headers and static libraries of Protocol buffers")
7261 "This package provides the headers and static library of Protocol buffers
7262 for other R packages to compile and link against.")
7263 (license license:bsd-3)))
7265 (define-public r-flowworkspace
7267 (name "r-flowworkspace")
7272 (uri (bioconductor-uri "flowWorkspace" version))
7275 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
7276 (properties `((upstream-name . "flowWorkspace")))
7277 (build-system r-build-system)
7280 (modify-phases %standard-phases
7281 (add-after 'unpack 'fix-linking
7283 (substitute* "src/Makevars"
7284 ;; This is to avoid having a plain directory on the list of
7285 ;; libraries to link.
7286 (("\\{h5lib\\}" match)
7287 (string-append match "/libhdf5.a")))
7290 `(("r-aws-s3" ,r-aws-s3)
7291 ("r-aws-signature" ,r-aws-signature)
7293 ("r-biobase" ,r-biobase)
7294 ("r-biocgenerics" ,r-biocgenerics)
7295 ("r-cytolib" ,r-cytolib)
7296 ("r-data-table" ,r-data-table)
7297 ("r-digest" ,r-digest)
7298 ("r-dplyr" ,r-dplyr)
7299 ("r-flowcore" ,r-flowcore)
7300 ("r-ggplot2" ,r-ggplot2)
7301 ("r-graph" ,r-graph)
7302 ("r-lattice" ,r-lattice)
7303 ("r-latticeextra" ,r-latticeextra)
7304 ("r-matrixstats" ,r-matrixstats)
7305 ("r-ncdfflow" ,r-ncdfflow)
7308 ("r-rcpparmadillo" ,r-rcpparmadillo)
7309 ("r-rcppparallel" ,r-rcppparallel)
7310 ("r-rgraphviz" ,r-rgraphviz)
7311 ("r-rhdf5lib" ,r-rhdf5lib)
7312 ("r-rprotobuflib" ,r-rprotobuflib)
7313 ("r-scales" ,r-scales)
7316 `(("r-knitr" ,r-knitr)))
7317 (home-page "https://bioconductor.org/packages/flowWorkspace/")
7318 (synopsis "Infrastructure for working with cytometry data")
7320 "This package is designed to facilitate comparison of automated gating
7321 methods against manual gating done in flowJo. This package allows you to
7322 import basic flowJo workspaces into BioConductor and replicate the gating from
7323 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
7324 samples, compensation, and transformation are performed so that the output
7325 matches the flowJo analysis.")
7326 (license license:artistic2.0)))
7328 (define-public r-flowstats
7330 (name "r-flowstats")
7335 (uri (bioconductor-uri "flowStats" version))
7338 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
7339 (properties `((upstream-name . "flowStats")))
7340 (build-system r-build-system)
7342 `(("r-biobase" ,r-biobase)
7343 ("r-biocgenerics" ,r-biocgenerics)
7344 ("r-cluster" ,r-cluster)
7346 ("r-flowcore" ,r-flowcore)
7347 ("r-flowviz" ,r-flowviz)
7348 ("r-flowworkspace" ,r-flowworkspace)
7349 ("r-kernsmooth" ,r-kernsmooth)
7351 ("r-lattice" ,r-lattice)
7353 ("r-ncdfflow" ,r-ncdfflow)
7354 ("r-rcolorbrewer" ,r-rcolorbrewer)
7355 ("r-rrcov" ,r-rrcov)))
7356 (home-page "http://www.github.com/RGLab/flowStats")
7357 (synopsis "Statistical methods for the analysis of flow cytometry data")
7359 "This package provides methods and functionality to analyze flow data
7360 that is beyond the basic infrastructure provided by the @code{flowCore}
7362 (license license:artistic2.0)))
7364 (define-public r-opencyto
7371 (uri (bioconductor-uri "openCyto" version))
7374 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
7375 (properties `((upstream-name . "openCyto")))
7376 (build-system r-build-system)
7378 `(("r-biobase" ,r-biobase)
7379 ("r-biocgenerics" ,r-biocgenerics)
7381 ("r-data-table" ,r-data-table)
7382 ("r-flowclust" ,r-flowclust)
7383 ("r-flowcore" ,r-flowcore)
7384 ("r-flowstats" ,r-flowstats)
7385 ("r-flowviz" ,r-flowviz)
7386 ("r-flowworkspace" ,r-flowworkspace)
7387 ("r-graph" ,r-graph)
7388 ("r-gtools" ,r-gtools)
7390 ("r-lattice" ,r-lattice)
7392 ("r-ncdfflow" ,r-ncdfflow)
7394 ("r-r-utils" ,r-r-utils)
7396 ("r-rcolorbrewer" ,r-rcolorbrewer)
7398 ("r-rrcov" ,r-rrcov)))
7400 `(("r-knitr" ,r-knitr)))
7401 (home-page "https://bioconductor.org/packages/openCyto")
7402 (synopsis "Hierarchical gating pipeline for flow cytometry data")
7404 "This package is designed to facilitate the automated gating methods in a
7405 sequential way to mimic the manual gating strategy.")
7406 (license license:artistic2.0)))
7408 (define-public r-cytoml
7415 (uri (bioconductor-uri "CytoML" version))
7418 "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1"))))
7419 (properties `((upstream-name . "CytoML")))
7420 (build-system r-build-system)
7423 (modify-phases %standard-phases
7424 (add-after 'unpack 'fix-linking
7426 (substitute* "src/Makevars.in"
7427 ;; This is to avoid having a plain directory on the list of
7428 ;; libraries to link.
7429 (("\\{h5lib\\}" match)
7430 (string-append match "/libhdf5.a")))
7433 `(("libxml2" ,libxml2)
7436 `(("r-base64enc" ,r-base64enc)
7438 ("r-biobase" ,r-biobase)
7439 ("r-corpcor" ,r-corpcor)
7440 ("r-cytolib" ,r-cytolib)
7441 ("r-data-table" ,r-data-table)
7442 ("r-dplyr" ,r-dplyr)
7443 ("r-flowcore" ,r-flowcore)
7444 ("r-flowworkspace" ,r-flowworkspace)
7445 ("r-ggcyto" ,r-ggcyto)
7446 ("r-graph" ,r-graph)
7447 ("r-jsonlite" ,r-jsonlite)
7448 ("r-lattice" ,r-lattice)
7449 ("r-opencyto" ,r-opencyto)
7453 ("r-rcpparmadillo" ,r-rcpparmadillo)
7454 ("r-rcppparallel" ,r-rcppparallel)
7455 ("r-rgraphviz" ,r-rgraphviz)
7456 ("r-rhdf5lib" ,r-rhdf5lib)
7457 ("r-rprotobuflib" ,r-rprotobuflib)
7458 ("r-runit" ,r-runit)
7459 ("r-tibble" ,r-tibble)
7462 ("r-yaml" ,r-yaml)))
7464 `(("r-knitr" ,r-knitr)))
7465 (home-page "https://github.com/RGLab/CytoML")
7466 (synopsis "GatingML interface for cross platform cytometry data sharing")
7468 "This package provides an interface to implementations of the GatingML2.0
7469 standard to exchange gated cytometry data with other software platforms.")
7470 (license license:artistic2.0)))
7472 (define-public r-flowsom
7479 (uri (bioconductor-uri "FlowSOM" version))
7482 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
7483 (properties `((upstream-name . "FlowSOM")))
7484 (build-system r-build-system)
7486 `(("r-biocgenerics" ,r-biocgenerics)
7487 ("r-consensusclusterplus" ,r-consensusclusterplus)
7488 ("r-cytoml" ,r-cytoml)
7489 ("r-flowcore" ,r-flowcore)
7490 ("r-flowworkspace" ,r-flowworkspace)
7491 ("r-igraph" ,r-igraph)
7492 ("r-rcolorbrewer" ,r-rcolorbrewer)
7495 (home-page "https://bioconductor.org/packages/FlowSOM/")
7496 (synopsis "Visualize and interpret cytometry data")
7498 "FlowSOM offers visualization options for cytometry data, by using
7499 self-organizing map clustering and minimal spanning trees.")
7500 (license license:gpl2+)))
7502 (define-public r-mixomics
7509 (uri (bioconductor-uri "mixOmics" version))
7512 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
7513 (properties `((upstream-name . "mixOmics")))
7514 (build-system r-build-system)
7516 `(("r-corpcor" ,r-corpcor)
7517 ("r-dplyr" ,r-dplyr)
7518 ("r-ellipse" ,r-ellipse)
7519 ("r-ggrepel" ,r-ggrepel)
7520 ("r-ggplot2" ,r-ggplot2)
7521 ("r-gridextra" ,r-gridextra)
7522 ("r-igraph" ,r-igraph)
7523 ("r-lattice" ,r-lattice)
7525 ("r-matrixstats" ,r-matrixstats)
7526 ("r-rarpack" ,r-rarpack)
7527 ("r-rcolorbrewer" ,r-rcolorbrewer)
7528 ("r-reshape2" ,r-reshape2)
7529 ("r-tidyr" ,r-tidyr)))
7531 `(("r-knitr" ,r-knitr)))
7532 (home-page "http://www.mixOmics.org")
7533 (synopsis "Multivariate methods for exploration of biological datasets")
7535 "mixOmics offers a wide range of multivariate methods for the exploration
7536 and integration of biological datasets with a particular focus on variable
7537 selection. The package proposes several sparse multivariate models we have
7538 developed to identify the key variables that are highly correlated, and/or
7539 explain the biological outcome of interest. The data that can be analysed
7540 with mixOmics may come from high throughput sequencing technologies, such as
7541 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
7542 also beyond the realm of omics (e.g. spectral imaging). The methods
7543 implemented in mixOmics can also handle missing values without having to
7544 delete entire rows with missing data.")
7545 (license license:gpl2+)))
7547 (define-public r-depecher
7548 (package ;Source/Weave error
7554 (uri (bioconductor-uri "DepecheR" version))
7557 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
7558 (properties `((upstream-name . "DepecheR")))
7559 (build-system r-build-system)
7561 `(("r-beanplot" ,r-beanplot)
7562 ("r-dosnow" ,r-dosnow)
7563 ("r-dplyr" ,r-dplyr)
7565 ("r-foreach" ,r-foreach)
7566 ("r-ggplot2" ,r-ggplot2)
7567 ("r-gmodels" ,r-gmodels)
7568 ("r-gplots" ,r-gplots)
7570 ("r-matrixstats" ,r-matrixstats)
7571 ("r-mixomics" ,r-mixomics)
7572 ("r-moments" ,r-moments)
7574 ("r-rcppeigen" ,r-rcppeigen)
7575 ("r-reshape2" ,r-reshape2)
7576 ("r-robustbase" ,r-robustbase)
7577 ("r-viridis" ,r-viridis)))
7579 `(("r-knitr" ,r-knitr)))
7580 (home-page "https://bioconductor.org/packages/DepecheR/")
7581 (synopsis "Identify traits of clusters in high-dimensional entities")
7583 "The purpose of this package is to identify traits in a dataset that can
7584 separate groups. This is done on two levels. First, clustering is performed,
7585 using an implementation of sparse K-means. Secondly, the generated clusters
7586 are used to predict outcomes of groups of individuals based on their
7587 distribution of observations in the different clusters. As certain clusters
7588 with separating information will be identified, and these clusters are defined
7589 by a sparse number of variables, this method can reduce the complexity of
7590 data, to only emphasize the data that actually matters.")
7591 (license license:expat)))
7593 (define-public r-rcistarget
7595 (name "r-rcistarget")
7600 (uri (bioconductor-uri "RcisTarget" version))
7603 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
7604 (properties `((upstream-name . "RcisTarget")))
7605 (build-system r-build-system)
7607 `(("r-aucell" ,r-aucell)
7608 ("r-biocgenerics" ,r-biocgenerics)
7609 ("r-data-table" ,r-data-table)
7610 ("r-feather" ,r-feather)
7611 ("r-gseabase" ,r-gseabase)
7612 ("r-r-utils" ,r-r-utils)
7613 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7615 `(("r-knitr" ,r-knitr)))
7616 (home-page "https://aertslab.org/#scenic")
7617 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
7619 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
7620 over-represented on a gene list. In a first step, RcisTarget selects DNA
7621 motifs that are significantly over-represented in the surroundings of the
7622 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
7623 achieved by using a database that contains genome-wide cross-species rankings
7624 for each motif. The motifs that are then annotated to TFs and those that have
7625 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
7626 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
7627 genes in the gene-set that are ranked above the leading edge).")
7628 (license license:gpl3)))
7630 (define-public r-cicero
7637 (uri (bioconductor-uri "cicero" version))
7640 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
7641 (build-system r-build-system)
7643 `(("r-assertthat" ,r-assertthat)
7644 ("r-biobase" ,r-biobase)
7645 ("r-biocgenerics" ,r-biocgenerics)
7646 ("r-data-table" ,r-data-table)
7647 ("r-dplyr" ,r-dplyr)
7649 ("r-genomicranges" ,r-genomicranges)
7650 ("r-ggplot2" ,r-ggplot2)
7651 ("r-glasso" ,r-glasso)
7653 ("r-igraph" ,r-igraph)
7654 ("r-iranges" ,r-iranges)
7655 ("r-matrix" ,r-matrix)
7656 ("r-monocle" ,r-monocle)
7658 ("r-reshape2" ,r-reshape2)
7659 ("r-s4vectors" ,r-s4vectors)
7660 ("r-stringi" ,r-stringi)
7661 ("r-stringr" ,r-stringr)
7662 ("r-tibble" ,r-tibble)
7663 ("r-tidyr" ,r-tidyr)
7664 ("r-vgam" ,r-vgam)))
7666 `(("r-knitr" ,r-knitr)))
7667 (home-page "https://bioconductor.org/packages/cicero/")
7668 (synopsis "Predict cis-co-accessibility from single-cell data")
7670 "Cicero computes putative cis-regulatory maps from single-cell chromatin
7671 accessibility data. It also extends the monocle package for use in chromatin
7672 accessibility data.")
7673 (license license:expat)))
7675 ;; This is the latest commit on the "monocle3" branch.
7676 (define-public r-cicero-monocle3
7677 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
7679 (package (inherit r-cicero)
7680 (name "r-cicero-monocle3")
7681 (version (git-version "1.3.2" revision commit))
7686 (url "https://github.com/cole-trapnell-lab/cicero-release")
7688 (file-name (git-file-name name version))
7691 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
7693 `(("r-monocle3" ,r-monocle3)
7694 ,@(alist-delete "r-monocle"
7695 (package-propagated-inputs r-cicero)))))))
7697 (define-public r-circrnaprofiler
7699 (name "r-circrnaprofiler")
7704 (uri (bioconductor-uri "circRNAprofiler" version))
7707 "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
7709 `((upstream-name . "circRNAprofiler")))
7710 (build-system r-build-system)
7712 `(("r-annotationhub" ,r-annotationhub)
7713 ("r-biostrings" ,r-biostrings)
7714 ("r-bsgenome" ,r-bsgenome)
7715 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7716 ("r-deseq2" ,r-deseq2)
7717 ("r-dplyr" ,r-dplyr)
7718 ("r-edger" ,r-edger)
7719 ("r-genomeinfodb" ,r-genomeinfodb)
7720 ("r-genomicranges" ,r-genomicranges)
7721 ("r-ggplot2" ,r-ggplot2)
7722 ("r-gwascat" ,r-gwascat)
7723 ("r-iranges" ,r-iranges)
7724 ("r-magrittr" ,r-magrittr)
7725 ("r-r-utils" ,r-r-utils)
7726 ("r-readr" ,r-readr)
7727 ("r-reshape2" ,r-reshape2)
7728 ("r-rlang" ,r-rlang)
7729 ("r-rtracklayer" ,r-rtracklayer)
7730 ("r-s4vectors" ,r-s4vectors)
7731 ("r-seqinr" ,r-seqinr)
7732 ("r-stringi" ,r-stringi)
7733 ("r-stringr" ,r-stringr)
7734 ("r-universalmotif" ,r-universalmotif)))
7736 `(("r-knitr" ,r-knitr)))
7738 "https://github.com/Aufiero/circRNAprofiler")
7740 "Computational framework for the downstream analysis of circular RNA's")
7742 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
7743 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
7744 framework allows to combine and analyze circRNAs previously detected by
7745 multiple publicly available annotation-based circRNA detection tools. It
7746 covers different aspects of circRNAs analysis from differential expression
7747 analysis, evolutionary conservation, biogenesis to functional analysis.")
7748 (license license:gpl3)))
7750 (define-public r-cistopic
7751 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
7755 (version (git-version "0.2.1" revision commit))
7760 (url "https://github.com/aertslab/cisTopic")
7762 (file-name (git-file-name name version))
7765 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
7766 (build-system r-build-system)
7768 `(("r-aucell" ,r-aucell)
7769 ("r-data-table" ,r-data-table)
7770 ("r-dplyr" ,r-dplyr)
7771 ("r-dosnow" ,r-dosnow)
7773 ("r-feather" ,r-feather)
7774 ("r-fitdistrplus" ,r-fitdistrplus)
7775 ("r-genomicranges" ,r-genomicranges)
7776 ("r-ggplot2" ,r-ggplot2)
7778 ("r-matrix" ,r-matrix)
7780 ("r-rcistarget" ,r-rcistarget)
7781 ("r-rtracklayer" ,r-rtracklayer)
7782 ("r-s4vectors" ,r-s4vectors)))
7783 (home-page "https://github.com/aertslab/cisTopic")
7784 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
7786 "The sparse nature of single cell epigenomics data can be overruled using
7787 probabilistic modelling methods such as @dfn{Latent Dirichlet
7788 Allocation} (LDA). This package allows the probabilistic modelling of
7789 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
7790 includes functionalities to identify cell states based on the contribution of
7791 cisTopics and explore the nature and regulatory proteins driving them.")
7792 (license license:gpl3))))
7794 (define-public r-genie3
7801 (uri (bioconductor-uri "GENIE3" version))
7804 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
7805 (properties `((upstream-name . "GENIE3")))
7806 (build-system r-build-system)
7807 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
7809 `(("r-knitr" ,r-knitr)))
7810 (home-page "https://bioconductor.org/packages/GENIE3")
7811 (synopsis "Gene network inference with ensemble of trees")
7813 "This package implements the GENIE3 algorithm for inferring gene
7814 regulatory networks from expression data.")
7815 (license license:gpl2+)))
7817 (define-public r-roc
7824 (uri (bioconductor-uri "ROC" version))
7827 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
7828 (properties `((upstream-name . "ROC")))
7829 (build-system r-build-system)
7831 `(("r-knitr" ,r-knitr)))
7832 (home-page "https://www.bioconductor.org/packages/ROC/")
7833 (synopsis "Utilities for ROC curves")
7835 "This package provides utilities for @dfn{Receiver Operating
7836 Characteristic} (ROC) curves, with a focus on micro arrays.")
7837 (license license:artistic2.0)))
7839 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
7841 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
7846 (uri (bioconductor-uri
7847 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
7848 version 'annotation))
7851 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
7854 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
7855 (build-system r-build-system)
7856 (propagated-inputs `(("r-minfi" ,r-minfi)))
7858 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
7859 (synopsis "Annotation for Illumina's 450k methylation arrays")
7861 "This package provides manifests and annotation for Illumina's 450k array
7863 (license license:artistic2.0)))
7865 (define-public r-watermelon
7867 (name "r-watermelon")
7872 (uri (bioconductor-uri "wateRmelon" version))
7875 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
7876 (properties `((upstream-name . "wateRmelon")))
7877 (build-system r-build-system)
7879 `(("r-biobase" ,r-biobase)
7880 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
7881 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
7882 ("r-illuminaio" ,r-illuminaio)
7883 ("r-limma" ,r-limma)
7885 ("r-matrixstats" ,r-matrixstats)
7886 ("r-methylumi" ,r-methylumi)
7888 (home-page "https://bioconductor.org/packages/wateRmelon/")
7889 (synopsis "Illumina 450 methylation array normalization and metrics")
7891 "The standard index of DNA methylation (beta) is computed from methylated
7892 and unmethylated signal intensities. Betas calculated from raw signal
7893 intensities perform well, but using 11 methylomic datasets we demonstrate that
7894 quantile normalization methods produce marked improvement. The commonly used
7895 procedure of normalizing betas is inferior to the separate normalization of M
7896 and U, and it is also advantageous to normalize Type I and Type II assays
7897 separately. This package provides 15 flavours of betas and three performance
7898 metrics, with methods for objects produced by the @code{methylumi} and
7899 @code{minfi} packages.")
7900 (license license:gpl3)))
7902 (define-public r-gdsfmt
7909 (uri (bioconductor-uri "gdsfmt" version))
7912 "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
7913 (modules '((guix build utils)))
7914 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
7915 ;; them and link with system libraries instead.
7918 (for-each delete-file-recursively
7922 (substitute* "src/Makevars"
7923 (("all: \\$\\(SHLIB\\)") "all:")
7924 (("\\$\\(SHLIB\\): liblzma.a") "")
7925 (("(ZLIB|LZ4)/.*") "")
7926 (("CoreArray/dVLIntGDS.cpp.*")
7927 "CoreArray/dVLIntGDS.cpp")
7928 (("CoreArray/dVLIntGDS.o.*")
7929 "CoreArray/dVLIntGDS.o")
7930 (("PKG_LIBS = ./liblzma.a")
7931 "PKG_LIBS = -llz4"))
7932 (substitute* "src/CoreArray/dStream.h"
7933 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
7934 (string-append "include <" header ">")))
7936 (properties `((upstream-name . "gdsfmt")))
7937 (build-system r-build-system)
7943 `(("r-knitr" ,r-knitr)))
7944 (home-page "http://corearray.sourceforge.net/")
7946 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
7948 "This package provides a high-level R interface to CoreArray @dfn{Genomic
7949 Data Structure} (GDS) data files, which are portable across platforms with
7950 hierarchical structure to store multiple scalable array-oriented data sets
7951 with metadata information. It is suited for large-scale datasets, especially
7952 for data which are much larger than the available random-access memory. The
7953 @code{gdsfmt} package offers efficient operations specifically designed for
7954 integers of less than 8 bits, since a diploid genotype, like
7955 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
7956 byte. Data compression and decompression are available with relatively
7957 efficient random access. It is also allowed to read a GDS file in parallel
7958 with multiple R processes supported by the package @code{parallel}.")
7959 (license license:lgpl3)))
7961 (define-public r-bigmelon
7968 (uri (bioconductor-uri "bigmelon" version))
7971 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
7972 (properties `((upstream-name . "bigmelon")))
7973 (build-system r-build-system)
7975 `(("r-biobase" ,r-biobase)
7976 ("r-biocgenerics" ,r-biocgenerics)
7977 ("r-gdsfmt" ,r-gdsfmt)
7978 ("r-geoquery" ,r-geoquery)
7979 ("r-methylumi" ,r-methylumi)
7980 ("r-minfi" ,r-minfi)
7981 ("r-watermelon" ,r-watermelon)))
7982 (home-page "https://bioconductor.org/packages/bigmelon/")
7983 (synopsis "Illumina methylation array analysis for large experiments")
7985 "This package provides methods for working with Illumina arrays using the
7986 @code{gdsfmt} package.")
7987 (license license:gpl3)))
7989 (define-public r-seqbias
7996 (uri (bioconductor-uri "seqbias" version))
7999 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
8000 (properties `((upstream-name . "seqbias")))
8001 (build-system r-build-system)
8003 `(("r-biostrings" ,r-biostrings)
8004 ("r-genomicranges" ,r-genomicranges)
8005 ("r-rhtslib" ,r-rhtslib)))
8006 (home-page "https://bioconductor.org/packages/seqbias/")
8007 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
8009 "This package implements a model of per-position sequencing bias in
8010 high-throughput sequencing data using a simple Bayesian network, the structure
8011 and parameters of which are trained on a set of aligned reads and a reference
8013 (license license:lgpl3)))
8015 (define-public r-snplocs-hsapiens-dbsnp144-grch37
8017 (name "r-snplocs-hsapiens-dbsnp144-grch37")
8021 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
8022 version 'annotation))
8025 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
8026 (build-system r-build-system)
8027 ;; As this package provides little more than a very large data file it
8028 ;; doesn't make sense to build substitutes.
8029 (arguments `(#:substitutable? #f))
8031 `(("r-biocgenerics" ,r-biocgenerics)
8032 ("r-s4vectors" ,r-s4vectors)
8033 ("r-iranges" ,r-iranges)
8034 ("r-genomeinfodb" ,r-genomeinfodb)
8035 ("r-genomicranges" ,r-genomicranges)
8036 ("r-bsgenome" ,r-bsgenome)
8037 ("r-biostrings" ,r-biostrings)))
8039 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
8040 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
8041 (description "This package provides SNP locations and alleles for Homo
8042 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
8043 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
8044 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
8045 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
8046 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
8047 the mitochondrion chromosome. Therefore, the SNPs in this package can be
8048 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
8049 correct position but this injection will exclude chrM (i.e. nothing will be
8050 injected in that sequence).")
8051 (license license:artistic2.0)))
8053 (define-public r-reqon
8060 (uri (bioconductor-uri "ReQON" version))
8063 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
8064 (properties `((upstream-name . "ReQON")))
8065 (build-system r-build-system)
8067 `(("r-rjava" ,r-rjava)
8068 ("r-rsamtools" ,r-rsamtools)
8069 ("r-seqbias" ,r-seqbias)))
8070 (home-page "https://bioconductor.org/packages/ReQON/")
8071 (synopsis "Recalibrating quality of nucleotides")
8073 "This package provides an implementation of an algorithm for
8074 recalibrating the base quality scores for aligned sequencing data in BAM
8076 (license license:gpl2)))
8078 (define-public r-wavcluster
8080 (name "r-wavcluster")
8085 (uri (bioconductor-uri "wavClusteR" version))
8088 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
8089 (properties `((upstream-name . "wavClusteR")))
8090 (build-system r-build-system)
8092 `(("r-biocgenerics" ,r-biocgenerics)
8093 ("r-biostrings" ,r-biostrings)
8094 ("r-foreach" ,r-foreach)
8095 ("r-genomicfeatures" ,r-genomicfeatures)
8096 ("r-genomicranges" ,r-genomicranges)
8097 ("r-ggplot2" ,r-ggplot2)
8098 ("r-hmisc" ,r-hmisc)
8099 ("r-iranges" ,r-iranges)
8100 ("r-mclust" ,r-mclust)
8101 ("r-rsamtools" ,r-rsamtools)
8102 ("r-rtracklayer" ,r-rtracklayer)
8103 ("r-s4vectors" ,r-s4vectors)
8104 ("r-seqinr" ,r-seqinr)
8105 ("r-stringr" ,r-stringr)))
8107 `(("r-knitr" ,r-knitr)))
8108 (home-page "https://bioconductor.org/packages/wavClusteR/")
8109 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
8111 "This package provides an integrated pipeline for the analysis of
8112 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
8113 sequencing errors, SNPs and additional non-experimental sources by a non-
8114 parametric mixture model. The protein binding sites (clusters) are then
8115 resolved at high resolution and cluster statistics are estimated using a
8116 rigorous Bayesian framework. Post-processing of the results, data export for
8117 UCSC genome browser visualization and motif search analysis are provided. In
8118 addition, the package integrates RNA-Seq data to estimate the False
8119 Discovery Rate of cluster detection. Key functions support parallel multicore
8120 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
8121 be applied to the analysis of other NGS data obtained from experimental
8122 procedures that induce nucleotide substitutions (e.g. BisSeq).")
8123 (license license:gpl2)))
8125 (define-public r-timeseriesexperiment
8127 (name "r-timeseriesexperiment")
8132 (uri (bioconductor-uri "TimeSeriesExperiment" version))
8135 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
8137 `((upstream-name . "TimeSeriesExperiment")))
8138 (build-system r-build-system)
8140 `(("r-deseq2" ,r-deseq2)
8141 ("r-dplyr" ,r-dplyr)
8142 ("r-dynamictreecut" ,r-dynamictreecut)
8143 ("r-edger" ,r-edger)
8144 ("r-ggplot2" ,r-ggplot2)
8145 ("r-hmisc" ,r-hmisc)
8146 ("r-limma" ,r-limma)
8147 ("r-magrittr" ,r-magrittr)
8148 ("r-proxy" ,r-proxy)
8149 ("r-s4vectors" ,r-s4vectors)
8150 ("r-summarizedexperiment" ,r-summarizedexperiment)
8151 ("r-tibble" ,r-tibble)
8152 ("r-tidyr" ,r-tidyr)
8153 ("r-vegan" ,r-vegan)
8154 ("r-viridis" ,r-viridis)))
8156 `(("r-knitr" ,r-knitr)))
8157 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
8158 (synopsis "Analysis for short time-series data")
8160 "This package is a visualization and analysis toolbox for short time
8161 course data which includes dimensionality reduction, clustering, two-sample
8162 differential expression testing and gene ranking techniques. The package also
8163 provides methods for retrieving enriched pathways.")
8164 (license license:lgpl3+)))
8166 (define-public r-variantfiltering
8168 (name "r-variantfiltering")
8173 (uri (bioconductor-uri "VariantFiltering" version))
8176 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
8178 `((upstream-name . "VariantFiltering")))
8179 (build-system r-build-system)
8181 `(("r-annotationdbi" ,r-annotationdbi)
8182 ("r-biobase" ,r-biobase)
8183 ("r-biocgenerics" ,r-biocgenerics)
8184 ("r-biocparallel" ,r-biocparallel)
8185 ("r-biostrings" ,r-biostrings)
8186 ("r-bsgenome" ,r-bsgenome)
8188 ("r-genomeinfodb" ,r-genomeinfodb)
8189 ("r-genomicfeatures" ,r-genomicfeatures)
8190 ("r-genomicranges" ,r-genomicranges)
8191 ("r-genomicscores" ,r-genomicscores)
8192 ("r-graph" ,r-graph)
8194 ("r-iranges" ,r-iranges)
8196 ("r-rsamtools" ,r-rsamtools)
8197 ("r-s4vectors" ,r-s4vectors)
8198 ("r-shiny" ,r-shiny)
8199 ("r-shinyjs" ,r-shinyjs)
8200 ("r-shinythemes" ,r-shinythemes)
8201 ("r-shinytree" ,r-shinytree)
8202 ("r-summarizedexperiment" ,r-summarizedexperiment)
8203 ("r-variantannotation" ,r-variantannotation)
8204 ("r-xvector" ,r-xvector)))
8205 (home-page "https://github.com/rcastelo/VariantFiltering")
8206 (synopsis "Filtering of coding and non-coding genetic variants")
8208 "Filter genetic variants using different criteria such as inheritance
8209 model, amino acid change consequence, minor allele frequencies across human
8210 populations, splice site strength, conservation, etc.")
8211 (license license:artistic2.0)))
8213 (define-public r-genomegraphs
8215 (name "r-genomegraphs")
8220 (uri (bioconductor-uri "GenomeGraphs" version))
8223 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
8224 (properties `((upstream-name . "GenomeGraphs")))
8225 (build-system r-build-system)
8227 `(("r-biomart" ,r-biomart)))
8228 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
8229 (synopsis "Plotting genomic information from Ensembl")
8231 "Genomic data analyses requires integrated visualization of known genomic
8232 information and new experimental data. GenomeGraphs uses the biomaRt package
8233 to perform live annotation queries to Ensembl and translates this to e.g.
8234 gene/transcript structures in viewports of the grid graphics package. This
8235 results in genomic information plotted together with your data. Another
8236 strength of GenomeGraphs is to plot different data types such as array CGH,
8237 gene expression, sequencing and other data, together in one plot using the
8238 same genome coordinate system.")
8239 (license license:artistic2.0)))
8241 (define-public r-wavetiling
8243 (name "r-wavetiling")
8248 (uri (bioconductor-uri "waveTiling" version))
8251 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
8252 (properties `((upstream-name . "waveTiling")))
8253 (build-system r-build-system)
8255 `(("r-affy" ,r-affy)
8256 ("r-biobase" ,r-biobase)
8257 ("r-biostrings" ,r-biostrings)
8258 ("r-genomegraphs" ,r-genomegraphs)
8259 ("r-genomicranges" ,r-genomicranges)
8260 ("r-iranges" ,r-iranges)
8261 ("r-oligo" ,r-oligo)
8262 ("r-oligoclasses" ,r-oligoclasses)
8263 ("r-preprocesscore" ,r-preprocesscore)
8264 ("r-waveslim" ,r-waveslim)))
8265 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
8266 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
8268 "This package is designed to conduct transcriptome analysis for tiling
8269 arrays based on fast wavelet-based functional models.")
8270 (license license:gpl2+)))
8272 (define-public r-variancepartition
8274 (name "r-variancepartition")
8279 (uri (bioconductor-uri "variancePartition" version))
8282 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
8284 `((upstream-name . "variancePartition")))
8285 (build-system r-build-system)
8287 `(("r-biobase" ,r-biobase)
8288 ("r-biocparallel" ,r-biocparallel)
8289 ("r-colorramps" ,r-colorramps)
8290 ("r-doparallel" ,r-doparallel)
8291 ("r-foreach" ,r-foreach)
8292 ("r-ggplot2" ,r-ggplot2)
8293 ("r-gplots" ,r-gplots)
8294 ("r-iterators" ,r-iterators)
8295 ("r-limma" ,r-limma)
8297 ("r-lmertest" ,r-lmertest)
8299 ("r-pbkrtest" ,r-pbkrtest)
8300 ("r-progress" ,r-progress)
8301 ("r-reshape2" ,r-reshape2)
8302 ("r-scales" ,r-scales)))
8304 `(("r-knitr" ,r-knitr)))
8305 (home-page "https://bioconductor.org/packages/variancePartition/")
8306 (synopsis "Analyze variation in gene expression experiments")
8308 "This is a package providing tools to quantify and interpret multiple
8309 sources of biological and technical variation in gene expression experiments.
8310 It uses a linear mixed model to quantify variation in gene expression
8311 attributable to individual, tissue, time point, or technical variables. The
8312 package includes dream differential expression analysis for repeated
8314 (license license:gpl2+)))
8316 (define-public r-htqpcr
8323 (uri (bioconductor-uri "HTqPCR" version))
8326 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
8327 (properties `((upstream-name . "HTqPCR")))
8328 (build-system r-build-system)
8330 `(("r-affy" ,r-affy)
8331 ("r-biobase" ,r-biobase)
8332 ("r-gplots" ,r-gplots)
8333 ("r-limma" ,r-limma)
8334 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8335 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
8336 "groups/bertone/software/HTqPCR.pdf"))
8337 (synopsis "Automated analysis of high-throughput qPCR data")
8339 "Analysis of Ct values from high throughput quantitative real-time
8340 PCR (qPCR) assays across multiple conditions or replicates. The input data
8341 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
8342 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
8343 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
8344 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
8345 loading, quality assessment, normalization, visualization and parametric or
8346 non-parametric testing for statistical significance in Ct values between
8347 features (e.g. genes, microRNAs).")
8348 (license license:artistic2.0)))
8350 (define-public r-unifiedwmwqpcr
8352 (name "r-unifiedwmwqpcr")
8357 (uri (bioconductor-uri "unifiedWMWqPCR" version))
8360 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
8362 `((upstream-name . "unifiedWMWqPCR")))
8363 (build-system r-build-system)
8365 `(("r-biocgenerics" ,r-biocgenerics)
8366 ("r-htqpcr" ,r-htqpcr)))
8367 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
8368 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
8370 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
8371 data. This modified test allows for testing differential expression in qPCR
8373 (license license:gpl2+)))
8375 (define-public r-universalmotif
8377 (name "r-universalmotif")
8382 (uri (bioconductor-uri "universalmotif" version))
8385 "0pmi5mp5v0srr482vlkfmkp28bywq969fvv9g5kjl5rxki963zmr"))))
8387 `((upstream-name . "universalmotif")))
8388 (build-system r-build-system)
8391 (modify-phases %standard-phases
8392 (add-after 'unpack 'fix-reference-to-strip
8394 (substitute* "src/Makevars"
8395 (("/usr/bin/strip") (which "strip"))))))))
8397 `(("r-biocgenerics" ,r-biocgenerics)
8398 ("r-biostrings" ,r-biostrings)
8399 ("r-ggplot2" ,r-ggplot2)
8400 ("r-ggseqlogo" ,r-ggseqlogo)
8401 ("r-iranges" ,r-iranges)
8404 ("r-rcppthread" ,r-rcppthread)
8405 ("r-rdpack" ,r-rdpack)
8406 ("r-rlang" ,r-rlang)
8407 ("r-s4vectors" ,r-s4vectors)
8408 ("r-yaml" ,r-yaml)))
8410 `(("r-knitr" ,r-knitr)))
8412 "https://bioconductor.org/packages/universalmotif/")
8414 "Specific structures importer, modifier, and exporter for R")
8416 "This package allows importing most common @dfn{specific structure}
8417 (motif) types into R for use by functions provided by other Bioconductor
8418 motif-related packages. Motifs can be exported into most major motif formats
8419 from various classes as defined by other Bioconductor packages. A suite of
8420 motif and sequence manipulation and analysis functions are included, including
8421 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
8422 motifs, and others.")
8423 (license license:gpl3)))
8425 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
8427 (define-public r-activedriverwgs
8429 (name "r-activedriverwgs")
8434 (uri (cran-uri "ActiveDriverWGS" version))
8437 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
8439 `((upstream-name . "ActiveDriverWGS")))
8440 (build-system r-build-system)
8442 `(("r-biostrings" ,r-biostrings)
8443 ("r-bsgenome" ,r-bsgenome)
8444 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8445 ("r-genomeinfodb" ,r-genomeinfodb)
8446 ("r-genomicranges" ,r-genomicranges)
8447 ("r-iranges" ,r-iranges)
8448 ("r-s4vectors" ,r-s4vectors)))
8450 `(("r-knitr" ,r-knitr)))
8451 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
8452 (synopsis "Driver discovery tool for cancer whole genomes")
8454 "This package provides a method for finding an enrichment of cancer
8455 simple somatic mutations (SNVs and Indels) in functional elements across the
8456 human genome. ActiveDriverWGS detects coding and noncoding driver elements
8457 using whole genome sequencing data.")
8458 (license license:gpl3)))
8460 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
8462 (define-public r-activepathways
8464 (name "r-activepathways")
8469 (uri (cran-uri "ActivePathways" version))
8472 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
8474 `((upstream-name . "ActivePathways")))
8475 (build-system r-build-system)
8477 `(("r-data-table" ,r-data-table)
8478 ("r-ggplot2" ,r-ggplot2)))
8480 `(("r-knitr" ,r-knitr)))
8481 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
8482 (synopsis "Multivariate pathway enrichment analysis")
8484 "This package represents an integrative method of analyzing multi omics
8485 data that conducts enrichment analysis of annotated gene sets. ActivePathways
8486 uses a statistical data fusion approach, rationalizes contributing evidence
8487 and highlights associated genes, improving systems-level understanding of
8488 cellular organization in health and disease.")
8489 (license license:gpl3)))
8491 (define-public r-bgmix
8498 (uri (bioconductor-uri "BGmix" version))
8501 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
8502 (properties `((upstream-name . "BGmix")))
8503 (build-system r-build-system)
8505 `(("r-kernsmooth" ,r-kernsmooth)))
8506 (home-page "https://bioconductor.org/packages/BGmix/")
8507 (synopsis "Bayesian models for differential gene expression")
8509 "This package provides fully Bayesian mixture models for differential
8511 (license license:gpl2)))
8513 (define-public r-bgx
8520 (uri (bioconductor-uri "bgx" version))
8523 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
8524 (properties `((upstream-name . "bgx")))
8525 (build-system r-build-system)
8527 `(("r-affy" ,r-affy)
8528 ("r-biobase" ,r-biobase)
8529 ("r-gcrma" ,r-gcrma)
8530 ("r-rcpp" ,r-rcpp)))
8531 (home-page "https://bioconductor.org/packages/bgx/")
8532 (synopsis "Bayesian gene expression")
8534 "This package provides tools for Bayesian integrated analysis of
8535 Affymetrix GeneChips.")
8536 (license license:gpl2)))
8538 (define-public r-bhc
8545 (uri (bioconductor-uri "BHC" version))
8548 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
8549 (properties `((upstream-name . "BHC")))
8550 (build-system r-build-system)
8551 (home-page "https://bioconductor.org/packages/BHC/")
8552 (synopsis "Bayesian hierarchical clustering")
8554 "The method implemented in this package performs bottom-up hierarchical
8555 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
8556 in the data and Bayesian model selection to decide at each step which clusters
8557 to merge. This avoids several limitations of traditional methods, for example
8558 how many clusters there should be and how to choose a principled distance
8559 metric. This implementation accepts multinomial (i.e. discrete, with 2+
8560 categories) or time-series data. This version also includes a randomised
8561 algorithm which is more efficient for larger data sets.")
8562 (license license:gpl3)))
8564 (define-public r-bicare
8571 (uri (bioconductor-uri "BicARE" version))
8574 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
8575 (properties `((upstream-name . "BicARE")))
8576 (build-system r-build-system)
8578 `(("r-biobase" ,r-biobase)
8579 ("r-gseabase" ,r-gseabase)
8580 ("r-multtest" ,r-multtest)))
8581 (home-page "http://bioinfo.curie.fr")
8582 (synopsis "Biclustering analysis and results exploration")
8584 "This is a package for biclustering analysis and exploration of
8586 (license license:gpl2)))
8588 (define-public r-bifet
8595 (uri (bioconductor-uri "BiFET" version))
8598 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
8599 (properties `((upstream-name . "BiFET")))
8600 (build-system r-build-system)
8602 `(("r-genomicranges" ,r-genomicranges)
8603 ("r-poibin" ,r-poibin)))
8605 `(("r-knitr" ,r-knitr)))
8606 (home-page "https://bioconductor.org/packages/BiFET")
8607 (synopsis "Bias-free footprint enrichment test")
8609 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
8610 over-represented in target regions compared to background regions after
8611 correcting for the bias arising from the imbalance in read counts and GC
8612 contents between the target and background regions. For a given TF k, BiFET
8613 tests the null hypothesis that the target regions have the same probability of
8614 having footprints for the TF k as the background regions while correcting for
8615 the read count and GC content bias.")
8616 (license license:gpl3)))
8618 (define-public r-rsbml
8625 (uri (bioconductor-uri "rsbml" version))
8628 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
8629 (properties `((upstream-name . "rsbml")))
8630 (build-system r-build-system)
8632 `(("libsbml" ,libsbml)
8635 `(("r-biocgenerics" ,r-biocgenerics)
8636 ("r-graph" ,r-graph)))
8638 `(("pkg-config" ,pkg-config)))
8639 (home-page "http://www.sbml.org")
8640 (synopsis "R support for SBML")
8642 "This package provides an R interface to libsbml for SBML parsing,
8643 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
8644 (license license:artistic2.0)))
8646 (define-public r-hypergraph
8648 (name "r-hypergraph")
8653 (uri (bioconductor-uri "hypergraph" version))
8656 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
8657 (properties `((upstream-name . "hypergraph")))
8658 (build-system r-build-system)
8660 `(("r-graph" ,r-graph)))
8661 (home-page "https://bioconductor.org/packages/hypergraph")
8662 (synopsis "Hypergraph data structures")
8664 "This package implements some simple capabilities for representing and
8665 manipulating hypergraphs.")
8666 (license license:artistic2.0)))
8668 (define-public r-hyperdraw
8670 (name "r-hyperdraw")
8675 (uri (bioconductor-uri "hyperdraw" version))
8678 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
8679 (properties `((upstream-name . "hyperdraw")))
8680 (build-system r-build-system)
8681 (inputs `(("graphviz" ,graphviz)))
8683 `(("r-graph" ,r-graph)
8684 ("r-hypergraph" ,r-hypergraph)
8685 ("r-rgraphviz" ,r-rgraphviz)))
8686 (home-page "https://bioconductor.org/packages/hyperdraw")
8687 (synopsis "Visualizing hypergraphs")
8689 "This package provides functions for visualizing hypergraphs.")
8690 (license license:gpl2+)))
8692 (define-public r-biggr
8699 (uri (bioconductor-uri "BiGGR" version))
8702 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
8703 (properties `((upstream-name . "BiGGR")))
8704 (build-system r-build-system)
8706 `(("r-hyperdraw" ,r-hyperdraw)
8707 ("r-hypergraph" ,r-hypergraph)
8709 ("r-limsolve" ,r-limsolve)
8710 ("r-rsbml" ,r-rsbml)
8711 ("r-stringr" ,r-stringr)))
8712 (home-page "https://bioconductor.org/packages/BiGGR/")
8713 (synopsis "Constraint based modeling using metabolic reconstruction databases")
8715 "This package provides an interface to simulate metabolic reconstruction
8716 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
8717 reconstruction databases. The package facilitates @dfn{flux balance
8718 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
8719 networks and estimated fluxes can be visualized with hypergraphs.")
8720 (license license:gpl3+)))
8722 (define-public r-bigmemoryextras
8724 (name "r-bigmemoryextras")
8729 (uri (bioconductor-uri "bigmemoryExtras" version))
8732 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
8734 `((upstream-name . "bigmemoryExtras")))
8735 (build-system r-build-system)
8737 `(("r-bigmemory" ,r-bigmemory)))
8739 `(("r-knitr" ,r-knitr)))
8740 (home-page "https://github.com/phaverty/bigmemoryExtras")
8741 (synopsis "Extension of the bigmemory package")
8743 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
8744 safety and convenience features to the @code{filebacked.big.matrix} class from
8745 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
8746 monitoring and gracefully restoring the connection to on-disk data and it also
8747 protects against accidental data modification with a file-system-based
8748 permissions system. Utilities are provided for using @code{BigMatrix}-derived
8749 classes as @code{assayData} matrices within the @code{Biobase} package's
8750 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
8751 related to attaching to, and indexing into, file-backed matrices with
8752 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
8753 a file-backed matrix with factor properties.")
8754 (license license:artistic2.0)))
8756 (define-public r-bigpint
8763 (uri (bioconductor-uri "bigPint" version))
8766 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
8767 (properties `((upstream-name . "bigPint")))
8768 (build-system r-build-system)
8770 `(("r-delayedarray" ,r-delayedarray)
8771 ("r-dplyr" ,r-dplyr)
8772 ("r-ggally" ,r-ggally)
8773 ("r-ggplot2" ,r-ggplot2)
8774 ("r-gridextra" ,r-gridextra)
8775 ("r-hexbin" ,r-hexbin)
8776 ("r-hmisc" ,r-hmisc)
8777 ("r-htmlwidgets" ,r-htmlwidgets)
8778 ("r-plotly" ,r-plotly)
8780 ("r-rcolorbrewer" ,r-rcolorbrewer)
8781 ("r-reshape" ,r-reshape)
8782 ("r-shiny" ,r-shiny)
8783 ("r-shinycssloaders" ,r-shinycssloaders)
8784 ("r-shinydashboard" ,r-shinydashboard)
8785 ("r-stringr" ,r-stringr)
8786 ("r-summarizedexperiment" ,r-summarizedexperiment)
8787 ("r-tidyr" ,r-tidyr)))
8789 `(("r-knitr" ,r-knitr)))
8790 (home-page "https://github.com/lindsayrutter/bigPint")
8791 (synopsis "Big multivariate data plotted interactively")
8793 "This package provides methods for visualizing large multivariate
8794 datasets using static and interactive scatterplot matrices, parallel
8795 coordinate plots, volcano plots, and litre plots. It includes examples for
8796 visualizing RNA-sequencing datasets and differentially expressed genes.")
8797 (license license:gpl3)))
8799 (define-public r-chemminer
8801 (name "r-chemminer")
8806 (uri (bioconductor-uri "ChemmineR" version))
8809 "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
8810 (properties `((upstream-name . "ChemmineR")))
8811 (build-system r-build-system)
8813 `(("r-base64enc" ,r-base64enc)
8815 ("r-biocgenerics" ,r-biocgenerics)
8817 ("r-digest" ,r-digest)
8819 ("r-ggplot2" ,r-ggplot2)
8820 ("r-gridextra" ,r-gridextra)
8823 ("r-rcurl" ,r-rcurl)
8824 ("r-rjson" ,r-rjson)
8825 ("r-rsvg" ,r-rsvg)))
8827 `(("r-knitr" ,r-knitr)))
8828 (home-page "https://github.com/girke-lab/ChemmineR")
8829 (synopsis "Cheminformatics toolkit for R")
8831 "ChemmineR is a cheminformatics package for analyzing drug-like small
8832 molecule data in R. It contains functions for efficient processing of large
8833 numbers of molecules, physicochemical/structural property predictions,
8834 structural similarity searching, classification and clustering of compound
8835 libraries with a wide spectrum of algorithms. In addition, it offers
8836 visualization functions for compound clustering results and chemical
8838 (license license:artistic2.0)))
8840 (define-public r-bioassayr
8842 (name "r-bioassayr")
8847 (uri (bioconductor-uri "bioassayR" version))
8850 "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5"))))
8851 (properties `((upstream-name . "bioassayR")))
8852 (build-system r-build-system)
8854 `(("r-biocgenerics" ,r-biocgenerics)
8855 ("r-chemminer" ,r-chemminer)
8857 ("r-matrix" ,r-matrix)
8858 ("r-rjson" ,r-rjson)
8859 ("r-rsqlite" ,r-rsqlite)
8862 `(("r-knitr" ,r-knitr)))
8863 (home-page "https://github.com/girke-lab/bioassayR")
8864 (synopsis "Cross-target analysis of small molecule bioactivity")
8866 "bioassayR is a computational tool that enables simultaneous analysis of
8867 thousands of bioassay experiments performed over a diverse set of compounds
8868 and biological targets. Unique features include support for large-scale
8869 cross-target analyses of both public and custom bioassays, generation of
8870 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
8871 preloaded database that provides access to a substantial portion of publicly
8872 available bioactivity data.")
8873 (license license:artistic2.0)))
8875 (define-public r-biobroom
8882 (uri (bioconductor-uri "biobroom" version))
8885 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
8886 (properties `((upstream-name . "biobroom")))
8887 (build-system r-build-system)
8889 `(("r-biobase" ,r-biobase)
8890 ("r-broom" ,r-broom)
8891 ("r-dplyr" ,r-dplyr)
8892 ("r-tidyr" ,r-tidyr)))
8894 `(("r-knitr" ,r-knitr)))
8895 (home-page "https://github.com/StoreyLab/biobroom")
8896 (synopsis "Turn Bioconductor objects into tidy data frames")
8898 "This package contains methods for converting standard objects
8899 constructed by bioinformatics packages, especially those in Bioconductor, and
8900 converting them to @code{tidy} data. It thus serves as a complement to the
8901 @code{broom} package, and follows the same tidy, augment, glance division of
8902 tidying methods. Tidying data makes it easy to recombine, reshape and
8903 visualize bioinformatics analyses.")
8904 ;; Any version of the LGPL.
8905 (license license:lgpl3+)))
8907 (define-public r-graphite
8914 (uri (bioconductor-uri "graphite" version))
8917 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
8918 (properties `((upstream-name . "graphite")))
8919 (build-system r-build-system)
8921 `(("r-annotationdbi" ,r-annotationdbi)
8922 ("r-checkmate" ,r-checkmate)
8923 ("r-graph" ,r-graph)
8925 ("r-rappdirs" ,r-rappdirs)))
8926 (home-page "https://bioconductor.org/packages/graphite/")
8927 (synopsis "Networks from pathway databases")
8929 "Graphite provides networks derived from eight public pathway databases,
8930 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
8932 (license license:agpl3+)))
8934 (define-public r-reactomepa
8936 (name "r-reactomepa")
8941 (uri (bioconductor-uri "ReactomePA" version))
8944 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
8945 (properties `((upstream-name . "ReactomePA")))
8946 (build-system r-build-system)
8948 `(("r-annotationdbi" ,r-annotationdbi)
8950 ("r-enrichplot" ,r-enrichplot)
8951 ("r-ggplot2" ,r-ggplot2)
8952 ("r-ggraph" ,r-ggraph)
8953 ("r-graphite" ,r-graphite)
8954 ("r-igraph" ,r-igraph)
8955 ("r-reactome-db" ,r-reactome-db)))
8957 `(("r-knitr" ,r-knitr)))
8958 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
8959 (synopsis "Reactome pathway analysis")
8961 "This package provides functions for pathway analysis based on the
8962 REACTOME pathway database. It implements enrichment analysis, gene set
8963 enrichment analysis and several functions for visualization.")
8964 (license license:gpl2)))
8966 (define-public r-ebarrays
8973 (uri (bioconductor-uri "EBarrays" version))
8976 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
8977 (properties `((upstream-name . "EBarrays")))
8978 (build-system r-build-system)
8980 `(("r-biobase" ,r-biobase)
8981 ("r-cluster" ,r-cluster)
8982 ("r-lattice" ,r-lattice)))
8983 (home-page "https://bioconductor.org/packages/EBarrays/")
8984 (synopsis "Gene clustering and differential expression identification")
8986 "EBarrays provides tools for the analysis of replicated/unreplicated
8988 (license license:gpl2+)))
8990 (define-public r-bioccasestudies
8992 (name "r-bioccasestudies")
8997 (uri (bioconductor-uri "BiocCaseStudies" version))
9000 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
9002 `((upstream-name . "BiocCaseStudies")))
9003 (build-system r-build-system)
9004 (propagated-inputs `(("r-biobase" ,r-biobase)))
9005 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
9006 (synopsis "Support for the case studies monograph")
9008 "This package provides software and data to support the case studies
9010 (license license:artistic2.0)))
9012 (define-public r-bioccheck
9014 (name "r-bioccheck")
9018 (uri (bioconductor-uri "BiocCheck" version))
9021 "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
9023 `((upstream-name . "BiocCheck")))
9024 (build-system r-build-system)
9027 (modify-phases %standard-phases
9028 ;; This package can be used by calling BiocCheck(<package>) from
9029 ;; within R, or by running R CMD BiocCheck <package>. This phase
9030 ;; makes sure the latter works. For this to work, the BiocCheck
9031 ;; script must be somewhere on the PATH (not the R bin directory).
9032 (add-after 'install 'install-bioccheck-subcommand
9033 (lambda* (#:key outputs #:allow-other-keys)
9034 (let* ((out (assoc-ref outputs "out"))
9035 (dest-dir (string-append out "/bin"))
9037 (string-append out "/site-library/BiocCheck/script/")))
9039 (symlink (string-append script-dir "/checkBadDeps.R")
9040 (string-append dest-dir "/checkBadDeps.R"))
9041 (symlink (string-append script-dir "/BiocCheck")
9042 (string-append dest-dir "/BiocCheck")))
9045 `(("r-codetools" ,r-codetools)
9046 ("r-graph" ,r-graph)
9048 ("r-knitr" ,r-knitr)
9049 ("r-optparse" ,r-optparse)
9050 ("r-biocmanager" ,r-biocmanager)
9051 ("r-biocviews" ,r-biocviews)
9052 ("r-stringdist" ,r-stringdist)))
9054 `(("r-knitr" ,r-knitr)))
9055 (home-page "https://bioconductor.org/packages/BiocCheck")
9056 (synopsis "Executes Bioconductor-specific package checks")
9057 (description "This package contains tools to perform additional quality
9058 checks on R packages that are to be submitted to the Bioconductor repository.")
9059 (license license:artistic2.0)))
9061 (define-public r-biocgraph
9063 (name "r-biocgraph")
9068 (uri (bioconductor-uri "biocGraph" version))
9071 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
9072 (properties `((upstream-name . "biocGraph")))
9073 (build-system r-build-system)
9075 `(("r-biocgenerics" ,r-biocgenerics)
9076 ("r-geneplotter" ,r-geneplotter)
9077 ("r-graph" ,r-graph)
9078 ("r-rgraphviz" ,r-rgraphviz)))
9079 (home-page "https://bioconductor.org/packages/biocGraph/")
9080 (synopsis "Graph examples and use cases in Bioinformatics")
9082 "This package provides examples and code that make use of the
9083 different graph related packages produced by Bioconductor.")
9084 (license license:artistic2.0)))
9086 (define-public r-biocstyle
9088 (name "r-biocstyle")
9092 (uri (bioconductor-uri "BiocStyle" version))
9095 "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
9097 `((upstream-name . "BiocStyle")))
9098 (build-system r-build-system)
9100 `(("r-biocmanager" ,r-biocmanager)
9101 ("r-bookdown" ,r-bookdown)
9102 ("r-knitr" ,r-knitr)
9103 ("r-rmarkdown" ,r-rmarkdown)
9104 ("r-yaml" ,r-yaml)))
9106 `(("r-knitr" ,r-knitr)))
9107 (home-page "https://bioconductor.org/packages/BiocStyle")
9108 (synopsis "Bioconductor formatting styles")
9109 (description "This package provides standard formatting styles for
9110 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
9112 (license license:artistic2.0)))
9114 (define-public r-biocviews
9116 (name "r-biocviews")
9120 (uri (bioconductor-uri "biocViews" version))
9123 "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
9125 `((upstream-name . "biocViews")))
9126 (build-system r-build-system)
9128 `(("r-biobase" ,r-biobase)
9129 ("r-biocmanager" ,r-biocmanager)
9130 ("r-graph" ,r-graph)
9132 ("r-rcurl" ,r-rcurl)
9134 ("r-runit" ,r-runit)))
9135 (home-page "https://bioconductor.org/packages/biocViews")
9136 (synopsis "Bioconductor package categorization helper")
9137 (description "The purpose of biocViews is to create HTML pages that
9138 categorize packages in a Bioconductor package repository according to keywords,
9139 also known as views, in a controlled vocabulary.")
9140 (license license:artistic2.0)))
9142 (define-public r-experimenthub
9144 (name "r-experimenthub")
9149 (uri (bioconductor-uri "ExperimentHub" version))
9152 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
9153 (properties `((upstream-name . "ExperimentHub")))
9154 (build-system r-build-system)
9156 `(("r-annotationhub" ,r-annotationhub)
9157 ("r-biocfilecache" ,r-biocfilecache)
9158 ("r-biocgenerics" ,r-biocgenerics)
9159 ("r-biocmanager" ,r-biocmanager)
9161 ("r-rappdirs" ,r-rappdirs)
9162 ("r-s4vectors" ,r-s4vectors)))
9164 `(("r-knitr" ,r-knitr)))
9165 (home-page "https://bioconductor.org/packages/ExperimentHub/")
9166 (synopsis "Client to access ExperimentHub resources")
9168 "This package provides a client for the Bioconductor ExperimentHub web
9169 resource. ExperimentHub provides a central location where curated data from
9170 experiments, publications or training courses can be accessed. Each resource
9171 has associated metadata, tags and date of modification. The client creates
9172 and manages a local cache of files retrieved enabling quick and reproducible
9174 (license license:artistic2.0)))
9176 (define-public r-grohmm
9183 (uri (bioconductor-uri "groHMM" version))
9186 "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
9187 (properties `((upstream-name . "groHMM")))
9188 (build-system r-build-system)
9190 `(("r-genomeinfodb" ,r-genomeinfodb)
9191 ("r-genomicalignments" ,r-genomicalignments)
9192 ("r-genomicranges" ,r-genomicranges)
9193 ("r-iranges" ,r-iranges)
9195 ("r-rtracklayer" ,r-rtracklayer)
9196 ("r-s4vectors" ,r-s4vectors)))
9197 (home-page "https://github.com/Kraus-Lab/groHMM")
9198 (synopsis "GRO-seq analysis pipeline")
9200 "This package provides a pipeline for the analysis of GRO-seq data.")
9201 (license license:gpl3+)))
9203 (define-public r-multiassayexperiment
9205 (name "r-multiassayexperiment")
9210 (uri (bioconductor-uri "MultiAssayExperiment" version))
9213 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
9215 `((upstream-name . "MultiAssayExperiment")))
9216 (build-system r-build-system)
9218 `(("r-biobase" ,r-biobase)
9219 ("r-biocgenerics" ,r-biocgenerics)
9220 ("r-genomicranges" ,r-genomicranges)
9221 ("r-iranges" ,r-iranges)
9222 ("r-s4vectors" ,r-s4vectors)
9223 ("r-summarizedexperiment" ,r-summarizedexperiment)
9224 ("r-tidyr" ,r-tidyr)))
9226 `(("r-knitr" ,r-knitr)))
9227 (home-page "https://waldronlab.io/MultiAssayExperiment/")
9228 (synopsis "Integration of multi-omics experiments in Bioconductor")
9230 "MultiAssayExperiment harmonizes data management of multiple assays
9231 performed on an overlapping set of specimens. It provides a familiar
9232 Bioconductor user experience by extending concepts from
9233 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
9234 classes for individual assays, and allowing subsetting by genomic ranges or
9236 (license license:artistic2.0)))
9238 (define-public r-bioconcotk
9240 (name "r-bioconcotk")
9245 (uri (bioconductor-uri "BiocOncoTK" version))
9248 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
9249 (properties `((upstream-name . "BiocOncoTK")))
9250 (build-system r-build-system)
9252 `(("r-bigrquery" ,r-bigrquery)
9254 ("r-complexheatmap" ,r-complexheatmap)
9255 ("r-curatedtcgadata" ,r-curatedtcgadata)
9257 ("r-dplyr" ,r-dplyr)
9259 ("r-genomicfeatures" ,r-genomicfeatures)
9260 ("r-genomicranges" ,r-genomicranges)
9261 ("r-ggplot2" ,r-ggplot2)
9262 ("r-ggpubr" ,r-ggpubr)
9263 ("r-graph" ,r-graph)
9265 ("r-iranges" ,r-iranges)
9266 ("r-magrittr" ,r-magrittr)
9268 ("r-rgraphviz" ,r-rgraphviz)
9269 ("r-rjson" ,r-rjson)
9270 ("r-s4vectors" ,r-s4vectors)
9271 ("r-scales" ,r-scales)
9272 ("r-shiny" ,r-shiny)
9273 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9275 `(("r-knitr" ,r-knitr)))
9276 (home-page "https://bioconductor.org/packages/BiocOncoTK")
9277 (synopsis "Bioconductor components for general cancer genomics")
9279 "The purpose of this package is to provide a central interface to various
9280 tools for genome-scale analysis of cancer studies.")
9281 (license license:artistic2.0)))
9283 (define-public r-biocor
9290 (uri (bioconductor-uri "BioCor" version))
9293 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
9294 (properties `((upstream-name . "BioCor")))
9295 (build-system r-build-system)
9297 `(("r-biocparallel" ,r-biocparallel)
9298 ("r-gseabase" ,r-gseabase)
9299 ("r-matrix" ,r-matrix)))
9301 `(("r-knitr" ,r-knitr)))
9302 (home-page "https://llrs.github.io/BioCor/")
9303 (synopsis "Functional similarities")
9305 "This package provides tools to calculate functional similarities based
9306 on the pathways described on KEGG and REACTOME or in gene sets. These
9307 similarities can be calculated for pathways or gene sets, genes, or clusters
9308 and combined with other similarities. They can be used to improve networks,
9309 gene selection, testing relationships, and so on.")
9310 (license license:expat)))
9312 (define-public r-biocpkgtools
9314 (name "r-biocpkgtools")
9319 (uri (bioconductor-uri "BiocPkgTools" version))
9322 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
9323 (properties `((upstream-name . "BiocPkgTools")))
9324 (build-system r-build-system)
9326 `(("r-biocfilecache" ,r-biocfilecache)
9327 ("r-biocmanager" ,r-biocmanager)
9328 ("r-biocviews" ,r-biocviews)
9329 ("r-dplyr" ,r-dplyr)
9332 ("r-graph" ,r-graph)
9333 ("r-htmltools" ,r-htmltools)
9334 ("r-htmlwidgets" ,r-htmlwidgets)
9336 ("r-igraph" ,r-igraph)
9337 ("r-jsonlite" ,r-jsonlite)
9338 ("r-magrittr" ,r-magrittr)
9339 ("r-rappdirs" ,r-rappdirs)
9341 ("r-readr" ,r-readr)
9343 ("r-rlang" ,r-rlang)
9344 ("r-rvest" ,r-rvest)
9345 ("r-stringr" ,r-stringr)
9346 ("r-tibble" ,r-tibble)
9347 ("r-tidyr" ,r-tidyr)
9348 ("r-tidyselect" ,r-tidyselect)
9349 ("r-xml2" ,r-xml2)))
9351 `(("r-knitr" ,r-knitr)))
9352 (home-page "https://github.com/seandavi/BiocPkgTools")
9353 (synopsis "Collection of tools for learning about Bioconductor packages")
9355 "Bioconductor has a rich ecosystem of metadata around packages, usage,
9356 and build status. This package is a simple collection of functions to access
9357 that metadata from R. The goal is to expose metadata for data mining and
9358 value-added functionality such as package searching, text mining, and
9359 analytics on packages.")
9360 (license license:expat)))
9362 (define-public r-biocset
9369 (uri (bioconductor-uri "BiocSet" version))
9372 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
9373 (properties `((upstream-name . "BiocSet")))
9374 (build-system r-build-system)
9376 `(("r-annotationdbi" ,r-annotationdbi)
9377 ("r-biocio" ,r-biocio)
9378 ("r-dplyr" ,r-dplyr)
9379 ("r-keggrest" ,r-keggrest)
9380 ("r-ontologyindex" ,r-ontologyindex)
9382 ("r-rlang" ,r-rlang)
9383 ("r-s4vectors" ,r-s4vectors)
9384 ("r-tibble" ,r-tibble)
9385 ("r-tidyr" ,r-tidyr)))
9387 `(("r-knitr" ,r-knitr)))
9389 "https://bioconductor.org/packages/BiocSet")
9391 "Representing Different Biological Sets")
9393 "BiocSet displays different biological sets in a triple tibble format.
9394 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
9395 The user has the ability to activate one of these three tibbles to perform
9396 common functions from the @code{dplyr} package. Mapping functionality and
9397 accessing web references for elements/sets are also available in BiocSet.")
9398 (license license:artistic2.0)))
9400 (define-public r-biocworkflowtools
9402 (name "r-biocworkflowtools")
9407 (uri (bioconductor-uri "BiocWorkflowTools" version))
9410 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
9412 `((upstream-name . "BiocWorkflowTools")))
9413 (build-system r-build-system)
9415 `(("r-biocstyle" ,r-biocstyle)
9416 ("r-bookdown" ,r-bookdown)
9417 ("r-git2r" ,r-git2r)
9419 ("r-knitr" ,r-knitr)
9420 ("r-rmarkdown" ,r-rmarkdown)
9421 ("r-rstudioapi" ,r-rstudioapi)
9422 ("r-stringr" ,r-stringr)
9423 ("r-usethis" ,r-usethis)))
9425 `(("r-knitr" ,r-knitr)))
9426 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
9427 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
9429 "This package provides functions to ease the transition between
9430 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
9431 (license license:expat)))
9433 (define-public r-biodist
9440 (uri (bioconductor-uri "bioDist" version))
9443 "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
9444 (properties `((upstream-name . "bioDist")))
9445 (build-system r-build-system)
9447 `(("r-biobase" ,r-biobase)
9448 ("r-kernsmooth" ,r-kernsmooth)))
9449 (home-page "https://bioconductor.org/packages/bioDist/")
9450 (synopsis "Different distance measures")
9452 "This package provides a collection of software tools for calculating
9453 distance measures.")
9454 (license license:artistic2.0)))
9456 (define-public r-pcatools
9463 (uri (bioconductor-uri "PCAtools" version))
9466 "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
9467 (properties `((upstream-name . "PCAtools")))
9468 (build-system r-build-system)
9470 `(("r-beachmat" ,r-beachmat)
9472 ("r-biocparallel" ,r-biocparallel)
9473 ("r-biocsingular" ,r-biocsingular)
9474 ("r-cowplot" ,r-cowplot)
9475 ("r-delayedarray" ,r-delayedarray)
9476 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9477 ("r-dqrng" ,r-dqrng)
9478 ("r-ggplot2" ,r-ggplot2)
9479 ("r-ggrepel" ,r-ggrepel)
9480 ("r-lattice" ,r-lattice)
9481 ("r-matrix" ,r-matrix)
9483 ("r-reshape2" ,r-reshape2)))
9484 (native-inputs `(("r-knitr" ,r-knitr)))
9485 (home-page "https://github.com/kevinblighe/PCAtools")
9486 (synopsis "PCAtools: everything Principal Components Analysis")
9488 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
9489 structure of the data without the need to build any model to represent it.
9490 This \"summary\" of the data is arrived at through a process of reduction that
9491 can transform the large number of variables into a lesser number that are
9492 uncorrelated (i.e. the 'principal components'), while at the same time being
9493 capable of easy interpretation on the original data. PCAtools provides
9494 functions for data exploration via PCA, and allows the user to generate
9495 publication-ready figures. PCA is performed via @code{BiocSingular}; users
9496 can also identify an optimal number of principal components via different
9497 metrics, such as the elbow method and Horn's parallel analysis, which has
9498 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
9499 dimensional mass cytometry data.")
9500 (license license:gpl3)))
9502 (define-public r-rgreat
9509 (uri (bioconductor-uri "rGREAT" version))
9512 "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
9513 (properties `((upstream-name . "rGREAT")))
9514 (build-system r-build-system)
9516 `(("r-genomicranges" ,r-genomicranges)
9517 ("r-getoptlong" ,r-getoptlong)
9518 ("r-iranges" ,r-iranges)
9519 ("r-rcurl" ,r-rcurl)
9520 ("r-rjson" ,r-rjson)))
9521 (native-inputs `(("r-knitr" ,r-knitr)))
9522 (home-page "https://github.com/jokergoo/rGREAT")
9523 (synopsis "Client for GREAT analysis")
9525 "This package makes GREAT (Genomic Regions Enrichment of Annotations
9526 Tool) analysis automatic by constructing a HTTP POST request according to
9527 user's input and automatically retrieving results from GREAT web server.")
9528 (license license:expat)))
9530 (define-public r-m3c
9537 (uri (bioconductor-uri "M3C" version))
9540 "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
9541 (properties `((upstream-name . "M3C")))
9542 (build-system r-build-system)
9544 `(("r-cluster" ,r-cluster)
9545 ("r-corpcor" ,r-corpcor)
9546 ("r-doparallel" ,r-doparallel)
9547 ("r-dosnow" ,r-dosnow)
9548 ("r-foreach" ,r-foreach)
9549 ("r-ggplot2" ,r-ggplot2)
9550 ("r-matrix" ,r-matrix)
9551 ("r-matrixcalc" ,r-matrixcalc)
9552 ("r-rtsne" ,r-rtsne)
9553 ("r-umap" ,r-umap)))
9554 (native-inputs `(("r-knitr" ,r-knitr)))
9555 (home-page "https://bioconductor.org/packages/M3C")
9556 (synopsis "Monte Carlo reference-based consensus clustering")
9558 "M3C is a consensus clustering algorithm that uses a Monte Carlo
9559 simulation to eliminate overestimation of @code{K} and can reject the null
9560 hypothesis @code{K=1}.")
9561 (license license:agpl3+)))
9563 (define-public r-icens
9570 (uri (bioconductor-uri "Icens" version))
9573 "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
9574 (properties `((upstream-name . "Icens")))
9575 (build-system r-build-system)
9577 `(("r-survival" ,r-survival)))
9578 (home-page "https://bioconductor.org/packages/Icens")
9579 (synopsis "NPMLE for censored and truncated data")
9581 "This package provides many functions for computing the
9582 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
9584 (license license:artistic2.0)))
9586 ;; This is a CRAN package but it depends on r-icens, which is published on
9588 (define-public r-interval
9595 (uri (cran-uri "interval" version))
9598 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
9599 (properties `((upstream-name . "interval")))
9600 (build-system r-build-system)
9602 `(("r-icens" ,r-icens)
9603 ("r-mlecens" ,r-mlecens)
9605 ("r-survival" ,r-survival)))
9606 (home-page "https://cran.r-project.org/web/packages/interval/")
9607 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
9609 "This package provides functions to fit nonparametric survival curves,
9610 plot them, and perform logrank or Wilcoxon type tests.")
9611 (license license:gpl2+)))
9613 ;; This is a CRAN package, but it depends on r-interval, which depends on a
9614 ;; Bioconductor package.
9615 (define-public r-fhtest
9622 (uri (cran-uri "FHtest" version))
9625 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
9626 (properties `((upstream-name . "FHtest")))
9627 (build-system r-build-system)
9629 `(("r-interval" ,r-interval)
9630 ("r-kmsurv" ,r-kmsurv)
9633 ("r-survival" ,r-survival)))
9634 (home-page "https://cran.r-project.org/web/packages/FHtest/")
9635 (synopsis "Tests for survival data based on the Fleming-Harrington class")
9637 "This package provides functions to compare two or more survival curves
9641 @item The Fleming-Harrington test for right-censored data based on
9642 permutations and on counting processes.
9643 @item An extension of the Fleming-Harrington test for interval-censored data
9644 based on a permutation distribution and on a score vector distribution.
9647 (license license:gpl2+)))
9649 (define-public r-fourcseq
9656 (uri (bioconductor-uri "FourCSeq" version))
9658 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
9659 (properties `((upstream-name . "FourCSeq")))
9660 (build-system r-build-system)
9662 `(("r-biobase" ,r-biobase)
9663 ("r-biostrings" ,r-biostrings)
9664 ("r-deseq2" ,r-deseq2)
9666 ("r-genomicalignments" ,r-genomicalignments)
9667 ("r-genomicranges" ,r-genomicranges)
9668 ("r-ggbio" ,r-ggbio)
9669 ("r-ggplot2" ,r-ggplot2)
9670 ("r-gtools" ,r-gtools)
9672 ("r-matrix" ,r-matrix)
9673 ("r-reshape2" ,r-reshape2)
9674 ("r-rsamtools" ,r-rsamtools)
9675 ("r-rtracklayer" ,r-rtracklayer)
9676 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9678 `(("r-knitr" ,r-knitr)))
9680 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
9681 (synopsis "Analysis of multiplexed 4C sequencing data")
9683 "This package is an R package dedicated to the analysis of (multiplexed)
9684 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
9685 interactions between DNA elements and identify differential interactions
9686 between conditions. The statistical analysis in R starts with individual bam
9687 files for each sample as inputs. To obtain these files, the package contains
9688 a Python script to demultiplex libraries and trim off primer sequences. With
9689 a standard alignment software the required bam files can be then be
9691 (license license:gpl3+)))
9693 (define-public r-preprocesscore
9695 (name "r-preprocesscore")
9700 (uri (bioconductor-uri "preprocessCore" version))
9703 "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
9705 `((upstream-name . "preprocessCore")))
9706 (build-system r-build-system)
9707 (home-page "https://github.com/bmbolstad/preprocessCore")
9708 (synopsis "Collection of pre-processing functions")
9710 "This package provides a library of core pre-processing and normalization
9712 (license license:lgpl2.0+)))
9714 (define-public r-s4vectors
9716 (name "r-s4vectors")
9720 (uri (bioconductor-uri "S4Vectors" version))
9723 "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh"))))
9725 `((upstream-name . "S4Vectors")))
9726 (build-system r-build-system)
9728 `(("r-biocgenerics" ,r-biocgenerics)))
9729 (home-page "https://bioconductor.org/packages/S4Vectors")
9730 (synopsis "S4 implementation of vectors and lists")
9732 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
9733 classes and a set of generic functions that extend the semantic of ordinary
9734 vectors and lists in R. Package developers can easily implement vector-like
9735 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
9736 In addition, a few low-level concrete subclasses of general interest (e.g.
9737 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
9738 S4Vectors package itself.")
9739 (license license:artistic2.0)))
9741 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
9742 ;; Bioconductor package.
9743 (define-public r-wgcna
9750 (uri (cran-uri "WGCNA" version))
9753 "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
9754 (properties `((upstream-name . "WGCNA")))
9755 (build-system r-build-system)
9757 `(("r-annotationdbi" ,r-annotationdbi)
9758 ("r-doparallel" ,r-doparallel)
9759 ("r-dynamictreecut" ,r-dynamictreecut)
9760 ("r-fastcluster" ,r-fastcluster)
9761 ("r-foreach" ,r-foreach)
9762 ("r-go-db" ,r-go-db)
9763 ("r-hmisc" ,r-hmisc)
9764 ("r-impute" ,r-impute)
9766 ("r-survival" ,r-survival)
9767 ("r-matrixstats" ,r-matrixstats)
9768 ("r-preprocesscore" ,r-preprocesscore)))
9770 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
9771 (synopsis "Weighted correlation network analysis")
9773 "This package provides functions necessary to perform Weighted
9774 Correlation Network Analysis on high-dimensional data. It includes functions
9775 for rudimentary data cleaning, construction and summarization of correlation
9776 networks, module identification and functions for relating both variables and
9777 modules to sample traits. It also includes a number of utility functions for
9778 data manipulation and visualization.")
9779 (license license:gpl2+)))
9781 (define-public r-rgraphviz
9783 (name "r-rgraphviz")
9788 (uri (bioconductor-uri "Rgraphviz" version))
9791 "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
9792 (properties `((upstream-name . "Rgraphviz")))
9793 (build-system r-build-system)
9796 (modify-phases %standard-phases
9797 (add-after 'unpack 'make-reproducible
9799 ;; The replacement value is taken from src/graphviz/builddate.h
9800 (substitute* "src/graphviz/configure"
9801 (("VERSION_DATE=.*")
9802 "VERSION_DATE=20200427.2341\n"))
9804 ;; FIXME: Rgraphviz bundles the sources of an older variant of
9805 ;; graphviz. It does not build with the latest version of graphviz, so
9806 ;; we do not add graphviz to the inputs.
9807 (inputs `(("zlib" ,zlib)))
9809 `(("r-graph" ,r-graph)))
9811 `(("pkg-config" ,pkg-config)))
9812 (home-page "https://bioconductor.org/packages/Rgraphviz")
9813 (synopsis "Plotting capabilities for R graph objects")
9815 "This package interfaces R with the graphviz library for plotting R graph
9816 objects from the @code{graph} package.")
9817 (license license:epl1.0)))
9819 (define-public r-fithic
9825 (uri (bioconductor-uri "FitHiC" version))
9828 "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
9829 (properties `((upstream-name . "FitHiC")))
9830 (build-system r-build-system)
9832 `(("r-data-table" ,r-data-table)
9833 ("r-fdrtool" ,r-fdrtool)
9834 ("r-rcpp" ,r-rcpp)))
9836 `(("r-knitr" ,r-knitr)))
9837 (home-page "https://bioconductor.org/packages/FitHiC")
9838 (synopsis "Confidence estimation for intra-chromosomal contact maps")
9840 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
9841 intra-chromosomal contact maps produced by genome-wide genome architecture
9842 assays such as Hi-C.")
9843 (license license:gpl2+)))
9845 (define-public r-hitc
9851 (uri (bioconductor-uri "HiTC" version))
9854 "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
9855 (properties `((upstream-name . "HiTC")))
9856 (build-system r-build-system)
9858 `(("r-biostrings" ,r-biostrings)
9859 ("r-genomeinfodb" ,r-genomeinfodb)
9860 ("r-genomicranges" ,r-genomicranges)
9861 ("r-iranges" ,r-iranges)
9862 ("r-matrix" ,r-matrix)
9863 ("r-rcolorbrewer" ,r-rcolorbrewer)
9864 ("r-rtracklayer" ,r-rtracklayer)))
9865 (home-page "https://bioconductor.org/packages/HiTC")
9866 (synopsis "High throughput chromosome conformation capture analysis")
9868 "The HiTC package was developed to explore high-throughput \"C\" data
9869 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
9870 quality controls, normalization, visualization, and further analysis are also
9872 (license license:artistic2.0)))
9874 (define-public r-hdf5array
9876 (name "r-hdf5array")
9881 (uri (bioconductor-uri "HDF5Array" version))
9884 "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
9885 (properties `((upstream-name . "HDF5Array")))
9886 (build-system r-build-system)
9889 (modify-phases %standard-phases
9890 (add-after 'unpack 'fix-linking
9892 (substitute* "src/Makevars"
9893 ;; This is to avoid having a plain directory on the list of
9894 ;; libraries to link.
9895 (("\\(RHDF5LIB_LIBS\\)" match)
9896 (string-append match "/libhdf5.a")))
9901 `(("r-biocgenerics" ,r-biocgenerics)
9902 ("r-delayedarray" ,r-delayedarray)
9903 ("r-iranges" ,r-iranges)
9904 ("r-matrix" ,r-matrix)
9905 ("r-rhdf5" ,r-rhdf5)
9906 ("r-rhdf5lib" ,r-rhdf5lib)
9907 ("r-s4vectors" ,r-s4vectors)))
9908 (home-page "https://bioconductor.org/packages/HDF5Array")
9909 (synopsis "HDF5 back end for DelayedArray objects")
9910 (description "This package provides an array-like container for convenient
9911 access and manipulation of HDF5 datasets. It supports delayed operations and
9913 (license license:artistic2.0)))
9915 (define-public r-rhdf5lib
9922 (uri (bioconductor-uri "Rhdf5lib" version))
9925 "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
9926 (modules '((guix build utils)))
9929 ;; Delete bundled binaries
9930 (delete-file-recursively "src/wininclude/")
9931 (delete-file-recursively "src/winlib-4.9.3/")
9932 (delete-file-recursively "src/winlib-8.3.0/")
9933 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
9935 (properties `((upstream-name . "Rhdf5lib")))
9936 (build-system r-build-system)
9939 (modify-phases %standard-phases
9940 (add-after 'unpack 'do-not-use-bundled-hdf5
9941 (lambda* (#:key inputs #:allow-other-keys)
9942 (for-each delete-file '("configure" "configure.ac"))
9943 ;; Do not make other packages link with the proprietary libsz.
9944 (substitute* "R/zzz.R"
9945 ((" \"%s/libsz.a\"") ""))
9946 (with-directory-excursion "src"
9947 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
9948 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
9950 ;; Remove timestamp and host system information to make
9951 ;; the build reproducible.
9952 (substitute* "hdf5/src/libhdf5.settings.in"
9953 (("Configured on: @CONFIG_DATE@")
9954 "Configured on: Guix")
9955 (("Uname information:.*")
9956 "Uname information: Linux\n")
9957 ;; Remove unnecessary store reference.
9959 "C Compiler: GCC\n"))
9960 (rename-file "hdf5/src/libhdf5.settings.in"
9961 "hdf5/src/libhdf5.settings")
9962 (rename-file "Makevars.in" "Makevars")
9963 (substitute* "Makevars"
9964 (("@ZLIB_LIB@") "-lz")
9965 (("@ZLIB_INCLUDE@") "")
9966 (("HDF5_CXX_LIB=.*")
9967 (string-append "HDF5_CXX_LIB="
9968 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
9970 (string-append "HDF5_LIB="
9971 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
9972 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
9973 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
9974 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
9975 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
9977 (string-append "HDF5_HL_LIB="
9978 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
9979 (("HDF5_HL_CXX_LIB=.*")
9980 (string-append "HDF5_HL_CXX_LIB="
9981 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
9982 ;; szip is non-free software
9983 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
9984 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
9989 `(("hdf5" ,hdf5-1.10)))
9991 `(("hdf5-source" ,(package-source hdf5-1.10))
9992 ("r-knitr" ,r-knitr)))
9993 (home-page "https://bioconductor.org/packages/Rhdf5lib")
9994 (synopsis "HDF5 library as an R package")
9995 (description "This package provides C and C++ HDF5 libraries for use in R
9997 (license license:artistic2.0)))
9999 (define-public r-beachmat
10001 (name "r-beachmat")
10006 (uri (bioconductor-uri "beachmat" version))
10009 "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
10010 (build-system r-build-system)
10012 `(("r-biocgenerics" ,r-biocgenerics)
10013 ("r-delayedarray" ,r-delayedarray)
10014 ("r-matrix" ,r-matrix)))
10016 `(("r-knitr" ,r-knitr)))
10017 (home-page "https://bioconductor.org/packages/beachmat")
10018 (synopsis "Compiling Bioconductor to handle each matrix type")
10019 (description "This package provides a consistent C++ class interface for a
10020 variety of commonly used matrix types, including sparse and HDF5-backed
10022 (license license:gpl3)))
10024 ;; This package includes files that have been taken from kentutils. Some
10025 ;; parts of kentutils are not released under a free license, but this package
10026 ;; only uses files that are also found in the free parts of kentutils.
10027 (define-public r-cner
10034 (uri (bioconductor-uri "CNEr" version))
10036 (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
10037 (properties `((upstream-name . "CNEr")))
10038 (build-system r-build-system)
10039 (inputs `(("zlib" ,zlib)))
10041 `(("r-annotate" ,r-annotate)
10042 ("r-biocgenerics" ,r-biocgenerics)
10043 ("r-biostrings" ,r-biostrings)
10045 ("r-genomeinfodb" ,r-genomeinfodb)
10046 ("r-genomicalignments" ,r-genomicalignments)
10047 ("r-genomicranges" ,r-genomicranges)
10048 ("r-ggplot2" ,r-ggplot2)
10049 ("r-go-db" ,r-go-db)
10050 ("r-iranges" ,r-iranges)
10051 ("r-keggrest" ,r-keggrest)
10052 ("r-powerlaw" ,r-powerlaw)
10053 ("r-r-utils" ,r-r-utils)
10054 ("r-readr" ,r-readr)
10055 ("r-reshape2" ,r-reshape2)
10056 ("r-rsqlite" ,r-rsqlite)
10057 ("r-rtracklayer" ,r-rtracklayer)
10058 ("r-s4vectors" ,r-s4vectors)
10059 ("r-xvector" ,r-xvector)))
10061 `(("r-knitr" ,r-knitr)))
10062 (home-page "https://github.com/ge11232002/CNEr")
10063 (synopsis "CNE Detection and Visualization")
10065 "This package provides tools for large-scale identification and
10066 advanced visualization of sets of conserved noncoding elements.")
10067 ;; For all files in src/ucsc "license is hereby granted for all use -
10068 ;; public, private or commercial"; this includes those files that don't
10069 ;; have a license header, because they are included in the free parts of
10070 ;; the kentutils package.
10071 (license (list license:gpl2
10072 (license:non-copyleft
10073 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
10075 (define-public r-tfbstools
10077 (name "r-tfbstools")
10082 (uri (bioconductor-uri "TFBSTools" version))
10085 "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
10086 (properties `((upstream-name . "TFBSTools")))
10087 (build-system r-build-system)
10089 `(("r-biobase" ,r-biobase)
10090 ("r-biocgenerics" ,r-biocgenerics)
10091 ("r-biocparallel" ,r-biocparallel)
10092 ("r-biostrings" ,r-biostrings)
10093 ("r-bsgenome" ,r-bsgenome)
10094 ("r-catools" ,r-catools)
10097 ("r-dirichletmultinomial" ,r-dirichletmultinomial)
10098 ("r-genomeinfodb" ,r-genomeinfodb)
10099 ("r-genomicranges" ,r-genomicranges)
10100 ("r-gtools" ,r-gtools)
10101 ("r-iranges" ,r-iranges)
10102 ("r-rsqlite" ,r-rsqlite)
10103 ("r-rtracklayer" ,r-rtracklayer)
10104 ("r-s4vectors" ,r-s4vectors)
10105 ("r-seqlogo" ,r-seqlogo)
10106 ("r-tfmpvalue" ,r-tfmpvalue)
10108 ("r-xvector" ,r-xvector)))
10109 (native-inputs `(("r-knitr" ,r-knitr)))
10110 (home-page "https://github.com/ge11232002/TFBSTools")
10111 (synopsis "Transcription factor binding site (TFBS) analysis")
10113 "TFBSTools is a package for the analysis and manipulation of
10114 transcription factor binding sites. It includes matrices conversion
10115 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
10116 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
10117 scan putative TFBS from sequence/alignment, query JASPAR database and
10118 provides a wrapper of de novo motif discovery software.")
10119 (license license:gpl2)))
10121 (define-public r-motifmatchr
10123 (name "r-motifmatchr")
10128 (uri (bioconductor-uri "motifmatchr" version))
10131 "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z"))))
10132 (properties `((upstream-name . "motifmatchr")))
10133 (build-system r-build-system)
10135 `(("r-biostrings" ,r-biostrings)
10136 ("r-bsgenome" ,r-bsgenome)
10137 ("r-genomeinfodb" ,r-genomeinfodb)
10138 ("r-genomicranges" ,r-genomicranges)
10139 ("r-iranges" ,r-iranges)
10140 ("r-matrix" ,r-matrix)
10142 ("r-rcpparmadillo" ,r-rcpparmadillo)
10143 ("r-rsamtools" ,r-rsamtools)
10144 ("r-s4vectors" ,r-s4vectors)
10145 ("r-summarizedexperiment" ,r-summarizedexperiment)
10146 ("r-tfbstools" ,r-tfbstools)))
10147 (native-inputs `(("r-knitr" ,r-knitr)))
10148 (home-page "https://bioconductor.org/packages/motifmatchr")
10149 (synopsis "Fast motif matching in R")
10151 "Quickly find motif matches for many motifs and many sequences.
10152 This package wraps C++ code from the MOODS motif calling library.")
10153 (license license:gpl3)))
10155 (define-public r-chromvar
10157 (name "r-chromvar")
10162 (uri (bioconductor-uri "chromVAR" version))
10164 (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819"))))
10165 (properties `((upstream-name . "chromVAR")))
10166 (build-system r-build-system)
10168 `(("r-biocgenerics" ,r-biocgenerics)
10169 ("r-biocparallel" ,r-biocparallel)
10170 ("r-biostrings" ,r-biostrings)
10171 ("r-bsgenome" ,r-bsgenome)
10173 ("r-genomeinfodb" ,r-genomeinfodb)
10174 ("r-genomicranges" ,r-genomicranges)
10175 ("r-ggplot2" ,r-ggplot2)
10176 ("r-iranges" ,r-iranges)
10177 ("r-matrix" ,r-matrix)
10178 ("r-miniui" ,r-miniui)
10179 ("r-nabor" ,r-nabor)
10180 ("r-plotly" ,r-plotly)
10181 ("r-rcolorbrewer" ,r-rcolorbrewer)
10183 ("r-rcpparmadillo" ,r-rcpparmadillo)
10184 ("r-rsamtools" ,r-rsamtools)
10185 ("r-rtsne" ,r-rtsne)
10186 ("r-s4vectors" ,r-s4vectors)
10187 ("r-shiny" ,r-shiny)
10188 ("r-summarizedexperiment" ,r-summarizedexperiment)
10189 ("r-tfbstools" ,r-tfbstools)))
10190 (native-inputs `(("r-knitr" ,r-knitr)))
10191 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
10192 (synopsis "Determine chromatin variation across regions")
10194 "This package @code{r-chromvar} determines variation in chromatin
10195 accessibility across sets of annotations or peaks. @code{r-chromvar} is
10196 designed primarily for single-cell or sparse chromatin accessibility data like
10197 single cell assay for transposase-accessible chromatin using
10198 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
10199 sequence (@code{DNAse-seq}) experiments.")
10200 (license license:expat)))
10202 (define-public r-singlecellexperiment
10204 (name "r-singlecellexperiment")
10209 (uri (bioconductor-uri "SingleCellExperiment" version))
10212 "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
10214 `((upstream-name . "SingleCellExperiment")))
10215 (build-system r-build-system)
10217 `(("r-biocgenerics" ,r-biocgenerics)
10218 ("r-s4vectors" ,r-s4vectors)
10219 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10221 `(("r-knitr" ,r-knitr)))
10222 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
10223 (synopsis "S4 classes for single cell data")
10224 (description "This package defines an S4 class for storing data from
10225 single-cell experiments. This includes specialized methods to store and
10226 retrieve spike-in information, dimensionality reduction coordinates and size
10227 factors for each cell, along with the usual metadata for genes and
10229 (license license:gpl3)))
10231 (define-public r-scuttle
10238 (uri (bioconductor-uri "scuttle" version))
10241 "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
10242 (properties `((upstream-name . "scuttle")))
10243 (build-system r-build-system)
10245 `(("r-beachmat" ,r-beachmat)
10246 ("r-biocgenerics" ,r-biocgenerics)
10247 ("r-biocparallel" ,r-biocparallel)
10248 ("r-delayedarray" ,r-delayedarray)
10249 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10250 ("r-genomicranges" ,r-genomicranges)
10251 ("r-matrix" ,r-matrix)
10253 ("r-s4vectors" ,r-s4vectors)
10254 ("r-singlecellexperiment" ,r-singlecellexperiment)
10255 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10256 (native-inputs `(("r-knitr" ,r-knitr)))
10257 (home-page "https://bioconductor.org/packages/scuttle")
10258 (synopsis "Single-cell RNA-Seq analysis utilities")
10260 "This package provides basic utility functions for performing single-cell
10261 analyses, focusing on simple normalization, quality control and data
10262 transformations. It also provides some helper functions to assist development
10263 of other packages.")
10264 (license license:gpl3)))
10266 (define-public r-scater
10272 (uri (bioconductor-uri "scater" version))
10275 "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609"))))
10276 (build-system r-build-system)
10278 `(("r-biocgenerics" ,r-biocgenerics)
10279 ("r-biocneighbors" ,r-biocneighbors)
10280 ("r-biocparallel" ,r-biocparallel)
10281 ("r-biocsingular" ,r-biocsingular)
10282 ("r-delayedarray" ,r-delayedarray)
10283 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10284 ("r-ggbeeswarm" ,r-ggbeeswarm)
10285 ("r-ggplot2" ,r-ggplot2)
10286 ("r-gridextra" ,r-gridextra)
10287 ("r-matrix" ,r-matrix)
10288 ("r-rlang" ,r-rlang)
10289 ("r-s4vectors" ,r-s4vectors)
10290 ("r-scuttle" ,r-scuttle)
10291 ("r-singlecellexperiment" ,r-singlecellexperiment)
10292 ("r-summarizedexperiment" ,r-summarizedexperiment)
10293 ("r-viridis" ,r-viridis)))
10295 `(("r-knitr" ,r-knitr)))
10296 (home-page "https://github.com/davismcc/scater")
10297 (synopsis "Single-cell analysis toolkit for gene expression data in R")
10298 (description "This package provides a collection of tools for doing
10299 various analyses of single-cell RNA-seq gene expression data, with a focus on
10301 (license license:gpl2+)))
10303 (define-public r-scran
10310 (uri (bioconductor-uri "scran" version))
10313 "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
10314 (build-system r-build-system)
10316 `(("r-beachmat" ,r-beachmat)
10318 ("r-biocgenerics" ,r-biocgenerics)
10319 ("r-biocneighbors" ,r-biocneighbors)
10320 ("r-biocparallel" ,r-biocparallel)
10321 ("r-biocsingular" ,r-biocsingular)
10322 ("r-bluster" ,r-bluster)
10323 ("r-delayedarray" ,r-delayedarray)
10324 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10325 ("r-dqrng" ,r-dqrng)
10326 ("r-edger" ,r-edger)
10327 ("r-igraph" ,r-igraph)
10328 ("r-limma" ,r-limma)
10329 ("r-matrix" ,r-matrix)
10331 ("r-s4vectors" ,r-s4vectors)
10332 ("r-scuttle" ,r-scuttle)
10333 ("r-singlecellexperiment" ,r-singlecellexperiment)
10334 ("r-statmod" ,r-statmod)
10335 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10337 `(("r-knitr" ,r-knitr)))
10338 (home-page "https://bioconductor.org/packages/scran")
10339 (synopsis "Methods for single-cell RNA-Seq data analysis")
10340 (description "This package implements a variety of low-level analyses of
10341 single-cell RNA-seq data. Methods are provided for normalization of
10342 cell-specific biases, assignment of cell cycle phase, and detection of highly
10343 variable and significantly correlated genes.")
10344 (license license:gpl3)))
10346 (define-public r-sparsematrixstats
10348 (name "r-sparsematrixstats")
10353 (uri (bioconductor-uri "sparseMatrixStats" version))
10356 "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
10358 `((upstream-name . "sparseMatrixStats")))
10359 (build-system r-build-system)
10361 `(("r-matrix" ,r-matrix)
10362 ("r-matrixgenerics" ,r-matrixgenerics)
10363 ("r-matrixstats" ,r-matrixstats)
10364 ("r-rcpp" ,r-rcpp)))
10365 (native-inputs `(("r-knitr" ,r-knitr)))
10366 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
10367 (synopsis "Summary statistics for rows and columns of sparse matrices")
10369 "This package provides high performance functions for row and column
10370 operations on sparse matrices. Currently, the optimizations are limited to
10371 data in the column sparse format.")
10372 (license license:expat)))
10374 (define-public r-delayedmatrixstats
10376 (name "r-delayedmatrixstats")
10381 (uri (bioconductor-uri "DelayedMatrixStats" version))
10384 "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
10386 `((upstream-name . "DelayedMatrixStats")))
10387 (build-system r-build-system)
10389 `(("r-biocparallel" ,r-biocparallel)
10390 ("r-delayedarray" ,r-delayedarray)
10391 ("r-hdf5array" ,r-hdf5array)
10392 ("r-iranges" ,r-iranges)
10393 ("r-matrix" ,r-matrix)
10394 ("r-matrixgenerics" ,r-matrixgenerics)
10395 ("r-matrixstats" ,r-matrixstats)
10396 ("r-s4vectors" ,r-s4vectors)
10397 ("r-sparsematrixstats" ,r-sparsematrixstats)))
10399 `(("r-knitr" ,r-knitr)))
10400 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
10401 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
10403 "This package provides a port of the @code{matrixStats} API for use with
10404 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
10405 contains high-performing functions operating on rows and columns of
10406 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
10407 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
10408 are optimized per data type and for subsetted calculations such that both
10409 memory usage and processing time is minimized.")
10410 (license license:expat)))
10412 (define-public r-mscoreutils
10414 (name "r-mscoreutils")
10419 (uri (bioconductor-uri "MsCoreUtils" version))
10422 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
10423 (properties `((upstream-name . "MsCoreUtils")))
10424 (build-system r-build-system)
10426 `(("r-mass" ,r-mass)
10428 ("r-s4vectors" ,r-s4vectors)))
10430 `(("r-knitr" ,r-knitr)))
10431 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
10432 (synopsis "Core utils for mass spectrometry data")
10434 "This package defines low-level functions for mass spectrometry data and
10435 is independent of any high-level data structures. These functions include
10436 mass spectra processing functions (noise estimation, smoothing, binning),
10437 quantitative aggregation functions (median polish, robust summarisation,
10438 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
10439 well as misc helper functions, that are used across high-level data structure
10440 within the R for Mass Spectrometry packages.")
10441 (license license:artistic2.0)))
10443 (define-public r-biocio
10450 (uri (bioconductor-uri "BiocIO" version))
10453 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
10454 (properties `((upstream-name . "BiocIO")))
10455 (build-system r-build-system)
10457 `(("r-biocgenerics" ,r-biocgenerics)
10458 ("r-genomicranges" ,r-genomicranges)
10459 ("r-rcurl" ,r-rcurl)
10460 ("r-s4vectors" ,r-s4vectors)))
10462 `(("r-knitr" ,r-knitr)))
10463 (home-page "https://bioconductor.org/packages/BiocIO")
10464 (synopsis "Standard input and output for Bioconductor packages")
10466 "This package implements `import()` and `export()` standard generics for
10467 importing and exporting biological data formats. `import()` supports
10468 whole-file as well as chunk-wise iterative import. The `import()` interface
10469 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
10470 row or element-like components of the file resource), `select()` (on
10471 column-like components of the file resource) and `collect()`. The `import()`
10472 interface optionally provides transparent access to remote (e.g. via https)
10473 as well as local access. Developers can register a file extension, e.g.,
10474 `.loom` for dispatch from character-based URIs to specific `import()` /
10475 `export()` methods based on classes representing file types, e.g.,
10477 (license license:artistic2.0)))
10479 (define-public r-msmseda
10486 (uri (bioconductor-uri "msmsEDA" version))
10489 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
10490 (properties `((upstream-name . "msmsEDA")))
10491 (build-system r-build-system)
10493 `(("r-gplots" ,r-gplots)
10495 ("r-msnbase" ,r-msnbase)
10496 ("r-rcolorbrewer" ,r-rcolorbrewer)))
10498 "https://bioconductor.org/packages/msmsEDA")
10499 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
10501 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
10502 experiments, and visualize de influence of the involved factors.")
10503 (license license:gpl2)))
10505 (define-public r-msmstests
10507 (name "r-msmstests")
10512 (uri (bioconductor-uri "msmsTests" version))
10515 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
10516 (properties `((upstream-name . "msmsTests")))
10517 (build-system r-build-system)
10519 `(("r-edger" ,r-edger)
10520 ("r-msmseda" ,r-msmseda)
10521 ("r-msnbase" ,r-msnbase)
10522 ("r-qvalue" ,r-qvalue)))
10524 "https://bioconductor.org/packages/msmsTests")
10525 (synopsis "Differential LC-MS/MS expression tests")
10527 "This packages provides statistical tests for label-free LC-MS/MS data
10528 by spectral counts, to discover differentially expressed proteins between two
10529 biological conditions. Three tests are available: Poisson GLM regression,
10530 quasi-likelihood GLM regression, and the negative binomial of the edgeR
10531 package.The three models admit blocking factors to control for nuissance
10532 variables.To assure a good level of reproducibility a post-test filter is
10533 available, where we may set the minimum effect size considered biologicaly
10534 relevant, and the minimum expression of the most abundant condition.")
10535 (license license:gpl2)))
10537 (define-public r-catalyst
10539 (name "r-catalyst")
10544 (uri (bioconductor-uri "CATALYST" version))
10547 "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
10548 (properties `((upstream-name . "CATALYST")))
10549 (build-system r-build-system)
10551 `(("r-circlize" ,r-circlize)
10552 ("r-complexheatmap" ,r-complexheatmap)
10553 ("r-consensusclusterplus" ,r-consensusclusterplus)
10554 ("r-cowplot" ,r-cowplot)
10555 ("r-data-table" ,r-data-table)
10556 ("r-dplyr" ,r-dplyr)
10558 ("r-flowcore" ,r-flowcore)
10559 ("r-flowsom" ,r-flowsom)
10560 ("r-ggplot2" ,r-ggplot2)
10561 ("r-ggrepel" ,r-ggrepel)
10562 ("r-ggridges" ,r-ggridges)
10563 ("r-gridextra" ,r-gridextra)
10564 ("r-magrittr" ,r-magrittr)
10565 ("r-matrix" ,r-matrix)
10566 ("r-matrixstats" ,r-matrixstats)
10568 ("r-purrr" ,r-purrr)
10569 ("r-rcolorbrewer" ,r-rcolorbrewer)
10570 ("r-reshape2" ,r-reshape2)
10571 ("r-rtsne" ,r-rtsne)
10572 ("r-s4vectors" ,r-s4vectors)
10573 ("r-scales" ,r-scales)
10574 ("r-scater" ,r-scater)
10575 ("r-singlecellexperiment" ,r-singlecellexperiment)
10576 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10578 `(("r-knitr" ,r-knitr)))
10580 "https://github.com/HelenaLC/CATALYST")
10581 (synopsis "Cytometry data analysis tools")
10583 "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
10584 cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
10585 reporters to label antibodies, thereby substantially decreasing spectral
10586 overlap and allowing for examination of over 50 parameters at the single cell
10587 level. While spectral overlap is significantly less pronounced in CyTOF than
10588 flow cytometry, spillover due to detection sensitivity, isotopic impurities,
10589 and oxide formation can impede data interpretability. We designed
10590 CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
10591 preprocessing of cytometry data, including i) normalization using bead
10592 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
10593 (license license:gpl2+)))
10595 (define-public r-erma
10602 (uri (bioconductor-uri "erma" version))
10605 "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
10606 (build-system r-build-system)
10608 `(("r-annotationdbi" ,r-annotationdbi)
10609 ("r-biobase" ,r-biobase)
10610 ("r-biocgenerics" ,r-biocgenerics)
10611 ("r-biocparallel" ,r-biocparallel)
10612 ("r-genomeinfodb" ,r-genomeinfodb)
10613 ("r-genomicfiles" ,r-genomicfiles)
10614 ("r-genomicranges" ,r-genomicranges)
10615 ("r-ggplot2" ,r-ggplot2)
10616 ("r-homo-sapiens" ,r-homo-sapiens)
10617 ("r-iranges" ,r-iranges)
10618 ("r-rtracklayer" ,r-rtracklayer)
10619 ("r-s4vectors" ,r-s4vectors)
10620 ("r-shiny" ,r-shiny)
10621 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10623 `(("r-knitr" ,r-knitr)))
10624 (home-page "https://bioconductor.org/packages/erma")
10625 (synopsis "Epigenomic road map adventures")
10627 "The epigenomics road map describes locations of epigenetic marks in DNA
10628 from a variety of cell types. Of interest are locations of histone
10629 modifications, sites of DNA methylation, and regions of accessible chromatin.
10630 This package presents a selection of elements of the road map including
10631 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
10632 by Ernst and Kellis.")
10633 (license license:artistic2.0)))
10635 (define-public r-ggbio
10642 (uri (bioconductor-uri "ggbio" version))
10645 "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
10646 (build-system r-build-system)
10649 (modify-phases %standard-phases
10650 ;; See https://github.com/tengfei/ggbio/issues/117
10651 ;; This fix will be included in the next release.
10652 (add-after 'unpack 'fix-typo
10654 (substitute* "R/GGbio-class.R"
10655 (("fechable") "fetchable"))
10658 `(("r-annotationdbi" ,r-annotationdbi)
10659 ("r-annotationfilter" ,r-annotationfilter)
10660 ("r-biobase" ,r-biobase)
10661 ("r-biocgenerics" ,r-biocgenerics)
10662 ("r-biostrings" ,r-biostrings)
10663 ("r-biovizbase" ,r-biovizbase)
10664 ("r-bsgenome" ,r-bsgenome)
10665 ("r-ensembldb" ,r-ensembldb)
10666 ("r-genomeinfodb" ,r-genomeinfodb)
10667 ("r-genomicalignments" ,r-genomicalignments)
10668 ("r-genomicfeatures" ,r-genomicfeatures)
10669 ("r-genomicranges" ,r-genomicranges)
10670 ("r-ggally" ,r-ggally)
10671 ("r-ggplot2" ,r-ggplot2)
10672 ("r-gridextra" ,r-gridextra)
10673 ("r-gtable" ,r-gtable)
10674 ("r-hmisc" ,r-hmisc)
10675 ("r-iranges" ,r-iranges)
10676 ("r-organismdbi" ,r-organismdbi)
10677 ("r-reshape2" ,r-reshape2)
10678 ("r-rlang" ,r-rlang)
10679 ("r-rsamtools" ,r-rsamtools)
10680 ("r-rtracklayer" ,r-rtracklayer)
10681 ("r-s4vectors" ,r-s4vectors)
10682 ("r-scales" ,r-scales)
10683 ("r-summarizedexperiment" ,r-summarizedexperiment)
10684 ("r-variantannotation" ,r-variantannotation)))
10686 `(("r-knitr" ,r-knitr)))
10687 (home-page "http://www.tengfei.name/ggbio/")
10688 (synopsis "Visualization tools for genomic data")
10690 "The ggbio package extends and specializes the grammar of graphics for
10691 biological data. The graphics are designed to answer common scientific
10692 questions, in particular those often asked of high throughput genomics data.
10693 All core Bioconductor data structures are supported, where appropriate. The
10694 package supports detailed views of particular genomic regions, as well as
10695 genome-wide overviews. Supported overviews include ideograms and grand linear
10696 views. High-level plots include sequence fragment length, edge-linked
10697 interval to data view, mismatch pileup, and several splicing summaries.")
10698 (license license:artistic2.0)))
10700 (define-public r-gqtlbase
10702 (name "r-gqtlbase")
10707 (uri (bioconductor-uri "gQTLBase" version))
10710 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
10711 (properties `((upstream-name . "gQTLBase")))
10712 (build-system r-build-system)
10715 (modify-phases %standard-phases
10716 ;; This is an upstream bug.
10717 (add-after 'unpack 'fix-imports
10719 (substitute* "NAMESPACE"
10720 ((".*maxffmode.*") "")
10721 (("importFrom\\(ff,.*") "import(ff)\n"))
10724 `(("r-batchjobs" ,r-batchjobs)
10725 ("r-bbmisc" ,r-bbmisc)
10726 ("r-biocgenerics" ,r-biocgenerics)
10728 ("r-doparallel" ,r-doparallel)
10730 ("r-ffbase" ,r-ffbase)
10731 ("r-foreach" ,r-foreach)
10732 ("r-genomicfiles" ,r-genomicfiles)
10733 ("r-genomicranges" ,r-genomicranges)
10734 ("r-rtracklayer" ,r-rtracklayer)
10735 ("r-s4vectors" ,r-s4vectors)
10736 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10738 `(("r-knitr" ,r-knitr)))
10739 (home-page "https://bioconductor.org/packages/gQTLBase")
10740 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
10742 "The purpose of this package is to simplify the storage and interrogation
10743 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
10745 (license license:artistic2.0)))
10747 (define-public r-gqtlstats
10749 (name "r-gqtlstats")
10754 (uri (bioconductor-uri "gQTLstats" version))
10757 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
10758 (properties `((upstream-name . "gQTLstats")))
10759 (build-system r-build-system)
10761 `(("r-annotationdbi" ,r-annotationdbi)
10762 ("r-batchjobs" ,r-batchjobs)
10763 ("r-bbmisc" ,r-bbmisc)
10764 ("r-beeswarm" ,r-beeswarm)
10765 ("r-biobase" ,r-biobase)
10766 ("r-biocgenerics" ,r-biocgenerics)
10767 ("r-doparallel" ,r-doparallel)
10768 ("r-dplyr" ,r-dplyr)
10770 ("r-ffbase" ,r-ffbase)
10771 ("r-foreach" ,r-foreach)
10772 ("r-genomeinfodb" ,r-genomeinfodb)
10773 ("r-genomicfeatures" ,r-genomicfeatures)
10774 ("r-genomicfiles" ,r-genomicfiles)
10775 ("r-genomicranges" ,r-genomicranges)
10776 ("r-ggbeeswarm" ,r-ggbeeswarm)
10777 ("r-ggplot2" ,r-ggplot2)
10778 ("r-gqtlbase" ,r-gqtlbase)
10779 ("r-hardyweinberg" ,r-hardyweinberg)
10780 ("r-homo-sapiens" ,r-homo-sapiens)
10781 ("r-iranges" ,r-iranges)
10782 ("r-limma" ,r-limma)
10784 ("r-plotly" ,r-plotly)
10785 ("r-reshape2" ,r-reshape2)
10786 ("r-s4vectors" ,r-s4vectors)
10787 ("r-shiny" ,r-shiny)
10788 ("r-snpstats" ,r-snpstats)
10789 ("r-summarizedexperiment" ,r-summarizedexperiment)
10790 ("r-variantannotation" ,r-variantannotation)))
10792 `(("r-knitr" ,r-knitr)))
10793 (home-page "https://bioconductor.org/packages/gQTLstats")
10794 (synopsis "Computationally efficient analysis for eQTL and allied studies")
10796 "This package provides tools for the computationally efficient analysis
10797 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
10798 The software in this package aims to support refinements and functional
10799 interpretation of members of a collection of association statistics on a
10800 family of feature/genome hypotheses.")
10801 (license license:artistic2.0)))
10803 (define-public r-gviz
10810 (uri (bioconductor-uri "Gviz" version))
10813 "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1"))))
10814 (properties `((upstream-name . "Gviz")))
10815 (build-system r-build-system)
10817 `(("r-annotationdbi" ,r-annotationdbi)
10818 ("r-biobase" ,r-biobase)
10819 ("r-biocgenerics" ,r-biocgenerics)
10820 ("r-biomart" ,r-biomart)
10821 ("r-biostrings" ,r-biostrings)
10822 ("r-biovizbase" ,r-biovizbase)
10823 ("r-bsgenome" ,r-bsgenome)
10824 ("r-digest" ,r-digest)
10825 ("r-ensembldb" ,r-ensembldb)
10826 ("r-genomeinfodb" ,r-genomeinfodb)
10827 ("r-genomicalignments" ,r-genomicalignments)
10828 ("r-genomicfeatures" ,r-genomicfeatures)
10829 ("r-genomicranges" ,r-genomicranges)
10830 ("r-iranges" ,r-iranges)
10831 ("r-lattice" ,r-lattice)
10832 ("r-latticeextra" ,r-latticeextra)
10833 ("r-matrixstats" ,r-matrixstats)
10834 ("r-rcolorbrewer" ,r-rcolorbrewer)
10835 ("r-rsamtools" ,r-rsamtools)
10836 ("r-rtracklayer" ,r-rtracklayer)
10837 ("r-s4vectors" ,r-s4vectors)
10838 ("r-xvector" ,r-xvector)))
10840 `(("r-knitr" ,r-knitr)))
10841 (home-page "https://bioconductor.org/packages/Gviz")
10842 (synopsis "Plotting data and annotation information along genomic coordinates")
10844 "Genomic data analyses requires integrated visualization of known genomic
10845 information and new experimental data. Gviz uses the biomaRt and the
10846 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
10847 and translates this to e.g. gene/transcript structures in viewports of the
10848 grid graphics package. This results in genomic information plotted together
10850 (license license:artistic2.0)))
10852 (define-public r-gwascat
10859 (uri (bioconductor-uri "gwascat" version))
10862 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
10863 (build-system r-build-system)
10865 `(("r-annotationdbi" ,r-annotationdbi)
10866 ("r-biocfilecache" ,r-biocfilecache)
10867 ("r-biostrings" ,r-biostrings)
10868 ("r-genomeinfodb" ,r-genomeinfodb)
10869 ("r-genomicfeatures" ,r-genomicfeatures)
10870 ("r-genomicranges" ,r-genomicranges)
10871 ("r-iranges" ,r-iranges)
10872 ("r-readr" ,r-readr)
10873 ("r-s4vectors" ,r-s4vectors)
10874 ("r-snpstats" ,r-snpstats)
10875 ("r-variantannotation" ,r-variantannotation)))
10877 `(("r-knitr" ,r-knitr)))
10878 (home-page "https://bioconductor.org/packages/gwascat")
10879 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
10881 "This package provides tools for representing and modeling data in the
10882 EMBL-EBI GWAS catalog.")
10883 (license license:artistic2.0)))
10885 (define-public r-kegggraph
10887 (name "r-kegggraph")
10892 (uri (bioconductor-uri "KEGGgraph" version))
10894 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
10895 (properties `((upstream-name . "KEGGgraph")))
10896 (build-system r-build-system)
10898 `(("r-graph" ,r-graph)
10899 ("r-rcurl" ,r-rcurl)
10901 (home-page "https://bioconductor.org/packages/KEGGgraph")
10902 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
10904 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
10905 object as well as a collection of tools to analyze, dissect and visualize these
10906 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
10907 maintaining all essential pathway attributes. The package offers
10908 functionalities including parsing, graph operation, visualization and etc.")
10909 (license license:gpl2+)))
10911 (define-public r-ldblock
10918 (uri (bioconductor-uri "ldblock" version))
10921 "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
10922 (build-system r-build-system)
10924 `(("r-biocgenerics" ,r-biocgenerics)
10925 ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
10926 ("r-ensembldb" ,r-ensembldb)
10927 ("r-genomeinfodb" ,r-genomeinfodb)
10928 ("r-genomicfiles" ,r-genomicfiles)
10930 ("r-matrix" ,r-matrix)
10931 ("r-rsamtools" ,r-rsamtools)
10932 ("r-snpstats" ,r-snpstats)
10933 ("r-variantannotation" ,r-variantannotation)))
10935 `(("r-knitr" ,r-knitr)))
10936 (home-page "https://bioconductor.org/packages/ldblock")
10937 (synopsis "Data structures for linkage disequilibrium measures in populations")
10939 "This package defines data structures for @dfn{linkage
10940 disequilibrium} (LD) measures in populations. Its purpose is to simplify
10941 handling of existing population-level data for the purpose of flexibly
10942 defining LD blocks.")
10943 (license license:artistic2.0)))
10945 ;; This is a CRAN package, but it depends on r-snpstats, which is a
10946 ;; Bioconductor package.
10947 (define-public r-ldheatmap
10949 (name "r-ldheatmap")
10954 (uri (cran-uri "LDheatmap" version))
10957 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
10958 (properties `((upstream-name . "LDheatmap")))
10959 (build-system r-build-system)
10961 `(("r-genetics" ,r-genetics)
10963 ("r-snpstats" ,r-snpstats)))
10964 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
10965 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
10967 "This package provides tools to produce a graphical display, as a heat
10968 map, of measures of pairwise linkage disequilibria between SNPs. Users may
10969 optionally include the physical locations or genetic map distances of each SNP
10971 (license license:gpl3)))
10973 (define-public r-pathview
10975 (name "r-pathview")
10980 (uri (bioconductor-uri "pathview" version))
10982 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
10983 (properties `((upstream-name . "pathview")))
10984 (build-system r-build-system)
10986 `(("r-annotationdbi" ,r-annotationdbi)
10987 ("r-graph" ,r-graph)
10988 ("r-kegggraph" ,r-kegggraph)
10989 ("r-keggrest" ,r-keggrest)
10990 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
10992 ("r-rgraphviz" ,r-rgraphviz)
10994 (home-page "https://pathview.uncc.edu/")
10995 (synopsis "Tool set for pathway based data integration and visualization")
10997 "@code{r-pathview} is a tool set for pathway based data integration and
10998 visualization. It maps and renders a wide variety of biological data on
10999 relevant pathway graphs. All users need is to supply their data and specify
11000 the target pathway. This package automatically downloads the pathway graph
11001 data, parses the data file, maps user data to the pathway, and render pathway
11002 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
11003 integrates with pathway and gene set (enrichment) analysis tools for
11004 large-scale and fully automated analysis.")
11005 (license license:gpl3+)))
11007 (define-public r-snpstats
11009 (name "r-snpstats")
11014 (uri (bioconductor-uri "snpStats" version))
11017 "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
11018 (properties `((upstream-name . "snpStats")))
11019 (build-system r-build-system)
11020 (inputs `(("zlib" ,zlib)))
11022 `(("r-biocgenerics" ,r-biocgenerics)
11023 ("r-matrix" ,r-matrix)
11024 ("r-survival" ,r-survival)
11025 ("r-zlibbioc" ,r-zlibbioc)))
11026 (home-page "https://bioconductor.org/packages/snpStats")
11027 (synopsis "Methods for SNP association studies")
11029 "This package provides classes and statistical methods for large
11030 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
11031 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
11032 (license license:gpl3)))
11034 (define-public r-chromstar
11036 (name "r-chromstar")
11041 (uri (bioconductor-uri "chromstaR" version))
11044 "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1"))))
11045 (properties `((upstream-name . "chromstaR")))
11046 (build-system r-build-system)
11048 `(("r-bamsignals" ,r-bamsignals)
11049 ("r-biocgenerics" ,r-biocgenerics)
11050 ("r-chromstardata" ,r-chromstardata)
11051 ("r-doparallel" ,r-doparallel)
11052 ("r-foreach" ,r-foreach)
11053 ("r-genomeinfodb" ,r-genomeinfodb)
11054 ("r-genomicalignments" ,r-genomicalignments)
11055 ("r-genomicranges" ,r-genomicranges)
11056 ("r-ggplot2" ,r-ggplot2)
11057 ("r-iranges" ,r-iranges)
11058 ("r-mvtnorm" ,r-mvtnorm)
11059 ("r-reshape2" ,r-reshape2)
11060 ("r-rsamtools" ,r-rsamtools)
11061 ("r-s4vectors" ,r-s4vectors)))
11062 (native-inputs `(("r-knitr" ,r-knitr)))
11063 (home-page "https://github.com/ataudt/chromstaR")
11064 (synopsis "Chromatin state analysis for ChIP-Seq data")
11066 "This package implements functions for combinatorial and differential
11067 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
11068 export to genome browser viewable files, and functi ons for enrichment
11070 (license license:artistic2.0)))
11072 (define-public r-sushi
11078 (uri (bioconductor-uri "Sushi" version))
11081 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
11082 (properties `((upstream-name . "Sushi")))
11083 (build-system r-build-system)
11085 `(("r-biomart" ,r-biomart)
11087 (home-page "https://bioconductor.org/packages/Sushi")
11088 (synopsis "Tools for visualizing genomics data")
11090 "This package provides flexible, quantitative, and integrative genomic
11091 visualizations for publication-quality multi-panel figures.")
11092 (license license:gpl2+)))