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 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
5 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
7 ;;; This file is part of GNU Guix.
9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
10 ;;; under the terms of the GNU General Public License as published by
11 ;;; the Free Software Foundation; either version 3 of the License, or (at
12 ;;; your option) any later version.
14 ;;; GNU Guix is distributed in the hope that it will be useful, but
15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 ;;; GNU General Public License for more details.
19 ;;; You should have received a copy of the GNU General Public License
20 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
22 (define-module (gnu packages bioconductor)
23 #:use-module ((guix licenses) #:prefix license:)
24 #:use-module (guix packages)
25 #:use-module (guix download)
26 #:use-module (guix git-download)
27 #:use-module (guix build-system r)
28 #:use-module (gnu packages)
29 #:use-module (gnu packages base)
30 #:use-module (gnu packages bioinformatics)
31 #:use-module (gnu packages cran)
32 #:use-module (gnu packages compression)
33 #:use-module (gnu packages gcc)
34 #:use-module (gnu packages graph)
35 #:use-module (gnu packages graphviz)
36 #:use-module (gnu packages haskell-xyz)
37 #:use-module (gnu packages image)
38 #:use-module (gnu packages maths)
39 #:use-module (gnu packages netpbm)
40 #:use-module (gnu packages perl)
41 #:use-module (gnu packages pkg-config)
42 #:use-module (gnu packages statistics)
43 #:use-module (gnu packages web)
44 #:use-module (gnu packages xml)
45 #:use-module (srfi srfi-1))
50 (define-public r-reactome-db
52 (name "r-reactome-db")
57 (uri (bioconductor-uri "reactome.db" version 'annotation))
60 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
61 (properties `((upstream-name . "reactome.db")))
62 (build-system r-build-system)
64 `(("r-annotationdbi" ,r-annotationdbi)))
65 (home-page "https://bioconductor.org/packages/reactome.db/")
66 (synopsis "Annotation maps for reactome")
68 "This package provides a set of annotation maps for the REACTOME
69 database, assembled using data from REACTOME.")
70 (license license:cc-by4.0)))
72 (define-public r-bsgenome-celegans-ucsc-ce6
74 (name "r-bsgenome-celegans-ucsc-ce6")
78 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
82 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
84 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
85 (build-system r-build-system)
87 `(("r-bsgenome" ,r-bsgenome)))
89 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
90 (synopsis "Full genome sequences for Worm")
92 "This package provides full genome sequences for Caenorhabditis
93 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
95 (license license:artistic2.0)))
97 (define-public r-bsgenome-celegans-ucsc-ce10
99 (name "r-bsgenome-celegans-ucsc-ce10")
103 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
104 version 'annotation))
107 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
109 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
110 (build-system r-build-system)
112 `(("r-bsgenome" ,r-bsgenome)))
114 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
115 (synopsis "Full genome sequences for Worm")
117 "This package provides full genome sequences for Caenorhabditis
118 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
120 (license license:artistic2.0)))
122 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
124 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
128 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
129 version 'annotation))
132 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
134 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
135 (build-system r-build-system)
137 `(("r-bsgenome" ,r-bsgenome)))
139 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
140 (synopsis "Full genome sequences for Fly")
142 "This package provides full genome sequences for Drosophila
143 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
145 (license license:artistic2.0)))
147 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
149 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
153 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
154 version 'annotation))
157 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
159 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
160 (build-system r-build-system)
162 `(("r-bsgenome" ,r-bsgenome)))
164 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
165 (synopsis "Full genome sequences for Fly")
167 "This package provides full genome sequences for Drosophila
168 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
169 Biostrings objects.")
170 (license license:artistic2.0)))
172 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
174 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
178 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
179 version 'annotation))
182 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
184 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
185 (build-system r-build-system)
187 `(("r-bsgenome" ,r-bsgenome)
188 ("r-bsgenome-dmelanogaster-ucsc-dm3"
189 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
190 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
191 (synopsis "Full masked genome sequences for Fly")
193 "This package provides full masked genome sequences for Drosophila
194 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
195 Biostrings objects. The sequences are the same as in
196 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
197 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
198 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
199 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
200 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
201 (license license:artistic2.0)))
203 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
205 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
209 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
210 version 'annotation))
213 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
215 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
216 (build-system r-build-system)
218 `(("r-bsgenome" ,r-bsgenome)))
220 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
221 (synopsis "Full genome sequences for Homo sapiens")
223 "This package provides full genome sequences for Homo sapiens from
224 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
225 (license license:artistic2.0)))
227 (define-public r-bsgenome-hsapiens-ncbi-grch38
229 (name "r-bsgenome-hsapiens-ncbi-grch38")
234 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
235 version 'annotation))
238 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
239 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
240 (build-system r-build-system)
241 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
243 "https://bioconductor.org/packages/release/data/annotation/html/\
244 BSgenome.Hsapiens.NCBI.GRCh38.html")
245 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
247 "This package provides full genome sequences for Homo sapiens (Human) as
248 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
249 (license license:artistic2.0)))
251 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
253 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
257 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
258 version 'annotation))
261 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
263 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
264 (build-system r-build-system)
266 `(("r-bsgenome" ,r-bsgenome)
267 ("r-bsgenome-hsapiens-ucsc-hg19"
268 ,r-bsgenome-hsapiens-ucsc-hg19)))
269 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
270 (synopsis "Full masked genome sequences for Homo sapiens")
272 "This package provides full genome sequences for Homo sapiens (Human) as
273 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
274 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
275 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
276 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
277 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
278 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
280 (license license:artistic2.0)))
282 (define-public r-bsgenome-mmusculus-ucsc-mm9
284 (name "r-bsgenome-mmusculus-ucsc-mm9")
288 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
289 version 'annotation))
292 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
294 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
295 (build-system r-build-system)
297 `(("r-bsgenome" ,r-bsgenome)))
299 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
300 (synopsis "Full genome sequences for Mouse")
302 "This package provides full genome sequences for Mus musculus (Mouse) as
303 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
304 (license license:artistic2.0)))
306 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
308 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
312 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
313 version 'annotation))
316 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
318 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
319 (build-system r-build-system)
321 `(("r-bsgenome" ,r-bsgenome)
322 ("r-bsgenome-mmusculus-ucsc-mm9"
323 ,r-bsgenome-mmusculus-ucsc-mm9)))
324 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
325 (synopsis "Full masked genome sequences for Mouse")
327 "This package provides full genome sequences for Mus musculus (Mouse) as
328 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
329 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
330 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
331 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
332 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
333 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
335 (license license:artistic2.0)))
337 (define-public r-bsgenome-mmusculus-ucsc-mm10
339 (name "r-bsgenome-mmusculus-ucsc-mm10")
343 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
344 version 'annotation))
347 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
349 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
350 (build-system r-build-system)
352 `(("r-bsgenome" ,r-bsgenome)))
354 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
355 (synopsis "Full genome sequences for Mouse")
357 "This package provides full genome sequences for Mus
358 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
359 in Biostrings objects.")
360 (license license:artistic2.0)))
362 (define-public r-org-ce-eg-db
364 (name "r-org-ce-eg-db")
368 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
371 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
373 `((upstream-name . "org.Ce.eg.db")))
374 (build-system r-build-system)
376 `(("r-annotationdbi" ,r-annotationdbi)))
377 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
378 (synopsis "Genome wide annotation for Worm")
380 "This package provides mappings from Entrez gene identifiers to various
381 annotations for the genome of the model worm Caenorhabditis elegans.")
382 (license license:artistic2.0)))
384 (define-public r-org-dm-eg-db
386 (name "r-org-dm-eg-db")
390 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
393 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
395 `((upstream-name . "org.Dm.eg.db")))
396 (build-system r-build-system)
398 `(("r-annotationdbi" ,r-annotationdbi)))
399 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
400 (synopsis "Genome wide annotation for Fly")
402 "This package provides mappings from Entrez gene identifiers to various
403 annotations for the genome of the model fruit fly Drosophila melanogaster.")
404 (license license:artistic2.0)))
406 (define-public r-org-dr-eg-db
408 (name "r-org-dr-eg-db")
412 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
415 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
417 `((upstream-name . "org.Dr.eg.db")))
418 (build-system r-build-system)
420 `(("r-annotationdbi" ,r-annotationdbi)))
421 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
422 (synopsis "Annotation for Zebrafish")
424 "This package provides genome wide annotations for Zebrafish, primarily
425 based on mapping using Entrez Gene identifiers.")
426 (license license:artistic2.0)))
428 (define-public r-org-hs-eg-db
430 (name "r-org-hs-eg-db")
434 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
437 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
439 `((upstream-name . "org.Hs.eg.db")))
440 (build-system r-build-system)
442 `(("r-annotationdbi" ,r-annotationdbi)))
443 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
444 (synopsis "Genome wide annotation for Human")
446 "This package contains genome-wide annotations for Human, primarily based
447 on mapping using Entrez Gene identifiers.")
448 (license license:artistic2.0)))
450 (define-public r-org-mm-eg-db
452 (name "r-org-mm-eg-db")
456 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
459 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
461 `((upstream-name . "org.Mm.eg.db")))
462 (build-system r-build-system)
464 `(("r-annotationdbi" ,r-annotationdbi)))
465 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
466 (synopsis "Genome wide annotation for Mouse")
468 "This package provides mappings from Entrez gene identifiers to various
469 annotations for the genome of the model mouse Mus musculus.")
470 (license license:artistic2.0)))
472 (define-public r-bsgenome-hsapiens-ucsc-hg19
474 (name "r-bsgenome-hsapiens-ucsc-hg19")
478 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
479 version 'annotation))
482 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
484 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
485 (build-system r-build-system)
487 `(("r-bsgenome" ,r-bsgenome)))
489 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
490 (synopsis "Full genome sequences for Homo sapiens")
492 "This package provides full genome sequences for Homo sapiens as provided
493 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
494 (license license:artistic2.0)))
496 (define-public r-ensdb-hsapiens-v75
498 (name "r-ensdb-hsapiens-v75")
503 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
506 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
508 `((upstream-name . "EnsDb.Hsapiens.v75")))
509 (build-system r-build-system)
511 `(("r-ensembldb" ,r-ensembldb)))
512 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
513 (synopsis "Ensembl based annotation package")
515 "This package exposes an annotation database generated from Ensembl.")
516 (license license:artistic2.0)))
518 (define-public r-genelendatabase
520 (name "r-genelendatabase")
525 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
528 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
530 `((upstream-name . "geneLenDataBase")))
531 (build-system r-build-system)
533 `(("r-rtracklayer" ,r-rtracklayer)
534 ("r-genomicfeatures" ,r-genomicfeatures)))
535 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
536 (synopsis "Lengths of mRNA transcripts for a number of genomes")
538 "This package provides the lengths of mRNA transcripts for a number of
539 genomes and gene ID formats, largely based on the UCSC table browser.")
540 (license license:lgpl2.0+)))
542 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
544 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
548 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
549 version 'annotation))
552 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
554 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
555 (build-system r-build-system)
557 `(("r-genomicfeatures" ,r-genomicfeatures)))
559 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
560 (synopsis "Annotation package for human genome in TxDb format")
562 "This package provides an annotation database of Homo sapiens genome
563 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
564 track. The database is exposed as a @code{TxDb} object.")
565 (license license:artistic2.0)))
567 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
569 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
573 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
574 version 'annotation))
577 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
579 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
580 (build-system r-build-system)
582 `(("r-genomicfeatures" ,r-genomicfeatures)))
584 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
585 (synopsis "Annotation package for human genome in TxDb format")
587 "This package provides an annotation database of Homo sapiens genome
588 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
589 track. The database is exposed as a @code{TxDb} object.")
590 (license license:artistic2.0)))
592 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
594 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
598 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
599 version 'annotation))
602 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
604 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
605 (build-system r-build-system)
607 `(("r-genomicfeatures" ,r-genomicfeatures)
608 ("r-annotationdbi" ,r-annotationdbi)))
610 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
611 (synopsis "Annotation package for mouse genome in TxDb format")
613 "This package provides an annotation database of Mouse genome data. It
614 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
615 database is exposed as a @code{TxDb} object.")
616 (license license:artistic2.0)))
618 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
620 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
624 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
625 version 'annotation))
628 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
630 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
631 (build-system r-build-system)
633 `(("r-bsgenome" ,r-bsgenome)
634 ("r-genomicfeatures" ,r-genomicfeatures)
635 ("r-annotationdbi" ,r-annotationdbi)))
637 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
638 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
640 "This package loads a TxDb object, which is an R interface to
641 prefabricated databases contained in this package. This package provides
642 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
643 based on the knownGene track.")
644 (license license:artistic2.0)))
646 (define-public r-txdb-celegans-ucsc-ce6-ensgene
648 (name "r-txdb-celegans-ucsc-ce6-ensgene")
653 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
654 version 'annotation))
657 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
659 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
660 (build-system r-build-system)
662 `(("r-annotationdbi" ,r-annotationdbi)
663 ("r-genomicfeatures" ,r-genomicfeatures)))
664 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
665 (synopsis "Annotation package for C elegans TxDb objects")
667 "This package exposes a C elegans annotation database generated from UCSC
668 by exposing these as TxDb objects.")
669 (license license:artistic2.0)))
671 (define-public r-fdb-infiniummethylation-hg19
673 (name "r-fdb-infiniummethylation-hg19")
677 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
678 version 'annotation))
681 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
683 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
684 (build-system r-build-system)
686 `(("r-biostrings" ,r-biostrings)
687 ("r-genomicfeatures" ,r-genomicfeatures)
688 ("r-annotationdbi" ,r-annotationdbi)
689 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
690 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
691 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
692 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
694 "This is an annotation package for Illumina Infinium DNA methylation
695 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
697 (license license:artistic2.0)))
699 (define-public r-illuminahumanmethylationepicmanifest
701 (name "r-illuminahumanmethylationepicmanifest")
705 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
706 version 'annotation))
709 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
711 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
712 (build-system r-build-system)
714 `(("r-minfi" ,r-minfi)))
715 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
716 (synopsis "Manifest for Illumina's EPIC methylation arrays")
718 "This is a manifest package for Illumina's EPIC methylation arrays.")
719 (license license:artistic2.0)))
721 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
722 ;; from Bioconductor.
723 (define-public r-deconstructsigs
725 (name "r-deconstructsigs")
729 (uri (cran-uri "deconstructSigs" version))
732 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
734 `((upstream-name . "deconstructSigs")))
735 (build-system r-build-system)
737 `(("r-bsgenome" ,r-bsgenome)
738 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
739 ("r-genomeinfodb" ,r-genomeinfodb)
740 ("r-reshape2" ,r-reshape2)))
741 (home-page "https://github.com/raerose01/deconstructSigs")
742 (synopsis "Identifies signatures present in a tumor sample")
743 (description "This package takes sample information in the form of the
744 fraction of mutations in each of 96 trinucleotide contexts and identifies
745 the weighted combination of published signatures that, when summed, most
746 closely reconstructs the mutational profile.")
747 (license license:gpl2+)))
749 ;; This is a CRAN package, but it depends on Bioconductor packages.
757 (uri (cran-uri "NMF" version))
760 "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq"))))
761 (properties `((upstream-name . "NMF")))
762 (build-system r-build-system)
764 `(("r-cluster" ,r-cluster)
765 ("r-biobase" ,r-biobase)
766 ("r-biocmanager" ,r-biocmanager)
767 ("r-bigmemory" ,r-bigmemory) ; suggested
768 ("r-synchronicity" ,r-synchronicity) ; suggested
769 ("r-colorspace" ,r-colorspace)
770 ("r-digest" ,r-digest)
771 ("r-doparallel" ,r-doparallel)
772 ("r-foreach" ,r-foreach)
773 ("r-ggplot2" ,r-ggplot2)
774 ("r-gridbase" ,r-gridbase)
775 ("r-pkgmaker" ,r-pkgmaker)
776 ("r-rcolorbrewer" ,r-rcolorbrewer)
777 ("r-registry" ,r-registry)
778 ("r-reshape2" ,r-reshape2)
779 ("r-rngtools" ,r-rngtools)
780 ("r-stringr" ,r-stringr)))
781 (home-page "http://renozao.github.io/NMF")
782 (synopsis "Algorithms and framework for nonnegative matrix factorization")
784 "This package provides a framework to perform Non-negative Matrix
785 Factorization (NMF). The package implements a set of already published
786 algorithms and seeding methods, and provides a framework to test, develop and
787 plug new or custom algorithms. Most of the built-in algorithms have been
788 optimized in C++, and the main interface function provides an easy way of
789 performing parallel computations on multicore machines.")
790 (license license:gpl2+)))
792 (define-public r-do-db
798 (uri (bioconductor-uri "DO.db" version 'annotation))
801 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
803 `((upstream-name . "DO.db")))
804 (build-system r-build-system)
806 `(("r-annotationdbi" ,r-annotationdbi)))
807 (home-page "https://www.bioconductor.org/packages/DO.db/")
808 (synopsis "Annotation maps describing the entire Disease Ontology")
810 "This package provides a set of annotation maps describing the entire
812 (license license:artistic2.0)))
814 (define-public r-pfam-db
821 (uri (bioconductor-uri "PFAM.db" version 'annotation))
824 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
825 (properties `((upstream-name . "PFAM.db")))
826 (build-system r-build-system)
828 `(("r-annotationdbi" ,r-annotationdbi)))
829 (home-page "https://bioconductor.org/packages/PFAM.db")
830 (synopsis "Set of protein ID mappings for PFAM")
832 "This package provides a set of protein ID mappings for PFAM, assembled
833 using data from public repositories.")
834 (license license:artistic2.0)))
836 (define-public r-phastcons100way-ucsc-hg19
838 (name "r-phastcons100way-ucsc-hg19")
843 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
844 version 'annotation))
847 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
849 `((upstream-name . "phastCons100way.UCSC.hg19")))
850 (build-system r-build-system)
852 `(("r-bsgenome" ,r-bsgenome)
853 ("r-genomeinfodb" ,r-genomeinfodb)
854 ("r-genomicranges" ,r-genomicranges)
855 ("r-genomicscores" ,r-genomicscores)
856 ("r-iranges" ,r-iranges)
857 ("r-s4vectors" ,r-s4vectors)))
858 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
859 (synopsis "UCSC phastCons conservation scores for hg19")
861 "This package provides UCSC phastCons conservation scores for the human
862 genome (hg19) calculated from multiple alignments with other 99 vertebrate
864 (license license:artistic2.0)))
869 (define-public r-abadata
875 (uri (bioconductor-uri "ABAData" version 'experiment))
878 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
880 `((upstream-name . "ABAData")))
881 (build-system r-build-system)
883 `(("r-annotationdbi" ,r-annotationdbi)))
884 (home-page "https://www.bioconductor.org/packages/ABAData/")
885 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
887 "This package provides the data for the gene expression enrichment
888 analysis conducted in the package ABAEnrichment. The package includes three
889 datasets which are derived from the Allen Brain Atlas:
892 @item Gene expression data from Human Brain (adults) averaged across donors,
893 @item Gene expression data from the Developing Human Brain pooled into five
894 age categories and averaged across donors, and
895 @item a developmental effect score based on the Developing Human Brain
899 All datasets are restricted to protein coding genes.")
900 (license license:gpl2+)))
902 (define-public r-arrmdata
908 (uri (bioconductor-uri "ARRmData" version 'experiment))
911 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
913 `((upstream-name . "ARRmData")))
914 (build-system r-build-system)
915 (home-page "https://www.bioconductor.org/packages/ARRmData/")
916 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
918 "This package provides raw beta values from 36 samples across 3 groups
919 from Illumina 450k methylation arrays.")
920 (license license:artistic2.0)))
922 (define-public r-hsmmsinglecell
924 (name "r-hsmmsinglecell")
928 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
931 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
933 `((upstream-name . "HSMMSingleCell")))
934 (build-system r-build-system)
935 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
936 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
938 "Skeletal myoblasts undergo a well-characterized sequence of
939 morphological and transcriptional changes during differentiation. In this
940 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
941 under high mitogen conditions (GM) and then differentiated by switching to
942 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
943 hundred cells taken over a time-course of serum-induced differentiation.
944 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
945 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
946 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
947 which were then sequenced to a depth of ~4 million reads per library,
948 resulting in a complete gene expression profile for each cell.")
949 (license license:artistic2.0)))
957 (uri (bioconductor-uri "ALL" version 'experiment))
960 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
961 (properties `((upstream-name . "ALL")))
962 (build-system r-build-system)
964 `(("r-biobase" ,r-biobase)))
965 (home-page "https://bioconductor.org/packages/ALL")
966 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
968 "The data consist of microarrays from 128 different individuals with
969 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
970 are available. The data have been normalized (using rma) and it is the
971 jointly normalized data that are available here. The data are presented in
972 the form of an @code{exprSet} object.")
973 (license license:artistic2.0)))
975 (define-public r-affydata
982 (uri (bioconductor-uri "affydata" version 'experiment))
985 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
986 (properties `((upstream-name . "affydata")))
987 (build-system r-build-system)
989 `(("r-affy" ,r-affy)))
990 (home-page "https://bioconductor.org/packages/affydata/")
991 (synopsis "Affymetrix data for demonstration purposes")
993 "This package provides example datasets that represent 'real world
994 examples' of Affymetrix data, unlike the artificial examples included in the
995 package @code{affy}.")
996 (license license:gpl2+)))
998 (define-public r-curatedtcgadata
1000 (name "r-curatedtcgadata")
1005 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1008 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1010 `((upstream-name . "curatedTCGAData")))
1011 (build-system r-build-system)
1013 `(("r-annotationhub" ,r-annotationhub)
1014 ("r-experimenthub" ,r-experimenthub)
1015 ("r-hdf5array" ,r-hdf5array)
1016 ("r-multiassayexperiment" ,r-multiassayexperiment)
1017 ("r-s4vectors" ,r-s4vectors)
1018 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1019 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1020 (synopsis "Curated data from The Cancer Genome Atlas")
1022 "This package provides publicly available data from The Cancer Genome
1023 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1024 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1025 number, mutation, microRNA, protein, and others) with clinical / pathological
1026 data. It also links assay barcodes with patient identifiers, enabling
1027 harmonized subsetting of rows (features) and columns (patients / samples)
1028 across the entire multi-'omics experiment.")
1029 (license license:artistic2.0)))
1034 (define-public r-biocversion
1036 (name "r-biocversion")
1041 (uri (bioconductor-uri "BiocVersion" version))
1044 "0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f"))))
1045 (properties `((upstream-name . "BiocVersion")))
1046 (build-system r-build-system)
1047 (home-page "https://bioconductor.org/packages/BiocVersion/")
1048 (synopsis "Set the appropriate version of Bioconductor packages")
1050 "This package provides repository information for the appropriate version
1052 (license license:artistic2.0)))
1054 (define-public r-biocgenerics
1056 (name "r-biocgenerics")
1060 (uri (bioconductor-uri "BiocGenerics" version))
1063 "1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn"))))
1065 `((upstream-name . "BiocGenerics")))
1066 (build-system r-build-system)
1067 (home-page "https://bioconductor.org/packages/BiocGenerics")
1068 (synopsis "S4 generic functions for Bioconductor")
1070 "This package provides S4 generic functions needed by many Bioconductor
1072 (license license:artistic2.0)))
1074 (define-public r-affycomp
1081 (uri (bioconductor-uri "affycomp" version))
1084 "0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js"))))
1085 (properties `((upstream-name . "affycomp")))
1086 (build-system r-build-system)
1087 (propagated-inputs `(("r-biobase" ,r-biobase)))
1088 (home-page "https://bioconductor.org/packages/affycomp/")
1089 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1091 "The package contains functions that can be used to compare expression
1092 measures for Affymetrix Oligonucleotide Arrays.")
1093 (license license:gpl2+)))
1095 (define-public r-affycompatible
1097 (name "r-affycompatible")
1102 (uri (bioconductor-uri "AffyCompatible" version))
1105 "10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks"))))
1107 `((upstream-name . "AffyCompatible")))
1108 (build-system r-build-system)
1110 `(("r-biostrings" ,r-biostrings)
1111 ("r-rcurl" ,r-rcurl)
1113 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1114 (synopsis "Work with Affymetrix GeneChip files")
1116 "This package provides an interface to Affymetrix chip annotation and
1117 sample attribute files. The package allows an easy way for users to download
1118 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1119 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1120 Command Console} (AGCC)-compatible sample annotation files.")
1121 (license license:artistic2.0)))
1123 (define-public r-affycontam
1125 (name "r-affycontam")
1130 (uri (bioconductor-uri "affyContam" version))
1133 "0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l"))))
1134 (properties `((upstream-name . "affyContam")))
1135 (build-system r-build-system)
1137 `(("r-affy" ,r-affy)
1138 ("r-affydata" ,r-affydata)
1139 ("r-biobase" ,r-biobase)))
1140 (home-page "https://bioconductor.org/packages/affyContam/")
1141 (synopsis "Structured corruption of Affymetrix CEL file data")
1143 "Microarray quality assessment is a major concern of microarray analysts.
1144 This package provides some simple approaches to in silico creation of quality
1145 problems in CEL-level data to help evaluate performance of quality metrics.")
1146 (license license:artistic2.0)))
1148 (define-public r-affycoretools
1150 (name "r-affycoretools")
1155 (uri (bioconductor-uri "affycoretools" version))
1158 "1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw"))))
1159 (properties `((upstream-name . "affycoretools")))
1160 (build-system r-build-system)
1162 `(("r-affy" ,r-affy)
1163 ("r-annotationdbi" ,r-annotationdbi)
1164 ("r-biobase" ,r-biobase)
1165 ("r-biocgenerics" ,r-biocgenerics)
1167 ("r-edger" ,r-edger)
1168 ("r-gcrma" ,r-gcrma)
1169 ("r-glimma" ,r-glimma)
1170 ("r-ggplot2" ,r-ggplot2)
1171 ("r-gostats" ,r-gostats)
1172 ("r-gplots" ,r-gplots)
1173 ("r-hwriter" ,r-hwriter)
1174 ("r-lattice" ,r-lattice)
1175 ("r-limma" ,r-limma)
1176 ("r-oligoclasses" ,r-oligoclasses)
1177 ("r-reportingtools" ,r-reportingtools)
1178 ("r-rsqlite" ,r-rsqlite)
1179 ("r-s4vectors" ,r-s4vectors)
1180 ("r-xtable" ,r-xtable)))
1181 (home-page "https://bioconductor.org/packages/affycoretools/")
1182 (synopsis "Functions for analyses with Affymetrix GeneChips")
1184 "This package provides various wrapper functions that have been written
1185 to streamline the more common analyses that a Biostatistician might see.")
1186 (license license:artistic2.0)))
1188 (define-public r-affxparser
1190 (name "r-affxparser")
1195 (uri (bioconductor-uri "affxparser" version))
1198 "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40"))))
1199 (properties `((upstream-name . "affxparser")))
1200 (build-system r-build-system)
1201 (home-page "https://github.com/HenrikBengtsson/affxparser")
1202 (synopsis "Affymetrix File Parsing SDK")
1204 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1205 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1206 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1207 are supported. Currently, there are methods for reading @dfn{chip definition
1208 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1209 either in full or in part. For example, probe signals from a few probesets
1210 can be extracted very quickly from a set of CEL files into a convenient list
1212 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1214 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1216 (define-public r-annotate
1223 (uri (bioconductor-uri "annotate" version))
1226 "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy"))))
1227 (build-system r-build-system)
1229 `(("r-annotationdbi" ,r-annotationdbi)
1230 ("r-biobase" ,r-biobase)
1231 ("r-biocgenerics" ,r-biocgenerics)
1233 ("r-rcurl" ,r-rcurl)
1235 ("r-xtable" ,r-xtable)))
1237 "https://bioconductor.org/packages/annotate")
1238 (synopsis "Annotation for microarrays")
1239 (description "This package provides R environments for the annotation of
1241 (license license:artistic2.0)))
1243 (define-public r-hpar
1250 (uri (bioconductor-uri "hpar" version))
1253 "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m"))))
1254 (build-system r-build-system)
1255 (home-page "https://bioconductor.org/packages/hpar/")
1256 (synopsis "Human Protein Atlas in R")
1257 (description "This package provides a simple interface to and data from
1258 the Human Protein Atlas project.")
1259 (license license:artistic2.0)))
1261 (define-public r-regioner
1268 (uri (bioconductor-uri "regioneR" version))
1271 "0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9"))))
1272 (properties `((upstream-name . "regioneR")))
1273 (build-system r-build-system)
1275 `(("r-biostrings" ,r-biostrings)
1276 ("r-bsgenome" ,r-bsgenome)
1277 ("r-genomeinfodb" ,r-genomeinfodb)
1278 ("r-genomicranges" ,r-genomicranges)
1279 ("r-iranges" ,r-iranges)
1280 ("r-memoise" ,r-memoise)
1281 ("r-rtracklayer" ,r-rtracklayer)
1282 ("r-s4vectors" ,r-s4vectors)))
1283 (home-page "https://bioconductor.org/packages/regioneR/")
1284 (synopsis "Association analysis of genomic regions")
1285 (description "This package offers a statistical framework based on
1286 customizable permutation tests to assess the association between genomic
1287 region sets and other genomic features.")
1288 (license license:artistic2.0)))
1290 (define-public r-reportingtools
1292 (name "r-reportingtools")
1297 (uri (bioconductor-uri "ReportingTools" version))
1300 "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w"))))
1302 `((upstream-name . "ReportingTools")))
1303 (build-system r-build-system)
1305 `(("r-annotate" ,r-annotate)
1306 ("r-annotationdbi" ,r-annotationdbi)
1307 ("r-biobase" ,r-biobase)
1308 ("r-biocgenerics" ,r-biocgenerics)
1309 ("r-category" ,r-category)
1310 ("r-deseq2" ,r-deseq2)
1311 ("r-edger" ,r-edger)
1312 ("r-ggbio" ,r-ggbio)
1313 ("r-ggplot2" ,r-ggplot2)
1314 ("r-gostats" ,r-gostats)
1315 ("r-gseabase" ,r-gseabase)
1316 ("r-hwriter" ,r-hwriter)
1317 ("r-iranges" ,r-iranges)
1318 ("r-knitr" ,r-knitr)
1319 ("r-lattice" ,r-lattice)
1320 ("r-limma" ,r-limma)
1321 ("r-pfam-db" ,r-pfam-db)
1322 ("r-r-utils" ,r-r-utils)
1324 (home-page "https://bioconductor.org/packages/ReportingTools/")
1325 (synopsis "Tools for making reports in various formats")
1327 "The ReportingTools package enables users to easily display reports of
1328 analysis results generated from sources such as microarray and sequencing
1329 data. The package allows users to create HTML pages that may be viewed on a
1330 web browser, or in other formats. Users can generate tables with sortable and
1331 filterable columns, make and display plots, and link table entries to other
1332 data sources such as NCBI or larger plots within the HTML page. Using the
1333 package, users can also produce a table of contents page to link various
1334 reports together for a particular project that can be viewed in a web
1336 (license license:artistic2.0)))
1338 (define-public r-geneplotter
1340 (name "r-geneplotter")
1345 (uri (bioconductor-uri "geneplotter" version))
1348 "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx"))))
1349 (build-system r-build-system)
1351 `(("r-annotate" ,r-annotate)
1352 ("r-annotationdbi" ,r-annotationdbi)
1353 ("r-biobase" ,r-biobase)
1354 ("r-biocgenerics" ,r-biocgenerics)
1355 ("r-lattice" ,r-lattice)
1356 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1357 (home-page "https://bioconductor.org/packages/geneplotter")
1358 (synopsis "Graphics functions for genomic data")
1360 "This package provides functions for plotting genomic data.")
1361 (license license:artistic2.0)))
1363 (define-public r-oligoclasses
1365 (name "r-oligoclasses")
1370 (uri (bioconductor-uri "oligoClasses" version))
1373 "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf"))))
1374 (properties `((upstream-name . "oligoClasses")))
1375 (build-system r-build-system)
1377 `(("r-affyio" ,r-affyio)
1378 ("r-biobase" ,r-biobase)
1379 ("r-biocgenerics" ,r-biocgenerics)
1380 ("r-biocmanager" ,r-biocmanager)
1381 ("r-biostrings" ,r-biostrings)
1384 ("r-foreach" ,r-foreach)
1385 ("r-genomicranges" ,r-genomicranges)
1386 ("r-iranges" ,r-iranges)
1387 ("r-rsqlite" ,r-rsqlite)
1388 ("r-s4vectors" ,r-s4vectors)
1389 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1390 (home-page "https://bioconductor.org/packages/oligoClasses/")
1391 (synopsis "Classes for high-throughput arrays")
1393 "This package contains class definitions, validity checks, and
1394 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1396 (license license:gpl2+)))
1398 (define-public r-oligo
1405 (uri (bioconductor-uri "oligo" version))
1408 "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3"))))
1409 (properties `((upstream-name . "oligo")))
1410 (build-system r-build-system)
1411 (inputs `(("zlib" ,zlib)))
1413 `(("r-affxparser" ,r-affxparser)
1414 ("r-affyio" ,r-affyio)
1415 ("r-biobase" ,r-biobase)
1416 ("r-biocgenerics" ,r-biocgenerics)
1417 ("r-biostrings" ,r-biostrings)
1420 ("r-oligoclasses" ,r-oligoclasses)
1421 ("r-preprocesscore" ,r-preprocesscore)
1422 ("r-rsqlite" ,r-rsqlite)
1423 ("r-zlibbioc" ,r-zlibbioc)))
1424 (home-page "https://bioconductor.org/packages/oligo/")
1425 (synopsis "Preprocessing tools for oligonucleotide arrays")
1427 "This package provides a package to analyze oligonucleotide
1428 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1429 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1430 (license license:lgpl2.0+)))
1432 (define-public r-qvalue
1439 (uri (bioconductor-uri "qvalue" version))
1442 "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j"))))
1443 (build-system r-build-system)
1445 `(("r-ggplot2" ,r-ggplot2)
1446 ("r-reshape2" ,r-reshape2)))
1447 (home-page "http://github.com/jdstorey/qvalue")
1448 (synopsis "Q-value estimation for false discovery rate control")
1450 "This package takes a list of p-values resulting from the simultaneous
1451 testing of many hypotheses and estimates their q-values and local @dfn{false
1452 discovery rate} (FDR) values. The q-value of a test measures the proportion
1453 of false positives incurred when that particular test is called significant.
1454 The local FDR measures the posterior probability the null hypothesis is true
1455 given the test's p-value. Various plots are automatically generated, allowing
1456 one to make sensible significance cut-offs. The software can be applied to
1457 problems in genomics, brain imaging, astrophysics, and data mining.")
1458 ;; Any version of the LGPL.
1459 (license license:lgpl3+)))
1461 (define-public r-diffbind
1468 (uri (bioconductor-uri "DiffBind" version))
1471 "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2"))))
1472 (properties `((upstream-name . "DiffBind")))
1473 (build-system r-build-system)
1477 `(("r-amap" ,r-amap)
1478 ("r-biocparallel" ,r-biocparallel)
1479 ("r-deseq2" ,r-deseq2)
1480 ("r-dplyr" ,r-dplyr)
1481 ("r-edger" ,r-edger)
1482 ("r-genomicalignments" ,r-genomicalignments)
1483 ("r-genomicranges" ,r-genomicranges)
1484 ("r-ggplot2" ,r-ggplot2)
1485 ("r-ggrepel" ,r-ggrepel)
1486 ("r-gplots" ,r-gplots)
1487 ("r-iranges" ,r-iranges)
1488 ("r-lattice" ,r-lattice)
1489 ("r-limma" ,r-limma)
1490 ("r-locfit" ,r-locfit)
1491 ("r-rcolorbrewer" , r-rcolorbrewer)
1493 ("r-rhtslib" ,r-rhtslib)
1494 ("r-rsamtools" ,r-rsamtools)
1495 ("r-s4vectors" ,r-s4vectors)
1496 ("r-summarizedexperiment" ,r-summarizedexperiment)
1497 ("r-systempiper" ,r-systempiper)))
1498 (home-page "https://bioconductor.org/packages/DiffBind")
1499 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1501 "This package computes differentially bound sites from multiple
1502 ChIP-seq experiments using affinity (quantitative) data. Also enables
1503 occupancy (overlap) analysis and plotting functions.")
1504 (license license:artistic2.0)))
1506 (define-public r-ripseeker
1508 (name "r-ripseeker")
1513 (uri (bioconductor-uri "RIPSeeker" version))
1516 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1517 (properties `((upstream-name . "RIPSeeker")))
1518 (build-system r-build-system)
1520 `(("r-s4vectors" ,r-s4vectors)
1521 ("r-iranges" ,r-iranges)
1522 ("r-genomicranges" ,r-genomicranges)
1523 ("r-summarizedexperiment" ,r-summarizedexperiment)
1524 ("r-rsamtools" ,r-rsamtools)
1525 ("r-genomicalignments" ,r-genomicalignments)
1526 ("r-rtracklayer" ,r-rtracklayer)))
1527 (home-page "https://bioconductor.org/packages/RIPSeeker")
1529 "Identifying protein-associated transcripts from RIP-seq experiments")
1531 "This package infers and discriminates RIP peaks from RIP-seq alignments
1532 using two-state HMM with negative binomial emission probability. While
1533 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1534 a suite of bioinformatics tools integrated within this self-contained software
1535 package comprehensively addressing issues ranging from post-alignments
1536 processing to visualization and annotation.")
1537 (license license:gpl2)))
1539 (define-public r-multtest
1546 (uri (bioconductor-uri "multtest" version))
1549 "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari"))))
1550 (build-system r-build-system)
1552 `(("r-survival" ,r-survival)
1553 ("r-biocgenerics" ,r-biocgenerics)
1554 ("r-biobase" ,r-biobase)
1555 ("r-mass" ,r-mass)))
1556 (home-page "https://bioconductor.org/packages/multtest")
1557 (synopsis "Resampling-based multiple hypothesis testing")
1559 "This package can do non-parametric bootstrap and permutation
1560 resampling-based multiple testing procedures (including empirical Bayes
1561 methods) for controlling the family-wise error rate (FWER), generalized
1562 family-wise error rate (gFWER), tail probability of the proportion of
1563 false positives (TPPFP), and false discovery rate (FDR). Several choices
1564 of bootstrap-based null distribution are implemented (centered, centered
1565 and scaled, quantile-transformed). Single-step and step-wise methods are
1566 available. Tests based on a variety of T- and F-statistics (including
1567 T-statistics based on regression parameters from linear and survival models
1568 as well as those based on correlation parameters) are included. When probing
1569 hypotheses with T-statistics, users may also select a potentially faster null
1570 distribution which is multivariate normal with mean zero and variance
1571 covariance matrix derived from the vector influence function. Results are
1572 reported in terms of adjusted P-values, confidence regions and test statistic
1573 cutoffs. The procedures are directly applicable to identifying differentially
1574 expressed genes in DNA microarray experiments.")
1575 (license license:lgpl3)))
1577 (define-public r-graph
1583 (uri (bioconductor-uri "graph" version))
1586 "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc"))))
1587 (build-system r-build-system)
1589 `(("r-biocgenerics" ,r-biocgenerics)))
1590 (home-page "https://bioconductor.org/packages/graph")
1591 (synopsis "Handle graph data structures in R")
1593 "This package implements some simple graph handling capabilities for R.")
1594 (license license:artistic2.0)))
1596 ;; This is a CRAN package, but it depends on a Bioconductor package.
1597 (define-public r-ggm
1604 (uri (cran-uri "ggm" version))
1607 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1608 (properties `((upstream-name . "ggm")))
1609 (build-system r-build-system)
1611 `(("r-graph" ,r-graph)
1612 ("r-igraph" ,r-igraph)))
1613 (home-page "https://cran.r-project.org/package=ggm")
1614 (synopsis "Functions for graphical Markov models")
1616 "This package provides functions and datasets for maximum likelihood
1617 fitting of some classes of graphical Markov models.")
1618 (license license:gpl2+)))
1620 (define-public r-codedepends
1622 (name "r-codedepends")
1627 (uri (cran-uri "CodeDepends" version))
1630 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1631 (properties `((upstream-name . "CodeDepends")))
1632 (build-system r-build-system)
1634 `(("r-codetools" ,r-codetools)
1635 ("r-graph" ,r-graph)
1637 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
1638 (synopsis "Analysis of R code for reproducible research and code comprehension")
1640 "This package provides tools for analyzing R expressions or blocks of
1641 code and determining the dependencies between them. It focuses on R scripts,
1642 but can be used on the bodies of functions. There are many facilities
1643 including the ability to summarize or get a high-level view of code,
1644 determining dependencies between variables, code improvement suggestions.")
1645 ;; Any version of the GPL
1646 (license (list license:gpl2+ license:gpl3+))))
1648 (define-public r-chippeakanno
1650 (name "r-chippeakanno")
1655 (uri (bioconductor-uri "ChIPpeakAnno" version))
1658 "0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc"))))
1659 (properties `((upstream-name . "ChIPpeakAnno")))
1660 (build-system r-build-system)
1662 `(("r-annotationdbi" ,r-annotationdbi)
1663 ("r-biobase" ,r-biobase)
1664 ("r-biocgenerics" ,r-biocgenerics)
1665 ("r-biocmanager" ,r-biocmanager)
1666 ("r-biomart" ,r-biomart)
1667 ("r-biostrings" ,r-biostrings)
1668 ("r-bsgenome" ,r-bsgenome)
1670 ("r-delayedarray" ,r-delayedarray)
1671 ("r-ensembldb" ,r-ensembldb)
1672 ("r-genomeinfodb" ,r-genomeinfodb)
1673 ("r-genomicalignments" ,r-genomicalignments)
1674 ("r-genomicfeatures" ,r-genomicfeatures)
1675 ("r-genomicranges" ,r-genomicranges)
1676 ("r-go-db" ,r-go-db)
1677 ("r-graph" ,r-graph)
1679 ("r-iranges" ,r-iranges)
1680 ("r-limma" ,r-limma)
1681 ("r-matrixstats" ,r-matrixstats)
1682 ("r-multtest" ,r-multtest)
1684 ("r-regioner" ,r-regioner)
1685 ("r-rsamtools" ,r-rsamtools)
1686 ("r-rtracklayer" ,r-rtracklayer)
1687 ("r-s4vectors" ,r-s4vectors)
1688 ("r-seqinr" ,r-seqinr)
1689 ("r-summarizedexperiment" ,r-summarizedexperiment)
1690 ("r-venndiagram" ,r-venndiagram)))
1691 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
1692 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1694 "The package includes functions to retrieve the sequences around the peak,
1695 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1696 custom features such as most conserved elements and other transcription factor
1697 binding sites supplied by users. Starting 2.0.5, new functions have been added
1698 for finding the peaks with bi-directional promoters with summary statistics
1699 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1700 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1701 enrichedGO (addGeneIDs).")
1702 (license license:gpl2+)))
1704 (define-public r-marray
1710 (uri (bioconductor-uri "marray" version))
1712 (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl"))))
1713 (build-system r-build-system)
1715 `(("r-limma" ,r-limma)))
1716 (home-page "https://bioconductor.org/packages/marray")
1717 (synopsis "Exploratory analysis for two-color spotted microarray data")
1718 (description "This package contains class definitions for two-color spotted
1719 microarray data. It also includes functions for data input, diagnostic plots,
1720 normalization and quality checking.")
1721 (license license:lgpl2.0+)))
1723 (define-public r-cghbase
1729 (uri (bioconductor-uri "CGHbase" version))
1731 (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x"))))
1732 (properties `((upstream-name . "CGHbase")))
1733 (build-system r-build-system)
1735 `(("r-biobase" ,r-biobase)
1736 ("r-marray" ,r-marray)))
1737 (home-page "https://bioconductor.org/packages/CGHbase")
1738 (synopsis "Base functions and classes for arrayCGH data analysis")
1739 (description "This package contains functions and classes that are needed by
1740 the @code{arrayCGH} packages.")
1741 (license license:gpl2+)))
1743 (define-public r-cghcall
1749 (uri (bioconductor-uri "CGHcall" version))
1751 (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s"))))
1752 (properties `((upstream-name . "CGHcall")))
1753 (build-system r-build-system)
1755 `(("r-biobase" ,r-biobase)
1756 ("r-cghbase" ,r-cghbase)
1757 ("r-impute" ,r-impute)
1758 ("r-dnacopy" ,r-dnacopy)
1759 ("r-snowfall" ,r-snowfall)))
1760 (home-page "https://bioconductor.org/packages/CGHcall")
1761 (synopsis "Base functions and classes for arrayCGH data analysis")
1762 (description "This package contains functions and classes that are needed by
1763 @code{arrayCGH} packages.")
1764 (license license:gpl2+)))
1766 (define-public r-qdnaseq
1772 (uri (bioconductor-uri "QDNAseq" version))
1774 (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq"))))
1775 (properties `((upstream-name . "QDNAseq")))
1776 (build-system r-build-system)
1778 `(("r-biobase" ,r-biobase)
1779 ("r-cghbase" ,r-cghbase)
1780 ("r-cghcall" ,r-cghcall)
1781 ("r-dnacopy" ,r-dnacopy)
1782 ("r-future" ,r-future)
1783 ("r-future-apply" ,r-future-apply)
1784 ("r-genomicranges" ,r-genomicranges)
1785 ("r-iranges" ,r-iranges)
1786 ("r-matrixstats" ,r-matrixstats)
1787 ("r-r-utils" ,r-r-utils)
1788 ("r-rsamtools" ,r-rsamtools)))
1789 (home-page "https://bioconductor.org/packages/QDNAseq")
1790 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1791 (description "The genome is divided into non-overlapping fixed-sized bins,
1792 number of sequence reads in each counted, adjusted with a simultaneous
1793 two-dimensional loess correction for sequence mappability and GC content, and
1794 filtered to remove spurious regions in the genome. Downstream steps of
1795 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1797 (license license:gpl2+)))
1799 (define-public r-bayseq
1806 (uri (bioconductor-uri "baySeq" version))
1809 "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk"))))
1810 (properties `((upstream-name . "baySeq")))
1811 (build-system r-build-system)
1813 `(("r-abind" ,r-abind)
1814 ("r-edger" ,r-edger)
1815 ("r-genomicranges" ,r-genomicranges)))
1816 (home-page "https://bioconductor.org/packages/baySeq/")
1817 (synopsis "Bayesian analysis of differential expression patterns in count data")
1819 "This package identifies differential expression in high-throughput count
1820 data, such as that derived from next-generation sequencing machines,
1821 calculating estimated posterior likelihoods of differential expression (or
1822 more complex hypotheses) via empirical Bayesian methods.")
1823 (license license:gpl3)))
1825 (define-public r-chipcomp
1832 (uri (bioconductor-uri "ChIPComp" version))
1835 "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg"))))
1836 (properties `((upstream-name . "ChIPComp")))
1837 (build-system r-build-system)
1839 `(("r-biocgenerics" ,r-biocgenerics)
1840 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1841 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1842 ("r-genomeinfodb" ,r-genomeinfodb)
1843 ("r-genomicranges" ,r-genomicranges)
1844 ("r-iranges" ,r-iranges)
1845 ("r-limma" ,r-limma)
1846 ("r-rsamtools" ,r-rsamtools)
1847 ("r-rtracklayer" ,r-rtracklayer)
1848 ("r-s4vectors" ,r-s4vectors)))
1849 (home-page "https://bioconductor.org/packages/ChIPComp")
1850 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1852 "ChIPComp implements a statistical method for quantitative comparison of
1853 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1854 sites across multiple conditions considering matching control in ChIP-seq
1856 ;; Any version of the GPL.
1857 (license license:gpl3+)))
1859 (define-public r-riboprofiling
1861 (name "r-riboprofiling")
1866 (uri (bioconductor-uri "RiboProfiling" version))
1869 "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx"))))
1870 (properties `((upstream-name . "RiboProfiling")))
1871 (build-system r-build-system)
1873 `(("r-biocgenerics" ,r-biocgenerics)
1874 ("r-biostrings" ,r-biostrings)
1875 ("r-data-table" ,r-data-table)
1876 ("r-genomeinfodb" ,r-genomeinfodb)
1877 ("r-genomicalignments" ,r-genomicalignments)
1878 ("r-genomicfeatures" ,r-genomicfeatures)
1879 ("r-genomicranges" ,r-genomicranges)
1880 ("r-ggbio" ,r-ggbio)
1881 ("r-ggplot2" ,r-ggplot2)
1882 ("r-iranges" ,r-iranges)
1884 ("r-reshape2" ,r-reshape2)
1885 ("r-rsamtools" ,r-rsamtools)
1886 ("r-rtracklayer" ,r-rtracklayer)
1887 ("r-s4vectors" ,r-s4vectors)
1888 ("r-sqldf" ,r-sqldf)))
1889 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1890 (synopsis "Ribosome profiling data analysis")
1891 (description "Starting with a BAM file, this package provides the
1892 necessary functions for quality assessment, read start position recalibration,
1893 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1894 of count data: pairs, log fold-change, codon frequency and coverage
1895 assessment, principal component analysis on codon coverage.")
1896 (license license:gpl3)))
1898 (define-public r-riboseqr
1905 (uri (bioconductor-uri "riboSeqR" version))
1908 "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm"))))
1909 (properties `((upstream-name . "riboSeqR")))
1910 (build-system r-build-system)
1912 `(("r-abind" ,r-abind)
1913 ("r-bayseq" ,r-bayseq)
1914 ("r-genomeinfodb" ,r-genomeinfodb)
1915 ("r-genomicranges" ,r-genomicranges)
1916 ("r-iranges" ,r-iranges)
1917 ("r-rsamtools" ,r-rsamtools)
1918 ("r-seqlogo" ,r-seqlogo)))
1919 (home-page "https://bioconductor.org/packages/riboSeqR/")
1920 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1922 "This package provides plotting functions, frameshift detection and
1923 parsing of genetic sequencing data from ribosome profiling experiments.")
1924 (license license:gpl3)))
1926 (define-public r-interactionset
1928 (name "r-interactionset")
1933 (uri (bioconductor-uri "InteractionSet" version))
1936 "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh"))))
1938 `((upstream-name . "InteractionSet")))
1939 (build-system r-build-system)
1941 `(("r-biocgenerics" ,r-biocgenerics)
1942 ("r-genomeinfodb" ,r-genomeinfodb)
1943 ("r-genomicranges" ,r-genomicranges)
1944 ("r-iranges" ,r-iranges)
1945 ("r-matrix" ,r-matrix)
1947 ("r-s4vectors" ,r-s4vectors)
1948 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1949 (home-page "https://bioconductor.org/packages/InteractionSet")
1950 (synopsis "Base classes for storing genomic interaction data")
1952 "This package provides the @code{GInteractions},
1953 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1954 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1956 (license license:gpl3)))
1958 (define-public r-genomicinteractions
1960 (name "r-genomicinteractions")
1965 (uri (bioconductor-uri "GenomicInteractions" version))
1968 "0mqb899wah5n7bp2lajhwy2zpqqhi18plza3i3m51rfl9n62smph"))))
1970 `((upstream-name . "GenomicInteractions")))
1971 (build-system r-build-system)
1973 `(("r-biobase" ,r-biobase)
1974 ("r-biocgenerics" ,r-biocgenerics)
1975 ("r-data-table" ,r-data-table)
1976 ("r-dplyr" ,r-dplyr)
1977 ("r-genomeinfodb" ,r-genomeinfodb)
1978 ("r-genomicranges" ,r-genomicranges)
1979 ("r-ggplot2" ,r-ggplot2)
1980 ("r-gridextra" ,r-gridextra)
1982 ("r-igraph" ,r-igraph)
1983 ("r-interactionset" ,r-interactionset)
1984 ("r-iranges" ,r-iranges)
1985 ("r-rsamtools" ,r-rsamtools)
1986 ("r-rtracklayer" ,r-rtracklayer)
1987 ("r-s4vectors" ,r-s4vectors)
1988 ("r-stringr" ,r-stringr)))
1990 `(("r-knitr" ,r-knitr)))
1991 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1992 (synopsis "R package for handling genomic interaction data")
1994 "This R package provides tools for handling genomic interaction data,
1995 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1996 information and producing various plots and statistics.")
1997 (license license:gpl3)))
1999 (define-public r-ctc
2006 (uri (bioconductor-uri "ctc" version))
2009 "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d"))))
2010 (build-system r-build-system)
2011 (propagated-inputs `(("r-amap" ,r-amap)))
2012 (home-page "https://bioconductor.org/packages/ctc/")
2013 (synopsis "Cluster and tree conversion")
2015 "This package provides tools for exporting and importing classification
2016 trees and clusters to other programs.")
2017 (license license:gpl2)))
2019 (define-public r-goseq
2026 (uri (bioconductor-uri "goseq" version))
2029 "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv"))))
2030 (build-system r-build-system)
2032 `(("r-annotationdbi" ,r-annotationdbi)
2033 ("r-biasedurn" ,r-biasedurn)
2034 ("r-biocgenerics" ,r-biocgenerics)
2035 ("r-genelendatabase" ,r-genelendatabase)
2036 ("r-go-db" ,r-go-db)
2037 ("r-mgcv" ,r-mgcv)))
2038 (home-page "https://bioconductor.org/packages/goseq/")
2039 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2041 "This package provides tools to detect Gene Ontology and/or other user
2042 defined categories which are over/under represented in RNA-seq data.")
2043 (license license:lgpl2.0+)))
2045 (define-public r-glimma
2052 (uri (bioconductor-uri "Glimma" version))
2055 "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r"))))
2056 (properties `((upstream-name . "Glimma")))
2057 (build-system r-build-system)
2059 `(("r-edger" ,r-edger)
2060 ("r-jsonlite" ,r-jsonlite)
2061 ("r-s4vectors" ,r-s4vectors)))
2062 (home-page "https://github.com/Shians/Glimma")
2063 (synopsis "Interactive HTML graphics")
2065 "This package generates interactive visualisations for analysis of
2066 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2067 HTML page. The interactions are built on top of the popular static
2068 representations of analysis results in order to provide additional
2070 (license license:lgpl3)))
2072 (define-public r-rots
2079 (uri (bioconductor-uri "ROTS" version))
2082 "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm"))))
2083 (properties `((upstream-name . "ROTS")))
2084 (build-system r-build-system)
2086 `(("r-biobase" ,r-biobase)
2087 ("r-rcpp" ,r-rcpp)))
2088 (home-page "https://bioconductor.org/packages/ROTS/")
2089 (synopsis "Reproducibility-Optimized Test Statistic")
2091 "This package provides tools for calculating the
2092 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2094 (license license:gpl2+)))
2096 (define-public r-plgem
2103 (uri (bioconductor-uri "plgem" version))
2106 "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v"))))
2107 (build-system r-build-system)
2109 `(("r-biobase" ,r-biobase)
2110 ("r-mass" ,r-mass)))
2111 (home-page "http://www.genopolis.it")
2112 (synopsis "Detect differential expression in microarray and proteomics datasets")
2114 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2115 model the variance-versus-mean dependence that exists in a variety of
2116 genome-wide datasets, including microarray and proteomics data. The use of
2117 PLGEM has been shown to improve the detection of differentially expressed
2118 genes or proteins in these datasets.")
2119 (license license:gpl2)))
2121 (define-public r-inspect
2128 (uri (bioconductor-uri "INSPEcT" version))
2131 "0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp"))))
2132 (properties `((upstream-name . "INSPEcT")))
2133 (build-system r-build-system)
2135 `(("r-biobase" ,r-biobase)
2136 ("r-biocgenerics" ,r-biocgenerics)
2137 ("r-biocparallel" ,r-biocparallel)
2138 ("r-deseq2" ,r-deseq2)
2139 ("r-desolve" ,r-desolve)
2140 ("r-gdata" ,r-gdata)
2141 ("r-genomeinfodb" ,r-genomeinfodb)
2142 ("r-genomicalignments" ,r-genomicalignments)
2143 ("r-genomicfeatures" ,r-genomicfeatures)
2144 ("r-genomicranges" ,r-genomicranges)
2145 ("r-iranges" ,r-iranges)
2146 ("r-kernsmooth" ,r-kernsmooth)
2147 ("r-plgem" ,r-plgem)
2149 ("r-rootsolve" ,r-rootsolve)
2150 ("r-rsamtools" ,r-rsamtools)
2151 ("r-s4vectors" ,r-s4vectors)
2152 ("r-shiny" ,r-shiny)
2153 ("r-summarizedexperiment" ,r-summarizedexperiment)
2154 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2155 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2156 (home-page "https://bioconductor.org/packages/INSPEcT")
2157 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2159 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2160 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2161 order to evaluate synthesis, processing and degradation rates and assess via
2162 modeling the rates that determines changes in mature mRNA levels.")
2163 (license license:gpl2)))
2165 (define-public r-dnabarcodes
2167 (name "r-dnabarcodes")
2172 (uri (bioconductor-uri "DNABarcodes" version))
2175 "0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd"))))
2176 (properties `((upstream-name . "DNABarcodes")))
2177 (build-system r-build-system)
2180 ("r-matrix" ,r-matrix)
2181 ("r-rcpp" ,r-rcpp)))
2182 (home-page "https://bioconductor.org/packages/DNABarcodes")
2183 (synopsis "Create and analyze DNA barcodes")
2185 "This package offers tools to create DNA barcode sets capable of
2186 correcting insertion, deletion, and substitution errors. Existing barcodes
2187 can be analyzed regarding their minimal, maximal and average distances between
2188 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2189 demultiplexed, i.e. assigned to their original reference barcode.")
2190 (license license:gpl2)))
2192 (define-public r-ruvseq
2199 (uri (bioconductor-uri "RUVSeq" version))
2202 "1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj"))))
2203 (properties `((upstream-name . "RUVSeq")))
2204 (build-system r-build-system)
2206 `(("r-biobase" ,r-biobase)
2207 ("r-edaseq" ,r-edaseq)
2208 ("r-edger" ,r-edger)
2209 ("r-mass" ,r-mass)))
2210 (home-page "https://github.com/drisso/RUVSeq")
2211 (synopsis "Remove unwanted variation from RNA-Seq data")
2213 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2214 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2216 (license license:artistic2.0)))
2218 (define-public r-biocneighbors
2220 (name "r-biocneighbors")
2225 (uri (bioconductor-uri "BiocNeighbors" version))
2228 "1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6"))))
2229 (properties `((upstream-name . "BiocNeighbors")))
2230 (build-system r-build-system)
2232 `(("r-biocparallel" ,r-biocparallel)
2233 ("r-matrix" ,r-matrix)
2235 ("r-rcppannoy" ,r-rcppannoy)
2236 ("r-rcpphnsw" ,r-rcpphnsw)
2237 ("r-s4vectors" ,r-s4vectors)))
2238 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2239 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2241 "This package implements exact and approximate methods for nearest
2242 neighbor detection, in a framework that allows them to be easily switched
2243 within Bioconductor packages or workflows. The exact algorithm is implemented
2244 using pre-clustering with the k-means algorithm. Functions are also provided
2245 to search for all neighbors within a given distance. Parallelization is
2246 achieved for all methods using the BiocParallel framework.")
2247 (license license:gpl3)))
2249 (define-public r-biocsingular
2251 (name "r-biocsingular")
2256 (uri (bioconductor-uri "BiocSingular" version))
2259 "1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407"))))
2260 (properties `((upstream-name . "BiocSingular")))
2261 (build-system r-build-system)
2263 `(("r-beachmat" ,r-beachmat)
2264 ("r-biocgenerics" ,r-biocgenerics)
2265 ("r-biocparallel" ,r-biocparallel)
2266 ("r-delayedarray" ,r-delayedarray)
2267 ("r-irlba" ,r-irlba)
2268 ("r-matrix" ,r-matrix)
2271 ("r-s4vectors" ,r-s4vectors)))
2272 (home-page "https://github.com/LTLA/BiocSingular")
2273 (synopsis "Singular value decomposition for Bioconductor packages")
2275 "This package implements exact and approximate methods for singular value
2276 decomposition and principal components analysis, in a framework that allows
2277 them to be easily switched within Bioconductor packages or workflows. Where
2278 possible, parallelization is achieved using the BiocParallel framework.")
2279 (license license:gpl3)))
2281 (define-public r-destiny
2288 (uri (bioconductor-uri "destiny" version))
2291 "1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi"))))
2292 (build-system r-build-system)
2294 `(("r-biobase" ,r-biobase)
2295 ("r-biocgenerics" ,r-biocgenerics)
2296 ("r-ggplot-multistats" ,r-ggplot-multistats)
2297 ("r-ggplot2" ,r-ggplot2)
2298 ("r-ggthemes" ,r-ggthemes)
2299 ("r-irlba" ,r-irlba)
2300 ("r-knn-covertree" ,r-knn-covertree)
2301 ("r-matrix" ,r-matrix)
2302 ("r-pcamethods" ,r-pcamethods)
2303 ("r-proxy" ,r-proxy)
2305 ("r-rcppeigen" ,r-rcppeigen)
2306 ("r-rcpphnsw" ,r-rcpphnsw)
2307 ("r-rspectra" ,r-rspectra)
2308 ("r-scales" ,r-scales)
2309 ("r-scatterplot3d" ,r-scatterplot3d)
2310 ("r-singlecellexperiment" ,r-singlecellexperiment)
2311 ("r-smoother" ,r-smoother)
2312 ("r-summarizedexperiment" ,r-summarizedexperiment)
2313 ("r-tidyr" ,r-tidyr)
2314 ("r-tidyselect" ,r-tidyselect)
2316 (home-page "https://bioconductor.org/packages/destiny/")
2317 (synopsis "Create and plot diffusion maps")
2318 (description "This package provides tools to create and plot diffusion
2320 ;; Any version of the GPL
2321 (license license:gpl3+)))
2323 (define-public r-savr
2330 (uri (bioconductor-uri "savR" version))
2333 "1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf"))))
2334 (properties `((upstream-name . "savR")))
2335 (build-system r-build-system)
2337 `(("r-ggplot2" ,r-ggplot2)
2338 ("r-gridextra" ,r-gridextra)
2339 ("r-reshape2" ,r-reshape2)
2340 ("r-scales" ,r-scales)
2342 (home-page "https://github.com/bcalder/savR")
2343 (synopsis "Parse and analyze Illumina SAV files")
2345 "This package provides tools to parse Illumina Sequence Analysis
2346 Viewer (SAV) files, access data, and generate QC plots.")
2347 (license license:agpl3+)))
2349 (define-public r-chipexoqual
2351 (name "r-chipexoqual")
2356 (uri (bioconductor-uri "ChIPexoQual" version))
2359 "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0"))))
2360 (properties `((upstream-name . "ChIPexoQual")))
2361 (build-system r-build-system)
2363 `(("r-biocparallel" ,r-biocparallel)
2364 ("r-biovizbase" ,r-biovizbase)
2365 ("r-broom" ,r-broom)
2366 ("r-data-table" ,r-data-table)
2367 ("r-dplyr" ,r-dplyr)
2368 ("r-genomeinfodb" ,r-genomeinfodb)
2369 ("r-genomicalignments" ,r-genomicalignments)
2370 ("r-genomicranges" ,r-genomicranges)
2371 ("r-ggplot2" ,r-ggplot2)
2372 ("r-hexbin" ,r-hexbin)
2373 ("r-iranges" ,r-iranges)
2374 ("r-rcolorbrewer" ,r-rcolorbrewer)
2375 ("r-rmarkdown" ,r-rmarkdown)
2376 ("r-rsamtools" ,r-rsamtools)
2377 ("r-s4vectors" ,r-s4vectors)
2378 ("r-scales" ,r-scales)
2379 ("r-viridis" ,r-viridis)))
2380 (home-page "https://github.com/keleslab/ChIPexoQual")
2381 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2383 "This package provides a quality control pipeline for ChIP-exo/nexus
2385 (license license:gpl2+)))
2387 (define-public r-copynumber
2389 (name "r-copynumber")
2393 (uri (bioconductor-uri "copynumber" version))
2396 "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj"))))
2397 (build-system r-build-system)
2399 `(("r-s4vectors" ,r-s4vectors)
2400 ("r-iranges" ,r-iranges)
2401 ("r-genomicranges" ,r-genomicranges)
2402 ("r-biocgenerics" ,r-biocgenerics)))
2403 (home-page "https://bioconductor.org/packages/copynumber")
2404 (synopsis "Segmentation of single- and multi-track copy number data")
2406 "This package segments single- and multi-track copy number data by a
2407 penalized least squares regression method.")
2408 (license license:artistic2.0)))
2410 (define-public r-dnacopy
2417 (uri (bioconductor-uri "DNAcopy" version))
2420 "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw"))))
2421 (properties `((upstream-name . "DNAcopy")))
2422 (build-system r-build-system)
2423 (native-inputs `(("gfortran" ,gfortran)))
2424 (home-page "https://bioconductor.org/packages/DNAcopy")
2425 (synopsis "DNA copy number data analysis")
2427 "This package implements the @dfn{circular binary segmentation} (CBS)
2428 algorithm to segment DNA copy number data and identify genomic regions with
2429 abnormal copy number.")
2430 (license license:gpl2+)))
2432 ;; This is a CRAN package, but it uncharacteristically depends on a
2433 ;; Bioconductor package.
2434 (define-public r-htscluster
2436 (name "r-htscluster")
2441 (uri (cran-uri "HTSCluster" version))
2444 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2445 (properties `((upstream-name . "HTSCluster")))
2446 (build-system r-build-system)
2448 `(("r-capushe" ,r-capushe)
2449 ("r-edger" ,r-edger)
2450 ("r-plotrix" ,r-plotrix)))
2451 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2452 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2454 "This package provides a Poisson mixture model is implemented to cluster
2455 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2456 estimation is performed using either the EM or CEM algorithm, and the slope
2457 heuristics are used for model selection (i.e., to choose the number of
2459 (license license:gpl3+)))
2461 (define-public r-deds
2468 (uri (bioconductor-uri "DEDS" version))
2471 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2472 (properties `((upstream-name . "DEDS")))
2473 (build-system r-build-system)
2474 (home-page "https://bioconductor.org/packages/DEDS/")
2475 (synopsis "Differential expression via distance summary for microarray data")
2477 "This library contains functions that calculate various statistics of
2478 differential expression for microarray data, including t statistics, fold
2479 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2480 also implements a new methodology called DEDS (Differential Expression via
2481 Distance Summary), which selects differentially expressed genes by integrating
2482 and summarizing a set of statistics using a weighted distance approach.")
2483 ;; Any version of the LGPL.
2484 (license license:lgpl3+)))
2486 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2488 (define-public r-nbpseq
2495 (uri (cran-uri "NBPSeq" version))
2498 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2499 (properties `((upstream-name . "NBPSeq")))
2500 (build-system r-build-system)
2502 `(("r-qvalue" ,r-qvalue)))
2503 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2504 (synopsis "Negative binomial models for RNA-Seq data")
2506 "This package provides negative binomial models for two-group comparisons
2507 and regression inferences from RNA-sequencing data.")
2508 (license license:gpl2)))
2510 (define-public r-ebseq
2517 (uri (bioconductor-uri "EBSeq" version))
2520 "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6"))))
2521 (properties `((upstream-name . "EBSeq")))
2522 (build-system r-build-system)
2524 `(("r-blockmodeling" ,r-blockmodeling)
2525 ("r-gplots" ,r-gplots)
2526 ("r-testthat" ,r-testthat)))
2527 (home-page "https://bioconductor.org/packages/EBSeq")
2528 (synopsis "Differential expression analysis of RNA-seq data")
2530 "This package provides tools for differential expression analysis at both
2531 gene and isoform level using RNA-seq data")
2532 (license license:artistic2.0)))
2534 (define-public r-lpsymphony
2536 (name "r-lpsymphony")
2541 (uri (bioconductor-uri "lpsymphony" version))
2544 "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv"))))
2545 (build-system r-build-system)
2547 `(("gfortran" ,gfortran)
2550 `(("pkg-config" ,pkg-config)))
2551 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2552 (synopsis "Symphony integer linear programming solver in R")
2554 "This package was derived from Rsymphony. The package provides an R
2555 interface to SYMPHONY, a linear programming solver written in C++. The main
2556 difference between this package and Rsymphony is that it includes the solver
2557 source code, while Rsymphony expects to find header and library files on the
2558 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2559 to install interface to SYMPHONY.")
2560 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2561 ;; lpsimphony is released under the same terms.
2562 (license license:epl1.0)))
2564 (define-public r-ihw
2571 (uri (bioconductor-uri "IHW" version))
2574 "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x"))))
2575 (properties `((upstream-name . "IHW")))
2576 (build-system r-build-system)
2578 `(("r-biocgenerics" ,r-biocgenerics)
2579 ("r-fdrtool" ,r-fdrtool)
2580 ("r-lpsymphony" ,r-lpsymphony)
2581 ("r-slam" ,r-slam)))
2582 (home-page "https://bioconductor.org/packages/IHW")
2583 (synopsis "Independent hypothesis weighting")
2585 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2586 procedure that increases power compared to the method of Benjamini and
2587 Hochberg by assigning data-driven weights to each hypothesis. The input to
2588 IHW is a two-column table of p-values and covariates. The covariate can be
2589 any continuous-valued or categorical variable that is thought to be
2590 informative on the statistical properties of each hypothesis test, while it is
2591 independent of the p-value under the null hypothesis.")
2592 (license license:artistic2.0)))
2594 (define-public r-icobra
2601 (uri (bioconductor-uri "iCOBRA" version))
2604 "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz"))))
2605 (properties `((upstream-name . "iCOBRA")))
2606 (build-system r-build-system)
2608 `(("r-dplyr" ,r-dplyr)
2610 ("r-ggplot2" ,r-ggplot2)
2611 ("r-limma" ,r-limma)
2612 ("r-reshape2" ,r-reshape2)
2614 ("r-scales" ,r-scales)
2615 ("r-shiny" ,r-shiny)
2616 ("r-shinybs" ,r-shinybs)
2617 ("r-shinydashboard" ,r-shinydashboard)
2618 ("r-upsetr" ,r-upsetr)))
2619 (home-page "https://bioconductor.org/packages/iCOBRA")
2620 (synopsis "Comparison and visualization of ranking and assignment methods")
2622 "This package provides functions for calculation and visualization of
2623 performance metrics for evaluation of ranking and binary
2624 classification (assignment) methods. It also contains a Shiny application for
2625 interactive exploration of results.")
2626 (license license:gpl2+)))
2628 (define-public r-mast
2635 (uri (bioconductor-uri "MAST" version))
2638 "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga"))))
2639 (properties `((upstream-name . "MAST")))
2640 (build-system r-build-system)
2642 `(("r-abind" ,r-abind)
2643 ("r-biobase" ,r-biobase)
2644 ("r-biocgenerics" ,r-biocgenerics)
2645 ("r-data-table" ,r-data-table)
2646 ("r-ggplot2" ,r-ggplot2)
2648 ("r-progress" ,r-progress)
2649 ("r-reshape2" ,r-reshape2)
2650 ("r-s4vectors" ,r-s4vectors)
2651 ("r-singlecellexperiment" ,r-singlecellexperiment)
2652 ("r-stringr" ,r-stringr)
2653 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2655 `(("r-knitr" ,r-knitr)))
2656 (home-page "https://github.com/RGLab/MAST/")
2657 (synopsis "Model-based analysis of single cell transcriptomics")
2659 "This package provides methods and models for handling zero-inflated
2660 single cell assay data.")
2661 (license license:gpl2+)))
2663 (define-public r-monocle
2670 (uri (bioconductor-uri "monocle" version))
2673 "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2"))))
2674 (build-system r-build-system)
2676 `(("r-biobase" ,r-biobase)
2677 ("r-biocgenerics" ,r-biocgenerics)
2678 ("r-biocviews" ,r-biocviews)
2679 ("r-cluster" ,r-cluster)
2680 ("r-combinat" ,r-combinat)
2681 ("r-ddrtree" ,r-ddrtree)
2682 ("r-densityclust" ,r-densityclust)
2683 ("r-dplyr" ,r-dplyr)
2684 ("r-fastica" ,r-fastica)
2685 ("r-ggplot2" ,r-ggplot2)
2686 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2687 ("r-igraph" ,r-igraph)
2688 ("r-irlba" ,r-irlba)
2689 ("r-limma" ,r-limma)
2691 ("r-matrix" ,r-matrix)
2692 ("r-matrixstats" ,r-matrixstats)
2693 ("r-pheatmap" ,r-pheatmap)
2695 ("r-proxy" ,r-proxy)
2696 ("r-qlcmatrix" ,r-qlcmatrix)
2699 ("r-reshape2" ,r-reshape2)
2700 ("r-rtsne" ,r-rtsne)
2702 ("r-stringr" ,r-stringr)
2703 ("r-tibble" ,r-tibble)
2705 ("r-viridis" ,r-viridis)))
2706 (home-page "https://bioconductor.org/packages/monocle")
2707 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2709 "Monocle performs differential expression and time-series analysis for
2710 single-cell expression experiments. It orders individual cells according to
2711 progress through a biological process, without knowing ahead of time which
2712 genes define progress through that process. Monocle also performs
2713 differential expression analysis, clustering, visualization, and other useful
2714 tasks on single cell expression data. It is designed to work with RNA-Seq and
2715 qPCR data, but could be used with other types as well.")
2716 (license license:artistic2.0)))
2718 (define-public r-monocle3
2726 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2728 (file-name (git-file-name name version))
2731 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2732 (build-system r-build-system)
2734 `(("r-biobase" ,r-biobase)
2735 ("r-biocgenerics" ,r-biocgenerics)
2736 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2737 ("r-dplyr" ,r-dplyr)
2738 ("r-ggplot2" ,r-ggplot2)
2739 ("r-ggrepel" ,r-ggrepel)
2741 ("r-htmlwidgets" ,r-htmlwidgets)
2742 ("r-igraph" ,r-igraph)
2743 ("r-irlba" ,r-irlba)
2744 ("r-limma" ,r-limma)
2745 ("r-lmtest" ,r-lmtest)
2747 ("r-matrix" ,r-matrix)
2748 ("r-matrix-utils" ,r-matrix-utils)
2749 ("r-pbapply" ,r-pbapply)
2750 ("r-pbmcapply" ,r-pbmcapply)
2751 ("r-pheatmap" ,r-pheatmap)
2752 ("r-plotly" ,r-plotly)
2754 ("r-proxy" ,r-proxy)
2756 ("r-purrr" ,r-purrr)
2759 ("r-rcppparallel" ,r-rcppparallel)
2760 ("r-reshape2" ,r-reshape2)
2761 ("r-reticulate" ,r-reticulate)
2762 ("r-rhpcblasctl" ,r-rhpcblasctl)
2763 ("r-rtsne" ,r-rtsne)
2764 ("r-shiny" ,r-shiny)
2766 ("r-spdep" ,r-spdep)
2767 ("r-speedglm" ,r-speedglm)
2768 ("r-stringr" ,r-stringr)
2769 ("r-singlecellexperiment" ,r-singlecellexperiment)
2770 ("r-tibble" ,r-tibble)
2771 ("r-tidyr" ,r-tidyr)
2773 ("r-viridis" ,r-viridis)))
2774 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2775 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2777 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2778 (license license:expat)))
2780 (define-public r-noiseq
2787 (uri (bioconductor-uri "NOISeq" version))
2790 "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4"))))
2791 (properties `((upstream-name . "NOISeq")))
2792 (build-system r-build-system)
2794 `(("r-biobase" ,r-biobase)
2795 ("r-matrix" ,r-matrix)))
2796 (home-page "https://bioconductor.org/packages/NOISeq")
2797 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2799 "This package provides tools to support the analysis of RNA-seq
2800 expression data or other similar kind of data. It provides exploratory plots
2801 to evaluate saturation, count distribution, expression per chromosome, type of
2802 detected features, features length, etc. It also supports the analysis of
2803 differential expression between two experimental conditions with no parametric
2805 (license license:artistic2.0)))
2807 (define-public r-scdd
2814 (uri (bioconductor-uri "scDD" version))
2817 "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4"))))
2818 (properties `((upstream-name . "scDD")))
2819 (build-system r-build-system)
2822 ("r-biocparallel" ,r-biocparallel)
2823 ("r-ebseq" ,r-ebseq)
2824 ("r-fields" ,r-fields)
2825 ("r-ggplot2" ,r-ggplot2)
2826 ("r-mclust" ,r-mclust)
2827 ("r-outliers" ,r-outliers)
2828 ("r-s4vectors" ,r-s4vectors)
2829 ("r-scran" ,r-scran)
2830 ("r-singlecellexperiment" ,r-singlecellexperiment)
2831 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2832 (home-page "https://github.com/kdkorthauer/scDD")
2833 (synopsis "Mixture modeling of single-cell RNA-seq data")
2835 "This package implements a method to analyze single-cell RNA-seq data
2836 utilizing flexible Dirichlet Process mixture models. Genes with differential
2837 distributions of expression are classified into several interesting patterns
2838 of differences between two conditions. The package also includes functions
2839 for simulating data with these patterns from negative binomial
2841 (license license:gpl2)))
2843 (define-public r-scone
2850 (uri (bioconductor-uri "scone" version))
2853 "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp"))))
2854 (build-system r-build-system)
2856 `(("r-aroma-light" ,r-aroma-light)
2857 ("r-biocparallel" ,r-biocparallel)
2859 ("r-class" ,r-class)
2860 ("r-cluster" ,r-cluster)
2861 ("r-compositions" ,r-compositions)
2862 ("r-diptest" ,r-diptest)
2863 ("r-edger" ,r-edger)
2865 ("r-gplots" ,r-gplots)
2866 ("r-hexbin" ,r-hexbin)
2867 ("r-limma" ,r-limma)
2868 ("r-matrixstats" ,r-matrixstats)
2869 ("r-mixtools" ,r-mixtools)
2870 ("r-rarpack" ,r-rarpack)
2871 ("r-rcolorbrewer" ,r-rcolorbrewer)
2872 ("r-rhdf5" ,r-rhdf5)
2873 ("r-ruvseq" ,r-ruvseq)
2874 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2875 (home-page "https://bioconductor.org/packages/scone")
2876 (synopsis "Single cell overview of normalized expression data")
2878 "SCONE is an R package for comparing and ranking the performance of
2879 different normalization schemes for single-cell RNA-seq and other
2880 high-throughput analyses.")
2881 (license license:artistic2.0)))
2883 (define-public r-geoquery
2890 (uri (bioconductor-uri "GEOquery" version))
2893 "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5"))))
2894 (properties `((upstream-name . "GEOquery")))
2895 (build-system r-build-system)
2897 `(("r-biobase" ,r-biobase)
2898 ("r-dplyr" ,r-dplyr)
2900 ("r-limma" ,r-limma)
2901 ("r-magrittr" ,r-magrittr)
2902 ("r-readr" ,r-readr)
2903 ("r-tidyr" ,r-tidyr)
2904 ("r-xml2" ,r-xml2)))
2905 (home-page "https://github.com/seandavi/GEOquery/")
2906 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2908 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2909 microarray data. Given the rich and varied nature of this resource, it is
2910 only natural to want to apply BioConductor tools to these data. GEOquery is
2911 the bridge between GEO and BioConductor.")
2912 (license license:gpl2)))
2914 (define-public r-illuminaio
2916 (name "r-illuminaio")
2921 (uri (bioconductor-uri "illuminaio" version))
2924 "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh"))))
2925 (build-system r-build-system)
2927 `(("r-base64" ,r-base64)))
2928 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2929 (synopsis "Parse Illumina microarray output files")
2931 "This package provides tools for parsing Illumina's microarray output
2932 files, including IDAT.")
2933 (license license:gpl2)))
2935 (define-public r-siggenes
2942 (uri (bioconductor-uri "siggenes" version))
2945 "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4"))))
2946 (build-system r-build-system)
2948 `(("r-biobase" ,r-biobase)
2949 ("r-multtest" ,r-multtest)
2950 ("r-scrime" ,r-scrime)))
2951 (home-page "https://bioconductor.org/packages/siggenes/")
2953 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2955 "This package provides tools for the identification of differentially
2956 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2957 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2958 Bayes Analyses of Microarrays} (EBAM).")
2959 (license license:lgpl2.0+)))
2961 (define-public r-bumphunter
2963 (name "r-bumphunter")
2968 (uri (bioconductor-uri "bumphunter" version))
2971 "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv"))))
2972 (build-system r-build-system)
2974 `(("r-annotationdbi" ,r-annotationdbi)
2975 ("r-biocgenerics" ,r-biocgenerics)
2976 ("r-dorng" ,r-dorng)
2977 ("r-foreach" ,r-foreach)
2978 ("r-genomeinfodb" ,r-genomeinfodb)
2979 ("r-genomicfeatures" ,r-genomicfeatures)
2980 ("r-genomicranges" ,r-genomicranges)
2981 ("r-iranges" ,r-iranges)
2982 ("r-iterators" ,r-iterators)
2983 ("r-limma" ,r-limma)
2984 ("r-locfit" ,r-locfit)
2985 ("r-matrixstats" ,r-matrixstats)
2986 ("r-s4vectors" ,r-s4vectors)))
2987 (home-page "https://github.com/ririzarr/bumphunter")
2988 (synopsis "Find bumps in genomic data")
2990 "This package provides tools for finding bumps in genomic data in order
2991 to identify differentially methylated regions in epigenetic epidemiology
2993 (license license:artistic2.0)))
2995 (define-public r-minfi
3002 (uri (bioconductor-uri "minfi" version))
3005 "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3"))))
3006 (build-system r-build-system)
3008 `(("r-beanplot" ,r-beanplot)
3009 ("r-biobase" ,r-biobase)
3010 ("r-biocgenerics" ,r-biocgenerics)
3011 ("r-biocparallel" ,r-biocparallel)
3012 ("r-biostrings" ,r-biostrings)
3013 ("r-bumphunter" ,r-bumphunter)
3014 ("r-data-table" ,r-data-table)
3015 ("r-delayedarray" ,r-delayedarray)
3016 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3017 ("r-genefilter" ,r-genefilter)
3018 ("r-genomeinfodb" ,r-genomeinfodb)
3019 ("r-genomicranges" ,r-genomicranges)
3020 ("r-geoquery" ,r-geoquery)
3021 ("r-hdf5array" ,r-hdf5array)
3022 ("r-illuminaio" ,r-illuminaio)
3023 ("r-iranges" ,r-iranges)
3024 ("r-lattice" ,r-lattice)
3025 ("r-limma" ,r-limma)
3027 ("r-mclust" ,r-mclust)
3029 ("r-nor1mix" ,r-nor1mix)
3030 ("r-preprocesscore" ,r-preprocesscore)
3031 ("r-quadprog" ,r-quadprog)
3032 ("r-rcolorbrewer" ,r-rcolorbrewer)
3033 ("r-reshape" ,r-reshape)
3034 ("r-s4vectors" ,r-s4vectors)
3035 ("r-siggenes" ,r-siggenes)
3036 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3037 (home-page "https://github.com/hansenlab/minfi")
3038 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3040 "This package provides tools to analyze and visualize Illumina Infinium
3041 methylation arrays.")
3042 (license license:artistic2.0)))
3044 (define-public r-methylumi
3046 (name "r-methylumi")
3051 (uri (bioconductor-uri "methylumi" version))
3054 "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w"))))
3055 (build-system r-build-system)
3057 `(("r-annotate" ,r-annotate)
3058 ("r-annotationdbi" ,r-annotationdbi)
3059 ("r-biobase" ,r-biobase)
3060 ("r-biocgenerics" ,r-biocgenerics)
3061 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3062 ("r-genefilter" ,r-genefilter)
3063 ("r-genomeinfodb" ,r-genomeinfodb)
3064 ("r-genomicranges" ,r-genomicranges)
3065 ("r-ggplot2" ,r-ggplot2)
3066 ("r-illuminaio" ,r-illuminaio)
3067 ("r-iranges" ,r-iranges)
3068 ("r-lattice" ,r-lattice)
3069 ("r-matrixstats" ,r-matrixstats)
3070 ("r-minfi" ,r-minfi)
3071 ("r-reshape2" ,r-reshape2)
3072 ("r-s4vectors" ,r-s4vectors)
3073 ("r-scales" ,r-scales)
3074 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3075 (home-page "https://bioconductor.org/packages/methylumi")
3076 (synopsis "Handle Illumina methylation data")
3078 "This package provides classes for holding and manipulating Illumina
3079 methylation data. Based on eSet, it can contain MIAME information, sample
3080 information, feature information, and multiple matrices of data. An
3081 \"intelligent\" import function, methylumiR can read the Illumina text files
3082 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3083 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3084 background correction, and quality control features for GoldenGate, Infinium,
3085 and Infinium HD arrays are also included.")
3086 (license license:gpl2)))
3088 (define-public r-lumi
3095 (uri (bioconductor-uri "lumi" version))
3098 "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm"))))
3099 (build-system r-build-system)
3101 `(("r-affy" ,r-affy)
3102 ("r-annotate" ,r-annotate)
3103 ("r-annotationdbi" ,r-annotationdbi)
3104 ("r-biobase" ,r-biobase)
3106 ("r-genomicfeatures" ,r-genomicfeatures)
3107 ("r-genomicranges" ,r-genomicranges)
3108 ("r-kernsmooth" ,r-kernsmooth)
3109 ("r-lattice" ,r-lattice)
3111 ("r-methylumi" ,r-methylumi)
3113 ("r-nleqslv" ,r-nleqslv)
3114 ("r-preprocesscore" ,r-preprocesscore)
3115 ("r-rsqlite" ,r-rsqlite)))
3116 (home-page "https://bioconductor.org/packages/lumi")
3117 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3119 "The lumi package provides an integrated solution for the Illumina
3120 microarray data analysis. It includes functions of Illumina
3121 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3122 variance stabilization, normalization and gene annotation at the probe level.
3123 It also includes the functions of processing Illumina methylation microarrays,
3124 especially Illumina Infinium methylation microarrays.")
3125 (license license:lgpl2.0+)))
3127 (define-public r-linnorm
3134 (uri (bioconductor-uri "Linnorm" version))
3137 "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67"))))
3138 (properties `((upstream-name . "Linnorm")))
3139 (build-system r-build-system)
3141 `(("r-amap" ,r-amap)
3142 ("r-apcluster" ,r-apcluster)
3143 ("r-ellipse" ,r-ellipse)
3144 ("r-fastcluster" ,r-fastcluster)
3146 ("r-ggdendro" ,r-ggdendro)
3147 ("r-ggplot2" ,r-ggplot2)
3148 ("r-gmodels" ,r-gmodels)
3149 ("r-igraph" ,r-igraph)
3150 ("r-limma" ,r-limma)
3152 ("r-mclust" ,r-mclust)
3154 ("r-rcpparmadillo" ,r-rcpparmadillo)
3155 ("r-rtsne" ,r-rtsne)
3156 ("r-statmod" ,r-statmod)
3157 ("r-vegan" ,r-vegan)
3159 (home-page "http://www.jjwanglab.org/Linnorm/")
3160 (synopsis "Linear model and normality based transformation method")
3162 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3163 count data or any large scale count data. It transforms such datasets for
3164 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3165 the following pipelines are implemented:
3168 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3169 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3170 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3171 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3172 @item Differential expression analysis or differential peak detection using
3173 limma (@code{Linnorm.limma})
3174 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3175 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3176 @item Stable gene selection for scRNA-seq data; for users without or who do
3177 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3178 @item Data imputation (@code{Linnorm.DataImput}).
3181 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3182 @code{RnaXSim} function is included for simulating RNA-seq data for the
3183 evaluation of DEG analysis methods.")
3184 (license license:expat)))
3186 (define-public r-ioniser
3193 (uri (bioconductor-uri "IONiseR" version))
3196 "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f"))))
3197 (properties `((upstream-name . "IONiseR")))
3198 (build-system r-build-system)
3200 `(("r-biocgenerics" ,r-biocgenerics)
3201 ("r-biocparallel" ,r-biocparallel)
3202 ("r-biostrings" ,r-biostrings)
3203 ("r-bit64" ,r-bit64)
3204 ("r-dplyr" ,r-dplyr)
3205 ("r-ggplot2" ,r-ggplot2)
3206 ("r-magrittr" ,r-magrittr)
3207 ("r-rhdf5" ,r-rhdf5)
3208 ("r-shortread" ,r-shortread)
3209 ("r-stringr" ,r-stringr)
3210 ("r-tibble" ,r-tibble)
3211 ("r-tidyr" ,r-tidyr)
3212 ("r-xvector" ,r-xvector)))
3213 (home-page "https://bioconductor.org/packages/IONiseR/")
3214 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3216 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3217 MinION data. It extracts summary statistics from a set of fast5 files and can
3218 be used either before or after base calling. In addition to standard
3219 summaries of the read-types produced, it provides a number of plots for
3220 visualising metrics relative to experiment run time or spatially over the
3221 surface of a flowcell.")
3222 (license license:expat)))
3224 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3225 (define-public r-gkmsvm
3232 (uri (cran-uri "gkmSVM" version))
3235 "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p"))))
3236 (properties `((upstream-name . "gkmSVM")))
3237 (build-system r-build-system)
3239 `(("r-kernlab" ,r-kernlab)
3242 ("r-seqinr" ,r-seqinr)))
3243 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3244 (synopsis "Gapped-kmer support vector machine")
3246 "This R package provides tools for training gapped-kmer SVM classifiers
3247 for DNA and protein sequences. This package supports several sequence
3248 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3249 (license license:gpl2+)))
3251 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3252 (define-public r-mutoss
3259 (uri (cran-uri "mutoss" version))
3262 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3263 (properties `((upstream-name . "mutoss")))
3264 (build-system r-build-system)
3266 `(("r-multcomp" ,r-multcomp)
3267 ("r-multtest" ,r-multtest)
3268 ("r-mvtnorm" ,r-mvtnorm)
3269 ("r-plotrix" ,r-plotrix)))
3270 (home-page "https://github.com/kornl/mutoss/")
3271 (synopsis "Unified multiple testing procedures")
3273 "This package is designed to ease the application and comparison of
3274 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3275 are standardized and usable by the accompanying mutossGUI package.")
3276 ;; Any version of the GPL.
3277 (license (list license:gpl2+ license:gpl3+))))
3279 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3280 ;; from Bioconductor, so we put it here.
3281 (define-public r-metap
3288 (uri (cran-uri "metap" version))
3291 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3292 (build-system r-build-system)
3294 `(("r-lattice" ,r-lattice)
3295 ("r-mutoss" ,r-mutoss)
3296 ("r-rdpack" ,r-rdpack)
3297 ("r-tfisher" ,r-tfisher)))
3298 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3299 (synopsis "Meta-analysis of significance values")
3301 "The canonical way to perform meta-analysis involves using effect sizes.
3302 When they are not available this package provides a number of methods for
3303 meta-analysis of significance values including the methods of Edgington,
3304 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3305 published results; and a routine for graphical display.")
3306 (license license:gpl2)))
3308 (define-public r-triform
3315 (uri (bioconductor-uri "triform" version))
3318 "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9"))))
3319 (build-system r-build-system)
3321 `(("r-biocgenerics" ,r-biocgenerics)
3322 ("r-iranges" ,r-iranges)
3323 ("r-yaml" ,r-yaml)))
3324 (home-page "https://bioconductor.org/packages/triform/")
3325 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3327 "The Triform algorithm uses model-free statistics to identify peak-like
3328 distributions of TF ChIP sequencing reads, taking advantage of an improved
3329 peak definition in combination with known profile characteristics.")
3330 (license license:gpl2)))
3332 (define-public r-varianttools
3334 (name "r-varianttools")
3339 (uri (bioconductor-uri "VariantTools" version))
3342 "0aafcprsqbn1xl8jqnxfl8r2d0lmzhssqpr26lam2cprh3yk0xiv"))))
3343 (properties `((upstream-name . "VariantTools")))
3344 (build-system r-build-system)
3346 `(("r-biobase" ,r-biobase)
3347 ("r-biocgenerics" ,r-biocgenerics)
3348 ("r-biocparallel" ,r-biocparallel)
3349 ("r-biostrings" ,r-biostrings)
3350 ("r-bsgenome" ,r-bsgenome)
3351 ("r-genomeinfodb" ,r-genomeinfodb)
3352 ("r-genomicfeatures" ,r-genomicfeatures)
3353 ("r-genomicranges" ,r-genomicranges)
3354 ("r-iranges" ,r-iranges)
3355 ("r-matrix" ,r-matrix)
3356 ("r-rsamtools" ,r-rsamtools)
3357 ("r-rtracklayer" ,r-rtracklayer)
3358 ("r-s4vectors" ,r-s4vectors)
3359 ("r-variantannotation" ,r-variantannotation)))
3360 (home-page "https://bioconductor.org/packages/VariantTools/")
3361 (synopsis "Tools for exploratory analysis of variant calls")
3363 "Explore, diagnose, and compare variant calls using filters. The
3364 VariantTools package supports a workflow for loading data, calling single
3365 sample variants and tumor-specific somatic mutations or other sample-specific
3366 variant types (e.g., RNA editing). Most of the functions operate on
3367 alignments (BAM files) or datasets of called variants. The user is expected
3368 to have already aligned the reads with a separate tool, e.g., GSNAP via
3370 (license license:artistic2.0)))
3372 (define-public r-heatplus
3379 (uri (bioconductor-uri "Heatplus" version))
3382 "1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1"))))
3383 (properties `((upstream-name . "Heatplus")))
3384 (build-system r-build-system)
3386 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3387 (home-page "https://github.com/alexploner/Heatplus")
3388 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3390 "This package provides tools to display a rectangular heatmap (intensity
3391 plot) of a data matrix. By default, both samples (columns) and features (row)
3392 of the matrix are sorted according to a hierarchical clustering, and the
3393 corresponding dendrogram is plotted. Optionally, panels with additional
3394 information about samples and features can be added to the plot.")
3395 (license license:gpl2+)))
3397 (define-public r-gosemsim
3404 (uri (bioconductor-uri "GOSemSim" version))
3407 "1r8yx6qw6d6602cp8aspzl3shi1l1zqcrc8fm9d5wg01sw1whs05"))))
3408 (properties `((upstream-name . "GOSemSim")))
3409 (build-system r-build-system)
3411 `(("r-annotationdbi" ,r-annotationdbi)
3412 ("r-go-db" ,r-go-db)
3413 ("r-rcpp" ,r-rcpp)))
3415 `(("r-knitr" ,r-knitr)))
3416 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3417 (synopsis "GO-terms semantic similarity measures")
3419 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3420 quantitative ways to compute similarities between genes and gene groups, and
3421 have became important basis for many bioinformatics analysis approaches.
3422 GOSemSim is an R package for semantic similarity computation among GO terms,
3423 sets of GO terms, gene products and gene clusters.")
3424 (license license:artistic2.0)))
3426 (define-public r-anota
3433 (uri (bioconductor-uri "anota" version))
3436 "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m"))))
3437 (build-system r-build-system)
3439 `(("r-multtest" ,r-multtest)
3440 ("r-qvalue" ,r-qvalue)))
3441 (home-page "https://bioconductor.org/packages/anota/")
3442 (synopsis "Analysis of translational activity")
3444 "Genome wide studies of translational control is emerging as a tool to
3445 study various biological conditions. The output from such analysis is both
3446 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3447 involved in translation (the actively translating mRNA level) for each mRNA.
3448 The standard analysis of such data strives towards identifying differential
3449 translational between two or more sample classes - i.e. differences in
3450 actively translated mRNA levels that are independent of underlying differences
3451 in cytosolic mRNA levels. This package allows for such analysis using partial
3452 variances and the random variance model. As 10s of thousands of mRNAs are
3453 analyzed in parallel the library performs a number of tests to assure that
3454 the data set is suitable for such analysis.")
3455 (license license:gpl3)))
3457 (define-public r-sigpathway
3459 (name "r-sigpathway")
3464 (uri (bioconductor-uri "sigPathway" version))
3467 "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb"))))
3468 (properties `((upstream-name . "sigPathway")))
3469 (build-system r-build-system)
3470 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3471 (synopsis "Pathway analysis")
3473 "This package is used to conduct pathway analysis by calculating the NT_k
3474 and NE_k statistics in a statistical framework for determining whether a
3475 specified group of genes for a pathway has a coordinated association with a
3476 phenotype of interest.")
3477 (license license:gpl2)))
3479 (define-public r-fgsea
3486 (uri (bioconductor-uri "fgsea" version))
3489 "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1"))))
3490 (build-system r-build-system)
3493 ("r-biocparallel" ,r-biocparallel)
3494 ("r-data-table" ,r-data-table)
3495 ("r-fastmatch" ,r-fastmatch)
3496 ("r-ggplot2" ,r-ggplot2)
3497 ("r-gridextra" ,r-gridextra)
3498 ("r-matrix" ,r-matrix)
3499 ("r-rcpp" ,r-rcpp)))
3500 (home-page "https://github.com/ctlab/fgsea/")
3501 (synopsis "Fast gene set enrichment analysis")
3503 "The package implements an algorithm for fast gene set enrichment
3504 analysis. Using the fast algorithm allows to make more permutations and get
3505 more fine grained p-values, which allows to use accurate stantard approaches
3506 to multiple hypothesis correction.")
3507 (license license:expat)))
3509 (define-public r-dose
3516 (uri (bioconductor-uri "DOSE" version))
3519 "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5"))))
3520 (properties `((upstream-name . "DOSE")))
3521 (build-system r-build-system)
3523 `(("r-annotationdbi" ,r-annotationdbi)
3524 ("r-biocparallel" ,r-biocparallel)
3525 ("r-do-db" ,r-do-db)
3526 ("r-fgsea" ,r-fgsea)
3527 ("r-ggplot2" ,r-ggplot2)
3528 ("r-gosemsim" ,r-gosemsim)
3529 ("r-qvalue" ,r-qvalue)
3530 ("r-reshape2" ,r-reshape2)
3531 ("r-s4vectors" ,r-s4vectors)))
3532 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3533 (synopsis "Disease ontology semantic and enrichment analysis")
3535 "This package implements five methods proposed by Resnik, Schlicker,
3536 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3537 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3538 including hypergeometric model and gene set enrichment analysis are also
3539 implemented for discovering disease associations of high-throughput biological
3541 (license license:artistic2.0)))
3543 (define-public r-enrichplot
3545 (name "r-enrichplot")
3550 (uri (bioconductor-uri "enrichplot" version))
3553 "0707f5ll58psh7pr001cmmk5di7dprnbry1cy2mw20vn8p24nf3x"))))
3554 (build-system r-build-system)
3556 `(("r-annotationdbi" ,r-annotationdbi)
3557 ("r-cowplot" ,r-cowplot)
3559 ("r-europepmc" ,r-europepmc)
3560 ("r-ggplot2" ,r-ggplot2)
3561 ("r-ggplotify" ,r-ggplotify)
3562 ("r-ggraph" ,r-ggraph)
3563 ("r-ggridges" ,r-ggridges)
3564 ("r-gosemsim" ,r-gosemsim)
3565 ("r-gridextra" ,r-gridextra)
3566 ("r-igraph" ,r-igraph)
3567 ("r-purrr" ,r-purrr)
3568 ("r-rcolorbrewer" ,r-rcolorbrewer)
3569 ("r-reshape2" ,r-reshape2)))
3570 (home-page "https://github.com/GuangchuangYu/enrichplot")
3571 (synopsis "Visualization of functional enrichment result")
3573 "The enrichplot package implements several visualization methods for
3574 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3575 All the visualization methods are developed based on ggplot2 graphics.")
3576 (license license:artistic2.0)))
3578 (define-public r-clusterprofiler
3580 (name "r-clusterprofiler")
3585 (uri (bioconductor-uri "clusterProfiler" version))
3588 "08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg"))))
3590 `((upstream-name . "clusterProfiler")))
3591 (build-system r-build-system)
3593 `(("r-annotationdbi" ,r-annotationdbi)
3595 ("r-enrichplot" ,r-enrichplot)
3596 ("r-ggplot2" ,r-ggplot2)
3597 ("r-go-db" ,r-go-db)
3598 ("r-gosemsim" ,r-gosemsim)
3599 ("r-magrittr" ,r-magrittr)
3601 ("r-qvalue" ,r-qvalue)
3602 ("r-rvcheck" ,r-rvcheck)
3603 ("r-tidyr" ,r-tidyr)))
3604 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3605 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3607 "This package implements methods to analyze and visualize functional
3608 profiles (GO and KEGG) of gene and gene clusters.")
3609 (license license:artistic2.0)))
3611 (define-public r-mlinterfaces
3613 (name "r-mlinterfaces")
3618 (uri (bioconductor-uri "MLInterfaces" version))
3621 "05bg7qcrv485m03rkyq3qg5hrr1m3y7zx49bipwaivzqm3s1mbw5"))))
3622 (properties `((upstream-name . "MLInterfaces")))
3623 (build-system r-build-system)
3625 `(("r-annotate" ,r-annotate)
3626 ("r-biobase" ,r-biobase)
3627 ("r-biocgenerics" ,r-biocgenerics)
3628 ("r-cluster" ,r-cluster)
3631 ("r-gdata" ,r-gdata)
3632 ("r-genefilter" ,r-genefilter)
3633 ("r-ggvis" ,r-ggvis)
3634 ("r-hwriter" ,r-hwriter)
3636 ("r-mlbench" ,r-mlbench)
3638 ("r-rcolorbrewer" ,r-rcolorbrewer)
3639 ("r-rpart" ,r-rpart)
3640 ("r-sfsmisc" ,r-sfsmisc)
3641 ("r-shiny" ,r-shiny)
3642 ("r-threejs" ,r-threejs)))
3643 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3644 (synopsis "Interfaces to R machine learning procedures")
3646 "This package provides uniform interfaces to machine learning code for
3647 data in R and Bioconductor containers.")
3648 ;; Any version of the LGPL.
3649 (license license:lgpl2.1+)))
3651 (define-public r-annaffy
3658 (uri (bioconductor-uri "annaffy" version))
3661 "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16"))))
3662 (build-system r-build-system)
3665 (modify-phases %standard-phases
3666 (add-after 'unpack 'remove-reference-to-non-free-data
3668 (substitute* "DESCRIPTION"
3672 `(("r-annotationdbi" ,r-annotationdbi)
3673 ("r-biobase" ,r-biobase)
3675 ("r-go-db" ,r-go-db)))
3676 (home-page "https://bioconductor.org/packages/annaffy/")
3677 (synopsis "Annotation tools for Affymetrix biological metadata")
3679 "This package provides functions for handling data from Bioconductor
3680 Affymetrix annotation data packages. It produces compact HTML and text
3681 reports including experimental data and URL links to many online databases.
3682 It allows searching of biological metadata using various criteria.")
3683 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3684 ;; the LGPL 2.1 is included.
3685 (license license:lgpl2.1+)))
3687 (define-public r-a4core
3694 (uri (bioconductor-uri "a4Core" version))
3697 "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df"))))
3698 (properties `((upstream-name . "a4Core")))
3699 (build-system r-build-system)
3701 `(("r-biobase" ,r-biobase)
3702 ("r-glmnet" ,r-glmnet)))
3703 (home-page "https://bioconductor.org/packages/a4Core")
3704 (synopsis "Automated Affymetrix array analysis core package")
3706 "This is the core package for the automated analysis of Affymetrix
3708 (license license:gpl3)))
3710 (define-public r-a4classif
3712 (name "r-a4classif")
3717 (uri (bioconductor-uri "a4Classif" version))
3720 "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn"))))
3721 (properties `((upstream-name . "a4Classif")))
3722 (build-system r-build-system)
3724 `(("r-a4core" ,r-a4core)
3725 ("r-a4preproc" ,r-a4preproc)
3726 ("r-glmnet" ,r-glmnet)
3727 ("r-mlinterfaces" ,r-mlinterfaces)
3730 ("r-varselrf" ,r-varselrf)))
3731 (home-page "https://bioconductor.org/packages/a4Classif/")
3732 (synopsis "Automated Affymetrix array analysis classification package")
3734 "This is the classification package for the automated analysis of
3735 Affymetrix arrays.")
3736 (license license:gpl3)))
3738 (define-public r-a4preproc
3740 (name "r-a4preproc")
3745 (uri (bioconductor-uri "a4Preproc" version))
3748 "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd"))))
3749 (properties `((upstream-name . "a4Preproc")))
3750 (build-system r-build-system)
3752 `(("r-annotationdbi" ,r-annotationdbi)))
3753 (home-page "https://bioconductor.org/packages/a4Preproc/")
3754 (synopsis "Automated Affymetrix array analysis preprocessing package")
3756 "This is a package for the automated analysis of Affymetrix arrays. It
3757 is used for preprocessing the arrays.")
3758 (license license:gpl3)))
3760 (define-public r-a4reporting
3762 (name "r-a4reporting")
3767 (uri (bioconductor-uri "a4Reporting" version))
3770 "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5"))))
3771 (properties `((upstream-name . "a4Reporting")))
3772 (build-system r-build-system)
3774 `(("r-annaffy" ,r-annaffy)
3775 ("r-xtable" ,r-xtable)))
3776 (home-page "https://bioconductor.org/packages/a4Reporting/")
3777 (synopsis "Automated Affymetrix array analysis reporting package")
3779 "This is a package for the automated analysis of Affymetrix arrays. It
3780 provides reporting features.")
3781 (license license:gpl3)))
3783 (define-public r-a4base
3790 (uri (bioconductor-uri "a4Base" version))
3793 "0dgqyq4dnlcik5qqygnhxlhfr98sh6kmdcj2qllhrwyk0lmsfk01"))))
3794 (properties `((upstream-name . "a4Base")))
3795 (build-system r-build-system)
3797 `(("r-a4core" ,r-a4core)
3798 ("r-a4preproc" ,r-a4preproc)
3799 ("r-annaffy" ,r-annaffy)
3800 ("r-annotationdbi" ,r-annotationdbi)
3801 ("r-biobase" ,r-biobase)
3802 ("r-genefilter" ,r-genefilter)
3803 ("r-glmnet" ,r-glmnet)
3804 ("r-gplots" ,r-gplots)
3805 ("r-limma" ,r-limma)
3807 ("r-multtest" ,r-multtest)))
3808 (home-page "https://bioconductor.org/packages/a4Base/")
3809 (synopsis "Automated Affymetrix array analysis base package")
3811 "This package provides basic features for the automated analysis of
3812 Affymetrix arrays.")
3813 (license license:gpl3)))
3822 (uri (bioconductor-uri "a4" version))
3825 "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4"))))
3826 (build-system r-build-system)
3828 `(("r-a4base" ,r-a4base)
3829 ("r-a4classif" ,r-a4classif)
3830 ("r-a4core" ,r-a4core)
3831 ("r-a4preproc" ,r-a4preproc)
3832 ("r-a4reporting" ,r-a4reporting)))
3833 (home-page "https://bioconductor.org/packages/a4/")
3834 (synopsis "Automated Affymetrix array analysis umbrella package")
3836 "This package provides a software suite for the automated analysis of
3837 Affymetrix arrays.")
3838 (license license:gpl3)))
3840 (define-public r-abseqr
3847 (uri (bioconductor-uri "abseqR" version))
3850 "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa"))))
3851 (properties `((upstream-name . "abseqR")))
3852 (build-system r-build-system)
3854 `(("pandoc" ,ghc-pandoc)))
3856 `(("r-biocparallel" ,r-biocparallel)
3857 ("r-biocstyle" ,r-biocstyle)
3858 ("r-circlize" ,r-circlize)
3859 ("r-flexdashboard" ,r-flexdashboard)
3860 ("r-ggcorrplot" ,r-ggcorrplot)
3861 ("r-ggdendro" ,r-ggdendro)
3862 ("r-ggplot2" ,r-ggplot2)
3863 ("r-gridextra" ,r-gridextra)
3864 ("r-knitr" ,r-knitr)
3865 ("r-plotly" ,r-plotly)
3868 ("r-rcolorbrewer" ,r-rcolorbrewer)
3869 ("r-reshape2" ,r-reshape2)
3870 ("r-rmarkdown" ,r-rmarkdown)
3871 ("r-stringr" ,r-stringr)
3872 ("r-vegan" ,r-vegan)
3873 ("r-venndiagram" ,r-venndiagram)))
3874 (home-page "https://github.com/malhamdoosh/abseqR")
3875 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3877 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3878 sequencing datasets generated from antibody libraries and abseqR is one of its
3879 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3880 capabilities and allows them to generate interactive HTML reports for the
3881 convenience of viewing and sharing with other researchers. Additionally,
3882 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3883 further downstream analysis on its output.")
3884 (license license:gpl3)))
3886 (define-public r-bacon
3893 (uri (bioconductor-uri "bacon" version))
3896 "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86"))))
3897 (build-system r-build-system)
3899 `(("r-biocparallel" ,r-biocparallel)
3900 ("r-ellipse" ,r-ellipse)
3901 ("r-ggplot2" ,r-ggplot2)))
3902 (home-page "https://bioconductor.org/packages/bacon/")
3903 (synopsis "Controlling bias and inflation in association studies")
3905 "Bacon can be used to remove inflation and bias often observed in
3906 epigenome- and transcriptome-wide association studies. To this end bacon
3907 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3908 fitting a three-component normal mixture on z-scores.")
3909 (license license:gpl2+)))
3911 (define-public r-rgadem
3918 (uri (bioconductor-uri "rGADEM" version))
3921 "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h"))))
3922 (properties `((upstream-name . "rGADEM")))
3923 (build-system r-build-system)
3925 `(("r-biostrings" ,r-biostrings)
3926 ("r-bsgenome" ,r-bsgenome)
3927 ("r-genomicranges" ,r-genomicranges)
3928 ("r-iranges" ,r-iranges)
3929 ("r-seqlogo" ,r-seqlogo)))
3930 (home-page "https://bioconductor.org/packages/rGADEM/")
3931 (synopsis "De novo sequence motif discovery")
3933 "rGADEM is an efficient de novo motif discovery tool for large-scale
3934 genomic sequence data.")
3935 (license license:artistic2.0)))
3937 (define-public r-motiv
3944 (uri (bioconductor-uri "MotIV" version))
3947 "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k"))))
3948 (properties `((upstream-name . "MotIV")))
3949 (build-system r-build-system)
3953 `(("r-biocgenerics" ,r-biocgenerics)
3954 ("r-biostrings" ,r-biostrings)
3955 ("r-genomicranges" ,r-genomicranges)
3956 ("r-iranges" ,r-iranges)
3957 ("r-lattice" ,r-lattice)
3958 ("r-rgadem" ,r-rgadem)
3959 ("r-s4vectors" ,r-s4vectors)))
3960 (home-page "https://bioconductor.org/packages/MotIV/")
3961 (synopsis "Motif identification and validation")
3963 "This package is used for the identification and validation of sequence
3964 motifs. It makes use of STAMP for comparing a set of motifs to a given
3965 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3966 distributions, modules and filter motifs.")
3967 (license license:gpl2)))
3969 (define-public r-motifstack
3971 (name "r-motifstack")
3976 (uri (bioconductor-uri "motifStack" version))
3979 "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg"))))
3980 (properties `((upstream-name . "motifStack")))
3981 (build-system r-build-system)
3983 `(("r-ade4" ,r-ade4)
3984 ("r-biostrings" ,r-biostrings)
3985 ("r-ggplot2" ,r-ggplot2)
3986 ("r-grimport2" ,r-grimport2)
3987 ("r-htmlwidgets" ,r-htmlwidgets)
3988 ("r-motiv" ,r-motiv)
3989 ("r-scales" ,r-scales)
3991 (home-page "https://bioconductor.org/packages/motifStack/")
3992 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3994 "The motifStack package is designed for graphic representation of
3995 multiple motifs with different similarity scores. It works with both DNA/RNA
3996 sequence motifs and amino acid sequence motifs. In addition, it provides the
3997 flexibility for users to customize the graphic parameters such as the font
3998 type and symbol colors.")
3999 (license license:gpl2+)))
4001 (define-public r-genomicscores
4003 (name "r-genomicscores")
4008 (uri (bioconductor-uri "GenomicScores" version))
4011 "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj"))))
4012 (properties `((upstream-name . "GenomicScores")))
4013 (build-system r-build-system)
4015 `(("r-annotationhub" ,r-annotationhub)
4016 ("r-biobase" ,r-biobase)
4017 ("r-biocgenerics" ,r-biocgenerics)
4018 ("r-biostrings" ,r-biostrings)
4019 ("r-bsgenome" ,r-bsgenome)
4020 ("r-genomeinfodb" ,r-genomeinfodb)
4021 ("r-genomicranges" ,r-genomicranges)
4022 ("r-iranges" ,r-iranges)
4023 ("r-s4vectors" ,r-s4vectors)
4025 (home-page "https://github.com/rcastelo/GenomicScores/")
4026 (synopsis "Work with genome-wide position-specific scores")
4028 "This package provides infrastructure to store and access genome-wide
4029 position-specific scores within R and Bioconductor.")
4030 (license license:artistic2.0)))
4032 (define-public r-atacseqqc
4034 (name "r-atacseqqc")
4039 (uri (bioconductor-uri "ATACseqQC" version))
4042 "18zf90iksglbs13cwr4jjwsv332a19lf4bpdmy69jz8bpwrklv22"))))
4043 (properties `((upstream-name . "ATACseqQC")))
4044 (build-system r-build-system)
4046 `(("r-biocgenerics" ,r-biocgenerics)
4047 ("r-biostrings" ,r-biostrings)
4048 ("r-bsgenome" ,r-bsgenome)
4049 ("r-chippeakanno" ,r-chippeakanno)
4050 ("r-edger" ,r-edger)
4051 ("r-genomeinfodb" ,r-genomeinfodb)
4052 ("r-genomicalignments" ,r-genomicalignments)
4053 ("r-genomicranges" ,r-genomicranges)
4054 ("r-genomicscores" ,r-genomicscores)
4055 ("r-iranges" ,r-iranges)
4056 ("r-kernsmooth" ,r-kernsmooth)
4057 ("r-limma" ,r-limma)
4058 ("r-motifstack" ,r-motifstack)
4059 ("r-preseqr" ,r-preseqr)
4060 ("r-randomforest" ,r-randomforest)
4061 ("r-rsamtools" ,r-rsamtools)
4062 ("r-rtracklayer" ,r-rtracklayer)
4063 ("r-s4vectors" ,r-s4vectors)))
4065 `(("r-knitr" ,r-knitr)))
4066 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4067 (synopsis "ATAC-seq quality control")
4069 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4070 sequencing, is a rapid and sensitive method for chromatin accessibility
4071 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4072 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4073 assess whether their ATAC-seq experiment is successful. It includes
4074 diagnostic plots of fragment size distribution, proportion of mitochondria
4075 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4077 (license license:gpl2+)))
4079 (define-public r-gofuncr
4086 (uri (bioconductor-uri "GOfuncR" version))
4089 "1wk7ja6f5il8jx8v05ijzcs9pijp3b953h566ya66xp7dz5jg9rb"))))
4090 (properties `((upstream-name . "GOfuncR")))
4091 (build-system r-build-system)
4093 `(("r-annotationdbi" ,r-annotationdbi)
4094 ("r-genomicranges" ,r-genomicranges)
4095 ("r-gtools" ,r-gtools)
4096 ("r-iranges" ,r-iranges)
4097 ("r-mapplots" ,r-mapplots)
4099 ("r-vioplot" ,r-vioplot)))
4101 `(("r-knitr" ,r-knitr)))
4102 (home-page "https://bioconductor.org/packages/GOfuncR/")
4103 (synopsis "Gene ontology enrichment using FUNC")
4105 "GOfuncR performs a gene ontology enrichment analysis based on the
4106 ontology enrichment software FUNC. GO-annotations are obtained from
4107 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4108 included in the package and updated regularly. GOfuncR provides the standard
4109 candidate vs background enrichment analysis using the hypergeometric test, as
4110 well as three additional tests:
4113 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4114 @item a binomial test that is used when genes are associated with two counts,
4116 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4117 associated with four counts.
4120 To correct for multiple testing and interdependency of the tests, family-wise
4121 error rates are computed based on random permutations of the gene-associated
4122 variables. GOfuncR also provides tools for exploring the ontology graph and
4123 the annotations, and options to take gene-length or spatial clustering of
4124 genes into account. It is also possible to provide custom gene coordinates,
4125 annotations and ontologies.")
4126 (license license:gpl2+)))
4128 (define-public r-abaenrichment
4130 (name "r-abaenrichment")
4135 (uri (bioconductor-uri "ABAEnrichment" version))
4138 "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp"))))
4139 (properties `((upstream-name . "ABAEnrichment")))
4140 (build-system r-build-system)
4142 `(("r-abadata" ,r-abadata)
4143 ("r-data-table" ,r-data-table)
4144 ("r-gofuncr" ,r-gofuncr)
4145 ("r-gplots" ,r-gplots)
4146 ("r-gtools" ,r-gtools)
4147 ("r-rcpp" ,r-rcpp)))
4148 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4149 (synopsis "Gene expression enrichment in human brain regions")
4151 "The package ABAEnrichment is designed to test for enrichment of user
4152 defined candidate genes in the set of expressed genes in different human brain
4153 regions. The core function @code{aba_enrich} integrates the expression of the
4154 candidate gene set (averaged across donors) and the structural information of
4155 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4156 (license license:gpl2+)))
4158 (define-public r-annotationfuncs
4160 (name "r-annotationfuncs")
4165 (uri (bioconductor-uri "AnnotationFuncs" version))
4168 "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq"))))
4170 `((upstream-name . "AnnotationFuncs")))
4171 (build-system r-build-system)
4173 `(("r-annotationdbi" ,r-annotationdbi)
4175 (home-page "https://www.iysik.com/r/annotationfuncs")
4176 (synopsis "Annotation translation functions")
4178 "This package provides functions for handling translating between
4179 different identifieres using the Biocore Data Team data-packages (e.g.
4180 @code{org.Bt.eg.db}).")
4181 (license license:gpl2)))
4183 (define-public r-annotationtools
4185 (name "r-annotationtools")
4190 (uri (bioconductor-uri "annotationTools" version))
4193 "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i"))))
4195 `((upstream-name . "annotationTools")))
4196 (build-system r-build-system)
4197 (propagated-inputs `(("r-biobase" ,r-biobase)))
4198 (home-page "https://bioconductor.org/packages/annotationTools/")
4199 (synopsis "Annotate microarrays and perform gene expression analyses")
4201 "This package provides functions to annotate microarrays, find orthologs,
4202 and integrate heterogeneous gene expression profiles using annotation and
4203 other molecular biology information available as flat file database (plain
4205 ;; Any version of the GPL.
4206 (license (list license:gpl2+))))
4208 (define-public r-allelicimbalance
4210 (name "r-allelicimbalance")
4215 (uri (bioconductor-uri "AllelicImbalance" version))
4218 "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc"))))
4220 `((upstream-name . "AllelicImbalance")))
4221 (build-system r-build-system)
4223 `(("r-annotationdbi" ,r-annotationdbi)
4224 ("r-biocgenerics" ,r-biocgenerics)
4225 ("r-biostrings" ,r-biostrings)
4226 ("r-bsgenome" ,r-bsgenome)
4227 ("r-genomeinfodb" ,r-genomeinfodb)
4228 ("r-genomicalignments" ,r-genomicalignments)
4229 ("r-genomicfeatures" ,r-genomicfeatures)
4230 ("r-genomicranges" ,r-genomicranges)
4231 ("r-gridextra" ,r-gridextra)
4233 ("r-iranges" ,r-iranges)
4234 ("r-lattice" ,r-lattice)
4235 ("r-latticeextra" ,r-latticeextra)
4237 ("r-rsamtools" ,r-rsamtools)
4238 ("r-s4vectors" ,r-s4vectors)
4239 ("r-seqinr" ,r-seqinr)
4240 ("r-summarizedexperiment" ,r-summarizedexperiment)
4241 ("r-variantannotation" ,r-variantannotation)))
4242 (home-page "https://github.com/pappewaio/AllelicImbalance")
4243 (synopsis "Investigate allele-specific expression")
4245 "This package provides a framework for allele-specific expression
4246 investigation using RNA-seq data.")
4247 (license license:gpl3)))
4249 (define-public r-aucell
4256 (uri (bioconductor-uri "AUCell" version))
4259 "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky"))))
4260 (properties `((upstream-name . "AUCell")))
4261 (build-system r-build-system)
4263 `(("r-biocgenerics" ,r-biocgenerics)
4264 ("r-data-table" ,r-data-table)
4265 ("r-gseabase" ,r-gseabase)
4266 ("r-mixtools" ,r-mixtools)
4267 ("r-r-utils" ,r-r-utils)
4268 ("r-s4vectors" ,r-s4vectors)
4269 ("r-shiny" ,r-shiny)
4270 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4271 (home-page "https://bioconductor.org/packages/AUCell/")
4272 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4274 "AUCell allows to identify cells with active gene sets (e.g. signatures,
4275 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4276 Under the Curve} (AUC) to calculate whether a critical subset of the input
4277 gene set is enriched within the expressed genes for each cell. The
4278 distribution of AUC scores across all the cells allows exploring the relative
4279 expression of the signature. Since the scoring method is ranking-based,
4280 AUCell is independent of the gene expression units and the normalization
4281 procedure. In addition, since the cells are evaluated individually, it can
4282 easily be applied to bigger datasets, subsetting the expression matrix if
4284 (license license:gpl3)))
4286 (define-public r-ebimage
4293 (uri (bioconductor-uri "EBImage" version))
4296 "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs"))))
4297 (properties `((upstream-name . "EBImage")))
4298 (build-system r-build-system)
4300 `(("r-abind" ,r-abind)
4301 ("r-biocgenerics" ,r-biocgenerics)
4302 ("r-fftwtools" ,r-fftwtools)
4303 ("r-htmltools" ,r-htmltools)
4304 ("r-htmlwidgets" ,r-htmlwidgets)
4306 ("r-locfit" ,r-locfit)
4308 ("r-rcurl" ,r-rcurl)
4309 ("r-tiff" ,r-tiff)))
4311 `(("r-knitr" ,r-knitr))) ; for vignettes
4312 (home-page "https://github.com/aoles/EBImage")
4313 (synopsis "Image processing and analysis toolbox for R")
4315 "EBImage provides general purpose functionality for image processing and
4316 analysis. In the context of (high-throughput) microscopy-based cellular
4317 assays, EBImage offers tools to segment cells and extract quantitative
4318 cellular descriptors. This allows the automation of such tasks using the R
4319 programming language and facilitates the use of other tools in the R
4320 environment for signal processing, statistical modeling, machine learning and
4321 visualization with image data.")
4322 ;; Any version of the LGPL.
4323 (license license:lgpl2.1+)))
4325 (define-public r-yamss
4332 (uri (bioconductor-uri "yamss" version))
4335 "12jr7hbrwhb1gfjadj1024hv80ra22miy46dn40nmsrbklkfn3rw"))))
4336 (build-system r-build-system)
4338 `(("r-biocgenerics" ,r-biocgenerics)
4339 ("r-data-table" ,r-data-table)
4340 ("r-ebimage" ,r-ebimage)
4341 ("r-iranges" ,r-iranges)
4342 ("r-limma" ,r-limma)
4343 ("r-matrix" ,r-matrix)
4345 ("r-s4vectors" ,r-s4vectors)
4346 ("r-summarizedexperiment"
4347 ,r-summarizedexperiment)))
4348 (home-page "https://github.com/hansenlab/yamss")
4349 (synopsis "Tools for high-throughput metabolomics")
4351 "This package provides tools to analyze and visualize high-throughput
4352 metabolomics data acquired using chromatography-mass spectrometry. These tools
4353 preprocess data in a way that enables reliable and powerful differential
4355 (license license:artistic2.0)))
4357 (define-public r-gtrellis
4364 (uri (bioconductor-uri "gtrellis" version))
4367 "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z"))))
4368 (build-system r-build-system)
4370 `(("r-circlize" ,r-circlize)
4371 ("r-genomicranges" ,r-genomicranges)
4372 ("r-getoptlong" ,r-getoptlong)
4373 ("r-iranges" ,r-iranges)))
4374 (home-page "https://github.com/jokergoo/gtrellis")
4375 (synopsis "Genome level Trellis layout")
4377 "Genome level Trellis graph visualizes genomic data conditioned by
4378 genomic categories (e.g. chromosomes). For each genomic category, multiple
4379 dimensional data which are represented as tracks describe different features
4380 from different aspects. This package provides high flexibility to arrange
4381 genomic categories and to add self-defined graphics in the plot.")
4382 (license license:expat)))
4384 (define-public r-somaticsignatures
4386 (name "r-somaticsignatures")
4391 (uri (bioconductor-uri "SomaticSignatures" version))
4394 "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z"))))
4396 `((upstream-name . "SomaticSignatures")))
4397 (build-system r-build-system)
4399 `(("r-biobase" ,r-biobase)
4400 ("r-biostrings" ,r-biostrings)
4401 ("r-genomeinfodb" ,r-genomeinfodb)
4402 ("r-genomicranges" ,r-genomicranges)
4403 ("r-ggbio" ,r-ggbio)
4404 ("r-ggplot2" ,r-ggplot2)
4405 ("r-iranges" ,r-iranges)
4407 ("r-pcamethods" ,r-pcamethods)
4408 ("r-proxy" ,r-proxy)
4409 ("r-reshape2" ,r-reshape2)
4410 ("r-s4vectors" ,r-s4vectors)
4411 ("r-variantannotation" ,r-variantannotation)))
4412 (home-page "https://github.com/juliangehring/SomaticSignatures")
4413 (synopsis "Somatic signatures")
4415 "This package identifies mutational signatures of @dfn{single nucleotide
4416 variants} (SNVs). It provides a infrastructure related to the methodology
4417 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4418 decomposition algorithms.")
4419 (license license:expat)))
4421 (define-public r-yapsa
4428 (uri (bioconductor-uri "YAPSA" version))
4431 "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926"))))
4432 (properties `((upstream-name . "YAPSA")))
4433 (build-system r-build-system)
4435 `(("r-circlize" ,r-circlize)
4436 ("r-complexheatmap" ,r-complexheatmap)
4437 ("r-corrplot" ,r-corrplot)
4438 ("r-dendextend" ,r-dendextend)
4439 ("r-genomeinfodb" ,r-genomeinfodb)
4440 ("r-genomicranges" ,r-genomicranges)
4441 ("r-getoptlong" ,r-getoptlong)
4442 ("r-ggplot2" ,r-ggplot2)
4443 ("r-gridextra" ,r-gridextra)
4444 ("r-gtrellis" ,r-gtrellis)
4445 ("r-keggrest" ,r-keggrest)
4447 ("r-pmcmr" ,r-pmcmr)
4448 ("r-reshape2" ,r-reshape2)
4449 ("r-somaticsignatures" ,r-somaticsignatures)
4450 ("r-variantannotation" ,r-variantannotation)))
4451 (home-page "https://bioconductor.org/packages/YAPSA/")
4452 (synopsis "Yet another package for signature analysis")
4454 "This package provides functions and routines useful in the analysis of
4455 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4456 functions to perform a signature analysis with known signatures and a
4457 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4459 (license license:gpl3)))
4461 (define-public r-gcrma
4468 (uri (bioconductor-uri "gcrma" version))
4471 "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx"))))
4472 (build-system r-build-system)
4474 `(("r-affy" ,r-affy)
4475 ("r-affyio" ,r-affyio)
4476 ("r-biobase" ,r-biobase)
4477 ("r-biocmanager" ,r-biocmanager)
4478 ("r-biostrings" ,r-biostrings)
4479 ("r-xvector" ,r-xvector)))
4480 (home-page "https://bioconductor.org/packages/gcrma/")
4481 (synopsis "Background adjustment using sequence information")
4483 "Gcrma adjusts for background intensities in Affymetrix array data which
4484 include optical noise and @dfn{non-specific binding} (NSB). The main function
4485 @code{gcrma} converts background adjusted probe intensities to expression
4486 measures using the same normalization and summarization methods as a
4487 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4488 to estimate probe affinity to NSB. The sequence information is summarized in
4489 a more complex way than the simple GC content. Instead, the base types (A, T,
4490 G or C) at each position along the probe determine the affinity of each probe.
4491 The parameters of the position-specific base contributions to the probe
4492 affinity is estimated in an NSB experiment in which only NSB but no
4493 gene-specific bidning is expected.")
4494 ;; Any version of the LGPL
4495 (license license:lgpl2.1+)))
4497 (define-public r-simpleaffy
4499 (name "r-simpleaffy")
4504 (uri (bioconductor-uri "simpleaffy" version))
4507 "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs"))))
4508 (build-system r-build-system)
4510 `(("r-affy" ,r-affy)
4511 ("r-biobase" ,r-biobase)
4512 ("r-biocgenerics" ,r-biocgenerics)
4513 ("r-gcrma" ,r-gcrma)
4514 ("r-genefilter" ,r-genefilter)))
4515 (home-page "https://bioconductor.org/packages/simpleaffy/")
4516 (synopsis "Very simple high level analysis of Affymetrix data")
4518 "This package provides high level functions for reading Affy @file{.CEL}
4519 files, phenotypic data, and then computing simple things with it, such as
4520 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4521 library. It also has some basic scatter plot functions and mechanisms for
4522 generating high resolution journal figures.")
4523 (license license:gpl2+)))
4525 (define-public r-yaqcaffy
4532 (uri (bioconductor-uri "yaqcaffy" version))
4535 "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz"))))
4536 (build-system r-build-system)
4538 `(("r-simpleaffy" ,r-simpleaffy)))
4539 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4540 (synopsis "Affymetrix quality control and reproducibility analysis")
4542 "This is a package that can be used for quality control of Affymetrix
4543 GeneChip expression data and reproducibility analysis of human whole genome
4544 chips with the MAQC reference datasets.")
4545 (license license:artistic2.0)))
4547 (define-public r-quantro
4554 (uri (bioconductor-uri "quantro" version))
4557 "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m"))))
4558 (build-system r-build-system)
4560 `(("r-biobase" ,r-biobase)
4561 ("r-doparallel" ,r-doparallel)
4562 ("r-foreach" ,r-foreach)
4563 ("r-ggplot2" ,r-ggplot2)
4564 ("r-iterators" ,r-iterators)
4565 ("r-minfi" ,r-minfi)
4566 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4567 (home-page "https://bioconductor.org/packages/quantro/")
4568 (synopsis "Test for when to use quantile normalization")
4570 "This package provides a data-driven test for the assumptions of quantile
4571 normalization using raw data such as objects that inherit eSets (e.g.
4572 ExpressionSet, MethylSet). Group level information about each sample (such as
4573 Tumor / Normal status) must also be provided because the test assesses if
4574 there are global differences in the distributions between the user-defined
4576 (license license:gpl3+)))
4578 (define-public r-yarn
4585 (uri (bioconductor-uri "yarn" version))
4588 "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp"))))
4589 (build-system r-build-system)
4591 `(("r-biobase" ,r-biobase)
4592 ("r-biomart" ,r-biomart)
4593 ("r-downloader" ,r-downloader)
4594 ("r-edger" ,r-edger)
4595 ("r-gplots" ,r-gplots)
4596 ("r-limma" ,r-limma)
4597 ("r-matrixstats" ,r-matrixstats)
4598 ("r-preprocesscore" ,r-preprocesscore)
4599 ("r-quantro" ,r-quantro)
4600 ("r-rcolorbrewer" ,r-rcolorbrewer)
4601 ("r-readr" ,r-readr)))
4602 (home-page "https://bioconductor.org/packages/yarn/")
4603 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4605 "Expedite large RNA-Seq analyses using a combination of previously
4606 developed tools. YARN is meant to make it easier for the user in performing
4607 basic mis-annotation quality control, filtering, and condition-aware
4608 normalization. YARN leverages many Bioconductor tools and statistical
4609 techniques to account for the large heterogeneity and sparsity found in very
4610 large RNA-seq experiments.")
4611 (license license:artistic2.0)))
4613 (define-public r-roar
4620 (uri (bioconductor-uri "roar" version))
4623 "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06"))))
4624 (build-system r-build-system)
4626 `(("r-biocgenerics" ,r-biocgenerics)
4627 ("r-genomeinfodb" ,r-genomeinfodb)
4628 ("r-genomicalignments" ,r-genomicalignments)
4629 ("r-genomicranges" ,r-genomicranges)
4630 ("r-iranges" ,r-iranges)
4631 ("r-rtracklayer" ,r-rtracklayer)
4632 ("r-s4vectors" ,r-s4vectors)
4633 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4634 (home-page "https://github.com/vodkatad/roar/")
4635 (synopsis "Identify differential APA usage from RNA-seq alignments")
4637 "This package provides tools for identifying preferential usage of APA
4638 sites, comparing two biological conditions, starting from known alternative
4639 sites and alignments obtained from standard RNA-seq experiments.")
4640 (license license:gpl3)))
4642 (define-public r-xbseq
4649 (uri (bioconductor-uri "XBSeq" version))
4652 "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp"))))
4653 (properties `((upstream-name . "XBSeq")))
4654 (build-system r-build-system)
4656 `(("r-biobase" ,r-biobase)
4657 ("r-deseq2" ,r-deseq2)
4658 ("r-dplyr" ,r-dplyr)
4659 ("r-ggplot2" ,r-ggplot2)
4660 ("r-locfit" ,r-locfit)
4661 ("r-magrittr" ,r-magrittr)
4662 ("r-matrixstats" ,r-matrixstats)
4663 ("r-pracma" ,r-pracma)
4664 ("r-roar" ,r-roar)))
4665 (home-page "https://github.com/Liuy12/XBSeq")
4666 (synopsis "Test for differential expression for RNA-seq data")
4668 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4669 expression} (DE), where a statistical model was established based on the
4670 assumption that observed signals are the convolution of true expression
4671 signals and sequencing noises. The mapped reads in non-exonic regions are
4672 considered as sequencing noises, which follows a Poisson distribution. Given
4673 measurable observed signal and background noise from RNA-seq data, true
4674 expression signals, assuming governed by the negative binomial distribution,
4675 can be delineated and thus the accurate detection of differential expressed
4677 (license license:gpl3+)))
4679 (define-public r-massspecwavelet
4681 (name "r-massspecwavelet")
4686 (uri (bioconductor-uri "MassSpecWavelet" version))
4689 "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7"))))
4691 `((upstream-name . "MassSpecWavelet")))
4692 (build-system r-build-system)
4694 `(("r-waveslim" ,r-waveslim)))
4695 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4696 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4698 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4699 data mainly through the use of wavelet transforms. It supports peak detection
4700 based on @dfn{Continuous Wavelet Transform} (CWT).")
4701 (license license:lgpl2.0+)))
4703 (define-public r-xcms
4710 (uri (bioconductor-uri "xcms" version))
4713 "0bfl56v3l6k31i11l09nx1yqfjy6z5yragm6k83z4w0mpgk18y7g"))))
4714 (build-system r-build-system)
4716 `(("r-biobase" ,r-biobase)
4717 ("r-biocgenerics" ,r-biocgenerics)
4718 ("r-biocparallel" ,r-biocparallel)
4719 ("r-iranges" ,r-iranges)
4720 ("r-lattice" ,r-lattice)
4721 ("r-massspecwavelet" ,r-massspecwavelet)
4722 ("r-msnbase" ,r-msnbase)
4723 ("r-multtest" ,r-multtest)
4726 ("r-protgenerics" ,r-protgenerics)
4728 ("r-rcolorbrewer" ,r-rcolorbrewer)
4729 ("r-robustbase" ,r-robustbase)
4730 ("r-s4vectors" ,r-s4vectors)))
4731 (home-page "https://bioconductor.org/packages/xcms/")
4732 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4734 "This package provides a framework for processing and visualization of
4735 chromatographically separated and single-spectra mass spectral data. It
4736 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4737 data for high-throughput, untargeted analyte profiling.")
4738 (license license:gpl2+)))
4740 (define-public r-wrench
4747 (uri (bioconductor-uri "Wrench" version))
4750 "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm"))))
4751 (properties `((upstream-name . "Wrench")))
4752 (build-system r-build-system)
4754 `(("r-limma" ,r-limma)
4755 ("r-locfit" ,r-locfit)
4756 ("r-matrixstats" ,r-matrixstats)))
4757 (home-page "https://github.com/HCBravoLab/Wrench")
4758 (synopsis "Wrench normalization for sparse count data")
4760 "Wrench is a package for normalization sparse genomic count data, like
4761 that arising from 16s metagenomic surveys.")
4762 (license license:artistic2.0)))
4764 (define-public r-wiggleplotr
4766 (name "r-wiggleplotr")
4771 (uri (bioconductor-uri "wiggleplotr" version))
4774 "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m"))))
4775 (build-system r-build-system)
4777 `(("r-assertthat" ,r-assertthat)
4778 ("r-cowplot" ,r-cowplot)
4779 ("r-dplyr" ,r-dplyr)
4780 ("r-genomeinfodb" ,r-genomeinfodb)
4781 ("r-genomicranges" ,r-genomicranges)
4782 ("r-ggplot2" ,r-ggplot2)
4783 ("r-iranges" ,r-iranges)
4784 ("r-purrr" ,r-purrr)
4785 ("r-rtracklayer" ,r-rtracklayer)
4786 ("r-s4vectors" ,r-s4vectors)))
4787 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4788 (synopsis "Make read coverage plots from BigWig files")
4790 "This package provides tools to visualize read coverage from sequencing
4791 experiments together with genomic annotations (genes, transcripts, peaks).
4792 Introns of long transcripts can be rescaled to a fixed length for better
4793 visualization of exonic read coverage.")
4794 (license license:asl2.0)))
4796 (define-public r-widgettools
4798 (name "r-widgettools")
4803 (uri (bioconductor-uri "widgetTools" version))
4806 "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5"))))
4807 (properties `((upstream-name . "widgetTools")))
4808 (build-system r-build-system)
4809 (home-page "https://bioconductor.org/packages/widgetTools/")
4810 (synopsis "Tools for creating interactive tcltk widgets")
4812 "This package contains tools to support the construction of tcltk
4814 ;; Any version of the LGPL.
4815 (license license:lgpl3+)))
4817 (define-public r-webbioc
4824 (uri (bioconductor-uri "webbioc" version))
4827 "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62"))))
4828 (build-system r-build-system)
4830 `(("netpbm" ,netpbm)
4833 `(("r-affy" ,r-affy)
4834 ("r-annaffy" ,r-annaffy)
4835 ("r-biobase" ,r-biobase)
4836 ("r-biocmanager" ,r-biocmanager)
4837 ("r-gcrma" ,r-gcrma)
4838 ("r-multtest" ,r-multtest)
4839 ("r-qvalue" ,r-qvalue)
4841 (home-page "https://www.bioconductor.org/")
4842 (synopsis "Bioconductor web interface")
4844 "This package provides an integrated web interface for doing microarray
4845 analysis using several of the Bioconductor packages. It is intended to be
4846 deployed as a centralized bioinformatics resource for use by many users.
4847 Currently only Affymetrix oligonucleotide analysis is supported.")
4848 (license license:gpl2+)))
4850 (define-public r-zfpkm
4857 (uri (bioconductor-uri "zFPKM" version))
4860 "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n"))))
4861 (properties `((upstream-name . "zFPKM")))
4862 (build-system r-build-system)
4864 `(("r-checkmate" ,r-checkmate)
4865 ("r-dplyr" ,r-dplyr)
4866 ("r-ggplot2" ,r-ggplot2)
4867 ("r-summarizedexperiment" ,r-summarizedexperiment)
4868 ("r-tidyr" ,r-tidyr)))
4869 (home-page "https://github.com/ronammar/zFPKM/")
4870 (synopsis "Functions to facilitate zFPKM transformations")
4872 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4873 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4875 (license license:gpl3)))
4877 (define-public r-rbowtie2
4884 (uri (bioconductor-uri "Rbowtie2" version))
4887 "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5"))))
4888 (properties `((upstream-name . "Rbowtie2")))
4889 (build-system r-build-system)
4892 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4893 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4895 "This package provides an R wrapper of the popular @code{bowtie2}
4896 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4897 rapid adapter trimming, identification, and read merging.")
4898 (license license:gpl3+)))
4900 (define-public r-progeny
4907 (uri (bioconductor-uri "progeny" version))
4910 "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq"))))
4911 (build-system r-build-system)
4912 (propagated-inputs `(("r-biobase" ,r-biobase)))
4913 (home-page "https://github.com/saezlab/progeny")
4914 (synopsis "Pathway responsive gene activity inference")
4916 "This package provides a function to infer pathway activity from gene
4917 expression. It contains the linear model inferred in the publication
4918 \"Perturbation-response genes reveal signaling footprints in cancer gene
4920 (license license:asl2.0)))
4922 (define-public r-arrmnormalization
4924 (name "r-arrmnormalization")
4929 (uri (bioconductor-uri "ARRmNormalization" version))
4932 "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1"))))
4934 `((upstream-name . "ARRmNormalization")))
4935 (build-system r-build-system)
4936 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4937 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4938 (synopsis "Adaptive robust regression normalization for methylation data")
4940 "This is a package to perform the @dfn{Adaptive Robust Regression
4941 method} (ARRm) for the normalization of methylation data from the Illumina
4942 Infinium HumanMethylation 450k assay.")
4943 (license license:artistic2.0)))
4945 (define-public r-biocfilecache
4947 (name "r-biocfilecache")
4952 (uri (bioconductor-uri "BiocFileCache" version))
4955 "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6"))))
4956 (properties `((upstream-name . "BiocFileCache")))
4957 (build-system r-build-system)
4959 `(("r-curl" ,r-curl)
4961 ("r-dbplyr" ,r-dbplyr)
4962 ("r-dplyr" ,r-dplyr)
4964 ("r-rappdirs" ,r-rappdirs)
4965 ("r-rsqlite" ,r-rsqlite)))
4966 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4967 (synopsis "Manage files across sessions")
4969 "This package creates a persistent on-disk cache of files that the user
4970 can add, update, and retrieve. It is useful for managing resources (such as
4971 custom Txdb objects) that are costly or difficult to create, web resources,
4972 and data files used across sessions.")
4973 (license license:artistic2.0)))
4975 (define-public r-iclusterplus
4977 (name "r-iclusterplus")
4982 (uri (bioconductor-uri "iClusterPlus" version))
4985 "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37"))))
4986 (properties `((upstream-name . "iClusterPlus")))
4987 (build-system r-build-system)
4988 (native-inputs `(("gfortran" ,gfortran)))
4989 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4990 (synopsis "Integrative clustering of multi-type genomic data")
4992 "iClusterPlus is developed for integrative clustering analysis of
4993 multi-type genomic data and is an enhanced version of iCluster proposed and
4994 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4995 from the experiments where biological samples (e.g. tumor samples) are
4996 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4997 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4998 on. In the iClusterPlus model, binary observations such as somatic mutation
4999 are modeled as Binomial processes; categorical observations such as copy
5000 number states are realizations of Multinomial random variables; counts are
5001 modeled as Poisson random processes; and continuous measures are modeled by
5002 Gaussian distributions.")
5003 (license license:gpl2+)))
5005 (define-public r-rbowtie
5012 (uri (bioconductor-uri "Rbowtie" version))
5015 "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4"))))
5016 (properties `((upstream-name . "Rbowtie")))
5017 (build-system r-build-system)
5020 (home-page "https://bioconductor.org/packages/Rbowtie/")
5021 (synopsis "R bowtie wrapper")
5023 "This package provides an R wrapper around the popular bowtie short read
5024 aligner and around SpliceMap, a de novo splice junction discovery and
5026 (license license:artistic2.0)))
5028 (define-public r-sgseq
5035 (uri (bioconductor-uri "SGSeq" version))
5038 "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw"))))
5039 (properties `((upstream-name . "SGSeq")))
5040 (build-system r-build-system)
5042 `(("r-annotationdbi" ,r-annotationdbi)
5043 ("r-biocgenerics" ,r-biocgenerics)
5044 ("r-biostrings" ,r-biostrings)
5045 ("r-genomeinfodb" ,r-genomeinfodb)
5046 ("r-genomicalignments" ,r-genomicalignments)
5047 ("r-genomicfeatures" ,r-genomicfeatures)
5048 ("r-genomicranges" ,r-genomicranges)
5049 ("r-igraph" ,r-igraph)
5050 ("r-iranges" ,r-iranges)
5051 ("r-rsamtools" ,r-rsamtools)
5052 ("r-rtracklayer" ,r-rtracklayer)
5053 ("r-runit" ,r-runit)
5054 ("r-s4vectors" ,r-s4vectors)
5055 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5056 (home-page "https://bioconductor.org/packages/SGSeq/")
5057 (synopsis "Splice event prediction and quantification from RNA-seq data")
5059 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5060 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5061 represented as a splice graph, which can be obtained from existing annotation
5062 or predicted from the mapped sequence reads. Splice events are identified
5063 from the graph and are quantified locally using structurally compatible reads
5064 at the start or end of each splice variant. The software includes functions
5065 for splice event prediction, quantification, visualization and
5067 (license license:artistic2.0)))
5069 (define-public r-rhisat2
5076 (uri (bioconductor-uri "Rhisat2" version))
5079 "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49"))))
5080 (properties `((upstream-name . "Rhisat2")))
5081 (build-system r-build-system)
5084 (modify-phases %standard-phases
5085 (add-after 'unpack 'make-reproducible
5087 (substitute* "src/Makefile"
5088 (("`hostname`") "guix")
5090 ;; Avoid shelling out to "which".
5091 (("^CC =.*") (which "gcc"))
5092 (("^CPP =.*") (which "g++")))
5095 `(("r-genomicfeatures" ,r-genomicfeatures)
5096 ("r-genomicranges" ,r-genomicranges)
5097 ("r-sgseq" ,r-sgseq)))
5098 (home-page "https://github.com/fmicompbio/Rhisat2")
5099 (synopsis "R Wrapper for HISAT2 sequence aligner")
5101 "This package provides an R interface to the HISAT2 spliced short-read
5102 aligner by Kim et al. (2015). The package contains wrapper functions to
5103 create a genome index and to perform the read alignment to the generated
5105 (license license:gpl3)))
5107 (define-public r-quasr
5114 (uri (bioconductor-uri "QuasR" version))
5117 "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv"))))
5118 (properties `((upstream-name . "QuasR")))
5119 (build-system r-build-system)
5123 `(("r-annotationdbi" ,r-annotationdbi)
5124 ("r-biobase" ,r-biobase)
5125 ("r-biocgenerics" ,r-biocgenerics)
5126 ("r-biocmanager" ,r-biocmanager)
5127 ("r-biocparallel" ,r-biocparallel)
5128 ("r-biostrings" ,r-biostrings)
5129 ("r-bsgenome" ,r-bsgenome)
5130 ("r-genomeinfodb" ,r-genomeinfodb)
5131 ("r-genomicalignments" ,r-genomicalignments)
5132 ("r-genomicfeatures" ,r-genomicfeatures)
5133 ("r-genomicfiles" ,r-genomicfiles)
5134 ("r-genomicranges" ,r-genomicranges)
5135 ("r-iranges" ,r-iranges)
5136 ("r-rbowtie" ,r-rbowtie)
5137 ("r-rhisat2" ,r-rhisat2)
5138 ("r-rhtslib" ,r-rhtslib)
5139 ("r-rsamtools" ,r-rsamtools)
5140 ("r-rtracklayer" ,r-rtracklayer)
5141 ("r-s4vectors" ,r-s4vectors)
5142 ("r-shortread" ,r-shortread)))
5143 (home-page "https://bioconductor.org/packages/QuasR/")
5144 (synopsis "Quantify and annotate short reads in R")
5146 "This package provides a framework for the quantification and analysis of
5147 short genomic reads. It covers a complete workflow starting from raw sequence
5148 reads, over creation of alignments and quality control plots, to the
5149 quantification of genomic regions of interest.")
5150 (license license:gpl2)))
5152 (define-public r-rqc
5159 (uri (bioconductor-uri "Rqc" version))
5162 "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m"))))
5163 (properties `((upstream-name . "Rqc")))
5164 (build-system r-build-system)
5166 `(("r-biocgenerics" ,r-biocgenerics)
5167 ("r-biocparallel" ,r-biocparallel)
5168 ("r-biocstyle" ,r-biocstyle)
5169 ("r-biostrings" ,r-biostrings)
5170 ("r-biovizbase" ,r-biovizbase)
5171 ("r-genomicalignments" ,r-genomicalignments)
5172 ("r-genomicfiles" ,r-genomicfiles)
5173 ("r-ggplot2" ,r-ggplot2)
5174 ("r-iranges" ,r-iranges)
5175 ("r-knitr" ,r-knitr)
5176 ("r-markdown" ,r-markdown)
5179 ("r-reshape2" ,r-reshape2)
5180 ("r-rsamtools" ,r-rsamtools)
5181 ("r-s4vectors" ,r-s4vectors)
5182 ("r-shiny" ,r-shiny)
5183 ("r-shortread" ,r-shortread)))
5184 (home-page "https://github.com/labbcb/Rqc")
5185 (synopsis "Quality control tool for high-throughput sequencing data")
5187 "Rqc is an optimized tool designed for quality control and assessment of
5188 high-throughput sequencing data. It performs parallel processing of entire
5189 files and produces a report which contains a set of high-resolution
5191 (license license:gpl2+)))
5193 (define-public r-birewire
5200 (uri (bioconductor-uri "BiRewire" version))
5203 "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q"))))
5204 (properties `((upstream-name . "BiRewire")))
5205 (build-system r-build-system)
5207 `(("r-igraph" ,r-igraph)
5208 ("r-matrix" ,r-matrix)
5210 ("r-tsne" ,r-tsne)))
5211 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5212 (synopsis "Tools for randomization of bipartite graphs")
5214 "This package provides functions for bipartite network rewiring through N
5215 consecutive switching steps and for the computation of the minimal number of
5216 switching steps to be performed in order to maximise the dissimilarity with
5217 respect to the original network. It includes functions for the analysis of
5218 the introduced randomness across the switching steps and several other
5219 routines to analyse the resulting networks and their natural projections.")
5220 (license license:gpl3)))
5222 (define-public r-birta
5229 (uri (bioconductor-uri "birta" version))
5232 "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg"))))
5233 (build-system r-build-system)
5235 `(("r-biobase" ,r-biobase)
5236 ("r-limma" ,r-limma)
5237 ("r-mass" ,r-mass)))
5238 (home-page "https://bioconductor.org/packages/birta")
5239 (synopsis "Bayesian inference of regulation of transcriptional activity")
5241 "Expression levels of mRNA molecules are regulated by different
5242 processes, comprising inhibition or activation by transcription factors and
5243 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5244 Inference of Regulation of Transcriptional Activity) uses the regulatory
5245 networks of transcription factors and miRNAs together with mRNA and miRNA
5246 expression data to predict switches in regulatory activity between two
5247 conditions. A Bayesian network is used to model the regulatory structure and
5248 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5249 (license license:gpl2+)))
5251 (define-public r-multidataset
5253 (name "r-multidataset")
5258 (uri (bioconductor-uri "MultiDataSet" version))
5261 "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj"))))
5262 (properties `((upstream-name . "MultiDataSet")))
5263 (build-system r-build-system)
5265 `(("r-biobase" ,r-biobase)
5266 ("r-biocgenerics" ,r-biocgenerics)
5267 ("r-genomicranges" ,r-genomicranges)
5268 ("r-ggplot2" ,r-ggplot2)
5269 ("r-ggrepel" ,r-ggrepel)
5270 ("r-iranges" ,r-iranges)
5271 ("r-limma" ,r-limma)
5272 ("r-qqman" ,r-qqman)
5273 ("r-s4vectors" ,r-s4vectors)
5274 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5275 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5276 (synopsis "Implementation of MultiDataSet and ResultSet")
5278 "This package provides an implementation of the BRGE's (Bioinformatic
5279 Research Group in Epidemiology from Center for Research in Environmental
5280 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5281 integrating multi omics data sets and ResultSet is a container for omics
5282 results. This package contains base classes for MEAL and rexposome
5284 (license license:expat)))
5286 (define-public r-ropls
5293 (uri (bioconductor-uri "ropls" version))
5296 "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a"))))
5297 (build-system r-build-system)
5299 `(("r-biobase" ,r-biobase)
5300 ("r-multidataset" ,r-multidataset)))
5302 `(("r-knitr" ,r-knitr))) ; for vignettes
5303 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5304 (synopsis "Multivariate analysis and feature selection of omics data")
5306 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5307 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5308 regression, classification, and feature selection of omics data where the
5309 number of variables exceeds the number of samples and with multicollinearity
5310 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5311 separately model the variation correlated (predictive) to the factor of
5312 interest and the uncorrelated (orthogonal) variation. While performing
5313 similarly to PLS, OPLS facilitates interpretation.
5315 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5316 analysis and feature selection of omics data. In addition to scores, loadings
5317 and weights plots, the package provides metrics and graphics to determine the
5318 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5319 validity of the model by permutation testing, detect outliers, and perform
5320 feature selection (e.g. with Variable Importance in Projection or regression
5322 (license license:cecill)))
5324 (define-public r-biosigner
5326 (name "r-biosigner")
5331 (uri (bioconductor-uri "biosigner" version))
5334 "0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl"))))
5335 (build-system r-build-system)
5337 `(("r-biobase" ,r-biobase)
5338 ("r-e1071" ,r-e1071)
5339 ("r-multidataset" ,r-multidataset)
5340 ("r-randomforest" ,r-randomforest)
5341 ("r-ropls" ,r-ropls)))
5343 `(("r-knitr" ,r-knitr)))
5344 (home-page "https://bioconductor.org/packages/biosigner/")
5345 (synopsis "Signature discovery from omics data")
5347 "Feature selection is critical in omics data analysis to extract
5348 restricted and meaningful molecular signatures from complex and high-dimension
5349 data, and to build robust classifiers. This package implements a method to
5350 assess the relevance of the variables for the prediction performances of the
5351 classifier. The approach can be run in parallel with the PLS-DA, Random
5352 Forest, and SVM binary classifiers. The signatures and the corresponding
5353 'restricted' models are returned, enabling future predictions on new
5355 (license license:cecill)))
5357 (define-public r-annotatr
5364 (uri (bioconductor-uri "annotatr" version))
5367 "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj"))))
5368 (build-system r-build-system)
5370 `(("r-annotationdbi" ,r-annotationdbi)
5371 ("r-annotationhub" ,r-annotationhub)
5372 ("r-dplyr" ,r-dplyr)
5373 ("r-genomeinfodb" ,r-genomeinfodb)
5374 ("r-genomicfeatures" ,r-genomicfeatures)
5375 ("r-genomicranges" ,r-genomicranges)
5376 ("r-ggplot2" ,r-ggplot2)
5377 ("r-iranges" ,r-iranges)
5378 ("r-readr" ,r-readr)
5379 ("r-regioner" ,r-regioner)
5380 ("r-reshape2" ,r-reshape2)
5381 ("r-rtracklayer" ,r-rtracklayer)
5382 ("r-s4vectors" ,r-s4vectors)))
5383 (home-page "https://bioconductor.org/packages/annotatr/")
5384 (synopsis "Annotation of genomic regions to genomic annotations")
5386 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5387 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5388 to investigate the intersecting genomic annotations. Such annotations include
5389 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5390 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5391 enhancers. The annotatr package provides an easy way to summarize and
5392 visualize the intersection of genomic sites/regions with genomic
5394 (license license:gpl3)))
5396 (define-public r-rsubread
5403 (uri (bioconductor-uri "Rsubread" version))
5406 "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy"))))
5407 (properties `((upstream-name . "Rsubread")))
5408 (build-system r-build-system)
5409 (inputs `(("zlib" ,zlib)))
5410 (home-page "https://bioconductor.org/packages/Rsubread/")
5411 (synopsis "Subread sequence alignment and counting for R")
5413 "This package provides tools for alignment, quantification and analysis
5414 of second and third generation sequencing data. It includes functionality for
5415 read mapping, read counting, SNP calling, structural variant detection and
5416 gene fusion discovery. It can be applied to all major sequencing techologies
5417 and to both short and long sequence reads.")
5418 (license license:gpl3)))
5420 (define-public r-flowutils
5422 (name "r-flowutils")
5427 (uri (bioconductor-uri "flowUtils" version))
5430 "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81"))))
5431 (properties `((upstream-name . "flowUtils")))
5432 (build-system r-build-system)
5434 `(("r-biobase" ,r-biobase)
5435 ("r-corpcor" ,r-corpcor)
5436 ("r-flowcore" ,r-flowcore)
5437 ("r-graph" ,r-graph)
5438 ("r-runit" ,r-runit)
5440 (home-page "https://github.com/jspidlen/flowUtils")
5441 (synopsis "Utilities for flow cytometry")
5443 "This package provides utilities for flow cytometry data.")
5444 (license license:artistic2.0)))
5446 (define-public r-consensusclusterplus
5448 (name "r-consensusclusterplus")
5453 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5456 "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4"))))
5458 `((upstream-name . "ConsensusClusterPlus")))
5459 (build-system r-build-system)
5462 ("r-biobase" ,r-biobase)
5463 ("r-cluster" ,r-cluster)))
5464 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5465 (synopsis "Clustering algorithm")
5467 "This package provides an implementation of an algorithm for determining
5468 cluster count and membership by stability evidence in unsupervised analysis.")
5469 (license license:gpl2)))
5471 (define-public r-cytolib
5478 (uri (bioconductor-uri "cytolib" version))
5481 "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9"))))
5482 (properties `((upstream-name . "cytolib")))
5483 (build-system r-build-system)
5484 (home-page "https://bioconductor.org/packages/cytolib/")
5485 (synopsis "C++ infrastructure for working with gated cytometry")
5487 "This package provides the core data structure and API to represent and
5488 interact with gated cytometry data.")
5489 (license license:artistic2.0)))
5491 (define-public r-flowcore
5498 (uri (bioconductor-uri "flowCore" version))
5501 "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2"))))
5502 (properties `((upstream-name . "flowCore")))
5503 (build-system r-build-system)
5506 ("r-biobase" ,r-biobase)
5507 ("r-biocgenerics" ,r-biocgenerics)
5508 ("r-cytolib" ,r-cytolib)
5509 ("r-matrixstats" ,r-matrixstats)
5510 ("r-rcpp" ,r-rcpp)))
5511 (home-page "https://bioconductor.org/packages/flowCore")
5512 (synopsis "Basic structures for flow cytometry data")
5514 "This package provides S4 data structures and basic functions to deal
5515 with flow cytometry data.")
5516 (license license:artistic2.0)))
5518 (define-public r-flowmeans
5520 (name "r-flowmeans")
5525 (uri (bioconductor-uri "flowMeans" version))
5528 "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h"))))
5529 (properties `((upstream-name . "flowMeans")))
5530 (build-system r-build-system)
5532 `(("r-biobase" ,r-biobase)
5533 ("r-feature" ,r-feature)
5534 ("r-flowcore" ,r-flowcore)
5535 ("r-rrcov" ,r-rrcov)))
5536 (home-page "https://bioconductor.org/packages/flowMeans")
5537 (synopsis "Non-parametric flow cytometry data gating")
5539 "This package provides tools to identify cell populations in Flow
5540 Cytometry data using non-parametric clustering and segmented-regression-based
5541 change point detection.")
5542 (license license:artistic2.0)))
5544 (define-public r-ncdfflow
5551 (uri (bioconductor-uri "ncdfFlow" version))
5554 "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i"))))
5555 (properties `((upstream-name . "ncdfFlow")))
5556 (build-system r-build-system)
5561 ("r-biobase" ,r-biobase)
5562 ("r-biocgenerics" ,r-biocgenerics)
5563 ("r-flowcore" ,r-flowcore)
5565 ("r-rcpparmadillo" ,r-rcpparmadillo)
5566 ("r-rhdf5lib" ,r-rhdf5lib)
5567 ("r-zlibbioc" ,r-zlibbioc)))
5568 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5569 (synopsis "HDF5 based storage for flow cytometry data")
5571 "This package provides HDF5 storage based methods and functions for
5572 manipulation of flow cytometry data.")
5573 (license license:artistic2.0)))
5575 (define-public r-ggcyto
5582 (uri (bioconductor-uri "ggcyto" version))
5585 "16jwdslhmj1nsa28wmaircy15cq7qn8nsyiawinjv711qiqhgw50"))))
5586 (properties `((upstream-name . "ggcyto")))
5587 (build-system r-build-system)
5589 `(("r-data-table" ,r-data-table)
5590 ("r-flowcore" ,r-flowcore)
5591 ("r-flowworkspace" ,r-flowworkspace)
5592 ("r-ggplot2" ,r-ggplot2)
5593 ("r-gridextra" ,r-gridextra)
5594 ("r-ncdfflow" ,r-ncdfflow)
5596 ("r-rcolorbrewer" ,r-rcolorbrewer)
5597 ("r-rlang" ,r-rlang)
5598 ("r-scales" ,r-scales)))
5600 `(("r-knitr" ,r-knitr)))
5601 (home-page "https://github.com/RGLab/ggcyto/issues")
5602 (synopsis "Visualize Cytometry data with ggplot")
5604 "With the dedicated fortify method implemented for @code{flowSet},
5605 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
5606 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
5607 and some custom layers also make it easy to add gates and population
5608 statistics to the plot.")
5609 (license license:artistic2.0)))
5611 (define-public r-flowviz
5618 (uri (bioconductor-uri "flowViz" version))
5621 "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7"))))
5622 (properties `((upstream-name . "flowViz")))
5623 (build-system r-build-system)
5625 `(("r-biobase" ,r-biobase)
5626 ("r-flowcore" ,r-flowcore)
5627 ("r-hexbin" ,r-hexbin)
5628 ("r-idpmisc" ,r-idpmisc)
5629 ("r-kernsmooth" ,r-kernsmooth)
5630 ("r-lattice" ,r-lattice)
5631 ("r-latticeextra" ,r-latticeextra)
5633 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5634 (home-page "https://bioconductor.org/packages/flowViz/")
5635 (synopsis "Visualization for flow cytometry")
5637 "This package provides visualization tools for flow cytometry data.")
5638 (license license:artistic2.0)))
5640 (define-public r-flowclust
5642 (name "r-flowclust")
5647 (uri (bioconductor-uri "flowClust" version))
5650 "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s"))))
5651 (properties `((upstream-name . "flowClust")))
5652 (build-system r-build-system)
5655 (list "--configure-args=--enable-bundled-gsl=no")))
5657 `(("r-biobase" ,r-biobase)
5658 ("r-biocgenerics" ,r-biocgenerics)
5660 ("r-corpcor" ,r-corpcor)
5661 ("r-ellipse" ,r-ellipse)
5662 ("r-flowcore" ,r-flowcore)
5663 ("r-flowviz" ,r-flowviz)
5664 ("r-graph" ,r-graph)
5665 ("r-mnormt" ,r-mnormt)))
5669 `(("pkg-config" ,pkg-config)))
5670 (home-page "https://bioconductor.org/packages/flowClust")
5671 (synopsis "Clustering for flow cytometry")
5673 "This package provides robust model-based clustering using a t-mixture
5674 model with Box-Cox transformation.")
5675 (license license:artistic2.0)))
5677 ;; TODO: this package bundles an old version of protobuf. It's not easy to
5678 ;; make it use our protobuf package instead.
5679 (define-public r-rprotobuflib
5681 (name "r-rprotobuflib")
5686 (uri (bioconductor-uri "RProtoBufLib" version))
5689 "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm"))))
5690 (properties `((upstream-name . "RProtoBufLib")))
5691 (build-system r-build-system)
5694 (modify-phases %standard-phases
5695 (add-after 'unpack 'unpack-bundled-sources
5697 (with-directory-excursion "src"
5698 (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
5700 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
5701 (synopsis "C++ headers and static libraries of Protocol buffers")
5703 "This package provides the headers and static library of Protocol buffers
5704 for other R packages to compile and link against.")
5705 (license license:bsd-3)))
5707 (define-public r-flowworkspace
5709 (name "r-flowworkspace")
5714 (uri (bioconductor-uri "flowWorkspace" version))
5717 "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn"))))
5718 (properties `((upstream-name . "flowWorkspace")))
5719 (build-system r-build-system)
5722 ("r-biobase" ,r-biobase)
5723 ("r-biocgenerics" ,r-biocgenerics)
5724 ("r-cytolib" ,r-cytolib)
5725 ("r-data-table" ,r-data-table)
5726 ("r-digest" ,r-digest)
5727 ("r-dplyr" ,r-dplyr)
5728 ("r-flowcore" ,r-flowcore)
5729 ("r-flowviz" ,r-flowviz)
5730 ("r-graph" ,r-graph)
5731 ("r-gridextra" ,r-gridextra)
5732 ("r-lattice" ,r-lattice)
5733 ("r-latticeextra" ,r-latticeextra)
5734 ("r-matrixstats" ,r-matrixstats)
5735 ("r-ncdfflow" ,r-ncdfflow)
5737 ("r-rcolorbrewer" ,r-rcolorbrewer)
5739 ("r-rcppparallel" ,r-rcppparallel)
5740 ("r-rgraphviz" ,r-rgraphviz)
5741 ("r-rprotobuflib" ,r-rprotobuflib)
5742 ("r-scales" ,r-scales)
5743 ("r-stringr" ,r-stringr)))
5744 (home-page "https://bioconductor.org/packages/flowWorkspace/")
5745 (synopsis "Infrastructure for working with cytometry data")
5747 "This package is designed to facilitate comparison of automated gating
5748 methods against manual gating done in flowJo. This package allows you to
5749 import basic flowJo workspaces into BioConductor and replicate the gating from
5750 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
5751 samples, compensation, and transformation are performed so that the output
5752 matches the flowJo analysis.")
5753 (license license:artistic2.0)))
5755 (define-public r-flowstats
5757 (name "r-flowstats")
5762 (uri (bioconductor-uri "flowStats" version))
5765 "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w"))))
5766 (properties `((upstream-name . "flowStats")))
5767 (build-system r-build-system)
5769 `(("r-biobase" ,r-biobase)
5770 ("r-biocgenerics" ,r-biocgenerics)
5771 ("r-cluster" ,r-cluster)
5773 ("r-flowcore" ,r-flowcore)
5774 ("r-flowviz" ,r-flowviz)
5775 ("r-flowworkspace" ,r-flowworkspace)
5776 ("r-kernsmooth" ,r-kernsmooth)
5778 ("r-lattice" ,r-lattice)
5780 ("r-ncdfflow" ,r-ncdfflow)
5781 ("r-rcolorbrewer" ,r-rcolorbrewer)
5782 ("r-rrcov" ,r-rrcov)))
5783 (home-page "http://www.github.com/RGLab/flowStats")
5784 (synopsis "Statistical methods for the analysis of flow cytometry data")
5786 "This package provides methods and functionality to analyze flow data
5787 that is beyond the basic infrastructure provided by the @code{flowCore}
5789 (license license:artistic2.0)))
5791 (define-public r-opencyto
5798 (uri (bioconductor-uri "openCyto" version))
5801 "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb"))))
5802 (properties `((upstream-name . "openCyto")))
5803 (build-system r-build-system)
5805 `(("r-biobase" ,r-biobase)
5806 ("r-biocgenerics" ,r-biocgenerics)
5808 ("r-data-table" ,r-data-table)
5809 ("r-flowclust" ,r-flowclust)
5810 ("r-flowcore" ,r-flowcore)
5811 ("r-flowstats" ,r-flowstats)
5812 ("r-flowviz" ,r-flowviz)
5813 ("r-flowworkspace" ,r-flowworkspace)
5814 ("r-graph" ,r-graph)
5815 ("r-gtools" ,r-gtools)
5817 ("r-lattice" ,r-lattice)
5819 ("r-ncdfflow" ,r-ncdfflow)
5821 ("r-r-utils" ,r-r-utils)
5823 ("r-rcolorbrewer" ,r-rcolorbrewer)
5825 ("r-rrcov" ,r-rrcov)))
5826 (home-page "https://bioconductor.org/packages/openCyto")
5827 (synopsis "Hierarchical gating pipeline for flow cytometry data")
5829 "This package is designed to facilitate the automated gating methods in a
5830 sequential way to mimic the manual gating strategy.")
5831 (license license:artistic2.0)))
5833 (define-public r-cytoml
5840 (uri (bioconductor-uri "CytoML" version))
5843 "0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz"))))
5844 (properties `((upstream-name . "CytoML")))
5845 (build-system r-build-system)
5847 `(("libxml2" ,libxml2)))
5849 `(("r-base64enc" ,r-base64enc)
5851 ("r-biobase" ,r-biobase)
5852 ("r-corpcor" ,r-corpcor)
5853 ("r-cytolib" ,r-cytolib)
5854 ("r-data-table" ,r-data-table)
5855 ("r-dplyr" ,r-dplyr)
5856 ("r-flowcore" ,r-flowcore)
5857 ("r-flowworkspace" ,r-flowworkspace)
5858 ("r-ggcyto" ,r-ggcyto)
5859 ("r-graph" ,r-graph)
5860 ("r-jsonlite" ,r-jsonlite)
5861 ("r-lattice" ,r-lattice)
5862 ("r-ncdfflow" ,r-ncdfflow)
5863 ("r-opencyto" ,r-opencyto)
5867 ("r-rcppparallel" ,r-rcppparallel)
5868 ("r-rgraphviz" ,r-rgraphviz)
5869 ("r-rprotobuflib" ,r-rprotobuflib)
5870 ("r-runit" ,r-runit)
5872 ("r-yaml" ,r-yaml)))
5874 `(("r-knitr" ,r-knitr)))
5875 (home-page "https://github.com/RGLab/CytoML")
5876 (synopsis "GatingML interface for cross platform cytometry data sharing")
5878 "This package provides an interface to implementations of the GatingML2.0
5879 standard to exchange gated cytometry data with other software platforms.")
5880 (license license:artistic2.0)))
5882 (define-public r-flowsom
5889 (uri (bioconductor-uri "FlowSOM" version))
5892 "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5"))))
5893 (properties `((upstream-name . "FlowSOM")))
5894 (build-system r-build-system)
5896 `(("r-biocgenerics" ,r-biocgenerics)
5897 ("r-consensusclusterplus" ,r-consensusclusterplus)
5898 ("r-cytoml" ,r-cytoml)
5899 ("r-flowcore" ,r-flowcore)
5900 ("r-flowworkspace" ,r-flowworkspace)
5901 ("r-igraph" ,r-igraph)
5902 ("r-rcolorbrewer" ,r-rcolorbrewer)
5905 (home-page "https://bioconductor.org/packages/FlowSOM/")
5906 (synopsis "Visualize and interpret cytometry data")
5908 "FlowSOM offers visualization options for cytometry data, by using
5909 self-organizing map clustering and minimal spanning trees.")
5910 (license license:gpl2+)))
5912 (define-public r-mixomics
5919 (uri (bioconductor-uri "mixOmics" version))
5922 "0307vhx9ck24rxqbvq15815ssxcc226sl2la060n204b51wi9jaa"))))
5923 (properties `((upstream-name . "mixOmics")))
5924 (build-system r-build-system)
5926 `(("r-corpcor" ,r-corpcor)
5927 ("r-dplyr" ,r-dplyr)
5928 ("r-ellipse" ,r-ellipse)
5929 ("r-ggplot2" ,r-ggplot2)
5930 ("r-gridextra" ,r-gridextra)
5931 ("r-igraph" ,r-igraph)
5932 ("r-lattice" ,r-lattice)
5934 ("r-matrixstats" ,r-matrixstats)
5935 ("r-rarpack" ,r-rarpack)
5936 ("r-rcolorbrewer" ,r-rcolorbrewer)
5937 ("r-reshape2" ,r-reshape2)
5938 ("r-tidyr" ,r-tidyr)))
5939 (home-page "http://www.mixOmics.org")
5940 (synopsis "Multivariate methods for exploration of biological datasets")
5942 "mixOmics offers a wide range of multivariate methods for the exploration
5943 and integration of biological datasets with a particular focus on variable
5944 selection. The package proposes several sparse multivariate models we have
5945 developed to identify the key variables that are highly correlated, and/or
5946 explain the biological outcome of interest. The data that can be analysed
5947 with mixOmics may come from high throughput sequencing technologies, such as
5948 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5949 also beyond the realm of omics (e.g. spectral imaging). The methods
5950 implemented in mixOmics can also handle missing values without having to
5951 delete entire rows with missing data.")
5952 (license license:gpl2+)))
5954 (define-public r-depecher
5961 (uri (bioconductor-uri "DepecheR" version))
5964 "199j2kw0xnw7y4v1gakm2jgyc7zzlj8xh0570f2yjq55gp1kggbm"))))
5965 (properties `((upstream-name . "DepecheR")))
5966 (build-system r-build-system)
5968 `(("r-beanplot" ,r-beanplot)
5969 ("r-dosnow" ,r-dosnow)
5970 ("r-dplyr" ,r-dplyr)
5972 ("r-foreach" ,r-foreach)
5973 ("r-ggplot2" ,r-ggplot2)
5974 ("r-gplots" ,r-gplots)
5976 ("r-matrixstats" ,r-matrixstats)
5977 ("r-mixomics" ,r-mixomics)
5978 ("r-moments" ,r-moments)
5980 ("r-rcppeigen" ,r-rcppeigen)
5981 ("r-reshape2" ,r-reshape2)
5982 ("r-robustbase" ,r-robustbase)
5983 ("r-viridis" ,r-viridis)))
5985 `(("r-knitr" ,r-knitr)))
5986 (home-page "https://bioconductor.org/packages/DepecheR/")
5987 (synopsis "Identify traits of clusters in high-dimensional entities")
5989 "The purpose of this package is to identify traits in a dataset that can
5990 separate groups. This is done on two levels. First, clustering is performed,
5991 using an implementation of sparse K-means. Secondly, the generated clusters
5992 are used to predict outcomes of groups of individuals based on their
5993 distribution of observations in the different clusters. As certain clusters
5994 with separating information will be identified, and these clusters are defined
5995 by a sparse number of variables, this method can reduce the complexity of
5996 data, to only emphasize the data that actually matters.")
5997 (license license:expat)))
5999 (define-public r-rcistarget
6001 (name "r-rcistarget")
6006 (uri (bioconductor-uri "RcisTarget" version))
6009 "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw"))))
6010 (properties `((upstream-name . "RcisTarget")))
6011 (build-system r-build-system)
6013 `(("r-aucell" ,r-aucell)
6014 ("r-biocgenerics" ,r-biocgenerics)
6015 ("r-data-table" ,r-data-table)
6016 ("r-feather" ,r-feather)
6017 ("r-gseabase" ,r-gseabase)
6018 ("r-r-utils" ,r-r-utils)
6019 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6020 (home-page "https://aertslab.org/#scenic")
6021 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6023 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6024 over-represented on a gene list. In a first step, RcisTarget selects DNA
6025 motifs that are significantly over-represented in the surroundings of the
6026 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6027 achieved by using a database that contains genome-wide cross-species rankings
6028 for each motif. The motifs that are then annotated to TFs and those that have
6029 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6030 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6031 genes in the gene-set that are ranked above the leading edge).")
6032 (license license:gpl3)))
6034 (define-public r-cicero
6041 (uri (bioconductor-uri "cicero" version))
6044 "1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld"))))
6045 (build-system r-build-system)
6047 `(("r-assertthat" ,r-assertthat)
6048 ("r-biobase" ,r-biobase)
6049 ("r-biocgenerics" ,r-biocgenerics)
6050 ("r-data-table" ,r-data-table)
6051 ("r-dplyr" ,r-dplyr)
6053 ("r-genomicranges" ,r-genomicranges)
6054 ("r-ggplot2" ,r-ggplot2)
6055 ("r-glasso" ,r-glasso)
6057 ("r-igraph" ,r-igraph)
6058 ("r-iranges" ,r-iranges)
6059 ("r-matrix" ,r-matrix)
6060 ("r-monocle" ,r-monocle)
6062 ("r-reshape2" ,r-reshape2)
6063 ("r-s4vectors" ,r-s4vectors)
6064 ("r-stringr" ,r-stringr)
6065 ("r-tibble" ,r-tibble)
6066 ("r-tidyr" ,r-tidyr)
6067 ("r-vgam" ,r-vgam)))
6069 `(("r-knitr" ,r-knitr)))
6070 (home-page "https://bioconductor.org/packages/cicero/")
6071 (synopsis "Predict cis-co-accessibility from single-cell data")
6073 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6074 accessibility data. It also extends the monocle package for use in chromatin
6075 accessibility data.")
6076 (license license:expat)))
6078 ;; This is the latest commit on the "monocle3" branch.
6079 (define-public r-cicero-monocle3
6080 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6082 (package (inherit r-cicero)
6083 (name "r-cicero-monocle3")
6084 (version (git-version "1.3.2" revision commit))
6089 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
6091 (file-name (git-file-name name version))
6094 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6096 `(("r-monocle3" ,r-monocle3)
6097 ,@(alist-delete "r-monocle"
6098 (package-propagated-inputs r-cicero)))))))
6100 (define-public r-cistopic
6101 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6105 (version (git-version "0.2.1" revision commit))
6110 (url "https://github.com/aertslab/cisTopic.git")
6112 (file-name (git-file-name name version))
6115 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6116 (build-system r-build-system)
6118 `(("r-aucell" ,r-aucell)
6119 ("r-data-table" ,r-data-table)
6120 ("r-dplyr" ,r-dplyr)
6121 ("r-dosnow" ,r-dosnow)
6123 ("r-feather" ,r-feather)
6124 ("r-fitdistrplus" ,r-fitdistrplus)
6125 ("r-genomicranges" ,r-genomicranges)
6126 ("r-ggplot2" ,r-ggplot2)
6128 ("r-matrix" ,r-matrix)
6130 ("r-rcistarget" ,r-rcistarget)
6131 ("r-rtracklayer" ,r-rtracklayer)
6132 ("r-s4vectors" ,r-s4vectors)))
6133 (home-page "https://github.com/aertslab/cisTopic")
6134 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6136 "The sparse nature of single cell epigenomics data can be overruled using
6137 probabilistic modelling methods such as @dfn{Latent Dirichlet
6138 Allocation} (LDA). This package allows the probabilistic modelling of
6139 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6140 includes functionalities to identify cell states based on the contribution of
6141 cisTopics and explore the nature and regulatory proteins driving them.")
6142 (license license:gpl3))))
6144 (define-public r-genie3
6151 (uri (bioconductor-uri "GENIE3" version))
6154 "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l"))))
6155 (properties `((upstream-name . "GENIE3")))
6156 (build-system r-build-system)
6157 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6158 (home-page "https://bioconductor.org/packages/GENIE3")
6159 (synopsis "Gene network inference with ensemble of trees")
6161 "This package implements the GENIE3 algorithm for inferring gene
6162 regulatory networks from expression data.")
6163 (license license:gpl2+)))
6165 (define-public r-roc
6172 (uri (bioconductor-uri "ROC" version))
6175 "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y"))))
6176 (properties `((upstream-name . "ROC")))
6177 (build-system r-build-system)
6179 `(("r-knitr" ,r-knitr)))
6180 (home-page "https://www.bioconductor.org/packages/ROC/")
6181 (synopsis "Utilities for ROC curves")
6183 "This package provides utilities for @dfn{Receiver Operating
6184 Characteristic} (ROC) curves, with a focus on micro arrays.")
6185 (license license:artistic2.0)))
6187 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6189 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6194 (uri (bioconductor-uri
6195 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6196 version 'annotation))
6199 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6202 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6203 (build-system r-build-system)
6204 (propagated-inputs `(("r-minfi" ,r-minfi)))
6206 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6207 (synopsis "Annotation for Illumina's 450k methylation arrays")
6209 "This package provides manifests and annotation for Illumina's 450k array
6211 (license license:artistic2.0)))
6213 (define-public r-watermelon
6215 (name "r-watermelon")
6220 (uri (bioconductor-uri "wateRmelon" version))
6223 "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0"))))
6224 (properties `((upstream-name . "wateRmelon")))
6225 (build-system r-build-system)
6227 `(("r-biobase" ,r-biobase)
6228 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6229 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6230 ("r-illuminaio" ,r-illuminaio)
6231 ("r-limma" ,r-limma)
6233 ("r-matrixstats" ,r-matrixstats)
6234 ("r-methylumi" ,r-methylumi)
6236 (home-page "https://bioconductor.org/packages/wateRmelon/")
6237 (synopsis "Illumina 450 methylation array normalization and metrics")
6239 "The standard index of DNA methylation (beta) is computed from methylated
6240 and unmethylated signal intensities. Betas calculated from raw signal
6241 intensities perform well, but using 11 methylomic datasets we demonstrate that
6242 quantile normalization methods produce marked improvement. The commonly used
6243 procedure of normalizing betas is inferior to the separate normalization of M
6244 and U, and it is also advantageous to normalize Type I and Type II assays
6245 separately. This package provides 15 flavours of betas and three performance
6246 metrics, with methods for objects produced by the @code{methylumi} and
6247 @code{minfi} packages.")
6248 (license license:gpl3)))
6250 (define-public r-gdsfmt
6257 (uri (bioconductor-uri "gdsfmt" version))
6260 "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9"))
6261 (modules '((guix build utils)))
6262 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6263 ;; them and link with system libraries instead.
6266 (for-each delete-file-recursively
6270 (substitute* "src/Makevars"
6271 (("all: \\$\\(SHLIB\\)") "all:")
6272 (("\\$\\(SHLIB\\): liblzma.a") "")
6273 (("(ZLIB|LZ4)/.*") "")
6274 (("CoreArray/dVLIntGDS.cpp.*")
6275 "CoreArray/dVLIntGDS.cpp")
6276 (("CoreArray/dVLIntGDS.o.*")
6277 "CoreArray/dVLIntGDS.o")
6278 (("PKG_LIBS = ./liblzma.a")
6279 "PKG_LIBS = -llz4"))
6280 (substitute* "src/CoreArray/dStream.h"
6281 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6282 (string-append "include <" header ">")))
6284 (properties `((upstream-name . "gdsfmt")))
6285 (build-system r-build-system)
6290 (home-page "http://corearray.sourceforge.net/")
6292 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6294 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6295 Data Structure} (GDS) data files, which are portable across platforms with
6296 hierarchical structure to store multiple scalable array-oriented data sets
6297 with metadata information. It is suited for large-scale datasets, especially
6298 for data which are much larger than the available random-access memory. The
6299 @code{gdsfmt} package offers efficient operations specifically designed for
6300 integers of less than 8 bits, since a diploid genotype, like
6301 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6302 byte. Data compression and decompression are available with relatively
6303 efficient random access. It is also allowed to read a GDS file in parallel
6304 with multiple R processes supported by the package @code{parallel}.")
6305 (license license:lgpl3)))
6307 (define-public r-bigmelon
6314 (uri (bioconductor-uri "bigmelon" version))
6317 "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls"))))
6318 (properties `((upstream-name . "bigmelon")))
6319 (build-system r-build-system)
6321 `(("r-biobase" ,r-biobase)
6322 ("r-biocgenerics" ,r-biocgenerics)
6323 ("r-gdsfmt" ,r-gdsfmt)
6324 ("r-geoquery" ,r-geoquery)
6325 ("r-methylumi" ,r-methylumi)
6326 ("r-minfi" ,r-minfi)
6327 ("r-watermelon" ,r-watermelon)))
6328 (home-page "https://bioconductor.org/packages/bigmelon/")
6329 (synopsis "Illumina methylation array analysis for large experiments")
6331 "This package provides methods for working with Illumina arrays using the
6332 @code{gdsfmt} package.")
6333 (license license:gpl3)))
6335 (define-public r-seqbias
6342 (uri (bioconductor-uri "seqbias" version))
6345 "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq"))))
6346 (properties `((upstream-name . "seqbias")))
6347 (build-system r-build-system)
6349 `(("r-biostrings" ,r-biostrings)
6350 ("r-genomicranges" ,r-genomicranges)
6351 ("r-rhtslib" ,r-rhtslib)))
6353 `(("zlib" ,zlib))) ; This comes from rhtslib.
6354 (home-page "https://bioconductor.org/packages/seqbias/")
6355 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6357 "This package implements a model of per-position sequencing bias in
6358 high-throughput sequencing data using a simple Bayesian network, the structure
6359 and parameters of which are trained on a set of aligned reads and a reference
6361 (license license:lgpl3)))
6363 (define-public r-reqon
6370 (uri (bioconductor-uri "ReQON" version))
6373 "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx"))))
6374 (properties `((upstream-name . "ReQON")))
6375 (build-system r-build-system)
6377 `(("r-rjava" ,r-rjava)
6378 ("r-rsamtools" ,r-rsamtools)
6379 ("r-seqbias" ,r-seqbias)))
6380 (home-page "https://bioconductor.org/packages/ReQON/")
6381 (synopsis "Recalibrating quality of nucleotides")
6383 "This package provides an implementation of an algorithm for
6384 recalibrating the base quality scores for aligned sequencing data in BAM
6386 (license license:gpl2)))
6388 (define-public r-wavcluster
6390 (name "r-wavcluster")
6395 (uri (bioconductor-uri "wavClusteR" version))
6398 "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y"))))
6399 (properties `((upstream-name . "wavClusteR")))
6400 (build-system r-build-system)
6402 `(("r-biocgenerics" ,r-biocgenerics)
6403 ("r-biostrings" ,r-biostrings)
6404 ("r-foreach" ,r-foreach)
6405 ("r-genomicfeatures" ,r-genomicfeatures)
6406 ("r-genomicranges" ,r-genomicranges)
6407 ("r-ggplot2" ,r-ggplot2)
6408 ("r-hmisc" ,r-hmisc)
6409 ("r-iranges" ,r-iranges)
6410 ("r-mclust" ,r-mclust)
6411 ("r-rsamtools" ,r-rsamtools)
6412 ("r-rtracklayer" ,r-rtracklayer)
6413 ("r-s4vectors" ,r-s4vectors)
6414 ("r-seqinr" ,r-seqinr)
6415 ("r-stringr" ,r-stringr)
6416 ("r-wmtsa" ,r-wmtsa)))
6417 (home-page "https://bioconductor.org/packages/wavClusteR/")
6418 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6420 "This package provides an integrated pipeline for the analysis of
6421 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6422 sequencing errors, SNPs and additional non-experimental sources by a non-
6423 parametric mixture model. The protein binding sites (clusters) are then
6424 resolved at high resolution and cluster statistics are estimated using a
6425 rigorous Bayesian framework. Post-processing of the results, data export for
6426 UCSC genome browser visualization and motif search analysis are provided. In
6427 addition, the package allows to integrate RNA-Seq data to estimate the False
6428 Discovery Rate of cluster detection. Key functions support parallel multicore
6429 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6430 be applied to the analysis of other NGS data obtained from experimental
6431 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6432 (license license:gpl2)))
6434 (define-public r-timeseriesexperiment
6436 (name "r-timeseriesexperiment")
6441 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6444 "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm"))))
6446 `((upstream-name . "TimeSeriesExperiment")))
6447 (build-system r-build-system)
6449 `(("r-deseq2" ,r-deseq2)
6450 ("r-dplyr" ,r-dplyr)
6451 ("r-dynamictreecut" ,r-dynamictreecut)
6452 ("r-edger" ,r-edger)
6453 ("r-ggplot2" ,r-ggplot2)
6454 ("r-hmisc" ,r-hmisc)
6455 ("r-limma" ,r-limma)
6456 ("r-magrittr" ,r-magrittr)
6457 ("r-proxy" ,r-proxy)
6458 ("r-s4vectors" ,r-s4vectors)
6459 ("r-summarizedexperiment" ,r-summarizedexperiment)
6460 ("r-tibble" ,r-tibble)
6461 ("r-tidyr" ,r-tidyr)
6462 ("r-vegan" ,r-vegan)
6463 ("r-viridis" ,r-viridis)))
6464 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6465 (synopsis "Analysis for short time-series data")
6467 "This package is a visualization and analysis toolbox for short time
6468 course data which includes dimensionality reduction, clustering, two-sample
6469 differential expression testing and gene ranking techniques. The package also
6470 provides methods for retrieving enriched pathways.")
6471 (license license:lgpl3+)))
6473 (define-public r-variantfiltering
6475 (name "r-variantfiltering")
6480 (uri (bioconductor-uri "VariantFiltering" version))
6483 "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8"))))
6485 `((upstream-name . "VariantFiltering")))
6486 (build-system r-build-system)
6488 `(("r-annotationdbi" ,r-annotationdbi)
6489 ("r-biobase" ,r-biobase)
6490 ("r-biocgenerics" ,r-biocgenerics)
6491 ("r-biocparallel" ,r-biocparallel)
6492 ("r-biostrings" ,r-biostrings)
6493 ("r-bsgenome" ,r-bsgenome)
6495 ("r-genomeinfodb" ,r-genomeinfodb)
6496 ("r-genomicfeatures" ,r-genomicfeatures)
6497 ("r-genomicranges" ,r-genomicranges)
6498 ("r-genomicscores" ,r-genomicscores)
6499 ("r-graph" ,r-graph)
6501 ("r-iranges" ,r-iranges)
6503 ("r-rsamtools" ,r-rsamtools)
6504 ("r-s4vectors" ,r-s4vectors)
6505 ("r-shiny" ,r-shiny)
6506 ("r-shinyjs" ,r-shinyjs)
6507 ("r-shinythemes" ,r-shinythemes)
6508 ("r-shinytree" ,r-shinytree)
6509 ("r-summarizedexperiment" ,r-summarizedexperiment)
6510 ("r-variantannotation" ,r-variantannotation)
6511 ("r-xvector" ,r-xvector)))
6512 (home-page "https://github.com/rcastelo/VariantFiltering")
6513 (synopsis "Filtering of coding and non-coding genetic variants")
6515 "Filter genetic variants using different criteria such as inheritance
6516 model, amino acid change consequence, minor allele frequencies across human
6517 populations, splice site strength, conservation, etc.")
6518 (license license:artistic2.0)))
6520 (define-public r-genomegraphs
6522 (name "r-genomegraphs")
6527 (uri (bioconductor-uri "GenomeGraphs" version))
6530 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
6531 (properties `((upstream-name . "GenomeGraphs")))
6532 (build-system r-build-system)
6534 `(("r-biomart" ,r-biomart)))
6535 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
6536 (synopsis "Plotting genomic information from Ensembl")
6538 "Genomic data analyses requires integrated visualization of known genomic
6539 information and new experimental data. GenomeGraphs uses the biomaRt package
6540 to perform live annotation queries to Ensembl and translates this to e.g.
6541 gene/transcript structures in viewports of the grid graphics package. This
6542 results in genomic information plotted together with your data. Another
6543 strength of GenomeGraphs is to plot different data types such as array CGH,
6544 gene expression, sequencing and other data, together in one plot using the
6545 same genome coordinate system.")
6546 (license license:artistic2.0)))
6548 (define-public r-wavetiling
6550 (name "r-wavetiling")
6555 (uri (bioconductor-uri "waveTiling" version))
6558 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
6559 (properties `((upstream-name . "waveTiling")))
6560 (build-system r-build-system)
6562 `(("r-affy" ,r-affy)
6563 ("r-biobase" ,r-biobase)
6564 ("r-biostrings" ,r-biostrings)
6565 ("r-genomegraphs" ,r-genomegraphs)
6566 ("r-genomicranges" ,r-genomicranges)
6567 ("r-iranges" ,r-iranges)
6568 ("r-oligo" ,r-oligo)
6569 ("r-oligoclasses" ,r-oligoclasses)
6570 ("r-preprocesscore" ,r-preprocesscore)
6571 ("r-waveslim" ,r-waveslim)))
6572 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
6573 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
6575 "This package is designed to conduct transcriptome analysis for tiling
6576 arrays based on fast wavelet-based functional models.")
6577 (license license:gpl2+)))
6579 (define-public r-variancepartition
6581 (name "r-variancepartition")
6586 (uri (bioconductor-uri "variancePartition" version))
6589 "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g"))))
6591 `((upstream-name . "variancePartition")))
6592 (build-system r-build-system)
6594 `(("r-biobase" ,r-biobase)
6595 ("r-biocparallel" ,r-biocparallel)
6596 ("r-colorramps" ,r-colorramps)
6597 ("r-doparallel" ,r-doparallel)
6598 ("r-foreach" ,r-foreach)
6599 ("r-ggplot2" ,r-ggplot2)
6600 ("r-gplots" ,r-gplots)
6601 ("r-iterators" ,r-iterators)
6602 ("r-limma" ,r-limma)
6604 ("r-lmertest" ,r-lmertest)
6606 ("r-pbkrtest" ,r-pbkrtest)
6607 ("r-progress" ,r-progress)
6608 ("r-reshape2" ,r-reshape2)
6609 ("r-scales" ,r-scales)))
6610 (home-page "https://bioconductor.org/packages/variancePartition/")
6611 (synopsis "Analyze variation in gene expression experiments")
6613 "This is a package providing tools to quantify and interpret multiple
6614 sources of biological and technical variation in gene expression experiments.
6615 It uses a linear mixed model to quantify variation in gene expression
6616 attributable to individual, tissue, time point, or technical variables. The
6617 package includes dream differential expression analysis for repeated
6619 (license license:gpl2+)))
6621 (define-public r-htqpcr
6628 (uri (bioconductor-uri "HTqPCR" version))
6631 "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx"))))
6632 (properties `((upstream-name . "HTqPCR")))
6633 (build-system r-build-system)
6635 `(("r-affy" ,r-affy)
6636 ("r-biobase" ,r-biobase)
6637 ("r-gplots" ,r-gplots)
6638 ("r-limma" ,r-limma)
6639 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6640 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
6641 "groups/bertone/software/HTqPCR.pdf"))
6642 (synopsis "Automated analysis of high-throughput qPCR data")
6644 "Analysis of Ct values from high throughput quantitative real-time
6645 PCR (qPCR) assays across multiple conditions or replicates. The input data
6646 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
6647 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
6648 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
6649 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
6650 loading, quality assessment, normalization, visualization and parametric or
6651 non-parametric testing for statistical significance in Ct values between
6652 features (e.g. genes, microRNAs).")
6653 (license license:artistic2.0)))
6655 (define-public r-unifiedwmwqpcr
6657 (name "r-unifiedwmwqpcr")
6662 (uri (bioconductor-uri "unifiedWMWqPCR" version))
6665 "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj"))))
6667 `((upstream-name . "unifiedWMWqPCR")))
6668 (build-system r-build-system)
6670 `(("r-biocgenerics" ,r-biocgenerics)
6671 ("r-htqpcr" ,r-htqpcr)))
6672 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
6673 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
6675 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
6676 data. This modified test allows for testing differential expression in qPCR
6678 (license license:gpl2+)))
6680 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
6682 (define-public r-activedriverwgs
6684 (name "r-activedriverwgs")
6689 (uri (cran-uri "ActiveDriverWGS" version))
6692 "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
6694 `((upstream-name . "ActiveDriverWGS")))
6695 (build-system r-build-system)
6697 `(("r-biostrings" ,r-biostrings)
6698 ("r-bsgenome" ,r-bsgenome)
6699 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
6700 ("r-genomeinfodb" ,r-genomeinfodb)
6701 ("r-genomicranges" ,r-genomicranges)
6702 ("r-iranges" ,r-iranges)
6704 ("r-s4vectors" ,r-s4vectors)))
6705 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
6706 (synopsis "Driver discovery tool for cancer whole genomes")
6708 "This package provides a method for finding an enrichment of cancer
6709 simple somatic mutations (SNVs and Indels) in functional elements across the
6710 human genome. ActiveDriverWGS detects coding and noncoding driver elements
6711 using whole genome sequencing data.")
6712 (license license:gpl3)))
6714 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
6716 (define-public r-activepathways
6718 (name "r-activepathways")
6723 (uri (cran-uri "ActivePathways" version))
6726 "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20"))))
6728 `((upstream-name . "ActivePathways")))
6729 (build-system r-build-system)
6731 `(("r-data-table" ,r-data-table)
6732 ("r-ggplot2" ,r-ggplot2)
6733 ("r-metap" ,r-metap)))
6734 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
6735 (synopsis "Multivariate pathway enrichment analysis")
6737 "This package represents an integrative method of analyzing multi omics
6738 data that conducts enrichment analysis of annotated gene sets. ActivePathways
6739 uses a statistical data fusion approach, rationalizes contributing evidence
6740 and highlights associated genes, improving systems-level understanding of
6741 cellular organization in health and disease.")
6742 (license license:gpl3)))
6744 (define-public r-bgmix
6751 (uri (bioconductor-uri "BGmix" version))
6754 "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683"))))
6755 (properties `((upstream-name . "BGmix")))
6756 (build-system r-build-system)
6758 `(("r-kernsmooth" ,r-kernsmooth)))
6759 (home-page "https://bioconductor.org/packages/BGmix/")
6760 (synopsis "Bayesian models for differential gene expression")
6762 "This package provides fully Bayesian mixture models for differential
6764 (license license:gpl2)))
6766 (define-public r-bgx
6773 (uri (bioconductor-uri "bgx" version))
6776 "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm"))))
6777 (properties `((upstream-name . "bgx")))
6778 (build-system r-build-system)
6780 `(("r-affy" ,r-affy)
6781 ("r-biobase" ,r-biobase)
6782 ("r-gcrma" ,r-gcrma)
6783 ("r-rcpp" ,r-rcpp)))
6784 (home-page "https://bioconductor.org/packages/bgx/")
6785 (synopsis "Bayesian gene expression")
6787 "This package provides tools for Bayesian integrated analysis of
6788 Affymetrix GeneChips.")
6789 (license license:gpl2)))
6791 (define-public r-bhc
6798 (uri (bioconductor-uri "BHC" version))
6801 "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh"))))
6802 (properties `((upstream-name . "BHC")))
6803 (build-system r-build-system)
6804 (home-page "https://bioconductor.org/packages/BHC/")
6805 (synopsis "Bayesian hierarchical clustering")
6807 "The method implemented in this package performs bottom-up hierarchical
6808 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
6809 in the data and Bayesian model selection to decide at each step which clusters
6810 to merge. This avoids several limitations of traditional methods, for example
6811 how many clusters there should be and how to choose a principled distance
6812 metric. This implementation accepts multinomial (i.e. discrete, with 2+
6813 categories) or time-series data. This version also includes a randomised
6814 algorithm which is more efficient for larger data sets.")
6815 (license license:gpl3)))
6817 (define-public r-bicare
6824 (uri (bioconductor-uri "BicARE" version))
6827 "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs"))))
6828 (properties `((upstream-name . "BicARE")))
6829 (build-system r-build-system)
6831 `(("r-biobase" ,r-biobase)
6832 ("r-gseabase" ,r-gseabase)
6833 ("r-multtest" ,r-multtest)))
6834 (home-page "http://bioinfo.curie.fr")
6835 (synopsis "Biclustering analysis and results exploration")
6837 "This is a package for biclustering analysis and exploration of
6839 (license license:gpl2)))
6841 (define-public r-bifet
6848 (uri (bioconductor-uri "BiFET" version))
6851 "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k"))))
6852 (properties `((upstream-name . "BiFET")))
6853 (build-system r-build-system)
6855 `(("r-genomicranges" ,r-genomicranges)
6856 ("r-poibin" ,r-poibin)))
6857 (home-page "https://bioconductor.org/packages/BiFET")
6858 (synopsis "Bias-free footprint enrichment test")
6860 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
6861 over-represented in target regions compared to background regions after
6862 correcting for the bias arising from the imbalance in read counts and GC
6863 contents between the target and background regions. For a given TF k, BiFET
6864 tests the null hypothesis that the target regions have the same probability of
6865 having footprints for the TF k as the background regions while correcting for
6866 the read count and GC content bias.")
6867 (license license:gpl3)))
6869 (define-public r-rsbml
6876 (uri (bioconductor-uri "rsbml" version))
6879 "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa"))))
6880 (properties `((upstream-name . "rsbml")))
6881 (build-system r-build-system)
6883 `(("libsbml" ,libsbml)
6886 `(("r-biocgenerics" ,r-biocgenerics)
6887 ("r-graph" ,r-graph)))
6889 `(("pkg-config" ,pkg-config)))
6890 (home-page "http://www.sbml.org")
6891 (synopsis "R support for SBML")
6893 "This package provides an R interface to libsbml for SBML parsing,
6894 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
6895 (license license:artistic2.0)))
6897 (define-public r-hypergraph
6899 (name "r-hypergraph")
6904 (uri (bioconductor-uri "hypergraph" version))
6907 "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m"))))
6908 (properties `((upstream-name . "hypergraph")))
6909 (build-system r-build-system)
6911 `(("r-graph" ,r-graph)))
6912 (home-page "https://bioconductor.org/packages/hypergraph")
6913 (synopsis "Hypergraph data structures")
6915 "This package implements some simple capabilities for representing and
6916 manipulating hypergraphs.")
6917 (license license:artistic2.0)))
6919 (define-public r-hyperdraw
6921 (name "r-hyperdraw")
6926 (uri (bioconductor-uri "hyperdraw" version))
6929 "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj"))))
6930 (properties `((upstream-name . "hyperdraw")))
6931 (build-system r-build-system)
6932 (inputs `(("graphviz" ,graphviz)))
6934 `(("r-graph" ,r-graph)
6935 ("r-hypergraph" ,r-hypergraph)
6936 ("r-rgraphviz" ,r-rgraphviz)))
6937 (home-page "https://bioconductor.org/packages/hyperdraw")
6938 (synopsis "Visualizing hypergraphs")
6940 "This package provides functions for visualizing hypergraphs.")
6941 (license license:gpl2+)))
6943 (define-public r-biggr
6950 (uri (bioconductor-uri "BiGGR" version))
6953 "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif"))))
6954 (properties `((upstream-name . "BiGGR")))
6955 (build-system r-build-system)
6957 `(("r-hyperdraw" ,r-hyperdraw)
6958 ("r-hypergraph" ,r-hypergraph)
6960 ("r-limsolve" ,r-limsolve)
6961 ("r-rsbml" ,r-rsbml)
6962 ("r-stringr" ,r-stringr)))
6963 (home-page "https://bioconductor.org/packages/BiGGR/")
6964 (synopsis "Constraint based modeling using metabolic reconstruction databases")
6966 "This package provides an interface to simulate metabolic reconstruction
6967 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
6968 reconstruction databases. The package facilitates @dfn{flux balance
6969 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
6970 networks and estimated fluxes can be visualized with hypergraphs.")
6971 (license license:gpl3+)))
6973 (define-public r-bigmemoryextras
6975 (name "r-bigmemoryextras")
6980 (uri (bioconductor-uri "bigmemoryExtras" version))
6983 "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq"))))
6985 `((upstream-name . "bigmemoryExtras")))
6986 (build-system r-build-system)
6988 `(("r-bigmemory" ,r-bigmemory)))
6989 (home-page "https://github.com/phaverty/bigmemoryExtras")
6990 (synopsis "Extension of the bigmemory package")
6992 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
6993 safety and convenience features to the @code{filebacked.big.matrix} class from
6994 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
6995 monitoring and gracefully restoring the connection to on-disk data and it also
6996 protects against accidental data modification with a filesystem-based
6997 permissions system. Utilities are provided for using @code{BigMatrix}-derived
6998 classes as @code{assayData} matrices within the @code{Biobase} package's
6999 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7000 related to attaching to, and indexing into, file-backed matrices with
7001 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7002 a file-backed matrix with factor properties.")
7003 (license license:artistic2.0)))
7005 (define-public r-bigpint
7012 (uri (bioconductor-uri "bigPint" version))
7015 "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs"))))
7016 (properties `((upstream-name . "bigPint")))
7017 (build-system r-build-system)
7019 `(("r-dplyr" ,r-dplyr)
7020 ("r-ggally" ,r-ggally)
7021 ("r-ggplot2" ,r-ggplot2)
7022 ("r-gridextra" ,r-gridextra)
7023 ("r-hexbin" ,r-hexbin)
7024 ("r-hmisc" ,r-hmisc)
7025 ("r-htmlwidgets" ,r-htmlwidgets)
7026 ("r-plotly" ,r-plotly)
7028 ("r-rcolorbrewer" ,r-rcolorbrewer)
7029 ("r-reshape" ,r-reshape)
7030 ("r-shiny" ,r-shiny)
7031 ("r-shinycssloaders" ,r-shinycssloaders)
7032 ("r-shinydashboard" ,r-shinydashboard)
7033 ("r-stringr" ,r-stringr)
7034 ("r-tidyr" ,r-tidyr)))
7036 `(("r-knitr" ,r-knitr)))
7037 (home-page "https://github.com/lindsayrutter/bigPint")
7038 (synopsis "Big multivariate data plotted interactively")
7040 "This package provides methods for visualizing large multivariate
7041 datasets using static and interactive scatterplot matrices, parallel
7042 coordinate plots, volcano plots, and litre plots. It includes examples for
7043 visualizing RNA-sequencing datasets and differentially expressed genes.")
7044 (license license:gpl3)))
7046 (define-public r-chemminer
7048 (name "r-chemminer")
7053 (uri (bioconductor-uri "ChemmineR" version))
7056 "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga"))))
7057 (properties `((upstream-name . "ChemmineR")))
7058 (build-system r-build-system)
7060 `(("r-base64enc" ,r-base64enc)
7062 ("r-biocgenerics" ,r-biocgenerics)
7064 ("r-digest" ,r-digest)
7066 ("r-ggplot2" ,r-ggplot2)
7067 ("r-gridextra" ,r-gridextra)
7070 ("r-rcurl" ,r-rcurl)
7071 ("r-rjson" ,r-rjson)
7072 ("r-rsvg" ,r-rsvg)))
7073 (home-page "https://github.com/girke-lab/ChemmineR")
7074 (synopsis "Cheminformatics toolkit for R")
7076 "ChemmineR is a cheminformatics package for analyzing drug-like small
7077 molecule data in R. It contains functions for efficient processing of large
7078 numbers of molecules, physicochemical/structural property predictions,
7079 structural similarity searching, classification and clustering of compound
7080 libraries with a wide spectrum of algorithms. In addition, it offers
7081 visualization functions for compound clustering results and chemical
7083 (license license:artistic2.0)))
7085 (define-public r-bioassayr
7087 (name "r-bioassayr")
7092 (uri (bioconductor-uri "bioassayR" version))
7095 "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw"))))
7096 (properties `((upstream-name . "bioassayR")))
7097 (build-system r-build-system)
7099 `(("r-biocgenerics" ,r-biocgenerics)
7100 ("r-chemminer" ,r-chemminer)
7102 ("r-matrix" ,r-matrix)
7103 ("r-rjson" ,r-rjson)
7104 ("r-rsqlite" ,r-rsqlite)
7106 (home-page "https://github.com/TylerBackman/bioassayR")
7107 (synopsis "Cross-target analysis of small molecule bioactivity")
7109 "bioassayR is a computational tool that enables simultaneous analysis of
7110 thousands of bioassay experiments performed over a diverse set of compounds
7111 and biological targets. Unique features include support for large-scale
7112 cross-target analyses of both public and custom bioassays, generation of
7113 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7114 preloaded database that provides access to a substantial portion of publicly
7115 available bioactivity data.")
7116 (license license:artistic2.0)))
7118 (define-public r-biobroom
7125 (uri (bioconductor-uri "biobroom" version))
7128 "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb"))))
7129 (properties `((upstream-name . "biobroom")))
7130 (build-system r-build-system)
7132 `(("r-biobase" ,r-biobase)
7133 ("r-broom" ,r-broom)
7134 ("r-dplyr" ,r-dplyr)
7135 ("r-tidyr" ,r-tidyr)))
7136 (home-page "https://github.com/StoreyLab/biobroom")
7137 (synopsis "Turn Bioconductor objects into tidy data frames")
7139 "This package contains methods for converting standard objects
7140 constructed by bioinformatics packages, especially those in Bioconductor, and
7141 converting them to @code{tidy} data. It thus serves as a complement to the
7142 @code{broom} package, and follows the same tidy, augment, glance division of
7143 tidying methods. Tidying data makes it easy to recombine, reshape and
7144 visualize bioinformatics analyses.")
7145 ;; Any version of the LGPL.
7146 (license license:lgpl3+)))
7148 (define-public r-graphite
7155 (uri (bioconductor-uri "graphite" version))
7158 "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd"))))
7159 (properties `((upstream-name . "graphite")))
7160 (build-system r-build-system)
7162 `(("r-annotationdbi" ,r-annotationdbi)
7163 ("r-checkmate" ,r-checkmate)
7164 ("r-graph" ,r-graph)
7166 ("r-rappdirs" ,r-rappdirs)))
7167 (home-page "https://bioconductor.org/packages/graphite/")
7168 (synopsis "Networks from pathway databases")
7170 "Graphite provides networks derived from eight public pathway databases,
7171 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7173 (license license:agpl3+)))
7175 (define-public r-reactomepa
7177 (name "r-reactomepa")
7182 (uri (bioconductor-uri "ReactomePA" version))
7185 "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1"))))
7186 (properties `((upstream-name . "ReactomePA")))
7187 (build-system r-build-system)
7189 `(("r-annotationdbi" ,r-annotationdbi)
7191 ("r-enrichplot" ,r-enrichplot)
7192 ("r-ggplot2" ,r-ggplot2)
7193 ("r-ggraph" ,r-ggraph)
7194 ("r-graphite" ,r-graphite)
7195 ("r-igraph" ,r-igraph)
7196 ("r-reactome-db" ,r-reactome-db)))
7197 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7198 (synopsis "Reactome pathway analysis")
7200 "This package provides functions for pathway analysis based on the
7201 REACTOME pathway database. It implements enrichment analysis, gene set
7202 enrichment analysis and several functions for visualization.")
7203 (license license:gpl2)))
7205 (define-public r-ebarrays
7212 (uri (bioconductor-uri "EBarrays" version))
7215 "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13"))))
7216 (properties `((upstream-name . "EBarrays")))
7217 (build-system r-build-system)
7219 `(("r-biobase" ,r-biobase)
7220 ("r-cluster" ,r-cluster)
7221 ("r-lattice" ,r-lattice)))
7222 (home-page "https://bioconductor.org/packages/EBarrays/")
7223 (synopsis "Gene clustering and differential expression identification")
7225 "EBarrays provides tools for the analysis of replicated/unreplicated
7227 (license license:gpl2+)))
7229 (define-public r-bioccasestudies
7231 (name "r-bioccasestudies")
7236 (uri (bioconductor-uri "BiocCaseStudies" version))
7239 "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd"))))
7241 `((upstream-name . "BiocCaseStudies")))
7242 (build-system r-build-system)
7243 (propagated-inputs `(("r-biobase" ,r-biobase)))
7244 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7245 (synopsis "Support for the case studies monograph")
7247 "This package provides software and data to support the case studies
7249 (license license:artistic2.0)))
7251 (define-public r-biocgraph
7253 (name "r-biocgraph")
7258 (uri (bioconductor-uri "biocGraph" version))
7261 "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw"))))
7262 (properties `((upstream-name . "biocGraph")))
7263 (build-system r-build-system)
7265 `(("r-biocgenerics" ,r-biocgenerics)
7266 ("r-geneplotter" ,r-geneplotter)
7267 ("r-graph" ,r-graph)
7268 ("r-rgraphviz" ,r-rgraphviz)))
7269 (home-page "https://bioconductor.org/packages/biocGraph/")
7270 (synopsis "Graph examples and use cases in Bioinformatics")
7272 "This package provides examples and code that make use of the
7273 different graph related packages produced by Bioconductor.")
7274 (license license:artistic2.0)))
7276 (define-public r-experimenthub
7278 (name "r-experimenthub")
7283 (uri (bioconductor-uri "ExperimentHub" version))
7286 "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24"))))
7287 (properties `((upstream-name . "ExperimentHub")))
7288 (build-system r-build-system)
7290 `(("r-annotationhub" ,r-annotationhub)
7291 ("r-biocfilecache" ,r-biocfilecache)
7292 ("r-biocgenerics" ,r-biocgenerics)
7293 ("r-biocmanager" ,r-biocmanager)
7295 ("r-rappdirs" ,r-rappdirs)
7296 ("r-s4vectors" ,r-s4vectors)))
7297 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7298 (synopsis "Client to access ExperimentHub resources")
7300 "This package provides a client for the Bioconductor ExperimentHub web
7301 resource. ExperimentHub provides a central location where curated data from
7302 experiments, publications or training courses can be accessed. Each resource
7303 has associated metadata, tags and date of modification. The client creates
7304 and manages a local cache of files retrieved enabling quick and reproducible
7306 (license license:artistic2.0)))
7308 (define-public r-multiassayexperiment
7310 (name "r-multiassayexperiment")
7315 (uri (bioconductor-uri "MultiAssayExperiment" version))
7318 "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi"))))
7320 `((upstream-name . "MultiAssayExperiment")))
7321 (build-system r-build-system)
7323 `(("r-biobase" ,r-biobase)
7324 ("r-biocgenerics" ,r-biocgenerics)
7325 ("r-genomicranges" ,r-genomicranges)
7326 ("r-iranges" ,r-iranges)
7327 ("r-s4vectors" ,r-s4vectors)
7328 ("r-summarizedexperiment" ,r-summarizedexperiment)
7329 ("r-tidyr" ,r-tidyr)))
7331 `(("r-knitr" ,r-knitr)))
7332 (home-page "https://waldronlab.io/MultiAssayExperiment/")
7333 (synopsis "Integration of multi-omics experiments in Bioconductor")
7335 "MultiAssayExperiment harmonizes data management of multiple assays
7336 performed on an overlapping set of specimens. It provides a familiar
7337 Bioconductor user experience by extending concepts from
7338 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7339 classes for individual assays, and allowing subsetting by genomic ranges or
7341 (license license:artistic2.0)))
7343 (define-public r-bioconcotk
7345 (name "r-bioconcotk")
7350 (uri (bioconductor-uri "BiocOncoTK" version))
7353 "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj"))))
7354 (properties `((upstream-name . "BiocOncoTK")))
7355 (build-system r-build-system)
7357 `(("r-bigrquery" ,r-bigrquery)
7359 ("r-complexheatmap" ,r-complexheatmap)
7360 ("r-curatedtcgadata" ,r-curatedtcgadata)
7362 ("r-dplyr" ,r-dplyr)
7364 ("r-genomicfeatures" ,r-genomicfeatures)
7365 ("r-genomicranges" ,r-genomicranges)
7366 ("r-ggplot2" ,r-ggplot2)
7367 ("r-ggpubr" ,r-ggpubr)
7368 ("r-graph" ,r-graph)
7370 ("r-iranges" ,r-iranges)
7371 ("r-magrittr" ,r-magrittr)
7373 ("r-rgraphviz" ,r-rgraphviz)
7374 ("r-rjson" ,r-rjson)
7375 ("r-s4vectors" ,r-s4vectors)
7376 ("r-scales" ,r-scales)
7377 ("r-shiny" ,r-shiny)
7378 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7379 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7380 (synopsis "Bioconductor components for general cancer genomics")
7382 "The purpose of this package is to provide a central interface to various
7383 tools for genome-scale analysis of cancer studies.")
7384 (license license:artistic2.0)))
7386 (define-public r-biocor
7393 (uri (bioconductor-uri "BioCor" version))
7396 "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl"))))
7397 (properties `((upstream-name . "BioCor")))
7398 (build-system r-build-system)
7400 `(("r-biocparallel" ,r-biocparallel)
7401 ("r-gseabase" ,r-gseabase)
7402 ("r-matrix" ,r-matrix)))
7403 (home-page "https://llrs.github.io/BioCor/")
7404 (synopsis "Functional similarities")
7406 "This package provides tools to calculate functional similarities based
7407 on the pathways described on KEGG and REACTOME or in gene sets. These
7408 similarities can be calculated for pathways or gene sets, genes, or clusters
7409 and combined with other similarities. They can be used to improve networks,
7410 gene selection, testing relationships, and so on.")
7411 (license license:expat)))
7413 (define-public r-biocpkgtools
7415 (name "r-biocpkgtools")
7420 (uri (bioconductor-uri "BiocPkgTools" version))
7423 "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a"))))
7424 (properties `((upstream-name . "BiocPkgTools")))
7425 (build-system r-build-system)
7427 `(("r-biocfilecache" ,r-biocfilecache)
7428 ("r-biocmanager" ,r-biocmanager)
7429 ("r-biocviews" ,r-biocviews)
7430 ("r-dplyr" ,r-dplyr)
7433 ("r-graph" ,r-graph)
7434 ("r-htmltools" ,r-htmltools)
7435 ("r-htmlwidgets" ,r-htmlwidgets)
7437 ("r-igraph" ,r-igraph)
7438 ("r-jsonlite" ,r-jsonlite)
7439 ("r-magrittr" ,r-magrittr)
7440 ("r-rappdirs" ,r-rappdirs)
7442 ("r-readr" ,r-readr)
7444 ("r-rlang" ,r-rlang)
7445 ("r-rvest" ,r-rvest)
7446 ("r-stringr" ,r-stringr)
7447 ("r-tibble" ,r-tibble)
7448 ("r-tidyr" ,r-tidyr)
7449 ("r-tidyselect" ,r-tidyselect)
7450 ("r-xml2" ,r-xml2)))
7452 `(("r-knitr" ,r-knitr)))
7453 (home-page "https://github.com/seandavi/BiocPkgTools")
7454 (synopsis "Collection of tools for learning about Bioconductor packages")
7456 "Bioconductor has a rich ecosystem of metadata around packages, usage,
7457 and build status. This package is a simple collection of functions to access
7458 that metadata from R. The goal is to expose metadata for data mining and
7459 value-added functionality such as package searching, text mining, and
7460 analytics on packages.")
7461 (license license:expat)))
7463 (define-public r-biocset
7470 (uri (bioconductor-uri "BiocSet" version))
7473 "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9"))))
7474 (properties `((upstream-name . "BiocSet")))
7475 (build-system r-build-system)
7477 `(("r-annotationdbi" ,r-annotationdbi)
7478 ("r-dplyr" ,r-dplyr)
7479 ("r-keggrest" ,r-keggrest)
7481 ("r-rlang" ,r-rlang)
7482 ("r-rtracklayer" ,r-rtracklayer)
7483 ("r-tibble" ,r-tibble)))
7485 "https://bioconductor.org/packages/BiocSet")
7487 "Representing Different Biological Sets")
7489 "BiocSet displays different biological sets in a triple tibble format.
7490 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
7491 The user has the ability to activate one of these three tibbles to perform
7492 common functions from the @code{dplyr} package. Mapping functionality and
7493 accessing web references for elements/sets are also available in BiocSet.")
7494 (license license:artistic2.0)))
7496 (define-public r-biocworkflowtools
7498 (name "r-biocworkflowtools")
7503 (uri (bioconductor-uri "BiocWorkflowTools" version))
7506 "1v4bhnpdkmllm7aghms9b7369hkrgz7mn69wbrqg1x42pgkf30ad"))))
7508 `((upstream-name . "BiocWorkflowTools")))
7509 (build-system r-build-system)
7511 `(("r-biocstyle" ,r-biocstyle)
7512 ("r-bookdown" ,r-bookdown)
7513 ("r-git2r" ,r-git2r)
7515 ("r-knitr" ,r-knitr)
7516 ("r-rmarkdown" ,r-rmarkdown)
7517 ("r-rstudioapi" ,r-rstudioapi)
7518 ("r-stringr" ,r-stringr)
7519 ("r-usethis" ,r-usethis)))
7520 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
7521 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
7523 "This package provides functions to ease the transition between
7524 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
7525 (license license:expat)))
7527 (define-public r-biodist
7534 (uri (bioconductor-uri "bioDist" version))
7537 "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q"))))
7538 (properties `((upstream-name . "bioDist")))
7539 (build-system r-build-system)
7541 `(("r-biobase" ,r-biobase)
7542 ("r-kernsmooth" ,r-kernsmooth)))
7543 (home-page "https://bioconductor.org/packages/bioDist/")
7544 (synopsis "Different distance measures")
7546 "This package provides a collection of software tools for calculating
7547 distance measures.")
7548 (license license:artistic2.0)))