1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 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-bsgenome-hsapiens-ucsc-hg38
498 (name "r-bsgenome-hsapiens-ucsc-hg38")
502 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
503 version 'annotation))
506 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
508 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
509 (build-system r-build-system)
511 `(("r-bsgenome" ,r-bsgenome)))
513 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
514 (synopsis "Full genome sequences for Homo sapiens")
516 "This package provides full genome sequences for Homo sapiens (Human)
517 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
518 (license license:artistic2.0)))
520 (define-public r-ensdb-hsapiens-v75
522 (name "r-ensdb-hsapiens-v75")
527 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
530 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
532 `((upstream-name . "EnsDb.Hsapiens.v75")))
533 (build-system r-build-system)
535 `(("r-ensembldb" ,r-ensembldb)))
536 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
537 (synopsis "Ensembl based annotation package")
539 "This package exposes an annotation database generated from Ensembl.")
540 (license license:artistic2.0)))
542 (define-public r-genelendatabase
544 (name "r-genelendatabase")
549 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
552 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
554 `((upstream-name . "geneLenDataBase")))
555 (build-system r-build-system)
557 `(("r-rtracklayer" ,r-rtracklayer)
558 ("r-genomicfeatures" ,r-genomicfeatures)))
559 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
560 (synopsis "Lengths of mRNA transcripts for a number of genomes")
562 "This package provides the lengths of mRNA transcripts for a number of
563 genomes and gene ID formats, largely based on the UCSC table browser.")
564 (license license:lgpl2.0+)))
566 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
568 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
572 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
573 version 'annotation))
576 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
578 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
579 (build-system r-build-system)
581 `(("r-genomicfeatures" ,r-genomicfeatures)))
583 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
584 (synopsis "Annotation package for human genome in TxDb format")
586 "This package provides an annotation database of Homo sapiens genome
587 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
588 track. The database is exposed as a @code{TxDb} object.")
589 (license license:artistic2.0)))
591 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
593 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
597 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
598 version 'annotation))
601 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
603 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
604 (build-system r-build-system)
606 `(("r-genomicfeatures" ,r-genomicfeatures)))
608 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
609 (synopsis "Annotation package for human genome in TxDb format")
611 "This package provides an annotation database of Homo sapiens genome
612 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
613 track. The database is exposed as a @code{TxDb} object.")
614 (license license:artistic2.0)))
616 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
618 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
622 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
623 version 'annotation))
626 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
628 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
629 (build-system r-build-system)
631 `(("r-genomicfeatures" ,r-genomicfeatures)
632 ("r-annotationdbi" ,r-annotationdbi)))
634 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
635 (synopsis "Annotation package for mouse genome in TxDb format")
637 "This package provides an annotation database of Mouse genome data. It
638 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
639 database is exposed as a @code{TxDb} object.")
640 (license license:artistic2.0)))
642 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
644 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
648 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
649 version 'annotation))
652 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
654 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
655 (build-system r-build-system)
657 `(("r-bsgenome" ,r-bsgenome)
658 ("r-genomicfeatures" ,r-genomicfeatures)
659 ("r-annotationdbi" ,r-annotationdbi)))
661 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
662 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
664 "This package loads a TxDb object, which is an R interface to
665 prefabricated databases contained in this package. This package provides
666 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
667 based on the knownGene track.")
668 (license license:artistic2.0)))
670 (define-public r-txdb-celegans-ucsc-ce6-ensgene
672 (name "r-txdb-celegans-ucsc-ce6-ensgene")
677 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
678 version 'annotation))
681 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
683 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
684 (build-system r-build-system)
686 `(("r-annotationdbi" ,r-annotationdbi)
687 ("r-genomicfeatures" ,r-genomicfeatures)))
688 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
689 (synopsis "Annotation package for C elegans TxDb objects")
691 "This package exposes a C elegans annotation database generated from UCSC
692 by exposing these as TxDb objects.")
693 (license license:artistic2.0)))
695 (define-public r-fdb-infiniummethylation-hg19
697 (name "r-fdb-infiniummethylation-hg19")
701 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
702 version 'annotation))
705 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
707 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
708 (build-system r-build-system)
710 `(("r-biostrings" ,r-biostrings)
711 ("r-genomicfeatures" ,r-genomicfeatures)
712 ("r-annotationdbi" ,r-annotationdbi)
713 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
714 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
715 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
716 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
718 "This is an annotation package for Illumina Infinium DNA methylation
719 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
721 (license license:artistic2.0)))
723 (define-public r-illuminahumanmethylationepicmanifest
725 (name "r-illuminahumanmethylationepicmanifest")
729 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
730 version 'annotation))
733 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
735 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
736 (build-system r-build-system)
738 `(("r-minfi" ,r-minfi)))
739 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
740 (synopsis "Manifest for Illumina's EPIC methylation arrays")
742 "This is a manifest package for Illumina's EPIC methylation arrays.")
743 (license license:artistic2.0)))
745 (define-public r-ideoviz
751 (uri (bioconductor-uri "IdeoViz" version))
754 "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50"))))
755 (build-system r-build-system)
757 `(("r-biobase" ,r-biobase)
758 ("r-iranges" ,r-iranges)
759 ("r-genomicranges" ,r-genomicranges)
760 ("r-rcolorbrewer" ,r-rcolorbrewer)
761 ("r-rtracklayer" ,r-rtracklayer)
762 ("r-genomeinfodb" ,r-genomeinfodb)))
763 (home-page "https://bioconductor.org/packages/IdeoViz/")
764 (synopsis "Plots data along a chromosomal ideogram")
765 (description "This package provides functions to plot data associated with
766 arbitrary genomic intervals along chromosomal ideogram.")
767 (license license:gpl2)))
769 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
770 ;; from Bioconductor.
771 (define-public r-deconstructsigs
773 (name "r-deconstructsigs")
777 (uri (cran-uri "deconstructSigs" version))
780 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
782 `((upstream-name . "deconstructSigs")))
783 (build-system r-build-system)
785 `(("r-bsgenome" ,r-bsgenome)
786 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
787 ("r-genomeinfodb" ,r-genomeinfodb)
788 ("r-reshape2" ,r-reshape2)))
789 (home-page "https://github.com/raerose01/deconstructSigs")
790 (synopsis "Identifies signatures present in a tumor sample")
791 (description "This package takes sample information in the form of the
792 fraction of mutations in each of 96 trinucleotide contexts and identifies
793 the weighted combination of published signatures that, when summed, most
794 closely reconstructs the mutational profile.")
795 (license license:gpl2+)))
797 ;; This is a CRAN package, but it depends on Bioconductor packages.
805 (uri (cran-uri "NMF" version))
808 "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq"))))
809 (properties `((upstream-name . "NMF")))
810 (build-system r-build-system)
812 `(("r-cluster" ,r-cluster)
813 ("r-biobase" ,r-biobase)
814 ("r-biocmanager" ,r-biocmanager)
815 ("r-bigmemory" ,r-bigmemory) ; suggested
816 ("r-synchronicity" ,r-synchronicity) ; suggested
817 ("r-colorspace" ,r-colorspace)
818 ("r-digest" ,r-digest)
819 ("r-doparallel" ,r-doparallel)
820 ("r-foreach" ,r-foreach)
821 ("r-ggplot2" ,r-ggplot2)
822 ("r-gridbase" ,r-gridbase)
823 ("r-pkgmaker" ,r-pkgmaker)
824 ("r-rcolorbrewer" ,r-rcolorbrewer)
825 ("r-registry" ,r-registry)
826 ("r-reshape2" ,r-reshape2)
827 ("r-rngtools" ,r-rngtools)
828 ("r-stringr" ,r-stringr)))
829 (home-page "http://renozao.github.io/NMF")
830 (synopsis "Algorithms and framework for nonnegative matrix factorization")
832 "This package provides a framework to perform Non-negative Matrix
833 Factorization (NMF). The package implements a set of already published
834 algorithms and seeding methods, and provides a framework to test, develop and
835 plug new or custom algorithms. Most of the built-in algorithms have been
836 optimized in C++, and the main interface function provides an easy way of
837 performing parallel computations on multicore machines.")
838 (license license:gpl2+)))
840 (define-public r-do-db
846 (uri (bioconductor-uri "DO.db" version 'annotation))
849 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
851 `((upstream-name . "DO.db")))
852 (build-system r-build-system)
854 `(("r-annotationdbi" ,r-annotationdbi)))
855 (home-page "https://www.bioconductor.org/packages/DO.db/")
856 (synopsis "Annotation maps describing the entire Disease Ontology")
858 "This package provides a set of annotation maps describing the entire
860 (license license:artistic2.0)))
862 (define-public r-pasilla
869 "http://bioconductor.org/packages/release/data/experiment"
870 "/src/contrib/pasilla_" version ".tar.gz"))
873 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
874 (build-system r-build-system)
876 `(("r-biocstyle" ,r-biocstyle)
877 ("r-dexseq" ,r-dexseq)
879 ("r-rmarkdown" ,r-rmarkdown)))
880 (home-page "https://www.bioconductor.org/packages/pasilla/")
881 (synopsis "Data package with per-exon and per-gene read counts")
882 (description "This package provides per-exon and per-gene read counts
883 computed for selected genes from RNA-seq data that were presented in the
884 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
885 by Brooks et al., Genome Research 2011.")
886 (license license:lgpl2.1+)))
888 (define-public r-pfam-db
895 (uri (bioconductor-uri "PFAM.db" version 'annotation))
898 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
899 (properties `((upstream-name . "PFAM.db")))
900 (build-system r-build-system)
902 `(("r-annotationdbi" ,r-annotationdbi)))
903 (home-page "https://bioconductor.org/packages/PFAM.db")
904 (synopsis "Set of protein ID mappings for PFAM")
906 "This package provides a set of protein ID mappings for PFAM, assembled
907 using data from public repositories.")
908 (license license:artistic2.0)))
910 (define-public r-phastcons100way-ucsc-hg19
912 (name "r-phastcons100way-ucsc-hg19")
917 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
918 version 'annotation))
921 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
923 `((upstream-name . "phastCons100way.UCSC.hg19")))
924 (build-system r-build-system)
926 `(("r-bsgenome" ,r-bsgenome)
927 ("r-genomeinfodb" ,r-genomeinfodb)
928 ("r-genomicranges" ,r-genomicranges)
929 ("r-genomicscores" ,r-genomicscores)
930 ("r-iranges" ,r-iranges)
931 ("r-s4vectors" ,r-s4vectors)))
932 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
933 (synopsis "UCSC phastCons conservation scores for hg19")
935 "This package provides UCSC phastCons conservation scores for the human
936 genome (hg19) calculated from multiple alignments with other 99 vertebrate
938 (license license:artistic2.0)))
943 (define-public r-abadata
949 (uri (bioconductor-uri "ABAData" version 'experiment))
952 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
954 `((upstream-name . "ABAData")))
955 (build-system r-build-system)
957 `(("r-annotationdbi" ,r-annotationdbi)))
958 (home-page "https://www.bioconductor.org/packages/ABAData/")
959 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
961 "This package provides the data for the gene expression enrichment
962 analysis conducted in the package ABAEnrichment. The package includes three
963 datasets which are derived from the Allen Brain Atlas:
966 @item Gene expression data from Human Brain (adults) averaged across donors,
967 @item Gene expression data from the Developing Human Brain pooled into five
968 age categories and averaged across donors, and
969 @item a developmental effect score based on the Developing Human Brain
973 All datasets are restricted to protein coding genes.")
974 (license license:gpl2+)))
976 (define-public r-arrmdata
982 (uri (bioconductor-uri "ARRmData" version 'experiment))
985 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
987 `((upstream-name . "ARRmData")))
988 (build-system r-build-system)
989 (home-page "https://www.bioconductor.org/packages/ARRmData/")
990 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
992 "This package provides raw beta values from 36 samples across 3 groups
993 from Illumina 450k methylation arrays.")
994 (license license:artistic2.0)))
996 (define-public r-hsmmsinglecell
998 (name "r-hsmmsinglecell")
1002 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1005 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
1007 `((upstream-name . "HSMMSingleCell")))
1008 (build-system r-build-system)
1009 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1010 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1012 "Skeletal myoblasts undergo a well-characterized sequence of
1013 morphological and transcriptional changes during differentiation. In this
1014 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1015 under high mitogen conditions (GM) and then differentiated by switching to
1016 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1017 hundred cells taken over a time-course of serum-induced differentiation.
1018 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1019 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1020 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1021 which were then sequenced to a depth of ~4 million reads per library,
1022 resulting in a complete gene expression profile for each cell.")
1023 (license license:artistic2.0)))
1025 (define-public r-all
1031 (uri (bioconductor-uri "ALL" version 'experiment))
1034 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1035 (properties `((upstream-name . "ALL")))
1036 (build-system r-build-system)
1038 `(("r-biobase" ,r-biobase)))
1039 (home-page "https://bioconductor.org/packages/ALL")
1040 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1042 "The data consist of microarrays from 128 different individuals with
1043 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1044 are available. The data have been normalized (using rma) and it is the
1045 jointly normalized data that are available here. The data are presented in
1046 the form of an @code{exprSet} object.")
1047 (license license:artistic2.0)))
1049 (define-public r-affydata
1056 (uri (bioconductor-uri "affydata" version 'experiment))
1059 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1060 (properties `((upstream-name . "affydata")))
1061 (build-system r-build-system)
1063 `(("r-affy" ,r-affy)))
1064 (home-page "https://bioconductor.org/packages/affydata/")
1065 (synopsis "Affymetrix data for demonstration purposes")
1067 "This package provides example datasets that represent 'real world
1068 examples' of Affymetrix data, unlike the artificial examples included in the
1069 package @code{affy}.")
1070 (license license:gpl2+)))
1072 (define-public r-coverageview
1074 (name "r-coverageview")
1078 (uri (bioconductor-uri "CoverageView" version))
1081 "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj"))))
1082 (build-system r-build-system)
1084 `(("r-s4vectors" ,r-s4vectors)
1085 ("r-iranges" ,r-iranges)
1086 ("r-genomicranges" ,r-genomicranges)
1087 ("r-genomicalignments" ,r-genomicalignments)
1088 ("r-rtracklayer" ,r-rtracklayer)
1089 ("r-rsamtools" ,r-rsamtools)))
1090 (home-page "https://bioconductor.org/packages/CoverageView/")
1091 (synopsis "Coverage visualization package for R")
1092 (description "This package provides a framework for the visualization of
1093 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1094 be also used for genome-wide nucleosome positioning experiments or other
1095 experiment types where it is important to have a framework in order to inspect
1096 how the coverage distributed across the genome.")
1097 (license license:artistic2.0)))
1099 (define-public r-cummerbund
1101 (name "r-cummerbund")
1105 (uri (bioconductor-uri "cummeRbund" version))
1108 "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc"))))
1109 (build-system r-build-system)
1111 `(("r-biobase" ,r-biobase)
1112 ("r-biocgenerics" ,r-biocgenerics)
1113 ("r-fastcluster", r-fastcluster)
1114 ("r-ggplot2" ,r-ggplot2)
1117 ("r-reshape2" ,r-reshape2)
1118 ("r-rsqlite" ,r-rsqlite)
1119 ("r-rtracklayer" ,r-rtracklayer)
1120 ("r-s4vectors" ,r-s4vectors)))
1121 (home-page "https://bioconductor.org/packages/cummeRbund/")
1122 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1123 (description "This package allows for persistent storage, access,
1124 exploration, and manipulation of Cufflinks high-throughput sequencing
1125 data. In addition, provides numerous plotting functions for commonly
1126 used visualizations.")
1127 (license license:artistic2.0)))
1129 (define-public r-curatedtcgadata
1131 (name "r-curatedtcgadata")
1136 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1139 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1141 `((upstream-name . "curatedTCGAData")))
1142 (build-system r-build-system)
1144 `(("r-annotationhub" ,r-annotationhub)
1145 ("r-experimenthub" ,r-experimenthub)
1146 ("r-hdf5array" ,r-hdf5array)
1147 ("r-multiassayexperiment" ,r-multiassayexperiment)
1148 ("r-s4vectors" ,r-s4vectors)
1149 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1150 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1151 (synopsis "Curated data from The Cancer Genome Atlas")
1153 "This package provides publicly available data from The Cancer Genome
1154 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1155 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1156 number, mutation, microRNA, protein, and others) with clinical / pathological
1157 data. It also links assay barcodes with patient identifiers, enabling
1158 harmonized subsetting of rows (features) and columns (patients / samples)
1159 across the entire multi-'omics experiment.")
1160 (license license:artistic2.0)))
1165 (define-public r-biocversion
1167 (name "r-biocversion")
1172 (uri (bioconductor-uri "BiocVersion" version))
1175 "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz"))))
1176 (properties `((upstream-name . "BiocVersion")))
1177 (build-system r-build-system)
1178 (home-page "https://bioconductor.org/packages/BiocVersion/")
1179 (synopsis "Set the appropriate version of Bioconductor packages")
1181 "This package provides repository information for the appropriate version
1183 (license license:artistic2.0)))
1185 (define-public r-biocgenerics
1187 (name "r-biocgenerics")
1191 (uri (bioconductor-uri "BiocGenerics" version))
1194 "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk"))))
1196 `((upstream-name . "BiocGenerics")))
1197 (build-system r-build-system)
1198 (home-page "https://bioconductor.org/packages/BiocGenerics")
1199 (synopsis "S4 generic functions for Bioconductor")
1201 "This package provides S4 generic functions needed by many Bioconductor
1203 (license license:artistic2.0)))
1205 (define-public r-affycomp
1212 (uri (bioconductor-uri "affycomp" version))
1215 "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0"))))
1216 (properties `((upstream-name . "affycomp")))
1217 (build-system r-build-system)
1218 (propagated-inputs `(("r-biobase" ,r-biobase)))
1219 (home-page "https://bioconductor.org/packages/affycomp/")
1220 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1222 "The package contains functions that can be used to compare expression
1223 measures for Affymetrix Oligonucleotide Arrays.")
1224 (license license:gpl2+)))
1226 (define-public r-affycompatible
1228 (name "r-affycompatible")
1233 (uri (bioconductor-uri "AffyCompatible" version))
1236 "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd"))))
1238 `((upstream-name . "AffyCompatible")))
1239 (build-system r-build-system)
1241 `(("r-biostrings" ,r-biostrings)
1242 ("r-rcurl" ,r-rcurl)
1244 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1245 (synopsis "Work with Affymetrix GeneChip files")
1247 "This package provides an interface to Affymetrix chip annotation and
1248 sample attribute files. The package allows an easy way for users to download
1249 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1250 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1251 Command Console} (AGCC)-compatible sample annotation files.")
1252 (license license:artistic2.0)))
1254 (define-public r-affycontam
1256 (name "r-affycontam")
1261 (uri (bioconductor-uri "affyContam" version))
1264 "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i"))))
1265 (properties `((upstream-name . "affyContam")))
1266 (build-system r-build-system)
1268 `(("r-affy" ,r-affy)
1269 ("r-affydata" ,r-affydata)
1270 ("r-biobase" ,r-biobase)))
1271 (home-page "https://bioconductor.org/packages/affyContam/")
1272 (synopsis "Structured corruption of Affymetrix CEL file data")
1274 "Microarray quality assessment is a major concern of microarray analysts.
1275 This package provides some simple approaches to in silico creation of quality
1276 problems in CEL-level data to help evaluate performance of quality metrics.")
1277 (license license:artistic2.0)))
1279 (define-public r-affycoretools
1281 (name "r-affycoretools")
1286 (uri (bioconductor-uri "affycoretools" version))
1289 "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s"))))
1290 (properties `((upstream-name . "affycoretools")))
1291 (build-system r-build-system)
1293 `(("r-affy" ,r-affy)
1294 ("r-annotationdbi" ,r-annotationdbi)
1295 ("r-biobase" ,r-biobase)
1296 ("r-biocgenerics" ,r-biocgenerics)
1298 ("r-edger" ,r-edger)
1299 ("r-gcrma" ,r-gcrma)
1300 ("r-glimma" ,r-glimma)
1301 ("r-ggplot2" ,r-ggplot2)
1302 ("r-gostats" ,r-gostats)
1303 ("r-gplots" ,r-gplots)
1304 ("r-hwriter" ,r-hwriter)
1305 ("r-lattice" ,r-lattice)
1306 ("r-limma" ,r-limma)
1307 ("r-oligoclasses" ,r-oligoclasses)
1308 ("r-reportingtools" ,r-reportingtools)
1309 ("r-rsqlite" ,r-rsqlite)
1310 ("r-s4vectors" ,r-s4vectors)
1311 ("r-xtable" ,r-xtable)))
1313 `(("r-knitr" ,r-knitr)))
1314 (home-page "https://bioconductor.org/packages/affycoretools/")
1315 (synopsis "Functions for analyses with Affymetrix GeneChips")
1317 "This package provides various wrapper functions that have been written
1318 to streamline the more common analyses that a Biostatistician might see.")
1319 (license license:artistic2.0)))
1321 (define-public r-affxparser
1323 (name "r-affxparser")
1328 (uri (bioconductor-uri "affxparser" version))
1331 "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq"))))
1332 (properties `((upstream-name . "affxparser")))
1333 (build-system r-build-system)
1334 (home-page "https://github.com/HenrikBengtsson/affxparser")
1335 (synopsis "Affymetrix File Parsing SDK")
1337 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1338 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1339 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1340 are supported. Currently, there are methods for reading @dfn{chip definition
1341 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1342 either in full or in part. For example, probe signals from a few probesets
1343 can be extracted very quickly from a set of CEL files into a convenient list
1345 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1347 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1349 (define-public r-annotate
1356 (uri (bioconductor-uri "annotate" version))
1359 "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w"))))
1360 (build-system r-build-system)
1362 `(("r-annotationdbi" ,r-annotationdbi)
1363 ("r-biobase" ,r-biobase)
1364 ("r-biocgenerics" ,r-biocgenerics)
1366 ("r-rcurl" ,r-rcurl)
1368 ("r-xtable" ,r-xtable)))
1370 "https://bioconductor.org/packages/annotate")
1371 (synopsis "Annotation for microarrays")
1372 (description "This package provides R environments for the annotation of
1374 (license license:artistic2.0)))
1376 (define-public r-hpar
1383 (uri (bioconductor-uri "hpar" version))
1386 "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9"))))
1387 (build-system r-build-system)
1389 `(("r-knitr" ,r-knitr)))
1390 (home-page "https://bioconductor.org/packages/hpar/")
1391 (synopsis "Human Protein Atlas in R")
1392 (description "This package provides a simple interface to and data from
1393 the Human Protein Atlas project.")
1394 (license license:artistic2.0)))
1396 (define-public r-regioner
1403 (uri (bioconductor-uri "regioneR" version))
1406 "10i21gxv0n7lrflhj5ja672xjizy1i4y4iq3pmjgbf0dpy1lxsih"))))
1407 (properties `((upstream-name . "regioneR")))
1408 (build-system r-build-system)
1410 `(("r-biostrings" ,r-biostrings)
1411 ("r-bsgenome" ,r-bsgenome)
1412 ("r-genomeinfodb" ,r-genomeinfodb)
1413 ("r-genomicranges" ,r-genomicranges)
1414 ("r-iranges" ,r-iranges)
1415 ("r-memoise" ,r-memoise)
1416 ("r-rtracklayer" ,r-rtracklayer)
1417 ("r-s4vectors" ,r-s4vectors)))
1419 `(("r-knitr" ,r-knitr)))
1420 (home-page "https://bioconductor.org/packages/regioneR/")
1421 (synopsis "Association analysis of genomic regions")
1422 (description "This package offers a statistical framework based on
1423 customizable permutation tests to assess the association between genomic
1424 region sets and other genomic features.")
1425 (license license:artistic2.0)))
1427 (define-public r-reportingtools
1429 (name "r-reportingtools")
1434 (uri (bioconductor-uri "ReportingTools" version))
1437 "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx"))))
1439 `((upstream-name . "ReportingTools")))
1440 (build-system r-build-system)
1442 `(("r-annotate" ,r-annotate)
1443 ("r-annotationdbi" ,r-annotationdbi)
1444 ("r-biobase" ,r-biobase)
1445 ("r-biocgenerics" ,r-biocgenerics)
1446 ("r-category" ,r-category)
1447 ("r-deseq2" ,r-deseq2)
1448 ("r-edger" ,r-edger)
1449 ("r-ggbio" ,r-ggbio)
1450 ("r-ggplot2" ,r-ggplot2)
1451 ("r-gostats" ,r-gostats)
1452 ("r-gseabase" ,r-gseabase)
1453 ("r-hwriter" ,r-hwriter)
1454 ("r-iranges" ,r-iranges)
1455 ("r-knitr" ,r-knitr)
1456 ("r-lattice" ,r-lattice)
1457 ("r-limma" ,r-limma)
1458 ("r-pfam-db" ,r-pfam-db)
1459 ("r-r-utils" ,r-r-utils)
1462 `(("r-knitr" ,r-knitr)))
1463 (home-page "https://bioconductor.org/packages/ReportingTools/")
1464 (synopsis "Tools for making reports in various formats")
1466 "The ReportingTools package enables users to easily display reports of
1467 analysis results generated from sources such as microarray and sequencing
1468 data. The package allows users to create HTML pages that may be viewed on a
1469 web browser, or in other formats. Users can generate tables with sortable and
1470 filterable columns, make and display plots, and link table entries to other
1471 data sources such as NCBI or larger plots within the HTML page. Using the
1472 package, users can also produce a table of contents page to link various
1473 reports together for a particular project that can be viewed in a web
1475 (license license:artistic2.0)))
1477 (define-public r-geneplotter
1479 (name "r-geneplotter")
1484 (uri (bioconductor-uri "geneplotter" version))
1487 "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5"))))
1488 (build-system r-build-system)
1490 `(("r-annotate" ,r-annotate)
1491 ("r-annotationdbi" ,r-annotationdbi)
1492 ("r-biobase" ,r-biobase)
1493 ("r-biocgenerics" ,r-biocgenerics)
1494 ("r-lattice" ,r-lattice)
1495 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1496 (home-page "https://bioconductor.org/packages/geneplotter")
1497 (synopsis "Graphics functions for genomic data")
1499 "This package provides functions for plotting genomic data.")
1500 (license license:artistic2.0)))
1502 (define-public r-oligoclasses
1504 (name "r-oligoclasses")
1509 (uri (bioconductor-uri "oligoClasses" version))
1512 "05jy9qz3ir4maxackr1xqlfi1czhy1qd22wwibjdhfh5dp534cpn"))))
1513 (properties `((upstream-name . "oligoClasses")))
1514 (build-system r-build-system)
1516 `(("r-affyio" ,r-affyio)
1517 ("r-biobase" ,r-biobase)
1518 ("r-biocgenerics" ,r-biocgenerics)
1519 ("r-biocmanager" ,r-biocmanager)
1520 ("r-biostrings" ,r-biostrings)
1523 ("r-foreach" ,r-foreach)
1524 ("r-genomicranges" ,r-genomicranges)
1525 ("r-iranges" ,r-iranges)
1526 ("r-rsqlite" ,r-rsqlite)
1527 ("r-s4vectors" ,r-s4vectors)
1528 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1529 (home-page "https://bioconductor.org/packages/oligoClasses/")
1530 (synopsis "Classes for high-throughput arrays")
1532 "This package contains class definitions, validity checks, and
1533 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1535 (license license:gpl2+)))
1537 (define-public r-oligo
1544 (uri (bioconductor-uri "oligo" version))
1547 "102szyiicws4c6l3k282236ml1m1vl9zmars4q1kdjfnvsyclfc4"))))
1548 (properties `((upstream-name . "oligo")))
1549 (build-system r-build-system)
1550 (inputs `(("zlib" ,zlib)))
1552 `(("r-affxparser" ,r-affxparser)
1553 ("r-affyio" ,r-affyio)
1554 ("r-biobase" ,r-biobase)
1555 ("r-biocgenerics" ,r-biocgenerics)
1556 ("r-biostrings" ,r-biostrings)
1559 ("r-oligoclasses" ,r-oligoclasses)
1560 ("r-preprocesscore" ,r-preprocesscore)
1561 ("r-rsqlite" ,r-rsqlite)
1562 ("r-zlibbioc" ,r-zlibbioc)))
1564 `(("r-knitr" ,r-knitr)))
1565 (home-page "https://bioconductor.org/packages/oligo/")
1566 (synopsis "Preprocessing tools for oligonucleotide arrays")
1568 "This package provides a package to analyze oligonucleotide
1569 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1570 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1571 (license license:lgpl2.0+)))
1573 (define-public r-qvalue
1580 (uri (bioconductor-uri "qvalue" version))
1583 "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f"))))
1584 (build-system r-build-system)
1586 `(("r-ggplot2" ,r-ggplot2)
1587 ("r-reshape2" ,r-reshape2)))
1589 `(("r-knitr" ,r-knitr)))
1590 (home-page "http://github.com/jdstorey/qvalue")
1591 (synopsis "Q-value estimation for false discovery rate control")
1593 "This package takes a list of p-values resulting from the simultaneous
1594 testing of many hypotheses and estimates their q-values and local @dfn{false
1595 discovery rate} (FDR) values. The q-value of a test measures the proportion
1596 of false positives incurred when that particular test is called significant.
1597 The local FDR measures the posterior probability the null hypothesis is true
1598 given the test's p-value. Various plots are automatically generated, allowing
1599 one to make sensible significance cut-offs. The software can be applied to
1600 problems in genomics, brain imaging, astrophysics, and data mining.")
1601 ;; Any version of the LGPL.
1602 (license license:lgpl3+)))
1604 (define-public r-diffbind
1611 (uri (bioconductor-uri "DiffBind" version))
1614 "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5"))))
1615 (properties `((upstream-name . "DiffBind")))
1616 (build-system r-build-system)
1620 `(("r-amap" ,r-amap)
1621 ("r-biocparallel" ,r-biocparallel)
1622 ("r-deseq2" ,r-deseq2)
1623 ("r-dplyr" ,r-dplyr)
1624 ("r-edger" ,r-edger)
1625 ("r-genomicalignments" ,r-genomicalignments)
1626 ("r-genomicranges" ,r-genomicranges)
1627 ("r-ggplot2" ,r-ggplot2)
1628 ("r-ggrepel" ,r-ggrepel)
1629 ("r-gplots" ,r-gplots)
1630 ("r-iranges" ,r-iranges)
1631 ("r-lattice" ,r-lattice)
1632 ("r-limma" ,r-limma)
1633 ("r-locfit" ,r-locfit)
1634 ("r-rcolorbrewer" , r-rcolorbrewer)
1636 ("r-rhtslib" ,r-rhtslib)
1637 ("r-rsamtools" ,r-rsamtools)
1638 ("r-s4vectors" ,r-s4vectors)
1639 ("r-summarizedexperiment" ,r-summarizedexperiment)
1640 ("r-systempiper" ,r-systempiper)))
1641 (home-page "https://bioconductor.org/packages/DiffBind")
1642 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1644 "This package computes differentially bound sites from multiple
1645 ChIP-seq experiments using affinity (quantitative) data. Also enables
1646 occupancy (overlap) analysis and plotting functions.")
1647 (license license:artistic2.0)))
1649 (define-public r-ripseeker
1651 (name "r-ripseeker")
1656 (uri (bioconductor-uri "RIPSeeker" version))
1659 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1660 (properties `((upstream-name . "RIPSeeker")))
1661 (build-system r-build-system)
1663 `(("r-s4vectors" ,r-s4vectors)
1664 ("r-iranges" ,r-iranges)
1665 ("r-genomicranges" ,r-genomicranges)
1666 ("r-summarizedexperiment" ,r-summarizedexperiment)
1667 ("r-rsamtools" ,r-rsamtools)
1668 ("r-genomicalignments" ,r-genomicalignments)
1669 ("r-rtracklayer" ,r-rtracklayer)))
1670 (home-page "https://bioconductor.org/packages/RIPSeeker")
1672 "Identifying protein-associated transcripts from RIP-seq experiments")
1674 "This package infers and discriminates RIP peaks from RIP-seq alignments
1675 using two-state HMM with negative binomial emission probability. While
1676 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1677 a suite of bioinformatics tools integrated within this self-contained software
1678 package comprehensively addressing issues ranging from post-alignments
1679 processing to visualization and annotation.")
1680 (license license:gpl2)))
1682 (define-public r-multtest
1689 (uri (bioconductor-uri "multtest" version))
1692 "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2"))))
1693 (build-system r-build-system)
1695 `(("r-survival" ,r-survival)
1696 ("r-biocgenerics" ,r-biocgenerics)
1697 ("r-biobase" ,r-biobase)
1698 ("r-mass" ,r-mass)))
1699 (home-page "https://bioconductor.org/packages/multtest")
1700 (synopsis "Resampling-based multiple hypothesis testing")
1702 "This package can do non-parametric bootstrap and permutation
1703 resampling-based multiple testing procedures (including empirical Bayes
1704 methods) for controlling the family-wise error rate (FWER), generalized
1705 family-wise error rate (gFWER), tail probability of the proportion of
1706 false positives (TPPFP), and false discovery rate (FDR). Several choices
1707 of bootstrap-based null distribution are implemented (centered, centered
1708 and scaled, quantile-transformed). Single-step and step-wise methods are
1709 available. Tests based on a variety of T- and F-statistics (including
1710 T-statistics based on regression parameters from linear and survival models
1711 as well as those based on correlation parameters) are included. When probing
1712 hypotheses with T-statistics, users may also select a potentially faster null
1713 distribution which is multivariate normal with mean zero and variance
1714 covariance matrix derived from the vector influence function. Results are
1715 reported in terms of adjusted P-values, confidence regions and test statistic
1716 cutoffs. The procedures are directly applicable to identifying differentially
1717 expressed genes in DNA microarray experiments.")
1718 (license license:lgpl3)))
1720 (define-public r-graph
1726 (uri (bioconductor-uri "graph" version))
1729 "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g"))))
1730 (build-system r-build-system)
1732 `(("r-biocgenerics" ,r-biocgenerics)))
1733 (home-page "https://bioconductor.org/packages/graph")
1734 (synopsis "Handle graph data structures in R")
1736 "This package implements some simple graph handling capabilities for R.")
1737 (license license:artistic2.0)))
1739 ;; This is a CRAN package, but it depends on a Bioconductor package.
1740 (define-public r-ggm
1747 (uri (cran-uri "ggm" version))
1750 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1751 (properties `((upstream-name . "ggm")))
1752 (build-system r-build-system)
1754 `(("r-graph" ,r-graph)
1755 ("r-igraph" ,r-igraph)))
1756 (home-page "https://cran.r-project.org/package=ggm")
1757 (synopsis "Functions for graphical Markov models")
1759 "This package provides functions and datasets for maximum likelihood
1760 fitting of some classes of graphical Markov models.")
1761 (license license:gpl2+)))
1763 (define-public r-codedepends
1765 (name "r-codedepends")
1770 (uri (cran-uri "CodeDepends" version))
1773 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1774 (properties `((upstream-name . "CodeDepends")))
1775 (build-system r-build-system)
1777 `(("r-codetools" ,r-codetools)
1778 ("r-graph" ,r-graph)
1780 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
1781 (synopsis "Analysis of R code for reproducible research and code comprehension")
1783 "This package provides tools for analyzing R expressions or blocks of
1784 code and determining the dependencies between them. It focuses on R scripts,
1785 but can be used on the bodies of functions. There are many facilities
1786 including the ability to summarize or get a high-level view of code,
1787 determining dependencies between variables, code improvement suggestions.")
1788 ;; Any version of the GPL
1789 (license (list license:gpl2+ license:gpl3+))))
1791 (define-public r-chippeakanno
1793 (name "r-chippeakanno")
1798 (uri (bioconductor-uri "ChIPpeakAnno" version))
1801 "199mlg0gwjy39afyk0ah6lzcm759bzxla4hgcajj0ay9jiibjqpa"))))
1802 (properties `((upstream-name . "ChIPpeakAnno")))
1803 (build-system r-build-system)
1805 `(("r-annotationdbi" ,r-annotationdbi)
1806 ("r-biobase" ,r-biobase)
1807 ("r-biocgenerics" ,r-biocgenerics)
1808 ("r-biocmanager" ,r-biocmanager)
1809 ("r-biomart" ,r-biomart)
1810 ("r-biostrings" ,r-biostrings)
1811 ("r-bsgenome" ,r-bsgenome)
1813 ("r-delayedarray" ,r-delayedarray)
1814 ("r-ensembldb" ,r-ensembldb)
1815 ("r-genomeinfodb" ,r-genomeinfodb)
1816 ("r-genomicalignments" ,r-genomicalignments)
1817 ("r-genomicfeatures" ,r-genomicfeatures)
1818 ("r-genomicranges" ,r-genomicranges)
1819 ("r-go-db" ,r-go-db)
1820 ("r-graph" ,r-graph)
1822 ("r-iranges" ,r-iranges)
1823 ("r-limma" ,r-limma)
1824 ("r-matrixstats" ,r-matrixstats)
1825 ("r-multtest" ,r-multtest)
1827 ("r-regioner" ,r-regioner)
1828 ("r-rsamtools" ,r-rsamtools)
1829 ("r-rtracklayer" ,r-rtracklayer)
1830 ("r-s4vectors" ,r-s4vectors)
1831 ("r-seqinr" ,r-seqinr)
1832 ("r-summarizedexperiment" ,r-summarizedexperiment)
1833 ("r-venndiagram" ,r-venndiagram)))
1835 `(("r-knitr" ,r-knitr)))
1836 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
1837 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1839 "The package includes functions to retrieve the sequences around the peak,
1840 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1841 custom features such as most conserved elements and other transcription factor
1842 binding sites supplied by users. Starting 2.0.5, new functions have been added
1843 for finding the peaks with bi-directional promoters with summary statistics
1844 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1845 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1846 enrichedGO (addGeneIDs).")
1847 (license license:gpl2+)))
1849 (define-public r-marray
1855 (uri (bioconductor-uri "marray" version))
1857 (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd"))))
1858 (build-system r-build-system)
1860 `(("r-limma" ,r-limma)))
1861 (home-page "https://bioconductor.org/packages/marray")
1862 (synopsis "Exploratory analysis for two-color spotted microarray data")
1863 (description "This package contains class definitions for two-color spotted
1864 microarray data. It also includes functions for data input, diagnostic plots,
1865 normalization and quality checking.")
1866 (license license:lgpl2.0+)))
1868 (define-public r-cghbase
1874 (uri (bioconductor-uri "CGHbase" version))
1876 (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf"))))
1877 (properties `((upstream-name . "CGHbase")))
1878 (build-system r-build-system)
1880 `(("r-biobase" ,r-biobase)
1881 ("r-marray" ,r-marray)))
1882 (home-page "https://bioconductor.org/packages/CGHbase")
1883 (synopsis "Base functions and classes for arrayCGH data analysis")
1884 (description "This package contains functions and classes that are needed by
1885 the @code{arrayCGH} packages.")
1886 (license license:gpl2+)))
1888 (define-public r-cghcall
1894 (uri (bioconductor-uri "CGHcall" version))
1896 (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg"))))
1897 (properties `((upstream-name . "CGHcall")))
1898 (build-system r-build-system)
1900 `(("r-biobase" ,r-biobase)
1901 ("r-cghbase" ,r-cghbase)
1902 ("r-impute" ,r-impute)
1903 ("r-dnacopy" ,r-dnacopy)
1904 ("r-snowfall" ,r-snowfall)))
1905 (home-page "https://bioconductor.org/packages/CGHcall")
1906 (synopsis "Base functions and classes for arrayCGH data analysis")
1907 (description "This package contains functions and classes that are needed by
1908 @code{arrayCGH} packages.")
1909 (license license:gpl2+)))
1911 (define-public r-qdnaseq
1917 (uri (bioconductor-uri "QDNAseq" version))
1919 (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86"))))
1920 (properties `((upstream-name . "QDNAseq")))
1921 (build-system r-build-system)
1923 `(("r-biobase" ,r-biobase)
1924 ("r-cghbase" ,r-cghbase)
1925 ("r-cghcall" ,r-cghcall)
1926 ("r-dnacopy" ,r-dnacopy)
1927 ("r-future" ,r-future)
1928 ("r-future-apply" ,r-future-apply)
1929 ("r-genomicranges" ,r-genomicranges)
1930 ("r-iranges" ,r-iranges)
1931 ("r-matrixstats" ,r-matrixstats)
1932 ("r-r-utils" ,r-r-utils)
1933 ("r-rsamtools" ,r-rsamtools)))
1934 (home-page "https://bioconductor.org/packages/QDNAseq")
1935 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1936 (description "The genome is divided into non-overlapping fixed-sized bins,
1937 number of sequence reads in each counted, adjusted with a simultaneous
1938 two-dimensional loess correction for sequence mappability and GC content, and
1939 filtered to remove spurious regions in the genome. Downstream steps of
1940 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1942 (license license:gpl2+)))
1944 (define-public r-bayseq
1951 (uri (bioconductor-uri "baySeq" version))
1954 "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj"))))
1955 (properties `((upstream-name . "baySeq")))
1956 (build-system r-build-system)
1958 `(("r-abind" ,r-abind)
1959 ("r-edger" ,r-edger)
1960 ("r-genomicranges" ,r-genomicranges)))
1961 (home-page "https://bioconductor.org/packages/baySeq/")
1962 (synopsis "Bayesian analysis of differential expression patterns in count data")
1964 "This package identifies differential expression in high-throughput count
1965 data, such as that derived from next-generation sequencing machines,
1966 calculating estimated posterior likelihoods of differential expression (or
1967 more complex hypotheses) via empirical Bayesian methods.")
1968 (license license:gpl3)))
1970 (define-public r-chipcomp
1977 (uri (bioconductor-uri "ChIPComp" version))
1980 "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp"))))
1981 (properties `((upstream-name . "ChIPComp")))
1982 (build-system r-build-system)
1984 `(("r-biocgenerics" ,r-biocgenerics)
1985 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1986 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1987 ("r-genomeinfodb" ,r-genomeinfodb)
1988 ("r-genomicranges" ,r-genomicranges)
1989 ("r-iranges" ,r-iranges)
1990 ("r-limma" ,r-limma)
1991 ("r-rsamtools" ,r-rsamtools)
1992 ("r-rtracklayer" ,r-rtracklayer)
1993 ("r-s4vectors" ,r-s4vectors)))
1994 (home-page "https://bioconductor.org/packages/ChIPComp")
1995 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1997 "ChIPComp implements a statistical method for quantitative comparison of
1998 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1999 sites across multiple conditions considering matching control in ChIP-seq
2001 ;; Any version of the GPL.
2002 (license license:gpl3+)))
2004 (define-public r-riboprofiling
2006 (name "r-riboprofiling")
2011 (uri (bioconductor-uri "RiboProfiling" version))
2014 "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha"))))
2015 (properties `((upstream-name . "RiboProfiling")))
2016 (build-system r-build-system)
2018 `(("r-biocgenerics" ,r-biocgenerics)
2019 ("r-biostrings" ,r-biostrings)
2020 ("r-data-table" ,r-data-table)
2021 ("r-genomeinfodb" ,r-genomeinfodb)
2022 ("r-genomicalignments" ,r-genomicalignments)
2023 ("r-genomicfeatures" ,r-genomicfeatures)
2024 ("r-genomicranges" ,r-genomicranges)
2025 ("r-ggbio" ,r-ggbio)
2026 ("r-ggplot2" ,r-ggplot2)
2027 ("r-iranges" ,r-iranges)
2029 ("r-reshape2" ,r-reshape2)
2030 ("r-rsamtools" ,r-rsamtools)
2031 ("r-rtracklayer" ,r-rtracklayer)
2032 ("r-s4vectors" ,r-s4vectors)
2033 ("r-sqldf" ,r-sqldf)))
2035 `(("r-knitr" ,r-knitr)))
2036 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2037 (synopsis "Ribosome profiling data analysis")
2038 (description "Starting with a BAM file, this package provides the
2039 necessary functions for quality assessment, read start position recalibration,
2040 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2041 of count data: pairs, log fold-change, codon frequency and coverage
2042 assessment, principal component analysis on codon coverage.")
2043 (license license:gpl3)))
2045 (define-public r-riboseqr
2052 (uri (bioconductor-uri "riboSeqR" version))
2055 "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk"))))
2056 (properties `((upstream-name . "riboSeqR")))
2057 (build-system r-build-system)
2059 `(("r-abind" ,r-abind)
2060 ("r-bayseq" ,r-bayseq)
2061 ("r-genomeinfodb" ,r-genomeinfodb)
2062 ("r-genomicranges" ,r-genomicranges)
2063 ("r-iranges" ,r-iranges)
2064 ("r-rsamtools" ,r-rsamtools)
2065 ("r-seqlogo" ,r-seqlogo)))
2066 (home-page "https://bioconductor.org/packages/riboSeqR/")
2067 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2069 "This package provides plotting functions, frameshift detection and
2070 parsing of genetic sequencing data from ribosome profiling experiments.")
2071 (license license:gpl3)))
2073 (define-public r-interactionset
2075 (name "r-interactionset")
2080 (uri (bioconductor-uri "InteractionSet" version))
2083 "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v"))))
2085 `((upstream-name . "InteractionSet")))
2086 (build-system r-build-system)
2088 `(("r-biocgenerics" ,r-biocgenerics)
2089 ("r-genomeinfodb" ,r-genomeinfodb)
2090 ("r-genomicranges" ,r-genomicranges)
2091 ("r-iranges" ,r-iranges)
2092 ("r-matrix" ,r-matrix)
2094 ("r-s4vectors" ,r-s4vectors)
2095 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2097 `(("r-knitr" ,r-knitr)))
2098 (home-page "https://bioconductor.org/packages/InteractionSet")
2099 (synopsis "Base classes for storing genomic interaction data")
2101 "This package provides the @code{GInteractions},
2102 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2103 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2105 (license license:gpl3)))
2107 (define-public r-genomicinteractions
2109 (name "r-genomicinteractions")
2114 (uri (bioconductor-uri "GenomicInteractions" version))
2117 "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy"))))
2119 `((upstream-name . "GenomicInteractions")))
2120 (build-system r-build-system)
2122 `(("r-biobase" ,r-biobase)
2123 ("r-biocgenerics" ,r-biocgenerics)
2124 ("r-data-table" ,r-data-table)
2125 ("r-dplyr" ,r-dplyr)
2126 ("r-genomeinfodb" ,r-genomeinfodb)
2127 ("r-genomicranges" ,r-genomicranges)
2128 ("r-ggplot2" ,r-ggplot2)
2129 ("r-gridextra" ,r-gridextra)
2131 ("r-igraph" ,r-igraph)
2132 ("r-interactionset" ,r-interactionset)
2133 ("r-iranges" ,r-iranges)
2134 ("r-rsamtools" ,r-rsamtools)
2135 ("r-rtracklayer" ,r-rtracklayer)
2136 ("r-s4vectors" ,r-s4vectors)
2137 ("r-stringr" ,r-stringr)))
2139 `(("r-knitr" ,r-knitr)))
2140 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2141 (synopsis "R package for handling genomic interaction data")
2143 "This R package provides tools for handling genomic interaction data,
2144 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2145 information and producing various plots and statistics.")
2146 (license license:gpl3)))
2148 (define-public r-ctc
2155 (uri (bioconductor-uri "ctc" version))
2158 "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6"))))
2159 (build-system r-build-system)
2160 (propagated-inputs `(("r-amap" ,r-amap)))
2161 (home-page "https://bioconductor.org/packages/ctc/")
2162 (synopsis "Cluster and tree conversion")
2164 "This package provides tools for exporting and importing classification
2165 trees and clusters to other programs.")
2166 (license license:gpl2)))
2168 (define-public r-goseq
2175 (uri (bioconductor-uri "goseq" version))
2178 "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym"))))
2179 (build-system r-build-system)
2181 `(("r-annotationdbi" ,r-annotationdbi)
2182 ("r-biasedurn" ,r-biasedurn)
2183 ("r-biocgenerics" ,r-biocgenerics)
2184 ("r-genelendatabase" ,r-genelendatabase)
2185 ("r-go-db" ,r-go-db)
2186 ("r-mgcv" ,r-mgcv)))
2187 (home-page "https://bioconductor.org/packages/goseq/")
2188 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2190 "This package provides tools to detect Gene Ontology and/or other user
2191 defined categories which are over/under represented in RNA-seq data.")
2192 (license license:lgpl2.0+)))
2194 (define-public r-glimma
2201 (uri (bioconductor-uri "Glimma" version))
2204 "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y"))))
2205 (properties `((upstream-name . "Glimma")))
2206 (build-system r-build-system)
2208 `(("r-edger" ,r-edger)
2209 ("r-jsonlite" ,r-jsonlite)
2210 ("r-s4vectors" ,r-s4vectors)))
2212 `(("r-knitr" ,r-knitr)))
2213 (home-page "https://github.com/Shians/Glimma")
2214 (synopsis "Interactive HTML graphics")
2216 "This package generates interactive visualisations for analysis of
2217 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2218 HTML page. The interactions are built on top of the popular static
2219 representations of analysis results in order to provide additional
2221 (license license:lgpl3)))
2223 (define-public r-rots
2230 (uri (bioconductor-uri "ROTS" version))
2233 "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm"))))
2234 (properties `((upstream-name . "ROTS")))
2235 (build-system r-build-system)
2237 `(("r-biobase" ,r-biobase)
2238 ("r-rcpp" ,r-rcpp)))
2239 (home-page "https://bioconductor.org/packages/ROTS/")
2240 (synopsis "Reproducibility-Optimized Test Statistic")
2242 "This package provides tools for calculating the
2243 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2245 (license license:gpl2+)))
2247 (define-public r-plgem
2254 (uri (bioconductor-uri "plgem" version))
2257 "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a"))))
2258 (build-system r-build-system)
2260 `(("r-biobase" ,r-biobase)
2261 ("r-mass" ,r-mass)))
2262 (home-page "http://www.genopolis.it")
2263 (synopsis "Detect differential expression in microarray and proteomics datasets")
2265 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2266 model the variance-versus-mean dependence that exists in a variety of
2267 genome-wide datasets, including microarray and proteomics data. The use of
2268 PLGEM has been shown to improve the detection of differentially expressed
2269 genes or proteins in these datasets.")
2270 (license license:gpl2)))
2272 (define-public r-inspect
2279 (uri (bioconductor-uri "INSPEcT" version))
2282 "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z"))))
2283 (properties `((upstream-name . "INSPEcT")))
2284 (build-system r-build-system)
2286 `(("r-biobase" ,r-biobase)
2287 ("r-biocgenerics" ,r-biocgenerics)
2288 ("r-biocparallel" ,r-biocparallel)
2289 ("r-deseq2" ,r-deseq2)
2290 ("r-desolve" ,r-desolve)
2291 ("r-gdata" ,r-gdata)
2292 ("r-genomeinfodb" ,r-genomeinfodb)
2293 ("r-genomicalignments" ,r-genomicalignments)
2294 ("r-genomicfeatures" ,r-genomicfeatures)
2295 ("r-genomicranges" ,r-genomicranges)
2296 ("r-iranges" ,r-iranges)
2297 ("r-kernsmooth" ,r-kernsmooth)
2298 ("r-plgem" ,r-plgem)
2300 ("r-rootsolve" ,r-rootsolve)
2301 ("r-rsamtools" ,r-rsamtools)
2302 ("r-rtracklayer" ,r-rtracklayer)
2303 ("r-s4vectors" ,r-s4vectors)
2304 ("r-shiny" ,r-shiny)
2305 ("r-summarizedexperiment" ,r-summarizedexperiment)
2306 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2307 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2309 `(("r-knitr" ,r-knitr)))
2310 (home-page "https://bioconductor.org/packages/INSPEcT")
2311 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2313 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2314 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2315 order to evaluate synthesis, processing and degradation rates and assess via
2316 modeling the rates that determines changes in mature mRNA levels.")
2317 (license license:gpl2)))
2319 (define-public r-dnabarcodes
2321 (name "r-dnabarcodes")
2326 (uri (bioconductor-uri "DNABarcodes" version))
2329 "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7"))))
2330 (properties `((upstream-name . "DNABarcodes")))
2331 (build-system r-build-system)
2334 ("r-matrix" ,r-matrix)
2335 ("r-rcpp" ,r-rcpp)))
2337 `(("r-knitr" ,r-knitr)))
2338 (home-page "https://bioconductor.org/packages/DNABarcodes")
2339 (synopsis "Create and analyze DNA barcodes")
2341 "This package offers tools to create DNA barcode sets capable of
2342 correcting insertion, deletion, and substitution errors. Existing barcodes
2343 can be analyzed regarding their minimal, maximal and average distances between
2344 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2345 demultiplexed, i.e. assigned to their original reference barcode.")
2346 (license license:gpl2)))
2348 (define-public r-ruvseq
2355 (uri (bioconductor-uri "RUVSeq" version))
2358 "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x"))))
2359 (properties `((upstream-name . "RUVSeq")))
2360 (build-system r-build-system)
2362 `(("r-biobase" ,r-biobase)
2363 ("r-edaseq" ,r-edaseq)
2364 ("r-edger" ,r-edger)
2365 ("r-mass" ,r-mass)))
2367 `(("r-knitr" ,r-knitr)))
2368 (home-page "https://github.com/drisso/RUVSeq")
2369 (synopsis "Remove unwanted variation from RNA-Seq data")
2371 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2372 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2374 (license license:artistic2.0)))
2376 (define-public r-biocneighbors
2378 (name "r-biocneighbors")
2383 (uri (bioconductor-uri "BiocNeighbors" version))
2386 "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy"))))
2387 (properties `((upstream-name . "BiocNeighbors")))
2388 (build-system r-build-system)
2390 `(("r-biocparallel" ,r-biocparallel)
2391 ("r-matrix" ,r-matrix)
2393 ("r-rcppannoy" ,r-rcppannoy)
2394 ("r-rcpphnsw" ,r-rcpphnsw)
2395 ("r-s4vectors" ,r-s4vectors)))
2397 `(("r-knitr" ,r-knitr)))
2398 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2399 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2401 "This package implements exact and approximate methods for nearest
2402 neighbor detection, in a framework that allows them to be easily switched
2403 within Bioconductor packages or workflows. The exact algorithm is implemented
2404 using pre-clustering with the k-means algorithm. Functions are also provided
2405 to search for all neighbors within a given distance. Parallelization is
2406 achieved for all methods using the BiocParallel framework.")
2407 (license license:gpl3)))
2409 (define-public r-biocsingular
2411 (name "r-biocsingular")
2416 (uri (bioconductor-uri "BiocSingular" version))
2419 "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih"))))
2420 (properties `((upstream-name . "BiocSingular")))
2421 (build-system r-build-system)
2423 `(("r-beachmat" ,r-beachmat)
2424 ("r-biocgenerics" ,r-biocgenerics)
2425 ("r-biocparallel" ,r-biocparallel)
2426 ("r-delayedarray" ,r-delayedarray)
2427 ("r-irlba" ,r-irlba)
2428 ("r-matrix" ,r-matrix)
2431 ("r-s4vectors" ,r-s4vectors)))
2433 `(("r-knitr" ,r-knitr)))
2434 (home-page "https://github.com/LTLA/BiocSingular")
2435 (synopsis "Singular value decomposition for Bioconductor packages")
2437 "This package implements exact and approximate methods for singular value
2438 decomposition and principal components analysis, in a framework that allows
2439 them to be easily switched within Bioconductor packages or workflows. Where
2440 possible, parallelization is achieved using the BiocParallel framework.")
2441 (license license:gpl3)))
2443 (define-public r-destiny
2450 (uri (bioconductor-uri "destiny" version))
2453 "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n"))))
2454 (build-system r-build-system)
2456 `(("r-biobase" ,r-biobase)
2457 ("r-biocgenerics" ,r-biocgenerics)
2458 ("r-ggplot-multistats" ,r-ggplot-multistats)
2459 ("r-ggplot2" ,r-ggplot2)
2460 ("r-ggthemes" ,r-ggthemes)
2461 ("r-irlba" ,r-irlba)
2462 ("r-knn-covertree" ,r-knn-covertree)
2463 ("r-matrix" ,r-matrix)
2464 ("r-nbconvertr" ,r-nbconvertr)
2465 ("r-pcamethods" ,r-pcamethods)
2466 ("r-proxy" ,r-proxy)
2468 ("r-rcppeigen" ,r-rcppeigen)
2469 ("r-rcpphnsw" ,r-rcpphnsw)
2470 ("r-rspectra" ,r-rspectra)
2471 ("r-scales" ,r-scales)
2472 ("r-scatterplot3d" ,r-scatterplot3d)
2473 ("r-singlecellexperiment" ,r-singlecellexperiment)
2474 ("r-smoother" ,r-smoother)
2475 ("r-summarizedexperiment" ,r-summarizedexperiment)
2476 ("r-tidyr" ,r-tidyr)
2477 ("r-tidyselect" ,r-tidyselect)
2480 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2481 (home-page "https://bioconductor.org/packages/destiny/")
2482 (synopsis "Create and plot diffusion maps")
2483 (description "This package provides tools to create and plot diffusion
2485 ;; Any version of the GPL
2486 (license license:gpl3+)))
2488 (define-public r-savr
2495 (uri (bioconductor-uri "savR" version))
2498 "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a"))))
2499 (properties `((upstream-name . "savR")))
2500 (build-system r-build-system)
2502 `(("r-ggplot2" ,r-ggplot2)
2503 ("r-gridextra" ,r-gridextra)
2504 ("r-reshape2" ,r-reshape2)
2505 ("r-scales" ,r-scales)
2507 (home-page "https://github.com/bcalder/savR")
2508 (synopsis "Parse and analyze Illumina SAV files")
2510 "This package provides tools to parse Illumina Sequence Analysis
2511 Viewer (SAV) files, access data, and generate QC plots.")
2512 (license license:agpl3+)))
2514 (define-public r-chipexoqual
2516 (name "r-chipexoqual")
2521 (uri (bioconductor-uri "ChIPexoQual" version))
2524 "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp"))))
2525 (properties `((upstream-name . "ChIPexoQual")))
2526 (build-system r-build-system)
2528 `(("r-biocparallel" ,r-biocparallel)
2529 ("r-biovizbase" ,r-biovizbase)
2530 ("r-broom" ,r-broom)
2531 ("r-data-table" ,r-data-table)
2532 ("r-dplyr" ,r-dplyr)
2533 ("r-genomeinfodb" ,r-genomeinfodb)
2534 ("r-genomicalignments" ,r-genomicalignments)
2535 ("r-genomicranges" ,r-genomicranges)
2536 ("r-ggplot2" ,r-ggplot2)
2537 ("r-hexbin" ,r-hexbin)
2538 ("r-iranges" ,r-iranges)
2539 ("r-rcolorbrewer" ,r-rcolorbrewer)
2540 ("r-rmarkdown" ,r-rmarkdown)
2541 ("r-rsamtools" ,r-rsamtools)
2542 ("r-s4vectors" ,r-s4vectors)
2543 ("r-scales" ,r-scales)
2544 ("r-viridis" ,r-viridis)))
2546 `(("r-knitr" ,r-knitr)))
2547 (home-page "https://github.com/keleslab/ChIPexoQual")
2548 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2550 "This package provides a quality control pipeline for ChIP-exo/nexus
2552 (license license:gpl2+)))
2554 (define-public r-copynumber
2556 (name "r-copynumber")
2560 (uri (bioconductor-uri "copynumber" version))
2563 "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my"))))
2564 (build-system r-build-system)
2566 `(("r-s4vectors" ,r-s4vectors)
2567 ("r-iranges" ,r-iranges)
2568 ("r-genomicranges" ,r-genomicranges)
2569 ("r-biocgenerics" ,r-biocgenerics)))
2570 (home-page "https://bioconductor.org/packages/copynumber")
2571 (synopsis "Segmentation of single- and multi-track copy number data")
2573 "This package segments single- and multi-track copy number data by a
2574 penalized least squares regression method.")
2575 (license license:artistic2.0)))
2577 (define-public r-dnacopy
2584 (uri (bioconductor-uri "DNAcopy" version))
2587 "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza"))))
2588 (properties `((upstream-name . "DNAcopy")))
2589 (build-system r-build-system)
2590 (native-inputs `(("gfortran" ,gfortran)))
2591 (home-page "https://bioconductor.org/packages/DNAcopy")
2592 (synopsis "DNA copy number data analysis")
2594 "This package implements the @dfn{circular binary segmentation} (CBS)
2595 algorithm to segment DNA copy number data and identify genomic regions with
2596 abnormal copy number.")
2597 (license license:gpl2+)))
2599 ;; This is a CRAN package, but it uncharacteristically depends on a
2600 ;; Bioconductor package.
2601 (define-public r-htscluster
2603 (name "r-htscluster")
2608 (uri (cran-uri "HTSCluster" version))
2611 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2612 (properties `((upstream-name . "HTSCluster")))
2613 (build-system r-build-system)
2615 `(("r-capushe" ,r-capushe)
2616 ("r-edger" ,r-edger)
2617 ("r-plotrix" ,r-plotrix)))
2618 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2619 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2621 "This package provides a Poisson mixture model is implemented to cluster
2622 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2623 estimation is performed using either the EM or CEM algorithm, and the slope
2624 heuristics are used for model selection (i.e., to choose the number of
2626 (license license:gpl3+)))
2628 (define-public r-deds
2635 (uri (bioconductor-uri "DEDS" version))
2638 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2639 (properties `((upstream-name . "DEDS")))
2640 (build-system r-build-system)
2641 (home-page "https://bioconductor.org/packages/DEDS/")
2642 (synopsis "Differential expression via distance summary for microarray data")
2644 "This library contains functions that calculate various statistics of
2645 differential expression for microarray data, including t statistics, fold
2646 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2647 also implements a new methodology called DEDS (Differential Expression via
2648 Distance Summary), which selects differentially expressed genes by integrating
2649 and summarizing a set of statistics using a weighted distance approach.")
2650 ;; Any version of the LGPL.
2651 (license license:lgpl3+)))
2653 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2655 (define-public r-nbpseq
2662 (uri (cran-uri "NBPSeq" version))
2665 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2666 (properties `((upstream-name . "NBPSeq")))
2667 (build-system r-build-system)
2669 `(("r-qvalue" ,r-qvalue)))
2670 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2671 (synopsis "Negative binomial models for RNA-Seq data")
2673 "This package provides negative binomial models for two-group comparisons
2674 and regression inferences from RNA-sequencing data.")
2675 (license license:gpl2)))
2677 (define-public r-ebseq
2684 (uri (bioconductor-uri "EBSeq" version))
2687 "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f"))))
2688 (properties `((upstream-name . "EBSeq")))
2689 (build-system r-build-system)
2691 `(("r-blockmodeling" ,r-blockmodeling)
2692 ("r-gplots" ,r-gplots)
2693 ("r-testthat" ,r-testthat)))
2694 (home-page "https://bioconductor.org/packages/EBSeq")
2695 (synopsis "Differential expression analysis of RNA-seq data")
2697 "This package provides tools for differential expression analysis at both
2698 gene and isoform level using RNA-seq data")
2699 (license license:artistic2.0)))
2701 (define-public r-karyoploter
2703 (name "r-karyoploter")
2707 (uri (bioconductor-uri "karyoploteR" version))
2710 "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs"))))
2711 (build-system r-build-system)
2713 `(("r-annotationdbi" ,r-annotationdbi)
2714 ("r-bamsignals" ,r-bamsignals)
2715 ("r-bezier" ,r-bezier)
2716 ("r-biovizbase" ,r-biovizbase)
2717 ("r-digest" ,r-digest)
2718 ("r-genomeinfodb" ,r-genomeinfodb)
2719 ("r-genomicfeatures" ,r-genomicfeatures)
2720 ("r-genomicranges" ,r-genomicranges)
2721 ("r-iranges" ,r-iranges)
2722 ("r-memoise" ,r-memoise)
2723 ("r-regioner" ,r-regioner)
2724 ("r-rsamtools" ,r-rsamtools)
2725 ("r-rtracklayer" ,r-rtracklayer)
2726 ("r-s4vectors" ,r-s4vectors)
2727 ("r-variantannotation" ,r-variantannotation)))
2729 `(("r-knitr" ,r-knitr)))
2730 (home-page "https://bioconductor.org/packages/karyoploteR/")
2731 (synopsis "Plot customizable linear genomes displaying arbitrary data")
2732 (description "This package creates karyotype plots of arbitrary genomes and
2733 offers a complete set of functions to plot arbitrary data on them. It mimicks
2734 many R base graphics functions coupling them with a coordinate change function
2735 automatically mapping the chromosome and data coordinates into the plot
2737 (license license:artistic2.0)))
2739 (define-public r-lpsymphony
2741 (name "r-lpsymphony")
2746 (uri (bioconductor-uri "lpsymphony" version))
2749 "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4"))))
2750 (build-system r-build-system)
2754 `(("pkg-config" ,pkg-config)
2755 ("r-knitr" ,r-knitr)))
2756 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2757 (synopsis "Symphony integer linear programming solver in R")
2759 "This package was derived from Rsymphony. The package provides an R
2760 interface to SYMPHONY, a linear programming solver written in C++. The main
2761 difference between this package and Rsymphony is that it includes the solver
2762 source code, while Rsymphony expects to find header and library files on the
2763 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2764 to install interface to SYMPHONY.")
2765 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2766 ;; lpsimphony is released under the same terms.
2767 (license license:epl1.0)))
2769 (define-public r-ihw
2776 (uri (bioconductor-uri "IHW" version))
2779 "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j"))))
2780 (properties `((upstream-name . "IHW")))
2781 (build-system r-build-system)
2783 `(("r-biocgenerics" ,r-biocgenerics)
2784 ("r-fdrtool" ,r-fdrtool)
2785 ("r-lpsymphony" ,r-lpsymphony)
2786 ("r-slam" ,r-slam)))
2788 `(("r-knitr" ,r-knitr)))
2789 (home-page "https://bioconductor.org/packages/IHW")
2790 (synopsis "Independent hypothesis weighting")
2792 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2793 procedure that increases power compared to the method of Benjamini and
2794 Hochberg by assigning data-driven weights to each hypothesis. The input to
2795 IHW is a two-column table of p-values and covariates. The covariate can be
2796 any continuous-valued or categorical variable that is thought to be
2797 informative on the statistical properties of each hypothesis test, while it is
2798 independent of the p-value under the null hypothesis.")
2799 (license license:artistic2.0)))
2801 (define-public r-icobra
2808 (uri (bioconductor-uri "iCOBRA" version))
2811 "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1"))))
2812 (properties `((upstream-name . "iCOBRA")))
2813 (build-system r-build-system)
2815 `(("r-dplyr" ,r-dplyr)
2817 ("r-ggplot2" ,r-ggplot2)
2818 ("r-limma" ,r-limma)
2819 ("r-reshape2" ,r-reshape2)
2821 ("r-scales" ,r-scales)
2822 ("r-shiny" ,r-shiny)
2823 ("r-shinybs" ,r-shinybs)
2824 ("r-shinydashboard" ,r-shinydashboard)
2825 ("r-upsetr" ,r-upsetr)))
2827 `(("r-knitr" ,r-knitr)))
2828 (home-page "https://bioconductor.org/packages/iCOBRA")
2829 (synopsis "Comparison and visualization of ranking and assignment methods")
2831 "This package provides functions for calculation and visualization of
2832 performance metrics for evaluation of ranking and binary
2833 classification (assignment) methods. It also contains a Shiny application for
2834 interactive exploration of results.")
2835 (license license:gpl2+)))
2837 (define-public r-mast
2844 (uri (bioconductor-uri "MAST" version))
2847 "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr"))))
2848 (properties `((upstream-name . "MAST")))
2849 (build-system r-build-system)
2851 `(("r-abind" ,r-abind)
2852 ("r-biobase" ,r-biobase)
2853 ("r-biocgenerics" ,r-biocgenerics)
2854 ("r-data-table" ,r-data-table)
2855 ("r-ggplot2" ,r-ggplot2)
2857 ("r-progress" ,r-progress)
2858 ("r-reshape2" ,r-reshape2)
2859 ("r-s4vectors" ,r-s4vectors)
2860 ("r-singlecellexperiment" ,r-singlecellexperiment)
2861 ("r-stringr" ,r-stringr)
2862 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2864 `(("r-knitr" ,r-knitr)))
2865 (home-page "https://github.com/RGLab/MAST/")
2866 (synopsis "Model-based analysis of single cell transcriptomics")
2868 "This package provides methods and models for handling zero-inflated
2869 single cell assay data.")
2870 (license license:gpl2+)))
2872 (define-public r-monocle
2879 (uri (bioconductor-uri "monocle" version))
2882 "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd"))))
2883 (build-system r-build-system)
2885 `(("r-biobase" ,r-biobase)
2886 ("r-biocgenerics" ,r-biocgenerics)
2887 ("r-biocviews" ,r-biocviews)
2888 ("r-cluster" ,r-cluster)
2889 ("r-combinat" ,r-combinat)
2890 ("r-ddrtree" ,r-ddrtree)
2891 ("r-densityclust" ,r-densityclust)
2892 ("r-dplyr" ,r-dplyr)
2893 ("r-fastica" ,r-fastica)
2894 ("r-ggplot2" ,r-ggplot2)
2895 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2896 ("r-igraph" ,r-igraph)
2897 ("r-irlba" ,r-irlba)
2898 ("r-limma" ,r-limma)
2900 ("r-matrix" ,r-matrix)
2901 ("r-matrixstats" ,r-matrixstats)
2902 ("r-pheatmap" ,r-pheatmap)
2904 ("r-proxy" ,r-proxy)
2905 ("r-qlcmatrix" ,r-qlcmatrix)
2908 ("r-reshape2" ,r-reshape2)
2909 ("r-rtsne" ,r-rtsne)
2911 ("r-stringr" ,r-stringr)
2912 ("r-tibble" ,r-tibble)
2914 ("r-viridis" ,r-viridis)))
2916 `(("r-knitr" ,r-knitr)))
2917 (home-page "https://bioconductor.org/packages/monocle")
2918 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2920 "Monocle performs differential expression and time-series analysis for
2921 single-cell expression experiments. It orders individual cells according to
2922 progress through a biological process, without knowing ahead of time which
2923 genes define progress through that process. Monocle also performs
2924 differential expression analysis, clustering, visualization, and other useful
2925 tasks on single cell expression data. It is designed to work with RNA-Seq and
2926 qPCR data, but could be used with other types as well.")
2927 (license license:artistic2.0)))
2929 (define-public r-monocle3
2937 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2939 (file-name (git-file-name name version))
2942 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2943 (build-system r-build-system)
2945 `(("r-biobase" ,r-biobase)
2946 ("r-biocgenerics" ,r-biocgenerics)
2947 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2948 ("r-dplyr" ,r-dplyr)
2949 ("r-ggplot2" ,r-ggplot2)
2950 ("r-ggrepel" ,r-ggrepel)
2952 ("r-htmlwidgets" ,r-htmlwidgets)
2953 ("r-igraph" ,r-igraph)
2954 ("r-irlba" ,r-irlba)
2955 ("r-limma" ,r-limma)
2956 ("r-lmtest" ,r-lmtest)
2958 ("r-matrix" ,r-matrix)
2959 ("r-matrix-utils" ,r-matrix-utils)
2960 ("r-pbapply" ,r-pbapply)
2961 ("r-pbmcapply" ,r-pbmcapply)
2962 ("r-pheatmap" ,r-pheatmap)
2963 ("r-plotly" ,r-plotly)
2965 ("r-proxy" ,r-proxy)
2967 ("r-purrr" ,r-purrr)
2970 ("r-rcppparallel" ,r-rcppparallel)
2971 ("r-reshape2" ,r-reshape2)
2972 ("r-reticulate" ,r-reticulate)
2973 ("r-rhpcblasctl" ,r-rhpcblasctl)
2974 ("r-rtsne" ,r-rtsne)
2975 ("r-shiny" ,r-shiny)
2977 ("r-spdep" ,r-spdep)
2978 ("r-speedglm" ,r-speedglm)
2979 ("r-stringr" ,r-stringr)
2980 ("r-singlecellexperiment" ,r-singlecellexperiment)
2981 ("r-tibble" ,r-tibble)
2982 ("r-tidyr" ,r-tidyr)
2984 ("r-viridis" ,r-viridis)))
2985 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2986 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2988 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2989 (license license:expat)))
2991 (define-public r-noiseq
2998 (uri (bioconductor-uri "NOISeq" version))
3001 "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33"))))
3002 (properties `((upstream-name . "NOISeq")))
3003 (build-system r-build-system)
3005 `(("r-biobase" ,r-biobase)
3006 ("r-matrix" ,r-matrix)))
3007 (home-page "https://bioconductor.org/packages/NOISeq")
3008 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3010 "This package provides tools to support the analysis of RNA-seq
3011 expression data or other similar kind of data. It provides exploratory plots
3012 to evaluate saturation, count distribution, expression per chromosome, type of
3013 detected features, features length, etc. It also supports the analysis of
3014 differential expression between two experimental conditions with no parametric
3016 (license license:artistic2.0)))
3018 (define-public r-scdd
3025 (uri (bioconductor-uri "scDD" version))
3028 "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx"))))
3029 (properties `((upstream-name . "scDD")))
3030 (build-system r-build-system)
3033 ("r-biocparallel" ,r-biocparallel)
3034 ("r-ebseq" ,r-ebseq)
3035 ("r-fields" ,r-fields)
3036 ("r-ggplot2" ,r-ggplot2)
3037 ("r-mclust" ,r-mclust)
3038 ("r-outliers" ,r-outliers)
3039 ("r-s4vectors" ,r-s4vectors)
3040 ("r-scran" ,r-scran)
3041 ("r-singlecellexperiment" ,r-singlecellexperiment)
3042 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3044 `(("r-knitr" ,r-knitr)))
3045 (home-page "https://github.com/kdkorthauer/scDD")
3046 (synopsis "Mixture modeling of single-cell RNA-seq data")
3048 "This package implements a method to analyze single-cell RNA-seq data
3049 utilizing flexible Dirichlet Process mixture models. Genes with differential
3050 distributions of expression are classified into several interesting patterns
3051 of differences between two conditions. The package also includes functions
3052 for simulating data with these patterns from negative binomial
3054 (license license:gpl2)))
3056 (define-public r-scone
3063 (uri (bioconductor-uri "scone" version))
3066 "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g"))))
3067 (build-system r-build-system)
3069 `(("r-aroma-light" ,r-aroma-light)
3070 ("r-biocparallel" ,r-biocparallel)
3072 ("r-class" ,r-class)
3073 ("r-cluster" ,r-cluster)
3074 ("r-compositions" ,r-compositions)
3075 ("r-diptest" ,r-diptest)
3076 ("r-edger" ,r-edger)
3078 ("r-gplots" ,r-gplots)
3079 ("r-hexbin" ,r-hexbin)
3080 ("r-limma" ,r-limma)
3081 ("r-matrixstats" ,r-matrixstats)
3082 ("r-mixtools" ,r-mixtools)
3083 ("r-rarpack" ,r-rarpack)
3084 ("r-rcolorbrewer" ,r-rcolorbrewer)
3085 ("r-rhdf5" ,r-rhdf5)
3086 ("r-ruvseq" ,r-ruvseq)
3087 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3089 `(("r-knitr" ,r-knitr)))
3090 (home-page "https://bioconductor.org/packages/scone")
3091 (synopsis "Single cell overview of normalized expression data")
3093 "SCONE is an R package for comparing and ranking the performance of
3094 different normalization schemes for single-cell RNA-seq and other
3095 high-throughput analyses.")
3096 (license license:artistic2.0)))
3098 (define-public r-geoquery
3105 (uri (bioconductor-uri "GEOquery" version))
3108 "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m"))))
3109 (properties `((upstream-name . "GEOquery")))
3110 (build-system r-build-system)
3112 `(("r-biobase" ,r-biobase)
3113 ("r-dplyr" ,r-dplyr)
3115 ("r-limma" ,r-limma)
3116 ("r-magrittr" ,r-magrittr)
3117 ("r-readr" ,r-readr)
3118 ("r-tidyr" ,r-tidyr)
3119 ("r-xml2" ,r-xml2)))
3121 `(("r-knitr" ,r-knitr)))
3122 (home-page "https://github.com/seandavi/GEOquery/")
3123 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3125 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3126 microarray data. Given the rich and varied nature of this resource, it is
3127 only natural to want to apply BioConductor tools to these data. GEOquery is
3128 the bridge between GEO and BioConductor.")
3129 (license license:gpl2)))
3131 (define-public r-illuminaio
3133 (name "r-illuminaio")
3138 (uri (bioconductor-uri "illuminaio" version))
3141 "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c"))))
3142 (build-system r-build-system)
3144 `(("r-base64" ,r-base64)))
3145 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3146 (synopsis "Parse Illumina microarray output files")
3148 "This package provides tools for parsing Illumina's microarray output
3149 files, including IDAT.")
3150 (license license:gpl2)))
3152 (define-public r-siggenes
3159 (uri (bioconductor-uri "siggenes" version))
3162 "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy"))))
3163 (build-system r-build-system)
3165 `(("r-biobase" ,r-biobase)
3166 ("r-multtest" ,r-multtest)
3167 ("r-scrime" ,r-scrime)))
3168 (home-page "https://bioconductor.org/packages/siggenes/")
3170 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3172 "This package provides tools for the identification of differentially
3173 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3174 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3175 Bayes Analyses of Microarrays} (EBAM).")
3176 (license license:lgpl2.0+)))
3178 (define-public r-bumphunter
3180 (name "r-bumphunter")
3185 (uri (bioconductor-uri "bumphunter" version))
3188 "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq"))))
3189 (build-system r-build-system)
3191 `(("r-annotationdbi" ,r-annotationdbi)
3192 ("r-biocgenerics" ,r-biocgenerics)
3193 ("r-dorng" ,r-dorng)
3194 ("r-foreach" ,r-foreach)
3195 ("r-genomeinfodb" ,r-genomeinfodb)
3196 ("r-genomicfeatures" ,r-genomicfeatures)
3197 ("r-genomicranges" ,r-genomicranges)
3198 ("r-iranges" ,r-iranges)
3199 ("r-iterators" ,r-iterators)
3200 ("r-limma" ,r-limma)
3201 ("r-locfit" ,r-locfit)
3202 ("r-matrixstats" ,r-matrixstats)
3203 ("r-s4vectors" ,r-s4vectors)))
3204 (home-page "https://github.com/ririzarr/bumphunter")
3205 (synopsis "Find bumps in genomic data")
3207 "This package provides tools for finding bumps in genomic data in order
3208 to identify differentially methylated regions in epigenetic epidemiology
3210 (license license:artistic2.0)))
3212 (define-public r-minfi
3219 (uri (bioconductor-uri "minfi" version))
3222 "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w"))))
3223 (build-system r-build-system)
3225 `(("r-beanplot" ,r-beanplot)
3226 ("r-biobase" ,r-biobase)
3227 ("r-biocgenerics" ,r-biocgenerics)
3228 ("r-biocparallel" ,r-biocparallel)
3229 ("r-biostrings" ,r-biostrings)
3230 ("r-bumphunter" ,r-bumphunter)
3231 ("r-data-table" ,r-data-table)
3232 ("r-delayedarray" ,r-delayedarray)
3233 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3234 ("r-genefilter" ,r-genefilter)
3235 ("r-genomeinfodb" ,r-genomeinfodb)
3236 ("r-genomicranges" ,r-genomicranges)
3237 ("r-geoquery" ,r-geoquery)
3238 ("r-hdf5array" ,r-hdf5array)
3239 ("r-illuminaio" ,r-illuminaio)
3240 ("r-iranges" ,r-iranges)
3241 ("r-lattice" ,r-lattice)
3242 ("r-limma" ,r-limma)
3244 ("r-mclust" ,r-mclust)
3246 ("r-nor1mix" ,r-nor1mix)
3247 ("r-preprocesscore" ,r-preprocesscore)
3248 ("r-quadprog" ,r-quadprog)
3249 ("r-rcolorbrewer" ,r-rcolorbrewer)
3250 ("r-reshape" ,r-reshape)
3251 ("r-s4vectors" ,r-s4vectors)
3252 ("r-siggenes" ,r-siggenes)
3253 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3255 `(("r-knitr" ,r-knitr)))
3256 (home-page "https://github.com/hansenlab/minfi")
3257 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3259 "This package provides tools to analyze and visualize Illumina Infinium
3260 methylation arrays.")
3261 (license license:artistic2.0)))
3263 (define-public r-methylumi
3265 (name "r-methylumi")
3270 (uri (bioconductor-uri "methylumi" version))
3273 "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr"))))
3274 (build-system r-build-system)
3276 `(("r-annotate" ,r-annotate)
3277 ("r-annotationdbi" ,r-annotationdbi)
3278 ("r-biobase" ,r-biobase)
3279 ("r-biocgenerics" ,r-biocgenerics)
3280 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3281 ("r-genefilter" ,r-genefilter)
3282 ("r-genomeinfodb" ,r-genomeinfodb)
3283 ("r-genomicranges" ,r-genomicranges)
3284 ("r-ggplot2" ,r-ggplot2)
3285 ("r-illuminaio" ,r-illuminaio)
3286 ("r-iranges" ,r-iranges)
3287 ("r-lattice" ,r-lattice)
3288 ("r-matrixstats" ,r-matrixstats)
3289 ("r-minfi" ,r-minfi)
3290 ("r-reshape2" ,r-reshape2)
3291 ("r-s4vectors" ,r-s4vectors)
3292 ("r-scales" ,r-scales)
3293 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3295 `(("r-knitr" ,r-knitr)))
3296 (home-page "https://bioconductor.org/packages/methylumi")
3297 (synopsis "Handle Illumina methylation data")
3299 "This package provides classes for holding and manipulating Illumina
3300 methylation data. Based on eSet, it can contain MIAME information, sample
3301 information, feature information, and multiple matrices of data. An
3302 \"intelligent\" import function, methylumiR can read the Illumina text files
3303 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3304 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3305 background correction, and quality control features for GoldenGate, Infinium,
3306 and Infinium HD arrays are also included.")
3307 (license license:gpl2)))
3309 (define-public r-lumi
3316 (uri (bioconductor-uri "lumi" version))
3319 "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9"))))
3320 (build-system r-build-system)
3322 `(("r-affy" ,r-affy)
3323 ("r-annotate" ,r-annotate)
3324 ("r-annotationdbi" ,r-annotationdbi)
3325 ("r-biobase" ,r-biobase)
3327 ("r-genomicfeatures" ,r-genomicfeatures)
3328 ("r-genomicranges" ,r-genomicranges)
3329 ("r-kernsmooth" ,r-kernsmooth)
3330 ("r-lattice" ,r-lattice)
3332 ("r-methylumi" ,r-methylumi)
3334 ("r-nleqslv" ,r-nleqslv)
3335 ("r-preprocesscore" ,r-preprocesscore)
3336 ("r-rsqlite" ,r-rsqlite)))
3337 (home-page "https://bioconductor.org/packages/lumi")
3338 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3340 "The lumi package provides an integrated solution for the Illumina
3341 microarray data analysis. It includes functions of Illumina
3342 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3343 variance stabilization, normalization and gene annotation at the probe level.
3344 It also includes the functions of processing Illumina methylation microarrays,
3345 especially Illumina Infinium methylation microarrays.")
3346 (license license:lgpl2.0+)))
3348 (define-public r-linnorm
3355 (uri (bioconductor-uri "Linnorm" version))
3358 "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp"))))
3359 (properties `((upstream-name . "Linnorm")))
3360 (build-system r-build-system)
3362 `(("r-amap" ,r-amap)
3363 ("r-apcluster" ,r-apcluster)
3364 ("r-ellipse" ,r-ellipse)
3365 ("r-fastcluster" ,r-fastcluster)
3367 ("r-ggdendro" ,r-ggdendro)
3368 ("r-ggplot2" ,r-ggplot2)
3369 ("r-gmodels" ,r-gmodels)
3370 ("r-igraph" ,r-igraph)
3371 ("r-limma" ,r-limma)
3373 ("r-mclust" ,r-mclust)
3375 ("r-rcpparmadillo" ,r-rcpparmadillo)
3376 ("r-rtsne" ,r-rtsne)
3377 ("r-statmod" ,r-statmod)
3378 ("r-vegan" ,r-vegan)
3381 `(("r-knitr" ,r-knitr)))
3382 (home-page "http://www.jjwanglab.org/Linnorm/")
3383 (synopsis "Linear model and normality based transformation method")
3385 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3386 count data or any large scale count data. It transforms such datasets for
3387 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3388 the following pipelines are implemented:
3391 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3392 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3393 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3394 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3395 @item Differential expression analysis or differential peak detection using
3396 limma (@code{Linnorm.limma})
3397 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3398 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3399 @item Stable gene selection for scRNA-seq data; for users without or who do
3400 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3401 @item Data imputation (@code{Linnorm.DataImput}).
3404 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3405 @code{RnaXSim} function is included for simulating RNA-seq data for the
3406 evaluation of DEG analysis methods.")
3407 (license license:expat)))
3409 (define-public r-ioniser
3416 (uri (bioconductor-uri "IONiseR" version))
3419 "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w"))))
3420 (properties `((upstream-name . "IONiseR")))
3421 (build-system r-build-system)
3423 `(("r-biocgenerics" ,r-biocgenerics)
3424 ("r-biocparallel" ,r-biocparallel)
3425 ("r-biostrings" ,r-biostrings)
3426 ("r-bit64" ,r-bit64)
3427 ("r-dplyr" ,r-dplyr)
3428 ("r-ggplot2" ,r-ggplot2)
3429 ("r-magrittr" ,r-magrittr)
3430 ("r-rhdf5" ,r-rhdf5)
3431 ("r-shortread" ,r-shortread)
3432 ("r-stringr" ,r-stringr)
3433 ("r-tibble" ,r-tibble)
3434 ("r-tidyr" ,r-tidyr)
3435 ("r-xvector" ,r-xvector)))
3437 `(("r-knitr" ,r-knitr)))
3438 (home-page "https://bioconductor.org/packages/IONiseR/")
3439 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3441 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3442 MinION data. It extracts summary statistics from a set of fast5 files and can
3443 be used either before or after base calling. In addition to standard
3444 summaries of the read-types produced, it provides a number of plots for
3445 visualising metrics relative to experiment run time or spatially over the
3446 surface of a flowcell.")
3447 (license license:expat)))
3449 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3450 (define-public r-gkmsvm
3457 (uri (cran-uri "gkmSVM" version))
3460 "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p"))))
3461 (properties `((upstream-name . "gkmSVM")))
3462 (build-system r-build-system)
3464 `(("r-kernlab" ,r-kernlab)
3467 ("r-seqinr" ,r-seqinr)))
3468 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3469 (synopsis "Gapped-kmer support vector machine")
3471 "This R package provides tools for training gapped-kmer SVM classifiers
3472 for DNA and protein sequences. This package supports several sequence
3473 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3474 (license license:gpl2+)))
3476 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3477 (define-public r-mutoss
3484 (uri (cran-uri "mutoss" version))
3487 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3488 (properties `((upstream-name . "mutoss")))
3489 (build-system r-build-system)
3491 `(("r-multcomp" ,r-multcomp)
3492 ("r-multtest" ,r-multtest)
3493 ("r-mvtnorm" ,r-mvtnorm)
3494 ("r-plotrix" ,r-plotrix)))
3495 (home-page "https://github.com/kornl/mutoss/")
3496 (synopsis "Unified multiple testing procedures")
3498 "This package is designed to ease the application and comparison of
3499 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3500 are standardized and usable by the accompanying mutossGUI package.")
3501 ;; Any version of the GPL.
3502 (license (list license:gpl2+ license:gpl3+))))
3504 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3505 ;; from Bioconductor, so we put it here.
3506 (define-public r-metap
3513 (uri (cran-uri "metap" version))
3516 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3517 (build-system r-build-system)
3519 `(("r-lattice" ,r-lattice)
3520 ("r-mutoss" ,r-mutoss)
3521 ("r-rdpack" ,r-rdpack)
3522 ("r-tfisher" ,r-tfisher)))
3523 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3524 (synopsis "Meta-analysis of significance values")
3526 "The canonical way to perform meta-analysis involves using effect sizes.
3527 When they are not available this package provides a number of methods for
3528 meta-analysis of significance values including the methods of Edgington,
3529 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3530 published results; and a routine for graphical display.")
3531 (license license:gpl2)))
3533 (define-public r-triform
3540 (uri (bioconductor-uri "triform" version))
3543 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3544 (build-system r-build-system)
3546 `(("r-biocgenerics" ,r-biocgenerics)
3547 ("r-iranges" ,r-iranges)
3548 ("r-yaml" ,r-yaml)))
3549 (home-page "https://bioconductor.org/packages/triform/")
3550 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3552 "The Triform algorithm uses model-free statistics to identify peak-like
3553 distributions of TF ChIP sequencing reads, taking advantage of an improved
3554 peak definition in combination with known profile characteristics.")
3555 (license license:gpl2)))
3557 (define-public r-varianttools
3559 (name "r-varianttools")
3564 (uri (bioconductor-uri "VariantTools" version))
3567 "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx"))))
3568 (properties `((upstream-name . "VariantTools")))
3569 (build-system r-build-system)
3571 `(("r-biobase" ,r-biobase)
3572 ("r-biocgenerics" ,r-biocgenerics)
3573 ("r-biocparallel" ,r-biocparallel)
3574 ("r-biostrings" ,r-biostrings)
3575 ("r-bsgenome" ,r-bsgenome)
3576 ("r-genomeinfodb" ,r-genomeinfodb)
3577 ("r-genomicfeatures" ,r-genomicfeatures)
3578 ("r-genomicranges" ,r-genomicranges)
3579 ("r-iranges" ,r-iranges)
3580 ("r-matrix" ,r-matrix)
3581 ("r-rsamtools" ,r-rsamtools)
3582 ("r-rtracklayer" ,r-rtracklayer)
3583 ("r-s4vectors" ,r-s4vectors)
3584 ("r-variantannotation" ,r-variantannotation)))
3585 (home-page "https://bioconductor.org/packages/VariantTools/")
3586 (synopsis "Tools for exploratory analysis of variant calls")
3588 "Explore, diagnose, and compare variant calls using filters. The
3589 VariantTools package supports a workflow for loading data, calling single
3590 sample variants and tumor-specific somatic mutations or other sample-specific
3591 variant types (e.g., RNA editing). Most of the functions operate on
3592 alignments (BAM files) or datasets of called variants. The user is expected
3593 to have already aligned the reads with a separate tool, e.g., GSNAP via
3595 (license license:artistic2.0)))
3597 (define-public r-heatplus
3604 (uri (bioconductor-uri "Heatplus" version))
3607 "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw"))))
3608 (properties `((upstream-name . "Heatplus")))
3609 (build-system r-build-system)
3611 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3612 (home-page "https://github.com/alexploner/Heatplus")
3613 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3615 "This package provides tools to display a rectangular heatmap (intensity
3616 plot) of a data matrix. By default, both samples (columns) and features (row)
3617 of the matrix are sorted according to a hierarchical clustering, and the
3618 corresponding dendrogram is plotted. Optionally, panels with additional
3619 information about samples and features can be added to the plot.")
3620 (license license:gpl2+)))
3622 (define-public r-gosemsim
3629 (uri (bioconductor-uri "GOSemSim" version))
3632 "0mg4d8whq90iyl2jjj5dx3kyar17yqn00jvia3b4a8lhmjw8l1hk"))))
3633 (properties `((upstream-name . "GOSemSim")))
3634 (build-system r-build-system)
3636 `(("r-annotationdbi" ,r-annotationdbi)
3637 ("r-go-db" ,r-go-db)
3638 ("r-rcpp" ,r-rcpp)))
3640 `(("r-knitr" ,r-knitr)))
3641 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3642 (synopsis "GO-terms semantic similarity measures")
3644 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3645 quantitative ways to compute similarities between genes and gene groups, and
3646 have became important basis for many bioinformatics analysis approaches.
3647 GOSemSim is an R package for semantic similarity computation among GO terms,
3648 sets of GO terms, gene products and gene clusters.")
3649 (license license:artistic2.0)))
3651 (define-public r-anota
3658 (uri (bioconductor-uri "anota" version))
3661 "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm"))))
3662 (build-system r-build-system)
3664 `(("r-multtest" ,r-multtest)
3665 ("r-qvalue" ,r-qvalue)))
3666 (home-page "https://bioconductor.org/packages/anota/")
3667 (synopsis "Analysis of translational activity")
3669 "Genome wide studies of translational control is emerging as a tool to
3670 study various biological conditions. The output from such analysis is both
3671 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3672 involved in translation (the actively translating mRNA level) for each mRNA.
3673 The standard analysis of such data strives towards identifying differential
3674 translational between two or more sample classes - i.e. differences in
3675 actively translated mRNA levels that are independent of underlying differences
3676 in cytosolic mRNA levels. This package allows for such analysis using partial
3677 variances and the random variance model. As 10s of thousands of mRNAs are
3678 analyzed in parallel the library performs a number of tests to assure that
3679 the data set is suitable for such analysis.")
3680 (license license:gpl3)))
3682 (define-public r-sigpathway
3684 (name "r-sigpathway")
3689 (uri (bioconductor-uri "sigPathway" version))
3692 "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5"))))
3693 (properties `((upstream-name . "sigPathway")))
3694 (build-system r-build-system)
3695 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3696 (synopsis "Pathway analysis")
3698 "This package is used to conduct pathway analysis by calculating the NT_k
3699 and NE_k statistics in a statistical framework for determining whether a
3700 specified group of genes for a pathway has a coordinated association with a
3701 phenotype of interest.")
3702 (license license:gpl2)))
3704 (define-public r-fgsea
3711 (uri (bioconductor-uri "fgsea" version))
3714 "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc"))))
3715 (build-system r-build-system)
3718 ("r-biocparallel" ,r-biocparallel)
3719 ("r-data-table" ,r-data-table)
3720 ("r-fastmatch" ,r-fastmatch)
3721 ("r-ggplot2" ,r-ggplot2)
3722 ("r-gridextra" ,r-gridextra)
3723 ("r-matrix" ,r-matrix)
3724 ("r-rcpp" ,r-rcpp)))
3726 `(("r-knitr" ,r-knitr)))
3727 (home-page "https://github.com/ctlab/fgsea/")
3728 (synopsis "Fast gene set enrichment analysis")
3730 "The package implements an algorithm for fast gene set enrichment
3731 analysis. Using the fast algorithm makes more permutations and gets
3732 more fine grained p-values, which allows using accurate standard approaches
3733 to multiple hypothesis correction.")
3734 (license license:expat)))
3736 (define-public r-dose
3743 (uri (bioconductor-uri "DOSE" version))
3746 "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8"))))
3747 (properties `((upstream-name . "DOSE")))
3748 (build-system r-build-system)
3750 `(("r-annotationdbi" ,r-annotationdbi)
3751 ("r-biocparallel" ,r-biocparallel)
3752 ("r-do-db" ,r-do-db)
3753 ("r-fgsea" ,r-fgsea)
3754 ("r-ggplot2" ,r-ggplot2)
3755 ("r-gosemsim" ,r-gosemsim)
3756 ("r-qvalue" ,r-qvalue)
3757 ("r-reshape2" ,r-reshape2)))
3759 `(("r-knitr" ,r-knitr)))
3760 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3761 (synopsis "Disease ontology semantic and enrichment analysis")
3763 "This package implements five methods proposed by Resnik, Schlicker,
3764 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3765 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3766 including hypergeometric model and gene set enrichment analysis are also
3767 implemented for discovering disease associations of high-throughput biological
3769 (license license:artistic2.0)))
3771 (define-public r-enrichplot
3773 (name "r-enrichplot")
3778 (uri (bioconductor-uri "enrichplot" version))
3781 "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7"))))
3782 (build-system r-build-system)
3784 `(("r-annotationdbi" ,r-annotationdbi)
3785 ("r-cowplot" ,r-cowplot)
3787 ("r-europepmc" ,r-europepmc)
3788 ("r-ggplot2" ,r-ggplot2)
3789 ("r-ggplotify" ,r-ggplotify)
3790 ("r-ggraph" ,r-ggraph)
3791 ("r-ggridges" ,r-ggridges)
3792 ("r-gosemsim" ,r-gosemsim)
3793 ("r-gridextra" ,r-gridextra)
3794 ("r-igraph" ,r-igraph)
3796 ("r-purrr" ,r-purrr)
3797 ("r-rcolorbrewer" ,r-rcolorbrewer)
3798 ("r-reshape2" ,r-reshape2)
3799 ("r-scatterpie" ,r-scatterpie)))
3801 `(("r-knitr" ,r-knitr)))
3802 (home-page "https://github.com/GuangchuangYu/enrichplot")
3803 (synopsis "Visualization of functional enrichment result")
3805 "The enrichplot package implements several visualization methods for
3806 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3807 All the visualization methods are developed based on ggplot2 graphics.")
3808 (license license:artistic2.0)))
3810 (define-public r-clusterprofiler
3812 (name "r-clusterprofiler")
3817 (uri (bioconductor-uri "clusterProfiler" version))
3820 "0m7919gzrd2fddb4kcznwpshhab1ha2yppnkxg11zmh40wcdawyi"))))
3822 `((upstream-name . "clusterProfiler")))
3823 (build-system r-build-system)
3825 `(("r-annotationdbi" ,r-annotationdbi)
3827 ("r-downloader" ,r-downloader)
3828 ("r-dplyr" ,r-dplyr)
3829 ("r-enrichplot" ,r-enrichplot)
3830 ("r-go-db" ,r-go-db)
3831 ("r-gosemsim" ,r-gosemsim)
3832 ("r-magrittr" ,r-magrittr)
3834 ("r-qvalue" ,r-qvalue)
3835 ("r-rvcheck" ,r-rvcheck)
3836 ("r-tidyr" ,r-tidyr)))
3838 `(("r-knitr" ,r-knitr)))
3839 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3840 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3842 "This package implements methods to analyze and visualize functional
3843 profiles (GO and KEGG) of gene and gene clusters.")
3844 (license license:artistic2.0)))
3846 (define-public r-mlinterfaces
3848 (name "r-mlinterfaces")
3853 (uri (bioconductor-uri "MLInterfaces" version))
3856 "05bg7qcrv485m03rkyq3qg5hrr1m3y7zx49bipwaivzqm3s1mbw5"))))
3857 (properties `((upstream-name . "MLInterfaces")))
3858 (build-system r-build-system)
3860 `(("r-annotate" ,r-annotate)
3861 ("r-biobase" ,r-biobase)
3862 ("r-biocgenerics" ,r-biocgenerics)
3863 ("r-cluster" ,r-cluster)
3866 ("r-gdata" ,r-gdata)
3867 ("r-genefilter" ,r-genefilter)
3868 ("r-ggvis" ,r-ggvis)
3869 ("r-hwriter" ,r-hwriter)
3871 ("r-mlbench" ,r-mlbench)
3873 ("r-rcolorbrewer" ,r-rcolorbrewer)
3874 ("r-rpart" ,r-rpart)
3875 ("r-sfsmisc" ,r-sfsmisc)
3876 ("r-shiny" ,r-shiny)
3877 ("r-threejs" ,r-threejs)))
3878 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3879 (synopsis "Interfaces to R machine learning procedures")
3881 "This package provides uniform interfaces to machine learning code for
3882 data in R and Bioconductor containers.")
3883 ;; Any version of the LGPL.
3884 (license license:lgpl2.1+)))
3886 (define-public r-annaffy
3893 (uri (bioconductor-uri "annaffy" version))
3896 "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16"))))
3897 (build-system r-build-system)
3900 (modify-phases %standard-phases
3901 (add-after 'unpack 'remove-reference-to-non-free-data
3903 (substitute* "DESCRIPTION"
3907 `(("r-annotationdbi" ,r-annotationdbi)
3908 ("r-biobase" ,r-biobase)
3910 ("r-go-db" ,r-go-db)))
3911 (home-page "https://bioconductor.org/packages/annaffy/")
3912 (synopsis "Annotation tools for Affymetrix biological metadata")
3914 "This package provides functions for handling data from Bioconductor
3915 Affymetrix annotation data packages. It produces compact HTML and text
3916 reports including experimental data and URL links to many online databases.
3917 It allows searching of biological metadata using various criteria.")
3918 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3919 ;; the LGPL 2.1 is included.
3920 (license license:lgpl2.1+)))
3922 (define-public r-a4core
3929 (uri (bioconductor-uri "a4Core" version))
3932 "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df"))))
3933 (properties `((upstream-name . "a4Core")))
3934 (build-system r-build-system)
3936 `(("r-biobase" ,r-biobase)
3937 ("r-glmnet" ,r-glmnet)))
3938 (home-page "https://bioconductor.org/packages/a4Core")
3939 (synopsis "Automated Affymetrix array analysis core package")
3941 "This is the core package for the automated analysis of Affymetrix
3943 (license license:gpl3)))
3945 (define-public r-a4classif
3947 (name "r-a4classif")
3952 (uri (bioconductor-uri "a4Classif" version))
3955 "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn"))))
3956 (properties `((upstream-name . "a4Classif")))
3957 (build-system r-build-system)
3959 `(("r-a4core" ,r-a4core)
3960 ("r-a4preproc" ,r-a4preproc)
3961 ("r-glmnet" ,r-glmnet)
3962 ("r-mlinterfaces" ,r-mlinterfaces)
3965 ("r-varselrf" ,r-varselrf)))
3966 (home-page "https://bioconductor.org/packages/a4Classif/")
3967 (synopsis "Automated Affymetrix array analysis classification package")
3969 "This is the classification package for the automated analysis of
3970 Affymetrix arrays.")
3971 (license license:gpl3)))
3973 (define-public r-a4preproc
3975 (name "r-a4preproc")
3980 (uri (bioconductor-uri "a4Preproc" version))
3983 "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd"))))
3984 (properties `((upstream-name . "a4Preproc")))
3985 (build-system r-build-system)
3987 `(("r-annotationdbi" ,r-annotationdbi)))
3988 (home-page "https://bioconductor.org/packages/a4Preproc/")
3989 (synopsis "Automated Affymetrix array analysis preprocessing package")
3991 "This is a package for the automated analysis of Affymetrix arrays. It
3992 is used for preprocessing the arrays.")
3993 (license license:gpl3)))
3995 (define-public r-a4reporting
3997 (name "r-a4reporting")
4002 (uri (bioconductor-uri "a4Reporting" version))
4005 "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5"))))
4006 (properties `((upstream-name . "a4Reporting")))
4007 (build-system r-build-system)
4009 `(("r-annaffy" ,r-annaffy)
4010 ("r-xtable" ,r-xtable)))
4011 (home-page "https://bioconductor.org/packages/a4Reporting/")
4012 (synopsis "Automated Affymetrix array analysis reporting package")
4014 "This is a package for the automated analysis of Affymetrix arrays. It
4015 provides reporting features.")
4016 (license license:gpl3)))
4018 (define-public r-a4base
4025 (uri (bioconductor-uri "a4Base" version))
4028 "1a0yk05ikk1hr1vpxynydrb5xb1hj4hdqlh9zd13n83ir89dss83"))))
4029 (properties `((upstream-name . "a4Base")))
4030 (build-system r-build-system)
4032 `(("r-a4core" ,r-a4core)
4033 ("r-a4preproc" ,r-a4preproc)
4034 ("r-annaffy" ,r-annaffy)
4035 ("r-annotationdbi" ,r-annotationdbi)
4036 ("r-biobase" ,r-biobase)
4037 ("r-genefilter" ,r-genefilter)
4038 ("r-glmnet" ,r-glmnet)
4039 ("r-gplots" ,r-gplots)
4040 ("r-limma" ,r-limma)
4042 ("r-multtest" ,r-multtest)))
4043 (home-page "https://bioconductor.org/packages/a4Base/")
4044 (synopsis "Automated Affymetrix array analysis base package")
4046 "This package provides basic features for the automated analysis of
4047 Affymetrix arrays.")
4048 (license license:gpl3)))
4057 (uri (bioconductor-uri "a4" version))
4060 "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4"))))
4061 (build-system r-build-system)
4063 `(("r-a4base" ,r-a4base)
4064 ("r-a4classif" ,r-a4classif)
4065 ("r-a4core" ,r-a4core)
4066 ("r-a4preproc" ,r-a4preproc)
4067 ("r-a4reporting" ,r-a4reporting)))
4068 (home-page "https://bioconductor.org/packages/a4/")
4069 (synopsis "Automated Affymetrix array analysis umbrella package")
4071 "This package provides a software suite for the automated analysis of
4072 Affymetrix arrays.")
4073 (license license:gpl3)))
4075 (define-public r-abseqr
4082 (uri (bioconductor-uri "abseqR" version))
4085 "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa"))))
4086 (properties `((upstream-name . "abseqR")))
4087 (build-system r-build-system)
4089 `(("pandoc" ,ghc-pandoc)))
4091 `(("r-biocparallel" ,r-biocparallel)
4092 ("r-biocstyle" ,r-biocstyle)
4093 ("r-circlize" ,r-circlize)
4094 ("r-flexdashboard" ,r-flexdashboard)
4095 ("r-ggcorrplot" ,r-ggcorrplot)
4096 ("r-ggdendro" ,r-ggdendro)
4097 ("r-ggplot2" ,r-ggplot2)
4098 ("r-gridextra" ,r-gridextra)
4099 ("r-knitr" ,r-knitr)
4100 ("r-plotly" ,r-plotly)
4103 ("r-rcolorbrewer" ,r-rcolorbrewer)
4104 ("r-reshape2" ,r-reshape2)
4105 ("r-rmarkdown" ,r-rmarkdown)
4106 ("r-stringr" ,r-stringr)
4107 ("r-vegan" ,r-vegan)
4108 ("r-venndiagram" ,r-venndiagram)))
4109 (home-page "https://github.com/malhamdoosh/abseqR")
4110 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4112 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4113 sequencing datasets generated from antibody libraries and abseqR is one of its
4114 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4115 capabilities and allows them to generate interactive HTML reports for the
4116 convenience of viewing and sharing with other researchers. Additionally,
4117 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4118 further downstream analysis on its output.")
4119 (license license:gpl3)))
4121 (define-public r-bacon
4128 (uri (bioconductor-uri "bacon" version))
4131 "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86"))))
4132 (build-system r-build-system)
4134 `(("r-biocparallel" ,r-biocparallel)
4135 ("r-ellipse" ,r-ellipse)
4136 ("r-ggplot2" ,r-ggplot2)))
4138 `(("r-knitr" ,r-knitr)))
4139 (home-page "https://bioconductor.org/packages/bacon/")
4140 (synopsis "Controlling bias and inflation in association studies")
4142 "Bacon can be used to remove inflation and bias often observed in
4143 epigenome- and transcriptome-wide association studies. To this end bacon
4144 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4145 fitting a three-component normal mixture on z-scores.")
4146 (license license:gpl2+)))
4148 (define-public r-rgadem
4155 (uri (bioconductor-uri "rGADEM" version))
4158 "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h"))))
4159 (properties `((upstream-name . "rGADEM")))
4160 (build-system r-build-system)
4162 `(("r-biostrings" ,r-biostrings)
4163 ("r-bsgenome" ,r-bsgenome)
4164 ("r-genomicranges" ,r-genomicranges)
4165 ("r-iranges" ,r-iranges)
4166 ("r-seqlogo" ,r-seqlogo)))
4167 (home-page "https://bioconductor.org/packages/rGADEM/")
4168 (synopsis "De novo sequence motif discovery")
4170 "rGADEM is an efficient de novo motif discovery tool for large-scale
4171 genomic sequence data.")
4172 (license license:artistic2.0)))
4174 (define-public r-motiv
4181 (uri (bioconductor-uri "MotIV" version))
4184 "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k"))))
4185 (properties `((upstream-name . "MotIV")))
4186 (build-system r-build-system)
4190 `(("r-biocgenerics" ,r-biocgenerics)
4191 ("r-biostrings" ,r-biostrings)
4192 ("r-genomicranges" ,r-genomicranges)
4193 ("r-iranges" ,r-iranges)
4194 ("r-lattice" ,r-lattice)
4195 ("r-rgadem" ,r-rgadem)
4196 ("r-s4vectors" ,r-s4vectors)))
4197 (home-page "https://bioconductor.org/packages/MotIV/")
4198 (synopsis "Motif identification and validation")
4200 "This package is used for the identification and validation of sequence
4201 motifs. It makes use of STAMP for comparing a set of motifs to a given
4202 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4203 distributions, modules and filter motifs.")
4204 (license license:gpl2)))
4206 (define-public r-motifdb
4212 (uri (bioconductor-uri "MotifDb" version))
4214 (base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc"))))
4215 (properties `((upstream-name . "MotifDb")))
4216 (build-system r-build-system)
4218 `(("r-biocgenerics" ,r-biocgenerics)
4219 ("r-biostrings" ,r-biostrings)
4220 ("r-iranges" ,r-iranges)
4221 ("r-rtracklayer" ,r-rtracklayer)
4222 ("r-s4vectors" ,r-s4vectors)
4223 ("r-splitstackshape" ,r-splitstackshape)))
4224 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4225 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4226 (description "This package provides more than 2000 annotated position
4227 frequency matrices from nine public sources, for multiple organisms.")
4228 (license license:artistic2.0)))
4230 (define-public r-motifbreakr
4232 (name "r-motifbreakr")
4236 (uri (bioconductor-uri "motifbreakR" version))
4238 (base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n"))))
4239 (properties `((upstream-name . "motifbreakR")))
4240 (build-system r-build-system)
4242 `(("r-grimport" ,r-grimport)
4243 ("r-stringr" ,r-stringr)
4244 ("r-biocgenerics" ,r-biocgenerics)
4245 ("r-s4vectors" ,r-s4vectors)
4246 ("r-iranges" ,r-iranges)
4247 ("r-genomeinfodb" ,r-genomeinfodb)
4248 ("r-genomicranges" ,r-genomicranges)
4249 ("r-biostrings" ,r-biostrings)
4250 ("r-bsgenome" ,r-bsgenome)
4251 ("r-rtracklayer" ,r-rtracklayer)
4252 ("r-variantannotation" ,r-variantannotation)
4253 ("r-biocparallel" ,r-biocparallel)
4254 ("r-motifstack" ,r-motifstack)
4256 ("r-matrixstats" ,r-matrixstats)
4257 ("r-tfmpvalue" ,r-tfmpvalue)
4258 ("r-motifdb" ,r-motifdb)))
4259 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4260 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4261 (description "This package allows biologists to judge in the first place
4262 whether the sequence surrounding the polymorphism is a good match, and in
4263 the second place how much information is gained or lost in one allele of
4264 the polymorphism relative to another. This package gives a choice of
4265 algorithms for interrogation of genomes with motifs from public sources:
4267 @item a weighted-sum probability matrix;
4268 @item log-probabilities;
4269 @item weighted by relative entropy.
4272 This package can predict effects for novel or previously described variants in
4273 public databases, making it suitable for tasks beyond the scope of its original
4274 design. Lastly, it can be used to interrogate any genome curated within
4276 (license license:gpl2+)))
4278 (define-public r-motifstack
4280 (name "r-motifstack")
4285 (uri (bioconductor-uri "motifStack" version))
4288 "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg"))))
4289 (properties `((upstream-name . "motifStack")))
4290 (build-system r-build-system)
4292 `(("r-ade4" ,r-ade4)
4293 ("r-biostrings" ,r-biostrings)
4294 ("r-ggplot2" ,r-ggplot2)
4295 ("r-grimport2" ,r-grimport2)
4296 ("r-htmlwidgets" ,r-htmlwidgets)
4297 ("r-motiv" ,r-motiv)
4298 ("r-scales" ,r-scales)
4300 (home-page "https://bioconductor.org/packages/motifStack/")
4301 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4303 "The motifStack package is designed for graphic representation of
4304 multiple motifs with different similarity scores. It works with both DNA/RNA
4305 sequence motifs and amino acid sequence motifs. In addition, it provides the
4306 flexibility for users to customize the graphic parameters such as the font
4307 type and symbol colors.")
4308 (license license:gpl2+)))
4310 (define-public r-genomicscores
4312 (name "r-genomicscores")
4317 (uri (bioconductor-uri "GenomicScores" version))
4320 "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj"))))
4321 (properties `((upstream-name . "GenomicScores")))
4322 (build-system r-build-system)
4324 `(("r-annotationhub" ,r-annotationhub)
4325 ("r-biobase" ,r-biobase)
4326 ("r-biocgenerics" ,r-biocgenerics)
4327 ("r-biostrings" ,r-biostrings)
4328 ("r-bsgenome" ,r-bsgenome)
4329 ("r-genomeinfodb" ,r-genomeinfodb)
4330 ("r-genomicranges" ,r-genomicranges)
4331 ("r-iranges" ,r-iranges)
4332 ("r-s4vectors" ,r-s4vectors)
4334 (home-page "https://github.com/rcastelo/GenomicScores/")
4335 (synopsis "Work with genome-wide position-specific scores")
4337 "This package provides infrastructure to store and access genome-wide
4338 position-specific scores within R and Bioconductor.")
4339 (license license:artistic2.0)))
4341 (define-public r-atacseqqc
4343 (name "r-atacseqqc")
4348 (uri (bioconductor-uri "ATACseqQC" version))
4351 "1g07ni134cyl3jd9y19afip39kxddfgpm1jjm0rhrm7jgssp24in"))))
4352 (properties `((upstream-name . "ATACseqQC")))
4353 (build-system r-build-system)
4355 `(("r-biocgenerics" ,r-biocgenerics)
4356 ("r-biostrings" ,r-biostrings)
4357 ("r-bsgenome" ,r-bsgenome)
4358 ("r-chippeakanno" ,r-chippeakanno)
4359 ("r-edger" ,r-edger)
4360 ("r-genomeinfodb" ,r-genomeinfodb)
4361 ("r-genomicalignments" ,r-genomicalignments)
4362 ("r-genomicranges" ,r-genomicranges)
4363 ("r-genomicscores" ,r-genomicscores)
4364 ("r-iranges" ,r-iranges)
4365 ("r-kernsmooth" ,r-kernsmooth)
4366 ("r-limma" ,r-limma)
4367 ("r-motifstack" ,r-motifstack)
4368 ("r-preseqr" ,r-preseqr)
4369 ("r-randomforest" ,r-randomforest)
4370 ("r-rsamtools" ,r-rsamtools)
4371 ("r-rtracklayer" ,r-rtracklayer)
4372 ("r-s4vectors" ,r-s4vectors)))
4374 `(("r-knitr" ,r-knitr)))
4375 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4376 (synopsis "ATAC-seq quality control")
4378 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4379 sequencing, is a rapid and sensitive method for chromatin accessibility
4380 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4381 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4382 assess whether their ATAC-seq experiment is successful. It includes
4383 diagnostic plots of fragment size distribution, proportion of mitochondria
4384 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4386 (license license:gpl2+)))
4388 (define-public r-gofuncr
4395 (uri (bioconductor-uri "GOfuncR" version))
4398 "1wk7ja6f5il8jx8v05ijzcs9pijp3b953h566ya66xp7dz5jg9rb"))))
4399 (properties `((upstream-name . "GOfuncR")))
4400 (build-system r-build-system)
4402 `(("r-annotationdbi" ,r-annotationdbi)
4403 ("r-genomicranges" ,r-genomicranges)
4404 ("r-gtools" ,r-gtools)
4405 ("r-iranges" ,r-iranges)
4406 ("r-mapplots" ,r-mapplots)
4408 ("r-vioplot" ,r-vioplot)))
4410 `(("r-knitr" ,r-knitr)))
4411 (home-page "https://bioconductor.org/packages/GOfuncR/")
4412 (synopsis "Gene ontology enrichment using FUNC")
4414 "GOfuncR performs a gene ontology enrichment analysis based on the
4415 ontology enrichment software FUNC. GO-annotations are obtained from
4416 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4417 included in the package and updated regularly. GOfuncR provides the standard
4418 candidate vs background enrichment analysis using the hypergeometric test, as
4419 well as three additional tests:
4422 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4423 @item a binomial test that is used when genes are associated with two counts,
4425 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4426 associated with four counts.
4429 To correct for multiple testing and interdependency of the tests, family-wise
4430 error rates are computed based on random permutations of the gene-associated
4431 variables. GOfuncR also provides tools for exploring the ontology graph and
4432 the annotations, and options to take gene-length or spatial clustering of
4433 genes into account. It is also possible to provide custom gene coordinates,
4434 annotations and ontologies.")
4435 (license license:gpl2+)))
4437 (define-public r-abaenrichment
4439 (name "r-abaenrichment")
4444 (uri (bioconductor-uri "ABAEnrichment" version))
4447 "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp"))))
4448 (properties `((upstream-name . "ABAEnrichment")))
4449 (build-system r-build-system)
4451 `(("r-abadata" ,r-abadata)
4452 ("r-data-table" ,r-data-table)
4453 ("r-gofuncr" ,r-gofuncr)
4454 ("r-gplots" ,r-gplots)
4455 ("r-gtools" ,r-gtools)
4456 ("r-rcpp" ,r-rcpp)))
4457 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4458 (synopsis "Gene expression enrichment in human brain regions")
4460 "The package ABAEnrichment is designed to test for enrichment of user
4461 defined candidate genes in the set of expressed genes in different human brain
4462 regions. The core function @code{aba_enrich} integrates the expression of the
4463 candidate gene set (averaged across donors) and the structural information of
4464 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4465 (license license:gpl2+)))
4467 (define-public r-annotationfuncs
4469 (name "r-annotationfuncs")
4474 (uri (bioconductor-uri "AnnotationFuncs" version))
4477 "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq"))))
4479 `((upstream-name . "AnnotationFuncs")))
4480 (build-system r-build-system)
4482 `(("r-annotationdbi" ,r-annotationdbi)
4484 (home-page "https://www.iysik.com/r/annotationfuncs")
4485 (synopsis "Annotation translation functions")
4487 "This package provides functions for handling translating between
4488 different identifieres using the Biocore Data Team data-packages (e.g.
4489 @code{org.Bt.eg.db}).")
4490 (license license:gpl2)))
4492 (define-public r-annotationtools
4494 (name "r-annotationtools")
4499 (uri (bioconductor-uri "annotationTools" version))
4502 "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i"))))
4504 `((upstream-name . "annotationTools")))
4505 (build-system r-build-system)
4506 (propagated-inputs `(("r-biobase" ,r-biobase)))
4507 (home-page "https://bioconductor.org/packages/annotationTools/")
4508 (synopsis "Annotate microarrays and perform gene expression analyses")
4510 "This package provides functions to annotate microarrays, find orthologs,
4511 and integrate heterogeneous gene expression profiles using annotation and
4512 other molecular biology information available as flat file database (plain
4514 ;; Any version of the GPL.
4515 (license (list license:gpl2+))))
4517 (define-public r-allelicimbalance
4519 (name "r-allelicimbalance")
4524 (uri (bioconductor-uri "AllelicImbalance" version))
4527 "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc"))))
4529 `((upstream-name . "AllelicImbalance")))
4530 (build-system r-build-system)
4532 `(("r-annotationdbi" ,r-annotationdbi)
4533 ("r-biocgenerics" ,r-biocgenerics)
4534 ("r-biostrings" ,r-biostrings)
4535 ("r-bsgenome" ,r-bsgenome)
4536 ("r-genomeinfodb" ,r-genomeinfodb)
4537 ("r-genomicalignments" ,r-genomicalignments)
4538 ("r-genomicfeatures" ,r-genomicfeatures)
4539 ("r-genomicranges" ,r-genomicranges)
4540 ("r-gridextra" ,r-gridextra)
4542 ("r-iranges" ,r-iranges)
4543 ("r-lattice" ,r-lattice)
4544 ("r-latticeextra" ,r-latticeextra)
4546 ("r-rsamtools" ,r-rsamtools)
4547 ("r-s4vectors" ,r-s4vectors)
4548 ("r-seqinr" ,r-seqinr)
4549 ("r-summarizedexperiment" ,r-summarizedexperiment)
4550 ("r-variantannotation" ,r-variantannotation)))
4551 (home-page "https://github.com/pappewaio/AllelicImbalance")
4552 (synopsis "Investigate allele-specific expression")
4554 "This package provides a framework for allele-specific expression
4555 investigation using RNA-seq data.")
4556 (license license:gpl3)))
4558 (define-public r-aucell
4565 (uri (bioconductor-uri "AUCell" version))
4568 "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky"))))
4569 (properties `((upstream-name . "AUCell")))
4570 (build-system r-build-system)
4572 `(("r-biocgenerics" ,r-biocgenerics)
4573 ("r-data-table" ,r-data-table)
4574 ("r-gseabase" ,r-gseabase)
4575 ("r-mixtools" ,r-mixtools)
4576 ("r-r-utils" ,r-r-utils)
4577 ("r-s4vectors" ,r-s4vectors)
4578 ("r-shiny" ,r-shiny)
4579 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4580 (home-page "https://bioconductor.org/packages/AUCell/")
4581 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4583 "AUCell identifies cells with active gene sets (e.g. signatures,
4584 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4585 Under the Curve} (AUC) to calculate whether a critical subset of the input
4586 gene set is enriched within the expressed genes for each cell. The
4587 distribution of AUC scores across all the cells allows exploring the relative
4588 expression of the signature. Since the scoring method is ranking-based,
4589 AUCell is independent of the gene expression units and the normalization
4590 procedure. In addition, since the cells are evaluated individually, it can
4591 easily be applied to bigger datasets, subsetting the expression matrix if
4593 (license license:gpl3)))
4595 (define-public r-ebimage
4602 (uri (bioconductor-uri "EBImage" version))
4605 "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs"))))
4606 (properties `((upstream-name . "EBImage")))
4607 (build-system r-build-system)
4609 `(("r-abind" ,r-abind)
4610 ("r-biocgenerics" ,r-biocgenerics)
4611 ("r-fftwtools" ,r-fftwtools)
4612 ("r-htmltools" ,r-htmltools)
4613 ("r-htmlwidgets" ,r-htmlwidgets)
4615 ("r-locfit" ,r-locfit)
4617 ("r-rcurl" ,r-rcurl)
4618 ("r-tiff" ,r-tiff)))
4620 `(("r-knitr" ,r-knitr))) ; for vignettes
4621 (home-page "https://github.com/aoles/EBImage")
4622 (synopsis "Image processing and analysis toolbox for R")
4624 "EBImage provides general purpose functionality for image processing and
4625 analysis. In the context of (high-throughput) microscopy-based cellular
4626 assays, EBImage offers tools to segment cells and extract quantitative
4627 cellular descriptors. This allows the automation of such tasks using the R
4628 programming language and facilitates the use of other tools in the R
4629 environment for signal processing, statistical modeling, machine learning and
4630 visualization with image data.")
4631 ;; Any version of the LGPL.
4632 (license license:lgpl2.1+)))
4634 (define-public r-yamss
4641 (uri (bioconductor-uri "yamss" version))
4644 "12jr7hbrwhb1gfjadj1024hv80ra22miy46dn40nmsrbklkfn3rw"))))
4645 (build-system r-build-system)
4647 `(("r-biocgenerics" ,r-biocgenerics)
4648 ("r-data-table" ,r-data-table)
4649 ("r-ebimage" ,r-ebimage)
4650 ("r-iranges" ,r-iranges)
4651 ("r-limma" ,r-limma)
4652 ("r-matrix" ,r-matrix)
4654 ("r-s4vectors" ,r-s4vectors)
4655 ("r-summarizedexperiment"
4656 ,r-summarizedexperiment)))
4657 (home-page "https://github.com/hansenlab/yamss")
4658 (synopsis "Tools for high-throughput metabolomics")
4660 "This package provides tools to analyze and visualize high-throughput
4661 metabolomics data acquired using chromatography-mass spectrometry. These tools
4662 preprocess data in a way that enables reliable and powerful differential
4664 (license license:artistic2.0)))
4666 (define-public r-gtrellis
4673 (uri (bioconductor-uri "gtrellis" version))
4676 "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z"))))
4677 (build-system r-build-system)
4679 `(("r-circlize" ,r-circlize)
4680 ("r-genomicranges" ,r-genomicranges)
4681 ("r-getoptlong" ,r-getoptlong)
4682 ("r-iranges" ,r-iranges)))
4683 (home-page "https://github.com/jokergoo/gtrellis")
4684 (synopsis "Genome level Trellis layout")
4686 "Genome level Trellis graph visualizes genomic data conditioned by
4687 genomic categories (e.g. chromosomes). For each genomic category, multiple
4688 dimensional data which are represented as tracks describe different features
4689 from different aspects. This package provides high flexibility to arrange
4690 genomic categories and to add self-defined graphics in the plot.")
4691 (license license:expat)))
4693 (define-public r-somaticsignatures
4695 (name "r-somaticsignatures")
4700 (uri (bioconductor-uri "SomaticSignatures" version))
4703 "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z"))))
4705 `((upstream-name . "SomaticSignatures")))
4706 (build-system r-build-system)
4708 `(("r-biobase" ,r-biobase)
4709 ("r-biostrings" ,r-biostrings)
4710 ("r-genomeinfodb" ,r-genomeinfodb)
4711 ("r-genomicranges" ,r-genomicranges)
4712 ("r-ggbio" ,r-ggbio)
4713 ("r-ggplot2" ,r-ggplot2)
4714 ("r-iranges" ,r-iranges)
4716 ("r-pcamethods" ,r-pcamethods)
4717 ("r-proxy" ,r-proxy)
4718 ("r-reshape2" ,r-reshape2)
4719 ("r-s4vectors" ,r-s4vectors)
4720 ("r-variantannotation" ,r-variantannotation)))
4721 (home-page "https://github.com/juliangehring/SomaticSignatures")
4722 (synopsis "Somatic signatures")
4724 "This package identifies mutational signatures of @dfn{single nucleotide
4725 variants} (SNVs). It provides a infrastructure related to the methodology
4726 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4727 decomposition algorithms.")
4728 (license license:expat)))
4730 (define-public r-yapsa
4737 (uri (bioconductor-uri "YAPSA" version))
4740 "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926"))))
4741 (properties `((upstream-name . "YAPSA")))
4742 (build-system r-build-system)
4744 `(("r-circlize" ,r-circlize)
4745 ("r-complexheatmap" ,r-complexheatmap)
4746 ("r-corrplot" ,r-corrplot)
4747 ("r-dendextend" ,r-dendextend)
4748 ("r-genomeinfodb" ,r-genomeinfodb)
4749 ("r-genomicranges" ,r-genomicranges)
4750 ("r-getoptlong" ,r-getoptlong)
4751 ("r-ggplot2" ,r-ggplot2)
4752 ("r-gridextra" ,r-gridextra)
4753 ("r-gtrellis" ,r-gtrellis)
4754 ("r-keggrest" ,r-keggrest)
4756 ("r-pmcmr" ,r-pmcmr)
4757 ("r-reshape2" ,r-reshape2)
4758 ("r-somaticsignatures" ,r-somaticsignatures)
4759 ("r-variantannotation" ,r-variantannotation)))
4760 (home-page "https://bioconductor.org/packages/YAPSA/")
4761 (synopsis "Yet another package for signature analysis")
4763 "This package provides functions and routines useful in the analysis of
4764 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4765 functions to perform a signature analysis with known signatures and a
4766 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4768 (license license:gpl3)))
4770 (define-public r-gcrma
4777 (uri (bioconductor-uri "gcrma" version))
4780 "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx"))))
4781 (build-system r-build-system)
4783 `(("r-affy" ,r-affy)
4784 ("r-affyio" ,r-affyio)
4785 ("r-biobase" ,r-biobase)
4786 ("r-biocmanager" ,r-biocmanager)
4787 ("r-biostrings" ,r-biostrings)
4788 ("r-xvector" ,r-xvector)))
4789 (home-page "https://bioconductor.org/packages/gcrma/")
4790 (synopsis "Background adjustment using sequence information")
4792 "Gcrma adjusts for background intensities in Affymetrix array data which
4793 include optical noise and @dfn{non-specific binding} (NSB). The main function
4794 @code{gcrma} converts background adjusted probe intensities to expression
4795 measures using the same normalization and summarization methods as a
4796 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4797 to estimate probe affinity to NSB. The sequence information is summarized in
4798 a more complex way than the simple GC content. Instead, the base types (A, T,
4799 G or C) at each position along the probe determine the affinity of each probe.
4800 The parameters of the position-specific base contributions to the probe
4801 affinity is estimated in an NSB experiment in which only NSB but no
4802 gene-specific bidning is expected.")
4803 ;; Any version of the LGPL
4804 (license license:lgpl2.1+)))
4806 (define-public r-simpleaffy
4808 (name "r-simpleaffy")
4813 (uri (bioconductor-uri "simpleaffy" version))
4816 "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs"))))
4817 (build-system r-build-system)
4819 `(("r-affy" ,r-affy)
4820 ("r-biobase" ,r-biobase)
4821 ("r-biocgenerics" ,r-biocgenerics)
4822 ("r-gcrma" ,r-gcrma)
4823 ("r-genefilter" ,r-genefilter)))
4824 (home-page "https://bioconductor.org/packages/simpleaffy/")
4825 (synopsis "Very simple high level analysis of Affymetrix data")
4827 "This package provides high level functions for reading Affy @file{.CEL}
4828 files, phenotypic data, and then computing simple things with it, such as
4829 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4830 library. It also has some basic scatter plot functions and mechanisms for
4831 generating high resolution journal figures.")
4832 (license license:gpl2+)))
4834 (define-public r-yaqcaffy
4841 (uri (bioconductor-uri "yaqcaffy" version))
4844 "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz"))))
4845 (build-system r-build-system)
4847 `(("r-simpleaffy" ,r-simpleaffy)))
4848 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4849 (synopsis "Affymetrix quality control and reproducibility analysis")
4851 "This is a package that can be used for quality control of Affymetrix
4852 GeneChip expression data and reproducibility analysis of human whole genome
4853 chips with the MAQC reference datasets.")
4854 (license license:artistic2.0)))
4856 (define-public r-quantro
4863 (uri (bioconductor-uri "quantro" version))
4866 "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m"))))
4867 (build-system r-build-system)
4869 `(("r-biobase" ,r-biobase)
4870 ("r-doparallel" ,r-doparallel)
4871 ("r-foreach" ,r-foreach)
4872 ("r-ggplot2" ,r-ggplot2)
4873 ("r-iterators" ,r-iterators)
4874 ("r-minfi" ,r-minfi)
4875 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4876 (home-page "https://bioconductor.org/packages/quantro/")
4877 (synopsis "Test for when to use quantile normalization")
4879 "This package provides a data-driven test for the assumptions of quantile
4880 normalization using raw data such as objects that inherit eSets (e.g.
4881 ExpressionSet, MethylSet). Group level information about each sample (such as
4882 Tumor / Normal status) must also be provided because the test assesses if
4883 there are global differences in the distributions between the user-defined
4885 (license license:gpl3+)))
4887 (define-public r-yarn
4894 (uri (bioconductor-uri "yarn" version))
4897 "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp"))))
4898 (build-system r-build-system)
4900 `(("r-biobase" ,r-biobase)
4901 ("r-biomart" ,r-biomart)
4902 ("r-downloader" ,r-downloader)
4903 ("r-edger" ,r-edger)
4904 ("r-gplots" ,r-gplots)
4905 ("r-limma" ,r-limma)
4906 ("r-matrixstats" ,r-matrixstats)
4907 ("r-preprocesscore" ,r-preprocesscore)
4908 ("r-quantro" ,r-quantro)
4909 ("r-rcolorbrewer" ,r-rcolorbrewer)
4910 ("r-readr" ,r-readr)))
4911 (home-page "https://bioconductor.org/packages/yarn/")
4912 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4914 "Expedite large RNA-Seq analyses using a combination of previously
4915 developed tools. YARN is meant to make it easier for the user in performing
4916 basic mis-annotation quality control, filtering, and condition-aware
4917 normalization. YARN leverages many Bioconductor tools and statistical
4918 techniques to account for the large heterogeneity and sparsity found in very
4919 large RNA-seq experiments.")
4920 (license license:artistic2.0)))
4922 (define-public r-roar
4929 (uri (bioconductor-uri "roar" version))
4932 "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06"))))
4933 (build-system r-build-system)
4935 `(("r-biocgenerics" ,r-biocgenerics)
4936 ("r-genomeinfodb" ,r-genomeinfodb)
4937 ("r-genomicalignments" ,r-genomicalignments)
4938 ("r-genomicranges" ,r-genomicranges)
4939 ("r-iranges" ,r-iranges)
4940 ("r-rtracklayer" ,r-rtracklayer)
4941 ("r-s4vectors" ,r-s4vectors)
4942 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4943 (home-page "https://github.com/vodkatad/roar/")
4944 (synopsis "Identify differential APA usage from RNA-seq alignments")
4946 "This package provides tools for identifying preferential usage of APA
4947 sites, comparing two biological conditions, starting from known alternative
4948 sites and alignments obtained from standard RNA-seq experiments.")
4949 (license license:gpl3)))
4951 (define-public r-xbseq
4958 (uri (bioconductor-uri "XBSeq" version))
4961 "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp"))))
4962 (properties `((upstream-name . "XBSeq")))
4963 (build-system r-build-system)
4965 `(("r-biobase" ,r-biobase)
4966 ("r-deseq2" ,r-deseq2)
4967 ("r-dplyr" ,r-dplyr)
4968 ("r-ggplot2" ,r-ggplot2)
4969 ("r-locfit" ,r-locfit)
4970 ("r-magrittr" ,r-magrittr)
4971 ("r-matrixstats" ,r-matrixstats)
4972 ("r-pracma" ,r-pracma)
4973 ("r-roar" ,r-roar)))
4974 (home-page "https://github.com/Liuy12/XBSeq")
4975 (synopsis "Test for differential expression for RNA-seq data")
4977 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4978 expression} (DE), where a statistical model was established based on the
4979 assumption that observed signals are the convolution of true expression
4980 signals and sequencing noises. The mapped reads in non-exonic regions are
4981 considered as sequencing noises, which follows a Poisson distribution. Given
4982 measurable observed signal and background noise from RNA-seq data, true
4983 expression signals, assuming governed by the negative binomial distribution,
4984 can be delineated and thus the accurate detection of differential expressed
4986 (license license:gpl3+)))
4988 (define-public r-massspecwavelet
4990 (name "r-massspecwavelet")
4995 (uri (bioconductor-uri "MassSpecWavelet" version))
4998 "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7"))))
5000 `((upstream-name . "MassSpecWavelet")))
5001 (build-system r-build-system)
5003 `(("r-waveslim" ,r-waveslim)))
5004 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5005 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5007 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5008 data mainly through the use of wavelet transforms. It supports peak detection
5009 based on @dfn{Continuous Wavelet Transform} (CWT).")
5010 (license license:lgpl2.0+)))
5012 (define-public r-xcms
5019 (uri (bioconductor-uri "xcms" version))
5022 "0bfl56v3l6k31i11l09nx1yqfjy6z5yragm6k83z4w0mpgk18y7g"))))
5023 (build-system r-build-system)
5025 `(("r-biobase" ,r-biobase)
5026 ("r-biocgenerics" ,r-biocgenerics)
5027 ("r-biocparallel" ,r-biocparallel)
5028 ("r-iranges" ,r-iranges)
5029 ("r-lattice" ,r-lattice)
5030 ("r-massspecwavelet" ,r-massspecwavelet)
5031 ("r-msnbase" ,r-msnbase)
5032 ("r-multtest" ,r-multtest)
5035 ("r-protgenerics" ,r-protgenerics)
5037 ("r-rcolorbrewer" ,r-rcolorbrewer)
5038 ("r-robustbase" ,r-robustbase)
5039 ("r-s4vectors" ,r-s4vectors)))
5040 (home-page "https://bioconductor.org/packages/xcms/")
5041 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5043 "This package provides a framework for processing and visualization of
5044 chromatographically separated and single-spectra mass spectral data. It
5045 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5046 data for high-throughput, untargeted analyte profiling.")
5047 (license license:gpl2+)))
5049 (define-public r-wrench
5056 (uri (bioconductor-uri "Wrench" version))
5059 "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm"))))
5060 (properties `((upstream-name . "Wrench")))
5061 (build-system r-build-system)
5063 `(("r-limma" ,r-limma)
5064 ("r-locfit" ,r-locfit)
5065 ("r-matrixstats" ,r-matrixstats)))
5066 (home-page "https://github.com/HCBravoLab/Wrench")
5067 (synopsis "Wrench normalization for sparse count data")
5069 "Wrench is a package for normalization sparse genomic count data, like
5070 that arising from 16s metagenomic surveys.")
5071 (license license:artistic2.0)))
5073 (define-public r-wiggleplotr
5075 (name "r-wiggleplotr")
5080 (uri (bioconductor-uri "wiggleplotr" version))
5083 "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m"))))
5084 (build-system r-build-system)
5086 `(("r-assertthat" ,r-assertthat)
5087 ("r-cowplot" ,r-cowplot)
5088 ("r-dplyr" ,r-dplyr)
5089 ("r-genomeinfodb" ,r-genomeinfodb)
5090 ("r-genomicranges" ,r-genomicranges)
5091 ("r-ggplot2" ,r-ggplot2)
5092 ("r-iranges" ,r-iranges)
5093 ("r-purrr" ,r-purrr)
5094 ("r-rtracklayer" ,r-rtracklayer)
5095 ("r-s4vectors" ,r-s4vectors)))
5096 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5097 (synopsis "Make read coverage plots from BigWig files")
5099 "This package provides tools to visualize read coverage from sequencing
5100 experiments together with genomic annotations (genes, transcripts, peaks).
5101 Introns of long transcripts can be rescaled to a fixed length for better
5102 visualization of exonic read coverage.")
5103 (license license:asl2.0)))
5105 (define-public r-widgettools
5107 (name "r-widgettools")
5112 (uri (bioconductor-uri "widgetTools" version))
5115 "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5"))))
5116 (properties `((upstream-name . "widgetTools")))
5117 (build-system r-build-system)
5118 (home-page "https://bioconductor.org/packages/widgetTools/")
5119 (synopsis "Tools for creating interactive tcltk widgets")
5121 "This package contains tools to support the construction of tcltk
5123 ;; Any version of the LGPL.
5124 (license license:lgpl3+)))
5126 (define-public r-webbioc
5133 (uri (bioconductor-uri "webbioc" version))
5136 "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62"))))
5137 (build-system r-build-system)
5139 `(("netpbm" ,netpbm)
5142 `(("r-affy" ,r-affy)
5143 ("r-annaffy" ,r-annaffy)
5144 ("r-biobase" ,r-biobase)
5145 ("r-biocmanager" ,r-biocmanager)
5146 ("r-gcrma" ,r-gcrma)
5147 ("r-multtest" ,r-multtest)
5148 ("r-qvalue" ,r-qvalue)
5150 (home-page "https://www.bioconductor.org/")
5151 (synopsis "Bioconductor web interface")
5153 "This package provides an integrated web interface for doing microarray
5154 analysis using several of the Bioconductor packages. It is intended to be
5155 deployed as a centralized bioinformatics resource for use by many users.
5156 Currently only Affymetrix oligonucleotide analysis is supported.")
5157 (license license:gpl2+)))
5159 (define-public r-zfpkm
5166 (uri (bioconductor-uri "zFPKM" version))
5169 "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n"))))
5170 (properties `((upstream-name . "zFPKM")))
5171 (build-system r-build-system)
5173 `(("r-checkmate" ,r-checkmate)
5174 ("r-dplyr" ,r-dplyr)
5175 ("r-ggplot2" ,r-ggplot2)
5176 ("r-summarizedexperiment" ,r-summarizedexperiment)
5177 ("r-tidyr" ,r-tidyr)))
5178 (home-page "https://github.com/ronammar/zFPKM/")
5179 (synopsis "Functions to facilitate zFPKM transformations")
5181 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5182 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5184 (license license:gpl3)))
5186 (define-public r-rbowtie2
5193 (uri (bioconductor-uri "Rbowtie2" version))
5196 "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5"))))
5197 (properties `((upstream-name . "Rbowtie2")))
5198 (build-system r-build-system)
5201 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5202 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5204 "This package provides an R wrapper of the popular @code{bowtie2}
5205 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5206 rapid adapter trimming, identification, and read merging.")
5207 (license license:gpl3+)))
5209 (define-public r-progeny
5216 (uri (bioconductor-uri "progeny" version))
5219 "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq"))))
5220 (build-system r-build-system)
5221 (propagated-inputs `(("r-biobase" ,r-biobase)))
5222 (home-page "https://github.com/saezlab/progeny")
5223 (synopsis "Pathway responsive gene activity inference")
5225 "This package provides a function to infer pathway activity from gene
5226 expression. It contains the linear model inferred in the publication
5227 \"Perturbation-response genes reveal signaling footprints in cancer gene
5229 (license license:asl2.0)))
5231 (define-public r-arrmnormalization
5233 (name "r-arrmnormalization")
5238 (uri (bioconductor-uri "ARRmNormalization" version))
5241 "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1"))))
5243 `((upstream-name . "ARRmNormalization")))
5244 (build-system r-build-system)
5245 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5246 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5247 (synopsis "Adaptive robust regression normalization for methylation data")
5249 "This is a package to perform the @dfn{Adaptive Robust Regression
5250 method} (ARRm) for the normalization of methylation data from the Illumina
5251 Infinium HumanMethylation 450k assay.")
5252 (license license:artistic2.0)))
5254 (define-public r-biocfilecache
5256 (name "r-biocfilecache")
5261 (uri (bioconductor-uri "BiocFileCache" version))
5264 "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6"))))
5265 (properties `((upstream-name . "BiocFileCache")))
5266 (build-system r-build-system)
5268 `(("r-curl" ,r-curl)
5270 ("r-dbplyr" ,r-dbplyr)
5271 ("r-dplyr" ,r-dplyr)
5273 ("r-rappdirs" ,r-rappdirs)
5274 ("r-rsqlite" ,r-rsqlite)))
5275 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5276 (synopsis "Manage files across sessions")
5278 "This package creates a persistent on-disk cache of files that the user
5279 can add, update, and retrieve. It is useful for managing resources (such as
5280 custom Txdb objects) that are costly or difficult to create, web resources,
5281 and data files used across sessions.")
5282 (license license:artistic2.0)))
5284 (define-public r-iclusterplus
5286 (name "r-iclusterplus")
5291 (uri (bioconductor-uri "iClusterPlus" version))
5294 "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37"))))
5295 (properties `((upstream-name . "iClusterPlus")))
5296 (build-system r-build-system)
5297 (native-inputs `(("gfortran" ,gfortran)))
5298 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5299 (synopsis "Integrative clustering of multi-type genomic data")
5301 "iClusterPlus is developed for integrative clustering analysis of
5302 multi-type genomic data and is an enhanced version of iCluster proposed and
5303 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5304 from the experiments where biological samples (e.g. tumor samples) are
5305 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5306 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5307 on. In the iClusterPlus model, binary observations such as somatic mutation
5308 are modeled as Binomial processes; categorical observations such as copy
5309 number states are realizations of Multinomial random variables; counts are
5310 modeled as Poisson random processes; and continuous measures are modeled by
5311 Gaussian distributions.")
5312 (license license:gpl2+)))
5314 (define-public r-rbowtie
5321 (uri (bioconductor-uri "Rbowtie" version))
5324 "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4"))))
5325 (properties `((upstream-name . "Rbowtie")))
5326 (build-system r-build-system)
5329 (home-page "https://bioconductor.org/packages/Rbowtie/")
5330 (synopsis "R bowtie wrapper")
5332 "This package provides an R wrapper around the popular bowtie short read
5333 aligner and around SpliceMap, a de novo splice junction discovery and
5335 (license license:artistic2.0)))
5337 (define-public r-sgseq
5344 (uri (bioconductor-uri "SGSeq" version))
5347 "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw"))))
5348 (properties `((upstream-name . "SGSeq")))
5349 (build-system r-build-system)
5351 `(("r-annotationdbi" ,r-annotationdbi)
5352 ("r-biocgenerics" ,r-biocgenerics)
5353 ("r-biostrings" ,r-biostrings)
5354 ("r-genomeinfodb" ,r-genomeinfodb)
5355 ("r-genomicalignments" ,r-genomicalignments)
5356 ("r-genomicfeatures" ,r-genomicfeatures)
5357 ("r-genomicranges" ,r-genomicranges)
5358 ("r-igraph" ,r-igraph)
5359 ("r-iranges" ,r-iranges)
5360 ("r-rsamtools" ,r-rsamtools)
5361 ("r-rtracklayer" ,r-rtracklayer)
5362 ("r-runit" ,r-runit)
5363 ("r-s4vectors" ,r-s4vectors)
5364 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5365 (home-page "https://bioconductor.org/packages/SGSeq/")
5366 (synopsis "Splice event prediction and quantification from RNA-seq data")
5368 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5369 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5370 represented as a splice graph, which can be obtained from existing annotation
5371 or predicted from the mapped sequence reads. Splice events are identified
5372 from the graph and are quantified locally using structurally compatible reads
5373 at the start or end of each splice variant. The software includes functions
5374 for splice event prediction, quantification, visualization and
5376 (license license:artistic2.0)))
5378 (define-public r-rhisat2
5385 (uri (bioconductor-uri "Rhisat2" version))
5388 "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49"))))
5389 (properties `((upstream-name . "Rhisat2")))
5390 (build-system r-build-system)
5393 (modify-phases %standard-phases
5394 (add-after 'unpack 'make-reproducible
5396 (substitute* "src/Makefile"
5397 (("`hostname`") "guix")
5399 ;; Avoid shelling out to "which".
5400 (("^CC =.*") (which "gcc"))
5401 (("^CPP =.*") (which "g++")))
5404 `(("r-genomicfeatures" ,r-genomicfeatures)
5405 ("r-genomicranges" ,r-genomicranges)
5406 ("r-sgseq" ,r-sgseq)))
5407 (home-page "https://github.com/fmicompbio/Rhisat2")
5408 (synopsis "R Wrapper for HISAT2 sequence aligner")
5410 "This package provides an R interface to the HISAT2 spliced short-read
5411 aligner by Kim et al. (2015). The package contains wrapper functions to
5412 create a genome index and to perform the read alignment to the generated
5414 (license license:gpl3)))
5416 (define-public r-quasr
5423 (uri (bioconductor-uri "QuasR" version))
5426 "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv"))))
5427 (properties `((upstream-name . "QuasR")))
5428 (build-system r-build-system)
5432 `(("r-annotationdbi" ,r-annotationdbi)
5433 ("r-biobase" ,r-biobase)
5434 ("r-biocgenerics" ,r-biocgenerics)
5435 ("r-biocmanager" ,r-biocmanager)
5436 ("r-biocparallel" ,r-biocparallel)
5437 ("r-biostrings" ,r-biostrings)
5438 ("r-bsgenome" ,r-bsgenome)
5439 ("r-genomeinfodb" ,r-genomeinfodb)
5440 ("r-genomicalignments" ,r-genomicalignments)
5441 ("r-genomicfeatures" ,r-genomicfeatures)
5442 ("r-genomicfiles" ,r-genomicfiles)
5443 ("r-genomicranges" ,r-genomicranges)
5444 ("r-iranges" ,r-iranges)
5445 ("r-rbowtie" ,r-rbowtie)
5446 ("r-rhisat2" ,r-rhisat2)
5447 ("r-rhtslib" ,r-rhtslib)
5448 ("r-rsamtools" ,r-rsamtools)
5449 ("r-rtracklayer" ,r-rtracklayer)
5450 ("r-s4vectors" ,r-s4vectors)
5451 ("r-shortread" ,r-shortread)))
5452 (home-page "https://bioconductor.org/packages/QuasR/")
5453 (synopsis "Quantify and annotate short reads in R")
5455 "This package provides a framework for the quantification and analysis of
5456 short genomic reads. It covers a complete workflow starting from raw sequence
5457 reads, over creation of alignments and quality control plots, to the
5458 quantification of genomic regions of interest.")
5459 (license license:gpl2)))
5461 (define-public r-rqc
5468 (uri (bioconductor-uri "Rqc" version))
5471 "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m"))))
5472 (properties `((upstream-name . "Rqc")))
5473 (build-system r-build-system)
5475 `(("r-biocgenerics" ,r-biocgenerics)
5476 ("r-biocparallel" ,r-biocparallel)
5477 ("r-biocstyle" ,r-biocstyle)
5478 ("r-biostrings" ,r-biostrings)
5479 ("r-biovizbase" ,r-biovizbase)
5480 ("r-genomicalignments" ,r-genomicalignments)
5481 ("r-genomicfiles" ,r-genomicfiles)
5482 ("r-ggplot2" ,r-ggplot2)
5483 ("r-iranges" ,r-iranges)
5484 ("r-knitr" ,r-knitr)
5485 ("r-markdown" ,r-markdown)
5488 ("r-reshape2" ,r-reshape2)
5489 ("r-rsamtools" ,r-rsamtools)
5490 ("r-s4vectors" ,r-s4vectors)
5491 ("r-shiny" ,r-shiny)
5492 ("r-shortread" ,r-shortread)))
5493 (home-page "https://github.com/labbcb/Rqc")
5494 (synopsis "Quality control tool for high-throughput sequencing data")
5496 "Rqc is an optimized tool designed for quality control and assessment of
5497 high-throughput sequencing data. It performs parallel processing of entire
5498 files and produces a report which contains a set of high-resolution
5500 (license license:gpl2+)))
5502 (define-public r-birewire
5509 (uri (bioconductor-uri "BiRewire" version))
5512 "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q"))))
5513 (properties `((upstream-name . "BiRewire")))
5514 (build-system r-build-system)
5516 `(("r-igraph" ,r-igraph)
5517 ("r-matrix" ,r-matrix)
5519 ("r-tsne" ,r-tsne)))
5520 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5521 (synopsis "Tools for randomization of bipartite graphs")
5523 "This package provides functions for bipartite network rewiring through N
5524 consecutive switching steps and for the computation of the minimal number of
5525 switching steps to be performed in order to maximise the dissimilarity with
5526 respect to the original network. It includes functions for the analysis of
5527 the introduced randomness across the switching steps and several other
5528 routines to analyse the resulting networks and their natural projections.")
5529 (license license:gpl3)))
5531 (define-public r-birta
5538 (uri (bioconductor-uri "birta" version))
5541 "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg"))))
5542 (build-system r-build-system)
5544 `(("r-biobase" ,r-biobase)
5545 ("r-limma" ,r-limma)
5546 ("r-mass" ,r-mass)))
5547 (home-page "https://bioconductor.org/packages/birta")
5548 (synopsis "Bayesian inference of regulation of transcriptional activity")
5550 "Expression levels of mRNA molecules are regulated by different
5551 processes, comprising inhibition or activation by transcription factors and
5552 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5553 Inference of Regulation of Transcriptional Activity) uses the regulatory
5554 networks of transcription factors and miRNAs together with mRNA and miRNA
5555 expression data to predict switches in regulatory activity between two
5556 conditions. A Bayesian network is used to model the regulatory structure and
5557 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5558 (license license:gpl2+)))
5560 (define-public r-multidataset
5562 (name "r-multidataset")
5567 (uri (bioconductor-uri "MultiDataSet" version))
5570 "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj"))))
5571 (properties `((upstream-name . "MultiDataSet")))
5572 (build-system r-build-system)
5574 `(("r-biobase" ,r-biobase)
5575 ("r-biocgenerics" ,r-biocgenerics)
5576 ("r-genomicranges" ,r-genomicranges)
5577 ("r-ggplot2" ,r-ggplot2)
5578 ("r-ggrepel" ,r-ggrepel)
5579 ("r-iranges" ,r-iranges)
5580 ("r-limma" ,r-limma)
5581 ("r-qqman" ,r-qqman)
5582 ("r-s4vectors" ,r-s4vectors)
5583 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5584 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5585 (synopsis "Implementation of MultiDataSet and ResultSet")
5587 "This package provides an implementation of the BRGE's (Bioinformatic
5588 Research Group in Epidemiology from Center for Research in Environmental
5589 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5590 integrating multi omics data sets and ResultSet is a container for omics
5591 results. This package contains base classes for MEAL and rexposome
5593 (license license:expat)))
5595 (define-public r-ropls
5602 (uri (bioconductor-uri "ropls" version))
5605 "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a"))))
5606 (build-system r-build-system)
5608 `(("r-biobase" ,r-biobase)
5609 ("r-multidataset" ,r-multidataset)))
5611 `(("r-knitr" ,r-knitr))) ; for vignettes
5612 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5613 (synopsis "Multivariate analysis and feature selection of omics data")
5615 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5616 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5617 regression, classification, and feature selection of omics data where the
5618 number of variables exceeds the number of samples and with multicollinearity
5619 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5620 separately model the variation correlated (predictive) to the factor of
5621 interest and the uncorrelated (orthogonal) variation. While performing
5622 similarly to PLS, OPLS facilitates interpretation.
5624 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5625 analysis and feature selection of omics data. In addition to scores, loadings
5626 and weights plots, the package provides metrics and graphics to determine the
5627 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5628 validity of the model by permutation testing, detect outliers, and perform
5629 feature selection (e.g. with Variable Importance in Projection or regression
5631 (license license:cecill)))
5633 (define-public r-biosigner
5635 (name "r-biosigner")
5640 (uri (bioconductor-uri "biosigner" version))
5643 "0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl"))))
5644 (build-system r-build-system)
5646 `(("r-biobase" ,r-biobase)
5647 ("r-e1071" ,r-e1071)
5648 ("r-multidataset" ,r-multidataset)
5649 ("r-randomforest" ,r-randomforest)
5650 ("r-ropls" ,r-ropls)))
5652 `(("r-knitr" ,r-knitr)))
5653 (home-page "https://bioconductor.org/packages/biosigner/")
5654 (synopsis "Signature discovery from omics data")
5656 "Feature selection is critical in omics data analysis to extract
5657 restricted and meaningful molecular signatures from complex and high-dimension
5658 data, and to build robust classifiers. This package implements a method to
5659 assess the relevance of the variables for the prediction performances of the
5660 classifier. The approach can be run in parallel with the PLS-DA, Random
5661 Forest, and SVM binary classifiers. The signatures and the corresponding
5662 'restricted' models are returned, enabling future predictions on new
5664 (license license:cecill)))
5666 (define-public r-annotatr
5673 (uri (bioconductor-uri "annotatr" version))
5676 "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj"))))
5677 (build-system r-build-system)
5679 `(("r-annotationdbi" ,r-annotationdbi)
5680 ("r-annotationhub" ,r-annotationhub)
5681 ("r-dplyr" ,r-dplyr)
5682 ("r-genomeinfodb" ,r-genomeinfodb)
5683 ("r-genomicfeatures" ,r-genomicfeatures)
5684 ("r-genomicranges" ,r-genomicranges)
5685 ("r-ggplot2" ,r-ggplot2)
5686 ("r-iranges" ,r-iranges)
5687 ("r-readr" ,r-readr)
5688 ("r-regioner" ,r-regioner)
5689 ("r-reshape2" ,r-reshape2)
5690 ("r-rtracklayer" ,r-rtracklayer)
5691 ("r-s4vectors" ,r-s4vectors)))
5692 (home-page "https://bioconductor.org/packages/annotatr/")
5693 (synopsis "Annotation of genomic regions to genomic annotations")
5695 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5696 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5697 to investigate the intersecting genomic annotations. Such annotations include
5698 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5699 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5700 enhancers. The annotatr package provides an easy way to summarize and
5701 visualize the intersection of genomic sites/regions with genomic
5703 (license license:gpl3)))
5705 (define-public r-rsubread
5712 (uri (bioconductor-uri "Rsubread" version))
5715 "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy"))))
5716 (properties `((upstream-name . "Rsubread")))
5717 (build-system r-build-system)
5718 (inputs `(("zlib" ,zlib)))
5719 (home-page "https://bioconductor.org/packages/Rsubread/")
5720 (synopsis "Subread sequence alignment and counting for R")
5722 "This package provides tools for alignment, quantification and analysis
5723 of second and third generation sequencing data. It includes functionality for
5724 read mapping, read counting, SNP calling, structural variant detection and
5725 gene fusion discovery. It can be applied to all major sequencing techologies
5726 and to both short and long sequence reads.")
5727 (license license:gpl3)))
5729 (define-public r-flowutils
5731 (name "r-flowutils")
5736 (uri (bioconductor-uri "flowUtils" version))
5739 "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81"))))
5740 (properties `((upstream-name . "flowUtils")))
5741 (build-system r-build-system)
5743 `(("r-biobase" ,r-biobase)
5744 ("r-corpcor" ,r-corpcor)
5745 ("r-flowcore" ,r-flowcore)
5746 ("r-graph" ,r-graph)
5747 ("r-runit" ,r-runit)
5749 (home-page "https://github.com/jspidlen/flowUtils")
5750 (synopsis "Utilities for flow cytometry")
5752 "This package provides utilities for flow cytometry data.")
5753 (license license:artistic2.0)))
5755 (define-public r-consensusclusterplus
5757 (name "r-consensusclusterplus")
5762 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5765 "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4"))))
5767 `((upstream-name . "ConsensusClusterPlus")))
5768 (build-system r-build-system)
5771 ("r-biobase" ,r-biobase)
5772 ("r-cluster" ,r-cluster)))
5773 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5774 (synopsis "Clustering algorithm")
5776 "This package provides an implementation of an algorithm for determining
5777 cluster count and membership by stability evidence in unsupervised analysis.")
5778 (license license:gpl2)))
5780 (define-public r-cytolib
5787 (uri (bioconductor-uri "cytolib" version))
5790 "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9"))))
5791 (properties `((upstream-name . "cytolib")))
5792 (build-system r-build-system)
5793 (home-page "https://bioconductor.org/packages/cytolib/")
5794 (synopsis "C++ infrastructure for working with gated cytometry")
5796 "This package provides the core data structure and API to represent and
5797 interact with gated cytometry data.")
5798 (license license:artistic2.0)))
5800 (define-public r-flowcore
5807 (uri (bioconductor-uri "flowCore" version))
5810 "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2"))))
5811 (properties `((upstream-name . "flowCore")))
5812 (build-system r-build-system)
5815 ("r-biobase" ,r-biobase)
5816 ("r-biocgenerics" ,r-biocgenerics)
5817 ("r-cytolib" ,r-cytolib)
5818 ("r-matrixstats" ,r-matrixstats)
5819 ("r-rcpp" ,r-rcpp)))
5820 (home-page "https://bioconductor.org/packages/flowCore")
5821 (synopsis "Basic structures for flow cytometry data")
5823 "This package provides S4 data structures and basic functions to deal
5824 with flow cytometry data.")
5825 (license license:artistic2.0)))
5827 (define-public r-flowmeans
5829 (name "r-flowmeans")
5834 (uri (bioconductor-uri "flowMeans" version))
5837 "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h"))))
5838 (properties `((upstream-name . "flowMeans")))
5839 (build-system r-build-system)
5841 `(("r-biobase" ,r-biobase)
5842 ("r-feature" ,r-feature)
5843 ("r-flowcore" ,r-flowcore)
5844 ("r-rrcov" ,r-rrcov)))
5845 (home-page "https://bioconductor.org/packages/flowMeans")
5846 (synopsis "Non-parametric flow cytometry data gating")
5848 "This package provides tools to identify cell populations in Flow
5849 Cytometry data using non-parametric clustering and segmented-regression-based
5850 change point detection.")
5851 (license license:artistic2.0)))
5853 (define-public r-ncdfflow
5860 (uri (bioconductor-uri "ncdfFlow" version))
5863 "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i"))))
5864 (properties `((upstream-name . "ncdfFlow")))
5865 (build-system r-build-system)
5870 ("r-biobase" ,r-biobase)
5871 ("r-biocgenerics" ,r-biocgenerics)
5872 ("r-flowcore" ,r-flowcore)
5874 ("r-rcpparmadillo" ,r-rcpparmadillo)
5875 ("r-rhdf5lib" ,r-rhdf5lib)
5876 ("r-zlibbioc" ,r-zlibbioc)))
5877 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5878 (synopsis "HDF5 based storage for flow cytometry data")
5880 "This package provides HDF5 storage based methods and functions for
5881 manipulation of flow cytometry data.")
5882 (license license:artistic2.0)))
5884 (define-public r-ggcyto
5891 (uri (bioconductor-uri "ggcyto" version))
5894 "16jwdslhmj1nsa28wmaircy15cq7qn8nsyiawinjv711qiqhgw50"))))
5895 (properties `((upstream-name . "ggcyto")))
5896 (build-system r-build-system)
5898 `(("r-data-table" ,r-data-table)
5899 ("r-flowcore" ,r-flowcore)
5900 ("r-flowworkspace" ,r-flowworkspace)
5901 ("r-ggplot2" ,r-ggplot2)
5902 ("r-gridextra" ,r-gridextra)
5903 ("r-ncdfflow" ,r-ncdfflow)
5905 ("r-rcolorbrewer" ,r-rcolorbrewer)
5906 ("r-rlang" ,r-rlang)
5907 ("r-scales" ,r-scales)))
5909 `(("r-knitr" ,r-knitr)))
5910 (home-page "https://github.com/RGLab/ggcyto/issues")
5911 (synopsis "Visualize Cytometry data with ggplot")
5913 "With the dedicated fortify method implemented for @code{flowSet},
5914 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
5915 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
5916 and some custom layers also make it easy to add gates and population
5917 statistics to the plot.")
5918 (license license:artistic2.0)))
5920 (define-public r-flowviz
5927 (uri (bioconductor-uri "flowViz" version))
5930 "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7"))))
5931 (properties `((upstream-name . "flowViz")))
5932 (build-system r-build-system)
5934 `(("r-biobase" ,r-biobase)
5935 ("r-flowcore" ,r-flowcore)
5936 ("r-hexbin" ,r-hexbin)
5937 ("r-idpmisc" ,r-idpmisc)
5938 ("r-kernsmooth" ,r-kernsmooth)
5939 ("r-lattice" ,r-lattice)
5940 ("r-latticeextra" ,r-latticeextra)
5942 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5943 (home-page "https://bioconductor.org/packages/flowViz/")
5944 (synopsis "Visualization for flow cytometry")
5946 "This package provides visualization tools for flow cytometry data.")
5947 (license license:artistic2.0)))
5949 (define-public r-flowclust
5951 (name "r-flowclust")
5956 (uri (bioconductor-uri "flowClust" version))
5959 "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s"))))
5960 (properties `((upstream-name . "flowClust")))
5961 (build-system r-build-system)
5964 (list "--configure-args=--enable-bundled-gsl=no")))
5966 `(("r-biobase" ,r-biobase)
5967 ("r-biocgenerics" ,r-biocgenerics)
5969 ("r-corpcor" ,r-corpcor)
5970 ("r-ellipse" ,r-ellipse)
5971 ("r-flowcore" ,r-flowcore)
5972 ("r-flowviz" ,r-flowviz)
5973 ("r-graph" ,r-graph)
5974 ("r-mnormt" ,r-mnormt)))
5978 `(("pkg-config" ,pkg-config)))
5979 (home-page "https://bioconductor.org/packages/flowClust")
5980 (synopsis "Clustering for flow cytometry")
5982 "This package provides robust model-based clustering using a t-mixture
5983 model with Box-Cox transformation.")
5984 (license license:artistic2.0)))
5986 ;; TODO: this package bundles an old version of protobuf. It's not easy to
5987 ;; make it use our protobuf package instead.
5988 (define-public r-rprotobuflib
5990 (name "r-rprotobuflib")
5995 (uri (bioconductor-uri "RProtoBufLib" version))
5998 "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm"))))
5999 (properties `((upstream-name . "RProtoBufLib")))
6000 (build-system r-build-system)
6003 (modify-phases %standard-phases
6004 (add-after 'unpack 'unpack-bundled-sources
6006 (with-directory-excursion "src"
6007 (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
6009 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6010 (synopsis "C++ headers and static libraries of Protocol buffers")
6012 "This package provides the headers and static library of Protocol buffers
6013 for other R packages to compile and link against.")
6014 (license license:bsd-3)))
6016 (define-public r-flowworkspace
6018 (name "r-flowworkspace")
6023 (uri (bioconductor-uri "flowWorkspace" version))
6026 "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn"))))
6027 (properties `((upstream-name . "flowWorkspace")))
6028 (build-system r-build-system)
6031 ("r-biobase" ,r-biobase)
6032 ("r-biocgenerics" ,r-biocgenerics)
6033 ("r-cytolib" ,r-cytolib)
6034 ("r-data-table" ,r-data-table)
6035 ("r-digest" ,r-digest)
6036 ("r-dplyr" ,r-dplyr)
6037 ("r-flowcore" ,r-flowcore)
6038 ("r-flowviz" ,r-flowviz)
6039 ("r-graph" ,r-graph)
6040 ("r-gridextra" ,r-gridextra)
6041 ("r-lattice" ,r-lattice)
6042 ("r-latticeextra" ,r-latticeextra)
6043 ("r-matrixstats" ,r-matrixstats)
6044 ("r-ncdfflow" ,r-ncdfflow)
6046 ("r-rcolorbrewer" ,r-rcolorbrewer)
6048 ("r-rcppparallel" ,r-rcppparallel)
6049 ("r-rgraphviz" ,r-rgraphviz)
6050 ("r-rprotobuflib" ,r-rprotobuflib)
6051 ("r-scales" ,r-scales)
6052 ("r-stringr" ,r-stringr)))
6053 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6054 (synopsis "Infrastructure for working with cytometry data")
6056 "This package is designed to facilitate comparison of automated gating
6057 methods against manual gating done in flowJo. This package allows you to
6058 import basic flowJo workspaces into BioConductor and replicate the gating from
6059 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6060 samples, compensation, and transformation are performed so that the output
6061 matches the flowJo analysis.")
6062 (license license:artistic2.0)))
6064 (define-public r-flowstats
6066 (name "r-flowstats")
6071 (uri (bioconductor-uri "flowStats" version))
6074 "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w"))))
6075 (properties `((upstream-name . "flowStats")))
6076 (build-system r-build-system)
6078 `(("r-biobase" ,r-biobase)
6079 ("r-biocgenerics" ,r-biocgenerics)
6080 ("r-cluster" ,r-cluster)
6082 ("r-flowcore" ,r-flowcore)
6083 ("r-flowviz" ,r-flowviz)
6084 ("r-flowworkspace" ,r-flowworkspace)
6085 ("r-kernsmooth" ,r-kernsmooth)
6087 ("r-lattice" ,r-lattice)
6089 ("r-ncdfflow" ,r-ncdfflow)
6090 ("r-rcolorbrewer" ,r-rcolorbrewer)
6091 ("r-rrcov" ,r-rrcov)))
6092 (home-page "http://www.github.com/RGLab/flowStats")
6093 (synopsis "Statistical methods for the analysis of flow cytometry data")
6095 "This package provides methods and functionality to analyze flow data
6096 that is beyond the basic infrastructure provided by the @code{flowCore}
6098 (license license:artistic2.0)))
6100 (define-public r-opencyto
6107 (uri (bioconductor-uri "openCyto" version))
6110 "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb"))))
6111 (properties `((upstream-name . "openCyto")))
6112 (build-system r-build-system)
6114 `(("r-biobase" ,r-biobase)
6115 ("r-biocgenerics" ,r-biocgenerics)
6117 ("r-data-table" ,r-data-table)
6118 ("r-flowclust" ,r-flowclust)
6119 ("r-flowcore" ,r-flowcore)
6120 ("r-flowstats" ,r-flowstats)
6121 ("r-flowviz" ,r-flowviz)
6122 ("r-flowworkspace" ,r-flowworkspace)
6123 ("r-graph" ,r-graph)
6124 ("r-gtools" ,r-gtools)
6126 ("r-lattice" ,r-lattice)
6128 ("r-ncdfflow" ,r-ncdfflow)
6130 ("r-r-utils" ,r-r-utils)
6132 ("r-rcolorbrewer" ,r-rcolorbrewer)
6134 ("r-rrcov" ,r-rrcov)))
6135 (home-page "https://bioconductor.org/packages/openCyto")
6136 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6138 "This package is designed to facilitate the automated gating methods in a
6139 sequential way to mimic the manual gating strategy.")
6140 (license license:artistic2.0)))
6142 (define-public r-cytoml
6149 (uri (bioconductor-uri "CytoML" version))
6152 "0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz"))))
6153 (properties `((upstream-name . "CytoML")))
6154 (build-system r-build-system)
6156 `(("libxml2" ,libxml2)))
6158 `(("r-base64enc" ,r-base64enc)
6160 ("r-biobase" ,r-biobase)
6161 ("r-corpcor" ,r-corpcor)
6162 ("r-cytolib" ,r-cytolib)
6163 ("r-data-table" ,r-data-table)
6164 ("r-dplyr" ,r-dplyr)
6165 ("r-flowcore" ,r-flowcore)
6166 ("r-flowworkspace" ,r-flowworkspace)
6167 ("r-ggcyto" ,r-ggcyto)
6168 ("r-graph" ,r-graph)
6169 ("r-jsonlite" ,r-jsonlite)
6170 ("r-lattice" ,r-lattice)
6171 ("r-ncdfflow" ,r-ncdfflow)
6172 ("r-opencyto" ,r-opencyto)
6176 ("r-rcppparallel" ,r-rcppparallel)
6177 ("r-rgraphviz" ,r-rgraphviz)
6178 ("r-rprotobuflib" ,r-rprotobuflib)
6179 ("r-runit" ,r-runit)
6181 ("r-yaml" ,r-yaml)))
6183 `(("r-knitr" ,r-knitr)))
6184 (home-page "https://github.com/RGLab/CytoML")
6185 (synopsis "GatingML interface for cross platform cytometry data sharing")
6187 "This package provides an interface to implementations of the GatingML2.0
6188 standard to exchange gated cytometry data with other software platforms.")
6189 (license license:artistic2.0)))
6191 (define-public r-flowsom
6198 (uri (bioconductor-uri "FlowSOM" version))
6201 "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5"))))
6202 (properties `((upstream-name . "FlowSOM")))
6203 (build-system r-build-system)
6205 `(("r-biocgenerics" ,r-biocgenerics)
6206 ("r-consensusclusterplus" ,r-consensusclusterplus)
6207 ("r-cytoml" ,r-cytoml)
6208 ("r-flowcore" ,r-flowcore)
6209 ("r-flowworkspace" ,r-flowworkspace)
6210 ("r-igraph" ,r-igraph)
6211 ("r-rcolorbrewer" ,r-rcolorbrewer)
6214 (home-page "https://bioconductor.org/packages/FlowSOM/")
6215 (synopsis "Visualize and interpret cytometry data")
6217 "FlowSOM offers visualization options for cytometry data, by using
6218 self-organizing map clustering and minimal spanning trees.")
6219 (license license:gpl2+)))
6221 (define-public r-mixomics
6228 (uri (bioconductor-uri "mixOmics" version))
6231 "0b457yg8mwqlrn5l344w8qcj8v2ghlj1wdx1ysxbncqvqx7nvgig"))))
6232 (properties `((upstream-name . "mixOmics")))
6233 (build-system r-build-system)
6235 `(("r-corpcor" ,r-corpcor)
6236 ("r-dplyr" ,r-dplyr)
6237 ("r-ellipse" ,r-ellipse)
6238 ("r-ggplot2" ,r-ggplot2)
6239 ("r-gridextra" ,r-gridextra)
6240 ("r-igraph" ,r-igraph)
6241 ("r-lattice" ,r-lattice)
6243 ("r-matrixstats" ,r-matrixstats)
6244 ("r-rarpack" ,r-rarpack)
6245 ("r-rcolorbrewer" ,r-rcolorbrewer)
6246 ("r-reshape2" ,r-reshape2)
6247 ("r-tidyr" ,r-tidyr)))
6249 `(("r-knitr" ,r-knitr)))
6250 (home-page "http://www.mixOmics.org")
6251 (synopsis "Multivariate methods for exploration of biological datasets")
6253 "mixOmics offers a wide range of multivariate methods for the exploration
6254 and integration of biological datasets with a particular focus on variable
6255 selection. The package proposes several sparse multivariate models we have
6256 developed to identify the key variables that are highly correlated, and/or
6257 explain the biological outcome of interest. The data that can be analysed
6258 with mixOmics may come from high throughput sequencing technologies, such as
6259 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6260 also beyond the realm of omics (e.g. spectral imaging). The methods
6261 implemented in mixOmics can also handle missing values without having to
6262 delete entire rows with missing data.")
6263 (license license:gpl2+)))
6265 (define-public r-depecher
6272 (uri (bioconductor-uri "DepecheR" version))
6275 "199j2kw0xnw7y4v1gakm2jgyc7zzlj8xh0570f2yjq55gp1kggbm"))))
6276 (properties `((upstream-name . "DepecheR")))
6277 (build-system r-build-system)
6279 `(("r-beanplot" ,r-beanplot)
6280 ("r-dosnow" ,r-dosnow)
6281 ("r-dplyr" ,r-dplyr)
6283 ("r-foreach" ,r-foreach)
6284 ("r-ggplot2" ,r-ggplot2)
6285 ("r-gplots" ,r-gplots)
6287 ("r-matrixstats" ,r-matrixstats)
6288 ("r-mixomics" ,r-mixomics)
6289 ("r-moments" ,r-moments)
6291 ("r-rcppeigen" ,r-rcppeigen)
6292 ("r-reshape2" ,r-reshape2)
6293 ("r-robustbase" ,r-robustbase)
6294 ("r-viridis" ,r-viridis)))
6296 `(("r-knitr" ,r-knitr)))
6297 (home-page "https://bioconductor.org/packages/DepecheR/")
6298 (synopsis "Identify traits of clusters in high-dimensional entities")
6300 "The purpose of this package is to identify traits in a dataset that can
6301 separate groups. This is done on two levels. First, clustering is performed,
6302 using an implementation of sparse K-means. Secondly, the generated clusters
6303 are used to predict outcomes of groups of individuals based on their
6304 distribution of observations in the different clusters. As certain clusters
6305 with separating information will be identified, and these clusters are defined
6306 by a sparse number of variables, this method can reduce the complexity of
6307 data, to only emphasize the data that actually matters.")
6308 (license license:expat)))
6310 (define-public r-rcistarget
6312 (name "r-rcistarget")
6317 (uri (bioconductor-uri "RcisTarget" version))
6320 "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw"))))
6321 (properties `((upstream-name . "RcisTarget")))
6322 (build-system r-build-system)
6324 `(("r-aucell" ,r-aucell)
6325 ("r-biocgenerics" ,r-biocgenerics)
6326 ("r-data-table" ,r-data-table)
6327 ("r-feather" ,r-feather)
6328 ("r-gseabase" ,r-gseabase)
6329 ("r-r-utils" ,r-r-utils)
6330 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6331 (home-page "https://aertslab.org/#scenic")
6332 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6334 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6335 over-represented on a gene list. In a first step, RcisTarget selects DNA
6336 motifs that are significantly over-represented in the surroundings of the
6337 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6338 achieved by using a database that contains genome-wide cross-species rankings
6339 for each motif. The motifs that are then annotated to TFs and those that have
6340 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6341 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6342 genes in the gene-set that are ranked above the leading edge).")
6343 (license license:gpl3)))
6345 (define-public r-cicero
6352 (uri (bioconductor-uri "cicero" version))
6355 "1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld"))))
6356 (build-system r-build-system)
6358 `(("r-assertthat" ,r-assertthat)
6359 ("r-biobase" ,r-biobase)
6360 ("r-biocgenerics" ,r-biocgenerics)
6361 ("r-data-table" ,r-data-table)
6362 ("r-dplyr" ,r-dplyr)
6364 ("r-genomicranges" ,r-genomicranges)
6365 ("r-ggplot2" ,r-ggplot2)
6366 ("r-glasso" ,r-glasso)
6368 ("r-igraph" ,r-igraph)
6369 ("r-iranges" ,r-iranges)
6370 ("r-matrix" ,r-matrix)
6371 ("r-monocle" ,r-monocle)
6373 ("r-reshape2" ,r-reshape2)
6374 ("r-s4vectors" ,r-s4vectors)
6375 ("r-stringr" ,r-stringr)
6376 ("r-tibble" ,r-tibble)
6377 ("r-tidyr" ,r-tidyr)
6378 ("r-vgam" ,r-vgam)))
6380 `(("r-knitr" ,r-knitr)))
6381 (home-page "https://bioconductor.org/packages/cicero/")
6382 (synopsis "Predict cis-co-accessibility from single-cell data")
6384 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6385 accessibility data. It also extends the monocle package for use in chromatin
6386 accessibility data.")
6387 (license license:expat)))
6389 ;; This is the latest commit on the "monocle3" branch.
6390 (define-public r-cicero-monocle3
6391 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6393 (package (inherit r-cicero)
6394 (name "r-cicero-monocle3")
6395 (version (git-version "1.3.2" revision commit))
6400 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
6402 (file-name (git-file-name name version))
6405 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6407 `(("r-monocle3" ,r-monocle3)
6408 ,@(alist-delete "r-monocle"
6409 (package-propagated-inputs r-cicero)))))))
6411 (define-public r-cistopic
6412 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6416 (version (git-version "0.2.1" revision commit))
6421 (url "https://github.com/aertslab/cisTopic.git")
6423 (file-name (git-file-name name version))
6426 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6427 (build-system r-build-system)
6429 `(("r-aucell" ,r-aucell)
6430 ("r-data-table" ,r-data-table)
6431 ("r-dplyr" ,r-dplyr)
6432 ("r-dosnow" ,r-dosnow)
6434 ("r-feather" ,r-feather)
6435 ("r-fitdistrplus" ,r-fitdistrplus)
6436 ("r-genomicranges" ,r-genomicranges)
6437 ("r-ggplot2" ,r-ggplot2)
6439 ("r-matrix" ,r-matrix)
6441 ("r-rcistarget" ,r-rcistarget)
6442 ("r-rtracklayer" ,r-rtracklayer)
6443 ("r-s4vectors" ,r-s4vectors)))
6444 (home-page "https://github.com/aertslab/cisTopic")
6445 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6447 "The sparse nature of single cell epigenomics data can be overruled using
6448 probabilistic modelling methods such as @dfn{Latent Dirichlet
6449 Allocation} (LDA). This package allows the probabilistic modelling of
6450 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6451 includes functionalities to identify cell states based on the contribution of
6452 cisTopics and explore the nature and regulatory proteins driving them.")
6453 (license license:gpl3))))
6455 (define-public r-genie3
6462 (uri (bioconductor-uri "GENIE3" version))
6465 "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l"))))
6466 (properties `((upstream-name . "GENIE3")))
6467 (build-system r-build-system)
6468 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6469 (home-page "https://bioconductor.org/packages/GENIE3")
6470 (synopsis "Gene network inference with ensemble of trees")
6472 "This package implements the GENIE3 algorithm for inferring gene
6473 regulatory networks from expression data.")
6474 (license license:gpl2+)))
6476 (define-public r-roc
6483 (uri (bioconductor-uri "ROC" version))
6486 "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y"))))
6487 (properties `((upstream-name . "ROC")))
6488 (build-system r-build-system)
6490 `(("r-knitr" ,r-knitr)))
6491 (home-page "https://www.bioconductor.org/packages/ROC/")
6492 (synopsis "Utilities for ROC curves")
6494 "This package provides utilities for @dfn{Receiver Operating
6495 Characteristic} (ROC) curves, with a focus on micro arrays.")
6496 (license license:artistic2.0)))
6498 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6500 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6505 (uri (bioconductor-uri
6506 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6507 version 'annotation))
6510 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6513 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6514 (build-system r-build-system)
6515 (propagated-inputs `(("r-minfi" ,r-minfi)))
6517 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6518 (synopsis "Annotation for Illumina's 450k methylation arrays")
6520 "This package provides manifests and annotation for Illumina's 450k array
6522 (license license:artistic2.0)))
6524 (define-public r-watermelon
6526 (name "r-watermelon")
6531 (uri (bioconductor-uri "wateRmelon" version))
6534 "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0"))))
6535 (properties `((upstream-name . "wateRmelon")))
6536 (build-system r-build-system)
6538 `(("r-biobase" ,r-biobase)
6539 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6540 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6541 ("r-illuminaio" ,r-illuminaio)
6542 ("r-limma" ,r-limma)
6544 ("r-matrixstats" ,r-matrixstats)
6545 ("r-methylumi" ,r-methylumi)
6547 (home-page "https://bioconductor.org/packages/wateRmelon/")
6548 (synopsis "Illumina 450 methylation array normalization and metrics")
6550 "The standard index of DNA methylation (beta) is computed from methylated
6551 and unmethylated signal intensities. Betas calculated from raw signal
6552 intensities perform well, but using 11 methylomic datasets we demonstrate that
6553 quantile normalization methods produce marked improvement. The commonly used
6554 procedure of normalizing betas is inferior to the separate normalization of M
6555 and U, and it is also advantageous to normalize Type I and Type II assays
6556 separately. This package provides 15 flavours of betas and three performance
6557 metrics, with methods for objects produced by the @code{methylumi} and
6558 @code{minfi} packages.")
6559 (license license:gpl3)))
6561 (define-public r-gdsfmt
6568 (uri (bioconductor-uri "gdsfmt" version))
6571 "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9"))
6572 (modules '((guix build utils)))
6573 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6574 ;; them and link with system libraries instead.
6577 (for-each delete-file-recursively
6581 (substitute* "src/Makevars"
6582 (("all: \\$\\(SHLIB\\)") "all:")
6583 (("\\$\\(SHLIB\\): liblzma.a") "")
6584 (("(ZLIB|LZ4)/.*") "")
6585 (("CoreArray/dVLIntGDS.cpp.*")
6586 "CoreArray/dVLIntGDS.cpp")
6587 (("CoreArray/dVLIntGDS.o.*")
6588 "CoreArray/dVLIntGDS.o")
6589 (("PKG_LIBS = ./liblzma.a")
6590 "PKG_LIBS = -llz4"))
6591 (substitute* "src/CoreArray/dStream.h"
6592 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6593 (string-append "include <" header ">")))
6595 (properties `((upstream-name . "gdsfmt")))
6596 (build-system r-build-system)
6601 (home-page "http://corearray.sourceforge.net/")
6603 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6605 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6606 Data Structure} (GDS) data files, which are portable across platforms with
6607 hierarchical structure to store multiple scalable array-oriented data sets
6608 with metadata information. It is suited for large-scale datasets, especially
6609 for data which are much larger than the available random-access memory. The
6610 @code{gdsfmt} package offers efficient operations specifically designed for
6611 integers of less than 8 bits, since a diploid genotype, like
6612 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6613 byte. Data compression and decompression are available with relatively
6614 efficient random access. It is also allowed to read a GDS file in parallel
6615 with multiple R processes supported by the package @code{parallel}.")
6616 (license license:lgpl3)))
6618 (define-public r-bigmelon
6625 (uri (bioconductor-uri "bigmelon" version))
6628 "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls"))))
6629 (properties `((upstream-name . "bigmelon")))
6630 (build-system r-build-system)
6632 `(("r-biobase" ,r-biobase)
6633 ("r-biocgenerics" ,r-biocgenerics)
6634 ("r-gdsfmt" ,r-gdsfmt)
6635 ("r-geoquery" ,r-geoquery)
6636 ("r-methylumi" ,r-methylumi)
6637 ("r-minfi" ,r-minfi)
6638 ("r-watermelon" ,r-watermelon)))
6639 (home-page "https://bioconductor.org/packages/bigmelon/")
6640 (synopsis "Illumina methylation array analysis for large experiments")
6642 "This package provides methods for working with Illumina arrays using the
6643 @code{gdsfmt} package.")
6644 (license license:gpl3)))
6646 (define-public r-seqbias
6653 (uri (bioconductor-uri "seqbias" version))
6656 "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq"))))
6657 (properties `((upstream-name . "seqbias")))
6658 (build-system r-build-system)
6660 `(("r-biostrings" ,r-biostrings)
6661 ("r-genomicranges" ,r-genomicranges)
6662 ("r-rhtslib" ,r-rhtslib)))
6664 `(("zlib" ,zlib))) ; This comes from rhtslib.
6665 (home-page "https://bioconductor.org/packages/seqbias/")
6666 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6668 "This package implements a model of per-position sequencing bias in
6669 high-throughput sequencing data using a simple Bayesian network, the structure
6670 and parameters of which are trained on a set of aligned reads and a reference
6672 (license license:lgpl3)))
6674 (define-public r-snplocs-hsapiens-dbsnp144-grch37
6676 (name "r-snplocs-hsapiens-dbsnp144-grch37")
6680 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
6681 version 'annotation))
6684 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
6685 (build-system r-build-system)
6686 ;; As this package provides little more than a very large data file it
6687 ;; doesn't make sense to build substitutes.
6688 (arguments `(#:substitutable? #f))
6690 `(("r-biocgenerics" ,r-biocgenerics)
6691 ("r-s4vectors" ,r-s4vectors)
6692 ("r-iranges" ,r-iranges)
6693 ("r-genomeinfodb" ,r-genomeinfodb)
6694 ("r-genomicranges" ,r-genomicranges)
6695 ("r-bsgenome" ,r-bsgenome)
6696 ("r-biostrings" ,r-biostrings)))
6698 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
6699 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
6700 (description "This package provides SNP locations and alleles for Homo
6701 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
6702 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
6703 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
6704 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
6705 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
6706 the mitochondrion chromosome. Therefore, the SNPs in this package can be
6707 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
6708 correct position but this injection will exclude chrM (i.e. nothing will be
6709 injected in that sequence).")
6710 (license license:artistic2.0)))
6712 (define-public r-reqon
6719 (uri (bioconductor-uri "ReQON" version))
6722 "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx"))))
6723 (properties `((upstream-name . "ReQON")))
6724 (build-system r-build-system)
6726 `(("r-rjava" ,r-rjava)
6727 ("r-rsamtools" ,r-rsamtools)
6728 ("r-seqbias" ,r-seqbias)))
6729 (home-page "https://bioconductor.org/packages/ReQON/")
6730 (synopsis "Recalibrating quality of nucleotides")
6732 "This package provides an implementation of an algorithm for
6733 recalibrating the base quality scores for aligned sequencing data in BAM
6735 (license license:gpl2)))
6737 (define-public r-wavcluster
6739 (name "r-wavcluster")
6744 (uri (bioconductor-uri "wavClusteR" version))
6747 "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y"))))
6748 (properties `((upstream-name . "wavClusteR")))
6749 (build-system r-build-system)
6751 `(("r-biocgenerics" ,r-biocgenerics)
6752 ("r-biostrings" ,r-biostrings)
6753 ("r-foreach" ,r-foreach)
6754 ("r-genomicfeatures" ,r-genomicfeatures)
6755 ("r-genomicranges" ,r-genomicranges)
6756 ("r-ggplot2" ,r-ggplot2)
6757 ("r-hmisc" ,r-hmisc)
6758 ("r-iranges" ,r-iranges)
6759 ("r-mclust" ,r-mclust)
6760 ("r-rsamtools" ,r-rsamtools)
6761 ("r-rtracklayer" ,r-rtracklayer)
6762 ("r-s4vectors" ,r-s4vectors)
6763 ("r-seqinr" ,r-seqinr)
6764 ("r-stringr" ,r-stringr)
6765 ("r-wmtsa" ,r-wmtsa)))
6766 (home-page "https://bioconductor.org/packages/wavClusteR/")
6767 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6769 "This package provides an integrated pipeline for the analysis of
6770 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6771 sequencing errors, SNPs and additional non-experimental sources by a non-
6772 parametric mixture model. The protein binding sites (clusters) are then
6773 resolved at high resolution and cluster statistics are estimated using a
6774 rigorous Bayesian framework. Post-processing of the results, data export for
6775 UCSC genome browser visualization and motif search analysis are provided. In
6776 addition, the package integrates RNA-Seq data to estimate the False
6777 Discovery Rate of cluster detection. Key functions support parallel multicore
6778 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6779 be applied to the analysis of other NGS data obtained from experimental
6780 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6781 (license license:gpl2)))
6783 (define-public r-timeseriesexperiment
6785 (name "r-timeseriesexperiment")
6790 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6793 "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm"))))
6795 `((upstream-name . "TimeSeriesExperiment")))
6796 (build-system r-build-system)
6798 `(("r-deseq2" ,r-deseq2)
6799 ("r-dplyr" ,r-dplyr)
6800 ("r-dynamictreecut" ,r-dynamictreecut)
6801 ("r-edger" ,r-edger)
6802 ("r-ggplot2" ,r-ggplot2)
6803 ("r-hmisc" ,r-hmisc)
6804 ("r-limma" ,r-limma)
6805 ("r-magrittr" ,r-magrittr)
6806 ("r-proxy" ,r-proxy)
6807 ("r-s4vectors" ,r-s4vectors)
6808 ("r-summarizedexperiment" ,r-summarizedexperiment)
6809 ("r-tibble" ,r-tibble)
6810 ("r-tidyr" ,r-tidyr)
6811 ("r-vegan" ,r-vegan)
6812 ("r-viridis" ,r-viridis)))
6813 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6814 (synopsis "Analysis for short time-series data")
6816 "This package is a visualization and analysis toolbox for short time
6817 course data which includes dimensionality reduction, clustering, two-sample
6818 differential expression testing and gene ranking techniques. The package also
6819 provides methods for retrieving enriched pathways.")
6820 (license license:lgpl3+)))
6822 (define-public r-variantfiltering
6824 (name "r-variantfiltering")
6829 (uri (bioconductor-uri "VariantFiltering" version))
6832 "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8"))))
6834 `((upstream-name . "VariantFiltering")))
6835 (build-system r-build-system)
6837 `(("r-annotationdbi" ,r-annotationdbi)
6838 ("r-biobase" ,r-biobase)
6839 ("r-biocgenerics" ,r-biocgenerics)
6840 ("r-biocparallel" ,r-biocparallel)
6841 ("r-biostrings" ,r-biostrings)
6842 ("r-bsgenome" ,r-bsgenome)
6844 ("r-genomeinfodb" ,r-genomeinfodb)
6845 ("r-genomicfeatures" ,r-genomicfeatures)
6846 ("r-genomicranges" ,r-genomicranges)
6847 ("r-genomicscores" ,r-genomicscores)
6848 ("r-graph" ,r-graph)
6850 ("r-iranges" ,r-iranges)
6852 ("r-rsamtools" ,r-rsamtools)
6853 ("r-s4vectors" ,r-s4vectors)
6854 ("r-shiny" ,r-shiny)
6855 ("r-shinyjs" ,r-shinyjs)
6856 ("r-shinythemes" ,r-shinythemes)
6857 ("r-shinytree" ,r-shinytree)
6858 ("r-summarizedexperiment" ,r-summarizedexperiment)
6859 ("r-variantannotation" ,r-variantannotation)
6860 ("r-xvector" ,r-xvector)))
6861 (home-page "https://github.com/rcastelo/VariantFiltering")
6862 (synopsis "Filtering of coding and non-coding genetic variants")
6864 "Filter genetic variants using different criteria such as inheritance
6865 model, amino acid change consequence, minor allele frequencies across human
6866 populations, splice site strength, conservation, etc.")
6867 (license license:artistic2.0)))
6869 (define-public r-genomegraphs
6871 (name "r-genomegraphs")
6876 (uri (bioconductor-uri "GenomeGraphs" version))
6879 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
6880 (properties `((upstream-name . "GenomeGraphs")))
6881 (build-system r-build-system)
6883 `(("r-biomart" ,r-biomart)))
6884 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
6885 (synopsis "Plotting genomic information from Ensembl")
6887 "Genomic data analyses requires integrated visualization of known genomic
6888 information and new experimental data. GenomeGraphs uses the biomaRt package
6889 to perform live annotation queries to Ensembl and translates this to e.g.
6890 gene/transcript structures in viewports of the grid graphics package. This
6891 results in genomic information plotted together with your data. Another
6892 strength of GenomeGraphs is to plot different data types such as array CGH,
6893 gene expression, sequencing and other data, together in one plot using the
6894 same genome coordinate system.")
6895 (license license:artistic2.0)))
6897 (define-public r-wavetiling
6899 (name "r-wavetiling")
6904 (uri (bioconductor-uri "waveTiling" version))
6907 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
6908 (properties `((upstream-name . "waveTiling")))
6909 (build-system r-build-system)
6911 `(("r-affy" ,r-affy)
6912 ("r-biobase" ,r-biobase)
6913 ("r-biostrings" ,r-biostrings)
6914 ("r-genomegraphs" ,r-genomegraphs)
6915 ("r-genomicranges" ,r-genomicranges)
6916 ("r-iranges" ,r-iranges)
6917 ("r-oligo" ,r-oligo)
6918 ("r-oligoclasses" ,r-oligoclasses)
6919 ("r-preprocesscore" ,r-preprocesscore)
6920 ("r-waveslim" ,r-waveslim)))
6921 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
6922 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
6924 "This package is designed to conduct transcriptome analysis for tiling
6925 arrays based on fast wavelet-based functional models.")
6926 (license license:gpl2+)))
6928 (define-public r-variancepartition
6930 (name "r-variancepartition")
6935 (uri (bioconductor-uri "variancePartition" version))
6938 "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g"))))
6940 `((upstream-name . "variancePartition")))
6941 (build-system r-build-system)
6943 `(("r-biobase" ,r-biobase)
6944 ("r-biocparallel" ,r-biocparallel)
6945 ("r-colorramps" ,r-colorramps)
6946 ("r-doparallel" ,r-doparallel)
6947 ("r-foreach" ,r-foreach)
6948 ("r-ggplot2" ,r-ggplot2)
6949 ("r-gplots" ,r-gplots)
6950 ("r-iterators" ,r-iterators)
6951 ("r-limma" ,r-limma)
6953 ("r-lmertest" ,r-lmertest)
6955 ("r-pbkrtest" ,r-pbkrtest)
6956 ("r-progress" ,r-progress)
6957 ("r-reshape2" ,r-reshape2)
6958 ("r-scales" ,r-scales)))
6959 (home-page "https://bioconductor.org/packages/variancePartition/")
6960 (synopsis "Analyze variation in gene expression experiments")
6962 "This is a package providing tools to quantify and interpret multiple
6963 sources of biological and technical variation in gene expression experiments.
6964 It uses a linear mixed model to quantify variation in gene expression
6965 attributable to individual, tissue, time point, or technical variables. The
6966 package includes dream differential expression analysis for repeated
6968 (license license:gpl2+)))
6970 (define-public r-htqpcr
6977 (uri (bioconductor-uri "HTqPCR" version))
6980 "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx"))))
6981 (properties `((upstream-name . "HTqPCR")))
6982 (build-system r-build-system)
6984 `(("r-affy" ,r-affy)
6985 ("r-biobase" ,r-biobase)
6986 ("r-gplots" ,r-gplots)
6987 ("r-limma" ,r-limma)
6988 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6989 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
6990 "groups/bertone/software/HTqPCR.pdf"))
6991 (synopsis "Automated analysis of high-throughput qPCR data")
6993 "Analysis of Ct values from high throughput quantitative real-time
6994 PCR (qPCR) assays across multiple conditions or replicates. The input data
6995 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
6996 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
6997 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
6998 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
6999 loading, quality assessment, normalization, visualization and parametric or
7000 non-parametric testing for statistical significance in Ct values between
7001 features (e.g. genes, microRNAs).")
7002 (license license:artistic2.0)))
7004 (define-public r-unifiedwmwqpcr
7006 (name "r-unifiedwmwqpcr")
7011 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7014 "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj"))))
7016 `((upstream-name . "unifiedWMWqPCR")))
7017 (build-system r-build-system)
7019 `(("r-biocgenerics" ,r-biocgenerics)
7020 ("r-htqpcr" ,r-htqpcr)))
7021 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7022 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7024 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7025 data. This modified test allows for testing differential expression in qPCR
7027 (license license:gpl2+)))
7029 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7031 (define-public r-activedriverwgs
7033 (name "r-activedriverwgs")
7038 (uri (cran-uri "ActiveDriverWGS" version))
7041 "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
7043 `((upstream-name . "ActiveDriverWGS")))
7044 (build-system r-build-system)
7046 `(("r-biostrings" ,r-biostrings)
7047 ("r-bsgenome" ,r-bsgenome)
7048 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7049 ("r-genomeinfodb" ,r-genomeinfodb)
7050 ("r-genomicranges" ,r-genomicranges)
7051 ("r-iranges" ,r-iranges)
7053 ("r-s4vectors" ,r-s4vectors)))
7054 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7055 (synopsis "Driver discovery tool for cancer whole genomes")
7057 "This package provides a method for finding an enrichment of cancer
7058 simple somatic mutations (SNVs and Indels) in functional elements across the
7059 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7060 using whole genome sequencing data.")
7061 (license license:gpl3)))
7063 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7065 (define-public r-activepathways
7067 (name "r-activepathways")
7072 (uri (cran-uri "ActivePathways" version))
7075 "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20"))))
7077 `((upstream-name . "ActivePathways")))
7078 (build-system r-build-system)
7080 `(("r-data-table" ,r-data-table)
7081 ("r-ggplot2" ,r-ggplot2)
7082 ("r-metap" ,r-metap)))
7084 `(("r-knitr" ,r-knitr)))
7085 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7086 (synopsis "Multivariate pathway enrichment analysis")
7088 "This package represents an integrative method of analyzing multi omics
7089 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7090 uses a statistical data fusion approach, rationalizes contributing evidence
7091 and highlights associated genes, improving systems-level understanding of
7092 cellular organization in health and disease.")
7093 (license license:gpl3)))
7095 (define-public r-bgmix
7102 (uri (bioconductor-uri "BGmix" version))
7105 "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683"))))
7106 (properties `((upstream-name . "BGmix")))
7107 (build-system r-build-system)
7109 `(("r-kernsmooth" ,r-kernsmooth)))
7110 (home-page "https://bioconductor.org/packages/BGmix/")
7111 (synopsis "Bayesian models for differential gene expression")
7113 "This package provides fully Bayesian mixture models for differential
7115 (license license:gpl2)))
7117 (define-public r-bgx
7124 (uri (bioconductor-uri "bgx" version))
7127 "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm"))))
7128 (properties `((upstream-name . "bgx")))
7129 (build-system r-build-system)
7131 `(("r-affy" ,r-affy)
7132 ("r-biobase" ,r-biobase)
7133 ("r-gcrma" ,r-gcrma)
7134 ("r-rcpp" ,r-rcpp)))
7135 (home-page "https://bioconductor.org/packages/bgx/")
7136 (synopsis "Bayesian gene expression")
7138 "This package provides tools for Bayesian integrated analysis of
7139 Affymetrix GeneChips.")
7140 (license license:gpl2)))
7142 (define-public r-bhc
7149 (uri (bioconductor-uri "BHC" version))
7152 "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh"))))
7153 (properties `((upstream-name . "BHC")))
7154 (build-system r-build-system)
7155 (home-page "https://bioconductor.org/packages/BHC/")
7156 (synopsis "Bayesian hierarchical clustering")
7158 "The method implemented in this package performs bottom-up hierarchical
7159 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7160 in the data and Bayesian model selection to decide at each step which clusters
7161 to merge. This avoids several limitations of traditional methods, for example
7162 how many clusters there should be and how to choose a principled distance
7163 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7164 categories) or time-series data. This version also includes a randomised
7165 algorithm which is more efficient for larger data sets.")
7166 (license license:gpl3)))
7168 (define-public r-bicare
7175 (uri (bioconductor-uri "BicARE" version))
7178 "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs"))))
7179 (properties `((upstream-name . "BicARE")))
7180 (build-system r-build-system)
7182 `(("r-biobase" ,r-biobase)
7183 ("r-gseabase" ,r-gseabase)
7184 ("r-multtest" ,r-multtest)))
7185 (home-page "http://bioinfo.curie.fr")
7186 (synopsis "Biclustering analysis and results exploration")
7188 "This is a package for biclustering analysis and exploration of
7190 (license license:gpl2)))
7192 (define-public r-bifet
7199 (uri (bioconductor-uri "BiFET" version))
7202 "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k"))))
7203 (properties `((upstream-name . "BiFET")))
7204 (build-system r-build-system)
7206 `(("r-genomicranges" ,r-genomicranges)
7207 ("r-poibin" ,r-poibin)))
7208 (home-page "https://bioconductor.org/packages/BiFET")
7209 (synopsis "Bias-free footprint enrichment test")
7211 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7212 over-represented in target regions compared to background regions after
7213 correcting for the bias arising from the imbalance in read counts and GC
7214 contents between the target and background regions. For a given TF k, BiFET
7215 tests the null hypothesis that the target regions have the same probability of
7216 having footprints for the TF k as the background regions while correcting for
7217 the read count and GC content bias.")
7218 (license license:gpl3)))
7220 (define-public r-rsbml
7227 (uri (bioconductor-uri "rsbml" version))
7230 "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa"))))
7231 (properties `((upstream-name . "rsbml")))
7232 (build-system r-build-system)
7234 `(("libsbml" ,libsbml)
7237 `(("r-biocgenerics" ,r-biocgenerics)
7238 ("r-graph" ,r-graph)))
7240 `(("pkg-config" ,pkg-config)))
7241 (home-page "http://www.sbml.org")
7242 (synopsis "R support for SBML")
7244 "This package provides an R interface to libsbml for SBML parsing,
7245 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7246 (license license:artistic2.0)))
7248 (define-public r-hypergraph
7250 (name "r-hypergraph")
7255 (uri (bioconductor-uri "hypergraph" version))
7258 "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m"))))
7259 (properties `((upstream-name . "hypergraph")))
7260 (build-system r-build-system)
7262 `(("r-graph" ,r-graph)))
7263 (home-page "https://bioconductor.org/packages/hypergraph")
7264 (synopsis "Hypergraph data structures")
7266 "This package implements some simple capabilities for representing and
7267 manipulating hypergraphs.")
7268 (license license:artistic2.0)))
7270 (define-public r-hyperdraw
7272 (name "r-hyperdraw")
7277 (uri (bioconductor-uri "hyperdraw" version))
7280 "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj"))))
7281 (properties `((upstream-name . "hyperdraw")))
7282 (build-system r-build-system)
7283 (inputs `(("graphviz" ,graphviz)))
7285 `(("r-graph" ,r-graph)
7286 ("r-hypergraph" ,r-hypergraph)
7287 ("r-rgraphviz" ,r-rgraphviz)))
7288 (home-page "https://bioconductor.org/packages/hyperdraw")
7289 (synopsis "Visualizing hypergraphs")
7291 "This package provides functions for visualizing hypergraphs.")
7292 (license license:gpl2+)))
7294 (define-public r-biggr
7301 (uri (bioconductor-uri "BiGGR" version))
7304 "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif"))))
7305 (properties `((upstream-name . "BiGGR")))
7306 (build-system r-build-system)
7308 `(("r-hyperdraw" ,r-hyperdraw)
7309 ("r-hypergraph" ,r-hypergraph)
7311 ("r-limsolve" ,r-limsolve)
7312 ("r-rsbml" ,r-rsbml)
7313 ("r-stringr" ,r-stringr)))
7314 (home-page "https://bioconductor.org/packages/BiGGR/")
7315 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7317 "This package provides an interface to simulate metabolic reconstruction
7318 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7319 reconstruction databases. The package facilitates @dfn{flux balance
7320 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7321 networks and estimated fluxes can be visualized with hypergraphs.")
7322 (license license:gpl3+)))
7324 (define-public r-bigmemoryextras
7326 (name "r-bigmemoryextras")
7331 (uri (bioconductor-uri "bigmemoryExtras" version))
7334 "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq"))))
7336 `((upstream-name . "bigmemoryExtras")))
7337 (build-system r-build-system)
7339 `(("r-bigmemory" ,r-bigmemory)))
7340 (home-page "https://github.com/phaverty/bigmemoryExtras")
7341 (synopsis "Extension of the bigmemory package")
7343 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7344 safety and convenience features to the @code{filebacked.big.matrix} class from
7345 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7346 monitoring and gracefully restoring the connection to on-disk data and it also
7347 protects against accidental data modification with a filesystem-based
7348 permissions system. Utilities are provided for using @code{BigMatrix}-derived
7349 classes as @code{assayData} matrices within the @code{Biobase} package's
7350 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7351 related to attaching to, and indexing into, file-backed matrices with
7352 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7353 a file-backed matrix with factor properties.")
7354 (license license:artistic2.0)))
7356 (define-public r-bigpint
7363 (uri (bioconductor-uri "bigPint" version))
7366 "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs"))))
7367 (properties `((upstream-name . "bigPint")))
7368 (build-system r-build-system)
7370 `(("r-dplyr" ,r-dplyr)
7371 ("r-ggally" ,r-ggally)
7372 ("r-ggplot2" ,r-ggplot2)
7373 ("r-gridextra" ,r-gridextra)
7374 ("r-hexbin" ,r-hexbin)
7375 ("r-hmisc" ,r-hmisc)
7376 ("r-htmlwidgets" ,r-htmlwidgets)
7377 ("r-plotly" ,r-plotly)
7379 ("r-rcolorbrewer" ,r-rcolorbrewer)
7380 ("r-reshape" ,r-reshape)
7381 ("r-shiny" ,r-shiny)
7382 ("r-shinycssloaders" ,r-shinycssloaders)
7383 ("r-shinydashboard" ,r-shinydashboard)
7384 ("r-stringr" ,r-stringr)
7385 ("r-tidyr" ,r-tidyr)))
7387 `(("r-knitr" ,r-knitr)))
7388 (home-page "https://github.com/lindsayrutter/bigPint")
7389 (synopsis "Big multivariate data plotted interactively")
7391 "This package provides methods for visualizing large multivariate
7392 datasets using static and interactive scatterplot matrices, parallel
7393 coordinate plots, volcano plots, and litre plots. It includes examples for
7394 visualizing RNA-sequencing datasets and differentially expressed genes.")
7395 (license license:gpl3)))
7397 (define-public r-chemminer
7399 (name "r-chemminer")
7404 (uri (bioconductor-uri "ChemmineR" version))
7407 "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga"))))
7408 (properties `((upstream-name . "ChemmineR")))
7409 (build-system r-build-system)
7411 `(("r-base64enc" ,r-base64enc)
7413 ("r-biocgenerics" ,r-biocgenerics)
7415 ("r-digest" ,r-digest)
7417 ("r-ggplot2" ,r-ggplot2)
7418 ("r-gridextra" ,r-gridextra)
7421 ("r-rcurl" ,r-rcurl)
7422 ("r-rjson" ,r-rjson)
7423 ("r-rsvg" ,r-rsvg)))
7424 (home-page "https://github.com/girke-lab/ChemmineR")
7425 (synopsis "Cheminformatics toolkit for R")
7427 "ChemmineR is a cheminformatics package for analyzing drug-like small
7428 molecule data in R. It contains functions for efficient processing of large
7429 numbers of molecules, physicochemical/structural property predictions,
7430 structural similarity searching, classification and clustering of compound
7431 libraries with a wide spectrum of algorithms. In addition, it offers
7432 visualization functions for compound clustering results and chemical
7434 (license license:artistic2.0)))
7436 (define-public r-bioassayr
7438 (name "r-bioassayr")
7443 (uri (bioconductor-uri "bioassayR" version))
7446 "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw"))))
7447 (properties `((upstream-name . "bioassayR")))
7448 (build-system r-build-system)
7450 `(("r-biocgenerics" ,r-biocgenerics)
7451 ("r-chemminer" ,r-chemminer)
7453 ("r-matrix" ,r-matrix)
7454 ("r-rjson" ,r-rjson)
7455 ("r-rsqlite" ,r-rsqlite)
7458 `(("r-knitr" ,r-knitr)))
7459 (home-page "https://github.com/TylerBackman/bioassayR")
7460 (synopsis "Cross-target analysis of small molecule bioactivity")
7462 "bioassayR is a computational tool that enables simultaneous analysis of
7463 thousands of bioassay experiments performed over a diverse set of compounds
7464 and biological targets. Unique features include support for large-scale
7465 cross-target analyses of both public and custom bioassays, generation of
7466 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7467 preloaded database that provides access to a substantial portion of publicly
7468 available bioactivity data.")
7469 (license license:artistic2.0)))
7471 (define-public r-biobroom
7478 (uri (bioconductor-uri "biobroom" version))
7481 "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb"))))
7482 (properties `((upstream-name . "biobroom")))
7483 (build-system r-build-system)
7485 `(("r-biobase" ,r-biobase)
7486 ("r-broom" ,r-broom)
7487 ("r-dplyr" ,r-dplyr)
7488 ("r-tidyr" ,r-tidyr)))
7489 (home-page "https://github.com/StoreyLab/biobroom")
7490 (synopsis "Turn Bioconductor objects into tidy data frames")
7492 "This package contains methods for converting standard objects
7493 constructed by bioinformatics packages, especially those in Bioconductor, and
7494 converting them to @code{tidy} data. It thus serves as a complement to the
7495 @code{broom} package, and follows the same tidy, augment, glance division of
7496 tidying methods. Tidying data makes it easy to recombine, reshape and
7497 visualize bioinformatics analyses.")
7498 ;; Any version of the LGPL.
7499 (license license:lgpl3+)))
7501 (define-public r-graphite
7508 (uri (bioconductor-uri "graphite" version))
7511 "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd"))))
7512 (properties `((upstream-name . "graphite")))
7513 (build-system r-build-system)
7515 `(("r-annotationdbi" ,r-annotationdbi)
7516 ("r-checkmate" ,r-checkmate)
7517 ("r-graph" ,r-graph)
7519 ("r-rappdirs" ,r-rappdirs)))
7520 (home-page "https://bioconductor.org/packages/graphite/")
7521 (synopsis "Networks from pathway databases")
7523 "Graphite provides networks derived from eight public pathway databases,
7524 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7526 (license license:agpl3+)))
7528 (define-public r-reactomepa
7530 (name "r-reactomepa")
7535 (uri (bioconductor-uri "ReactomePA" version))
7538 "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1"))))
7539 (properties `((upstream-name . "ReactomePA")))
7540 (build-system r-build-system)
7542 `(("r-annotationdbi" ,r-annotationdbi)
7544 ("r-enrichplot" ,r-enrichplot)
7545 ("r-ggplot2" ,r-ggplot2)
7546 ("r-ggraph" ,r-ggraph)
7547 ("r-graphite" ,r-graphite)
7548 ("r-igraph" ,r-igraph)
7549 ("r-reactome-db" ,r-reactome-db)))
7550 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7551 (synopsis "Reactome pathway analysis")
7553 "This package provides functions for pathway analysis based on the
7554 REACTOME pathway database. It implements enrichment analysis, gene set
7555 enrichment analysis and several functions for visualization.")
7556 (license license:gpl2)))
7558 (define-public r-ebarrays
7565 (uri (bioconductor-uri "EBarrays" version))
7568 "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13"))))
7569 (properties `((upstream-name . "EBarrays")))
7570 (build-system r-build-system)
7572 `(("r-biobase" ,r-biobase)
7573 ("r-cluster" ,r-cluster)
7574 ("r-lattice" ,r-lattice)))
7575 (home-page "https://bioconductor.org/packages/EBarrays/")
7576 (synopsis "Gene clustering and differential expression identification")
7578 "EBarrays provides tools for the analysis of replicated/unreplicated
7580 (license license:gpl2+)))
7582 (define-public r-bioccasestudies
7584 (name "r-bioccasestudies")
7589 (uri (bioconductor-uri "BiocCaseStudies" version))
7592 "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd"))))
7594 `((upstream-name . "BiocCaseStudies")))
7595 (build-system r-build-system)
7596 (propagated-inputs `(("r-biobase" ,r-biobase)))
7597 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7598 (synopsis "Support for the case studies monograph")
7600 "This package provides software and data to support the case studies
7602 (license license:artistic2.0)))
7604 (define-public r-biocgraph
7606 (name "r-biocgraph")
7611 (uri (bioconductor-uri "biocGraph" version))
7614 "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw"))))
7615 (properties `((upstream-name . "biocGraph")))
7616 (build-system r-build-system)
7618 `(("r-biocgenerics" ,r-biocgenerics)
7619 ("r-geneplotter" ,r-geneplotter)
7620 ("r-graph" ,r-graph)
7621 ("r-rgraphviz" ,r-rgraphviz)))
7622 (home-page "https://bioconductor.org/packages/biocGraph/")
7623 (synopsis "Graph examples and use cases in Bioinformatics")
7625 "This package provides examples and code that make use of the
7626 different graph related packages produced by Bioconductor.")
7627 (license license:artistic2.0)))
7629 (define-public r-experimenthub
7631 (name "r-experimenthub")
7636 (uri (bioconductor-uri "ExperimentHub" version))
7639 "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24"))))
7640 (properties `((upstream-name . "ExperimentHub")))
7641 (build-system r-build-system)
7643 `(("r-annotationhub" ,r-annotationhub)
7644 ("r-biocfilecache" ,r-biocfilecache)
7645 ("r-biocgenerics" ,r-biocgenerics)
7646 ("r-biocmanager" ,r-biocmanager)
7648 ("r-rappdirs" ,r-rappdirs)
7649 ("r-s4vectors" ,r-s4vectors)))
7650 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7651 (synopsis "Client to access ExperimentHub resources")
7653 "This package provides a client for the Bioconductor ExperimentHub web
7654 resource. ExperimentHub provides a central location where curated data from
7655 experiments, publications or training courses can be accessed. Each resource
7656 has associated metadata, tags and date of modification. The client creates
7657 and manages a local cache of files retrieved enabling quick and reproducible
7659 (license license:artistic2.0)))
7661 (define-public r-multiassayexperiment
7663 (name "r-multiassayexperiment")
7668 (uri (bioconductor-uri "MultiAssayExperiment" version))
7671 "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi"))))
7673 `((upstream-name . "MultiAssayExperiment")))
7674 (build-system r-build-system)
7676 `(("r-biobase" ,r-biobase)
7677 ("r-biocgenerics" ,r-biocgenerics)
7678 ("r-genomicranges" ,r-genomicranges)
7679 ("r-iranges" ,r-iranges)
7680 ("r-s4vectors" ,r-s4vectors)
7681 ("r-summarizedexperiment" ,r-summarizedexperiment)
7682 ("r-tidyr" ,r-tidyr)))
7684 `(("r-knitr" ,r-knitr)))
7685 (home-page "https://waldronlab.io/MultiAssayExperiment/")
7686 (synopsis "Integration of multi-omics experiments in Bioconductor")
7688 "MultiAssayExperiment harmonizes data management of multiple assays
7689 performed on an overlapping set of specimens. It provides a familiar
7690 Bioconductor user experience by extending concepts from
7691 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7692 classes for individual assays, and allowing subsetting by genomic ranges or
7694 (license license:artistic2.0)))
7696 (define-public r-bioconcotk
7698 (name "r-bioconcotk")
7703 (uri (bioconductor-uri "BiocOncoTK" version))
7706 "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj"))))
7707 (properties `((upstream-name . "BiocOncoTK")))
7708 (build-system r-build-system)
7710 `(("r-bigrquery" ,r-bigrquery)
7712 ("r-complexheatmap" ,r-complexheatmap)
7713 ("r-curatedtcgadata" ,r-curatedtcgadata)
7715 ("r-dplyr" ,r-dplyr)
7717 ("r-genomicfeatures" ,r-genomicfeatures)
7718 ("r-genomicranges" ,r-genomicranges)
7719 ("r-ggplot2" ,r-ggplot2)
7720 ("r-ggpubr" ,r-ggpubr)
7721 ("r-graph" ,r-graph)
7723 ("r-iranges" ,r-iranges)
7724 ("r-magrittr" ,r-magrittr)
7726 ("r-rgraphviz" ,r-rgraphviz)
7727 ("r-rjson" ,r-rjson)
7728 ("r-s4vectors" ,r-s4vectors)
7729 ("r-scales" ,r-scales)
7730 ("r-shiny" ,r-shiny)
7731 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7732 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7733 (synopsis "Bioconductor components for general cancer genomics")
7735 "The purpose of this package is to provide a central interface to various
7736 tools for genome-scale analysis of cancer studies.")
7737 (license license:artistic2.0)))
7739 (define-public r-biocor
7746 (uri (bioconductor-uri "BioCor" version))
7749 "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl"))))
7750 (properties `((upstream-name . "BioCor")))
7751 (build-system r-build-system)
7753 `(("r-biocparallel" ,r-biocparallel)
7754 ("r-gseabase" ,r-gseabase)
7755 ("r-matrix" ,r-matrix)))
7756 (home-page "https://llrs.github.io/BioCor/")
7757 (synopsis "Functional similarities")
7759 "This package provides tools to calculate functional similarities based
7760 on the pathways described on KEGG and REACTOME or in gene sets. These
7761 similarities can be calculated for pathways or gene sets, genes, or clusters
7762 and combined with other similarities. They can be used to improve networks,
7763 gene selection, testing relationships, and so on.")
7764 (license license:expat)))
7766 (define-public r-biocpkgtools
7768 (name "r-biocpkgtools")
7773 (uri (bioconductor-uri "BiocPkgTools" version))
7776 "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a"))))
7777 (properties `((upstream-name . "BiocPkgTools")))
7778 (build-system r-build-system)
7780 `(("r-biocfilecache" ,r-biocfilecache)
7781 ("r-biocmanager" ,r-biocmanager)
7782 ("r-biocviews" ,r-biocviews)
7783 ("r-dplyr" ,r-dplyr)
7786 ("r-graph" ,r-graph)
7787 ("r-htmltools" ,r-htmltools)
7788 ("r-htmlwidgets" ,r-htmlwidgets)
7790 ("r-igraph" ,r-igraph)
7791 ("r-jsonlite" ,r-jsonlite)
7792 ("r-magrittr" ,r-magrittr)
7793 ("r-rappdirs" ,r-rappdirs)
7795 ("r-readr" ,r-readr)
7797 ("r-rlang" ,r-rlang)
7798 ("r-rvest" ,r-rvest)
7799 ("r-stringr" ,r-stringr)
7800 ("r-tibble" ,r-tibble)
7801 ("r-tidyr" ,r-tidyr)
7802 ("r-tidyselect" ,r-tidyselect)
7803 ("r-xml2" ,r-xml2)))
7805 `(("r-knitr" ,r-knitr)))
7806 (home-page "https://github.com/seandavi/BiocPkgTools")
7807 (synopsis "Collection of tools for learning about Bioconductor packages")
7809 "Bioconductor has a rich ecosystem of metadata around packages, usage,
7810 and build status. This package is a simple collection of functions to access
7811 that metadata from R. The goal is to expose metadata for data mining and
7812 value-added functionality such as package searching, text mining, and
7813 analytics on packages.")
7814 (license license:expat)))
7816 (define-public r-biocset
7823 (uri (bioconductor-uri "BiocSet" version))
7826 "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9"))))
7827 (properties `((upstream-name . "BiocSet")))
7828 (build-system r-build-system)
7830 `(("r-annotationdbi" ,r-annotationdbi)
7831 ("r-dplyr" ,r-dplyr)
7832 ("r-keggrest" ,r-keggrest)
7834 ("r-rlang" ,r-rlang)
7835 ("r-rtracklayer" ,r-rtracklayer)
7836 ("r-tibble" ,r-tibble)))
7838 "https://bioconductor.org/packages/BiocSet")
7840 "Representing Different Biological Sets")
7842 "BiocSet displays different biological sets in a triple tibble format.
7843 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
7844 The user has the ability to activate one of these three tibbles to perform
7845 common functions from the @code{dplyr} package. Mapping functionality and
7846 accessing web references for elements/sets are also available in BiocSet.")
7847 (license license:artistic2.0)))
7849 (define-public r-biocworkflowtools
7851 (name "r-biocworkflowtools")
7856 (uri (bioconductor-uri "BiocWorkflowTools" version))
7859 "0z28s572wg9qxv52dmixxz1xf1z3fyp2j7kzk0k32fp628918wr6"))))
7861 `((upstream-name . "BiocWorkflowTools")))
7862 (build-system r-build-system)
7864 `(("r-biocstyle" ,r-biocstyle)
7865 ("r-bookdown" ,r-bookdown)
7866 ("r-git2r" ,r-git2r)
7868 ("r-knitr" ,r-knitr)
7869 ("r-rmarkdown" ,r-rmarkdown)
7870 ("r-rstudioapi" ,r-rstudioapi)
7871 ("r-stringr" ,r-stringr)
7872 ("r-usethis" ,r-usethis)))
7874 `(("r-knitr" ,r-knitr)))
7875 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
7876 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
7878 "This package provides functions to ease the transition between
7879 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
7880 (license license:expat)))
7882 (define-public r-biodist
7889 (uri (bioconductor-uri "bioDist" version))
7892 "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q"))))
7893 (properties `((upstream-name . "bioDist")))
7894 (build-system r-build-system)
7896 `(("r-biobase" ,r-biobase)
7897 ("r-kernsmooth" ,r-kernsmooth)))
7898 (home-page "https://bioconductor.org/packages/bioDist/")
7899 (synopsis "Different distance measures")
7901 "This package provides a collection of software tools for calculating
7902 distance measures.")
7903 (license license:artistic2.0)))