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-ensdb-hsapiens-v75
498 (name "r-ensdb-hsapiens-v75")
503 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
506 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
508 `((upstream-name . "EnsDb.Hsapiens.v75")))
509 (build-system r-build-system)
511 `(("r-ensembldb" ,r-ensembldb)))
512 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
513 (synopsis "Ensembl based annotation package")
515 "This package exposes an annotation database generated from Ensembl.")
516 (license license:artistic2.0)))
518 (define-public r-genelendatabase
520 (name "r-genelendatabase")
525 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
528 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
530 `((upstream-name . "geneLenDataBase")))
531 (build-system r-build-system)
533 `(("r-rtracklayer" ,r-rtracklayer)
534 ("r-genomicfeatures" ,r-genomicfeatures)))
535 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
536 (synopsis "Lengths of mRNA transcripts for a number of genomes")
538 "This package provides the lengths of mRNA transcripts for a number of
539 genomes and gene ID formats, largely based on the UCSC table browser.")
540 (license license:lgpl2.0+)))
542 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
544 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
548 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
549 version 'annotation))
552 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
554 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
555 (build-system r-build-system)
557 `(("r-genomicfeatures" ,r-genomicfeatures)))
559 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
560 (synopsis "Annotation package for human genome in TxDb format")
562 "This package provides an annotation database of Homo sapiens genome
563 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
564 track. The database is exposed as a @code{TxDb} object.")
565 (license license:artistic2.0)))
567 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
569 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
573 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
574 version 'annotation))
577 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
579 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
580 (build-system r-build-system)
582 `(("r-genomicfeatures" ,r-genomicfeatures)))
584 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
585 (synopsis "Annotation package for human genome in TxDb format")
587 "This package provides an annotation database of Homo sapiens genome
588 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
589 track. The database is exposed as a @code{TxDb} object.")
590 (license license:artistic2.0)))
592 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
594 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
598 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
599 version 'annotation))
602 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
604 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
605 (build-system r-build-system)
607 `(("r-genomicfeatures" ,r-genomicfeatures)
608 ("r-annotationdbi" ,r-annotationdbi)))
610 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
611 (synopsis "Annotation package for mouse genome in TxDb format")
613 "This package provides an annotation database of Mouse genome data. It
614 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
615 database is exposed as a @code{TxDb} object.")
616 (license license:artistic2.0)))
618 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
620 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
624 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
625 version 'annotation))
628 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
630 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
631 (build-system r-build-system)
633 `(("r-bsgenome" ,r-bsgenome)
634 ("r-genomicfeatures" ,r-genomicfeatures)
635 ("r-annotationdbi" ,r-annotationdbi)))
637 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
638 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
640 "This package loads a TxDb object, which is an R interface to
641 prefabricated databases contained in this package. This package provides
642 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
643 based on the knownGene track.")
644 (license license:artistic2.0)))
646 (define-public r-txdb-celegans-ucsc-ce6-ensgene
648 (name "r-txdb-celegans-ucsc-ce6-ensgene")
653 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
654 version 'annotation))
657 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
659 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
660 (build-system r-build-system)
662 `(("r-annotationdbi" ,r-annotationdbi)
663 ("r-genomicfeatures" ,r-genomicfeatures)))
664 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
665 (synopsis "Annotation package for C elegans TxDb objects")
667 "This package exposes a C elegans annotation database generated from UCSC
668 by exposing these as TxDb objects.")
669 (license license:artistic2.0)))
671 (define-public r-fdb-infiniummethylation-hg19
673 (name "r-fdb-infiniummethylation-hg19")
677 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
678 version 'annotation))
681 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
683 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
684 (build-system r-build-system)
686 `(("r-biostrings" ,r-biostrings)
687 ("r-genomicfeatures" ,r-genomicfeatures)
688 ("r-annotationdbi" ,r-annotationdbi)
689 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
690 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
691 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
692 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
694 "This is an annotation package for Illumina Infinium DNA methylation
695 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
697 (license license:artistic2.0)))
699 (define-public r-illuminahumanmethylationepicmanifest
701 (name "r-illuminahumanmethylationepicmanifest")
705 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
706 version 'annotation))
709 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
711 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
712 (build-system r-build-system)
714 `(("r-minfi" ,r-minfi)))
715 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
716 (synopsis "Manifest for Illumina's EPIC methylation arrays")
718 "This is a manifest package for Illumina's EPIC methylation arrays.")
719 (license license:artistic2.0)))
721 (define-public r-ideoviz
727 (uri (bioconductor-uri "IdeoViz" version))
730 "0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil"))))
731 (build-system r-build-system)
733 `(("r-biobase" ,r-biobase)
734 ("r-iranges" ,r-iranges)
735 ("r-genomicranges" ,r-genomicranges)
736 ("r-rcolorbrewer" ,r-rcolorbrewer)
737 ("r-rtracklayer" ,r-rtracklayer)
738 ("r-genomeinfodb" ,r-genomeinfodb)))
739 (home-page "https://bioconductor.org/packages/IdeoViz/")
740 (synopsis "Plots data along a chromosomal ideogram")
741 (description "This package provides functions to plot data associated with
742 arbitrary genomic intervals along chromosomal ideogram.")
743 (license license:gpl2)))
745 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
746 ;; from Bioconductor.
747 (define-public r-deconstructsigs
749 (name "r-deconstructsigs")
753 (uri (cran-uri "deconstructSigs" version))
756 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
758 `((upstream-name . "deconstructSigs")))
759 (build-system r-build-system)
761 `(("r-bsgenome" ,r-bsgenome)
762 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
763 ("r-genomeinfodb" ,r-genomeinfodb)
764 ("r-reshape2" ,r-reshape2)))
765 (home-page "https://github.com/raerose01/deconstructSigs")
766 (synopsis "Identifies signatures present in a tumor sample")
767 (description "This package takes sample information in the form of the
768 fraction of mutations in each of 96 trinucleotide contexts and identifies
769 the weighted combination of published signatures that, when summed, most
770 closely reconstructs the mutational profile.")
771 (license license:gpl2+)))
773 ;; This is a CRAN package, but it depends on Bioconductor packages.
781 (uri (cran-uri "NMF" version))
784 "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq"))))
785 (properties `((upstream-name . "NMF")))
786 (build-system r-build-system)
788 `(("r-cluster" ,r-cluster)
789 ("r-biobase" ,r-biobase)
790 ("r-biocmanager" ,r-biocmanager)
791 ("r-bigmemory" ,r-bigmemory) ; suggested
792 ("r-synchronicity" ,r-synchronicity) ; suggested
793 ("r-colorspace" ,r-colorspace)
794 ("r-digest" ,r-digest)
795 ("r-doparallel" ,r-doparallel)
796 ("r-foreach" ,r-foreach)
797 ("r-ggplot2" ,r-ggplot2)
798 ("r-gridbase" ,r-gridbase)
799 ("r-pkgmaker" ,r-pkgmaker)
800 ("r-rcolorbrewer" ,r-rcolorbrewer)
801 ("r-registry" ,r-registry)
802 ("r-reshape2" ,r-reshape2)
803 ("r-rngtools" ,r-rngtools)
804 ("r-stringr" ,r-stringr)))
805 (home-page "http://renozao.github.io/NMF")
806 (synopsis "Algorithms and framework for nonnegative matrix factorization")
808 "This package provides a framework to perform Non-negative Matrix
809 Factorization (NMF). The package implements a set of already published
810 algorithms and seeding methods, and provides a framework to test, develop and
811 plug new or custom algorithms. Most of the built-in algorithms have been
812 optimized in C++, and the main interface function provides an easy way of
813 performing parallel computations on multicore machines.")
814 (license license:gpl2+)))
816 (define-public r-do-db
822 (uri (bioconductor-uri "DO.db" version 'annotation))
825 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
827 `((upstream-name . "DO.db")))
828 (build-system r-build-system)
830 `(("r-annotationdbi" ,r-annotationdbi)))
831 (home-page "https://www.bioconductor.org/packages/DO.db/")
832 (synopsis "Annotation maps describing the entire Disease Ontology")
834 "This package provides a set of annotation maps describing the entire
836 (license license:artistic2.0)))
838 (define-public r-pasilla
845 "http://bioconductor.org/packages/release/data/experiment"
846 "/src/contrib/pasilla_" version ".tar.gz"))
849 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
850 (build-system r-build-system)
852 `(("r-biocstyle" ,r-biocstyle)
853 ("r-dexseq" ,r-dexseq)
855 ("r-rmarkdown" ,r-rmarkdown)))
856 (home-page "https://www.bioconductor.org/packages/pasilla/")
857 (synopsis "Data package with per-exon and per-gene read counts")
858 (description "This package provides per-exon and per-gene read counts
859 computed for selected genes from RNA-seq data that were presented in the
860 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
861 by Brooks et al., Genome Research 2011.")
862 (license license:lgpl2.1+)))
864 (define-public r-pfam-db
871 (uri (bioconductor-uri "PFAM.db" version 'annotation))
874 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
875 (properties `((upstream-name . "PFAM.db")))
876 (build-system r-build-system)
878 `(("r-annotationdbi" ,r-annotationdbi)))
879 (home-page "https://bioconductor.org/packages/PFAM.db")
880 (synopsis "Set of protein ID mappings for PFAM")
882 "This package provides a set of protein ID mappings for PFAM, assembled
883 using data from public repositories.")
884 (license license:artistic2.0)))
886 (define-public r-phastcons100way-ucsc-hg19
888 (name "r-phastcons100way-ucsc-hg19")
893 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
894 version 'annotation))
897 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
899 `((upstream-name . "phastCons100way.UCSC.hg19")))
900 (build-system r-build-system)
902 `(("r-bsgenome" ,r-bsgenome)
903 ("r-genomeinfodb" ,r-genomeinfodb)
904 ("r-genomicranges" ,r-genomicranges)
905 ("r-genomicscores" ,r-genomicscores)
906 ("r-iranges" ,r-iranges)
907 ("r-s4vectors" ,r-s4vectors)))
908 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
909 (synopsis "UCSC phastCons conservation scores for hg19")
911 "This package provides UCSC phastCons conservation scores for the human
912 genome (hg19) calculated from multiple alignments with other 99 vertebrate
914 (license license:artistic2.0)))
919 (define-public r-abadata
925 (uri (bioconductor-uri "ABAData" version 'experiment))
928 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
930 `((upstream-name . "ABAData")))
931 (build-system r-build-system)
933 `(("r-annotationdbi" ,r-annotationdbi)))
934 (home-page "https://www.bioconductor.org/packages/ABAData/")
935 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
937 "This package provides the data for the gene expression enrichment
938 analysis conducted in the package ABAEnrichment. The package includes three
939 datasets which are derived from the Allen Brain Atlas:
942 @item Gene expression data from Human Brain (adults) averaged across donors,
943 @item Gene expression data from the Developing Human Brain pooled into five
944 age categories and averaged across donors, and
945 @item a developmental effect score based on the Developing Human Brain
949 All datasets are restricted to protein coding genes.")
950 (license license:gpl2+)))
952 (define-public r-arrmdata
958 (uri (bioconductor-uri "ARRmData" version 'experiment))
961 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
963 `((upstream-name . "ARRmData")))
964 (build-system r-build-system)
965 (home-page "https://www.bioconductor.org/packages/ARRmData/")
966 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
968 "This package provides raw beta values from 36 samples across 3 groups
969 from Illumina 450k methylation arrays.")
970 (license license:artistic2.0)))
972 (define-public r-hsmmsinglecell
974 (name "r-hsmmsinglecell")
978 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
981 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
983 `((upstream-name . "HSMMSingleCell")))
984 (build-system r-build-system)
985 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
986 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
988 "Skeletal myoblasts undergo a well-characterized sequence of
989 morphological and transcriptional changes during differentiation. In this
990 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
991 under high mitogen conditions (GM) and then differentiated by switching to
992 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
993 hundred cells taken over a time-course of serum-induced differentiation.
994 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
995 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
996 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
997 which were then sequenced to a depth of ~4 million reads per library,
998 resulting in a complete gene expression profile for each cell.")
999 (license license:artistic2.0)))
1001 (define-public r-all
1007 (uri (bioconductor-uri "ALL" version 'experiment))
1010 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1011 (properties `((upstream-name . "ALL")))
1012 (build-system r-build-system)
1014 `(("r-biobase" ,r-biobase)))
1015 (home-page "https://bioconductor.org/packages/ALL")
1016 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1018 "The data consist of microarrays from 128 different individuals with
1019 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1020 are available. The data have been normalized (using rma) and it is the
1021 jointly normalized data that are available here. The data are presented in
1022 the form of an @code{exprSet} object.")
1023 (license license:artistic2.0)))
1025 (define-public r-affydata
1032 (uri (bioconductor-uri "affydata" version 'experiment))
1035 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1036 (properties `((upstream-name . "affydata")))
1037 (build-system r-build-system)
1039 `(("r-affy" ,r-affy)))
1040 (home-page "https://bioconductor.org/packages/affydata/")
1041 (synopsis "Affymetrix data for demonstration purposes")
1043 "This package provides example datasets that represent 'real world
1044 examples' of Affymetrix data, unlike the artificial examples included in the
1045 package @code{affy}.")
1046 (license license:gpl2+)))
1048 (define-public r-curatedtcgadata
1050 (name "r-curatedtcgadata")
1055 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1058 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1060 `((upstream-name . "curatedTCGAData")))
1061 (build-system r-build-system)
1063 `(("r-annotationhub" ,r-annotationhub)
1064 ("r-experimenthub" ,r-experimenthub)
1065 ("r-hdf5array" ,r-hdf5array)
1066 ("r-multiassayexperiment" ,r-multiassayexperiment)
1067 ("r-s4vectors" ,r-s4vectors)
1068 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1069 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1070 (synopsis "Curated data from The Cancer Genome Atlas")
1072 "This package provides publicly available data from The Cancer Genome
1073 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1074 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1075 number, mutation, microRNA, protein, and others) with clinical / pathological
1076 data. It also links assay barcodes with patient identifiers, enabling
1077 harmonized subsetting of rows (features) and columns (patients / samples)
1078 across the entire multi-'omics experiment.")
1079 (license license:artistic2.0)))
1084 (define-public r-biocversion
1086 (name "r-biocversion")
1091 (uri (bioconductor-uri "BiocVersion" version))
1094 "0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f"))))
1095 (properties `((upstream-name . "BiocVersion")))
1096 (build-system r-build-system)
1097 (home-page "https://bioconductor.org/packages/BiocVersion/")
1098 (synopsis "Set the appropriate version of Bioconductor packages")
1100 "This package provides repository information for the appropriate version
1102 (license license:artistic2.0)))
1104 (define-public r-biocgenerics
1106 (name "r-biocgenerics")
1110 (uri (bioconductor-uri "BiocGenerics" version))
1113 "1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn"))))
1115 `((upstream-name . "BiocGenerics")))
1116 (build-system r-build-system)
1117 (home-page "https://bioconductor.org/packages/BiocGenerics")
1118 (synopsis "S4 generic functions for Bioconductor")
1120 "This package provides S4 generic functions needed by many Bioconductor
1122 (license license:artistic2.0)))
1124 (define-public r-affycomp
1131 (uri (bioconductor-uri "affycomp" version))
1134 "0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js"))))
1135 (properties `((upstream-name . "affycomp")))
1136 (build-system r-build-system)
1137 (propagated-inputs `(("r-biobase" ,r-biobase)))
1138 (home-page "https://bioconductor.org/packages/affycomp/")
1139 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1141 "The package contains functions that can be used to compare expression
1142 measures for Affymetrix Oligonucleotide Arrays.")
1143 (license license:gpl2+)))
1145 (define-public r-affycompatible
1147 (name "r-affycompatible")
1152 (uri (bioconductor-uri "AffyCompatible" version))
1155 "10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks"))))
1157 `((upstream-name . "AffyCompatible")))
1158 (build-system r-build-system)
1160 `(("r-biostrings" ,r-biostrings)
1161 ("r-rcurl" ,r-rcurl)
1163 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1164 (synopsis "Work with Affymetrix GeneChip files")
1166 "This package provides an interface to Affymetrix chip annotation and
1167 sample attribute files. The package allows an easy way for users to download
1168 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1169 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1170 Command Console} (AGCC)-compatible sample annotation files.")
1171 (license license:artistic2.0)))
1173 (define-public r-affycontam
1175 (name "r-affycontam")
1180 (uri (bioconductor-uri "affyContam" version))
1183 "0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l"))))
1184 (properties `((upstream-name . "affyContam")))
1185 (build-system r-build-system)
1187 `(("r-affy" ,r-affy)
1188 ("r-affydata" ,r-affydata)
1189 ("r-biobase" ,r-biobase)))
1190 (home-page "https://bioconductor.org/packages/affyContam/")
1191 (synopsis "Structured corruption of Affymetrix CEL file data")
1193 "Microarray quality assessment is a major concern of microarray analysts.
1194 This package provides some simple approaches to in silico creation of quality
1195 problems in CEL-level data to help evaluate performance of quality metrics.")
1196 (license license:artistic2.0)))
1198 (define-public r-affycoretools
1200 (name "r-affycoretools")
1205 (uri (bioconductor-uri "affycoretools" version))
1208 "1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw"))))
1209 (properties `((upstream-name . "affycoretools")))
1210 (build-system r-build-system)
1212 `(("r-affy" ,r-affy)
1213 ("r-annotationdbi" ,r-annotationdbi)
1214 ("r-biobase" ,r-biobase)
1215 ("r-biocgenerics" ,r-biocgenerics)
1217 ("r-edger" ,r-edger)
1218 ("r-gcrma" ,r-gcrma)
1219 ("r-glimma" ,r-glimma)
1220 ("r-ggplot2" ,r-ggplot2)
1221 ("r-gostats" ,r-gostats)
1222 ("r-gplots" ,r-gplots)
1223 ("r-hwriter" ,r-hwriter)
1224 ("r-lattice" ,r-lattice)
1225 ("r-limma" ,r-limma)
1226 ("r-oligoclasses" ,r-oligoclasses)
1227 ("r-reportingtools" ,r-reportingtools)
1228 ("r-rsqlite" ,r-rsqlite)
1229 ("r-s4vectors" ,r-s4vectors)
1230 ("r-xtable" ,r-xtable)))
1231 (home-page "https://bioconductor.org/packages/affycoretools/")
1232 (synopsis "Functions for analyses with Affymetrix GeneChips")
1234 "This package provides various wrapper functions that have been written
1235 to streamline the more common analyses that a Biostatistician might see.")
1236 (license license:artistic2.0)))
1238 (define-public r-affxparser
1240 (name "r-affxparser")
1245 (uri (bioconductor-uri "affxparser" version))
1248 "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40"))))
1249 (properties `((upstream-name . "affxparser")))
1250 (build-system r-build-system)
1251 (home-page "https://github.com/HenrikBengtsson/affxparser")
1252 (synopsis "Affymetrix File Parsing SDK")
1254 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1255 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1256 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1257 are supported. Currently, there are methods for reading @dfn{chip definition
1258 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1259 either in full or in part. For example, probe signals from a few probesets
1260 can be extracted very quickly from a set of CEL files into a convenient list
1262 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1264 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1266 (define-public r-annotate
1273 (uri (bioconductor-uri "annotate" version))
1276 "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy"))))
1277 (build-system r-build-system)
1279 `(("r-annotationdbi" ,r-annotationdbi)
1280 ("r-biobase" ,r-biobase)
1281 ("r-biocgenerics" ,r-biocgenerics)
1283 ("r-rcurl" ,r-rcurl)
1285 ("r-xtable" ,r-xtable)))
1287 "https://bioconductor.org/packages/annotate")
1288 (synopsis "Annotation for microarrays")
1289 (description "This package provides R environments for the annotation of
1291 (license license:artistic2.0)))
1293 (define-public r-hpar
1300 (uri (bioconductor-uri "hpar" version))
1303 "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m"))))
1304 (build-system r-build-system)
1305 (home-page "https://bioconductor.org/packages/hpar/")
1306 (synopsis "Human Protein Atlas in R")
1307 (description "This package provides a simple interface to and data from
1308 the Human Protein Atlas project.")
1309 (license license:artistic2.0)))
1311 (define-public r-regioner
1318 (uri (bioconductor-uri "regioneR" version))
1321 "0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9"))))
1322 (properties `((upstream-name . "regioneR")))
1323 (build-system r-build-system)
1325 `(("r-biostrings" ,r-biostrings)
1326 ("r-bsgenome" ,r-bsgenome)
1327 ("r-genomeinfodb" ,r-genomeinfodb)
1328 ("r-genomicranges" ,r-genomicranges)
1329 ("r-iranges" ,r-iranges)
1330 ("r-memoise" ,r-memoise)
1331 ("r-rtracklayer" ,r-rtracklayer)
1332 ("r-s4vectors" ,r-s4vectors)))
1333 (home-page "https://bioconductor.org/packages/regioneR/")
1334 (synopsis "Association analysis of genomic regions")
1335 (description "This package offers a statistical framework based on
1336 customizable permutation tests to assess the association between genomic
1337 region sets and other genomic features.")
1338 (license license:artistic2.0)))
1340 (define-public r-reportingtools
1342 (name "r-reportingtools")
1347 (uri (bioconductor-uri "ReportingTools" version))
1350 "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w"))))
1352 `((upstream-name . "ReportingTools")))
1353 (build-system r-build-system)
1355 `(("r-annotate" ,r-annotate)
1356 ("r-annotationdbi" ,r-annotationdbi)
1357 ("r-biobase" ,r-biobase)
1358 ("r-biocgenerics" ,r-biocgenerics)
1359 ("r-category" ,r-category)
1360 ("r-deseq2" ,r-deseq2)
1361 ("r-edger" ,r-edger)
1362 ("r-ggbio" ,r-ggbio)
1363 ("r-ggplot2" ,r-ggplot2)
1364 ("r-gostats" ,r-gostats)
1365 ("r-gseabase" ,r-gseabase)
1366 ("r-hwriter" ,r-hwriter)
1367 ("r-iranges" ,r-iranges)
1368 ("r-knitr" ,r-knitr)
1369 ("r-lattice" ,r-lattice)
1370 ("r-limma" ,r-limma)
1371 ("r-pfam-db" ,r-pfam-db)
1372 ("r-r-utils" ,r-r-utils)
1374 (home-page "https://bioconductor.org/packages/ReportingTools/")
1375 (synopsis "Tools for making reports in various formats")
1377 "The ReportingTools package enables users to easily display reports of
1378 analysis results generated from sources such as microarray and sequencing
1379 data. The package allows users to create HTML pages that may be viewed on a
1380 web browser, or in other formats. Users can generate tables with sortable and
1381 filterable columns, make and display plots, and link table entries to other
1382 data sources such as NCBI or larger plots within the HTML page. Using the
1383 package, users can also produce a table of contents page to link various
1384 reports together for a particular project that can be viewed in a web
1386 (license license:artistic2.0)))
1388 (define-public r-geneplotter
1390 (name "r-geneplotter")
1395 (uri (bioconductor-uri "geneplotter" version))
1398 "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx"))))
1399 (build-system r-build-system)
1401 `(("r-annotate" ,r-annotate)
1402 ("r-annotationdbi" ,r-annotationdbi)
1403 ("r-biobase" ,r-biobase)
1404 ("r-biocgenerics" ,r-biocgenerics)
1405 ("r-lattice" ,r-lattice)
1406 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1407 (home-page "https://bioconductor.org/packages/geneplotter")
1408 (synopsis "Graphics functions for genomic data")
1410 "This package provides functions for plotting genomic data.")
1411 (license license:artistic2.0)))
1413 (define-public r-oligoclasses
1415 (name "r-oligoclasses")
1420 (uri (bioconductor-uri "oligoClasses" version))
1423 "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf"))))
1424 (properties `((upstream-name . "oligoClasses")))
1425 (build-system r-build-system)
1427 `(("r-affyio" ,r-affyio)
1428 ("r-biobase" ,r-biobase)
1429 ("r-biocgenerics" ,r-biocgenerics)
1430 ("r-biocmanager" ,r-biocmanager)
1431 ("r-biostrings" ,r-biostrings)
1434 ("r-foreach" ,r-foreach)
1435 ("r-genomicranges" ,r-genomicranges)
1436 ("r-iranges" ,r-iranges)
1437 ("r-rsqlite" ,r-rsqlite)
1438 ("r-s4vectors" ,r-s4vectors)
1439 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1440 (home-page "https://bioconductor.org/packages/oligoClasses/")
1441 (synopsis "Classes for high-throughput arrays")
1443 "This package contains class definitions, validity checks, and
1444 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1446 (license license:gpl2+)))
1448 (define-public r-oligo
1455 (uri (bioconductor-uri "oligo" version))
1458 "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3"))))
1459 (properties `((upstream-name . "oligo")))
1460 (build-system r-build-system)
1461 (inputs `(("zlib" ,zlib)))
1463 `(("r-affxparser" ,r-affxparser)
1464 ("r-affyio" ,r-affyio)
1465 ("r-biobase" ,r-biobase)
1466 ("r-biocgenerics" ,r-biocgenerics)
1467 ("r-biostrings" ,r-biostrings)
1470 ("r-oligoclasses" ,r-oligoclasses)
1471 ("r-preprocesscore" ,r-preprocesscore)
1472 ("r-rsqlite" ,r-rsqlite)
1473 ("r-zlibbioc" ,r-zlibbioc)))
1474 (home-page "https://bioconductor.org/packages/oligo/")
1475 (synopsis "Preprocessing tools for oligonucleotide arrays")
1477 "This package provides a package to analyze oligonucleotide
1478 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1479 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1480 (license license:lgpl2.0+)))
1482 (define-public r-qvalue
1489 (uri (bioconductor-uri "qvalue" version))
1492 "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j"))))
1493 (build-system r-build-system)
1495 `(("r-ggplot2" ,r-ggplot2)
1496 ("r-reshape2" ,r-reshape2)))
1497 (home-page "http://github.com/jdstorey/qvalue")
1498 (synopsis "Q-value estimation for false discovery rate control")
1500 "This package takes a list of p-values resulting from the simultaneous
1501 testing of many hypotheses and estimates their q-values and local @dfn{false
1502 discovery rate} (FDR) values. The q-value of a test measures the proportion
1503 of false positives incurred when that particular test is called significant.
1504 The local FDR measures the posterior probability the null hypothesis is true
1505 given the test's p-value. Various plots are automatically generated, allowing
1506 one to make sensible significance cut-offs. The software can be applied to
1507 problems in genomics, brain imaging, astrophysics, and data mining.")
1508 ;; Any version of the LGPL.
1509 (license license:lgpl3+)))
1511 (define-public r-diffbind
1518 (uri (bioconductor-uri "DiffBind" version))
1521 "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2"))))
1522 (properties `((upstream-name . "DiffBind")))
1523 (build-system r-build-system)
1527 `(("r-amap" ,r-amap)
1528 ("r-biocparallel" ,r-biocparallel)
1529 ("r-deseq2" ,r-deseq2)
1530 ("r-dplyr" ,r-dplyr)
1531 ("r-edger" ,r-edger)
1532 ("r-genomicalignments" ,r-genomicalignments)
1533 ("r-genomicranges" ,r-genomicranges)
1534 ("r-ggplot2" ,r-ggplot2)
1535 ("r-ggrepel" ,r-ggrepel)
1536 ("r-gplots" ,r-gplots)
1537 ("r-iranges" ,r-iranges)
1538 ("r-lattice" ,r-lattice)
1539 ("r-limma" ,r-limma)
1540 ("r-locfit" ,r-locfit)
1541 ("r-rcolorbrewer" , r-rcolorbrewer)
1543 ("r-rhtslib" ,r-rhtslib)
1544 ("r-rsamtools" ,r-rsamtools)
1545 ("r-s4vectors" ,r-s4vectors)
1546 ("r-summarizedexperiment" ,r-summarizedexperiment)
1547 ("r-systempiper" ,r-systempiper)))
1548 (home-page "https://bioconductor.org/packages/DiffBind")
1549 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1551 "This package computes differentially bound sites from multiple
1552 ChIP-seq experiments using affinity (quantitative) data. Also enables
1553 occupancy (overlap) analysis and plotting functions.")
1554 (license license:artistic2.0)))
1556 (define-public r-ripseeker
1558 (name "r-ripseeker")
1563 (uri (bioconductor-uri "RIPSeeker" version))
1566 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1567 (properties `((upstream-name . "RIPSeeker")))
1568 (build-system r-build-system)
1570 `(("r-s4vectors" ,r-s4vectors)
1571 ("r-iranges" ,r-iranges)
1572 ("r-genomicranges" ,r-genomicranges)
1573 ("r-summarizedexperiment" ,r-summarizedexperiment)
1574 ("r-rsamtools" ,r-rsamtools)
1575 ("r-genomicalignments" ,r-genomicalignments)
1576 ("r-rtracklayer" ,r-rtracklayer)))
1577 (home-page "https://bioconductor.org/packages/RIPSeeker")
1579 "Identifying protein-associated transcripts from RIP-seq experiments")
1581 "This package infers and discriminates RIP peaks from RIP-seq alignments
1582 using two-state HMM with negative binomial emission probability. While
1583 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1584 a suite of bioinformatics tools integrated within this self-contained software
1585 package comprehensively addressing issues ranging from post-alignments
1586 processing to visualization and annotation.")
1587 (license license:gpl2)))
1589 (define-public r-multtest
1596 (uri (bioconductor-uri "multtest" version))
1599 "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari"))))
1600 (build-system r-build-system)
1602 `(("r-survival" ,r-survival)
1603 ("r-biocgenerics" ,r-biocgenerics)
1604 ("r-biobase" ,r-biobase)
1605 ("r-mass" ,r-mass)))
1606 (home-page "https://bioconductor.org/packages/multtest")
1607 (synopsis "Resampling-based multiple hypothesis testing")
1609 "This package can do non-parametric bootstrap and permutation
1610 resampling-based multiple testing procedures (including empirical Bayes
1611 methods) for controlling the family-wise error rate (FWER), generalized
1612 family-wise error rate (gFWER), tail probability of the proportion of
1613 false positives (TPPFP), and false discovery rate (FDR). Several choices
1614 of bootstrap-based null distribution are implemented (centered, centered
1615 and scaled, quantile-transformed). Single-step and step-wise methods are
1616 available. Tests based on a variety of T- and F-statistics (including
1617 T-statistics based on regression parameters from linear and survival models
1618 as well as those based on correlation parameters) are included. When probing
1619 hypotheses with T-statistics, users may also select a potentially faster null
1620 distribution which is multivariate normal with mean zero and variance
1621 covariance matrix derived from the vector influence function. Results are
1622 reported in terms of adjusted P-values, confidence regions and test statistic
1623 cutoffs. The procedures are directly applicable to identifying differentially
1624 expressed genes in DNA microarray experiments.")
1625 (license license:lgpl3)))
1627 (define-public r-graph
1633 (uri (bioconductor-uri "graph" version))
1636 "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc"))))
1637 (build-system r-build-system)
1639 `(("r-biocgenerics" ,r-biocgenerics)))
1640 (home-page "https://bioconductor.org/packages/graph")
1641 (synopsis "Handle graph data structures in R")
1643 "This package implements some simple graph handling capabilities for R.")
1644 (license license:artistic2.0)))
1646 ;; This is a CRAN package, but it depends on a Bioconductor package.
1647 (define-public r-ggm
1654 (uri (cran-uri "ggm" version))
1657 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1658 (properties `((upstream-name . "ggm")))
1659 (build-system r-build-system)
1661 `(("r-graph" ,r-graph)
1662 ("r-igraph" ,r-igraph)))
1663 (home-page "https://cran.r-project.org/package=ggm")
1664 (synopsis "Functions for graphical Markov models")
1666 "This package provides functions and datasets for maximum likelihood
1667 fitting of some classes of graphical Markov models.")
1668 (license license:gpl2+)))
1670 (define-public r-codedepends
1672 (name "r-codedepends")
1677 (uri (cran-uri "CodeDepends" version))
1680 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1681 (properties `((upstream-name . "CodeDepends")))
1682 (build-system r-build-system)
1684 `(("r-codetools" ,r-codetools)
1685 ("r-graph" ,r-graph)
1687 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
1688 (synopsis "Analysis of R code for reproducible research and code comprehension")
1690 "This package provides tools for analyzing R expressions or blocks of
1691 code and determining the dependencies between them. It focuses on R scripts,
1692 but can be used on the bodies of functions. There are many facilities
1693 including the ability to summarize or get a high-level view of code,
1694 determining dependencies between variables, code improvement suggestions.")
1695 ;; Any version of the GPL
1696 (license (list license:gpl2+ license:gpl3+))))
1698 (define-public r-chippeakanno
1700 (name "r-chippeakanno")
1705 (uri (bioconductor-uri "ChIPpeakAnno" version))
1708 "0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc"))))
1709 (properties `((upstream-name . "ChIPpeakAnno")))
1710 (build-system r-build-system)
1712 `(("r-annotationdbi" ,r-annotationdbi)
1713 ("r-biobase" ,r-biobase)
1714 ("r-biocgenerics" ,r-biocgenerics)
1715 ("r-biocmanager" ,r-biocmanager)
1716 ("r-biomart" ,r-biomart)
1717 ("r-biostrings" ,r-biostrings)
1718 ("r-bsgenome" ,r-bsgenome)
1720 ("r-delayedarray" ,r-delayedarray)
1721 ("r-ensembldb" ,r-ensembldb)
1722 ("r-genomeinfodb" ,r-genomeinfodb)
1723 ("r-genomicalignments" ,r-genomicalignments)
1724 ("r-genomicfeatures" ,r-genomicfeatures)
1725 ("r-genomicranges" ,r-genomicranges)
1726 ("r-go-db" ,r-go-db)
1727 ("r-graph" ,r-graph)
1729 ("r-iranges" ,r-iranges)
1730 ("r-limma" ,r-limma)
1731 ("r-matrixstats" ,r-matrixstats)
1732 ("r-multtest" ,r-multtest)
1734 ("r-regioner" ,r-regioner)
1735 ("r-rsamtools" ,r-rsamtools)
1736 ("r-rtracklayer" ,r-rtracklayer)
1737 ("r-s4vectors" ,r-s4vectors)
1738 ("r-seqinr" ,r-seqinr)
1739 ("r-summarizedexperiment" ,r-summarizedexperiment)
1740 ("r-venndiagram" ,r-venndiagram)))
1741 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
1742 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1744 "The package includes functions to retrieve the sequences around the peak,
1745 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1746 custom features such as most conserved elements and other transcription factor
1747 binding sites supplied by users. Starting 2.0.5, new functions have been added
1748 for finding the peaks with bi-directional promoters with summary statistics
1749 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1750 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1751 enrichedGO (addGeneIDs).")
1752 (license license:gpl2+)))
1754 (define-public r-marray
1760 (uri (bioconductor-uri "marray" version))
1762 (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl"))))
1763 (build-system r-build-system)
1765 `(("r-limma" ,r-limma)))
1766 (home-page "https://bioconductor.org/packages/marray")
1767 (synopsis "Exploratory analysis for two-color spotted microarray data")
1768 (description "This package contains class definitions for two-color spotted
1769 microarray data. It also includes functions for data input, diagnostic plots,
1770 normalization and quality checking.")
1771 (license license:lgpl2.0+)))
1773 (define-public r-cghbase
1779 (uri (bioconductor-uri "CGHbase" version))
1781 (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x"))))
1782 (properties `((upstream-name . "CGHbase")))
1783 (build-system r-build-system)
1785 `(("r-biobase" ,r-biobase)
1786 ("r-marray" ,r-marray)))
1787 (home-page "https://bioconductor.org/packages/CGHbase")
1788 (synopsis "Base functions and classes for arrayCGH data analysis")
1789 (description "This package contains functions and classes that are needed by
1790 the @code{arrayCGH} packages.")
1791 (license license:gpl2+)))
1793 (define-public r-cghcall
1799 (uri (bioconductor-uri "CGHcall" version))
1801 (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s"))))
1802 (properties `((upstream-name . "CGHcall")))
1803 (build-system r-build-system)
1805 `(("r-biobase" ,r-biobase)
1806 ("r-cghbase" ,r-cghbase)
1807 ("r-impute" ,r-impute)
1808 ("r-dnacopy" ,r-dnacopy)
1809 ("r-snowfall" ,r-snowfall)))
1810 (home-page "https://bioconductor.org/packages/CGHcall")
1811 (synopsis "Base functions and classes for arrayCGH data analysis")
1812 (description "This package contains functions and classes that are needed by
1813 @code{arrayCGH} packages.")
1814 (license license:gpl2+)))
1816 (define-public r-qdnaseq
1822 (uri (bioconductor-uri "QDNAseq" version))
1824 (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq"))))
1825 (properties `((upstream-name . "QDNAseq")))
1826 (build-system r-build-system)
1828 `(("r-biobase" ,r-biobase)
1829 ("r-cghbase" ,r-cghbase)
1830 ("r-cghcall" ,r-cghcall)
1831 ("r-dnacopy" ,r-dnacopy)
1832 ("r-future" ,r-future)
1833 ("r-future-apply" ,r-future-apply)
1834 ("r-genomicranges" ,r-genomicranges)
1835 ("r-iranges" ,r-iranges)
1836 ("r-matrixstats" ,r-matrixstats)
1837 ("r-r-utils" ,r-r-utils)
1838 ("r-rsamtools" ,r-rsamtools)))
1839 (home-page "https://bioconductor.org/packages/QDNAseq")
1840 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1841 (description "The genome is divided into non-overlapping fixed-sized bins,
1842 number of sequence reads in each counted, adjusted with a simultaneous
1843 two-dimensional loess correction for sequence mappability and GC content, and
1844 filtered to remove spurious regions in the genome. Downstream steps of
1845 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1847 (license license:gpl2+)))
1849 (define-public r-bayseq
1856 (uri (bioconductor-uri "baySeq" version))
1859 "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk"))))
1860 (properties `((upstream-name . "baySeq")))
1861 (build-system r-build-system)
1863 `(("r-abind" ,r-abind)
1864 ("r-edger" ,r-edger)
1865 ("r-genomicranges" ,r-genomicranges)))
1866 (home-page "https://bioconductor.org/packages/baySeq/")
1867 (synopsis "Bayesian analysis of differential expression patterns in count data")
1869 "This package identifies differential expression in high-throughput count
1870 data, such as that derived from next-generation sequencing machines,
1871 calculating estimated posterior likelihoods of differential expression (or
1872 more complex hypotheses) via empirical Bayesian methods.")
1873 (license license:gpl3)))
1875 (define-public r-chipcomp
1882 (uri (bioconductor-uri "ChIPComp" version))
1885 "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg"))))
1886 (properties `((upstream-name . "ChIPComp")))
1887 (build-system r-build-system)
1889 `(("r-biocgenerics" ,r-biocgenerics)
1890 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1891 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1892 ("r-genomeinfodb" ,r-genomeinfodb)
1893 ("r-genomicranges" ,r-genomicranges)
1894 ("r-iranges" ,r-iranges)
1895 ("r-limma" ,r-limma)
1896 ("r-rsamtools" ,r-rsamtools)
1897 ("r-rtracklayer" ,r-rtracklayer)
1898 ("r-s4vectors" ,r-s4vectors)))
1899 (home-page "https://bioconductor.org/packages/ChIPComp")
1900 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1902 "ChIPComp implements a statistical method for quantitative comparison of
1903 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1904 sites across multiple conditions considering matching control in ChIP-seq
1906 ;; Any version of the GPL.
1907 (license license:gpl3+)))
1909 (define-public r-riboprofiling
1911 (name "r-riboprofiling")
1916 (uri (bioconductor-uri "RiboProfiling" version))
1919 "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx"))))
1920 (properties `((upstream-name . "RiboProfiling")))
1921 (build-system r-build-system)
1923 `(("r-biocgenerics" ,r-biocgenerics)
1924 ("r-biostrings" ,r-biostrings)
1925 ("r-data-table" ,r-data-table)
1926 ("r-genomeinfodb" ,r-genomeinfodb)
1927 ("r-genomicalignments" ,r-genomicalignments)
1928 ("r-genomicfeatures" ,r-genomicfeatures)
1929 ("r-genomicranges" ,r-genomicranges)
1930 ("r-ggbio" ,r-ggbio)
1931 ("r-ggplot2" ,r-ggplot2)
1932 ("r-iranges" ,r-iranges)
1934 ("r-reshape2" ,r-reshape2)
1935 ("r-rsamtools" ,r-rsamtools)
1936 ("r-rtracklayer" ,r-rtracklayer)
1937 ("r-s4vectors" ,r-s4vectors)
1938 ("r-sqldf" ,r-sqldf)))
1939 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1940 (synopsis "Ribosome profiling data analysis")
1941 (description "Starting with a BAM file, this package provides the
1942 necessary functions for quality assessment, read start position recalibration,
1943 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1944 of count data: pairs, log fold-change, codon frequency and coverage
1945 assessment, principal component analysis on codon coverage.")
1946 (license license:gpl3)))
1948 (define-public r-riboseqr
1955 (uri (bioconductor-uri "riboSeqR" version))
1958 "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm"))))
1959 (properties `((upstream-name . "riboSeqR")))
1960 (build-system r-build-system)
1962 `(("r-abind" ,r-abind)
1963 ("r-bayseq" ,r-bayseq)
1964 ("r-genomeinfodb" ,r-genomeinfodb)
1965 ("r-genomicranges" ,r-genomicranges)
1966 ("r-iranges" ,r-iranges)
1967 ("r-rsamtools" ,r-rsamtools)
1968 ("r-seqlogo" ,r-seqlogo)))
1969 (home-page "https://bioconductor.org/packages/riboSeqR/")
1970 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1972 "This package provides plotting functions, frameshift detection and
1973 parsing of genetic sequencing data from ribosome profiling experiments.")
1974 (license license:gpl3)))
1976 (define-public r-interactionset
1978 (name "r-interactionset")
1983 (uri (bioconductor-uri "InteractionSet" version))
1986 "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh"))))
1988 `((upstream-name . "InteractionSet")))
1989 (build-system r-build-system)
1991 `(("r-biocgenerics" ,r-biocgenerics)
1992 ("r-genomeinfodb" ,r-genomeinfodb)
1993 ("r-genomicranges" ,r-genomicranges)
1994 ("r-iranges" ,r-iranges)
1995 ("r-matrix" ,r-matrix)
1997 ("r-s4vectors" ,r-s4vectors)
1998 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1999 (home-page "https://bioconductor.org/packages/InteractionSet")
2000 (synopsis "Base classes for storing genomic interaction data")
2002 "This package provides the @code{GInteractions},
2003 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2004 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2006 (license license:gpl3)))
2008 (define-public r-genomicinteractions
2010 (name "r-genomicinteractions")
2015 (uri (bioconductor-uri "GenomicInteractions" version))
2018 "01ps97cs29qvzy5piq2l2k0yyr56rmg5cycfiqhbbvqpjrfvy60g"))))
2020 `((upstream-name . "GenomicInteractions")))
2021 (build-system r-build-system)
2023 `(("r-biobase" ,r-biobase)
2024 ("r-biocgenerics" ,r-biocgenerics)
2025 ("r-data-table" ,r-data-table)
2026 ("r-dplyr" ,r-dplyr)
2027 ("r-genomeinfodb" ,r-genomeinfodb)
2028 ("r-genomicranges" ,r-genomicranges)
2029 ("r-ggplot2" ,r-ggplot2)
2030 ("r-gridextra" ,r-gridextra)
2032 ("r-igraph" ,r-igraph)
2033 ("r-interactionset" ,r-interactionset)
2034 ("r-iranges" ,r-iranges)
2035 ("r-rsamtools" ,r-rsamtools)
2036 ("r-rtracklayer" ,r-rtracklayer)
2037 ("r-s4vectors" ,r-s4vectors)
2038 ("r-stringr" ,r-stringr)))
2040 `(("r-knitr" ,r-knitr)))
2041 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2042 (synopsis "R package for handling genomic interaction data")
2044 "This R package provides tools for handling genomic interaction data,
2045 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2046 information and producing various plots and statistics.")
2047 (license license:gpl3)))
2049 (define-public r-ctc
2056 (uri (bioconductor-uri "ctc" version))
2059 "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d"))))
2060 (build-system r-build-system)
2061 (propagated-inputs `(("r-amap" ,r-amap)))
2062 (home-page "https://bioconductor.org/packages/ctc/")
2063 (synopsis "Cluster and tree conversion")
2065 "This package provides tools for exporting and importing classification
2066 trees and clusters to other programs.")
2067 (license license:gpl2)))
2069 (define-public r-goseq
2076 (uri (bioconductor-uri "goseq" version))
2079 "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv"))))
2080 (build-system r-build-system)
2082 `(("r-annotationdbi" ,r-annotationdbi)
2083 ("r-biasedurn" ,r-biasedurn)
2084 ("r-biocgenerics" ,r-biocgenerics)
2085 ("r-genelendatabase" ,r-genelendatabase)
2086 ("r-go-db" ,r-go-db)
2087 ("r-mgcv" ,r-mgcv)))
2088 (home-page "https://bioconductor.org/packages/goseq/")
2089 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2091 "This package provides tools to detect Gene Ontology and/or other user
2092 defined categories which are over/under represented in RNA-seq data.")
2093 (license license:lgpl2.0+)))
2095 (define-public r-glimma
2102 (uri (bioconductor-uri "Glimma" version))
2105 "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r"))))
2106 (properties `((upstream-name . "Glimma")))
2107 (build-system r-build-system)
2109 `(("r-edger" ,r-edger)
2110 ("r-jsonlite" ,r-jsonlite)
2111 ("r-s4vectors" ,r-s4vectors)))
2112 (home-page "https://github.com/Shians/Glimma")
2113 (synopsis "Interactive HTML graphics")
2115 "This package generates interactive visualisations for analysis of
2116 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2117 HTML page. The interactions are built on top of the popular static
2118 representations of analysis results in order to provide additional
2120 (license license:lgpl3)))
2122 (define-public r-rots
2129 (uri (bioconductor-uri "ROTS" version))
2132 "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm"))))
2133 (properties `((upstream-name . "ROTS")))
2134 (build-system r-build-system)
2136 `(("r-biobase" ,r-biobase)
2137 ("r-rcpp" ,r-rcpp)))
2138 (home-page "https://bioconductor.org/packages/ROTS/")
2139 (synopsis "Reproducibility-Optimized Test Statistic")
2141 "This package provides tools for calculating the
2142 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2144 (license license:gpl2+)))
2146 (define-public r-plgem
2153 (uri (bioconductor-uri "plgem" version))
2156 "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v"))))
2157 (build-system r-build-system)
2159 `(("r-biobase" ,r-biobase)
2160 ("r-mass" ,r-mass)))
2161 (home-page "http://www.genopolis.it")
2162 (synopsis "Detect differential expression in microarray and proteomics datasets")
2164 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2165 model the variance-versus-mean dependence that exists in a variety of
2166 genome-wide datasets, including microarray and proteomics data. The use of
2167 PLGEM has been shown to improve the detection of differentially expressed
2168 genes or proteins in these datasets.")
2169 (license license:gpl2)))
2171 (define-public r-inspect
2178 (uri (bioconductor-uri "INSPEcT" version))
2181 "0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp"))))
2182 (properties `((upstream-name . "INSPEcT")))
2183 (build-system r-build-system)
2185 `(("r-biobase" ,r-biobase)
2186 ("r-biocgenerics" ,r-biocgenerics)
2187 ("r-biocparallel" ,r-biocparallel)
2188 ("r-deseq2" ,r-deseq2)
2189 ("r-desolve" ,r-desolve)
2190 ("r-gdata" ,r-gdata)
2191 ("r-genomeinfodb" ,r-genomeinfodb)
2192 ("r-genomicalignments" ,r-genomicalignments)
2193 ("r-genomicfeatures" ,r-genomicfeatures)
2194 ("r-genomicranges" ,r-genomicranges)
2195 ("r-iranges" ,r-iranges)
2196 ("r-kernsmooth" ,r-kernsmooth)
2197 ("r-plgem" ,r-plgem)
2199 ("r-rootsolve" ,r-rootsolve)
2200 ("r-rsamtools" ,r-rsamtools)
2201 ("r-s4vectors" ,r-s4vectors)
2202 ("r-shiny" ,r-shiny)
2203 ("r-summarizedexperiment" ,r-summarizedexperiment)
2204 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2205 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2206 (home-page "https://bioconductor.org/packages/INSPEcT")
2207 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2209 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2210 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2211 order to evaluate synthesis, processing and degradation rates and assess via
2212 modeling the rates that determines changes in mature mRNA levels.")
2213 (license license:gpl2)))
2215 (define-public r-dnabarcodes
2217 (name "r-dnabarcodes")
2222 (uri (bioconductor-uri "DNABarcodes" version))
2225 "0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd"))))
2226 (properties `((upstream-name . "DNABarcodes")))
2227 (build-system r-build-system)
2230 ("r-matrix" ,r-matrix)
2231 ("r-rcpp" ,r-rcpp)))
2232 (home-page "https://bioconductor.org/packages/DNABarcodes")
2233 (synopsis "Create and analyze DNA barcodes")
2235 "This package offers tools to create DNA barcode sets capable of
2236 correcting insertion, deletion, and substitution errors. Existing barcodes
2237 can be analyzed regarding their minimal, maximal and average distances between
2238 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2239 demultiplexed, i.e. assigned to their original reference barcode.")
2240 (license license:gpl2)))
2242 (define-public r-ruvseq
2249 (uri (bioconductor-uri "RUVSeq" version))
2252 "1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj"))))
2253 (properties `((upstream-name . "RUVSeq")))
2254 (build-system r-build-system)
2256 `(("r-biobase" ,r-biobase)
2257 ("r-edaseq" ,r-edaseq)
2258 ("r-edger" ,r-edger)
2259 ("r-mass" ,r-mass)))
2260 (home-page "https://github.com/drisso/RUVSeq")
2261 (synopsis "Remove unwanted variation from RNA-Seq data")
2263 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2264 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2266 (license license:artistic2.0)))
2268 (define-public r-biocneighbors
2270 (name "r-biocneighbors")
2275 (uri (bioconductor-uri "BiocNeighbors" version))
2278 "1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6"))))
2279 (properties `((upstream-name . "BiocNeighbors")))
2280 (build-system r-build-system)
2282 `(("r-biocparallel" ,r-biocparallel)
2283 ("r-matrix" ,r-matrix)
2285 ("r-rcppannoy" ,r-rcppannoy)
2286 ("r-rcpphnsw" ,r-rcpphnsw)
2287 ("r-s4vectors" ,r-s4vectors)))
2288 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2289 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2291 "This package implements exact and approximate methods for nearest
2292 neighbor detection, in a framework that allows them to be easily switched
2293 within Bioconductor packages or workflows. The exact algorithm is implemented
2294 using pre-clustering with the k-means algorithm. Functions are also provided
2295 to search for all neighbors within a given distance. Parallelization is
2296 achieved for all methods using the BiocParallel framework.")
2297 (license license:gpl3)))
2299 (define-public r-biocsingular
2301 (name "r-biocsingular")
2306 (uri (bioconductor-uri "BiocSingular" version))
2309 "1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407"))))
2310 (properties `((upstream-name . "BiocSingular")))
2311 (build-system r-build-system)
2313 `(("r-beachmat" ,r-beachmat)
2314 ("r-biocgenerics" ,r-biocgenerics)
2315 ("r-biocparallel" ,r-biocparallel)
2316 ("r-delayedarray" ,r-delayedarray)
2317 ("r-irlba" ,r-irlba)
2318 ("r-matrix" ,r-matrix)
2321 ("r-s4vectors" ,r-s4vectors)))
2322 (home-page "https://github.com/LTLA/BiocSingular")
2323 (synopsis "Singular value decomposition for Bioconductor packages")
2325 "This package implements exact and approximate methods for singular value
2326 decomposition and principal components analysis, in a framework that allows
2327 them to be easily switched within Bioconductor packages or workflows. Where
2328 possible, parallelization is achieved using the BiocParallel framework.")
2329 (license license:gpl3)))
2331 (define-public r-destiny
2338 (uri (bioconductor-uri "destiny" version))
2341 "1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi"))))
2342 (build-system r-build-system)
2344 `(("r-biobase" ,r-biobase)
2345 ("r-biocgenerics" ,r-biocgenerics)
2346 ("r-ggplot-multistats" ,r-ggplot-multistats)
2347 ("r-ggplot2" ,r-ggplot2)
2348 ("r-ggthemes" ,r-ggthemes)
2349 ("r-irlba" ,r-irlba)
2350 ("r-knn-covertree" ,r-knn-covertree)
2351 ("r-matrix" ,r-matrix)
2352 ("r-pcamethods" ,r-pcamethods)
2353 ("r-proxy" ,r-proxy)
2355 ("r-rcppeigen" ,r-rcppeigen)
2356 ("r-rcpphnsw" ,r-rcpphnsw)
2357 ("r-rspectra" ,r-rspectra)
2358 ("r-scales" ,r-scales)
2359 ("r-scatterplot3d" ,r-scatterplot3d)
2360 ("r-singlecellexperiment" ,r-singlecellexperiment)
2361 ("r-smoother" ,r-smoother)
2362 ("r-summarizedexperiment" ,r-summarizedexperiment)
2363 ("r-tidyr" ,r-tidyr)
2364 ("r-tidyselect" ,r-tidyselect)
2367 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2368 (home-page "https://bioconductor.org/packages/destiny/")
2369 (synopsis "Create and plot diffusion maps")
2370 (description "This package provides tools to create and plot diffusion
2372 ;; Any version of the GPL
2373 (license license:gpl3+)))
2375 (define-public r-savr
2382 (uri (bioconductor-uri "savR" version))
2385 "1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf"))))
2386 (properties `((upstream-name . "savR")))
2387 (build-system r-build-system)
2389 `(("r-ggplot2" ,r-ggplot2)
2390 ("r-gridextra" ,r-gridextra)
2391 ("r-reshape2" ,r-reshape2)
2392 ("r-scales" ,r-scales)
2394 (home-page "https://github.com/bcalder/savR")
2395 (synopsis "Parse and analyze Illumina SAV files")
2397 "This package provides tools to parse Illumina Sequence Analysis
2398 Viewer (SAV) files, access data, and generate QC plots.")
2399 (license license:agpl3+)))
2401 (define-public r-chipexoqual
2403 (name "r-chipexoqual")
2408 (uri (bioconductor-uri "ChIPexoQual" version))
2411 "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0"))))
2412 (properties `((upstream-name . "ChIPexoQual")))
2413 (build-system r-build-system)
2415 `(("r-biocparallel" ,r-biocparallel)
2416 ("r-biovizbase" ,r-biovizbase)
2417 ("r-broom" ,r-broom)
2418 ("r-data-table" ,r-data-table)
2419 ("r-dplyr" ,r-dplyr)
2420 ("r-genomeinfodb" ,r-genomeinfodb)
2421 ("r-genomicalignments" ,r-genomicalignments)
2422 ("r-genomicranges" ,r-genomicranges)
2423 ("r-ggplot2" ,r-ggplot2)
2424 ("r-hexbin" ,r-hexbin)
2425 ("r-iranges" ,r-iranges)
2426 ("r-rcolorbrewer" ,r-rcolorbrewer)
2427 ("r-rmarkdown" ,r-rmarkdown)
2428 ("r-rsamtools" ,r-rsamtools)
2429 ("r-s4vectors" ,r-s4vectors)
2430 ("r-scales" ,r-scales)
2431 ("r-viridis" ,r-viridis)))
2432 (home-page "https://github.com/keleslab/ChIPexoQual")
2433 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2435 "This package provides a quality control pipeline for ChIP-exo/nexus
2437 (license license:gpl2+)))
2439 (define-public r-copynumber
2441 (name "r-copynumber")
2445 (uri (bioconductor-uri "copynumber" version))
2448 "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj"))))
2449 (build-system r-build-system)
2451 `(("r-s4vectors" ,r-s4vectors)
2452 ("r-iranges" ,r-iranges)
2453 ("r-genomicranges" ,r-genomicranges)
2454 ("r-biocgenerics" ,r-biocgenerics)))
2455 (home-page "https://bioconductor.org/packages/copynumber")
2456 (synopsis "Segmentation of single- and multi-track copy number data")
2458 "This package segments single- and multi-track copy number data by a
2459 penalized least squares regression method.")
2460 (license license:artistic2.0)))
2462 (define-public r-dnacopy
2469 (uri (bioconductor-uri "DNAcopy" version))
2472 "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw"))))
2473 (properties `((upstream-name . "DNAcopy")))
2474 (build-system r-build-system)
2475 (native-inputs `(("gfortran" ,gfortran)))
2476 (home-page "https://bioconductor.org/packages/DNAcopy")
2477 (synopsis "DNA copy number data analysis")
2479 "This package implements the @dfn{circular binary segmentation} (CBS)
2480 algorithm to segment DNA copy number data and identify genomic regions with
2481 abnormal copy number.")
2482 (license license:gpl2+)))
2484 ;; This is a CRAN package, but it uncharacteristically depends on a
2485 ;; Bioconductor package.
2486 (define-public r-htscluster
2488 (name "r-htscluster")
2493 (uri (cran-uri "HTSCluster" version))
2496 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2497 (properties `((upstream-name . "HTSCluster")))
2498 (build-system r-build-system)
2500 `(("r-capushe" ,r-capushe)
2501 ("r-edger" ,r-edger)
2502 ("r-plotrix" ,r-plotrix)))
2503 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2504 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2506 "This package provides a Poisson mixture model is implemented to cluster
2507 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2508 estimation is performed using either the EM or CEM algorithm, and the slope
2509 heuristics are used for model selection (i.e., to choose the number of
2511 (license license:gpl3+)))
2513 (define-public r-deds
2520 (uri (bioconductor-uri "DEDS" version))
2523 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2524 (properties `((upstream-name . "DEDS")))
2525 (build-system r-build-system)
2526 (home-page "https://bioconductor.org/packages/DEDS/")
2527 (synopsis "Differential expression via distance summary for microarray data")
2529 "This library contains functions that calculate various statistics of
2530 differential expression for microarray data, including t statistics, fold
2531 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2532 also implements a new methodology called DEDS (Differential Expression via
2533 Distance Summary), which selects differentially expressed genes by integrating
2534 and summarizing a set of statistics using a weighted distance approach.")
2535 ;; Any version of the LGPL.
2536 (license license:lgpl3+)))
2538 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2540 (define-public r-nbpseq
2547 (uri (cran-uri "NBPSeq" version))
2550 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2551 (properties `((upstream-name . "NBPSeq")))
2552 (build-system r-build-system)
2554 `(("r-qvalue" ,r-qvalue)))
2555 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2556 (synopsis "Negative binomial models for RNA-Seq data")
2558 "This package provides negative binomial models for two-group comparisons
2559 and regression inferences from RNA-sequencing data.")
2560 (license license:gpl2)))
2562 (define-public r-ebseq
2569 (uri (bioconductor-uri "EBSeq" version))
2572 "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6"))))
2573 (properties `((upstream-name . "EBSeq")))
2574 (build-system r-build-system)
2576 `(("r-blockmodeling" ,r-blockmodeling)
2577 ("r-gplots" ,r-gplots)
2578 ("r-testthat" ,r-testthat)))
2579 (home-page "https://bioconductor.org/packages/EBSeq")
2580 (synopsis "Differential expression analysis of RNA-seq data")
2582 "This package provides tools for differential expression analysis at both
2583 gene and isoform level using RNA-seq data")
2584 (license license:artistic2.0)))
2586 (define-public r-lpsymphony
2588 (name "r-lpsymphony")
2593 (uri (bioconductor-uri "lpsymphony" version))
2596 "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv"))))
2597 (build-system r-build-system)
2599 `(("gfortran" ,gfortran)
2602 `(("pkg-config" ,pkg-config)))
2603 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2604 (synopsis "Symphony integer linear programming solver in R")
2606 "This package was derived from Rsymphony. The package provides an R
2607 interface to SYMPHONY, a linear programming solver written in C++. The main
2608 difference between this package and Rsymphony is that it includes the solver
2609 source code, while Rsymphony expects to find header and library files on the
2610 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2611 to install interface to SYMPHONY.")
2612 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2613 ;; lpsimphony is released under the same terms.
2614 (license license:epl1.0)))
2616 (define-public r-ihw
2623 (uri (bioconductor-uri "IHW" version))
2626 "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x"))))
2627 (properties `((upstream-name . "IHW")))
2628 (build-system r-build-system)
2630 `(("r-biocgenerics" ,r-biocgenerics)
2631 ("r-fdrtool" ,r-fdrtool)
2632 ("r-lpsymphony" ,r-lpsymphony)
2633 ("r-slam" ,r-slam)))
2634 (home-page "https://bioconductor.org/packages/IHW")
2635 (synopsis "Independent hypothesis weighting")
2637 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2638 procedure that increases power compared to the method of Benjamini and
2639 Hochberg by assigning data-driven weights to each hypothesis. The input to
2640 IHW is a two-column table of p-values and covariates. The covariate can be
2641 any continuous-valued or categorical variable that is thought to be
2642 informative on the statistical properties of each hypothesis test, while it is
2643 independent of the p-value under the null hypothesis.")
2644 (license license:artistic2.0)))
2646 (define-public r-icobra
2653 (uri (bioconductor-uri "iCOBRA" version))
2656 "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz"))))
2657 (properties `((upstream-name . "iCOBRA")))
2658 (build-system r-build-system)
2660 `(("r-dplyr" ,r-dplyr)
2662 ("r-ggplot2" ,r-ggplot2)
2663 ("r-limma" ,r-limma)
2664 ("r-reshape2" ,r-reshape2)
2666 ("r-scales" ,r-scales)
2667 ("r-shiny" ,r-shiny)
2668 ("r-shinybs" ,r-shinybs)
2669 ("r-shinydashboard" ,r-shinydashboard)
2670 ("r-upsetr" ,r-upsetr)))
2671 (home-page "https://bioconductor.org/packages/iCOBRA")
2672 (synopsis "Comparison and visualization of ranking and assignment methods")
2674 "This package provides functions for calculation and visualization of
2675 performance metrics for evaluation of ranking and binary
2676 classification (assignment) methods. It also contains a Shiny application for
2677 interactive exploration of results.")
2678 (license license:gpl2+)))
2680 (define-public r-mast
2687 (uri (bioconductor-uri "MAST" version))
2690 "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga"))))
2691 (properties `((upstream-name . "MAST")))
2692 (build-system r-build-system)
2694 `(("r-abind" ,r-abind)
2695 ("r-biobase" ,r-biobase)
2696 ("r-biocgenerics" ,r-biocgenerics)
2697 ("r-data-table" ,r-data-table)
2698 ("r-ggplot2" ,r-ggplot2)
2700 ("r-progress" ,r-progress)
2701 ("r-reshape2" ,r-reshape2)
2702 ("r-s4vectors" ,r-s4vectors)
2703 ("r-singlecellexperiment" ,r-singlecellexperiment)
2704 ("r-stringr" ,r-stringr)
2705 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2707 `(("r-knitr" ,r-knitr)))
2708 (home-page "https://github.com/RGLab/MAST/")
2709 (synopsis "Model-based analysis of single cell transcriptomics")
2711 "This package provides methods and models for handling zero-inflated
2712 single cell assay data.")
2713 (license license:gpl2+)))
2715 (define-public r-monocle
2722 (uri (bioconductor-uri "monocle" version))
2725 "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2"))))
2726 (build-system r-build-system)
2728 `(("r-biobase" ,r-biobase)
2729 ("r-biocgenerics" ,r-biocgenerics)
2730 ("r-biocviews" ,r-biocviews)
2731 ("r-cluster" ,r-cluster)
2732 ("r-combinat" ,r-combinat)
2733 ("r-ddrtree" ,r-ddrtree)
2734 ("r-densityclust" ,r-densityclust)
2735 ("r-dplyr" ,r-dplyr)
2736 ("r-fastica" ,r-fastica)
2737 ("r-ggplot2" ,r-ggplot2)
2738 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2739 ("r-igraph" ,r-igraph)
2740 ("r-irlba" ,r-irlba)
2741 ("r-limma" ,r-limma)
2743 ("r-matrix" ,r-matrix)
2744 ("r-matrixstats" ,r-matrixstats)
2745 ("r-pheatmap" ,r-pheatmap)
2747 ("r-proxy" ,r-proxy)
2748 ("r-qlcmatrix" ,r-qlcmatrix)
2751 ("r-reshape2" ,r-reshape2)
2752 ("r-rtsne" ,r-rtsne)
2754 ("r-stringr" ,r-stringr)
2755 ("r-tibble" ,r-tibble)
2757 ("r-viridis" ,r-viridis)))
2758 (home-page "https://bioconductor.org/packages/monocle")
2759 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2761 "Monocle performs differential expression and time-series analysis for
2762 single-cell expression experiments. It orders individual cells according to
2763 progress through a biological process, without knowing ahead of time which
2764 genes define progress through that process. Monocle also performs
2765 differential expression analysis, clustering, visualization, and other useful
2766 tasks on single cell expression data. It is designed to work with RNA-Seq and
2767 qPCR data, but could be used with other types as well.")
2768 (license license:artistic2.0)))
2770 (define-public r-monocle3
2778 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2780 (file-name (git-file-name name version))
2783 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2784 (build-system r-build-system)
2786 `(("r-biobase" ,r-biobase)
2787 ("r-biocgenerics" ,r-biocgenerics)
2788 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2789 ("r-dplyr" ,r-dplyr)
2790 ("r-ggplot2" ,r-ggplot2)
2791 ("r-ggrepel" ,r-ggrepel)
2793 ("r-htmlwidgets" ,r-htmlwidgets)
2794 ("r-igraph" ,r-igraph)
2795 ("r-irlba" ,r-irlba)
2796 ("r-limma" ,r-limma)
2797 ("r-lmtest" ,r-lmtest)
2799 ("r-matrix" ,r-matrix)
2800 ("r-matrix-utils" ,r-matrix-utils)
2801 ("r-pbapply" ,r-pbapply)
2802 ("r-pbmcapply" ,r-pbmcapply)
2803 ("r-pheatmap" ,r-pheatmap)
2804 ("r-plotly" ,r-plotly)
2806 ("r-proxy" ,r-proxy)
2808 ("r-purrr" ,r-purrr)
2811 ("r-rcppparallel" ,r-rcppparallel)
2812 ("r-reshape2" ,r-reshape2)
2813 ("r-reticulate" ,r-reticulate)
2814 ("r-rhpcblasctl" ,r-rhpcblasctl)
2815 ("r-rtsne" ,r-rtsne)
2816 ("r-shiny" ,r-shiny)
2818 ("r-spdep" ,r-spdep)
2819 ("r-speedglm" ,r-speedglm)
2820 ("r-stringr" ,r-stringr)
2821 ("r-singlecellexperiment" ,r-singlecellexperiment)
2822 ("r-tibble" ,r-tibble)
2823 ("r-tidyr" ,r-tidyr)
2825 ("r-viridis" ,r-viridis)))
2826 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2827 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2829 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2830 (license license:expat)))
2832 (define-public r-noiseq
2839 (uri (bioconductor-uri "NOISeq" version))
2842 "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4"))))
2843 (properties `((upstream-name . "NOISeq")))
2844 (build-system r-build-system)
2846 `(("r-biobase" ,r-biobase)
2847 ("r-matrix" ,r-matrix)))
2848 (home-page "https://bioconductor.org/packages/NOISeq")
2849 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2851 "This package provides tools to support the analysis of RNA-seq
2852 expression data or other similar kind of data. It provides exploratory plots
2853 to evaluate saturation, count distribution, expression per chromosome, type of
2854 detected features, features length, etc. It also supports the analysis of
2855 differential expression between two experimental conditions with no parametric
2857 (license license:artistic2.0)))
2859 (define-public r-scdd
2866 (uri (bioconductor-uri "scDD" version))
2869 "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4"))))
2870 (properties `((upstream-name . "scDD")))
2871 (build-system r-build-system)
2874 ("r-biocparallel" ,r-biocparallel)
2875 ("r-ebseq" ,r-ebseq)
2876 ("r-fields" ,r-fields)
2877 ("r-ggplot2" ,r-ggplot2)
2878 ("r-mclust" ,r-mclust)
2879 ("r-outliers" ,r-outliers)
2880 ("r-s4vectors" ,r-s4vectors)
2881 ("r-scran" ,r-scran)
2882 ("r-singlecellexperiment" ,r-singlecellexperiment)
2883 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2884 (home-page "https://github.com/kdkorthauer/scDD")
2885 (synopsis "Mixture modeling of single-cell RNA-seq data")
2887 "This package implements a method to analyze single-cell RNA-seq data
2888 utilizing flexible Dirichlet Process mixture models. Genes with differential
2889 distributions of expression are classified into several interesting patterns
2890 of differences between two conditions. The package also includes functions
2891 for simulating data with these patterns from negative binomial
2893 (license license:gpl2)))
2895 (define-public r-scone
2902 (uri (bioconductor-uri "scone" version))
2905 "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp"))))
2906 (build-system r-build-system)
2908 `(("r-aroma-light" ,r-aroma-light)
2909 ("r-biocparallel" ,r-biocparallel)
2911 ("r-class" ,r-class)
2912 ("r-cluster" ,r-cluster)
2913 ("r-compositions" ,r-compositions)
2914 ("r-diptest" ,r-diptest)
2915 ("r-edger" ,r-edger)
2917 ("r-gplots" ,r-gplots)
2918 ("r-hexbin" ,r-hexbin)
2919 ("r-limma" ,r-limma)
2920 ("r-matrixstats" ,r-matrixstats)
2921 ("r-mixtools" ,r-mixtools)
2922 ("r-rarpack" ,r-rarpack)
2923 ("r-rcolorbrewer" ,r-rcolorbrewer)
2924 ("r-rhdf5" ,r-rhdf5)
2925 ("r-ruvseq" ,r-ruvseq)
2926 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2927 (home-page "https://bioconductor.org/packages/scone")
2928 (synopsis "Single cell overview of normalized expression data")
2930 "SCONE is an R package for comparing and ranking the performance of
2931 different normalization schemes for single-cell RNA-seq and other
2932 high-throughput analyses.")
2933 (license license:artistic2.0)))
2935 (define-public r-geoquery
2942 (uri (bioconductor-uri "GEOquery" version))
2945 "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5"))))
2946 (properties `((upstream-name . "GEOquery")))
2947 (build-system r-build-system)
2949 `(("r-biobase" ,r-biobase)
2950 ("r-dplyr" ,r-dplyr)
2952 ("r-limma" ,r-limma)
2953 ("r-magrittr" ,r-magrittr)
2954 ("r-readr" ,r-readr)
2955 ("r-tidyr" ,r-tidyr)
2956 ("r-xml2" ,r-xml2)))
2957 (home-page "https://github.com/seandavi/GEOquery/")
2958 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2960 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2961 microarray data. Given the rich and varied nature of this resource, it is
2962 only natural to want to apply BioConductor tools to these data. GEOquery is
2963 the bridge between GEO and BioConductor.")
2964 (license license:gpl2)))
2966 (define-public r-illuminaio
2968 (name "r-illuminaio")
2973 (uri (bioconductor-uri "illuminaio" version))
2976 "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh"))))
2977 (build-system r-build-system)
2979 `(("r-base64" ,r-base64)))
2980 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2981 (synopsis "Parse Illumina microarray output files")
2983 "This package provides tools for parsing Illumina's microarray output
2984 files, including IDAT.")
2985 (license license:gpl2)))
2987 (define-public r-siggenes
2994 (uri (bioconductor-uri "siggenes" version))
2997 "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4"))))
2998 (build-system r-build-system)
3000 `(("r-biobase" ,r-biobase)
3001 ("r-multtest" ,r-multtest)
3002 ("r-scrime" ,r-scrime)))
3003 (home-page "https://bioconductor.org/packages/siggenes/")
3005 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3007 "This package provides tools for the identification of differentially
3008 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3009 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3010 Bayes Analyses of Microarrays} (EBAM).")
3011 (license license:lgpl2.0+)))
3013 (define-public r-bumphunter
3015 (name "r-bumphunter")
3020 (uri (bioconductor-uri "bumphunter" version))
3023 "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv"))))
3024 (build-system r-build-system)
3026 `(("r-annotationdbi" ,r-annotationdbi)
3027 ("r-biocgenerics" ,r-biocgenerics)
3028 ("r-dorng" ,r-dorng)
3029 ("r-foreach" ,r-foreach)
3030 ("r-genomeinfodb" ,r-genomeinfodb)
3031 ("r-genomicfeatures" ,r-genomicfeatures)
3032 ("r-genomicranges" ,r-genomicranges)
3033 ("r-iranges" ,r-iranges)
3034 ("r-iterators" ,r-iterators)
3035 ("r-limma" ,r-limma)
3036 ("r-locfit" ,r-locfit)
3037 ("r-matrixstats" ,r-matrixstats)
3038 ("r-s4vectors" ,r-s4vectors)))
3039 (home-page "https://github.com/ririzarr/bumphunter")
3040 (synopsis "Find bumps in genomic data")
3042 "This package provides tools for finding bumps in genomic data in order
3043 to identify differentially methylated regions in epigenetic epidemiology
3045 (license license:artistic2.0)))
3047 (define-public r-minfi
3054 (uri (bioconductor-uri "minfi" version))
3057 "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3"))))
3058 (build-system r-build-system)
3060 `(("r-beanplot" ,r-beanplot)
3061 ("r-biobase" ,r-biobase)
3062 ("r-biocgenerics" ,r-biocgenerics)
3063 ("r-biocparallel" ,r-biocparallel)
3064 ("r-biostrings" ,r-biostrings)
3065 ("r-bumphunter" ,r-bumphunter)
3066 ("r-data-table" ,r-data-table)
3067 ("r-delayedarray" ,r-delayedarray)
3068 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3069 ("r-genefilter" ,r-genefilter)
3070 ("r-genomeinfodb" ,r-genomeinfodb)
3071 ("r-genomicranges" ,r-genomicranges)
3072 ("r-geoquery" ,r-geoquery)
3073 ("r-hdf5array" ,r-hdf5array)
3074 ("r-illuminaio" ,r-illuminaio)
3075 ("r-iranges" ,r-iranges)
3076 ("r-lattice" ,r-lattice)
3077 ("r-limma" ,r-limma)
3079 ("r-mclust" ,r-mclust)
3081 ("r-nor1mix" ,r-nor1mix)
3082 ("r-preprocesscore" ,r-preprocesscore)
3083 ("r-quadprog" ,r-quadprog)
3084 ("r-rcolorbrewer" ,r-rcolorbrewer)
3085 ("r-reshape" ,r-reshape)
3086 ("r-s4vectors" ,r-s4vectors)
3087 ("r-siggenes" ,r-siggenes)
3088 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3089 (home-page "https://github.com/hansenlab/minfi")
3090 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3092 "This package provides tools to analyze and visualize Illumina Infinium
3093 methylation arrays.")
3094 (license license:artistic2.0)))
3096 (define-public r-methylumi
3098 (name "r-methylumi")
3103 (uri (bioconductor-uri "methylumi" version))
3106 "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w"))))
3107 (build-system r-build-system)
3109 `(("r-annotate" ,r-annotate)
3110 ("r-annotationdbi" ,r-annotationdbi)
3111 ("r-biobase" ,r-biobase)
3112 ("r-biocgenerics" ,r-biocgenerics)
3113 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3114 ("r-genefilter" ,r-genefilter)
3115 ("r-genomeinfodb" ,r-genomeinfodb)
3116 ("r-genomicranges" ,r-genomicranges)
3117 ("r-ggplot2" ,r-ggplot2)
3118 ("r-illuminaio" ,r-illuminaio)
3119 ("r-iranges" ,r-iranges)
3120 ("r-lattice" ,r-lattice)
3121 ("r-matrixstats" ,r-matrixstats)
3122 ("r-minfi" ,r-minfi)
3123 ("r-reshape2" ,r-reshape2)
3124 ("r-s4vectors" ,r-s4vectors)
3125 ("r-scales" ,r-scales)
3126 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3127 (home-page "https://bioconductor.org/packages/methylumi")
3128 (synopsis "Handle Illumina methylation data")
3130 "This package provides classes for holding and manipulating Illumina
3131 methylation data. Based on eSet, it can contain MIAME information, sample
3132 information, feature information, and multiple matrices of data. An
3133 \"intelligent\" import function, methylumiR can read the Illumina text files
3134 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3135 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3136 background correction, and quality control features for GoldenGate, Infinium,
3137 and Infinium HD arrays are also included.")
3138 (license license:gpl2)))
3140 (define-public r-lumi
3147 (uri (bioconductor-uri "lumi" version))
3150 "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm"))))
3151 (build-system r-build-system)
3153 `(("r-affy" ,r-affy)
3154 ("r-annotate" ,r-annotate)
3155 ("r-annotationdbi" ,r-annotationdbi)
3156 ("r-biobase" ,r-biobase)
3158 ("r-genomicfeatures" ,r-genomicfeatures)
3159 ("r-genomicranges" ,r-genomicranges)
3160 ("r-kernsmooth" ,r-kernsmooth)
3161 ("r-lattice" ,r-lattice)
3163 ("r-methylumi" ,r-methylumi)
3165 ("r-nleqslv" ,r-nleqslv)
3166 ("r-preprocesscore" ,r-preprocesscore)
3167 ("r-rsqlite" ,r-rsqlite)))
3168 (home-page "https://bioconductor.org/packages/lumi")
3169 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3171 "The lumi package provides an integrated solution for the Illumina
3172 microarray data analysis. It includes functions of Illumina
3173 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3174 variance stabilization, normalization and gene annotation at the probe level.
3175 It also includes the functions of processing Illumina methylation microarrays,
3176 especially Illumina Infinium methylation microarrays.")
3177 (license license:lgpl2.0+)))
3179 (define-public r-linnorm
3186 (uri (bioconductor-uri "Linnorm" version))
3189 "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67"))))
3190 (properties `((upstream-name . "Linnorm")))
3191 (build-system r-build-system)
3193 `(("r-amap" ,r-amap)
3194 ("r-apcluster" ,r-apcluster)
3195 ("r-ellipse" ,r-ellipse)
3196 ("r-fastcluster" ,r-fastcluster)
3198 ("r-ggdendro" ,r-ggdendro)
3199 ("r-ggplot2" ,r-ggplot2)
3200 ("r-gmodels" ,r-gmodels)
3201 ("r-igraph" ,r-igraph)
3202 ("r-limma" ,r-limma)
3204 ("r-mclust" ,r-mclust)
3206 ("r-rcpparmadillo" ,r-rcpparmadillo)
3207 ("r-rtsne" ,r-rtsne)
3208 ("r-statmod" ,r-statmod)
3209 ("r-vegan" ,r-vegan)
3211 (home-page "http://www.jjwanglab.org/Linnorm/")
3212 (synopsis "Linear model and normality based transformation method")
3214 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3215 count data or any large scale count data. It transforms such datasets for
3216 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3217 the following pipelines are implemented:
3220 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3221 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3222 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3223 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3224 @item Differential expression analysis or differential peak detection using
3225 limma (@code{Linnorm.limma})
3226 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3227 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3228 @item Stable gene selection for scRNA-seq data; for users without or who do
3229 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3230 @item Data imputation (@code{Linnorm.DataImput}).
3233 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3234 @code{RnaXSim} function is included for simulating RNA-seq data for the
3235 evaluation of DEG analysis methods.")
3236 (license license:expat)))
3238 (define-public r-ioniser
3245 (uri (bioconductor-uri "IONiseR" version))
3248 "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f"))))
3249 (properties `((upstream-name . "IONiseR")))
3250 (build-system r-build-system)
3252 `(("r-biocgenerics" ,r-biocgenerics)
3253 ("r-biocparallel" ,r-biocparallel)
3254 ("r-biostrings" ,r-biostrings)
3255 ("r-bit64" ,r-bit64)
3256 ("r-dplyr" ,r-dplyr)
3257 ("r-ggplot2" ,r-ggplot2)
3258 ("r-magrittr" ,r-magrittr)
3259 ("r-rhdf5" ,r-rhdf5)
3260 ("r-shortread" ,r-shortread)
3261 ("r-stringr" ,r-stringr)
3262 ("r-tibble" ,r-tibble)
3263 ("r-tidyr" ,r-tidyr)
3264 ("r-xvector" ,r-xvector)))
3265 (home-page "https://bioconductor.org/packages/IONiseR/")
3266 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3268 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3269 MinION data. It extracts summary statistics from a set of fast5 files and can
3270 be used either before or after base calling. In addition to standard
3271 summaries of the read-types produced, it provides a number of plots for
3272 visualising metrics relative to experiment run time or spatially over the
3273 surface of a flowcell.")
3274 (license license:expat)))
3276 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3277 (define-public r-gkmsvm
3284 (uri (cran-uri "gkmSVM" version))
3287 "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p"))))
3288 (properties `((upstream-name . "gkmSVM")))
3289 (build-system r-build-system)
3291 `(("r-kernlab" ,r-kernlab)
3294 ("r-seqinr" ,r-seqinr)))
3295 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3296 (synopsis "Gapped-kmer support vector machine")
3298 "This R package provides tools for training gapped-kmer SVM classifiers
3299 for DNA and protein sequences. This package supports several sequence
3300 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3301 (license license:gpl2+)))
3303 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3304 (define-public r-mutoss
3311 (uri (cran-uri "mutoss" version))
3314 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3315 (properties `((upstream-name . "mutoss")))
3316 (build-system r-build-system)
3318 `(("r-multcomp" ,r-multcomp)
3319 ("r-multtest" ,r-multtest)
3320 ("r-mvtnorm" ,r-mvtnorm)
3321 ("r-plotrix" ,r-plotrix)))
3322 (home-page "https://github.com/kornl/mutoss/")
3323 (synopsis "Unified multiple testing procedures")
3325 "This package is designed to ease the application and comparison of
3326 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3327 are standardized and usable by the accompanying mutossGUI package.")
3328 ;; Any version of the GPL.
3329 (license (list license:gpl2+ license:gpl3+))))
3331 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3332 ;; from Bioconductor, so we put it here.
3333 (define-public r-metap
3340 (uri (cran-uri "metap" version))
3343 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3344 (build-system r-build-system)
3346 `(("r-lattice" ,r-lattice)
3347 ("r-mutoss" ,r-mutoss)
3348 ("r-rdpack" ,r-rdpack)
3349 ("r-tfisher" ,r-tfisher)))
3350 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3351 (synopsis "Meta-analysis of significance values")
3353 "The canonical way to perform meta-analysis involves using effect sizes.
3354 When they are not available this package provides a number of methods for
3355 meta-analysis of significance values including the methods of Edgington,
3356 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3357 published results; and a routine for graphical display.")
3358 (license license:gpl2)))
3360 (define-public r-triform
3367 (uri (bioconductor-uri "triform" version))
3370 "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9"))))
3371 (build-system r-build-system)
3373 `(("r-biocgenerics" ,r-biocgenerics)
3374 ("r-iranges" ,r-iranges)
3375 ("r-yaml" ,r-yaml)))
3376 (home-page "https://bioconductor.org/packages/triform/")
3377 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3379 "The Triform algorithm uses model-free statistics to identify peak-like
3380 distributions of TF ChIP sequencing reads, taking advantage of an improved
3381 peak definition in combination with known profile characteristics.")
3382 (license license:gpl2)))
3384 (define-public r-varianttools
3386 (name "r-varianttools")
3391 (uri (bioconductor-uri "VariantTools" version))
3394 "1x57shc3slcbnc807ra1nwnjr37sqjh04n2xfwd469m4hkjb0jzh"))))
3395 (properties `((upstream-name . "VariantTools")))
3396 (build-system r-build-system)
3398 `(("r-biobase" ,r-biobase)
3399 ("r-biocgenerics" ,r-biocgenerics)
3400 ("r-biocparallel" ,r-biocparallel)
3401 ("r-biostrings" ,r-biostrings)
3402 ("r-bsgenome" ,r-bsgenome)
3403 ("r-genomeinfodb" ,r-genomeinfodb)
3404 ("r-genomicfeatures" ,r-genomicfeatures)
3405 ("r-genomicranges" ,r-genomicranges)
3406 ("r-iranges" ,r-iranges)
3407 ("r-matrix" ,r-matrix)
3408 ("r-rsamtools" ,r-rsamtools)
3409 ("r-rtracklayer" ,r-rtracklayer)
3410 ("r-s4vectors" ,r-s4vectors)
3411 ("r-variantannotation" ,r-variantannotation)))
3412 (home-page "https://bioconductor.org/packages/VariantTools/")
3413 (synopsis "Tools for exploratory analysis of variant calls")
3415 "Explore, diagnose, and compare variant calls using filters. The
3416 VariantTools package supports a workflow for loading data, calling single
3417 sample variants and tumor-specific somatic mutations or other sample-specific
3418 variant types (e.g., RNA editing). Most of the functions operate on
3419 alignments (BAM files) or datasets of called variants. The user is expected
3420 to have already aligned the reads with a separate tool, e.g., GSNAP via
3422 (license license:artistic2.0)))
3424 (define-public r-heatplus
3431 (uri (bioconductor-uri "Heatplus" version))
3434 "1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1"))))
3435 (properties `((upstream-name . "Heatplus")))
3436 (build-system r-build-system)
3438 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3439 (home-page "https://github.com/alexploner/Heatplus")
3440 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3442 "This package provides tools to display a rectangular heatmap (intensity
3443 plot) of a data matrix. By default, both samples (columns) and features (row)
3444 of the matrix are sorted according to a hierarchical clustering, and the
3445 corresponding dendrogram is plotted. Optionally, panels with additional
3446 information about samples and features can be added to the plot.")
3447 (license license:gpl2+)))
3449 (define-public r-gosemsim
3456 (uri (bioconductor-uri "GOSemSim" version))
3459 "1r8yx6qw6d6602cp8aspzl3shi1l1zqcrc8fm9d5wg01sw1whs05"))))
3460 (properties `((upstream-name . "GOSemSim")))
3461 (build-system r-build-system)
3463 `(("r-annotationdbi" ,r-annotationdbi)
3464 ("r-go-db" ,r-go-db)
3465 ("r-rcpp" ,r-rcpp)))
3467 `(("r-knitr" ,r-knitr)))
3468 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3469 (synopsis "GO-terms semantic similarity measures")
3471 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3472 quantitative ways to compute similarities between genes and gene groups, and
3473 have became important basis for many bioinformatics analysis approaches.
3474 GOSemSim is an R package for semantic similarity computation among GO terms,
3475 sets of GO terms, gene products and gene clusters.")
3476 (license license:artistic2.0)))
3478 (define-public r-anota
3485 (uri (bioconductor-uri "anota" version))
3488 "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m"))))
3489 (build-system r-build-system)
3491 `(("r-multtest" ,r-multtest)
3492 ("r-qvalue" ,r-qvalue)))
3493 (home-page "https://bioconductor.org/packages/anota/")
3494 (synopsis "Analysis of translational activity")
3496 "Genome wide studies of translational control is emerging as a tool to
3497 study various biological conditions. The output from such analysis is both
3498 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3499 involved in translation (the actively translating mRNA level) for each mRNA.
3500 The standard analysis of such data strives towards identifying differential
3501 translational between two or more sample classes - i.e. differences in
3502 actively translated mRNA levels that are independent of underlying differences
3503 in cytosolic mRNA levels. This package allows for such analysis using partial
3504 variances and the random variance model. As 10s of thousands of mRNAs are
3505 analyzed in parallel the library performs a number of tests to assure that
3506 the data set is suitable for such analysis.")
3507 (license license:gpl3)))
3509 (define-public r-sigpathway
3511 (name "r-sigpathway")
3516 (uri (bioconductor-uri "sigPathway" version))
3519 "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb"))))
3520 (properties `((upstream-name . "sigPathway")))
3521 (build-system r-build-system)
3522 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3523 (synopsis "Pathway analysis")
3525 "This package is used to conduct pathway analysis by calculating the NT_k
3526 and NE_k statistics in a statistical framework for determining whether a
3527 specified group of genes for a pathway has a coordinated association with a
3528 phenotype of interest.")
3529 (license license:gpl2)))
3531 (define-public r-fgsea
3538 (uri (bioconductor-uri "fgsea" version))
3541 "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1"))))
3542 (build-system r-build-system)
3545 ("r-biocparallel" ,r-biocparallel)
3546 ("r-data-table" ,r-data-table)
3547 ("r-fastmatch" ,r-fastmatch)
3548 ("r-ggplot2" ,r-ggplot2)
3549 ("r-gridextra" ,r-gridextra)
3550 ("r-matrix" ,r-matrix)
3551 ("r-rcpp" ,r-rcpp)))
3552 (home-page "https://github.com/ctlab/fgsea/")
3553 (synopsis "Fast gene set enrichment analysis")
3555 "The package implements an algorithm for fast gene set enrichment
3556 analysis. Using the fast algorithm makes more permutations and gets
3557 more fine grained p-values, which allows using accurate standard approaches
3558 to multiple hypothesis correction.")
3559 (license license:expat)))
3561 (define-public r-dose
3568 (uri (bioconductor-uri "DOSE" version))
3571 "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5"))))
3572 (properties `((upstream-name . "DOSE")))
3573 (build-system r-build-system)
3575 `(("r-annotationdbi" ,r-annotationdbi)
3576 ("r-biocparallel" ,r-biocparallel)
3577 ("r-do-db" ,r-do-db)
3578 ("r-fgsea" ,r-fgsea)
3579 ("r-ggplot2" ,r-ggplot2)
3580 ("r-gosemsim" ,r-gosemsim)
3581 ("r-qvalue" ,r-qvalue)
3582 ("r-reshape2" ,r-reshape2)
3583 ("r-s4vectors" ,r-s4vectors)))
3585 `(("r-knitr" ,r-knitr)))
3586 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3587 (synopsis "Disease ontology semantic and enrichment analysis")
3589 "This package implements five methods proposed by Resnik, Schlicker,
3590 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3591 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3592 including hypergeometric model and gene set enrichment analysis are also
3593 implemented for discovering disease associations of high-throughput biological
3595 (license license:artistic2.0)))
3597 (define-public r-enrichplot
3599 (name "r-enrichplot")
3604 (uri (bioconductor-uri "enrichplot" version))
3607 "0707f5ll58psh7pr001cmmk5di7dprnbry1cy2mw20vn8p24nf3x"))))
3608 (build-system r-build-system)
3610 `(("r-annotationdbi" ,r-annotationdbi)
3611 ("r-cowplot" ,r-cowplot)
3613 ("r-europepmc" ,r-europepmc)
3614 ("r-ggplot2" ,r-ggplot2)
3615 ("r-ggplotify" ,r-ggplotify)
3616 ("r-ggraph" ,r-ggraph)
3617 ("r-ggridges" ,r-ggridges)
3618 ("r-gosemsim" ,r-gosemsim)
3619 ("r-gridextra" ,r-gridextra)
3620 ("r-igraph" ,r-igraph)
3621 ("r-purrr" ,r-purrr)
3622 ("r-rcolorbrewer" ,r-rcolorbrewer)
3623 ("r-reshape2" ,r-reshape2)))
3624 (home-page "https://github.com/GuangchuangYu/enrichplot")
3625 (synopsis "Visualization of functional enrichment result")
3627 "The enrichplot package implements several visualization methods for
3628 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3629 All the visualization methods are developed based on ggplot2 graphics.")
3630 (license license:artistic2.0)))
3632 (define-public r-clusterprofiler
3634 (name "r-clusterprofiler")
3639 (uri (bioconductor-uri "clusterProfiler" version))
3642 "08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg"))))
3644 `((upstream-name . "clusterProfiler")))
3645 (build-system r-build-system)
3647 `(("r-annotationdbi" ,r-annotationdbi)
3649 ("r-enrichplot" ,r-enrichplot)
3650 ("r-ggplot2" ,r-ggplot2)
3651 ("r-go-db" ,r-go-db)
3652 ("r-gosemsim" ,r-gosemsim)
3653 ("r-magrittr" ,r-magrittr)
3655 ("r-qvalue" ,r-qvalue)
3656 ("r-rvcheck" ,r-rvcheck)
3657 ("r-tidyr" ,r-tidyr)))
3658 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3659 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3661 "This package implements methods to analyze and visualize functional
3662 profiles (GO and KEGG) of gene and gene clusters.")
3663 (license license:artistic2.0)))
3665 (define-public r-mlinterfaces
3667 (name "r-mlinterfaces")
3672 (uri (bioconductor-uri "MLInterfaces" version))
3675 "05bg7qcrv485m03rkyq3qg5hrr1m3y7zx49bipwaivzqm3s1mbw5"))))
3676 (properties `((upstream-name . "MLInterfaces")))
3677 (build-system r-build-system)
3679 `(("r-annotate" ,r-annotate)
3680 ("r-biobase" ,r-biobase)
3681 ("r-biocgenerics" ,r-biocgenerics)
3682 ("r-cluster" ,r-cluster)
3685 ("r-gdata" ,r-gdata)
3686 ("r-genefilter" ,r-genefilter)
3687 ("r-ggvis" ,r-ggvis)
3688 ("r-hwriter" ,r-hwriter)
3690 ("r-mlbench" ,r-mlbench)
3692 ("r-rcolorbrewer" ,r-rcolorbrewer)
3693 ("r-rpart" ,r-rpart)
3694 ("r-sfsmisc" ,r-sfsmisc)
3695 ("r-shiny" ,r-shiny)
3696 ("r-threejs" ,r-threejs)))
3697 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3698 (synopsis "Interfaces to R machine learning procedures")
3700 "This package provides uniform interfaces to machine learning code for
3701 data in R and Bioconductor containers.")
3702 ;; Any version of the LGPL.
3703 (license license:lgpl2.1+)))
3705 (define-public r-annaffy
3712 (uri (bioconductor-uri "annaffy" version))
3715 "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16"))))
3716 (build-system r-build-system)
3719 (modify-phases %standard-phases
3720 (add-after 'unpack 'remove-reference-to-non-free-data
3722 (substitute* "DESCRIPTION"
3726 `(("r-annotationdbi" ,r-annotationdbi)
3727 ("r-biobase" ,r-biobase)
3729 ("r-go-db" ,r-go-db)))
3730 (home-page "https://bioconductor.org/packages/annaffy/")
3731 (synopsis "Annotation tools for Affymetrix biological metadata")
3733 "This package provides functions for handling data from Bioconductor
3734 Affymetrix annotation data packages. It produces compact HTML and text
3735 reports including experimental data and URL links to many online databases.
3736 It allows searching of biological metadata using various criteria.")
3737 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3738 ;; the LGPL 2.1 is included.
3739 (license license:lgpl2.1+)))
3741 (define-public r-a4core
3748 (uri (bioconductor-uri "a4Core" version))
3751 "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df"))))
3752 (properties `((upstream-name . "a4Core")))
3753 (build-system r-build-system)
3755 `(("r-biobase" ,r-biobase)
3756 ("r-glmnet" ,r-glmnet)))
3757 (home-page "https://bioconductor.org/packages/a4Core")
3758 (synopsis "Automated Affymetrix array analysis core package")
3760 "This is the core package for the automated analysis of Affymetrix
3762 (license license:gpl3)))
3764 (define-public r-a4classif
3766 (name "r-a4classif")
3771 (uri (bioconductor-uri "a4Classif" version))
3774 "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn"))))
3775 (properties `((upstream-name . "a4Classif")))
3776 (build-system r-build-system)
3778 `(("r-a4core" ,r-a4core)
3779 ("r-a4preproc" ,r-a4preproc)
3780 ("r-glmnet" ,r-glmnet)
3781 ("r-mlinterfaces" ,r-mlinterfaces)
3784 ("r-varselrf" ,r-varselrf)))
3785 (home-page "https://bioconductor.org/packages/a4Classif/")
3786 (synopsis "Automated Affymetrix array analysis classification package")
3788 "This is the classification package for the automated analysis of
3789 Affymetrix arrays.")
3790 (license license:gpl3)))
3792 (define-public r-a4preproc
3794 (name "r-a4preproc")
3799 (uri (bioconductor-uri "a4Preproc" version))
3802 "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd"))))
3803 (properties `((upstream-name . "a4Preproc")))
3804 (build-system r-build-system)
3806 `(("r-annotationdbi" ,r-annotationdbi)))
3807 (home-page "https://bioconductor.org/packages/a4Preproc/")
3808 (synopsis "Automated Affymetrix array analysis preprocessing package")
3810 "This is a package for the automated analysis of Affymetrix arrays. It
3811 is used for preprocessing the arrays.")
3812 (license license:gpl3)))
3814 (define-public r-a4reporting
3816 (name "r-a4reporting")
3821 (uri (bioconductor-uri "a4Reporting" version))
3824 "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5"))))
3825 (properties `((upstream-name . "a4Reporting")))
3826 (build-system r-build-system)
3828 `(("r-annaffy" ,r-annaffy)
3829 ("r-xtable" ,r-xtable)))
3830 (home-page "https://bioconductor.org/packages/a4Reporting/")
3831 (synopsis "Automated Affymetrix array analysis reporting package")
3833 "This is a package for the automated analysis of Affymetrix arrays. It
3834 provides reporting features.")
3835 (license license:gpl3)))
3837 (define-public r-a4base
3844 (uri (bioconductor-uri "a4Base" version))
3847 "1a0yk05ikk1hr1vpxynydrb5xb1hj4hdqlh9zd13n83ir89dss83"))))
3848 (properties `((upstream-name . "a4Base")))
3849 (build-system r-build-system)
3851 `(("r-a4core" ,r-a4core)
3852 ("r-a4preproc" ,r-a4preproc)
3853 ("r-annaffy" ,r-annaffy)
3854 ("r-annotationdbi" ,r-annotationdbi)
3855 ("r-biobase" ,r-biobase)
3856 ("r-genefilter" ,r-genefilter)
3857 ("r-glmnet" ,r-glmnet)
3858 ("r-gplots" ,r-gplots)
3859 ("r-limma" ,r-limma)
3861 ("r-multtest" ,r-multtest)))
3862 (home-page "https://bioconductor.org/packages/a4Base/")
3863 (synopsis "Automated Affymetrix array analysis base package")
3865 "This package provides basic features for the automated analysis of
3866 Affymetrix arrays.")
3867 (license license:gpl3)))
3876 (uri (bioconductor-uri "a4" version))
3879 "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4"))))
3880 (build-system r-build-system)
3882 `(("r-a4base" ,r-a4base)
3883 ("r-a4classif" ,r-a4classif)
3884 ("r-a4core" ,r-a4core)
3885 ("r-a4preproc" ,r-a4preproc)
3886 ("r-a4reporting" ,r-a4reporting)))
3887 (home-page "https://bioconductor.org/packages/a4/")
3888 (synopsis "Automated Affymetrix array analysis umbrella package")
3890 "This package provides a software suite for the automated analysis of
3891 Affymetrix arrays.")
3892 (license license:gpl3)))
3894 (define-public r-abseqr
3901 (uri (bioconductor-uri "abseqR" version))
3904 "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa"))))
3905 (properties `((upstream-name . "abseqR")))
3906 (build-system r-build-system)
3908 `(("pandoc" ,ghc-pandoc)))
3910 `(("r-biocparallel" ,r-biocparallel)
3911 ("r-biocstyle" ,r-biocstyle)
3912 ("r-circlize" ,r-circlize)
3913 ("r-flexdashboard" ,r-flexdashboard)
3914 ("r-ggcorrplot" ,r-ggcorrplot)
3915 ("r-ggdendro" ,r-ggdendro)
3916 ("r-ggplot2" ,r-ggplot2)
3917 ("r-gridextra" ,r-gridextra)
3918 ("r-knitr" ,r-knitr)
3919 ("r-plotly" ,r-plotly)
3922 ("r-rcolorbrewer" ,r-rcolorbrewer)
3923 ("r-reshape2" ,r-reshape2)
3924 ("r-rmarkdown" ,r-rmarkdown)
3925 ("r-stringr" ,r-stringr)
3926 ("r-vegan" ,r-vegan)
3927 ("r-venndiagram" ,r-venndiagram)))
3928 (home-page "https://github.com/malhamdoosh/abseqR")
3929 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3931 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3932 sequencing datasets generated from antibody libraries and abseqR is one of its
3933 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3934 capabilities and allows them to generate interactive HTML reports for the
3935 convenience of viewing and sharing with other researchers. Additionally,
3936 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3937 further downstream analysis on its output.")
3938 (license license:gpl3)))
3940 (define-public r-bacon
3947 (uri (bioconductor-uri "bacon" version))
3950 "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86"))))
3951 (build-system r-build-system)
3953 `(("r-biocparallel" ,r-biocparallel)
3954 ("r-ellipse" ,r-ellipse)
3955 ("r-ggplot2" ,r-ggplot2)))
3957 `(("r-knitr" ,r-knitr)))
3958 (home-page "https://bioconductor.org/packages/bacon/")
3959 (synopsis "Controlling bias and inflation in association studies")
3961 "Bacon can be used to remove inflation and bias often observed in
3962 epigenome- and transcriptome-wide association studies. To this end bacon
3963 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3964 fitting a three-component normal mixture on z-scores.")
3965 (license license:gpl2+)))
3967 (define-public r-rgadem
3974 (uri (bioconductor-uri "rGADEM" version))
3977 "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h"))))
3978 (properties `((upstream-name . "rGADEM")))
3979 (build-system r-build-system)
3981 `(("r-biostrings" ,r-biostrings)
3982 ("r-bsgenome" ,r-bsgenome)
3983 ("r-genomicranges" ,r-genomicranges)
3984 ("r-iranges" ,r-iranges)
3985 ("r-seqlogo" ,r-seqlogo)))
3986 (home-page "https://bioconductor.org/packages/rGADEM/")
3987 (synopsis "De novo sequence motif discovery")
3989 "rGADEM is an efficient de novo motif discovery tool for large-scale
3990 genomic sequence data.")
3991 (license license:artistic2.0)))
3993 (define-public r-motiv
4000 (uri (bioconductor-uri "MotIV" version))
4003 "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k"))))
4004 (properties `((upstream-name . "MotIV")))
4005 (build-system r-build-system)
4009 `(("r-biocgenerics" ,r-biocgenerics)
4010 ("r-biostrings" ,r-biostrings)
4011 ("r-genomicranges" ,r-genomicranges)
4012 ("r-iranges" ,r-iranges)
4013 ("r-lattice" ,r-lattice)
4014 ("r-rgadem" ,r-rgadem)
4015 ("r-s4vectors" ,r-s4vectors)))
4016 (home-page "https://bioconductor.org/packages/MotIV/")
4017 (synopsis "Motif identification and validation")
4019 "This package is used for the identification and validation of sequence
4020 motifs. It makes use of STAMP for comparing a set of motifs to a given
4021 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4022 distributions, modules and filter motifs.")
4023 (license license:gpl2)))
4025 (define-public r-motifdb
4031 (uri (bioconductor-uri "MotifDb" version))
4033 (base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc"))))
4034 (properties `((upstream-name . "MotifDb")))
4035 (build-system r-build-system)
4037 `(("r-biocgenerics" ,r-biocgenerics)
4038 ("r-biostrings" ,r-biostrings)
4039 ("r-iranges" ,r-iranges)
4040 ("r-rtracklayer" ,r-rtracklayer)
4041 ("r-s4vectors" ,r-s4vectors)
4042 ("r-splitstackshape" ,r-splitstackshape)))
4043 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4044 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4045 (description "This package provides more than 2000 annotated position
4046 frequency matrices from nine public sources, for multiple organisms.")
4047 (license license:artistic2.0)))
4049 (define-public r-motifbreakr
4051 (name "r-motifbreakr")
4055 (uri (bioconductor-uri "motifbreakR" version))
4057 (base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n"))))
4058 (properties `((upstream-name . "motifbreakR")))
4059 (build-system r-build-system)
4061 `(("r-grimport" ,r-grimport)
4062 ("r-stringr" ,r-stringr)
4063 ("r-biocgenerics" ,r-biocgenerics)
4064 ("r-s4vectors" ,r-s4vectors)
4065 ("r-iranges" ,r-iranges)
4066 ("r-genomeinfodb" ,r-genomeinfodb)
4067 ("r-genomicranges" ,r-genomicranges)
4068 ("r-biostrings" ,r-biostrings)
4069 ("r-bsgenome" ,r-bsgenome)
4070 ("r-rtracklayer" ,r-rtracklayer)
4071 ("r-variantannotation" ,r-variantannotation)
4072 ("r-biocparallel" ,r-biocparallel)
4073 ("r-motifstack" ,r-motifstack)
4075 ("r-matrixstats" ,r-matrixstats)
4076 ("r-tfmpvalue" ,r-tfmpvalue)
4077 ("r-motifdb" ,r-motifdb)))
4078 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4079 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4080 (description "This package allows biologists to judge in the first place
4081 whether the sequence surrounding the polymorphism is a good match, and in
4082 the second place how much information is gained or lost in one allele of
4083 the polymorphism relative to another. This package gives a choice of
4084 algorithms for interrogation of genomes with motifs from public sources:
4086 @item a weighted-sum probability matrix;
4087 @item log-probabilities;
4088 @item weighted by relative entropy.
4091 This package can predict effects for novel or previously described variants in
4092 public databases, making it suitable for tasks beyond the scope of its original
4093 design. Lastly, it can be used to interrogate any genome curated within
4095 (license license:gpl2+)))
4097 (define-public r-motifstack
4099 (name "r-motifstack")
4104 (uri (bioconductor-uri "motifStack" version))
4107 "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg"))))
4108 (properties `((upstream-name . "motifStack")))
4109 (build-system r-build-system)
4111 `(("r-ade4" ,r-ade4)
4112 ("r-biostrings" ,r-biostrings)
4113 ("r-ggplot2" ,r-ggplot2)
4114 ("r-grimport2" ,r-grimport2)
4115 ("r-htmlwidgets" ,r-htmlwidgets)
4116 ("r-motiv" ,r-motiv)
4117 ("r-scales" ,r-scales)
4119 (home-page "https://bioconductor.org/packages/motifStack/")
4120 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4122 "The motifStack package is designed for graphic representation of
4123 multiple motifs with different similarity scores. It works with both DNA/RNA
4124 sequence motifs and amino acid sequence motifs. In addition, it provides the
4125 flexibility for users to customize the graphic parameters such as the font
4126 type and symbol colors.")
4127 (license license:gpl2+)))
4129 (define-public r-genomicscores
4131 (name "r-genomicscores")
4136 (uri (bioconductor-uri "GenomicScores" version))
4139 "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj"))))
4140 (properties `((upstream-name . "GenomicScores")))
4141 (build-system r-build-system)
4143 `(("r-annotationhub" ,r-annotationhub)
4144 ("r-biobase" ,r-biobase)
4145 ("r-biocgenerics" ,r-biocgenerics)
4146 ("r-biostrings" ,r-biostrings)
4147 ("r-bsgenome" ,r-bsgenome)
4148 ("r-genomeinfodb" ,r-genomeinfodb)
4149 ("r-genomicranges" ,r-genomicranges)
4150 ("r-iranges" ,r-iranges)
4151 ("r-s4vectors" ,r-s4vectors)
4153 (home-page "https://github.com/rcastelo/GenomicScores/")
4154 (synopsis "Work with genome-wide position-specific scores")
4156 "This package provides infrastructure to store and access genome-wide
4157 position-specific scores within R and Bioconductor.")
4158 (license license:artistic2.0)))
4160 (define-public r-atacseqqc
4162 (name "r-atacseqqc")
4167 (uri (bioconductor-uri "ATACseqQC" version))
4170 "1g07ni134cyl3jd9y19afip39kxddfgpm1jjm0rhrm7jgssp24in"))))
4171 (properties `((upstream-name . "ATACseqQC")))
4172 (build-system r-build-system)
4174 `(("r-biocgenerics" ,r-biocgenerics)
4175 ("r-biostrings" ,r-biostrings)
4176 ("r-bsgenome" ,r-bsgenome)
4177 ("r-chippeakanno" ,r-chippeakanno)
4178 ("r-edger" ,r-edger)
4179 ("r-genomeinfodb" ,r-genomeinfodb)
4180 ("r-genomicalignments" ,r-genomicalignments)
4181 ("r-genomicranges" ,r-genomicranges)
4182 ("r-genomicscores" ,r-genomicscores)
4183 ("r-iranges" ,r-iranges)
4184 ("r-kernsmooth" ,r-kernsmooth)
4185 ("r-limma" ,r-limma)
4186 ("r-motifstack" ,r-motifstack)
4187 ("r-preseqr" ,r-preseqr)
4188 ("r-randomforest" ,r-randomforest)
4189 ("r-rsamtools" ,r-rsamtools)
4190 ("r-rtracklayer" ,r-rtracklayer)
4191 ("r-s4vectors" ,r-s4vectors)))
4193 `(("r-knitr" ,r-knitr)))
4194 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4195 (synopsis "ATAC-seq quality control")
4197 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4198 sequencing, is a rapid and sensitive method for chromatin accessibility
4199 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4200 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4201 assess whether their ATAC-seq experiment is successful. It includes
4202 diagnostic plots of fragment size distribution, proportion of mitochondria
4203 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4205 (license license:gpl2+)))
4207 (define-public r-gofuncr
4214 (uri (bioconductor-uri "GOfuncR" version))
4217 "1wk7ja6f5il8jx8v05ijzcs9pijp3b953h566ya66xp7dz5jg9rb"))))
4218 (properties `((upstream-name . "GOfuncR")))
4219 (build-system r-build-system)
4221 `(("r-annotationdbi" ,r-annotationdbi)
4222 ("r-genomicranges" ,r-genomicranges)
4223 ("r-gtools" ,r-gtools)
4224 ("r-iranges" ,r-iranges)
4225 ("r-mapplots" ,r-mapplots)
4227 ("r-vioplot" ,r-vioplot)))
4229 `(("r-knitr" ,r-knitr)))
4230 (home-page "https://bioconductor.org/packages/GOfuncR/")
4231 (synopsis "Gene ontology enrichment using FUNC")
4233 "GOfuncR performs a gene ontology enrichment analysis based on the
4234 ontology enrichment software FUNC. GO-annotations are obtained from
4235 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4236 included in the package and updated regularly. GOfuncR provides the standard
4237 candidate vs background enrichment analysis using the hypergeometric test, as
4238 well as three additional tests:
4241 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4242 @item a binomial test that is used when genes are associated with two counts,
4244 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4245 associated with four counts.
4248 To correct for multiple testing and interdependency of the tests, family-wise
4249 error rates are computed based on random permutations of the gene-associated
4250 variables. GOfuncR also provides tools for exploring the ontology graph and
4251 the annotations, and options to take gene-length or spatial clustering of
4252 genes into account. It is also possible to provide custom gene coordinates,
4253 annotations and ontologies.")
4254 (license license:gpl2+)))
4256 (define-public r-abaenrichment
4258 (name "r-abaenrichment")
4263 (uri (bioconductor-uri "ABAEnrichment" version))
4266 "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp"))))
4267 (properties `((upstream-name . "ABAEnrichment")))
4268 (build-system r-build-system)
4270 `(("r-abadata" ,r-abadata)
4271 ("r-data-table" ,r-data-table)
4272 ("r-gofuncr" ,r-gofuncr)
4273 ("r-gplots" ,r-gplots)
4274 ("r-gtools" ,r-gtools)
4275 ("r-rcpp" ,r-rcpp)))
4276 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4277 (synopsis "Gene expression enrichment in human brain regions")
4279 "The package ABAEnrichment is designed to test for enrichment of user
4280 defined candidate genes in the set of expressed genes in different human brain
4281 regions. The core function @code{aba_enrich} integrates the expression of the
4282 candidate gene set (averaged across donors) and the structural information of
4283 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4284 (license license:gpl2+)))
4286 (define-public r-annotationfuncs
4288 (name "r-annotationfuncs")
4293 (uri (bioconductor-uri "AnnotationFuncs" version))
4296 "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq"))))
4298 `((upstream-name . "AnnotationFuncs")))
4299 (build-system r-build-system)
4301 `(("r-annotationdbi" ,r-annotationdbi)
4303 (home-page "https://www.iysik.com/r/annotationfuncs")
4304 (synopsis "Annotation translation functions")
4306 "This package provides functions for handling translating between
4307 different identifieres using the Biocore Data Team data-packages (e.g.
4308 @code{org.Bt.eg.db}).")
4309 (license license:gpl2)))
4311 (define-public r-annotationtools
4313 (name "r-annotationtools")
4318 (uri (bioconductor-uri "annotationTools" version))
4321 "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i"))))
4323 `((upstream-name . "annotationTools")))
4324 (build-system r-build-system)
4325 (propagated-inputs `(("r-biobase" ,r-biobase)))
4326 (home-page "https://bioconductor.org/packages/annotationTools/")
4327 (synopsis "Annotate microarrays and perform gene expression analyses")
4329 "This package provides functions to annotate microarrays, find orthologs,
4330 and integrate heterogeneous gene expression profiles using annotation and
4331 other molecular biology information available as flat file database (plain
4333 ;; Any version of the GPL.
4334 (license (list license:gpl2+))))
4336 (define-public r-allelicimbalance
4338 (name "r-allelicimbalance")
4343 (uri (bioconductor-uri "AllelicImbalance" version))
4346 "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc"))))
4348 `((upstream-name . "AllelicImbalance")))
4349 (build-system r-build-system)
4351 `(("r-annotationdbi" ,r-annotationdbi)
4352 ("r-biocgenerics" ,r-biocgenerics)
4353 ("r-biostrings" ,r-biostrings)
4354 ("r-bsgenome" ,r-bsgenome)
4355 ("r-genomeinfodb" ,r-genomeinfodb)
4356 ("r-genomicalignments" ,r-genomicalignments)
4357 ("r-genomicfeatures" ,r-genomicfeatures)
4358 ("r-genomicranges" ,r-genomicranges)
4359 ("r-gridextra" ,r-gridextra)
4361 ("r-iranges" ,r-iranges)
4362 ("r-lattice" ,r-lattice)
4363 ("r-latticeextra" ,r-latticeextra)
4365 ("r-rsamtools" ,r-rsamtools)
4366 ("r-s4vectors" ,r-s4vectors)
4367 ("r-seqinr" ,r-seqinr)
4368 ("r-summarizedexperiment" ,r-summarizedexperiment)
4369 ("r-variantannotation" ,r-variantannotation)))
4370 (home-page "https://github.com/pappewaio/AllelicImbalance")
4371 (synopsis "Investigate allele-specific expression")
4373 "This package provides a framework for allele-specific expression
4374 investigation using RNA-seq data.")
4375 (license license:gpl3)))
4377 (define-public r-aucell
4384 (uri (bioconductor-uri "AUCell" version))
4387 "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky"))))
4388 (properties `((upstream-name . "AUCell")))
4389 (build-system r-build-system)
4391 `(("r-biocgenerics" ,r-biocgenerics)
4392 ("r-data-table" ,r-data-table)
4393 ("r-gseabase" ,r-gseabase)
4394 ("r-mixtools" ,r-mixtools)
4395 ("r-r-utils" ,r-r-utils)
4396 ("r-s4vectors" ,r-s4vectors)
4397 ("r-shiny" ,r-shiny)
4398 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4399 (home-page "https://bioconductor.org/packages/AUCell/")
4400 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4402 "AUCell identifies cells with active gene sets (e.g. signatures,
4403 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4404 Under the Curve} (AUC) to calculate whether a critical subset of the input
4405 gene set is enriched within the expressed genes for each cell. The
4406 distribution of AUC scores across all the cells allows exploring the relative
4407 expression of the signature. Since the scoring method is ranking-based,
4408 AUCell is independent of the gene expression units and the normalization
4409 procedure. In addition, since the cells are evaluated individually, it can
4410 easily be applied to bigger datasets, subsetting the expression matrix if
4412 (license license:gpl3)))
4414 (define-public r-ebimage
4421 (uri (bioconductor-uri "EBImage" version))
4424 "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs"))))
4425 (properties `((upstream-name . "EBImage")))
4426 (build-system r-build-system)
4428 `(("r-abind" ,r-abind)
4429 ("r-biocgenerics" ,r-biocgenerics)
4430 ("r-fftwtools" ,r-fftwtools)
4431 ("r-htmltools" ,r-htmltools)
4432 ("r-htmlwidgets" ,r-htmlwidgets)
4434 ("r-locfit" ,r-locfit)
4436 ("r-rcurl" ,r-rcurl)
4437 ("r-tiff" ,r-tiff)))
4439 `(("r-knitr" ,r-knitr))) ; for vignettes
4440 (home-page "https://github.com/aoles/EBImage")
4441 (synopsis "Image processing and analysis toolbox for R")
4443 "EBImage provides general purpose functionality for image processing and
4444 analysis. In the context of (high-throughput) microscopy-based cellular
4445 assays, EBImage offers tools to segment cells and extract quantitative
4446 cellular descriptors. This allows the automation of such tasks using the R
4447 programming language and facilitates the use of other tools in the R
4448 environment for signal processing, statistical modeling, machine learning and
4449 visualization with image data.")
4450 ;; Any version of the LGPL.
4451 (license license:lgpl2.1+)))
4453 (define-public r-yamss
4460 (uri (bioconductor-uri "yamss" version))
4463 "12jr7hbrwhb1gfjadj1024hv80ra22miy46dn40nmsrbklkfn3rw"))))
4464 (build-system r-build-system)
4466 `(("r-biocgenerics" ,r-biocgenerics)
4467 ("r-data-table" ,r-data-table)
4468 ("r-ebimage" ,r-ebimage)
4469 ("r-iranges" ,r-iranges)
4470 ("r-limma" ,r-limma)
4471 ("r-matrix" ,r-matrix)
4473 ("r-s4vectors" ,r-s4vectors)
4474 ("r-summarizedexperiment"
4475 ,r-summarizedexperiment)))
4476 (home-page "https://github.com/hansenlab/yamss")
4477 (synopsis "Tools for high-throughput metabolomics")
4479 "This package provides tools to analyze and visualize high-throughput
4480 metabolomics data acquired using chromatography-mass spectrometry. These tools
4481 preprocess data in a way that enables reliable and powerful differential
4483 (license license:artistic2.0)))
4485 (define-public r-gtrellis
4492 (uri (bioconductor-uri "gtrellis" version))
4495 "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z"))))
4496 (build-system r-build-system)
4498 `(("r-circlize" ,r-circlize)
4499 ("r-genomicranges" ,r-genomicranges)
4500 ("r-getoptlong" ,r-getoptlong)
4501 ("r-iranges" ,r-iranges)))
4502 (home-page "https://github.com/jokergoo/gtrellis")
4503 (synopsis "Genome level Trellis layout")
4505 "Genome level Trellis graph visualizes genomic data conditioned by
4506 genomic categories (e.g. chromosomes). For each genomic category, multiple
4507 dimensional data which are represented as tracks describe different features
4508 from different aspects. This package provides high flexibility to arrange
4509 genomic categories and to add self-defined graphics in the plot.")
4510 (license license:expat)))
4512 (define-public r-somaticsignatures
4514 (name "r-somaticsignatures")
4519 (uri (bioconductor-uri "SomaticSignatures" version))
4522 "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z"))))
4524 `((upstream-name . "SomaticSignatures")))
4525 (build-system r-build-system)
4527 `(("r-biobase" ,r-biobase)
4528 ("r-biostrings" ,r-biostrings)
4529 ("r-genomeinfodb" ,r-genomeinfodb)
4530 ("r-genomicranges" ,r-genomicranges)
4531 ("r-ggbio" ,r-ggbio)
4532 ("r-ggplot2" ,r-ggplot2)
4533 ("r-iranges" ,r-iranges)
4535 ("r-pcamethods" ,r-pcamethods)
4536 ("r-proxy" ,r-proxy)
4537 ("r-reshape2" ,r-reshape2)
4538 ("r-s4vectors" ,r-s4vectors)
4539 ("r-variantannotation" ,r-variantannotation)))
4540 (home-page "https://github.com/juliangehring/SomaticSignatures")
4541 (synopsis "Somatic signatures")
4543 "This package identifies mutational signatures of @dfn{single nucleotide
4544 variants} (SNVs). It provides a infrastructure related to the methodology
4545 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4546 decomposition algorithms.")
4547 (license license:expat)))
4549 (define-public r-yapsa
4556 (uri (bioconductor-uri "YAPSA" version))
4559 "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926"))))
4560 (properties `((upstream-name . "YAPSA")))
4561 (build-system r-build-system)
4563 `(("r-circlize" ,r-circlize)
4564 ("r-complexheatmap" ,r-complexheatmap)
4565 ("r-corrplot" ,r-corrplot)
4566 ("r-dendextend" ,r-dendextend)
4567 ("r-genomeinfodb" ,r-genomeinfodb)
4568 ("r-genomicranges" ,r-genomicranges)
4569 ("r-getoptlong" ,r-getoptlong)
4570 ("r-ggplot2" ,r-ggplot2)
4571 ("r-gridextra" ,r-gridextra)
4572 ("r-gtrellis" ,r-gtrellis)
4573 ("r-keggrest" ,r-keggrest)
4575 ("r-pmcmr" ,r-pmcmr)
4576 ("r-reshape2" ,r-reshape2)
4577 ("r-somaticsignatures" ,r-somaticsignatures)
4578 ("r-variantannotation" ,r-variantannotation)))
4579 (home-page "https://bioconductor.org/packages/YAPSA/")
4580 (synopsis "Yet another package for signature analysis")
4582 "This package provides functions and routines useful in the analysis of
4583 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4584 functions to perform a signature analysis with known signatures and a
4585 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4587 (license license:gpl3)))
4589 (define-public r-gcrma
4596 (uri (bioconductor-uri "gcrma" version))
4599 "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx"))))
4600 (build-system r-build-system)
4602 `(("r-affy" ,r-affy)
4603 ("r-affyio" ,r-affyio)
4604 ("r-biobase" ,r-biobase)
4605 ("r-biocmanager" ,r-biocmanager)
4606 ("r-biostrings" ,r-biostrings)
4607 ("r-xvector" ,r-xvector)))
4608 (home-page "https://bioconductor.org/packages/gcrma/")
4609 (synopsis "Background adjustment using sequence information")
4611 "Gcrma adjusts for background intensities in Affymetrix array data which
4612 include optical noise and @dfn{non-specific binding} (NSB). The main function
4613 @code{gcrma} converts background adjusted probe intensities to expression
4614 measures using the same normalization and summarization methods as a
4615 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4616 to estimate probe affinity to NSB. The sequence information is summarized in
4617 a more complex way than the simple GC content. Instead, the base types (A, T,
4618 G or C) at each position along the probe determine the affinity of each probe.
4619 The parameters of the position-specific base contributions to the probe
4620 affinity is estimated in an NSB experiment in which only NSB but no
4621 gene-specific bidning is expected.")
4622 ;; Any version of the LGPL
4623 (license license:lgpl2.1+)))
4625 (define-public r-simpleaffy
4627 (name "r-simpleaffy")
4632 (uri (bioconductor-uri "simpleaffy" version))
4635 "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs"))))
4636 (build-system r-build-system)
4638 `(("r-affy" ,r-affy)
4639 ("r-biobase" ,r-biobase)
4640 ("r-biocgenerics" ,r-biocgenerics)
4641 ("r-gcrma" ,r-gcrma)
4642 ("r-genefilter" ,r-genefilter)))
4643 (home-page "https://bioconductor.org/packages/simpleaffy/")
4644 (synopsis "Very simple high level analysis of Affymetrix data")
4646 "This package provides high level functions for reading Affy @file{.CEL}
4647 files, phenotypic data, and then computing simple things with it, such as
4648 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4649 library. It also has some basic scatter plot functions and mechanisms for
4650 generating high resolution journal figures.")
4651 (license license:gpl2+)))
4653 (define-public r-yaqcaffy
4660 (uri (bioconductor-uri "yaqcaffy" version))
4663 "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz"))))
4664 (build-system r-build-system)
4666 `(("r-simpleaffy" ,r-simpleaffy)))
4667 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4668 (synopsis "Affymetrix quality control and reproducibility analysis")
4670 "This is a package that can be used for quality control of Affymetrix
4671 GeneChip expression data and reproducibility analysis of human whole genome
4672 chips with the MAQC reference datasets.")
4673 (license license:artistic2.0)))
4675 (define-public r-quantro
4682 (uri (bioconductor-uri "quantro" version))
4685 "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m"))))
4686 (build-system r-build-system)
4688 `(("r-biobase" ,r-biobase)
4689 ("r-doparallel" ,r-doparallel)
4690 ("r-foreach" ,r-foreach)
4691 ("r-ggplot2" ,r-ggplot2)
4692 ("r-iterators" ,r-iterators)
4693 ("r-minfi" ,r-minfi)
4694 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4695 (home-page "https://bioconductor.org/packages/quantro/")
4696 (synopsis "Test for when to use quantile normalization")
4698 "This package provides a data-driven test for the assumptions of quantile
4699 normalization using raw data such as objects that inherit eSets (e.g.
4700 ExpressionSet, MethylSet). Group level information about each sample (such as
4701 Tumor / Normal status) must also be provided because the test assesses if
4702 there are global differences in the distributions between the user-defined
4704 (license license:gpl3+)))
4706 (define-public r-yarn
4713 (uri (bioconductor-uri "yarn" version))
4716 "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp"))))
4717 (build-system r-build-system)
4719 `(("r-biobase" ,r-biobase)
4720 ("r-biomart" ,r-biomart)
4721 ("r-downloader" ,r-downloader)
4722 ("r-edger" ,r-edger)
4723 ("r-gplots" ,r-gplots)
4724 ("r-limma" ,r-limma)
4725 ("r-matrixstats" ,r-matrixstats)
4726 ("r-preprocesscore" ,r-preprocesscore)
4727 ("r-quantro" ,r-quantro)
4728 ("r-rcolorbrewer" ,r-rcolorbrewer)
4729 ("r-readr" ,r-readr)))
4730 (home-page "https://bioconductor.org/packages/yarn/")
4731 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4733 "Expedite large RNA-Seq analyses using a combination of previously
4734 developed tools. YARN is meant to make it easier for the user in performing
4735 basic mis-annotation quality control, filtering, and condition-aware
4736 normalization. YARN leverages many Bioconductor tools and statistical
4737 techniques to account for the large heterogeneity and sparsity found in very
4738 large RNA-seq experiments.")
4739 (license license:artistic2.0)))
4741 (define-public r-roar
4748 (uri (bioconductor-uri "roar" version))
4751 "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06"))))
4752 (build-system r-build-system)
4754 `(("r-biocgenerics" ,r-biocgenerics)
4755 ("r-genomeinfodb" ,r-genomeinfodb)
4756 ("r-genomicalignments" ,r-genomicalignments)
4757 ("r-genomicranges" ,r-genomicranges)
4758 ("r-iranges" ,r-iranges)
4759 ("r-rtracklayer" ,r-rtracklayer)
4760 ("r-s4vectors" ,r-s4vectors)
4761 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4762 (home-page "https://github.com/vodkatad/roar/")
4763 (synopsis "Identify differential APA usage from RNA-seq alignments")
4765 "This package provides tools for identifying preferential usage of APA
4766 sites, comparing two biological conditions, starting from known alternative
4767 sites and alignments obtained from standard RNA-seq experiments.")
4768 (license license:gpl3)))
4770 (define-public r-xbseq
4777 (uri (bioconductor-uri "XBSeq" version))
4780 "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp"))))
4781 (properties `((upstream-name . "XBSeq")))
4782 (build-system r-build-system)
4784 `(("r-biobase" ,r-biobase)
4785 ("r-deseq2" ,r-deseq2)
4786 ("r-dplyr" ,r-dplyr)
4787 ("r-ggplot2" ,r-ggplot2)
4788 ("r-locfit" ,r-locfit)
4789 ("r-magrittr" ,r-magrittr)
4790 ("r-matrixstats" ,r-matrixstats)
4791 ("r-pracma" ,r-pracma)
4792 ("r-roar" ,r-roar)))
4793 (home-page "https://github.com/Liuy12/XBSeq")
4794 (synopsis "Test for differential expression for RNA-seq data")
4796 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4797 expression} (DE), where a statistical model was established based on the
4798 assumption that observed signals are the convolution of true expression
4799 signals and sequencing noises. The mapped reads in non-exonic regions are
4800 considered as sequencing noises, which follows a Poisson distribution. Given
4801 measurable observed signal and background noise from RNA-seq data, true
4802 expression signals, assuming governed by the negative binomial distribution,
4803 can be delineated and thus the accurate detection of differential expressed
4805 (license license:gpl3+)))
4807 (define-public r-massspecwavelet
4809 (name "r-massspecwavelet")
4814 (uri (bioconductor-uri "MassSpecWavelet" version))
4817 "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7"))))
4819 `((upstream-name . "MassSpecWavelet")))
4820 (build-system r-build-system)
4822 `(("r-waveslim" ,r-waveslim)))
4823 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4824 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4826 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4827 data mainly through the use of wavelet transforms. It supports peak detection
4828 based on @dfn{Continuous Wavelet Transform} (CWT).")
4829 (license license:lgpl2.0+)))
4831 (define-public r-xcms
4838 (uri (bioconductor-uri "xcms" version))
4841 "0bfl56v3l6k31i11l09nx1yqfjy6z5yragm6k83z4w0mpgk18y7g"))))
4842 (build-system r-build-system)
4844 `(("r-biobase" ,r-biobase)
4845 ("r-biocgenerics" ,r-biocgenerics)
4846 ("r-biocparallel" ,r-biocparallel)
4847 ("r-iranges" ,r-iranges)
4848 ("r-lattice" ,r-lattice)
4849 ("r-massspecwavelet" ,r-massspecwavelet)
4850 ("r-msnbase" ,r-msnbase)
4851 ("r-multtest" ,r-multtest)
4854 ("r-protgenerics" ,r-protgenerics)
4856 ("r-rcolorbrewer" ,r-rcolorbrewer)
4857 ("r-robustbase" ,r-robustbase)
4858 ("r-s4vectors" ,r-s4vectors)))
4859 (home-page "https://bioconductor.org/packages/xcms/")
4860 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4862 "This package provides a framework for processing and visualization of
4863 chromatographically separated and single-spectra mass spectral data. It
4864 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4865 data for high-throughput, untargeted analyte profiling.")
4866 (license license:gpl2+)))
4868 (define-public r-wrench
4875 (uri (bioconductor-uri "Wrench" version))
4878 "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm"))))
4879 (properties `((upstream-name . "Wrench")))
4880 (build-system r-build-system)
4882 `(("r-limma" ,r-limma)
4883 ("r-locfit" ,r-locfit)
4884 ("r-matrixstats" ,r-matrixstats)))
4885 (home-page "https://github.com/HCBravoLab/Wrench")
4886 (synopsis "Wrench normalization for sparse count data")
4888 "Wrench is a package for normalization sparse genomic count data, like
4889 that arising from 16s metagenomic surveys.")
4890 (license license:artistic2.0)))
4892 (define-public r-wiggleplotr
4894 (name "r-wiggleplotr")
4899 (uri (bioconductor-uri "wiggleplotr" version))
4902 "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m"))))
4903 (build-system r-build-system)
4905 `(("r-assertthat" ,r-assertthat)
4906 ("r-cowplot" ,r-cowplot)
4907 ("r-dplyr" ,r-dplyr)
4908 ("r-genomeinfodb" ,r-genomeinfodb)
4909 ("r-genomicranges" ,r-genomicranges)
4910 ("r-ggplot2" ,r-ggplot2)
4911 ("r-iranges" ,r-iranges)
4912 ("r-purrr" ,r-purrr)
4913 ("r-rtracklayer" ,r-rtracklayer)
4914 ("r-s4vectors" ,r-s4vectors)))
4915 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4916 (synopsis "Make read coverage plots from BigWig files")
4918 "This package provides tools to visualize read coverage from sequencing
4919 experiments together with genomic annotations (genes, transcripts, peaks).
4920 Introns of long transcripts can be rescaled to a fixed length for better
4921 visualization of exonic read coverage.")
4922 (license license:asl2.0)))
4924 (define-public r-widgettools
4926 (name "r-widgettools")
4931 (uri (bioconductor-uri "widgetTools" version))
4934 "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5"))))
4935 (properties `((upstream-name . "widgetTools")))
4936 (build-system r-build-system)
4937 (home-page "https://bioconductor.org/packages/widgetTools/")
4938 (synopsis "Tools for creating interactive tcltk widgets")
4940 "This package contains tools to support the construction of tcltk
4942 ;; Any version of the LGPL.
4943 (license license:lgpl3+)))
4945 (define-public r-webbioc
4952 (uri (bioconductor-uri "webbioc" version))
4955 "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62"))))
4956 (build-system r-build-system)
4958 `(("netpbm" ,netpbm)
4961 `(("r-affy" ,r-affy)
4962 ("r-annaffy" ,r-annaffy)
4963 ("r-biobase" ,r-biobase)
4964 ("r-biocmanager" ,r-biocmanager)
4965 ("r-gcrma" ,r-gcrma)
4966 ("r-multtest" ,r-multtest)
4967 ("r-qvalue" ,r-qvalue)
4969 (home-page "https://www.bioconductor.org/")
4970 (synopsis "Bioconductor web interface")
4972 "This package provides an integrated web interface for doing microarray
4973 analysis using several of the Bioconductor packages. It is intended to be
4974 deployed as a centralized bioinformatics resource for use by many users.
4975 Currently only Affymetrix oligonucleotide analysis is supported.")
4976 (license license:gpl2+)))
4978 (define-public r-zfpkm
4985 (uri (bioconductor-uri "zFPKM" version))
4988 "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n"))))
4989 (properties `((upstream-name . "zFPKM")))
4990 (build-system r-build-system)
4992 `(("r-checkmate" ,r-checkmate)
4993 ("r-dplyr" ,r-dplyr)
4994 ("r-ggplot2" ,r-ggplot2)
4995 ("r-summarizedexperiment" ,r-summarizedexperiment)
4996 ("r-tidyr" ,r-tidyr)))
4997 (home-page "https://github.com/ronammar/zFPKM/")
4998 (synopsis "Functions to facilitate zFPKM transformations")
5000 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5001 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5003 (license license:gpl3)))
5005 (define-public r-rbowtie2
5012 (uri (bioconductor-uri "Rbowtie2" version))
5015 "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5"))))
5016 (properties `((upstream-name . "Rbowtie2")))
5017 (build-system r-build-system)
5020 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5021 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5023 "This package provides an R wrapper of the popular @code{bowtie2}
5024 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5025 rapid adapter trimming, identification, and read merging.")
5026 (license license:gpl3+)))
5028 (define-public r-progeny
5035 (uri (bioconductor-uri "progeny" version))
5038 "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq"))))
5039 (build-system r-build-system)
5040 (propagated-inputs `(("r-biobase" ,r-biobase)))
5041 (home-page "https://github.com/saezlab/progeny")
5042 (synopsis "Pathway responsive gene activity inference")
5044 "This package provides a function to infer pathway activity from gene
5045 expression. It contains the linear model inferred in the publication
5046 \"Perturbation-response genes reveal signaling footprints in cancer gene
5048 (license license:asl2.0)))
5050 (define-public r-arrmnormalization
5052 (name "r-arrmnormalization")
5057 (uri (bioconductor-uri "ARRmNormalization" version))
5060 "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1"))))
5062 `((upstream-name . "ARRmNormalization")))
5063 (build-system r-build-system)
5064 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5065 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5066 (synopsis "Adaptive robust regression normalization for methylation data")
5068 "This is a package to perform the @dfn{Adaptive Robust Regression
5069 method} (ARRm) for the normalization of methylation data from the Illumina
5070 Infinium HumanMethylation 450k assay.")
5071 (license license:artistic2.0)))
5073 (define-public r-biocfilecache
5075 (name "r-biocfilecache")
5080 (uri (bioconductor-uri "BiocFileCache" version))
5083 "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6"))))
5084 (properties `((upstream-name . "BiocFileCache")))
5085 (build-system r-build-system)
5087 `(("r-curl" ,r-curl)
5089 ("r-dbplyr" ,r-dbplyr)
5090 ("r-dplyr" ,r-dplyr)
5092 ("r-rappdirs" ,r-rappdirs)
5093 ("r-rsqlite" ,r-rsqlite)))
5094 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5095 (synopsis "Manage files across sessions")
5097 "This package creates a persistent on-disk cache of files that the user
5098 can add, update, and retrieve. It is useful for managing resources (such as
5099 custom Txdb objects) that are costly or difficult to create, web resources,
5100 and data files used across sessions.")
5101 (license license:artistic2.0)))
5103 (define-public r-iclusterplus
5105 (name "r-iclusterplus")
5110 (uri (bioconductor-uri "iClusterPlus" version))
5113 "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37"))))
5114 (properties `((upstream-name . "iClusterPlus")))
5115 (build-system r-build-system)
5116 (native-inputs `(("gfortran" ,gfortran)))
5117 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5118 (synopsis "Integrative clustering of multi-type genomic data")
5120 "iClusterPlus is developed for integrative clustering analysis of
5121 multi-type genomic data and is an enhanced version of iCluster proposed and
5122 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5123 from the experiments where biological samples (e.g. tumor samples) are
5124 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5125 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5126 on. In the iClusterPlus model, binary observations such as somatic mutation
5127 are modeled as Binomial processes; categorical observations such as copy
5128 number states are realizations of Multinomial random variables; counts are
5129 modeled as Poisson random processes; and continuous measures are modeled by
5130 Gaussian distributions.")
5131 (license license:gpl2+)))
5133 (define-public r-rbowtie
5140 (uri (bioconductor-uri "Rbowtie" version))
5143 "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4"))))
5144 (properties `((upstream-name . "Rbowtie")))
5145 (build-system r-build-system)
5148 (home-page "https://bioconductor.org/packages/Rbowtie/")
5149 (synopsis "R bowtie wrapper")
5151 "This package provides an R wrapper around the popular bowtie short read
5152 aligner and around SpliceMap, a de novo splice junction discovery and
5154 (license license:artistic2.0)))
5156 (define-public r-sgseq
5163 (uri (bioconductor-uri "SGSeq" version))
5166 "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw"))))
5167 (properties `((upstream-name . "SGSeq")))
5168 (build-system r-build-system)
5170 `(("r-annotationdbi" ,r-annotationdbi)
5171 ("r-biocgenerics" ,r-biocgenerics)
5172 ("r-biostrings" ,r-biostrings)
5173 ("r-genomeinfodb" ,r-genomeinfodb)
5174 ("r-genomicalignments" ,r-genomicalignments)
5175 ("r-genomicfeatures" ,r-genomicfeatures)
5176 ("r-genomicranges" ,r-genomicranges)
5177 ("r-igraph" ,r-igraph)
5178 ("r-iranges" ,r-iranges)
5179 ("r-rsamtools" ,r-rsamtools)
5180 ("r-rtracklayer" ,r-rtracklayer)
5181 ("r-runit" ,r-runit)
5182 ("r-s4vectors" ,r-s4vectors)
5183 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5184 (home-page "https://bioconductor.org/packages/SGSeq/")
5185 (synopsis "Splice event prediction and quantification from RNA-seq data")
5187 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5188 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5189 represented as a splice graph, which can be obtained from existing annotation
5190 or predicted from the mapped sequence reads. Splice events are identified
5191 from the graph and are quantified locally using structurally compatible reads
5192 at the start or end of each splice variant. The software includes functions
5193 for splice event prediction, quantification, visualization and
5195 (license license:artistic2.0)))
5197 (define-public r-rhisat2
5204 (uri (bioconductor-uri "Rhisat2" version))
5207 "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49"))))
5208 (properties `((upstream-name . "Rhisat2")))
5209 (build-system r-build-system)
5212 (modify-phases %standard-phases
5213 (add-after 'unpack 'make-reproducible
5215 (substitute* "src/Makefile"
5216 (("`hostname`") "guix")
5218 ;; Avoid shelling out to "which".
5219 (("^CC =.*") (which "gcc"))
5220 (("^CPP =.*") (which "g++")))
5223 `(("r-genomicfeatures" ,r-genomicfeatures)
5224 ("r-genomicranges" ,r-genomicranges)
5225 ("r-sgseq" ,r-sgseq)))
5226 (home-page "https://github.com/fmicompbio/Rhisat2")
5227 (synopsis "R Wrapper for HISAT2 sequence aligner")
5229 "This package provides an R interface to the HISAT2 spliced short-read
5230 aligner by Kim et al. (2015). The package contains wrapper functions to
5231 create a genome index and to perform the read alignment to the generated
5233 (license license:gpl3)))
5235 (define-public r-quasr
5242 (uri (bioconductor-uri "QuasR" version))
5245 "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv"))))
5246 (properties `((upstream-name . "QuasR")))
5247 (build-system r-build-system)
5251 `(("r-annotationdbi" ,r-annotationdbi)
5252 ("r-biobase" ,r-biobase)
5253 ("r-biocgenerics" ,r-biocgenerics)
5254 ("r-biocmanager" ,r-biocmanager)
5255 ("r-biocparallel" ,r-biocparallel)
5256 ("r-biostrings" ,r-biostrings)
5257 ("r-bsgenome" ,r-bsgenome)
5258 ("r-genomeinfodb" ,r-genomeinfodb)
5259 ("r-genomicalignments" ,r-genomicalignments)
5260 ("r-genomicfeatures" ,r-genomicfeatures)
5261 ("r-genomicfiles" ,r-genomicfiles)
5262 ("r-genomicranges" ,r-genomicranges)
5263 ("r-iranges" ,r-iranges)
5264 ("r-rbowtie" ,r-rbowtie)
5265 ("r-rhisat2" ,r-rhisat2)
5266 ("r-rhtslib" ,r-rhtslib)
5267 ("r-rsamtools" ,r-rsamtools)
5268 ("r-rtracklayer" ,r-rtracklayer)
5269 ("r-s4vectors" ,r-s4vectors)
5270 ("r-shortread" ,r-shortread)))
5271 (home-page "https://bioconductor.org/packages/QuasR/")
5272 (synopsis "Quantify and annotate short reads in R")
5274 "This package provides a framework for the quantification and analysis of
5275 short genomic reads. It covers a complete workflow starting from raw sequence
5276 reads, over creation of alignments and quality control plots, to the
5277 quantification of genomic regions of interest.")
5278 (license license:gpl2)))
5280 (define-public r-rqc
5287 (uri (bioconductor-uri "Rqc" version))
5290 "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m"))))
5291 (properties `((upstream-name . "Rqc")))
5292 (build-system r-build-system)
5294 `(("r-biocgenerics" ,r-biocgenerics)
5295 ("r-biocparallel" ,r-biocparallel)
5296 ("r-biocstyle" ,r-biocstyle)
5297 ("r-biostrings" ,r-biostrings)
5298 ("r-biovizbase" ,r-biovizbase)
5299 ("r-genomicalignments" ,r-genomicalignments)
5300 ("r-genomicfiles" ,r-genomicfiles)
5301 ("r-ggplot2" ,r-ggplot2)
5302 ("r-iranges" ,r-iranges)
5303 ("r-knitr" ,r-knitr)
5304 ("r-markdown" ,r-markdown)
5307 ("r-reshape2" ,r-reshape2)
5308 ("r-rsamtools" ,r-rsamtools)
5309 ("r-s4vectors" ,r-s4vectors)
5310 ("r-shiny" ,r-shiny)
5311 ("r-shortread" ,r-shortread)))
5312 (home-page "https://github.com/labbcb/Rqc")
5313 (synopsis "Quality control tool for high-throughput sequencing data")
5315 "Rqc is an optimized tool designed for quality control and assessment of
5316 high-throughput sequencing data. It performs parallel processing of entire
5317 files and produces a report which contains a set of high-resolution
5319 (license license:gpl2+)))
5321 (define-public r-birewire
5328 (uri (bioconductor-uri "BiRewire" version))
5331 "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q"))))
5332 (properties `((upstream-name . "BiRewire")))
5333 (build-system r-build-system)
5335 `(("r-igraph" ,r-igraph)
5336 ("r-matrix" ,r-matrix)
5338 ("r-tsne" ,r-tsne)))
5339 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5340 (synopsis "Tools for randomization of bipartite graphs")
5342 "This package provides functions for bipartite network rewiring through N
5343 consecutive switching steps and for the computation of the minimal number of
5344 switching steps to be performed in order to maximise the dissimilarity with
5345 respect to the original network. It includes functions for the analysis of
5346 the introduced randomness across the switching steps and several other
5347 routines to analyse the resulting networks and their natural projections.")
5348 (license license:gpl3)))
5350 (define-public r-birta
5357 (uri (bioconductor-uri "birta" version))
5360 "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg"))))
5361 (build-system r-build-system)
5363 `(("r-biobase" ,r-biobase)
5364 ("r-limma" ,r-limma)
5365 ("r-mass" ,r-mass)))
5366 (home-page "https://bioconductor.org/packages/birta")
5367 (synopsis "Bayesian inference of regulation of transcriptional activity")
5369 "Expression levels of mRNA molecules are regulated by different
5370 processes, comprising inhibition or activation by transcription factors and
5371 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5372 Inference of Regulation of Transcriptional Activity) uses the regulatory
5373 networks of transcription factors and miRNAs together with mRNA and miRNA
5374 expression data to predict switches in regulatory activity between two
5375 conditions. A Bayesian network is used to model the regulatory structure and
5376 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5377 (license license:gpl2+)))
5379 (define-public r-multidataset
5381 (name "r-multidataset")
5386 (uri (bioconductor-uri "MultiDataSet" version))
5389 "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj"))))
5390 (properties `((upstream-name . "MultiDataSet")))
5391 (build-system r-build-system)
5393 `(("r-biobase" ,r-biobase)
5394 ("r-biocgenerics" ,r-biocgenerics)
5395 ("r-genomicranges" ,r-genomicranges)
5396 ("r-ggplot2" ,r-ggplot2)
5397 ("r-ggrepel" ,r-ggrepel)
5398 ("r-iranges" ,r-iranges)
5399 ("r-limma" ,r-limma)
5400 ("r-qqman" ,r-qqman)
5401 ("r-s4vectors" ,r-s4vectors)
5402 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5403 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5404 (synopsis "Implementation of MultiDataSet and ResultSet")
5406 "This package provides an implementation of the BRGE's (Bioinformatic
5407 Research Group in Epidemiology from Center for Research in Environmental
5408 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5409 integrating multi omics data sets and ResultSet is a container for omics
5410 results. This package contains base classes for MEAL and rexposome
5412 (license license:expat)))
5414 (define-public r-ropls
5421 (uri (bioconductor-uri "ropls" version))
5424 "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a"))))
5425 (build-system r-build-system)
5427 `(("r-biobase" ,r-biobase)
5428 ("r-multidataset" ,r-multidataset)))
5430 `(("r-knitr" ,r-knitr))) ; for vignettes
5431 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5432 (synopsis "Multivariate analysis and feature selection of omics data")
5434 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5435 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5436 regression, classification, and feature selection of omics data where the
5437 number of variables exceeds the number of samples and with multicollinearity
5438 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5439 separately model the variation correlated (predictive) to the factor of
5440 interest and the uncorrelated (orthogonal) variation. While performing
5441 similarly to PLS, OPLS facilitates interpretation.
5443 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5444 analysis and feature selection of omics data. In addition to scores, loadings
5445 and weights plots, the package provides metrics and graphics to determine the
5446 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5447 validity of the model by permutation testing, detect outliers, and perform
5448 feature selection (e.g. with Variable Importance in Projection or regression
5450 (license license:cecill)))
5452 (define-public r-biosigner
5454 (name "r-biosigner")
5459 (uri (bioconductor-uri "biosigner" version))
5462 "0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl"))))
5463 (build-system r-build-system)
5465 `(("r-biobase" ,r-biobase)
5466 ("r-e1071" ,r-e1071)
5467 ("r-multidataset" ,r-multidataset)
5468 ("r-randomforest" ,r-randomforest)
5469 ("r-ropls" ,r-ropls)))
5471 `(("r-knitr" ,r-knitr)))
5472 (home-page "https://bioconductor.org/packages/biosigner/")
5473 (synopsis "Signature discovery from omics data")
5475 "Feature selection is critical in omics data analysis to extract
5476 restricted and meaningful molecular signatures from complex and high-dimension
5477 data, and to build robust classifiers. This package implements a method to
5478 assess the relevance of the variables for the prediction performances of the
5479 classifier. The approach can be run in parallel with the PLS-DA, Random
5480 Forest, and SVM binary classifiers. The signatures and the corresponding
5481 'restricted' models are returned, enabling future predictions on new
5483 (license license:cecill)))
5485 (define-public r-annotatr
5492 (uri (bioconductor-uri "annotatr" version))
5495 "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj"))))
5496 (build-system r-build-system)
5498 `(("r-annotationdbi" ,r-annotationdbi)
5499 ("r-annotationhub" ,r-annotationhub)
5500 ("r-dplyr" ,r-dplyr)
5501 ("r-genomeinfodb" ,r-genomeinfodb)
5502 ("r-genomicfeatures" ,r-genomicfeatures)
5503 ("r-genomicranges" ,r-genomicranges)
5504 ("r-ggplot2" ,r-ggplot2)
5505 ("r-iranges" ,r-iranges)
5506 ("r-readr" ,r-readr)
5507 ("r-regioner" ,r-regioner)
5508 ("r-reshape2" ,r-reshape2)
5509 ("r-rtracklayer" ,r-rtracklayer)
5510 ("r-s4vectors" ,r-s4vectors)))
5511 (home-page "https://bioconductor.org/packages/annotatr/")
5512 (synopsis "Annotation of genomic regions to genomic annotations")
5514 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5515 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5516 to investigate the intersecting genomic annotations. Such annotations include
5517 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5518 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5519 enhancers. The annotatr package provides an easy way to summarize and
5520 visualize the intersection of genomic sites/regions with genomic
5522 (license license:gpl3)))
5524 (define-public r-rsubread
5531 (uri (bioconductor-uri "Rsubread" version))
5534 "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy"))))
5535 (properties `((upstream-name . "Rsubread")))
5536 (build-system r-build-system)
5537 (inputs `(("zlib" ,zlib)))
5538 (home-page "https://bioconductor.org/packages/Rsubread/")
5539 (synopsis "Subread sequence alignment and counting for R")
5541 "This package provides tools for alignment, quantification and analysis
5542 of second and third generation sequencing data. It includes functionality for
5543 read mapping, read counting, SNP calling, structural variant detection and
5544 gene fusion discovery. It can be applied to all major sequencing techologies
5545 and to both short and long sequence reads.")
5546 (license license:gpl3)))
5548 (define-public r-flowutils
5550 (name "r-flowutils")
5555 (uri (bioconductor-uri "flowUtils" version))
5558 "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81"))))
5559 (properties `((upstream-name . "flowUtils")))
5560 (build-system r-build-system)
5562 `(("r-biobase" ,r-biobase)
5563 ("r-corpcor" ,r-corpcor)
5564 ("r-flowcore" ,r-flowcore)
5565 ("r-graph" ,r-graph)
5566 ("r-runit" ,r-runit)
5568 (home-page "https://github.com/jspidlen/flowUtils")
5569 (synopsis "Utilities for flow cytometry")
5571 "This package provides utilities for flow cytometry data.")
5572 (license license:artistic2.0)))
5574 (define-public r-consensusclusterplus
5576 (name "r-consensusclusterplus")
5581 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5584 "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4"))))
5586 `((upstream-name . "ConsensusClusterPlus")))
5587 (build-system r-build-system)
5590 ("r-biobase" ,r-biobase)
5591 ("r-cluster" ,r-cluster)))
5592 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5593 (synopsis "Clustering algorithm")
5595 "This package provides an implementation of an algorithm for determining
5596 cluster count and membership by stability evidence in unsupervised analysis.")
5597 (license license:gpl2)))
5599 (define-public r-cytolib
5606 (uri (bioconductor-uri "cytolib" version))
5609 "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9"))))
5610 (properties `((upstream-name . "cytolib")))
5611 (build-system r-build-system)
5612 (home-page "https://bioconductor.org/packages/cytolib/")
5613 (synopsis "C++ infrastructure for working with gated cytometry")
5615 "This package provides the core data structure and API to represent and
5616 interact with gated cytometry data.")
5617 (license license:artistic2.0)))
5619 (define-public r-flowcore
5626 (uri (bioconductor-uri "flowCore" version))
5629 "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2"))))
5630 (properties `((upstream-name . "flowCore")))
5631 (build-system r-build-system)
5634 ("r-biobase" ,r-biobase)
5635 ("r-biocgenerics" ,r-biocgenerics)
5636 ("r-cytolib" ,r-cytolib)
5637 ("r-matrixstats" ,r-matrixstats)
5638 ("r-rcpp" ,r-rcpp)))
5639 (home-page "https://bioconductor.org/packages/flowCore")
5640 (synopsis "Basic structures for flow cytometry data")
5642 "This package provides S4 data structures and basic functions to deal
5643 with flow cytometry data.")
5644 (license license:artistic2.0)))
5646 (define-public r-flowmeans
5648 (name "r-flowmeans")
5653 (uri (bioconductor-uri "flowMeans" version))
5656 "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h"))))
5657 (properties `((upstream-name . "flowMeans")))
5658 (build-system r-build-system)
5660 `(("r-biobase" ,r-biobase)
5661 ("r-feature" ,r-feature)
5662 ("r-flowcore" ,r-flowcore)
5663 ("r-rrcov" ,r-rrcov)))
5664 (home-page "https://bioconductor.org/packages/flowMeans")
5665 (synopsis "Non-parametric flow cytometry data gating")
5667 "This package provides tools to identify cell populations in Flow
5668 Cytometry data using non-parametric clustering and segmented-regression-based
5669 change point detection.")
5670 (license license:artistic2.0)))
5672 (define-public r-ncdfflow
5679 (uri (bioconductor-uri "ncdfFlow" version))
5682 "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i"))))
5683 (properties `((upstream-name . "ncdfFlow")))
5684 (build-system r-build-system)
5689 ("r-biobase" ,r-biobase)
5690 ("r-biocgenerics" ,r-biocgenerics)
5691 ("r-flowcore" ,r-flowcore)
5693 ("r-rcpparmadillo" ,r-rcpparmadillo)
5694 ("r-rhdf5lib" ,r-rhdf5lib)
5695 ("r-zlibbioc" ,r-zlibbioc)))
5696 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5697 (synopsis "HDF5 based storage for flow cytometry data")
5699 "This package provides HDF5 storage based methods and functions for
5700 manipulation of flow cytometry data.")
5701 (license license:artistic2.0)))
5703 (define-public r-ggcyto
5710 (uri (bioconductor-uri "ggcyto" version))
5713 "16jwdslhmj1nsa28wmaircy15cq7qn8nsyiawinjv711qiqhgw50"))))
5714 (properties `((upstream-name . "ggcyto")))
5715 (build-system r-build-system)
5717 `(("r-data-table" ,r-data-table)
5718 ("r-flowcore" ,r-flowcore)
5719 ("r-flowworkspace" ,r-flowworkspace)
5720 ("r-ggplot2" ,r-ggplot2)
5721 ("r-gridextra" ,r-gridextra)
5722 ("r-ncdfflow" ,r-ncdfflow)
5724 ("r-rcolorbrewer" ,r-rcolorbrewer)
5725 ("r-rlang" ,r-rlang)
5726 ("r-scales" ,r-scales)))
5728 `(("r-knitr" ,r-knitr)))
5729 (home-page "https://github.com/RGLab/ggcyto/issues")
5730 (synopsis "Visualize Cytometry data with ggplot")
5732 "With the dedicated fortify method implemented for @code{flowSet},
5733 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
5734 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
5735 and some custom layers also make it easy to add gates and population
5736 statistics to the plot.")
5737 (license license:artistic2.0)))
5739 (define-public r-flowviz
5746 (uri (bioconductor-uri "flowViz" version))
5749 "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7"))))
5750 (properties `((upstream-name . "flowViz")))
5751 (build-system r-build-system)
5753 `(("r-biobase" ,r-biobase)
5754 ("r-flowcore" ,r-flowcore)
5755 ("r-hexbin" ,r-hexbin)
5756 ("r-idpmisc" ,r-idpmisc)
5757 ("r-kernsmooth" ,r-kernsmooth)
5758 ("r-lattice" ,r-lattice)
5759 ("r-latticeextra" ,r-latticeextra)
5761 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5762 (home-page "https://bioconductor.org/packages/flowViz/")
5763 (synopsis "Visualization for flow cytometry")
5765 "This package provides visualization tools for flow cytometry data.")
5766 (license license:artistic2.0)))
5768 (define-public r-flowclust
5770 (name "r-flowclust")
5775 (uri (bioconductor-uri "flowClust" version))
5778 "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s"))))
5779 (properties `((upstream-name . "flowClust")))
5780 (build-system r-build-system)
5783 (list "--configure-args=--enable-bundled-gsl=no")))
5785 `(("r-biobase" ,r-biobase)
5786 ("r-biocgenerics" ,r-biocgenerics)
5788 ("r-corpcor" ,r-corpcor)
5789 ("r-ellipse" ,r-ellipse)
5790 ("r-flowcore" ,r-flowcore)
5791 ("r-flowviz" ,r-flowviz)
5792 ("r-graph" ,r-graph)
5793 ("r-mnormt" ,r-mnormt)))
5797 `(("pkg-config" ,pkg-config)))
5798 (home-page "https://bioconductor.org/packages/flowClust")
5799 (synopsis "Clustering for flow cytometry")
5801 "This package provides robust model-based clustering using a t-mixture
5802 model with Box-Cox transformation.")
5803 (license license:artistic2.0)))
5805 ;; TODO: this package bundles an old version of protobuf. It's not easy to
5806 ;; make it use our protobuf package instead.
5807 (define-public r-rprotobuflib
5809 (name "r-rprotobuflib")
5814 (uri (bioconductor-uri "RProtoBufLib" version))
5817 "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm"))))
5818 (properties `((upstream-name . "RProtoBufLib")))
5819 (build-system r-build-system)
5822 (modify-phases %standard-phases
5823 (add-after 'unpack 'unpack-bundled-sources
5825 (with-directory-excursion "src"
5826 (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
5828 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
5829 (synopsis "C++ headers and static libraries of Protocol buffers")
5831 "This package provides the headers and static library of Protocol buffers
5832 for other R packages to compile and link against.")
5833 (license license:bsd-3)))
5835 (define-public r-flowworkspace
5837 (name "r-flowworkspace")
5842 (uri (bioconductor-uri "flowWorkspace" version))
5845 "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn"))))
5846 (properties `((upstream-name . "flowWorkspace")))
5847 (build-system r-build-system)
5850 ("r-biobase" ,r-biobase)
5851 ("r-biocgenerics" ,r-biocgenerics)
5852 ("r-cytolib" ,r-cytolib)
5853 ("r-data-table" ,r-data-table)
5854 ("r-digest" ,r-digest)
5855 ("r-dplyr" ,r-dplyr)
5856 ("r-flowcore" ,r-flowcore)
5857 ("r-flowviz" ,r-flowviz)
5858 ("r-graph" ,r-graph)
5859 ("r-gridextra" ,r-gridextra)
5860 ("r-lattice" ,r-lattice)
5861 ("r-latticeextra" ,r-latticeextra)
5862 ("r-matrixstats" ,r-matrixstats)
5863 ("r-ncdfflow" ,r-ncdfflow)
5865 ("r-rcolorbrewer" ,r-rcolorbrewer)
5867 ("r-rcppparallel" ,r-rcppparallel)
5868 ("r-rgraphviz" ,r-rgraphviz)
5869 ("r-rprotobuflib" ,r-rprotobuflib)
5870 ("r-scales" ,r-scales)
5871 ("r-stringr" ,r-stringr)))
5872 (home-page "https://bioconductor.org/packages/flowWorkspace/")
5873 (synopsis "Infrastructure for working with cytometry data")
5875 "This package is designed to facilitate comparison of automated gating
5876 methods against manual gating done in flowJo. This package allows you to
5877 import basic flowJo workspaces into BioConductor and replicate the gating from
5878 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
5879 samples, compensation, and transformation are performed so that the output
5880 matches the flowJo analysis.")
5881 (license license:artistic2.0)))
5883 (define-public r-flowstats
5885 (name "r-flowstats")
5890 (uri (bioconductor-uri "flowStats" version))
5893 "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w"))))
5894 (properties `((upstream-name . "flowStats")))
5895 (build-system r-build-system)
5897 `(("r-biobase" ,r-biobase)
5898 ("r-biocgenerics" ,r-biocgenerics)
5899 ("r-cluster" ,r-cluster)
5901 ("r-flowcore" ,r-flowcore)
5902 ("r-flowviz" ,r-flowviz)
5903 ("r-flowworkspace" ,r-flowworkspace)
5904 ("r-kernsmooth" ,r-kernsmooth)
5906 ("r-lattice" ,r-lattice)
5908 ("r-ncdfflow" ,r-ncdfflow)
5909 ("r-rcolorbrewer" ,r-rcolorbrewer)
5910 ("r-rrcov" ,r-rrcov)))
5911 (home-page "http://www.github.com/RGLab/flowStats")
5912 (synopsis "Statistical methods for the analysis of flow cytometry data")
5914 "This package provides methods and functionality to analyze flow data
5915 that is beyond the basic infrastructure provided by the @code{flowCore}
5917 (license license:artistic2.0)))
5919 (define-public r-opencyto
5926 (uri (bioconductor-uri "openCyto" version))
5929 "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb"))))
5930 (properties `((upstream-name . "openCyto")))
5931 (build-system r-build-system)
5933 `(("r-biobase" ,r-biobase)
5934 ("r-biocgenerics" ,r-biocgenerics)
5936 ("r-data-table" ,r-data-table)
5937 ("r-flowclust" ,r-flowclust)
5938 ("r-flowcore" ,r-flowcore)
5939 ("r-flowstats" ,r-flowstats)
5940 ("r-flowviz" ,r-flowviz)
5941 ("r-flowworkspace" ,r-flowworkspace)
5942 ("r-graph" ,r-graph)
5943 ("r-gtools" ,r-gtools)
5945 ("r-lattice" ,r-lattice)
5947 ("r-ncdfflow" ,r-ncdfflow)
5949 ("r-r-utils" ,r-r-utils)
5951 ("r-rcolorbrewer" ,r-rcolorbrewer)
5953 ("r-rrcov" ,r-rrcov)))
5954 (home-page "https://bioconductor.org/packages/openCyto")
5955 (synopsis "Hierarchical gating pipeline for flow cytometry data")
5957 "This package is designed to facilitate the automated gating methods in a
5958 sequential way to mimic the manual gating strategy.")
5959 (license license:artistic2.0)))
5961 (define-public r-cytoml
5968 (uri (bioconductor-uri "CytoML" version))
5971 "0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz"))))
5972 (properties `((upstream-name . "CytoML")))
5973 (build-system r-build-system)
5975 `(("libxml2" ,libxml2)))
5977 `(("r-base64enc" ,r-base64enc)
5979 ("r-biobase" ,r-biobase)
5980 ("r-corpcor" ,r-corpcor)
5981 ("r-cytolib" ,r-cytolib)
5982 ("r-data-table" ,r-data-table)
5983 ("r-dplyr" ,r-dplyr)
5984 ("r-flowcore" ,r-flowcore)
5985 ("r-flowworkspace" ,r-flowworkspace)
5986 ("r-ggcyto" ,r-ggcyto)
5987 ("r-graph" ,r-graph)
5988 ("r-jsonlite" ,r-jsonlite)
5989 ("r-lattice" ,r-lattice)
5990 ("r-ncdfflow" ,r-ncdfflow)
5991 ("r-opencyto" ,r-opencyto)
5995 ("r-rcppparallel" ,r-rcppparallel)
5996 ("r-rgraphviz" ,r-rgraphviz)
5997 ("r-rprotobuflib" ,r-rprotobuflib)
5998 ("r-runit" ,r-runit)
6000 ("r-yaml" ,r-yaml)))
6002 `(("r-knitr" ,r-knitr)))
6003 (home-page "https://github.com/RGLab/CytoML")
6004 (synopsis "GatingML interface for cross platform cytometry data sharing")
6006 "This package provides an interface to implementations of the GatingML2.0
6007 standard to exchange gated cytometry data with other software platforms.")
6008 (license license:artistic2.0)))
6010 (define-public r-flowsom
6017 (uri (bioconductor-uri "FlowSOM" version))
6020 "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5"))))
6021 (properties `((upstream-name . "FlowSOM")))
6022 (build-system r-build-system)
6024 `(("r-biocgenerics" ,r-biocgenerics)
6025 ("r-consensusclusterplus" ,r-consensusclusterplus)
6026 ("r-cytoml" ,r-cytoml)
6027 ("r-flowcore" ,r-flowcore)
6028 ("r-flowworkspace" ,r-flowworkspace)
6029 ("r-igraph" ,r-igraph)
6030 ("r-rcolorbrewer" ,r-rcolorbrewer)
6033 (home-page "https://bioconductor.org/packages/FlowSOM/")
6034 (synopsis "Visualize and interpret cytometry data")
6036 "FlowSOM offers visualization options for cytometry data, by using
6037 self-organizing map clustering and minimal spanning trees.")
6038 (license license:gpl2+)))
6040 (define-public r-mixomics
6047 (uri (bioconductor-uri "mixOmics" version))
6050 "0b457yg8mwqlrn5l344w8qcj8v2ghlj1wdx1ysxbncqvqx7nvgig"))))
6051 (properties `((upstream-name . "mixOmics")))
6052 (build-system r-build-system)
6054 `(("r-corpcor" ,r-corpcor)
6055 ("r-dplyr" ,r-dplyr)
6056 ("r-ellipse" ,r-ellipse)
6057 ("r-ggplot2" ,r-ggplot2)
6058 ("r-gridextra" ,r-gridextra)
6059 ("r-igraph" ,r-igraph)
6060 ("r-lattice" ,r-lattice)
6062 ("r-matrixstats" ,r-matrixstats)
6063 ("r-rarpack" ,r-rarpack)
6064 ("r-rcolorbrewer" ,r-rcolorbrewer)
6065 ("r-reshape2" ,r-reshape2)
6066 ("r-tidyr" ,r-tidyr)))
6068 `(("r-knitr" ,r-knitr)))
6069 (home-page "http://www.mixOmics.org")
6070 (synopsis "Multivariate methods for exploration of biological datasets")
6072 "mixOmics offers a wide range of multivariate methods for the exploration
6073 and integration of biological datasets with a particular focus on variable
6074 selection. The package proposes several sparse multivariate models we have
6075 developed to identify the key variables that are highly correlated, and/or
6076 explain the biological outcome of interest. The data that can be analysed
6077 with mixOmics may come from high throughput sequencing technologies, such as
6078 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6079 also beyond the realm of omics (e.g. spectral imaging). The methods
6080 implemented in mixOmics can also handle missing values without having to
6081 delete entire rows with missing data.")
6082 (license license:gpl2+)))
6084 (define-public r-depecher
6091 (uri (bioconductor-uri "DepecheR" version))
6094 "199j2kw0xnw7y4v1gakm2jgyc7zzlj8xh0570f2yjq55gp1kggbm"))))
6095 (properties `((upstream-name . "DepecheR")))
6096 (build-system r-build-system)
6098 `(("r-beanplot" ,r-beanplot)
6099 ("r-dosnow" ,r-dosnow)
6100 ("r-dplyr" ,r-dplyr)
6102 ("r-foreach" ,r-foreach)
6103 ("r-ggplot2" ,r-ggplot2)
6104 ("r-gplots" ,r-gplots)
6106 ("r-matrixstats" ,r-matrixstats)
6107 ("r-mixomics" ,r-mixomics)
6108 ("r-moments" ,r-moments)
6110 ("r-rcppeigen" ,r-rcppeigen)
6111 ("r-reshape2" ,r-reshape2)
6112 ("r-robustbase" ,r-robustbase)
6113 ("r-viridis" ,r-viridis)))
6115 `(("r-knitr" ,r-knitr)))
6116 (home-page "https://bioconductor.org/packages/DepecheR/")
6117 (synopsis "Identify traits of clusters in high-dimensional entities")
6119 "The purpose of this package is to identify traits in a dataset that can
6120 separate groups. This is done on two levels. First, clustering is performed,
6121 using an implementation of sparse K-means. Secondly, the generated clusters
6122 are used to predict outcomes of groups of individuals based on their
6123 distribution of observations in the different clusters. As certain clusters
6124 with separating information will be identified, and these clusters are defined
6125 by a sparse number of variables, this method can reduce the complexity of
6126 data, to only emphasize the data that actually matters.")
6127 (license license:expat)))
6129 (define-public r-rcistarget
6131 (name "r-rcistarget")
6136 (uri (bioconductor-uri "RcisTarget" version))
6139 "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw"))))
6140 (properties `((upstream-name . "RcisTarget")))
6141 (build-system r-build-system)
6143 `(("r-aucell" ,r-aucell)
6144 ("r-biocgenerics" ,r-biocgenerics)
6145 ("r-data-table" ,r-data-table)
6146 ("r-feather" ,r-feather)
6147 ("r-gseabase" ,r-gseabase)
6148 ("r-r-utils" ,r-r-utils)
6149 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6150 (home-page "https://aertslab.org/#scenic")
6151 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6153 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6154 over-represented on a gene list. In a first step, RcisTarget selects DNA
6155 motifs that are significantly over-represented in the surroundings of the
6156 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6157 achieved by using a database that contains genome-wide cross-species rankings
6158 for each motif. The motifs that are then annotated to TFs and those that have
6159 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6160 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6161 genes in the gene-set that are ranked above the leading edge).")
6162 (license license:gpl3)))
6164 (define-public r-cicero
6171 (uri (bioconductor-uri "cicero" version))
6174 "1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld"))))
6175 (build-system r-build-system)
6177 `(("r-assertthat" ,r-assertthat)
6178 ("r-biobase" ,r-biobase)
6179 ("r-biocgenerics" ,r-biocgenerics)
6180 ("r-data-table" ,r-data-table)
6181 ("r-dplyr" ,r-dplyr)
6183 ("r-genomicranges" ,r-genomicranges)
6184 ("r-ggplot2" ,r-ggplot2)
6185 ("r-glasso" ,r-glasso)
6187 ("r-igraph" ,r-igraph)
6188 ("r-iranges" ,r-iranges)
6189 ("r-matrix" ,r-matrix)
6190 ("r-monocle" ,r-monocle)
6192 ("r-reshape2" ,r-reshape2)
6193 ("r-s4vectors" ,r-s4vectors)
6194 ("r-stringr" ,r-stringr)
6195 ("r-tibble" ,r-tibble)
6196 ("r-tidyr" ,r-tidyr)
6197 ("r-vgam" ,r-vgam)))
6199 `(("r-knitr" ,r-knitr)))
6200 (home-page "https://bioconductor.org/packages/cicero/")
6201 (synopsis "Predict cis-co-accessibility from single-cell data")
6203 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6204 accessibility data. It also extends the monocle package for use in chromatin
6205 accessibility data.")
6206 (license license:expat)))
6208 ;; This is the latest commit on the "monocle3" branch.
6209 (define-public r-cicero-monocle3
6210 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6212 (package (inherit r-cicero)
6213 (name "r-cicero-monocle3")
6214 (version (git-version "1.3.2" revision commit))
6219 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
6221 (file-name (git-file-name name version))
6224 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6226 `(("r-monocle3" ,r-monocle3)
6227 ,@(alist-delete "r-monocle"
6228 (package-propagated-inputs r-cicero)))))))
6230 (define-public r-cistopic
6231 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6235 (version (git-version "0.2.1" revision commit))
6240 (url "https://github.com/aertslab/cisTopic.git")
6242 (file-name (git-file-name name version))
6245 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6246 (build-system r-build-system)
6248 `(("r-aucell" ,r-aucell)
6249 ("r-data-table" ,r-data-table)
6250 ("r-dplyr" ,r-dplyr)
6251 ("r-dosnow" ,r-dosnow)
6253 ("r-feather" ,r-feather)
6254 ("r-fitdistrplus" ,r-fitdistrplus)
6255 ("r-genomicranges" ,r-genomicranges)
6256 ("r-ggplot2" ,r-ggplot2)
6258 ("r-matrix" ,r-matrix)
6260 ("r-rcistarget" ,r-rcistarget)
6261 ("r-rtracklayer" ,r-rtracklayer)
6262 ("r-s4vectors" ,r-s4vectors)))
6263 (home-page "https://github.com/aertslab/cisTopic")
6264 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6266 "The sparse nature of single cell epigenomics data can be overruled using
6267 probabilistic modelling methods such as @dfn{Latent Dirichlet
6268 Allocation} (LDA). This package allows the probabilistic modelling of
6269 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6270 includes functionalities to identify cell states based on the contribution of
6271 cisTopics and explore the nature and regulatory proteins driving them.")
6272 (license license:gpl3))))
6274 (define-public r-genie3
6281 (uri (bioconductor-uri "GENIE3" version))
6284 "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l"))))
6285 (properties `((upstream-name . "GENIE3")))
6286 (build-system r-build-system)
6287 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6288 (home-page "https://bioconductor.org/packages/GENIE3")
6289 (synopsis "Gene network inference with ensemble of trees")
6291 "This package implements the GENIE3 algorithm for inferring gene
6292 regulatory networks from expression data.")
6293 (license license:gpl2+)))
6295 (define-public r-roc
6302 (uri (bioconductor-uri "ROC" version))
6305 "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y"))))
6306 (properties `((upstream-name . "ROC")))
6307 (build-system r-build-system)
6309 `(("r-knitr" ,r-knitr)))
6310 (home-page "https://www.bioconductor.org/packages/ROC/")
6311 (synopsis "Utilities for ROC curves")
6313 "This package provides utilities for @dfn{Receiver Operating
6314 Characteristic} (ROC) curves, with a focus on micro arrays.")
6315 (license license:artistic2.0)))
6317 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6319 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6324 (uri (bioconductor-uri
6325 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6326 version 'annotation))
6329 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6332 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6333 (build-system r-build-system)
6334 (propagated-inputs `(("r-minfi" ,r-minfi)))
6336 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6337 (synopsis "Annotation for Illumina's 450k methylation arrays")
6339 "This package provides manifests and annotation for Illumina's 450k array
6341 (license license:artistic2.0)))
6343 (define-public r-watermelon
6345 (name "r-watermelon")
6350 (uri (bioconductor-uri "wateRmelon" version))
6353 "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0"))))
6354 (properties `((upstream-name . "wateRmelon")))
6355 (build-system r-build-system)
6357 `(("r-biobase" ,r-biobase)
6358 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6359 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6360 ("r-illuminaio" ,r-illuminaio)
6361 ("r-limma" ,r-limma)
6363 ("r-matrixstats" ,r-matrixstats)
6364 ("r-methylumi" ,r-methylumi)
6366 (home-page "https://bioconductor.org/packages/wateRmelon/")
6367 (synopsis "Illumina 450 methylation array normalization and metrics")
6369 "The standard index of DNA methylation (beta) is computed from methylated
6370 and unmethylated signal intensities. Betas calculated from raw signal
6371 intensities perform well, but using 11 methylomic datasets we demonstrate that
6372 quantile normalization methods produce marked improvement. The commonly used
6373 procedure of normalizing betas is inferior to the separate normalization of M
6374 and U, and it is also advantageous to normalize Type I and Type II assays
6375 separately. This package provides 15 flavours of betas and three performance
6376 metrics, with methods for objects produced by the @code{methylumi} and
6377 @code{minfi} packages.")
6378 (license license:gpl3)))
6380 (define-public r-gdsfmt
6387 (uri (bioconductor-uri "gdsfmt" version))
6390 "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9"))
6391 (modules '((guix build utils)))
6392 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6393 ;; them and link with system libraries instead.
6396 (for-each delete-file-recursively
6400 (substitute* "src/Makevars"
6401 (("all: \\$\\(SHLIB\\)") "all:")
6402 (("\\$\\(SHLIB\\): liblzma.a") "")
6403 (("(ZLIB|LZ4)/.*") "")
6404 (("CoreArray/dVLIntGDS.cpp.*")
6405 "CoreArray/dVLIntGDS.cpp")
6406 (("CoreArray/dVLIntGDS.o.*")
6407 "CoreArray/dVLIntGDS.o")
6408 (("PKG_LIBS = ./liblzma.a")
6409 "PKG_LIBS = -llz4"))
6410 (substitute* "src/CoreArray/dStream.h"
6411 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6412 (string-append "include <" header ">")))
6414 (properties `((upstream-name . "gdsfmt")))
6415 (build-system r-build-system)
6420 (home-page "http://corearray.sourceforge.net/")
6422 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6424 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6425 Data Structure} (GDS) data files, which are portable across platforms with
6426 hierarchical structure to store multiple scalable array-oriented data sets
6427 with metadata information. It is suited for large-scale datasets, especially
6428 for data which are much larger than the available random-access memory. The
6429 @code{gdsfmt} package offers efficient operations specifically designed for
6430 integers of less than 8 bits, since a diploid genotype, like
6431 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6432 byte. Data compression and decompression are available with relatively
6433 efficient random access. It is also allowed to read a GDS file in parallel
6434 with multiple R processes supported by the package @code{parallel}.")
6435 (license license:lgpl3)))
6437 (define-public r-bigmelon
6444 (uri (bioconductor-uri "bigmelon" version))
6447 "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls"))))
6448 (properties `((upstream-name . "bigmelon")))
6449 (build-system r-build-system)
6451 `(("r-biobase" ,r-biobase)
6452 ("r-biocgenerics" ,r-biocgenerics)
6453 ("r-gdsfmt" ,r-gdsfmt)
6454 ("r-geoquery" ,r-geoquery)
6455 ("r-methylumi" ,r-methylumi)
6456 ("r-minfi" ,r-minfi)
6457 ("r-watermelon" ,r-watermelon)))
6458 (home-page "https://bioconductor.org/packages/bigmelon/")
6459 (synopsis "Illumina methylation array analysis for large experiments")
6461 "This package provides methods for working with Illumina arrays using the
6462 @code{gdsfmt} package.")
6463 (license license:gpl3)))
6465 (define-public r-seqbias
6472 (uri (bioconductor-uri "seqbias" version))
6475 "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq"))))
6476 (properties `((upstream-name . "seqbias")))
6477 (build-system r-build-system)
6479 `(("r-biostrings" ,r-biostrings)
6480 ("r-genomicranges" ,r-genomicranges)
6481 ("r-rhtslib" ,r-rhtslib)))
6483 `(("zlib" ,zlib))) ; This comes from rhtslib.
6484 (home-page "https://bioconductor.org/packages/seqbias/")
6485 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6487 "This package implements a model of per-position sequencing bias in
6488 high-throughput sequencing data using a simple Bayesian network, the structure
6489 and parameters of which are trained on a set of aligned reads and a reference
6491 (license license:lgpl3)))
6493 (define-public r-snplocs-hsapiens-dbsnp144-grch37
6495 (name "r-snplocs-hsapiens-dbsnp144-grch37")
6499 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
6500 version 'annotation))
6503 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
6504 (build-system r-build-system)
6505 ;; As this package provides little more than a very large data file it
6506 ;; doesn't make sense to build substitutes.
6507 (arguments `(#:substitutable? #f))
6509 `(("r-biocgenerics" ,r-biocgenerics)
6510 ("r-s4vectors" ,r-s4vectors)
6511 ("r-iranges" ,r-iranges)
6512 ("r-genomeinfodb" ,r-genomeinfodb)
6513 ("r-genomicranges" ,r-genomicranges)
6514 ("r-bsgenome" ,r-bsgenome)
6515 ("r-biostrings" ,r-biostrings)))
6517 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
6518 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
6519 (description "This package provides SNP locations and alleles for Homo
6520 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
6521 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
6522 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
6523 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
6524 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
6525 the mitochondrion chromosome. Therefore, the SNPs in this package can be
6526 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
6527 correct position but this injection will exclude chrM (i.e. nothing will be
6528 injected in that sequence).")
6529 (license license:artistic2.0)))
6531 (define-public r-reqon
6538 (uri (bioconductor-uri "ReQON" version))
6541 "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx"))))
6542 (properties `((upstream-name . "ReQON")))
6543 (build-system r-build-system)
6545 `(("r-rjava" ,r-rjava)
6546 ("r-rsamtools" ,r-rsamtools)
6547 ("r-seqbias" ,r-seqbias)))
6548 (home-page "https://bioconductor.org/packages/ReQON/")
6549 (synopsis "Recalibrating quality of nucleotides")
6551 "This package provides an implementation of an algorithm for
6552 recalibrating the base quality scores for aligned sequencing data in BAM
6554 (license license:gpl2)))
6556 (define-public r-wavcluster
6558 (name "r-wavcluster")
6563 (uri (bioconductor-uri "wavClusteR" version))
6566 "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y"))))
6567 (properties `((upstream-name . "wavClusteR")))
6568 (build-system r-build-system)
6570 `(("r-biocgenerics" ,r-biocgenerics)
6571 ("r-biostrings" ,r-biostrings)
6572 ("r-foreach" ,r-foreach)
6573 ("r-genomicfeatures" ,r-genomicfeatures)
6574 ("r-genomicranges" ,r-genomicranges)
6575 ("r-ggplot2" ,r-ggplot2)
6576 ("r-hmisc" ,r-hmisc)
6577 ("r-iranges" ,r-iranges)
6578 ("r-mclust" ,r-mclust)
6579 ("r-rsamtools" ,r-rsamtools)
6580 ("r-rtracklayer" ,r-rtracklayer)
6581 ("r-s4vectors" ,r-s4vectors)
6582 ("r-seqinr" ,r-seqinr)
6583 ("r-stringr" ,r-stringr)
6584 ("r-wmtsa" ,r-wmtsa)))
6585 (home-page "https://bioconductor.org/packages/wavClusteR/")
6586 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6588 "This package provides an integrated pipeline for the analysis of
6589 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6590 sequencing errors, SNPs and additional non-experimental sources by a non-
6591 parametric mixture model. The protein binding sites (clusters) are then
6592 resolved at high resolution and cluster statistics are estimated using a
6593 rigorous Bayesian framework. Post-processing of the results, data export for
6594 UCSC genome browser visualization and motif search analysis are provided. In
6595 addition, the package integrates RNA-Seq data to estimate the False
6596 Discovery Rate of cluster detection. Key functions support parallel multicore
6597 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6598 be applied to the analysis of other NGS data obtained from experimental
6599 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6600 (license license:gpl2)))
6602 (define-public r-timeseriesexperiment
6604 (name "r-timeseriesexperiment")
6609 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6612 "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm"))))
6614 `((upstream-name . "TimeSeriesExperiment")))
6615 (build-system r-build-system)
6617 `(("r-deseq2" ,r-deseq2)
6618 ("r-dplyr" ,r-dplyr)
6619 ("r-dynamictreecut" ,r-dynamictreecut)
6620 ("r-edger" ,r-edger)
6621 ("r-ggplot2" ,r-ggplot2)
6622 ("r-hmisc" ,r-hmisc)
6623 ("r-limma" ,r-limma)
6624 ("r-magrittr" ,r-magrittr)
6625 ("r-proxy" ,r-proxy)
6626 ("r-s4vectors" ,r-s4vectors)
6627 ("r-summarizedexperiment" ,r-summarizedexperiment)
6628 ("r-tibble" ,r-tibble)
6629 ("r-tidyr" ,r-tidyr)
6630 ("r-vegan" ,r-vegan)
6631 ("r-viridis" ,r-viridis)))
6632 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6633 (synopsis "Analysis for short time-series data")
6635 "This package is a visualization and analysis toolbox for short time
6636 course data which includes dimensionality reduction, clustering, two-sample
6637 differential expression testing and gene ranking techniques. The package also
6638 provides methods for retrieving enriched pathways.")
6639 (license license:lgpl3+)))
6641 (define-public r-variantfiltering
6643 (name "r-variantfiltering")
6648 (uri (bioconductor-uri "VariantFiltering" version))
6651 "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8"))))
6653 `((upstream-name . "VariantFiltering")))
6654 (build-system r-build-system)
6656 `(("r-annotationdbi" ,r-annotationdbi)
6657 ("r-biobase" ,r-biobase)
6658 ("r-biocgenerics" ,r-biocgenerics)
6659 ("r-biocparallel" ,r-biocparallel)
6660 ("r-biostrings" ,r-biostrings)
6661 ("r-bsgenome" ,r-bsgenome)
6663 ("r-genomeinfodb" ,r-genomeinfodb)
6664 ("r-genomicfeatures" ,r-genomicfeatures)
6665 ("r-genomicranges" ,r-genomicranges)
6666 ("r-genomicscores" ,r-genomicscores)
6667 ("r-graph" ,r-graph)
6669 ("r-iranges" ,r-iranges)
6671 ("r-rsamtools" ,r-rsamtools)
6672 ("r-s4vectors" ,r-s4vectors)
6673 ("r-shiny" ,r-shiny)
6674 ("r-shinyjs" ,r-shinyjs)
6675 ("r-shinythemes" ,r-shinythemes)
6676 ("r-shinytree" ,r-shinytree)
6677 ("r-summarizedexperiment" ,r-summarizedexperiment)
6678 ("r-variantannotation" ,r-variantannotation)
6679 ("r-xvector" ,r-xvector)))
6680 (home-page "https://github.com/rcastelo/VariantFiltering")
6681 (synopsis "Filtering of coding and non-coding genetic variants")
6683 "Filter genetic variants using different criteria such as inheritance
6684 model, amino acid change consequence, minor allele frequencies across human
6685 populations, splice site strength, conservation, etc.")
6686 (license license:artistic2.0)))
6688 (define-public r-genomegraphs
6690 (name "r-genomegraphs")
6695 (uri (bioconductor-uri "GenomeGraphs" version))
6698 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
6699 (properties `((upstream-name . "GenomeGraphs")))
6700 (build-system r-build-system)
6702 `(("r-biomart" ,r-biomart)))
6703 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
6704 (synopsis "Plotting genomic information from Ensembl")
6706 "Genomic data analyses requires integrated visualization of known genomic
6707 information and new experimental data. GenomeGraphs uses the biomaRt package
6708 to perform live annotation queries to Ensembl and translates this to e.g.
6709 gene/transcript structures in viewports of the grid graphics package. This
6710 results in genomic information plotted together with your data. Another
6711 strength of GenomeGraphs is to plot different data types such as array CGH,
6712 gene expression, sequencing and other data, together in one plot using the
6713 same genome coordinate system.")
6714 (license license:artistic2.0)))
6716 (define-public r-wavetiling
6718 (name "r-wavetiling")
6723 (uri (bioconductor-uri "waveTiling" version))
6726 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
6727 (properties `((upstream-name . "waveTiling")))
6728 (build-system r-build-system)
6730 `(("r-affy" ,r-affy)
6731 ("r-biobase" ,r-biobase)
6732 ("r-biostrings" ,r-biostrings)
6733 ("r-genomegraphs" ,r-genomegraphs)
6734 ("r-genomicranges" ,r-genomicranges)
6735 ("r-iranges" ,r-iranges)
6736 ("r-oligo" ,r-oligo)
6737 ("r-oligoclasses" ,r-oligoclasses)
6738 ("r-preprocesscore" ,r-preprocesscore)
6739 ("r-waveslim" ,r-waveslim)))
6740 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
6741 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
6743 "This package is designed to conduct transcriptome analysis for tiling
6744 arrays based on fast wavelet-based functional models.")
6745 (license license:gpl2+)))
6747 (define-public r-variancepartition
6749 (name "r-variancepartition")
6754 (uri (bioconductor-uri "variancePartition" version))
6757 "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g"))))
6759 `((upstream-name . "variancePartition")))
6760 (build-system r-build-system)
6762 `(("r-biobase" ,r-biobase)
6763 ("r-biocparallel" ,r-biocparallel)
6764 ("r-colorramps" ,r-colorramps)
6765 ("r-doparallel" ,r-doparallel)
6766 ("r-foreach" ,r-foreach)
6767 ("r-ggplot2" ,r-ggplot2)
6768 ("r-gplots" ,r-gplots)
6769 ("r-iterators" ,r-iterators)
6770 ("r-limma" ,r-limma)
6772 ("r-lmertest" ,r-lmertest)
6774 ("r-pbkrtest" ,r-pbkrtest)
6775 ("r-progress" ,r-progress)
6776 ("r-reshape2" ,r-reshape2)
6777 ("r-scales" ,r-scales)))
6778 (home-page "https://bioconductor.org/packages/variancePartition/")
6779 (synopsis "Analyze variation in gene expression experiments")
6781 "This is a package providing tools to quantify and interpret multiple
6782 sources of biological and technical variation in gene expression experiments.
6783 It uses a linear mixed model to quantify variation in gene expression
6784 attributable to individual, tissue, time point, or technical variables. The
6785 package includes dream differential expression analysis for repeated
6787 (license license:gpl2+)))
6789 (define-public r-htqpcr
6796 (uri (bioconductor-uri "HTqPCR" version))
6799 "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx"))))
6800 (properties `((upstream-name . "HTqPCR")))
6801 (build-system r-build-system)
6803 `(("r-affy" ,r-affy)
6804 ("r-biobase" ,r-biobase)
6805 ("r-gplots" ,r-gplots)
6806 ("r-limma" ,r-limma)
6807 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6808 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
6809 "groups/bertone/software/HTqPCR.pdf"))
6810 (synopsis "Automated analysis of high-throughput qPCR data")
6812 "Analysis of Ct values from high throughput quantitative real-time
6813 PCR (qPCR) assays across multiple conditions or replicates. The input data
6814 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
6815 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
6816 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
6817 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
6818 loading, quality assessment, normalization, visualization and parametric or
6819 non-parametric testing for statistical significance in Ct values between
6820 features (e.g. genes, microRNAs).")
6821 (license license:artistic2.0)))
6823 (define-public r-unifiedwmwqpcr
6825 (name "r-unifiedwmwqpcr")
6830 (uri (bioconductor-uri "unifiedWMWqPCR" version))
6833 "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj"))))
6835 `((upstream-name . "unifiedWMWqPCR")))
6836 (build-system r-build-system)
6838 `(("r-biocgenerics" ,r-biocgenerics)
6839 ("r-htqpcr" ,r-htqpcr)))
6840 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
6841 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
6843 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
6844 data. This modified test allows for testing differential expression in qPCR
6846 (license license:gpl2+)))
6848 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
6850 (define-public r-activedriverwgs
6852 (name "r-activedriverwgs")
6857 (uri (cran-uri "ActiveDriverWGS" version))
6860 "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
6862 `((upstream-name . "ActiveDriverWGS")))
6863 (build-system r-build-system)
6865 `(("r-biostrings" ,r-biostrings)
6866 ("r-bsgenome" ,r-bsgenome)
6867 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
6868 ("r-genomeinfodb" ,r-genomeinfodb)
6869 ("r-genomicranges" ,r-genomicranges)
6870 ("r-iranges" ,r-iranges)
6872 ("r-s4vectors" ,r-s4vectors)))
6873 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
6874 (synopsis "Driver discovery tool for cancer whole genomes")
6876 "This package provides a method for finding an enrichment of cancer
6877 simple somatic mutations (SNVs and Indels) in functional elements across the
6878 human genome. ActiveDriverWGS detects coding and noncoding driver elements
6879 using whole genome sequencing data.")
6880 (license license:gpl3)))
6882 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
6884 (define-public r-activepathways
6886 (name "r-activepathways")
6891 (uri (cran-uri "ActivePathways" version))
6894 "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20"))))
6896 `((upstream-name . "ActivePathways")))
6897 (build-system r-build-system)
6899 `(("r-data-table" ,r-data-table)
6900 ("r-ggplot2" ,r-ggplot2)
6901 ("r-metap" ,r-metap)))
6903 `(("r-knitr" ,r-knitr)))
6904 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
6905 (synopsis "Multivariate pathway enrichment analysis")
6907 "This package represents an integrative method of analyzing multi omics
6908 data that conducts enrichment analysis of annotated gene sets. ActivePathways
6909 uses a statistical data fusion approach, rationalizes contributing evidence
6910 and highlights associated genes, improving systems-level understanding of
6911 cellular organization in health and disease.")
6912 (license license:gpl3)))
6914 (define-public r-bgmix
6921 (uri (bioconductor-uri "BGmix" version))
6924 "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683"))))
6925 (properties `((upstream-name . "BGmix")))
6926 (build-system r-build-system)
6928 `(("r-kernsmooth" ,r-kernsmooth)))
6929 (home-page "https://bioconductor.org/packages/BGmix/")
6930 (synopsis "Bayesian models for differential gene expression")
6932 "This package provides fully Bayesian mixture models for differential
6934 (license license:gpl2)))
6936 (define-public r-bgx
6943 (uri (bioconductor-uri "bgx" version))
6946 "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm"))))
6947 (properties `((upstream-name . "bgx")))
6948 (build-system r-build-system)
6950 `(("r-affy" ,r-affy)
6951 ("r-biobase" ,r-biobase)
6952 ("r-gcrma" ,r-gcrma)
6953 ("r-rcpp" ,r-rcpp)))
6954 (home-page "https://bioconductor.org/packages/bgx/")
6955 (synopsis "Bayesian gene expression")
6957 "This package provides tools for Bayesian integrated analysis of
6958 Affymetrix GeneChips.")
6959 (license license:gpl2)))
6961 (define-public r-bhc
6968 (uri (bioconductor-uri "BHC" version))
6971 "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh"))))
6972 (properties `((upstream-name . "BHC")))
6973 (build-system r-build-system)
6974 (home-page "https://bioconductor.org/packages/BHC/")
6975 (synopsis "Bayesian hierarchical clustering")
6977 "The method implemented in this package performs bottom-up hierarchical
6978 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
6979 in the data and Bayesian model selection to decide at each step which clusters
6980 to merge. This avoids several limitations of traditional methods, for example
6981 how many clusters there should be and how to choose a principled distance
6982 metric. This implementation accepts multinomial (i.e. discrete, with 2+
6983 categories) or time-series data. This version also includes a randomised
6984 algorithm which is more efficient for larger data sets.")
6985 (license license:gpl3)))
6987 (define-public r-bicare
6994 (uri (bioconductor-uri "BicARE" version))
6997 "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs"))))
6998 (properties `((upstream-name . "BicARE")))
6999 (build-system r-build-system)
7001 `(("r-biobase" ,r-biobase)
7002 ("r-gseabase" ,r-gseabase)
7003 ("r-multtest" ,r-multtest)))
7004 (home-page "http://bioinfo.curie.fr")
7005 (synopsis "Biclustering analysis and results exploration")
7007 "This is a package for biclustering analysis and exploration of
7009 (license license:gpl2)))
7011 (define-public r-bifet
7018 (uri (bioconductor-uri "BiFET" version))
7021 "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k"))))
7022 (properties `((upstream-name . "BiFET")))
7023 (build-system r-build-system)
7025 `(("r-genomicranges" ,r-genomicranges)
7026 ("r-poibin" ,r-poibin)))
7027 (home-page "https://bioconductor.org/packages/BiFET")
7028 (synopsis "Bias-free footprint enrichment test")
7030 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7031 over-represented in target regions compared to background regions after
7032 correcting for the bias arising from the imbalance in read counts and GC
7033 contents between the target and background regions. For a given TF k, BiFET
7034 tests the null hypothesis that the target regions have the same probability of
7035 having footprints for the TF k as the background regions while correcting for
7036 the read count and GC content bias.")
7037 (license license:gpl3)))
7039 (define-public r-rsbml
7046 (uri (bioconductor-uri "rsbml" version))
7049 "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa"))))
7050 (properties `((upstream-name . "rsbml")))
7051 (build-system r-build-system)
7053 `(("libsbml" ,libsbml)
7056 `(("r-biocgenerics" ,r-biocgenerics)
7057 ("r-graph" ,r-graph)))
7059 `(("pkg-config" ,pkg-config)))
7060 (home-page "http://www.sbml.org")
7061 (synopsis "R support for SBML")
7063 "This package provides an R interface to libsbml for SBML parsing,
7064 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7065 (license license:artistic2.0)))
7067 (define-public r-hypergraph
7069 (name "r-hypergraph")
7074 (uri (bioconductor-uri "hypergraph" version))
7077 "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m"))))
7078 (properties `((upstream-name . "hypergraph")))
7079 (build-system r-build-system)
7081 `(("r-graph" ,r-graph)))
7082 (home-page "https://bioconductor.org/packages/hypergraph")
7083 (synopsis "Hypergraph data structures")
7085 "This package implements some simple capabilities for representing and
7086 manipulating hypergraphs.")
7087 (license license:artistic2.0)))
7089 (define-public r-hyperdraw
7091 (name "r-hyperdraw")
7096 (uri (bioconductor-uri "hyperdraw" version))
7099 "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj"))))
7100 (properties `((upstream-name . "hyperdraw")))
7101 (build-system r-build-system)
7102 (inputs `(("graphviz" ,graphviz)))
7104 `(("r-graph" ,r-graph)
7105 ("r-hypergraph" ,r-hypergraph)
7106 ("r-rgraphviz" ,r-rgraphviz)))
7107 (home-page "https://bioconductor.org/packages/hyperdraw")
7108 (synopsis "Visualizing hypergraphs")
7110 "This package provides functions for visualizing hypergraphs.")
7111 (license license:gpl2+)))
7113 (define-public r-biggr
7120 (uri (bioconductor-uri "BiGGR" version))
7123 "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif"))))
7124 (properties `((upstream-name . "BiGGR")))
7125 (build-system r-build-system)
7127 `(("r-hyperdraw" ,r-hyperdraw)
7128 ("r-hypergraph" ,r-hypergraph)
7130 ("r-limsolve" ,r-limsolve)
7131 ("r-rsbml" ,r-rsbml)
7132 ("r-stringr" ,r-stringr)))
7133 (home-page "https://bioconductor.org/packages/BiGGR/")
7134 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7136 "This package provides an interface to simulate metabolic reconstruction
7137 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7138 reconstruction databases. The package facilitates @dfn{flux balance
7139 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7140 networks and estimated fluxes can be visualized with hypergraphs.")
7141 (license license:gpl3+)))
7143 (define-public r-bigmemoryextras
7145 (name "r-bigmemoryextras")
7150 (uri (bioconductor-uri "bigmemoryExtras" version))
7153 "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq"))))
7155 `((upstream-name . "bigmemoryExtras")))
7156 (build-system r-build-system)
7158 `(("r-bigmemory" ,r-bigmemory)))
7159 (home-page "https://github.com/phaverty/bigmemoryExtras")
7160 (synopsis "Extension of the bigmemory package")
7162 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7163 safety and convenience features to the @code{filebacked.big.matrix} class from
7164 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7165 monitoring and gracefully restoring the connection to on-disk data and it also
7166 protects against accidental data modification with a filesystem-based
7167 permissions system. Utilities are provided for using @code{BigMatrix}-derived
7168 classes as @code{assayData} matrices within the @code{Biobase} package's
7169 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7170 related to attaching to, and indexing into, file-backed matrices with
7171 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7172 a file-backed matrix with factor properties.")
7173 (license license:artistic2.0)))
7175 (define-public r-bigpint
7182 (uri (bioconductor-uri "bigPint" version))
7185 "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs"))))
7186 (properties `((upstream-name . "bigPint")))
7187 (build-system r-build-system)
7189 `(("r-dplyr" ,r-dplyr)
7190 ("r-ggally" ,r-ggally)
7191 ("r-ggplot2" ,r-ggplot2)
7192 ("r-gridextra" ,r-gridextra)
7193 ("r-hexbin" ,r-hexbin)
7194 ("r-hmisc" ,r-hmisc)
7195 ("r-htmlwidgets" ,r-htmlwidgets)
7196 ("r-plotly" ,r-plotly)
7198 ("r-rcolorbrewer" ,r-rcolorbrewer)
7199 ("r-reshape" ,r-reshape)
7200 ("r-shiny" ,r-shiny)
7201 ("r-shinycssloaders" ,r-shinycssloaders)
7202 ("r-shinydashboard" ,r-shinydashboard)
7203 ("r-stringr" ,r-stringr)
7204 ("r-tidyr" ,r-tidyr)))
7206 `(("r-knitr" ,r-knitr)))
7207 (home-page "https://github.com/lindsayrutter/bigPint")
7208 (synopsis "Big multivariate data plotted interactively")
7210 "This package provides methods for visualizing large multivariate
7211 datasets using static and interactive scatterplot matrices, parallel
7212 coordinate plots, volcano plots, and litre plots. It includes examples for
7213 visualizing RNA-sequencing datasets and differentially expressed genes.")
7214 (license license:gpl3)))
7216 (define-public r-chemminer
7218 (name "r-chemminer")
7223 (uri (bioconductor-uri "ChemmineR" version))
7226 "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga"))))
7227 (properties `((upstream-name . "ChemmineR")))
7228 (build-system r-build-system)
7230 `(("r-base64enc" ,r-base64enc)
7232 ("r-biocgenerics" ,r-biocgenerics)
7234 ("r-digest" ,r-digest)
7236 ("r-ggplot2" ,r-ggplot2)
7237 ("r-gridextra" ,r-gridextra)
7240 ("r-rcurl" ,r-rcurl)
7241 ("r-rjson" ,r-rjson)
7242 ("r-rsvg" ,r-rsvg)))
7243 (home-page "https://github.com/girke-lab/ChemmineR")
7244 (synopsis "Cheminformatics toolkit for R")
7246 "ChemmineR is a cheminformatics package for analyzing drug-like small
7247 molecule data in R. It contains functions for efficient processing of large
7248 numbers of molecules, physicochemical/structural property predictions,
7249 structural similarity searching, classification and clustering of compound
7250 libraries with a wide spectrum of algorithms. In addition, it offers
7251 visualization functions for compound clustering results and chemical
7253 (license license:artistic2.0)))
7255 (define-public r-bioassayr
7257 (name "r-bioassayr")
7262 (uri (bioconductor-uri "bioassayR" version))
7265 "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw"))))
7266 (properties `((upstream-name . "bioassayR")))
7267 (build-system r-build-system)
7269 `(("r-biocgenerics" ,r-biocgenerics)
7270 ("r-chemminer" ,r-chemminer)
7272 ("r-matrix" ,r-matrix)
7273 ("r-rjson" ,r-rjson)
7274 ("r-rsqlite" ,r-rsqlite)
7277 `(("r-knitr" ,r-knitr)))
7278 (home-page "https://github.com/TylerBackman/bioassayR")
7279 (synopsis "Cross-target analysis of small molecule bioactivity")
7281 "bioassayR is a computational tool that enables simultaneous analysis of
7282 thousands of bioassay experiments performed over a diverse set of compounds
7283 and biological targets. Unique features include support for large-scale
7284 cross-target analyses of both public and custom bioassays, generation of
7285 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7286 preloaded database that provides access to a substantial portion of publicly
7287 available bioactivity data.")
7288 (license license:artistic2.0)))
7290 (define-public r-biobroom
7297 (uri (bioconductor-uri "biobroom" version))
7300 "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb"))))
7301 (properties `((upstream-name . "biobroom")))
7302 (build-system r-build-system)
7304 `(("r-biobase" ,r-biobase)
7305 ("r-broom" ,r-broom)
7306 ("r-dplyr" ,r-dplyr)
7307 ("r-tidyr" ,r-tidyr)))
7308 (home-page "https://github.com/StoreyLab/biobroom")
7309 (synopsis "Turn Bioconductor objects into tidy data frames")
7311 "This package contains methods for converting standard objects
7312 constructed by bioinformatics packages, especially those in Bioconductor, and
7313 converting them to @code{tidy} data. It thus serves as a complement to the
7314 @code{broom} package, and follows the same tidy, augment, glance division of
7315 tidying methods. Tidying data makes it easy to recombine, reshape and
7316 visualize bioinformatics analyses.")
7317 ;; Any version of the LGPL.
7318 (license license:lgpl3+)))
7320 (define-public r-graphite
7327 (uri (bioconductor-uri "graphite" version))
7330 "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd"))))
7331 (properties `((upstream-name . "graphite")))
7332 (build-system r-build-system)
7334 `(("r-annotationdbi" ,r-annotationdbi)
7335 ("r-checkmate" ,r-checkmate)
7336 ("r-graph" ,r-graph)
7338 ("r-rappdirs" ,r-rappdirs)))
7339 (home-page "https://bioconductor.org/packages/graphite/")
7340 (synopsis "Networks from pathway databases")
7342 "Graphite provides networks derived from eight public pathway databases,
7343 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7345 (license license:agpl3+)))
7347 (define-public r-reactomepa
7349 (name "r-reactomepa")
7354 (uri (bioconductor-uri "ReactomePA" version))
7357 "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1"))))
7358 (properties `((upstream-name . "ReactomePA")))
7359 (build-system r-build-system)
7361 `(("r-annotationdbi" ,r-annotationdbi)
7363 ("r-enrichplot" ,r-enrichplot)
7364 ("r-ggplot2" ,r-ggplot2)
7365 ("r-ggraph" ,r-ggraph)
7366 ("r-graphite" ,r-graphite)
7367 ("r-igraph" ,r-igraph)
7368 ("r-reactome-db" ,r-reactome-db)))
7369 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7370 (synopsis "Reactome pathway analysis")
7372 "This package provides functions for pathway analysis based on the
7373 REACTOME pathway database. It implements enrichment analysis, gene set
7374 enrichment analysis and several functions for visualization.")
7375 (license license:gpl2)))
7377 (define-public r-ebarrays
7384 (uri (bioconductor-uri "EBarrays" version))
7387 "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13"))))
7388 (properties `((upstream-name . "EBarrays")))
7389 (build-system r-build-system)
7391 `(("r-biobase" ,r-biobase)
7392 ("r-cluster" ,r-cluster)
7393 ("r-lattice" ,r-lattice)))
7394 (home-page "https://bioconductor.org/packages/EBarrays/")
7395 (synopsis "Gene clustering and differential expression identification")
7397 "EBarrays provides tools for the analysis of replicated/unreplicated
7399 (license license:gpl2+)))
7401 (define-public r-bioccasestudies
7403 (name "r-bioccasestudies")
7408 (uri (bioconductor-uri "BiocCaseStudies" version))
7411 "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd"))))
7413 `((upstream-name . "BiocCaseStudies")))
7414 (build-system r-build-system)
7415 (propagated-inputs `(("r-biobase" ,r-biobase)))
7416 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7417 (synopsis "Support for the case studies monograph")
7419 "This package provides software and data to support the case studies
7421 (license license:artistic2.0)))
7423 (define-public r-biocgraph
7425 (name "r-biocgraph")
7430 (uri (bioconductor-uri "biocGraph" version))
7433 "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw"))))
7434 (properties `((upstream-name . "biocGraph")))
7435 (build-system r-build-system)
7437 `(("r-biocgenerics" ,r-biocgenerics)
7438 ("r-geneplotter" ,r-geneplotter)
7439 ("r-graph" ,r-graph)
7440 ("r-rgraphviz" ,r-rgraphviz)))
7441 (home-page "https://bioconductor.org/packages/biocGraph/")
7442 (synopsis "Graph examples and use cases in Bioinformatics")
7444 "This package provides examples and code that make use of the
7445 different graph related packages produced by Bioconductor.")
7446 (license license:artistic2.0)))
7448 (define-public r-experimenthub
7450 (name "r-experimenthub")
7455 (uri (bioconductor-uri "ExperimentHub" version))
7458 "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24"))))
7459 (properties `((upstream-name . "ExperimentHub")))
7460 (build-system r-build-system)
7462 `(("r-annotationhub" ,r-annotationhub)
7463 ("r-biocfilecache" ,r-biocfilecache)
7464 ("r-biocgenerics" ,r-biocgenerics)
7465 ("r-biocmanager" ,r-biocmanager)
7467 ("r-rappdirs" ,r-rappdirs)
7468 ("r-s4vectors" ,r-s4vectors)))
7469 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7470 (synopsis "Client to access ExperimentHub resources")
7472 "This package provides a client for the Bioconductor ExperimentHub web
7473 resource. ExperimentHub provides a central location where curated data from
7474 experiments, publications or training courses can be accessed. Each resource
7475 has associated metadata, tags and date of modification. The client creates
7476 and manages a local cache of files retrieved enabling quick and reproducible
7478 (license license:artistic2.0)))
7480 (define-public r-multiassayexperiment
7482 (name "r-multiassayexperiment")
7487 (uri (bioconductor-uri "MultiAssayExperiment" version))
7490 "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi"))))
7492 `((upstream-name . "MultiAssayExperiment")))
7493 (build-system r-build-system)
7495 `(("r-biobase" ,r-biobase)
7496 ("r-biocgenerics" ,r-biocgenerics)
7497 ("r-genomicranges" ,r-genomicranges)
7498 ("r-iranges" ,r-iranges)
7499 ("r-s4vectors" ,r-s4vectors)
7500 ("r-summarizedexperiment" ,r-summarizedexperiment)
7501 ("r-tidyr" ,r-tidyr)))
7503 `(("r-knitr" ,r-knitr)))
7504 (home-page "https://waldronlab.io/MultiAssayExperiment/")
7505 (synopsis "Integration of multi-omics experiments in Bioconductor")
7507 "MultiAssayExperiment harmonizes data management of multiple assays
7508 performed on an overlapping set of specimens. It provides a familiar
7509 Bioconductor user experience by extending concepts from
7510 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7511 classes for individual assays, and allowing subsetting by genomic ranges or
7513 (license license:artistic2.0)))
7515 (define-public r-bioconcotk
7517 (name "r-bioconcotk")
7522 (uri (bioconductor-uri "BiocOncoTK" version))
7525 "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj"))))
7526 (properties `((upstream-name . "BiocOncoTK")))
7527 (build-system r-build-system)
7529 `(("r-bigrquery" ,r-bigrquery)
7531 ("r-complexheatmap" ,r-complexheatmap)
7532 ("r-curatedtcgadata" ,r-curatedtcgadata)
7534 ("r-dplyr" ,r-dplyr)
7536 ("r-genomicfeatures" ,r-genomicfeatures)
7537 ("r-genomicranges" ,r-genomicranges)
7538 ("r-ggplot2" ,r-ggplot2)
7539 ("r-ggpubr" ,r-ggpubr)
7540 ("r-graph" ,r-graph)
7542 ("r-iranges" ,r-iranges)
7543 ("r-magrittr" ,r-magrittr)
7545 ("r-rgraphviz" ,r-rgraphviz)
7546 ("r-rjson" ,r-rjson)
7547 ("r-s4vectors" ,r-s4vectors)
7548 ("r-scales" ,r-scales)
7549 ("r-shiny" ,r-shiny)
7550 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7551 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7552 (synopsis "Bioconductor components for general cancer genomics")
7554 "The purpose of this package is to provide a central interface to various
7555 tools for genome-scale analysis of cancer studies.")
7556 (license license:artistic2.0)))
7558 (define-public r-biocor
7565 (uri (bioconductor-uri "BioCor" version))
7568 "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl"))))
7569 (properties `((upstream-name . "BioCor")))
7570 (build-system r-build-system)
7572 `(("r-biocparallel" ,r-biocparallel)
7573 ("r-gseabase" ,r-gseabase)
7574 ("r-matrix" ,r-matrix)))
7575 (home-page "https://llrs.github.io/BioCor/")
7576 (synopsis "Functional similarities")
7578 "This package provides tools to calculate functional similarities based
7579 on the pathways described on KEGG and REACTOME or in gene sets. These
7580 similarities can be calculated for pathways or gene sets, genes, or clusters
7581 and combined with other similarities. They can be used to improve networks,
7582 gene selection, testing relationships, and so on.")
7583 (license license:expat)))
7585 (define-public r-biocpkgtools
7587 (name "r-biocpkgtools")
7592 (uri (bioconductor-uri "BiocPkgTools" version))
7595 "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a"))))
7596 (properties `((upstream-name . "BiocPkgTools")))
7597 (build-system r-build-system)
7599 `(("r-biocfilecache" ,r-biocfilecache)
7600 ("r-biocmanager" ,r-biocmanager)
7601 ("r-biocviews" ,r-biocviews)
7602 ("r-dplyr" ,r-dplyr)
7605 ("r-graph" ,r-graph)
7606 ("r-htmltools" ,r-htmltools)
7607 ("r-htmlwidgets" ,r-htmlwidgets)
7609 ("r-igraph" ,r-igraph)
7610 ("r-jsonlite" ,r-jsonlite)
7611 ("r-magrittr" ,r-magrittr)
7612 ("r-rappdirs" ,r-rappdirs)
7614 ("r-readr" ,r-readr)
7616 ("r-rlang" ,r-rlang)
7617 ("r-rvest" ,r-rvest)
7618 ("r-stringr" ,r-stringr)
7619 ("r-tibble" ,r-tibble)
7620 ("r-tidyr" ,r-tidyr)
7621 ("r-tidyselect" ,r-tidyselect)
7622 ("r-xml2" ,r-xml2)))
7624 `(("r-knitr" ,r-knitr)))
7625 (home-page "https://github.com/seandavi/BiocPkgTools")
7626 (synopsis "Collection of tools for learning about Bioconductor packages")
7628 "Bioconductor has a rich ecosystem of metadata around packages, usage,
7629 and build status. This package is a simple collection of functions to access
7630 that metadata from R. The goal is to expose metadata for data mining and
7631 value-added functionality such as package searching, text mining, and
7632 analytics on packages.")
7633 (license license:expat)))
7635 (define-public r-biocset
7642 (uri (bioconductor-uri "BiocSet" version))
7645 "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9"))))
7646 (properties `((upstream-name . "BiocSet")))
7647 (build-system r-build-system)
7649 `(("r-annotationdbi" ,r-annotationdbi)
7650 ("r-dplyr" ,r-dplyr)
7651 ("r-keggrest" ,r-keggrest)
7653 ("r-rlang" ,r-rlang)
7654 ("r-rtracklayer" ,r-rtracklayer)
7655 ("r-tibble" ,r-tibble)))
7657 "https://bioconductor.org/packages/BiocSet")
7659 "Representing Different Biological Sets")
7661 "BiocSet displays different biological sets in a triple tibble format.
7662 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
7663 The user has the ability to activate one of these three tibbles to perform
7664 common functions from the @code{dplyr} package. Mapping functionality and
7665 accessing web references for elements/sets are also available in BiocSet.")
7666 (license license:artistic2.0)))
7668 (define-public r-biocworkflowtools
7670 (name "r-biocworkflowtools")
7675 (uri (bioconductor-uri "BiocWorkflowTools" version))
7678 "0z28s572wg9qxv52dmixxz1xf1z3fyp2j7kzk0k32fp628918wr6"))))
7680 `((upstream-name . "BiocWorkflowTools")))
7681 (build-system r-build-system)
7683 `(("r-biocstyle" ,r-biocstyle)
7684 ("r-bookdown" ,r-bookdown)
7685 ("r-git2r" ,r-git2r)
7687 ("r-knitr" ,r-knitr)
7688 ("r-rmarkdown" ,r-rmarkdown)
7689 ("r-rstudioapi" ,r-rstudioapi)
7690 ("r-stringr" ,r-stringr)
7691 ("r-usethis" ,r-usethis)))
7693 `(("r-knitr" ,r-knitr)))
7694 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
7695 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
7697 "This package provides functions to ease the transition between
7698 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
7699 (license license:expat)))
7701 (define-public r-biodist
7708 (uri (bioconductor-uri "bioDist" version))
7711 "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q"))))
7712 (properties `((upstream-name . "bioDist")))
7713 (build-system r-build-system)
7715 `(("r-biobase" ,r-biobase)
7716 ("r-kernsmooth" ,r-kernsmooth)))
7717 (home-page "https://bioconductor.org/packages/bioDist/")
7718 (synopsis "Different distance measures")
7720 "This package provides a collection of software tools for calculating
7721 distance measures.")
7722 (license license:artistic2.0)))